bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stigmatized Professions and Ambiguous Subjects: Methodological Reflections from Sanitation Workers and Opioid Consumption in Sierra Leone
Authors: Bangura Ibrahim Bakarr , Leblond Nelly , Walker Julian Hugo 
Published: August 2024

Abstract
This paper explores ethical dilemmas in relation to practices of alcohol and drug consumption in the workplace by manual pit emptiers in Freetown, Sierra Leone. Based on observations and interviews with workers, we come to understand the consumption of painkillers and gin as a mechanism to alleviate stigma, rather than an issue of addiction. Indeed, the consumption of psychoactive substances before manual pit emptying appears as a performance to create a symbolic distance between the worker entering half-naked in a tank filled with faecal sludge and the social being, who would never do so in a ‘normal state of mind’. This analysis calls both for a deconstruction of the policies and rules that shape the sanitation sector as shameful and ‘inhuman’ and for proposals to ameliorate those conditions. Furthermore, we explore our positions as researchers on why revealing such practices can make sense in action-oriented research but also must be thought through ethically. Beyond the guidance of institutional ethics boards, the question of short- and long-term engagements with research subjects is central in shaping what ought or ought not to be investigated. We thus contribute to the discussions on how to support better science and practices with and for already stigmatized populations.
The association between long-term PM2.5 exposure and risk for pancreatic cancer: an application of social informatics
Authors: Bhavsar Nrupen A , Jowers Kay , Yang Lexie Z , Guha Sharmistha , Lin Xuan , Peskoe Sarah , McManus Hannah , McElroy Lisa , Bravo Mercedes , Reiter Jerome P , Whitsel Eric , Timmins Christopher 
Published: August 2024

Abstract
There is a profound need to identify modifiable risk factors to screen and prevent pancreatic cancer. Air pollution, including fine particulate matter (PM2.5), is increasingly recognized as a risk factor for cancer. We conducted a case-control study using data from the electronic health record (EHR) of Duke University Health System, 15-year residential history, NASA satellite fine particulate matter (PM2.5), and neighborhood socioeconomic data. Using deterministic and probabilistic linkage algorithms, we linked residential history and EHR data to quantify long-term PM2.5 exposure. Logistic regression models quantified the association between a 1 interquartile range (IQR) increase in PM2.5 concentration and pancreatic cancer risk. The study included 203 cases and 5027 controls (median age of 59 years, 62% female, 26% Black). Individuals with pancreatic cancer had higher average annual exposure (9.4 μg/m3) as compared to an IQR increase in average annual PM2.5, which was associated with greater odds of pancreatic cancer (odds ratio = 1.20; 95% CI, 1.00-1.44). These findings highlight the link between elevated PM2.5 exposure and increased pancreatic cancer risk. They may inform screening strategies for high-risk populations and guide air pollution policies to mitigate exposure.
This article is part of a Special Collection on Environmental Epidemiology.
Causal effects of competing obstetrical interventions: mediators of placental abruption and perinatal mortality
Authors: Ananth Cande V , Loh Wen Wei 
Published: August 2024

Abstract
Placental abruption, the premature placental separation, confers increased perinatal mortality risk with preterm delivery as an important pathway through which the risk appears mediated. Although pregnancies complicated by abruption are often delivered through an obstetrical intervention, many deliver spontaneously. We examined the contributions of clinician-initiated (PTDIND) and spontaneous (PTDSPT) preterm delivery at &lt; 37 weeks as competing causal mediators of the abruption-perinatal mortality association. Using the Consortium for Safe Labor (2002-2008) data (n = 203 990; 1.6% with abruption), we applied a potential outcomes-based mediation analysis to decompose the total effect into direct and mediator-specific indirect effects through PTDIND and PTDSPT. Each mediated effect describes the reduction in the counterfactual mortality risk if that preterm delivery subtype was shifted from its distribution under abruption to without abruption. The total effect risk ratio (RR) of abruption on perinatal mortality was 5.4 (95% CI, 4.6-6.3). The indirect effect RRs for PTDIND and PTDSPT were 1.5 (95% CI, 1.4-1.6) and 1.5 (95% CI, 1.5-1.6), respectively; these corresponded to mediated proportions of 25% each. These findings underscore that PTDIND and PTDSPT each play essential roles in shaping perinatal mortality risks associated with placental abruption.
Evolutionary algorithms simulating molecular evolution: a new field proposal
Authors: Browning Jr. James S L , Tauritz Daniel R , Beckmann John 
Published: August 2024

Abstract
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins—the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity of protein families, but compared with the massive search space of all possible amino acid sequences, the set of known functional families is minimal. One could say nature has a limited protein ”vocabulary.” A major question for computational biologists, therefore, is whether this vocabulary can be expanded to include useful proteins that went extinct long ago or have never evolved (yet). By merging evolutionary algorithms, machine learning, and bioinformatics, we can develop highly customized ”designer proteins.” We dub the new subfield of computational evolution, which employs evolutionary algorithms with DNA string representations, biologically accurate molecular evolution, and bioinformatics-informed fitness functions, Evolutionary Algorithms Simulating Molecular Evolution.
BioM2: biologically informed multi-stage machine learning for phenotype prediction using omics data
Authors: Zhang Shunjie , Li Pan , Wang Shenghan , Zhu Jijun , Huang Zhongting , Cai Fuqiang , Freidel Sebastian , Ling Fei , Schwarz Emanuel , Chen Junfang 
Published: August 2024

Abstract
Navigating the complex landscape of high-dimensional omics data with machine learning models presents a significant challenge. The integration of biological domain knowledge into these models has shown promise in creating more meaningful stratifications of predictor variables, leading to algorithms that are both more accurate and generalizable. However, the wider availability of machine learning tools capable of incorporating such biological knowledge remains limited. Addressing this gap, we introduce BioM2, a novel R package designed for biologically informed multistage machine learning. BioM2 uniquely leverages biological information to effectively stratify and aggregate high-dimensional biological data in the context of machine learning. Demonstrating its utility with genome-wide DNA methylation and transcriptome-wide gene expression data, BioM2 has shown to enhance predictive performance, surpassing traditional machine learning models that operate without the integration of biological knowledge. A key feature of BioM2 is its ability to rank predictor variables within biological categories, specifically Gene Ontology pathways. This functionality not only aids in the interpretability of the results but also enables a subsequent modular network analysis of these variables, shedding light on the intricate systems-level biology underpinning the predictive outcome. We have proposed a biologically informed multistage machine learning framework termed BioM2 for phenotype prediction based on omics data. BioM2 has been incorporated into the BioM2 CRAN package (https://cran.r-project.org/web/packages/BioM2/index.html).
Situational aesthetics in Ptolemaic culture
Authors: Bing Peter , Höschele Regina 
Published: August 2024

Abstract
The Ptolemies fostered a literature of exquisite polish and slender proportions, most strikingly embodied in Callimachus, whose aesthetic principles became synonymous with Alexandrian artistry. At the same time, however, they had a penchant for ostentatious display and gigantism, as evidenced, for example, in Ptolemy Philadelphus’ ‘Grand Procession’. While these two impulses might appear to be at odds, we argue that Ptolemaic patronage embraced a ‘situational aesthetic’, accommodating both the grandiose and the diminutive: these rulers understood that different situations (and their respective audiences) call for different aesthetic approaches.
pyTWMR: transcriptome-wide Mendelian randomization in python
Authors: Oreshkov Sergey , Lepik Kaido , Santoni Federico 
Published: August 2024

Abstract

Motivation
Mendelian randomization (MR) is a widely used approach to estimate causal effect of variation in gene expression on complex traits. Among several MR-based algorithms, transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) enables the uses of multiple SNPs as instruments and multiple gene expression traits as exposures to facilitate causal inference in observational studies.

Results
Here we present a Python-based implementation of TWMR and revTWMR. Our implementation offers GPU computational support for faster computations and robust computation mode resilient to highly correlated gene expressions and genetic variants

Availability and implementation
pyTWMR is available at github.com/soreshkov/pyTWMR.
Foodscapes for salmon and other mobile consumers in river networks
Authors: Rossi Gabriel J , Bellmore J Ryan , Armstrong Jonathan B , Jeffres Carson , Naman Sean M , Carlson Stephanie M , Grantham Theodore E , Kaylor Matthew J , White Seth , Katz Jacob , Power Mary E 
Published: August 2024

Abstract
Mobile consumers track fluctuating resources across heterogeneous landscapes to grow and survive. In river networks, the abundance and accessibility of food and the energetic consequences of foraging vary among habitats and through time, providing a shifting mosaic of growth opportunities for mobile consumers. However, a framework integrating the spatiotemporal dynamics of growth potential within riverscapes has been lacking. We present the concept of foodscapes to depict the dynamic changes in food abundance, food accessibility, and consumer physiology that contribute to spatial and temporal variation of fish growth in rivers. Drawing on case studies of salmonid fishes from Alaska to California, we illustrate how foodscapes can provide a plethora of foraging, growth, and life history opportunities that potentially contribute to population resilience. We identify knowledge gaps in understanding foodscapes and approaches for stewardship that focus on restoring diverse foraging and growth opportunities for fish and other mobile consumers in river networks.
Eco-emotional Responses to Climate Change: A Scoping Review of Social Work Literature
Authors: McCaffery Jillian , Boetto Heather 
Published: August 2024

Abstract
The existential threat of climate change to the future of human and non-human well-being evokes complex emotional responses. The aim of this study was to explore the extent and nature of social work literature relating to eco-emotions. Eco-emotions refer to a diverse array of emotional responses to climate change, for example, anxiety, anger and hope. A scoping review explored scholarly databases to examine literature relating to eco-emotions between 2000 and 2023. Data were extracted from the articles to synthesise key characteristics, and thematic analysis was undertaken to identify themes emerging from the data. The scoping review yielded a total of seven articles with a focus on worry, anxiety, hope and empathy. Themes identified were related to intergenerational relationships, eco-emotional fluidity and multidimensional practice. Drawing on the profession’s established knowledge base, eco-social work provides a framework for engaging with eco-emotions. Furthermore, acknowledging eco-emotions specific to First Nations peoples in the context of colonialism and incorporating Indigenous knowledges to improve planetary health are essential for a decolonised approach to eco-emotional practice. Given social work’s increasing engagement with climate change, this review highlights the need for greater awareness of and engagement with eco-emotions.
Synthesis of terminus-decorated aza[9]helicenes: control of interlayer interaction
Authors: Matsuo Yusuke , Seki Shu , Tanaka Takayuki 
Published: August 2024

Abstract
Azahelicenes are intriguing luminescent materials with a planar chirality. The properties of aza[9]helicene can be perturbed by attaching substituent at the termini. The impact of the terminal decoration has been investigated in view of structural and electronic aspects, leading to the control of interlayer interaction.
SoDCoD: a comprehensive database of Cu/Zn superoxide dismutase conformational diversity caused by ALS-linked gene mutations and other perturbations
Authors: Tabuchi Riko , Momozawa Yurika , Hayashi Yuki , Noma Hisashi , Ichijo Hidenori , Fujisawa Takao 
Published: August 2024

Abstract
A structural alteration in copper/zinc superoxide dismutase (SOD1) is one of the common features caused by amyotrophic lateral sclerosis (ALS)–linked mutations. Although a large number of SOD1 variants have been reported in ALS patients, the detailed structural properties of each variant are not well summarized. We present SoDCoD, a database of superoxide dismutase conformational diversity, collecting our comprehensive biochemical analyses of the structural changes in SOD1 caused by ALS-linked gene mutations and other perturbations. SoDCoD version 1.0 contains information about the properties of 188 types of SOD1 mutants, including structural changes and their binding to Derlin-1, as well as a set of genes contributing to the proteostasis of mutant-like wild-type SOD1. This database provides valuable insights into the diagnosis and treatment of ALS, particularly by targeting conformational alterations in SOD1.
Database URL: https://fujisawagroup.github.io/SoDCoDweb/
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop
Authors: Islamaj Rezarta , Wei Chih-Hsuan , Lai Po-Ting , Luo Ling , Coss Cathleen , Gokal Kochar Preeti , Miliaras Nicholas , Rodionov Oleg , Sekiya Keiko , Trinh Dorothy , Whitman Deborah , Lu Zhiyong 
Published: August 2024

Abstract
The automatic recognition of biomedical relationships is an important step in the semantic understanding of the information contained in the unstructured text of the published literature. The BioRED track at BioCreative VIII aimed to foster the development of such methods by providing the participants the BioRED-BC8 corpus, a collection of 1000 PubMed documents manually curated for diseases, gene/proteins, chemicals, cell lines, gene variants, and species, as well as pairwise relationships between them which are disease–gene, chemical–gene, disease–variant, gene–gene, chemical–disease, chemical–chemical, chemical–variant, and variant–variant. Furthermore, relationships are categorized into the following semantic categories: positive correlation, negative correlation, binding, conversion, drug interaction, comparison, cotreatment, and association. Unlike most of the previous publicly available corpora, all relationships are expressed at the document level as opposed to the sentence level, and as such, the entities are normalized to the corresponding concept identifiers of the standardized vocabularies, namely, diseases and chemicals are normalized to MeSH, genes (and proteins) to National Center for Biotechnology Information (NCBI) Gene, species to NCBI Taxonomy, cell lines to Cellosaurus, and gene/protein variants to Single Nucleotide Polymorphism Database. Finally, each annotated relationship is categorized as ‘novel’ depending on whether it is a novel finding or experimental verification in the publication it is expressed in. This distinction helps differentiate novel findings from other relationships in the same text that provides known facts and/or background knowledge. The BioRED-BC8 corpus uses the previous BioRED corpus of 600 PubMed articles as the training dataset and includes a set of newly published 400 articles to serve as the test data for the challenge. All test articles were manually annotated for the BioCreative VIII challenge by expert biocurators at the National Library of Medicine, using the original annotation guidelines, where each article is doubly annotated in a three-round annotation process until full agreement is reached between all curators. This manuscript details the characteristics of the BioRED-BC8 corpus as a critical resource for biomedical named entity recognition and relation extraction. Using this new resource, we have demonstrated advancements in biomedical text-mining algorithm development.
Database URL: https://codalab.lisn.upsaclay.fr/competitions/16381
Changes in Endoscopic Activity and Classification of Lesions With Panenteric Capsule Endoscopy in Patients Treated for Crohn’s Disease—A Prospective Blinded Comparison With Ileocolonoscopy, Fecal Calprotectin, and C-Reactive Protein
Authors: Brodersen Jacob Broder , Kjeldsen Jens , Juel Mie Agerbæk , Knudsen Torben , Rafaelsen Søren Rafael , Jensen Michael Dam 
Published: August 2024

Abstract

Background and Aims
Panenteric capsule endoscopy (PCE) is a minimally invasive modality that may replace ileocolonoscopy (IC) in selected patients with Crohn’s disease (CD). This study aimed to evaluate the dynamics of repeated assessment with PCE in patients receiving medical treatment for ileocolonic CD.

Methods
This prospective, blinded, multicenter study included patients with endoscopically active CD. Patients were scheduled for IC, PCE, fecal calprotectin, and C-reactive protein before and 12 weeks after treatment with corticosteroids or biological therapy. The endoscopic disease activity was assessed with the Simple Endoscopic Score for Crohn’s Disease (SES-CD).

Results
Thirty-one patients entered the study, and PCE visualized 148 (95.5%) and 128 (82.6%) ileocolonic bowel segments before and after medical treatment, respectively. The median SES-CD decreased from 14 (interquartile range [IQR] 8-17) to 5 (IQR 0-14) (p &lt; 0.001) and 14 (IQR 10-17) to 6 (IQR 3-12) (p &lt; 0.001) with IC and PCE, respectively. The repeated measures correlation between PCE and IC was very strong (r = 0.77, p &lt; 0.001), strong compared to fecal calprotectin (r = 0.42, p = 0.003), and moderate compared to C-reactive protein (r = 0.36, p = 0.005). The mean scores for ulcer size, ulcerated surface, and affected surface were comparable between PCE and IC both before and after treatment. PCE had a sensitivity and specificity of 80.6% (95% confidence interval [95% CI] 62.5-92.5) and 93.8% (95% CI 79.2-99.2), respectively, for ulcer healing compared to IC.

Conclusions
PCE is responsive in patients treated for CD and may serve as a minimally invasive alternative to IC in selected patients.
Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis
Authors: Jangi Sushrut , Zhao Naisi , Hsia Katie , Park Young Soo , Michaud Dominique S , Yoon Hyuk 
Published: August 2024

Abstract

Background and Aims
While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.

Methods
Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn’s & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n = 166) and activity (n = 46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort.

Results
CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.

Conclusions
Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.
Epigenetics of violence against women: a systematic review of the literature
Authors: Bailo Paolo , Piccinini Andrea , Barbara Giussy , Caruso Palmina , Bollati Valentina , Gaudi Simona 
Published: August 2024

Abstract
Violence against women is a pervasive global issue with profound impacts on victims’ well-being, extending across cultural boundaries. Besides immediate physical harm, it triggers mental health consequences such as post-traumatic stress disorder (PTSD). Indeed, it is the trauma experienced during a violent event that can lead to epigenetic modifications, ultimately contributing to the onset of PTSD. While research on the epigenetic effects of trauma initially focused on war veterans and disaster survivors, there is a dearth of studies on violence against women. In this article, we performed a systematic review aimed to fill this gap, examining existing studies on the epigenetic impact of violence on women. The review assessed sample sizes, study validity, and gene-specific investigations. Currently, there is insufficient data for a comprehensive meta-analysis, highlighting a nascent stage in understanding this complex issue. Future research is crucial for deeper insights into the epigenetic mechanisms related to violence against women, contributing to improved interventions and support healthcare systems for affected individuals.