bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs
Authors: Maity Arijit , Winnerdy Fernaldo Richtia , Chang Weili Denyse , Chen Gang , Phan Anh Tuân 
Published: February 2020

Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
Rare cause of emergency in the first week of life: congenital hepatoblastoma (case report)
Authors: Yoo Gloria Ha Young , Mugarab-Samedi Veronica , Hansen Gregory , Miller Grant , Givelichian Laurence , Kalaniti Kaarthigeyan , Daspal Sibasis 
Published: February 2020

Abstract
During the first week of life, a sudden deterioration in a newborn commonly includes investigations to rule out infections, lung pathologies, cardiac lesions, neurological insults, metabolic disorders or gastrointestinal emergencies. It is unusual, however, to consider malignancy as the primary causative factor. In this case report, we describe a rare and unusual presentation of congenital hepatoblastoma, its complications and management in a neonate with multi-organ dysfunction. A term infant presented with sudden deterioration, hemodynamic instability and an acute abdomen on his 4th day of life. Surgical exploration revealed a ruptured neoplasm that pathology diagnosed as a congenital hepatoblastoma. After the patient was stabilized, chemotherapy was initiated. At present, the patient is 8 months old and under continuous follow-up of oncology service. This case highlights the importance of considering rare diagnoses including congenital malignancy when investigating and managing a sick newborn with multi-organ dysfunction.
49 years of normal functioning Starr–Edwards aortic valve prosthesis
Authors: Sabouni Mouhamed Amr , Baumeister Robin H , Traverse Paul 
Published: February 2020

Abstract
Although it is no longer in production, the Starr–Edwards valve has successfully replaced hundreds of thousands of heart valves in the past 50 years of its use. We report on the case of a valve in the aortic position still functioning 49 years after implantation without replacement, showcasing the valve’s durability.
Investigation of Fluid-driven Carbonation of a Hydrated, Forearc Mantle Wedge using Serpentinite Cores in High-pressure Experiments
Authors: Sieber Melanie J , Yaxley Gregory M , Hermann Jörg 
Published: February 2020

AbstractHigh-pressure experiments were performed to investigate the effectiveness, rate and mechanism of carbonation of serpentinites by a carbon-saturated COH fluid at 1·5–2·5 GPa and 375–700 °C. This allows a better understanding of the fate and redistribution of slab-derived carbonic fluids when they react with the partially hydrated mantle within and above the subducting slab under pressure and temperature conditions corresponding to the forearc mantle. Interactions between carbon-saturated CO2–H2O–CH4 fluids and serpentinite were investigated using natural serpentinite cylinders with natural grain sizes and shapes in piston-cylinder experiments. The volatile composition of post-run fluids was quantified by gas chromatography. Solid phases were examined by Raman spectroscopy, electron microscopy and laser ablation inductively coupled plasma mass spectrometry. Textures, porosity and phase abundances of recovered rock cores were visualized and quantified by three-dimensional, high-resolution computed tomography. We find that carbonation of serpentinites is efficient at sequestering CO2 from the interacting fluid into newly formed magnesite. Time-series experiments demonstrate that carbonation is completed within ∼96 h at 2 GPa and 600 °C. With decreasing CO2,aq antigorite is replaced first by magnesite + quartz followed by magnesite + talc + chlorite in distinct, metasomatic fronts. Above antigorite stability magnesite + enstatite + talc + chlorite occur additionally. The formation of fluid-permeable reaction zones enhances the reaction rate and efficiency of carbonation. Carbonation probably occurs via an interface-coupled replacement process, whereby interconnected porosity is present within reaction zones after the experiment. Consequently, carbonation of serpentinites is self-promoting and efficient even if fluid flow is channelized into veins. We conclude that significant amounts of carbonates may accumulate, over time, in the hydrated forearc mantle.
Resolving a spacetime singularity with field transformations
Authors: Naruko Atsushi , Yoo Chul-Moon , Sasaki Misao 
Published: February 2020

Abstract
It is widely believed that classical gravity breaks down and quantum gravity is needed to deal with a singularity. We show that there is a class of spacetime curvature singularities which can be resolved with metric and matter field transformations. As an example, we consider an anisotropic power-law inflation model with scalar and gauge fields in which a space-like curvature singularity exists at the beginning of time. First, we provide a transformation of the metric to the flat geometry, i.e. the Minkowski metric. The transformation removes the curvature singularity located at the origin of time. An essential difference from previous work in the literature is that the origin of time is not sent to past infinity by the transformation but it remains at a finite time in the past. Thus the geometry becomes extensible beyond the singularity. In general, matter fields are still singular in their original form after such a metric transformation. However, we explicitly show that there is a case in which the singular behavior of the matter fields can be completely removed by a redefinition of matter fields. Thus, for the first time, we have resolved a class of initial cosmic singularities and successfully extended the spacetime beyond the singularity in the framework of classical gravity.
Thermal state of transiently accreting neutron stars with additional heating beyond deep crustal heating
Authors: Liu Helei , Hashimoto Masa-aki , Lü Guoliang , Matsuo Yasuhide , Wen Dehua , Noda Tsuneo 
Published: February 2020

Abstract
As some neutron star transients require an additional unknown heat source (referred to as “shallow heating”) to explain their high temperatures at the beginning of quiescence, we investigate the effect of shallow heating as well as compressional heating on the thermal state of transiently accreting neutron stars with the use of evolutionary calculations in the present work. Through comparing our theoretical predictions of the equilibrium redshifted luminosities $(L_{\gamma}^{\infty})$ produced by both deep crustal heating and shallow heating/compressional heating for different time-averaged mass-accretion rates $\langle\dot{M}\rangle$ with 35 updated observations of soft X-ray transients, the results show that both shallow heating and compressional heating make significant contributions to the equilibrium redshifted luminosity. The hotter sources (XTE J1701, MAXI J0556, EXO 0748, Aql X-1 etc.) with higher accretion rates are more likely to be explained with the effect of shallow heating or compressional heating. In addition, for a proper shallow heat $q_\mathrm{sh}$ and mass-accretion rate $\dot{M}$, the effect of shallow heating could be simulated by compressional heating.
Significance of Ethnic Factors in Immunosuppressive Therapy Management After Organ Transplantation
Authors: Yamada Takaaki , Zhang Mengyu , Masuda Satohiro 
Published: February 2020

Abstract:Clinical outcomes after organ transplantation have greatly improved in the past 2 decades with the discovery and development of immunosuppressive drugs such as calcineurin inhibitors, antiproliferative agents, and mammalian target of rapamycin inhibitors. However, individualized dosage regimens have not yet been fully established for these drugs except for therapeutic drug monitoring-based dosage modification because of extensive interindividual variations in immunosuppressive drug pharmacokinetics. The variations in immunosuppressive drug pharmacokinetics are attributed to interindividual variations in the functional activity of cytochrome P450 enzymes, UDP-glucuronosyltransferases, and ATP-binding cassette subfamily B member 1 (known as P-glycoprotein or multidrug resistance 1) in the liver and small intestine. Some genetic variations have been found to be involved to at least some degree in pharmacokinetic variations in post-transplant immunosuppressive therapy. It is well known that the frequencies and effect size of minor alleles vary greatly between different races. Thus, ethnic considerations might provide useful information for optimizing individualized immunosuppressive therapy after organ transplantation. Here, we review ethnic factors affecting the pharmacokinetics of immunosuppressive drugs requiring therapeutic drug monitoring, including tacrolimus, cyclosporine, mycophenolate mofetil, sirolimus, and everolimus.
Teaching Those Who Care How to Care for a Person With Substance Use Disorder
Authors: Dion Kimberly , Griggs Stephanie 
Published: February 2020

Background
Substance use disorder (SUD) is on the rise globally, and nurses are not prepared to care for this population.

Purpose
The purpose was to determine if a 4-hour antistigma intervention improved prelicensure student nurse attitudes and perceived stigma toward people with SUD.

Methods
This was a nonrandomized quasi-experimental survey study. Participants completed the 20-item Drug and Drug Problems Perception Questionnaire (DDPPQ), the 8-item Perceived Stigma of Substance Abuse Scale (PSAS), and the 13-item Marlowe-Crowne Social Desirability Scale at baseline and repeated the DDPPQ and PSAS postintervention. Paired t tests were used to determine the mean differences in the total DDPPQ and total PSAS scores.

Results
After the antistigma intervention, there was a significant improvement in overall therapeutic attitudes (t = 8.4, df = 108, P < .001) and perceived stigma (t = −2.5, df = 108, P = .01) in undergraduate nursing students (n = 126).

Conclusions
Incorporating antistigma educational approaches may lead to more involvement and compassionate care for people with SUD.
General theory of topological explanations and explanatory asymmetry
Authors: Kostić Daniel 
Published: February 2020

In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological propertyAto explain some physical or dynamical propertyB. Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a particular system; a criterion for describing counterfactual dependencies in two explanatory modes, i.e. the vertical and the horizontal and, finally, a third perspectival one that tells us when to use the vertical and when to use the horizontal mode. In the second step, I show how this general theory of topological explanations accounts for explanatory asymmetry in both the vertical and horizontal explanatory modes. Finally, in the third step, I argue that this theory is universally applicable across biological sciences, which helps in unifying essential concepts of biological networks.This article is part of the theme issue ‘Unifying the essential concepts of biological networks: biological insights and philosophical foundations'.
Influence of physical activity and sleep duration on the retinal and choroidal structure in diabetic patients: An SS-OCT study
Authors: Liu Sen , Wang Wei , Qiu Zihan , He Miao , Huang Wenyong 
Published: February 2020

ABSTRACTPurposeTo assess the association between physical activity, sleep duration, sitting time, and alterations of posterior segment structures with swept-source optical coherence tomography (SS-OCT).MethodsPatients with diabetic retinopathy (DR) were recruited, and diabetic patients without retinopathy (non-DR) who matched for age and duration of diabetes were used as control. The physical activity, siting time, and sleep duration were obtained by using standardized questionnaire. OCT parameters included: retinal nerve fibre layer (RNFL) thickness, ganglion cell inner plexiform layer (GC-IPL) thickness, retinal thickness, and choroidal thickness (CT). Linear regression was conducted to analyse the association.ResultsEach group included 116 diabetic patients. Average macular CT was positively correlated with metabolic equivalents (MET) only in the DR group, independent of age, gender, and other potential confounding factors (β = 1.163, P = 0.006). Average macular CT was also positively correlated with sleep duration only in the non-DR group, independent of age, gender, and other potential confounding factors (β = 10.54, P = 0.031). No correlation was found between MET, sleep duration, and other OCT parameters. Sitting time was not significantly correlated with OCT parameters either.ConclusionsPhysical activity and sleep duration are both positively correlated with macular choroidal thickness; this suggests that more time in physical activity and sleep benefit the retina, while there was no association between sedentary time and OCT parameters. Further studies are warranted to clarify the underlying mechanisms and the role of physical activity and sleep in CT alterations and DR.
Postprandial changes in gastrointestinal function and transit in cystic fibrosis assessed by magnetic resonance imaging
Authors: Ng C. , Dellschaft N. S. , Hoad C. L. , Marciani L. , Ban L. , Prayle A. P. , Barr H. L. , Jaudszus A. , Mainz J. G. , Spiller R. , Gowland P. , Major G. , Smyth A.R. 
Published: February 2020

AbstractBackground and AimsCystic fibrosis (CF) is a multi-system genetic disorder affecting >72,000 people worldwide. Most people with CF experience gastrointestinal symptoms and some will develop complications such as distal intestinal obstruction syndrome. However the mechanisms of symptoms and complications are not understood. We evaluated gut function and transit of CF using magnetic resonance imaging (MRI). Our hypotheses were: oro-caecal transit time (OCTT) is longer in CF, with lower small bowel water content (SBWC).MethodsTwelve people with CF at a tertiary centre and 12 age and sex-matched controls underwent serial MRIs over 1 day, with meals at set times. The primary endpoint was OCTT, assessed by the appearance of a food bolus in the caecum. Other measures included SBWC, colonic volume, gastric half-emptying time and gastrointestinal symptoms.ResultsOCTT was longer in CF (controls 210 minutes [173, 315] vs. CF 330 minutes [270, >360], p=0.04). There was no difference in gastric half-emptying times (controls 80 minutes [66, 88] vs. CF 97 [71, 128], p=0.3). Corrected SBWC was higher in CF (controls 34 L.min/m2[28, 41] vs. CF 63 L.min/m2[36, 80], p=0.021), with minimal second post-prandial decrease suggesting impaired ileal emptying. Corrected colonic volumes were higher in CF (controls 123 L.min/m2[89, 146] vs. CF 186 L.min/m2[166, 209], p=0.012). There were no differences in gastrointestinal symptoms.ConclusionsSignificant differences in gut function and transit exist between CF and controls. Our methodology provides a platform for studying gastrointestinal function in CF and has identified new potential mechanisms of dysfunction.ClinicalTrials.govNCT03566550
PERFORMANCE OF GOOGLE TRENDS FOR EARLY DETECTION OF DENGUE INFECTION EPIDEMICS IN JAKARTA AND YOGYAKARTA
Authors: Husnayain Atina , Lestari Setyarini Hestu , Tarmizi Siti Nadia , Fuad Anis 
Published: February 2020

ABSTRACTBackgroundEarly detection of disease outbreak is among the most critical role of the sub-national authorities as mandated by the health decentralization policy. Given the continuous growth of Internet penetration and dependencies of the society on the digital ecosystem, it is essential to investigate the potential innovations to improve the existing surveillance system using digital epidemiology. Several studies, including in Indonesia, have assessed the roles of Google Trends (GT) to improve dengue surveillance systems. However, they were mostly located in specific areas or national level only. No reports are available to compare the performance of GT for early detection of dengue outbreak among high burdened provinces.AimsThis study aimed to examine the correlation between GT data on dengue-related query terms with the official dengue surveillance reports in Jakarta and Yogyakarta Province.MethodsRelative Search Volume of GT data for dengue were collected from the area of Jakarta and Yogyakarta between 2012 to 2016. Those data were compared with the official dengue reports from the Indonesian Ministry of Health using Pearson’s correlation and Time-lag correlation, performed with Stata version 13.ResultsGT data are positively correlated with the routine surveillance report in Jakarta (r = 0.723, p-value= 0.000) and Yogyakarta Province (r = 0.715, p-value= 0.000). In Jakarta, search term of ‘DBD’ demonstrated a very strong correlation for lag-1 (r =0.828, p-value= 0.000). This finding indicates that GT data could possibly detect the dengue outbreak a month earlier, especially in Jakarta. Hence, GT data can be used to monitor disease dynamics and improve the public awareness of a potential outbreak in near-real-time.ConclusionGT data were positively correlated with the routine surveillance report in Jakarta and Yogyakarta Province. Early warning system utilizing GT data is potentially more accurate in Jakarta than in Yogyakarta. We assume that it is related with the larger population as well as the Internet use activities that drives the higher volume of Google search on dengue in Jakarta compared to Yogyakarta. Further studies involving other digital data sources, for example, Twitter, online news, and administrative data from the national health insurance are essential to strengthen the current surveillance system with the new digital epidemiology approach.
Early Phylogenetic Estimate Of The Effective Reproduction Number Of 2019-nCoV
Authors: Lai Alessia , Bergna Annalisa , Acciarri Carla , Galli Massimo , Zehender Gianguglielmo 
Published: February 2020

ABSTRACTTo reconstruct the evolutionary dynamics of the 2019 novel coronavirus, 52 2019-nCOV genomes available on 04 February 2020 at GISAID were analysed.The two models used to estimate the reproduction number (coalescent-based exponential growth and a birth-death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10−4 subs/site/year (range 1.1×10−4–15×10−4).The estimated R value was 2.6 (range 2.1-5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days.This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.
The serial interval of COVID-19 from publicly reported confirmed cases
Authors: Du Zhanwei , Xu Xiaoke , Wu Ye , Wang Lin , Cowling Benjamin J. , Meyers Lauren Ancel 
Published: February 2020

Short AbstractWe estimate the distribution of serial intervals for 468 confirmed cases of COVID-19 reported in 93 Chinese cities by February 8, 2020. The mean and standard deviation are 3.96 (95% CI 3.53-4.39) and 4.75 (95% CI 4.46-5.07) days, respectively, with 12.6% of reports indicating pre-symptomatic transmission.One sentence summaryWe estimate the distribution of serial intervals for 468 confirmed cases of COVID-19 reported in 93 Chinese cities by February 8, 2020.
Application of the Adaptive Validation Design to estimate the association between transmasculine/transfeminine status and self-inflicted injury among transgender and gender-nonconforming children and adolescents
Authors: Collin Lindsay J. , MacLehose Richard F. , Ahern Thomas P. , Goodman Michael , Lash Timothy L. 
Published: February 2020

AbstractBackgroundAn internal validation substudy compares an imperfect measurement of a variable with a gold standard measurement in a subset of the study population. Validation data permit calculation of a bias-adjusted estimate, expected to equal the association that would have been observed had the gold standard measurement been available for the entire study population. Guidance on optimal sampling of participants to include in validation substudies has not considered monitoring validation data as they accrue. In this paper, we develop and apply the framework of Bayesian monitoring to determine when sufficient validation data have been collected to yield a bias-adjusted estimate of association with a prespecified level of precision.MethodsWe demonstrate the utility of this method using the Study of Transition, Outcomes and Gender—a cohort study of transgender and gender non-conforming children and adolescents. Transmasculine and transfeminine status were determined from the gender code in the electronic medical record at cohort enrollment. This status is known to be misclassified because it can indicate either gender identity or sex recorded at birth. Our interest is in the association between transmasculine and transfeminine status and self-inflicted injury. To address possible exposure misclassification, we demonstrate the method’s ability to determine when sufficient validation data have been collected to calculate a bias-adjusted estimate of association that is less than 80% greater than the precision of the conventional estimate.ResultsIn the conventional age-adjusted analysis, we observed that transmasculine children and adolescents were 1.80-fold more likely to inflict self-harm than transfeminine youths (95%CI 1.27, 2.55). Using the adaptive validation approach, 200 cohort members were required for validation to yield a bias-adjusted estimate of OR=3.03 (95%CI 1.76, 5.56), which was similar to the bias-adjusted estimate using complete validation data (OR=2.63, 95%CI 1.67, 4.23).ConclusionsOur method provides a novel approach to effective and efficient estimation of classification parameters as validation data accrue. This method can be applied within the context of any parent epidemiologic study design, and modified to meet alternative criteria given specific study or validation study objectives.