bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surface plasmon dispersion and modes on the graphene metasurface with periodical ribbon arrays
Authors: Liu Yong-Qiang , Li Liangsheng , Yin Hongcheng 
Published: June 2020

Abstract
Graphene plasmonics on the structured metasurface demonstrate many exotic properties which can combine novel nanomaterials and well-established plasmonics, providing unique opportunities to develop a series of novel photonic, plasmonic and optoelectronic devices across a wideband spectrum. Dispersion theory and its propagating characteristics of surface plasmon polaritons (SSPs) mode along the graphene metasurface can provide a powerful guidance to design related devices and systems. In this paper, the fundamental dispersion theory and the numerical studies of graphene SSPs (GSPs) on a graphene metasurface i.e. periodical ribbon arrays which are bounded by a superstrate and substrate dielectric are presented. The dispersion expression of GSPs is deduced and revealed by a modal expansion method combined with periodical boundary conditions on the structure. According to this fully analytical dispersion expression of SSPs mode on the graphene metasurface, the dispersion characteristics, propagation loss and field profiles of SSPs mode with different graphene material parameters (e.g. graphene ribbon width and chemical potential) and bounded dielectric mediums are studied and analyzed in detail in terahertz (THz) band. Moreover, the dynamical tunable dispersion characteristics of SSPs mode on the graphene metasurface via electrostatic gating of a ground metal plate can be readily obtained by applying a graphene biased voltage model to this analytical dispersion theory. The presented studies on the dispersion theory of the graphene metasurface provide an analytical method to understand the propagation characteristics of SSPs mode on the structure. Besides, the calculation results on the structure can also be used to design some novel graphene-based optoelectronic and plasmonic devices with planar gradient-index distributions such as couplers, tunable focused lens and enhanced radiation sources in THz band.
Regime-Centered and Court-Centered Understandings: The Reception of American Constitutional Law in Contemporary China†
Authors: Liu Han 
Published: June 2020

Abstract
American constitutional law haunts the contemporary Chinese constitutional imagination. China’s reception of American constitutional law occurred in two major stages. In the first stage, which spanned from the 1980s to the early 1990s, Chinese intellectuals understood American constitutionalism as a particular political regime to be politically criticized or objectively appraised, with the tripartite separation of powers overwhelmingly highlighted as a core feature of the American constitutional-political system. In the second stage, which began in the late 1990s, a paradigmatic shift from a political, regime-centered perspective to a legalized, court-centered approach occurred in China’s introductions to and studies of American constitutionalism. The U.S. Supreme Court and the concept of judicial review now primarily preoccupy most Chinese constitutional minds; these features of the American system have formed the focal points of reference for Chinese constitutional reform. This shift from the first stage to the second reflects both ideological and social changes since the economic reform in China, as well as international impacts.
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
Authors: Srivastava Avi , Malik Laraib , Sarkar Hirak , Patro Rob 
Published: June 2020

Abstract

Motivation
Droplet-based single-cell RNA-seq (dscRNA-seq) data are being generated at an unprecedented pace, and the accurate estimation of gene-level abundances for each cell is a crucial first step in most dscRNA-seq analyses. When pre-processing the raw dscRNA-seq data to generate a count matrix, care must be taken to account for the potentially large number of multi-mapping locations per read. The sparsity of dscRNA-seq data, and the strong 3’ sampling bias, makes it difficult to disambiguate cases where there is no uniquely mapping read to any of the candidate target genes.

Results
We introduce a Bayesian framework for information sharing across cells within a sample, or across multiple modalities of data using the same sample, to improve gene quantification estimates for dscRNA-seq data. We use an anchor-based approach to connect cells with similar gene-expression patterns, and learn informative, empirical priors which we provide to alevin’s gene multi-mapping resolution algorithm. This improves the quantification estimates for genes with no uniquely mapping reads (i.e. when there is no unique intra-cellular information). We show our new model improves the per cell gene-level estimates and provides a principled framework for information sharing across multiple modalities. We test our method on a combination of simulated and real datasets under various setups.

Availability and implementation
The information sharing model is included in alevin and is implemented in C++14. It is available as open-source software, under GPL v3, at https://github.com/COMBINE-lab/salmon as of version 1.1.0.
GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form
Authors: Meng Qingxi , Ochoa Idoia , Hernaez Mikel 
Published: June 2020

Abstract

Motivation
Sequencing data are often summarized at different annotation levels for further analysis, generally using the general feature format (GFF) or its descendants, gene transfer format (GTF) and GFF3. Existing utilities for accessing these files, like gffutils and gffread, do not focus on reducing the storage space, significantly increasing it in some cases. We propose GPress, a framework for querying GFF files in a compressed form. GPress can also incorporate and compress expression files from both bulk and single-cell RNA-Seq experiments, supporting simultaneous queries on both the GFF and expression files. In brief, GPress applies transformations to the data which are then compressed with the general lossless compressor BSC. To support queries, GPress compresses the data in blocks and creates several index tables for fast retrieval.

Results
We tested GPress on several GFF files of different organisms, and showed that it achieves on average a 61% reduction in size with respect to gzip (the current de facto compressor for GFF files) while being able to retrieve all annotations for a given identifier or a range of coordinates in a few seconds (when run in a common laptop). In contrast, gffutils provides faster retrieval but doubles the size of the GFF files. When additionally linking an expression file, we show that GPress can reduce its size by more than 68% when compared to gzip (for both bulk and single-cell RNA-Seq experiments), while still retrieving the information within seconds. Finally, applying BSC to the data streams generated by GPress instead of to the original file shows a size reduction of more than 44% on average.

Availability and implementation
GPress is freely available at https://github.com/qm2/gpress.

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulation, power evaluation and sample size recommendation for single-cell RNA-seq
Authors: Su Kenong , Wu Zhijin , Wu Hao 
Published: June 2020

Abstract

Motivation
Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge.

Results
We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA-sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship. The data simulator in POWSC outperforms two other state-of-art simulators in capturing key characteristics of real datasets. The power assessor in POWSC provides a variety of power evaluations including stratified and marginal power analyses for DEs characterized by two forms (phase transition or magnitude tuning), under different comparison scenarios. In addition, POWSC offers information for optimizing the tradeoffs between sample size and sequencing depth with the same total reads.

Availability and implementation
POWSC is an open-source R package available online at https://github.com/suke18/POWSC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome
Authors: Casimiro-Soriguer C S , Rigual M M , Brokate-Llanos A M , Muñoz M J , Garzón A , Pérez-Pulido A J , Jimenez J 
Published: June 2020

Abstract

Motivation
Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance.

Results
AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes.

Availability and implementation
AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans.

Supplementary information
Supplementary data are available at Bioinformatics online.
Is Childhood Obesity a Child Protection Concern?
Authors: Nelson Peter , Bissell Paul , Homer Catherine , Pollard Lee , Powell-Hoyland Vanessa 
Published: June 2020

AbstractChildhood obesity is a key public health concern. Obesity has an impact on morbidity and mortality, child development, and has links to child sexual abuse. The costs of childhood obesity on the health service and society are well recognised. Whether childhood obesity should also be a child protection concern has divided commentators and professionals. They pose a juxtaposition questioning whether childhood obesity is a consequence of neglect and obese children should potentially be removed from parents who do not seek to reduce their child’s weight, whilst expressing resistance to a role focused on bodily surveillance. This research sought to identify existing practice, through interviews (N23) and focus groups (N3:24) with key professional stakeholders, from social care, health and education, in one area in the UK. The research aimed to explore the decision-making, views and experiences of those working with obesity and the child protection system. The data were subject to Framework Analysis. Key findings include multi-agency working, personal and professional standpoint, and the complex and nuanced impact of individual and agency thresholds on practice. The research demonstrates how the tensions surrounding a child protection paradigm impact on individual and agency practice, potentially inhibiting the support offered to service users.
Age-Related Compensatory Reconfiguration of PFC Connections during Episodic Memory Retrieval
Authors: Deng Lifu , Stanley Mathew L , Monge Zachary A , Wing Erik A , Geib Benjamin R , Davis Simon W , Cabeza Roberto 
Published: June 2020

AbstractDuring demanding cognitive tasks, older adults (OAs) frequently show greater prefrontal cortex (PFC) activity than younger adults (YAs). This age-related increase in PFC activity is often associated with enhanced cognitive performance, suggesting functional compensation. However, the brain is a complex network of interconnected regions, and it is unclear how network connectivity of PFC regions differs for OAs versus YAs. To investigate this, we examined the age-related difference on the functional brain networks mediating episodic memory retrieval. YAs and OAs participants encoded and recalled visual scenes, and age-related differences in network topology during memory retrieval were investigated as a function of memory performance. We measured both changes in functional integration and reconfiguration in connectivity patterns. The study yielded three main findings. First, PFC regions were more functionally integrated with the rest of the brain network in OAs. Critically, this age-related increase in PFC integration was associated with better retrieval performance. Second, PFC regions showed stronger performance-related reconfiguration of connectivity patterns in OAs. Finally, the PFC reconfiguration increases in OAs tracked reconfiguration reductions in the medial temporal lobe (MTL)—a core episodic memory region, suggesting that PFC connectivity in OAs may be compensating for MTL deficits.
Development of an HPLC Method for the Determination of Meropenem/Vaborbactam in Biological and Aqueous Matrixes
Authors: Sutherland Christina A , Nicolau David P 
Published: June 2020

Abstract
A HPLC method was developed and validated to analyze meropenem and vaborbactam simultaneously in murine plasma and saline matrixes. A 60-μL volume of extracted sample was injected onto a 5-μm BDS Phenyl-Hypersil C18 reversed-phase column and analyzed with a UV detector set at 298 nm for the first 4.9 min and switched to 240 nm. The mobile phase contained a mixture of methanol and 25-mM sodium phosphate buffer set at a flow rate of 1.0 mL/min for the 16 min run time. Cefuroxime was used as the internal standard. The standard curves were linear over a range of 0.25–50 μg/mL. The precision and accuracy for 0.25 μg/mL (LLQ) in plasma for both compounds were &lt;4.8% and &gt;98.9%, respectively. Interday and intraday precision and accuracy for all QC plasma samples for both compounds were &lt;6.2% and &gt;95.7%, respectively. This methodology details a reproducible assay for both compounds using a single extraction with good accuracy and precision.
Social Distancing Alters the Clinical Course of COVID-19 in Young Adults: A Comparative Cohort Study
Authors: Bielecki Michel , Züst Roland , Siegrist Denise , Meyerhofer Daniele , Crameri Giovanni Andrea Gerardo , Stanga Zeno , Stettbacher Andreas , Buehrer Thomas Werner , Deuel Jeremy Werner 
Published: June 2020

Abstract

Background
Social distancing and stringent hygiene seem to be effective in reducing the number of transmitted virus particles, and therefore the infectivity, of coronavirus disease 2019 (COVID-19) and could alter the mode of transmission of the disease. However, it is not known if such practices can change the clinical course in infected individuals.

Methods
We prospectively studied an outbreak of COVID-19 in Switzerland among a population of 508 predominantly male soldiers with a median age of 21 years. We followed the number of infections in 2 spatially separated cohorts with almost identical baseline characteristics with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) before and after implementation of stringent social distancing.

Results
Of the 354 soldiers infected prior to the implementation of social distancing, 30% fell ill from COVID-19, while no soldier in a group of 154, in which infections appeared after implementation of social distancing, developed COVID-19 despite the detection of viral RNA in the nasal and virus-specific antibodies within this group.

Conclusions
Social distancing not only can slow the spread of SARS-CoV-2 in a cohort of young, healthy adults but it can also prevent the outbreak of COVID-19 while still inducing an immune response and colonizing nasal passages. Viral inoculum during infection or mode of transmission may be a key factor determining the clinical course of COVID-19.
A heart transplant after total artificial heart support: initial and long-term results
Authors: David Charles-Henri , Lacoste Philippe , Nanjaiah Prakash , Bizouarn Philippe , Lepoivre Thierry , Michel Magali , Pattier Sabine , Toquet Claire , Périgaud Christian , Mugniot Antoine , Al Habash Ousama , Petit Thierry , Groleau Nicolas , Rozec Bertrand , Trochu Jean Noel , Roussel Jean Christian , Sénage Thomas 
Published: June 2020

Abstract

OBJECTIVES

At our centre, the SynCardia temporary Total Artificial Heart (TAH-t) (SynCardia Systems, LLC, Tucson, AZ, USA) is used to provide long-term support for patients with biventricular failure as a bridge to a transplant. However, a heart transplant (HT) after such support remains challenging. The aim of this retrospective study was to assess the immediate and long-term results following an HT in the cohort of patients who had a TAH-t implant.

METHODS
A total of 73 patients were implanted with the TAH-t between 1988 and 2019 in our centre. Of these 73 consecutive patients, 50 (68%) received an HT and are included in this retrospective analysis of prospectively collected data.

RESULTS
In the selected cohort, in-hospital mortality after an HT was 10% (n = 5). The median intensive care unit stay was 33 days (range 5–278). The median hospital stay was 41 days (range 28–650). A partial or total pericardiectomy was performed during the HT procedure in 21 patients (42%) due to a severe pericardial reaction. Long-term survival rates after an HT at 5, 10 and 12 years were 79.1 ± 5.9% (n = 32), 76.5 ± 6.3% (n = 22) and 72.4 ± 7.1% (n = 12), respectively, which was similar to the long-term survival for a primary HT without TAH-t during the same period (n = 686). An HT performed within 3–6 months post-TAH-t implantation appeared to provide the best survival (P = 0.007). Eight (16%) patients required chronic dialysis during the subsequent follow-up period, with 3 patients requiring a kidney transplant.

CONCLUSIONS
The long-term outcomes with the SynCardia TAH-t as a bridge to transplant in patients with severe biventricular failure are very encouraging. Our review noted that an HT following TAH-t can be technically challenging, especially in the case of a severe pericardial reaction, with potential pitfalls that should be recognized preoperatively.
Why is preventing antibiotic resistance so hard? Analysis of failed resistance management
Authors: Zhou Shiwei , Barbosa Camilo , Woods Robert J 
Published: June 2020

Abstract
We describe the case of a patient with pancreatitis followed by intra-abdominal infection in which source control was not achieved. Antimicrobial therapy led to the emergence of resistance in multiple organisms through multiple population dynamics processes. While the initial insult was not due to infection, subsequent infections with resistant organisms contributed to a poor outcome for the patient. Though resistance evolution was a known risk, it was difficult to predict the next organism that would arise in the setting of antibiotic pressure and its resistance profile. This case illustrates the clinical challenge of antibiotic resistance that current approaches cannot readily prevent.
LAY SUMMARY
Why is antibiotic resistance management so complex? Distinct evolutionary processes unfold when antibiotic treatment is initiated that lead, separately and together, to the undesired outcome of antibiotic resistance. This clinical case exemplifies some of those processes and highlights the dire need for evolutionary risk assessments to be incorporated into clinical decision making.
Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation
Authors: Li Zhipeng , Shen Junshi , Xu Yixuan , Zhu Weiyun 
Published: June 2020

ABSTRACT
Urea is a cost-effective replacement for feed proteins in ruminant diets. However, its metabolism by the rumen microbiome is not fully understood. Here, rumen contents were collected from 18 male sheep fed one of the following three treatments: a low N basal diet with no urea (UC, 0 g/kg dry matter (DM)), low urea (LU, 10 g/kg DM) and high urea (HU, 30 g/kg DM). Principal coordinate analysis showed that the microbial composition and functional profiles of the LU treatment significantly differed from the UC and HU treatments. The genera Prevotella, Succinivibrio, Succinatimonas and Megasphaera were higher in the LU rumen, while the genera Clostridium, Ruminococcus and Butyrivibrio were enriched in the UC and HU rumen. The aspartate–glutamate and arginine–proline metabolic pathways and valine, leucine and isoleucine biosynthesis were higher in the LU rumen. The cysteine and methionine metabolism, lysine degradation and fructose and pentose phosphate metabolism pathways were higher in the UC and HU rumen. The protozoa population in the HU treatment was higher than in the UC and LU treatments. These findings suggest that the rumen microbiome of sheep fed low N diet with different urea supplementation are significantly different.
Polyphasic taxonomic analysis of Sinimarinibacterium arenosum sp. nov., a halophilic bacterium isolated from marine sediment
Authors: Kim Jong-Hwa , Baek Jihye , Yoon Jung-Hoon , Sukhoom Ampaitip , Kim Wonyong 
Published: June 2020

ABSTRACT
A Gram stain-negative, aerobic, motile, rod-shaped bacterial strain, designated CAU 1509T, was isolated from marine sediment, and its taxonomic position was determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1509T formed a distinct lineage within the genus Sinimarinibacterium with the highest 16S rRNA gene sequence similarity to Sinimarinibacterium flocculans NH6–24T (97.0%). Similar to another member of Sinimarinibacterium, ubiquinone-8 (Q-8) was the predominant quinone, whereas C16:0, summed feature 3 (C16:1ω7c/ω6c) and summed feature 8 (C18:1ω7c/ω6c) were the major cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, four unidentified glycolipids and three unidentified aminolipids. Strain CAU 1509T has a genome of 4.54 Mb, including 4251 coding sequences, 6 rRNAs and 50 tRNAs, with a genomic DNA G+C content of 63.2 mol%. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain CAU 1509T should be classified as a novel species of the genus Sinimarinibacterium, for which the name Sinimarinibacterium arenosum sp. nov. is proposed. The type strain is CAU 1509T (= KCTC 72000T = NBRC 113698T).
The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability
Authors: Börlin Christoph S , Nielsen Jens , Siewers Verena 
Published: June 2020

ABSTRACT
The main transcriptional regulator of leucine biosynthesis in the yeast Saccharomyces cerevisiae is the transcription factor Leu3. It has previously been reported that Leu3 always binds to its target genes, but requires activation to induce their expression. In a recent large-scale study of high-resolution transcription factor binding site identification, we showed that Leu3 has divergent binding sites in different cultivation conditions, thereby questioning the results of earlier studies. Here, we present a follow-up study using chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate the influence of leucine supplementation on Leu3 binding activity and strength. With this new data set we are able to show that Leu3 exhibits changes in binding activity in response to changing levels of leucine availability.