bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethnic Disparities in Hospitalization for COVID-19: a Community-Based Cohort Study in the UK
Authors: Lassale Camille , Gaye Bamba , Hamer Mark , Gale Catharine R , Batty G David
Published: May 2020

Importance: Differentials in COVID-19 incidence, hospitalization and mortality according to ethnicity are being reported but their origin is uncertain.
Objective: We aimed to explain any ethnic differentials in COVID-19 hospitalization based on socioeconomic, lifestyle, mental and physical health factors.
Design: Prospective cohort study with national registry linkage to hospitalisation for COVID-19.
Setting: Community-dwelling.
Participants: 340,966 men and women (mean age 56.2 (SD=8.1) years; 54.3% women) residing in England from the UK Biobank study.
Exposures: Ethnicity classified as White, Black, Asian, and Others.
Main Outcome(s) and Measure(s): Cases of COVID-19 serious enough to warrant a hospital admission in England from 16-March-2020 to 26-April-2020.
Results: There were 640 COVID-19 cases (571/324,306 White, 31/4,485 Black, 21/5,732 Asian, 17/5,803 Other). Compared to the White study members and after adjusting for age and sex, Black individuals had over a 4-fold increased risk of being hospitalised (odds ratio; 95% confidence interval: =4.32; 3.00-6.23), and there was a doubling of risk in the Asian group (2.12; 1.37, 3.28) and the Other non-white group (1.84; 1.13, 2.99). After controlling for 15 confounding factors which included neighbourhood deprivation, education, number in household, smoking, markers of body size, inflammation, and glycated haemoglobin, these effect estimates were attenuated by 33% for Blacks, 52% for Asians and 43% for Other, but remained raised for Blacks (2.66; 1.82, 3.91), Asian (1.43; 0.91, 2.26) and other non-white groups (1.41; 0.87, 2.31).
Conclusions and Relevance: Our findings show clear ethnic differences in risk of hospitalization for COVID-19 which do not appear to be fully explained by known explanatory factors. If replicated, our results have implications for health policy, including the targeting of prevention advice and vaccination coverage.
Association of PNPLA3 rs738409 G/C gene polymorphism with nonalcoholic fatty liver disease in children: a meta-analysis
Authors: Tang Shan , Zhang Jing , Mei Tingting , Guo Haiqing , Wei Xinhuan , Zhang Wenyan , Liu Yali , Liang Shan , Fan Zuopeng , Ma Lixia , Lin Wei , Liu Yirong , Qiu Lixia , Yu Haibin
Published: May 2020

Objective:To systematically review the association of PNPLA3 rs738409 G/C gene polymorphism with non-alcoholic fatty liver disease(NAFLD) in children.
Design: Systematic review and meta-analysis.
Data sources and study selection: We searched MEDLINE, PubMed, EMBASE, and CENTRAL databases from inception to May 2019. Case-control studies assessing the relationship between PNPLA3 rs738409 G/C gene polymorphism with non-alcoholic fatty liver disease in children were selected according to inclusion and exclusion criteria.
Data extraction and analyses: First author's surname, publication year, country, total numbers of patients in the case and control groups, sex ratio, and body mass index (BMI), as well as the numbers of cases and controls with the C/C, C/G and G/G genotypes were extracted from the included studies. Random effects model was used to quantify the association between the PNPLA3 rs738409 G/C gene polymorphism and the susceptibility of children's NAFLD. Fixed effects model was used to quantify the relationship between the PNPLA3 rs738409 G/C gene polymorphism and the severity of NAFLD in children.
Results: A total of nine case-control studies were included in this meta-analysis containing data of 1173 children with NAFLD and 1792 healthy controls. Five studies compared NAFLD children and non-NAFLD healthy populations. Statistical analysis showed that PNPLA3 gene polymorphism was significantly associated with children's NAFLD in the allele contrast, dominant, recessive and over dominant models (G vs C,OR=3.343, 95% CI=1.524-7.334; GG+GC vs CC,OR=3.157, 95% CI=1.446-6.892;GG vs GC+CC,OR=5.692, 95% CI=1.941-16.689; GG+CC vs GC,OR=2.756, 95% CI=1.729-4.392). Four case-control studies compared Children with nonalcoholic fatty liver(NAFL) and children with nonalcoholic steatohepatitis(NASH). The results showed that the PNPLA3 gene polymorphism was also significantly associated with the severity of NAFLD in children in recessive gene model(GG vs GC+CC,OR = 14.43, 95% CI = 5.985-34.997); The Egger's test revealed no significant publication bias.
Conclusions: Meta-analysis showed that PNPLA3 gene polymorphism was significantly associated with susceptibility and severity of NAFLD in children.
trial registration number： CRD42019134056.
Outdoor PM2.5 Concentration and Rate of Change in COVID-19 Infection in Provincial Capital Cities in China
Authors: Han Yang , Lam Jacqueline CK , Li Victor OK , Crowcroft Jon , Fu Jinqi , Downey Jocelyn , Gozes Illana
Published: May 2020

Motivated by earlier findings that exposure to daily outdoor PM2.5 (P) may increase the risk of influenza infection, our study examines if immediate exposure to outdoor P will modify the rate of change in the daily number of COVID-19 infections (R), for (1) the high infection provincial capital cities in China and (2) Wuhan, China, using regression modelling. A multiple linear regression model was constructed to model the statistical relationship between P and R in China and in Wuhan, from 1 January to 20 March 2020. We carefully accounted for potential key confounders and addressed collinearity. The causal relationship between P and R, and the interaction effect between key variables were investigated. A causal relationship between P and R across the high infection provincial capital cities in China was established via matching. A higher P resulted in a higher R in China. A 10 µg/m3 increase in P gave a 1.5% increase in R (p < 0.001). An interaction analysis between P and absolute humidity (AH) showed a statistically significant negative relationship between P × AH and R (p < 0.05). When AH was $ 5.8 g/m3, a higher P and AH gave a higher R. In contrast, when AH ≥ 5.8 g/m3, the effect of a higher P was counteracted by the effect of a higher AH, resulting in a lower R. Given that P can exacerbate R, we recommend the installation of air purifiers and better air ventilation to reduce the effect of P on R. Further, given the increasing discussions/observations that COVID-19 can be airborne, we highly recommend the wearing of surgical masks to keep one from contracting COVID-19 via the viral-particulate transmission pathway.
A modified SEIR Model with Confinement and Lockdown of COVID-19 for Costa Rica
Authors: de-Camino-Beck Tomas
Published: May 2020

The fast moving post-modern society allows for individuals to move fast in and between different countries, making it a perfect situation for the spread of emerging diseases. COVID-19 emerged with properties of a highly contagious disease, that has spread rapidly around the world. SIR/SEIR models are generally used to explain the dynamics of epidemics, however Coronavirus has shown dynamics with constant non-pharmaceutical interventions, making it difficult to model with these simple models. We extend an SEIR model to include a confinement compartment (SEICR) and use this to explain data from COVID-19 epidemic in Costa Rica. Then we discuss possible second wave of infection by adding a time varying function in the model to simulate cyclic interventions.
Does Heat Thermotherapy Improve Cardiovascular and Cardiometabolic Health? A Systematic Review and Narrative Synthesis of the Literature
Authors: Price Ben S. , Lucas Samuel J.E. , Gifford Rachel E. , Cable Nigel T. , Lucas Rebekah A.I.
Published: May 2020

Objective: To assess the efficacy of heat thermotherapy to improve cardiovascular and cardiometabolic health, and to compare potential heat thermotherapy moderating factors.
Design: Systematic review and narrative synthesis.
Data Sources: Electronic databases (MEDLINE, EMBASE and Web of Science) were searched up to 6th February 2020.
Eligibility criteria for selecting studies: Journal articles with adult participants, a controlled trial study design, and a passive heating stimulus with a cardiovascular or cardiometabolic health outcome were included.
Results: From 1036 articles, 39 articles met the inclusion criteria. Heat thermotherapy was delivered acutely (one bout; n=19), short term (2-15 bouts; n=6) and chronically (>15 bouts; n=14), via either hot water immersion (n=26; water temperature 38-43 °C) or heated air exposure (n=11; air temperature 31-90 °C), or water perfused suit/handheld device (n=2). Heat exposure ranged from 10 to 240 minutes. Cardiovascular and cardiometabolic measurement techniques varied across studies, alongside participant age (≤35 years, n=376; >35 ≤60 years, n=335 and >60 years, n=350) and health status. 21/27 studies measuring cardiovascular outcomes reported positive health benefits, including increased flow-mediated dilation (1.3-5.3%) and lower systolic blood pressure (4-16 mm Hg). 15/22 studies measuring cardiometabolic outcomes reported positive health benefits, including reduced postprandial glucose (-0.89 to -0.5 mmol.L -1) and C-reactive protein concentrations (-0.9 to -10.94 mg.L-1).
Conclusion: Overall, 29/39 studies demonstrated significant positive cardiovascular or cardiometabolic health benefits from heat thermotherapy across various population demographics, despite varied study design and modality. Heat thermotherapy is an efficacious treatment for cardiovascular disease alongside pharmaceutical and exercise-based interventions.
Eruption of COVID-19 like illness in a remote village in Papua (Indonesia)
Authors: van Burg Elco , van Burg-Verhage Wijnanda
Published: May 2020

Background
The COVID-19 pandemic is creating significant challenges for healthcare infrastructure for countries of all development and resource levels. Low-and-middle resource countries face even larger challenges, as their resources are stretched and often insufficient under normal circumstances. A village in the Papuan highlands of Indonesia; small, isolated, accessed only by small plane or trekking has experienced an outbreak typical of COVID-19.

Methodology/Principal Findings
This description was compiled from patient care records by lay healthcare workers in M20 (a pseudonym) during and after an outbreak and from medical doctors responding to online requests for help. We assume that, for reasons given, the outbreak that has been described was COVID-19. The dense social structure of the village resulted in a rapid infection of 90-95% of the population. Physical distancing and isolation measures were used, but probably implemented suboptimal and too late, and their effect on the illness course was unclear. The relatively young population, with a majority of women, probably influenced the impact of the epidemic, resulting in only two deaths so far.

Conclusions/Significance
This outbreak pattern of suspected SARS-CoV-2 in a village in the highlands of Papua (Indonesia) presents a unique report of the infection of an entire village population over five weeks. The age distribution, common in Papuan highland villages may have reduced case fatality rate (CFR) in this context and that might be the case in similar remote areas since survival to old age is already very limited and CFR among younger people is lower.
Efficacy and Safety of Hydroxychloroquine and Chloroquine for COVID-19: A systematic review
Authors: Singh Sonal , Moore Thomas J
Published: May 2020

BACKGROUND:
Hydroxychloroquine and chloroquine are widely used to treat hospitalized COVID-19 patients primarily based on antiviral activity in in vitro studies. Our objective was to systematically evaluate their efficacy and safety in hospitalized patients with COVID-19.

METHODS:
We systematically reviewed PubMed, ClinicalTrials.gov, and Medrxviv for studies of hydroxychloroquine and chloroquine in COVID-19 hospitalized patients on April 26, 2020. We evaluated the quality of trials and observational studies using the Jadad criteria and Newcastle Ottawa Scale, respectively.

RESULTS:
After a review of 175 citations, we included 5 clinical trials (total of 345 patients), 9 observational studies (n = 2529), and 6 additional studies (n = 775) reporting on the QT interval. Three studies reported treatment benefits including two studies reporting benefit on virologic outcomes, which was statistically significant in one study, and another reported significant improvement on cough symptoms. Three studies reported that treatment was potentially harmful, including an significantly increased risk of mortality in two studies and increased need for respiratory support in another. Eight studies were unable to detect improvements on virologic outcomes (n = 3) or pneumonia or transfer to ICU/death (n = 5). The proportion of participants with critical QTc intervals of ≥ 500 ms or an increase of ≥ 60 ms from baseline ranged from 8.3% to 36% (n = 8). One clinical trial and six observational studies were of good quality. The remaining studies were of poor quality.

CONCLUSIONS:
Our systematic review of reported clinical studies did not identify substantial evidence to support the efficacy of hydroxychloroquine or chloroquine in hospitalized COVID-19 patients and raises questions about potential harm from QT prolongation and increased mortality.
Ethnic and regional variation in hospital mortality from COVID-19 in Brazil
Authors: Baqui Pedro Otavio , Bica Ioana , Marra Valerio , Ercole Ari , Van Der Schaar Mihaela
Published: May 2020

Background: The COVID-19 pandemic is quickly spreading throughout Brazil, which is rapidly ascending the ranking of countries with the highest number of cases and deaths. A particularly unstable federal regime and fragile socioeconomic situation is likely to have contributed to the impact of the disease. Amid this crisis there is substantial concern in the possible socioeconomic, geopolitical and ethnic inequity of the impact of COVID-19 on the country's particularly diverse population.

Methods: We performed a cross-sectional observational study of COVID-19 hospital mortality using observational data from the SIVEP-Gripe dataset. We present descriptive statistics to quantify the COVID-19 pandemic in Brazil. We assess the importance of regional factors such as education, income and health either on a state-by-state basis or by splitting Brazil into a North and a Central-South region. Mixed-effects survival analysis was used to estimate the effects of ethnicity and comorbidity at an individual level in the context of regional variation.

Findings: Our results show that, compared to branco comparators, hospitalised pardo and preto Brazilians have significantly higher risk of mortality, with hazard ratios and 95% CI of 1.47 (1.33-1.58) and 1.32 (1.15-1.52), respectively. In particular, pardo ethnicity was the second most important risk factor (after age). We also found that hospitalised Brazilians in North regions tend to have more comorbidities than in the Central-South, with similar proportions between the various ethnic groups. Finally, we found that states in the North have a higher hazard ratio as compared to the Central-South, and that Rio de Janeiro obtained one of the highest hazard ratios, similar to the ones of the more underdeveloped Pernambuco and Amazonas.

Interpretation: Our results can be interpreted according to the interplay of two independent, but correlated, effects: i) mortality by COVID-19 increases going North (vertical effect), ii) mortality increases for the pardo and preto population (horizontal effect). We speculate that the vertical effect is driven by increasing levels of comorbidity in Northern regions where levels of socioeconomic development are lower, whereas the horizontal effect may be related to lower levels of healthcare access or availability (including intensive care) for pardo and preto Brazilians. For most states the vertical and horizontal effects are correlated giving a larger cumulative mortality. However, Rio de Janeiro was found to be an outlier to this trend: It has an ethnicity composition (horizontal effect) similar to the states in the North region, despite high levels of socioeconomic development (vertical effect). Our analysis motivates an urgent effort on the part of Brazilian authorities to consider how the national response to COVID-19 can better protect pardo and preto Brazilians as well as the population of poorer states from their higher death risk from SARS-CoV-2 infection.
“Subtherapeutic concentrations of first-line antitubercular agents in pediatric patients and its association with tuberculosis treatment outcome: protocol for a systematic review and meta-analysis”
Authors: Chachaima-Mar Jorge , Sánchez-Velazco Diana , Ugarte-Gil Cesar
Published: May 2020

Pediatric tuberculosis is a neglected disease that is receiving more attention lately. Some studies found that serum levels of first line antituberculosis drugs do not reach reference concentrations in children. However, these reference ranges were validated in an adult sample. Thus, we do not know if subtherapeutic concentrations of antitubercular agents in children are associated with negative outcomes.

Objective

To estimate the association between subtherapeutic concentrations of first-line antitubercular drugs with clinical outcomes of treatment.

Methods

We propose to do a systematic review and meta-analysis. In order to do so, we will perform an electronic search in Medline, SCOPUS, Web of Science and Global Index Medicus. There will be no restriction of language nor date of publication. First, we will screen titles and abstracts; then we will screen through the full text of the article. Both phases will be done by 2 independent authors. Data extraction will be performed using a data abstraction form by two independent authors. The quality of the studies will be checked with standardized tools according to the design of the study, and will also be performed by duplicate. We will present the main characteristics of each included study through tables. The heterogeneity between studies will be assessed through the I2 statistic. If appropriate, we will use the random-effects model to calculate the pooled estimate. We will evaluate the publication bias through visual inspection of the funnel plot and Egger’s test. Pre-arranged subgroup and sensitivity analysis will be performed.

Results

We will publish the results of this systematic review in a peer-reviewed journal.

Conclusions

This systematic review will provide up-to-date evidence regarding serum concentration in pediatric patients and its association with outcomes. With the analysis we plan, we will offer important recommendations regarding the dosage of the first line antitubercular agents in children, and the modifications that may be needed.

Conflicts of interest

All the authors declare to have no conflict of interest.

Funding

This study did not receive funding from the public, commercial or not-for-profit sectors.
Identification of severity zones for mitigation strategy assessment COVID-19 outbreak in Malaysia
Authors: Ahmad Tahir , Ashaari Azmirul , Awang Siti Rahmah , Mamat Siti Salwana , Mohamad Wan Munirah Wan , Fuad Amirul Aizad Ahmad , Hassan Nurfarhana
Published: May 2020

The objective of this research is to identify severity zones for the COVID-19 outbreak in Malaysia. The technique employed for the purpose is fuzzy graph that can accommodate scarcity, quantity, and availability of data set. Two published sets of data by the Ministry of Health of Malaysia are used to implement the technique. The obtained results can offer descriptive insight, reflection, assessment, and strategizing actions in combating the pandemic.
Syndromic Surveillance for COVID-19 in Canada
Authors: Lapointe-Shaw Lauren , Rader Benjamin , Astley Christina M. , Hawkins Jared B. , Bhatia Deepit , Schatten William J. , Lee Todd C. , Liu Jessica J. , Ivers Noah M. , Stall Nathan M. , Gournis Effie , Tuite Ashleigh R. , Fisman David N. , Bogoch Isaac I. , Brownstein John S.
Published: May 2020

Background

Syndromic surveillance through web or phone-based polling has been used to track the course of infectious diseases worldwide. Our study objective was to describe the characteristics, symptoms, and self-reported testing rates of respondents in three different COVID-19 symptom surveys in Canada.

Methods

Data sources consisted of two distinct Canada-wide web-based surveys, and phone polling in Ontario. All three sources contained self-reported information on COVID-19 symptoms and testing. In addition to describing respondent characteristics, we examined symptom frequency and the testing rate among the symptomatic, as well as rates of symptoms and testing across respondent groups.

Results

We found that 1.6% of respondents experienced a symptom on the day of their survey, 15% of Ontario households had a symptom in the previous week, and 44% of Canada-wide respondents had a symptom in the previous month over March-April 2020. Across the three surveys, SARS-CoV-2-testing was reported in 2-9% of symptomatic responses. Women, younger and middle-aged adults (versus older adults) and Indigenous/First nations/Inuit/Métis were more likely to report at least one symptom, and visible minorities were more likely to report the combination of fever with cough or shortness of breath.

Interpretation

The low rate of testing among those reporting symptoms suggests significant opportunity to expand testing among community-dwelling residents of Canada. Syndromic surveillance data can supplement public health reports and provide much-needed context to gauge the adequacy of current SARS-CoV-2 testing rates.
Estimating prevalence of subjective cognitive decline in and across international cohort studies of aging: A COSMIC study
Authors: Roehr Susanne , Pabst Alexander , Riedel-Heller Steffi G. , Jessen Frank , Turana Yuda , Handajani Yvonne S. , Brayne Carol , Matthews Fiona E. , Stephan Blosso C.M. , Lipton Richard B. , Katz Mindy J. , Wang Cuiling , Guerchet Maëlenn , Preux Pierre-Marie , Mbelesso Pascal , Ritchie Karen , Ancelin Marie-Laure , Carrière Isabelle , Guaita Antonio , Davin Annalisa , Vaccaro Roberta , Kim Ki Woong , Han Ji Won , Suh Seung Wan , Shahar Suzana , Din Normah C. , Vanoh Divya , van Boxtel Martin , Köhler Sebastian , Ganguli Mary , Jacobsen Erin P. , Snitz Beth E. , Anstey Kaaren J. , Cherbuin Nicolas , Kumagai Shuzo , Chen Sanmei , Narazaki Kenji , Ng Tze Pin , Gao Qi , Gwee Xin Yi , Brodaty Henry , Kochan Nicole A. , Trollor Julian , Lobo Antonio , López-Antón Raúl , Santabárbara Javier , Crawford John D. , Lipnicki Darren M. , Sachdev Perminder S.
Published: May 2020

Subjective cognitive decline (SCD) is recognized as a risk stage for Alzheimer`s disease (AD) and other dementias, but its prevalence is not well known. We aimed to use uniform criteria to better estimate SCD prevalence across international cohorts. Therefore, we combined individual participant data for 16 cohorts from 15 countries (members of the COSMIC consortium) and used qualitative and quantitative (Item Response Theory/IRT) harmonization techniques to estimate SCD prevalence. The sample comprised 39,387 cognitively unimpaired individuals above age 60. The prevalence of SCD across studies was around one quarter with both qualitative harmonization/QH (23.8%, 95%CI=23.3%-24.4%) and IRT (25.6%, 95%CI=25.1%-26.1%); however, prevalence estimates varied largely between studies (QH: 6.1%, 95%CI=5.1%-7.0%, to 52.7%, 95%CI=47.4%-58.0%; IRT: 7.8%, 95%%CI=6.8%-8.9%, to 52.7%, 95%CI = 47.4%-58.0%). Across studies, SCD prevalence was higher in men than women, in lower levels of education, in individuals with Asian and African ancestry compared to European ancestry, in lower- and middle-income countries compared to high-income countries, and in studies conducted in later decades. Data harmonization and application of uniform criteria across diverse cohorts yielded more accurate estimates of SCD prevalence. Having a quarter of older individuals with SCD warrants further investigation of its significance, as a risk stage for AD and other dementias, and of ways to help individuals with SCD who seek medical advice.
Sensitive quantitative and rapid immunochromatographic diagnosis of clinical samples by scanning electron microscopy - preparing for future outbreaks
Authors: Kawasaki Hideya , Suzuki Hiromi , Maekawa Masato , Hariyama Takahiko
Published: May 2020

Background

As pathogens such as influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can easily cause pandemics, rapid diagnostic tests are crucial for implementing efficient quarantine measures, providing effective treatments to patients, and preventing or containing a pandemic infection. Here, we developed the immunochromatography-NanoSuit® method, an improved immunochromatography method combined with a conventional scanning electron microscope (SEM), which enables observation of immunocomplexes labeled with a colloidal metal.

Methods and Findings

The detection ability of our method is comparable to that of real-time reverse transcription-polymerase chain reaction and the detection time is approximately 15 min. Our new immunochromatography-NanoSuit® method suppresses cellulose deformity and makes it possible to easily focus and acquire high-resolution images of gold/platinum labeled immunocomplexes of viruses such as influenza A, without the need for conductive treatment as with conventional SEM. Electron microscopy (EM)-based diagnosis of influenza A exhibited 94% clinical sensitivity (29/31) (95% confidence interval [95%CI]: 78.58–99.21%) and 100% clinical specificity (95%CI: 97.80–100%). EM-based diagnosis was significantly more sensitive (71.2%) than macroscopic diagnosis (14.3%), especially in the lower influenza A-RNA copy number group. The detection ability of our method is comparable to that of real-time reverse transcription-polymerase chain reaction.

Conclusions

This simple and highly sensitive quantitative analysis method involving immunochromatography can be utilized to diagnose various infections in humans and livestock, including highly infectious diseases such as COVID-19.
Novel Approach for Microbiome Analysis Using Bacterial Replication Rates and Causal Inference with Applications
Authors: Stebliankin Vitalii , Sazal Musfiqur Rahman , Valdes Camilo , Mathee Kalai , Narasimhan Giri
Published: May 2020

Motivation: Metagenomics sequencing data can be used to compute not just the relative abundance profile, but also the replication rates of every taxon in the microbiome sample. We investigate how the dynamics implied by the replication rates can be used to understand the antibiotic response in microbiomes, given the significant variation in the types of antibiotics and the types of response by different taxa. The analysis is further expanded by factoring in the resistome of the microbiomes, which can be readily profiled from the metagenomic sequence data. The fact that some antibiotics such as β -lactams target replicating cells makes it even more critical to use replication rates to analyze the antibiotic response. Results: We introduce a novel approach for metagenomic analysis that integrates microbial community profiling, replication rate calculation, and causal structural learning to analyze the antibiotic response. First, we developed PeTRi, which involves efficient cluster computation of bacterial replication rates from metagenomic sequence data. Second, we integrate the abundance profile, replication profile, resistome profile, and environmental variables to perform causality analysis. Finally, we applied the integrated analysis to the data from an infant gut microbiome study. Conclusions from our analysis are as follows: (i) Microbes tend to lower their replication rates in response to β -lactams; (ii) The presence of antibiotic resistance genes combined with the causality analysis strongly suggest that genes fosA5, oqxA, kpnF, arnA, and acrA provides resistance for the taxon K. pneumoniae, allowing it to replicate and dominate the microbiome after the drug ticarcillin-clavulanate was administered; and (iii) Human and donor milk strongly influence the resistome of the infant gut microbiome.
Malacological survey in a bottle of water: A comparative study between manual sampling and environmental DNA metabarcoding approaches
Authors: Mulero Stephen , Toulza Eve , Loisier Anaïs , Zimmerman Meryl , Allienne Jean-François , Foata Joséphine , Quilichini Yann , Pointier Jean-Pierre , Rey Olivier , Boissier Jérôme
Published: May 2020

Abstract

To assess the effect of anthropogenic activities on ecosystems, it is of prime importance to develop new tools enabling a rapid characterisation of ecological communities. Freshwater ecosystems are particularly impacted and threatened by human activities and need thorough attention to preserve their biodiversity and the ecological services they provide. Studying such ecosystems is generally difficult because the associated organisms are hard to sample and to monitor. We present a ready to use environmental metabarcoding diagnostic tool to characterise and monitor the freshwater malacofauna from water samples. The efficiency of this new tool was compared to a classical malacological survey at 19 sampled sites from 10 distinct rivers distributed over Corsica Island (France). Our eDNA monitoring tool demonstrated a remarkable ability to reconstitute the local malacofauna compared to the malacological survey, with 97.1% of species detection confirmed by both methods. The present tool successfully detected the 11 freshwater snail species previously reported in Corsica by malacological survey but was limited at the genus level for some species. Moreover, our malacological survey allowed an update of the local distribution of a wide diversity of freshwater snails including invasive species (i.e.Potamopyrgus antipodarumandPhysa acuta) as well as snail hosts of pathogens of medical and veterinary importance (i.e.Bulinus truncatusandGalba truncatula).
Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm
Authors: Bjånes David A. , Fisher Lee E. , Gaunt Robert A. , Weber Douglas J.
Published: May 2020

Bjånes DA, Fisher LE, Gaunt RA, Weber DJ

Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm.bioRxivFirst published May 21, 2020. Extracellular microelectrodes frequently record neural activity from more than one neuron in the vicinity of the electrode. The process of labeling each recorded spike waveform with the identity of its source neuron is called spike sorting and is often approached from an abstracted statistical perspective. However, these approaches do not consider neurophysiological realities and may ignore important features that could improve the accuracy of these methods. Further, standard algorithms typically require selection of at least one free parameter, which can have significant effects on the quality of the output. We describe a Heuristic Spike Sorting Tuner (HSST) that determines the optimal choice of the free parameters for a given spike sorting algorithm based on the neurophysiological qualification of unit isolation and signal discrimination. A set of heuristic metrics are used to score the output of a spike sorting algorithm over a range of free parameters resulting in optimal sorting quality. We demonstrate that these metrics can be used to tune parameters in several spike sorting algorithms. The HSST algorithm shows robustness to variations in signal to noise ratio, number and relative size of units per channel. Moreover, the HSST algorithm is computationally efficient, operates unsupervised, and is parallelizable for batch processing.

NEW & NOTEWORTHY

HSST incorporates known neurophysiological priors of extracellular neural recordings while simultaneously taking advantage of powerful abstract mathematical tools. Rather than simply selecting free parameters prior to running a sorting algorithm, HSST executes a sorting algorithm across a range of input parameters, using heuristic metrics to detect which spike-sorting output is most physiologically plausible. This novel approach enables unsupervised spike-sorting exceeding the performance of previous methods, thereby enabling the processing of large data sets with confidence.
Distributed functions of prefrontal and parietal cortices during sequential categorical decisions
Authors: Zhou Yang , Rosen Matthew , Swaminathan Sruthi K. , Masse Nicolas Y. , Zhu Oliver , Freedman David J.
Published: May 2020

The ability to compare sequential sensory inputs is crucial for solving many behavioral tasks. To understand the neuronal mechanisms underlying sequential decisions, we compared neuronal responses in the prefrontal cortex (PFC) and the lateral and medial intra-parietal (LIP and MIP) areas in monkeys trained to decide whether sequentially presented stimuli were from matching (M) or nonmatching (NM) categories. We found that PFC leads the M/NM decision process relying on nonlinear neuronal integration of sensory and mnemonic information, whereas LIP and MIP are more involved in sensory evaluation and motor planning, respectively. Furthermore, multi-module recurrent neural networks trained on the same task exhibited the key features of PFC and LIP encoding, including nonlinear integrative encoding in the PFC-like module which was crucial for M/NM decisions. Together, our results illuminate the relative functions of LIP, PFC, and MIP in sensory, cognitive and motor functions, and suggest that nonlinear integration of task-related variables in PFC is important for mediating sequential decisions.
A Biphasic Approach for Characterizing Tensile, Compressive, and Hydraulic Properties of the Sclera
Authors: Brown Dillon M. , Pardue Machelle T. , Ethier C. Ross
Published: May 2020

Measuring the biomechanical properties of the mouse sclera is of great interest, since altered scleral properties are features of many common ocular pathologies, and the mouse is a powerful species for studying genetic factors in disease. Here, a poroelastic material model is used to analyze data from unconfined compression testing of both pig and mouse sclera, and the tensile modulus, compressive modulus, and permeability of the sclera are obtained at three levels of compressive strain. Values for all three properties measured simultaneously by unconfined compression of pig sclera were comparable to previously reported values measured by tests specific for each property, i.e., compression tests, biaxial tensile tests, and falling-head permeability assays. The repeatability of the approach was evaluated using test-retest experimental paradigm on pig sclera. Repeatability was low for measured compressive stiffness, indicating permanent changes to the samples occurring after the first test. However, reasonable repeatability for tensile stiffness and permeability was observed. The intrinsic material properties of the mouse sclera were measured for the first time. Tensile stiffness and permeability of the sclera in both species were seen to be dependent on the state of compressive strain. We conclude that unconfined compression testing of sclera, when analyzed with poroelastic theory, can be used as a powerful tool to phenotype mouse scleral changes in future genotype-phenotype association studies.

Statement of Significance

Ocular biomechanics is strongly influenced by the sclera, the outermost white coat of the eye. Many ocular diseases are believed to be influenced by pathological changes to scleral microstructure and biomechanics, making intrinsic biomechanical properties an important outcome measure in many studies. However, the small mouse eye precludes the use of most traditional biomechanical characterization techniques. Here, we show that unconfined compression testing analyzed with poroelastic theory can produce measurements of biomechanical properties in the pig sclera comparable to those measured by other traditional techniques. Importantly, this technique can be successfully applied to the mouse sclera, enabling more widespread use of the species as a model for ocular disease.
A streamlined, cost-effective, and specific method to deplete transcripts for RNA-seq
Authors: Baldwin Amber , Morris Adam R , Mukherjee Neelanjan
Published: May 2020

RNA-sequencing is a powerful and increasingly prevalent method to answer biological questions. Depletion of ribosomal RNA (rRNA), which accounts for 80% of total RNA, is an extremely important step to increase the power of RNA-seq. Selection for polyadenylated RNA is a commonly used approach that excludes rRNA, as well as, important non-polyadenylated RNAs, such as histones, circular RNAs, and many long noncoding RNAs. Commercial methods to deplete rRNA are cost-prohibitive and the gold standard method is no longer available as a standalone kit. Alternative non-commercial methods suffer from inconsistent depletion. Through careful characterization of all reaction parameters, we developed an optimized RNaseH-based depletion of human rRNA. Our method exhibited comparable or better rRNA depletion compared to commercial kits at a fraction of the cost and across a wide-range of input RNA amounts.
KDM2B Silencing Elicits a Paracrine Mechanism Which Destabilizes SLUG, Promoting Differentiation of Basal-Like Breast Cancer Cells.
Authors: Fraile Elia-Aguado , Soysal Burak , Anastas Vollter , Soysal Zeynep Tugce , Serebrennikova Oksana , Paraskevopoulou Maria D. , Chavdoula Evangelia , Tsichlis Philip N.
Published: May 2020

KDM2B is a JmjC domain H3K36me2/H3K36me1 demethylase, which immortalizes cells in culture and contributes to the biology of both embryonic and adult stem cells, including cancer stem cells. Here we show that the silencing of KDM2B activates a tyrosine kinase receptor-dependent paracrine mechanism, which results in the downregulation of SNAI2 (SLUG), SNAI1 (SNAIL) and SOX9, which also contribute to the biology of stem and progenitor cells. The downregulation of these molecules is posttranscriptional and in the case of SNAI2-encoded SLUG, it is due to calpain-dependent proteolytic degradation. SLUG abundance in normally growing cells is under the homeostatic control of GSK3, which phosphorylates SLUG and tags it for proteasomal degradation. The paracrine mechanism activated by KDM2B depletion, activates FGFR1 and EGFR family members, and blocks the homeostatic SLUG degradation by inactivating GSK3. This, however, sensitizes SLUG to classical calpains, which are also activated in KDM2B-depleted cells via Ca2+ influx and calpastatin downregulation. The switch in SLUG degradation pathways, results in the rapid degradation of SLUG and the differentiation of breast cancer stem cells, revealing an unexpected mechanism of stem cell regulation by a lysine demethylase.
Paradigms about the COVID-19 pandemic: knowledge, attitudes and practices from medical students
Authors: Eddy Lincango-Naranjo , Paola Solis-Pazmino , Santiago Rodriguez-Villafuerte , Jose Lincango-Naranjo , Paul Vinueza-Moreano , Giuseppe Barberis-Barcia , Carlos Ruiz-Sosa , Giovanni Rojas-Velasco , Derek Gravholt , Nataly Espinoza-Suarez , Elizabeth Golembiewski , Percy Soto-Becerra
Published: May 2020

Background

As the disease caused by the new coronavirus has spread globally, economic instability in healthcare systems has been significant, and the lack of knowledge, positive attitudes and appropriate practices among people has led to the magnification of this disease. This reality is especially accentuated in Ecuador where, although many healthcare workers have been called to help in the regions most affected, the shortage of them combined with cultural and macroeconomic factors have led Ecuador to face the most aggressive outbreak in Latin America. In this context, the participation on the front line of final year medical students is indispensable. For that reason, appropriate training on COVID-19 for final year medical students is an urgent need that universities and health systems must guarantee. We aimed to describe the knowledge, attitudes and practices in Ecuadorian final year medical students in order to identify the knowledge gaps, perceptions and behavior patterns which could guide the design of better medical education curricula regarding COVID-19.

Methods

This was a cross-sectional 33-item online survey conducted between April 6 to April 20 assessing the knowledge, attitudes, and practices toward the diagnosis, treatment, prevention, and prognosis toward COVID-19 in Ecuadorian final year medical students. It was sent by email and by Facebook and WhatsApp.

Results

A total of 309 students responded to the survey. 88% of students scored high (≥ 70% correct) for knowledge of the disease. The majority of students were pessimistic about possible government actions, which is reflected in the negative attitude towards the control of COVID-19 in Ecuador and volunteering during the outbreak (77%, and 58% of the students, respectively). Moreover, 91% of students said they did not have adequate protective equipment or training in their health facilities.

Conclusions

The high level of students’ knowledge, with coexisting negative attitudes, suggests Ecuador has a capable upcoming workforce that could benefit from an opportunity to strengthen, improve and advance their training in preparation for COVID-19. Creating a national curriculum may be one of the most effective ways for all students to be trained, while simultaneously focusing on the students’ most pressing concerns. Hopefully with this, negative attitudes will improve and students will be better qualified.
Common and separable neurofunctional dysregulations characterize obsessive-compulsive, substance use, and gaming disorders – evidence from an activation likelihood meta-analysis of functional imaging studies
Authors: Klugah-Brown Benjamin , Zhou Xinqi , Pradhan Basant K. , Zweerings Jana , Mathiak Klaus , Biswal Bharat , Becker Benjamin
Published: May 2020

Background

Compulsivity and loss of behavioral control represent core symptoms in obsessive-compulsive disorder (OCD), substance use disorder (SUD), and internet gaming disorder (IGD). Despite animal models suggesting compulsivity mediated by cortico-striatal circuits and several neuroimaging case-control studies positing common/distinct neurofunctional alterations in these disorders a systematic examination is still lacking.

Aims

The present study capitalized on previous case-control fMRI studies to determine shared and disorder-specific neurofunctional alterations among three disorders.

Methods

Task-based fMRI studies in SUD, OCD, and IGD were obtained. Coordinate-based meta-analyses were performed within each disorder. Next contrast and conjunction meta-analyses were done to determine differential and common neurofunctional alterations between the disorders. Task-paradigm were group according to RDoC domains to determine contributions of underlying behavioral domains. Find pre-registration of the study here (https://osf.io/j8wct/).

Results

144 articles were included representing 6897 individuals (SUD=2418, controls=2332; IGD=361, controls=360; OCD=715, controls=711). Conjunction meta-analyses revealed shared alterations in anterior insular cortex between OCD, and pooled as-well-as separate SUDs. SUD exhibited pronounced dorso-striatal alterations as compared to both, OCD and IGD. IGD shared frontal, particularly cingulate alterations with all SUDs. IGD demonstrated temporal alterations compared to both, SUD and OCD. No robust overlap between IGD and OCD was observed. Across the disorders, neurofunctional alterations were mainly contributed to by cognitive systems and positive valence RDoC domains.

Conclusion

The present findings indicate that neurofunctional dysregulations in prefrontal regions engaged in regulatory control share neurofunctional alterations across substance and behavioral addictions, while shared neurofunctional dysregulations in the anterior insula may mediate compulsivity in substance addiction and obsessive-compulsive disorders.
COVID-19 in Bangladesh: Measuring differences in individual precautionary behaviors among young adults
Authors: Imtiaz Asif , Khan Noor Muhammad , Hossain Md. Akram
Published: May 2020

Aim

The novel coronavirus disease 2019 (COVID-19) has already hit Bangladesh, and various control measures have been taken to flatten the epidemic curve. Due to the current demographic distribution in Bangladesh, young adults are vital to the demography of the country. Therefore, their precautionary behavior is very important to ensure the success of preventive policies. This exploratory study examined the differences in the adoption of precautionary behaviors among young adults, and estimated and compared the predictors of precautionary behavior adoption among young adults living in the capital city Dhaka and a nearby district, Tangail.

Subject and Methods

A total of 350 respondents from each district participated in the study. ANOVA and two-sample t-tests were utilized to detect differences in precautionary behavior across demographic groups of young adults, and quantile regression modeling was used to find the predictors of adopting precautionary behaviors and to compare these predictors between the two districts.

Results

Individuals who had a postgraduate education and had good mental health tended to show better precautionary behaviors in Dhaka. Female respondents from Tangail who had no psychological distress took precautionary behaviors more often than their counterparts. However, no significant differences in the adoption of precautionary behaviors to prevent COVID-19 among young adults were found between the two districts. Better self-control ability, higher education and good mental health emerged as factors that significantly shaped the precautionary behaviors of young adults in this study.

Conclusion

Having better knowledge did not ensure better adoption of precautionary behaviors among the participants. In effect, the government’s strong intervention to keep people at home and distant from each other and continued lockdown for several more days are probable immediate solutions. At the same time, the economic burden on lower-income people should be addressed.
Prone Cardiopulmonary Resuscitation: A Rapid Scoping and Expanded Grey Literature Review for the covid-19 Pandemic
Authors: Douma Matthew J , Mackenzie Ella , Loch Tess , Tan Maria C. , Anderson Dustin , Picard Christopher , Milovanovic Lazar , O’Dochartaigh Domhnall , Brindley Peter G
Published: May 2020

Prone Cardiopulmonary Resuscitation

A Rapid Scoping and Expanded Grey Literature Review for the COVID-19 Pandemic

Aim

To rapidly identify and summarize the available science on prone resuscitation. To determine the value of undertaking a systematic review on this topic; and to identify knowledge gaps to aid future research, education and guidelines.

Methods

This review was guided by specific methodological framework and reporting items (PRISMA-ScR). We included studies, cases and grey literature regarding prone position and CPR/cardiac arrest. The databases searched were MEDLINE, Embase, CINAHL, Cochrane CENTRAL, Cochrane Database of Systematic Reviews, Scopus and Google Scholar. Expanded grey literature searching included internet search engine, targeted websites and social media.

Results

Of 453 identified studies, 24 (5%) studies met our inclusion criteria. There were four prone resuscitation-relevant studies examining: blood and tidal volumes generated by prone compressions; prone compression quality metrics on a manikin; and chest computed tomography scans for compression landmarking. Twenty case reports/series described the resuscitation of 25 prone patients. Prone compression quality was assessed by invasive blood pressure monitoring, exhaled carbon dioxide and pulse palpation. Recommended compression location was zero-to-two vertebral segments below the scapulae. Twenty of 25 cases (80%) survived prone resuscitation, although few cases reported long term outcome. Seven cases described full neurological recovery.

Conclusion

This scoping review did not identify sufficient evidence to justify a systematic review or modified resuscitation guidelines. It remains reasonable to initiate resuscitation in the prone position if turning the patient supine would lead to delays or risk to providers or patients. Prone resuscitation quality can be judged using end-tidal CO2, and arterial pressure tracing, with patients turned supine if insufficient.