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ISSN / EISSN : 1932-6203 / 1932-6203
Current Publisher: Public Library of Science (PLoS) (10.1371)
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Udo Buchholz, Heiko Juergen Jahn, Bonita Brodhun, Ann-Sophie Lehfeld, Marina M. Lewandowsky, Franziska Reber, Kristin Adler, Jacqueline Bochmann, Christina Förster, Madlen Koch, et al.
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0241724

Abstract:
Introduction Sources of infection of most cases of community-acquired Legionnaires’ disease (CALD) are unknown. Objective Identification of sources of infection of CALD. Setting Berlin; December 2016–May 2019. Participants Adult cases of CALD reported to district health authorities and consenting to the study; age and hospital matched controls. Main outcome measure Percentage of cases of CALD with attributed source of infection. Methods Analysis of secondary patient samples for monoclonal antibody (MAb) type (and sequence type); questionnaire-based interviews, analysis of standard household water samples for Legionella concentration followed by MAb (and sequence) typing of Legionella pneumophila serogroup 1 (Lp1) isolates; among cases taking of additional water samples to identify the infectious source as appropriate; recruitment of control persons for comparison of exposure history and Legionella in standard household water samples. For each case an appraisal matrix was filled in to attribute any of three source types (external (non-residence) source, residential non-drinking water (RnDW) source (not directly from drinking water outlet), residential drinking water (RDW) as source) using three evidence types (microbiological results, cluster evidence, analytical-comparative evidence (using added information from controls)). Results Inclusion of 111 study cases and 202 controls. Median age of cases was 67 years (range 25–93 years), 74 (67%) were male. Among 65 patients with urine typable for MAb type we found a MAb 3/1-positive strain in all of them. Compared to controls being a case was not associated with a higher Legionella concentration in standard household water samples, however, the presence of a MAb 3/1-positive strain was significantly associated (odds ratio (OR) = 4.9, 95% confidence interval (CI) 1.7 to 11). Thus, a source was attributed by microbiological evidence if it contained a MAb 3/1-positive strain. A source was attributed by cluster evidence if at least two cases were exposed to the same source. Statistically significant general source types were attributed by calculating the population attributable risk (analytical-comparative evidence). We identified an external source in 16 (14%) cases, and RDW as source in 28 (25%). Wearing inadequately disinfected dentures was the only RnDW source significantly associated with cases (OR = 3.2, 95% CI 1.3 to 7.8) and led to an additional 8% of cases with source attribution, for a total of 48% of cases attributed. Conclusion Using the appraisal matrix we attributed almost half of all cases of CALD to an infectious source, predominantly RDW. Risk for LD seems to be conferred primarily by the type of Legionella rather than the amount. Dentures as a new infectious source needs further, in particular, integrated microbiological, molecular and epidemiological confirmation.
Shreya Banerjee, Indrani Roy Chowdhury
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0241994

Abstract:
Objective The study attempts (a) to compute the degree of socio-economic inequity in health care utilization and (b) to decompose and analyze the drivers of socio-economic inequity in health care utilization among adults (20–59 years) in India during the periods 2014 and 2017–18. Data source The analysis has been done by using the unit level data of Social Consumption: Health (Schedule number 25.0), of National sample Survey (NSS), corresponding to the 71st and 75th rounds. Methods Odds ratios were computed through logistic regression analysis to examine the effect of the socio-economic status on the health seeking behaviour of the ailing adult population in India. Concentration Indices (CIs) were calculated to quantify the magnitude of socio-economic inequity in health care utilization. Further, the CIs were decomposed to find out the share of the major contributory factors in the overall inequity. Results The regression results revealed that socio-economic status continues to show a strong association with treatment seeking behavior among the adults in India. The positive estimates of CIs across both the rounds of NSS suggested that health care utilization among the adults continues to be concentrated within the higher socio-economic status, although the magnitude of inequity in health care utilization has shrunk from 0.0336 in 2014 to 0.0230 in 2017–18. However, the relative contribution of poor economic status to the overall explained inequities in health care utilisation observed a rise in its share from 31% in 2014 to 45% in 2017–18. Conclusion To reduce inequities in health care utilization, policies should address issues related to both supply and demand sides. Revamping the public health infrastructure is the foremost necessary condition from the supply side to ensure equitable health care access to the poor. Therefore, it is warranted that India ramps up investments and raises the budgetary allocation in the health care infrastructure and human resources, much beyond the current spending of 1.28% of its GDP as public expenditure on health. Further, to reduce the existing socio-economic inequities from the demand side, there is an urgent need to strengthen the redistributive mechanisms by tightening the various social security networks through efficient targeting and broadening the outreach capacity to the vulnerable and marginalized sections of the population.
Seung-Young Roh, Jong-Il Choi, Min Sun Kim, Eun Young Cho, Yun Gi Kim, Kwang-No Lee, Jaemin Shim, Jin Seok Kim, Young-Hoon Kim
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0242799

Abstract:
The incidence of sudden cardiac arrest (SCA) in Asians is lower than that seen in Western populations, but there are few available data on the incidence and associated cardiac etiology of SCA in Asians. From 2002 to 2013, patients with SCA were analyzed using a cohort from the South Korean National Health Insurance Service (NHIS) coded database. Sudden unexplained death syndrome (SUDS) was defined as cryptogenic arrest, excluding that of non-cardiac origin, coronary artery disease (CAD), cardiomyopathy (CM), and valvular heart disease. During the 12-year study period, 5,973 patients (0.53%) from the total cohort of 1,125,691 had a cardiac arrest code. The overall incidence of arrest was 48.7 per 100,000 person-years (95% CI 16.6–18.0). The incidence of primary SCA excluding those of non-cardiac origin was 16.1 per 100,000 person-years (95% CI 15.4–16.8). It was higher in males than in females (18.1 vs. 14.1 per 100,000 person-years). CAD was the most common cause of SCA (59.4%), and followed by CM (13.9%). SUDS accounted for 14.7% of SCA events. The risk of SCA had increased gradually from over 25 years old. Heart failure, atrial fibrillation and hypertension are major factors associated with SCA incidence. Our findings outline epidemiologic data for SCA and the proportion of associated cardiac etiology leads SCA in a large population.
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0240414

Abstract:
The availability of reliable commercial information is considered a key feature of inter-regional trade if the Roman economy was highly integrated. However, the extent to which archaeological and historical sources of inter-regional trade reflect the degree of economic integration is still not fully understood, a question which lies at the heart of current debates in Roman Studies. Ceramic tableware offers one of the only comparable and quantifiable sources of information for Roman inter-regional trade over centuries-long time periods. The distribution patterns and stylistic features of tablewares from the East Mediterranean dated between 200 BC and AD 300 suggest a competitive market where buying decisions might have been influenced by access to reliable commercial information. We contribute to this debate by representing three competing hypotheses in an agent-based model: success-biased social learning of tableware buying strategies (requiring access to reliable commercial information from all traders), unbiased social learning (requiring limited access), and independent learning (requiring no access). We use approximate Bayesian computation (ABC) to evaluate which hypothesis best describes archaeologically observed tableware distribution patterns. Our results revealed success-bias is not a viable theory and we demonstrate instead that local innovation (independent learning) is a plausible driving factor in inter-regional tableware trade. We also suggest that tableware distribution should instead be explored as a small component of long-distance trade cargoes dominated by foodstuffs, metals, and building materials.
Steve Goodacre, Ben Thomas, Ellen Lee, Laura Sutton, Amanda Loban, Simon Waterhouse, Richard Simmonds, Katie Biggs, Carl Marincowitz, Jose Schutter, et al.
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0240206

Abstract:
Background Hospital emergency departments play a crucial role in the initial assessment and management of suspected COVID-19 infection. This needs to be guided by studies of people presenting with suspected COVID-19, including those admitted and discharged, and those who do not ultimately have COVID-19 confirmed. We aimed to characterise patients attending emergency departments with suspected COVID-19, including subgroups based on sex, ethnicity and COVID-19 test results. Methods and findings We undertook a mixed prospective and retrospective observational cohort study in 70 emergency departments across the United Kingdom (UK). We collected presenting data from 22445 people attending with suspected COVID-19 between 26 March 2020 and 28 May 2020. Outcomes were admission to hospital, COVID-19 result, organ support (respiratory, cardiovascular or renal), and death, by record review at 30 days. Mean age was 58.4 years, 11200 (50.4%) were female and 11034 (49.6%) male. Adults (age >16 years) were acutely unwell (median NEWS2 score of 4), frequently had limited performance status (46.9%) and had high rates of admission (67.1%), COVID-19 positivity (31.2%), organ support (9.8%) and death (15.5%). Children had much lower rates of admission (27.4%), COVID-19 positivity (1.2%), organ support (1.4%) and death (0.3%). Similar numbers of men and women presented to the ED, but men were more likely to be admitted (72.9% v 61.4%), require organ support (12.2% v 7.7%) and die (18.2% v 13.0%). Black or Asian adults tended to be younger than White adults (median age 54, 50 and 67 years), were less likely to have impaired performance status (43.1%, 26.8% and 51.6%), be admitted to hospital (60.8%, 57.3%, 69.6%) or die (11.6%, 11.2%, 16.4%), but were more likely to require organ support (15.9%, 14.3%, 8.9%) or have a positive COVID-19 test (40.8%, 42.1%, 30.0%). Adults admitted with suspected and confirmed COVID-19 had similar age, performance status and comorbidities (except chronic lung disease) to those who did not have COVID-19 confirmed, but were much more likely to need organ support (22.2% v 8.9%) or die (32.1% v 15.5%). Conclusions Important differences exist between patient groups presenting to the emergency department with suspected COVID-19. Adults and children differ markedly and require different approaches to emergency triage. Admission and adverse outcome rates among adults suggest that policies to avoid unnecessary ED attendance achieved their aim. Subsequent COVID-19 confirmation confers a worse prognosis and greater need for organ support. Registration ISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533.
Jan Göpel, Jan Schüngel, Benjamin Stuch, Rüdiger Schaldach
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0225914

Abstract:
The ongoing trend toward agricultural intensification in Southern Amazonia makes it essential to explore the future impacts of this development on the extent of natural habitats and biodiversity. This type of analysis requires information on future pathways of land-use and land-cover change (LULCC) under different socio-economic conditions and policy settings. For this purpose, the spatially explicit land-use change model LandSHIFT was applied to calculate a set of high-resolution land-use change scenarios for the Brazilian states Para and Mato Grosso. The period of the analysis were the years 2010–2030. The resulting land-use maps were combined with maps depicting vertebrate species diversity in order to examine the impact of natural habitat loss on species ranges as well as the overall LULCC-induced effect on vertebrate diversity as expressed by the Biodiversity Intactness Index (BII). The results of this study indicate a general decrease in biodiversity intactness in all investigated scenarios. However, agricultural intensification combined with diversified environmental protection policies show least impact of LULCC on vertebrate species richness and conservation of natural habitats compared to scenarios with low agricultural intensification or scenarios with less effective conservation policies.
Shengwang Du, Junyi Li, Naizheng Bian
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0238220

Abstract:
The development of high-throughput sequencing technology has generated huge amounts DNA data. Many general compression algorithms are not ideal for compressing DNA data, such as the LZ77 algorithm. On the basis of Nour and Sharawi’s method,we propose a new, lossless and reference-free method to increase the compression performance. The original sequences are converted into eight intermediate files and six final files. Then, the LZ77 algorithm is used to compress the six final files. The results show that the compression time is decreased by 83% and the decompression time is decreased by 54% on average.The compression rate is almost the same as Nour and Sharawi’s method which is the fastest method so far. What’s more, our method has a wider range of application than Nour and Sharawi’s method. Compared to some very advanced compression tools at present, such as XM and FCM-Mx, the time for compression in our method is much smaller, on average decreasing the time by more than 90%.
Jan A. Stratmann, Raphael Lacko, Olivier Ballo, Shabnam Shaid, Wolfgang Gleiber, Maria J. G. T. Vehreschild, Thomas Wichelhaus, Claudia Reinheimer, Stephan Göttig, Volkhard A. J. Kempf, et al.
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0242544

Abstract:
Objectives Multidrug-resistant organisms (MDRO) are considered an emerging threat worldwide. Data covering the clinical impact of MDRO colonization in patients with solid malignancies, however, is widely missing. We sought to determine the impact of MDRO colonization in patients who have been diagnosed with Non-small cell lung cancer (NSCLC) who are at known high-risk for invasive infections. Materials and methods Patients who were screened for MDRO colonization within a 90-day period after NSCLC diagnosis of all stages were included in this single-center retrospective study. Results Two hundred and ninety-five patients were included of whom 24 patients (8.1%) were screened positive for MDRO colonization (MDROpos) at first diagnosis. Enterobacterales were by far the most frequent MDRO detected with a proportion of 79.2% (19/24). MDRO colonization was present across all disease stages and more present in patients with concomitant diabetes mellitus. Median overall survival was significantly inferior in the MDROpos study group with a median OS of 7.8 months (95% CI, 0.0–19.9 months) compared to a median OS of 23.9 months (95% CI, 17.6–30.1 months) in the MDROneg group in univariate (p = 0.036) and multivariate analysis (P = 0.02). Exploratory analyses suggest a higher rate of non-cancer-related-mortality in MDROpos patients compared to MDROneg patients (p = 0.002) with an increased rate of fatal infections in MDROpos patients (p = 0.0002). Conclusions MDRO colonization is an independent risk factor for inferior OS in patients diagnosed with NSCLC due to a higher rate of fatal infections. Empirical antibiotic treatment approaches should cover formerly detected MDR commensals in cases of (suspected) invasive infections.
Liviu Badea, Emil Stănescu
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0242858

Abstract:
Linking phenotypes to specific gene expression profiles is an extremely important problem in biology, which has been approached mainly by correlation methods or, more fundamentally, by studying the effects of gene perturbations. However, genome-wide perturbations involve extensive experimental efforts, which may be prohibitive for certain organisms. On the other hand, the characterization of the various phenotypes frequently requires an expert’s subjective interpretation, such as a histopathologist’s description of tissue slide images in terms of complex visual features (e.g. ‘acinar structures’). In this paper, we use Deep Learning to eliminate the inherent subjective nature of these visual histological features and link them to genomic data, thus establishing a more precisely quantifiable correlation between transcriptomes and phenotypes. Using a dataset of whole slide images with matching gene expression data from 39 normal tissue types, we first developed a Deep Learning tissue classifier with an accuracy of 94%. Then we searched for genes whose expression correlates with features inferred by the classifier and demonstrate that Deep Learning can automatically derive visual (phenotypical) features that are well correlated with the transcriptome and therefore biologically interpretable. As we are particularly concerned with interpretability and explainability of the inferred histological models, we also develop visualizations of the inferred features and compare them with gene expression patterns determined by immunohistochemistry. This can be viewed as a first step toward bridging the gap between the level of genes and the cellular organization of tissues.
Fekade Wondemagegn, Tsegaye Berkessa
Published: 25 November 2020
PLOS ONE, Volume 15; doi:10.1371/journal.pone.0242701

Abstract:
Introduction Data on the sexual behavior among people living with human immunodeficiency virus (PLHIV) dwelling at HIV prevalent setting located at the periphery of Ethiopia is lacking. Therefore, this study was designed to investigate sexual practice of patients following their antiretroviral therapy (ART) service and factors affecting their behavior. Materials and methods A facility based cross-sectional study design was employed to assess risky sexual practice and associated factors among HIV positive adults attending ART clinics in Gambella town, Southwest Ethiopia. Risky sexual practice is defined as a custom of getting in at least one of the following practices such as condom-unprotected sex with any partner, having two or more sexual partners and practicing casual sex in the last three months. A total of 352 randomly selected clients were interviewed by using a structured questionnaire. The multivariable logistic regression model was used to examine the association between covariates and the outcome variable. Results Majority of the study participants were engaged at least in one of the risky sexual practices (79.8% confidence interval (CI): 75.3% - 83.9%). The multivariable analysis found that the odds of risky sexual practice were higher among individuals who use substances (‘khat’ users (AOR: 3.82, 95%CI:1.30–11.22), smoke cigarette (AOR:4.90, 95%CI:1.19–12.60), consume alcohol (AOR: 2.59, 95%CI:1.28–5.21)); those who never discuss about safe sex with their partner/s (AOR: 2.21, 95%CI:1.16–4.21); those who have been in attachment for longer duration (more than four years) with their partner (AOR: 3.56, 95%CI: 1.32–9.62); and groups who desire to bear children in their future life (AOR: 3.15, 95%CI:1.40–7.04) as compared to their respective comparison groups. Conclusions A significant number of participants were engaged at least in one of the risky sexual practices which potentially result in super infection by a new or/and drug resistant viral strain/s, and onward transmission of the virus. Thus, an HIV intervention program which focuses on the identified factors has to be implemented to mitigate risk of unsafe sexual behavior of this population group and move towards ending the HIV/Acquired Immunodeficiency Syndrome (AIDS) epidemic.
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