bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentially avoidable mortality among adults with intellectual disability
Authors: Thygesen Lau Caspar , Klitgaard Marie Borring , Sabers Anne , Kjellberg Jakob , Søndergaard Jens , Sørensen Jeppe , Sonne Marie , Juel Knud , Michelsen Susan Ishøy 
Published: August 2024

Abstract
Persons with intellectual disabilities (ID) face pronounced health disparities. The aim of this study was to describe premature mortality by causes of death and avoidable mortality among persons with ID compared to the general Danish population. This study is based on a Danish nationwide cohort of adults (aged 18–74 years) with ID (n = 57 663) and an age- and sex-matched reference cohort (n = 607 097) which was established by linkage between several registers. The cohorts were followed in the Register of Causes of Death between 2000 and 2020. Causes of death were categorized into preventable, treatable, or unavoidable deaths using the OECD/Eurostat classification and furthermore categorized into specific interventions. We compared the observed and expected number of deaths by calculating standardized mortality ratio (SMR). Among persons with ID the number of deaths was 9400 whereof 5437 (58%) were avoidable. SMR for preventable deaths, e.g. by reducing smoking and alcohol intake or by vaccination, was 2.62 (95% CI, 2.51–2.73), and SMR for treatable deaths, e.g. by earlier diagnosis and treatment, was 6.00 (5.72–6.29). Unavoidable mortality was also six-fold increased (SMR = 6.03; 5.84–6.22). Preventable deaths were higher for persons with mild ID compared to severe ID, while treatable and unavoidable mortality were highest for persons with severe ID. The study confirmed that persons with ID have an amplified risk of mortality across all categories. There is a need for competence development of social care and healthcare personnel and reasonable adjustment of health promotion programs and healthcare services for people with ID.
Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus
Authors: Christodoulides Nicholas , Urgiles Veronica L , Guayasamin Juan M , Savage Anna E 
Published: August 2024

Abstract
The genus Pristimantis diversified in the tropical Andes mountains and is the most speciose genus of terrestrial vertebrates. Pristimantis are notable among frogs in that they thrive at high elevations (&gt;2,000 m) and are direct developers without a tadpole stage. Despite their ecological significance, little is known about the genetic and physiological traits enabling their success. We conducted transcriptomic analysis on seven Pristimantis species sampled across elevations in the Ecuadorean Andes to explore three hypotheses for their success: (i) unique genes are under selection relative to all other frogs, (ii) common selection occurs across all direct developers, or (iii) common selection occurs across all high-elevation frog clades. Comparative analysis with 34 frog species revealed unique positive selection in Pristimantis genes related to aerobic respiration, hemostasis, signaling, cellular transportation of proteins and ions, and immunity. Additionally, we detected positive selection across all direct developers for genes associated with oxygenase activity and metal ion binding. While many genes under selection in Pristimantis were not positively selected in other high-elevation frog species, we identified some shared genes and pathways linked to lipid metabolism, innate immunity, and cellular redox processes. We observed more positive selection in duplicated- versus single-copy genes, while relaxed purifying selection was prevalent in single-copy genes. Notably, copy number of an innate immunity complement gene was positively correlated with Pristimantis species elevation. Our findings contribute novel insights into the genetic basis of adaptation in Pristimantis and provide a foundation for future studies on the evolutionary mechanisms leading to direct development and coping with high elevations.
Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing
Authors: Li Yanguo , Lin Chen , Chu Yidian , Wei Zhengyu , Ding Qi , Gu Shanshan , Deng Hongxia , Liao Qi , Shen Zhisen 
Published: August 2024

Abstract
Cancer stem cells (CSCs) constitute a pivotal element within the tumor microenvironment (TME), driving the initiation and progression of cancer. However, the identification of CSCs and their underlying molecular mechanisms in laryngeal squamous cell carcinoma (LSCC) remains a formidable challenge. Here, we employed single-cell RNA sequencing of matched primary tumor tissues, paracancerous tissues, and local lymph nodes from three LSCC patients to comprehensively characterize the CSCs in LSCC. Two distinct clusters of stem cells originating from epithelial populations were delineated and verified as CSCs and normal stem cells (NSCs), respectively. CSCs were abundant in the paracancerous tissues compared to those in the tumor tissues. CSCs showed high expression of stem cell marker genes such as PROM1, ALDH1A1, and SOX4, and increased the activity of tumor-related hypoxia, Wnt/β-catenin, and Notch signaling pathways. We then explored the intricate crosstalk between CSCs and the TME cells and identified targets within the TME that related with CSCs. We also found eight marker genes of CSCs that were correlated significantly with the prognosis of LSCC patients. Furthermore, bioinformatics analyses showed that drugs such as erlotinib, OSI-027, and ibrutinib selectively targeted the CSC-specifically expressed genes. In conclusion, our results represent the first comprehensive characterization of CSC properties in LSCC at the single-cell level.
Computational Strategies and Algorithms for Inferring Cellular Composition of Spatial Transcriptomics Data
Authors: Liu Xiuying , Ren Xianwen 
Published: August 2024

Abstract
Spatial transcriptomics technology has been an essential and powerful method for delineating tissue architecture at the molecular level. However, due to the limitations of the current spatial techniques, the cellular information cannot be directly measured but instead spatial spots typically varying from a diameter of 0.2 to 100 µm are characterized. Therefore, it is vital to apply computational strategies for inferring the cellular composition within each spatial spot. The main objective of this review is to summarize the most recent progresses in estimating the exact cellular proportions for each spatial spot, and to prospect the future directions of this field.
The art of tartness: the genetics of organic acid content in fresh fruits
Authors: Miao Shixue , Wei Xiaoyu , Zhu Lingcheng , Ma Baiquan , Li Mingjun 
Published: August 2024

Abstract
Organic acids are major determinants of fruit flavor and a primary focus of fruit crop breeding. The accumulation of organic acids is determined by their synthesis, degradation, and transport, all of which are manipulated by sophisticated genetic mechanisms. Constant exploration of the genetic basis of organic acid accumulation, especially through linkage analysis, association analysis, and evolutionary analysis, have identified numerous loci in recent decades. In this review, the genetic loci and genes responsible for malate and citrate contents in fruits are discussed from the genetic perspective. Technologies such as gene transformation and genome editing as well as efficient breeding using marker-assisted selection (MAS) and genomic selection (GS) are expected to break the bottleneck of traditional fruit crop breeding and promote fruit quality improvement.
Eosinophil Depletion as a Potential Therapeutic Strategy in Acute and Chronic Intestinal Inflammation Based on a Dextran Sulfate Sodium Colitis Model
Authors: Jacobs Inge , Deleu Sara , Cremer Jonathan , De Hertogh Gert , Vermeire Séverine , Breynaert Christine , Vanuytsel Tim , Verstockt Bram 
Published: August 2024

Abstract

Background
A role for eosinophils in intestinal inflammation and fibrosis in the context of inflammatory bowel disease has been suggested, yet the precise nature, whether causal or secondary remains debated. Hence, it remains unclear whether targeting eosinophils should be further explored as a treatment option in inflammatory bowel disease.

Methods
Acute and chronic dextran sulfate sodium colitis was induced in wild-type C57BL/6 mice. Eosinophils were depleted by anti-CCR3 injections before colitis induction in a chronic model and after colitis onset in an acute model in order to investigate the impact of eosinophil depletion on pre-existing colitis. Inflammation was assessed using the disease activity index, macroscopic damage, and histological disease activity score. In the chronic model, fibrosis was assessed by examining colon weight/length ratio, collagen deposition through Martius Scarlet Blue staining, hydroxyproline assay, and COL1A1 expression. Protein and gene expression were assessed using the Meso Scale Discovery platform and real-time quantitative polymerase chain reaction.

Results
In the acute and chronic colitis model, eosinophil depletion resulted in reduced disease activity and faster recovery, as observed via the total area under the curve of the disease activity index (P = .004 and P = .02, respectively), macroscopic damage score (P = .009 and P = .08, respectively), and histological disease activity score (P = .09 and P = .002, respectively). In the acute model, the accelerated recovery was accompanied by an increase in interleukin (IL)-10 (P = .03) and a decrease in IL-4 (P = .03) and IL-6 (P = .009). Colon weight/length ratio and collagen deposition were not affected by eosinophil depletion.

Conclusions
Eosinophil depletion prevents and decreases intestinal inflammation in a preclinical dextran sulfate sodium model without affecting fibrosis. These results pave the way for exploring eosinophil depletion as a novel treatment modality in addressing intestinal inflammation.
Assessing the Value of Histology and Anatomic Segment Evaluation Among Patients Undergoing Pouchoscopy
Authors: Dave Mili , Power Sydney , Herfarth Hans H , Barnes Edward L 
Published: August 2024

Abstract

Background
The value of histologic assessment after ileal pouch-anal anastomosis (IPAA) has not been definitively determined. We evaluated the correlation between histology and endoscopic findings, as well as the proportion of patients with inflammation in areas beyond the pouch body on their initial pouchoscopy after IPAA.

Methods
In a retrospective cohort study, we evaluated patients who underwent IPAA for UC between 2012 and 2020 and subsequently underwent a pouchoscopy with routine biopsies of the pouch body, pre-pouch ileum, and rectal cuff. We compared endoscopic and histologic assessments in each location using χ2 testing and Spearman correlation, as well as the development of pouchitis and Crohn’s-like disease of the pouch (CLDP) in longitudinal follow-up.

Results
Among 126 patients, the median time to pouchoscopy after IPAA was 384 days, with 82 patients (65%) having inflammation of the pouch body. Significantly more patients with pouch body inflammation had histologic inflammation compared with patients without pouch body inflammation (96% vs 22%, P &lt; .001, r = 0.769). Additionally, 16 patients (13%) were found to have endoscopic inflammation of the pre-pouch ileum with corresponding histologic inflammation in 88%; of these, 31% later developed CLDP. In contrast, 13% of patients with no endoscopic inflammation displayed histologic inflammation, with none later developing CLDP. Forty-six percent of patients had rectal cuff inflammation (correlation with histologic inflammation r = 0.580).

Conclusions
In our evaluation, the added benefit of histology in the presence of visible endoscopic inflammation for disease activity assessment scores is unclear. The prognostic value of histologic inflammation without endoscopic inflammation warrants a longitudinal study.
Predicting trawl catches using environmental DNA
Authors: Guri Gledis , Shelton Andrew Olaf , Kelly Ryan P , Yoccoz Nigel , Johansen Torild , Præbel Kim , Hanebrekke Tanja , Ray Jessica Louise , Fall Johanna , Westgaard Jon-Ivar 
Published: August 2024

Abstract
Quantifying the biomass, or number of individuals, diversity, and distribution of marine species is a critical aspect of understanding and managing marine ecosystems. In recent years, there has been growing interest in using environmental DNA (eDNA) for marine ecosystem management and biodiversity assessment. However, the main challenge hindering eDNA applicability has been the inability to infer absolute species abundances from multispecies analysis (eDNA metabarcoding). In this study, we demonstrate a way forward by estimating the abundance of commercially important fish species in a Norwegian fjord using a joint Bayesian statistical model of traditional trawl-catch data and molecular data derived from eDNA. Using this model, we accurately predict out-of-sample trawl catches using eDNA alone. Moreover, our model provides empirical estimates for key processes linking marine eDNA concentration to the fish population abundance estimated from trawl observations, including trawl catchability, DNA shedding, degradation, dilution, transport, recovery rate, and isolation efficiency. These processes, including amplification efficiencies correcting for Polymerase Chain Reaction (PCR) bias, are species-specific and enable the translation of eDNA metabarcoding data into abundances. These findings have broad implications for the use of eDNA in marine ecosystem management and conservation efforts.
Outcomes of surgical ablation for atrial fibrillation in on- versus off-pump coronary artery bypass grafting
Authors: Vroomen Mindy , Franke Ulrich , Senges Jochen , Friedrich Ivar , Fischlein Theodor , Lewalter Thorsten , Ouarrak Taoufik , Niemann Bernd , Liebold Andreas , Hanke Thorsten , Doll Nicolas , Albert Marc 
Published: August 2024

Abstract

OBJECTIVES
A considerable number of patients undergoing coronary artery bypass grafting surgery suffer from atrial fibrillation and should be treated concomitantly. This manuscript evaluates the impact of on-pump versus off-pump bypass grafting on the applied lesion set and rhythm outcome.

METHODS
Between January 2017 and April 2020, patients who underwent combined bypass grafting and surgical ablation for atrial fibrillation were consecutively enrolled in the German CArdioSurgEry Atrial Fibrillation registry (CASE-AF, 17 centres). Data were prospectively collected. Follow-up was planned after one year.

RESULTS
A total of 224 patients were enrolled. No differences in baseline characteristics were seen between on- and off-pump bypass grafting, especially not in type of atrial fibrillation and left atrial size. In the on-pump group (n = 171, 76%), pulmonary vein isolation and an extended left atrial lesion set were performed more often compared to off-pump bypass grafting (58% vs 26%, 33 vs 9%, respectively, P &lt; 0.001). In off-pump bypass grafting a box isolating the atrial posterior wall was the dominant lesion (72% off-pump vs 42% on-pump, P &lt; 0.001). Left atrial appendage management was comparable in on-pump versus off-pump bypass grafting (94% vs 91%, P = 0.37). Sinus rhythm at follow-up was confirmed in 61% in the on-pump group and in 65% in the off-pump group (P = 0.66). No differences were seen in in-hospital or follow-up complication-rates between the two groups.

CONCLUSIONS
In coronary artery bypass grafting patients undergoing concomitant atrial fibrillation ablation, our data suggests that the technique applied for myocardial revascularization (off-pump vs on-pump) leads to differences in the ablation lesion set, but not in safety and effectiveness.
Vaccine Effectiveness Against Anal HPV Among Men Who Have Sex With Men Aged 18–45 Years Attending Sexual Health Clinics in 3 United States Cities, 2018–2023
Authors: DeSisto Carla L , Winer Rachel L , Querec Troy D , Dada Damilola , Pathela Preeti , Asbel Lenore , Lin John , Tang Jennifer , Iqbal Alfred , Meites Elissa , Unger Elizabeth R , Markowitz Lauri E 
Published: August 2024

Abstract

Background
We assessed human papillomavirus (HPV) vaccine effectiveness (VE) against anal HPV among men who have sex with men (MSM) in 2018–2023.

Methods
Residual anal specimens from MSM without HIV aged 18–45 years were tested for HPV. We calculated adjusted prevalence ratios (aPR) and 95% confidence intervals (CI) for associations between vaccination (≥1 dose) and quadrivalent vaccine (4vHPV)-type prevalence adjusting for city, race/ethnicity, and nonvaccine-type HPV prevalence, stratified by age group (18–26, 27–45 years). VE was calculated as (1 − aPR) × 100.

Results
Among 2802 persons aged 18–26, 4vHPV-type prevalence was lower in those vaccinated at age &lt;18 (aPR = 0.13; 95% CI, .08–.22; VE = 87%) and those vaccinated ≥2 years before specimen collection (aPR = 0.52; 95% CI, .42–.64; VE = 48%) compared with unvaccinated persons. Among 3548 persons aged 27–45, 4vHPV-type prevalence was lower in those vaccinated at ages 18–26 (aPR = 0.68; 95% CI, .57–.82; VE = 32%) and those vaccinated ≥2 years before specimen collection (aPR = 0.66; 95% CI, .57–.77; VE = 33%) compared with unvaccinated persons. While we observed no VE in persons vaccinated at age &gt;26 overall, 4vHPV-type prevalence was lower in the subgroup vaccinated ≥2 years before specimen collection (aPR = 0.71; 95% CI, .56–.89; VE = 29%).

Conclusions
We found high VE against anal 4vHPV-type prevalence among MSM aged 18–26 who were vaccinated at age &lt;18. Lower VE was observed among MSM aged 27–45 who were vaccinated at age 18–26 or ≥2 years before specimen collection. While ideally vaccination should be given at younger ages, vaccination can prevent some future infections in this population.
Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses
Authors: Berrios Louis , Venturini Andressa M , Ansell Tillson Bertie , Tok Esther , Johnson William , Willing Claire E , Peay Kabir G 
Published: August 2024

Abstract
Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.
Leveraging multi-site electronic health data for characterization of subtypes: a pilot study of dementia in the N3C Clinical Tenant
Authors: Sharma Suchetha , Liu Jiebei , Abramowitz Amy Caroline , Geary Carol Reynolds , Johnston Karen C , Manning Carol , Van Horn John Darrell , Zhou Andrea , Anzalone Alfred J , Loomba Johanna , Pfaff Emily , Brown Don 
Published: August 2024

Abstract

Objectives
To provide a foundational methodology for differentiating comorbidity patterns in subphenotypes through investigation of a multi-site dementia patient dataset.

Materials and Methods
Employing the National Clinical Cohort Collaborative Tenant Pilot (N3C Clinical) dataset, our approach integrates machine learning algorithms—logistic regression and eXtreme Gradient Boosting (XGBoost)—with a diagnostic hierarchical model for nuanced classification of dementia subtypes based on comorbidities and gender. The methodology is enhanced by multi-site EHR data, implementing a hybrid sampling strategy combining 65% Synthetic Minority Over-sampling Technique (SMOTE), 35% Random Under-Sampling (RUS), and Tomek Links for class imbalance. The hierarchical model further refines the analysis, allowing for layered understanding of disease patterns.

Results
The study identified significant comorbidity patterns associated with diagnosis of Alzheimer's, Vascular, and Lewy Body dementia subtypes. The classification models achieved accuracies up to 69% for Alzheimer's/Vascular dementia and highlighted challenges in distinguishing Dementia with Lewy Bodies. The hierarchical model elucidates the complexity of diagnosing Dementia with Lewy Bodies and reveals the potential impact of regional clinical practices on dementia classification.

Conclusion
Our methodology underscores the importance of leveraging multi-site datasets and tailored sampling techniques for dementia research. This framework holds promise for extending to other disease subtypes, offering a pathway to more nuanced and generalizable insights into dementia and its complex interplay with comorbid conditions.

Discussion
This study underscores the critical role of multi-site data analyzes in understanding the relationship between comorbidities and disease subtypes. By utilizing diverse healthcare data, we emphasize the need to consider site-specific differences in clinical practices and patient demographics. Despite challenges like class imbalance and variability in EHR data, our findings highlight the essential contribution of multi-site data to developing accurate and generalizable models for disease classification.
Does ostracism/rejection impact self-disclosures? Examining the appeal of perceived social affordances after social threat
Authors: Grady Sara M , Eden Allison , Tamborini Ron 
Published: August 2024

Abstract
Two studies examine how experiencing a social need threat (ostracism and rejection) impacts subsequent preferences for self-disclosure to various digital audiences. Findings consider how contextual/situational factors like need threats may impact the appeal of two established perceived social affordances of media: personalization and privacy/visibility. Participants took part in a (bogus) social media activity to elicit feelings of inclusion/ostracization/rejection and then were asked about sharing their media preferences with various potential audiences. Results show that social need threats have no significant impact on privacy preferences but do affect preferences for sharing with some audiences and not others. Notably, ostracized and rejected participants show different patterns of preferences, suggesting these forms of social need threat may have distinct impacts on future self-disclosures. Implications for online relationship development and community building are considered in the discussion.