bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel germline BMPR1A variant (c.72_73delGA) in a Japanese family with hereditary mixed polyposis syndrome
Authors: Miyahara Yosuke , Ishida Hideyuki , Kawabe Koichi , Eto Hiroyuki , Kasai Toyotaka , Ito Tetsuya , Kaneko Kou , Arai Motohiro , Kamae Nao , Momose Shuji , Eguchi Hidetaka , Okazaki Yasushi 
Published: April 2020

Abstract
Hereditary mixed polyposis syndrome (HMPS) is a rare autosomal dominant disorder characterized by a mixture of typical and/or atypical juvenile polyps, adenomas and hyperplastic polyps, resulting in an increased risk of colorectal cancer. In HMPS, four different germline BMPR1A variants from five unrelated families have been reported. This study is the first to report HMPS within a Japanese family. The proband underwent repeated colonoscopic polypectomies over a 5-year period, since the age of 67. Histological examination of these resected polyps revealed adenomas, juvenile-like polyps and hyperplastic changes. Genetic testing was conducted to identify the causative genes for hereditary gastrointestinal cancer syndromes, including BMPR1A. We detected a germline variant, c.72_73delGA, in BMPR1A. The proband’s elder brother, younger sister and nephew have also undergone repeated colonoscopic polypectomies at other clinics. His sister and nephew underwent genetic testing, and the same BMPR1A variant was identified.
Protective Effectiveness of Long-Lasting Permethrin Impregnated Clothing Against Tick Bites in an Endemic Lyme Disease Setting: A Randomized Control Trial Among Outdoor Workers
Authors: Mitchell Cedar , Dyer Megan , Lin Feng-Chang , Bowman Natalie , Mather Thomas , Meshnick Steven 
Published: April 2020

Abstract
Tick-borne diseases are a growing threat to public health in the United States, especially among outdoor workers who experience high occupational exposure to ticks. Long-lasting permethrin-impregnated clothing has demonstrated high initial protection against bites from blacklegged ticks, Ixodes scapularis Say (Acari: Ixodidae), in laboratory settings, and sustained protection against bites from the lone star tick, Amblyomma americanum (L.) (Acari: Ixodidae), in field tests. However, long-lasting permethrin impregnation of clothing has not been field tested among outdoor workers who are frequently exposed to blacklegged ticks. We conducted a 2-yr randomized, placebo-controlled, double-blinded trial among 82 outdoor workers in Rhode Island and southern Massachusetts. Participants in the treatment arm wore factory-impregnated permethrin clothing, and the control group wore sham-treated clothing. Outdoor working hours, tick encounters, and bites were recorded weekly to assess protective effectiveness of long-lasting permethrin-impregnated garments. Factory-impregnated clothing significantly reduced tick bites by 65% in the first study year and by 50% in the second year for a 2-yr protective effect of 58%. No significant difference in other tick bite prevention method utilization occurred between treatment and control groups, and no treatment-related adverse outcomes were reported. Factory permethrin impregnation of clothing is safe and effective for the prevention of tick bites among outdoor workers whose primary exposure is to blacklegged ticks in the northeastern United States.
X-ray variability analysis of a large series of XMM–Newton +NuSTAR observations of NGC 3227
Authors: Lobban A P , Turner T J , Reeves J N , Braito V , Miller L 
Published: April 2020

ABSTRACT
We present a series of X-ray variability results from a long XMM–Newton + NuSTAR campaign on the bright, variable AGN NGC 3227. We present an analysis of the light curves, showing that the source displays typically softer-when-brighter behaviour, although also undergoes significant spectral hardening during one observation which we interpret as due to an occultation event by a cloud of absorbing gas. We spectrally decompose the data and show that the bulk of the variability is continuum-driven and, through rms variability analysis, strongly enhanced in the soft band. We show that the source largely conforms to linear rms-flux behaviour and we compute X-ray power spectra, detecting moderate evidence for a bend in the power spectrum, consistent with existing scaling relations. Additionally, we compute X-ray Fourier time lags using both the XMM–Newton and – through maximum-likelihood methods – NuSTAR data, revealing a strong low-frequency hard lag and evidence for a soft lag at higher frequencies, which we discuss in terms of reverberation models.
Molecular cross-sections for high-resolution spectroscopy of super-Earths, warm Neptunes, and hot Jupiters
Authors: Gandhi Siddharth , Brogi Matteo , Yurchenko Sergei N , Tennyson Jonathan , Coles Phillip A , Webb Rebecca K , Birkby Jayne L , Guilluy Gloria , Hawker George A , Madhusudhan Nikku , Bonomo Aldo S , Sozzetti Alessandro 
Published: April 2020

ABSTRACT
High-resolution spectroscopy (HRS) has been used to detect a number of species in the atmospheres of hot Jupiters. Key to such detections is accurately and precisely modelled spectra for cross-correlation against the R ≳ 20 000 observations. There is a need for the latest generation of opacities which form the basis for high signal-to-noise detections using such spectra. In this study we present and make publicly available cross-sections for six molecular species, H2O, CO, HCN, CH4, NH3, and CO2 using the latest line lists most suitable for low- and high-resolution spectroscopy. We focus on the infrared (0.95–5 μm) and between 500 and 1500 K where these species have strong spectral signatures. We generate these cross-sections on a grid of pressures and temperatures typical for the photospheres of super-Earth, warm Neptunes, and hot Jupiters using the latest H2 and He pressure broadening. We highlight the most prominent infrared spectral features by modelling three representative exoplanets, GJ 1214 b, GJ 3470 b, and HD 189733 b, which encompass a wide range in temperature, mass, and radii. In addition, we verify the line lists for H2O, CO, and HCN with previous high-resolution observations of hot Jupiters. However, we are unable to detect CH4 with our new cross-sections from HRS observations of HD 102195 b. These high-accuracy opacities are critical for atmospheric detections with HRS and will be continually updated as new data become available.
Sustained research fund and dedicated research center to prepare for the next pandemic
Authors: Jia Hongpeng , Wu Min 
Published: April 2020

AbstractThe current COVID-19 pandemic caused by the SARS-CoV-2 virus is imposing a great threat to human lives and international panic the like of which has not been seen since WWII, resulting in financial crisis, disturbance to daily life, transportation shutdown, industry disruption, and country/city lockdown in every corner of the globe. The inability to effectively contain the virus indicates that our investment and attention to research, prevention, and development of treatment for this type of deadly virus are insufficient, considering that it has been 18 years since outbreak of the "brother" coronavirus, SARS-CoV. The biggest lesson learned from acrimonious past experiences is that humans quickly forget and do not continue to support related research when a pandemic has passed. This is a wake-up call for governments, industry, and private foundations to work together and to take extraordinary measures to sustain research support and establish comprehensive research centers. Only this level of response may give us hope to prepare for the future and adequately deal with the next potential pandemic caused by emerging devastating viral infections.
Mapping the Burden of COVID-19 in the United States
Authors: Miller Ian F. , Becker Alexander D. , Grenfell Bryan T. , Metcalf C. Jessica E. 
Published: April 2020

AbstractAs of April 5th 2020, SARS-CoV-2 has resulted in over 273,000 confirmed infections in the United States of America. Incidence continues to rise. As the epidemic threatens to overwhelm health care systems, identifying regions where the expected disease burden is likely to be high relative to the rest of the country is critical for enabling prudent and effective distribution of emergency resources. Across all global regions affected by the pandemic, an elevated risk of severe outcomes has consistently been observed in older age groups. Using age-specific mortality patterns in tandem with demographic data, we map a projection of the cumulative burden of COVID-19 and the associated cumulative burden on the healthcare system at the county-scale in the United States for a scenario in which 20% of the population of each county acquires infection. We identify regions that may be particularly impacted relative to the rest of the country, and observe a general trend that per capita disease burden and relative healthcare system demand may be highest away from major population centers.
A streamlined approach to rapidly detect SARS-CoV-2 infection, avoiding RNA purification
Authors: Marzinotto Stefania , Mio Catia , Cifù Adriana , Verardo Roberto , Pipan Corrado , Schneider Claudio , Curcio Francesco 
Published: April 2020

AbstractIn the current pandemic, the presence of SARS-CoV-2 RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients’ infectiveness. Recently, the demand for laboratory reagents has greatly increased; in particular, there is a worldwide shortage of RNA extraction kits. Here, we describe a fast, simple and inexpensive method for the detection of SARS CoV-2 RNA, which includes a pretreatment with Proteinase K and a heating-cooling cycle before the amplification. This method bypasses the RNA extraction step; it leads to a higher amount of available viral RNA compared to the automated extraction methods, and generates the same profile in the subsequent amplification phase.
A modification to the Maquet Flow-i anaesthesia machine for ICU ventilation
Authors: Robinson Andrew J. , London William , Kotan Laszlo , Downing Warwick 
Published: April 2020

AbstractThe authors present an easily manufactured modification of Getinge Group’s Maquet Flow-i anaesthesia machine that gives it potential to be used long-term as an Intensive Care ventilator for emergency circumstances. There are some 7000 such machines in use worldwide, which could assist in increasing ICU ventilated bed capacity in a number of nations. The authors believe this modification has potential as a solution to increasing ventilator numbers for the COVID-19 pandemic, in hospitals where the Flow-i is underutilised for its designed purpose during this emergency. The technical drawing files are downloadable on the GrabCAD website and are Creative Commons (CC-BY 4.0) licensed to allow local manufacture of the modification. We welcome other Flow-i users and engineers to join us in troubleshooting this project on the associated GrabCAD discussion group during this ‘pre-print’ phase of research.
Toward respiratory support of critically ill COVID-19 patients using repurposed kidney hollow fiber membrane dialysers to oxygenate the blood
Authors: Rubin David M. , Stacey Neil , Matambo Tonderayi , Vale Claudia Do , Sussman Martin J. , Snyman Tracy , Mer Mervyn , Hildebrandt Diane 
Published: April 2020

AbstractThe COVID-19 pandemic has highlighted resource constraints in respiratory support. The oxygen transfer characteristics of a hollow fiber membrane dialyser were investigated with a view to repurposing the device as a low-cost, readily available blood oxygenator. Oxygen transfer in a low-flux hollow fiber dialyser with a polysulfone membrane was studied by passing first water and then blood through the dialyser in counter-current to high-purity oxygen. Oxygen transfer rates of about 15% of the nominal 250 ml(STP)/min of a typical adult oxygen consumption rate were achieved for blood flow rates of 500ml/min. Using two such dialysis devices in parallel could provide up to 30% of the nominal oxygen consumption. Specific hollow fiber dialysis devices operating with suitable pumps in a veno-venous access configuration, could provide a cost-effective and readily available supplementation of respiratory support in the face of severe resource constraints.
Early Stage Prediction of US County Vulnerability to the COVID-19 Pandemic
Authors: Mehta Mihir , Julaiti Juxihong , Griffin Paul , Kumara Soundar 
Published: April 2020

AbstractImportanceThe rapid spread of COVID-19 means that government and health services providers have little time to plan and design effective response policies. It is therefore important to rapidly provide accurate predictions of how vulnerable geographic regions such as counties are to the spread.ObjectiveDeveloping county level prediction around near future disease movement for COVID-19 occurrences using publicly available data.DesignOriginal Investigation; Decision Analytical Model Study for County Level COVID-19 occurrences using data from March 14-31, 2020.SettingDisease spread prediction for US counties.ParticipantsAll US county level granularity based on data fused from multiple publicly available sources inclusive of health statistics, demographics, and geographical features.Exposure(s) (for observational studies)Daily county level reported COVID-19 occurrences from March 14-31, 2020.Main Outcome(s) and Measure(s)We developed a 3-stage model to quantify, firstly the probability of COVID-19 occurrence for unaffected counties using XGBoost classifier and secondly, the number of potential occurrences of a county via XGBoost regression. Thirdly, these results are combined to compute the county level risk. This risk is then used as an estimated after-five-day-vulnerability of the county.ResultsUsing data from March 14-31, 2020, the model shows a sensitivity over 71.5% and specificity over 94%.Conclusions and RelevanceWe found that population, population density, percentage of people aged 70 or greater and prevalence of comorbidities play an important role in predicting COVID-19 occurrences. We found a positive association between affected and urban counties as well as less vulnerable and rural counties. The developed model can be used for identification of vulnerable counties and potential data discrepancies. Limited testing facilities and delayed results introduces significant variation in reported cases and produces a bias in the model.Trial RegistrationNot ApplicableKey PointsQuestionWhat are key factors that define the vulnerability of counties in the US to cases of the COVID-19 virus?FindingsIn this epidemiological study based on publicly available data, we develop a model that predicts vulnerability to COVID-19 for each US county in terms of likelihood of going from no documented cases to at least one case within five days and in terms of number of occurrences of the virus.MeaningPredicting county vulnerability to COVID-19 can assist health organizations to better plan for resource and workforce needs.
Noisy Pooled PCR for Virus Testing
Authors: Zhu Junan , Rivera Kristina , Baron Dror 
Published: April 2020

AbstractFast testing can help mitigate the coronavirus disease 2019 (COVID-19) pandemic. Despite their accuracy for single sample analysis, infectious diseases diagnostic tools, like RT-PCR, require substantial resources to test large populations. We develop a scalable approach for determining the viral status of pooled patient samples. Our approach converts group testing to a linear inverse problem, where false positives and negatives are interpreted as generated by a noisy communication channel, and a message passing algorithm estimates the illness status of patients. Numerical results reveal that our approach estimates patient illness using fewer pooled measurements than existing noisy group testing algorithms. Our approach can easily be extended to various applications, including where false negatives must be minimized. Finally, in a Utopian world we would have collaborated with RT-PCR experts; it is difficult to form such connections during a pandemic.We welcome new collaborators to reach out and help improve this work!
Accelerometry-assessed sleep duration and timing in late childhood and adolescence in Scottish schoolchildren: a feasibility study
Authors: Lyall Laura M. , Sangha Natasha , Wyse Cathy , Hindle Elaine , Haughton Dawn , Campbell Kate , Brown Judith , Moore Laurence , Simpson Sharon A. , Inchley Joanna C. , Smith Daniel J. 
Published: April 2020

AbstractChildren and adolescents commonly suffer from sleep and circadian rhythm disturbances, which may contribute to poorer mental health and wellbeing during this critical developmental phase. Many studies however rely on self-reported sleep measures. This study assessed whether accelerometry data collection was feasible within the school setting as a method for investigating the extent of sleep and circadian disruption, and associations with subjective wellbeing, in Scotland. Fourteen days of wrist-worn accelerometry data were collected from 69 pupils, aged 10-14 years. Objective measures of sleep timing, sleep duration and circadian rest-activity patterns were derived. Questionnaires assessed subjective sleep timing, depressive symptoms, and experiences of wearing the accelerometer. Pupils slept on average less than 8 hours per night, failing to meet standard age-specific recommendations. Sleep timing was later and duration longer on weekends compared to weekdays (B = 0.87, 95% confidence interval (CI) 0.70, 1.04; B = 0.49, 95% CI 0.29, 0.69), indicating social jetlag. Lower daytime activity was correlated with higher depressive symptoms (r = -0.84, p = 0.008). Compared to primary school pupils, secondary pupils had shorter sleep window duration and lower circadian relative amplitude. Over half of participants reported some discomfort/inconvenience wearing the accelerometer. These data highlight that inadequate sleep is prevalent in this sample of schoolchildren. Future, larger scale investigations will examine in more detail the associations between sleep, circadian function and physical activity with mental health and wellbeing.
Identification and Estimation of Undetected COVID-19 Cases Using Testing Data from Iceland
Authors: Aspelund Karl M. , Droste Michael , Stock James H. , Walker Christopher D. 
Published: April 2020

AbstractIn the early stages of the COVID-19 pandemic, international testing efforts tended to target individuals whose symptoms and/or jobs placed them at a high presumed risk of infection. Testing regimes of this sort potentially result in a high proportion of cases going undetected. Quantifying this parameter, which we refer to as the undetected rate, is an important contribution to the analysis of the spread of the SARS-CoV-2 virus. We show that partial identification techniques can credibly deal with the data problems that common COVID-19 testing programs induce (i.e. excluding quarantined individuals from testing and low participation in random screening programs). We use public data from two Icelandic testing regimes during the first month of the outbreak and estimate an identified interval for the undetected rate. Our main approach estimates that the undetected rate was between 89% and 93% before the medical system broadened its eligibility criteria and between 80% and 90% after.
Association Between BCG Policy is Significantly Confounded by Age and is Unlikely to Alter Infection or Mortality Rates
Authors: Kirov Stefan 
Published: April 2020

AbstractRecently a number of publications looked at the association between COVID-19 morbidity and mortality on one hand and countries’ policies with respect to BCG vaccination on the other. This connection arises from differences in the rates of infection in countries where BCG vaccination is mandatory compared to countries where mandatory vaccination no longer exists or was never implemented in the first place. In at least 2 preprint publications the authors expressed the view that the “known immunological benefits” of BCG vaccination may be behind the biological mechanism of such observation.One study accounted for different income levels in different groups. Another study did not attempted to do so, instead exploring the differences between countries where a booster shot is given vs others where no such practice exists (finding no connection).Both of these studies did not explore other potential confounding factors. Meanwhile the press has focused on these headlines and pushed the narrative that BCG vaccination is causally linked to infection and mortality rates. This poses a serious challenge, demonstrated by the recently initiated clinical trials on BCG vaccination within the COVID19 context.This study shows that population age is a very significant confounding factor that explains the rates of infections much better and has a solid biology mechanism which explains this correlation. It suggests that BCG vaccination may have little or no causal link to infection rates and advises that any follow up studies should control for several confounding factors, such as population age, ethnicity, rates of certain chronic diseases, time from community spread start date, major public policy decisions and income levels.
Association of County-Level Socioeconomic and Political Characteristics with Engagement in Social Distancing for COVID-19
Authors: Kavanagh Nolan M. , Goel Rishi R. , Venkataramani Atheendar S. 
Published: April 2020

AbstractThe U.S. is the epicenter of the coronavirus disease 2019 (COVID-19) pandemic. In response, governments have implemented measures to slow transmission through “social distancing.” However, the practice of social distancing may depend on prevailing socioeconomic conditions and beliefs. Using 15–17 million anonymized cell phone records, we find that lower per capita income and greater Republican orientation were associated with significantly reduced social distancing among U.S. counties. These associations persisted after adjusting for county-level sociodemographic and labor market characteristics as well as state fixed effects. These results may help policymakers and health professionals identify communities that are most vulnerable to transmission and direct resources and communications accordingly.
Gaussian Statistics and Data-Assimilated Model of Mortality due to COVID-19: China, USA, Italy, Spain, UK, Iran, and the World Total
Authors: Lee T.-W. , Park J.E. , Hung David 
Published: April 2020

ABSTRACTCovid-19 is characterized by rapid transmission and severe symptoms, leading to deaths in some cases (ranging from 1.5 to 12% of the affected, depending on the country). We identify the Gaussian nature of mortality due to covid-19, as shown in China where it appears to have run its course (during the first sweep of the pandemic at least) and other coutnries, and also in Imperial College modeling. Gaussian distribution involves three parameters, the height, peak location and the width, and the streaming data can be used to infer function value, slope and inflection location as a minimum set of constraints to estimate the subsequent trajectories. Thus, we apply the Gaussian function template as the basis for a data-assimilated model of covid-19 trajectories, first to USA, United Kingdom (UK), Iran and the world total in this study. As more data become available, the Gaussian trajectories are updated, for other nations and also for state-by-state projections in USA.