bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scattering in gapped graphene quantum dot with magnetic flux
Authors: Lemaalem Bouchaib , Belouad Abdelhadi , Mekkaoui Miloud , Jellal Ahmed 
Published: September 2020

Abstract
We study the propagation of electrons in a circular quantum dot of gapped graphene subject to the magnetic flux ϕ. We present analytical expressions for the eigenstates, scattering coefficients, scattering efficiency and radial component of the reflected current. We identify different scattering regimes as a function of the physical parameters such as the incident electronic energy, potential barrier, radius of quantum dot, gap and ϕ. We choose two values of the flux ϕ = 1/2, 3/2 and show that for low energy of the incident electron, the scattering resonances appear and the far-field scattered current presents distinct preferred scattering directions.
Acoustoelectric imaging of deep dipoles in a human head phantom for guiding treatment of epilepsy
Authors: Barragan Andres , Preston Chet , Alvarez Alex , Bera Tushar , Qin Yexian , Weinand Martin , Kasoff Willard , Witte Russell S 
Published: September 2020

Abstract

Objective. This study employs a human head model with real skull to demonstrate the feasibility of transcranial acoustoelectric brain imaging (tABI) as a new modality for electrical mapping of deep dipole sources during treatment of epilepsy with much better resolution and accuracy than conventional mapping methods. Approach. This technique exploits an interaction between a focused ultrasound (US) beam and tissue resistivity to localize current source densities as deep as 63 mm at high spatial resolution (1 to 4 mm) and resolve fast time-varying currents with sub-ms precision. Main results. Detection thresholds through a thick segment of the human skull at biologically safe US intensities was below 0.5 mA and within range of strong currents generated by the human brain. Significance. This work suggests that 4D tABI may emerge as a revolutionary modality for real-time high-resolution mapping of neuronal currents for the purpose of monitoring, staging, and guiding treatment of epilepsy and other brain disorders characterized by abnormal rhythms.
Comparison of signal decomposition techniques for analysis of human cortical signals
Authors: Duraivel Suseendrakumar , Rao Akshay T , Lu Charles W , Bentley J Nicole , Stacey William C , Chestek Cynthia A , Patil Parag G 
Published: September 2020

Abstract

Objective. Conventional neural signal analysis methods assume that features of interest are linear, time-invariant signals confined to well-delineated spectral bands. However, new evidence suggests that neural signals exhibit important non-stationary characteristics with ill-defined spectral distributions. These features pose a need for signal processing algorithms that can characterize temporal and spectral features of non-linear time series. This study compares the effectiveness of four algorithms in extracting neural information for use in decoding cortical signals: Fast Fourier Transform bandpass filtering (FFT), principal spectral component analysis (PSCA), wavelet analysis (WA), and empirical mode decomposition (EMD). Approach. Electrocorticographic signals were recorded from the motor and sensory cortex of two epileptic patients performing finger movements. Each signal processing algorithm was used to extract beta (10–30 Hz) and gamma (66–114 Hz) band power to detect thumb movement and decode finger flexions, respectively. Naïve-Bayes (NB), support vector machine (SVM), and linear discriminant analysis (LDA) classifiers using each signal were validated using leave-one-out cross-validation. Main results. Decoders using all four signal decompositions achieved above 90% average accuracy in finger movement detection using beta power. When decoding individual finger flexion using gamma, the PSCA NB classifiers achieved 78 ± 4% accuracy while FFT, WA, and EMD analysis achieved accuracies of 73 ± 8%, 68 ± 7%, and 62 ± 3% respectively, with similar results using SVM and LDA. Significance. These results illustrate the relative levels of useful information contributed by each decomposition method in the case of finger movement decoding, which can inform the development of effective neural decoding pipelines. Further analyses could compare performance using more specific non-sinusoidal features, such as transients and phase-amplitude coupling.
A combination of hydrogen bonding and chemical covalent crosslinking to fabricate a novel swim-bladder-derived dry heart valve material yields advantageous mechanical and biological properties
Authors: Lan Xiaorong , Zhao Qianting , Zhang Jiayi , Lei Yang , Wang Yunbing 
Published: September 2020

Abstract
The current biological valve products used in transcatheter aortic valve replacement (TAVR) are mainly made of glutaraldehyde (GLUT)-crosslinked porcine and bovine pericardia, which need to be transported and stored in GLUT solution. This leads to prolonged preparation time and the presence of GLUT residue. Therefore, there has been interest in developing TAVR valves using a pre-crimped valve (also known as a dry valve). Herein, a natural, inexpensive, and widely available swim bladder was selected as the source of a biological valve functioning as a dry valve and was obtained via acellular processes and crosslinking fixation. With the help of multiple hydrogen bonds between polyphenols (represented by procyanidin and curcumin) and tissue, as well as the chemical crosslinking of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC) with tissue, we found that this novel combined crosslinking method was able to successfully crosslink with an acellular swim bladder. The stabilities, mechanical properties, resistance to pre-folding/pre-compressing, flattening capability in water, hemocompatibility, cytocompatibility, and anti-calcification capability were systematically measured via a series of experiments. We demonstrated that this dry valve resulting from a combination of EDC/polyphenols exhibited superior properties compared with those of a control pericardial-based valve.
Use of Ethanol-Based Hand Disinfectants: Source of Increased Ethyl Glucuronide Levels in Hair?
Authors: Scholz Clementine , Baumgartner Markus R , Madry Milena M 
Published: September 2020

Abstract

Aim
Due to the COVID-19 pandemic increasing the use of hand disinfectants, we investigated the effect of frequent use of ethanol-based hand disinfectants (EBHD) on the levels of the alcohol marker ethyl glucuronide (EtG) in hair.

Method
Hair samples were collected from 10 health professionals (8 nondrinkers, 2 rarely drinking individuals) and EtG was examined in hair.

Result
EtG (~2 pg/mg) was only detected in the hair sample of a nondrinker using EBHD 60–70 times per working day.

Conclusion
Our data provide no evidence that frequent EBHD use results in hair EtG levels above the recommended Society of Hair Testing cutoff for repeated alcohol consumption (5 pg/mg).
Irregular adaxial–abaxial polarity rearrangement contributes to the monosymmetric-to-asymmetric transformation of Canna indica stamen
Authors: Tian Xueyi , Li Xiaorong , Yu Qianxia , Zhao Haichan , Song Juanjuan , Liao Jingping 
Published: September 2020

AbstractIn flowering plants, lateral organs including stamens develop according to the precise regulation of adaxial–abaxial polarity. However, the polarity establishment process is poorly understood in asymmetric stamens. Canna indica (Zingiberales: Cannaceae) is a common ornamental plant with an asymmetric stamen comprising a one-theca anther and a petaloid appendage. In this study, we depicted the monosymmetric-to-asymmetric morphogenesis of C. indica stamen, and the morphogenesis of the monosymmetric stamen of a sister species was used as a contrast. We chose a HD-ZIP III gene family member and a YABBY family member as the adaxial and abaxial polarity marker genes, respectively, and tested their expression using mRNA in situ hybridization. The expression patterns of the two genes changed dynamically and asymmetrically during the stamen development process. Compared with their homologues in Arabidopsis thaliana, these two genes exhibited some specific expression patterns. We hypothesize that the distinctive adaxial–abaxial polarity participates in the irregular morphogenesis of C. indica stamen, which mediates the putative stamen-to-petaloid staminode conversion in this species.
History in Person: A Longitudinal Study of a Language Learner’s Experience at Home and Abroad
Authors: Lee Sheng-Hsun 
Published: September 2020

Abstract
This study explores the longitudinal pathway of social identification traveled by a US learner of Chinese, Tom. Focusing on the historical production of persons, I analyze interactional recordings, instructional artifacts, and participant interviews collected over three years of qualitative inquiry. The analysis articulates how Tom’s narrative of intercultural encounters was reframed, rekeyed, and recycled at home and abroad. Along the way, Tom was identified as (i) an avid learner of Chinese in a language classroom in the USA; (ii) an ignorant foreigner while studying in China; and (iii) a political outcast upon his return to the USA whose intercultural experience abroad, nevertheless, afforded his classmates an opportunity to appreciate a more ethno-relative perspective. The consonance and dissonance of identification are results of interplay between history in person and history in institutionalized struggles. This interplay must be considered to understand the (re)making of language-learning identities across historical time, social space, and communicative modes. The findings illustrate how history, social identification, and engagement in intercultural communication mutually inform each other in and beyond transnational mobility.
Brief iPad-Based Assessment of Cognitive Functioning with ImPACT® Quick Test: Prevalence of Low Scores Using Multivariate Base Rates
Authors: Wallace Jessica , Schatz Philip , Covassin Tracey , Iverson Grant L 
Published: September 2020

AbstractObjectiveThe ImPACT® Quick Test is a brief iPad-based battery of neurocognitive tests that has been standardized on a sample of children, adolescents, and adults (ages 12–70). This study provides information on the prevalence of ImPACT® Quick Test scores falling below specific percentiles in the normative sample to aid in clinical interpretation and reduce the risk of over-interpreting, or misinterpreting, a single low score.MethodParticipants were 683 individuals ranging in age from 12 to 70, who were assessed individually. The ImPACT® Quick Test includes five subtests, contributing to three factor scores: motor speed, memory, and attention tracker. The prevalence of low factor scores, stratified by age and sex, were calculated using multivariate base rates.ResultsIn the total sample, obtaining 1 or more scores below the 25th percentile was common (base rate, BR = 47.2%), but obtaining 2 or more scores in this range was uncommon (BR = 15.3%). Similarly, obtaining 1 or more scores below the 16th percentile was common (BR = 31.4%), but obtaining two or more scores in this range was uncommon (BR = 6.9%). There were small differences in BRs between sexes and the number of low scores was fairly similar across the age groups.ConclusionResults from this study parallel previous work illustrating that a substantial percentage of healthy individuals will obtain one or more low test scores when administered a brief battery of cognitive tests. Given that some healthy individuals will obtain a single score below expected cut-offs, clinicians should caution against overinterpreting a single low test score.
A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear
Authors: Cai Jinpu , Xu Yuyang , Zhang Wen , Ding Shiying , Sun Yuewei , Lyu Jingyi , Duan Meiyu , Liu Shuai , Huang Lan , Zhou Fengfeng 
Published: September 2020

AbstractMotivation: DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. Methods: This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. Results: A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
3-Dimensional Printed Alternative to the Standard Synthetic Flocked Nasopharyngeal Swabs Used for Coronavirus Disease 2019 Testing
Authors: Decker Summer J , Goldstein Todd A , Ford Jonathan M , Teng Michael N , Pugliese Robert S , Berry Gregory J , Pettengill Matthew , Silbert Suzane , Hazelton Todd R , Wilson Jason W , Shine Kristy , Wang Zi-Xuan , Hutchinson Morgan , Castagnaro Joseph , Bloom Ona E , Breining Dwayne A , Goldsmith Barbara M , Sinnott John T , O’Donnell Donna Gentile , Crawford James M , Lockwood Charles J , Kim Kami 
Published: September 2020

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), can be detected in respiratory samples by real-time reverse transcriptase polymerase chain reaction (RT-PCR) or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs.MethodsWe developed a 3-dimensional printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at 3 clinical sites (n = 291) using 3 SARS-CoV-2 emergency use authorization tests: a modified version of the Centers for Disease Control and Prevention (CDC) RT-PCR Diagnostic Panel and 2 commercial automated formats, Roche Cobas and NeuMoDx.ResultsThe cycle threshold—C(t)—values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (P = .152 and P = .092), with the RNase P target performing significantly better in the 3DP swabs (P &lt; .001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (P = .05 and P = .05) as well as the NeuMoDx assay (P = .401 and P = .484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901).ConclusionsThe 3DP swabs were equivalent to standard FLNP in 3 testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed onsite are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.
Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression
Authors: de Vries Sophie , de Vries Jan , Archibald John M , Slamovits Claudio H 
Published: September 2020

ABSTRACTOomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
Abundance of Noncircular Intrahepatic Hepatitis B Virus DNA May Reflect Frequent Integration Into Human DNA in Chronically Infected Patients
Authors: Rydell Gustaf E , Larsson Simon B , Prakash Kasthuri , Andersson Maria , Norder Heléne , Hellstrand Kristoffer , Norkrans Gunnar , Lindh Magnus 
Published: September 2020

Abstract

Background
Hepatitis B virus (HBV) integration has implications for cancer development and surface antigen (HBsAg) production, but methods to quantify integrations are lacking. The aim of this study was to develop a droplet digital PCR (ddPCR) assay discriminating between circular and integrated HBV DNA, and to relate the distribution between the two forms to other HBV markers.

Methods
ddPCR with primers spanning the typical linearization breakpoint in the HBV genome allowed for quantification of the absolute copy numbers of total and circular HBV DNA, and calculation of linear HBV DNA.

Results
Analysis of 70 liver biopsies from patients with chronic HBV infection revealed that the fraction of linear HBV DNA, which includes integrations, was higher in HBeAg-negative patients than HBeAg-positive. The ratio between HBsAg and HBV DNA levels in serum correlated with the intrahepatic proportion of linear HBV DNA. Furthermore, ddPCR experiments on serum samples and experiments with nuclease indicated the contribution of encapsidated double-stranded linear DNA and replication intermediates to be limited.

Conclusions
The degree of integration of intrahepatic HBV DNA in the HBeAg-negative stage may be higher than previously anticipated, and integrated DNA may explain the persistence of high HBsAg serum levels in patients with low HBV DNA levels.
Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection
Authors: Grier Alex , Gill Ann L , Kessler Haeja A , Corbett Anthony , Bandyopadhyay Sanjukta , Java James , Holden-Wiltse Jeanne , Falsey Ann R , Topham David J , Mariani Thomas J , Caserta Mary T , Walsh Edward E , Gill Steven R 
Published: September 2020

Abstract

Background
Respiratory syncytial virus (RSV) is a leading cause of infant respiratory disease. Infant airway microbiota has been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respiratory disease susceptibility and severity, are unknown.

Methods
We carried out 16S rRNA microbiota profiling of infants in the first year of life from (1) a cross-sectional cohort of 89 RSV-infected infants sampled during illness and 102 matched healthy controls, and (2) a matched longitudinal cohort of 12 infants who developed RSV infection and 12 who did not, sampled before, during, and after infection.

Results
We identified 12 taxa significantly associated with RSV infection. All 12 taxa were differentially abundant during infection, with 8 associated with disease severity. Nasal microbiota composition was more discriminative of healthy vs infected than of disease severity.

Conclusions
Our findings elucidate the chronology of nasal microbiota dysbiosis and suggest an altered developmental trajectory associated with RSV infection. Microbial temporal dynamics reveal indicators of disease risk, correlates of illness and severity, and impact of RSV infection on microbiota composition.
Postmortem Findings in Italian Patients With COVID-19: A Descriptive Full Autopsy Study of Cases With and Without Comorbidities
Authors: Falasca Laura , Nardacci Roberta , Colombo Daniele , Lalle Eleonora , Di Caro Antonino , Nicastri Emanuele , Antinori Andrea , Petrosillo Nicola , Marchioni Luisa , Biava Gianluigi , D’Offizi Gianpiero , Palmieri Fabrizio , Goletti Delia , Zumla Alimuddin , Ippolito Giuseppe , Piacentini Mauro , Del Nonno Franca 
Published: September 2020

AbstractBackgroundDescriptions of the pathological features of coronavirus disease-2019 (COVID-19) caused by the novel zoonotic pathogen severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emanate from tissue biopsies, case reports, and small postmortem studies restricted to the lung and specific organs. Whole-body autopsy studies of COVID-19 patients have been sparse.MethodsTo further define the pathology caused by SARS-CoV-2 across all body organs, we performed autopsies on 22 patients with COVID-19 (18 with comorbidities and 4 without comorbidities) who died at the National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS Hospital, Rome, Italy. Tissues from the lung, heart, liver, kidney, spleen, and bone marrow (but not the brain) were examined. Only lung tissues were subject to transmission electron microscopy.ResultsCOVID-19 caused multisystem pathology. Pulmonary and cardiovascular involvement were dominant pathological features. Extrapulmonary manifestations included hepatic, kidney, splenic, and bone marrow involvement, and microvascular injury and thrombosis were also detected. These findings were similar in patients with or without preexisting medical comorbidities.ConclusionsSARS-CoV-2 infection causes multisystem disease and significant pathology in most organs in patients with and without comorbidities.