bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Approach to STRIDE-II in Real-Life Settings: Analysis and Practical Recommendations
Authors: Ricart Elena , Bastida Guillermo , Carpio Daniel , Ceballos Daniel , Ginard Daniel , Marín-Jimenéz Ignacio , Menchén Luis , Muñoz Fernando , González-Lama Yago 
Published: October 2024

Abstract

Background
We aimed to (1) analyze the applicability of the updated Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE-II) recommendations in real-world clinical practice, (2) identify barriers to their implementation, and (3) propose practical measures to overcome these obstacles.

Methods
This qualitative study was based on a survey, a literature review, and expert opinions. Nine inflammatory bowel disease (IBD) experts identified 7 areas likely to be controversial or potential implementation barriers in daily clinical practice: endoscopy, histology, ultrasound, quality of life, biomarkers, symptom control, and patient-reported outcomes (PROs). Based on this, a survey was carried out among educational course participants. The experts discussed the literature review and survey results and proposed several statements and practical actions.

Results
A total of 55 gastroenterologists answered the survey. The reported difficulty level in reaching STRIDE-II treatment goals in clinical practice was high. Only 22% of participants performed clinical remission assessments using clinical indexes and PROs. Seventy percent of responders did not use fecal calprotectin cutoffs and considered changes from the previous levels instead. Mucosal healing as a long-term therapeutic goal was considered necessary to be individualized in specific patient subgroups (eg, elderly/fragile patients, multiple treatment failures, and last-line therapies). Other barriers, like the lack of access to imaging techniques or insufficient knowledge and skills among healthcare professionals, were detected. The experts suggested adding less stringent treatment goals and measurements, patient stratification, local adaptations, educational activities, and research.

Conclusions
STRIDE-II recommendations face various implementation barriers needing careful evaluation in order to enhance their adoption in clinical practice, and ultimately improve outcomes in IBD patients.
A history of susceptibility to parasites and divergence in solitary, gregarious and agonistic behaviors of embiopterans
Authors: Arias Emily A , Schatz Andrew M , Kliefoth Soondree E , Rooks Edward C , Edgerly Janice S 
Published: October 2024

Abstract
Two species of Haploembia Ramburi (Oligotomidae: Embioptera), nonnative detritivores found in the western USA, display solitary tendencies, not typical for webspinners that usually share silk galleries. Reports from the 1960s based on native populations in Italy highlighted the impact of a gregarine that depressed male sterility and female survivorship in Haploembia solieri (Rambur). Sympatric asexual Haploembia tarsalis (Ross) lives a normal lifespan when parasitized, albeit suffering from reduced fecundity. Our goal is to characterize behavioral repertoires as individuals interact and to develop methods for future investigations focused on the impact of the little-known parasite. We quantified individual responses to conspecifics or other species in 10-min dyadic interactions and, in a 3-day trial, determined whether they aggregated when given dispersed resources. Replicated groups of four adult female H. solieri or H. tarsalis settled away from each other over the 3-day trials. In 10-min bouts of same or different species pairs, focal insects bolted back, retreated and attempted to escape when they encountered one another, especially when the opponent was H. tarsalis. Males courted conspecific females, but were dramatically repelled by H. tarsalis. Serving as a positive control, Oligotoma nigra (Hagen) (Oligotomidae) adult females paired with conspecifics displayed typical webspinner behaviors by sitting together, sharing silk. Haploembia solieri males did not respond negatively to O. nigra, not known to be parasitized by the gregarine, but did so when paired with H. tarsalis. Results align with the prediction that susceptibility to parasitism may have led to antisocial behaviors observed in two Haploembia species.
Sociodemographic differences in the response to changes in COVID-19 testing guidelines
Authors: Sharma Shambhavi , Li Huiqi , Löve Jesper , Nwaru Chioma , Gisslén Magnus , Byfors Sara , Hammar Niklas , Nilsson Anton , Björk Jonas , Nyberg Fredrik , Bonander Carl 
Published: October 2024

Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, Sweden emphasized voluntary guidelines over mandates. We exploited a rapid change and reversal of the Public Health Agency of Sweden’s COVID-19 testing guidelines for vaccinated and recently infected individuals as a quasi-experiment to examine sociodemographic differences in the response to changes in pandemic guidelines. We analyzed daily polymerase chain reaction tests from 1 October 2021 to 15 December 2021, for vaccinated or recently infected adults (≥20 years; n = 1 596 321) from three Swedish regions (Stockholm, Örebro, and Dalarna). Using interrupted time series analysis, we estimated abrupt changes in testing rates at the two dates when the guidelines were changed (1 November and 22 November). Stratified analysis and meta-regression were employed to explore sociodemographic differences in the strength of the response to the guideline changes. Testing rates declined substantially when guideline against testing of vaccinated and recently infected individuals came into effect on 1 November [testing rate ratio: 0.50 (95% confidence interval, CI 0.41, 0.61)], and increased again from these lowered levels by a similar amount upon its reversal on 22 November [testing rate ratio: 2.19 (95% CI: 1.69, 2.85)]. Being Sweden-born, having higher household income, or higher education, were all associated with a stronger adherent response to the guideline changes. Adjusting for stratum-specific baseline testing rates and test-positivity did not influence the results. Our findings suggest that the population was responsive to the rapid changes in testing guidelines, but with clear sociodemographic differences in the strength of the response.
Indirect genetic effects increase the heritable variation available to selection and are largest for behaviors: a meta-analysis
Authors: Santostefano Francesca , Moiron Maria , Sánchez-Tójar Alfredo , Fisher David N 
Published: October 2024

Abstract
The evolutionary potential of traits is governed by the amount of heritable variation available to selection. While this is typically quantified based on genetic variation in a focal individual for its own traits (direct genetic effects, DGEs), when social interactions occur, genetic variation in interacting partners can influence a focal individual’s traits (indirect genetic effects, IGEs). Theory and studies on domesticated species have suggested IGEs can greatly impact evolutionary trajectories, but whether this is true more broadly remains unclear. Here, we perform a systematic review and meta-analysis to quantify the amount of trait variance explained by IGEs and the contribution of IGEs to predictions of adaptive potential. We identified 180 effect sizes from 47 studies across 21 species and found that, on average, IGEs of a single social partner account for a small but statistically significant amount of phenotypic variation (0.03). As IGEs affect the trait values of each interacting group member and due to a typically positive—although statistically nonsignificant—correlation with DGEs (rDGE-IGE = 0.26), IGEs ultimately increase trait heritability substantially from 0.27 (narrow-sense heritability) to 0.45 (total heritable variance). This 66% average increase in heritability suggests IGEs can increase the amount of genetic variation available to selection. Furthermore, whilst showing considerable variation across studies, IGEs were most prominent for behaviors and, to a lesser extent, for reproduction and survival, in contrast to morphological, metabolic, physiological, and development traits. Our meta-analysis, therefore, shows that IGEs tend to enhance the evolutionary potential of traits, especially for those tightly related to interactions with other individuals, such as behavior and reproduction.
A chromosome-scale genome assembly of Timorese crabgrass (Digitaria radicosa): a useful genomic resource for the Poaceae
Authors: Minoji Koki , Sakai Toshiyuki 
Published: October 2024

Abstract
Timorese crabgrass (Digitaria radicosa) is a grass species commonly found in Southeast Asia and Oceania. Digitaria species have high intraspecific and interspecific genetic and phenotypic diversity, suggesting their potential usefulness as a genetic resource. However, as the only high-quality reference genome available is for a tetraploid Digitaria species, a reference genome of the diploid species D. radicosa would be a useful resource for genomic studies of Digitaria and Poaceae plants. Here, we present a chromosome-level genome assembly of D. radicosa and describe its genetic characteristics; we also illustrate its usefulness as a genomic resource for Poaceae. We constructed a 441.6-Mb draft assembly consisting of 61 contigs with an N50 contig length of 41.5 Mb, using PacBio HiFi long reads. We predicted 26,577 protein-coding genes, reaching a Benchmarking Universal Single-Copy Orthologs score of 96.5%. To demonstrate the usefulness of the D. radicosa reference genome, we investigated the evolution of Digitaria species and the genetic diversity of Japanese Digitaria plants based on our new reference genome. We also defined the syntenic blocks between D. radicosa and 2 Poaceae crops, fonio and rice, and the diverse distribution of representative resistance genes in D. radicosa. The D. radicosa reference genome presented here should help elucidate the genetic relatedness of Digitaria species and the genetic diversity of Digitaria plants. In addition, the D. radicosa genome will be an important genomic resource for Poaceae genomics and crop breeding.
Glial peroxisome dysfunction induces axonal swelling and neuroinflammation in Drosophila
Authors: Sodders Maggie , Das Anurag , Bai Hua 
Published: October 2024

Abstract
Glial cells are known to influence neuronal functions through glia–neuron communication. The present study aims to elucidate the mechanism behind peroxisome-mediated glia–neuron communication using Drosophila neuromuscular junction (NMJ) as a model system. We observe a high abundance of peroxisomes in the abdominal NMJ of adult Drosophila. Interestingly, glia-specific knockdown of peroxisome import receptor protein, Pex5, significantly increases axonal area and volume and leads to axon swelling. The enlarged axonal structure is likely deleterious, as the flies with glia-specific knockdown of Pex5 exhibit age-dependent locomotion defects. In addition, impaired peroxisomal ether lipid biosynthesis in glial cells also induces axon swelling. Consistent with our previous work, defective peroxisomal import function upregulates pro-inflammatory cytokine upd3 in glial cells, while glia-specific overexpression of upd3 induces axonal swelling. Furthermore, motor neuron-specific activation of the JAK-STAT pathway through hop overexpression results in axon swelling. Our findings demonstrated that impairment of glial peroxisomes alters axonal morphology, neuroinflammation, and motor neuron function.
Analysis of actionable gene fusions in a large cohort of Chinese patients with colorectal cancer
Authors: Kou Fu-Rong , Li Jian , Wang Zheng-Hang , Xu Ting , Qian Juan-Juan , Zhang En-Li , Zhang Li-Jun , Shen Lin , Wang Xi-Cheng 
Published: October 2024

Abstract

Background
The prevalence of gene fusion is extremely low in unselected patients with colorectal cancer (CRC). Published data on gene fusions are limited by relatively small sample sizes, with a primary focus on Western populations. This study aimed to analyse actionable gene fusions in a large consecutive Chinese CRC population.

Methods
This study included 5,534 consecutive CRC patients from the Genecast database. Genomic profiling was performed using a panel of 769 cancer-related genes. Data for 34 CRC patients with actionable gene fusions were also collected from cBioPortal and ChimerSeq.

Results
Among 5,534 CRC patients, 54 (0.98%) had actionable gene fusions, with NTRK1/2/3 being the most common fusion (0.38%), accounting for 38.9% (21/54) of those with fusions. Actionable gene fusion enrichment was higher in patients with microsatellite instability-high (MSI-H) (6.7% vs. 0.5%, P &lt; 0.001), RAS/BRAF wildtype (2.0% vs. 0.2%, P &lt; 0.001) and RNF43 mutation (7.7% vs. 0.4%, P &lt; 0.001) than in patients with microsatellite stability/MSI-low, RAS/BRAF mutation and RNF43 wildtype, respectively. When these markers were combined, the fusion detection rate increased. Among patients with RAS/BRAF wildtype and MSI-H, fusions were detected in 20.3% of patients. The fusion detection rate further increased to 37.5% when RNF43 mutation was added. The fusion detection rate was also higher in colon cancer than in rectal cancer. No significant differences in clinical or molecular features were found in patients with actionable gene fusions between the Genecast, cBioPortal, and ChimerSeq databases.

Conclusions
Approximately 1% of the unselected Chinese CRC population carries actionable gene fusions, mostly involving NTRK. Actionable gene fusions are more prevalent in MSI-H, RAS/BRAF wildtype, or RNF43-mutated CRC, as well as in colon cancer. Mapping of these molecular markers can markedly increase the fusion detection rate, which can help clinicians select candidates for fusion testing and targeted therapy.
A dominance hypothesis argument for historical genetic gains and the fixation of heterosis in octoploid strawberry
Authors: Feldmann Mitchell J , Pincot Dominique D A , Seymour Danelle K , Famula Randi A , Jiménez Nicolás P , López Cindy M , Cole Glenn S , Knapp Steven J 
Published: October 2024

Abstract
Heterosis was the catalyst for the domestication of cultivated strawberry (Fragaria×ananassa), an interspecific hybrid species that originated in the 1700s. The hybrid origin was discovered because the phenotypes of spontaneous hybrids transgressed those of their parent species. The transgressions included fruit yield increases and other genetic gains in the twentieth century that sparked the global expansion of strawberry production. The importance of heterosis to the agricultural success of the hybrid species, however, has remained a mystery. Here we show that heterosis has disappeared (become fixed) among improved hybrids within a population (the California population) that has been under long-term selection for increased fruit yield, weight, and firmness. We found that the highest yielding hybrids are among the most highly inbred (59–79%), which seems counterintuitive for a highly heterozygous, outbreeder carrying heavy genetic loads. Although faint remnants of heterosis were discovered, the between-parent allele frequency differences and dispersed favorable dominant alleles necessary for heterosis have decreased nearly genome-wide within the California population. Conversely, heterosis was prevalent and significant among wide hybrids, especially for fruit count, a significant driver of genetic gains for fruit yield. We attributed the disappearance (fixation) of heterosis within the California population to increased homozygosity of favorable dominant alleles and inbreeding associated with selection, random genetic drift, and selective sweeps. Despite historical inbreeding, the highest yielding hybrids reported to-date are estimated to be heterozygous for 20,370–44,280 of 97,000–108,000 genes in the octoploid genome, the equivalent of an entire diploid genome or more.
A Lack of Food for Thought: Midlife Food Insecurity and Its Association With Subsequent Cognitive Ability of Older Americans
Authors: Zuo Dongmei 
Published: October 2024

Abstract

Objectives
The 50–59 age group in the United States experience higher levels of food insecurity (FI) compared to older adults. While previous research has identified an association between FI and cognition outcomes in older populations, limited research has examined midlife as a specific FI exposure window and the association of this hardship with long-run cognition outcomes.

Methods
Utilizing 14 waves of Health and Retirement Study (HRS) data (1995–2020), I applied mixed-effects models to assess the relationship between midlife FI exposure and later-life cognitive function, controlling for childhood disadvantages and other health-related and sociodemographic characteristics.

Results
Findings indicate that both cumulative FI duration and ever experiencing FI during ages 50–59 are significantly associated with subsequent cognitive decline. Specifically, ever experiencing FI during midlife was linked to a decrease in cognitive function by 0.07 standard units (95% confidence interval [CI], −0.13 to −0.003; p &lt; .05). In addition, each additional year of FI exposure during midlife was associated with a reduction in cognitive function by 0.01 standard units (95% CI: −0.03 to −0.003; p &lt; .05). These associations remained robust even after accounting for a range of potential confounders and covariates.

Discussion
The findings support the cumulative inequality model, suggesting that midlife FI is a significant predictor of lower cognitive function in later life. Both the timing and extent of FI during midlife are crucial factors in shaping cognitive health outcomes. Policy interventions targeting FI in the 50–59 age group could play a pivotal role in promoting healthy aging and mitigating cognitive decline in older adulthood.
High-quality assembly of the T2T genome for Isodon rubescens f. lushanensis reveals genomic structure variations between 2 typical forms of Isodon rubescens
Authors: Yang Hao , Lian Conglong , Liu Jinlu , Yu Hongwei , Zhao Le , He Ni , Liu Xiuyu , Xue Shujuan , Sun Xiaoya , Zhang Liping , Wang Lili , Yang Jingfan , Fu Yu , Ma Rui , Zhang Bao , Ye Lidan , Chen Suiqing 
Published: October 2024

Abstract

Background
Rabdosiae rubescentis herba (Isodon rubescens) is widely used as a folk medicine to treat esophageal cancer and sore throat in China. Its germplasm resources are abundant in China, with I. rubescens (Hemsl.) Hara and I. rubescens f. lushanensis as 2 typical forms. I. rubescens (Hemsl.) Hara is featured by biosynthesis of the diterpenoid oridonin with strong anticancer activity, while I. rubescens f. lushanensis produces another diterpenoid with anticancer activity, lushanrubescensin. However, the biosynthetic pathways of both still need to be fully understood. In particular, little is known about the genetic background of I. rubescens f. lushanensis.

Findings
We used Pacific Biosciences (PacBio) single-molecule real-time and Nanopore Ultra-long sequencing platforms, respectively, and obtained 139.07 Gb of high-quality data, with a sequencing depth of about 328×. We also obtained a high-quality reference genome for I. rubescens f. lushanensis, with a genome size of 349 Mb and a contig N50 of 28.8 Mb. The heterozygosity of the genome is 1.7% and the repeatability is 83.43%. In total, 34,865 protein-coding genes were predicted. Moreover, we found that most of the variant or unique genes in the diterpenoid synthesis pathways of I. rubescens f. lushanensis and I. rubescens (Hemsl.) Hara were enriched in diterpene synthases.

Conclusions
We provide the first genome sequence and gene annotation for the I. rubescens f. lushanensis, which provides molecular evidence for understanding the chemotypic differences of I. rubescens.
CBioProfiler: A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization
Authors: Liu Xiaoping , Wang Zisong , Shi Hongjie , Li Sheng , Wang Xinghuan 
Published: October 2024

Abstract
Cancer is a leading cause of death worldwide, and the identification of biomarkers and subtypes that can predict the long-term survival of cancer patients is essential for their risk stratification, treatment, and prognosis. However, there are currently no standardized tools for exploring cancer biomarkers or subtypes. In this study, we introduced Cancer Biomarker and subtype Profiler (CBioProfiler), a web server and standalone application that includes two pipelines for analyzing cancer biomarkers and subtypes. The cancer biomarker pipeline consists of five modules for identifying and annotating cancer survival-related biomarkers using multiple survival-related machine learning algorithms. The cancer subtype pipeline includes three modules for data preprocessing, subtype identification using multiple unsupervised machine learning methods, and subtype evaluation and validation. CBioProfiler also includes CuratedCancerPrognosisData, a novel R package that integrates reviewed and curated gene expression and clinical data from 268 studies. These studies cover 43 common blood and solid tumors and draw upon 47,686 clinical samples. The web server is available at https://www.cbioprofiler.com/ and https://cbioprofiler.znhospital.cn/CBioProfiler/, and the standalone app and source code can be found at https://github.com/liuxiaoping2020/CBioProfiler.
RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells
Authors: Xu Ping , Yuan Zhiheng , Lu Xiaohua , Zhou Peng , Qiu Ding , Qiao Zhenghao , Zhou Zhongcheng , Guan Li , Jia Yongkang , He Xuan , Sun Ling , Wan Youzhong , Wang Ming , Yu Yang 
Published: October 2024

Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular diversity with unprecedented resolution. However, many current methods are limited in capturing full-length transcripts and discerning strand orientation. Here, we present RAG-seq, an innovative strand-specific total RNA sequencing technique that combines not-so-random (NSR) primers with Tn5 transposase-mediated tagmentation. RAG-seq overcomes previous limitations by delivering comprehensive transcript coverage and maintaining strand orientation, which are essential for accurate quantification of overlapping genes and detection of antisense transcripts. Through optimized reverse transcription with oligo-dT primers, rRNA depletion via Depletion of Abundant Sequences by Hybridization (DASH), and linear amplification, RAG-seq enhances sensitivity and reproducibility, especially for low-input samples and single cells. Application to mouse oocytes and early embryos highlights RAG-seq’s superior performance in identifying stage-specific antisense transcripts, shedding light on their regulatory roles during early development. This advancement represents a significant leap in transcriptome analysis within complex biological contexts.
Purging Disloyal Courts in Democratic Transitions and Judicial Preferences
Authors: Garoupa Nuno 
Published: October 2024

ABSTRACT∞
In this article, I examine court-purging in democratic transitions through the lens of judicial preferences. Specifically, I address the debate on how court-purging during a democratic transition affects the likelihood of future court-purging. I argue that the prevailing assumption is one of static, sincere judicial preferences. In contrast, I explicitly recognize the role of dynamic judicial preferences and incentives. This recognition suggests that transitional court-purging could be minimal and cautious, while the broader judicial context may eventually achieve the same policy outcomes. The dynamic perspective is crucial for understanding past court-purging strategies and for informing the conceptual debate about the rule of law in transitional justice.