bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy transport in

Z3

chiral clock model
Authors: Nishad Naveen , Sreejith G J 
Published: December 2021

Abstract
We characterize the energy transport in a one dimensional

Z

3

chiral clock model. The model generalizes the

Z

2

symmetric Transverse Field Ising Model (TFIM). The model is parametrized by a chirality parameter θ, in addition to f and J which are analogous to the transverse field and the nearest neighbor spin coupling in the TFIM. Unlike the well-studied TFIM and XYZ models, this model does not transform to a fermionic system. We use a matrix product states implementation of the Lindblad master equation to obtain the Non-Equilibrium Steady State (NESS) in systems of sizes up to 48. We present the estimated NESS current and its scaling exponent γ as a function of θ at different f/J. The estimated γ(f/J, θ) points to ballistic energy transport along a line of integrable points f = J cos 3θ in the parameter space; all other points deviate from ballistic transport. Analysis of finite size effects within the available system sizes suggest diffusive behavior away from the integrable points.
Structural, optical, and potential broad-spectrum antibacterial properties of CuO-Ag nanoparticles biosynthesized using the extract of Diospyros discolor Willd
Authors: Handayani Windri , Imawan Cuk , Umar Aminah , Yasman  , Yunilawati Retno , Djuhana Dede 
Published: December 2021

Abstract
The development of new material properties for antimicrobial agents to address the problem of antibiotic resistance is currently being explored. Silver and copper exhibit oligodynamic properties, which inhibit the growth of microorganisms. These properties are stronger at the nanoscale than the macroscale, especially for bimetallic nanoparticles (NPs). In this study, we synthesized bimetallic CuO and Ag NPs using Diospyros discolor Willd. (Velvet apple) leaf extract with three different ratios of Cu and Ag precursors: 1:0.01, 1:0.1, and 1:1 (v/v). In addition, the optical properties of these NPs were characterised using UV-Vis spectrophotometer, which showed the typical absorbance peak in the range of 300–400 nm. The size and shape of the CuO and Ag nanoparticles were analysed using a scanning electron microscope (SEM) and transmission electron microscope (TEM) images. The SEM and TEM images showed leaf-shaped CuO nanoplates and spherical AgNPs. Furthermore, the crystalline properties were analysed using x-ray diffraction (XRD). This study produced CuO-Ag nanoclusters with a particular morphology, size, and composition. The antibacterial assay showed potential broad-spectrum activity for Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis) as well as Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa).
Super-resolution imaging of negative-refractive graded-index photonic crystal flat lens
Authors: Liang Binming , Huang Xiao , Zheng Jihong 
Published: December 2021

Abstract
Photonic crystal (PC) not only breaks through the diffraction limit of traditional lenses but also can realize super-resolution imaging. Improving the resolution is the key task of PC imaging. The main work of this paper is to use a graded-index Photonic crystal (GPC) flat lens to improve the image resolution. An air-hole type two-dimensional (2D) GPC structure based on silicon medium is proposed in this paper. Numerical simulations through RSoft reveal that when the medium in the imaging area is air, the full width at half maximum (FWHM) value of a single image reaches

0.362
λ
.

According to the Rayleigh criterion, the images of two point sources

0.57
λ

apart can also be distinguished. In the imaging system composed of cedar oil and GPC flat lens, the FWHM value of a single image reaches

0.34
λ
.

In addition, the images of multiple point sources

0.49
λ

apart can still be distinguished.
On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library
Authors: Ferrer-Bonsoms Juan A , Morales Xabier , Afshar Pegah T , Wong Wing H , Rubio Angel 
Published: December 2021

Abstract

Motivation
Isoform deconvolution is an NP-hard problem. The accuracy of the proposed solutions is far from perfect. At present, it is not known if gene structure and isoform concentration can be uniquely inferred given paired-end reads, and there is no objective method to select the fragment length to improve the number of identifiable genes. Different pieces of evidence suggest that the optimal fragment length is gene-dependent, stressing the need for a method that selects the fragment length according to a reasonable trade-off across all the genes in the whole genome.

Results
A gene is considered to be identifiable if it is possible to get both the structure and concentration of its transcripts univocally. Here, we present a method to state the identifiability of this deconvolution problem. Assuming a given transcriptome and that the coverage is sufficient to interrogate all junction reads of the transcripts, this method states whether or not a gene is identifiable given the read length and fragment length distribution. Applying this method using different read and fragment length combinations, the optimal average fragment length for the human transcriptome is around 400–600 nt for coding genes and 150–200 nt for long non-coding RNAs. The optimal read length is the largest one that fits in the fragment length. It is also discussed the potential profit of combining several libraries to reconstruct the transcriptome. Combining two libraries of very different fragment lengths results in a significant improvement in gene identifiability.

Availability and implementation
Code is available in GitHub (https://github.com/JFerrer-B/transcriptome-identifiability).

Supplementary information
Supplementary data are available at Bioinformatics online.
Completing gene trees without species trees in sub-quadratic time
Authors: Mai Uyen , Mirarab Siavash 
Published: December 2021

Abstract

Motivation
As genome-wide reconstruction of phylogenetic trees becomes more widespread, limitations of available data are being appreciated more than ever before. One issue is that phylogenomic datasets are riddled with missing data, and gene trees, in particular, almost always lack representatives from some species otherwise available in the dataset. Since many downstream applications of gene trees require or can benefit from access to complete gene trees, it will be beneficial to algorithmically complete gene trees. Also, gene trees are often unrooted, and rooting them is useful for downstream applications. While completing and rooting a gene tree with respect to a given species tree has been studied, those problems are not studied in depth when we lack such a reference species tree.

Results
We study completion of gene trees without a need for a reference species tree. We formulate an optimization problem to complete the gene trees while minimizing their quartet distance to the given set of gene trees. We extend a seminal algorithm by Brodal et al. to solve this problem in quasi-linear time. In simulated studies and on a large empirical data, we show that completion of gene trees using other gene trees is relatively accurate and, unlike the case where a species tree is available, is unbiased.

Availability and implementation
Our method, tripVote, is available at https://github.com/uym2/tripVote.

Supplementary information
Supplementary data are available at Bioinformatics online.
CACONET: a novel classification framework for microbial correlation networks
Authors: Xu Yuanwei , Nash Katrina , Acharjee Animesh , Gkoutos Georgios V 
Published: December 2021

Abstract

Motivation
Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease.

Results
We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility.

Availability and implementation
CACONET is available at https://github.com/yuanwxu/corr-net-classify.

Supplementary information
Supplementary data are available at Bioinformatics online.
How effective is laparoscopic redo-antireflux surgery?
Authors: Fuchs K H , Breithaupt W , Varga G , Babic B , Eckhoff J , Meining A 
Published: December 2021

Summary
Background: The failure-rate after primary antireflux surgery ranges from 3 to 30%. Reasons for failures are multifactorial. The aim of this study is to gain insight into the complex reasons for, and management of, failure after antireflux surgery. Methods: Patients were selected for redo-surgery after a diagnostic workup consisting of history and physical examination, upper gastrointestinal endoscopy, quality-of-life assessment, screening for somatoform disorders, esophageal manometry, 24-hour-pH-impedance monitoring, and selective radiographic studies such as Barium-sandwich for esophageal passage and delayed gastric emptying. Perioperative and follow-up data were compiled between 2004 and 2017. Results: In total, 578 datasets were analyzed. The patient cohort undergoing a first redo-procedure (n = 401) consisted of 36 patients after in-house primary LF and 365 external referrals (mean age: 62.1 years [25–87]; mean BMI 26 [20–34]). The majority of patients underwent a repeated total or partial laparoscopic fundoplication. Major reasons for failure were migration and insufficient mobilization during the primary operation. With each increasing number of required redo-operations, the complexity of the redo-procedure itself increased, follow-up quality-of-life decreased (GIQLI: 106; 101; and 100), and complication rate increased (intraoperative: 6,4–10%; postoperative: 4,5–19%/first to third redo). After three redo-operations, resections were frequently necessary (morbidity: 42%). Conclusions: Providing a careful patient selection, primary redo-antireflux procedures have proven to be highly successful. It is often the final chance for a satisfying result may be achieved upon performing a second redo-procedure. A third revision may solve critical problems, such as severe pain and/or inadequate nutritional intake. When resection is required, quality of life cannot be entirely normalized.
Natural language processing tool for automatic diseases and drugs recognition from electronic health records in polish- pilot study
Authors: Maciejewski C M , Krajsman M K , Ozieranski K O , Basza M B , Gawalko M G , Lodzinski P L , Opolski G O , Grabowski M G , Cacko A C , Balsam P B 
Published: December 2021

Abstract

Background
An estimate of 80% of data gathered in electronic health records is unstructured, textual information that cannot be utilized for research purposes until it is manually coded into a database. Manual coding is a both cost and time- consuming process. Natural language processing (NLP) techniques may be utilized for extraction of structured data from text. However, little is known about the accuracy of data obtained through these methods.

Purpose
To evaluate the possibility of employing NLP techniques in order to obtain data regarding risk factors needed for CHA2DS2VASc scale calculation and detection of antithrombotic medication prescribed in the population of atrial fibrillation (AF) patients of a cardiology ward.

Methods
An automatic tool for diseases and drugs recognition based on regular expressions rules was designed through cooperation of physicians and IT specialists. Records of 194 AF patients discharged from a cardiology ward were manually reviewed by a physician- annotator as a comparator for the automatic approach.

Results
Median CHA2DS2VASc score calculated by the automatic was 3 (IQR 2–4) versus 3 points (IQR 2–4) for the manual method (p=0.66). High agreement between CHA2DS2VASc scores calculated by both methods was present (Kendall's W=0.979; p&lt;0.001). In terms of anticoagulant recognition, the automatic tool misqualified the drug prescribed in 4 cases.

Conclusion
NLP-based techniques are a promising tools for obtaining structured data for research purposes from electronic health records in polish. Tight cooperation of physicians and IT specialists is crucial for establishing accurate recognition patterns.

Funding Acknowledgement
Type of funding sources: None.
The Influence of Race and Gender on Receiving Assistance With Daily Activities Among Older Americans
Authors: Fabius Chanee D , Parker Lauren J , Thorpe Roland J 
Published: December 2021

Abstract

Background and Objectives
Nearly 8.2 million community-dwelling, older Medicare beneficiaries receive support from long-term services and supports (LTSS) with routine daily activities. Prior work demonstrates disability-related disparities; however, it is unclear whether these patterns persist among LTSS recipients and across specific sets of activities. We examine race and gender differences in receiving help with self-care (e.g., eating), mobility (e.g., getting around the house), and household (e.g., shopping) activities in a nationally representative sample of community-dwelling Medicare beneficiaries receiving LTSS.

Research Design and Methods
Cross-sectional analysis of 1,808 White and Black older adults receiving assistance with routine daily activities in the 2015 National Health and Aging Trends Study. Bivariate statistics were used to describe the sample and provide comparisons of characteristics by race and gender. Logistic regression models examined race and gender differences in receiving assistance with self-care, mobility, and household activities after adjusting for sociodemographic and health characteristics.

Results
Race and gender differences were observed across all sociodemographic and health characteristics, as well as for all forms of assistance. Relative to White men, Black men had lower odds of receiving help with self-care activities. White and black women had higher odds and Black men had lower odds of getting help with mobility activities than White men. Black men and White and Black women all had higher odds of receiving assistance with household tasks compared to White men.

Discussion and Implications
Our findings indicate that, despite prior evidence of disability-related disparities, the receipt of help with self-care, mobility, and household activities varies by race and gender. Findings reveal several target areas for future research. Future work should examine the role of cultural and social preferences for care, as well as the appropriateness of help, as evidenced by health service use and changes in quality of life.
Temporal Changes in the Treatment Paradigm and Long-term Prognosis of Patients With Crohn’s Disease: A Hospital-Based Cohort Study in China
Authors: Yao Lingya , Chen Haotian , Shao Bule , Liu Jing , Wang Chaohui , Zhang Zhou , Cao Qian 
Published: December 2021

Abstract

Background
The temporal trends in medical treatment and long-term outcomes of patients with Crohn’s disease (CD) have not been well elucidated in China over the past 2 decades. Accordingly, we aimed to evaluate the treatment paradigm and long-term clinical course of Chinese patients with CD in a hospital-based cohort.

Methods
All adult patients newly diagnosed with CD (n = 1338) between 1999 and 2019 in the Sir Run Run Shaw Hospital were included in this cohort. Medication utilization, disease outcomes, and risk factors were investigated.

Results
Overall, 48.7%, 35.6%, 67.8%, and 61.6% of patients used 5-aminosalicylates (5-ASA), corticosteroids, thiopurines, and infliximab (IFX), respectively. The cumulative risk of 5-ASA and corticosteroid initiation decreased during follow-up, whereas that of IFX initiation increased. Throughout a median follow-up duration of 26.4 (interquartile range, 12.0–49.2) months, a total of 486 and 300 patients underwent hospitalization and surgery, respectively. Of the 1097 patients with B1/B2 disease behavior at diagnosis, 10.3% experienced phenotype progression. The hospitalization rate decreased after 2015; however, surgery and phenotype progression rates did not significantly change. A Cox regression analysis indicated that IFX use since diagnosis was a contributing factor for lower rates of hospitalization and phenotype progression, whereas thiopurine use was associated with a lower surgery rate.

Conclusions
Infliximab use was observed to increase as 5-ASA and corticosteroid use decreased. Additionally, hospitalization rates decreased following temporal changes in IFX management, yet the surgery and phenotype progression rates remained the same.
Flight and Dietary Antioxidants Influence Antioxidant Expression and Activity in a Migratory Bird
Authors: DeMoranville Kristen J , Carter Wales A , Pierce Barbara J , McWilliams Scott R 
Published: December 2021

SynopsisEcologically relevant factors such as exercise and diet quality can directly influence how physiological systems work including those involved in maintaining oxidative balance; however, to our knowledge, no studies to date have focused on how such factors directly affect expression of key components of the endogenous antioxidant system (i.e., transcription factors, select antioxidant genes, and corresponding antioxidant enzymes) in several metabolically active tissues of a migratory songbird. We conducted a three-factor experiment that tested the following hypotheses: (H1) Daily flying over several weeks increases the expression of transcription factors NRF2 and PPARs as well as endogenous antioxidant genes (i.e., CAT, SOD1, SOD2, GPX1, GPX4), and upregulates endogenous antioxidant enzyme activities (i.e., CAT, SOD, GPx). (H2) Songbirds fed diets composed of more 18:2n-6 PUFA are more susceptible to oxidative damage and thus upregulate their endogenous antioxidant system compared with when fed diets with less PUFA. (H3) Songbirds fed dietary anthocyanins gain additional antioxidant protection and thus upregulate their endogenous antioxidant system less compared with songbirds not fed anthocyanins. Flight training increased the expression of 3 of the 6 antioxidant genes and transcription factors measured in the liver, consistent with H1, but for only one gene (SOD2) in the pectoralis. Dietary fat quality had no effect on antioxidant pathways (H2), whereas dietary anthocyanins increased the expression of select antioxidant enzymes in the pectoralis, but not in the liver (H3). These tissue-specific differences in response to flying and dietary antioxidants are likely explained by functional differences between tissues as well as fundamental differences in their turnover rates. The consumption of dietary antioxidants along with regular flying enables birds during migration to stimulate the expression of genes involved in antioxidant protection likely through increasing the transcriptional activity of NRF2 and PPARs, and thereby demonstrates for the first time that these relevant ecological factors affect the regulation of key antioxidant pathways in wild birds. What remains to be demonstrated is how the extent of these ecological factors (i.e., intensity or duration of flight, amounts of dietary antioxidants) influences the regulation of these antioxidant pathways and thus oxidative balance.
Applying requisite imagination to safeguard electronic health record transitions
Authors: Sittig Dean F , Lakhani Priti , Singh Hardeep 
Published: December 2021

Abstract
Over the next decade, many health care organizations (HCOs) will transition from one electronic health record (EHR) to another; some forced by hospital acquisition and others by choice in search of better EHRs. Herein, we apply principles of Requisite Imagination, or the ability to imagine key aspects of the future one is planning, to offer 6 recommendations on how to proactively safeguard these transitions. First, HCOs should implement a proactive leadership structure that values communication. Second, HCOs should implement proactive risk assessment and testing processes. Third, HCOs should anticipate and reduce unwarranted variation in their EHR and clinical processes. Fourth, HCOs should establish a culture of conscious inquiry with routine system monitoring. Fifth, HCOs should foresee and reduce information access problems. Sixth, HCOs should support their workforce through difficult EHR transitions. Proactive approaches using Requisite Imagination principles outlined here can help ensure safe, effective, and economically sound EHR transitions.
Novel experimental apparatus for laboratory measurements of phototaxis: A comparison between amphipod species
Authors: Kennedy Melissa D , Barberio Angelo , Connaughton Victoria P 
Published: December 2021

AbstractIntricate adaptations to visual systems have allowed amphipods to thrive in extreme habitats like caves. In addition to rearranging ocular dioptric elements, adaptations have also been made to photobehaviors to accommodate the environmental conditions of their habitats. Given the prevalence or absence of discernible eyes or photoreceptors across species, phototaxis is a commonly used behavior to assess light sensing mechanisms. Amphipod photobehaviors have increasingly been utilized within neuroethological and ecotoxicological studies but the quality of light used during laboratory experiments is often overlooked. We describe a novel experimental chamber that allows for accurate and efficient measurement of phototaxis under precisely controlled light conditions. We used this experimental chamber to test phototaxis in two related amphipod species, one subterranean (Stygobromus tenuis potomacusHolsinger, 1967) and one surface dwelling (Crangonyx shoemakeriHubricht & Mackin, 1940). Our results confirm that the behaviors of these species are indicative of natural photopreferences and that in certain populations, these preferences vary with light quality. This low cost and efficient method could easily be applied to a variety of animal models and light conditions, allowing for a reproducible and high throughput method to measure phototaxis in laboratory trials.