bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjuvant modified FOLFIRINOX for resected pancreatic adenocarcinoma: clinical insights and genomic features from a large contemporary cohort
Authors: Keane Fergus , O’Connor Catherine , Moss Drew , Chou Joanne F , Perry Maria A , Crowley Fionnuala , Saxena Parima , Chan Amelia , Schoenfeld Joshua D , Singhal Anupriya , Park Wungki , Cowzer Darren , Harrold Emily , Varghese Anna M , El Dika Imane , Crane Christopher , Harding James J , Abou-Alfa Ghassan K , Kingham T Peter , Wei Alice C , Yu Kenneth H , D’Angelica Michael I , Balachandran Vinod P , Drebin Jeffrey , Jarnagin William R , Bandlamudi Chaitanya , Kelsen David , Capanu Marinela , Soares Kevin C , Balogun Fiyinfolu , O’Reilly Eileen M 
Published: October 2024

Abstract

Background
Adjuvant modified leucovorin calcium, fluorouracil, irinotecan hydrochloride, and oxaliplatin (FOLFIRINOX) is standard of care for fit individuals with resected pancreatic ductal adenocarcinoma (PDAC). Data are limited on adjuvant modified FOLFIRINOX outcomes outside clinical trials.

Methods
We queried institutional databases to identify patients with resected PDAC who received 1 or more doses of adjuvant modified FOLFIRINOX. Primary endpoints were recurrence-free survival (RFS) and overall survival. Secondary endpoints were clinical factors and genomic features associated with outcomes. We estimated RFS and overall survival by using the Kaplan-Meier method. A Cox proportional hazards regression model was used to associate clinicogenomic features with survival outcomes.

Results
A search revealed 147 individuals with PDAC between January 2015 and January 2023. Median patient age was 67 years, with 57 (39%) patients older than 70 years. Unfavorable prognostic features included 52 (36%) patients with N2 nodal status, 115 (78%) patients with lymphovascular invasion, and 133 (90%) patients with perineural invasion. Median time from surgery to initiation of modified FOLFIRINOX was 1.78 months (IQR = 1.45-2.12). In total, 124 (84%) patients completed 12 doses; 98 (67%) patients stopped oxaliplatin early because of neuropathy (median = 10 doses, range = 4-12 doses). Further dosing characteristics are summarized in Table S3, with a median follow-up of 35.1 months, a median RFS of 26 months (95% confidence interval [CI] = 19 to 39), and a median overall survival not reached. For the cohort older than 70 years of age, the median RFS was 23 months (95% CI = 14 to not reached) and the median overall survival was 51 months (95% CI = 37 to not reached). Modified FOLFIRINOX started sooner than 8 weeks from resection was associated with improved RFS (hazard ratio = 0.62, 95% CI = 0.41 to 0.96; P = .033) and overall survival (hazard ratio = 0.53, 95% CI = 0.3 to 0.94; P = .030). KRAS variation and whole-genome doubling trended to shorter RFS and overall survival. Homologous recombination deficiency status did not confer improved survival outcomes.

Conclusions
Adjuvant modified FOLFIRINOX was effective and tolerated in patients with resected PDAC in a nontrial setting, including for patients older than 70 years of age.
Internal migration and multidimensional wellbeing: a case study of North-South migration in Ghana
Authors: Darko Francis Diawuo , Schech Susanne , Saikia Udoy 
Published: October 2024

Abstract
Migration is widely regarded as a principal form of activity available to many of the world’s poor to improve their household’s standard of living. This paper investigates whether and in what ways internal migrants benefit from moving within Ghana’s North-South migration context. This research uses an innovative multidimensional wellbeing framework to assess the effects of migration on migrants’ wellbeing based on six domains: living standards, health, education, community vitality, environmental resilience, and governance. The wellbeing survey of 251 northern Ghanaian migrants working in the informal economic sector within the Sunyani municipality discovered that although most migrants reported improved living standards, a majority could not attain overall wellbeing due to low health and education wellbeing scores. Exploring the relationship between income and wellbeing across domains, the study found a weak positive association, and the complex interplay of factors beyond income was evident. This study challenges the conventional perspective that equates income with the attainment of wellbeing and argues that a multidimensional wellbeing framework permits a more nuanced understanding of the impacts of migration. It highlights the need for the government to actively monitor and address the wellbeing of internal migrants within the Ghanaian context.
SLICK: Strong Lensing Identification of Candidates Kindred in gravitational wave data
Authors: Magare Sourabh , More Anupreeta , Choudhary Sunil 
Published: October 2024

ABSTRACT
By the end of the next decade, we hope to have detected strongly lensed gravitational waves by galaxies or clusters. Although there exist optimal methods for identifying lensed signal, it is shown that machine learning (ML) algorithms can give comparable performance but are orders of magnitude faster than non-ML methods. We present the SLICK pipeline which comprises a parallel network based on deep learning. We analyse the Q-transform maps (QT maps) and the Sine-Gaussian projection (SGP) maps generated for the binary black hole signals injected in Gaussian as well as real noise. We compare our network performance with the previous work and find that the efficiency of our model is higher by a factor of 5 at a false positive rate of 0.001. Further, we show that including SGP maps with QT maps data result in a better performance than analysing QT maps alone. When combined with sky localization constraints, we hope to get unprecedented accuracy in the predictions than previously possible. We also evaluate our model on the real events detected by the LIGO–Virgo collaboration and find that, at a threshold of 0.75 our network correctly classifies all of them, consistent with non-detection of lensing.
Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages
Authors: Wen Jiejie , Zhang Haobo , Chu Dongliang , Chen Xiaoke , Feng Jingru , Wang Yucen , Liu Guanxi , Zhang Yuhao , Li Yuxue , Ning Kang 
Published: October 2024

Abstract
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.
Impact of antidepressant use on survival outcomes in glioma patients: A systematic review and meta-analysis
Authors: Ge Yulu , Cao Yaning , Wang Qi , Wang Yu , Ma Wenbin 
Published: October 2024

Abstract

Background
Depression is common among glioma patients, and antidepressants are frequently prescribed to manage symptoms. Understanding the impact of antidepressants on glioma patient survival is crucial for informing treatment strategies.

Methods
A systematic search was conducted in PubMed and EMBASE databases for studies published from January 1994 to March 2024. The search strategy included terms related to overall survival, prognosis, antidepressants, and gliomas. A manual search was performed in the reference lists. According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guideline, 2 authors independently extracted data. Statistical analysis was performed using Review Manager (version 5.4.1) software, employing a random effects model based on study heterogeneity. The primary outcome was overall survival (OS). Hazard ratios (HRs) were used to present survival differences between the 2 arms. HRs after correcting for confounders were prioritized for extraction.

Results
Seven retrospective cohort studies involving 5579 patients were analyzed. Selective serotonin reuptake inhibitors (SSRIs) showed no significant survival difference in all glioma patients (HR = 1.34, 95% confidence interval [CI]: 0.66–2.70) and in GBM patients (HR = 1.05, 95% CI: 0.45–2.46), while non-SSRIs had an unfavorable impact on OS in GBMs (HR = 3.54, 95% CI: 2.51–4.99). When considering LGG, both SSRIs and non-SSRIs usage demonstrated associations with poorer survival outcomes (SSRIs: HR = 3.26, 95%CI: 2.19–4.85; Non-SSRIs: HR = 7.71, 95% CI: 4.25–14.00).

Conclusions
Antidepressant use was not significantly associated with better survival outcomes, emphasizing the need for reconsidering the real effects of antidepressant medication. Future clinical research should address patient heterogeneity to better clarify the effects of antidepressants on glioma survival.
A Content Analysis of Illicit Tobacco-Related Crimes Reported in Australian Media
Authors: Meciar Isabel , Puljević Cheneal , Holland Alice , Gartner Coral 
Published: October 2024

Abstract

Introduction
Australian survey and seizure data suggest a growing illicit tobacco market. As an illicit product, accurately tracking trends in illicit tobacco growing, manufacture, and sales is challenging. We examined trends in Australian illicit tobacco-related crimes using a content analysis of news articles.

Aims and Methods
We analyzed Australian news articles identified in the Factiva database and government press releases describing Australian illicit tobacco-related crimes reported between January 2000 and December 2023. Sources were coded for crime type, location, product type, dollar value of seized products, methods of distribution or storage, agencies involved, and other crimes involved.

Results
We identified 447 crimes reported in 389 sources. The number of illicit tobacco-related crimes reported increased between 2000 and 2023. The most common crimes were possession of illicit tobacco (n = 196/43.7%) and smuggling (n = 187/41.8%), and the most common product type was “illicit cigarettes” (n = 197/44.1%). The most common distribution/storage method reported was via residential premises (n = 98/21.9%). One-hundred and twenty incidents involved other crimes such as financial crimes involving money laundering (n = 59/13.2%). Across all included news articles, the quantity of seized products totaled 827 529 307 cigarette sticks, 76 185 cartons, 668 687 packs, 239 hectares (of land growing tobacco plants), and 2 149 000 plants of illicit tobacco between 2000 and 2023. The median value (worth; AUD) of each seizure was $1 500 000 (range $43 to $67 000 000).

Conclusions
Australian media reporting on illicit tobacco-related crimes increased over the past two decades, particularly since 2018. These findings highlight a need for improved border detection measures, investment in enforcement, and other deterrent activities.

Implications
This media analysis complements trends identified in national survey data that indicate a growing illicit tobacco market in Australia since 2013 with a marked increase since 2018. While survey data suggests that the Australian tobacco tax policy, which has included regular large tax increases since 2010, has decreased consumer demand for tobacco overall, it may have also incentivized criminal networks to supply illicit tobacco products due to it being a “low risk” and “high reward” activity. Controlling the Australian illicit tobacco market should be a policy priority.
Vitamin D as a Modifiable Risk Factor for Juvenile Idiopathic Arthritis: A Systematic Review and Meta-analysis of Observational Studies Comparing Baseline Vitamin D in Children with JIA to Individuals Without
Authors: Zang Kathleen , Bhatia Resham , Xue Elizabeth , Bennett Kalia J , Luo Katherine H , Malvankar-Mehta Monali S 
Published: October 2024

Abstract

Context
The varying interactions contributing to the development of juvenile idiopathic arthritis (JIA) drive the struggle to understand its etiology. Among the environmental risk factors, vitamin D has been posited to have a component in disease progression, acting as an inflammatory mediator.

Objective
To investigate the correlation between serum 25-hydroxyvitamin D [25(OH)D] levels, indicative of vitamin D, among patients diagnosed with JIA compared with control participants. The aim was to elucidate potential therapeutic implications of vitamin D in the management of JIA.

Data Sources
A systematic search of 6 electronic databases (MEDLINE, Embase, Scopus, CINAHL, Web of Science, and Cochrane Library) was performed until February 2023. Inclusion criteria required participants to be &lt;16 years old (either clinically diagnosed with JIA or a matched control participant), with vitamin D levels measured through serum laboratory methods. Exclusion criteria omitted studies in which participants used vitamin D supplementation or medications affecting vitamin D levels without corresponding statistical analyses on their association with vitamin D levels.

Data Extraction
Each article was reviewed by at least 2 independent reviewers to assess eligibility for analysis.

Data Analysis
Data were qualitatively analyzed to compare means of serum 25(OH)D levels (ng/mL) between patients with JIA and control participants, followed by a meta-analysis to obtain effect size.

Results
Ten eligible studies were included qualitatively, and eight were included in the meta-analysis. Seven studies found a statistically significant difference in vitamin D levels between control participants and patients with JIA, with five of these reporting a lower mean vitamin D level in patients with JIA. A random-effects model using standardized mean difference found a statistically significant difference in vitamin D levels between control participants and patients with JIA (–0.49; 95% CI, –0.92 to –0.06).

Conclusions
The findings from the analysis indicate vitamin D levels were lower in patients with JIA as compared with healthy control participants at baseline. It is recommended that research into vitamin D supplementation and JIA should be conducted.
Characterization of the Calmodulin-Like Protein Family in Chara braunii and their Conserved Interaction with the Calmodulin-Binding Transcription Activator Family
Authors: Symonds Kyle , Wali Udo , Duff Liam , Snedden Wayne A 
Published: October 2024

Abstract
Calcium sensor proteins play important roles by detecting changes in intracellular calcium and relaying that information onto downstream targets through protein–protein interaction. Very little is known about calcium sensors from plant species that predate land colonization and the evolution of embryophytes. Here, we examined the genome of the multicellular algae, Chara braunii, for orthologs to the evolutionarily conserved calcium sensor calmodulin (CaM) and for CaM-like (CML) proteins. We identified one CaM and eight CML isoforms that range in size from 16.4 to 21.3 kDa and are predicted to have between two to four calcium-binding (EF-hand) domains. Using recombinant protein, we tested whether CbCaM and CbCML1–CbCML7 possess biochemical properties of typical calcium sensors. CbCaM and the CbCMLs all displayed high-affinity calcium binding with estimated global KD,app values in the physiological µM range. In response to calcium binding, CbCaM and the CbCMLs exhibited varying degrees of increase in exposed hydrophobicity, suggesting that different calcium-induced conformational changes occur among isoforms. We found many examples of putative CaM targets encoded in the C. braunii genome and explored the ability of CbCaM and CbCMLs to interact in planta with a representative putative target, a C. braunii CaM-binding transcription factor (CbCAMTA1). CbCaM, CbCML2 and CbCML4 each associated with the C-terminal region of CbCAMTA1. Collectively, our data support the hypothesis that complex calcium signaling and sensing networks involving CaM and CMLs evolved early in the green lineage. Similarly, it seems likely that calcium-mediated regulation of transcription occurs in C. braunii via CAMTAs and is an ancient trait predating embryophytic emergence.
College Educated Religious Conservatives’ Support for Capital Punishment
Authors: Schwadel Philip , Anderson Amy L 
Published: October 2024

Abstract
Higher education is associated with reduced support for capital punishment among white Americans. Conservative religion, however, is associated with moral foundations and schemas that lead to greater support for capital punishment, which we expect moderate the association between education and views of capital punishment. Using nationally representative survey data, we found that the negative association between higher education and support for the death penalty was attenuated for white religious conservatives. This finding did not apply to nonwhite Americans. We conclude with a discussion of how the moral worldview associated with conservative religion may affect the future of capital punishment, by addressing how the association between higher education and views of capital punishment is contingent on other individual and contextual factors, and by situating the results within the contemporary American context that is characterized by political polarization and the decline of religion.
USP13 overexpression in BMSCs enhances anti-apoptotic ability and guards against methylprednisolone-induced osteonecrosis in rats
Authors: Jiang Yixin , Fan Xiaoli , Yu Yaling , Ge Hongfan , Liu Chengyin , Zhang Yanyan , Yu Lingyun , Yin Wen , Zhou Zhenlei 
Published: October 2024

Abstract
Methylprednisolone (MPS) use is linked to increased cases of osteonecrosis of the femoral head (ONFH). Bone marrow mesenchymal stem cells (BMSCs) have shown potential for treating MPS-induced ONFH, but their effectiveness is limited by high apoptosis rates post-transplantation. We developed a pretreatment strategy for BMSCs to improve their viability. In a rat model of MPS-induced ONFH, we evaluated the effects of USP13 overexpression in BMSCs through micro-CT, HE staining, and TUNEL staining. USP13-overexpressing BMSCs significantly reduced ONFH severity compared to plain BMSCs and direct lentivirus injection. USP13 also protected BMSCs from MPS-induced apoptosis by modulating PTEN and reducing AKT phosphorylation. This led to decreased expression of apoptotic genes and proteins in USP13-overexpressing BMSCs. Our findings highlight USP13 as a promising target for enhancing BMSC survival and efficacy in treating MPS-induced ONFH.
Adaptation of an evidence-based, preventive intervention to promote mental health in Hispanic adolescents: eHealth Familias Unidas Mental Health
Authors: Perrino Tatiana , Lozano Alyssa , Estrada Yannine , Tapia Maria I , Brown C Hendricks , Horigian Viviana E , Beardslee William R , Prado Guillermo 
Published: October 2024

Abstract
Youth internalizing symptoms (i.e., depression and anxiety), suicide ideation and attempts have been rising in recent years, including among Hispanics. Disparities in mental healthcare are concerning and require intervention, ideally prevention or early intervention. Familias Unidas is a culturally-syntonic, family-centered intervention effective in reducing youth drug use and sexual risk, with evidence of unanticipated effects on internalizing symptoms. This paper describes the systematic process used to adapt the eHealth version of the Familias Unidas intervention to more directly address internalizing symptoms and suicide risk in preparation for an effectiveness-implementation hybrid trial for youth with elevated internalizing symptoms, a history of suicide ideation/attempts, or poor parent-youth communication. The resulting eHealth Familias Unidas Mental Health intervention is described. Guided by a 4-phase framework, the steps in the adaptation process involved: assessment of the community and intervention delivery setting (pediatric primary care clinics); integration of previous intervention research, including intervention mechanisms of action; and expert and community consultation via focus groups. Focus group analyses showed that youth and parents perceived that the intervention was helpful. Their feedback was categorized into themes that were used to directly target mental health by addressing technology use, parent mental health, and social support. Effective and scalable preventive interventions are needed to address mental health disparities. The systematic adaptation process described in this paper is an efficient approach to expanding interventions while maintaining known, empirical and theoretical mechanisms of action. Findings from the ongoing effectiveness-implementation trial will be critical.
Historical biogeography of North American killifishes (Cyprinodontiformes) recapitulates geographical history in the Gulf of México watershed
Authors: Hernández-Ávila Sonia Gabriela , Hoagstrom Christopher W , Matamoros Wilfredo A 
Published: October 2024

Abstract
We analysed phylogenetic relationships within a major clade of Cyprinodontiformes (Teleostei) that includes five families of North American killifishes. We used DNA sequences from five genes for 130 species, with four fossil calibrations and three secondary calibrations, to generate a time-calibrated phylogeny. We estimated diversification rates, ancestral areas, and ancestral habitats for each node. Findings were interpreted within a detailed biogeographical synthesis. The results indicate that the clade arose in the Eocene along the Gulf of México coast. The speciation rate was uniform through time, except for acceleration in Cyprinodontidae after ~10.9 Mya. In other families, neither viviparity nor marine-to-freshwater transition was associated with accelerated speciation. Sea-level fluctuations might have created a speciation pump by stimulating cycles of dispersal and vicariance along the coast. Diversification also included many cases of inland immigration from coastal ancestors. For upland lineages, ancient river drainages accord with lineage distributions, including enigmatic disjunctions in Goodeidae and Fundulus. Diversification in uplands occurred via barrier displacement within alluvial or tectonically active landscapes. Killifishes also display high environmental tolerance and persist within harsh, peripheral environments unsuitable for most other fishes. Hence, a combination of clade antiquity, adaptability, dynamic geography, and persistence can explain the living diversity of New World killifishes.