bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain engineering of the electronic and thermoelectric properties of titanium trisulphide monolayers
Authors: Saiz Fernan , Rurali Riccardo 
Published: April 2020

Abstract
The goal of this work is to evaluate the effect of mechanical strain on a number of electronic and thermoelectric properties of TiS3 monolayers. We have used density-functional theory (DFT) calculations at the hybrid HSE06 level to evaluate the response of the electronic band gap and mobilities, as well as the thermopower, the electrical conductivity, the electronic contribution to the thermal conductivity and the power factor. Our calculations indicate that the band gaps can be increased by 44.25%, reaching a value of 1.55 eV from that of the undeformed case of 1.07 eV. The behaviour of HSE06 band gaps agrees well with that calculated at the G0W0 level of theory. We evaluate the variation of electron mobilities with strain and discuss the possible causes of the existent disagreement between experiments and simulations. In addition, our calculations predict small changes in the Seebeck coefficient, whose S

y
component can be enhanced by up to 11% with a compression of 5% along the y-axis. On the other hand, the electrical conductivity experiences higher variations, nearly doubling its value from the undeformed case under the semiconductor regime of doping and mechanical deformation. Finally, our predicted power factors can be enhanced by nearly twice under the same conditions by which the electrical conductivity is also improved, indicating that the latter drives the optimisation of the former.
Dual-Outcome Intention-to-Treat Analyses in the Women’s Health Initiative Randomized Controlled Hormone Therapy Trials
Authors: Prentice Ross L , Aragaki Aaron K , Chlebowski Rowan T , Zhao Shanshan , Anderson Garnet L , Rossouw Jacques E , Wallace Robert , Banack Hailey , Shadyab Aladdin H , Qi Lihong , Snively Beverly M , Gass Margery , Manson JoAnn E 
Published: April 2020

Abstract
Dual-outcome intention-to-treat hazard rate analyses have potential to complement single-outcome analyses for the evaluation of treatments or exposures in relation to multivariate time-to-response outcomes. Here we consider pairs formed from important clinical outcomes to obtain further insight into influences of menopausal hormone therapy on chronic disease. As part of the Women’s Health Initiative, randomized, placebo-controlled hormone therapy trials of conjugated equine estrogens (CEE) among posthysterectomy participants and of these same estrogens plus medroxyprogesterone acetate (MPA) among participants with an intact uterus were carried out at 40 US clinical centers (1993–2016). These data provide the context for analyses covering the trial intervention periods and a nearly 20-year (median) cumulative duration of follow-up. The rates of multiple outcome pairs were significantly influenced by hormone therapy, especially over cumulative follow-up, providing potential clinical and mechanistic insights. For example, among women randomized to either regimen, hazard ratios for pairs defined by fracture during intervention followed by death from any cause were reduced and hazard ratios for pairs defined by gallbladder disease followed by death were increased, though these findings may primarily reflect single-outcome associations. In comparison, hazard ratios for diabetes followed by death were reduced with CEE but not with CEE + MPA, and those for hypertension followed by death were increased with CEE + MPA but not with CEE.
Unravelling change in forest ground floras. A commentary on: ‘Temporal patterns of seed germination in early spring-flowering temperate woodland geophytes are modified by warming’
Authors: Kirby Keith J 
Published: April 2020

This article comments on:Rosemary J Newton, Fiona R Hay, Richard H Ellis, Temporal patterns of seed germination in early spring-flowering temperate woodland geophytes are modified by warming, Annals of Botany, Volume 125, Issue 7, 4 June 2020, Pages 1013–1023, https://doi.org/10.1093/aob/mcaa025
APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms
Authors: Wang Ruijia , Tian Bin 
Published: April 2020

Abstract

Summary
Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. APA is dynamically regulated under different growth and differentiation conditions. Here, we present a bioinformatics package, named APAlyzer, for examining 3′UTR APA, intronic APA and gene expression changes using RNA-seq data and annotated polyadenylation sites in the PolyA_DB database. Using APAlyzer and data from the GTEx database, we present APA profiles across human tissues.

Availability and implementation
APAlyzer is freely available at https://bioconductor.org/packages/release/bioc/html/APAlyzer.html as an R/Bioconductor package.

Supplementary information
Supplementary data are available at Bioinformatics online.
Characteristics of Household Transmission of COVID-19
Authors: Li Wei , Zhang Bo , Lu Jianhua , Liu Shihua , Chang Zhiqiang , Peng Cao , Liu Xinghua , Zhang Peng , Ling Yan , Tao Kaixiong , Chen Jianying 
Published: April 2020

AbstractBackgroundSince December 2019, SARS-CoV-2 has extended to most parts of China with &gt;80 000 cases and to at least 100 countries with &gt;60 000 international cases as of 15 March 2020. Here we used a household cohort study to determine the features of household transmission of COVID-19.MethodsA total of 105 index patients and 392 household contacts were enrolled. Both index patients and household members were tested by SARS-CoV-2 RT-PCR. Information on all recruited individuals was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to contact members were computed and the risk factors for transmission within the household were estimated.ResultsSecondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% compared with 17.1% for adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% compared with 16.9% for contacts without quarantined index patients. The secondary attack rate to contacts who were spouses of index cases was 27.8% compared with 17.3% for other adult members in the households.ConclusionsThe secondary attack rate of SARS-CoV-2 in household is 16.3%. Age of household contacts and spousal relationship to the index case are risk factors for transmission of SARS-CoV-2 within a household. Quarantine of index patients at home since onset of symptoms is useful to prevent the transmission of SARS-Co-2 within a household.
Duration of Viral Shedding of Discharged Patients With Severe COVID-19
Authors: Zhou Bo , She Jianqing , Wang Yadan , Ma Xiancang 
Published: April 2020

AbstractCOVID-19 has drawn global intensive attention. We analyzed the duration of viral shedding and the total time from illness onset to discharge in groups. This has important implications for making decisions for isolation of discharged patients and to provide guidance for the duration of hospitalization of patients with severe COVID-19.
Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion
Authors: Jensen Sarah Ø , Øgaard Nadia , Nielsen Hans Jørgen , Bramsen Jesper B , Andersen Claus L 
Published: April 2020

Abstract

Background
Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion.

Methods
Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)–specific methylation markers KCNQ5, C9orf50, and CLIP4 and compared with previously reported single-strand assays. Performance was tested in tumor and leukocyte DNA, and the ability to detect ctDNA was investigated in plasma from 43 patients with CRC stages I to IV and 42 colonoscopy-confirmed healthy controls.

Results
Dual-strand assays quantified close to 100% of methylated control DNA input, whereas single-strand assays quantified approximately 50%. Furthermore, dual-strand assays showed a 2-fold increase in the number of methylated DNA copies detected when applied to DNA purified from tumor tissue and plasma from CRC patients. When the results of the 3 DNA methylation markers were combined into a ctDNA detection test and applied to plasma, the dual-strand assay format detected 86% of the cancers compared with 74% for the single-strand assay format. The specificity was 100% for both the dual- and single-strand test formats.

Conclusion
Dual-strand assays enabled more sensitive detection of methylated ctDNA than single-strand assays.
Sex differences in aortic valve calcification in severe aortic valve stenosis: association between computer tomography assessed calcification and valvular calcium concentrations
Authors: Linde Louise , Carter-Storch Rasmus , Christensen Nicolaj Lyhne , Øvrehus Kristian Altern , Diederichsen Axel Cosmus Pyndt , Laursen Kristian , Jensen Pia Søndergaard , Rasmussen Lars Melholt , Møller Jacob Eifer , Dahl Jordi Sanchez 
Published: April 2020

Abstract

Aims
The aims of this study were to investigate the correlation and sex differences between total valve calcium, valve calcium concentration, and aortic valve calcification (AVC) in explanted valves from patients with severe aortic valve stenosis undergoing aortic valve replacement (AVR).

Methods and results
Sixty-nine patients with severe aortic stenosis (AS) scheduled for elective AVR underwent echocardiography and cardiac computed tomography (CT) prior to surgery (AVCin vivo) and CT of the explanted aortic valve (AVCex vivo). Explanted valves were prepared in acid solution, sonicated, and analysed with Arsenazo III dye to estimate total valve calcium and valve calcium concentration. Median AVCex vivo was 2082 (1421–2973) AU; mean valve calcium concentration was 1.43 ± 0.42 µmol Ca2+/mg tissue; median total valve calcium 156 (111–255) mg Ca2+, and valve calcium density 52 (35–81) mg/cm2. AVC displayed a strong correlation with total valve calcium (R2 = 0.98, P &lt; 0.001) and a moderate correlation with valve calcium concentration (R2 = 0.62, P &lt; 0.001). Valvular calcium concentration was associated with sex, aortic valve area, and mean gradient. After adjusting for age and estimated glomerular filtration rate, sex and mean gradient remained associated with valve calcium concentrations.

Conclusion
AVC score provides a strong estimate for total valve calcium but to a lesser degree calcium concentration in the valve tissue of patients with severe AS. Females presented lower valvular calcium concentrations than males irrespective of AS severity, adding evidence and providing support to the important point that sex differences in valvular calcium concentration in AS does not reflect valvular size.
The myocardial phenotype of Fabry disease pre-hypertrophy and pre-detectable storage
Authors: Augusto João B , Johner Nicolas , Shah Dipen , Nordin Sabrina , Knott Kristopher D , Rosmini Stefania , Lau Clement , Alfarih Mashael , Hughes Rebecca , Seraphim Andreas , Vijapurapu Ravi , Bhuva Anish , Lin Linda , Ojrzyńska Natalia , Geberhiwot Tarekegn , Captur Gabriella , Ramaswami Uma , Steeds Richard P , Kozor Rebecca , Hughes Derralynn , Moon James C , Namdar Mehdi 
Published: April 2020

Abstract

Aims
Cardiac involvement in Fabry disease (FD) occurs prior to left ventricular hypertrophy (LVH) and is characterized by low myocardial native T1 with sphingolipid storage reflected by cardiovascular magnetic resonance (CMR) and electrocardiogram (ECG) changes. We hypothesize that a pre-storage myocardial phenotype might occur even earlier, prior to T1 lowering.

Methods and results
FD patients and age-, sex-, and heart rate-matched healthy controls underwent same-day ECG with advanced analysis and multiparametric CMR [cines, global longitudinal strain (GLS), T1 and T2 mapping, stress perfusion (myocardial blood flow, MBF), and late gadolinium enhancement (LGE)]. One hundred and fourteen Fabry patients (46 ± 13 years, 61% female) and 76 controls (49 ± 15 years, 50% female) were included. In pre-LVH FD (n = 72, 63%), a low T1 (n = 32/72, 44%) was associated with a constellation of ECG and functional abnormalities compared to normal T1 FD patients and controls. However, pre-LVH FD with normal T1 (n = 40/72, 56%) also had abnormalities compared to controls: reduced GLS (−18 ± 2 vs. −20 ± 2%, P &lt; 0.001), microvascular changes (lower MBF 2.5 ± 0.7 vs. 3.0 ± 0.8 mL/g/min, P = 0.028), subtle T2 elevation (50 ± 4 vs. 48 ± 2 ms, P = 0.027), and limited LGE (%LGE 0.3 ± 1.1 vs. 0%, P = 0.004). ECG abnormalities included shorter P-wave duration (88 ± 12 vs. 94 ± 15 ms, P = 0.010) and T-wave peak time (Tonset – Tpeak; 104 ± 28 vs. 115 ± 20 ms, P = 0.015), resulting in a more symmetric T wave with lower T-wave time ratio (Tonset – Tpeak)/(Tpeak – Tend) (1.5 ± 0.4 vs. 1.8 ± 0.4, P &lt; 0.001) compared to controls.

Conclusion
FD has a measurable myocardial phenotype pre-LVH and pre-detectable myocyte storage with microvascular dysfunction, subtly impaired GLS and altered atrial depolarization and ventricular repolarization intervals.
Auxiliary information resolution effects on small area estimation in plantation forest inventory
Authors: Green P Corey , Burkhart Harold E , Coulston John W , Radtke Philip J , Thomas Valerie A 
Published: April 2020

AbstractIn forest inventory, traditional ground-based resource assessments are often expensive and time-consuming forcing managers to reduce sample sizes to meet budgetary and logistical constraints. Small area estimation (SAE) is a class of statistical estimators that uses a combination of traditional survey data and linearly related auxiliary information to improve estimate precision. These techniques have been shown to improve the precision of stand-level inventory estimates in loblolly pine plantations using lidar height percentiles and thinning status as covariates. In this study, the effects of reduced lidar point-cloud densities and lower digital elevation model (DEM) spatial resolutions were investigated for total planted volume estimates using area-level SAE models. In the managed Piedmont pine plantation conditions evaluated, lower lidar point-cloud densities and DEM spatial resolutions were found to have minimal effects on estimates and precision. The results of this study are promising to those interested in incorporating SAE methods into forest inventory programs.
Outcomes of a single-step endoscopic ultrasound-guided drainage of pancreatic-fluid collections using an electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent with and without fluoroscopy
Authors: Olaiya Babatunde , Mekaroonkamol Parit , Li Bai-Wen , Massaad Julia , Vachaparambil Cicily T , Xu Jennifer , Lamm Vladamir , Luo Hui , Shen Shan-Shan , Chen Hui-Min , Keilin Steve , Willingham Field F , Cai Qiang 
Published: April 2020

AbstractBackgroundFluoroscopy is often used during the endoscopic drainage of pancreatic-fluid collections (PFCs). An electrocautery-enhanced coaxial lumen-apposing, self-expanding metal stent (ELAMS) facilitates a single-step procedure and may avoid the need for fluoroscopy. This study compares the treatment outcomes using ELAMS with and without fluoroscopy.MethodsPatients with PFCs who had cystogastrostomy from January 2014 to February 2017 were enrolled. Two groups were studied based on fluoroscopy use. Technical success was defined as uneventful insertion of ELAMS at time of procedure. Clinical success was defined as (i) clinical resolution of symptoms after the procedure and (ii) &gt;75% reduction in cyst size on computed tomography 8 weeks after stent placement. Adverse events including bleeding, stent migration, and infection were recorded.ResultsA total of 21 patients (13 males) had PFCs drainage with ELAMS in the study period. The mean age was 51.6 ± 14.2 years. Thirteen patients had walled-off necrosis while eight had a pancreatic pseudocyst. The mean size of the PFCs was 11.3 ± 3.3 cm. Fluoroscopy was used in seven cases (33%) and was associated with a longer procedure time compared to non-fluoroscopy (43.1 ± 10.4 vs 33.3 ± 10.5 min, P = 0.025). This association was independent of the size, location, or type of PFCs. Fluoroscopy had no effect on the technical success rates. In fluoroless procedures, the clinical resolution was 91% as compared to 71% in fluoroscopy procedures (P = 0.52) and the radiologic resolution was 57% as compared to 71% in fluoroscopy procedures (P = 0. 65). Three cases of stent migration/displacement occurred in the fluoroless procedures.ConclusionsELAMS may avoid the need for fluoroscopy during cystogastrostomy. Procedures without fluoroscopy were significantly shorter and fluoroscopy use had no impact on the technical or clinical success rates.
Species-level evaluation of the human respiratory microbiome
Authors: Ibironke Olufunmilola , McGuinness Lora R , Lu Shou-En , Wang Yaquan , Hussain Sabiha , Weisel Clifford P , Kerkhof Lee J 
Published: April 2020

Abstract

Background
Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract.

Findings
Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ~600,000 rRNA reads passing quality assurance/quality control (70–95% identify; &gt;1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (&gt;750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (&lt;5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis.

Conclusions
Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, &gt;100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.
Building envelope and energy saving case study: a residential building in Al-Riyadh, Saudi Arabia
Authors: Al-Qahtani Laila Amer Hashem , Elgizawi Lamis Saad Eldeen 
Published: April 2020

Abstract
Around the world, most energy is consumed by buildings; residential buildings consume 40% of energy globally. In the Kingdom of Saudi Arabia (KSA), buildings consume 50% of all energy, and 70% of the buildings in the KSA are not insulated well. Creating an envelope is a key to decreasing energy consumption and providing thermal comfort and healthy internal spaces. Thus, the main aim of this study is to test the effect of selected passive cooling strategies by using a simulation program to evaluate a variety of envelope (floor, external and internal walls and roofs) thermal characteristic proposals to create an eco-interior space, to provide the most comfortable conditions for users and to save energy in buildings in hot climates in Riyadh, Saudi Arabia. One residential building case was selected, and some of the passive cooling strategies were tested. Simulation software—Design Builder—was used to calculate the total energy consumption in 1 year and compare the results before and after applying these strategies to the selected residential building.
Robust integrated covariance intersection fusion Kalman estimators for networked mixed uncertain time-varying systems
Authors: Gao Yuan , Deng Zili 
Published: April 2020

Abstract
For the multisensor time-varying networked mixed uncertain systems with random one-step sensor delays and uncertain-variance multiplicative and linearly dependent additive white noises, a new augmented state method with fictitious noises is presented, by which the original system is transformed into a standard system without delays and with uncertain-variance fictitious white noises. According to the minimax robust estimation principle and the Kalman filtering theory, based on the worst-case system with the conservative upper bounds of uncertain noise variances, the local and integrated covariance intersection (ICI) fused robust time-varying Kalman estimators (filter, predictor and smoother) are presented respectively in the sense that their actual estimation error variances are guaranteed to have the corresponding minimal upper bounds for all admissible uncertainties. Their robustness is proved by the extended Lyapunov equation method, and their accuracy relations are compared based on the traces of the variance matrices and the covariance ellipsoids, respectively. Specially, a universal ICI fusion robust Kalman filtering method of integrating the local robust estimators and their conservative cross-covariances is presented. It overcomes the drawbacks of the original covariance intersection (CI) fusion method and improves robust accuracy of the original CI fuser. A simulation example applied to two-mass spring system shows the effectiveness of the proposed methods and results.
Strongyloides stercoralis Coinfection Is Associated With Greater Disease Severity, Higher Bacterial Burden, and Elevated Plasma Matrix Metalloproteinases in Pulmonary Tuberculosis
Authors: Kumar Nathella P , Kathamuthu Gokul R , Moideen Kadar , Banurekha Vaithilingam V , Nair Dina , Fay Michael P , Nutman Thomas B , Babu Subash 
Published: April 2020

AbstractBackgroundHelminths and tuberculosis (TB) largely overlap at the population level. Whether helminth infections influence disease severity and bacterial burdens in TB is not well understood.MethodsThis study was conducted to examine the disease severity in a cohort of pulmonary TB (PTB) individuals with (Ss+) or without (Ss−) seropositivity for Strongyloides stercoralis infection.ResultsSs+ was associated with increased risk of cavitation (odds ratio [OR], 4.54; 95% confidence interval [CI], 2.33–9.04; P &lt; .0001) and bilateral lung involvement (OR, 5.97; 95% CI, 3.03–12.09; P &lt; .0001) in PTB individuals. Ss+ was also associated with higher bacterial burdens (OR, 7.57; 95% CI, 4.18–14.05; P &lt; .0001) in PTB individuals. After multivariate analysis adjusting for covariates, Ss+ was still associated with greater risk of cavitation (adjusted OR [aOR], 3.99; 95% CI, 1.73–9.19; P = .0014), bilateral lung involvement (aOR, 4.09; 95% CI, 1.78–9.41; P = .0011), and higher bacterial burden (aOR, 9.32; 95% CI, 6.30–13.96; P &lt; .0001). Finally, Ss+ was also associated with higher plasma levels of matrix metalloproteinases ([MMP]-1, -2, -7, -8, and -9) in PTB individuals.ConclusionsTherefore, our data demonstrate that coexistent Ss infection is associated with greater disease severity and higher bacterial burden in PTB. Our data also demonstrate enhanced plasma levels of MMPs in coinfected individuals, suggesting a plausible biological mechanism for these effects.