bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncRNA H19 promoted alcohol-associated liver disease through dysregulation of alternative splicing and methionine metabolism
Authors: Yang Zhihong , Jiang Yanchao , Ma Jing , Wang Li , Han Sen , Huda Nazmul , Kusumanchi Praveen , Gao Hui , Thoudam Themis , Sun Zhaoli , Liangpunsakul Suthat 
Published: August 2024

Background and Aims:Long noncoding RNAs constitute a significant portion of the human genome. Among these, lncRNA H19, initially identified for its high expression during fetal development followed by a decline in the liver postnatally, re-emerges in various liver diseases. However, its specific role in alcohol-associated liver disease (ALD) remains unclear.Approach and Results:Elevated H19 levels were detected in peripheral blood and livers of patients with alcohol-associated cirrhosis and hepatitis, as well as in livers of ethanol-fed mice. Hepatic overexpression of H19 exacerbated ethanol-induced liver steatosis and injury. Metabolomics analysis revealed decreased methionine levels in H19-overexpressed mouse livers, attributable to H19-mediated inhibition of betaine homocysteine methyltransferase (BHMT), a crucial enzyme in methionine synthesis. H19 regulated BHMT alternative splicing through polypyrimidine tract-binding protein 1 (PTBP1), resulting in a reduced Bhmt protein-coding variant. The maternally specific knockout of H19 (H19Mat+/−) or liver-specific knockout of the H19 differentially methylated domain (H19DMDHep−/−) in ethanol-fed mice upregulated BHMT expression and ameliorated hepatic steatosis. Furthermore, BHMT restoration counteracted H19-induced ethanol-mediated hepatic steatosis.Conclusions:This study identifies a novel mechanism whereby H19, via PTBP1–mediated BHMT regulation, influences methionine metabolism in ALD. Targeting the H19-PTBP1-BHMT pathway may offer new therapeutic avenues for ALD.
Length of hospital stay and its predictors among burn patients in a resource limited setting: a multicenter prospective longitudinal study
Authors: Baraka Samuel Mandro , Kiswezi Ahmed , Edyedu Isaac , Molen Selamo Fabrice , Muhumuza Joshua , Kyomukama Lauben , Zawadi Gift Vulwaghe , Okedi Xaviour Francis 
Published: August 2024

Introduction:
There is a paucity of data relating to length of hospital stay (LOS) among burn patients managed in hospitals with no burn units, yet this constitute a big percentage of hospitals in low-income countries. This study was aimed at determining the predictors of length of stay at three hospitals in a resource limited setting.

Methods:
This was a prospective longitudinal multicentre study that enrolled burn patients with moderate and severe burns according to the American Burn Association (ABA) admitted at three tertiary hospitals in western Uganda. Follow up was done till discharge. LOS and its predictors were determined using logistic regression in SPSS version 26. The cut off for prolonged hospital stay was a length of stay above the median which was 8 days.

Results:
This study included 101 patients with majority in the age bracket of 18–55 (56.4%). Majority were males (69.3%) from a rural setting (61.4%) and were accidentally burnt (95.0%) at home (75.2%). The median LOS was 8 days. The variables that independently predicted increased LOS were receiving medical attention after 12 h (P=0.002), burn severity according to the ABA (P=0.017), and type of procedure done (P<0.001).

Conclusion:
The factors independently associated with increased LOS were; time to medical attention, burn severity, and type of procedure done. Measures to ensure timely medical attention can reduce the length of stay among patients with burns even in the absence of a burn unit.
Antegrade and retrograde laser excision and ureterotomy laser for ureteral polyp causing total ureteral stenosis following left ureteral stones removal: a case report and literature review
Authors: Yusuf Krisna A. W. , Atmoko Widi , Rahman Fakhri , Birowo Ponco , Rasyid Nur 
Published: August 2024

Background:
Ureteral polyps are rare, and the clinical manifestations are typically nonspecific. Obstruction from ureteral polyps can lead to ureteral stone formation. Excision using a less invasive approach is the most commonly performed procedure. Here, the authors report a patient with left proximal and distal ureteral polyps treated with laser excision after removal of the right kidney and left ureteral stone using a combined antegrade and retrograde route. This case is interesting because there was complete ureteral blockage, and polyps were found on the proximal and distal sides of the stenotic area.

Case Presentation:
A 55-year-old female patient came to our center with bilateral flank pain. Initially, the diagnosis was bilateral hydronephrosis, but after ureteroscopy (URS) was performed, proximal and distal ureteral polyps were identified. The polyp was excised using a Thulium laser, followed by DJ-stent placement.

Discussion:
Imaging with intravenous pyelography, CT, or retrograde urography can help diagnose ureteral polyps. Removal of the polyp’s base using ureteroscopy with laser coagulation allows for identification and histologic diagnosis. Endoscopic treatment has become the most commonly used treatment for ureteral polyps.

Conclusion:
Ureteral polyps are rare, and preoperative diagnosis may be difficult. Laser excision with stent placement after primary polyp removal has been reported in many studies to have good outcomes.
Eradicating the Loneliness Epidemic: One Phone Call at a Time
Authors: Feldmiller Ethan , Messner Lynnae , Gona Sridhar Rao , Joshi Maulik 
Published: August 2024

ABSTRACT
Loneliness and social isolation are serious problems that can impose negative consequences on individual well-being. Research suggests that loneliness can lead to an increased risk of depression, anxiety, and other health issues. Meritus Health, recognizing that loneliness is an issue within its community, has set a goal to comprehensively eradicate loneliness. As part of this effort, Meritus implemented the Care Caller program in November of 2021 through which a volunteer is paired up with a patient from our institution who has indicated that they are lonely. Each duo then finds a weekly cadence to share in 15- to 30-minute phone calls to facilitate meaningful social interaction. As of July 2023, the program has 500 participants enrolled with 47 volunteers and 2 full-time employees, and over 350 people are called weekly. In the last fiscal year, over 75,000 minutes have been spent on the phone between care callers and participants with promising results. Of the 172 participants who have been in the program for 4+ months, 166 have indicated that they felt less lonely, yielding a success rate of 97%. Meritus Health continues to further this program by increasing the number of care callers and utilization of Plan-Do-Study-Act rapid improvement.
Challenges Meeting 21st Century Cures Act Patient Identity Interoperability and Information Blocking Rules
Authors: Gellert George A. , Erwich Mark E. , Krivicky Herdman Sara 
Published: August 2024

ABSTRACT

Objective:
Gather insights into healthcare organization (HCO) preparedness for new 21st Century Cures Act information blocking disincentives and challenges in achieving greater accuracy /interoperability of patient identity/data.

Methods:
Survey of 197 U.S. healthcare executives (54.7% response rate), included 46 health systems (23.4%), 141 hospitals (71.6%), and 10 payer organizations (5.1%), evaluated organizational gaps in patient identity data management/interoperability and preparation for information deblocking.

Results:
Healthcare organizations are unprepared to meet information deblocking requirements and manage increased data influx/exchange. Although 61% have invested in meeting requirements, only 36% have capabilities in place. Majorities reported inability to comply with information blocking rules (59%), communicate electronic patient activity notifications to other organizations (56%), or share/receive patient-level information with patients and other HCOs (57%). Across 12 critical functionalities, 57% lacked key capabilities; 97% reported inadequate patient data/identity management/interoperability as data volume expands, adversely affecting care quality/safety and outcomes; and 57% envision patient data-matching errors precipitating a healthcare crisis in 5–10 years.

Conclusions:
Many HCOs are unprepared to meet new Cures Act information blocking requirements and resultant increase of internal/external patient data volumes. Next generation master data management, enterprise master patient index, and referential matching technologies can improve HCO patient identity and data management, and information interoperability.
Functional traits and soil water availability shape competitive interactions in a diploid-polyploid complex
Authors: Rodríguez-Parra Alba , López-Jurado Javier , Mateos-Naranjo Enrique , Balao Francisco 
Published: August 2024

SummaryEven within those polyploid plant species that become established initially, only a few persist in the long term. Competitive interactions between polyploids and their ancestral cytotypes in secondary contact zones can contribute to local extinctions. Environmental factors such as water availability and functional trait divergence may influence these interactions.We conducted a greenhouse competition experiment with four cytotypes (2x, 4x, 6x, and 12x) ofDianthus broteriunder two contrasting irrigation regimes. We estimated niche and fitness differences and predicted the pairwise competitive outcomes. Additionally, we explored the influence of leaf physiological functional traits (SLA, AN, gs, LDMC, Fv/Fm, andiWUE) on competitive interactions.Soil water availability modified the competitive dynamics between cytotypes and predicted competitive exclusion. Under high water availability, lower ploidy levels (2x and 4x) outcompeted higher ploidy cytotypes (12x, 6x), while the latter exhibited greater competitive abilities under low water availability. These differences were explained by functional traits related to competitive effects (SLA) and competition tolerance (AN, Fv/Fm, andiWUE).Synthesis:Our study emphasizes that the long-term fate of polyploids largely depends on water availability, with high polyploids having a competitive advantage in arid environments. This ultimately highlights the role of functional traits in shaping the competitive dynamics between cytotypes.
Chronic intermittent alcohol yields sex-specific disruptions in cortical-striatal-limbic oscillations
Authors: Hewitt Kelly A. , Nicholson Skylar E. , Peterson Madilyn J. , Dwiel Lucas L. , Henricks Angela M. 
Published: August 2024

ABSTRACTBackgroundWhile the neurobiology of alcohol use disorder (AUD) has been extensively researched, the vast majority of these studies included only male organisms. However, there are significant sex differences in both the causes and consequences of alcohol misuse and dependence, suggesting sex-specific neurobiological mechanisms. The current study used a rodent model to determine whether chronic alcohol exposure impacts sex-specific neural circuits, and whether these changes contribute to the development of alcohol misuse.MethodsMale and female Sprague-Dawley rats were trained to self-administer 10% alcohol before implanting bilateral electrodes into the infralimbic medial prefrontal cortex (IL), nucleus accumbens shell (NAcSh), and central nucleus of the amygdala (CeA). Half of the rats were then exposed to four weeks of chronic intermittent alcohol (CIA) vapor (14 hours on/10 hours off). During acute withdrawal (6-8 after the vapor turns off), local field potentials (LFPs) were recorded from the IL, NAcSh, and CeA during 30-minute self-administration sessions. Using an unbiased machine learning approach, we built predictive models to determine whether/which LFP features could distinguish CIA-exposed from control rats in each sex, as well as if any of these LFP features correlated with rates of alcohol self-administration.ResultsFemale rats self-administered more alcohol in general compared to males, but only males exposed to CIA showed increased alcohol intake during acute withdrawal. LFPs predicted CIA exposure in both sexes better than chance estimates, but models built on IL and NAcSh oscillations performed the best in males, while models built on IL and CeA LFPs performed best in females. High γ LFPs recorded in the NAcSh correlated with rates of alcohol self-administration in males exposed to CIA, while only left-right NAcSh β coherence correlated with drinking in control females.ConclusionsThese data provide support for the hypothesis that the neural circuits driving alcohol dependence development are sex-specific, and that high frequency oscillations in the NAcSh may be related to the increased drinking observed in males exposed to CIA. Overall, these data add to our understanding of the neurobiological underpinnings behind the sex differences observed in AUD and offer promising biomarkers for future therapeutic research.
An explainable graph neural network approach for effectively integrating multi-omics with prior knowledge to identify biomarkers from interacting biological domains
Authors: Tripathy Rohit K. , Frohock Zachary , Wang Hong , Cary Gregory A. , Keegan Stephen , Carter Gregory W. , Li Yi 
Published: August 2024

AbstractThe rapid growth of multi-omics datasets, in addition to the wealth of existing biological prior knowledge, necessitates the development of effective methods for their integration. Such methods are essential for building predictive models and identifying disease-related molecular markers. We propose a framework for supervised integration of multi-omics data with biological priors represented as knowledge graphs. Our framework leverages graph neural networks (GNNs) to model the relationships among features from high-dimensional ‘omics data and set transformers to integrate low-dimensional representations of ‘omics features. Furthermore, our framework incorporates explainability methods to elucidate important biomarkers and extract interaction relationships between biological quantities of interest. We demonstrate the effectiveness of our approach by applying it to Alzheimer’s disease (AD) multi-omics data from the ROSMAP cohort, showing that the integration of transcriptomics and proteomics data with AD biological domain network priors improves the prediction accuracy of AD status and highlights functional AD biomarkers.
Spatiotemporal Decomposition of Whole-Brain Alpha Traveling Waves
Authors: Li Yichao , Hong Bo 
Published: August 2024

AbstractSpontaneously emerging traveling waves are present within the spatiotemporal patterns of alpha-band EEG oscillations, but current analysis methods are limited in parsing the diversity of global wave structures and their correlation with brain functions. To address this limitation, we constructed a rigorous mathematical framework, Weakly Orthogonal Conjugate Contrast Analysis (WOCCA), which decomposes the whole-brain EEG alpha oscillations into directionally independent traveling waves. For the first time, we systematically characterized propagating components in alpha-band resting-state EEG as a combination of rotational, longitudinal, and horizontal traveling wave patterns. The intensity, directionality, and morphological characteristics of these wave patterns account for the differences between cognitive states during rest and consciousness levels under sedation. Moreover, our WOCCA decomposition encompassed the state transition dynamics captured by EEG Microstate Analysis, a conventional analysis framework for alpha waves. These results not only established a novel approach for identifying and analyzing traveling waves but also provided evidence for the relationship between wave directionality and cooperative interactions in brain network.
Validating genuine changes in Heartbeat Evoked Potentials using Pseudotrials and Surrogate Procedures
Authors: Steinfath Paul , Herzog Nadine , Fourcade Antonin , Sander Christian , Nikulin Vadim , Villringer Arno 
Published: August 2024

AbstractThe brain continuously receives interoceptive information about the state and function of our internal organs. For instance, each time the heart beats, the brain responds by generating time-locked activity, known as heartbeat evoked potentials (HEP). When investigating HEPs, it is essential to adequately control for heartbeat-independent confounding activity to avoid false interpretation. In the present study, we highlight the pitfalls of uncontrolled analyses and advocate for the use of surrogate heartbeat analysis and pseudotrial correction, which are promising tools to control for spurious results. Surrogate heartbeat analysis involves shuffling the timing of heartbeats to verify the time-locking of HEP effects. Pseudotrial correction works by subtracting heartbeat-independent activity from HEPs. In this study we employ both procedures, validate them in simulations and apply them to real EEG data. Using EEG recordings obtained during the performance of an auditory novelty oddball task in a large population, we show that, without control analyses, pre-stimulus HEPs appear inversely related to task-related measures such as P300 event-related potential amplitudes and reaction time speed. However, these effects disappear after carefully controlling for heartbeat-unrelated EEG activity. Additionally, in real and simulated data, we show that pseudotrial correction has the potential to remove task-related confounds from HEPs, thereby uncovering real heartbeat-related effects that otherwise could be missed. This study therefore highlights issues that can arise when analyzing HEPs during tasks, provides solutions to overcome them, and gives recommendations for future studies to avoid pitfalls when analyzing and designing behavioral paradigms with HEPs.
Ischemic lesions to inferior frontal cortex alter the dynamics of conscious visual perception
Authors: Fritsch M. , Michely J. , Jaeckel L. , Rangus I. , Riegler C. , Scheitz J. , Nolte CH , Sterzer P. , Weilnhammer V. 
Published: August 2024

AbstractWhether the prefrontal cortex is part of the neural correlates of conscious visual perception has been subject to longstanding debate. Recent work, using functional magnetic resonance imaging (fMRI) and repetitive transcranial magnetic stimulation (rTMS) to induce virtual lesions, has illustrated a key role of the right inferior frontal cortex (IFC) in the detection and resolution of perceptual ambiguities. Here, we sought to validate an active role of the IFC in conscious perception by evaluating how loss-of-function in patients with ischemic stroke in this region influences processing of ambiguous visual information. To this end, twenty-three patients (11 female, mean age 70.65 ± 1.2 years) with chronic (>6 months), right-hemispheric ischemic stroke lesions within the MCA-territory (9 patients with IFC lesions, 14 without) performed a bistable perception task, having to report the perceived direction of rotation of an ambiguous random-dot-kinematogram (RDK). As hypothesized, patients with IFC lesions showed significantly fewer perceptual changes compared to patients without IFC lesions (IFC 44.9 ± 46.3 s, non-IFC 28.2 ± 37.1 s, T(182.9) =3.1, p = 2.2 x 10-3). Importantly, this effect remained significant when controlling for age, sex, stroke severity and lesion volume (T(5.97) = −2.9, p =0.026). Our results support the notion that the IFC is crucial for resolving perceptual ambiguities, suggesting an active role of frontal cortex in shaping conscious visual experience.
funkea: Functional Enrichment Analysis in Python
Authors: Tenmann Benjamin , Close Karina , Rodriguez-Martinez Andrea , Abujudeh Samer 
Published: August 2024

AbstractAdvancements in Genome-wide association studies (GWAS) have led to the discovery of numerous genetic variants potentially linked to various traits, necessitating effective methods to interpret and summarise these vast data sets. We introducefunkea, a Python package designed to fill this need by providing functional enrichment analysis methods. This tool encompasses popular enrichment approaches under a unified interface and leverages Spark for virtually limitless scale. This allows researchers to conduct pathway, cell-type, and tissue enrichment analysis across diverse annotation datasets. Ultimately, thefunkeaPython package delivers a highly flexible and scalable solution for functional enrichment analysis in the context of modern genetics workflows.https://github.com/BenevolentAI/funkea
Multimodal 3D Image Registration for Mapping Brain Disorders
Authors: Mahmood Hassan , Islam Syed Mohammed Shamsul , Iqbal Asim 
Published: August 2024

AbstractWe introduce an AI-driven approach for robust 3D brain image registration, addressing challenges posed by diverse hardware scanners and imaging sites. Our model trained using an SSIM-driven loss function, prioritizes structural coherence over voxel-wise intensity matching, making it uniquely robust to inter-scanner and intra-modality variations. This innovative end-to-end framework combines global alignment and non-rigid registration modules, specifically designed to handle structural, intensity, and domain variances in 3D brain imaging data. Our approach outperforms the baseline model in handling these shifts, achieving results that align closely with clinical ground-truth measurements. We demonstrate its efficacy on 3D brain data from healthy individuals and dementia patients, with particular success in quantifying brain atrophy, a key biomarker for Alzheimer’s disease and other brain disorders. By effectively managing variability in multisite, multi-scanner neuroimaging studies, our approach enhances the precision of atrophy measurements for clinical trials and longitudinal studies. This advancement promises to improve diagnostic and prognostic capabilities for neurodegenerative disorders.
Glymphatic clearance is enhanced during sleep
Authors: Kroesbergen Erik , Riesselmann Laurence V. , Gomolka Ryszard S. , Plá Virginia , Esmail Tina , Stenmo Visti H. , Kovács E. Rebeka , Nielsen Elise S. , Goldman Steven A. , Nedergaard Maiken , Weikop Pia , Mori Yuki 
Published: August 2024

AbstractWe here revisited the concept that glymphatic clearance is enhanced by sleep and anesthesia. Utilizing dynamic magnetic resonance imaging (MRI), single photon emission computed tomography (SPECT), and fluorescent fiber photometry, we report brain glymphatic clearance is enhanced by both sleep and anesthesia, and sharply suppressed by wakefulness. Another key finding was that less tracer enters the brains of awake animals and that brain clearance across different brain states can only be compared after adjusting for the injected tracer dose.