bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proposal of a modified classification for hilar cholangiocarcinoma
Authors: Xiang Shuai , Chen Xiao-Ping 
Published: December 2023

Abstract
Hilar cholangiocarcinoma is a malignant tumor that originates from the left and right hepatic ducts and their confluence. It is highly malignant and associated with a poor prognosis. Surgical resection is the only available curative treatment option. A scientific classification system can aid in the preoperative assessment of resectability and guide the development of appropriate surgical strategies. Several classification systems are available, with the Bismuth-Corlette (BC) classification being the earliest and most widely used. Similar to many other classifications, the BC classification relies on the secondary branching of the bile ducts as an important anatomical landmark, making it unsuitable for cases with variations in the bile duct anatomy. With advances in understanding the hepatic plate and anatomical structures at the hilum, the secondary bile ducts are no longer considered important anatomical landmarks. Therefore, modifications to the BC classification are needed to align with modern anatomical improvements and advancements in surgical techniques. Herein, we propose a modification to the BC classification. In this new system, the boundary of the hilar plate is considered as limit of the proximal ductal margin and used as an anatomical landmark, rather than the concept of “secondary bile ducts” in the BC classification.
Transcriptomic and Proteomic Characterization of the Immune Response to Elective Spinal Reconstructive Surgery: Impact of Aging and Comparison with Traumatic Injury Response
Authors: Bonaroti Jillian W , Ozel Mehves , Chen Tianmeng , Darby Jennifer L , Sun Xuejing , Moheimani Hamed , Reitz Katherine M , Kar Upendra K , Zuckerbraun Brian S , Das Jishnu , Okonkwo David O , Billiar Timothy R 
Published: December 2023

BACKGROUND:
Major surgery triggers trauma-like stress responses linked to age, surgery duration, and blood loss, resembling polytrauma. This similarity suggests elective surgery as a surrogate model for studying polytrauma immune responses. We investigated stress responses across age groups and compared them with those of polytrauma patients.

STUDY DESIGN:
Patients undergoing major spinal reconstruction surgery were divided into older (age >65 years, n = 5) and young (age 18 to 39 years, n = 6) groups. A comparison group consisted of matched trauma patients (n = 8). Blood samples were collected before, during, and after surgery. Bone marrow mononuclear cells and peripheral blood mononuclear cells were analyzed using cellular indexing of transcriptomes and epitopes sequencing or single-cell RNA sequencing. Plasma was subjected to dual-platform proteomic analysis (SomaLogic and O-link).

RESULTS:
Response to polytrauma was highest within 4 hours. By comparison, the response to surgery was highest at 24 hours. Both insults triggered significant changes in cluster of differentiation 14 monocytes, with increased inflammation and lower major histocompatibility complex-class 2 expression. Older patient’s cluster of differentiation 14 monocytes displayed higher inflammation and less major histocompatibility complex-class 2 suppression; a trend was also seen in bone marrow mononuclear cells. Although natural killer cells were markedly activated after polytrauma, they were suppressed after surgery, especially in older patients. In plasma, innate immunity proteins dominated at 24 hours, shifting to adaptive immunity proteins by 6 weeks with heightened inflammation in older patients. Senescence-associated secretory phenotype proteins were higher in older patients at baseline and further elevated during and after surgery.

CONCLUSIONS:
Although both major surgery and polytrauma initiate immune and stress responses, substantial differences exist in timing and cellular profiles, suggesting major elective surgery is not a suitable surrogate for the polytrauma response. Nonetheless, distinct responses in young vs older patients highlight the utility of elective spinal in studying patient-specific factors affecting outcomes after major elective surgery.
AN OVERVIEW OF THE IMPACT OF SOCIAL SUPPORT ON NURSE BURN OUT IN HOSPITALS
Authors: Riu Silvia Dewi Mayasari , Pandin Moses Glorino Rumambo 
Published: December 2023

ABSTRACTIntroductionThe nursing profession is one of the most difficult and stressful occupations. Nurses have a great responsibility in providing health care to clients, which often involves emotional, complex, and high-risk situations. Social support is emotional, informational and practical assistance provided by individuals or groups to others in certain situations. Burnout syndrome is a chronic stress condition that affects many individuals including nurses. This condition often arises as a result of excessive workload, high physical and emotional demands and imbalance between work and personal life plus the occurrence of a global pandemic.MethodThe author used the literature review method by searching for references via the internet. The literature search used Sciencedirect, Pubmed, and Medline and Google Scholar with keywords in English: “social support”, “burnout”. The inclusion criteria in this research were articles that discussed social support on burnout, were in English, published in the last 5 years (2018-2023), explored in the article was the influence of social support on burnout, and a comprehensive examination of the full article is provided. Exclusion criteria were articles that did not discuss social support on burnout.ResultFrom the literature search, it was obtained 16 journal articles that were relevant with the research objectives.ConclusionSocial support has an important role as a protective factor that can reduce the risk of burnout in individuals, especially among professionals or workers who experience high workloads. Good social support can provide the emotional, instrumental, and informational resources needed to cope with daily stress and pressure.SuggestionSocial support can be considered a form of “natural protection” against burnout, and efforts to strengthen social support networks can be an effective strategy in preventing and coping burnout at various levels of life and professions.
Clinical utility of plasma Aβ42/40 ratio by LC-MS/MS in Alzheimer’s disease assessment
Authors: Weber Darren M. , Taylor Steven W. , Lagier Robert J. , Kim Jueun C. , Goldman Scott M. , Clarke Nigel J. , Vaillancourt David E. , Duara Ranjan , McFarland Karen N. , Wang Wei-en , Golde Todd E. , Racke Michael K. 
Published: December 2023

ABSTRACTINTRODUCTIONPlasma Aβ42/40 ratio can be used to help predict amyloid PET status, but its clinical utility in Alzheimer’s disease (AD) assessment is unclear.METHODSAβ42/40 ratio was measured by LC-MS/MS in 250 specimens with associated amyloid PET imaging, diagnosis, and demographic data, and 6,192 consecutive clinical specimens submitted for Aβ42/40 testing.RESULTSHigh diagnostic sensitivity and negative predictive value (NPV) for Aβ-PET positivity were observed, consistent with the clinical performance of other plasma LC-MS/MS assays, but with greater separation between Aβ42/40 values for individuals with positive vs negative Aβ-PET results. Assuming a moderate prevalence of Aβ-PET positivity, a cutpoint was identified with 99% NPV, which could help predict that AD is likely not the cause of patients’ cognitive impairment and help reduce PET evaluation by about 40%.DISCUSSIONUsing high-throughput plasma Aβ42/40 LC-MS/MS assays can help reduce PET evaluations in patients with low likelihood of AD pathology, allowing for cost savings.HighlightsA new plasma LC-MS/MS assay for the Aβ42/Aβ40 ratio has clinical utility in AD assessment.Performance was assessed using specimens with a moderate prevalence of Aβ-PET positivity.Analysis was extrapolated to 6,192 consecutive clinical specimens submitted for ratio testing.Assay cutpoints were proposed to help suggest clinical management decisions.Based on the assay’s high NPV, costly PET evaluations may be avoided for many individuals.Research in ContextSystematic ReviewAβ42/Aβ40 ratio data were analyzed from 250 ADRC cohort participants and 6,192 plasma specimens submitted for Aβ42/40 ratio testing by LC-MS/MS at Quest Diagnostics.InterpretationBased on its high NPV, the assay identifies individuals likely to have negative amyloid PET results. Higher discriminatory power and larger fold-changes between PET-positive and negative individuals were observed compared with previous studies. Our “real-world” data set, combined with known performance characteristics, allows us to suggest cutpoints and clinical decisions based on plasma Aβ42/40 ratios.Future DirectionsLongitudinal plasma specimens from individuals who convert from PET-negative to positive, or that transition from cognitively normal to MCI and AD, will improve understanding of the prognostic utility of the Aβ42/40 ratio. Using Aβ42/40 ratio alone or combined with other biomarkers, to follow patients with cognitive impairment may yield insights regarding their disease conditions and progression and who may benefit from disease-modifying therapeutics.
Racial and Ethnic Disparities in Healthcare Utilization and Mortality by Neighborhood Poverty among Individuals with Congenital Heart Defects, four U.S. Surveillance Sites, 2011-2013
Authors: Raskind-Hood Cheryl L. , Kancherla Vijaya , Ivey Lindsey C. , Rodriguez Fred H. , Sullivan Anaclare M. , Lui George K. , Botto Lorenzo , Feldkamp Marcia , Li Jennifer S. , D’Ottavio Alfred , Farr Sherry L. , Glidewell Jill , Book Wendy M. 
Published: December 2023

ABSTRACTBACKGROUNDSocioeconomic factors may lead to a disproportionate impact on healthcare utilization and mortality among individuals with congenital heart defects (CHD) by race, ethnicity, and socio-economic factors. How neighborhood poverty affects racial and ethnic disparities in healthcare utilization and mortality among individuals with CHD across the lifespan is not well described.METHODSIndividuals, 1-64 years, with at least one CHD-related ICD-9-CM code were identified from healthcare encounters between 01/01/2011-12/31/2013 from four U.S. sites. Residence was classified into lower or higher poverty neighborhoods based on ZCTA from the 2014 American Community Survey 5-Year Estimates. Multivariable logistic regression models, adjusting for site, sex, CHD anatomic severity, and insurance evaluated associations between race and ethnicity, and healthcare utilization and mortality, stratified by neighborhood poverty.RESULTSOf 31,542 individuals, 22.2% were non-Hispanic Black (nHB) and 17.0% Hispanic. In high poverty neighborhoods, nHB (44.4%) and Hispanic (47.7%) individuals, respectively, were more likely to be hospitalized (aOR)=1.2 [95%CI=1.0-1.3] and aOR=1.3 [95%CI=1.2-1.5]) and have ED visits (aOR=1.3 [95%CI=1.2-1.5] and aOR=1.7 [95%CI=1.5-2.0]) compared to non-Hispanic White (nHW) individuals. In high poverty neighborhoods, nHB individuals with CHD had 1.7 times the odds of mortality compared to nHW individuals in high poverty neighborhoods (95%CI=1.1-2.7). Racial and ethnic disparities in healthcare utilization were similar in low poverty neighborhoods, but disparities in mortality were attenuated (aOR for nHB=1.2 [95%CI=0.9-1.7]).CONCLUSIONSRacial and ethnic disparities in healthcare utilization were found among individuals with CHD in low and high poverty neighborhoods, but mortality disparities were larger in high poverty neighborhoods. Understanding individual- and community-level social determinants of health, including access to healthcare, may help address racial and ethnic inequities in healthcare utilization and mortality among individuals with CHD.
Changes in the structure of spontaneous speech predict the disruption of hierarchical brain organization in first-episode psychosis
Authors: He Rui , Alonso-Sánchez Maria Francisca , Sepulcre Jorge , Palaniyappan Lena , Hinzen Wolfram 
Published: December 2023

AbstractPsychosis implicates changes across a broad range of cognitive functions. These functions are cortically organized in the form of a hierarchy ranging from primary sensorimotor (unimodal) to higher-order association cortices, which involve functions such as language (transmodal). Language has long been documented as undergoing structural changes in psychosis. We hypothesized that these changes as revealed in spontaneous speech patterns may act as readouts of alterations in the configuration of this unimodal-to-transmodal axis of cortical organization in psychosis. Results from 29 patients with first-episodic psychosis (FEP) and 29 controls scanned with 7T resting-state fMRI confirmed a compression of the cortical hierarchy in FEP, which affected metrics of the hierarchical distance between the sensorimotor and default mode networks, and of the hierarchical organization within the semantic network. These organizational changes were predicted by graphs representing semantic and syntactic associations between meaningful units in speech produced during picture descriptions. These findings unite psychosis, language, and the cortical hierarchy in a single conceptual scheme, which helps to situate language within the neurocognition of psychosis and opens the clinical prospect for mental dysfunction to become computationally measurable in spontaneous speech.
Steady-state neuron-predominant LINE-1 encoded ORF1p protein and LINE-1 RNA increase with aging in the mouse and human brain
Authors: Bonnifet Tom , Sinnassamy Sandra , Massiani-Beaudoin Olivia , Mailly Philippe , Monnet Héloïse , Loew Damarys , Lombard Berangère , Servant Nicolas , Joshi Rajiv L. , Fuchs Julia 
Published: December 2023

AbstractRecent studies have established a reciprocal causal link between aging and the activation of transposable elements, characterized in particular by a de-repression of LINE-1 retrotransposons. These LINE-1 elements represent 21% of the human genome, but only a minority of these sequences retain the coding potential essential for their mobility. LINE-1 encoded proteins can induce cell toxicity implicated in aging and neurodegenerative diseases. However, our knowledge of the expression and localization of LINE-1-encoded proteins in the central nervous system is limited. Using a novel approach combining atlas-based brain mapping with deep-learning algorithms on large-scale pyramidal brain images, we unveil a heterogeneous, neuron-predominant and widespread ORF1p expression throughout the murine brain at steady-state. In aged mice, ORF1p expression increases significantly which is corroborated in human post-mortem dopaminergic neurons by an increase in young LINE-1 elements including those with open reading frames. Mass spectrometry analysis of endogenous mouse ORF1p revealed novel, neuron-specific protein interactors. These findings contribute to a comprehensive description of the dynamics of LINE-1 and ORF1p expression in the brain at steady-state and in aging and provide insights on ORF1p protein interactions in the brain.
Structured dynamics in the algorithmic agent
Authors: Ruffini G. , Castaldo F. , Vohryzek J. 
Published: December 2023

AbstractIn the Kolmogorov Theory of Consciousness, algorithmic agents utilize inferred compressive models to track coarse-grained data produced by simplified world models, capturing regularities that structure subjective experience and guide action planning. Here, we study the dynamical aspects of this framework by examining how the requirement of tracking natural data drives the structural and dynamical properties of the agent. We first formalize the notion ofgenerative modelusing the language of symmetry from group theory, specifically employing Lie pseudogroups to describe the continuous transformations that characterize invariance in natural data. Then, adopting a generic neural network as a proxy for the agent dynamical system and drawing parallels to Noether’s theorem in physics, we demonstrate that data tracking forces the agent to mirror the symmetry properties of the generative world model. This dual constraint on the agent’s constitutive parameters and dynamical repertoire enforces a hierarchical organization consistent with the manifold hypothesis in the neural network. Our findings bridge perspectives from algorithmic information theory (Kolmogorov complexity, compressive modeling), symmetry (group theory), and dynamics (conservation laws, reduced manifolds), offering insights into the neural correlates of agenthood and structured experience in natural systems, as well as the design of artificial intelligence and computational models of the brain.HighlightsLie generative models are formalized using Lie pseudogroups, linking algorithmic simplicity, recursion, and compositionality with symmetry.Neural networks inherit structural constraints reflecting the symmetries in Lie-generated data.Similarly, agents, instantiated as neural networks tracking world Lie-generated data, reflect Lie structure and reduced-dimensional dynamical manifolds.Compositional structure in world data induces coarse-grained constraints, resulting in reduced manifolds that reflect the underlying generative process.Mutual Algorithmic Information (MAI) between the agent and the world emerges as shared symmetries in their dynamical interactions.These findings provide new insights for neuroscience, AI design, and computational brain modeling, emphasizing the interplay between data structure and agent dynamics.
Keratinocyte Piezo1 drives paclitaxel-induced mechanical hypersensitivity
Authors: Mikesell Alexander R , Isaeva Elena , Schulte Marie L , Menzel Anthony D , Sriram Anvitha , Prahl Megan M , Shin Seung Min , Sadler Katelyn E , Yu Hongwei , Stucky Cheryl L 
Published: December 2023

AbstractRecent work demonstrates that epidermal keratinocytes are critical for normal touch sensation. However, it is unknown if keratinocytes contribute to touch evoked pain and hypersensitivity following tissue injury. Here, we used inhibitory optogenetic and chemogenetic techniques to determine the extent to which keratinocyte activity contributes to the severe neuropathic pain that accompanies chemotherapeutic treatment. We found that keratinocyte inhibition largely alleviates paclitaxel-induced mechanical hypersensitivity. Furthermore, we found that paclitaxel exposure sensitizes mouse and human keratinocytes to mechanical stimulation through the keratinocyte mechanotransducer Piezo1. These findings demonstrate the contribution of non-neuronal cutaneous cells to neuropathic pain and pave the way for the development of new pain-relief strategies that target epidermal keratinocytes and Piezo1.SummarySensitization of the keratinocyte mechanotransducer Piezo1 drives paclitaxel-induced touch pain.
Shared features underlying compact genomes and extreme habitat use in chironomid midges
Authors: Nell Lucas A. , Weng Yi-Ming , Phillips Joseph S. , Botsch Jamieson C. , Book K. Riley , Einarsson Árni , Ives Anthony R. , Schoville Sean D. 
Published: December 2023

AbstractNon-biting midges (family Chironomidae) are found throughout the world in a diverse array of aquatic and terrestrial habitats, can often tolerate harsh conditions such as hypoxia or desiccation, and have consistently compact genomes. Yet we know little about the shared molecular basis for these attributes and how they have evolved across the family. Here, we address these questions by first creating high-quality, annotated reference assemblies forTanytarsus gracilentus(subfamily Chironominae, tribe Tanytarsini) andParochlus steinenii(subfamily Podonominae). Using these and other publicly available assemblies, we created a time-calibrated phylogenomic tree for family Chironomidae with outgroups from order Diptera. We used this phylogeny to test for features associated with compact genomes, as well as examining patterns of gene family evolution and positive selection that may underlie chironomid habitat tolerances. Our results suggest that compact genomes evolved in the most recent common ancestor of Chironomidae and Ceratopogonidae, and that this occurred mainly through reductions in non-coding regions (introns, intergenic sequences, and repeat elements). Gene families that significantly expanded in Chironomidae included biological processes that may relate to tolerance of stressful environments, such as temperature homeostasis, inflammatory response, melanization defense response, and trehalose transport. We identified a number of genes with evidence for positive selection in Chironomidae, notably sulfonylurea receptor, peroxiredoxin-1, and protein kinase D. Our results help to understand the genomic basis for the small genomes and extreme habitat use in this widely distributed group.Significance StatementChironomid midges are known for having small genomes and being able to tolerate many forms of environmental stress, yet little is known of the shared features of their genomes that may underlie these traits. We found that reductions in non-coding regions coincide with small chironomid genomes, and we identified duplicated and/or selected genes that may equip chironomids to tolerate harsh conditions. These results describe the key genomic changes in chironomid midges that may explain their ability to inhabit a range of extreme habitats across the world.
Micro-DeMix: A mixture beta-multinomial model for investigating the fecal microbiome compositions
Authors: Liu Ruoqian , Wang Yue , Cheng Dan 
Published: December 2023

AbstractExtensive research has uncovered the involvement of the human gut microbiome in various facets of human health, including metabolism, nutrition, physiology, and immune function. Researchers often study fecal microbiota as a proxy for understanding the gut microbiome. However, it has been demonstrated that this approach may not suffice to yield a comprehensive understanding of the entire gut microbial community. Emerging research is revealing the heterogeneity of the gut microbiome across different gastrointestinal (GI) locations in both composition and functions. While spatial metagenomics approach has been developed to address these variations in mice, limitations arise when applying it to human-subject research, primarily due to its invasive nature. With these restrictions, we introduce Micro-DeMix, a mixture beta-multinomial model that decomposes the fecal microbiome at compositional level to understand the heterogeneity of the gut microbiome across various GI locations and extract meaningful insights about the biodiversity of the gut microbiome. Moreover, Micro-DeMix facilitates the discovery of differentially abundant microbes between GI regions through a hypothesis testing framework. We utilize the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project to demonstrate the effectiveness and efficiency of the proposed Micro-DeMix.Key MessagesKey MessagesMicro-DeMix is a computational tool for understanding the heterogeneity of the gut microbiome across GI locations.Micro-DeMix facilitates the detection of differentially abundant microbes along the GI tract.Micro-DeMix detects that in IBD populations, the lower GI tract exhibits a larger abun-dance of Firmicutes and Bacteroidetes, whereas the upper GI tract is predominated by Proteobacteria and Firmicutes.