bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevention and Management of Posterior Wound Complications Following Oncologic Spine Surgery: Narrative Review of Available Evidence and Proposed Clinical Decision-Making Algorithm
Authors: Leary Owen P. , Setty Aayush , Gong Jung Ho , Ali Rohaid , Fridley Jared S. , Fisher Charles G. , Sahgal Arjun , Rhines Laurence D. , Reynolds Jeremy J. , Lazáry Áron , Laufer Ilya , Gasbarrini Alessandro , Dea Nicolas , Verlaan Jorrit-Jan , Bettegowda Chetan , Boriani Stefano , Mesfin Addisu , Luzzati Alessandro , Shin John H. , Cecchinato Riccardo , Hornicek Francis J. , Goodwin Matthew L. , Gokaslan Ziya L. 
Published: January 2025

Study Design Narrative Review. Objective Contextualized by a narrative review of recent literature, we propose a wound complication prevention and management algorithm for spinal oncology patients. We highlight available strategies and motivate future research to identify optimal and individualized wound management for this population. Methods We conducted a search of recent studies (2010-2022) using relevant keywords to identify primary literature in support of current strategies for wound complication prevention and management following spine tumor surgery. When primary literature specific to spine tumor cases was not available, data were extrapolated from studies of other spine surgery populations. Results were compiled into a proposed clinical algorithm to guide practice considering available evidence. Results Based on available literature, we recommend individualized stratification of patients according to identifiable risk factors for wound complication and propose several interventions which might be employed preventatively, including intrawound antibiotic administration, negative pressure wound therapy, and primary flap closure of the surgical wound. Of these, the available evidence, weighing possible risks vs benefits, most strongly favors primary flap closure of surgical wounds, particularly for patients with multiple risk factors. A secondary algorithm to guide management of wound complications is also proposed. Conclusions Wound complications such as SSI and dehiscence remain a significant source of morbidity following spine tumor surgery. Triaging patients on an individualized basis according to risk factors for complication may aid in selecting appropriate prophylactic strategies to prevent these complications. Future research in this area is still needed to strengthen recommendations.
Defining Spine Cancer Pain Syndromes: A Systematic Review and Proposed Terminology
Authors: Pahuta Markian , Laufer Ilya , Lo Sheng-fu Larry , Boriani Stefano , Fisher Charles , Dea Nicolas , Weber Michael H. , Chou Dean , Sahgal Arjun , Rhines Laurence , Reynolds Jeremy , Lazary Aron , Gasbarrinni Alessandro , Verlaan Jorrit-Jan , Gokaslan Ziya , Bettegowda Chetan , Sarraj Mohamed , Barzilai Ori ,   On behalf of the AO Spine Knowledge Forum Tumor
Published: January 2025

Study Design Systematic Review. Objectives Formalized terminology for pain experienced by spine cancer patients is lacking. The common descriptors of spine cancer pain as mechanical or non-mechanical is not exhaustive. Misdiagnosed spinal pain may lead to ineffective treatment recommendations for cancer patients. Methods We conducted a systematic review of pain terminology that may be relevant to spinal oncology patients. We provide a comprehensive and unbiased summary of the existing evidence, not limited to the spine surgery literature, and subsequently consolidate these data into a practical, clinically relevant nomenclature for spine oncologists. Results Our literature search identified 3515 unique citations. Through title and abstract screening, 3407 citations were excluded, resulting in 54 full-text citations for review. Pain in cancer patients is typically described as nociceptive pain (somatic vs visceral), neurologic pain and treatment related pain. Conclusions We consolidate the terminology used in the literature and consolidated into clinically relevant nomenclature of biologic tumor pain, mechanical pain, radicular pain, neuropathic pain, and treatment related pain. This review helps standardize terminology for cancer-related pain which may help clinicians identify pain generators.
Evaluation of the Soda Tax on Obesity and Diabetes in California: A Cost-Effectiveness Analysis
Authors: Zhao Fan , Gidwani Risha , Wang May C. , Chen Liwei , Nianogo Roch A. 
Published: January 2025

Introduction. Consumption of sugar-sweetened beverages (SSBs) contributes to weight gain, obesity, and diabetes. Soda tax has been proposed to reduce consumption of SSBs. What remains unclear is whether the soda tax has an effect on health and health care costs. We evaluated the cost-effectiveness of a 1-cent-per-ounce soda tax on obesity and diabetes in California. Methods. A microsimulation state-transition model was used to evaluate the cost-effectiveness of the soda tax. Health outcomes were measured in quality-adjusted life-years (QALYs). Health care costs were projected from 2015 to 2035. Results. In a simulated cohort of Californian adults, the soda tax policy prevented 2.28 million cases of overweight (95% confidence interval [CI] −0.06 to 6.63) and 0.49 million cases of obesity (95% CI −0.19 to 1.18). From the health care perspective, the incremental cost-effectiveness ratio of the soda tax was $124,839 dollars per QALY (95% CI −1,151,983 to 557,660). From the health care perspective, the soda tax policy was cost-effective 80% of the time in the probabilistic sensitivity analysis using a willingness-to-pay threshold of $100,000 per QALY. Conclusions. The 1-cent-per-ounce soda tax reduced the number of obesity cases, diabetes cases, and related complications. In addition, the soda tax policy implemented in California was cost-effective most of the time. Highlights Question: What remains unclear is whether the soda tax has an effect on health and health care costs. Findings: The 1-cent-per-ounce soda tax reduced the number of obesity cases, diabetes, and related complications. In addition, the soda tax policy brought large amounts of revenue. Meaning: This study provides additional evidence regarding the health care costs and cost-effectiveness related to the implementation of a soda tax.
Lower expression of BIN1's neuronal isoform in vulnerable excitatory neurons increases risk in Alzheimer's disease
Authors: Ranganathan Rajesh , Li Siwen , Sapozhnikov Georgy , Wang Shoutang , Song You-Qiang 
Published: January 2025

Background:  Neurons in Alzheimer's disease (AD) experience elevated DNA damage, with DNA repair sites enriched at enhancer regions of genes essential for neuronal survival. Excitatory neurons in the cortical superficial layers expressing CUX2 and RORB (Cux2+/Rorb+), are selectively vulnerable in AD, but their relationship to single nucleotide polymorphisms (SNPs) in AD genome-wide association studies (GWAS) is unclear. Objective:  This study aimed to identify and characterize functional AD-GWAS SNPs using single-nucleus RNA sequencing data, focusing on selectively vulnerable neurons and DNA repair hotspots. Methods:  Filters were applied to identify candidate SNPs based on overlap with repair hotspots, RNA expression, transcription factor binding, AD association, and epigenetic significance. In vitro assays and analyses of large datasets from bulk RNA-seq (n = 1894), proteomics (n = 400), and single-nucleus RNA-seq (n = 424, 1.6 M cells) were conducted. Results:  BIN1 SNP, rs78710909, met multiple criteria - located in an AD-GWAS locus, repair hotspot, and promoter region. rs78710909C exhibits 1.52× higher AD risk and 5.4× differential transcription factor binding. In vitro, rs78710909C shows greater enhancer activity and weaker p53 but stronger E2F1 binding. BIN1's neuronal isoform is neuroprotective, but its AD expression is lower (p < 0.01). Moreover, only in AD and Cux2+/Rorb + neurons, rs78710909C is associated with a lower average BIN1 neuronal isoform ratio (p < 0.01). The genes upregulated in neurons with lower neuronal isoform ratio were associated with the hallmarks of AD pathology. Conclusions:  In a disease-relevant mechanism, the BIN1 SNP rs78710909C is associated with a lower ratio of BIN1's neuronal isoform which increases the vulnerability of specific excitatory neurons in AD patients.
Sleep disturbances and their correlation with memory impairment in patients with Alzheimer's disease and amnestic mild cognitive impairment
Authors: Cui Linyang , Wan Yahui , Lu Yunyao , Meng Meng , Zhang Nan 
Published: January 2025

Background Episodic memory impairment is the core clinical feature of patients with typical Alzheimer's disease (AD) at an early stage. Since sleep plays a very important role in memory consolidation, the relationship between memory impairment and sleep disorders in AD patients is worthy of investigation. Objective To investigate sleep disturbances and their correlations with memory impairment in patients with AD and amnestic mild cognitive impairment (aMCI). Methods Forty-three patients with AD, 43 patients with aMCI, and 43 cognitively unimpaired controls (CUCs) were recruited and subjected to memory assessment via the Hopkins Verbal Learning Test–Revised and objective sleep evaluation via polysomnography (PSG). Results The total sleep time and the percentages of nonrapid eye movement (NREM) sleep stage 3 (N3) and the rapid eye movement (REM) were lower, while the percentages of NREM sleep stage 2 (N2) were greater in the AD and aMCI groups than in the CUC group (all p < 0.01). Compared with the CUC group, the AD group also presented a longer sleep latency and higher NREM sleep stage 1 (N1) percentage, apnea-hypopnea index (AHI), periodic limb movements during sleep index (PLMSI), and arousal index (AI). Both total learning scores and delayed recall scores were positively correlated with the N3 sleep percentage and negatively correlated with the AHI and PLMSI (all p < 0.01). Recognition scores were positively correlated with the N3 sleep percentage and negatively correlated with the AI (all p < 0.01). Conclusions Our results suggest that sleep disturbance is correlated with learning and memory disability in AD and aMCI patients. PSG is useful for screening and monitoring AD.
Natural language processing to identify suicidal ideation and anhedonia in major depressive disorder
Authors: Vance L. Alexander , Way Leslie , Kulkarni Deepali , Palmer Emily O. C. , Ghosh Abhijit , Unruh Melissa , Chan Kelly M. Y. , Girdhari Amey , Sarkar Joydeep 
Published: January 2025

Abstract

Background
Anhedonia and suicidal ideation are symptoms of major depressive disorder (MDD) that are not regularly captured in structured scales but may be captured in unstructured clinical notes. Natural language processing (NLP) techniques may be used to extract longitudinal data on suicidal behaviors and anhedonia within unstructured clinical notes. This study assessed the accuracy of using NLP techniques on electronic health records (EHRs) to identify these symptoms among patients with MDD.

Methods
EHR-derived, de-identified data were used from the NeuroBlu Database (version 23R1), a longitudinal behavioral health real-world database. Mental health clinicians annotated instances of anhedonia and suicidal symptoms in clinical notes creating a ground truth. Interrater reliability (IRR) was calculated using Krippendorff’s alpha. A novel transformer architecture-based NLP model was trained on clinical notes to recognize linguistic patterns and contextual cues. Each sentence was categorized into one of four labels: (1) anhedonia; (2) suicidal ideation without intent or plan; (3) suicidal ideation with intent or plan; (4) absence of suicidal ideation or anhedonia. The model was assessed using positive predictive values (PPV), negative predictive values, sensitivity, specificity, F1-score, and AUROC.

Results
The model was trained, tested, and validated on 2,198, 1,247, and 1,016 distinct clinical notes, respectively. IRR was 0.80. For anhedonia, suicidal ideation with intent or plan, and suicidal ideation without intent or plan the model achieved a PPV of 0.98, 0.93, and 0.87, an F1-score of 0.98, 0.91, and 0.89 during training and a PPV of 0.99, 0.95, and 0.87 and F1-score of 0.99, 0.95, and 0.89 during validation.

Conclusions
NLP techniques can leverage contextual information in EHRs to identify anhedonia and suicidal symptoms in patients with MDD. Integrating structured and unstructured data offers a comprehensive view of MDD’s trajectory, helping healthcare providers deliver timely, effective interventions. Addressing current limitations will further enhance NLP models, enabling more accurate extraction of critical clinical features and supporting personalized, proactive mental health care.
Adaptive evolution of stress response genes in parasites aligns with host niche diversity
Authors: Cruz-Laufer Armando J. , Vanhove Maarten P. M. , Bachmann Lutz , Barson Maxwell , Bassirou Hassan , Bitja Nyom Arnold R. , Geraerts Mare , Hahn Christoph , Huyse Tine , Kasembele Gyrhaiss Kapepula , Njom Samuel , Resl Philipp , Smeets Karen , Kmentová Nikol 
Published: January 2025

Abstract

Background
Stress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness. We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses.

Results
We assembled the sequences of 48 stress-related genes and report the first foraging (For) gene orthologs in flatworms. We found duplications of heat shock (Hsp) and oxidative stress genes in Cichlidogyrus compared to Kapentagyrus. We also observed positive selection patterns in genes related to mitochondrial protein import (H
sp) and behaviour (For) in species of Cichlidogyrus infecting East African cichlids—a host lineage under adaptive radiation. These patterns are consistent with a potential adaptation linked to a co-radiation of these parasites and their hosts. Additionally, the absence of cytochrome P450 and kappa and sigma-class glutathione S-transferases in monogenean flatworms is reported, genes considered essential for metazoan life.

Conclusions
This study potentially identifies the first molecular function linked to a flatworm radiation. Furthermore, the observed gene duplications and positive selection indicate the potentially important role of stress responses for the ecological adaptation of parasite species.
The Calicophoron daubneyi genome provides new insight into mechanisms of feeding, eggshell synthesis and parasite-microbe interactions
Authors: Clancy Shauna M. , Whitehead Mark , Oliver Nicola A. M. , Huson Kathryn M. , Kyle Jake , Demartini Daniel , Irvine Allister , Santos Fernanda Godoy , Kajugu Paul-Emile , Hanna Robert E. B. , Huws Sharon A. , Morphew Russell M. , Waite J. Herbert , Haldenby Sam , Robinson Mark W. 
Published: January 2025

Abstract

Background

The rumen fluke, Calicophoron daubneyi, is the major paramphistome species infecting ruminants within Europe. Adult flukes reside within the rumen where they are in direct contact with a unique collection of microorganisms. Here, we report a 1.76-Gb draft genome for C. daubneyi, the first for any paramphistome species.

Results
Several gene families have undergone specific expansion in C. daubneyi, including the peptidoglycan-recognition proteins (PGRPs) and DM9 domain-containing proteins, which function as pattern-recognition receptors, as well as the saposin-like proteins with putative antibacterial properties, and are upregulated upon arrival of the fluke in the microbe-rich rumen. We describe the first characterisation of a helminth PGRP and show that a recombinant C. daubneyi PGRP binds to the surface of bacteria, including obligate anaerobes from the rumen, via specific interaction with cell wall peptidoglycan. We reveal that C. daubneyi eggshell proteins lack L-DOPA typically required for eggshell crosslinking in trematodes and propose that C. daubneyi employs atypical eggshell crosslinking chemistry that produces eggs with greater stability. Finally, although extracellular digestion of rumen ciliates occurs within the C. daubneyi gut, unique ultrastructural and biochemical adaptations of the gastrodermal cells suggest that adult flukes also acquire nutrients via uptake of volatile fatty acids from rumen fluid.

Conclusions
Our findings suggest that unique selective pressures, associated with inhabiting a host environment so rich in microbial diversity, have driven the evolution of molecular and morphological adaptations that enable C. daubneyi to defend itself against microorganisms, feed and reproduce within the rumen.
Potential drug targets for asthma identified through mendelian randomization analysis
Authors: Chen Xingxuan , Shang Yu , Shen Danting , Shi Si , Wen Zhe , Li Lijuan , Chen Hong 
Published: January 2025

Abstract

Background
The emergence of new molecular targeted drugs marks a breakthrough in asthma treatment, particularly for severe cases. Yet, options for moderate-to-severe asthma treatment remain limited, highlighting the urgent need for novel therapeutic drug targets. In this study, we aimed to identify new treatment targets for asthma using the Mendelian randomization method and large-scale genome-wide association data (GWAS).

Methods
We utilized GWAS data from the UK Biobank (comprising 56,167 patients and 352,255 control subjects) and the FinnGen cohort (including 23,834 patients and 228,085 control subjects). Genetic instruments for 734 plasma proteins and 154 cerebrospinal fluid proteins were derived from recently published GWAS. Bidirectional Mendelian randomization analysis, Steiger filtering, colocalization, and phenotype scanning were employed for reverse causal inference detection, further substantiating the Mendelian randomization results. A protein-protein interaction network was also constructed to reveal potential associations between proteins and asthma medications.

Results
Under Bonferroni significance conditions, Mendelian randomization analysis revealed causal relationships between seven proteins and asthma. In plasma, we observed that an increase of one standard deviation in IL1R1[1.30 (95% CI 1.20–1.42)], IL7R[1.07 (95% CI 1.04–1.11)], ECM1[1.03 (95% CI 1.02–1.05)], and CD200R1[1.18 (95% CI 1.09–1.27)] were associated with an increased risk of asthma, while an increase in ADAM19 [0.87 (95% CI 0.82–0.92)] was found to be protective. In the brain, each 10-fold increase in IL-6 sRa [1.29 (95% CI 1.15–1.45)] was associated with an increased risk of asthma, while an increase in Layilin [0.61 (95% CI 0.51–0.73)] was found to be protective. None of the seven proteins exhibited a reverse causal relationship. Colocalization analysis indicated that ECM1 (coloc.abf-PPH4 = 0.953), IL-6 sRa (coloc.abf-PPH4 = 0.966), and layilin (coloc.abf-PPH4 = 0.975) shared the same genetic variation as in asthma.

Conclusion
A causal relationship exists between genetically determined protein levels of IL1R1, IL7R, ECM1, CD200R1, ADAM19, IL-6 sRa, and Layilin (LAYN) and asthma. Moreover, the identified proteins may serve as attractive drug targets for asthma, especially ECM1 and Layilin (LAYN). However, further research is required to comprehensively understand the roles of these proteins in the occurrence and progression of asthma.
Factors affecting communication time in an emergency medical communication centers
Authors: Bensoussan Melisande , Vanier Mathilde , Loeb Thomas , Boutet Jérémie , Lapostolle Frédéric , Reuter Paul-Georges 
Published: January 2025

Abstract

Background
Emergency Medical Communication Centres (EMCCs) play a crucial role in emergency care by ensuring timely responses through telephone triage. However, extended communication times can impede accessibility, patient triage, and decision-making. Identifying the factors influencing communication duration is essential for improving EMCC efficiency.

Objective
This study aims to identify temporal, human, and contextual factors associated with prolonged communication times in an EMCC where decision-making is conducted by physicians.

Methods
We conducted a retrospective observational study of all calls received at a French EMCC between March 1 and December 31, 2019. A total of 108,548 patient medical files were analyzed, excluding calls from medical personnel or hospitals. We examined the total communication time (from call initiation to decision) and the medical communication time (physician involvement). Bivariate and multivariate logistic regressions were used to identify factors associated with prolonged communication times.

Results
The median total communication time was 7 min [IQR 5–11], and the median medical communication time was 3 min [IQR 2–4]. Psychiatric reasons for calling (OR = 1.75) and elderly patients (OR = 1.58) were associated with longer communication times. Calls leading to medical advice (OR = 1.48) and calls during weekends or nighttime were also significant factors. Conversely, calls for trauma or from nursing homes, and those handled by emergency physicians, were associated with shorter durations.

Conclusion
Several factors influence communication times in EMCCs, including patient demographics, reason for the call, and time of day.
Suboptimal but intact integration of Bayesian components during perceptual decision-making in autism
Authors: Fazioli Laurina , Hadad Bat-Sheva , Denison Rachel N. , Yashar Amit 
Published: January 2025

Abstract

Background
Alterations in sensory perception, a core phenotype of autism, are attributed to imbalanced integration of sensory information and prior knowledge during perceptual statistical (Bayesian) inference. This hypothesis has gained momentum in recent years, partly because it can be implemented both at the computational level, as in Bayesian perception, and at the level of canonical neural microcircuitry, as in predictive coding. However, empirical investigations have yielded conflicting results with evidence remaining limited. Critically, previous studies did not assess the independent contributions of priors and sensory uncertainty to the inference.

Method
We addressed this gap by quantitatively assessing both the independent and interdependent contributions of priors and sensory uncertainty to perceptual decision-making in autistic and non-autistic individuals (N = 126) during an orientation categorization task.

Results
Contrary to common views, autistic individuals integrated the two Bayesian components into their decision behavior, and did so indistinguishably from non-autistic individuals. Both groups adjusted their decision criteria in a suboptimal manner.

Limitations
This study focuses on explicit priors in a perceptual categorization task and high-functioning adults. Thus, although the findings provide strong evidence against a general and basic alteration in prior integration in autism, they cannot rule out more specific cases of reduced prior effect – such as due to implicit prior learning, particular level of decision making (e.g., social), and level of functioning of the autistic person.

Conclusions
These results reveal intact inference for autistic individuals during perceptual decision-making, challenging the notion that Bayesian computations are fundamentally altered in autism.