bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances in functional and structural imaging of the brainstem: implications for disease
Authors: Cai Jiayue , Wang Yuheng , McKeown Martin J. 
Published: June 2024

Purpose of review
The brainstem's complex anatomy and relatively small size means that structural and functional assessment of this structure is done less frequently compared to other brain areas. However, recent years have seen substantial progress in brainstem imaging, enabling more detailed investigations into its structure and function, as well as its role in neuropathology.

Recent findings
Advancements in ultrahigh field MRI technology have allowed for unprecedented spatial resolution in brainstem imaging, facilitating the new creation of detailed brainstem-specific atlases. Methodological improvements have significantly enhanced the accuracy of physiological (cardiac and respiratory) noise correction within brainstem imaging studies. These technological and methodological advancements have allowed for in-depth analyses of the brainstem's anatomy, including quantitative assessments and examinations of structural connectivity within both gray and white matter. Furthermore, functional studies, including assessments of activation patterns and functional connectivity, have revealed the brainstem's roles in both specialized functions and broader neural integration. Notably, these investigations have identified alterations in brainstem structure and function associated with various neurological disorders.

Summary
The aforementioned developments have allowed for a greater appreciation of the importance of the brainstem in the wider context of neuroscience and clinical neurology.
A dynamic transmission model for assessing the impact of pneumococcal vaccination in the United States
Authors: Malik Tufail M , Bakker Kevin M , Oidtman Rachel J , Sharomi Oluwaseun , Meleleo Giulio , Nachbar Robert B , Elbasha Elamin H 
Published: June 2024

AbstractStreptococcus pneumoniae(SP) is a bacterial pathogen that kills more than 300,000 children every year across the globe. Multiple vaccines exist that prevent pneumococcal disease, with each vaccine covering a variable number of the more than 100 known serotypes. Due to the high effectiveness of these vaccines, each new pneumococcal conjugate vaccine (PCV) introduction has resulted in a decrease in vaccine-type disease and a shift in the serotype distribution towards non-vaccine types in a phenomenon called serotype replacement. Here, an age-structured compartmental model was created that reproduced historical carriage transmission dynamics in the United States and was used to evaluate the population-level impact of new vaccine introductions into the pediatric population. The model incorporates co-colonization and serotype competition, which drives replacement of the vaccine types by the non-vaccine types. The model was calibrated to historical age- and serotype-specific invasive pneumococcal disease (IPD) data from the United States. Vaccine-specific coverage and effectiveness were integrated in accordance with the recommended timelines for each age group. Demographic parameters were derived from US-population-specific databases, while population mixing patterns were informed by US-specific published literature on age-group based mixing matrices. The calibrated model was then used to project the epidemiological impact of PCV15, a 15-valent pneumococcal vaccine, compared with the status quo vaccination with PCV13 and demonstrated the value of added serotypes in PCV15. Projections revealed that PCV15 would reduce IPD incidence by 6.04% (range: 6.01% to 6.06%) over 10 years when compared to PCV13.
Sex differences in the associations of socioeconomic factors and cognitive performance with family history of Alzheimer’s disease
Authors: He Jun , Cabrera-Mendoza Brenda , Friligkou Eleni , Mecca Adam P. , van Dyck Christopher H. , Pathak Gita A. , Polimanti Renato 
Published: June 2024

ABSTRACTINTRODUCTIONWhile higher socioeconomic factors (SEF) and cognitive performance (CP) have been associated with reduced Alzheimer’s disease (AD) risk, recent evidence highlighted that these factors may have opposite effects on family history of AD (FHAD).METHODSLeveraging data from the UK Biobank (N=448,100) and the All of Us Research Program (N=240,319), we applied generalized linear regression models, polygenic risk scoring (PRS), and one-sample Mendelian randomization (MR) to test the sex-specific SEF and CP associations with AD and FHAD.RESULTSObservational and genetically informed analyses highlighted that higher SEF and CP were associated with reduced AD and sibling-FHAD, while these factors were associated with increased parent-FHAD. We also observed that population minorities may present different patterns with respect to sibling-FHAD vs. parent-FHAD. Sex differences in FHAD associations were identified in ancestry-specific and SEF PRS and MR results.DISCUSSIONThis study contributes to understanding the sex-specific relationships linking SEF and CP to FHAD, highlighting the potential role of reporting, recall, and surviving-related dynamics.
Machine learning and the labour market: A portrait of occupational and worker inequities in Canada
Authors: Jetha Arif , Liao Qing , Vahid Shahidi Faraz , Vu Viet , Biswas Aviroop , Smith Brendan , Smith Peter 
Published: June 2024

ABSTRACTIntroductionMachine learning (ML) is increasingly used by Canadian workplaces. Concerningly, the impact of ML may be inequitable and disrupt social determinants of health. The aim of this study is to estimate the number of workers in occupations highly exposed to ML and describe differences in ML exposure represents according to occupational and worker sociodemographic factors.MethodsCanadian occupations were scored according to the extent to which they were made up of job tasks that could be performed by ML. Eight years of data from Canada’s Labour Force Survey were pooled and the number of Canadians in occupations with high or low exposed to machine learning were estimated. The relationship between gender, hourly wages, educational attainment and occupational job skills, experience and training requirements and ML exposure was examined using stratified logistic regression models.ResultsApproximately, 1.9 million Canadians are working in occupations with high ML exposure and 744,250 workers were employed in occupations with low ML exposure. Women were more likely to be employed in occupations with high ML exposure than men. Workers with greater educational attainment and in occupations with higher wages and greater job skills requirements were more likely to experience high ML exposure. Women, especially those with less educational attainment and in jobs with greater job skills, training and experience requirements, were disproportionately exposed to ML.ConclusionML has the potential to widen inequities in the working population. Disadvantaged segments of the workforce may be most likely to be employed in occupations with high ML exposure. ML may have a gendered effect and disproportionately impact certain groups of women when compared to men. We provide a critical evidence base to develop strategic responses that ensure inclusion in a working world where ML is commonplace.KEY MESSAGESWhat is already known on this topicThe Canadian labour market is undergoing an artificial intelligence (AI) revolution that has the potential to have widespread impact on a range of occupations and worker groups.It is unclear how which the adoption of machine learning (ML), an AI subfield, within the working world might contribute to inequities within the labour market.What this study addsSegments of the workforce which have been previously disadvantaged may be most likely to work in occupations most likely to be affected by ML.ML may have a gendered effect and disproportionately impact some groups of women when compared to men.How this study might affect research, practice or policyFindings can inform targeted policies and programs that optimize the economic benefits of ML while addressing disparities that can emerge because of the adoption of the technology on workers.
Impact and Assessment of Mechanical Tension in Bowel Anastomosis: a Scoping Review
Authors: Khalid Muhammad Usman , Ali Danish , Wu Jie Ying , Khan Aimal 
Published: June 2024

AbstractBackgroundWhile tension on anastomoses is primarily regarded as a critical factor in anastomotic leaks and failure, assessing this tension is based on subjective surgeon estimation. There is currently no clinically available tool to assess mechanical tension on an anastomosis objectively. Some animal and human studies have previously evaluated anastomotic tension, but no comprehensive review discusses the different methods and types of tension measured.ObjectivesTo summarize the current state of the literature regarding the measurement and impact of tension on bowel anastomoses.DesignThis scoping review was conducted with a systematic search of literature in the PubMed, SCOPUS, and EMBASE databases. Key terms used were anastomoses/anastomosis, tension, bowel, surgery, intestine, tissue, small bowel, large bowel, bowel, mucosal tissue, and other corollary terms. Data were synthesized in tables, and summarized paragraphically, with studies assessed using the New-Castle Ottawa scale where possible. Emphasis was placed on method of tension assessment, outcomes, and factors relating to tension.ResultsAnastomotic leak and tension are strongly associated, with the presence of tension making leaks up to 10 times more likely. While freedom from tension has traditionally been measured via the surrogate measure of adequate bowel mobilization, this remains a subjective and imprecise method. The literature describes several techniques to allow adequate mobilization, such as splenic flexure mobilization or division of the omentum. However, basing the estimate of tension on subjective assessment has some inherent drawbacks. Animal and cadaveric studies have been the frontier for objective measurement of wall tension, with the use of scaffolds, suture types, and prostheses to bolster the natural tolerance of the bowel. However, these tend to use tensiometers to measure tension, along with automated machines or pulley and ratcheting systems to increase tension in specified intervals. These are universally destructive due to their design of measuring maximal tensile load as well as not being easily adaptable to the operating room.ConclusionsThe current literature does not study objective measurement of bowel tension in live human subjects. Bowel mobilization is a common method to reduce tension, but it relies on subjective judgment, which varies between surgeons. Given the recognized importance of tension, developing an objective, safe, intra-operative method to measure bowel wall tension would be a valuable surgical tool.
Who participates in ‘participatory design’ of WASH infrastructure: a mixed-methods process evaluation
Authors: Mink Thea L. , Salinger Allison P. , Francis Naomi , Batagol Becky , Burge Kerrie , Ilhamsyah Noor , Malumu Losalini , Marzaman Liza , Prescott Michaela , Putri Nur Intan , Sinharoy Sheela S. 
Published: June 2024

AbstractInclusive participation is critical for community-based water, sanitation and hygiene (WASH) interventions, especially in complex environments such as urban informal settlements. We conducted a mixed-methods, theory-driven process evaluation to evaluate participation, barriers to participation, and participant satisfaction within the Revitalising Informal Settlements and their Environments (RISE) trial in Makassar, Indonesia and Suva, Fiji (ACTRN12618000633280;https://www.anzctr.org.au/).RISE conducted participatory design activities, including community-level design workshops and household visits, to co-design WASH infrastructure. Household surveys, conducted with women and men after RISE participatory design in Makassar (N=320) and Suva (N=503), captured self-reported participation in RISE activities and satisfaction with influence over RISE decision-making. We used multivariable regression models to assess socio-demographic predictors of participation and satisfaction. Qualitative data were also collected after participatory design and analyzed thematically.Most respondents from Makassar (89%) and Suva (75%) participated in at least one RISE co-design activity. Statistically significant predictors of participation included gender, age, and marital status in Makassar and disability status and education in Suva. Most participants in Makassar (66%) and Suva (70%) were satisfied with their level of influence over RISE decision-making. In Makassar, no significant predictors of satisfaction were identified. In Suva, significant predictors of satisfaction included gender, religion, and marital status, with women wantingmoreinfluence and religious minorities and unmarried participants wantinglessinfluence over decisions. Qualitative data showed that most participants felt satisfied by RISE’s inclusive and participatory design, although some residents reported distrust with RISE and feeling excluded from activities by community representatives.While RISE participatory design activities achieved good reach and satisfaction overall, we identified specific gender and social inequities in participation and influence over decision-making. We recommend that WASH interventions reflect on the quality of their engagement with communities and local organizations in order to identify and appropriately include groups of interest.
Increased 5-HT2Areceptor signalling efficacy differentiates serotonergic psychedelics from non-psychedelics
Authors: Ippolito Aurelija , Vasudevan Sri , Hurley Shaun , Gilmour Gary , Westhorpe Frederick , Churchill Grant , Sharp Trevor 
Published: June 2024

ABSTRACTBackground and PurposeSerotonergic psychedelic drugs are under renewed investigation for the potential treatment of several psychiatric disorders. While all serotonergic psychedelics have 5-HT2Areceptor activity, the explanation for why some 5-HT2Areceptor agonists are not psychedelic is unknown. To address this question, we investigated the 5-HT2Areceptor signalling bias and efficacy of a panel of psychedelics and non-psychedelics.Experimental ApproachG -coupled (Ca2+and IP) and β-arrestin2 signalling effects of eight chemically diverse psychedelics (psilocin, 5-MeO-DMT, LSD, mescaline, 25B-NBOMe and DOI) and non-psychedelics (lisuride and TBG) were characterised using SH-SY5Y cells expressing recombinant human 5-HT2Areceptors. Measurements of signalling efficacy and bias were derived from dose-responses curves for each agonist, compared to 5-HT. Follow-up experiments sought to confirm the generality of findings using rat C6 cells expressing endogenous 5-HT2Areceptors.Key ResultsIn SH-SY5Y cells, all psychedelics were partial agonists at both 5-HT2Areceptor signalling pathways and none showed significant signalling bias. In comparison, in SH-SY5Y cells the non-psychedelics lisuride and TBG were not distinguishable from psychedelics in terms of biased agonist properties, but both exhibited the lowest 5-HT2Areceptor signalling efficacy of all drugs tested, a result confirmed in C6 cells.Conclusion and ImplicationsIn summary, all psychedelics tested were unbiased, partial 5-HT2Areceptor agonists. Importantly, the non-psychedelics lisuride and TBG were discriminated from psychedelics, not through biased signalling but rather by relatively low efficacy. Thus, 5-HT2Areceptor signalling efficacy and not bias provides a possible explanation for why some 5-HT2Areceptor agonists are not psychedelic.
Central place foragers, prey depletion halos, and how behavioral niche partitioning promotes consumer coexistence
Authors: Rueffler Claus , Lehmann Laurent 
Published: June 2024

AbstractMany seabirds congregate in large colonies for breeding, a time when they are central place foragers. An influential idea in seabird ecology posits that competition during breeding results in an area of reduced prey availability around colonies, a phenomenon known as Ashmole’s halo, and that this limits colony size. This idea has gained empirical support, including the finding that species coexisting within a colony might be able to do so by foraging on a single prey species but at different distances. Here, we provide a comprehensive mathematical model for central place foragers exploiting a single prey in a two-dimensional environment, where the prey distribution is the result of intrinsic birth and death, movement in space and mortality due to foraging birds (we also consider a variant tailored toward colonial social insects). Bird predation at different distances occurs according to an ideal free foraging distribution that maximizes prey delivery under flight and search costs. We fully characterize the birds’ ideal free distribution and the prey distribution it generates. Our results show that prey depletion halos around breeding colonies are a robust phenomenon and that the birds’ ideal free distribution is sensitive to prey movement. Furthermore, coexistence of several seabird species on a single prey easily emerges through behavioral niche partitioning whenever trait differences between species entail trade-offs between efficiently exploiting a scarce prey close to the colony and a more abundant prey far away. Such behavioral-based coexistence-inducing mechanism should generalize to other habitat and diet choice scenarios.Significance statementThis study presents a mathematical model to explore the distribution of foraging trips among seabirds breeding on isolated islands, providing insight into the emergence of prey depletion halos around colonies. Our findings reveal that such halos are a robust feature of central place foraging, independent of prey dynamics. Additionally, the model shows that trait-mediated niche partitioning promotes coexistence among species through behavioral segregation into different circular zones around the island. This partitioning occurs despite a shared preference to forage close to the island, where flight costs are lowest. The study advances understanding of ecological coexistence mechanisms and suggests broader applicability to other predator-prey systems beyond seabird ecology, offering a new perspective on community assembly under shared preferences.
Confinement modulates axial patterning in regenerating Hydra
Authors: Maroudas-Sacks Yonit , Garion Liora , Suganthan S , Popović Marko , Keren Kinneret 
Published: June 2024

AbstractThe establishment of the body plan is a major step in animal morphogenesis. The role of mechanical forces and feedback in patterning the body plan remains unclear. Here we explore this question, by studying regenerating Hydra tissues confined in narrow cylindrical channels which constrain their morphology. We find that frustration between the orientation of the channel and the inherited axis in the regenerating tissues can lead to the formation of a multiaxial body plan. The morphological outcome is directly related to the pattern of nematic topological defects that emerges in the organization of the supracellular actomyosin fibers. When the inherited axis, which can be read out from the initial alignment of the supracellular fibers in the confined spheroid, is parallel to the channel’s axis, the tissue regenerates normally into animals with a single body axis aligned with the channel. However, regenerating spheroids that are confined in a frustrated perpendicular configuration often develop excess defects (including negatively-charged -½ defects) and regenerate into multiaxial morphologies. The influence of mechanical constraints on the regenerated body plan argues against an axial patterning mechanism that is based solely on inherited gradients of biochemical morphogens. We further show that the dependence of the regeneration outcomes on the initial tissue orientation can be recapitulated by a biophysical model which considers the coupled dynamics of the nematic organization of the actomyosin fibers and a morphogen concentration field, incorporating a mechanochemical feedback loop involving strain-dependent morphogen production at defect sites.
Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition
Authors: Nourani Esmaeil , Koutrouli Mikaela , Xie Yijia , Vagiaki Danai , Pyysalo Sampo , Nastou Katerina , Brunak Søren , Juhl Jensen Lars 
Published: June 2024

AbstractMotivationDespite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This is in part because no named entity recognition (NER) system exists, which can comprehensively detect all types of LSFs in text. The task is challenging due to their inherent diversity, lack of a comprehensive LSF classification for dictionary-based NER, and lack of a corpus for deep learning-based NER.ResultsWe present a novel Lifestyle Factor Ontology (LSFO), which we used to develop a dictionarybased system for recognition and normalization of LSFs. Additionally, we introduce a manually annotated corpus for LSFs (LSF200) suitable for training and evaluation of NER systems, and use it to train a transformer-based system. Evaluating the performance of both NER systems on the corpus revealed an F-score of 64% for the dictionary-based system and 76% for the transformer-based system. Largescale application of these systems on PubMed abstracts and PMC Open Access articles identified over 300 million mentions of LSF in the biomedical literature.AvailabilityLSFO, the annotated LSF200 corpus, and the detected LSFs in PubMed and PMC-OA articles using both NER systems, are available under open licenses via the following GitHub repository:https://github.com/EsmaeilNourani/LSFO-expansion. This repository contains links to two associated GitHub repositories and a Zenodo project related to the study. LSFO is also available at BioPortal:https://bioportal.bioontology.org/ontologies/LSFO.Contactkaterina.nastou@cpr.ku.dk,soren.brunak@cpr.ku.dk,lars.juhl.jensen@cpr.ku.dkSupplementary informationSupplementary data are available atBioinformaticsonline.
Wavenumber-dependent transmission of subthreshold waves on electrical synapses network model ofCaenorhabditis elegans
Authors: Chang Iksoo , Chung Taegon , Kim Sangyeol 
Published: June 2024

AbstractRecent experimental studies showed that electrically coupled neural networks like in mammalian inferior olive nucleus generate synchronized rhythmic activity by the subthreshold sinusoidal-like oscillations of the membrane voltage. Understanding the basic mechanism and its implication of such phenomena in the nervous system bears fundamental importance and requires preemptively the connectome information of a given nervous system. Inspired by these necessities of developing a theoretical and computational model to this end and, however, in the absence of connectome information for the inferior olive nucleus, here we investigated interference phenomena of the subthreshold oscillations in the reference systemCaenorhabditis elegansfor which the structural anatomical connectome was completely known recently. We evaluated how strongly the sinusoidal wave was transmitted between arbitrary two cells in the model network. The region of cell-pairs that are good at transmitting waves changed according to the wavenumber of the wave, for which we named a wavenumber-dependent transmission map. Also, we unraveled that 1) the transmission of all cell-pairs disappeared beyond a threshold wavenumber, 2) long-distance and regular patterned transmission existed in the body-wall muscles part of the model network, and 3) major hub cell-pairs of the transmission were identified for many wavenumber conditions. A theoretical and computational model presented in this study provided fundamental insight for understanding how the multi-path constructive/destructive interference of the subthreshold oscillations propagating on electrically coupled neural networks could generate wavenumber-dependent synchronized rhythmic activity.