bluuebunny/crossref_metadata_2025 huggingface dataset:
Modelling the linkage between coral assemblage structure and pattern of environmental forcing
Authors: Sandin Stuart A. , Eynaud Yoan , Williams Gareth J. , Edwards Clinton B. , McNamara Dylan E.
Published: October 2020

Geographical comparisons suggest that coral reef communities can vary as a function of their environmental context, differing not just in terms of total coral cover but also in terms of relative abundance (or coverage) of coral taxa. While much work has considered how shifts in benthic reef dynamics can shift dominance of stony corals relative to algal and other benthic competitors, the relative performance of coral types under differing patterns of environmental disturbance has received less attention. We construct an empirically-grounded numerical model to simulate coral assemblage dynamics under a spectrum of disturbance regimes, contrasting hydrodynamic disturbances (which cause morphology-specific, whole-colony mortality) with disturbances that cause mortality independently of colony morphology. We demonstrate that the relative representation of morphological types within a coral assemblage shows limited connection to the intensity, and essentially no connection to the frequency, of hydrodynamic disturbances. Morphological types of corals that are more vulnerable to mortality owing to hydrodynamic disturbance tend to grow faster, with rates sufficiently high to recover benthic coverage during inter-disturbance intervals. By contrast, we show that factors causing mortality without linkage to morphology, including those that cause only partial colony loss, more dramatically shift coral assemblage structure, disproportionately favouring fast-growing tabular morphologies. Furthermore, when intensity and likelihood of such disturbances increases, assemblages do not adapt smoothly and instead reveal a heightened level of temporal variance, beyond which reefs demonstrate drastically reduced coral coverage. Our findings highlight that adaptation of coral reef benthic assemblages depends on the nature of disturbances, with hydrodynamic disturbances having little to no effect on the capacity of reef coral communities to resist and recover with sustained coral dominance.
Growth and behaviour of blue mussels, a re-emerging polar resident, follow a strong annual rhythm shaped by the extreme high Arctic light regime
Authors: Tran Damien , Andrade Hector , Durier Guillaume , Ciret Pierre , Leopold Peter , Sow Mohamedou , Ballantine Carl , Camus Lionel , Berge Jørgen , Perrigault Mickael
Published: October 2020

Polar regions are currently warming at a rate above the global average. One issue of concern is the consequences on biodiversity in relation to the Northward latitudinal shift in distribution of temperate species. In the present study, lasting almost two years, we examined two phenological traits, i.e. the shell growth and behavioural rhythm of a recently re-established species in the high Arctic, the blue mussel
Mytilus
sp. We compared this with a native species, the Islandic scallop
Chlamys islandica
. We show marked differences in the examined traits between the two species. In
Mytilus
sp., a clear annual pattern of shell growth strongly correlated to the valve behaviour rhythmicity, whereas
C. islandica
exhibited a shell growth pattern with a total absence of annual rhythmicity of behaviour. The shell growth was highly correlated to the photoperiod for the mussels but weaker for the scallops. The water temperature cycle was a very weak parameter to anticipate the phenology traits of both species. This study shows that the new resident in the high Arctic,
Mytilus
sp., is a highly adaptive species, and therefore a promising bioindicator to study the consequences of biodiversity changes due to global warming.
Susceptibility to misinformation about COVID-19 around the world
Authors: Roozenbeek Jon , Schneider Claudia R. , Dryhurst Sarah , Kerr John , Freeman Alexandra L. J. , Recchia Gabriel , van der Bles Anne Marthe , van der Linden Sander
Published: October 2020

Misinformation about COVID-19 is a major threat to public health. Using five national samples from the UK (n=1050 andn=1150), Ireland (n= 700), the USA (n= 700), Spain (n=700) and Mexico (n=700), we examine predictors of belief in the most common statements about the virus that contain misinformation. We also investigate the prevalence of belief in COVID-19 misinformation across different countries and the role of belief in such misinformation in predicting relevant health behaviours. We find that while public belief in misinformation about COVID-19 is not particularly common, a substantial proportion views this type of misinformation as highly reliable in each country surveyed. In addition, a small group of participants find common factual information about the virus highly unreliable. We also find that increased susceptibility to misinformation negatively affects people's self-reported compliance with public health guidance about COVID-19, as well as people's willingness to get vaccinated against the virus and to recommend the vaccine to vulnerable friends and family. Across all countries surveyed, we find that higher trust in scientists and having higher numeracy skills were associated with lower susceptibility to coronavirus-related misinformation. Taken together, these results demonstrate a clear link between susceptibility to misinformation and both vaccine hesitancy and a reduced likelihood to comply with health guidance measures, and suggest that interventions which aim to improve critical thinking and trust in science may be a promising avenue for future research.
Analogue neuro-memristive convolutional dropout nets
Authors: Krestinskaya O. , James A. P.
Published: October 2020

Randomly switching neurons ON/OFF while training and inference process is an interesting characteristic of biological neural networks, that potentially results in inherent adaptability and creativity expressed by human mind. Dropouts inspire from this random switching behaviour and in the artificial neural network they are used as a regularization techniques to reduce the impact of over-fitting during the training. The energy-efficient digital implementations of convolutional neural networks (CNN) have been on the rise for edge computing IoT applications. Pruning larger networks and optimization for performance accuracy has been the main direction of work in this field. As opposed to this approach, we propose to build a near-sensor analogue CNN with high-density memristor crossbar arrays. Since several active elements such as amplifiers are used in analogue designs, energy efficiency becomes a main challenge. To address this, we extend the idea of using dropouts in training to also the inference stage. The CNN implementations require a subsampling layer, which is implemented as a mean pooling layer in the design to ensure lower energy consumption. Along with the dropouts, we also investigate the effect of non-idealities of memristor and that of the network.
Stability and memory-loss go hand-in-hand: three results in dynamics and computation
Authors: Manjunath G.
Published: October 2020

The search for universal laws that help establish a relationship between dynamics and computation is driven by recent expansionist initiatives in biologically inspired computing. A general setting to understand both such dynamics and computation is a driven dynamical system that responds to a temporal input. Surprisingly, we find memory-loss a feature of driven systems to forget their internal states helps provide unambiguous answers to the following fundamental stability questions that have been unanswered for decades: what is necessary and sufficient so that slightly different inputs still lead to mostly similar responses? How does changing the driven system’s parameters affect stability? What is the mathematical definition of the edge-of-criticality? We anticipate our results to be timely in understanding and designing biologically inspired computers that are entering an era of dedicated hardware implementations for neuromorphic computing and state-of-the-art reservoir computing applications.
Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland
Authors: Ramezani Mohaddaseh , Pourmohyadini Mohammad , Nikou Mahdi Moshtaghi , Makzum Somaye , Schumann Peter , Clermont Dominique , Criscuolo Alexis , Amoozegar Mohammad Ali , Kämpfer Peter , Spröer Cathrin
Published: October 2020

We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2)T, isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3–15 % NaCl (w/v; optimum, 5 %), pH 7.0–9.0 (optimum, pH 7.5–8.0) and 15–35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2)T to the class

Gammaproteobacteria

and the genus

Halomonas

with highest similarity to

Halomonas daqiaonensis

YCSA28T (98.4 %) and

Halomonas ventosae

Al12T (97.9 %). Experimental and in silico DNA–DNA hybridization values were 42.7 and 35.1% with

H. daqiaonensis

IBRC-M 10931T and 48 and 35.2% with

H. ventosae

IBRC-M 10566T, respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against

H. ventosae

Al12T and

H. daqiaonensis

YCSA28T were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C16 : 0 cyclo, C19 : 0 ω8c, C16 : 1 ω7c and/or iso-C15:0 2-OH, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2)T could be classified as a novel species in the genus

Halomonas

for which the name Halomonas lysinitropha sp. nov. is proposed. The type strain is 3(2)T (=IBRC M 10929T=LMG 29450T=CIP 111708T).
Tabrizicola algicola sp. nov. isolated from culture of microalga Ettlia sp.
Authors: Park Chan-Yeong , Chun Seong-Jun , Jin Chunzhi , Le Ve Van , Cui Yingshun , Kim Song-Yeon , Ahn Chi-Yong , Oh Hee-Mock
Published: October 2020

A novel Gram-stain-negative, aerobic, non-spore-forming, non-motile, and rod-shaped bacterium, strain ETT8T was isolated from a chemostat culture of microalga Ettlia sp. YC001. Optimal growth was with 0–2% NaCl and at 25–37 °C on R2A medium. Phylogenetic analysis based on the 16S rRNA gene and genome sequence showed that strain ETT8T belongs to the genus

Tabrizicola

, with the close neighbours being

T. sediminis

DRYC-M-16T (98.1 %),

T. alkalilacus

DJCT (97.6 %),

T. fusiformis

SY72T (96.9 %),

T. piscis

K13M18T (96.8 %), and

T. aquatica

RCRI19T (96.5 %). The genomic comparison of strain ETT8T with type species in the genus

Tabrizicola

was analysed using the genome-to-genome distance calculator (GGDC), average nucleotide identity (ANI), and average amino acid identity (AAI) (values indicated ≤17.7, ≤75.4 and ≤71.9 %, respectively). The genomic DNA G+C content of strain ETT8T was 64.4 %, plus C18 : 1
 ω6c and C18 : 0-iso were the major fatty acids and Q-10 the major respiratory quinone. Strain ETT8T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine aminolipid, and four unidentified lipids as the major polar lipids. Based on the chemotaxonomic, genotypic, and phenotype results, strain ETT8T was recognized as a novel species of the genus

Tabrizicola

for which the name Tabrizicola algicola sp. nov. is proposed. The type strain is ETT8T (=KCTC 72206T=JCM 31893T=MCC 4339T).
Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales
Authors: Secaira-Morocho Henry , Castillo José A. , Driks Adam
Published: October 2020

Among members of the Bacillales order, there are several species capable of forming a structure called an endospore. Endospores enable bacteria to survive under unfavourable growth conditions and germinate when environmental conditions are favourable again. Spore-coat proteins are found in a multilayered proteinaceous structure encasing the spore core and the cortex. They are involved in coat assembly, cortex synthesis and germination. Here, we aimed to determine the diversity and evolutionary processes that have influenced spore-coat genes in various spore-forming species of Bacillales using an in silico approach. For this, we used sequence similarity searching algorithms to determine the diversity of coat genes across 161 genomes of Bacillales. The results suggest that among Bacillales, there is a well-conserved core genome, composed mainly by morphogenetic coat proteins and spore-coat proteins involved in germination. However, some spore-coat proteins are taxa-specific. The best-conserved genes among different species may promote adaptation to changeable environmental conditions. Because most of the

Bacillus

species harbour complete or almost complete sets of spore-coat genes, we focused on this genus in greater depth. Phylogenetic reconstruction revealed eight monophyletic groups in the

Bacillus

genus, of which three are newly discovered. We estimated the selection pressures acting over spore-coat genes in these monophyletic groups using classical and modern approaches and detected horizontal gene transfer (HGT) events, which have been further confirmed by scanning the genomes to find traces of insertion sequences. Although most of the genes are under purifying selection, there are several cases with individual sites evolving under positive selection. Finally, the HGT results confirm that sporulation is an ancestral feature in

Bacillus

.
How Policies on Restaurants, Bars, Nightclubs, Masks, Schools, and Travel Influenced Swiss COVID-19 Reproduction Ratios
Authors: Sruthi C. K. , Biswal Malay Ranjan , Saraswat Brijesh , Joshi Himanshu , Prakash Meher K.
Published: October 2020

The role of complete lockdowns in reducing the reproduction ratios (Rt) of COVID-19 is now established. However, the persisting reality in many countries is no longer a complete lockdown, but restrictions of varying degrees using different choices of Non-pharmaceutical interaction (NPI) policies. A scientific basis for understanding the effectiveness of these graded NPI policies in reducing the Rtis urgently needed to address the concerns on personal liberties and economic activities. In this work, we develop a systematic relation between the degrees of NPIs implemented by the 26 cantons in Switzerland during March 9 – September 13 and their respective contributions to the Rt. Using a machine learning framework, we find that Rtwhich should ideally be lower than 1.0, has significant contributions in the post-lockdown scenario from the different activities - restaurants (0.0523 (CI. 0.0517-0.0528)), bars (0.030 (CI. 0.029-0.030)), and nightclubs (0.154 (CI. 0.154-0.156)). Activities which keep the land-borders open (0.177 (CI. 0.175-0.178)), and tourism related activities contributed comparably 0.177 (CI. 0.175-0.178). However, international flights with a quarantine did not add further to the Rtof the cantons. The requirement of masks in public transport and secondary schools contributed to an overall 0.025 (CI. 0.018-0.030) reduction in Rt, compared to the baseline usage even when there are no mandates. Although causal relations are not guaranteed by the model framework, it nevertheless provides a fine-grained justification for the relative merits of choice and the degree of the NPIs and a data-driven strategy for mitigating Rt.
High Food Insecurity in Latinx Families and Associated COVID-19 Infection in the Greater Bay Area, California
Authors: Escobar Milagro , Mendez Andrea DeCastro , Encinas Maria Romero , Wojcicki Janet M
Published: October 2020

Background

Food insecurity impacts nearly one-in-four Latinx households in the United States and has been exacerbated by the novel coronavirus or COVID-19 pandemic.

Methods

We examined the impact of COVID-19 on household and child food security in three preexisting, longitudinal, Latinx urban cohorts in the San Francisco Bay Area (N=375 households, 1,875 individuals). Households were initially recruited during pregnancy and postpartum at Zuckerberg San Francisco General Hospital (ZSFG) and UCSF Benioff prior to the COVID-19 pandemic. For this COVID sub-study, participants responded to a 15-minute telephonic interview. Participants answered 18 questions from the US Food Security Food Module (US HFSSM), described food consumption, housing and employment status, and history of COVID-19 infection as per community or hospital-based testing. Food security and insecurity levels were compared with prior year metrics.

Results

We found low levels of household food security in Latinx families (by cohort: 29.2%; 34.2%; 60.0%) and child food security (56.9%; 54.1%; 78.0%) with differences between cohorts explained by self-reported levels of education and employment status. Food security levels were much lower than those reported previously in two cohorts where data had been recorded from prior years. Reported history of COVID-19 infection in households was 4.8% (95% Confidence Interval (CI); 1.5-14.3%); 7.2% (95%CI; 3.6-13.9%) and 3.5% (95%CI; 1.7-7.2%) by cohort and was associated with food insecurity in the two larger cohorts (p=0.03; p=0.01 respectively).

Conclusions

Latinx families in the Bay Area with children are experiencing a sharp rise in food insecurity levels during the COVID-19 epidemic. Food insecurity, similar to other indices of poverty, is associated with increased risk for COVID-19 infection. Comprehensive interventions are needed to address food insecurity in Latinx populations and further studies are needed to better assess independent associations between household food insecurity, poor nutritional health and risk of COVID-19 infection.
Symptom-based testing in a compartmental model of COVID-19
Authors: Bartha Ferenc A. , Karsai János , Tekeli Tamás , Röst Gergely
Published: October 2020

Testing and isolation of cases is an important component of our strategies to fight SARS-CoV-2. In this work, we consider a compartmental model for COVID-19 including a nonlinear term representing symptom-based testing. We analyze how the considered clinical spectrum of symptoms and the testing rate affect the outcome and the severity of the outbreak.
Evaluation of different stool extraction methods for metabolomics measurements in human fecal samples
Authors: Erben Vanessa , Poschet Gernot , Schrotz-King Petra , Brenner Hermann
Published: October 2020

Background

Measurement of metabolomics in human stool samples is of great interest for a broad range of applications in biomedical research including early detection of colorectal neoplasms. However, due to the complexity of metabolites there is no consensus on how to process samples for stool metabolomics measurements to obtain a broad coverage of hydrophilic and hydrophobic substances.

Methods

We used frozen stool samples (50mg) from healthy study participants. Stool samples were processed after thawing using 8 different processing protocols and different solvents. Metabolites were measured afterwards using the MxP® Quant 500 kit (Biocrates). The best performing protocol was subsequently applied to compare stool samples of participants with different dietary habits.

Results

In this study, we were able to determine up to 340 metabolites of various chemical classes extracted from stool samples of healthy study participants with 8 different protocols. Polar metabolites such as amino acids could be measured with each method while other metabolite classes, particular lipid species, are more dependent on the solvent or combination of solvents used. Only a small number of triglycerides or acylcarnitines were detected in human feces. Extraction efficiency was higher for protocols using isopropanol or those using ethanol or methanol and MTBE including an evaporation and concentration step than for other protocols. We detected significant fecal metabolite differences between vegetarians, semi-vegetarians and non-vegetarians.

Conclusion

For the evaluation of metabolites in fecal samples we found protocols using solvents like isopropanol and those using ethanol or methanol and MTBE including an evaporation and concentration step to be superior over others tested in this study.
Predicting Olfactory Loss In Chronic Rhinosinusitis Using Machine Learning
Authors: Ramakrishnan Vijay R. , Arbet Jaron , Mace Jess C. , Suresh Krithika , Smith Stephanie Shintani , Soler Zachary M. , Smith Timothy L.
Published: October 2020

Objective

Compare machine learning (ML) based predictive analytics methods to traditional logistic regression in classification of olfactory dysfunction in chronic rhinosinusitis (CRS-OD), and identify predictors within a large multi-institutional cohort of refractory CRS patients.

Methods

Adult CRS patients enrolled in a prospective, multi-institutional, observational cohort study were assessed for baseline CRS-OD using a smell identification test (SIT) or brief SIT (bSIT). Four different ML methods were compared to traditional logistic regression for classification of CRS normosmics versus CRS-OD.

Results

Data were collected for 611 study participants who met inclusion criteria between April 2011 and July 2015. 34% of enrolled patients demonstrated olfactory loss on psychophysical testing. Differences between CRS normosmics and those with smell loss included objective disease measures (CT and endoscopy scores), age, sex, prior surgeries, socioeconomic status, steroid use, polyp presence, asthma, and aspirin sensitivity. Most ML methods performed favorably in terms of predictive ability. Top predictors include factors previously reported in the literature, as well as several socioeconomic factors.

Conclusion

Olfactory dysfunction is a variable phenomenon in CRS patients. ML methods perform well compared to traditional logistic regression in classification of normosmia versus smell loss in CRS, and are able to include numerous risk factors into prediction models. Several actionable features were identified as risk factors for CRS-OD. These results suggest that ML methods may be useful for current understanding and future study of hyposmia secondary to sinonasal disease, the most common cause of persistent olfactory loss in the general population.
Predictors of mortality in hospitalized COVID-19 patients in Athens, Greece
Authors: Giannoglou Dimitrios , Meimeti Evangelia , Provatopoulou Xenia , Stathopoulos Konstantinos , Roukas Ioannis –Kriton , Galanis Petros
Published: October 2020

Background

The epidemic of COVID-19 has rapidly spread worldwide, with millions of confirmed cases and related deaths. Numerous efforts are being made to clarify how the infection progresses and potential factors associated with disease severity and mortality. We investigated the mortality in Greek hospitalized COVID-19 patients and also the predictors of this mortality.

Methods

Study population included 512 COVID-19 patients admitted to the hospitals of the Attica region of Greece. Patients’ demographic characteristics, comorbidities, allergies, previous vaccination for seasonal influenza virus, admission to ICU, intubation, and death were recorded. Potential predictors of in-hospital mortality were identified by regression analysis.

Results

The mean age of hospitalized patients was 60.4 years, and was higher in patients who deceased. The most common comorbidities were respiratory diseases, hypertension, gastrointestinal disorders, dyslipidemia, mental health diseases, asthma, diabetes mellitus and cardiovascular diseases. The need for ICU care and intubation was significantly higher among patients who died. The mortality rate was 15.8% (81 out of 512). Age ≥65 years, cancer, chronic kidney disease, endocrine diseases, central nervous system disorders, anemia, and intubation were independently associated with increased in-hospital mortality, while allergies and previous influenza vaccination were associated with decreased in-hospital mortality.

Conclusion

Our finding of a beneficial effect of allergies and influenza vaccination against COVID-19 infection merits further investigation, as it may shed light in the mechanisms underlying disease progression and severity. Most importantly, it may assist in the implementation of efficient protective measures and public healthcare policies.
School education during the SARS-CoV-2 pandemic - Which concept is safe, feasible and environmentally sound?
Authors: Kähler Christian J. , Fuchs Thomas , Mutsch Benedikt , Hain Rainer
Published: October 2020

Overview

The future belongs to children and they need education to shape the future with foresight and intention. Children therefore have the right to education, according to Article 29 of the UN Convention on the Rights of the Child [1]. However, professional education is not everything, because children must also experience their strengths and weaknesses together and educate each other to be responsible and considerate people, so that they become socially valuable personalities. Only in this way can they shape the future in a peaceful and humane way. Therefore, attending school is essential. However, children also have the right to protection and care by their parents and the state, because the welfare of the child must also be given priority in accordance with Article 3 of the UN Convention on the Rights of the Child. The question is therefore how schooling in community schools can be realized during the SARS-CoV-2 pandemic without exposing children to an unnecessary risk of infection. It is not only about the children, because if the children are at risk, then so are their parents and grandparents and ultimately society as a whole. There are numerous concepts that promise safety in schools during the pandemic. When selecting concepts, the costs must of course be weighed against the benefits. People rightly expect an efficient use of resources. This means that either the set goal is achieved with the least possible resources or that the available resources are used to achieve the greatest possible approximation to the goal. In addition to the financial resources, however, the long-term consequences for the state, the economy, the population and the environment under the pressure of the pandemic must also be taken into account. Social cohesion and democracy must not be jeopardized either. Various protection concepts are currently under discussion. Often the advantages are overstated and the disadvantages concealed. Furthermore, some arguments are based on assumptions that are not true. The aim of this study is to provide a comparative assessment of the main protection concepts and to demonstrate, with the help of experimental analyses, the extent to which the protection concepts are effective. We will show that a comparatively high level of safety against infection in classrooms can be technically ensured without exposing children to masks. At the same time, the protection concept makes economic sense and the burden on the environment is comparatively low, so that infection prevention and climate protection do not have to be weighed against each other, because infection prevention and climate protection are political and social goals that have to be achieved together.
Preventing COVID-19 spread in closed facilities by regular testing of employees – an efficient intervention in long-term care facilities and prisons?
Authors: Tsoungui Obama H. Christian , Adil M. Y. Nessma , Alawam N. Looli , Ngougoue N. Pierre M. , Ngwa Gideon A. , Teboh-Ewungkem Miranda , Schneider Kristan A.
Published: October 2020

Background

Different levels of control measures were introduced to contain the global COVID-19 pandemic, many of which have been controversial, particularly the comprehensive use of diagnostic tests. Regular testing of high-risk individuals (pre-existing conditions, older than 60 years of age) has been suggested by public health authorities. The WHO suggested the use of routine screening of residents, employees, and visitors of long-term care facilities (LTCF) to protect the resident risk group. Similar suggestions have been made by the WHO for other closed facilities including incarceration facilities (e.g., prisons or jails), wherein parts of the U.S., accelerated release of approved inmates is taken as a measure to mitigate COVID-19.

Methods and findings

Here, the simulation model underlying the pandemic preparedness tool CovidSim 1.1 (http://covidsim.eu/) is extended to investigate the effect of regularly testing of employees to protect immobile resident risk groups in closed facilities. The reduction in the number of infections and deaths within the risk group is investigated. Our simulations are adjusted to reflect the situation of LTCFs in Germany, and incarceration facilities in the U.S.

COVID-19 spreads in closed facilities due to contact with infected employees even under strict confinement of visitors in a pandemic scenario without targeted protective measures. Testing is only effective in conjunction with targeted contact reduction between the closed facility and the outside world – and will be most inefficient under strategies aiming for herd immunity. The frequency of testing, the quality of tests, and the waiting time for obtaining test results have noticeable effects. The exact reduction in the number of cases depends on disease prevalence in the population and the levels of contact reductions. Testing every 5 days with a good quality test and a processing time of 24 hours can lead up to a 40% reduction in the number of infections. However, the effects of testing vary substantially among types of closed facilities and can even be counterproductive in U.S. IFs.

Conclusions

The introduction of COVID-19 in closed facilities is unavoidable without a thorough screening of persons that can introduce the disease into the facility. Regular testing of employees in closed facilities can contribute to reducing the number of infections there, but is only meaningful as an accompanying measure, whose economic benefit needs to be assessed carefully.
Tracking the Progression & Influence of Beta-Amyloid Plaques Using Percolation Centrality and Collective Influence Algorithm: A Study using PET Images
Authors: Baboo Gautam Kumar , Prasad Raghav , Mahajan Pranav , Baths Veeky
Published: October 2020

(1) Background: Network analysis allows investigators to explore the many facets of brain networks, particularly the proliferation of disease. One of the hypotheses behind the disruption in brain networks in Alzheimer’s disease is the abnormal accumulation of beta-amyloid plaques and tau protein tangles. In this study, the potential use of percolation centrality to study beta-amyloid movement was studied as a feature of given PET image-based networks; (2) Methods: The PET image-based network construction is possible using a public access database - Alzheimer’s Disease Neuroimaging Initiative, which provided 551 scans. For each image, the Julich atlas provides 121 regions of interest, which are the network nodes. Besides, using the collective influence algorithm, the influential nodes for each scan are calculated; (3) Analysis of variance (p<0.05) yields the region of interest Gray Matter Broca’s Area for PiB tracer type for five nodal metrics. In comparison, AV45: the Gray Matter Hippocampus region is significant for three of the nodal metrics. Pairwise variance analysis between the clinical groups yields five and twelve statistically significant ROIs for AV45 and PiB, capable of distinguishing between pairs of clinical conditions. Multivariate linear regression between the percolation centrality values for nodes and psychometric assessment scores reveals Mini-Mental State Examination is reliable(4) Conclusion: percolation centrality effectively (41% of ROIs) indicates that the regions of interest that are part of the memory, visual-spatial skills, and language are crucial to the percolation of beta-amyloids within the brain network to the other widely used nodal metrics. Ranking the regions of interest based on the collective influence algorithm indicates the anatomical areas strongly influencing the beta-amyloid network.
News Coverage and Drug Shortages during the COVID-19 Pandemic
Authors: Catillon Maryaline , Majumder Maimuna S. , Manzi Shannon F. , Mandl Kenneth D.
Published: October 2020

Several drugs repurposed as COVID-19 treatment are in short supply. We collect data from MediaCloud and Google Health Trends about eight drugs proposed for repurposing as COVID-19 treatments and reported to be in shortage by the U.S. Food and Drug Administration (FDA) from January 1, 2020 through June 30, 2020. We find that news media coverage could have contributed to shortages due to hoarding by individuals and stockpiling by institutions, and that search trends appear to accurately discriminate between individual hoarding and institutional stockpiling.
Prone positioning of non-intubated patients with COVID-19 - A Systematic Review and Meta-analysis
Authors: Reddy Mallikarjuna Ponnapa , Subramaniam Ashwin , Lim Zheng Jie , Zubarev Alexandr , Afroz Afsana , Billah Baki , Blecher Gabriel , Tiruvoipati Ravindranath , Ramanathan Kollengode , Wong Suei Nee , Brodie Daniel , Fan Eddy , Shekar Kiran
Published: October 2020

Purpose

Several studies have reported adopting prone positioning (PP) in non-intubated patients with COVID-19-related hypoxaemic respiratory failure. This systematic review and meta-analysis evaluated the impact of PP on oxygenation and clinical outcomes.

Methods

We searched PubMed, Embase and COVID-19 living systematic review from December1st 2019 to July23rd 2020. We included studies that reported using PP in hypoxaemic, non-intubated adult COVID-19 patients. Primary outcome measure was the weighted mean difference (MD) in oxygenation parameters (PaO2/FiO2, PaO2 or SpO2) pre and post-PP.

Results

Fifteen single arm observational studies reporting PP in 449 patients were included. Substantial heterogeneity was noted in terms of, location within hospital where PP was instituted, respiratory supports, frequency and duration of PP. Significant improvement in oxygenation was reported post-PP: PaO2/FiO2, (MD 37.6, 95%CI 18.8, 56.5); PaO2, (MD 30.4 mmHg, 95%CI 10.9, 49.9); and SpO2, (MD 5.8%, 95%CI 3.7, 7.9). Patients with a pre-PP PaO2/FiO2 ≤150 experienced greater oxygenation improvements compared with those with a pre-PP PaO2/FiO2 >150 (MD 40.5, 95%CI −3.5, 84.6) vs. 37, 95%CI 17.1, 56.9). Respiratory rate decreased post-PP (MD −2.9, 95%CI −5.4, −0.4). Overall intubation and mortality rates were 21% (90/426) and 26% (101/390) respectively. No major adverse events were reported.

Conclusions

Despite significant variability in frequency and duration of PP and respiratory supports, PP was associated with improvements in oxygenation parameters without any reported serious adverse events. Major limitation being lack of control arm and adjustment for confounders. Clinical trials are required to determine the effect of awake PP on patient-centred outcomes.

Systematic review registration

Registration/protocol in PROSPERO (CRD42020194080).

What is the key question?

Is the novel approach of prone positioning in non-intubated patients associated with improvement in oxygenation?

What is the bottom line?

Prone position in non-intubated severe COIVD 19 suffers is associated with improvement of oxygenation while the short- and long-term patient centred out comes in this awake prone patient need more investigation.

Why read on?

Our study is first of its kind (Systematic review and Meta-analysis) summarising the evidence surrounding the less invasive innovate technique of prone position in non-intubated COVID-19 patients.
Using Satellite Images and Deep Learning to Identify Associations Between County-Level Mortality and Residential Neighborhood Features Proximal to Schools: A Cross-Sectional Study
Authors: Levy Joshua J. , Lebeaux Rebecca M. , Hoen Anne G. , Christensen Brock C. , Vaickus Louis J. , MacKenzie Todd A.
Published: October 2020

What is the relationship between mortality and satellite images as elucidated through the use of Convolutional Neural Networks?

Background

Following a century of increase, life expectancy in the United States has stagnated and begun to decline in recent decades. Using satellite images and street view images, prior work has demonstrated associations of the built environment with income, education, access to care and health factors such as obesity. However, assessment of learned image feature relationships with variation in crude mortality rate across the United States has been lacking.

Objective

We sought to investigate if county-level mortality rates in the U.S. could be predicted from satellite images.

Methods

Satellite images of neighborhoods surrounding schools were extracted with the Google Static Maps application programming interface for 430 counties representing approximately 68.9% of the US population. A convolutional neural network was trained using crude mortality rates for each county in 2015 to predict mortality. Learned image features were interpreted using Shapley Additive Feature Explanations, clustered, and compared to mortality and its associated covariate predictors.

Results

Predicted mortality from satellite images in a held-out test set of counties was strongly correlated to the true crude mortality rate (Pearson r=0.72). Direct prediction of mortality using a deep learning model across a cross-section of 430 U.S. counties identified key features in the environment (e.g. sidewalks, driveways and hiking trails) associated with lower mortality. Learned image features were clustered, and we identified 10 clusters that were associated with education, income, geographical region, race and age.

Conclusions

The application of deep learning techniques to remotely-sensed features of the built environment can serve as a useful predictor of mortality in the United States. Although we identified features that were largely associated with demographic information, future modeling approaches that directly identify image features associated with health-related outcomes have the potential to inform targeted public health interventions.
Molecular characterization of SARS-CoV-2 from Bangladesh: Implications in genetic diversity, possible origin of the virus, and functional significance of the mutations
Authors: Rahman Md. Marufur , Kader Shirmin Bintay , Rizvi S M Shahriar
Published: October 2020

In a try to understand the pathogenesis, evolution and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near complete SARS-CoV-2 genomes submitted in GISAID database from Bangladesh which were isolated between 30 March to 7 September, 2020. We then compared these genomes with Wuhan reference sequence and found 4160 mutation events including 2253 missense single nucleotide variations, 38 deletions and 10 insertions. The C>T nucleotide change was most prevalent (41% of all muations) possibly due to selective mutation pressure to reduce CpG sites to evade CpG targeted host immune response. The most frequent mutation that occurred in 98% isolates was 3037C>T which is a synonymous change that almost always accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp) and 23403A>G (D614G in spike protein). The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently most prevalent variant circulating all over the world. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. Our analysis revealed 5 large deletion events in ORF7a and ORF8 gene products that may be associated with less severity of the disease and increased viral clearance. Our phylogeny analysis identified most of the isolates belonged to the Nextstrain clade 20B (86%) and GISAID clade GR (88%). Most of our isolates shared common ancestors either directly with European countries or jointly with middle eastern countries as well as Australia and India. Interestingly, the 19B clade (GISAID S clade) was unique to Chittagong which was originally prevalent in China. This reveals possible multiple introduction of the virus in Bangladesh via different routes. Hence more genome sequencing and analysis with related clinical data is needed to interpret functional significance and better predict the disease dynamics that may be helpful for policy makers to control the COVID-19 pandemic in Bangladesh.
Postnatal fluoxetine treatment alters perineuronal net formation and maintenance in the hippocampus
Authors: Mukhopadhyay Sourish , Chatterjee Ashmita , Tiwari Praachi , Ghai Utkarsha , Vaidya Vidita A.
Published: October 2020

Elevation of serotonin via postnatal fluoxetine (PNFlx) treatment during critical temporal windows is hypothesized to perturb the development of limbic circuits thus establishing a substratum for persistent disruption of mood-related behavior. We examined the impact of PNFlx treatment on the formation and maintenance of perineuronal nets (PNNs), extracellular matrix (ECM) structures that deposit primarily around inhibitory interneurons, and mark the closure of critical period plasticity. PNFlx treatment evoked a significant decline in PNN number, with a robust reduction in PNNs deposited around parvalbumin (PV) interneurons, within the CA1 and CA3 hippocampal subfields at postnatal day 21 in Sprague-Dawley rat pups. While the reduction in CA1 subfield PNN number was still observed in adulthood, we observed no change in colocalization of PV-positive interneurons with PNNs in the hippocampi of adult PNFlx animals. PNFlx treatment did not alter hippocampal parvalbumin, calretinin, or reelin-positive neuron numbers in PNFlx animals at P21 or in adulthood. We did observe a small, but significant increase in somatostatin (SST)-positive interneurons in the DG subfield of PNFlx-treated animals in adulthood. This was accompanied by altered GABA-A receptor subunit composition, increased dendritic complexity of apical dendrites of CA1 pyramidal neurons, and enhanced neuronal activation revealed by increased c-Fos-positive cell numbers within hippocampi of PNFlx-treated animals in adulthood. These results indicate that PNFlx treatment alters the developmental trajectory of PNNs within the hippocampus, raising the possibility of a disruption of critical period plasticity and the establishment of an altered excitation-inhibition balance within this key limbic brain region.

Significance Statement

Clinical and preclinical studies indicate that developmental exposure to fluoxetine programs persistent dysregulation of mood-related behaviors. This is hypothesized to involve the disruption of the normal development of key brain regions, such as the hippocampus that regulate mood behaviors. We show that postnatal exposure to fluoxetine alters hippocampal perineuronal nets (PNNs), extracellular matrix structures that regulate plasticity and mark the closure of critical periods. The decline in PNNs is noted in early postnatal life, and persists into adulthood in specific hippocampal subfields. Adult animals with a history of postnatal fluoxetine exposure exhibit altered numbers of somatostatin interneurons, GABA receptor subunit expression and neuronal activation within the hippocampus. This indicates that postnatal fluoxetine disrupts the normal developmental trajectory of the hippocampus.
From more testing to smart testing: data-guided SARS-CoV-2 testing choices
Authors: van Beek Janko , Igloi Zsofia , Boelsums Timo , Fanoy Ewout , Gotz Hannelore , Molenkamp Richard , van Kampen Jeroen , GeurtsvanKessel Corine , van der Eijk Annemiek , van de Vijver David , Koopmans Marion
Published: October 2020

We present an in-depth analysis of data from drive through testing stations using rapid antigen detection tests (RDT’s), RT-PCR and virus culture, to assess the ability of RDT’s to detect infectious cases. We show that the detection limits of five commercially available RDT’s differ considerably, impacting the translation into the detection of infectious cases. We recommend careful fit-for-purpose testing before implementation of antigen RDT’s in routine testing algorithms as part of the COVID-19 response.
Background and concurrent factors predicting non-adherence to public health preventive measures during the chronic phase of the COVID-19 pandemic
Authors: Pollak Yehuda , Shoham Rachel , Dayan Haym , Seri Ortal Gabrieli , Berger Itai
Published: October 2020

To determine factors that predict non-adherence to preventive measures for COVID-19 during the chronic phase of the pandemic, a cross-sectional, general population survey was conducted in Israel. Sociodemographic, health-related, behavioral, and COVID-19-related characteristics were collected. Among 2055 participants, non-adherence was associated with male gender, young age, bachelorhood, being employed, lower decrease in income, low physical activity, psychological distress, ADHD symptoms, past risk-taking and anti-social behavior, low pro-sociality, perceived social norms favoring non-adherence, low perceived risk of COVID-19, low perceived efficacy of the preventive measures, and high perceived costs of adherence to the preventive measures. There appears to be a need for setting out and communicating preventive measures to specifically targeted at-risk populations.
Genome-wide association study identifies five risk loci for pernicious anemia and implicates the role of HLA-DR15 haplotype
Authors: Laisk Triin , Lepamets Maarja , Mägi Reedik
Published: October 2020

Pernicious anemia is a rare condition characterized by vitamin B12 deficiency anemia due to lack of intrinsic factor, often caused by autoimmune gastritis. Patients with pernicious anemia have a higher incidence of other autoimmune disorders, such as type 1 diabetes, vitiligo and autoimmune thyroid issues. Therefore, the disease has a clear autoimmune basis, although the genetic susceptibility factors have thus far remained poorly studied. We conducted a genome-wide association study meta-analysis in 2,166 cases and 659,516 European controls from population-based biobanks and identified genome-wide significant signals in or near thePTPN22 (rs6679677, p=1.91 ⨯ 10−24, OR=1.63), PNPT1(rs12616502, p=3.14 ⨯ 10−8, OR=1.70),HLA-DQB1(rs28414666, p=1.40 ⨯ 10−16, OR=1.38),IL2RA(rs2476491, p=1.90 ⨯ 10−8, OR=1.22) andAIRE(rs74203920, p=2.33 ⨯ 10−9, OR=1.83) genes, thus providing the first robust associations between pernicious anemia and genetic risk factors. We further mapped the susceptibility in the HLA region to the HLA-DR15 haplotype. Analysis of associated diagnoses and disease trajectories confirm the association between pernicious anemia and thyroid issues, vitiligo, gastritis, stomach cancer, osteoporosis and other diagnoses.