bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus
Authors: Maden Sean K. , Thompson Reid F. , Hansen Kasper D. , Nellore Abhinav 
Published: November 2020

AbstractWhile DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35,360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus (GEO). We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain, and one-third were from cancer patients. 19% of samples failed at least one of Illumina’s 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm, and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via therecountmethylationR/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
Authors: Hill Edward M. , Atkins Benjamin D. , Keeling Matt J. , Dyson Louise , Tildesley Michael J. 
Published: November 2020

AbstractBackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated.MethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create ‘COVID-secure’ workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics.ResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels.ConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.
CLINICAL APPLICATIONS OF MACHINE LEARNING ON COVID-19: THE USE OF A DECISION TREE ALGORITHM FOR THE ASSESSMENT OF PERCEIVED STRESS IN MEXICAN HEALTHCARE PROFESSIONALS
Authors: Delgado-Gallegos Juan Luis , Avilés-Rodriguez Gener , Padilla-Rivas Gerardo R. , Ángeles Cosio-León María De los , Franco-Villareal Héctor , Zuñiga-Violante Erika , Romo-Cardenas Gerardo Salvador , Islas Jose Francisco 
Published: November 2020

AbstractStress and anxiety have shown to be indirect effects of the COVID-19 pandemic, therefore managing stress becomes essential. One of the most affected populations by the pandemic are healthcare professionals. Thus, it is paramount to understand and categorize their perceived levels of stress, as it can be a detonating factor leading to mental illness. In our study, we used a machine learning prediction model to help measure perceived stress; a C5.0 decision tree algorithm was used to analyze and classify datasets obtained from healthcare professionals of the northeast region of Mexico. Our analysis showed that 6 out of 102 instances were incorrectly classified. Missing two cases for mild, three for moderate and 1 for severe (accuracy of 94.1%), statistical correlation analysis was performed to ensure integrity of the method, in addition we concluded that severe stress cases can be related mostly to high levels of Xenophobia and Compulsive stress.
Inward and outward effectiveness of cloth masks, a surgical mask, and a face shield
Authors: Pan Jin , Harb Charbel , Leng Weinan , Marr Linsey C. 
Published: November 2020

AbstractWe evaluated the effectiveness of 11 face coverings for material filtration efficiency, inward protection efficiency on a manikin, and outward protection efficiency on a manikin. At the most penetrating particle size, the vacuum bag, microfiber cloth, and surgical mask had material filtration efficiencies >50%, while the other materials had much lower filtration efficiencies. However, these efficiencies increased rapidly with particle size, and many materials had efficiencies >50% at 2 μm and >75% at 5 μm. The vacuum bag performed best, with efficiencies of 54-96% for all three metrics, depending on particle size. The thin acrylic and face shield performed worst. Inward protection efficiency and outward protection efficiency were similar for many masks; the two efficiencies diverged for stiffer materials and those worn more loosely (e.g., bandana) or more tightly (e.g., wrapped around the head) compared to a standard earloop mask. Discrepancies between material filtration efficiency and inward/outward protection efficiency indicated that the fit of the mask was important. We calculated that the particle size most likely to deposit in the respiratory tract when wearing a mask is ∼2 μm. Based on these findings, we recommend a three-layer mask consisting of outer layers of a flexible, tightly woven fabric and an inner layer consisting of a material designed to filter out particles. This combination should produce an overall efficiency of >70% at the most penetrating particle size and >90% for particles 1 μm and larger if the mask fits well.
Assortative social mixing and sex disparities in tuberculosis burden
Authors: Shaweno Debebe , Horton Katherine , Hayes Richard , Dodd Peter J. 
Published: November 2020

ABSTRACTGlobally, men have higher tuberculosis (TB) burden but the mechanisms underlying this sex disparity are not fully understood. Recent surveys of social mixing patterns have established moderate preferential within-sex mixing in many settings. This assortative mixing could amplify differences from other causes. We explored the impact of assortative mixing and factors differentially affecting disease progression and detection using a sex-stratified deterministic TB transmission model. We explored the influence of assortativity at disease-free and endemic equilibria, finding stronger effects during invasion and on increasing male:female prevalence (M:F) ratios than overall prevalence. Variance-based sensitivity analysis of endemic equilibria identified differential progression as the most important driver of M:F ratio uncertainty. We fitted our model to prevalence and notification data in examplar settings within a fully Bayesian framework. For our high M:F setting, random mixing reduced equilibrium M:F ratios by 12%(95%CrI 0 - 30%). Equalizing male case detection there led to a 20% (95%CrI 11 - 31%) reduction in M:F ratio over 10 years - insufficient to eliminate sex disparities. However, this potentially achievable improvement was associated with a meaningful 8%(95%CrI 4 - 14%) reduction in total TB prevalence over this time frame.
Acute nasal dryness in COVID-19
Authors: Navarra Jordi , Ruiz-Ceamanos Alba , Moreno Juan José , García-Basterrechea José María , de Haro-Licer Josep , Sinnett Scott , Spence Charles , Gallardo-Pujol David 
Published: November 2020

AbstractOne of the entry routes of SARS-CoV-2 is the nasal epithelium. Although mounting evidence suggests the presence of olfactory dysfunction, and even anosmia, in patients with COVID-19, it is not clear whether these patients also suffer from other “nasal” symptoms that may influence their olfaction. A group of 35 patients with COVID-19 (and a control group matched in gender and age) were surveyed about the presence of a variety of nasal symptoms that may be associated to drastic perturbations experienced in the nasal cavity (e.g., “excessive dryness” and/or a continual sensation of having had a “nasal douche”). We used a cross-sectional, retrospective survey, targeted at the general population by means of non-quoted, non-random, snowball sampling. Symptoms were assessed with absence/presence responses. The possible association between two continuously distributed latent variables from categorical variables was estimated by means of polychoric correlations. More than 68% of the patients reported at least one “nasal” symptom. The clinical group also experienced “a strange sensation in the nose” and having excessive nasal dryness significantly more often than the control group. Fifty-two percent of the patients (but only 3% of the control group) reported a constant sensation of having had a strong nasal douche. Nasal symptoms predominantly co-occurred with anosmia/hyposmia, and ageusia/hypogeusia, appeared principally before or during the other symptoms of COVID-19, and lasted for twelve days, in average. The presence of these nasal symptoms, and their early occurrence, could potentially facilitate early diagnosis of COVID-19 and initial social distancing efforts.
IMPACT OF THE CORONAVIRUS DISEASE 2019 PANDEMIC ON SURGICAL VOLUME IN JAPAN: A COHORT STUDY USING ADMINISTRATIVE DATA
Authors: Okuno Takuya , Takada Daisuke , Jung-ho Shin , Morishita Tetsuji , Itoshima Hisashi , Kunisawa Susumu , Imanaka Yuichi 
Published: November 2020

AbstractBackgroundInternationally, the Coronavirus Disease (COVID-19) pandemic has caused unprecedented challenges for surgical staff to minimise the exposure to COVID-19 or save medical resources without harmful outcomes for patients, in accordance with the statement of each surgical society. However, no research has empirically validated declines in Japanese surgical volume or compared decrease rates of surgeries during the COVID-19 pandemic.Material and MethodsWe extracted 672,772 available cases of patients aged > 15 years who were discharged between July 1, 2018, and June 30, 2020. After categorisation of surgery, we calculated descriptive statistics to compare the year-over-year trend and conducted interrupted time series analysis to validate the decline.ResultsThe year-over-year trend of all eight surgical categories decreased from April 2020 and reached a minimum in May 2020 (May: abdominal, 68.4%; thoracic, 85.8%; genitourinary, 78.6%; cardiovascular, 90.8%; neurosurgical, 69.1%; orthopaedic, 62.4%; ophthalmologic, 52.0%; ear/nose/throat, 27.3%). Interrupted time series analysis showed no significant trends in oncological and critical benign surgeries.ConclusionWe demonstrated and validated a trend of reduction in surgical volume in Japan using administrative data applying interrupted time series analyses. Low priority surgeries, as categorised by the statement of each society, showed obvious and statistically significant declines in case volume during the COVID-19 pandemic.
The detection and stability of the SARS-CoV-2 RNA biomarkers in wastewater influent in Helsinki, Finland
Authors: Hokajärvi Anna-Maria , Rytkönen Annastiina , Tiwari Ananda , Kauppinen Ari , Oikarinen Sami , Lehto Kirsi-Maarit , Kankaanpää Aino , Gunnar Teemu , Al-Hello Haider , Blomqvist Soile , Miettinen Ilkka T. , Savolainen-Kopra Carita , Pitkänen Tarja 
Published: November 2020

AbstractWastewater-based surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is used to monitor the population-level prevalence of the COVID-19 disease. In many cases, due to lockdowns or analytical delays, the analysis of wastewater samples might only be possible after prolonged storage. In this study, the effect of storage conditions on the RNA copy numbers of the SARS-CoV-2 virus in wastewater influent was studied and compared to the persistence of norovirus over time at 4°C, −20°C, and −75°C using the reverse-transcription quantitative PCR (RT-qPCR) assays E-Sarbeco, N2, and norovirus GII. For the first time in Finland, the presence of SARS-CoV-2 RNA was tested in 24 h composite influent wastewater samples collected from Viikinmäki wastewater treatment plant, Helsinki, Finland. The detected and quantified SARS-CoV-2 RNA copy numbers of the wastewater sample aliquots taken during 19–20 April 2020 and stored for 29, 64, and 84 days remained surprisingly stable. In the stored samples, the SARS betacoronavirus and SARS-CoV-2 copy numbers, but not the norovirus GII copy numbers, seemed slightly higher when analyzed from the pre-centrifuged pellet—that is, the particulate matter of the influent—as compared with the supernatant (i.e., water fraction) used for ultrafiltration, although the difference was not statistically significant. Furthermore, when wastewater was spiked with SARS-CoV-2, linear decay at 4°C was observed on the first 28 days, while no decay was visible within 58 days at −20°C or −75°C. In conclusion, freezing temperatures should be used for storage when immediate SARS-CoV-2 RNA analysis from the wastewater influent is not possible. Analysis of the particulate matter of the sample, in addition to the water fraction, can improve the detection frequency.
Association of plasma proteins with rate of cognitive decline and dementia: 20-year follow-up of the Whitehall II and ARIC cohort studies
Authors: Lindbohm Joni V. , Mars Nina , Walker Keenan A. , Singh-Manoux Archana , Livingston Gill , Brunner Eric J. , Sipilä Pyry N. , Saksela Kalle , Ferrie Jane E. , Lovering Ruth , Williams Stephen A. , Hingorani Aroon D. , Gottesman Rebecca F. , Zetterberg Henrik , Kivimäki Mika 
Published: November 2020

AbstractThe role of circulating proteins in Alzheimer’s disease and related dementias is unknown. Using a follow-up of two decades, 4953 plasma proteins, and discovery (Whitehall II) and replication cohort (ARIC), we examined plasma proteins associated with cognitive decline rate and dementia. After replication and adjustment for known dementia risk factors, fifteen proteins were associated with cognitive decline rate and dementia. None of these were amyloid, tau, or neurofilament-related proteins. Currently approved medications can target five of the proteins. The results support systemic pathogenesis of dementias, may aid in early diagnosis, and suggest potential targets for drug development.
The effects of developmental trauma on reinforcement learning and its relationship to psychotic experiences: a behavioural study
Authors: Rezaie Rowan , Modaffar Mustapha , Jung Paul , Hindocha Chandni , Bisby James A , Bloomfield Michael A P 
Published: November 2020

ABSTRACTBackgroundDevelopmental psychological trauma can impact several key neurocognitive domains, including reward processing, and is associated with increased risk of psychosis in adulthood. Aberrant reinforcement learning (RL), an important component of reward processing, has been implicated in the pathophysiology of psychosis by altering information processing through changes in hierarchical predictive coding. We therefore sought to investigate RL in survivors of developmental trauma and its relationship to psychotic experiences.MethodsWe recruited two groups of adults, one with self-reported exposure to multiple forms of developmental trauma (n=115), and a control group without any known history of maltreatment (n=85). Participants completed measures of psychotic experiences (Community Assessment of Psychic Experiences) and undertook a probabilistic selection task designed to assess RL from positive versus negative outcomes. We analysed group differences for main effects and investigated relationships between developmental trauma, RL and psychotic experiences using regression modelling and mediation analysis.ResultsDevelopmental trauma was associated with psychotic experiences (adjusted R2=0.41,p=0.004) and impaired RL (Fdf=6.291,89,p=0.014). Impaired RL mediated the association between developmental trauma and psychotic experiences (indirect effectβ= 0.60, 95% CI, 0.01–1.36).ConclusionsOur findings implicate aberrant RL as a possible mechanism through which developmental trauma may increase risk of psychosis. Further research is therefore warranted to understand the specific processes that characterise these putative trauma-induced vulnerability mechanisms and how they may contribute to the development of psychopathology.
Modeling and Sensitivity Analysis of Coronavirus Disease (COVID-19) Outbreak Prediction
Authors: Sedaghat Ahmad , Abbas Oloomi Seyed Amir , Malayer Mahdi Ashtian , Band Shahab S. , Mosavi Amir , Nadai Laszlo 
Published: November 2020

AbstractSusceptible-infectious-recovered-deceased (SIRD) model is an essential model for outbreak prediction. This paper evaluates the performance of the SIRD model for the outbreak of COVID-19 in Kuwait, which initiated on 24 February 2020 by five patients in Kuwait. This paper investigates the sensitivity of the SIRD model for the development of COVID-19 in Kuwait based on the duration of the progressed days of data. For Kuwait, we have fitted the SIRD model to COVID-19 data for 20, 40, 60, 80, 100, and 116 days of data and assessed the sensitivity of the model with the number of days of data. The parameters of the SIRD model are obtained using an optimization algorithm (lsqcurvefit) in MATLAB. The total population of 50,000 is equally applied for all Kuwait time intervals. Results of the SIRD model indicate that after 40 days, the peak infectious day can be adequately predicted. Although error percentage from sensitivity analysis suggests that different exposed population sizes are not correctly predicted. SIRD type models are too simple to robustly capture all features of COVID-19, and more precise methods are needed to tackle the correct trends of a pandemic.
Assessment of COVID-19 vaccine acceptance among healthcare workers in Los Angeles
Authors: Gadoth Adva , Halbrook Megan , Martin-Blais Rachel , Gray Ashley , Tobin Nicole H. , Ferbas Kathie G. , Aldrovandi Grace M. , Rimoin Anne W. 
Published: November 2020

AbstractImportanceHealthcare workers (HCW) are slated to be early recipients of SARS-CoV-2 vaccines due to increased risk of exposure to patients with COVID-19, and will be tasked with administering approved vaccines to the general population. As lynchpins of the vaccination effort, HCWs’ opinions of a vaccine’s safety and efficacy may affect both public perception and uptake of the vaccine. Therefore, it is crucial to understand and address potential hesitancy prior to vaccine administration.ObjectiveTo understand healthcare workers’ attitudes about vaccine safety, efficacy, and acceptability in the context of the COVID-19 pandemic, including acceptance of a novel coronavirus vaccine.Design, Setting, ParticipantsA cross-sectional survey was distributed to participants enrolled in a longitudinal cohort study surveilling SARS-CoV-2 infection among 1,093 volunteer sampled University of California, Los Angeles (UCLA) Health System employees. Surveys were completed online between September 24 and October 16, 2020. In total, 609 participants completed this supplemental survey.ResultsWe averaged a 9-statement Likert scale matrix scored from 1 (“strongly disagree”) to 5 (“strongly agree”) and found respondents overwhelmingly confident about vaccine safety (4.47); effectiveness (4.44); importance, self-protection, and community health (4.67). Notably, 47.3% of respondents reported unwillingness to participate in a coronavirus vaccine trial, and most (66.5%) intend to delay vaccination. The odds of reporting intent to delay coronavirus vaccine uptake were 4.15 times higher among nurses, 2.45 times higher among other personnel with patient contact roles, and 2.15 times higher among those without patient contact compared to doctors. Evolving SARS-CoV-2 science (76.0%), current political climate (57.6%), and fast-tracked vaccine development timeline (83.4%) were cited as primary variables impacting HCW decisions to undergo vaccination. Of note, these results were obtained prior to release of Phase III data from companies manufacturing vaccines in the U.S.Conclusions and RelevanceDespite overall confidence in vaccines, a majority of HCW expressed concerns over a novel coronavirus vaccine. A large proportion plan to delay vaccine uptake due to concerns about expedited development, emerging scientific discoveries, and the political climate. Forthcoming vaccination campaigns must address these unique points of coronavirus vaccine hesitancy in order to achieve adequate vaccine coverage.
Characterization of the first cultured free-living representative of Candidatus Izimaplasma uncovers its unique biology
Authors: Zheng Rikuan , Liu Rui , Shan Yeqi , Cai Ruining , Liu Ge , Sun Chaomin 
Published: November 2020

AbstractCandidatus Izimaplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes found in deep-sea methane seeps. Unfortunately, the paucity of marine isolates currently available has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we present a detailed description of the phenotypic traits, genomic data and central metabolisms tested in both laboratorial and deep-sea environments of the novel strain zrk13, which allows for the first time the reconstruction of the metabolic potential and lifestyle of a member of the tentatively defined Candidatus Izimaplasma. On the basis of the description of strain zrk13, the novel species and genus Xianfuyuplasma coldseepsis is proposed. Notably, DNA degradation driven by X. coldseepsis zrk13 was detected in both laboratorial and in situ conditions, strongly indicating it is indeed a key DNA degrader. Moreover, the putative genes determining degradation broadly distribute in the genomes of other Izimaplasma members. Given extracellular DNA is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor, Izimaplasma bacteria are thought to be important contributors to the biogeochemical cycling in the deep ocean.