bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jamming of multiple persistent random walkers in arbitrary spatial dimension
Authors: Metson M J , Evans M R , Blythe R A 
Published: November 2020

AbstractWe consider the persistent exclusion process in which a set of persistent random walkers interact via hard-core exclusion on a hypercubic lattice inddimensions. We work within the ballistic regime whereby particles continue to hop in the same direction over many lattice sites before reorienting. In the case of two particles, we find the mean first-passage time to a jammed state where the particles occupy adjacent sites and face each other. This is achieved within an approximation that amounts to embedding the one-dimensional system in a higher-dimensional reservoir. Numerical results demonstrate the validity of this approximation, even for small lattices. The results admit a straightforward generalization to dilute systems comprising more than two particles. A self-consistency condition on the validity of these results suggest that clusters may form at arbitrarily low densities in the ballistic regime, in contrast to what has been found in the diffusive limit.
In and around abelian anyon models
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Authors: Wang Liang , Wang Zhenghan 
Published: November 2020

Abstract
Anyon models are algebraic structures that model universal topological properties in topological phases of matter and can be regarded as mathematical characterization of topological order in two spacial dimensions. It is conjectured that every anyon model, or mathematically unitary modular tensor category, can be realized as the representation category of some chiral conformal field theory, or mathematically vertex operator algebra/local conformal net. This conjecture is known to be true for abelian anyon models providing support for the conjecture. We reexamine abelian anyon models from several different angles. First anyon models are algebraic data for both topological quantum field theories and chiral conformal field theories. While it is known that each abelian anyon model can be realized by a quantum abelian Chern–Simons (CS) theory and chiral conformal field theory, the construction is not algorithmic. Our goal is to provide such an explicit algorithm for a K-matrix in CS theory and a positive definite even one for a lattice conformal field theory. Secondly anyon models and chiral conformal field theories underlie the bulk-edge correspondence for topological phases of matter. But there are interesting subtleties in this correspondence when stability of the edge theory and topological symmetry are taken into consideration. Therefore, our focus is on the algorithmic reconstruction of extremal chiral conformal field theories with small central charges. Finally we conjecture that a much stronger reconstruction holds for abelian anyon models: every abelian anyon model can be realized as the representation category of some non-lattice extremal vertex operator algebra generalizing the moonshine realization of the trivial anyon model.
Dirac cones for bi- and trilayer Bernal-stacked graphene in a quantum graph model
Authors: de Oliveira César R , Rocha Vinícius L 
Published: November 2020

Abstract
A quantum graph model for a single sheet of graphene is extended to bilayer and trilayer Bernal-stacked graphene; the spectra are characterized and the dispersion relations explicitly obtained; Dirac cones are then proven to be present only for trilayer graphene, although the bilayer has a gapless parabolic band component. Our model rigorously exhibits basic facts from tight-binding calculations, effective two-dimensional models and a π-orbital continuum model with nearest-neighbour tunnelling that have been discussed in the physics literature.
Anthropogenic noise disrupts mate choice behaviors in femaleGryllus bimaculatus
Authors: Bent Adam M , Ings Thomas C , Mowles Sophie L 
Published: November 2020

AbstractBy assessing the sexual signals produced by conspecifics, individuals can make informed decisions on the best choice of mate, which can lead to reproductive fitness benefits. However, these communication systems are often vulnerable to disruption by conflicting with stimuli present in the environment. Anthropogenic noise may act as one such disruptive stimulus, leading to inefficient mate choice decisions and, thus, reductions to an animal’s fitness. In this study, the mate choice behaviors of female Gryllus bimaculatus were tested when presented with artificial male courtship songs of differing “quality” under different acoustic conditions. In ambient noise conditions, females significantly preferred mates paired with higher-quality songs, indicated by increased mating rates and reduced latency to mate. However, this mate selection pattern was disrupted in both traffic and white noise conditions. Additionally, “high-quality” courtship songs had an increased mounting latency in traffic and white noise conditions, when compared to ambient noise conditions. Making nonoptimal mating decisions, such as the ones seen here, can lead to deleterious fitness consequences, alter population dynamics, and weaken sexual selection, unless individuals adapt to cope with anthropogenic interference.
A comprehensive survey on computational methods of non-coding RNA and disease association prediction
Authors: Lei Xiujuan , Mudiyanselage Thosini Bamunu , Zhang Yuchen , Bian Chen , Lan Wei , Yu Ning , Pan Yi 
Published: November 2020

AbstractThe studies on relationships between non-coding RNAs and diseases are widely carried out in recent years. A large number of experimental methods and technologies of producing biological data have also been developed. However, due to their high labor cost and production time, nowadays, calculation-based methods, especially machine learning and deep learning methods, have received a lot of attention and been used commonly to solve these problems. From a computational point of view, this survey mainly introduces three common non-coding RNAs, i.e. miRNAs, lncRNAs and circRNAs, and the related computational methods for predicting their association with diseases. First, the mainstream databases of above three non-coding RNAs are introduced in detail. Then, we present several methods for RNA similarity and disease similarity calculations. Later, we investigate ncRNA-disease prediction methods in details and classify these methods into five types: network propagating, recommend system, matrix completion, machine learning and deep learning. Furthermore, we provide a summary of the applications of these five types of computational methods in predicting the associations between diseases and miRNAs, lncRNAs and circRNAs, respectively. Finally, the advantages and limitations of various methods are identified, and future researches and challenges are also discussed.
Evaluating single-cell cluster stability using the Jaccard similarity index
Authors: Tang Ming , Kaymaz Yasin , Logeman Brandon L , Eichhorn Stephen , Liang Zhengzheng S , Dulac Catherine , Sackton Timothy B 
Published: November 2020

Abstract

Motivation
One major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor and the resolution parameters, among others.

Results
Here, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat and estimation of cluster stability using the Jaccard similarity index and providing rich visualizations.

Availabilityand implementation
R package scclusteval: https://github.com/crazyhottommy/scclusteval Snakemake workflow: https://github.com/crazyhottommy/pyflow_seuratv3_parameter Tutorial: https://crazyhottommy.github.io/EvaluateSingleCellClustering/.
RP-HPLC Analysis of Phenolic Lignin Monomers with DAD and Coulometric Array Detection
Authors: Fischer Klaus , Höffler Susanne 
Published: November 2020

Abstract
An high performance liquid chromatography (HPLC) method, applying diode array (DAD) and coulometric array detection simultaneously, was developed to determine monomeric phenolic compounds in lignin hydrolysates. To allow for additional mass spectrometric detection, a formic acid gradient was designed as an alternative to the non-volatile phosphate buffer gradient. Within a total run time of 28 min, 10 out of 14 analytes were baseline separated by the formic acid gradient, and 8 compounds were completely resolved by the phosphate gradient. The dependence of the coulometric detection on cell potential, potential step width, eluent pH and eluent composition was comprehensively tested. Detection limits ≤20 μg/L were achieved by DAD detection for nine analytes and by coulometric array detection for all analytes, demonstrating the superior sensitivity of electrochemical detection. DAD offered better linearity and reproducibility. Inter-day precision of peak heights spanned from 0.26 to 2.00% (formic acid gradient) and from 0.75 to 2.85% (phosphate buffer gradient) operating the DAD detector, but it exceeded 10% for several compounds applying the coulometric array detector. The simultaneous operation of both detectors offered an enhanced certainty of substance identification. The appropriateness of the method was confirmed by the analysis of various hydrolysates of lignin-containing materials.
HPLC Detection and Antioxidant Capacity Determination of Brown, Red and Green Algal Pigments in Seaweed Extracts
Authors: Yalçın Sibel , Karakaş Özge , Okudan Emine Şükran , Başkan Kevser Sözgen , Çekiç Sema Demirci , Apak Reşat 
Published: November 2020

AbstractThis study was carried out to determine the main pigments in some different selected seaweeds and to reveal their antioxidant potential regarding the ever-increasing demand for utilization of marine pigments in human health and nutrition. The individual amounts of algal pigments were found by reverse phase high-performance liquid chromatography (HPLC) and their total antioxidant capacities (TAC) by two spectrophotometric TAC assays, namely: CUPRAC (CUPric ion Reducing Antioxidant Capacity) and ABTS/TEAC (2,2′-azinobis [3-ethyl benzo thiazoline-6-sulfonate])/(trolox equivalent antioxidant capacity). These two tests gave the same rank order for TAC. The TAC of HPLC-quantified compounds accounted for a relatively much lower percentage of the observed CUPRAC capacities of seaweed extracts, namely ranging from 11 to 68% for brown, from 4 to 41% for red and from 3 to 100% for green species, i.e., some TAC originated from chromatographically unidentified compounds. Fucoxanthin, chlorophyll a, and pheophytin a compounds were major pigments in brown algae. The relative carotenoid contents in red marine algae were generally lower than those of chlorophylls. Overall total quantities were quite low compared with those of brown species. In general, chlorophyll a and chlorophyll b were chiefly present in green algae, but β-carotene, violaxanthin and siphonaxanthin were also detected substantially higher in some species of green algae such as Caulerpa racemosa var. cylindracea and Codium fragile.
Very Low-Density Lipoprotein Cholesterol May Mediate a Substantial Component of the Effect of Obesity on Myocardial Infarction Risk: The Copenhagen General Population Study
Authors: Johansen Mia Ø , Nielsen Sune F , Afzal Shoaib , Vedel-Krogh Signe , Davey Smith George , Nordestgaard Børge G 
Published: November 2020

Abstract

Background
Individuals with obesity have higher concentrations of very low-density lipoprotein (VLDL) cholesterol and increased risk of myocardial infarction. We hypothesized that VLDL cholesterol explains a fraction of the excess myocardial infarction risk in individuals with obesity.

Methods
We included 29 010 individuals free of myocardial infarction at baseline, nested within 109 751 individuals from the Copenhagen General Population Study. During 10 years of follow-up, 2306 individuals developed myocardial infarction. Cholesterol content in large and small VLDLs, in intermediate-density lipoprotein (IDL), and in LDL was measured directly with nuclear magnetic resonance spectroscopy.

Results
Median concentrations of cholesterol in large and small VLDLs were 0.12 mmol/L (interquartile range [IQR], 0.07–0.20 mmol/L; 4.5 mg/dL [IQR, 2.6–6.9 mg/dL]) and 0.6 mmol/L (IQR, 0.5–0.8 mmol/L; 25 mg/dL [IQR, 20–30 mg/dL]) in individuals with obesity vs 0.06 mmol/L (IQR, 0.03–0.1 mmol/L; 2.2 mg/dL [IQR, 1.1–3.8 mg/dL]), and 0.5 mmol/L (IQR, 0.4–0.6 mmol/L; 20 mg/dL (IQR, 16–25 mg/dL]) in individuals with normal weight; in contrast, concentrations of IDL and LDL cholesterol were similar across body mass index (BMI) categories. Cholesterol in large and small VLDLs combined explained 40% (95% CI, 27%–53%) of the excess risk of myocardial infarction associated with higher BMI. In contrast, IDL and LDL cholesterol did not explain excess risk of myocardial infarction, whereas systolic blood pressure explained 17% (11%–23%) and diabetes mellitus explained 8.6% (3.2%–14%).

Conclusions
VLDL cholesterol explains a large fraction of excess myocardial infarction risk in individuals with obesity. These novel findings support a focus on cholesterol in VLDL for prevention of myocardial infarction and atherosclerotic cardiovascular disease in individuals with obesity.
MetaTropismDB: a database of organ-specific metastasis induced by human cancer cell lines in mouse models
Authors: Giulietti Matteo , Bastianoni Marco , Cecati Monia , Ruzzo Annamaria , Bracci Massimo , Malavolta Marco , Piacenza Francesco , Giacconi Robertina , Piva Francesco 
Published: November 2020

Abstract
The organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metastases. In order to shed light on this behaviour, several studies were performed by the injection of human cancer cell lines into immunocompromised mouse models. However, the information about these experiments is spread in the literature. For each xenograft experiment reported in the literature, we annotated both the experimental conditions and outcomes, including details on inoculated human cell lines, mouse models, injection methods, sites of metastasis, organs not colonized, rate of metastasis, latency time, overall survival and the involved genes. We created MetaTropismDB, a freely available database collecting hand-curated data useful to highlight the mechanisms of organ-specific metastasis. Currently, it stores the results of 513 experiments in which injections of 219 human cell lines have been carried out in mouse models. Notably, 296 genes involved in organotropic metastases have been collected. This specialized database allows the researchers to compare the current results about organotropism and plan future experiments in order to identify which tumour molecular signatures establish if and where the metastasis will develop.
Database URL: http://www.introni.it/Metastasis/metastasis.html
Exploring consensus for the optimal sealant use to prevent air leak following lung surgery: a modified Delphi survey from The European Society of Thoracic Surgeons
Authors: Brunelli Alessandro , Bölükbas Servet , Falcoz Pierre Emmanuel , Hansen Henrik , Jimenez Marcelo F. , Lardinois Didier , Scarci Marco , Viti Andrea , Walker Ian , Warren Tim 
Published: November 2020

Abstract

OBJECTIVES
The use of sealants is one of the methods available to reduce the occurrence of intraoperative air leaks. The objective of this modified Delphi survey among ESTS members is to understand the attitudes of clinicians to the optimal use of sealants in air leak management.

METHODS
To understand the attitudes of a wider sample of clinicians, a questionnaire was developed highlighting key issues through 37 statements. Respondents were invited to score their level of agreement with each. A modified Delphi methodology was used to review responses with a threshold of agreement for consensus of 75%.

RESULTS
A total of 258 responses were received (response rate 17%). Respondents agreed that prolonged air leaks are a common complication in thoracic surgery presenting a burden to the patient and increasing the costs of care. There is clear support for the use of sealants to reduce costs and improve the efficiency of healthcare provision and duration of chest tube use in selected high-risk patients with intraoperative air leak at the end of the lung surgery. Respondents also agreed that, due to often complex nature of thoracic surgery, sealants should be developed specifically for this application.

CONCLUSION
There is a clear role for sealants in the management of air leaks and certain surgical procedures demand their use (i.e. lung volume reduction surgery, decortication). This opinion-based consensus review helps to raise the debate about the burden of air leaks in thoracic surgery in order that this issue is recognized in practice and informs the optimal use of sealants in lung surgery.
Selective Sweeps in a Nutshell: The Genomic Footprint of Rapid Insecticide Resistance Evolution in the Almond Agroecosystem
Authors: Calla Bernarda , Demkovich Mark , Siegel Joel P , Viana João Paulo Gomes , Walden Kim K O , Robertson Hugh M , Berenbaum May R 
Published: November 2020

AbstractAmong the most familiar forms of human-driven evolution on ecological time scales is the rapid acquisition of resistance to pesticides by insects. Since the widespread adoption of synthetic organic insecticides in the mid-twentieth century, over 500 arthropod species have evolved resistance to at least one insecticide. Efforts to determine the genetic bases of insecticide resistance have historically focused on individual loci, but the availability of genomic tools has facilitated the screening of genome-wide characteristics. We resequenced three contemporary populations of the navel orangeworm (Amyelois transitella), the principal pest of almond orchards in California, differing in bifenthrin resistance status to examine insecticide-induced changes in the population genomic landscape of this species. We detected an exceptionally large region with virtually no polymorphisms, extending to up to 1.3 Mb in the resistant population. This selective sweep includes genes associated with pyrethroid and DDT resistance, including a cytochrome P450 gene cluster and the gene encoding the voltage-gated sodium channel para. Moreover, the sequence along the sweep is nearly identical in the genome assembled from a population founded in 1966, suggesting that the foundation for insecticide resistance may date back a half-century, when California’s Central Valley experienced massive area-wide applications of DDT for pest control.
Spousal Support, Spousal Strain, and Loneliness in Older Mexican Couples
Authors: Saenz Joseph L 
Published: November 2020

Abstract

Objectives
A growing body of research has identified factors related to loneliness among older adults. Fewer have investigated predictors of loneliness within married couples. This analysis investigates how spousal support and strain relate with loneliness within older couples (age 50+), and whether these associations are modified by functional limitation. The study focuses on Mexico, a country experiencing rapid aging occurring alongside historically limited institutional support for older adults, and where traditional gender roles extend to marriage.

Methods
The analytic sample consisted of 3,584 husband–wife dyads from the 2012 and 2015 Mexican Health and Aging Study. Loneliness was measured using the Three-Item Loneliness Scale. Associations between spousal support, strain, and loneliness were estimated within husband–wife dyads using the Actor–Partner Interdependence Model.

Results
Experiencing more spousal support was associated with less loneliness, whereas experiencing spousal strain was associated with more loneliness 3 years later among married adults. The associations between spousal support/strain and loneliness were stronger among husbands with limitations in activities of daily living (ADL) when compared to their counterparts without ADL limitations.

Discussion
Among married adults, spousal support and strain may be important factors to understand loneliness within marriage. Effects should be interpreted within the context of functional limitation.
Therapeutic effects of hysterosalpingography contrast media in infertile women: what do we know about the H2O in the H2Oil trial and why does it matter?
Authors: Peart Jane M , Sim Robert G , Hofman Paul L 
Published: November 2020

ABSTRACT
Recent interest in the use of oil-soluble contrast media (OSCM) for hysterosalpingography (HSG) and other tubal flushing procedures is largely the result of publication of the large, multicentre, randomized controlled H2Oil trial in the New England Journal of Medicine in 2017, addressing the long-held suspicion that pregnancy rates following HSG with OSCM are higher than if a water-soluble contrast media (WSCM) is used. However, the findings of this trial have been compromised by the WSCM selected for comparison with OSCM. The chosen WSCM belongs to a superceded class of ionic media, with an iodine concentration, osmolality and viscosity all lying at the extreme end of the range for water-soluble radiographic contrast. The requirement for safe, cheap, versatile WSCM for intravascular use during computerized tomography, angiography and interventional procedures has resulted in considerable refinement of WSCM, with current widespread use of non-ionic, low osmolality or iso-osmolar WSCM in radiology, including for HSG. However, the use of the earlier ionic, high osmolality agents such as that selected for the H2Oil trial persists for HSG in some centres, despite potential adverse effects on the endometrium and fallopian tubal epithelium compared with more modern, less toxic WSCM. Knowledge of the variety of physical and chemical characteristics of the available WSCM is essential for interpretation of the current literature and establishing the most effective and safe water-soluble agent to use for HSG. Design of future clinical trials to establish the potential superiority of OSCM over WSCM for fertility enhancement must include the use of the readily available, inexpensive modern WSCM. While the fertility rates following OSCM HSG have been shown to be high in women with idiopathic infertility, more robust trials are required before the widespread use of OSCM for HSG or other modalities such as ultrasound and laparoscopy should be adopted.