bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of full-genome analysis to diagnose rare monogenic disorders
Authors: Shieh Joseph T. , Penon-Portmann Monica , Wong Karen H. Y. , Levy-Sakin Michal , Verghese Michelle , Slavotinek Anne , Gallagher Renata C. , Mendelsohn Bryce A. , Tenney Jessica , Beleford Daniah , Perry Hazel , Chow Stephen K. , Sharo Andrew G. , Brenner Steven E. , Qi Zhongxia , Yu Jingwei , Klein Ophir D. , Martin David , Kwok Pui-Yan , Boffelli Dario 
Published: September 2021

AbstractCurrent genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.
Longevity leap: mind the healthspan gap
Authors: Garmany Armin , Yamada Satsuki , Terzic Andre 
Published: September 2021

AbstractLife expectancy has increased by three decades since the mid-twentieth century. Parallel healthspan expansion has however not followed, largely impeded by the pandemic of chronic diseases afflicting a growing older population. The lag in quality of life is a recognized challenge that calls for prioritization of disease-free longevity. Contemporary communal, clinical and research trends aspiring to extend the health horizon are here outlined in the context of an evolving epidemiology. A shared action integrating public and societal endeavors with emerging interventions that target age-related multimorbidity and frailty is needed. A multidimensional buildout of a curative perspective, boosted by modern anti-senescent and regenerative technology with augmented decision making, would require dedicated resources and cost-effective validation to responsibly bridge the healthspan-lifespan gap for a future of equitable global wellbeing.
Japanese encephalitis virus live attenuated vaccine strains display altered immunogenicity, virulence and genetic diversity
Authors: Davis Emily H. , Beck Andrew S. , Li Li , White Mellodee M. , Greenberg Marianne Banks , Thompson Jill K. , Widen Steven G. , Barrett Alan D. T. , Bourne Nigel 
Published: September 2021

AbstractJapanese encephalitis virus (JEV) is the etiological agent of Japanese encephalitis (JE). The most commonly used vaccine used to prevent JE is the live-attenuated strain SA14-14-2, which was generated by serial passage of the wild-type (WT) JEV strain SA14. Two other vaccine candidates, SA14-5-3 and SA14-2-8 were derived from SA14. Both were shown to be attenuated but lacked sufficient immunogenicity to be considered effective vaccines. To better contrast the SA14-14-2 vaccine with its less-immunogenic counterparts, genetic diversity, ribavirin sensitivity, mouse virulence and mouse immunogenicity of the three vaccines were investigated. Next generation sequencing demonstrated that SA14-14-2 was significantly more diverse than both SA14-5-3 and SA14-2-8, and was slightly less diverse than WT SA14. Notably, WT SA14 had unpredictable levels of diversity across its genome whereas SA14-14-2 is highly diverse, but genetic diversity is not random, rather the virus only tolerates variability at certain residues. Using Ribavirin sensitivity in vitro, it was found that SA14-14-2 has a lower fidelity replication complex compared to SA14-5-3 and SA14-2-8. Mouse virulence studies showed that SA14-2-8 was the most virulent of the three vaccine strains while SA14-14-2 had the most favorable combination of safety (virulence) and immunogenicity for all vaccines tested. SA14-14-2 contains genetic diversity and sensitivity to the antiviral Ribavirin similar to WT parent SA14, and this genetic diversity likely explains the (1) differences in genomic sequences reported for SA14-14-2 and (2) the encoding of major attenuation determinants by the viral E protein.
Paracetamol use during pregnancy — a call for precautionary action
Authors: Bauer Ann Z. , Swan Shanna H. , Kriebel David , Liew Zeyan , Taylor Hugh S. , Bornehag Carl-Gustaf , Andrade Anderson M. , Olsen Jørn , Jensen Rigmor H. , Mitchell Rod T. , Skakkebaek Niels E. , Jégou Bernard , Kristensen David M. 
Published: September 2021

AbstractParacetamol (N-acetyl-p-aminophenol (APAP), otherwise known as acetaminophen) is the active ingredient in more than 600 medications used to relieve mild to moderate pain and reduce fever. APAP is widely used by pregnant women as governmental agencies, including the FDA and EMA, have long considered APAP appropriate for use during pregnancy when used as directed. However, increasing experimental and epidemiological research suggests that prenatal exposure to APAP might alter fetal development, which could increase the risks of some neurodevelopmental, reproductive and urogenital disorders. Here we summarize this evidence and call for precautionary action through a focused research effort and by increasing awareness among health professionals and pregnant women. APAP is an important medication and alternatives for treatment of high fever and severe pain are limited. We recommend that pregnant women should be cautioned at the beginning of pregnancy to: forego APAP unless its use is medically indicated; consult with a physician or pharmacist if they are uncertain whether use is indicated and before using on a long-term basis; and minimize exposure by using the lowest effective dose for the shortest possible time. We suggest specific actions to implement these recommendations. This Consensus Statement reflects our concerns and is currently supported by 91 scientists, clinicians and public health professionals from across the globe.
Probabilistic risk assessment of solar particle events considering the cost of countermeasures to reduce the aviation radiation dose
Authors: Fujita Moe , Sato Tatsuhiko , Saito Susumu , Yamashiki Yosuke 
Published: September 2021

AbstractCosmic-ray exposure to flight crews and passengers, which is called aviation radiation exposure, is an important topic in radiological protection, particularly for solar energetic particles (SEP). We therefore assessed the risks associated with the countermeasure costs to reduce SEP doses and dose rates for eight flight routes during five ground level enhancements (GLE). A four-dimensional dose-rate database developed by the Warning System for Aviation Exposure to Solar Energetic Particles, WASAVIES, was employed in the SEP dose evaluation. As for the cost estimation, we considered two countermeasures; one is the cancellation of the flight, and the other is the reduction of flight altitudes. Then, we estimated the annual occurrence frequency of significant GLE events that would bring the maximum flight route dose and dose rate over 1.0 mSv and 80 μSv/h, respectively, based on past records of GLE as well as historically large events observed by the cosmogenic nuclide concentrations in tree rings and ice cores. Our calculations suggest that GLE events of a magnitude sufficient to exceed the above dose and dose rate thresholds, requiring a change in flight conditions, occur once every 47 and 17 years, respectively, and their conservatively-estimated annual risks associated with the countermeasure costs are up to around 1.5 thousand USD in the cases of daily-operated long-distance flights.
Simulation study on the effects of cancellous bone structure in the skull on ultrasonic wave propagation
Authors: Michimoto Itsuki , Miyashita Kazuki , Suzuyama Hidehisa , Yano Keita , Kobayashi Yasuyo , Saito Kozue , Matsukawa Mami 
Published: September 2021

AbstractThe transcranial Doppler method (TCD) enables the measurement of cerebral blood flow velocity and detection of emboli by applying an ultrasound probe to the temporal bone window, or the orbital or greater occipital foramina. TCD is widely used for evaluation of cerebral vasospasm after subarachnoid hemorrhage, early detection of patients with arterial stenosis, and the assessment of brain death. However, measurements often become difficult in older women. Among various factors contributing to this problem, we focused on the effect of the diploe in the skull bone on the penetration of ultrasound into the brain. In particular, the effect of the cancellous bone structure in the diploe was investigated. Using a 2D digital bone model, wave propagation through the skull bone was investigated using the finite-difference time-domain (FDTD) method. We fabricated digital bone models with similar structure but different BV/TV (bone volume/total volume) values in the diploe. At a BV/TV of approximately 50–60% (similar to that of older women), the minimum ultrasound amplitude was observed as a result of scattering and multiple reflections in the cancellous diploe. These results suggest that structural changes such as osteoporosis may be one factor hampering TCD measurements.
Effective and rugged analysis of glyphosate, glufosinate, and metabolites in Tenebrio molitor larva (mealworms) using liquid chromatography tandem mass spectrometry
Authors: Kim Leesun , Baek Sujn , Son Kyungae , Lee Hee-Dong , Choi Dal-Soon , Kim Chang Jo , Noh Hyun Ho 
Published: September 2021

AbstractTenebrio molitor larva (mealworms) has recently attracted attention as a protein source for food and feed. The larva is generally fed with wheat bran, which can be possibly contaminated with glyphosate. To establish food safe standards, a rugged and effective analytical method for glyphosate, aminomethylphosphonic acid, glufosinate, and their metabolites including 3-methylphosphinico-propionic acid, and N-acetyl glufosinate, in mealworms was optimized using liquid chromatography tandem mass spectrometry. An anionic polar pesticide column was used due to its high suitability for glyphosate. Acidified water and acetonitrile were used to extract the target compounds without contribution from various fatty and pigment interferences derived from brownish insects. Seven different clean-up procedures ((1) 50 mg C18 (2) 20 mg C18/Z-sep (3) PRiME hydrophilic-lipophilic balance (HLB) cartridge (4) 75 mg Z-sep, (5) 75 mg Z-sep+, (6) EMR-lipid cartridge, and (7) 50 mg ENVI-Carb) were compared. Due to its simplicity and cost-effectiveness, PRiME HLB was selected for clean-up. The recoveries of the target compounds were ranged from 86 to 96% with < 20% relative standard deviations. Therefore, this simple and effective method can be applied for the two pesticides and their metabolites in other edible insects or high-fat matrices.
Differences in the dynamics of community disaster resilience across the globe
Authors: Hochrainer-Stigler Stefan , Velev Stefan , Laurien Finn , Campbell Karen , Czajkowski Jeffrey , Keating Adriana , Mechler Reinhard 
Published: September 2021

AbstractThe consideration of disaster resilience as a multidimensional concept provides a viable and promising way forward for reducing risk and minimizing impacts today and in the future. What is missing is the understanding of the actual dynamics of resilience over time based on empirical evidence. This empirical understanding requires a consistent measure of resilience. To that end, a Technical Resilience Grading Standard for community flood resilience, was applied in a longitudinal study from 2016 to 2018 in 68 communities across the globe. We analyse the dynamics of disaster resilience using an advanced boosted regression tree modelling framework. The main outcome of our analysis is twofold: first, we found empirical evidence that the dynamics of resilience build on a typology of communities and that different community clusters experience different dynamics; and second, the dynamics of resilience follows transitional behaviour rather than a linear or continuous process. These are empirical insights that can provide ways forward, theoretically as well as practically, in the understanding of resilience as well as in regard to effective policy guidance to enhance disaster resilience.
A multilevel scenario based predictive analytics framework to model the community mental health and built environment nexus
Authors: Mukherjee Sayanti , Frimpong Boamah Emmanuel , Ganguly Prasangsha , Botchwey Nisha 
Published: September 2021

AbstractThe built environment affects mental health outcomes, but this relationship is less studied and understood. This article proposes a novel multi-level scenario-based predictive analytics framework (MSPAF) to explore the complex relationships between community mental health outcomes and the built environment conditions. The MSPAF combines rigorously validated interpretable machine learning algorithms and scenario-based sensitivity analysis to test various hypotheses on how the built environment impacts community mental health outcomes across the largest metropolitan areas in the US. Among other findings, our results suggest that declining socio-economic conditions of the built environment (e.g., poverty, low income, unemployment, decreased access to public health insurance) are significantly associated with increased reported mental health disorders. Similarly, physical conditions of the built environment (e.g., increased housing vacancies and increased travel costs) are significantly associated with increased reported mental health disorders. However, this positive relationship between the physical conditions of the built environment and mental health outcomes does not hold across all the metropolitan areas, suggesting a mixed effect of the built environment’s physical conditions on community mental health. We conclude by highlighting future opportunities of incorporating other variables and datasets into the MSPAF framework to test additional hypotheses on how the built environment impacts community mental health.
Prevalence and related factors of dyslipidemia among urban adults aged 35 to 79 years in Southwestern China
Authors: Huang Chuan , Zhang Wen-Qiang , Tang Wei-Wei , Liu Ya , Liu Jian-Xiong , Xu Rong-Hua , Zhao Shui-Ping , Wang Tzung-Dau , Huang Xiao-Bo 
Published: September 2021

AbstractThis study aimed to investigate the prevalence of dyslipidemia and its related factors among urban adults aged 35 to 79 years in Southwestern China. From September 2013 to March 2014, a multi-stage sampling was conducted, and a total of 10,221 people aged 35–79 years living in Chengdu and Chongqing were included. More than 30 investigators were trained in data collection, including questionnaire, anthropometric measurements and blood biomarkers testing. The prevalence of high triglycerides (≥ 2.3 mmol/L), high total cholesterol (≥ 6.2 mmol/L), high low-density lipoprotein cholesterol (≥ 4.1 mmol/L), low high-density lipoprotein cholesterol (< 1.0 mmol/L), and dyslipidemia were 15.7% (95% confidence interval, 15.0–16.4%), 5.4% (4.9–5.8%), 2.5% (2.2–2.8%), 5.7% (5.3–6.2%), and 27.4% (26.5–28.2%), respectively. The prevalence of dyslipidemia was positively correlated with higher education level, monthly income over 2000 CNY, smoking, hypertension, diabetes, overweight and obesity, and central obesity, and negatively correlated with daily physical exercise. The prevalence of dyslipidemia in Southwestern China is lower than the national average level, with high triglycerides being the most common form of dyslipidemia.
The quantum-mechanical Coulomb propagator in an L2 function representation
Authors: Gersbacher Rolf , Broad John T. 
Published: September 2021

AbstractThe quantum-mechanical Coulomb propagator is represented in a square-integrable basis of Sturmian functions. Herein, the Stieltjes integral containing the Coulomb spectral function as a weight is evaluated. The Coulomb propagator generally consists of two parts. The sum of the discrete part of the spectrum is extrapolated numerically, while three integration procedures are applied to the continuum part of the oscillating integral: the Gauss–Pollaczek quadrature, the Gauss–Legendre quadrature along the real axis, and a transformation into a contour integral in the complex plane with the subsequent Gauss–Legendre quadrature. Using the contour integral, the Coulomb propagator can be calculated very accurately from an L$$^2$$

2

basis. Using the three-term recursion relation of the Pollaczek polynomials, an effective algorithm is herein presented to reduce the number of integrations. Numerical results are presented and discussed for all procedures.
Testing covariance models for MEG source reconstruction of hippocampal activity
Authors: O’Neill George C. , Barry Daniel N. , Tierney Tim M. , Mellor Stephanie , Maguire Eleanor A. , Barnes Gareth R. 
Published: September 2021

AbstractBeamforming is one of the most commonly used source reconstruction methods for magneto- and electroencephalography (M/EEG). One underlying assumption, however, is that distant sources are uncorrelated and here we tested whether this is an appropriate model for the human hippocampal data. We revised the Empirical Bayesian Beamfomer (EBB) to accommodate specific a-priori correlated source models. We showed in simulation that we could use model evidence (as approximated by Free Energy) to distinguish between different correlated and uncorrelated source scenarios. Using group MEG data in which the participants performed a hippocampal-dependent task, we explored the possibility that the hippocampus or the cortex or both were correlated in their activity across hemispheres. We found that incorporating a correlated hippocampal source model significantly improved model evidence. Our findings help to explain why, up until now, the majority of MEG-reported hippocampal activity (typically making use of beamformers) has been estimated as unilateral.
Selective T3–T4 sympathicotomy versus gray ramicotomy on outcome and quality of life in hyperhidrosis patients: a randomized clinical trial
Authors: Vanaclocha Vicente , Guijarro-Jorge Ricardo , Saiz-Sapena Nieves , Granell-Gil Manuel , Ortiz-Criado José María , Mascarós Juan Manuel , Vanaclocha Leyre 
Published: September 2021

AbstractCompensatory hyperhidrosis is the leading cause of patients' dissatisfaction after thoracic sympathicotomy. The study aimed to reduce compensatory hyperhidrosis to increase patients’ satisfaction. A prospective randomized study on palmar hyperhidrosis, May 2016–September 2019. Twenty-one patients T3–T4sympathicotomy and 21 T3–T4gray ramicotomy. Data prospectively collected. Analysis at study's end. Focus on the sweating, temperature, quality of life baseline and postoperatively, compensatory hyperhidrosis, hand dryness, patients' satisfaction, and if they would undergo the procedure again and recommend it. No baseline differences between groups. Hyperhidrosis was controlled postoperatively in all patients. No mortality, serious complications, or recurrences. Sympathicotomy worse postoperative quality of life (49.05 (SD: 15.66, IR: 35.50–63.00) versus ramicotomy 24.30 (SD: 6.02, IR: 19.75–27.25). After ramicotomy, some residual sweating on the face, hands, and axillae. Compensatory sweating worse with sympathicotomy. Satisfaction higher with ramicotomy. Better results with ramicotomy than sympathicotomy regarding hand dryness, how many times a day the patients had to shower or change clothes, intention to undergo the procedure again or recommend it to somebody else, and how bothersome compensatory hyperhidrosis was. T3–T4gray ramicotomy had better results than T3–T4sympathicotomy, with less compensatory sweating and higher patients' satisfaction.
Distribution of Pb, Zn and Cd in stream and alluvial sediments in the area with past Zn smelting operations
Authors: Žibret Gorazd , Čeplak Barbara 
Published: September 2021

AbstractThe sources of Zn, Pb and Cd in alluvial and stream sediments have been studied in the area of historical Zn smelting tradition. 30 samples of stream sediments and samples from 4 alluvial sediment profiles were collected. Fractions 0.125–0.063 and < 0.063 mm were analysed by the means of ICP-MS prior 4-acid digestion. The highest levels of Zn, Cd and Pb were detected in the alluvial sediments in the closest vicinity to the abandoned slag and ore roasting residue waste dumps, reaching 96 and 4520 mg/kg, 522 and 26,800 mg/kg and 3.7 and 31 mg/kg for Pb, Zn and Cd in stream and alluvial sediments, respectively. The Voglajna River then transports contamination particles into the Savinja River, which afterwards flows into the Sava River. Consequently, the anomaly can even be detected in the Sava River, more than 30 km downstream. Higher levels of Pb, Zn and Cd have been found in fraction < 0.063 mm compared to 0.125–0.063 mm fraction. Impacts of historically contaminated soil erosion and in particular the wash-out of Zn-smelting waste from the improperly managed waste dump were recognised as the dominant sources of Zn, Cd and Pb in the stream and alluvial sediments.
On the role of hypocrisy in escaping the tragedy of the commons
Authors: Korman Amos , Vacus Robin 
Published: September 2021

AbstractWe study the emergence of cooperation in large spatial public goods games. Without employing severe social-pressure against “defectors”, or alternatively, significantly rewarding “cooperators”, theoretical models typically predict a system collapse in a way that is reminiscent of the “tragedy-of-the-commons” metaphor. Drawing on a dynamic network model, this paper demonstrates how cooperation can emerge when the social-pressure is mild. This is achieved with the aid of an additional behavior called “hypocrisy”, which appears to be cooperative from the external observer’s perspective but in fact hardly contributes to the social-welfare. Our model assumes that social-pressure is induced over both defectors and hypocritical players, though the extent of which may differ. Our main result indicates that the emergence of cooperation highly depends on the extent of social-pressure applied against hypocritical players. Setting it to be at some intermediate range below the one employed against defectors allows a system composed almost exclusively of defectors to transform into a fully cooperative one quickly. Conversely, when the social-pressure against hypocritical players is either too low or too high, the system remains locked in a degenerate configuration.
Evaluation of connectivity map shows limited reproducibility in drug repositioning
Authors: Lim Nathaniel , Pavlidis Paul 
Published: September 2021

AbstractThe Connectivity Map (CMap) is a popular resource designed for data-driven drug repositioning using a large transcriptomic compendium. However, evaluations of its performance are limited. We used two iterations of CMap (CMap 1 and 2) to assess their comparability and reliability. We queried CMap 2 with CMap 1-derived signatures, expecting CMap 2 would highly prioritize the queried compounds; the success rate was 17%. Analysis of previously published prioritizations yielded similar results. Low recall is caused by low differential expression (DE) reproducibility both between CMaps and within each CMap. DE strength was predictive of reproducibility, and is influenced by compound concentration and cell-line responsiveness. Reproducibility of CMap 2 sample expression levels was also lower than expected. We attempted to identify the “better” CMap by comparison with a third dataset, but they were mutually discordant. Our findings have implications for CMap usage and we suggest steps for investigators to limit false positives.