bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contribution of linguistic complexity to L2 learners’ perception on Chinese text comprehensibility and reading speed: a comparative judgment approach
Authors: Zhang Xiaopeng 
Published: January 2025

Abstract
This study delved into how linguistic complexity, gauged through various lexical, syntactic, and discoursal indices, correlates with the perception of text difficulty among learners acquiring Chinese as a second language (L2). This perception of difficulty underwent scrutiny via a comparative judgment task, wherein L2 raters appraised text comprehensibility and reading speed. A corpus of 250 Chinese texts was targeted, with 170 Chinese L2 learners participating as raters. Among these, eighty-five raters adjudicated pairs of texts, discerning the text posing greater comprehension challenge within each duo, while another eighty-five raters determined the text they could read faster within each pair. Stepwise linear regression models, which incorporate a range of linguistic indices, accounted for a substantial proportion of the variance in L2 learners’ judgments of comprehensibility and reading speed, respectively. Insights garnered from this study hold promise in enriching our comprehension of the elements influencing text difficulty in Chinese-L2 learners.
Social Determinants of Health and Cross-Sectional Cognitive Intra-Individual Variability in Adults from the Deep South Living with HIV
Authors: Del Bene Victor A , Fazeli Pariya L , Blake Jason A , Li Wei , Collette Christopher , Triebel Kristen L , Byun Jun Y , Jacob Alexandra E , Kamath Vidyulata , Vance David E 
Published: January 2025

Abstract
Cognitive intra-individual variability (IIV) is a sensitive marker of neuropathology and is increased in people with HIV (PWH). In a sample of PWH from the United States Deep South, we examined the relationship of cognitive IIV with cognitive impairment and social determinants of health (SDoH). This secondary analysis included 131 PWH from a larger cognitive training protocol. Our primary outcome measure was the coefficient of variation (CoV). We also included the individual standard deviation (iSD), with both calculated from demographically adjusted T-scores and unadjusted sample–based scores. Mixed-effects models investigated the relationship between IIV and cognitive impairment severity (i.e., Global Rating Score), SDoH, and clinical variables. Bivariate correlations were used to further explore these relationships. Greater cognitive IIV was associated with greater cognitive impairment in PWH, when accounting for demographic factors. When IIV is calculated from the sample, then IIV is no longer associated with cognitive impairment, but is associated with race (&gt;IIV in Black and African American participants). Demographically adjusted IIV is associated with global cognition, Wide Range Achievement Test–Fourth Edition reading score, and viral load (iSD only). No correlations were significant when using the unadjusted sample–based IIV metrics. In PWH from the Deep South, greater cognitive variability is seen in those with greater cognitive impairment, in Black participants, and in those with lower reading scores. Further research on the psychometric properties of IIV in HIV and other populations is needed, as results varied depending on the normative adjustments.
RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction
Authors: Bernard Clément , Postic Guillaume , Ghannay Sahar , Tahi Fariza 
Published: January 2025

Abstract

Motivation
Predicting the 3D structure of RNA is an ongoing challenge that has yet to be completely addressed despite continuous advancements. RNA 3D structures rely on distances between residues and base interactions but also backbone torsional angles. Knowing the torsional angles for each residue could help reconstruct its global folding, which is what we tackle in this work. This paper presents a novel approach for directly predicting RNA torsional angles from raw sequence data. Our method draws inspiration from the successful application of language models in various domains and adapts them to RNA.

Results
We have developed a language-based model, RNA-TorsionBERT, incorporating better sequential interactions for predicting RNA torsional and pseudo-torsional angles from the sequence only. Through extensive benchmarking, we demonstrate that our method improves the prediction of torsional angles compared to state-of-the-art methods. In addition, by using our predictive model, we have inferred a torsion angle-dependent scoring function, called TB-MCQ, that replaces the true reference angles by our model prediction. We show that it accurately evaluates the quality of near-native predicted structures, in terms of RNA backbone torsion angle values. Our work demonstrates promising results, suggesting the potential utility of language models in advancing RNA 3D structure prediction.

Availability and implementation
Source code is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr/evryrna/RNA-TorsionBERT.
High-throughput proteomics identifies inflammatory proteins associated with disease severity and genetic ancestry in patients with hidradenitis suppurativa
Authors: Dimitrion Peter M , Krevh Rachel , Veenstra Jesse , Ge James , Siddiqui Aamir , Ferguson Deangelo , Hans Aakash , Zuniga Bobby , Sidhu Kermanjot , Daveluy Steven , Hamzavi Iltefat , Zhou Li , Adrianto Indra , Mi Qing-Sheng 
Published: January 2025

Abstract

Background
Hidradenitis Suppurativa (HS) is a chronic inflammatory skin condition with a greater prevalence and disease burden in patients who identify as African American and those with a family history of HS, suggesting a strong genetic component to its pathogenesis.

Objective
To evaluate the relationship between plasma inflammatory protein expression, HS disease severity, and genetic ancestry in a diverse cohort of patients with Hidradenitis Suppurativa.

Methods
We performed a case-control study of patients with HS compared to age-, sex-, and ethnicity-matched healthy controls. We profiled circulating inflammatory proteins using Olink High-throughput proteomics and determined genetic ancestry from whole-genome sequencing data.

Results
Using linear regression, we identified novel proteins associated with HS after adjusting for age, sex, and ethnicity. Our analysis also revealed differences in the inflammatory proteome linked to disease severity. Specifically, we found that plasma IL6 levels can distinguish between different Hurley stages, indicating that IL6 may serve as a marker of disease severity. Additionally, we observed variations in inflammatory protein levels based on genetic ancestry: patients with predominantly African ancestry exhibited higher levels of inflammatory proteins associated with neutrophilic inflammation, while those with predominantly European ancestry showed increased levels of Th1-related inflammatory proteins.

Limitations
Single-center study. Limited sample size. Unable to account for treatment status or comorbidities that may influence the level of inflammatory cytokines.

Conclusion
Genetic ancestry and disease severity influence the plasma inflammatory profile in patients with HS.
Dermatologic surgery: An update on Secondary Intention Healing and Adjuncts: Part 2
Authors: Potluru Aparna , Barlow Richard , Pawlik Olga , Veitch David , Wernham Aaron 
Published: January 2025

Abstract
Secondary intention healing (SIH) is utilised by various surgical specialities. The formation of granulation tissue is crucial for initiating the healing process, necessitating robust support at this stage. Numerous adjunct therapies are available, with new developments aimed at treating both acute and chronic wounds undergoing SIH. This article continues from part 1, examining the efficacy of various adjunct therapies in promoting SIH. This article continues from part 1, examining the efficacy of various adjunct therapies in promoting SIH.
Intravenous Steroids Do Not Improve Short-Term Outcomes of Patients With Crohn’s Disease Presenting With an Acute Small Bowel Obstruction
Authors: Garcia Mariely , Debebe Anketse , Mahmood Farhan , Nirenberg Sharon , Rendon Alexa , Yang Eunyoung , Xiang Jiani , Colombel Jean-Frédéric , Kahan Tamara , Ghiasian Ghoncheh , Faye Adam S , Levine Irving , Farber Michael , Ramada Michael , Omoakhe Tisor , Sultan Keith , Sachar David B 
Published: January 2025

Abstract

Background
Intravenous (IV) steroids are commonly used to treat acute flares of Crohn’s disease (CD). However, it is unclear if they are beneficial in the setting of uncomplicated small bowel obstruction (SBO). We sought to examine if IV steroid administration improved short-term outcomes in patients with CD hospitalized for acute, uncomplicated SBO across three New York City hospital systems.

Methods
This retrospective study included patients ≥ 18 years old admitted between January 1, 2011, and December 31, 2019, with Crohn’s disease and an admission diagnosis of uncomplicated acute SBO, defined as cases without adhesions, fistula, phlegmon, and sepsis. Primary endpoints (length of stay and frequency of surgery) were compared between patients who received IV steroids upon admission and those who did not.

Results
Our analysis included 674 unique patients. Ninety-two (14%) received IV steroids, and 582 (86%) did not. IV steroid use did not result in shorter hospital stays (median days [IQR]: 3.0 (2.0-5.5) days vs 3.0 (2.0-6.0) days in the no-steroid group, P = .65) or reduce the need for surgery (4 patients (4.4%) vs 28 patients (4.8%) in the no-steroid group, P = .85). Sex, age, disease duration, concomitant biologic therapy, and NG tube placement did not independently contribute to either outcome.

Conclusions
These findings suggest that IV steroid administration for uncomplicated SBO in CD patients does not decrease hospital length of stay or need for surgery. Further research may help identify specific obstruction patterns or other therapies associated with different outcomes.
Efficacy and Safety of Mirikizumab in the Treatment of Moderately to Severely Active Ulcerative Colitis Regardless of Baseline Modified Mayo Score: Results From the Phase 3 LUCENT Trials
Authors: Abraham Bincy , Wu Jianmin , Vermeire Séverine , Melmed Gil , Ungaro Ryan , Charabaty Aline , Moses Richard , Chan-Diehl Faye , Paulissen Jerome , Zhu Baojin , Barnes Edward L , Ehrlich Adam C , Rubin David T 
Published: January 2025

Abstract

Background
The modified Mayo score (mMS) is a measure for ulcerative colitis (UC) disease activity. Recent US Food and Drug Administration guidance for moderately to severely active UC trials suggests that patients should have baseline mMS of 5–9 including an endoscopy score of at least 2, opposed to the previous range of 4–9. This disclosure reports results from patients with UC with baseline mMS of 5–9 who received mirikizumab, a monoclonal antibody directed against the interleukin-23 p19 subunit, or placebo in the phase 3 LUCENT trials.

Methods
Mirikizumab was evaluated in the randomized, double-blind, placebo-controlled LUCENT-1 (NCT03518086) and LUCENT-2 (NCT03524092) trials, and the ongoing long-term LUCENT-3 (NCT03519945) trial, which use mMS 4-9. Analyses for patients with baseline mMS of 5-9 (excluding patients with mMS of 4) were conducted according to LUCENT trial statistical analysis plans. Categorical efficacy endpoints were summarized using proportions and confidence intervals. Continuous efficacy endpoints are presented as least-squares mean (standard error) changes from baseline.

Results
Mirikizumab demonstrated efficacy for the primary endpoint of clinical remission and major secondary endpoints including clinical response, endoscopic improvement, histologic–endoscopic mucosal improvement/remission, bowel urgency remission, and corticosteroid-free remission. Importantly, mirikizumab exhibited greater improvements versus placebo in the Inflammatory Bowel Disease Questionnaire, fatigue, symptomatic remission, and work productivity. Finally, mirikizumab demonstrated long-term (104-week) sustained, durable efficacy across all studied endpoints. No new safety signals were identified during 2-year follow-up.

Conclusions
Mirikizumab delivered significant clinical benefit for patients with baseline mMS of 5-9 and demonstrated a favorable safety profile.
Endocrine dysfunction in long-term survivors of pediatric head and neck rhabdomyosarcoma
Authors: Morfouace Michele , Schoot Reineke A , Hol Marinka L F , Minard-Colin Veronique , Kolb Frederic , Bollé Stephanie , Kayembe Matumba T , Gaze Mark N , Sandler Eric , Knops Rutger R G , Merks Johannes H M , Smeele Ludwig E , Indelicato Daniel J , Slater Olga , van Santen Hanneke M 
Published: January 2025

Abstract

Objective
Survivors of pediatric head and neck rhabdomyosarcoma (HNRMS) are at risk of developing endocrinopathies following local treatment, resulting from radiation damage to the pituitary gland, hypothalamus, or thyroid gland, often at a young age. Our aim was to determine the prevalence of endocrine dysfunction in long-term HNRMS survivors and compare the prevalence of anterior pituitary insufficiency (API) among different local treatment strategies: external beam radiation with photons, external beam radiation with protons, microscopically radical surgery combined with external irradiation, and macroscopic radical surgery combined with brachytherapy.

Design and methods
Head and neck rhabdomyosarcoma survivors treated between 1993 and 2017, with ≥2 years of follow-up, without recurrent disease or secondary malignancy were eligible for this study. The presence of any endocrine dysfunction was assessed cross-sectionally using Common Terminology Criteria of Adverse Events grading, anthropometrics, and biochemical testing. Retrospective chart review was added to this clinical assessment.

Results
Ninety-six survivors with long follow-up time (median, 9 years) were included. Any endocrinopathy was present in 35% of survivors, with 88% having pituitary, 6% peripheral (thyroid), and 6% combined insufficiencies. None had gonadal insufficiency. Growth hormone deficiency was diagnosed in 31 (32%) survivors, with additional pituitary insufficiencies in 12 (39%). In 8%, central precocious puberty preceded API. None of the survivors given brachytherapy had API.

Conclusions
The prevalence of pituitary dysfunction in HNRMS survivors is high, emphasizing the importance of systematic endocrine assessment during follow-up, including pubertal development and growth. Efforts should be made to further reduce extraneous irradiation to endocrine organs to prevent dysfunction later in life.
Fine-scale spatial variation in fitness, inbreeding, and inbreeding depression in a wild ungulate
Authors: Hewett Anna M , Johnston Susan E , Albery Gregory F , Morris Alison , Morris Sean J , Pemberton Josephine M 
Published: January 2025

Abstract
Environmental stress can exacerbate inbreeding depression by amplifying differences between inbred and outbred individuals. In wild populations, where the environment is often unpredictable and stress can be highly detrimental, the interplay between inbreeding depression and environmental variation is potentially important. Here, we investigate variation in inbreeding level, fitness and strength of inbreeding depression across a fine-scale geographic area (~12 km2) in an individually monitored population of red deer (Cervus elaphus). We show that northern regions of the study area have lower birth weights, lower juvenile survival rates, and higher inbreeding coefficients. Such fine-scale differences in inbreeding coefficients could be caused by the mating system of red deer combined with female density variation. We then tested for an inbreeding depression-by-environment interaction (ID × E) in birth weight and juvenile survival, by fitting an interaction term between the inbreeding coefficient and geographic location. We find that inbreeding depression in juvenile survival is stronger in the harsher northern regions, indicating the presence of ID × E. We also highlight that the ability to infer ID × E is affected by the variation in inbreeding within each geographic region. Therefore, for future studies on ID × E in wild populations, we recommend first assessing whether inbreeding and traits vary spatially or temporally. Overall, this is one of only a handful of studies to find evidence for ID × E in a wild population—despite its prevalence in experimental systems—likely due to intense data demands or insufficient variation in environmental stress or inbreeding coefficients.
The Correlation Between Fecal Amino Acids, Colonic Mucosal Taste Receptors, and Clinical Features and Indicators of Ulcerative Colitis: A Multicenter Exploratory Study
Authors: Liu Yixin , Sha Sumei , Ran Qiuju , Shi Haitao , Ma Juan , Qin Bin , Li Yingchao , Wang Ning , Liu Xin , Wang Jinhai , Li Lu , Liu Na , Quan Xiaojing 
Published: January 2025

Abstract

Background
Patients with ulcerative colitis (UC) exhibit abnormal amino acid (AA) metabolism. Taste receptors play a crucial role in the detection of intestinal AAs. Nevertheless, it remains unclear whether UC patients exhibit abnormal expression of these receptors in the colon.

Methods
An observational, multicenter study was conducted involving adult patients with active UC and healthy controls (HCs), recruited from July 2023 to March 2024. Fresh feces and rectosigmoid mucosal tissues were obtained from each participant. The concentrations of fecal AAs and the expression of taste receptors, including calcium-sensing receptor (CaSR), G protein-coupled receptor family C group 6 member A (GPRC6A), taste receptor type 1 member 1 (T1R1), and metabotropic glutamate receptor 4 (mGLuR4), in the colon were measured. Additionally, the correlation between colonic mucosal taste receptors and clinical characteristics was evaluated.

Results
Except for GPRC6A, the expression levels of CaSR, mGLuR4, and T1R1 in the colonic mucosa of UC patients were significantly elevated compared to HC. The expression of CaSR was negatively correlated with C-reactive protein and erythrocyte sedimentation rate (ESR). T1R1 expression positively correlated with defecation frequency and an Improved Mayo Endoscopic Score. The total and subtype concentrations of fecal AAs were elevated in UC patients and demonstrated a negative correlation with ESR and fecal calprotectin.

Conclusions
The increased levels of taste receptors and fecal AAs in the colon of UC patients suggest an abnormal nutrient-sensing mechanism, potentially playing a crucial role in the development of the disease.
Pharmacokinetics and pharmacodynamics of an innovative psychedelic N,N-dimethyltryptamine/harmine formulation in healthy participants: a randomized controlled trial
Authors: Mueller Michael J , Aicher Helena D , Dornbierer Dario A , Marten Laurenz , Suay Dila , Meling Daniel , Elsner Claudius , Wicki Ilhui A , Müller Jovin , Poetzsch Sandra N , Caflisch Luzia , Hempe Alexandra , Steinhart Camilla P , Puchkov Maxim , Kost Jonas , Landolt Hans-Peter , Seifritz Erich , Quednow Boris B , Scheidegger Milan 
Published: January 2025

Abstract

Background
Recent interest in the clinical use of psychedelics has highlighted plant-derived medicines like ayahuasca showing rapid-acting and sustainable therapeutic effects in various psychiatric conditions. This traditional Amazonian plant decoction contains N,N-dimethyltryptamine (DMT) and β-carboline alkaloids such as harmine. However, its use is often accompanied by distressing effects like nausea, vomiting, and intense hallucinations, possibly due to complex pharmacokinetic/pharmacodynamic (PK-PD) interactions and lack of dose standardization.

Methods
This study addresses these limitations by testing a novel pharmaceutical formulation containing pure forms of DMT and harmine in a double-blind, randomized, placebo-controlled trial with 31 healthy male volunteers. We evaluated PK-PD by monitoring drug and metabolite plasma levels, subjective effects, adverse events, and cardiovascular parameters. Each participant received 3 randomized treatments: (1) 100 mg buccal harmine with 100 mg intranasal DMT, (2) 100 mg buccal harmine with intranasal placebo, and (3) full placebo, using a repeated-intermittent dosing scheme, such that 10 mg of DMT (or placebo) was administered every 15 minutes.

Results
N,N-dimethyltryptamine produced consistent PK profiles with Cmax values of 22.1 ng/mL and acute drug effects resembling the psychological effects of ayahuasca with a duration of 2–3 hours. Likewise, buccal harmine produced sustained-release PK profiles with Cmax values of 32.5 ng/mL but lacked distinguishable subjective effects compared to placebo. All drug conditions were safe and well tolerated, indicating the formulation’s suitability for clinical applications.

Conclusions
This study underscores the potential of a patient-oriented pharmaceutical formulation of DMT and harmine to reduce risks and improve therapeutic outcomes in treating mental health disorders.

Clinical trial registration number
Neurodynamics of prosocial emotional processing following serotonergic stimulation with N,N-dimethyltryptamine (DMT) and harmine in healthy subjects (NCT04716335) https://clinicaltrials.gov/ct2/show/NCT04716335
The role of pallidal substance P and neurokinin receptors in the consolidation of spatial memory of rats
Authors: Kertes Erika , Péczely László , Ollmann Tamás , László Kristóf , Berta Beáta , Kállai Veronika , Zagorácz Olga , Kovács Anita , Szabó Ádám , Karádi Zoltán , Lénárd László 
Published: January 2025

Abstract

Background
The tachykinin substance P (SP) facilitates learning and memory processes after its central administration. Activation of its different receptive sites, neurokinin-1 receptors (NK1Rs), as well as NK2Rs and NK3Rs, was shown to influence learning and memory. The basal ganglia have been confirmed to play an important role in the control of memory processes and spatial learning mechanisms, and as part of the basal ganglia, the globus pallidus (GP) may also be involved in this regulation. SP-immunoreactive fibers and terminals, as well as NK1Rs and NK3Rs, were shown to be present in the GP.

Methods
The present study aimed to examine whether the SP administered into the GP can influence spatial memory consolidation in the Morris water maze (MWM). Therefore, male Wistar rats received a post-trial microinjection of 0.4 µLf 10 ng SP, 100 ng SP, or vehicle solution. The possible involvement of pallidal NK1Rs and NK3Rs in the SP effects was also studied by applying WIN51708 for NK1R antagonism and SR142801 as a selective NK3R antagonist.

Results
Our results showed that the lower dose of SP significantly decreased escape latency on the second day compared to control animals, while the higher dose was ineffective. Prior treatment with the NK1R antagonist WIN51708 could not block, while the NK3R antagonist SR142801 inhibited the effects of SP on memory consolidation in the MWM.

Conclusions
Our results are the first to demonstrate that SP improves consolidation of spatial memory in the GP, and this effect is mediated through NK3Rs but not NK1Rs.