bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Risk Prediction and Clinical Guidance System for Evaluating Patients with Recurrent Infections
Authors: Rider Nicholas L. , Cahill Gina , Motazedi Tina , Wei Lei , Kurian Ashok , Noroski Lenora M. , Seeborg Filiz O. , Chinn Ivan K. , Roberts Kirk 
Published: June 2020

AbstractBackgroundPrimary immunodeficiency diseases represent an expanding set of heterogeneous conditions which are difficult to recognize clinically. Diagnostic rates outside of the newborn period have not changed appreciably. This concern underscores a need for novel methods of disease detection.ObjectiveWe built an artificial intelligence model to provide real-time risk assessment about primary immunodeficiency and to facilitate prescriptive analytics for initiating the most appropriate diagnostic work up. Our goal is to improve diagnostic rates for primary immunodeficiency and shorten time to diagnosis.MethodsWe extracted data from the Texas Children’s Hospital electronic health record on a large population of primary immunodeficiency patients (n = 1762) and age-matched set of controls (n = 1698). From the cohorts, clinically relevant prior probabilities were calculated enabling construction of a Bayesian network probabilistic model. Our model was constructed with clinical-immunology domain expertise, trained on a balanced cohort of 100 cases-controls and validated on an unseen balanced cohort of 150 cases-controls. Performance was measured by area under the receiver operator characteristic curve (AUROC).ResultsOur Bayesian network was accurate in classifying immunodeficiency patients from controls (AUROC = 0.945; p<0.0001) at a risk threshold of ≥6%. Additionally, the model was 89% accurate for categorizing validation cohort members into appropriate International Union of Immunological Societies diagnostic categories.ConclusionArtificial intelligence methods can classify risk for primary immunodeficiency and guide management. Our Bayesian network enables highly accurate, objective decision making about risk and guides the user towards the appropriate diagnostic evaluation for patients with recurrent infections.
Heterogeneity in risk, testing and outcome of COVID-19 across outbreak settings in the Greater Toronto Area, Canada: an observational study
Authors: Wang Linwei , Ma Huiting , Yiu Kristy C.Y. , Calzavara Andrew , Landsman David , Luong Linh , Chan Adrienne K. , Kustra Rafal , Kwong Jeffrey C , Boily Marie-Claude , Hwang Stephen , Straus Sharon , Baral Stefan D , Mishra Sharmistha 
Published: June 2020

AbstractBackgroundWe compared the risk of, testing for, and death following COVID-19 infection across three settings (long-term care homes (LTCH), shelters, the rest of the population) in the Greater Toronto Area (GTA), Canada.MethodsWe sourced person-level data from COVID-19 surveillance and reporting systems in Ontario, and examined settings with population-specific denominators (LTCH residents, shelters, and the rest of the population). We calculated cumulatively, the diagnosed cases per capita, proportion tested for COVID-19, daily and cumulative positivity, and case fatality proportion. We estimated the age- and sex-adjusted relative rate ratios for test positivity and case fatality using quasi-Poisson regression.ResultsBetween 01/23/2020-05/25/2020, we observed a shift in the proportion of cases: from travel-related and into LTCH and shelters. Cumulatively, compared to the rest of the population, the number of diagnosed cases per 100,000 was 59-fold and 18-fold higher among LTCH and shelter residents, respectively. By 05/25/2020, 77.2% of LTCH residents compared to 2.4% of the rest of the population had been tested. After adjusting for age and sex, LTCH residents were 2.5 times (95% confidence interval (CI): 2.3-2.8) more likely to test positive. Case fatality was 26.3% (915/3485), 0.7% (3/402), and 3.6% (506/14133) among LTCH residents, shelter population, and others in the GTA, respectively. After adjusting for age and sex, case fatality was 1.4-fold (95%CI: 1.1-1.9) higher among LTCH residents than the rest of the population.InterpretationHeterogeneity across micro-epidemics among specific populations in specific settings may reflect underlying heterogeneity in transmission risks, necessitating setting-specific COVID-19 prevention and mitigation strategies.
Dynamics of psychological responses to Covid-19 in India: A longitudinal study
Authors: Gopal Anvita , Sharma Anupam Joya , Subramanyam Malavika Ambale 
Published: June 2020

AbstractTo curb the spread of the novel coronavirus, India announced a nationwide lockdown on 24th March 2020 for 21 days, later extended for a longer time. This long period of lockdown greatly disrupted routine life and likely affecting citizens’ psychological well-being. The psychological toll of the pandemic on Indians is documented. However, no study has assessed whether the psychological toll changed over time due to repeated extensions of the lockdown. We followed up 159 Indian adults during the first two months of the lockdown to assess any change in their anxiety, stress, and depressive symptoms. Multilevel linear regression models of repeated observations nested within individuals, adjusted for socio-demographic covariates, showed that anxiety (β=0.81, CI: 0.03, 1.60), stress (β=0.51, CI: 0.32, 0.70), and depressive symptoms (β=0.37, CI: 0.13, 0.60) increased over time during the lockdown. This increase was higher among women than men independent of covariates. Individual resilience was negatively associated with the psychological outcomes. This suggests that the state needs to address the current mental health impacts of a long-drawn out lockdown and its long-term sequelae. Disproportionate burden on women needs immediate attention. Sustainable change requires addressing the root causes driving the gender inequalities in psychological distress during such crises.
PSEUDOMONAS AERUGINOSAVOLATILOME CHARACTERISTICS AND ADAPTATIONS IN CHRONIC CYSTIC FIBROSIS LUNG INFECTIONS
Authors: Davis Trenton J. , Karanjia Ava V. , Bhebhe Charity N. , West Sarah B. , Richardson Matthew , Bean Heather D. 
Published: June 2020

ABSTRACTPseudomonas aeruginosachronic lung infections in individuals with cystic fibrosis (CF) significantly reduce quality of life and increase morbidity and mortality. Tracking these infections is critical for monitoring patient health and informing treatments. We are working toward the development of novel breath-based biomarkers to track chronicP. aeruginosalung infectionsin situ. Using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS), we characterized thein vitrovolatile metabolomes (or volatilomes) of 81P. aeruginosaisolates collected from 17 CF patients over at least a five-year period of their chronic lung infections. We detected 539 volatiles produced by theP. aeruginosaisolates, 69 of which were core volatiles that were highly conserved. We found that each early infection isolate has a unique volatilome, and as infection progresses, the volatilomes of isolates from the same patient become increasingly dissimilar, to the point that these intra-patient isolates are no more similar to one another than to isolates from other patients. We observed that the size and chemical diversity ofP. aeruginosavolatilomes do not change over the course of chronic infections; however, the relative abundances of core hydrocarbons, alcohols, and aldehydes do change, and are correlated to changes in phenotypes associated with chronic infections. This study indicates that it may be feasible to trackP. aeruginosachronic lung infections by measuring changes to the infection volatilome, and lays the groundwork for exploring the translatability of this approach to direct measurement using patient breath.IMPORTANCEPseudomonas aeruginosais a leading cause of chronic lung infections in cystic fibrosis (CF), and are correlated with lung function declines. Significant clinical efforts are, therefore, aimed at detecting infections and tracking them for phenotypic changes, such as mucoidy and antibiotic resistance. Both the detection and tracking of lung infections relies on sputum cultures, but due to improvements in CF therapies, sputum production is declining though risks for lung infections persist. Therefore, we are working toward the development of breath-based diagnostics for CF lung infections. In this study we characterized of the volatile metabolomes of 81P. aeruginosaclinical isolates collected from 17 CF patients over a duration of at least five years of a chronic lung infection. We found that the volatilome ofP. aeruginosaadapts over time, and correlates to infection phenotype changes, suggesting it may be possible to track chronic CF lung infections with a breath test.
Ecological Specialization and Diversification in Birds
Authors: Crouch Nicholas M. A. , Ricklefs Robert E. , Igić Boris 
Published: June 2020

AbstractEcological specialization is widely thought to influence patterns of species richness by affecting rates at which species multiply and perish. Quantifying specialization is challenging, and using only one or a small number of ecological axes could bias estimates of overall specialization. Here, we calculate an index of specialization, based on seven measured traits, and estimate its effect on speciation and extinction rates in a large clade of birds. We find that speciation rate is independent of specialization, suggesting independence of local ecology and the geographic distributions of populations that promote allopatric species formation. Although some analyses suggest that more specialized species have higher extinction rates, leading to negative net diversification, this relationship is not consistently identified across our analyses. Our results suggest that specialization may drive diversification dynamics only on local scales or in specific clades, but is not generally responsible for macroevolutionary disparity in lineage diversification rates.
Auditory aversion in absolute pitch possessors
Authors: Rogenmoser Lars , Li H. Charles , Jäncke Lutz , Schlaug Gottfried 
Published: June 2020

ABSTRACTAbsolute pitch (AP) refers to the ability of identifying the pitch of a given tone without reliance on any reference pitch. The downside of possessing AP may be the experience of disturbance when exposed to out-of-tune tones. Here, we investigated this so-far unexplored phenomenon in AP, which we refer to as auditory aversion. Electroencephalography (EEG) was recorded in a sample of AP possessors and matched control musicians without AP while letting them perform a task underlying a so-called affective priming paradigm: Participants judged valenced pictures preceded by musical primes as quickly and accurately as possible. The primes were bimodal, presented as tones in combination with visual notations that either matched or mismatched the actually presented tone. Regardless of the prime condition, AP possessors performed more poorly in judging pleasant pictures and their EEG revealed later peaks at around 200 ms (P200) after prime onset. Their performance dropped when responding to pleasant pictures preceded by incongruent primes, especially when mistuned by one semitone. This interference was also reflected in an EEG deflection at around 400 ms (N400) after picture onset, preceding the behavior responses. These findings suggest that AP possessors process mistuned musical stimuli and pleasant pictures as affectively unrelated with each other, supporting an aversion towards out-of-tune tones in AP possessors. The longer prime-related P200 latencies exhibited by AP possessors suggest a delay in integrating musical stimuli, underlying an altered affinity towards pitch-label associations.
The effect of heavy metals on thiocyanate biodegradation by an autotrophic microbial consortium enriched from mine tailings
Authors: Shafiei Farhad , Watts Mathew P. , Pajank Lukas , Moreau John W. 
Published: June 2020

AbstractBioremediation systems represent an environmentally sustainable approach to degrading industrially-generated thiocyanate (SCN-), with low energy demand and operational costs, and high efficiency and substrate specificity. However, heavy metals present in mine tailings effluent may hamper process efficiency by poisoning thiocyanate-degrading microbial consortia. Here we experimentally tested the tolerance of an autotrophic SCN--degrading bacterial consortium enriched from gold mine tailings for Zn, Cu, Ni, Cr, and As. All of the selected metals inhibited SCN-biodegradation to different extents, depending on concentration. At pH of 7.8 and 30°C, complete inhibition of SCN-biodegradation by Zn, Cu, Ni, and Cr occurred at 20, 5, 10, and 6 mg L-1, respectively. Lower concentrations of these metals decreased the rate of SCN-biodegradation, with relatively long lag times. Interestingly, the microbial consortium tolerated As even at 500 mg L-1, although both the rate and extent of SCN-biodegradation were affected. This study highlights the importance of considering metal co-contamination in bioreactor design and operation for SCN-bioremediation at mine sites.Key pointsBoth the efficiency and rate of SCN-biodegradation were inhibited by heavy metals, to different degrees depending on type and concentration of metalThe autotrophic microbial consortium was capable of tolerating high levels of As
Specific ZNF274 binding interference at SNORD116 activates the maternal transcripts in Prader-Willi syndrome neurons
Authors: Langouët Maéva , Gorka Dea , Orniacki Clarisse , Dupont-Thibert Clémence M , Chung Michael S , Glatt-Deeley Heather R , Germain Noelle , Crandall Leann J , Cotney Justin L , Stoddard Christopher E , Lalande Marc , Chamberlain Stormy J 
Published: June 2020

AbstractPrader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay, and hyperphagia/obesity. This disorder is caused by the absence of paternally-expressed gene products from chromosome 15q11-q13. We previously demonstrated that knocking out ZNF274, a KRAB-domain zinc finger protein capable of recruiting epigenetic machinery to deposit the H3K9me3 repressive histone modification, can activate expression from the normally silent maternal allele of SNORD116 in neurons derived from PWS iPSCs. However, ZNF274 has many other targets in the genome in addition to SNORD116. Depleting ZNF274 will surely affect the expression of other important genes and disrupt other pathways. Here we used CRISPR/Cas9 to delete ZNF274 binding sites at the SNORD116 locus to determine whether activation of the maternal copy of SNORD116 could be achieved without altering ZNF274 protein levels. We obtained similar activation of gene expression from the normally silenced maternal allele in neurons derived from PWS iPSCs, compared to ZNF274 knockout, demonstrating that ZNF274 is directly involved in the repression of SNORD116. These results suggest that interfering with ZNF274 binding at the maternal SNORD116 locus is a potential therapeutic strategy for PWS.
Receptor utilization of angiotensin converting enzyme 2 (ACE2) indicates a narrower host range of SARS-CoV-2 than that of SARS-CoV
Authors: Qiu Ye , Wang Qiong , Li Jin-Yan , Liao Ce-Heng , Zhou Zhi-Jian , Ge Xing-Yi 
Published: June 2020

AbstractCoronavirus pandemics have become a huge threat to the public health worldwide in the recent decades. Typically, SARS-CoV caused SARS pandemic in 2003 and SARS-CoV-2 caused the COVID-19 pandemic recently. Both viruses have been reported to originate from bats. Thus, direct or indirect interspecies transmission from bats to humans is required for the viruses to cause pandemics. Receptor utilization is a key factor determining the host range of viruses which is critical to the interspecies transmission. Angiotensin converting enzyme 2 (ACE2) is the receptor of both SARS-CoV and SARS-CoV-2, but only ACE2s of certain animals can be utilized by the viruses. Here, we employed pseudovirus cell-entry assay to evaluate the receptor-utilizing capability of ACE2s of 20 animals by the two viruses and found that SARS-CoV-2 utilized less ACE2s than SARS-CoV, indicating a narrower host range of SARS-CoV-2. Meanwhile, pangolin CoV, another SARS-related coronavirus highly homologous to SARS-CoV-2 in its genome, yet showed similar ACE2 utilization profile with SARS-CoV rather than SARS-CoV-2. To clarify the mechanism underlying the receptor utilization, we compared the amino acid sequences of the 20 ACE2s and found 5 amino acid residues potentially critical for ACE2 utilization, including the N-terminal 20thand 42ndamino acids that may determine the different receptor utilization of SARS-CoV, SARS-CoV-2 and pangolin CoV. Our studies promote the understanding of receptor utilization of pandemic coronaviruses, potentially contributing to the virus tracing, intermediate host screening and epidemic prevention for pathogenic coronaviruses.
Reconciling Kinetic and Equilibrium Models of Bacterial Transcription
Authors: Morrison Muir , Razo-Mejia Manuel , Phillips Rob 
Published: June 2020

AbstractThe study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including fluorescence and sequencing readouts have raised the bar for what it means to quantitatively understand transcriptional regulation. In particular our understanding of the simplest genetic circuit is sufficiently refined both experimentally and theoretically that it has become possible to carefully discriminate between different conceptual pictures of how this regulatory system works. This regulatory motif, originally posited by Jacob and Monod in the 1960s, consists of a single transcriptional repressor binding to a promoter site and inhibiting transcription. In this paper, we show how seven distinct models of this so-called simple-repression motif, based both on equilibrium and kinetic thinking, can be used to derive the predicted levels of gene expression and shed light on the often surprising past success of the equilibrium models. These different models are then invoked to confront a variety of different data on mean, variance and full gene expression distributions, illustrating the extent to which such models can and cannot be distinguished, and suggesting a two-state model with a distribution of burst sizes as the most potent of the seven for describing the simple-repression motif.
Global research trend in the treatment of the new Coronavirus diseases (COVID-19): bibliometric analysis
Authors: Mbogning Fonkou Maxime Descartes , Yacouba Abdourahamane 
Published: June 2020

AbstractThe Coronavirus 2019 (COVID-19) pandemic has caused worldwide concern and has become a major medical problem. Vaccines and therapeutics are important interventions for the management of this outbreak. This study aims to used bibliometric methods to identify research trends in the domain of therapeutics and vaccines to cure patients with COVID-19 since the beginning of the pandemic.The Web of Science Core Collection database was retrieved for articles on therapeutic approaches to coronavirus disease management published between January 1, 2020 and May 20, 2020. Identified and analyzed the data included title, corresponding author, language, publication time, publication type, research focus.A total of 1569 articles on coronavirus therapeutic means from 84 countries were published in 620 journals. We note the remarkable progressive increase in the number of publications related to research on therapies and vaccines for COVID-19. The United States provided the largest number of articles (405), followed by China (364). Journal of Medical Virology published most of them (n = 40). 1005 (64.05%) were articles, 286 (18.23%) were letters, 230 (14.66%) were reviews. The terms “COVID- 19” or “SARS-CoV-2” or “Coronavirus” or “hydroxychloroquine” or “chloroquine” or “2019-nCOV” or “ACE2” or “treatment” or “remdesivir” or “pneumonia” were most frequently used, as shown in the density visualization map. A network analysis based on keyword co-occurrence revealed five distinct types of studies: clinical, biological, epidemiological, pandemic management, and therapeutics (vaccines and treatments).COVID-19 is a major disease that has had an impact on international public health at the global level. Several avenues for treatment and vaccines have been explored. Most of them focus on older drugs used to treat other diseases that have been effective for other types of coronaviruses. There is a discrepancy in the results obtained from the studies of the drugs included in this study. Randomized clinical trials are needed to evaluate older drugs and develop new treatment options.
Nearly Perfect Forecasting of the Total COVID-19 Cases in India: A Numerical Approach
Authors: Baruah Hemanta K. 
Published: June 2020

AbstractThere are standard computational and statistical techniques of forecasting the spread pattern of a pandemic. In this article, we are going to show how close the forecasts can be if we use a simple numerical approach that can be worked out using just a scientific calculator. Using a few recent data, short term forecasts can be found very easily. In this numerical technique, we need not make any assumptions, unlike in the cases of using computational and statistical methods. Such numerical forecasts would be nearly perfect unless the pandemic suddenly starts retarding during the period of the forecasts naturally or otherwise.
Delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults
Authors: Zazzara Maria Beatrice , Penfold Rose S. , Roberts Amy L. , Lee Karla A. , Dooley Hannah , Sudre Carole H. , Welch Carly , Bowyer Ruth C. E. , Visconti Alessia , Mangino Massimo , Freydin Maxim B. , El-Sayed Moustafa Julia S. , Small Kerrin , Murray Benjamin , Modat Marc , Wolf Jonathan , Ourselin Sebastien , Martin Finbarr C. , Steves Claire J. , Lochlainn Mary Ni 
Published: June 2020

AbstractBackgroundFrailty, increased vulnerability to physiological stressors, is associated with adverse outcomes. COVID-19 exhibits a more severe disease course in older, co-morbid adults. Awareness of atypical presentations is critical to facilitate early identification.ObjectiveTo assess how frailty affects presenting COVID-19 symptoms in older adults.DesignObservational cohort study of hospitalised older patients and self-report data for community-based older adults.SettingAdmissions to St Thomas’ Hospital, London with laboratory-confirmed COVID-19. Community-based data for 535 older adults using the COVID Symptom Study mobile application.SubjectsHospital cohort:patients aged 65 and over (n=322); unscheduled hospital admission between March 1st, 2020-May 5th, 2020; COVID-19 confirmed by RT-PCR of nasopharyngeal swab.Community-based cohort:participants aged 65 and over enrolled in the COVID Symptom Study (n=535); reported test-positive for COVID-19 from March 24th (application launch)-May 8th, 2020.MethodsMultivariate logistic regression analysis performed on age-matched samples from hospital and community-based cohorts to ascertain association of frailty with symptoms of confirmed COVID-19.ResultsHospital cohort:significantly higher prevalence of delirium in the frail sample, with no difference in fever or cough.Community-based cohort:significantly higher prevalence of probable delirium in frailer, older adults, and fatigue and shortness of breath.ConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.