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, Zaid Al-Ars, Koen Bertels
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249850

Abstract:
In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with a proof-of-concept example to target both the genomics research community and quantum application developers in a self-contained manner. The implementation and results on executing the algorithm from a set of DNA reads to a reconstructed sequence, on a gate-based quantum simulator, the D-Wave quantum annealing simulator and hardware are detailed. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/QE-Lab/QuASeR.
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248489

Abstract:
Accurate streamflow prediction plays a pivotal role in hydraulic project design, nonpoint source pollution estimation, and water resources planning and management. However, the highly non-linear relationship between rainfall and runoff makes prediction difficult with desirable accuracy. To improve the accuracy of monthly streamflow prediction, a seasonal Support Vector Regression (SVR) model coupled to the Soil and Water Assessment Tool (SWAT) model was developed for 13 subwatersheds in the Illinois River watershed (IRW), U.S. Terrain, precipitation, soil, land use and land cover, and monthly streamflow data were used to build the SWAT model. SWAT Streamflow output and the upstream drainage area were used as two input variables into SVR to build the hybrid SWAT-SVR model. The Calibration Uncertainty Procedure (SWAT-CUP) and Sequential Uncertainty Fitting-2 (SUFI-2) algorithms were applied to compare the model performance against SWAT-SVR. The spatial calibration and leave-one-out sampling methods were used to calibrate and validate the hybrid SWAT-SVR model. The results showed that the SWAT-SVR model had less deviation and better performance than SWAT-CUP simulations. SWAT-SVR predicted streamflow more accurately during the wet season than the dry season. The model worked well when it was applied to simulate medium flows with discharge between 5 m3 s-1 and 30 m3 s-1, and its applicable spatial scale fell between 500 to 3000 km2. The overall performance of the model on yearly time series is “Satisfactory”. This new SWAT-SVR model has not only the ability to capture intrinsic non-linear behaviors between rainfall and runoff while considering the mechanism of runoff generation but also can serve as a reliable regional tool for an ungauged or limited data watershed that has similar hydrologic characteristics with the IRW.
, , Kidist Hailu Akenew, Mahlet Tilahun Belete, Eyerusalem Teshome Tena, Genet Gebreselasie Gebretsadik, Aynalem Nebebe Tsegaw, Tigist Birru Woldemariam, Ashenafi Abate Woya, Amare Alemu Melese, et al.
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248108

Abstract:
Background Stunting is a well-established child-health indicator of chronic malnutrition, which reliably gives a picture of the past nutritional history and the prevailing environmental and socioeconomic circumstances. Objective To investigate the prevalence of stunting and associated factors among public primary school children of the Bahir Dar city. Method A cross-sectional study was carried out from March to June 2019. Data were coded and entered into the Epi-Data and exported to SPSS version 23 software. The pupil was stunted if the height- for-age was ≤ -2 SDs from the median growth standards according to the WHO. A descriptive summary was computed using frequency, percent, mean, median and standard deviation. A simple logistic regression model was fitted to identify associated factors between the independent variables and the dependent variable at a 95% confidence interval (CI) and p-value <0.05. Results 370 primary school pupils were included in the study with the mean age of 10.15 (± 2.23 SD) years. 51.6% of the pupils were females. The total prevalence of stunting was 15.13% (95%CI; 11%, 19%). The burden of stunting was higher in the age group of 11 years and older. Pupil’s age older than 11 years (AOR = 15. 6; 95%CI; 3.31, 73.45; p-value < 0. 001) and male sex (AOR = 7. 07; 95%CI: 2.51, 19.89; p-value < 0. 0002) were significantly associated with stunting. Conclusion The prevalence of stunting was relatively lower than the regional estimated stunting level. Older age and male sex were significantly associated with stunting.
, Christine Finn
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248620

Abstract:
Self-esteem has been shown to be both predictive of and predicted by characteristics of romantic relationships. While there is an increasing number of studies yielding support for reciprocal influences between self-esteem and perceived conflict in romantic relationships, longitudinal transactions between these constructs from both partners’ perspectives have not been studied systematically to date. Our aim was to close this gap. To that end, we examined the transactional and longitudinal interplay between self-esteem and perceived relationship conflict in continuing romantic couples from a dyadic perspective. Our sample consisted of N = 1,093 young adult female–male relationships from the German Family Panel. Individuals’ self-esteem, perceived conflict frequency, and their perceptions of their partners’ dysfunctional conflict styles (i.e., unconstructive behavior, withdrawal) were examined annually throughout a time span of five years. Based on dyadic bivariate latent change models, we tested our assumption that self-esteem and aspects of perceived relationship conflict are negatively interrelated within individuals and between partners both within and across time. We found one actor effect of self-esteem on changes in unconstructive behavior above and beyond initial unconstructive behavior levels, supporting self-broadcasting perspectives. Moreover, we found strong support for sociometer perspectives. Actor effects highlighted the importance of perceived conflict frequency for subsequent self-esteem changes. In addition, perceived conflict styles affected both partners’ self-esteem. The results imply that perceiving conflict is a between-person process, and might be more important for the development of self-esteem than vice versa.
Hiroko Enomoto, James Yeatts, Liliana Carbajal, B. Radha Krishnan, Jay P. Madan, Sandeep Laumas, Anthony T. Blikslager, Kristen M. Messenger
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249179

Abstract:
There is no FDA approved therapy for the treatment of celiac disease (CeD), aside from avoidance of dietary gluten. Larazotide acetate (LA) is a first in class oral peptide developed as a tight junction regulator, which is a lead candidate for management of CeD. A delayed release formulation was tested in vitro and predicted release in the mid duodenum and jejunum, the target site of CeD. The aim of this study was to follow the concentration versus time profile of orally administered LA in the small intestine using a porcine model. A sensitive liquid chromatography/tandem mass spectrometry method was developed to quantify LA concentrations in porcine intestinal fluid samples. Oral dosing of LA (1 mg total) in overnight fasted pigs resulted in time dependent appearance of LA in the distal duodenum and proximal jejunum. Peak LA concentrations (0.32–1.76 μM) occurred at 1 hour in the duodenum and in proximal jejunum following oral dosing, with the continued presence of LA (0.02–0.47 μM) in the distal duodenum and in proximal jejunum (0.00–0.43 μM) from 2 to 4 hours following oral dosing. The data shows that LA is available in detectable concentrations at the site of CeD.
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249707

Abstract:
Background The family is a key setting for health promotion. Contemporary health promoting family models can establish scaffolds for shaping health behaviors and can be useful tools for education and health promotion. Objectives The objective of this scoping review is to provide details as to how conceptual and theoretical models of the health promoting potential of the family are being used in health promotion contexts. Design Guided by PRISMA ScR guidelines, we used a three-step search strategy to find relevant papers. This included key-word searching electronic databases (Medline, PSycINFO, Embase, and CINAHL), searching the reference lists of included studies, and intentionally searching for grey literature (in textbooks, dissertations, thesis manuscripts and reports.) Results After applying inclusion and exclusion criteria, the overall search generated 113 included manuscripts/chapters with 118 unique models. Through our analysis of these models, three main themes were apparent: 1) ecological factors are central components to most models or conceptual frameworks; 2) models were attentive to cultural and other diversities, allowing room for a wide range of differences across family types, and for different and ever-expanding social norms and roles; and 3) the role of the child as a passive recipient of their health journey rather than as an active agent in promoting their own family health was highlighted as an important gap in many of the identified models. Conclusions This review contributes a synthesis of contemporary literature in this area and supports the priority of ecological frameworks and diversity of family contexts. It encourages researchers, practitioners and family stakeholders to recognize the value of the child as an active agent in shaping the health promoting potential of their family context.
, Yassine Merad, Mohamed Amine Merbouh
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249402

Abstract:
Introduction The Platelet Function Analyzer-100 (PFA-100) is a point of care instrument that simulates plug formation under high shear flow. The PFA-100 measures the time required to occlude the aperture in a biochemically active cartridge and is expressed in a term of closure time (CT). In Algeria, the reference values used in clinical laboratories are of Western origin. However, ethnic, genetic, dietary environmental, and diet differences between populations may affect reference intervals. We established the reference intervals of PFA-100 closure times in healthy Algerian adults according to the International Federation of Clinical Chemistry method, and we compared them with those of Western and Asian countries. Material and methods We enrolled 303 healthy blood donors in the study. 218 subjects met inclusion criteria. We analyzed the blood sample on the PFA-100 for CT with both the collagen epinephrine and collagen ADP cartridges. Results The reference intervals of PFA-100 collagen epinephrine CT and PFA-100 collagen ADP CT were 91–207 seconds and 71–144 seconds, respectively. Compared to Western and Asian populations, there were significant differences. The upper limits of CTs were higher for Algerians in this study. Our findings show that many healthy Algerians would be incorrectly identified as having a primary hemostasis abnormality according to the reference intervals of the manufacturer and scientific literature. Conclusion This report provides the first reference intervals for PFA-100 CTs in healthy Algerian adults. These results improve the accuracy of diagnosis and patient care in Algeria.
Wei-Chung Hsu, , Shou-Jen Lan
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249021

Abstract:
This study investigated home care aides’ (HCAs) oral health care experience, knowledge, and their intention to receive professional training, to explain and predict factors of their intention to receive such training. This cross-sectional study collected data through a structured questionnaire. HCAs affiliated with home care agencies in Taichung, Taiwan were recruited through purposive sampling. A total of 487 questionnaires were distributed from September to December 2015 with 280 valid responses collected (57.4%).This study predicted the factors of HCAs’ intention to receive oral health care training through a decision tree analysis. The decision tree model classified the respondents with an accuracy of 77.5%. The optimal predictor variable was oral health care knowledge (χ2 = 66.662, p < 0.0001). Among the low-scoring respondents on oral health care knowledge, 76.4% were classified in the “uninterested” group, whereas 84.8% of the high scorers were classified in the “interested” group. The second best predictor variable was whether oral health care is part of the job responsibility (χ2 = 7.979, p = 0.007). Among those who answered Yes, 92.9% were in the interested group, as were 76.5% of those who answered No. It is recommended to add “disease and oral care-related content” and “safety protection, assessment, and usage of oral care tools during practical oral care process” to the oral healthcare training course content for HCAs in order to improve HCAs’ oral healthcare knowledge and oral care skills. These research findings are valuable and may be taken into account in the future development of the in-service educational training of oral healthcare for HCAs.
, Demeke Kifle, Seyoum Leta, Maíra Mucci, Miquel Lürling
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249720

Abstract:
The massive growth of potentially toxic cyanobacteria in water supply reservoirs, such as Legedadi Reservoir (Ethiopia), poses a huge burden to water purification units and represents a serious threat to public health. In this study, we evaluated the efficiency of the flocculants/coagulants chitosan, Moringa oleifera seed (MOS), and poly-aluminium chloride (PAC) in settling cyanobacterial species present in the Legedadi Reservoir. We also tested whether coagulant-treated reservoir water promotes cyanobacteria growth. Our data showed that suspended solids in the turbid reservoir acted as ballast, thereby enhancing settling and hence the removal of cyanobacterial species coagulated with chitosan, Moringa oleifera seed, or their combination. Compared to other coagulants, MOS of 30 mg/L concentration, with the removal efficiency of 93.6%, was the most effective in removing cyanobacterial species without causing cell lysis. Contrary to our expectation, PAC was the least effective coagulant. Moreover, reservoir water treated with MOS alone or MOS combined with chitosan did not support any growth of cyanobacteria during the first two weeks of the experiment. Our data indicate that the efficacy of a flocculant/coagulant in the removal of cyanobacteria is influenced by the uniqueness of individual lakes/reservoirs, implying that mitigation methods should consider the unique characteristic of the lake/reservoir.
Correction
Donald A. Yee, William C. Glasgow, Nnaemeka F. Ezeakacha
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250288

, Ujjal Kumar Mukherjee, Dilip Chhajed, Jason Hirsbrunner,
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249084

Abstract:
Objectives Physician encounters with patients with type 2 diabetes act as motivation for self-management and lifestyle adjustments that are indispensable for diabetes treatment. We elucidate the sociodemographic sources of variation in encounter usage and the impact of encounter usage on glucose control, which can be used to recommend encounter usage for different sociodemographic strata of patients to reduce risks from Type 2 diabetes. Data and methods We analyzed data from a multi-facility clinic in the Midwestern United States on 2124 patients with type 2 diabetes, from 95 ZIP codes. A zero-inflated Poisson model was used to estimate the effects of various ZIP-code level sociodemographic variables on the encounter usage. A multinomial logistic regression model was built to estimate the effects of physical and telephonic encounters on patients’ glucose level transitions. Results from the two models were combined in marginal effect analyses. Results and conclusions Conditional on patients’ clinical status, demographics, and insurance status, significant inequality in patient encounters exists across ZIP codes with varying sociodemographic characteristics. One additional physical encounter in a six-month period marginally increases the probability of transition from a diabetic state to a pre-diabetic state by 4.3% and from pre-diabetic to the non-diabetic state by 3.2%. Combined marginal effect analyses illustrate that a ZIP code in the lower quartile of high school graduate percentage among all ZIP codes has 1 fewer physical encounter per six months marginally compared to a ZIP code at the upper quartile, which gives 5.4% average increase in the probability of transitioning from pre-diabetic to diabetic. Our results suggest that policymakers can target particular patient groups who may have inadequate encounters to engage in diabetes care, based on their immediate environmental sociodemographic characteristics, and design programs to increase their encounters to achieve better care outcomes.
Toshitaka Sugawara, , Jo Nishino, Shuichi Watanabe, Aya Maekawa, Yoshiya Ishikawa, Keiichi Akahoshi, Kosuke Ogawa, Hiroaki Ono, Atsushi Kudo, et al.
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249885

Abstract:
Background Even after curative resection, pancreatic ductal adenocarcinoma (PDAC) patients suffer a high rate of recurrence. There is an unmet need to predict which patients will experience early recurrence after resection in order to adjust treatment strategies. Methods Data of patients with resectable PDAC undergoing surgical resection between January 2005 and September 2018 were reviewed to stratify for early recurrence defined as occurring within 6 months of resection. Preoperative data including demographics, tumor markers, blood immune-inflammatory factors and clinicopathological data were examined. We employed Elastic Net, a sparse modeling method, to construct models predicting early recurrence using these multiple preoperative factors. As a result, seven preoperative factors were selected: age, duke pancreatic monoclonal antigen type 2 value, neutrophil:lymphocyte ratio, systemic immune-inflammation index, tumor size, lymph node metastasis and is peripancreatic invasion. Repeated 10-fold cross-validations were performed, and area under the receiver operating characteristic curve (AUC) and decision curve analysis were used to evaluate the usefulness of the models. Results A total of 136 patients was included in the final analysis, of which 35 (34%) experienced early recurrence. Using Elastic Net, we found that 7 of 14 preoperative factors were useful for the predictive model. The mean AUC of all models constructed in the repeated validation was superior to the standard marker CA 19–9 (0.718 vs 0.657), whereas the AUC of the model constructed from the entire patient cohort was 0.767. Decision curve analysis showed that the models had a higher mean net benefit across the majority of the range of reasonable threshold probabilities. Conclusion A model using multiple preoperative factors can improve prediction of early resectable PDAC recurrence.
Kalpana Sriraman, Ambreen Shaikh, Swapneil Parikh, Shreevatsa Udupa, Nirjhar Chatterjee, Jayanthi Shastri,
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249525

Abstract:
Infectious respiratory particles expelled by SARS-CoV-2 positive patients are attributed to be the key driver of COVID-19 transmission. Understanding how and by whom the virus is transmitted can help implement better disease control strategies. Here we have described the use of a noninvasive mask sampling method to detect and quantify SARS-CoV-2 RNA in respiratory particles expelled by COVID-19 patients and discussed its relationship to transmission risk. Respiratory particles of 31 symptomatic SARS-CoV-2 positive patients and 31 asymptomatic healthy volunteers were captured on N-95 masks layered with a gelatin membrane in a 30-minute process that involved talking/reading, coughing, and tidal breathing. SARS-CoV-2 viral RNA was detected and quantified using rRT-PCR in the mask and in concomitantly collected nasopharyngeal swab (NPS) samples. The data were analyzed with respect to patient demographics and clinical presentation. Thirteen of 31(41.9%) patients showed SARS-COV-2 positivity in both the mask and NPS samples, while 16 patients were mask negative but NPS positive. Two patients were both mask and NPS negative. All healthy volunteers except one were mask and NPS negative. The mask positive patients had significantly lower NPS Ct value (26) compared to mask negative patients (30.5) and were more likely to be rapid antigen test positive. The mask positive patients could be further grouped into low emitters (expelling 1000 viral copies). The study presents evidence for variation in emission of SARS-CoV-2 virus particles by COVID-19 patients reflecting differences in infectivity and transmission risk among individuals. The results conform to reported secondary infection rates and transmission and also suggest that mask sampling could be explored as an effective tool to assess individual transmission risks, at different time points and during different activities.
Correction
Belén Mesurado, María E. Oñate, Lucas M. Rodriguez, Natalia Putrino, Paulina Guerra, Claudia E. Vanney
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250287

Katherine M. Schafer, Grace Kennedy, , Philip Resnik
Published: 12 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249833

Abstract:
Theoretically-driven models of suicide have long guided suicidology; however, an approach employing machine learning models has recently emerged in the field. Some have suggested that machine learning models yield improved prediction as compared to theoretical approaches, but to date, this has not been investigated in a systematic manner. The present work directly compares widely researched theories of suicide (i.e., BioSocial, Biological, Ideation-to-Action, and Hopelessness Theories) to machine learning models, comparing the accuracy between the two differing approaches. We conducted literature searches using PubMed, PsycINFO, and Google Scholar, gathering effect sizes from theoretically-relevant constructs and machine learning models. Eligible studies were longitudinal research articles that predicted suicide ideation, attempts, or death published prior to May 1, 2020. 124 studies met inclusion criteria, corresponding to 330 effect sizes. Theoretically-driven models demonstrated suboptimal prediction of ideation (wOR = 2.87; 95% CI, 2.65–3.09; k = 87), attempts (wOR = 1.43; 95% CI, 1.34–1.51; k = 98), and death (wOR = 1.08; 95% CI, 1.01–1.15; k = 78). Generally, Ideation-to-Action (wOR = 2.41, 95% CI = 2.21–2.64, k = 60) outperformed Hopelessness (wOR = 1.83, 95% CI 1.71–1.96, k = 98), Biological (wOR = 1.04; 95% CI .97–1.11, k = 100), and BioSocial (wOR = 1.32, 95% CI 1.11–1.58, k = 6) theories. Machine learning provided superior prediction of ideation (wOR = 13.84; 95% CI, 11.95–16.03; k = 33), attempts (wOR = 99.01; 95% CI, 68.10–142.54; k = 27), and death (wOR = 17.29; 95% CI, 12.85–23.27; k = 7). Findings from our study indicated that across all theoretically-driven models, prediction of suicide-related outcomes was suboptimal. Notably, among theories of suicide, theories within the Ideation-to-Action framework provided the most accurate prediction of suicide-related outcomes. When compared to theoretically-driven models, machine learning models provided superior prediction of suicide ideation, attempts, and death.
Orsolya Kiss, Mate Babity, Attila Kovacs, Judit Skopal, Hajnalka Vago, Balint Karoly Lakatos, Csaba Bognar, Reka Rakoczi, Mark Zamodics, Lorinc Frivaldszky, et al.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249923

Abstract:
The significance of cardiology screening of referees is not well established. Cardiovascular risk factors and diseases were examined in asymptomatic Hungarian elite handball referees undergoing extended screening: personal/family history, physical examination, 12-lead ECG, laboratory tests, body-composition analysis, echocardiography, and cardiopulmonary exercise testing. Holter-ECG (n = 8), blood pressure monitorization (n = 10), cardiac magnetic resonance imaging (CMR; n = 27) and computer tomography (CCT; n = 4) were also carried out if needed. We examined 100 referees (age: 29.6±7.9years, male: 64, training: 4.3±2.0 hours/week), cardiovascular risk factors were: positive medical history: 24%, overweight: 10%, obesity: 3%, dyslipidaemia: 41%. Elevated resting blood pressure was measured in 38%. Stress-ECG was positive due to ECG-changes in 16%, due to elevated exercise blood pressure in 8%. Echocardiography and/or CMR identified abnormalities in 19%. A significant number of premature ventricular contractions was found on the Holter-ECG in two cases. The CCT showed myocardial bridge or coronary plaques in one-one case. We recommended lifestyle changes in 58%, new/modified antihypertensive or lipid-lowering therapy in 5%, iron-supplementation in 22%. By our results, a high percentage of elite Hungarian handball referees had cardiovascular risk factors or diseases, which, combined with physical and psychological stress, could increase the possibility of cardiovascular events. Our study draws attention to the importance of cardiac screening in elite handball referees.
Ricardo Abad, Orvil Collart, Prasanth Ganesan, A. J. Rogers, Mahmood I. Alhusseini, Miguel Rodrigo, ,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249873

Abstract:
Background The rotational activation created by spiral waves may be a mechanism for atrial fibrillation (AF), yet it is unclear how activation patterns obtained from endocardial baskets are influenced by the 3D geometric curvature of the atrium or ‘unfolding’ into 2D maps. We develop algorithms that can visualize spiral waves and their tip locations on curved atrial geometries. We use these algorithms to quantify differences in AF maps and spiral tip locations between 3D basket reconstructions, projection onto 3D anatomical shells and unfolded 2D surfaces. Methods We tested our algorithms in N = 20 patients in whom AF was recorded from 64-pole baskets (Abbott, CA). Phase maps were generated by non-proprietary software to identify the tips of spiral waves, indicated by phase singularities. The number and density of spiral tips were compared in patient-specific 3D shells constructed from the basket, as well as 3D maps from clinical electroanatomic mapping systems and 2D maps. Results Patients (59.4±12.7 yrs, 60% M) showed 1.7±0.8 phase singularities/patient, in whom ablation terminated AF in 11/20 patients (55%). There was no difference in the location of phase singularities, between 3D curved surfaces and 2D unfolded surfaces, with a median correlation coefficient between phase singularity density maps of 0.985 (0.978–0.990). No significant impact was noted by phase singularities location in more curved regions or relative to the basket location (p>0.1). Conclusions AF maps and phase singularities mapped by endocardial baskets are qualitatively and quantitatively similar whether calculated by 3D phase maps on patient-specific curved atrial geometries or in 2D. Phase maps on patient-specific geometries may be easier to interpret relative to critical structures for ablation planning.
Iva Trenevska, Amanda P. Anderson, Carol Bentley, Tasneem Hassanali, Sarah Wiblin, Shaun Maguire, Francesco Pezzella, ,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249967

Abstract:
T-cell receptor mimic (TCRm) antibodies have expanded the repertoire of antigens targetable by monoclonal antibodies, to include peptides derived from intracellular proteins that are presented by major histocompatibility complex class I (MHC-I) molecules on the cell surface. We have previously used this approach to target p53, which represents a valuable target for cancer immunotherapy because of the high frequency of its deregulation by mutation or other mechanisms. The T1-116C TCRm antibody targets the wild type p5365-73 peptide (RMPEAAPPV) presented by HLA-A*0201 (HLA-A2) and exhibited in vivo efficacy against triple receptor negative breast cancer xenografts. Here we report a comprehensive mutational analysis of the p53 RMPEAAPPV peptide to assess the T1-116C epitope and its peptide specificity. Antibody binding absolutely required the N-terminal arginine residue, while amino acids in the center of the peptide contributed little to specificity. Data mining the immune epitope database with the T1-116C binding consensus and validation of peptide recognition using the T2 stabilization assay identified additional tumor antigens targeted by T1-116C, including WT1, gp100, Tyrosinase and NY-ESO-1. Most peptides recognized by T1-116C were conserved in mice and human HLA-A2 transgenic mice showed no toxicity when treated with T1-116C in vivo. We conclude that comprehensive validation of TCRm antibody target specificity is critical for assessing their safety profile.
, Nadine Reichhart, Johannes Gonnermann, Norbert Kociok, Aline I. Riechardt, Enken Gundlach, Olaf Strauß, Antonia M. Joussen
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0245143

Abstract:
Tumor necrosis factor (TNF)α is an inflammatory cytokine likely to be involved in the process of corneal inflammation and neovascularization. In the present study we evaluate the role of the two receptors, TNF-receptor (TNF-R)p55 and TNF-Rp75, in the mouse model of suture-induced corneal neovascularization and lymphangiogenesis. Corneal neovascularization and lymphangiogenesis were induced by three 11–0 intrastromal corneal sutures in wild-type (WT) C57BL/6J mice and TNF-Rp55-deficient (TNF-Rp55d) and TNF-Rp75-deficient (TNF-Rp75d) mice. The mRNA expression of VEGF-A, VEGF-C, Lyve-1 and TNFα and its receptors was quantified by qPCR. The area covered with blood- or lymphatic vessels, respectively, was analyzed by immunohistochemistry of corneal flatmounts. Expression and localization of TNFα and its receptors was assessed by immunohistochemistry of sagittal sections and Western Blot. Both receptors are expressed in the murine cornea and are not differentially regulated by the genetic alteration. Both TNF-Rp55d and TNF-Rp75d mice showed a decrease in vascularized area compared to wild-type mice 14 days after suture treatment. After 21 days there were no differences detectable between the groups. The number of VEGF-A-expressing macrophages did not differ when comparing WT to TNF-Rp55d and TNF-Rp75d. The mRNA expression of lymphangiogenic markers VEGF-C or LYVE-1 does not increase after suture in all 3 groups and lymphangiogenesis showed a delayed effect only for TNF-Rp75d. TNFα mRNA and protein expression increased after suture treatment but showed no difference between the three groups. In the suture-induced mouse model, TNFα and its ligands TNF-Rp55 and TNF-Rp75 do not play a significant role in the pathogenesis of neovascularisation and lymphangiogenesis.
Romedan Delil, Beakal Zinab, Hassen Mosa, Ritbano Ahmed, Habtamu Hassen
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250037

Abstract:
Background Dietary diversity has continued to receive a global attention among pregnant women as they have been considered susceptible to malnutrition because of their increased nutrient demands. Thus, a variety of foodstuffs in their diet are necessary for ensuring the appropriateness of their nutrient consumptions. This study, therefore assessed the dietary diversity practice and its determinants among pregnant women attending antenatal clinic at Wachemo University Nigist Eleni Mohammed memorial referral hospital, Southern Ethiopia. Methods A hospital-based cross-sectional study was carried out on 303 participants from May 1 to June 15, 2019 using a systematic random sampling technique. Data were entered and analyzed using SPSS (version24.0). Both bivariate and multivariable logistic regression analyses were used to decide the association of each explanatory variable with the outcome variable. Odds ratio with their 95% confidence intervals was calculated to identify the presence and strength of association, and statistical significance was declared at p < 0.05. Results The overall prevalence of adequate dietary diversity practices was observed to be 42.6%. The determinants of dietary diversity practice included earning of a monthly income ≥2000 Ethiopian birr (AOR = 1.62; 95%CI:1.19–2.85), maternal educational level (AOR = 2.50; 95% CI: 1.05–6.12), educational status of partner (AOR = 2.45; 95% CI:1.20, 9.57), having a partner who was a government employee (AOR = 4; 95% CI:2.18–7.21), and the receiving of nutritional information (AOR = 1.35; 95% CI: 3.39–6.94). Conclusions The study indicated that the overall consumption of adequate dietary diversity practice was found to be low. Therefore, increasing household income, enhancing nutritional related information, advancing the academic level of both wife and her partner is essential to improve women’s dietary diversity practice.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250017

Abstract:
The coronavirus disease 2019 (COVID-19) outbreak spread to over 100 countries with a total of 100,000 cases during the first week of March 2020. Health care workers, as those on the frontline of the COVID-19 pandemic, are more susceptible to infection. Inadequate related knowledge and preventive behaviors among health care workers might lead to delayed treatment and result in the rapid spread of the infection. Therefore, this study evaluated the knowledge of health care workers with regard to COVID-19. A cross-sectional study was conducted from June 10–18, 2020. Participants were general practitioners, specialists, and nurses working at the forefront of the pandemic. Their knowledge, preventive behaviors, and risk perceptions concerning COVID-19 were evaluated using an online questionnaire created by our medical specialists. The questionnaire consisted of 29, 5, and 4 items about COVID-19 knowledge, preventive behaviors, and risk perceptions, respectively. A total of 251 health care workers completed the questionnaire. The mean age of the participants was 33.88±8.72 years old, and the sample consisted of 68 males (27.08%) and 183 females (72.91%). While there was no difference between the percentage of correct answers given by female and male participants to knowledge-based questions (p>0.05), the percentage of correct answers to the questions on preventive behaviors was significantly higher in female participants than in males (p<0.001). The overall average percentages of correct responses were 91.66% for knowledge-based questions and 85.96% for preventive behavior questions. The scores for knowledge-based questions were higher for medical specialists, whereas nurses scored higher on preventive behavior questions. Government hospital staff showed a significant difference in preventive behaviors compared to that of university hospitals (p<0.05). In addition, there was a positive correlation between knowledge scores and preventive behaviors. Although all the participants (100%) knew that contracting COVID-19 can lead to death, only 66.93% of them were willing to get vaccinated themselves. The knowledge level of health care workers concerning COVID-19 was above 90%, but the level of competence in terms of preventive behaviors was found to be low, especially in males.
Tor A. Klingen, Ying Chen, Hans Aas, ,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249767

Abstract:
Stromal elastosis is related to good prognosis in breast cancer and fibulin-2 helps to stabilize elastic fibers in basement membranes. Here, we examined the level of perivascular fibulin-2 expression in relation to elastosis content, vascular invasion, molecular subtypes, tumour detection mode, and patient prognosis in breast cancer. We performed a population based retrospective study of invasive breast cancers from the Norwegian Breast Screening Program (Vestfold County, 2004–2009) including 200 screen-detected and 82 interval cancers. Perivascular fibulin-2 staining was semi-quantitatively graded based on immunohistochemistry (1–3) and dichotomized as high expression (grade 2–3) and low expression (grade 1). Elastosis content was graded on a 4-tiered scale and dichotomized as high (score 3) and low (score 0–2) expression, whereas lymphatic (LVI) and blood vessel invasion (BVI) were recorded as absent or present by immunohistochemistry. High perivascular fibulin-2 expression was strongly related to stromal elastosis (p<0.001), and inversely associated with BVI and LVI (p<0.001 for both). High fibulin-2 was associated with luminal breast cancer subgroups (p<0.001) and inversely with interval cancers compared with screen-detected tumours (p<0.001). By univariate analysis, low perivascular fibulin-2 was associated with reduced recurrence-free survival (p = 0.002) and disease specific survival (p = 0.019). Low perivascular fibulin-2 expression was strongly related to vascular invasion, low stromal elastosis, non-luminal breast cancer subtypes, interval presentation, and adverse prognosis.
, Victor Daka, Panji Nkhoma, Mildred Zulu, Ephraim Zulu, Rabecca Tembo, Zifa Ngwira, Florence Mwaba, Musalula Sinkala,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248984

Abstract:
The malignant phenotype of tumour cells is fuelled by changes in the expression of various transcription factors, including some of the well-studied proteins such as p53 and Myc. Despite significant progress made, little is known about several other transcription factors, including ELF4, and how they help shape the oncogenic processes in cancer cells. To this end, we performed a bioinformatics analysis to facilitate a detailed understanding of how the expression variations of ELF4 in human cancers are related to disease outcomes and the cancer cell drug responses. Here, using ELF4 mRNA expression data of 9,350 samples from the Cancer Genome Atlas pan-cancer project, we identify two groups of patient’s tumours: those that expressed high ELF4 transcripts and those that expressed low ELF4 transcripts across 32 different human cancers. We uncover that patients segregated into these two groups are associated with different clinical outcomes. Further, we find that tumours that express high ELF4 mRNA levels tend to be of a higher-grade, afflict a significantly older patient population and have a significantly higher mutation burden. By analysing dose-response profiles to 397 anti-cancer drugs of 612 well-characterised human cancer cell lines, we discover that cell lines that expressed high ELF4 mRNA transcript are significantly less responsive to 129 anti-cancer drugs, and only significantly more response to three drugs: dasatinib, WH-4-023, and Ponatinib, all of which remarkably target the proto-oncogene tyrosine-protein kinase SRC and tyrosine-protein kinase ABL1. Collectively our analyses have shown that, across the 32 different human cancers, the patients afflicted with tumours that overexpress ELF4 tended to have a more aggressive disease that is also is more likely more refractory to most anti-cancer drugs, a finding upon which we could devise novel categorisation of patient tumours, treatment, and prognostic strategies.
, Deborah Sulem, Kerrie Mengersen, Vincent Rivoirard, Judith Rousseau
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250015

Abstract:
Hawkes processes are a form of self-exciting process that has been used in numerous applications, including neuroscience, seismology, and terrorism. While these self-exciting processes have a simple formulation, they can model incredibly complex phenomena. Traditionally Hawkes processes are a continuous-time process, however we enable these models to be applied to a wider range of problems by considering a discrete-time variant of Hawkes processes. We illustrate this through the novel coronavirus disease (COVID-19) as a substantive case study. While alternative models, such as compartmental and growth curve models, have been widely applied to the COVID-19 epidemic, the use of discrete-time Hawkes processes allows us to gain alternative insights. This paper evaluates the capability of discrete-time Hawkes processes by modelling daily mortality counts as distinct phases in the COVID-19 outbreak. We first consider the initial stage of exponential growth and the subsequent decline as preventative measures become effective. We then explore subsequent phases with more recent data. Various countries that have been adversely affected by the epidemic are considered, namely, Brazil, China, France, Germany, India, Italy, Spain, Sweden, the United Kingdom and the United States. These countries are all unique concerning the spread of the virus and their corresponding response measures. However, we find that this simple model is useful in accurately capturing the dynamics of the process, despite hidden interactions that are not directly modelled due to their complexity, and differences both within and between countries. The utility of this model is not confined to the current COVID-19 epidemic, rather this model could explain many other complex phenomena. It is of interest to have simple models that adequately describe these complex processes with unknown dynamics. As models become more complex, a simpler representation of the process can be desirable for the sake of parsimony.
Jonathan L. Crooke-Rosado, Sara C. Diaz-Mendez, Yamil E. Claudio-Roman, Nilsa M. Rivera,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249801

Abstract:
Crustaceans are major constituents of aquatic ecosystems and, as such, changes in their behavior and the structure and function of their bodies can serve as indicators of alterations in their immediate environment, such as those associated with climate change and anthropogenic contamination. We have used bioinformatics and a de novo transcriptome assembly approach to identify potential targets for developing specific antibodies to serve as nervous system function markers for freshwater prawns of the Macrobrachium spp. Total RNA was extracted from brain ganglia of Macrobrachium carcinus freshwater prawns and Illumina Next Generation Sequencing was performed using an Eel Pond mRNA Seq Protocol to construct a de novo transcriptome. Sequencing yielded 97,202,662 sequences: 47,630,546 paired and 1,941,570 singletons. Assembly with Trinity resulted in 197,898 assembled contigs from which 30,576 were annotated: 9,600 by orthology, 17,197 by homology, and 3,779 by transcript families. We looked for glutamate receptors contigs, due to their main role in crustacean excitatory neurotransmission, and found 138 contigs related to ionotropic receptors, 32 related to metabotropic receptors, and 18 to unidentified receptors. After performing multiple sequence alignments within different biological organisms and antigenicity analysis, we were able to develop antibodies for prawn AMPA ionotropic glutamate receptor 1, metabotropic glutamate receptor 1 and 4, and ionotropic NMDA glutamate receptor subunit 2B, with the expectation that the availability of these antibodies will help broaden knowledge regarding the underlying structural and functional mechanisms involved in prawn behavioral responses to environmental impacts. The Macrobrachium carcinus brain transcriptome can be an important tool for examining changes in many other nervous system molecules as a function of developmental stages, or in response to particular conditions or treatments.
Yu-Chi Chiu, Shih-Wei Lee, Chi-Wei Liu, Rebecca Chou-Jui Lin, Yung-Chia Huang, ,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249944

Abstract:
Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disease that reduces lung and respiratory function, with a high mortality rate. Severe and acute deterioration of COPD can easily lead to respiratory failure, resulting in personal, social, and medical burden. Recent studies have shown a high correlation between the gut microbiota and lung inflammation. In this study, we investigated the relationship between gut microbiota and COPD severity. A total of 60 COPD patients with varying severity according to GOLD guidelines were enrolled in this study. DNA was extracted from patients’ stool and 16S rRNA data analysis conducted using high-throughput sequencing followed by bioinformatics analysis. The richness of the gut microbiota was not associated with COPD severity. The gut microbiome is more similar in stage 1 and 2 COPD than stage 3+4 COPD. Fusobacterium and Aerococcus were more abundant in stage 3+4 COPD. Ruminococcaceae NK4A214 group and Lachnoclostridium were less abundant in stage 2–4, and Tyzzerella 4 and Dialister were less abundant in stage 1. However, the abundance of a Bacteroides was associated with blood eosinophils and lung function. This study suggests that no distinctive gut microbiota pattern is associated with the severity of COPD. The gut microbiome could affect COPD by gut inflammation shaping the host immune system.
, Yicheng Gao, Zhaoxu Zhang, Sijia Cheng, Shuangmei Zhang
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249313

Abstract:
Background Post-stroke spasm is currently a complex clinical problem that remains to be resolved. Due to its excellent efficacy and few side effects, clinicians have used fire acupuncture to treat post-stroke spasticity in China. Objectives The purpose of this study was to evaluate the clinical efficacy of fire acupuncture compared with conventional acupuncture to treat post-stroke spasms and provide a detailed summary of the commonly used acupoints. Methods Eight databases (MEDLINE/PubMed, Web of Science, the Cochrane database, EMBASE, CBM, CNKI, WanFang, and VIP) were searched for randomized controlled trials (RCTs) published from database inception through August 30, 2020. RCTs that compared fire acupuncture with conventional acupuncture as a treatment intervention for patients with spasticity after stroke were included. Revman 5.3 software was used to calculate risk ratios (RR) and standard mean differences (SMD) with 95% confidence intervals (CI). Methodological evaluation or critical appraisal of the included articles was assessed using RoB-2. Results Sixteen studies with a total of 1,118 patients were included. Although according to the standards of the Rob 2.0 tool, most studies are considered to have some problems. Comprehensive analysis of the results revealed a consistent trend indicating several advantages of using fire needles compared to conventional acupuncture in treating post-stroke spasms, including the effective rate, recovery rate, and improvement of multiple scales represented by MAS. Concerning secondary outcomes, using the scales of FMA, BI, or NDS in this random model meta-analysis, fire acupuncture exhibited better performance compared to acupuncture [SMD = 2.27, 95%CI [1.40,3.13 (random-effects model) ], [SMD = 1.46,95% CI [1.03,1.90 (random-effects model)], and [SMD = 0.90, 95%CI [0.44,1.35 (random-effects model)], respectively, with moderately high heterogeneity. When the effective rate was used as an outcome in the subgroup analysis, fire needles performed better than conventional acupuncture with respect to damage to the upper or lower limbs, and the thickness and depth of acupuncture. When the modified Ashworth scale (MAS) was used as the outcome, and the damage occurred in the lower extremity, the acupuncture depth exceeded 15mm, or the duration of stroke was longer than six months, the fire needles did not perform better than conventional acupuncture, [SMD = 0.01, 95%CI [-0.47,0.48 (fix-effects model)], [SMD = 0.21 [-0.51,0.93(random-effects model)], and [SMD = 0.76, 95%CI [-0.08,1.60 (random-effects model)], respectively. The acupoints identified with the highest frequencies in this study were Yang-meridian, including LI11-Quchi (nine times), LI4-Hegu (seven times), and ST36-Zusanli (five times). Moreover, no serious adverse effects were reported in any of the studies included in this analysis. Conclusions Despite several limitations, this was the first meta-analysis to focus on the treatment of post-stroke spasticity using fire needle acupuncture compared with conventional acupuncture. Our results confirmed that fire needles could provide a better clinical effect than conventional acupuncture, which will help standardize fire needle treatment strategies for post-stroke spasms.
Correction
Francisco Gil-Muñoz, Juan Gabriel Pérez-Pérez, Ana Quiñones, Amparo Primo-Capella, Jaime Cebolla, Mª Ángeles Forner-Giner, Maria L. Badenes, Mª Del Mar Naval
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250193

Fabian Ying,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249821

Abstract:
Since the outbreak of COVID-19 in early March 2020, supermarkets around the world have implemented different policies to reduce the virus transmission in stores to protect both customers and staff, such as restricting the maximum number of customers in a store, changes to the store layout, or enforcing a mandatory face covering policy. To quantitatively assess these mitigation methods, we formulate an agent-based model of customer movement in a supermarket (which we represent by a network) with a simple virus transmission model based on the amount of time a customer spends in close proximity to infectious customers (which we call the exposure time). We apply our model to synthetic store and shopping data to show how one can use our model to estimate exposure time and thereby the number of infections due to human-to-human contact in stores and how to model different store interventions. The source code is openly available under https://github.com/fabianying/covid19-supermarket-abm. We encourage retailers to use the model to find the most effective store policies that reduce virus transmission in stores and thereby protect both customers and staff.
, Paola Caroppo, Angela Spalatro, Luca Lavagnino, Giovanni Abbate Daga, Andrea Boghi, Mauro Bergui, Alessandro Cicerale, Benedetto Vitiello, Secondo Fassino, et al.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0231684

Abstract:
Aim The present study aims to extend the knowledge of the neural correlates of emotion processing in first episode subjects affected by anorexia nervosa (AN) or bulimia nervosa (BN). We applied an emotional distress paradigm targeting negative emotions thought to be relevant for interpersonal difficulties and therapeutic resistance mechanisms. Methods The current study applied to 44 female participants with newly diagnosed AN or BN and 20 matched controls a neuroimaging paradigm eliciting affective responses. The measurements also included an extensive assessment comprising clinical scales, neuropsychological tests, measures of emotion processing and empathy. Results AN and BN did not differ from controls in terms of emotional response, emotion matching, self-reported empathy and cognitive performance. However, eating disorder and psychopathological clinical scores, as well as alexithymia levels, were increased in AN and BN. On a neural level, no significant group differences emerged, even when focusing on a region of interest selected a priori: the amygdala. Some interesting findings put in relation the hippocampal activity with the level of Body Dissatisfaction of the participants, the relative importance of the key nodes for the common network in the decoding of different emotions (BN = right amygdala, AN = anterior cingulate area), and the qualitative profile of the deactivations. Conclusions Our data do not support the hypothesis that participants with AN or BN display reduced emotional responsiveness. However, peculiar characteristics in emotion processing could be associated to the three different groups. Therefore, relational difficulties in eating disorders, as well as therapeutic resistance, could be not secondary to a simple difficulty in feeling and identifying basic negative emotions in AN and BN participants.
, , Scott Richards-Jones, , , Christopher Stevenson, David Lawrence, Genevieve Pepin, Cathrine Mihalopoulos
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249902

Abstract:
Objective To examine the health care costs associated with mental disorders and subthreshold mental disorders within a nationally representative sample of children and adolescents in Australia. Method Data were derived from the Young Minds Matter Survey (N = 6,310). Mental disorders were classified using the Diagnostic Interview Schedule for Children Version IV. Participant data were linked to administrative data on health care costs. Adjusted generalized linear regression models and two-part models were used to estimate mean differences in costs between those with a mental disorder or subthreshold disorder and those without. Results Costs associated with health care attendances and medications were higher for children and adolescents with mental disorders and subthreshold mental disorders compared to those without a mental disorder. The additional population health care costs due to mental disorders amounted to AUD$234 million annually in children and adolescents, of which approximately 16% was attributed to out-of-pocket costs. Findings showed that those with subthreshold mental disorders or comorbid mental disorders have substantial additional costs of Medicare-funded medical and pharmaceutical services. Conclusion and implication Mental disorders in children and adolescents are associated with significant health care costs. Further research is needed to ensure that this population is receiving effective and efficient care.
Kassanesh Melese Tessema, Kebadnew Mulatu Mihirete, Endalkachew Worku Mengesha, Azezu Asres Nigussie,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249917

Abstract:
Background Maternal deaths remain high in Ethiopia mainly due to poor maternal health service utilization. Despite men are the chief decision-makers and economically dominant in Ethiopia, the impact of their involvement on maternal health services utilization is not clear. This study aimed to assess the association between male involvement and women’s use of institutional delivery, and factors influencing male partners’ involvement in institutional delivery. Methods A community based cross-sectional study was conducted between March and May, 2019. A total of 477 married men who have children less than one year of age were interviewed. Face-to-face interviews using a pre-tested and structured questionnaire were used for data collection. Bivariate and multiple logistic regressions were carried out. SPSS version 23 was used for data analysis. Results Overall 181 (37.9%) husbands/partners were involved in institutional delivery for the most recent child birth. Male partners involvement in institutional delivery was strongly associated with an increased odds of attending institutional delivery by spouse [AOR: 66.2, 95% CI: 24.8, 177.0]. Education [AOR: 0.33, 95% CI: 0.18–0.59], knowledge on maternal health [AOR: 1.67, 95% CI: 1.11–2.50], favourable attitude towards institutional delivery [AOR: 1.83, 95% CI: 1.23–2.71], and no fear while supporting spouse [AOR: 2.65, 95% CI: 1.28–5.50] were positively associated with male partners involvement in institutional delivery. Conclusion Male partner’s involvement in institutional delivery was inadequate. This study reported a significant beneficial impact of male involvement on maternal health through improved utilisation of institutional delivery. Therefore, maternal health interventions should target husbands as consumers of maternal health services, and healthcare/government policies that isolate or discourage men from having active engagement in maternal health should be improved.
, Ai Shibata, Kaori Ishii, Mohammad Javad Koohsari, Koichiro Oka
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248304

Abstract:
The purpose of this study was to identify typologies of diurnal sedentary behavior patterns and sociodemographic characteristics of desk-based workers. The sedentary time of 229 desk-based workers was measured using accelerometer devices. The within individual diurnal variations in sedentary time was calculated for both workdays and non-workdays. Diurnal variations in sedentary time during each time period (morning, afternoon, and evening) was calculated as the percentage of sedentary time during each time period divided by the percentage of the total sedentary time. A hierarchical cluster analysis (Ward’s method) was used to identify the optimal number of clusters. To refine the initial clusters, a non-hierarchical cluster analysis (k-means method) was performed. Four clusters were identified: stable sedentary cluster (46.7%), off-morning break cluster (26.6%), off-afternoon break cluster (8.3%), and evening sedentary cluster (18.3%). The stable sedentary cluster had the lowest variations in sedentary time throughout the day and the highest amount of total sedentary time. Participants in the off-morning and off-afternoon break clusters had nearly the same sedentary patterns but took short-term breaks during non-workday mornings or afternoons. The evening sedentary cluster had a completely different pattern, with a longer sedentary time during the evening both on workdays and non-workdays. Sociodemographic attributes such as sex, household income, educational attainment, employment status, sleep duration, and residential area, differed significantly between groups. Initiatives to address desk-based workers’ sedentary behavior need to focus not only on the workplace but also on the appropriate timing for reducing excessive sedentary time in non-work contexts depending on the characteristics and diurnal patterns of target subgroups.
, Valerio Bonavolontà, Laura Guidetti, , Lorenzo Innocenti, Ludovica Cardinali, Lavinia Falcioni, Selenia di Fronso, Gian Pietro Emerenziani, , et al.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249667

Abstract:
The purpose of this study was to validate the Volition in Exercise Questionnaire in Italian language (VEQ-I). The translation and cultural adaptation of the VEQ-I was conducted using the forward-backward translation method. VEQ-I eighteen items correspond to the six-factors structure of the original version. The construct validity was verified by the confirmatory factor analysis (CFA) (CFI = 0.960; TLI = 0.943; RMSEA = 0.039; and SRMR = 0.040). The eighteen items were well distributed in six subscales and the six-factors structure of the questionnaire was supported. Internal Consistency value of the questionnaire was investigated for each subscale of the VEQ-I. Cronbach’s alpha and Omega values of the Reasons, Postponing Training, Unrelated Thoughts, Self-Confidence, Approval from Others and Coping with Failure subscales were 0.76 (α) and 0.76 (ω), 0.76 (α) and 0.76 (ω), 0.87 (α) and 0.88 (ω), 0.85 (α) and 0.85 (ω), 0.70 (α) and 0.72 (ω) and 0.74 (α) and 0.74 (ω), respectively. They were acceptable in all the six subscales. The concurrent validity was assessed using the correlation among the subscales of VEQ-I measures and those contained in two questionnaires: Psychobiosocial States in Physical Education (PBS-SPE) and Exercise Motivations Inventory (EMI-2).
, Roland Marini Djang’Eing’A, Salomon Batina-Agasa, Charles Kayembe Tshilumba, Jérémie Muwonga Masidi, Marie-Pierre Hayette, Laurent Bélec
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249701

Abstract:
Background The burden of HIV, HBV, and HCV infections remains disproportionately high in sub-Saharan Africa, with high rates of co-infections. Multiplex rapid diagnostic tests for HIV, HBV and HCV serological testing with high analytical performances may improve the “cascade of screening” and quite possibly the linkage-to-care with reduced cost. Based on our previous field experience of HIV self-testing, we herein aimed at evaluating the practicability and acceptability of a prototype finger-stick whole-blood Triplex HIV/HCV/HBsAg self-test as a simultaneous serological screening tool for HIV, HBV, and HCV in the Democratic Republic of the Congo (DRC). Methods A cross-sectional multicentric study consisting of face-to-face, paper-based, and semi-structured questionnaires with a home-based and facility-based recruitment of untrained adult volunteers at risk of HIV, HBV, and HCV infections recruited from the general public was conducted in 2020 in urban and rural areas in the DRC. The practicability of the Triplex self-test was assessed by 3 substudies on the observation of self-test manipulation including the understanding of the instructions for use (IFU), on the interpretation of Triplex self-test results and on its acceptability. Results A total of 251 volunteers (mean age, 28 years; range, 18–49; 154 males) were included, from urban [160 (63.7%)] and rural [91 (36.3%)] areas. Overall, 242 (96.4%) participants performed the Triplex self-test and succeeded in obtaining a valid test result with an overall usability index of 89.2%. The correct use of the Triplex self-test was higher in urban areas than rural areas (51.2% versus 16.5%; aOR: 6.9). The use of video IFU in addition to paper-based IFU increased the correct manipulation and interpretation of the Triplex self-test. A total of 197 (78.5%) participants correctly interpreted the Triplex self-test results, whereas 54 (21.5%) misinterpreted their results, mainly the positive test results harboring low-intensity band (30/251; 12.0%), and preferentially the HBsAg band (12/44; 27.3%). The rates of acceptability of reuse, distribution of the Triplex self-test to third parties (partner, friend, or family member), linkage to the health care facility for confirmation of results and treatment, and confidence in the self-test results were very high, especially among participants from urban areas. Conclusions This pilot study shows evidence for the first time in sub-Saharan Africa on good practicability and high acceptability of a prototype Triplex HIV/HCV/HBsAg self-test for simultaneous diagnosis of three highly prevalent chronic viral infections, providing the rational basis of using self-test harboring four bands of interest, i.e. the control, HIV, HCV, and HBsAg bands. The relatively frequent misinterpretation of the Triplex self-test points however the necessity to improve the delivery of this prototype Triplex self-test probably in a supervised setting. Finally, these observations lay the foundations for the potential large-scale use of the Triplex self-test in populations living in sub-Saharan Africa at high risk for HIV, HBV, and HCV infections.
, Ludmilla Leidianne Limirio Souza, Alexandre Tadashi Inomata Bruce, Juliane De Almeida Crispim, Luiz Henrique Arroyo, Antônio Carlos Vieira Ramos, Thaís Zamboni Berra, , Alessandro Rolim Scholze, Fernanda Bruzadelli Paulino da Costa, et al.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249822

Abstract:
This study aimed to analyze the discourses of patients who were diagnosed with multidrug-resistant tuberculosis, the perception of why they acquired this health condition and barriers to seeking care in a priority city in Brazil during the COVID-19 pandemic. This was an exploratory qualitative study, which used the theoretical-methodological framework of the Discourse Analysis of French matrix, guided by the Consolidated Criteria for Reporting Qualitative Research. The study was conducted in Ribeirão Preto, São Paulo, Brazil. Seven participants were interviewed who were undergoing treatment at the time of the interview. The analysis of the participants’ discourses allowed the emergence of four discursive blocks: (1) impact of the social determinants in the development of multidrug-resistant tuberculosis, (2) barriers to seeking care and difficulties accessing health services, (3) perceptions of the side effects and their impact on multidrug-resistant tuberculosis treatment, and (4) tuberculosis and COVID-19: a necessary dialogue. Through discursive formations, these revealed the determinants of multidrug-resistant tuberculosis. Considering the complexity involved in the dynamics of multidrug-resistant tuberculosis, advancing in terms of equity in health, that is, in reducing unjust differences, is a challenge for public policies, especially at the current moment in Brazil, which is of accentuated economic, political and social crisis. The importance of psychosocial stressors and the lack of social support should also be highlighted as intermediary determinants of health. The study has also shown the situation of COVID-19, which consists of an important barrier for patients seeking care. Many patients reported fear, insecurity and worry with regard to returning to medical appointments, which might contribute to the worsening of tuberculosis in the scenario under study.
, Ignacio Rangel, Lena Serrander, Cecilia Magnusson, Jonas Halfvarson, Torbjörn Norén, Malin Bergman-Jungeström
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249861

Abstract:
Objective Fecal microbiota transplantation (FMT) is a highly effective treatment for Clostridioides difficile infection (CDI). However, the fecal transplant’s causal components translating into clearance of the CDI are yet to be identified. The commensal bacteria Faecalibacterium prausnitzii may be of great interest in this context, since it is one of the most common species of the healthy gut microbiota and produces metabolites with anti-inflammatory properties. Although there is mounting evidence that F. prausnitzii is an important regulator of intestinal homeostasis, data about its role in CDI and FMT are relatively scarce. Methods Stool samples from patients with recurrent CDI were collected to investigate the relative abundance of F. prausnitzii before and after FMT. Twenty-one patients provided fecal samples before the FMT procedure, at 2 weeks post-FMT, and at 2–4 months post-FMT. The relative abundance of F. prausnitzii was determined using quantitative polymerase chain reaction. Results The abundance of F. prausnitzii was elevated in samples (N = 9) from donors compared to pre-FMT samples (N = 15) from patients (adjusted P<0.001). No significant difference in the abundance of F. prausnitzii between responders (N = 11) and non-responders (N = 4) was found before FMT (P = 0.85). In patients with CDI, the abundance of F. prausnitzii significantly increased in the 2 weeks post-FMT samples (N = 14) compared to the pre-FMT samples (N = 15, adjusted P<0.001). The increase persisted 2–4 months post-FMT (N = 15) compared to pre-FMT samples (N = 15) (adjusted P<0.001). Conclusions FMT increases the relative abundance of F. prausnitzii in patients with recurrent CDI, and this microbial shift remains several months later. The baseline abundance of F. prausnitzii in donors or recipients was not associated with future treatment response, although a true predictive capacity cannot be excluded because of the limited sample size. Further studies are needed to discern whether F. prausnitzii plays an active role in the resolution of CDI.
, William Worodria, Sophie Nalukwago, Mary Nsereko, Ingvar Sanyu, Lalitha Rejani, Josephine Zawedde, David H. Canaday, Catherine M. Stein, Keith A. Chervenak, et al.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249477

Abstract:
Background The search for immune correlates of protection against Mycobacterium tuberculosis (MTB) infection in humans is limited by the focus on peripheral blood measures. Bronchoalveolar lavage (BAL) can safely be done and provides insight into cellular function in the lung where infection is first established. In this study, blood and lung samples were assayed to determine if heavily MTB exposed persons who resist development of latent MTB infection (RSTR) vs those who develop latent MTB infection (LTBI), differ in the make-up of resident BAL innate and adaptive immune cells. Methods Bronchoscopy was performed on 21 healthy long-term Ugandan RSTR and 25 LTBI participants. Immune cell distributions in BAL and peripheral blood were compared by differential cell counting and flow cytometry. Results The bronchoscopy procedure was well tolerated with few adverse reactions. Differential macrophage and lymphocyte frequencies in BAL differed between RSTR and LTBI. When corrected for age, this difference lost statistical significance. BAL CD4+ and CD8+ T cells were almost entirely composed of effector memory T cells in contrast to PBMC, and did not differ between RSTR and LTBI. BAL NKT, γδ T cells and NK cells also did not differ between RTSR and LTBI participants. There was a marginally significant increase (p = 0.034) in CD8 T effector memory cells re-expressing CD45RA (TEMRA) in PBMC of LTBI vs RSTR participants. Conclusion This observational case-control study comparing unstimulated BAL from RSTR vs LTBI, did not find evidence of large differences in the distribution of baseline BAL immune cells. PBMC TEMRA cell percentage was higher in LTBI relative to RSTR suggesting a role in the maintenance of latent MTB infection. Functional immune studies are required to determine if and how RSTR and LTBI BAL immune cells differ in response to MTB.
, Olivier Mascaro, Hugo Mercier, Gergely Csibra
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249958

Abstract:
Source representations play a role both in the formation of individual beliefs as well as in the social transmission of such beliefs. Both of these functions suggest that source information should be particularly useful in the context of interpersonal disagreement. Three experiments with an identical design (one original study and two replications) with 3- to 4-year-old-children (N = 100) assessed whether children’s source memory performance would improve in the face of disagreement and whether such an effect interacts with different types of sources (first- vs. second-hand). In a 2 x 2 repeated-measures design, children found out about the contents of a container either by looking inside or being told (IV1). Then they were questioned about the contents of the container by an interlocutor puppet who either agreed or disagreed with their answer (IV2). We measured children’s source memory performance in response to a free recall question (DV1) followed by a forced-choice question (DV2). Four-year-olds (but not three-year-olds) performed better in response to the free recall source memory question (but not the forced-choice question) when their interlocutor had disagreed with them compared to when it had agreed with them. Children were also better at recalling ‘having been told’ than ‘having seen’. These results demonstrate that by four years of age, source memory capacities are sensitive to the communicative context of assertions and serve social functions.
Prateek Dey, Sanjeev Kumar Sharma, Indrani Sarkar, , Padmanabhan Pramod, Venkata Hanumat Sastry Kochiganti, , Saurabh Singh Rathore, ,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0241098

Abstract:
Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.
Yan Chen, Yulu Zhao
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249359

Abstract:
A novel penalty for the proportional hazards model under the interval-censored failure time data structure is discussed, with which the subject of variable selection is rarely studied. The penalty comes from an idea to approximate some information criterion, e.g., the BIC or AIC, and the core process is to smooth the ℓ0 norm. Compared with usual regularization methods, the proposed approach is free of heavily time-consuming hyperparameter tuning. The efficiency is further improved by fitting the model and selecting variables in one step. To achieve this, sieve likelihood is introduced, which simultaneously estimates the coefficients and baseline cumulative hazards function. Furthermore, it is shown that the three desired properties for penalties, i.e., continuity, sparsity, and unbiasedness, are all guaranteed. Numerical results show that the proposed sparse estimation method is of great accuracy and efficiency. Finally, the method is used on data of Nigerian children and the key factors that have effects on child mortality are found.
Tianyu Zhang, Yanhua Wang, Peixun Zhang, Feng Xue, Dianying Zhang, Baoguo Jiang
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250009

Abstract:
The objective of this study is to establish an ankylosing spondylitis (AS) thoracolumbar fracture finite element (FE) model and provide a proper posterior fixation choice from the biomechanical perspective. The ankylosing spondylitis T9-L5 FE model was built and the range of motion (ROM) was compared to previous studies. The L1 transverse fracture was simulated and was separately fixed by five different patterns. The pull force and yielding force of the screws, the von Mises stress of the internal fixation, and the displacement of fracture site were analyzed to evaluate the proper fixation pattern for thoracolumbar fracture of AS. ROM of AS model was obviously restricted comparing to the normal vertebral experimental data. All the fixation patterns can stabilize the fracture. At least four levels of fixation can reduce the von Mises stress of the internal fixation. Four levels fixation has a higher pull force than the six levels fixation. Skipped level fixation did not reduce the stress, pull force and yielding force. The kyphosis correction did not change the biomechanical load. At least 4 levels fixation was needed for AS thoracolumbar fracture. The cemented screws should be chosen in 4 levels fixation to increase the holding of the screws. The skipped fixation has no advantage. The kyphosis correction can be chosen after weighing the pros and cons.
, Michael Skytte Petersen, Niels Høiby
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249733

Abstract:
Background Initially, the relative sizes of the asymptomatic and the symptomatic infected populations were not known for the COVID-19 pandemic and neither was the actual fatality rate. Therefore it was not clear either how the pandemic would impact the healthcare system. As a result it was initially predicted that the COVID-19 epidemic in Denmark would overwhelm the healthcare system and thus both the diagnosis and treatment of other hospital patients were compromised for an extended period. Aim To develop a mathematical model, which includes both asymptomatic and symptomatic infected persons, for early estimation of the epidemic’s course, its Infection Fatality Rate and the healthcare system load in Denmark, both retrospectively and prospectively. Methods The SEIRS (Susceptible—Exposed—Infected—Recovered—Susceptible) model including deaths outside hospitals and separate assessments of symptomatic and asymptomatic cases (based on seroprevalence) with different immunological memories. Optimal model parameters are in part identified by Monte Carlo based Least Square Error methods while micro-outbreaks are modeled by noise and explored in Monte Carlo simulations. Estimates for infected population sizes are obtained by using a quasi steady state method. Results The calculations and simulations made by the model were shown to fit with the observed development of the COVID-19 epidemic in Denmark. The antibody prevalence in the general population in May 2020 was 1.37%, which yields a relative frequency of symptomatic and asymptomatic cases of 1 to 5.2. Due to the large asymptomatic population, the Infection Mortality Rate was only 0.4%. However, with no non-pharmacological restrictions the COVID-19 death toll was calculated to have more than doubled the national average yearly deaths within a year. The transmission rate ℜ 0 was 5.4 in the initial free epidemic period, 0.4 in the lock-down period and 0.8–1.0 in the successive re-opening periods through August 2020. The large asymptomatic population made the termination of the epidemic difficult and micro-outbreaks occurred when the country re-opened. The estimated infected population size July 15 to August 15 was 2,100 and 12,200 for October 1–20, 2020. Conclusions The results of the model show, that COVID-19 has a low Infection Fatality Rate because the majority of infected persons are either asymptomatic or with few symptoms. A minority of the infected persons, therefore, requires hospitalization. That means that for a given infection pressure of both symptomatic and asymptomatic infected there will be a lower pressure on the capacity of the health care system than previously predicted. Further the epidemic will be difficult to terminate since about 84% of the infected individuals are asymptomatic but still contagious. The model may be useful if a major infection wave occurs in the autumn-winter season as it could make robust estimates both for the scale of an ongoing expanding epidemic and for the expected load on the healthcare system. The simulation may also be useful to evaluate different testing strategies based on estimated infected population sizes. The model can be adjusted and scaled to other regions and countries, which is illustrated with Spain and USA.
, , Cleuton Lima Miranda, Yennie Katarina Bredin, Maria João Ramos Pereira, Leandro Duarte
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0250016

Abstract:
Much evidence suggests that Amazonia and the Atlantic Forest were connected through at least three dispersion routes in the past: the Eastern route, the central route, and the Western route. However, few studies have assessed the use of these routes based on multiple species. Here we present a compilation of mammal species that potentially have dispersed between the two forest regions and which may serve to investigate these connections. We evaluate the present-day geographic distributions of mammals occurring in both Amazonia and the Atlantic Forest and the likely connective routes between these forests. We classified the species per habitat occupancy (strict forest specialists, species that prefer forest habitat, or generalists) and compiled the genetic data available for each species. We found 127 mammalian species presently occurring in both Amazonia and the Atlantic Forest for which, substantial genetic data was available. Hence, highlighting their potential for phylogeographic studies investigating the past connections between the two forests. Differently from what was previously proposed, the present-day geographic distribution of mammal species found in both Amazonia and the Atlantic Forest points to more species in the eastern portion of the dry diagonal (and adjoining forested habitats). The Central route was associated with the second most species. Although it remains to be seen how this present-day geography reflects the paleo dispersal routes, our results show the potential of using mammal species to investigate and bring new insights about the past connections between Amazonia and the Atlantic Forest.
, , Simon Zhou, Susan Carpenter
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249117

Abstract:
Macrophages and dendritic cells (DCs) are innate immune cells that play a key role in defense against pathogens. In vitro cultures of bone marrow-derived macrophages (BMDMs) and dendritic cells (BMDCs) are well-established and valuable methods for immunological studies. Typically, commercially available recombinant GM-CSF is utilized to generate BMDCs and is also used to culture alveolar macrophages. We have generated a new HEK-293T cell line expressing murine GM-CSF that secretes high levels of GM-CSF (~180 ng/ml) into complete media as an alternative to commercial GM-CSF. Differentiation of dendritic cells and expression of various markers were kinetically assessed using the GM-CSF HEK293T cell line, termed supGM-CSF and compared directly to purified commercial GMCSF. After 7–9 days of cell culture the supGM-CSF yielded twice as many viable cells compared to the commercial purified GM-CSF. In addition to differentiating BMDCs, the supGM-CSF can be utilized to culture functionally active alveolar macrophages. Collectively, our results show that supernatant from our GM-CSF HEK293T cell line supports the differentiation of mouse BMDCs or alveolar macrophage culturing, providing an economical alternative to purified GM-CSF.
Xiaoyan Sun, Huimin Zhu, Wenjuan Li, Li Zhao, Wenhua Li, Xiaoyong Li,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249977

Abstract:
Stress urinary incontinence (SUI) is a common condition in women and associated with extra-cellular matrix (ECM) reconstruction, which is mainly regulated by fibroblasts. However, the underlying mechanism remains obscure. Small extracellular vesicles (sEVs) play fundamental biological roles in various cellular functions. Some studies suggested that the sEVs were involved in the metabolism of ECM and the function of fibroblasts. The purpose of our study was to investigate the effect of sEVs secreted by vaginal fibroblasts on the pathogenesis of SUI. We showed that the fibroblasts of female anterior vaginal wall secreted sEVs. Moreover, fibroblasts of females with SUI had significantly elevated secretion of sEVs. The collagen contents, proliferation and migration capacity of fibroblasts were decreased when fibroblasts were co-cultured with fibroblasts-derived sEVs (fibroblast-sEVs) from SUI patients. Proteomic analysis revealed that fibroblast-sEVs contained various differentially expressed proteins including TIMP2, TGF-β and ABCC4, which were involved in signaling pathways of fibroblasts regulation. Therefore, we suggested that fibroblast-sEVs contributed to the pathogenesis of SUI through various proteins including TIMP2, TGF-β and ABCC4.
, Gabriella Do Vale Pereira, André Lopes, Rita Colen,
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0248356

Abstract:
New and more efficient methods to sustainably intensify Aquaculture production are essential to attain the seafood demand for direct human consumption in the near future. Nutrition has been identified as one strategy of early exposure that might affect animal early development and later phenotype. This strategy may have positive consequences in the modulation of fish digestive physiology, which will correlate with higher performance outputs. Thus, improving fish digestive efficiency will lead to higher productivity and lower biogenic emission from aquaculture facilities, minimising the impact on the environment while increasing the biological efficiency. An innovative in ovo nutritional modulation technique based on low-frequency ultrasounds was used to enhance the transport of amino acids across the embryo membranes. An early stimulus with either arginine or glutamine, both involved in gut maturation, was applied in zebrafish (Danio rerio) embryos at 3.5 hours post-fertilization (hpf). At 22 days post-fertilization (dpf), growth performance, digestive enzyme activities and gut microbiota composition were analysed to evaluate the larval nutrition-induced metabolic plasticity and the effects on fish digestive efficiency. Results showed that fish survival was not affected either by the sonophoresis technique or amino acid supplementation. Final dry weight at 22 dpf was statistically higher in larvae from glutamine treatment when compared to the control even with lower trypsin activity, suggesting a higher nutrient digestion capacity, due to a slightly modulation of gut microbiota. Higher arginine supplementation levels should be tested as strategy to enhance growth at later developmental stages. In conclusion, this study demonstrated the efficiency of sonophoresis technique for in ovo nutritional modulation and suggests that in ovo glutamine supplementation might promote growth at later developmental stage through a positive microbiota modulation.
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249835

Abstract:
The microbiome is a matter of interest for science, consumers and business. Our objective is to quantify that interest in academic journals and newspapers, both quantitatively and by study design. We calculated the number of articles on the microbiome from the total number of biomedicine articles featured in both PubMed and Spanish science news agency SINC, from 2008 to 2018. We used the Factiva database to identify news stories on microbiome papers in three general newspapers (The New York Times, The Times and El País) and three business newspapers (The Wall Street Journal, the Financial Times and Expansión), from 2007 to 2019. Then, we compared news stories with microbiome papers in PubMed, while also analyzing the frequencies of five study design types, both in the newspapers and in the papers themselves. Microbiome papers represented 0.8% of biomedicine papers in PubMed from 2008 to 2018 (increasing from 0.4% to 1.4%), while microbiome news published by SINC represented 1.6% of total biomedical news stories during the same period (increasing from 0.2% to 2.2%). The number of news stories on microbiome papers correlated with the number of microbiome papers (0.91, p < 0.001) featured in general newspapers, but not in business ones. News stories on microbiome papers represented 78.9% and 42.7% of all microbiome articles in general and business newspapers, respectively. Both media outlet types tended to over-report observational studies in humans while under-reporting environmental studies, while the representation of systematic reviews of randomized controlled trials, randomized controlled trials and animal/laboratory studies was similar when comparing newspapers and PubMed. The microbiome is receiving increasing attention in academic journals and newspapers. News stories on the microbiome in general and business newspapers are mostly based on research findings and are more interested in observational studies in humans and less in environmental studies compared to PubMed.
Youngsuk Lee, Van Giap Do, SeonAe Kim, Hunjoong Kweon, Tony K. McGhie
Published: 9 April 2021
PLOS ONE, Volume 16; doi:10.1371/journal.pone.0249975

Abstract:
Fruit abscission is a complex physiological process that is regulated by internal and environmental factors. During early development, apple fruit are exposed to extreme temperature fluctuations that are associated with premature fruit drop; however, their effect on fruit abscission is largely unknown. We hypothesized that fruit abscission is triggered by cold stress and investigated the molecular basis of premature fruit drop using RNA-Seq and metabolomics data from apple fruit undergoing abscission following cold stress in the field. Genes responsive to abscisic acid signaling and cell wall degradation were upregulated during abscission, consistent with the increased abscisic acid concentrations detected by liquid chromatography-mass spectrometry. We performed ex vivo cold shock experiments with excised tree subunits consisting of a branch, pedicel, and fruit. Abscission induction occurred in the cold-stressed subunits with concurrent upregulation of abscisic acid biosynthesis (MdNCED1) and metabolism (MdCYP707A) genes, and ethylene biosynthesis (MdACS1) and receptor (MdETR2) genes in the pedicel. Another key finding was the activation of cytoplasmic streaming in abscission-zone cells detected by electron microscopy. Our results provide a novel insight into the molecular basis of fruit abscission physiology in response to cold stress in apple.
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