bluuebunny/crossref_metadata_2025_split huggingface dataset:
CrossIsoFun: predicting isoform functions using the integration of multi-omics data
Authors: Liu Yiwei , Li Hong-Dong , Wang Jianxin 
Published: December 2024

Abstract

Motivation
Isoforms spliced from the same gene may carry distinct biological functions. Therefore, annotating functions at the isoform level provides valuable insights into the functional diversity of genomes. Since experimental approaches for determining isoform functions are time- and cost-demanding, computational methods have been proposed. In this case, multi-omics data integration helps enhance the model performance, providing complementary insights for isoform functions. However, current methods underperform in leveraging diverse omics data, primarily due to the limited power to integrate the heterogeneous feature domains. Besides, among the multi-omics data, isoform-isoform interactions (IIIs) are a key data source, as isoforms interact with each other to perform functions. Unfortunately, IIIs remain largely underutilized in isoform function predictions until now.

Results
We introduce CrossIsoFun, a multi-omics data analysis framework for isoform function prediction. CrossIsoFun combines omics-specific and cross-omics learning for data integration and function prediction. In detail, CrossIsoFun uses a graph convolutional network (GCN) as the omics-specific classifier for each data source. The initial label predictions from GCNs are forwarded to the View Correlation Discovery Network (VCDN) and processed as a cross-omics integrative representation. The representation is then used to produce final predictions of isoform functions. In addition, an antoencoder within a cycle-consistency generative adversarial network (cycleGAN) is designed to generate IIIs from PPIs and thereby enrich the interactomics data. Our method outperforms the state-of-the-art methods on three tissue-naive datasets and 15 tissue-specific datasets with mRNA expression, sequence, and PPI data. The prediction of CrossIsoFun is further validated by its consistency with subcellular localization and isoform-level annotations with literature support.

Availability and implementation
CrossIsoFun is freely available at https://github.com/genemine/CrossIsoFun.
Matching the general or the specific child with a foster home?
Authors: Järkestig Berggren Ulrika , Engwall Kristina , Bask Miia , Bergman Ann-Sofie 
Published: December 2024

Abstract
Matching a child with a foster home is a professional practice with considerable room for discretion since there are no specific guidelines in Sweden. The aim is to describe what knowledge do social workers’ assessments build upon in the matching process. The material consists of matching investigation files of 116 children from 6 municipalities in Sweden. A data form was used to assemble excerpts of descriptions of the child’s needs and how the family would be expected to meet the child’s needs. The findings show that social workers describe the child’s basic needs in line with the theory of Maslow and the ability of foster parents to form attachment and take a child perspective. Specific needs of the child are motioned regarding medical diagnoses and challenging behaviour of the child. This focus on basic needs is due to several circumstances, a shortage of available foster homes and that the matching social worker seldom meets the child, hence the child’s interests and wishes are seldom known. Implications for practice concern the right for children to be involved in the decision-making process and for the social worker to take in to account the specific needs of the child.
Increased cell-free DNA in CSF and serum of hip fracture patients with delirium
Authors: Bratseth Vibeke , Watne Leiv Otto , Neerland Bjørn Erik , Halaas Nathalie Bodd , Pollmann Christian Thomas , Karabeg Adi , Odegaard Olav Tobias , Sydnes Kristian , Zetterberg Henrik , Seljeflot Ingebjørg , Helseth Ragnhild 
Published: December 2024

Abstract
Delirium is a neuropsychiatric syndrome commonly presenting during acute illness. The pathophysiology of delirium is unknown, but neuroinflammation is suggested to play a role. In this cross-sectional study, we aimed to investigate whether cell-free DNA and markers of neutrophil extracellular traps in serum and CSF were associated with delirium and neuronal damage, assessed by neurofilament light chain. Hip fracture patients (n = 491) with a median (25, 75 percentiles) age of 83 (74, 88) years and 69% females were enrolled at Oslo University Hospital, Diakonhjemmet Hospital, Akershus University Hospital and Bærum Hospital. Delirium was assessed daily, pre- and postoperatively. Cognitively healthy adults (n = 32) with a median (25, 75 percentiles) age of 75 (70, 77) years and 53% females were included as controls. Cell-free DNA was measured by using the fluorescent nucleic acid stain Quant-iT PicoGreen® in serum and CSF. Myeloperoxidase-DNA and citrullinated histone H3 were analysed by enzyme-linked immunosorbent assay in serum. Hip fracture patients have significantly higher levels of cell-free DNA and neutrophil extracellular traps in blood than cognitively healthy controls. In hip fracture patients without dementia, cell-free DNA in CSF and serum was significantly higher in patients with (n = 68) versus without (n = 221) delirium after adjusting for age and sex (70 (59, 84) versus 62 (53, 77) ng/ml, P = 0.037) and 601 (504, 684) versus 508 (458, 572) ng/ml, P = 0.007, respectively). In the total hip fracture cohort, CSF levels of cell-free DNA and neurofilament light chain were significantly correlated after adjusting for age and sex (r = 0.441, P &lt; 0.001). The correlation was stronger in those with delirium (r = 0.468, P &lt; 0.001) and strongest in delirious patients without dementia (r = 0.765, P = 0.045). In delirious patients without dementia, significantly higher levels of cell-free DNA in CSF and serum were shown. The association between cell-free DNA and neurofilament light chain suggest simultaneous release of cell-free DNA and neuronal damage during delirium.
Bibliometric analysis of studies investigating the association between isotretinoin use and depression and suicide
Authors: Ünlü Açıkel Sezin , Sadettin Burak Açıkel 
Published: December 2024

Abstract

Background
Acne vulgaris has significant effects on the emotional and social wellbeing of an affected individual, leading to conditions like anxiety, depression and social isolation. Oral isotretinoin has been associated with various side-effects, including psychiatric concerns like depression and suicidal ideation. However, the connection between isotretinoin and these mental health issues remains controversial.

Objectives
To provide an overview of the literature on the subject by investigating data such as the effects of articles in the field on the literature as a whole, coauthorship and citation analysis.

Methods
A bibliometric analysis was conducted using the Web of Science database to search for studies from 1986 to 2024 with keywords related to isotretinoin, suicide and depression. Data were analysed using VOSviewer software to visualize the bibliometric networks and trends.

Results
For the study, 380 publications were identified, with a peak in 2018. The most common article types were original articles (60.3%), reviews (13.9%) and letters (12.1%). English is the predominant language of publication (93.4%). The h-index of these articles was 49, with an average of 23.0 citations per article. The top research areas included dermatology, pharmacology and psychiatry. The analysis highlights key authors and their contributions to the field.

Conclusions
The bibliometric analysis has revealed an evolving research landscape. The number of studies has increased since 2004, following the Food and Drug Administration’s black box warning in 2005. While early studies linked isotretinoin to psychiatric issues, recent data have shown a stronger association between acne and these conditions rather than the medication itself. This analysis underscores the importance of continuous research and re-evaluation of clinical guidelines based on emerging evidence.
Exit Interviews Exploring Patients’ Experience of Change in Crohn’s Disease Symptoms During the Mirikizumab Phase 3 Clinical Trial In Adult Patients With Moderately-to-Severely Crohn’s Disease
Authors: Hunter Gibble Theresa , Macey Jake , Makin Harriet , Rosu Rodica , Mellor Katie , Kitchen Helen , Hon Emily , Dubinsky Marla 
Published: December 2024

Abstract

Background
Exit interviews with patients who completed the Phase 3 VIVID-1 mirikizumab clinical trial for moderately-to-severely active Crohn’s disease explored the content validity of bowel urgency, stool frequency, and abdominal pain patient-reported outcome measures and perceptions of meaningful within-patient change and remission in these key Crohn’s disease symptoms.

Methodology
Cognitive debriefing explored patient understanding of the bowel urgency numeric rating scale (Urgency NRS), Crohn’s Disease Activity Index: Stool Frequency (CDAI-SF) and Abdominal Pain (CDAI-AP), and patient global rating/impression of severity/change (PGRS/PGIC). Perceptions of meaningful change and remission were explored qualitatively. Transcripts were analyzed using directed content and framework analysis.

Results
Interviewed participants (N = 62; mean age 44.8 years, 55% female, mean 12.0 years since Crohn’s disease diagnosis) were from the United States (n = 29), Czech Republic (n = 10), Poland (n = 8), Germany (n = 7), Canada (n = 4), Australia (n = 3), and the United Kingdom (n = 1). Participants understood the Urgency NRS, CDAI-SF, and CDAI-AP and could use them to rate their bowel urgency, stool frequency, and abdominal pain. Participants considered these symptoms when responding to the PGRS/PGIC. Meaningful change was described as symptom relief resulting in the ability to live daily life without pain or fear/need of rushing to the toilet. Most participants agreed with a proposed remission definition of ≤3 type 6/7 bowel movements and None/Mild abdominal pain.

Discussion
The Urgency NRS, CDAI-SF, and CDAI-AP are content-valid patient-reported outcome measures in Crohn’s disease. The PGRS/PGIC are conceptually related global assessments of bowel urgency, stool frequency, and abdominal pain. Patients considered reduction in these symptoms as meaningful and remission.
Multiple Ileal and Colonic Stenoses: Is It Always Crohn’s Disease?
Authors: Bencardino Sarah , Allocca Mariangela , Furfaro Federica , D’Amico Ferdinando , Parigi Tommaso Lorenzo , Danese Silvio , Zilli Alessandra 
Published: December 2024

Abstract
A 62-year-old woman presented with multiple ileal and colonic stenoses, initially suspected to be Crohn’s disease. Despite unremarkable endoscopic biopsies, surgery was performed due to clinical deterioration, and histological analysis confirmed the presence of metastatic breast cancer. This case highlights the importance of considering metastatic disease in the differential diagnosis of gastrointestinal (GI) strictures, particularly when inflammatory bowel disease markers are inconclusive or marginal. Clinicians should be aware of the potential for breast cancer to metastasize to the GI tract, which may present with symptoms mimicking primary GI diseases.
Catheter ablation of atrial flutter in an adult with a univentricular heart, common atrium, and single atrioventricular valve: a case report—‘complex things don’t always require a complex solution’
Authors: Ortíz-Avalos Martín , Galindo-Garza Silvia Melissa , Chavez-Collazos Chris Keith , Andrade-Cuellar Elias Noel , Rodríguez-Diez Gerardo 
Published: December 2024

Abstract

Background
The ‘univentricular’ heart encompasses a variety of congenital cardiac defects characterized by a single functional ventricle and an underdeveloped ventricular chamber. Surgical intervention, typically in infancy or childhood, aims to regulate pulmonary blood flow volume. In adulthood, untreated patients may experience limitations in physical activity and elevated morbidity due to persistent cyanosis and arrhythmias, notably after the Fontan procedure.

Case summary
A 38-year-old Mexican man with an unrepaired morphologically right single ventricle and a common atrium presented with palpitations. Diagnostic imaging revealed a hypertrophic systemic single ventricle with severe atrioventricular valve regurgitation and pulmonary stenosis. Despite ongoing anticoagulant and beta-blocker therapy, persistent symptoms prompted catheter ablation guided by CARTO-Merge®, a function that overlays computed tomography or magnetic resonance imaging onto a CARTO® electroanatomical map. Ablation along the cavo-annular isthmus was successfully performed, achieving arrhythmia termination. Post-ablation, the patient developed sinus rhythm and second-degree atrioventricular block, necessitating the implantation of an epicardial pacemaker.

Discussion
Atrial flutter ablation in univentricular hearts without prior surgery is rare. Such patients are predisposed to post-Fontan arrhythmias, often requiring intervention due to increased morbidity. Atrial flutter arises from scarred post-surgery regions, necessitating careful assessment and management. Our case demonstrates successful ablation in a complex congenital heart condition, highlighting the importance of comprehensive imaging, understanding arrhythmia mechanisms, and meticulous procedural techniques for optimal outcomes.
Aberration correction—impact on image quality and chamber quantification in transthoracic echocardiography
Authors: Berg Erik Andreas Rye , Espeland Torvald , Dalen Håvard , Grenne Bjørnar , Bjåstad Tore Grüner , Holte Espen , Måsøy Svein-Erik 
Published: December 2024

Abstract

Aims
To improve image quality (IQ) in echocardiography, an aberration correction (AC) algorithm has recently been implemented in commercial scanners. We aimed to study (i) the correlation of a subjective IQ-score and an objective IQ-metric [global image coherence (GIC)], (ii) if AC improved IQ; (iii) if AC affected average values and interobserver agreement of left ventricular (LV) size, LV longitudinal strain, and left atrial (LA) volume.

Methods and results
From 50 adult patients, where 45 (90%) had cardiovascular disease, unprocessed image data (channel data) were acquired from six standard transthoracic views. The data were processed with and without AC, resulting in 300 pairs of cine-loops. The cine-loops were randomly presented one-by-one to two blinded raters experienced in echocardiography. Both raters scored IQ subjectively from 1 (poor) to 4 (very good) and quantified LV dimensions, volumes and longitudinal strain, and LA volume. IQ-score correlated with GIC, Spearman rho 0.72, P &lt; 0.001. AC improved median IQ-score from 2.5 to 3.0 (Wilcoxon signed rank: P &lt; 0.001). The differences in average values of LV size, LV longitudinal strain, or LA volume with and without AC were not statistically significant and numerically minimal. Measured by intraclass correlation, interobserver agreement of these values was not significantly affected by AC.

Conclusion
Image quality-score strongly correlated with GIC. Aberration correction improved IQ. However, AC did not lead to statistically significant changes in average values or interobserver agreement of LV size, LV longitudinal strain or LA volume quantification. Likely, the major benefit of AC is enhanced visualization of anatomical details.
Sex-specific immunocompetence: resistance and tolerance can both be futile but not under the same circumstances
Authors: Brenninger Franziska A , Kovalov Viktor , Kokko Hanna 
Published: December 2024

Abstract
Immunocompetence evolution can involve a “resistance is futile” scenario if parasite encounter rates are so high that high investment in resistance only marginally delays infection. Here, we investigate two understudied aspects of “futility”: the mode of immunocompetence and sexual selection. First, immunocompetence is usefully categorized as reducing the rate of becoming infected (resistance) or reducing the negative fitness consequences of infection once it happened (tolerance). We compare the prospects of futility for resistance, tolerance, and their joint occurrence, showing that resistance futility arises with respect to parasite encounter rates, while tolerance futility arises with respect to parasite virulence. However, if the same host trait improves pleiotropically both resistance and tolerance, futility disappears altogether and immunity investment remains profitable when increasing parasite encounter rates, virulence, or both. Second, we examine how sexual selection strength impacts these findings. If one sex (typically males) is near the faster end of a fast-slow continuum of life histories, then life history patterns reflecting futility can evolve sex-specificity. The solutions often feature sexual dimorphism in immunocompetence, but not always in the direction of strong sexual selection yielding low immunity: sexual selection can select for faster and “sicker” lives, but if sexual selection also favors traits that impact parasite encounter rates, the results are strongly dependent on whether futility (along any axis) plays a role.
Meanings and Roles of Great-Grandparenthood: A Scoping Review
Authors: Talašová Zuzana , Souralová Adéla 
Published: December 2024

Abstract

Background and Objectives
Great-grandparenthood brings a new internal dynamic to intergenerational relationships in which contact between four generations is now the norm. In this scoping review, we sought to identify the roles of great-grandparents and what those roles entail.

Research Design and Methods
We performed a review using PRISMA-ScR to identify peer-reviewed studies investigating the roles of great-grandparents. The reviewed articles were selected from four databases. The article selection conditions were met by 23 studies that used quantitative or qualitative methods. The studies had to be published in English; the selected publications spanned eight countries.

Results
The scoping review covers a collection qualitative and quantitative research with different types of respondents (great-grandchild, grandparents, great-grandparents, etc.). An important element was a statement on great-grandparenting from at least one of the four generations. We selected 23 articles from an initial selection of 176 studies. The studies were heterogeneous in conceptual frameworks, collection methods, and interview conduct, with qualitative methods predominating over quantitative methods.

Discussion and Implications
Based on research on great-grandparenting, the roles of great-grandparents can be categorized as continuing, insignificant, or significant. Each role category has a specific function and each represents a different meaning for the great-grandparents within the family. Several factors and constraints frame the great-grandparent roles. Based on the research results, some characteristics are shared by all role categories despite the dividing elements.
Opaque ontology: neuroimaging classification of ICD-10 diagnostic groups in the UK Biobank
Authors: Easley Ty , Luo Xiaoke , Hannon Kayla , Lenzini Petra , Bijsterbosch Janine 
Published: December 2024

Abstract

Background
The use of machine learning to classify diagnostic cases versus controls defined based on diagnostic ontologies such as the International Classification of Diseases, Tenth Revision (ICD-10) from neuroimaging features is now commonplace across a wide range of diagnostic fields. However, transdiagnostic comparisons of such classifications are lacking. Such transdiagnostic comparisons are important to establish the specificity of classification models, set benchmarks, and assess the value of diagnostic ontologies.

Results
We investigated case-control classification accuracy in 17 different ICD-10 diagnostic groups from Chapter V (mental and behavioral disorders) and Chapter VI (diseases of the nervous system) using data from the UK Biobank. Classification models were trained using either neuroimaging (structural or functional brain magnetic resonance imaging feature sets) or sociodemographic features. Random forest classification models were adopted using rigorous shuffle-splits to estimate stability as well as accuracy of case-control classifications. Diagnostic classification accuracies were benchmarked against age classification (oldest vs. youngest) from the same feature sets and against additional classifier types (k-nearest neighbors and linear support vector machine). In contrast to age classification accuracy, which was high for all feature sets, few ICD-10 diagnostic groups were classified significantly above chance (namely, demyelinating diseases based on structural neuroimaging features and depression based on sociodemographic and functional neuroimaging features).

Conclusion
These findings highlight challenges with the current disease classification system, leading us to recommend caution with the use of ICD-10 diagnostic groups as target labels in brain-based disease prediction studies.
‘The Strength Even to Comprehend the Incomprehensible’: Rereading Adorno in the Age of Authoritarian Resurgence
Authors: Bakiner Onur 
Published: December 2024

ABSTRACT∞
This article reappraises Theodor W. Adorno’s call for ‘working through the past’ as an ethical practice in the wake of Auschwitz, and as a prescriptive model for rebuilding the collective, by situating Adorno’s 1959 lecture ‘What Does Coming to Terms with the Past Mean?’ and 1966 lecture ‘Education after Auschwitz’ in the totality of his corpus. Adorno’s reflections reveal the effort to build a positive political project in the wake of catastrophe, but its ethical demands on present generations complicate any practical proposal to address the past. Heralding contemporary transitional justice theory and practice in important ways, fruitful tensions in his lectures reveal the inherent difficulty of reckoning with past wrongs: rebuilding ethical life in the wake of Auschwitz presupposes the impossibility of a foundational metaphysics; understanding and overcoming past wrongs runs the risk of trivializing and relativizing them; and history should be understood as the unfolding of constellations of given conditions.