bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation of mass spectrometry-based proteomics data with Synthedia
Authors: Leeming Michael G , Ang Ching-Seng , Nie Shuai , Varshney Swati , Williamson Nicholas A 
Published: December 2022

Abstract

Motivation
A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies, but these do not extend to the rapidly developing field of data-independent acquisition (DIA) strategies.

Results
Here, we present Synthedia—a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters.

Availability and implementation
Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/).

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Integrative chromatin domain annotation through graph embedding of Hi-C data
Authors: Shokraneh Neda , Arab Mariam , Libbrecht Maxwell 
Published: December 2022

Abstract

Motivation
The organization of the genome into domains plays a central role in gene expression and other cellular activities. Researchers identify genomic domains mainly through two views: 1D functional assays such as ChIP-seq, and chromatin conformation assays such as Hi-C. Fully understanding domains requires integrative modeling that combines these two views. However, the predominant form of integrative modeling uses segmentation and genome annotation (SAGA) along with the rigid assumption that loci in contact are more likely to share the same domain type, which is not necessarily true for epigenomic domain types and genome-wide chromatin interactions.

Results
Here, we present an integrative approach that annotates domains using both 1D functional genomic signals and Hi-C measurements of genome-wide 3D interactions without the use of a pairwise prior. We do so by using a graph embedding to learn structural features corresponding to each genomic region, then inputting learned structural features along with functional genomic signals to a SAGA algorithm. We show that our domain types recapitulate well-known subcompartments with an additional granularity that distinguishes a combination of the spatial and functional states of the genomic regions. In particular, we identified a division of the previously identified A2 subcompartment such that the divided domain types have significantly varying expression levels.

Availability and implementation
https://github.com/nedashokraneh/IChDA.

Supplementary information
Supplementary data are available at Bioinformatics online.
A transformation perspective on marginal and conditional models
Authors: Barbanti Luisa , Hothorn Torsten 
Published: December 2022

Summary
Clustered observations are ubiquitous in controlled and observational studies and arise naturally in multicenter trials or longitudinal surveys. We present a novel model for the analysis of clustered observations where the marginal distributions are described by a linear transformation model and the correlations by a joint multivariate normal distribution. The joint model provides an analytic formula for the marginal distribution. Owing to the richness of transformation models, the techniques are applicable to any type of response variable, including bounded, skewed, binary, ordinal, or survival responses. We demonstrate how the common normal assumption for reaction times can be relaxed in the sleep deprivation benchmark data set and report marginal odds ratios for the notoriously difficult toe nail data. We furthermore discuss the analysis of two clinical trials aiming at the estimation of marginal treatment effects. In the first trial, pain was repeatedly assessed on a bounded visual analog scale and marginal proportional-odds models are presented. The second trial reported disease-free survival in rectal cancer patients, where the marginal hazard ratio from Weibull and Cox models is of special interest. An empirical evaluation compares the performance of the novel approach to general estimation equations for binary responses and to conditional mixed-effects models for continuous responses. An implementation is available in the tram add-on package to the R system and was benchmarked against established models in the literature.
Design and implementation of a new portable hybrid solar atmospheric water-generation system
Authors: Shafeian Nafise , Ranjbar A A , Gorji Tahereh B 
Published: December 2022

Abstract
During recent years, atmospheric water generation (AWG) has garnered significant attention among researchers as a viable solution to the water-scarcity problem. Generally, AWG requires dehumidification, which includes two main principles of refrigeration and sorption. Among refrigeration methods, thermoelectric coolers are suitable and, among sorption methods, it is best to utilize desiccant materials with high sorption capacity and low heat generation. In the present study, a portable hybrid/integrated solar AWG system was designed and tested under realistic conditions of Babol, Iran (36.5387°N, 52.6765°E) over four typical summer days between 14 and 31 August 2021. Two models (Models A and B) were designed and evaluated. Temperature, relative humidity, solar irradiance and water-production data were recorded to assess the system performance (i.e. the ratio between the generated water and consumed power in ml/W.hour) and economically analyse the system. Based on the results acquired, the maximum water production in the proposed configuration (acquired from Model B) was 2.12 l/m2.day at an average relative humidity and a temperature of 52% and 36°C, respectively. The desired AWG system had a system performance of 0.19 ml/W.hour, annual water production of 774.4 l/m2, production cost of 0.0246 $/l/m2 and a payback period of 1.19 years.
High-definition trans cranial direct current stimulation and its effects on cognitive function: a systematic review
Authors: Tedla Jaya Shanker , Sangadala Devika Rani , Reddy Ravi Shankar , Gular Kumar , Dixit Snehil 
Published: December 2022

Abstract
High-Definition Transcranial Direct Current Stimulation (HD-tDCS) is focal and improves higher mental functions. Due to the lack of published evidence, we conducted this review on the effect of HD-tDCS on cognitive functions in healthy and diseased individuals. We performed an electronic-data and gray-literature search to obtain the relevant studies for the review. The two distinct literature searches obtained a total of 468 studies. Out of these, a total of 12 studies were conducted on higher mental functions, and of these, two were on disordered consciousness, five were on memory, two were on speech, two were on cognition, and one was on execution. We submitted nine studies with control group to methodological quality assessment using the PEDro Scale. Remaining three studies underwent quality assessment by Quality Assessment Tool for Before-After (Pre-Post) Studies with No Control Group. We found that anodal HD-tDCS stimulation is significantly effective in treating disordered consciousness and improving memory, speech, cognition, and execution.
Reporting of Antimicrobial Resistance from Blood Cultures, an Antibacterial Resistance Leadership Group Survey Summary: Resistance Marker Reporting Practices from Positive Blood Cultures
Authors: Simner Patricia J , Dien Bard Jennifer , Doern Christopher , Kristie Johnson J , Westblade Lars , Yenokyan Gayane , Patel Robin , Hanson Kimberly E ,   for the Antibacterial Resistance Leadership Group
Published: December 2022

Abstract

Background
We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers.

Methods
A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey.

Results
Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as “detected”/“not detected” (16–22%) without interpretive guidance, to interpreting results (23–42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3–17%).

Conclusions
Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.
Moderate-intensity statin with ezetimibe vs. high-intensity statin in patients with diabetes and atherosclerotic cardiovascular disease in the RACING trial
Authors: Lee Yong-Joon , Cho Jae Young , You Seng Chan , Lee Yong-Ho , Yun Kyeong Ho , Cho Yun-Hyeong , Shin Won-Yong , Im Sang Wook , Kang Woong Chol , Park Yongwhi , Lee Sung Yoon , Lee Seung-Jun , Hong Sung-Jin , Ahn Chul-Min , Kim Byeong-Keuk , Ko Young-Guk , Choi Donghoon , Hong Myeong-Ki , Jang Yangsoo , Kim Jung-Sun 
Published: December 2022

AbstractAimsThis study evaluated the effect of moderate-intensity statin with ezetimibe combination therapy vs. high-intensity statin monotherapy among patients with diabetes mellitus (DM) and atherosclerotic cardiovascular disease (ASCVD).Methods and resultsThis was a pre-specified, stratified subgroup analysis of the DM cohort in the RACING trial. The primary outcome was a 3-year composite of cardiovascular death, major cardiovascular events, or non-fatal stroke. Among total patients, 1398 (37.0%) had DM at baseline. The incidence of the primary outcome was 10.0% and 11.3% among patients with DM randomized to ezetimibe combination therapy vs. high-intensity statin monotherapy (hazard ratio: 0.89; 95% confidence interval: 0.64–1.22; P = 0.460). Intolerance-related discontinuation or dose reduction of the study drug was observed in 5.2% and 8.7% of patients in each group, respectively (P = 0.014). LDL cholesterol levels &lt;70 mg/dL at 1, 2, and 3 years were observed in 81.0%, 83.1%, and 79.9% of patients in the ezetimibe combination therapy group, and 64.1%, 70.2%, and 66.8% of patients in the high-intensity statin monotherapy group (all P &lt; 0.001). In the total population, no significant interactions were found between DM status and therapy regarding primary outcome, intolerance-related discontinuation or dose reduction, and the proportion of patients with LDL cholesterol levels &lt;70 mg/dL.ConclusionEzetimibe combination therapy effects observed in the RACING trial population are preserved among patients with DM. This study supports moderate-intensity statin with ezetimibe combination therapy as a suitable alternative to high-intensity statins if the latter cannot be tolerated, or further reduction in LDL cholesterol is required among patients with DM and ASCVD.Clinical Trial RegistrationClinicalTrials.gov, Identifier:NCT03044665.
Heimat and Nation: Jewish Historians and the Construction of Regional Identities in Posen and Alsace-Lorraine during the German Empire
Authors: Seiter Mathias 
Published: December 2022

Abstract
The late nineteenth and early twentieth centuries saw a wave of interest in history among Jews in Germany. The popularity of the subject extended to those who lived at the geographic margins of the German Empire, in the Prussian Province of Posen and the Reichsland of Alsace-Lorraine. Living in borderlands in which national identities were contested, Jewish historians established and joined regional historical societies that looked to the local and regional past to construct identities. While Jewish historians in the German east worked alongside non-Jewish colleagues to create a German Heimat against the backdrop of ethnic strife between Germans and Poles, their co-religionists in Alsace-Lorraine tried to maintain a regional identity which preserved the cultural and historical uniqueness of the Franco-German borderland. These different visions of regional history and identity surfaced again in the responses to the establishment of a central German-Jewish archive in Berlin. Jews from Posen were instrumental in integrating the local Jewish past into a national German-Jewish narrative. However, in the Franco-German borderland, Jews were opposed to the idea of a national archive, which they saw as a challenge to their Alsace-Lorrainian Jewish identity. This article argues that Jewish historians engaged with and were part of the wider German discourses on Heimat, regionalism and localness. Although Jewish historians in Posen and Alsace-Lorraine differed in their understanding of these concepts, they used them as markers of identity which allowed Jews to define their position towards notions of Germanness and the idea of a German-Jewish community.
Live yeast supplementation altered the bacterial community’s composition and function in rumen and hindgut and alleviated the detrimental effects of heat stress on dairy cows
Authors: Li Zihao , Fan Yang , Bai Hao , Zhang Jiyou , Mao Shengyong , Jin Wei 
Published: December 2022

Abstract
The objective of this study was to investigate the effects of live yeast (LY, Saccharomyces cerevisiae) on the lactation performance, bacterial community, and functions in the rumen and hindgut of dairy cows under heat stress. Thirty-three multiparous (parity 3.9 ± 0.8) Holstein dairy cows (189.1 ± 6.6 d in milk at the beginning of the experiment) were randomly assigned to three groups (11 cows per treatment). Cows in the three groups were fed a diet without yeast (CON), with 10 g yeast/d/head (LY-10), and with 20 g yeast/d/head (LY-20). The yeast product contained 2.0 × 1010 CFU/g. Supplementing LY decreased the rectal temperature and respiratory rate of cows, and increased dry matter intake, milk yield, milk fat yield, milk protein yield, and milk lactose yield (P &lt; 0.001), yet decreased milk urea nitrogen concentration (P = 0.035). Interaction effects of treatment × week were observed for rectal temperature (P &lt; 0.05), respiratory rate (P &lt; 0.05), milk yield (P = 0.015), milk urea nitrogen (P = 0.001), milk protein yield (P = 0.008), and milk lactose yield (P = 0.030). In rumen, LY increased the concentrations of acetate, isobutyrate, isovaterate, valerate, total volatile fatty acids (VFAs), and NH3-N (P &lt; 0.05). Miseq sequencing of the 16S rRNA genes showed that LY increased the relative abundance of Prevotella and Prevotellaceae UCG-003 at the genus level with a series of enriched pathways in the metabolism of carbohydrates and protein. In fecal samples, LY did not affect the profile of VFAs (P &gt; 0.05). Clostridium sensu stricto 1 (P = 0.013) and Actinobacillus (P = 0.011) increased in the relative abundance by LY, whereas Bacteroides (P = 0.016) and Oscillospirales UCG-010 (P = 0.005) decreased with a series of enriched pathways in carbohydrate metabolism, secondary bile acid biosynthesis. In summary, LY supplementation altered the bacterial community’s composition and function in rumen and hindgut, and simultaneously alleviated the detrimental effects of heat stress on dairy cows. These findings provide extended insight into the effects of LY in the rumen and hindgut of dairy cows exposed to heat stress.
Who Supports the Huawei 5G Ban? Advancing a Two-Level Ideational Approach in International Relations
Authors: Lee Yoon Jin 
Published: December 2022

AbstractThe US allies’ decisions to ban or allow Huawei from building fifth-generation (5G) mobile broadband are significant to various actors, but their decisions have not been examined systematically. While related literatures point to relative bargaining power or domestic political constraints, I argue that strengths of pre-existing ideas, across national leader and national security institutional levels of analysis, help explain US allies’ positions. Specifically, I argue that the following three understandings are key: (1) China has aggressive intentions, (2) information and communications technology (ICT) system requires security, and (3) data privacy needs state protection. I argue that when the three key understandings are strong across national leader and national security institutional levels, the leader would likely adopt the Huawei 5G ban. On the other hand, when the three key understandings are weak across two levels, the leader would likely allow Huawei to partake in building 5G networks without tougher controls. I conduct a plausibility probe-based comparison of the decision cases of Australia and South Korea and find support for my hypotheses. The cross-national evidence calls for more attention to specific understandings—particular to action contexts—across at least two levels of analysis in explaining decisions of interest.
How Alive Is the Anti-Death Penalty Norm? Evidence from the British and French Treatment of ISIS Foreign Fighters
Authors: Efrat Asif , Richemond-Barak Daphné 
Published: December 2022

Abstract
This article enhances our understanding of international norms by developing a set of indicators to measure norm robustness at the domestic level. We apply these indicators to assess the robustness of the prohibition on the death penalty: a well-established international norm that terrorism-related cases have put to the test. In the United Kingdom, the government agreed to share information with the United States, possibly leading to the imposition of the death penalty on two ISIS foreign fighters of UK origin. France facilitated the trials of French ISIS fighters in Iraq, where they were sentenced to death. While the UK government, under public and judicial pressure, reversed its decision to cooperate with US authorities, the French government failed to acknowledge its violation of the death-penalty ban. We conclude that the anti-death penalty norm is more robust in the United Kingdom than in France. This case demonstrates how established democracies might break international human rights norms, and it reveals the nuances of the norm-decaying process.
Deep contextual disambiguation of homonyms and polysemants
Authors: Vakulenko Maksym O 
Published: December 2022

AbstractA new metric method for word sense disambiguation is put forward, being formulated within a phenomenological analogy to the wave function of an observable quantity in quantum mechanics where the actual meaning of a multivalued word (a homonym or a polysemant) is determined by its context. The choice of the actualized sense is determined by the minimal semantic distance between the semantics of possible word senses and that of the context, where the meanings of the word in question and the context follow from their semantic fields based on lexicographic hyperchains. In contrast to the common models, our method accounts for semantic polarity. The formulated method showed good results in disentangling polysemy, which was not possible to achieve within the contextualized embedding approacdh based on bidirectional encoder representations from transformers (BERT).
Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor
Authors: Fukuchi Satoshi , Noguchi Tamotsu , Anbo Hiroto , Homma Keiichi 
Published: December 2022

Abstract
Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, whereas the typical eukaryotic protein comprises multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer the internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the “small bang” model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them were subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat–mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analyzed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.
Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis
Authors: Behle Anna , Dietsch Maximilian , Goldschmidt Louis , Murugathas Wandana , Berwanger Lutz C , Burmester Jonas , Yao Lun , Brandt David , Busche Tobias , Kalinowski Jörn , Hudson Elton P , Ebenhöh Oliver , Axmann Ilka M , Machné Rainer 
Published: December 2022

Abstract
In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5’/3’ gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.