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Kohsuke Terada, Yorito Yanagida, Tomohiro Yan, Toshiki Funakoshi, Akio Hirama, Tetsuya Kashiwagi, Yukinao Sakai
Published: 7 July 2021
Renal Replacement Therapy, Volume 7, pp 1-7; doi:10.1186/s41100-021-00359-3

Abstract:
Background The Japanese population is aging quickly. New methods of supporting peritoneal dialysis (PD) for elderly patients are essential if we are to increase the number of such patients. Methods We established a two-way communication system between a central hospital and stations for visiting nurses. Home care nurses provided physicians at the central hospital with clinical findings for patients undergoing assisted PD. We compared 11 patients undergoing PD assisted by home care nurses in continuous interactive communication with the central hospital (cases) with 11 patients undergoing unassisted PD who were matched by sex, primary disease, estimated glomerular filtration rate at the start of PD, and age at the start of PD (controls). The variables compared were hospitalization due to heart failure, exit-site infection, peritonitis, and the composite of these causes during a 1-year period. In addition, we compared patient clinical factors between groups. Results Although differences in the number of hospitalizations attributable to exit-site infection, peritonitis, and heart failure were not significant, the difference in the number of hospitalizations attributable to a composite of these causes was significant. Exit-site scores were significantly better in the case group than in the control group. Conclusions PD assisted by home care nurses using an established continuous interactive communication system was associated with significantly better exit-site scores. Fewer cases than controls were hospitalized.
, Jun-Ichi Ando, Akihiro Kano, Hirokazu Kato, Gautam Ghosh, Kaushik Das
Progress in Earth and Planetary Science, Volume 8, pp 1-15; doi:10.1186/s40645-021-00435-6

Abstract:
Disentangling the temperature and depth of formation of fault rocks is critical for understanding their rheology, exhumation, and the evolution of fault zones. Estimation of fault rock temperatures mostly relies on conventional geothermometers of metamorphic minerals and element partitioning analysis, which are largely inapplicable in shallow crustal fault rocks. Here, we demonstrate the applicability of the carbonate clumped isotope thermometer in low-grade carbonate-bearing fault rocks from the Himalayan frontal wedge (northwest India). Coalescing carbonate clumped isotope thermometry and calcite e-twin morphology allows us to constrain the temperature and depth of formation of the two main thrusts of the Himalayan frontal wedge, the Nahan thrust (170 ± 10 °C; 6–7 km depth), and the Main Boundary thrust (262 ± 30 °C; 10–11 km depth). The integration of the adopted analytical techniques can promote the application of calcite-based clumped isotope thermometry to the fault zone processes and refinement of shallow crustal fault zone models.
Belal Hossain, , Mir Nurul Hasan Mahmud, Priya Lal Chandra Paul, Mst. Shetara Yesmin, Palash Kumar Kundu
Environmental Systems Research, Volume 10, pp 1-11; doi:10.1186/s40068-021-00239-z

Abstract:
Background Rainfall is the key contributor to provide soil moisture for wet season rice (T. Aman) cultivation. Erratic rainfall often causes water shortage resulting negative impact on plant growth and grain yield. The study aimed to determine suitable transplanting window that utilize maximum rainfall for T. Aman rice. Firstly, three years field experiment were conducted in Kushtia, Bangladesh from T. Aman, 2013 to 2015, and then the findings were implemented for another two adjacent locations, Panba and Rajshahi. The field experiment considered six transplanting dates of popular cultivar BR11 (growth duration 145 days) at 7 days interval starting from 10 July to 14 August. The CROPWAT 8.0 model was used to calculate crop water requirement (CWR), effective rainfall and irrigation demand (ID) from collected weather data in each growth phase of rice. Results In all locations T. Aman rice received enormous rainfall up to vegetative phase resulting no irrigation demand in all three tested years. The early transplanting received more rainfall in reproductive phase than late planting. Thus, Irrigation demand increased at reproductive phase with delay transplanting in moderate drought prone Kushtia, Pabna and Rajshahi. A significant relationship (R2 = 0.71) observed between reproductive phase ID and grain yield, while grain yield responded weakly with the ID at ripening phase. Based on yield performance 10–24 July found suitable transplanting window for BR11 in Kushtia. Considering the relationship between ID and grain yield, 10–17 July and 10–24 July considered the best transplanting window in Pabna and Rajshahi, respectively. Conclusions Location specific suitable transplanting windows were selected considering minimum ID at reproductive phase and the maximum grain yield. Delay in transplanting demanded more irrigation and reduced grain yield. Whereas, early transplanting utilized maximum rainfall, reduced ID in reproductive stage and ensured desired grain yield.
, Susanne F. McDermott, Julie K. Nielsen, Dave Fraser, Kimberly M. Rand
Published: 7 July 2021
Animal Biotelemetry, Volume 9, pp 1-18; doi:10.1186/s40317-021-00250-2

Abstract:
Background Pacific cod (Gadus macrocephalus) is an ecologically important species that supports a valuable commercial fishery throughout Alaska waters. Although its life history includes seasonal movement for spawning and feeding, little is known about its movement ecology. Here, we present results from the first study to use pop-up satellite archival tags (PSATs) to track the within-year movements of Pacific cod to understand their potential seasonal movement patterns within the Aleutian Islands. This study was part of a cooperative research project; tagging was conducted onboard commercial vessels during the winter fishing season while Pacific cod were aggregated to spawn in the central Aleutian Islands. Results Of the 36 PSATs deployed, we were able to obtain movement data from 13 Pacific cod that were at liberty between 60 and 360 days. We determined that three tagged Pacific cod were predated on by marine mammals and three were recaptured by the commercial fishery. Geolocation models were produced for four migrating individuals. Eight Pacific cod moved to a productive foraging ground near Seguam Island located 64 to 344 km from their release site and presumed spawning ground within a few weeks of their release. These movements indicate that some Pacific cod in the Aleutian Islands undergo seasonal migration. Three Pacific cod remained near their release locations (within 50 km) for more than 75 days suggesting the existence of partial migration in the population. Two Pacific cod undertook larger movements (378 and 394 km) during which they swam over deep passes and crossed several management boundaries highlighting the potential connectedness of Pacific cod throughout the Aleutian Islands. Conclusions This study provided important initial insights into the seasonal movement patterns of Pacific cod in the Aleutian Islands. Most tracked Pacific cod (77%) undertook migrations in the middle of March (64–394 km) from their winter spawning areas to summer foraging areas, but a few individuals remained in their capture location suggesting a partial migration strategy. Their ability to cross deep passes that were previously seen as potential barriers to movement has expanded our understanding of population connectivity.
Yan Dong
Published: 7 July 2021
Financial Innovation, Volume 7, pp 1-3; doi:10.1186/s40854-021-00273-x

, Ma. Mercedes T. Rodrigo
Research and Practice in Technology Enhanced Learning, Volume 16, pp 1-21; doi:10.1186/s41039-021-00171-x

Abstract:
The incubation effect (IE) is a problem-solving phenomenon composed of three phases: pre-incubation where one fails to solve a problem; incubation, a momentary break where time is spent away from the unsolved problem; and post-incubation where the unsolved problem is revisited and solved. Literature on IE was limited to experiments involving traditional classroom activities. This initial investigation showed evidence of IE instances in a computer-based learning environment. This paper consolidates the studies on IE among students playing an educational game called Physics Playground and presents further analysis to examine the incidence of post-incubation or the revisit to a previously unsolved problem. Prior work, which focused on predicting successful outcomes, includes a coarse-grained IE model developed with logistic regression on aggregated data and an improved model which leveraged long short-term memory (LSTM) combined with dimensionality reduction visualization technique and clustering on fine-grained data. The additional analysis which aims to understand factors that may trigger the post-incubation phase also used fine-grained data and LSTM to create a revisit model. Results show that time elapsed relative to the activity period and encountering a problem with a similar solution during incubation were possible factors in revisiting previously unsolved problems.
Tiantian Yu, Ruping Wang
EURASIP Journal on Wireless Communications and Networking, Volume 2021, pp 1-23; doi:10.1186/s13638-021-02021-2

Abstract:
Wireless communication refers to long-distance transmission communication between multiple nodes without propagation through conductors or cables, and wireless communication can be carried out by radio and electromagnetic waves, etc. Judging from the current situation, the home space positioning design of the medical and elderly care communities is not perfect, which affects the traditional home care. Wireless communication can give wisdom, coordination, and development space in the smart elderly care space positioning design, allowing the elderly to interact, contact, and know their precise location and behavior. This article mainly studies the design and implementation of smart pension space positioning under BIM technology. This paper introduces the frontier of Internet-of-things technology and the theory of sensor network topology control. It uses basic IoT technology to implement the "point, line, and surface" combination of personnel placement algorithms, sensor network communication protocols, topology checks, security models, sensor network wireless communication units, and wireless communication technology. The basic technology and communication technology of personnel deployment based on BIM technology are introduced, the development strategy of wireless communications node is studied, the installation of equipment radio personnel and communication equipment is designed, and the system management platform for the design and development of staff placement in pension institutions is provided. The Web site's information service management, standardized procedures, optimized services, provision of information, intelligent management, and pension services. The experimental results of this paper show that the smart pension space positioning under the BIM technology solves the management loopholes in nursing homes, shortage of nursing staff, inefficiency, lack of services, and family conflicts. It improves the efficiency of the elderly by 25% and the safety index by 23–27%. The development of wireless communication technology promotes the development of intelligent pension space. It will be an important future development direction for the smart community pension.
Sher Ahmad, Gabriela Vollet Marson, Waheed Ur Rehman, Mohammad Younas, Sarah Farrukh,
Environmental Sciences Europe, Volume 33, pp 1-18; doi:10.1186/s12302-021-00520-z

Abstract:
Background In this research work, a coupled heat and mass transfer model was developed for salt recovery from concentrated brine water through an osmotic membrane distillation (OMD) process in a hollow fiber membrane contactor (HFMC).The model was built based on the resistance-in-series concept for water transport across the hydrophobic membrane. The model was adopted to incorporate the effects of polarization layers such as temperature and concentration polarization, as well as viscosity changes during concentration. Results The modeling equations were numerically simulated in MATLAB® and were successfully validated with experimental data from literature with a deviation within the range of 1–5%. The model was then applied to study the effects of key process parameters like feed concentrations, osmotic solution concentration, feed, and osmotic solution flow rates and feed temperature on the overall heat and mass transfer coefficient as well as on water transport flux to improve the process efficiency. The mass balance modeling was applied to calculate the membrane area based on the simulated mass transfer coefficient. Finally, a scale-up for the MD process for salt recovery on an industrial scale was proposed. Conclusions This study highlights the effect of key parameters for salt recovery from wastewater using the membrane distillation process. Further, the applicability of the OMD process for salt recovery on large scale was investigated. Sensitivity analysis was performed to identify the key parameters. From the results of this study, it is concluded that the OMD process can be promising in salt recovery from wastewater.
, Ron Patrick Solfa, Thuy Linh Tran, Sophia Wohlfarth, Jonas Büttner, Oluyomi A. Osobajo, Afolabi Otitoju
Translational Medicine Communications, Volume 6, pp 1-13; doi:10.1186/s41231-021-00092-3

Abstract:
There is a growing debate on the linkage between social networking platforms and mental health disorder, such as depressive behaviour or depression. However, the relationship between Instagram use and depression or depressive behaviour has not been exhaustively examined. This review aims to examine these two variables. Only peer-reviewed journal articles that are published between October 2010 and December 2018 were sought in central and journal databases. Studies were selected based on predefined criteria and assessed for risk of bias and quality of evidence using GRADE. One thousand eight hundred fifty-six studies were the outcome of the search, out of which 9 meets all eligible criteria. Of the 9 studies, three-quarter was published between 2017 and 2018, covering five continents: (North America: 3; Asia: 2; Australia: 2; South America: 1, Europe: 1). The final included studies broadly examined young Instagram users between the age of 19 and 35. The synthesis affirmed a linkage between Instagram and symptoms of depression or depressive behaviour. Variables that moderate this relationship are social comparison, self-esteem built on validation and approval of others, social media dependence, gender, negative or insufficient feedback, poor self-rated attractiveness, Instagram broadcasting and loneliness, younger users and risk of anxiety, and the number of strangers that users follow. There is a strong relationship between Instagram use and mental health disorders such as depression or depressive behaviour; however, no in-depth direct causality is proven yet. Further studies are needed to unravel the direct causality puzzles.
Xuerui Wu, Andrés Calabia, , Weihua Bai, Peng Guo
Published: 7 July 2021
Geoscience Letters, Volume 8, pp 1-15; doi:10.1186/s40562-021-00195-7

Abstract:
In recent years, signal of opportunity reflectometry (SoOp-R) has become a promising remote sensing technique. This emerging technique employs the reflected signals from existing Global Navigation Satellite System (GNSS) or communication satellites to estimate geophysical parameters for Earth observation, such as wind speed, altimetry, significant wave height, soil moisture, etc. While its application for forest canopy monitoring is still in the initial stage, there are still many unknown relations between vegetation parameters and actual observations, and a proper theoretical basis needs to be established for simulation and analysis of the different observation geometries. In this paper, we develop a bistatic scattering model with various polarizations at different frequency bands. Our improved model is based on the first-order radiative transfer equation, and is developed based on the wave synthesis technique, after which it can be used for circular polarization signals in bistatic radar systems, i.e. the typical configuration of SoOp-R. We analyze the simulations of the P (0.25–0.5 GHz), L (0.5–1.5 GHz), C (4–8 GHz), and X (8–12 GHz) bands at the backscattering, specular cone, bistatic scattering, and perpendicular planes. The contributions of the different components to the total scattering are also analyzed. The results show that the coherent scattering at the specular cone is larger than the non-coherent scattering, while trunk-dominated forest canopy has strong scattering at the aforementioned different directions. Variations of canopy parameters such as trunk and branch diameters, tree density, and vegetation water content are also simulated at the specular cone plane, showing strong dependence on the final bistatic scattering observation. The simulation results show that the SoOp-R technique has a great potential for monitoring of canopy parameters.
, Philip J. Erickson, Yoshiharu Omura
Published: 7 July 2021
Earth, Planets and Space, Volume 73, pp 1-12; doi:10.1186/s40623-021-01467-4

Abstract:
Van Allen Probes in situ observations are used to examine detailed subpacket structure observed in strong VLF (very low frequency) rising-tone chorus elements observed at the time of a rapid MeV electron energization in the inner magnetosphere. Analysis of the frequency gap between lower and upper chorus-band waves identifies f ceEQ, the electron gyrofrequency in the equatorial wave generation region. Initial subpackets in these strong chorus rising-tone elements begin at a frequency near 1/4 f ceEQ and exhibit smooth gradual frequency increase across their > 10 ms temporal duration. A second much stronger subpacket is seen at frequencies around the local value of 1/4 f ce with small wave normal angle (< 10°) and steeply rising df/dt. Smooth frequency and phase variation across and between the initial subpackets support continuous phase trapping of resonant electrons and increased potential for MeV electron acceleration. The total energy gain for individual seed electrons with energies between 100 keV and 3 MeV ranges between 2 and 15%, in their nonlinear interaction with a single chorus element.
, Muhammad Abdulhaleem, Salah Eltahan, Moustafa Elhamami
Published: 7 July 2021
The Cardiothoracic Surgeon, Volume 29, pp 1-5; doi:10.1186/s43057-021-00051-6

Abstract:
Background Traumatic pneumothorax (PTx) is common in chest trauma. Its incidence ranges between 10 and 28%. Chest X-ray (CXR) is the traditional imaging for the potential traumatic PTx, while CT chest is considered the gold standard diagnostic tool. However, it requires that the patient to be transferred from the Emergency Department (ED) with its resuscitative facilities. Chest US (E-FAST) has emerged as a sensitive tool that can be used on bedside basis with much higher sensitivity than CXR. The objective of this study was to compare between accuracy and usefulness of the bedside US chest and CT chest in the diagnosis of traumatic PTx, as well as its ability to quantify its size. This was a prospective clinical study that included two hundred patients who have been admitted to the ED. The inclusion criteria included any patient with chest trauma. Exclusion criteria included patients with clinical surgical emphysema, patients with life threatening PTx, and patients who did not undergo CT chest. Results Forty-seven hemithoraces were proved positive for PTx by CT chest, while forty-five hemithoraces out of those 47 were confirmed by bedside chest US. The sensitivity for chest US is 95.74% in detection of traumatic PTx. No false-positive cases were diagnosed. All of the forty-five hemithoraces diagnosed by chest US have been confirmed by CT scan making a specificity of 100%. Conclusions Chest US is a useful rapid diagnostic tool in the diagnosis and quantification of the traumatic PTx at ED. It avoids the delay in transportation of the critically ill patients to perform CT chest.
Published: 7 July 2021
Heritage Science, Volume 9, pp 1-19; doi:10.1186/s40494-021-00548-7

Abstract:
Conservators, museologists, and architects make extremely complex decisions capable of affecting the way people perceive monuments. One might give this idea deeper consideration while pondering anastylosis. One of the things a designer should do when selecting a method of merging together parts of a damaged monument is answer the question whether the chosen method will facilitate the interest of onlookers in the presented object. In which case will the observers spend most of their time looking at the authentic relic fragments and distinguishing between the old and the new parts? The definitions in force do not explain how to approach this topic. By using eye-tracking research, we can learn how observers look at historical objects that have been reassembled again. By combining the observation of visual behaviours with a survey of people looking at such objects, it is possible to see how the process of classifying what is new and old actually works. This knowledge allows for more conscious approach to heritage management processes. In future, results of eye-tracking experiments should help experts plan sustainable conservation projects. Thanks to knowing the reactions of regular people, one will be able to establish conservation programmes in which the material preservation of a monument will reflect the way in which this object affects contemporary onlookers. Such an approach ought to result in real social and economic benefits.
Yichao Li, Sushil K. Jaiswal, Rupleen Kaur, Dana Alsaadi, Xiaoyu Liang, Frank Drews, Julie A. DeLoia, Thomas Krivak, Hanna M. Petrykowska, Valer Gotea, et al.
Published: 3 July 2021
BMC Cancer, Volume 21, pp 1-18; doi:10.1186/s12885-021-08276-8

Abstract:
Background The heterogeneous subtypes and stages of epithelial ovarian cancer (EOC) differ in their biological features, invasiveness, and response to chemotherapy, but the transcriptional regulators causing their differences remain nebulous. Methods In this study, we compared high-grade serous ovarian cancers (HGSOCs) to low malignant potential or serous borderline tumors (SBTs). Our aim was to discover new regulatory factors causing distinct biological properties of HGSOCs and SBTs. Results In a discovery dataset, we identified 11 differentially expressed genes (DEGs) between SBTs and HGSOCs. Their expression correctly classified 95% of 267 validation samples. Two of the DEGs, TMEM30B and TSPAN1, were significantly associated with worse overall survival in patients with HGSOC. We also identified 17 DEGs that distinguished stage II vs. III HGSOC. In these two DEG promoter sets, we identified significant enrichment of predicted transcription factor binding sites, including those of RARA, FOXF1, BHLHE41, and PITX1. Using published ChIP-seq data acquired from multiple non-ovarian cell types, we showed additional regulatory factors, including AP2-gamma/TFAP2C, FOXA1, and BHLHE40, bound at the majority of DEG promoters. Several of the factors are known to cooperate with and predict the presence of nuclear hormone receptor estrogen receptor alpha (ER-alpha). We experimentally confirmed ER-alpha and PITX1 presence at the DEGs by performing ChIP-seq analysis using the ovarian cancer cell line PEO4. Finally, RNA-seq analysis identified recurrent gene fusion events in our EOC tumor set. Some of these fusions were significantly associated with survival in HGSOC patients; however, the fusion genes are not regulated by the transcription factors identified for the DEGs. Conclusions These data implicate an estrogen-responsive regulatory network in the differential gene expression between ovarian cancer subtypes and stages, which includes PITX1. Importantly, the transcription factors associated with our DEG promoters are known to form the MegaTrans complex in breast cancer. This is the first study to implicate the MegaTrans complex in contributing to the distinct biological trajectories of malignant and indolent ovarian cancer subtypes.
Anne K. Erickson, Safa Abdalla, Alice Serenska, Bete Demeke, Gary L. Darmstadt
BMC Pregnancy and Childbirth, Volume 21, pp 1-11; doi:10.1186/s12884-021-03913-3

Abstract:
Background A strategy for reducing adverse pregnancy outcomes is the expanded implementation of maternity waiting homes (MWHs). We assessed factors influencing MWH use, as well as the association between MWH stay and obstetric outcomes in a hospital in rural Ethiopia. Methods Data from medical records of the Glenn C. Olson Memorial Primary Hospital obstetric ward were cross matched with records from the affiliated MWH between 1 and 2011 to 31 March 2014. Poisson regression with robust variance was conducted to estimate the relative risk (RR) of childbirth complications associated with MWH use vs. non-use. Five key informant interviews of a convenience sample of three MWH staff and two users were conducted and a thematic analysis performed of social, cultural, and economic factors underlying MWH use. Results During the study period, 489 women gave birth at the hospital, 93 of whom were MWH users. Common reasons for using the MWH were post-term status, previous caesarean section/myomectomy, malposition/malpresentation, and low-lying placenta, placenta previa, or antepartum hemorrhage, and hypertension or preeclampsia. MWH users were more likely than non-users to have had a previous caesarean Sec. (15.1 % vs. 5.3 %, p < 0.001) and to be post-term (21.5 % vs. 3.8 %, p < 0.001). MWH users were also more likely to undergo a caesarean Sec. (51.0 % vs. 35.4 %, p < 0.05) and less likely (p < 0.05) to have a spontaneous vaginal delivery (49.0 % vs. 63.6 %), obstructed labor (6.5 % vs. 14.4 %) or stillbirth (1.1 % vs. 8.6 %). MWH use (N = 93) was associated with a 77 % (adjusted RR = 0.23, 95 % Confidence Interval (CI) 0.12–0.46, p < 0.001) lower risk of childbirth complications, a 94 % (adjusted RR = 0.06, 95 % CI 0.01–0.43, p = 0.005) lower risk of fetal and newborn complications, and a 73 % (adjusted RR = 0.27, 95 % CI 0.13–0.56, p < 0.001) lower risk of maternal complications compared to MWH non-users (N = 396). Birth weight [median 3.5 kg (interquartile range 3.0-3.8) vs. 3.2 kg (2.8–3.5), p < 0.001] and 5-min Apgar scores (adjusted difference = 0.25, 95 % CI 0.06–0.44, p < 0.001) were also higher in offspring of MWH users. Opportunity costs due to missed work and need to arrange for care of children at home, long travel times, and lack of entertainment were suggested as key barriers to MWH utilization. Conclusions This observational, non-randomized study suggests that MWH usage was associated with significantly improved childbirth outcomes. Increasing facility quality, expanding services, and providing educational opportunities should be considered to increase MWH use.
Shaokun Wang, Li Pang, Zuolong Liu, Xiangwei Meng
Published: 3 July 2021
BMC Cancer, Volume 21, pp 1-13; doi:10.1186/s12885-021-08536-7

Abstract:
Background The change of immune cell infiltration essentially influences the process of colorectal cancer development. The infiltration of immune cells can be regulated by a variety of genes. Thus, modeling the immune microenvironment of colorectal cancer by analyzing the genes involved can be more conducive to the in-depth understanding of carcinogenesis and the progression thereof. Methods In this study, the number of stromal and immune cells in malignant tumor tissues were first estimated by using expression data (ESTIMATE) and cell-type identification with relative subsets of known RNA transcripts (CIBERSORT) to calculate the proportion of infiltrating immune cell and stromal components of colon cancer samples from the Cancer Genome Atlas database. Then the relationship between the TMN Classification and prognosis of malignant tumors was evaluated. Results By investigating differentially expressed genes using COX regression and protein-protein interaction network (PPI), the candidate hub gene serine protease inhibitor family E member 1 (SERPINE1) was found to be associated with immune cell infiltration. Gene Set Enrichment Analysis (GSEA) further projected the potential pathways with elevated SERPINE1 expression to carcinogenesis and immunity. CIBERSORT was subsequently utilized to investigate the relationship between the expression differences of SERPINE1 and immune cell infiltration and to identify eight immune cells associated with SERPINE1 expression. Conclusion We found that SERPINE1 plays a role in the remodeling of the colon cancer microenvironment and the infiltration of immune cells.
Takuya Tsujimura, Osamu Iida, Mitsutoshi Asai, Masaharu Masuda, Shin Okamoto, Takayuki Ishihara, Kiyonori Nanto, Takashi Kanda, Yasuhiro Matsuda, Yosuke Hata, et al.
Published: 3 July 2021
CVIR Endovascular, Volume 4, pp 1-6; doi:10.1186/s42155-021-00245-3

Abstract:
Background Although several clinical reports demonstrated a durable patency rate after a novel fluoropolymer-coated paclitaxel-eluting stent (Eluvia; Boston Scientific, Marlborough, MA, USA) placement, aneurysmal degeneration after drug-eluting stent (Eluvia) placement has raised clinical concerns. Here, we report a case with progressive aneurysm formation on serial angiography and intravascular ultrasound over 50 months after drug-eluting stent (Eluvia) placement for a superficial femoral artery atheromatous plaque. Case presentation A 79-year-old woman with right leg intermittent claudication at 100 m distance was referred to our hospital. Pre-procedural angiography showed long-segment severe stenosis from the middle-to-distal part of the right superficial femoral artery, and a 7 mm wide drug-eluting stent (Eluvia) was placed. However, the patient had a recurrence of intermittent claudication in the right lower extremity 25 months thereafter. Angiography revealed de novo stenosis in the distal part of the popliteal artery and proximal superficial femoral artery in-stent restenosis. Subsequently, the patient underwent endovascular therapy for these lesions. In addition, intravascular ultrasound at the time of endovascular therapy revealed femoral artery enlargement with a maximum vessel diameter of 10.0 mm at the distal edge of the stent. Intermittent claudication on the right side recurred again 50 months after drug-eluting stent (Eluvia). Angiography demonstrated de novo severe stenosis from the distal part of the superficial femoral artery to the middle part of the popliteal artery. Peri-stent contrast staining was found at the distal part of the drug-eluting stent (Eluvia) site. Intravascular ultrasound showed a further enlargement of maximum vessel diameter to 12.0 mm at the distal edge of the stent. Conclusions We report a case with progressive aneurysm degeneration on serial angiography and intravascular ultrasound over 50 months after drug-eluting stent (Eluvia) placement for a superficial femoral artery stenosis.
Nikolaos Giormezis, Anastassios Doudoulakakis, Katerina Tsilipounidaki, Maria Militsopoulou, George Kalogeras, Vasiliki Stamouli, Fevronia Kolonitsiou, Efthimia Petinaki, Evangelia Lebessi, Iris Spiliopoulou
Published: 3 July 2021
BMC Microbiology, Volume 21, pp 1-10; doi:10.1186/s12866-021-02272-5

Abstract:
Background Staphylococcus aureus causes various infections, including skin and soft tissue infections (SSTIs). In this study, methicillin-susceptible S. aureus (MSSA) from SSTIs among patients in three tertiary-care hospitals in Greece were studied in terms of antimicrobial resistance, clonal distribution, toxin and adhesin genes carriage. Results During a five-year period (2014–2018), 6145 S. aureus were recovered from 13,244 patients with SSTIs and tested for antimicrobial susceptibility. MSSA were 4806 (78.21 %) including 1484 isolates with mupirocin minimum inhibitory concentration (MIC) > 64 mg/L (30.88 %). Two hundred and sixty representative mupirocin-resistant MSSA were analyzed for genes encoding Panton-Valentine leukocidin (PVL, lukS/lukF-PV), exfoliative toxins (eta, etb), adhesin FnbA (fnbA) and resistance genes mupA (high-level resistance to mupirocin), fusB (fusidic acid), aminoglycosides’ modifying enzymes, ermA, ermC and msrA (macrolides/lincosamides) by PCRs. Strains were classified into clones by PFGE and MLST. All mupirocin-resistant MSSA were penicillin-resistant; 92.7 % expressed resistance to fusidic acid and 88.9 % to tobramycin. All 260 molecularly analyzed isolates were mupA-positive; all fusidic acid-resistant (241/260) carried fusB whereas, the tobramycin-resistant ones (230), ant(4′)-Ia. The majority carried eta (93.85 %), etb (98.08 %) and fnbA (88.85 %). PFGE typing revealed a mostly unvarying population; 260 MSSA were grouped into three types. One major eta/etb-positive clone comprising of 258/260 strains (99.2 %), PFGE type 1, was classified as ST121, including nine strains co-carrying PVL. Another PVL-positive strain was identified as ST1, and one toxins-negative as ST21. Conclusions A mupirocin-resistant MSSA clone, ST121, carrying resistance, exfoliative toxins and adhesin genes, was spread and predominated in SSTIs from patients in Greece during the five-year studied period.
Qinghui Kong, Suozhu Liu, Aoyun Li, Yaping Wang, Lihong Zhang, Mudassar Iqbal, Tariq Jamil, Zhenda Shang, Lang-Sizhu Suo, Jiakui Li
Published: 3 July 2021
BMC Microbiology, Volume 21, pp 1-10; doi:10.1186/s12866-021-02242-x

Abstract:
Background Diarrhea is an important ailment limiting the production of the Tibetan pig industry. Dynamic balance of the intestinal microbiota is important for the physiology of the animal. The objective of this work was to study fungal diversity in the feces of early weaning Tibetan piglets in different health conditions. Results In the present study, we performed high-throughput sequencing to characterize the fungal microbial diversity in healthy, diarrheal and treated Tibetan piglets at the Tibet Autonomous Region of the People’s Republic of China. The four alpha diversity indices (Chao1, ACE, Shannon and Simpson) revealed no significant differences in the richness across the different groups (P > 0.05). In all samples, the predominant fungal phyla were Ascomycota, Basidiomycota and Rozellomycota. Moreover, the healthy piglets showed a higher abundance of Ascomycota than the treated ones with a decreased level of Basidiomycota. One phylum (Rozellomycota) showed higher abundance in the diarrheal piglets than in the treated. At genus level, compared with that to the healthy group, the proportion of Derxomyces and Lecanicillium decreased, whereas that of Cortinarius and Kazachstania increased in the diarrheal group. The relative abundances of Derxomyces, Phyllozyma and Hydnum were higher in treated piglets than in the diarrheal ones. Conclusions A decreased relative abundance of beneficial fungi (e.g. Derxomyces and Lecanicillium) may cause diarrhea in the early-weaned Tibetan piglets. Addition of probiotics into the feed may prevent diarrhea at this stage. This study presented the fungal diversity in healthy, diarrheal and treated early-weaned Tibetan piglets.
Sasan Ghaffari, Monireh Torabi-Rahvar, Sajjad Aghayan, Zahra Jabbarpour, Kobra Moradzadeh, ,
Published: 3 July 2021
BMC Immunology, Volume 22, pp 1-9; doi:10.1186/s12865-021-00435-7

Abstract:
Background The successful ex vivo expansion of T-cells in great numbers is the cornerstone of adoptive cell therapy. We aimed to achieve the most optimal T-cell expansion condition by comparing the expansion of T-cells at various seeding densities, IL-2 concentrations, and bead-to-cell ratios. we first expanded the peripheral blood mononuclear cells (PBMCs) of a healthy donor at a range of 20 to 500 IU/mL IL-2 concentrations, 125 × 103 to 1.5 × 106 cell/mL, and 1:10 to 10:1 B:C (Bead-to-cell) ratios and compared the results. We then expanded the PBMC of three healthy donors using the optimized conditions and examined the growth kinetics. On day 28, CD3, CD4, and CD8 expression of the cell populations were analyzed by flow cytometry. Results T-cells of the first donor showed greater expansion results in IL-2 concentrations higher than 50 IU/mL compared to 20 IU/mL (P = 0.02). A seeding density of 250 × 103 cell/mL was superior to higher or lower densities in expanding T-cells (P = 0.025). Also, we witnessed a direct correlation between the B:C ratio and T-cell expansion, in which, in 5:1 and 10:1 B:C ratios T-cell significantly expanded more than lower B:C ratios. The results of PBMC expansions of three healthy donors were similar in growth kinetics. In the optimized condition, 96–98% of the lymphocyte population expressed CD3. While the majority of these cells expressed CD8, the mean expression of CD4 in the donors was 19.3, 16.5, and 20.4%. Conclusions Our methodology demonstrates an optimized culture condition for the production of large quantities of polyclonal T-cells, which could be useful for future clinical and research studies.
Yutaro Kanda, , Yoshitada Sakai, Zhongying Zhang, Takashi Yurube, Shingo Miyazaki, Yuji Kakiuchi, Yoshiki Takeoka, Ryu Tsujimoto, Kunihiko Miyazaki, et al.
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-9; doi:10.1186/s13018-021-02562-8

Abstract:
Background Few studies have addressed the impact of palliative surgery for cervical spine metastasis on patients’ performance status (PS) and quality of life (QOL). We investigated the surgical outcomes of patients with cervical spine metastasis and the risk factors for a poor outcome with a focus on the PS and QOL. Methods We prospectively analyzed patients with cervical spine metastasis who underwent palliative surgery from 2013 to 2018. The Eastern Cooperative Oncology Group PS (ECOGPS) and EuroQol 5-Dimension (EQ5D) score were assessed at study enrollment and 1, 3, and 6 months postoperatively. Neurological function was evaluated with Frankel grading. Univariate and multivariate analyses were performed to identify the risk factors for a poor surgical outcome, defined as no improvement or deterioration after improvement of the ECOGPS or EQ5D score within 3 months. Results Forty-six patients (mean age, 67.5 ± 11.7 years) were enrolled. Twelve postoperative complications occurred in 11 (23.9%) patients. The median ECOGPS improved from PS3 at study enrolment to PS2 at 1 month and PS1 at 3 and 6 months postoperatively. The mean EQ5D score improved from 0.085 ± 0.487 at study enrolment to 0.658 ± 0.356 at 1 month and 0.753 ± 0.312 at 3 months. A poor outcome was observed in 18 (39.1%) patients. The univariate analysis showed that variables with a P value of < 0.10 were sex (male), the revised Tokuhashi score, the new Katagiri score, the level of the main lesion, and the Frankel grade at baseline. The multivariate analysis identified the level of the main lesion (cervicothoracic junction) as the significant risk factor (odds ratio, 5.00; P = 0.025). Conclusions Palliative surgery for cervical spine metastasis improved the PS and QOL, but a cervicothoracic junction lesion could be a risk factor for a poor outcome.
, Lazaros Vlachopoulos, Karl Grob
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-8; doi:10.1186/s13018-021-02579-z

Abstract:
Background Corrective osteotomies for complex proximal femoral deformities can be challenging; wherefore, subsidies in preoperative planning and during surgical procedures are considered helpful. Three-dimensional (3D) planning and patient-specific instruments (PSI) are already established in different orthopedic procedures. This study gives an overview on this technique at the proximal femur and proposes a new indirect reduction technique using an angle blade plate. Methods Using computed tomography (CT) data, 3D models are generated serving for the preoperative 3D planning. Different guides are used for registration of the planning to the intraoperative situation and to perform the desired osteotomies with the following reduction task. A new valuable tool to perform the correction is the use of a combined osteotomy and implant-positioning guide, with indirect deformity reduction over an angle blade plate. Results An overview of the advantages of 3D planning and the use of PSI in complex corrective osteotomies at the proximal femur is provided. Furthermore, a new technique with indirect deformity reduction over an angle blade plate is introduced. Conclusion Using 3D planning and PSI for complex corrective osteotomies at the proximal femur can be a useful tool in understanding the individual deformity and performing the aimed deformity reduction. The indirect reduction over the implant is a simple and valuable tool in achieving the desired correction, and concurrently, surgical exposure can be limited to a subvastus approach.
Abbas Abdoli, , Seyed Houssein Saeed Banadaky, Rabeah Sarram
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-6; doi:10.1186/s13018-021-02566-4

Abstract:
Percutaneous release of the A1 pulley has been introduced as a therapeutic approach for trigger fingers and is suggested as an effective and safe alternative, where conservative treatments fail. The aim of the current study was to determine if percutaneous release with a 15° stab knife can effectively result in acceptable efficacy and lower complication rate. Methods In the present study, the percutaneous release of the A1 pulley was evaluated by percutaneous release using a 15° stab knife in 20 fresh-frozen cadaver hands (10 cadavers). One hundred fingers were finally included in the present study. The success rate of A1 pulley release as well as the complications of this method including digital vascular injury, A2 pulley injury, and superficial flexor tendon injury was evaluated, and finally, the data were analyzed by the SPSS software. Results The results showed a success rate of 75% for A1 pulley release in four fingers, followed by eleven fingers (90%) and eighty-five fingers (100%). Therefore, the A1 pulley was found to be completely released in eighty-five fingers (100%). Overall, the mean of A1 pulley release for these fingers was determined as 97.9%, indicating that percutaneous trigger finger release can be an effective technique using a 15° stab knife. Furthermore, our findings revealed no significant difference in the amount of A1 pulley release in each of the fingers in the right and left hands. Additionally, 17 fingers developed superficial scrape in flexor tendons, while 83 fingers showed no flexor tendons injuries and no other injuries (i.e., vascular, digital nerve, and A2 pulley injuries). Conclusions Percutaneous release of the A1 pulley using a 15° stab knife was contributed to acceptable efficacy and a relatively good safety in the cadaveric model.
Ye Peng, Gongzi Zhang, Shuwei Zhang, Xinran Ji, Junwei Li, Chengfei Du, Wen Zhao,
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-9; doi:10.1186/s13018-021-02581-5

Abstract:
Objective To compare the biomechanical stability of transsacral-transiliac screw fixation and lumbopelvic fixation for “H”- and “U”-type sacrum fractures with traumatic spondylopelvic dissociation. Methods Finite element models of “H”- and “U”-type sacrum fractures with traumatic spondylopelvic dissociation were created in this study. The models mimicked the standing position of a human. Fixation with transsacral-transiliac screw fixation, lumbopelvic fixation, and bilateral triangular fixation were simulated. Biomechanical tests of instability were performed, and the fracture gap displacement, anteflexion, rotation, and stress distribution after fixation were assessed. Results For H-type fractures, the three kinds of fixation ranked by stability were bilateral triangular fixation > lumbopelvic fixation > transsacral-transiliac screw fixation in the vertical and anteflexion directions, bilateral triangular fixation > transsacral-transiliac S1 and S2 screw fixation > lumbopelvic fixation in rotation. The largest displacements in the vertical, anteflexion, and rotational directions were 0.57234 mm, 0.37923 mm, and 0.13076 mm, respectively. For U-type fractures, these kinds of fixation ranked by stability were bilateral triangular fixation > lumbopelvic fixation > transsacral-transiliac S1 and S2 screw fixation > transsacral-transiliac S1 screw fixation in the vertical, anteflexion, and rotational directions. The largest displacements in the vertical, anteflexion, and rotational directions were 0.38296 mm, 0.33976 mm, and 0.05064 mm, respectively. Conclusion All these kinds of fixation met the mechanical criteria for clinical applications. The biomechanical analysis showed better bilateral balance with transsacral-transiliac screw fixation. The maximal displacement for these types of fixation was less than 1 mm. Percutaneous transsacral-transiliac screw fixation can be considered the best option among these kinds of fracture fixation.
Joshua Disatham, Lisa Brennan, Daniel Chauss, Jason Kantorow, Behdad Afzali, Marc Kantorow
Published: 3 July 2021
BMC Genomics, Volume 22, pp 1-20; doi:10.1186/s12864-021-07795-9

Abstract:
Background During eye lens development the embryonic vasculature regresses leaving the lens without a direct oxygen source. Both embryonically and throughout adult life, the lens contains a decreasing oxygen gradient from the surface to the core that parallels the natural differentiation of immature surface epithelial cells into mature core transparent fiber cells. These properties of the lens suggest a potential role for hypoxia and the master regulator of the hypoxic response, hypoxia-inducible transcription factor 1 (HIF1), in the regulation of genes required for lens fiber cell differentiation, structure and transparency. Here, we employed a multiomics approach combining CUT&RUN, RNA-seq and ATACseq analysis to establish the genomic complement of lens HIF1α binding sites, genes activated or repressed by HIF1α and the chromatin states of HIF1α-regulated genes. Results CUT&RUN analysis revealed 8375 HIF1α-DNA binding complexes in the chick lens genome. One thousand one hundred ninety HIF1α-DNA binding complexes were significantly clustered within chromatin accessible regions (χ2 test p < 1 × 10− 55) identified by ATACseq. Formation of the identified HIF1α-DNA complexes paralleled the activation or repression of 526 genes, 116 of which contained HIF1α binding sites within 10kB of the transcription start sites. Some of the identified HIF1α genes have previously established lens functions while others have novel functions never before examined in the lens. GO and pathway analysis of these genes implicate HIF1α in the control of a wide-variety of cellular pathways potentially critical for lens fiber cell formation, structure and function including glycolysis, cell cycle regulation, chromatin remodeling, Notch and Wnt signaling, differentiation, development, and transparency. Conclusions These data establish the first functional map of genomic HIF1α-DNA complexes in the eye lens. They identify HIF1α as an important regulator of a wide-variety of genes previously shown to be critical for lens formation and function and they reveal a requirement for HIF1α in the regulation of a wide-variety of genes not yet examined for lens function. They support a requirement for HIF1α in lens fiber cell formation, structure and function and they provide a basis for understanding the potential roles and requirements for HIF1α in the development, structure and function of more complex tissues.
, Cristina Marullo, Manila Bonciani, Milena Vainieri
BMC Health Services Research, Volume 21, pp 1-11; doi:10.1186/s12913-021-06628-5

Abstract:
Background Several technological innovations have been introduced in healthcare over the years, and their implementation proved crucial in addressing challenges of modern health. Healthcare workers have frequently been called upon to become familiar with technological innovations that pervade every aspect of their profession, changing their working schedule, habits, and daily actions. Purpose An in-depth analysis of the paths towards the acceptance and use of technology may facilitate the crafting and adoption of specific personnel policies taking into consideration definite levers, which appear to be different in relation to the age of nurses. Approach The strength of this study is the application of UTAUT model to analyse the acceptance of innovations by nurses in technology-intensive healthcare contexts. Multidimensional Item Response Theory is applied to identify the main dimensions characterizing the UTAUT model. Paths are tested through two stage regression models and validated using a SEM covariance analysis. Results The age is a moderator for the social influence: social influence, or peer opinion, matters more for young nurse. Conclusion The use of MIRT to identify the most important items for each construct of UTAUT model and an in-depth path analysis helps to identify which factors should be considered a leverage to foster nurses’ acceptance and intention to use new technologies (o technology-intensive devices). Practical implications Young nurses may benefit from the structuring of shifts with the most passionate colleagues (thus exploiting the social influence), the participation in ad hoc training courses (thus exploiting the facilitating conditions), while other nurses could benefit from policies that rely on the stressing of the perception of their expectations or the downsizing of their expectancy of the effort in using new technologies.
Omid Dadras, Seyed Ahmad Seyed Alinaghi, Amirali Karimi, Mehrzad MohsseniPour, Alireza Barzegary, Farzin Vahedi, Zahra Pashaei, Pegah Mirzapour, Amirata Fakhfouri, Ghazal Zargari, et al.
European Journal of Medical Research, Volume 26, pp 1-13; doi:10.1186/s40001-021-00539-1

Abstract:
Introduction Since the outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began, necessary measures to prevent virus transmission and reduce mortality have been implemented, including mandatory public use of masks, regular hand-sanitizing and hand-washing, social distancing, avoidance of crowds, remote work, and cancellation of public events. During and after the introduction of COVID-19 lockout, we performed a systematic review of available published literature to investigate the incidence of seasonal influenza and other respiratory viral infections. Methods PubMed, Embase, Web of Science, Scopus, Science Direct, Google Scholar, Research Gate, and the World Health Organization databases and websites were systematically searched for original studies concerning the impact of COVID-19 prevention means and measures on other common respiratory infectious diseases during the pandemic published by March 2021. Results The findings showed that the adherence to health protocols to prevent COVID-19 could help to reduce the incidence of other infectious diseases such as influenza, pneumonia, and Mycobacterium tuberculosis. Conclusion The implemented prevention measures and protocols might have reduced the incidence of influenza and some other common respiratory infections. However, controversies exist on this matter and future large population-based studies might provide further information to address these controversies.
Jing Wen, Ting Yang, Jiang Zhu, Min Guo, Xi Lai, Ting Tang, Li Chen, Jie Chen, Ming Xue,
Published: 3 July 2021
BMC Pediatrics, Volume 21, pp 1-9; doi:10.1186/s12887-021-02775-0

Abstract:
Background Vitamin A deficiency (VAD) and sleep disturbances have been reported in children with autism spectrum disorder (ASD). The influence of vitamin A (VA) levels on sleep regulation and sleep disturbances in ASD has garnered concern. The present study aimed to characterize the association of VA levels with sleep disturbances in children with ASD. Methods This cross-sectional study compared children with ASD (n = 856) to typically developing children (TDC; n = 316). We used the Children’s Sleep Habits Questionnaire to assess sleep disturbances, Childhood Autism Rating Scale to evaluate the severity of autism symptoms, and Autism Behavior Checklist and Social Responsiveness Scale to assess autism behaviors. Serum VA levels were estimated using high-performance liquid chromatography. Multivariable linear regression and two-way analysis of variance were performed to investigate if VAD was related to sleep disturbances in children with ASD. Results Children with ASD had lower serum VA levels and a higher prevalence of sleep disturbances than TDC did. The incidence of VAD in ASD children with sleep disturbances was higher, and the symptoms more severe than those without sleep disturbances and TDC. Interestingly, the interaction between VAD and sleep disturbances was associated with the severity of autism symptoms. Conclusion VAD and sleep disturbances are associated with the core symptoms of ASD in children. Regular monitoring of sleep and VA levels may be beneficial for children with ASD. Trial registration Chinese Clinical Trial Registry, registration number: ChiCTR-ROC-14005442, registration date: December 9th 2014.
Tsegaye Gebremedhin, Tesfa Sewunet Alamneh, Asebe Hagos, Beimnet Desalegn,
BMC Pregnancy and Childbirth, Volume 21, pp 1-10; doi:10.1186/s12884-021-03896-1

Abstract:
Background Mother-to-child transmission (MTCT) is the largest source of HIV infection in children below the age of 15 years, and more than 90% of pediatric HIV are infected through mother to child transmission. Without treatment, one-half of those infected children will die before the age of 2 years. Despite this, there is limited evidence on PMTCT and its determinants. Therefore, this study aimed to determine the factors affecting the PMTCT service utilisation in Ethiopia. Methods A two-stage stratified sampling technique was used to identify 4081 women from 2016 Ethiopian Demographic and Health Survey (EDHS). A multilevel mixed-effect binary logistic regression analysis was used to identify the individual and community level factors associated with PMTCT services utilisation. In the final model, a p-value of < 0.05 and Adjusted Odds Ratio (AOR) with 95% confidence interval (CI) were used to declare statistically significant factors with the utilisation. Results Overall, 21.9% (95% CI, 20.6–23.2) of the women were utilized PMTCT services. Educational status; primary (AOR: 1.65, 95% CI: 1.27–2.13), secondary (AOR: 1.52, 95% CI: 1.03–2.24) and higher school (AOR: 2.48, 95% CI: 1.45–4.22), poorer (AOR: 1.62, 95% CI: 1.12–2.37), middle (AOR: 1.82, 95% CI: 1.10–3.02), richer (AOR: 2.44, 95% CI: 1.42–4.21) and richest (AOR: 4.45, 95% CI: 2.43–8.14) wealth status and orthodox religion follower (AOR: 1.62, 95% CI: 1.22–2.16) were the individual level factors. Moreover, having basic (AOR: 1.66, 95% CI: 1.34–2.06) and comprehensive (AOR: 1.73, 95% CI: 1.38–2.18) knowledge on HIV prevention methods, having knowledge on MTCT of HIV (AOR: 2.69, 95% CI: 2.16–3.36) were also factors at individual level. Whereas, rural residence (AOR: 0.52, 95% CI: 0.32–0.85) was the community level factors that affects the utilization. Conclusions Less than one-fourth of the mothers had utilised the PMTCT services in Ethiopia. To increase the utilisation of the services, the health care providers should give emphases on counselling, awareness creation, and strengthen the existing frontline integrated health care services in the country.
, Siwaphon Paksee, Aphidet Duangya, Padchanee Sangthong, Sittiruk Roytrakul, Sucheewin Krobthong, Wipob Suttana, Nathupakorn Dechsupa
BMC Complementary Medicine and Therapies, Volume 21, pp 1-19; doi:10.1186/s12906-021-03363-6

Abstract:
Background Radioresistance can pose a significant obstacle to the effective treatment of breast cancers. Epithelial–mesenchymal transition (EMT) is a critical step in the acquisition of stem cell traits and radioresistance. Here, we investigated whether Maprang seed extract (MPSE), a gallotannin-rich extract of seed from Bouea macrophylla Griffith, could inhibit the radiation-induced EMT process and enhance the radiosensitivity of breast cancer cells. Methods Breast cancer cells were pre-treated with MPSE before irradiation (IR), the radiosensitizing activity of MPSE was assessed using the colony formation assay. Radiation-induced EMT and stemness phenotype were identified using breast cancer stem cells (CSCs) marker (CD24−/low/CD44+) and mammosphere formation assay. Cell motility was determined via the wound healing assay and transwell migration. Radiation-induced cell death was assessed via the apoptosis assay and SA-β-galactosidase staining for cellular senescence. CSCs- and EMT-related genes were confirmed by real-time PCR (qPCR) and Western blotting. Results Pre-treated with MPSE before irradiation could reduce the clonogenic activity and enhance radiosensitivity of breast cancer cell lines with sensitization enhancement ratios (SERs) of 2.33 and 1.35 for MCF7 and MDA-MB231cells, respectively. Pretreatment of breast cancer cells followed by IR resulted in an increased level of DNA damage maker (γ-H2A histone family member) and enhanced radiation-induced cell death. Irradiation induced EMT process, which displayed a significant EMT phenotype with a down-regulated epithelial marker E-cadherin and up-regulated mesenchymal marker vimentin in comparison with untreated breast cancer cells. Notably, we observed that pretreatment with MPSE attenuated the radiation-induced EMT process and decrease some stemness-like properties characterized by mammosphere formation and the CSC marker. Furthermore, pretreatment with MPSE attenuated the radiation-induced activation of the pro-survival pathway by decrease the expression of phosphorylation of ERK and AKT and sensitized breast cancer cells to radiation. Conclusion MPSE enhanced the radiosensitivity of breast cancer cells by enhancing IR-induced DNA damage and cell death, and attenuating the IR-induced EMT process and stemness phenotype via targeting survival pathways PI3K/AKT and MAPK in irradiated breast cancer cells. Our findings describe a novel strategy for increasing the efficacy of radiotherapy for breast cancer patients using a safer and low-cost natural product, MPSE.
Kaiwen Cai, Kefeng Luo, Jinjin Zhu, Kai Zhang, Shengkai Yu, Yi Ye,
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-8; doi:10.1186/s13018-021-02570-8

Abstract:
Study design A retrospective cohort study. Objective To investigate the radiological and clinical outcomes of patients with or without pedicle-screw rod fixation (PSRF) in OLIF surgery. Methods Between June 2017 and December 2019, 66 consecutive patients who underwent OLIF surgery at two centers were divided into stand-alone and combined groups according to whether or not PSRF was used. Imaging and clinical data were collected preoperatively, postoperatively, 3 and 6 months postoperatively, and at the last follow-up. Related coefficient and multiple linear regression analysis was used to detect the influencing factors of cage subsidence (CS). Results There was a lower baseline BMD in the combined group (p = 0.005). The combined group showed superior VAS score at 3 months postoperatively, although there was no difference in long-term VAS and ODI scores between the two groups. The foraminal height (FH) of the two groups was comparable at preoperatively, postoperatively, and 3 months postoperatively, but the combined group showed better maintenance of FH at 6 months postoperatively (p = 0.049) and last follow-up (p = 0.019). The total CS (tCS) of the combined group was lower than that of the stand-alone group during the whole follow-up period (all p ≤ 0.001). Multiple linear regression suggested that lower BMD was the risk factor for main CS, and PSRF could significantly reduce the BMD threshold for severe CS (−4.77 vs −1.38). Conclusions OLIF combined with PSRF can effectively avoid foraminal height loss and prevent severe CS, which may be more suitable for patients with osteoporosis or osteopenia and improve clinical outcomes.
Maliha Fansur, Nagib A. Yurdi,
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-8; doi:10.1186/s13018-021-02559-3

Abstract:
Background The purpose of total hip arthroplasty (THA) post-surgery and proper physiotherapy is positive recovery for the patient. Consideration is given to hip replacement biomechanics by ensuring no discrepancies in limb length (LL) and a stable prosthesis. Therefore, the patient must have proper preoperative planning and communication and a clear understanding of what to expect. Methods A prospective series of 59 THA operated by a single surgeon via Hardinge approach was studied, using an intraoperative calliper (CAL) to predict the change of LL and offset. We compared the results of the intraoperative changes before and after THA implantation with the reference of these values on anteroposterior x-ray pelvis. The importance of leg length balance and a good offset restoration is questioned, and the effect of component subsidence on leg length is considered. Results The average preoperative leg length discrepancy was −6.0 mm, postoperatively +3.6 mm. There was a strong correlation between the CAL measurements and the values on the x-ray (LL, r=0.873, p<0.01; offset, r=0.542, p<0.01). Reliability is better for limb length than for offset. These results are comparable within the literature and the statistical results from other studies reviewed. In addition, we evaluate the importance of subsidence of the prosthesis components for long-term results. Conclusion The intraoperative use of CAL gives excellent results in predicting the final LL and offset after THA. Considering subsidence of prosthesis components, a target zone around +5 mm might be more suitable for leg length directly postoperatively. Moreover, surgeons must discuss the topic of leg length discrepancy (LLD) intensively with the patient pre-operatively. Level of evidence Level 4, prospective cohort study
Shaobai Wang, Xiaolong Zeng, Liang Huangfu, Zhenyan Xie, Limin Ma, , Yu Zhang
Journal of Orthopaedic Surgery and Research, Volume 16, pp 1-7; doi:10.1186/s13018-021-02576-2

Abstract:
Background The Opti_Knee system, a marker-based motion capture system, tracks and analyzes the 6 degrees of freedom (6DOF) motion of the knee joint. However, the validation of the accuracy of this gait system had not been previously reported. The objective of this study was to validate and the system. Two healthy subjects were recruited for the study. Methods The 6DOF kinematics of the knee during flexion–extension and level walking cycles of the knee were recorded by Opti_Knee and compared to those from a biplanar fluoroscopy system. The root mean square error (RMSE) of knee kinematics in flexion–extension cycles were compared between the two systems to validate the accuracy at which they detect basic knee motions. The RMSE of kinematics at key events of gait cycles (level walking) were compared to validate the accuracy at which the systems detect functional knee motion. Pearson correlation tests were conducted to assess similarities in knee kinematic trends between the two systems. Results In flexion–extension cycles, the average translational accuracy (RMSE) was between 2.7 and 3.7 mm and the average rotational accuracy was between 1.7 and 3.8°. The Pearson correlation of coefficients for flexion–extension cycles was between 0.858 and 0.994 for translation and 0.995-0.999 for angles. In gait cycles, the RMSEs of angular knee kinematics were 2.3° for adduction/abduction, 3.2° for internal/external rotation, and 1.4° for flexion/extension. The RMSEs of translational kinematics were 4.2 mm for anterior/posterior translation, 3.3 mm for distal/proximal translation, and 3.2 mm for medial/lateral translation. The Pearson correlation of coefficients values was between 0.964 and 0.999 for angular kinematics and 0.883 and 0.938 for translational kinematics. Conclusion The Opti_Knee gait system exhibited acceptable accuracy and strong correlation strength compared to biplanar fluoroscopy. The Opti _Knee may serve as a promising portable clinical system for dynamic functional assessments of the knee.
Wang Wang, Jiangmiao Liu, Hai Wang, Tong Li,
Published: 3 July 2021
Plant Methods, Volume 17, pp 1-10; doi:10.1186/s13007-021-00774-x

Abstract:
Background CRISPR/Cas9 is a rapidly developing genome editing technology in various biological systems due to its efficiency, portability, simplicity and versatility. This editing technology has been successfully applied in in several important plants of Solanaceae such as tomato, tobacco, potato, petunia and groundcherry. Wolfberry ranked the sixth among solanaceous crops of outstanding importance in China following potato, tomato, eggplant, pepper and tobacco. To date, there has been no report on CRISPR/Cas9 technology to improve Lycium ruthenicum due to the unknown genome sequencing and the lack of efficient regeneration and genetic transformation systems. Results In this study, we have established an efficientregeneration and genetic transformation system of Lycium ruthenicum. We have used this system to validate target sites for fw2.2, a major fruit weight quantitative trait locus first identified from tomato and accounted for 30% of the variation in fruit size. In our experiments, the editing efficiency was very high, with 95.45% of the transgenic lines containing mutations in the fw2.2 target site. We obtained transgenic wolfberry plants containing four homozygous mutations and nine biallelic mutations in the fw2.2 gene. Conclusions These results suggest that CRISPR-based gene editing is effective for the improvement of black wolfberry traits, and we expect this approach to be routinely applied to this important economic fruit.
Yuan-Pin Lin, Hsing-Yi Liang, Yueh-Sheng Chen, Cheng-Hsien Lu, Yih-Ru Wu, Yung-Yee Chang, Wei-Che Lin
Journal of NeuroEngineering and Rehabilitation, Volume 18, pp 1-12; doi:10.1186/s12984-021-00897-1

Abstract:
Background Patients with Parkinson’s disease (PD) can develop impulse control disorders (ICDs) while undergoing a pharmacological treatment for motor control dysfunctions with a dopamine agonist (DA). Conventional clinical interviews or questionnaires can be biased and may not accurately diagnose at the early stage. A wearable electroencephalogram (EEG)-sensing headset paired with an examination procedure can be a potential user-friendly method to explore ICD-related signatures that can detect its early signs and progression by reflecting brain activity. Methods A stereotypical Go/NoGo test that targets impulse inhibition was performed on 59 individuals, including healthy controls, patients with PD, and patients with PD diagnosed by ICDs. We conducted two Go/NoGo sessions before and after the DA-pharmacological treatment for the PD and ICD groups. A low-cost LEGO-like EEG headset was used to record concurrent EEG signals. Then, we used the event-related potential (ERP) analytical framework to explore ICD-related EEG abnormalities after DA treatment. Results After the DA treatment, only the ICD-diagnosed PD patients made more behavioral errors and tended to exhibit the deterioration for the NoGo N2 and P3 peak amplitudes at fronto-central electrodes in contrast to the HC and PD groups. Particularly, the extent of the diminished NoGo-N2 amplitude was prone to be modulated by the ICD scores at Fz with marginal statistical significance (r = − 0.34, p = 0.07). Conclusions The low-cost LEGO-like EEG headset successfully captured ERP waveforms and objectively assessed ICD in patients with PD undergoing DA treatment. This objective neuro-evidence could provide complementary information to conventional clinical scales used to diagnose ICD adverse effects.
Julio Vallejos, Rodrigo Zoni, María Bangher, Silvina Villamandos, Angelina Bobadilla, Fabian Plano, Claudia Campias, Evangelina Chaparro Campias, Maria Fernanda Medina, Fernando Achinelli, et al.
Published: 2 July 2021
BMC Infectious Diseases, Volume 21, pp 1-11; doi:10.1186/s12879-021-06348-5

Abstract:
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has changed our lives. The scientific community has been investigating re-purposed treatments to prevent disease progression in coronavirus disease (COVID-19) patients. Objective To determine whether ivermectin treatment can prevent hospitalization in individuals with early COVID-19. Design, setting and participants: A randomized, double-blind, placebo-controlled study was conducted in non-hospitalized individuals with COVID-19 in Corrientes, Argentina. Patients with SARS-CoV-2 positive nasal swabs were contacted within 48 h by telephone to invite them to participate. The trial randomized 501 patients between August 19th 2020 and February 22nd 2021. Intervention Patients were randomized to ivermectin (N = 250) or placebo (N = 251) arms in a staggered dose, according to the patient’s weight, for 2 days. Main outcomes and measures The efficacy of ivermectin to prevent hospitalizations was evaluated as primary outcome. We evaluated secondary outcomes in relationship to safety and other efficacy end points. Results The mean age was 42 years (SD ± 15.5) and the median time since symptom onset to the inclusion was 4 days [interquartile range 3–6]. The primary outcome of hospitalization was met in 14/250 (5.6%) individuals in ivermectin group and 21/251 (8.4%) in placebo group (odds ratio 0.65; 95% confidence interval, 0.32–1.31; p = 0.227). Time to hospitalization was not statistically different between groups. The mean time from study enrollment to invasive mechanical ventilatory support (MVS) was 5.25 days (SD ± 1.71) in ivermectin group and 10 days (SD ± 2) in placebo group, (p = 0.019). There were no statistically significant differences in the other secondary outcomes including polymerase chain reaction test negativity and safety outcomes. Limitations Low percentage of hospitalization events, dose of ivermectin and not including only high-risk population. Conclusion Ivermectin had no significant effect on preventing hospitalization of patients with COVID-19. Patients who received ivermectin required invasive MVS earlier in their treatment. No significant differences were observed in any of the other secondary outcomes. Trial registration ClinicalTrials.gov NCT04529525.
International Journal of Geo-Engineering, Volume 12, pp 1-21; doi:10.1186/s40703-021-00147-2

Abstract:
In the sense of challenging economic situation, it is difficult to perform laboratory tests in a whole intended area to define the soil characteristics for whatever task or situation within an entire city. Hence, this study has used the spatial analysis through applying the inverse distance weighted (IDW) technique to integrate with the available data for 56 different soil samples collected from various depths of Kirkuk city. The studied characteristics were mainly classified to physical soil properties included gravel, sand, silt, and clay contents with chemical soil properties included organic and gypsum contents, pH content, sulfur trioxide, and total dissolved solids (TDS) content. Moreover, statistical investigations such as physico-chemical correlation, linear single and linear multi regression models have been applied. The results of this study have focused on constructing thematic digital maps for visualizing different physical and chemical characteristics of Kirkuk soil. In statistical analysis, negative linear correlations are obtained from the relation between the values of the pH, gypsum, organic, and SO3 contents with the increase of the gravel content, whereas a positive linear correlation is attained for the values of TDS content with the increase of the gravel content. Furthermore, the proposed linear multi regression model predicts the pH values reasonably where most of the values were close to the equality line. The obtained digital maps accompanied with the statistical models will provide comprehensive spatial, agricultural, chemical and mechanical visualizations of the nature and morphology of the soils in Kirkuk city.
Kurniawan Kurniawan, I Dewa Nyoman Wibawa, Gde Somayana, , I Made Mulyawan
Journal of Medical Case Reports, Volume 15, pp 1-6; doi:10.1186/s13256-021-02915-1

Abstract:
Background Hemobilia is a rare cause of upper gastrointestinal bleeding that originates from the biliary tract. It is infrequently considered in diagnosis, especially in the absence of abdominal trauma or history of hepatopancreatobiliary procedure, such as cholecystectomy, which can cause arterial pseudoaneurysm. Prompt diagnosis is crucial because its management strategy is distinct from other types of upper gastrointestinal bleeding. Here, we present a case of massive hemobilia caused by the rupture of a gastroduodenal artery pseudoaneurysm in a patient with a history of laparoscopic cholecystectomy 3 years prior to presentation. Case presentation A 44-year-old Indonesian female presented to the emergency department with complaint of hematemesis and melena accompanied by abdominal pain and icterus. History of an abdominal trauma was denied. However, she reported having undergone a laparoscopic cholecystectomy 3 years prior to presentation. On physical examination, we found anemic conjunctiva and icteric sclera. Nonvariceal bleeding was suspected, but esophagogastroduodenoscopy showed a blood clot at the ampulla of Vater. Angiography showed contrast extravasation from a gastroduodenal artery pseudoaneurysm. The patient underwent pseudoaneurysm ligation and excision surgery to stop the bleeding. After surgery, the patient’s vital signs were stable, and there was no sign of rebleeding. Conclusion Gastroduodenal artery pseudoaneurysm is a rare complication of laparoscopic cholecystectomy. The prolonged time interval, as compared with other postcholecystectomy hemobilia cases, resulted in hemobilia not being considered as an etiology of the gastrointestinal bleeding at presentation. Hemobilia should be considered as a possible etiology of gastrointestinal bleeding in patients with history of cholecystectomy, regardless of the time interval between the invasive procedure and onset of bleeding.
Published: 2 July 2021
Insights into Imaging, Volume 12, pp 1-21; doi:10.1186/s13244-021-01026-1

Abstract:
Lung cancer has the highest mortality rate of any tumour type. The main driver of lung tumour growth and development is uncontrolled cellular proliferation. Poor patient outcomes are partly the result of the limited range of effective anti-cancer therapies available and partly due to the limited accuracy of biomarkers to report on cell proliferation rates in patients. Accordingly, accurate methods of diagnosing, staging and assessing response to therapy are crucial to improve patient outcomes. One effective way of assessing cell proliferation is to employ non-invasive evaluation using 3'-deoxy-3'-[18F]fluorothymidine ([18F]FLT) positron emission tomography [18F]FLT-PET. [18F]FLT, unlike the most commonly used PET tracer [18F]fluorodeoxyglucose ([18F]FDG), can specifically report on cell proliferation and does not accumulate in inflammatory cells. Therefore, this radiotracer could exhibit higher specificity in diagnosis and staging, along with more accurate monitoring of therapy response at early stages in the treatment cycle. This review summarises and evaluates published studies on the clinical use of [18F]FLT to diagnose, stage and assess response to therapy in lung cancer.
Miguel A. Khoury, Karim Chamari, , Khalid Alkhelaifi, Trueba Ricardo, Couto Damián, Pieter D’Hooghe
Journal of Experimental Orthopaedics, Volume 8, pp 1-11; doi:10.1186/s40634-021-00358-7

Abstract:
Purpose Effect of ultrasound guided injections of autologous ASCs in chronic recalcitrant patellar tendinopathy. Methods Fourteen patients (16 knees, 12/2 males/females) with chronic, recalcitrant (unsuccessfully treated with nonoperative treatments) insertional PT underwent clinical evaluation and magnetic resonance imaging (MRI) before intervention. Stromal vascular fraction cells (SVF) were expanded by in-vitro culture and characterized by flow cytometry. Players were injected with three bi-weekly injections of ASCs followed by physiotherapy. They underwent serial clinical evaluations during a 12-month period with repeated MRI at 6-month post-injection. Results Victorian Institute of sports assessment-patellar tendon questionnaire (VISA-P) scores improved from 43.8 ± 4.9 at baseline to 58.1 ± 7.1, 70.3 ± 7.9 and 78.7 ± 7.5 at 3, 6, and12months follow-up, respectively. (p = 0.0004 comparing each variable with the previous one). Mean Visual analogue pain in sports (VAS-sport) score during practice significantly decreased from 7.4 ± 0.5 at baseline to 5.2 ± 1.5 9 (p = 0.0005), 3.3 ± 1.1 (p = 0.0004) and 1.5 ± 0.7 (P = 0.0004) at 3, 6, and 12 months, respectively. Mean Tegner-scores for patients were 8.0 ± 0.8 before injury and 2.3 ± 0.9 before treatment, thereafter, improving to 4.8 ± 0.8 and 7.2 ± 0.7 at 6- and 12- months, respectively (p = 0.0001). MRI assessed tendon width’ did not change over the first 6 months post-intervention. Significant changes were observed for: tendon thickness (12.8 ± 1.1 to 10.9 ± 0.7, P = 0.0001); tear length (9.3 ± 1.3 to 2.3 ± 0.7, P = 0.0001), tear width (6.3 ± 0.8 to 3.4 ± 0.4, P = 0.0001), and tear thickness (4.6 ± 0.4 to 2.6 ± 0., P = 0.0001) at baseline and 6 months, respectively. Conclusion Patients with recalcitrant insertional PT showed significant clinical improvement and structural repair at the patellar insertional tendinopathy after injections of autologous ASCs. Results of this study are promising and open a new biological therapeutic modality to treat PT.
Sowmya Chary, Karin Amrein, Djøra I. Soeteman, Sangeeta Mehta,
Published: 2 July 2021
Annals of Intensive Care, Volume 11, pp 1-8; doi:10.1186/s13613-021-00889-3

Abstract:
Background Bibliometric analyses show gender bias against women in scientific publications and citations. We hypothesized that a metric of an individual senior author’s inclusivity of women as first authors in critical care publications would predict gender inequality. Methods Using PubMed and Web of Science, we conducted a bibliometric analysis of original research publications in critical care from 2008 to 2018 in 11 specialty and general journals. Gender for first and senior authors was assigned by a gender determination application, and manually if needed. For all senior authors we defined the novel Female First Author Index (FFA-index) = #Female first authors in publications by an individual senior author/Total # publications by that senior author. We produced a novel interactive web-based application using the R package Shiny to increase potential utilization of the FFA-index. Results Of 7370 publications, 30.4% had female first authors and 15.5% had female senior authors. After adjustment for impact factor, journal, year of publication, number of authors, country, and gender determination accuracy, female senior authorship was associated with a 1.9-fold increase in female first authorship [OR = 1.85 (95% CI 1.62, 2.11); p < 0.001] compared with male senior authorship. The mean (SD) FFA-index for all individual senior authors was 30.5 (42.9); with a significant difference in FFA-index between male and female senior authors (27.6 versus 42.5, respectively; p < 0.001). The interactive web-based application (FFA-index App) produces the same FFA-index output as our study results. Conclusions Female representation at prominent authorship positions in critical care publications is still far from achieving gender parity. By creating an authorship index score, we propose a frame of reference for the advancement of female first authorship.
Tomas Urbina, Florence Canoui-Poitrine, Camille Hua, Richard Layese, Aline Alves, Rachida Ouedraogo, Romain Bosc, Emilie Sbidian, Olivier Chosidow, Armand Mekontso Dessap, et al.
Published: 2 July 2021
Annals of Intensive Care, Volume 11, pp 1-11; doi:10.1186/s13613-021-00891-9

Abstract:
Background Compared to other life-threatening infection survivors, long-term health-related quality of life (QOL) of patients surviving necrotizing soft-tissue infections (NSTI) and its determinants are little known. In this monocentric prospective cohort including NSTI survivors admitted between 2014 and 2017, QOL was assessed during a phone interview using the 36-Item Short-Form Health Survey (SF-36), the Hospital Anxiety and Depression (HAD), the activity of daily living (ADL), instrumental ADL (IADL) scales and the Impact of Event Scale-Revised (IES-R). The primary outcome measure was the SF-36 physical component summary (PCS). NSTI patients were compared according to intensive care unit (ICU) admission status. ICU survivors were matched on SAPS II with non-NSTI related septic shock survivors. Results Forty-nine NSTI survivors were phone-interviewed and included in the study. Median PCS was decreased compared to the reference population [− 0.97 (− 2.27; − 0.08) SD]. Previous cardiac disease was the only variable associated with PCS alteration [multivariate regression coefficient: − 8.86 (− 17.64; − 0.07), p = 0.048]. Of NSTI survivors, 15.2% had a HAD-D score ≥ 5 and 61.2% an IES-R score ≥ 33. ICU admission was not associated with lower PCS [35.21 (25.49–46.54) versus (vs) 41.82 (24.12–51.01), p = 0.516], but with higher IES-R score [14 (7.5–34) vs 7 (3–18), p = 0.035] and a higher proportion of HAD-D score ≥ 5 (28.6 vs 4.0%, p = 0.036). Compared to non-NSTI septic shock-matched controls, NSTI patients had similar PCS [33.81 (24.58; − 44.39) vs 44.87 (26.71; − 56.01), p = 0.706] but higher HAD-D [3.5 (1–7) vs 3 (1.5–6), p = 0.048] and IES-R scores [18 (8–35) vs 8 (3–19), p = 0.049]. Conclusions Long-term QOL in NSTI survivors is severely impaired, similarly to that of non-NSTI septic shock patients for physical compartments, but with more frequent depressive and/or post-traumatic stress disorders. Only ICU admission and previous cardiac disease were predictive of QOL impairment.
Shyam Sundar Santra, Apurba Ghosh, , Khaled Mohamed Khedher, Taher A. Nofal
Advances in Difference Equations, Volume 2021, pp 1-12; doi:10.1186/s13662-021-03474-x

Abstract:
In this work, we present new necessary and sufficient conditions for the oscillation of a class of second-order neutral delay impulsive differential equations. Our oscillation results complement, simplify and improve recent results on oscillation theory of this type of nonlinear neutral impulsive differential equations that appear in the literature. An example is provided to illustrate the value of the main results.
Celsus Ukelina Undie, Ewomazino Ibanga Nnana, Kalenebari Raymond Torporo
Published: 2 July 2021
African Journal of Urology, Volume 27, pp 1-6; doi:10.1186/s12301-021-00195-1

Abstract:
Background Uroliths are stones formed in the urinary tract. Analysis of stones helps to identify risk factors for their development and prevention of recurrence. Standard stone analysis using modern technology is not routinely done in Nigeria. This study sought to determine the chemical composition of urinary stones seen in Abuja, Nigeria. Methods This was a retrospective study on composition of uroliths. Urinary stones surgically removed from 155 patients through minimal access surgical procedures between January 2015 and August 2019 were analysed. Optical crystallography and infrared spectroscopy were used to determine the chemical composition of the urinary stones. Results A total of 155 urinary stones were assembled from the patients. More stones were removed from male patients and the male to female ratio was 1.9:1. Stones were rare in the extremes of age. The predominant location (89.7%) of stones was in the upper urinary tract. All stones were of mixed composition with calcium oxalate accounting for 93.55%. Calcium oxalate, calcium phosphate and uric acid stones were more common in the upper tract, while 2 of the 3 struvite stones were found in the lower tract. Conclusion Stones found in this study were of mixed composition with the most common constituent being Calcium oxalate and the least common, struvite.
Bao-Hui Li, Wen-Yi Yu,
Published: 2 July 2021
BMC Genomic Data, Volume 22, pp 1-17; doi:10.1186/s12863-021-00978-z

Abstract:
Background X chromosome inactivation (XCI) is that one of two chromosomes in mammalian females is silenced during early development of embryos. There has been a statistical measure for the degree of the skewness of XCI for qualitative traits. However, no method is available for such task at quantitative trait loci. Results In this article, we extend the existing statistical measure for the skewness of XCI for qualitative traits, and the likelihood ratio, Fieller’s and delta methods for constructing the corresponding confidence intervals, and make them accommodate quantitative traits. The proposed measure is a ratio of two linear regression coefficients when association exists. Noting that XCI may cause variance heterogeneity of the traits across different genotypes in females, we obtain the point estimate and confidence intervals of the measure by incorporating such information. The hypothesis testing of the proposed methods is also investigated. We conduct extensive simulation studies to assess the performance of the proposed methods. Simulation results demonstrate that the median of the point estimates of the measure is very close to the pre-specified true value. The likelihood ratio and Fieller’s methods control the size well, and have the similar test power and accurate coverage probability, which perform better than the delta method. So far, we are not aware of any association study for the X-chromosomal loci in the Minnesota Center for Twin and Family Research data. So, we apply our proposed methods to these data for their practical use and find that only the rs792959 locus, which is simultaneously associated with the illicit drug composite score and behavioral disinhibition composite score, may undergo XCI skewing. However, this needs to be confirmed by molecular genetics. Conclusions We recommend the Fieller’s method in practical use because it is a non-iterative procedure and has the similar performance to the likelihood ratio method.
Lior Galanti, Dennis Shasha,
Published: 2 July 2021
BMC Bioinformatics, Volume 22, pp 1-16; doi:10.1186/s12859-021-04267-5

Abstract:
Background Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on the ability to classify sequences based on correct decoding of these combinatorial barcodes. The probability of correct decoding is influenced by both sequence quality and the number and arrangement of barcodes. The rising complexity of experimental designs calls for a probability model that accounts for both sequencing errors and random noise, generalizes to multiple combinatorial tags, and can handle any barcoding scheme. The needs for reproducibility and community benchmark standards demand a peer-reviewed tool that preserves decoding quality scores and provides tunable control over classification confidence that balances precision and recall. Moreover, continuous improvements in sequencing throughput require a fast, parallelized and scalable implementation. Results and discussion We developed a flexible, robustly engineered software that performs probabilistic decoding and supports arbitrarily complex barcoding designs. Pheniqs computes the full posterior decoding error probability of observed barcodes by consulting basecalling quality scores and prior distributions, and reports sequences and confidence scores in Sequence Alignment/Map (SAM) fields. The product of posteriors for multiple independent barcodes provides an overall confidence score for each read. Pheniqs achieves greater accuracy than minimum edit distance or simple maximum likelihood estimation, and it scales linearly with core count to enable the classification of > 11 billion reads in 1 h 15 m using < 50 megabytes of memory. Pheniqs has been in production use for seven years in our genomics core facility. Conclusion We introduce a computationally efficient software that implements both probabilistic and minimum distance decoders and show that decoding barcodes using posterior probabilities is more accurate than available methods. Pheniqs allows fine-tuning of decoding sensitivity using intuitive confidence thresholds and is extensible with alternative decoders and new error models. Any arbitrary arrangement of barcodes is easily configured, enabling computation of combinatorial confidence scores for any barcoding strategy. An optimized multithreaded implementation assures that Pheniqs is faster and scales better with complex barcode sets than existing tools. Support for POSIX streams and multiple sequencing formats enables easy integration with automated analysis pipelines.
, Christian Fynbo Christiansen, Buket Öztürk Esen, Charlotte Suetta, Finn Erland Nielsen
Published: 2 July 2021
BMC Geriatrics, Volume 21, pp 1-11; doi:10.1186/s12877-021-02355-y

Abstract:
Background The mortality of older patients after early discharge from hospitals is sparsely described. Information on factors associated with mortality can help identify high-risk patients who may benefit from preventive interventions. The aim of this study was to examine whether demographic factors, comorbidity and admission diagnoses are predictors of 30-day mortality among acutely admitted older patients discharged within 24 h after admission. Methods All medical patients aged ≥65 years admitted acutely to Danish hospitals between 1 January 2013 and 30 June 2014 surviving a hospital stay of ≤24 h were included. Demographic factors, comorbidity, discharge diagnoses and mortality within 30 days were described using data from the Danish National Patient Registry and the Civil Registration System. Cox regression was used to estimate adjusted hazard ratios (aHR) with 95% confidence intervals (CI) for all-cause mortality. Results A total of 93,295 patients (49.4% men) with a median age of 75 years (interquartile range: 69–82 years), were included. Out of these, 2775 patients (3.0%; 95% CI 2.9–3.1%) died within 30 days after discharge. The 30-day mortality was increased in patients with age 76–85 years (aHR 1.59; 1.45–1.75) and 86+ years (aHR 3.35; 3.04–3.70), male gender (aHR 1.22; 1.11–1.33), a Charlson Comorbidity Index of 1–2 (aHR 2.15; 1.92–2.40) and 3+ (aHR 4.07; 3.65–4.54), and unmarried status (aHR 1.17; 1.08–1.27). Discharge diagnoses associated with 30-day mortality were heart failure (aHR 1.52; 1.17–1.95), respiratory failure (aHR 3.18; 2.46–4.11), dehydration (aHR 2.87; 2.51–3.29), constipation (aHR 1.31; 1.02–1.67), anemia (aHR 1.45; 1.27–1.66), pneumonia (aHR 2.24; 1.94–2.59), urinary tract infection (aHR 1.33; 1.14–1.55), dyspnea (aHR 1.57; 1.32–1.87) and suspicion of malignancy (aHR 2.06; 1.64–2.59). Conclusions Three percent had died within 30 days. High age, male gender, the comorbidity burden, unmarried status and several primary discharge diagnoses were identified as independent prognostic factors of 30-day all-cause mortality.
Sheida Shaafi, Fina Hadisi, Mahsa Mahmoudinezhad, Hamidreza Razmi, Seyed Aria Nejadghaderi,
Published: 2 July 2021
BMC Neurology, Volume 21, pp 1-8; doi:10.1186/s12883-021-02257-x

Abstract:
Background Stroke is a major cause of mortality and morbidity. Also, free radicals and oxidative stress are deleterious factor in the stroke progression. We aimed to evaluate the association between oxidative stress markers and odds of having risk factor for stroke or developing stroke. Methods The present case-control study was conducted on 556 participants in Imam-Reza hospital, Tabriz, Iran. Subjects were divided into three group, including individuals with acute ischemic stroke, those who were at risk of stroke, and healthy controls. All enrolled participants except for controls underwent neurological examinations and brain magnetic resonance imaging (MRI). Stroke-related disability and stroke severity were evaluated by modified Rankin Scale (mRS) and National Institutes of Health Stroke Scale (NIHSS), respectively. Serum malondialdehyde (MDA) level and total antioxidant capacity (TAC) were measured within 48 h of the initiation of stroke. One-way ANOVA and Chi-square tests were used for comparing characteristics between groups. Multivariable logistic regression was implemented for odds of stroke based on MDA and TAC quartiles. Also, Spearman’s correlation was utilized. Results Serum MDA, systolic and diastolic blood pressure, cholesterol, and triglyceride were significantly higher in the stroke group than controls. High levels of MDA were associated with increased development of stroke (P-value < 0.001), however TAC and MDA were not associated with having risk factors for stroke (P-value = 1.00 and 0.27, respectively). Also, TAC level was negatively associated with baseline (ρ = − 0.28; P-value = 0.04) and follow-up (ρ = − 0.31; P-value = 0.03) NIHSS scores. Moreover, MDA was correlated with mRS score at follow-up (ρ = − 0.26; P-value = 0.04). Conclusions The balance between antioxidants and oxidants markers might reveal a new approach in this context. Further studies are warranted to identify the source of oxidative stress as well as cessation of the production of oxygen radicals in stroke.
, Ryann Sohaney, Vidhit Puri, Benjamin Wagner, Amy Riddle, Sharon Dickinson, Lena Napolitano, Michael Heung, David Humes, Balazs Szamosfalvi
Published: 2 July 2021
BMC Nephrology, Volume 22, pp 1-12; doi:10.1186/s12882-021-02443-6

Abstract:
Background Regional citrate anticoagulation (RCA) for the prevention of clotting of the extracorporeal blood circuit during continuous kidney replacement therapy (CKRT) has been employed in limited fashion because of the complexity and complications associated with certain protocols. Hypertonic citrate infusion to achieve circuit anticoagulation results in variable systemic citrate- and sodium load and increases the risk of citrate accumulation and hypernatremia. The practice of “single starting calcium infusion rate for all patients” puts patients at risk for clinically significant hypocalcemia if filter effluent calcium losses exceed replacement. A fixed citrate to blood flow ratio, personalized effluent and pre-calculated calcium infusion dosing based on tables derived through kinetic analysis enable providers to use continuous veno-venous hemo-diafiltration (CVVHDF)-RCA in patients with liver citrate clearance of at least 6 L/h. Methods This was a single-center prospective observational study conducted in intensive care unit patients triaged to be treated with the novel pre-calculated CVVHDF-RCA “Non-shock” protocol. RCA efficacy outcomes were time to first hemofilter loss and circuit ionized calcium (iCa) levels. Safety outcomes were surrogate of citrate accumulation (TCa/iCa ratio) and the incidence of acid-base and electrolyte complications. Results Of 53 patients included in the study, 31 (59%) had acute kidney injury and 12 (22.6%) had the diagnosis of cirrhosis at the start of CVVHDF-RCA. The median first hemofilter life censored for causes other than clotting exceeded 70 h. The cumulative incidence of hypernatremia (Na > 148 mM), metabolic alkalosis (HCO3- > 30 mM), hypocalcemia (iCa < 0.9 mM) and hypercalcemia (iCa > 1.5 mM) were 1/47 (1%), 0/50 (0%), 1/53 (2%), 1/53 (2%) respectively and were not clinically significant. The median (25th–75th percentile) of the highest TCa/iCa ratio for every 24-h interval on CKRT was 1.99 (1.91–2.13). Conclusions The fixed citrate to blood flow ratio, as opposed to a titration approach, achieves adequate circuit iCa (< 0.4 mm/L) for any hematocrit level and plasma flow. The personalized dosing approach for calcium supplementation based on pre-calculated effluent calcium losses as opposed to the practice of “one starting dose for all” reduces the risk of clinically significant hypocalcemia. The fixed flow settings achieve clinically desirable steady state systemic electrolyte levels.
Alieh Gholaminejad, Mohammad Fathalipour,
Published: 2 July 2021
BMC Nephrology, Volume 22, pp 1-13; doi:10.1186/s12882-021-02447-2

Abstract:
Background Diabetic nephropathy (DN) is the major complication of diabetes mellitus, and leading cause of end-stage renal disease. The underlying molecular mechanism of DN is not yet completely clear. The aim of this study was to analyze a DN microarray dataset using weighted gene co-expression network analysis (WGCNA) algorithm for better understanding of DN pathogenesis and exploring key genes in the disease progression. Methods The identified differentially expressed genes (DEGs) in DN dataset GSE47183 were introduced to WGCNA algorithm to construct co-expression modules. STRING database was used for construction of Protein-protein interaction (PPI) networks of the genes in all modules and the hub genes were identified considering both the degree centrality in the PPI networks and the ranked lists of weighted networks. Gene ontology and Reactome pathway enrichment analyses were performed on each module to understand their involvement in the biological processes and pathways. Following validation of the hub genes in another DN dataset (GSE96804), their up-stream regulators, including microRNAs and transcription factors were predicted and a regulatory network comprising of all these molecules was constructed. Results After normalization and analysis of the dataset, 2475 significant DEGs were identified and clustered into six different co-expression modules by WGCNA algorithm. Then, DEGs of each module were subjected to functional enrichment analyses and PPI network constructions. Metabolic processes, cell cycle control, and apoptosis were among the top enriched terms. In the next step, 23 hub genes were identified among the modules in genes and five of them, including FN1, SLC2A2, FABP1, EHHADH and PIPOX were validated in another DN dataset. In the regulatory network, FN1 was the most affected hub gene and mir-27a and REAL were recognized as two main upstream-regulators of the hub genes. Conclusions The identified hub genes from the hearts of co-expression modules could widen our understanding of the DN development and might be of targets of future investigations, exploring their therapeutic potentials for treatment of this complicated disease.
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