bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fading on the beach: pigmentation plasticity adjusts coloration to substrate type in coastal Western spadefoot toads
Authors: Lorrain-Soligon Léa , Robin Frédéric , Lelong Vincent , Palier Sébastien , Jankovic Marko , Brischoux François 
Published: January 2025

Abstract
Animal species exhibit a wide range of coloration and patterns, which are under strong selection and often linked to individual quality, influencing mate choice, recognition, signaling, and interspecific interactions such as predator avoidance. In amphibians, coloration can vary based on individual traits as well as environmental conditions, including the coloration of their environment. In this study, we described the dorsal coloration (body coloration reticulated by dark patches) in 676 Western spadefoot toads (Pelobates cultripes) from the French Atlantic coast, comparing color variations across different substrates. In addition, we assessed color change in 18 toads transferred between bright and dark substrates. We demonstrated that the dorsal coloration varies based on capture locations (beach vs. inland) and associated substrate types (bright vs. dark), suggesting background color matching. We showed more pronounced effects in females, which might reflect varying predation risks. Experimentally, we showed that individuals can rapidly adjust their coloration to match the substrate within 24 h. Rapid color changes in response to substrate type indicate significant pigmentation plasticity. Bright individuals from sandy substrates showed less dorsal background (body) color change than dark inland individuals, while patch coloration responded differently depending on the substrate of origin. These findings highlight the complex interactions between substrate type, sex, and pigmentation plasticity. These interactions have potential costs and benefits, which might be linked to melanin production, which warrant further investigation.
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data
Authors: Poretsky Elly , Blake Victoria C , Andorf Carson M , Sen Taner Z 
Published: January 2025

Abstract
Curated resources at centralized repositories provide high-value service to users by enhancing data veracity. Curation, however, comes with a cost, as it requires dedicated time and effort from personnel with deep domain knowledge. In this paper, we investigate the performance of a large language model (LLM), specifically generative pre-trained transformer (GPT)-3.5 and GPT-4, in extracting and presenting data against a human curator. In order to accomplish this task, we used a small set of journal articles on wheat and barley genetics, focusing on traits, such as salinity tolerance and disease resistance, which are becoming more important. The 36 papers were then curated by a professional curator for the GrainGenes database (https://wheat.pw.usda.gov). In parallel, we developed a GPT-based retrieval-augmented generation question-answering system and compared how GPT performed in answering questions about traits and quantitative trait loci (QTLs). Our findings show that on average GPT-4 correctly categorized manuscripts 97% of the time, correctly extracted 80% of traits, and 61% of marker–trait associations. Furthermore, we assessed the ability of a GPT-based DataFrame agent to filter and summarize curated wheat genetics data, showing the potential of human and computational curators working side-by-side. In one case study, our findings show that GPT-4 was able to retrieve up to 91% of disease related, human-curated QTLs across the whole genome, and up to 96% across a specific genomic region through prompt engineering. Also, we observed that across most tasks, GPT-4 consistently outperformed GPT-3.5 while generating less hallucinations, suggesting that improvements in LLM models will make generative artificial intelligence a much more accurate companion for curators in extracting information from scientific literature. Despite their limitations, LLMs demonstrated a potential to extract and present information to curators and users of biological databases, as long as users are aware of potential inaccuracies and the possibility of incomplete information extraction.
Intersectionality of inequalities in revascularization and outcomes for acute coronary syndrome in England: nationwide linked cohort study
Authors: Roman Marius , Cheng Ann , Lai Florence Y , Aujla Hardeep , Sanders Julie , Dearling Jeremy , Murray Sarah , Loubani Mahmoud , Kunadian Vijay , Gale Chris , Murphy Gavin J 
Published: January 2025

Abstract

Background
Inequalities in access to care for women, people of non-white ethnicity, who live in areas of social deprivation, and with multiple long-term conditions lead to inequity of outcomes. We investigated the intersectionality of these causes of health inequality on coronary revascularization and clinical outcomes for admissions with acute coronary syndrome (ACS).

Methods and results
We included hospital admissions in England for types of ACS from April 2015 to April 2018 and linked Hospital Episode Statistics to the Office for National Statistics mortality data. The primary outcome was time to all-cause mortality. Time-to-event analyses examined the associations of sex, ethnicity, and socioeconomic deprivation with revascularization. Of 428 700 admissions with ACS, 212 015 (48.8%) received revascularization within 30 days. Women, black ethnicity, multimorbid, and frail patients were less likely to undergo revascularization. South Asian ethnicities had higher [hazard ratio (HR) = 1.15, 95% confidence interval (CI) 1.14–1.17] revascularization rates and comparable risk-adjusted survival but higher re-admission rates when compared to other ethnic groups. Women had higher 1-year all-cause [25.5% vs. 14.7%—ST-elevation myocardial infarction (STEMI); 24.9% vs. 18.7%—non-ST-elevation myocardial infarction (NSTEMI)] and cardiovascular (22.6% vs. 13.2%—STEMI; 20.3% vs. 15.6%—NSTEMI) mortality than men. After adjusting for confounders, women had a lower all-cause mortality when compared to men.

Discussion
Outcomes attributed to women and people of South Asian ethnicity may be attributable to age, comorbidity and frailty at presentation. Black ethnicity, geography, and social deprivation may be sources of inequality. These findings highlight the unmet need and may provide potential targets for interventions that address inequalities.
Effectiveness of psychological interventions in reducing post-traumatic stress among post-myocardial infarction patients: a systematic review and meta-analysis
Authors: Chew Tan Rouge , Yeo Tin Mei , Teo Jun Yi Claire , Seah Chuen Wei Alvin , Soh Cheers Shun Qin , Meng Jingjing , Wang Wenru 
Published: January 2025

Abstract

Aims
Myocardial infarction (MI) can lead to post-traumatic stress disorder (PTSD) which frequently occurs with anxiety and depression, impairing daily functioning and increasing the risk of recurrent cardiovascular events. While psychological interventions have shown promise in reducing anxiety and depression, their effectiveness for PTSD in post-MI patients remains unexplored. This systematic review and meta-analysis aim to evaluate the effectiveness of psychological interventions on PTSD, anxiety, and depression in post-MI patients.

Methods and results
A comprehensive search of databases (Cochrane, CINAHL, PubMed, PsycINFO, Scopus, Embase, Web of Science, CNKI, Wanfang, CBM, ProQuest Dissertations and Theses Global, ClinicalTrials.gov) was conducted until June 2024, identifying randomized controlled trials and quasi-experimental studies assessing psychological interventions in post-MI patients. Study quality was evaluated using the Cochrane Risk of Bias and ROBINS-I tools. Post-traumatic stress disorder outcomes were pooled using meta-analysis in RevMan 5.4. Narrative synthesis was conducted where meta-analysis was not feasible. Nine studies involving 1065 participants were included. Psychological interventions significantly reduced PTSD symptoms {standardized mean difference (SMD) = −0.43 [95% confidence interval (CI): −0.70 to −0.16, P = 0.002]}, anxiety, and depression post-intervention. Subgroup analyses found that intervention components influenced effectiveness, with first-line treatments [eye movement desensitization and reprocessing (EMDR) and cognitive-behavioural therapy (CBT)] demonstrating a medium effect (SMD = −0.40; 95% CI: −0.74 to −0.07; P = 0.02). No significant subgroup differences were found based on the control condition or geographical location of studies.

Conclusion
Psychological interventions, particularly CBT and EMDR, were effective in alleviating PTSD, anxiety, and depression in post-MI patients. Future high-quality research is needed to identify active components and optimize these psychological interventions.

Registration
Prospero CRD42024528138.
Life’s Essential 8 and cardiovascular disease in women with a history of adverse pregnancy outcomes
Authors: Chen Haozhang , Li Ruyi , Liu Sen , Zhao Shiyu , Guo Tianyu , Tian Shufan , Zhong Jiale , Tang Zijun , Ge Zhenghao , Xia Jiawei , Geng Tingting , Pan Xiongfei , Pan An , Qian Frank , Liu Gang 
Published: January 2025

Abstract

Aims
To assess whether better cardiovascular health (CVH) is associated with a lower long-term risk of cardiovascular disease (CVD) in women with a history of adverse pregnancy outcomes (APOs).

Methods and results
Using data from the UK Biobank prospective cohort, we included 2263 participants with prior APOs and 107 260 participants without prior APOs. Life's Essential 8 (LE8) score was assessed at baseline. Multivariable-adjusted Cox models were used to estimate the associations between LE8 score and CVD events. Over a median 13.5 years of follow-up, 11 134 incident CVD events were documented. Among women with prior APOs, the incidence of total CVD was significantly lower in the top tertile compared with the bottom tertile, with a hazard ratio (HR) [95% confidence interval (CI)] of 0.43 (0.29, 0.65). A similar trend was observed in women without APOs, with an HR (95% CI) of 0.55 (0.53, 0.58). With respect to the individual CVD outcomes, among women with APOs, only the associations with coronary heart disease (CHD), HR (95% CI) for T3 vs. T1: 0.30 (0.17, 0.55), and atrial fibrillation (AF): 0.47 (0.24, 0.91) achieved statistical significance. Women with high LE8 score and prior APOs had a similar long-term cardiovascular risk compared with women with high LE8 score and no prior APOs [0.95 (0.63, 1.44)].

Conclusion
Among women with a history of APOs, better CVH as assessed using LE8 was associated with a significantly lower incidence of CVD, particularly CHD and AF. The excess risk associated with APOs appears to be attenuated among those with a high LE8 score.
Operadic Kazhdan–Lusztig–Stanley Theory
Authors: Coron Basile 
Published: January 2025

Abstract
We introduce a new type of operad-like structure called a ${\mathcal{P}}$-operad, which depends on the choice of some collection of posets ${\mathcal{P}}$, and which is governed by chains in posets of ${\mathcal{P}}$. We introduce several examples of such structures that are related to classical poset theoretic notions such as poset homology, Cohen–Macaulayness, and lexicographic shellability. We then show that ${\mathcal{P}}$-operads form a satisfactory framework to categorify Kazhdan–Lusztig polynomials of geometric lattices and their $P$-kernel. In particular, this leads to a new proof of the positivity of the coefficients of Kazhdan–Lusztig polynomials of geometric lattices.
Increased discoverability of rare disease datasets through knowledge graph integration
Authors: Braun Ian , Hartley Emily , Olson Daniel , Matentzoglu Nicolas , Schaper Kevin , Walls Ramona , Vasilevsky Nicole 
Published: January 2025

Abstract

Objectives
Demonstrate a methodology for improving discoverability of rare disease datasets by enriching source data with biological associations.

Materials and Methods
We developed an extension of the Biolink semantic model to incorporate patient data and generated a knowledge graph (KG) comprising patient data and associations between biological entities in an existing KG, leveraging existing mappings and mapping standards.

Results
The enriched model of patient data can support a search application that is aware of biological associations and provides a semantic search interface to discover and summarize patient datasets within the broader biological context.

Discussion and Conclusion
Our methodology enriches datasets with a wealth of additional biological knowledge, improving discoverability. Using condition concepts, we illustrate techniques that could be applied to other entities within source data such as measurements and observations. This work provides a foundational framework for how source data can be modeled to improve accuracy of upstream language models for natural language querying.
Leveraging deep learning to detect stance in Spanish tweets on COVID-19 vaccination
Authors: Blanco Guillermo , Yáñez Martínez Rubén , Lourenço Anália 
Published: January 2025

Abstract

Objectives
The automatic detection of stance on social media is an important task for public health applications, especially in the context of health crises. Unfortunately, existing models are typically trained on English corpora. Considering the benefits of extending research to other widely spoken languages, the goal of this study is to develop stance detection models for social media posts in Spanish.

Materials and Methods
A corpus of 6170 tweets about COVID-19 vaccination, posted between March 1, 2020 and January 4, 2022, was manually annotated by native speakers. Traditional predictive models were compared with deep learning models to ascertain a baseline performance for the detection of stance in Spanish tweets. The evaluation focused on the ability of multilingual and language-specific embeddings to contextualize the topic of those short texts adequately.

Results
The BERT-Multi+BiLSTM combination yielded the best results (macroaveraged F1 and Matthews correlation coefficient scores of 0.86 and 0.79, respectively; interpolated area under the receiver operating curve [AUC] of 0.95 for tweets against vaccination and 0.85 in favor of vaccination and a score of 0.97 for tweets containing no stance information), closely followed by the BETO+BiLSTM and RoBERTa BNE-LSTM Spanish models and the term frequency-inverse document frequency+SVM model (average AUC decrease of 0.01). The main differentiating factor among these models was the ability to predict tweets against vaccination.

Discussion
The BERT Multi+BILSTM model outperformed the other models in terms of per class prediction capacity. The main assumption is that language-specific embeddings do not outperform multilingual embeddings or TF-IDF features because of the context of the topic. The inherent context of BERT or RoBERTa embeddings is general. So, these embeddings are not familiar with the slang commonly used on Twitter and, more specifically, during the pandemic.

Conclusion
The best performing model detects tweet stance with performance high enough to ensure its usefulness for public health applications, namely awareness campaigns, misinformation detection and other early intervention and prevention actions seeking to improve an individual’s well-being based on autoreported experiences and opinions. The dataset and code of the study are available on GitHub.
Association between urinary catecholamines and glucocorticoids and bone mineral density and osteoporosis in Puerto Rican adults
Authors: Fouhy Liam E , Mangano Kelsey M , Zhang Xiyuan , Hughes Bess Dawson , Cornell David J , Tucker Katherine L , Noel Sabrina E 
Published: January 2025

Abstract

Background
Chronic stress leads to elevated stress hormones, which may be linked to bone breakdown. Puerto Rican adults living on the US mainland have higher prevalence of stress than the general population, and higher and/or similar prevalence of osteoporosis compared with non-Hispanic Whites. The role of stress on bone remains unclear and may be modified by diet. A Dietary Approaches to Stop Hypertension (DASH) pattern, as a measure of dietary quality, was most protective for bone outcomes among Puerto Ricans.

Methods
In this cross-sectional study, 958 Boston Puerto Rican Health Study participants were included (aged: 59.9 ± 7.6 y). Stress markers (epinephrine, norepinephrine, cortisol) were collected via 12-hr urine samples and elevated concentrations were categorized using sex-specific cut-offs. Bone mineral density (BMD) was assessed via dual energy x-ray absorptiometry. Analysis of covariance models with least squares means were used to test differences in mean BMD between participants with elevated and non-elevated stress markers. Multivariable logistic regression examined associations between stress markers and osteoporosis in post-menopausal females and males. Models were adjusted for age, height, smoking, alcohol use, education, glucocorticoid use, and diabetes.

Results
Higher urinary epinephrine was associated with lower BMD at the lumbar spine (P=.012), femoral neck (P=.005), trochanter (P&lt;.001), and total hip (P&lt;.001) in Puerto Rican adults, and with higher odds of osteoporosis among males (OR = 4.01 [95%CI: 1.11, 14.5], P=.03). An interaction between DASH and norepinephrine was noted for post-menopausal females at the lumbar spine. No associations were noted for norepinephrine or cortisol (P&gt;.11), although higher urinary norepinephrine was associated with lower lumbar spine BMD in post-menopausal females not taking estrogen, with lower adherence to DASH (P=.03).

Conclusion
Higher urinary epinephrine and norepinephrine were associated with poorer bone outcomes in Puerto Rican adults, in a sex-specific manner, warranting future longitudinal studies to clarify associations. Dietary quality may moderate these associations.
Pea aphid wing plasticity variation has a multigenic basis
Authors: Driscoll Rose M H , Liu Xiaomi , McDonough Julia , Schmidt James , Brisson Jennifer A 
Published: January 2025

Abstract
Phenotypic plasticity, the ability of a single genotype to produce a range of phenotypes in response to environmental cues, can exhibit genetic variation like any trait. Discovering the genetic basis of plasticity and plasticity variation is critical to understand how populations will respond to the ongoing environmental challenges brought about by, for example, climate change. Here, we investigate the genetic basis of the pea aphid (Acyrthosiphon pisum) wing plasticity variation. In this species, genetically identical, highly fecund wingless and dispersive winged individuals are produced by pea aphid mothers in uncrowded versus crowded environments, respectively. We focus specifically on the genetic basis of the propensity to produce winged individuals in response to crowding. We crossed a low to a high plasticity line and examined plasticity variation in backcross progeny (F1 x low parent), finding that differences between lines had a strong genetic component and that multiple loci likely to contribute to this variation. Transcriptional profiling revealed a candidate gene, yellow-h, which was found within a genomic locus contributing to plasticity variation. Overall, we provide novel information about the genetic basis of an ecologically-relevant trait and contribute to the growing literature recognizing the importance of understanding the genetic basis of plasticity variation.
Early expansion of TIGIT+PD1+ effector memory CD4 T cells via agonistic effect of alefacept in new-onset type 1 diabetes
Authors: Higdon Lauren E , Cooney Laura A , Serti Elisavet , Suwannasaen Duangchan , Muir Virginia S , Wiedeman Alice E , Harris Kristina M , Pardo Jorge , Anderson Mark S , Speake Cate , Nepom Gerald T , Linsley Peter S , Sanda Srinath , Long S Alice 
Published: January 2025

Abstract
The CD2-depleting drug alefacept (LFA3-Ig) preserved beta cell function in new-onset type 1 diabetes (T1D) patients. The most promising biomarkers of response were late expansion of exhausted CD8 T cells and rare baseline inflammatory islet-reactive CD4 T cells, neither of which can be used to measure responses to drug in the weeks after treatment. Thus, we investigated whether early changes in T cell immunophenotypes could serve as biomarkers of drug activity. We characterized T cell responses by flow cytometry and identified an exhausted-like population of CD2low CD4 effector memory T cells coexpressing TIGIT and PD1 that expanded by 11 wk after the start of treatment. This population was not entirely spared from alefacept-mediated depletion in vivo or in vitro but recovered through homeostatic proliferation of CD2low cells in vivo. Proliferation of TIGIT+PD1+ effector memory CD4 T cells increased with treatment, with a concomitant reduction of proinflammatory cytokine production. The persistent increase of TIGIT+PD1+ effector memory CD4 T cells was specific to alefacept treatment; 2 other T cell depleting therapies, teplizumab and anti-thymocyte globulin, induced only a transient increase in this CD4 population. Our data suggest that the expanding TIGIT+PD1+ effector memory CD4 T cell population represents a promising biomarker of early treatment effects of alefacept. The nondepleting effects on proliferation and cytokine production also suggest agonistic activity by this CD2 targeted therapy.
Severe periocular ecchymosis following acupuncture therapy for dry eye: a report of two cases
Authors: Tsai Jarryl H J , Au Eong Jonathan T W , Au Eong Kah-Guan 
Published: January 2025

Abstract
Acupuncture is a complementary therapy used in many parts of the world to treat a variety of disorders. Two women aged 61 and 86 years old presented with painless bruising around their right eye for 3 and 10 days, respectively, following acupuncture therapy for dry eye. The younger woman was on oral acetylsalicylic acid 100 mg daily and it was her second episode of ocular bruising from a total of 20 therapy sessions. Clinical examination disclosed severe periocular ecchymosis in their right eye. There was no proptosis or globe perforation. The ecchymosis gradually resolved over a few weeks without any visual sequelae in both cases. Periocular acupuncture can cause severe periocular ecchymoses. Patients should be informed of this and other potentially sight-threatening complications associated with this form of treatment, and both acupuncture practitioners and ophthalmologists should be alert to recognize such complications early so that they can be appropriately managed.
Cecal volvulus after open right hepatectomy
Authors: Jensen Lasse R , Dohrn Niclas , Penninga Luit 
Published: January 2025

Abstract
Cecal volvulus, a rare cause of postoperative bowel obstruction, involves the twisting of the cecum and its mesentery, leading to the risk of ischemia. We present a case of cecal volvulus following open right hepatectomy in a patient in her 70s with no prior abdominal surgeries. On postoperative day six, after developing abdominal distension and pain, a CT scan revealed bowel obstruction and a cecal volvulus was suspected. Emergency laparotomy confirmed cecal volvulus with a highly mobile cecum, necessitating right hemicolectomy with end-ileostomy due to sepsis. The patient’s recovery was prolonged due to complications, including postoperative paralysis and fascial dehiscence. To our knowledge, this is the first documented case of cecal volvulus following right hepatectomy, likely due to altered anatomy and postoperative paralysis. This case underscores the importance of considering cecal volvulus in postoperative obstruction cases, especially following surgeries affecting right-sided visceral structures.