bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probability of aerosol transmission of SARS-CoV-2
Authors: Smith Scott H. , Somsen G. Aernout , van Rijn Cees , Kooij Stefan , van der Hoek Lia , Bem Reinout A. , Bonn Daniel 
Published: July 2020

ABSTRACTTransmission of SARS-CoV-2 leading to COVID-19 occurs through exhaled respiratory droplets from infected humans. Currently, however, there is much controversy over whether respiratory aerosol microdroplets play an important role as a route of transmission. By measuring and modeling the dynamics of exhaled respiratory droplets we can assess the relative contribution of aerosols in the spreading of SARS-CoV-2. We measure size distribution, total numbers and volumes of respiratory droplets, including aerosols, by speaking and coughing from healthy subjects. Dynamic modelling of exhaled respiratory droplets allows to account for aerosol persistence times in confined public spaces. The probability of infection by inhalation of aerosols when breathing in the same space can then be estimated using current estimates of viral load and infectivity of SARS-CoV-2. In line with the current known reproduction numbers, our study of transmission of SARS-CoV-2 suggests that aerosol transmission is an inefficient route, in particular from non or mildly symptomatic individuals.
Fully Automated Delineation of the Optic Radiation for Surgical Planning using Clinically Accessible Sequences
Authors: Reid Lee B , Martínez-Heras Eloy , Manjón Jose V , Jeffree Rosalind L. , Alexander Hamish , Trinder Julie , Solana Elisabeth , Llufriu Sara , Rose Stephen , Prior Marita , Fripp Jurgen 
Published: July 2020

1AbstractQuadrantanopia caused by inadvertent severing of Meyer’s Loop of the optic radiation is a well-recognised complication of temporal lobectomy for conditions such as epilepsy. Dissection studies indicate that the anterior extent of Meyer’s Loop varies considerably between individuals. Quantifying this for individual patients is thus an important step to improve the safety profile of temporal lobectomies. Previous attempts to delineate Meyer’s Loop using diffusion MRI tractography have had difficulty estimating its full anterior extent, required manual ROI placement, and/or relied on advanced diffusion sequences that cannot be acquired routinely in most clinics. Here we present CONSULT – a pipeline that can delineate the optic radiation from raw DICOM data in a completely automated way via a combination of robust preprocessing, segmentation, and alignment stages, plus simple improvements that bolster the efficiency and reliability of standard tractography. We tested CONSULT on 694 scans of predominantly healthy participants (538 unique brains), including both advanced acquisitions and simpler acquisitions that could be acquired in clinically acceptable timeframes. Delineations completed without error in 99.4% of the scans. The distance between Meyer’s Loop and the temporal pole closely matched both averages and ranges reported in dissection studies for all tested sequences. Median scan-rescan error of this distance was 1mm. When tested on two participants with considerable pathology, delineations were successful and realistic. Through this, we demonstrate not only how to identify Meyer’s Loop with clinically accessible sequences, but also that this can be achieved without fundamental changes to tractography algorithms or complex post-processing methods.HighlightsWe propose a fully automated means of delineating the optic radiation using diffusion MRI from DICOM dataAnatomical measurements from tractography of over 500 brains align well with previous dissection studiesThe proposed pipeline works well with clinically accessible and advanced acquisitionsMedian scan-rescan error was 1mmPlausible tractography was generated when pathology was present
Is it safe to lift COVID-19 travel bans? The Newfoundland story
Authors: Linka Kevin , Rahman Proton , Goriely Alain , Kuhl Ellen 
Published: July 2020

AbstractA key strategy to prevent a local outbreak during the COVID-19 pandemic is to restrict incoming travel. Once a region has successfully contained the disease, it becomes critical to decide when and how to reopen the borders. Here we explore the impact of border reopening for the example of Newfoundland and Labrador, a Canadian province that has enjoyed no new cases since late April, 2020. We combine a network epidemiology model with machine learning to infer parameters and predict the COVID-19 dynamics upon partial and total airport reopening, with perfect and imperfect quarantine conditions. Our study suggests that upon full reopening, every other day, a new COVID-19 case would enter the province. Under the current conditions, banning air travel from outside Canada is more efficient in managing the pandemic than fully reopening and quarantining 95% of the incoming population. Our study provides quantitative insights of the efficacy of travel restrictions and can inform political decision making in the controversy of reopening.“There is one and only one way to absolutely prevent it and that is by establishing absolute isolation. It is necessary to shut off those who are capable of giving off the virus from those who are capable of being infected, or vice versa.” The Lessons Of The Pandemic, Science 1919.
Determinants of Burnout and Other Aspects of Psychological Well-Being in Healthcare Workers During the COVID-19 Pandemic: A Multinational Cross-Sectional Study
Authors: Scott Alasdair , Tan Benjamin YQ , Huak Chan Yiong , Sia Ching-Hui , Xian Chua Ying , Goh Ee Teng , Zbikowska Gabriela , Dykowska Grazyna , Martin Guy , Kinross James , Przybylowicz Jan , Fedorowski Jaroslaw , Beatty Jasmine Winter , Clarke Jonathan , Sim Kang , Abhiram Kanneganti , Flott Kelsey , Lim Lucas JH , Wells Mary , Denning Max , Almonte Melanie T , Tan Melanie , Mason Sam , Purkayastha Sanjay , Yalamanchili Seema , Markar Sheraz , Ooi Shirley BS , Chidambaran Swathikan , Lifeng Tan , Sharma Vijay K , Sounderajah Viknesh 
Published: July 2020

ABSTRACTBackgroundThe Covid-19 pandemic has placed unprecedented pressure on healthcare systems and workers around the world. Such pressures may impact on working conditions, psychological wellbeing and perception of safety. In spite of this, no study has assessed the relationship between safety attitudes and psychological outcomes. Moreover, only limited studies have examined the relationship between personal characteristics and psychological outcomes during Covid-19.MethodsFrom 22nd March 2020 to 18th June 2020, healthcare workers from the United Kingdom, Poland, and Singapore were invited to participate using a self-administered questionnaire comprising the Safety Attitudes Questionnaire (SAQ), Oldenburg Burnout Inventory (OLBI) and Hospital Anxiety and Depression Scale (HADS) to evaluate safety culture, burnout and anxiety/depression. Multivariate logistic regression was used to determine predictors of burnout, anxiety and depression.ResultsOf 3,537 healthcare workers who participated in the study, 2,364 (67%) screened positive for burnout, 701 (20%) for anxiety, and 389 (11%) for depression. Significant predictors of burnout included patient-facing roles: doctor (OR 2.10; 95% CI 1.49-2.95), nurse (OR 1.38; 95% CI 1.04-1.84), and ‘other clinical’ (OR 2.02; 95% CI 1.45-2.82); being redeployed (OR 1.27; 95% CI 1.02-1.58), bottom quartile SAQ score (OR 2.43; 95% CI 1.98-2.99), anxiety (OR 4.87; 95% CI 3.92-6.06) and depression (OR 4.06; 95% CI 3.04-5.42). Factors significantly protective for burnout included being tested for SARS-CoV-2 (OR 0.64; 95% CI 0.51-0.82) and top quartile SAQ score (OR 0.30; 95% CI 0.22-0.40). Significant factors associated with anxiety and depression, included burnout, gender, safety attitudes and job role.ConclusionOur findings demonstrate a significant burden of burnout, anxiety, and depression amongst healthcare workers. A strong association was seen between SARS-CoV-2 testing, safety attitudes, gender, job role, redeployment and psychological state. These findings highlight the importance of targeted support services for at risk groups and proactive SARS-CoV-2 testing of healthcare workers.
Forecasting hospital demand in metropolitan areas during the current COVID-19 pandemic and estimates of lockdown-induced 2nd waves
Authors: Capistrán Marcos A. , Capella Antonio , Andrés Christen J. 
Published: July 2020

SummaryWe present a forecasting model aim to predict hospital occupancy in metropolitan areas during the current COVID-19 pandemic. Our SEIRD type model features asymptomatic and symptomatic infections with detailed hospital dynamics. We model explicitly branching probabilities and non-exponential residence times in each latent and infected compartments. Using both hospital admittance confirmed cases and deaths, we infer the contact rate and the initial conditions of the dynamical system, considering breakpoints to model lockdown interventions and the increase in effective population size due to lockdown relaxation. The latter features let us model lockdown-induced 2nd waves. Our Bayesian approach allows us to produce timely probabilistic forecasts of hospital demand. We have applied the model to analyze more than 70 metropolitan areas and 32 states in Mexico.
An overview of current mental health in the general population of Australia during the COVID-19 pandemic: Results from the COLLATE project
Authors: Rossell Susan L , Neill Erica , Phillipou Andrea , Tan Eric J , Toh Wei Lin , Van Rheenen Tamsyn E , Meyer Denny 
Published: July 2020

AbstractThe novel coronavirus disease (COVID-19) poses significant mental health challenges globally; however, to date, there is limited community level data. This study reports on the first wave of data from the COLLATE project (COvid-19 and you: mentaL heaLth in AusTralia now survEy), an ongoing study aimed at understanding the impact of the COVID-19 pandemic on the mental health and well-being of Australians. This paper addresses prevailing primary concerns related to the COVID-19 pandemic, current levels of negative emotions and risk factors predicting these negative emotions. On April 1st to 4th 2020, 5158 adult members of the Australian general public completed an online survey. Participants ranked their top ten current primary concerns about COVID-19, and completed standardized measures to ascertain levels of negative emotions (specifically, depression, anxiety and stress). Socio-demographic information was also collected and used in the assessment of risk factors. The top three primary concerns were all related to the health and well-being of family and loved ones. As expected, levels of negative emotion were exceptionally high. Modelling of predictors of negative emotions established several risk factors related to demographic variables, personal vulnerabilities, financial stresses, and social distancing experiences; particularly being young, being female, or having a mental illness diagnosis. The data provides important characterization of the current mental health of Australians during the COVID-19 pandemic. Critically, it appears that specific groups in the Australian community may need special attention to ensure their mental health is protected during these difficult times. The data further suggests the need for immediate action to combat high levels of psychological distress, along with the exacerbation of mental health conditions, in relation to the COVID-19 pandemic in Australia. These results may provide some direction for international researchers hoping to characterize similar issues in other countries.
Regeneration of Functional Retinal Ganglion Cells by Neuronal Identity Reprogramming
Authors: Wei Xiaohu , Zhang Zhenhao , Zeng Huan-huan , Wang Xue-Feng , Zhan Wenrong , Qiao Na , Chang Zhen , Liu Lu , Fan Chengyu , Yang Ziwei , Li Xiaoming , Yang Yang , Liu Hongjun 
Published: July 2020

SUMMARYDegeneration of retinal ganglion cells (RGCs) and their axons underlies vision loss in glaucoma and various optic neuropathies. There are currently no treatments available to restore lost vision in patients affected by these diseases. Regenerating RGCs and reconnecting the retina to the brain represent an ideal therapeutic strategy; however, mammals do not have a reservoir of retinal stem/progenitor cells poised to produce new neurons in adulthood. Here, we regenerated RGCs in adult mice by direct lineage reprogramming of retinal interneurons. We successfully converted amacrine and displaced amacrine interneurons into RGCs, and observed that regenerated RGCs projected axons into brain retinorecipient areas. They convey visual information to the brain in response to visual stimulation, and are able to transmit electrical signals to postsynaptic neurons, in both normal animals and in a diseased model. The generation of functional RGCs in adult mammals points to a therapeutic strategy for vision restoration in patients.
SARS-CoV-2 structural coverage map reveals state changes that disrupt host immunity
Authors: O’Donoghue Seán I. , Schafferhans Andrea , Sikta Neblina , Stolte Christian , Kaur Sandeep , Ho Bosco K. , Anderson Stuart , Procter James , Dallago Christian , Bordin Nicola , Adcock Matt , Rost Burkhard 
Published: July 2020

AbstractIn response to the COVID-19 pandemic, many life scientists are focused on SARS-CoV-2. To help them use available structural data, we systematically modeled all viral proteins using all related 3D structures, generating 872 models that provide detail not available elsewhere. To organise these models, we created a structural coverage map: a novel, one-stop visualization summarizing what is — and is not — known about the 3D structure of the viral proteome. The map highlights structural evidence for viral protein interactions, mimicry, and hijacking; it also helps researchers find 3D models of interest, which can then be mapped with UniProt, PredictProtein, or CATH features. The resulting Aquaria-COVID resource (https://aquaria.ws/covid) helps scientists understand molecular mechanisms underlying coronavirus infection. Based on insights gained using our resource, we propose mechanisms by which the virus may enter immune cells, sense the cell type, then switch focus from viral reproduction to disrupting host immune responses.SignificanceCurrently, much of the COVID-19 viral proteome has unknown molecular structure. To improve this, we generated ∼1,000 structural models, designed to capture multiple states for each viral protein. To organise these models, we created a structure coverage map: a novel, one-stop visualization summarizing what is — and is not — known about viral protein structure. We used these data to create an online resource, designed to help COVID-19 researchers gain insight into the key molecular processes that drive infection. Based on insights gained using our resource, we speculate that the virus may sense the type of cells it infects and, within certain cells, it may switch from reproduction to disruption of the immune system.
Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle
Authors: Yoshioka Kiyoshi , Nagahisa Hiroshi , Miura Fumihito , Araki Hiromitsu , Kamei Yasutomi , Kitajima Yasuo , Seko Daiki , Nogami Jumpei , Tsuchiya Yoshifumi , Okazaki Narihiro , Yonekura Akihiko , Ohba Seigo , Sumita Yoshinori , Chiba Ko , Ito Kosei , Asahina Izumi , Ogawa Yoshihiro , Ito Takashi , Ohkawa Yasuyuki , Ono Yusuke 
Published: July 2020

SUMMARYSkeletal muscle stem cells (satellite cells) are distributed throughout the body with heterogeneous properties that corresponds to region-specific pathophysiology. However, topographical genes that have functions remain unidentified in satellite cells of adult muscle. Here, we showed that expression of Homeobox (Hox)-A cluster genes, key regulators of the embryonic body plan, was robustly maintained in both muscles and satellite cells in adult mice and humans, which recapitulates their embryonic origin. We observed that regionally specific expressed Hox genes were linked to hypermethylation of the Hox-A locus. We examinedHoxa10inactivation in satellite cells and found it led to genomic instability and mitotic catastrophe, which resulted in a decline in the regionally specific regenerative ability of muscles in adult mice. Thus, our results showed that Hox gene expression profiles instill the embryonic history in satellite cells as positional memory, potentially modulating the region-specificity in adult skeletal muscles.
The role of alpha power in the suppression of anticipated distractors during verbal working memory
Authors: Sghirripa Sabrina , Graetz Lynton , Merkin Ashley , Rogasch Nigel C , Ridding Michael C , Semmler John G , Goldsworthy Mitchell R 
Published: July 2020

AbstractAs working memory (WM) is limited in capacity, it is important to direct neural resources towards processing task-relevant information while ignoring distractors. Neural oscillations in the alpha frequency band (8-12 Hz) have been suggested to play a role in the inhibition of task-irrelevant information during WM, although results are mixed, possibly due to differences in the type of WM task employed. Here, we examined the role of alpha power in inhibition of anticipated distractors of varying strength using a modified Sternberg task where the encoding and retention periods were temporally separated. We recorded EEG while 20 young adults completed the task and found: 1) slower reaction times in strong distractor trials compared to weak distractor trials; 2) increased alpha power in posterior regions from baseline prior to presentation of a distractor regardless of condition; and 3) no differences in alpha power between strong and weak distractor conditions. Our results suggest that parieto-occipital alpha power is increased prior to a distractor. However we could not find evidence that alpha power is further modulated by distractor strength.
Spatio-Temporal Correlates of Gene Expression and Cortical Morphology across Life Course and Aging
Authors: Qiu Anqi , Zhang Han , Kennedy Brian K. , Lee Annie 
Published: July 2020

AbstractEvidence from independent neuroimaging and genetic studies supports the concept that brain aging mirrors development. However, it is unclear whether mechanisms linking brain development and aging provide new insights to delay aging and potentially reverse it. This study determined biological mechanisms and phenotypic traits underpinning brain alterations across the life course and in aging by examining spatio-temporal correlations between gene expression and cortical volumes (n=3391) derived from the life course dataset (3-82 years) and the aging dataset (55-82 years). We revealed that a large proportion of genes whose expression was associated with cortical volume across the life course were in astrocytes. These genes, which showed up-regulation during development and down-regulation during aging, contributed to fundamental homeostatic functions of astrocytes crucial, in turn, for neuronal functions. Included among these genes were those encoding components of cAMP and Ras signal pathways, as well as retrograde endocannabinoid signaling. Genes associated with cortical volumes in the aging dataset were also enriched for the sphingolipid signaling pathway, renin-angiotensin system (RAS), proteasome, and TGF-beta signaling pathway, which is linked to the senescence-associated secretory phenotype. Neuroticism, drinking, and smoking were the common phenotypic traits in the life course and aging, while memory was the unique phenotype associated with aging. These findings provide biological mechanisms and phenotypic traits mirroring development and aging as well as unique to aging.
Genetic Diversity and Structure ofOryza rufipogonGriff. Populations in the Philippines
Authors: Labarosa Sandy Jan E. , Sevilla Neah Rosandra , Tabanao Dindo Agustin A. , Baldo Nenita B. , Ebuña Helen L.V. , Jamago Joy M. 
Published: July 2020

ABSTRACTOryza rufipogonGriff. or ‘Rufi’ is the wild progenitor of the cultivated rice,Oryza sativaL. In the Philippines, Rufi was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. Based on previous morphological diversity assessment, both populations are unique for at least three characters, i.e., leaf, culm, and awn lengths. Environmental parameters such as rainfall and air temperature also differed between the two lakes. With these, an assessment of Rufi’s genetic diversity at the molecular level is beneficial to further ascertain its usefulness in rice breeding and gain insights on its conservation status. Thus, this study estimated the degree of genetic diversity and determined the population structure of 41 samples of natural Rufi populations in the Philippines using SSR markers. A total of 98 genome wide polymorphic SSR markers were selected to examine the genetic diversity and structure of Rufi populations, along with seven rice cultivars for comparison. Results showed that Philippine Rufi populations have lower genetic diversity compared to cultivated rice accessions and other Rufi populations in Southeast Asia and China. This low genetic diversity suggested that Rufi populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness of their importance. A significant population structure and differentiation were determined using the STRUCTURE and phylogenetic analyses. Population differentiation might be due to geographic isolation which prevented gene flow between the two populations and the unique climatic conditions between the two lakes.
A Correspondence Between Normalization Strategies in Artificial and Biological Neural Networks
Authors: Shen Yang , Wang Julia , Navlakha Saket 
Published: July 2020

AbstractA fundamental challenge at the interface of machine learning and neuroscience is to uncover computational principles that are shared between artificial and biological neural networks. In deep learning, normalization methods, such as batch normalization, weight normalization, and their many variants, help to stabilize hidden unit activity and accelerate network training, and these methods have been called one of the most important recent innovations for optimizing deep networks. In the brain, homeostatic plasticity represents a set of mechanisms that also stabilize and normalize network activity to lie within certain ranges, and these mechanisms are critical for maintaining normal brain function. In this survey, we discuss parallels between artificial and biological normalization methods at four spatial scales: normalization of a single neuron’s activity, normalization of synaptic weights of a neuron, normalization of a layer of neurons, and normalization of a network of neurons. We argue that both types of methods are functionally equivalent — i.e., they both push activation patterns of hidden units towards a homeostatic state, where all neurons are equally used — and that such representations can increase coding capacity, discrimination, and regularization. As a proof of concept, we develop a neural normalization algorithm, inspired by a phenomena calledsynaptic scaling, and show that this algorithm performs competitively against existing normalization methods on several datasets. Overall, we hope this connection will inspire machine learners in three ways: to uncover new normalization algorithms based on established neurobiological principles; to help quantify the trade-offs of different homeostatic plasticity mechanisms used in the brain; and to offer insights about how stability may not hinder, but may actually promote, plasticity.