bluuebunny/crossref_metadata_2025 huggingface dataset:
Delayed endometrial preparation for the induction of luteolysis as a potential factor for improved reproductive performance in Angus beef heifers with high antral follicle counts
Authors: Kaps Martim , Quail Lacey K , Rosasco Shelby L , Snider Alexandria P , Zoca Saulo M , Epperson Kaitlin M , Rich Jerica J J , Miles Jeremy R , Crouse Matthew S , Keel Brittney N , Summers Adam F , Perry George A , Lents Clay A , Cushman Robert A
Published: October 2024

Antral follicle count (AFC) and anti-Müllerian hormone (AMH) concentrations are reflective for ovarian reserve and have been associated with improved reproductive performance in cattle. Key events for regulation of uterine receptivity are orchestrated by progesterone. As progesterone concentrations are greater in animals with high than low AFC, we tested the hypothesis, if the resulting improved uterine environment will lead to improved conceptus elongation and endometrial response to interferon tau. For four years, 10 heifers with lowest and highest AFC, respectively, were selected from 120 heifers. Reproductive tracts and blood samples for progesterone and AMH analysis were collected after synchronization and insemination. For a recovered conceptus, length was determined, and interferon tau (IFNT) transcript abundance was analyzed. Endometrial transcript abundance of interferon-stimulated gene 15 (ISG15) and oxytocin receptor (OXTR) were analyzed. Progesterone concentrations did not differ between low and high AFC groups (P = 0.1). A difference in conceptus length was not observed. Endometrial abundance of ISG15 did not differ between pregnant low and high AFC heifers. Abundance of OXTR was greater in open low AFC than open high AFC heifers (P < 0.01). Interaction of AMH and pregnancy status was determined, with greater AMH in pregnant than open high AFC heifers (P < 0.05). Improved uterine environment in high vs. low AFC heifers did not result in longer conceptuses or improved endometrial response. As the increase in OXTR transcript abundance was only detected in low AFC heifers, reported differences in reproductive performance might be associated with earlier initiation of luteolysis.
A modular curriculum to teach undergraduates ecological forecasting improves student and instructor confidence in their data science skills
Authors: Lofton Mary E , Moore Tadhg N , Woelmer Whitney M , Thomas R Quinn , Carey Cayelan C
Published: October 2024

Data science skills (e.g., analyzing, modeling, and visualizing large data sets) are increasingly needed by undergraduates in the life sciences. However, a lack of both student and instructor confidence in data science skills presents a barrier to their inclusion in undergraduate curricula. To reduce this barrier, we developed four teaching modules in the Macrosystems EDDIE (for environmental data-driven inquiry and exploration) program to introduce undergraduate students and instructors to ecological forecasting, an emerging subdiscipline that integrates multiple data science skills. Ecological forecasting aims to improve natural resource management by providing future predictions of ecosystems with uncertainty. We assessed module efficacy with 596 students and 26 instructors over 3 years and found that module completion increased students’ confidence in their understanding of ecological forecasting and instructors’ likelihood to work with long-term, high-frequency sensor network data. Our modules constitute one of the first formalized data science curricula on ecological forecasting for undergraduates.
Ultrasound strain elastography to improve diagnostic performance of breast lesions by reclassifying BI-RADS 3 and 4a lesions: a multicentre diagnostic study
Authors: Gu Yang , Tian Jiawei , Ran Haitao , Ren Weidong , Chang Cai , Yuan Jianjun , Kang Chunsong , Deng Youbin , Wang Hui , Luo Baoming , Guo Shenglan , Zhou Qi , Xue Ensheng , Zhan Weiwei , Zhou Qing , Li Jie , Zhou Ping , Zhang Chunquan , Chen Man , Gu Ying , Xu Jinfeng , Chen Wu , Zhang Yuhong , Li Jianchu , Wang Hongyan , Jiang Yuxin
Published: October 2024

Objectives

To investigate the added value of strain elastography (SE) by recategorizing ultrasound (US) breast imaging reporting and data system (BI-RADS) 3 and 4a lesions.

Methods

A total of 4371 patients underwent US and SE with BI-RADS 2-5 categories solid breast lesions were included from 32 hospitals. We evaluated the elastographic images according to elasticity scores (ES) and strain ratios (SR). Three combined methods (BI-RADS + ES, BI-RADS + SR, BI-RADS + ES + SR) and two reclassified methods were used (method one: upgrading BI-RADS 3 and downgrading BI-RADS 4a, method two: downgrading BI-RADS 4a alone). The diagnostic performance and the potential reduction of unnecessary biopsies were evaluated.

Results

Combining BI-RADS with SE had a higher area under the curve (AUC) than BI-RADS alone (0.822-0.898 vs 0.794, P < .01). For reclassified method one, the sensitivity, specificity, and accuracy were 99.36%, 66.70%, 78.36% for BI-RADS + ES and 98.01%, 66.45%, 77.72% for BI-RADS + SR, and 99.42%, 66.70%, 78.38% for BI-RADS + ES + SR, respectively. For reclassified method two, the sensitivity, specificity, and accuracy were 99.17%, 70.72%, 80.87% for BI-RADS + ES and 97.76%, 81.75%, 87.46% for BI-RADS + SR, and 99.23%, 69.83%, 80.32% for BI-RADS + ES + SR, respectively. Downgrading BI-RADS 4a alone had higher AUC, specificity, and accuracy (P < .01) and similar sensitivity (P > .05) to upgrading BI-RADS 3 and downgrading BI-RADS 4a. Combining SE with BI-RADS could help reduce unnecessary biopsies by 17.64%-55.20%.

Conclusions

Combining BI-RADS with SE improved the diagnostic performance in distinguishing benign from malignant lesions and could decrease false-positive breast biopsy rates. Downgrading BI-RADS 4a lesions alone might be sufficient for achieving good diagnostic performance.

Advances in knowledge

Downgrading BI-RADS category 4a lesions alone had higher AUC, specificity, and accuracy, and similar sensitivity to upgrading or downgrading BI-RADS category 3 and 4a lesions.
Understanding services provided to children in DFV shelters: Exposing the ‘invisible’ work
Authors: Bastian Carmela , Wendt Sarah , Cunningham Tessa , Bromley Amy
Published: October 2024

This study examines practice responses for children who reside in the context of domestic and family violence (DFV) shelters in Australia. DFV is a recognized form of child abuse and identified as such in child protection legislations, policies, and practice guidelines. The prevalence of children who experience DFV is unknown and underestimated. DFV shelters that provide crisis accommodation and case management services were traditionally established to respond to the needs of women and are therefore adult centred. Increasingly, practitioners employed in DFV shelters are also responding to the needs of children and young people; however, they are not resourced to do so. This qualitative study conducted in South Australia explores practice responses provided for children and young people while they are residing in a DFV shelter with their mothers. Data were extracted and analysed from the DFV shelter case files of seventeen women and their children using a co-designed data collection instrument. The findings provide insight into children’s experiences due to DFV. Practitioners in DFV shelters were found to be providing an array of services to children exposing this ‘invisible’ work. Understanding the complex needs and service provided to children have practice implications for the DFV sector.
Exploring patient perspectives on the relationship between hidradenitis suppurativa and body weight
Authors: Khalil Nada , Hussain Khawar , Patel Neil P
Published: October 2024

We conducted a questionnaire study of 40 patients attending the hidradenitis suppurativa (HS) clinic at our centre to explore patient perspectives on the relationship between HS and body weight. The most common obstacles to maintaining a healthy diet and regular exercise were time, cost and physical limitations related to HS. We identified a need for improved diagnosis of overweight/obesity, as well as an opportunity to improve patient education on the importance of maintaining a healthy body weight in HS, if clinician advice on weight management is to align with patients’ understanding of the condition.
Fear, learning, and the amygdala: a personal reflection in honor of Joseph LeDoux
Authors: LaBar Kevin S
Published: October 2024

In honor of Joseph LeDoux’s retirement from an illustrious career in science, I offer a personal reflection on how my graduate training experiences in his lab shaped my subsequent career trajectory and the development of my views on human amygdala function and the scientific enterprise. I discuss the values of openness to scientific exploration and of multi-methodological integration, both of which distinguished his laboratory over the years. I highlight the unique historical context in which the lab’s foundational discoveries on the emotional brain occurred and the importance of embracing new technologies to advance an understanding of brain–behavior relationships in affective neuroscience.
Optimizing the prediction of discard survival of bottom-trawled plaice based on vitality indicators
Authors: Uhlmann Sven Sebastian , Savina Esther , Karlsen Junita , Ampe Bart
Published: October 2024

Predicting the discard survival of aquatic animals after fisheries capture using vitality indicators (i.e. individual scores or indices of physical condition) is a resource-efficient approach compared to estimating discard survival from captive observation. But such indicators do not always lead to accurate and robust predictions. Individual scores of reflex impairments and injuries are typically given the same weight when being aggregated into an index, while some reflexes or injuries may contribute to mortality more than others. This study established an analytical methodology and created an index based on differential contributions of individual reflexes and injuries to optimize the prediction of discard survival of bottom-trawled European plaice (Pleuronectes platessa). The optimization procedures were applied to a dataset from vitality assessment of 1122 undersized plaice caught during 16 commercial fishing trips and 58 gear deployments in Belgium and Denmark. As welfare indicators, we considered and evaluated against post-capture survival of plaice: original vs. optimized reflex impairment and injury (R&I) index, number of absent reflexes, number of present injuries, number of absent reflexes and present injuries, categorical vitality score and individual reflex and injury scores. These were used in eight candidate generalized linear models (one without any vitality indicator) as explanatory variables to predict survival, with or without biological, environmental, technical and operational covariates, either at the individual fish or trip level. Bruising to the head and body were the most relevant predictors. The optimized R&I index did not perform better than any other vitality indicator, and all the indicators performed poorly in predicting survival probability both at the fish and trip levels without information on air exposure and seawater temperature. This means that they cannot be considered to be independent measures. The categorical vitality score provided a viable alternative to the more labour-intensive, scoring method of reflex responsiveness. Use of reflexes as proxies may not be accurate when they are not independent of environmental, biological or technical variables.
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

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

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

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

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

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

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

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 < 0.001), RAS/BRAF wildtype (2.0% vs. 0.2%, P < 0.001) and RNF43 mutation (7.7% vs. 0.4%, P < 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

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

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 < .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 < .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

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

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

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.
New insights and theoretical conditions for determining minor and major consolidations in the inverse DEA
Authors: Ghiyasi Mojtaba
Published: October 2024

Accepted by: Ali Emrouznejad

In the current paper, we propose new conditions for determining major and minor consolidation using the inverse data envelopment analysis models. We categorized the causes of major consolidation into pre and post-effect. Pre-effects may happen due to the omission of pre-merged units and post-effects are associated with the fact that the merged unit may not belong to the production set. The idea is described by numerical examples and graphical illustrations and an empirical analysis in banking also helps us to show the necessity, strength, and applicability of the proposed models for real-world applications.
A mathematical model on the impact of awareness and traditional medicine in the control of Ebola: case study of the 2014–2016 outbreaks in Sierra Leone and Liberia
Authors: Ouemba Tassé Arsène Jaurès , Tsanou Berge , Kum Cletus Kwa , Lubuma Jean
Published: October 2024

In the control of infectious diseases worldwide, awareness of the population occupies a prominent place. In Africa, there has been a long standing rivalry between traditional medicine and modern medicine. Any disease control strategy must take into account disease-oriented education, as this has a direct influence on the choice of treatment type to follow. In this work, we present a mathematical model that takes into consideration not only public health awareness but also the significant contribution of traditional medicine to the Ebola treatment effort. This study uses data from the 2014–2016 Ebola outbreaks in Sierra Leone and Liberia. Theoretically, we show that our model exhibits a trans-critical bifurcation at $\mathcal{R}_{c}=1$ and a backward bifurcation phenomenon whenever $\mathcal{R}_{c}^{c}<\mathcal{R}_{c}< 1$. While the disease persists when $\mathcal{R}_{c}>1$. In addition, a threshold number $\mathcal{T}_{0}$ is obtained, which ensures the global asymptotic stability of the disease-free equilibrium when its value is less than 1. Numerically, it is shown that the number of hospitalized infected cases increases more rapidly than the number of infected cases treated by traditional healers in both countries, suggesting that people have a high tendency to visit hospitals than visiting traditional healers. Our analysis reveals that during an Ebola outbreak, awareness messages should target the susceptible population for behaviour change in order to mitigate the spread of the disease. Calibrating the model, it fits well the weekly cumulative cases in Sierra Leone and Liberia, and their corresponding estimated control reproduction numbers are $0.5725$ and $0.8340$, respectively.
Three types of quasi-Trefftz functions for the 3D convected Helmholtz equation: construction and approximation properties
Authors: Imbert-Gérard Lise-Marie , Sylvand Guillaume
Published: October 2024

Trefftz methods are numerical methods for the approximation of solutions to boundary and/or initial value problems. They are Galerkin methods with particular test and trial functions, which solve locally the governing partial differential equation (PDE). This property is called the Trefftz property. Quasi-Trefftz methods were introduced to leverage the advantages of Trefftz methods for problems governed by variable coefficient PDEs, by relaxing the Trefftz property into a so-called quasi-Trefftz property: test and trial functions are not exact solutions, but rather local approximate solutions to the governing PDE. In order to develop quasi-Trefftz methods for aero-acoustics problems governed by the convected Helmholtz equation this work tackles the question of the definition, construction and approximation properties of three families of quasi-Trefftz functions: two based on generalizations on plane wave solutions, and one polynomial. The polynomial basis shows significant promise as it does not suffer from the ill-conditioning issue inherent to wave-like bases.
Simultaneous Cocirculation of 2 Genotypes of Dengue Virus Serotype 3 Causing a Large Outbreak in Sri Lanka in 2023
Authors: Ariyaratne Dinuka , Senadheera Bhagya , Kuruppu Heshan , Pramanayagam Jayadas Tibutius Thanesh , Gomes Laksiri , Ranasinghe Diyanath , Bary Farha , Wijewickrama Ananda , Agulilar Sully Márquez , Bennett Shannon , Jeewandara Chandima , Malavige Gathsaurie Neelika
Published: October 2024

Background

We observed a discrepancy between dengue NS1 antigen test and molecular diagnostics, with the emergence of dengue virus (DENV) serotype 3 in Sri Lanka, and sought to understand the cause for the rise in cases and high failure rates of molecular diagnostics.

Methods

Whole-genome sequencing was carried out in 22 DENV-3 samples. Phylogenetic and molecular clock analyses were done for genotype assignment and to understand the rate of evolution. Mutation analysis was done to understand the reasons for polymerase chain reaction (PCR) nondetection.

Results

We identified 2 DENV-3 genotypes (I and III) cocirculating. DENV-3 genotype III strains shared a common ancestor with a sequence from India collected in 2022, while DENV-3 genotype I, was found to share a common ancestor with DENV-3 sequences from China. DENV-3 genotype III was detected by the modified Centers for Disease Control and Prevention DENV-3 primers, whereas genotype I evaded detection due to key mutations at forward and reverse primer binding sites. We identified point mutations C744T and A756G in the forward primer binding sites and G795A in the reverse primer binding sites, which were not identified in DENV-3 genotype III. Furthermore, our Sri Lankan DENV-3 strains demonstrated a high root to tip ratio compared to the previous DENV-3 sequences, indicating a high mutation rate during the time of sampling (2017 to 2023).

Conclusions

The cocirculation of multiple genotypes associated with an increase in cases highlights the importance of continuous surveillance of DENVs to identify mutations resulting in nondetection by diagnostics and differences in virulence.
The law of perfidy and ruses of war at sea
Authors: Yoga Pornomo Rovan Astri , Bautista Lowell
Published: October 2024

The principle of distinction is a fundamental principle in the law of armed conflict, aimed at protecting civilians and civilian objects from direct attacks. Adherence to this principle is crucial for minimizing the humanitarian impact of warfare. Nevertheless, the longstanding practice of ruses of war, deeply embedded in customary international law, complicates the application of this principle in combat. While certain deceptive tactics are allowed, the line between acceptable ruses and forbidden acts of perfidy is often unclear, especially in naval warfare. The evolution of modern warfare technology further obscures these distinctions, raising important legal questions regarding their relevance today. This article critically examines the existing legal framework governing ruses and perfidy at sea and explores how these rules apply to contemporary naval operations. Finally, the article identifies key legal gaps and proposes pathways for reform to better align the law with current realities.
Regional changes of maximum dose insecticide responses in diamondback moth (Lepidoptera: Plutellidae) populations from Georgia and Florida, USA
Authors: Dunn Thomas P , Cremonez Paulo S G , Furuya Amanda , Brown Will S , Nagaoka Mirela M , Powell Chase B , Sparks Alton N , Smith Hugh , Riley David G , Champagne Donald E
Published: October 2024

Maximum dose bioassays were conducted to assess the efficacy of multiple registered active ingredients for diamondback moth (DBM), Plutella xylostella (L.), control in Georgia and Florida from 2021 to 2023 as a follow-up to an earlier study. Low efficacy (<40% mortality) was recorded for the highest labeled rate of Bacillus thuringiensis var. kurstaki strain ATBS-351 in Georgia, as well as chlorantraniliprole, cyantraniliprole, and cyclaniliprole in Georgia and Florida. The active ingredients with the highest efficacy (>80% mortality) in both states were naled, emamectin benzoate, and spinetoram. Independent analysis of data by state indicated that the efficacy of bifenthrin, chlorantraniliprole, cyantraniliprole, tolfenpyrad, and methomyl was higher in Florida populations than in Georgia populations. In addition, a comparison of these data to a recent DBM maximum dose survey in the same region suggested that these DBM populations have rapidly developed high levels of resistance to cyantraniliprole and cyclaniliprole. This work provides growers in the region with a recent ranking of insecticide efficacy that documents the loss of control for certain active ingredients, which assists pest managers in the planning of ongoing insecticide rotations for DBM resistance management.
Examining the psychometric properties of the CEFIS-AYA using item response theory
Authors: Howe Meghan M , Miller Steven A , Tran Susan , Buscemi Joanna , Bugno Lindsey , Greenley Rachel N
Published: October 2024

Objective

The COVID-19 Exposure and Family Impact Scale, Adolescent and Young Adult Version (CEFIS-AYA; Schwartz, L. A., Lewis, A. M., Alderfer, M. A., Vega, G., Barakat, L. P., King-Dowling, S., Psihogios, A. M., Canter, K. S., Crosby, L., Arasteh, K., Enlow, P., Hildenbrand, A. K., Kassam-Adams, N., Pai, A., Phan, T. L., Price, J., Schultz, C. L., Sood, E., Wood, J., & Kazak, A. (2022). COVID-19 exposure and family impact scales for adolescents and young adults. Journal of Pediatric Psychology, 47, 631–640. https://doi.org/10.1093/jpepsy/jsac036) was developed to assess the pandemic’s effects on adolescents and young adults (AYA). Via principal component analysis, measure developers examined the structure and reliability of the CEFIS-AYA and identified seven exposure and five impact components. This study built upon prior work through use of item response theory (IRT) models to characterize the dimensionality of the CEFIS-AYA, determine the strength of relations between items and underlying trait(s), and examine associations between trait scores and pandemic-related distress.

Methods

This was a secondary analysis of data collected between July 2020 and July 2021 from three studies of emerging adults (ages 18–29; N = 834).

Results

The CEFIS-AYA structure was multidimensional, with the strongest support for five traits. Trait 1 represented pandemic impact on social/emotional functioning and self-care. Trait 2 reflected other pandemic disruptions. Trait 3 represented pandemic disruptions to education and/or other milestones. Trait 4 represented pandemic impact on physical well-being. Trait 5 assessed pandemic disruptions to work/financial circumstances. Item loadings and parameters indicated variability in how consistently trait level was associated with item endorsement. Trait scores did not predict distress, except that increases in Trait 3 were associated with lower distress.

Conclusions

The present study examined the psychometric properties of the CEFIS-AYA among emerging adults using a statistical framework better suited for modeling categorical data. The identified dimensional structure was relatively consistent with the initial psychometric evaluation of the CEFIS-AYA, albeit more parsimonious. However, replication is critical in light of sample demographic characteristics.