bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic value of circulating tumor DNA in different cancer types detected by ultra-low-pass whole-genome sequencing: a systematic review and patient-level survival data meta-analysis
Authors: Sogbe Miguel , Aliseda Daniel , Sangro Paloma , de la Torre-Aláez Manuel , Sangro Bruno , Argemi Josepmaria 
Published: November 2024

Abstract
Ultra-low-pass whole-genome sequencing (ULP-WGS) (≤0.5 × coverage) of plasma cell-free DNA (cfDNA) has emerged as a low-cost, promising tool to assess the circulating tumor DNA (ctDNA) fraction. This meta-analysis aims to summarize the current findings and comprehensively investigate the prognostic value of baseline ctDNA detected by ULP-WGS in solid tumors. A systematic review was carried out by searching PubMed/MEDLINE and Scopus databases to identify eligible studies conducted between January 2014 and January 2024. Inclusion criteria comprised studies with reported overall survival and progression-free survival outcomes across therapy-naïve patients with different solid tumors. All patients underwent baseline ULP-WGS of plasma cfDNA and were categorized as ctDNA positive (tumor fraction ≥10%) or negative (tumor fraction &lt;10%). A one-stage meta-analysis was performed using patient-level survival data reconstructed from published articles. A Cox proportional hazards model with shared frailty was used to assess the difference in survival between arms. A total of six studies, comprising 620 patients (367 negative ctDNA and 253 positive ctDNA), were included in the overall survival analysis, while five studies, involving 349 patients (212 negative ctDNA and 137 positive ctDNA), were included in the progression-free survival analysis. The meta-analysis showed that patients with baseline positive ctDNA had a significantly higher risk of death (HR = 2.60, 95% CI: 2.01–3.36) and disease progression (HR = 2.28, 95% CI: 1.71–3.05) compared to those with negative ctDNA. The presence of a positive ctDNA at baseline is associated with increased risk of death and progression in patients with same-stage cancer.
Synesthesia is linked to large and extensive differences in brain structure and function as determined by whole-brain biomarkers derived from the HCP (Human Connectome Project) cortical parcellation approach
Authors: Ward Jamie , Simner Julia , Simpson Ivor , Rae Charlotte , del Rio Magda , Eccles Jessica A , Racey Chris 
Published: November 2024

Abstract
There is considerable interest in understanding the developmental origins and health implications of individual differences in brain structure and function. In this pre-registered study we demonstrate that a hidden subgroup within the general population—people with synesthesia (e.g. who “hear” colors)—show a distinctive behavioral phenotype and wide-ranging differences in brain structure and function. We assess the performance of 13 different brain-based biomarkers (structural and functional MRI) for classifying synesthetes against general population samples, using machine learning models. The features in these models were derived from subject-specific parcellations of the cortex using the Human Connectome Project approach. All biomarkers performed above chance with intracortical myelin being a particularly strong predictor that has not been implicated in synesthesia before. Resting state data show widespread changes in the functional connectome (including less hub-based connectivity). These brain-based individual differences within the neurotypical population can be as large as those that differentiate neurotypical from clinical brain states.
Prediction models for ischemic stroke and bleeding in dialysis patients: a systematic review and meta-analysis
Authors: Travlos Christoforos K , Chirgwin-Dasgupta Adario , Trinh Emilie , Sniderman Allan D , Alam Ahsan , Mavrakanas Thomas A 
Published: November 2024

ABSTRACT

Background
Patients with kidney failure on maintenance dialysis have a high stroke and bleeding risk. Multivariable prediction models can be used to estimate the risk of ischemic stroke and bleeding. A systematic review and meta-analysis was performed to determine the performance of the existing models in patients on dialysis.

Methods
MEDLINE and Embase databases were searched, from inception through 12 January 2024, for studies of prediction models for stroke or bleeding, derived or validated in dialysis cohorts. Discrimination measures for models with c-statistic data from three or more cohorts were pooled by random effects meta-analysis and a 95% prediction interval (PI) was calculated. Risk of bias was assessed using PROBAST. The review was conducted according to the PRISMA statement and the CHARMS checklist.

Results
Eight studies were included in this systematic review. All the included studies validated pre-existing models that were derived in cohorts from the general population. None of the identified studies reported the development of a new dialysis specific prediction model for stroke, while dialysis specific risk scores for bleeding were proposed by two studies. In meta-analysis of c-statistics, the CHA2DS2-VASc, CHADS2, ATRIA, HEMORR(2)HAGES and HAS-BLED scores showed very poor discriminative ability in the dialysis population. Six of the eight included studies were at low or unclear risk of bias and certainty of evidence was moderate.

Conclusions
The existing prediction models for stroke and bleeding have very poor performance in the dialysis population. New dialysis-specific risk scores should be developed to guide clinical decision making in these patients.
Addition of ammonium acetate to torula yeast borax and its effect on captures of three species of economically important fruit flies (Diptera: Tephritidae)
Authors: Shelly Todd E , Fezza Thomas J , Kurashima Rick S 
Published: November 2024

Abstract
Many countries operate continuous trapping programs to detect invasive fruit flies (Diptera: Tephritidae) that threaten fruit and vegetable production. Food-based attractants are an important component of these programs, as they are generalized baits that attract both sexes of all target species. However, food baits are considered weak attractants, and the development of improved food attractants would benefit surveillance efforts. Prior work on protein bait sprays demonstrated that the addition of ammonium acetate increased their attractiveness to tephritid fruit flies, and the present study was conducted to determine whether adding ammonium acetate to torula yeast borax solution (a commonly used food bait) similarly increased its attractiveness. Four field experiments were performed in Hawaii comparing captures of Ceratitis capitata (Wiedemann), Bactrocera dorsalis (Hendel), and Zeugodacus cucurbitae (Coquillett) in Multilure traps baited with standard torula yeast borax solution or with the standard solution plus 1% ammonium acetate. Captures of C. capitata and B. dorsalis were significantly higher for the ammonium acetate-supplemented solution, while results for Z. cucurbitae were inconsistent. In one experiment involving only C. capitata, an additional bait having 5% ammonium acetate was included, and captures for both 1% and 5% ammonium acetate exceeded the standard solution but did not differ from one another. Sex ratios of captured flies were similar between food baits for all three species. These results are compared with similar studies on Anastrepha spp., and implications for surveillance programs are discussed.
Aortoesophageal fistula 19 years after radiotherapy for oesophageal cancer: a case report
Authors: Sakakibara Satoshi , Marumoto Akira 
Published: November 2024

Abstract

Background
Aortoesophageal fistula (AEF) is a life-threatening disease that causes massive bleeding, sepsis, and ultimately death. Therefore, emergency treatments are required. Recently, cases of AEF treated with thoracic endovascular aortic repair (TEVAR) have been reported.

Case summary
An 84-year-old man was referred to a local hospital with massive haematemesis and transient loss of consciousness. The patient’s medical history included radiotherapy for oesophageal cancer 19 years before presentation. Gastrofiberscopy revealed an ulcer in the thoracic oesophagus and no recurrence of oesophageal cancer. Computed tomography (CT) showed that the same area was adjacent to the thoracic aorta and that there was no thoracic aortic aneurysm. The patient was then transferred to our institution for surgical treatment. We diagnosed the patient with an AEF caused by radiotherapy of the oesophagus. Therefore, TEVAR was performed. Due to the patient’s advanced age, condition, and the possibility of strong adhesions, there was a high risk that they would be unable to tolerate oesophagectomy to prevent stent graft infection. Therefore, antibiotic therapy was initiated. However, CT revealed a stent graft infection 24 days after TEVAR. The patient died of sepsis 27 days after the procedure.

Discussion
We describe the first case of AEF as a very late complication of radiotherapy for oesophageal cancer. Surgery to repair oesophageal defects is necessary to prevent stent graft infection. However, the decision for such surgery should be made on a case-by-case basis, taking into account the patient’s condition and ability to tolerate the procedure.
Survival of a patient following initial left ventricular assist device implantation and two successive left ventricular assist device exchanges: case report
Authors: Scarsella Luca , Bentley Alexander , Amer Mohamed Ishaq , Thal Serge C 
Published: November 2024

Abstract

Background
Initially conceptualized as a bridge to heart transplantation, the left ventricular assist device (LVAD) has become an important option for improving survival in patients with severe heart failure and poor prognosis.

Case summary
We report the case of a patient suffering from severe chronic heart failure, complicated by ST-elevation myocardial infarction due to left main coronary artery stenosis (NYHA IV, INTERMACS profile 1). Despite support with veno-arterial extracorporeal membrane oxygenation, inotropes, and catecholamine therapy, the patient’s cardiac function did not recover sufficiently. Consequently, the decision was made to proceed with LVAD implantation as destination therapy. The initial LVAD implantation was uneventful, and the patient received anticoagulant therapy according to standard operating procedure. However, pump thrombosis occurred on the first post-operative day, necessitating an LVAD exchange. Following an extended stay in the cardiac surgery intensive care unit, the patient was eventually discharged. Approximately 15 months later, the patient developed a driveline infection, involving most of the intrapericardial components of the LVAD. A second LVAD exchange was required, and the patient received a third LVAD. To mitigate the risk of recurrent infection, suppressive antibiotic therapy with ampicillin/sulbactam was initiated.

Discussion
This is the first reported case of a patient surviving three LVAD implantations and highlights an instance of off-label use of lifelong antibiotic therapy following a driveline infection.
Discrimination in track recommendation but not in grading: experimental evidence among primary school teachers in Hungary
Authors: Kisfalusi Dorottya , Hermann Zoltán , Keller Tamás 
Published: November 2024

Abstract
This study examines discrimination in teacher assessments and track recommendations against Roma minority students in Hungary. We conducted a pre-registered randomized experiment among 413 primary school teachers. Participating teachers evaluated six mathematics or literacy and grammar tests with fictitious, randomized student names and recommended a high school track. Our results show mixed evidence for discrimination against Roma students: teachers do not discriminate in test evaluations but do so in high school track recommendations, though this latter effect is small. We find that contextual factors play a substantial role in discrimination in track recommendations: teachers who receive tests with fewer Roma than non-Roma names discriminate against Roma students, whereas teachers who receive tests with more Roma names do not. In the latter case, non-Roma students receive similarly low track recommendations as Roma students in both experimental conditions. The results are consistent with stereotype-based theories of discrimination.
Revascularization in frail patients with acute coronary syndromes: a retrospective longitudinal study
Authors: Roman Marius , Miksza Joanne , Lai Florence Yuk-Lin , Sze Shirley , Poppe Katrina , Doughty Rob , Squire Iain , Murphy Gavin James 
Published: November 2024

Abstract

Background and Aims
Frailty is increasingly prevalent in people presenting with acute coronary syndrome (ACS). This high-risk group is typically excluded from trials of interventions in ACS, and there is uncertainty about the risks and benefits of invasive management.

Methods
Patients with an ACS diagnosis between 2010 and 2015 in England were identified from Hospital Episode Statistics, with linked Office for National Statistics mortality data. Frailty was defined by the Hospital Frailty Risk Score. Causal inference analysis used regional variation in revascularization as an instrumental variable to estimate average treatment effects of revascularization on cardiovascular mortality up to 5 years in people presenting with ACS and low-, intermediate-, or high-risk frailty.

Results
The analysis included 565 378 ACS patients, of whom 11.6% (n = 65 522) were at intermediate risk and 4.7% (n = 26 504) were at high risk of frailty. Intermediate and high frailty risks were associated with reduced likelihood of echocardiography, invasive angiography, or revascularization and increased likelihood of mortality and major adverse cardiovascular events compared with low frailty risk. Cardiovascular death at 5 years was 78.6%, 77.3%, and 75.7% in people at low, intermediate, and high frailty risk, respectively. Instrumental variable analysis suggested that revascularization resulted in a higher absolute reduction in cardiovascular mortality in high and intermediate frail risk patients compared with low risk at 1-year post-ACS.

Conclusions
Frailty is common in people presenting with ACS, where cardiovascular causes are the principal mode of death. Revascularization is associated with short- and long-term survival benefits in people at intermediate and high risk of frailty after adjustment for measured and unmeasured confounders.
The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki
Authors: Rayamajhi Niraj , Rivera-Colón Angel G , Minhas Bushra Fazal , Cheng C H Christina , Catchen Julian M 
Published: November 2024

Abstract
The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high-quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein-coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.
Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome
Authors: Cheung Kelton , Rollins Lee Ann , Hammond Jillian M , Barton Kirston , Ferguson James M , Eyck Harrison J F , Shine Richard , Edwards Richard J 
Published: November 2024

Abstract
Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMTs) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false-positive detection of NUMTs is common when handling repeat-rich sequences, while fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10× linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n = 5,310), indicating the gene-containing regions were well assembled. We used 3 complementary methods (NUMTFinder, dinumt, and PALMER) to study the NUMT landscape of the cane toad genome. All 3 methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.
Balancing selfing and outcrossing: the genetics and cell biology of nematodes with three sexual morphs
Authors: Adams Sally , Tandonnet Sophie , Pires-daSilva Andre 
Published: November 2024

Abstract
Trioecy, a rare reproductive system where hermaphrodites, females, and males coexist, is found in certain algae, plants, and animals. Though it has evolved independently multiple times, its rarity suggests it may be an unstable or transitory evolutionary strategy. In the well-studied Caenorhabditis elegans, attempts to engineer a trioecious strain have reverted to the hermaphrodite/male system, reinforcing this view. However, these studies did not consider the sex-determination systems of naturally stable trioecious species. The discovery of free-living nematodes of the Auanema genus, which have naturally stable trioecy, provides an opportunity to study these systems. In Auanema, females produce only oocytes, while hermaphrodites produce both oocytes and sperm for self-fertilization. Crosses between males and females primarily produce daughters (XX hermaphrodites and females), while male-hermaphrodite crosses result in sons only. These skewed sex ratios are due to X-chromosome drive during spermatogenesis, where males produce only X-bearing sperm through asymmetric cell division. The stability of trioecy in Auanema is influenced by maternal control over sex determination and environmental cues. These factors offer insights into the genetic and environmental dynamics that maintain trioecy, potentially explaining its evolutionary stability in certain species.
Implementing the WHO ICOPE Program in Clinical Practice: Three Years of Lessons From Monitoring 27 082 Participants Using the ICOPE Monitor Digital Tool
Authors: Berbon Caroline , Takeda Catherine , Balardy Laurent , Lafont Christine , Tavassoli Néda , Carrie Isabelle , Guyonnet Sophie , de Kerimel Justine , Mathieu Céline , Pennetier Delphine , Bezombes Véronique , Nourhashemi Fatemeh , Vellas Bruno , Andrieu Sandrine , Soto-Martin Maria-Eugenia 
Published: November 2024

Abstract

Background
To describe the implementation of the ICOPE program in France using a digital tool in order to: (1) describe the characteristics of people completing the screener, identifying differences across assessors (healthcare professionals (HCPs), non-HCPs, or self-assessment); (2) describe the characteristics of follow-up and assessments for people with abnormal screening test; and (3) describe the recommendations in the intervention care plans for people with a decline in intrinsic capacity.

Methods
A descriptive study, presenting the results at initial screening, as well as at assessment when needed, and the recommendations issued during Step 3. We compared these results based on whether the participant was enrolled by an HCP, by a non-HCP, or by self-assessment.

Results
A total of 27 082 participants were enrolled. 67.9% were registered by HCPs. 90.8% participants screened positive at Step 1. Participants who completed the self-assessment were significantly younger (70.9 years vs 76.4 for HCPs or 77.9 for non-HCPs, p &lt; .01) and less frequently had alerts in Step 1 (83.8% vs 90.8% for HCPs or 94.8% for non-HCPs). Step 2 in-depth assessments were carried out for 8.9% of the participants. In Step 2, only the SPPB showed significantly better motor abilities in individuals enrolled through self-assessment (median and IQR: 11 (10–12) vs 10 (8–12) for HCPs and 10 (7–12) for non-HCPs). Prevention care plans were proposed, mainly physical activity (n = 833, 33.7%) and nutrition counseling (n = 1 233, 51.7%).

Conclusions
This study highlights the major role of HCPs in the implementation of the ICOPE program. Self-assessment enables the enrollment of more robust seniors, allowing for an early detection and treatment.
De novoscreening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation
Authors: Huang Rong , Shi Mijuan , Luo Lifei , Yang Cheng , Ou Mi , Zhang Wanting , Liao Lanjie , Li Yongming , Xia Xiao-Qin , Zhu Zuoyan , Wang Yaping 
Published: November 2024

AbstractBackgroundMutants are important for the discovery of functional genes and creation of germplasm resources. Mutant acquisition depends on the efficiency of mutation technology and screening methods. CRISPR-Cas9 technology is an efficient gene editing technology mainly used for editing a few genes or target sites, which has not been applied for the construction of random mutant libraries and for the de novo discovery of functional genes.ResultsIn this study, we first sequenced and assembled the chromosome-level genome of wild-type rare minnow (Gobiocypris rarus) as a susceptible model of hemorrhagic disease, obtained a 956.05 Mb genome sequence, assembled the sequence into 25 chromosomes, and annotated 26,861 protein-coding genes. Thereafter, CRISPR-Cas9 technology was applied to randomly mutate the whole genome of rare minnow with the conserved bases (TATAWAW and ATG) of the promoter and coding regions as the target sites. The survival rate of hemorrhagic disease in the rare minnow gradually increased from 0% (the entire wild-type population died after infection) to 38.24% (F3 generation). Finally, 7 susceptible genes were identified via genome comparative analysis and cell-level verification based on the rare minnow genome.ConclusionsThe results provided the genomic resources for wild-type rare minnow, and confirmed that the random mutation system designed using CRISPR-Cas9 technology in this study is simple and efficient and is suitable for the de novo discovery of functional genes and creation of a germplasm resource related to qualitative traits.