bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptomic score to classify the inflammation-dysplasia-cancer sequence lesions in Inflammatory Bowel Disease
Authors: Cremer Anneline , Rosewick Nicolas , Kelsey Maxfield , Trépo Eric , Libert Frédérick , De Vos Martine , Baert Filip , Moreels Tom , Louis Edouard , Rahier Jean-François , Demetter Pieter , Sedivy John M , Vermeire Séverine , Franchimont Denis 
Published: February 2025

Abstract

Background and aims
Inflammatory bowel disease (IBD) is associated with a higher risk of developing colorectal cancer, according to the inflammation-dysplasia-cancer (IDC) sequence from inflammation to colitis-associated colorectal cancer (CAC). The objective of this study was to identify and generate a transcriptomic signature and score, related to the IDC sequence, that could ultimately classify dysplasia and cancer in IBD.

Methods
Demographics, clinical parameters, histological characteristics and RNA-sequencing data were evaluated on 134 formalin-fixed paraffin-embedded lesions from 2 independent cohorts of IBD patients with low- or high-grade dysplasia (LGD, HGD) and/or CAC. An ordinal logistic regression screened for significant IDC sequence-associated genes that were computed in a transcriptomic signature score.

Results
Principal component analysis and unsupervised clustering on 1% of the most variable genes showed a good clustering between the 4 lesion groups (Normal Mucosa, Inflamed Mucosa, LGD/HGD, and CAC). A gene signature was identified on 27 genes that correlated with the lesion groups in the exploratory cohort. The most weighted gene in this transcriptomic signature was the long non-coding regulatory RNA KCNQ1OT1, a gate keeper against genomic instability and transposon activation. Based on these 27- genes expression, we built and validated a transcriptomic signature score to classify dysplasia and CAC. The overall accuracy of the transcriptomic signature score was 85.71% in the exploratory cohort and 90.91% in the validation cohort.

Conclusion
We identified a tissue-based transcriptomic score to classify IDC lesions in IBD patients and uncovered some of the pivotal genes in the carcinogenesis related to inflammation in IBD.
Incremental value of multiparametric cardiac magnetic resonance imaging for non-invasive identification of significant acute cardiac allograft rejection: a prospective and biopsy-proven study
Authors: Zhou Pengyu , Dong Zhixiang , Hu Xiaoying , Yang Shujuan , Wang Jiaxin , Ma Xuan , Tang Yun , Xu Jing , Wei Zhuxin , Jia Xi , Chen Xingrui , Liu Yujie , Xiang Xiaorui , Huang Jie , Zhao Shihua 
Published: February 2025

Abstract

Aims
This study aimed to evaluate the association between cardiac magnetic resonance imaging (CMR) multiparameters and significant acute cardiac allograft rejection (SR), and assess the incremental value of CMR multiparameters over conventional serum examinations for identifying SR.

Methods and results
Heart transplantation (HTx) recipients with endomyocardial biopsy and healthy controls were prospectively recruited for CMR assessment. CMR feature tracking was performed to evaluate the left ventricular (LV) global strain in all three directions. The last serum examinations including N-terminal pro-brain natriuretic peptide (NT-proBNP) before anti-rejection therapy were recorded. Participants were divided into three groups: control, SR [acute cellular rejection grade ≥ 2R and/or antibody-mediated rejection (AMR) grade ≥ pAMR1], and NSR (non-SR). Finally, 30 controls (43.3 ± 13.6 years, 26 males) and 51 HTx recipients comprising 23 SRs (48.6 ± 12.6 years, 24 males) and 28 NSRs (42.7 ± 14.9 years, 16 males) were enrolled for analysis. Compared with NSRs, SRs showed elevated NT-proBNP (7797.0 ± 7527.6 pg/mL vs. 3334.6 ± 5935.3 pg/mL, P &lt; 0.001), worse LV global longitudinal strain (GLS) (−9.7 ± 3.1% vs. −13.1 ± 2.9%, P &lt; 0.001), and increased native T1 (1384 ± 80.1 ms vs. 1321 ± 69.9 ms, P &lt; 0.001) and T2 values (50.9 ± 2.7 ms vs. 45.7 ± 4.3 ms, P &lt; 0.001). In multivariable analysis, LVGLS (OR = 0.76, 95% CI, 0.59–0.98, P = 0.03) and T2 value (OR = 1.35, 95% CI, 1.10–1.65, P = 0.01) were independently associated with SR after NT-proBNP adjustment. Furthermore, the likelihood ratio test showed LVGLS (P = 0.002) and T2 value (P &lt; 0.001) had incremental value over NT-proBNP for identifying SR.

Conclusion
LVGLS and T2 value were independently associated with SR, providing incremental value for non-invasive identification of significant rejection in HTx recipients.
Prospective seaweed systems for North-West European waters
Authors: Zaat Loekie M , van den Burg Sander W K , Ketelaar Tijs , Koppenberg Maximilian , Möhring Niklas , Meuwissen Miranda P M 
Published: February 2025

Abstract
Seaweed is a potential source of sustainable food, feed, cosmetics, biomaterials, and biostimulants. Seaweed is currently mainly grown in Asia, and it is unclear which seaweed systems are best suited for North-West European waters. We use an expert workshop and a written feedback round to identify prospective seaweed systems, including the cultivation site and post-harvest stages, for three different contexts. Independent of the context, there is a preference for cultivating multiple species and having a high level of automation. Depending on the context, the optimal choice with regards to scale, substrate, seeding technique, and the integration of seaweed farming with (shell)fish species differs. Profitability of the systems, availability of (large-scale) processing facilities and ships to go offshore, uncertainty of buyers, and obstacles in seed stock availability, permits, and building infrastructures present key challenges and risks. The identified seaweed systems serve as input to the policy debate around alternative resource production in Europe and can help in developing standards for seaweed system design. Furthermore, researchers and technology providers can use the prospective systems for future profitability assessments and directions for technology developments.
INFLAMMATORY CYTOKINES DURING PREGNANCY PREDICT POSTPARTUM ANXIETY: FINDINGS FROM A PROSPECTIVE PREGNANCY COHORT
Authors: Rommel *Anna Sophie , Gigase Frederieke , Kaplan Carly 
Published: February 2025

Abstract

Background
Studies have linked inflammation with both depression and anxiety disorders. Pregnancy confers large- scale immune changes, and elevated inflammatory cytokines (particularly IL-1b and IL-6) during pregnancy have been associated with postpartum depression. However, the relationship between pregnancy cytokines and postpartum anxiety has not been thoroughly explored.

Methods
We included 716 participants from Generation C, a prospective pregnancy cohort in New York City (recruited from April 2020 - February 2022). Anxiety symptoms were assessed 1-8 months postpartum via the Generalized Anxiety Disorder (GAD) questionnaire. Cytokine levels were measured in blood from routine draws throughout pregnancy. Using quantile regressions, the relationship between cytokine levels (log-transformed) and continuously measured postpartum anxiety symptoms was investigated separately for 4 cytokines (IL-6, IL-17A, IL-1b, and CRP). The analyses were adjusted for maternal race/ethnicity, maternal education, parity, SARS-CoV-2 infection status during pregnancy, and GAD response timing.

Results
Participants' mean age was 33.0 (SD=4.91). 74 (10.34%) individuals were Asian, 85 (11.87%) were,192 (26.82%) Hispanic, and 327 individuals (45.67%) were white. Mean GAD score was 2.9 (SD=3.6), and 43 (6%) participants scored above the clinical cutoff (&gt;10) for moderate/high anxiety. After adjustment, IL-17A was significantly associated with increased GAD score at the 75% quantile (b=0.70, SE=0.24, p=0.004). IL-6, IL-1b and CRP were not significantly associated with postpartum anxiety.

Conclusion
These findings suggest a significant link between pregnancy inflammation and postpartum anxiety among those experiencing the highest anxiety symptoms. While specific mechanisms require further exploration, this relationship not only advances our understanding of postpartum mental health but may also encourage investigation into novel applications of anti-inflammatory medications in the field of psychiatry.
SLOW BUT STEADY: ORAL KETAMINE AS AN EFFECTIVE ADJUNCT IN DEPRESSION, ANXIETY AND PTSD
Authors: Sulis *William 
Published: February 2025

Abstract
Intravenous and intranasal Ketamine have become important options for the rapid relief of symptoms in PTSD, Suicidality and in Treatment Resistant Depression and Anxiety. However, they are costly, require at least an out- patient clinic setting and have relatively short lived benefits. I present a pilot study examining 8 patients treated with oral Ketamine, 5 mg/kg for 12 treatments. Treatment was well tolerated with mild to moderate hypertension and drowsiness the main side effects. Treatment response during the administration phase was minimal to modest at best. Nevertheless over subsequent weeks, 7 subjects experienced significant improvement in symptom severity and daily function which has persisted for nearly 18 months in follow up. One subject dropped out. Oral Ketamine warrants further study as a possible adjunctive treatment in resistant cases.
STRUCTURAL, FUNCTIONAL, AND METABOLIC SIGNATURES OF POSTPARTUM DEPRESSION: A SYSTEMATIC REVIEW
Authors: Horakova *Anna , Nemcova Hana , Mohr Pavel , Sebela Antonin 
Published: February 2025

Abstract

Objective
Postpartum depression (PPD) is a serious condition with debilitating consequences for the mother, offspring, and the whole family. The scope of negative outcomes of PPD highlights the need to specify effective diagnostics and treatment which might differ from major depressive disorder (MDD). In order to improve our clinical care, we need to better understand the underlying neuropathological mechanisms of PPD. Therefore, we conducted a systematic review of published neuroimaging studies assessing functional, structural, and metabolic correlates of PPD.

Methods
Relevant papers were identified using a search code for English-written studies in the PubMed, Scopus, and Web of Science databases published by March 2022. Included were studies with structural magnetic resonance imaging, functional magnetic resonance imaging, both resting-state and task-related, magnetic resonance spectroscopy, or positron emission tomography. The findings were analyzed to assess signatures in PPD- diagnosed women compared to healthy controls. The review protocol was registered in PROSPERO (CRD42022313794).

Results
The total of 3,368 references were initially identified. After the removal of duplicates and non-applicable papers, the search yielded 74 full-text studies assessed for eligibility. Of them, 26 met the inclusion criteria and their findings were analyzed and synthesized. The results showed consistent functional, structural, and metabolic changes in the default mode network and the salient network in women with PPD. During emotion-related tasks, PPD was associated with changes in the corticolimbic system activity, especially the amygdala.

Discussion
This review offers a comprehensive summary of neuroimaging signatures in PPD-diagnosed women. It indicates the brain regions and networks which show functional, structural, and metabolic changes. Our findings offer better understanding of the nature of PPD, which clearly copies some features of MDD, while differs in others.
IMPACT OF CHILDHOOD MALTREATMENT ON COGNITIVE FUNCTION IN YOUNG ADULTS
Authors: Lee *Sang Won , Kim Kyungmin , Kim Min Seok 
Published: February 2025

Abstract

Background
Childhood maltreatment could have a negative impact on emotional1 and cognitive2 development, and it can be vulnerable factors for mental illness.

Aim & Objectives
This study aimed to demonstrate the effects of maltreatment on cognitive function in young adults by using various cognitive measurements, including computerized test.

Methods
We recruited 149 healthy individuals with and without maltreatment experiences and conducted the Wechsler Adult Intelligence Scale IV (WAIS-IV) and computerized battery for measuring cognitive function. To evaluate childhood maltreatment experiences, we used the Early Trauma Inventory Self Report-Short Form (ETISR-SF).

Results
Among the WAIS-IV subscales, the perceptual reasoning, working memory, and processing speed scores were lower after controlling for age, sex, education, and depressive symptoms in the maltreatment group than in the no-maltreatment group (all, p &lt;0.01, Table 1). Among the cognitive function variables measured by CNS-VS, psychomotor speed, reaction time, cognitive flexibility, processing speed, executive function, working memory, sustained attention, and motor speed were significantly lower in the maltreatment group than in the no-maltreatment group (all, p &lt;0.05).

Discussion & Conclusion
This study highlights the childhood maltreatment effects on cognitive function in young adulthood. Also, our results suggest that cognitive interventions for cognitive function in individuals with a history of childhood maltreatment could be effective for enhancing the resilience of the individuals.

References
Teicher, M. H., &Samson, J. A. (2016). Annual Research Review: Enduring neurobiological effects of childhood abuse and neglect. J Child Psychol Psychiatry, 57, 241-266. Su, Y. Y., D'Arcy, C., Yuan, S., &Meng, X. F. (2019). How does childhood maltreatment influence ensuing cognitive functioning among people with the exposure of childhood maltreatment? A systematic review of prospective cohort studies. Journal of Affective Disorders, 252, 278-293.
Applying the Human Factors Analysis and Classification System (HFACS) within Root Cause Analysis (RCA) to Prevent Medical Errors and Enhancing Patient Safety Culture: Insights from a Medical Center
Authors: Lee Jiun-Yih , Huang Chien-Hsien , Sie Yi-An , Yang Pei-Ching , Su Chun-Cheng , Chang Jui-Ting 
Published: February 2025

Abstract
Introduction: Enhancing patient safety and minimizing medical errors are crucial in healthcare. While Root Cause Analysis (RCA) is commonly used to investigate adverse events, its lack of human factors integration limit its effectiveness. The Human Factors Analysis and Classification System (HFACS), adapted from aviation to healthcare, systematically identifies human and organizational factors. However, the integration of HFACS into RCA and the impact of HFACS-RCA implementation remain underexplored. Therefore, this study aims to: provide a practical case of HFACS integration into RCA and explore the effects of HFACS-RCA implementation.
Methodology: This study integrates HFACS into the RCA process at a medical center in Taiwan, examining an incident involving unsterilized instruments distributed from the Central Sterile Supply Room (CSR) to the ICU. This study employed a before-and-after study design to examine the impact of the HFACS-RCA intervention. The primary outcome measures were the changes in scores across the eight dimensions of the Taiwan Patient Safety Culture Survey (TPSC) before and after the intervention.
Results: A one-year follow-up of the CSR case showed no similar incidents. HFACS-RCA significantly improved TPSC scores in unit safety climate (p=0.05), feelings towards management (p=0.05), and job satisfaction (p=0.05), while the other dimensions showed no significant changes.
Conclusion: HFACS-RCA application offers a comprehensive framework for identifying and mitigating factors contributing to medical errors, improving patient safety, and setting a precedent for future healthcare safety management research and practice.
Indirect effects of the COVID-19 pandemic on healthcare contacts, quality of care, and social disparities across essential healthcare domains
Authors: Knudsen Søren Valgreen , Jensen Henry , Mainz Jan , Baandrup Lone , Gögenur Ismail , Jensen Jens Winther , Johnsen Søren Paaske , Lassen Jens Flensted , Løkke Anders , Mackenhauer Julie , Mortensen Laust Hvas , Møller Henrik , Olesen Tina Bech 
Published: February 2025

Abstract

Background
The COVID-19 pandemic significantly affected global healthcare systems, revealing their resilience to crises. Despite this, national-level research on its impact across key healthcare domains—such as acute and chronic disease management, cancer screening and care, mental health, and palliative care—is scarce. This study examines the pandemic’s impact on contacts, quality of care, and social disparity in these healthcare domains to guide better preparedness for future health emergencies.

Methods
The study utilized data from the Danish National Clinical Quality Registries, covering January 2015 to June 2022, to create a nationwide cohort for comparing healthcare metrics across the pandemic’s phases and the prepandemic period. Healthcare contacts were assessed through descriptive analyses, while the quality of care and social disparities were analysed using multivariable regression models, providing estimated prevalence ratios and 95% confidence intervals.

Results
The first wave of the COVID-19 pandemic in Denmark led to community and healthcare lockdowns, which were associated with fewer hospital contacts and reduced participation in national cancer screening programs. However, a gradual recovery towards prepandemic levels was found, with the exceptions of chronic obstructive pulmonary disease contacts and colorectal cancer incidence. Overall, the quality of care across various healthcare domains in Denmark remained largely unchanged or improved slightly during the pandemic. However, social disparities in contacts were increased across all examined healthcare domains, with patients who were immigrants, living alone, had limited educational level or low income experiencing reduced contact compared to the prepandemic period.

Conclusions
Overall, the Danish healthcare system appeared to be resilient and largely unaffected throughout the pandemic, and the quality of care in several healthcare domains remained high. Nevertheless, the increasing social disparities in healthcare contacts during the pandemic demands attention. In preparing for future health crises, it is important to address and mitigate potential social inequalities, focusing on achieving equity in healthcare.
Extracting Herbrand systems from refutation schemata
Authors: Leitsch Alexander , Lolic Anela 
Published: February 2025

Abstract
An inductive proof can be represented as a proof schema, i.e. as a parameterized sequence of proofs defined in a primitive recursive way. A corresponding cut-elimination method, called schematic cut-elimination by resolution, can be used to analyse these proofs, and to extract their (schematic) Herbrand sequents, even though Herbrand’s theorem in general does not hold for proofs with induction inferences. This work focuses on the most crucial part of the schematic cut-elimination method, which is to construct a refutation of a schematic formula that represents the cut-structure of the original proof schema. We develop a new framework for schematic substitutions and define a unification algorithm for resolution schemata. Moreover, we introduce a new calculus for the refutation of formula schemata that is simpler and more expressive than previous formalisms. Finally, we show that this new formalism allows the extraction of a structure from the refutation schema, called a Herbrand system, which represents its Herbrand sequent.
Phylogeography Analysis Reveals Rabies Epidemiology, Evolution, and Transmission in the Philippines
Authors: Zhang Liang , Cruz Jeffrey , Tian Yao , Wang Yuyang , Jiang Jianfeng , Gonzales Riva Marie , Azul Rachel R , Peña Rainelda C Dela , Sun Sheng , Liu Yan , Jiang Tao , Fang Liqun , Tu Changchun , Gong Wenjie , Feng Ye 
Published: February 2025

Abstract
Rabies, caused by rabies virus, is a severe public health problem in the Philippines, where animal rabies epidemiology had been extensively investigated, but little is known about the national epidemiologic situations since 2010. Here, we report a 12-year nationwide animal rabies surveillance with systematic phylogenetic analysis, in which 353 whole genomes of rabies viruses collected from animal rabies cases between 2018 and 2022 were obtained. The phylogenetic and spatial–temporal evolutionary analyses showed that rabies viruses in the Philippines were exclusively classified into the SEA4 subclade within the Asian clade, but forming three major geographically specific lineages. Intra-island spread predominates the rabies transmission in three major island regions, while the inter-island transmission, between major island regions, is very limited, likely due to ocean barriers. Overall, our findings have provided the most comprehensive dataset on the infected animal species, geographic distribution, transmission dynamics, genetic diversity of rabies viruses, and transmission risk factors, thus established a basis to support WOAH-endorsed national control program for dog-mediated rabies in the Philippines.
VEXAS syndrome through a rheumatologist’s lens: insights from a Spanish national cohort
Authors: García-Escudero Paula , López-Gómez Marta , López Berta Magallares , Dorta Alicia García , Frade-Sosa Beatriz , Lizarzaburu Meritxell Sallés , Rúa-Figueroa Íñigo , Fiallo Dolly Viviana , Toyos Sáenz de Miera Francisco Javier , Melero-Gonzalez Rafael Benito , Dios Santos Diego , Miranda José Alberto , Belando Clara García , Boselli Giuliano , Boteanu Alina Lucica , Villalobos Lourdes , Selaya Cristina Corrales , Sieiro Santos Cristiana , Álvarez Elvira Díez , Font Judit , Alonso Elena Riera , Araguás Ernesto Trallero , Merayo Eugenia Enríquez , Rodriguez-Laguna María , Monjo Irene , Gómez Ignacio Vázquez , Vela-Casasempere Paloma , Merino Carolina , Martínez Marta Ibáñez , Beriain José Ángel Hernández , Ruiz-Román Alberto , Calvo-Alén Jaime 
Published: February 2025

Abstract

Objectives
To describe the clinical spectrum of VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, and somatic) syndrome in patients managed by rheumatology units and analyse genotype–phenotype correlations.

Methods
A multicentre, cross-sectional, retrospective study was conducted across 126 Spanish hospitals. Patients with VEXAS syndrome diagnosed between December 2020 and January 2024 were included. Demographic data, clinical manifestations, laboratory findings, genetic analyses, treatments and outcomes were collected from medical records.

Results
Thirty-nine male patients were included (mean age at diagnosis: 72.78 years). Common manifestations were cutaneous lesions (87.18%), polyarthritis (82.05%) and fever (79.49%). Renal involvement was observed in 20.51% of patients. Genetic testing confirmed ubiquitin-like modifier-activating enzyme 1 mutations in all cases: 18 M41L, 14 M41T, 6 M41V and 1 novel mutation of unknown significance at site c.209T&gt;A. The M41V mutation was significantly associated with renal involvement, while M41T was linked to deep vein thrombosis and thrombocytopaenia. Glucocorticoids were used in all patients, with improved response rates post-diagnosis (55.26% vs 97.14%) probably influenced by an increase in administered doses. IL-6 inhibitors and JAK inhibitors showed promising response rates (75% and 76.92%, respectively).

Conclusions
This study provides insights into the clinical spectrum of VEXAS syndrome in rheumatology settings, highlighting a higher prevalence of joint symptoms and renal involvement than previously reported. Genotype–phenotype correlations were observed, with M41V significantly associated with renal involvement and M41T linked to deep vein thrombosis and thrombocytopaenia. A new, presumably causative variant of VEXAS syndrome at site c.209T&gt;A was described. These findings contribute to the growing understanding of VEXAS syndrome and may inform future diagnostic and treatment strategies.