bluuebunny/crossref_metadata_2025_split huggingface dataset:
T1 mapping magnetic resonance imaging predicts decline of kidney function
Authors: Huber Aurélie , Aslam Ibtisam , Crowe Lindsey , Pruijm Menno , de Perrot Thomas , de Seigneux Sophie , Vallée Jean-Paul , Berchtold Lena 
Published: February 2025

Abstract

Background
Renal cortical interstitial fibrosis, typically assessed by biopsy, is crucial for kidney function prognosis. MRI is a promising method to assess fibrosis non-invasively. Diffusion-Weighted (DW) MRI correlates with renal fibrosis and predicts kidney function decline in chronic kidney disease (CKD) and kidney allograft patients. This study evaluates whether T1 and T2 mapping predict kidney function decline and if their simultaneous use enhances the predictive power of a DW-MRI-based model.

Methods
We prospectively included 197 patients (42 CKD, 155 allograft kidneys). Each underwent a biopsy followed by multiparametric MRI without contrast within a week. Over a median follow-up of 2.2 years, laboratory parameters were recorded. Primary endpoint was a rapid decline in kidney function (GFR reduction &gt; 30%) or replacement therapy initiation. T1 and T2 mapping sequences’ ability to predict poor renal outcome was examined using multivariable Cox regression models, incorporating MRI-derived parameters, eGFR, and proteinuria.

Results
Renal outcome occurred in 54 patients after a median of 1.1 years (IQR 0.9–2.1). Univariable survival analysis showed cortical T1 was associated with poor renal outcome (HR: 3.02 [1.44–6.33]), while T2 sequences had no significant predictive value. Adding cortical T1 to the established model (ΔADC, eGFR, proteinuria) did not improve the hazard ratio (from 4.62 [1.56–13.67] to 4.36 [1.46–13.02]) and marginally increased Harrell's C-index (0.77 to 0.79). Adjusting the regression model for ΔT2 yielded no enhancement in predictive power.

Conclusions
Cortical T1 is strongly associated with poor renal outcome but did not enhance prognostic power of the DW-MRI-based model.
T-helper cell phenotypes are repeatable, positively correlated, and associated with helminth infection in wild Soay sheep
Authors: Corripio-Miyar Yolanda , Hayward Adam D , Lemon Hannah , Bal Xavier , Cunnea Cameron , Kenyon Fiona , Pilkington Jill G , Pemberton Josephine M , Nussey Daniel H , McNeilly Tom N 
Published: February 2025

Abstract

Background
T-helper (Th) cells co-ordinate immune responses to ensure that infections with diverse parasites are controlled effectively. Helminth parasites such as gastrointestinal nematodes (GIN) are generally associated with T-helper type 2 (Th2) responses, while intracellular parasites are associated with Th1 responses. Although laboratory models have reported that Th1 and Th2 can be antagonistic, this has been challenged by studies of natural infections.

Methods
Between 2019 and 2022 we completed 759 captures of 538 wild Soay sheep (1–4 captures per animal) and monitored body weight, parasite egg counts, Th phenotypes, cytokines, and GIN-specific antibodies.

Results
While different Th cell counts, cytokines and antibody isotypes were generally positively correlated with each other, no strong positive associations were observed between these measurements. Cell counts had low repeatability (among-individual variation) across 4 years, while antibody levels were highly repeatable. The Th1 and Th2 cytokines Interferon-gamma (IFN-γ) and Interleukin-4 (IL-4) were moderately repeatable and were positively correlated at both the between- and within-individual levels independent of body condition or parasite exposure. IL-4 was negatively associated with GIN faecal egg count, while IFN-γ was negatively associated with coccidian faecal oocyst count, suggesting that these cytokines reflect resistance to these parasites. None of our immune markers were strongly associated with lamb survival.

Conclusions
Our results provide insights into how different aspects of immune function interact to produce effective responses to complex infections but suggest longer-term data collection is required to address the causes of these interactions and to detect fitness consequences of variation in T cell phenotypes under natural conditions.
Informal social interactions, academic achievement and behavior: Evidence from peers on the school bus
Authors: Lenard Matthew A , Silliman Mikko 
Published: February 2025

Abstract
We study the effects of informal social interactions on academic achievement and behavior using idiosyncratic variation in peer groups stemming from changes in bus routes across elementary, middle, and high school. Our results suggest that student interactions outside the classroom—especially in adolescence—may be an important factor in the education production function for both academic and, particularly, behavioral skills. The effects of interactions on the bus are also related to neighborhood measures—suggesting that one way that interactions on the bus may matter is by amplifying interactions in the neighborhood.
Descriptive analysis and outcomes of PitNETs treated surgically during pregnancy and postpartum
Authors: Odot Cindy , Brière Mathilde , Villa Chiara , Henry Théophraste , Gaillard Stephan , Caron Philippe , Groussin Lionel , Reznik Yves , Rod Anne , Ghorra Camille , Raffin-Sanson Marie-Laure , Baussart Bertrand , Hage Mirella 
Published: February 2025

Abstract

Objective
Data on pituitary neuroendocrine tumors (PitNETs) surgically treated during pregnancy is limited, and no studies have compared these cases to those treated in non-pregnant women. This study aimed to describe the clinical, radiological, and histological profiles of patients treated surgically for PitNETs during pregnancy and evaluate long-term prognosis.

Design
This study was multicentric, observational and retrospective.

Methods
We included 10 patients from 5 university hospitals who underwent surgical treatment for PitNETs during pregnancy or within 12 months postpartum, along with 30 matched non-pregnant controls treated surgically for PitNETs. Clinical and histological data, as well as progression-free survival without additional treatment, were compared between pregnant and non-pregnant patients.

Results and Conclusions
Among the 10 PitNETs, 4 were corticotropic, 2 gonadotropic, 2 lactotropic, and 2 somatotropic. The primary surgical indication (tumour syndrome with or without failure of medical treatment) was similar between the two groups: 7/10 vs 19/30 (p = 1.00). There was no statistically significant difference in volume (p = 0.072) or radiological invasion markers (optic chiasm compression, p = 0.059, and cavernous sinus invasion, p = 0.274). However, PitNETs in pregnant women showed higher mitotic activity (p = 0.038) and were more frequently classified as grade 2b (Trouillas clinicopathological classification; p=0.049). The need for second-line treatment was also more frequent (p = 0.005). PitNETs requiring surgical treatment during pregnancy are characterized by increased proliferative activity and progression after surgery. Despite this, the long-term prognosis remains favorable. These results need confirmation in a larger study.
Biochemical characterization of diaminopimelate decarboxylase from the hyperthermophile Thermotoga maritima
Authors: Miyamoto Tetsuya , Yazawa Akari , Mishima Rio , Sakai-Kato Kumiko 
Published: February 2025

Abstract
The peptidoglycan stem peptides of the hyperthermophile Thermotoga maritima contain an unusual D-lysine (D-Lys) alongside the usual D-alanine and D-glutamate. We identified a Lys racemase that catalyzes racemization between L-Lys and D-Lys, and a diaminopimelate (Dpm) epimerase that catalyzes epimerization between LL-Dpm and meso-Dpm. Herein, we characterized a Dpm decarboxylase (TM1517) that catalyzes the conversion of meso-Dpm to L-Lys. TM1517 displayed high decarboxylase activity toward meso-Dpm but no activity toward LL-Dpm. D-Lys was not detected in the decarboxylation of meso-Dpm. The pH and temperature dependencies and kinetic parameters of decarboxylase activity were determined. Although other amino acid metabolizing activities of TM1517 were investigated, TM1517 did not exhibit any activities. Therefore, TM1517 is a Dpm decarboxylase associated with L- and D-Lys biosynthesis in T. maritima.
Challenges in elucidating ethylene glycol metabolism in Saccharomyces cerevisiae
Authors: Senatore Vittorio Giorgio , Masotti Fiorella , Milanesi Riccardo , Ceccarossi Sofia , Maestroni Letizia , Serra Immacolata , Branduardi Paola 
Published: February 2025

Abstract
Polyethylene terephthalate (PET) is one of the most used polymers in the packaging industry; enzymatic recycling is emerging as a sustainable strategy to deal with waste PET, producing the virgin monomers terephthalic acid and ethylene glycol (EG). These monomers can be feedstocks for further microbial transformations. While EG metabolism has been uncovered in bacteria, in yeast the pathway for the oxidation to glycolic acid (GA) has only been proposed, but never experimentally elucidated.
In this work, we investigated in Saccharomyces cerevisiae the potential contribution to this metabolism of two endogenous genes, YLL056C (a putative alcohol dehydrogenase) and GOR1 (glyoxylate reductase). Secondly, the possible role of alcohol dehydrogenases (ADHs) was considered, too. Finally, two heterologous genes (gox0313 from Gluconobacter oxydans and AOX1 from Komagataella phaffii) were expressed with the intent to push EG oxidation towards GA. Our main findings revealed that i) Gor1, Yll056c and ADHs are not involved in EG oxidation, ii) the bottleneck of the catabolism is the first step in the pathway, due to the endogenous mechanisms for aldehyde detoxification. Multiomics studies are required to completely elucidate the pathway for EG catabolism, while further engineering directed towards relieving the bottleneck is needed to fully unleash the potential of yeasts for the upcycling of EG to GA.
Genome-wide association studies dissect the genetic architecture of seed and yield component traits in cowpea (Vigna unguiculata L. Walp)
Authors: Akinmade Habib , Ferreira Rebecca Caroline Ulbricht , Leite Andrade Mario Henrique Murad , Fernandes Claudio , Sipowicz Pablo , Muñoz-Amatriaín María , Rios Esteban 
Published: February 2025

Abstract
The identification of loci related to seed and yield component traits in cowpea constitutes a key step for improvement through marker-assisted selection (MAS). Furthermore, seed morphology has an impact on industrial processing and influences consumer and farmer preferences. In this study, we performed genome-wide association studies (GWAS) on a mini-core collection of cowpea to dissect the genetic architecture and detect genomic regions associated with seed morphological traits and yield components. Phenotypic data were measured both manually and by high-throughput image-based approaches to test associations with 41,533 single-nucleotide polymorphism markers using the FarmCPU model. From genome-associated regions, we also investigated putative candidate genes involved in the variation of the phenotypic traits. We detected 42 marker-trait associations for pod length and hundred seed weight, length, width, perimeter, and area of the seed. Candidate genes encoding leucine-rich repeat-containing (LRR) and F-box proteins, known to be associated with seed size, were identified; in addition, we identified candidate genes encoding PPR (Pentatricopeptide repeat) proteins, recognized to have an important role in seed development in several crops. Our findings provide insights into natural variation in cowpea for yield-related traits and valuable information for MAS breeding strategies in this and other closely related crops.
Employment Status and Life Satisfaction Among Older Adults: Disentangling the Gendered Effects of Entering and Exiting Employment
Authors: Park Sujeong , Kim Jinho 
Published: February 2025

Abstract

Background and Objectives
This study examines the relationship between employment transitions and life satisfaction among Korean adults aged 65 and older, with a focus on the distinct effects of entering and exiting employment. Moreover, the study explores whether these associations vary by gender.

Research Design and Methods
Utilizing data from the Korean Longitudinal Study of Ageing, the study employed innovative asymmetric fixed effects models to separately assess the impacts of entering and exiting employment. Gender-stratified analyses were also conducted to explore potential differences in these effects between men and women.

Results
Conventional fixed effects models suggested that employment status is not significantly related to life satisfaction in older adults. However, the asymmetric fixed effects models revealed a more nuanced picture: entering employment is associated with an increase in life satisfaction while exiting employment shows no significant association. The gender-stratified analysis further indicated that for men, entering employment improved life satisfaction, while exiting had no effect. In contrast, for older women, entering employment did not enhance life satisfaction, but exiting employment had a positive impact.

Discussion and Implications
These findings highlight the need for gender-sensitive employment policies for older adults, aimed at enhancing their well-being based on their unique experiences of employment transitions.
Cold atmospheric plasma pretreatment on the extraction of bioactive compounds from Scutellaria baicalensis Georgi
Authors: Zhang Jiaming , Chu Jiangnan , Wu Zhengwei 
Published: February 2025

Abstract
Scutellaria baicalensis Georgi (SBG) is a traditional medicinal plant for its anti-inflammatory, antibacterial and antiviral properties. Nevertheless, the current conventional means of extracting the bioactive compounds of SBG are less efficient, and this study aimed to improve the extraction efficiency of flavonoids from SBG by pretreatment with cold atmospheric pressure plasma (CAP) technique. The results showed that CAP pretreatment could facilitate an increase in the specific surface area, a reduction in particle size, thus increasing the area in contact to the extraction solvent. The reactive oxygen of CAP can also degrade cell wall components. Ultimately, the extraction efficiency of flavonoids was improved by 8.25%–59.77%. In conclusion, this study demonstrated that CAP is an effective method to enhance the extraction efficiency of SBG bioactive compounds, indicating the potential to improve the nutritional and functional properties of plants in the food industry.
Inhibition of PDE4B ameliorates cognitive defects in the model of alcoholic dementia in 3×Tg-AD mice via PDE4B/cAMP/PKA signaling
Authors: Sun Rongzhen , Han Mei , Lin Yuanyuan , Ma Shengyao , Tu Huan , Yang Xueliang , Zhang Fang , Zhang Han-Ting 
Published: February 2025

Abstract

Background
Chronic, heavy alcohol use may lead to permanent brain damage, cognitive impairment, and dementia. One of the most serious consequences is alcoholic dementia (AlD). Phosphodiesterase-4 (PDE4) inhibitors have been shown to exhibit beneficial effects on cognition deficits and alcoholism. However, it is not known whether PDE4 inhibitors can be used to treat AlD. A33, a relatively selective PDE4B inhibitor, is absent of the emetic effect associated with PDE4D. The effect of A33 on memory and cognition in AlD remains unclear.

Methods
We investigated the effects of A33 and the PDE4 inhibitor rolipram on memory and cognition using an AlD animal model, i.e., APP/PS1/Tau mice drinking alcohol in the two-bottle choice test, with or without A33 or rolipram treatment for 3 wk. The animal groups were compared in behavioral tests related to learning and memory. Neurochemical measures were conducted to explore the underlying mechanism of A33.

Results
Compared to WT controls, AlD mice showed impairments of learning ability and memory in the behavior tests; this was attenuated by treatment of rolipram or A33. In addition, administration of rolipram or A33 in AlD mice further alleviated neuropathological alterations in the hippocampus, including Aβ expression and deposition; rolipram or A33 also decreased the levels of inflammatory cytokines, including IL-1β, IL-6, and TNF-α, as well as NF-κB. Further, rolipram or A33 decreased the activation of microglia while increased cAMP levels in the hippocampus of AlD mice.

Conclusions
These results revealed that the alleviation of the cognitive impairment of AlD in APP/PS1/Tau triple transgenic mice by rolipram or A33 was linked to the action of the PDE4B/cAMP/PKA signaling pathway. A33 can be a promising therapeutic agent for AlD-related cognitive dysfunction.
Human Challenge Models for Vaccine Development – Strengths, Limitations and Expansion into Endemic Settings: a HIC-Vac Meeting Report
Authors: Wagstaffe Helen R , Ascough Stephanie , Openshaw Peter J M ,   HIC-Vac meeting contributors
Published: February 2025

Abstract
The HIC-Vac network is a unique association of researchers focused on the development and use of Human Infection Challenge (HIC, otherwise known as Controlled Human Infection Models or CHIM) studies for vaccine and therapeutic development, particularly for pathogens of high global impact. The 5th annual meeting of the HIC-Vac network was held on 1st-3rd November 2023. The theme of the meeting was capacity-building in endemic settings particularly in Low- and Middle-Income Countries (LMIC), where pathogens cause the greatest morbidity and mortality. In this report we highlight the strengths and limitations of HIC and expansion of such studies into endemic settings, noting that immune responses and vaccine efficacy differ across diverse settings and populations. The consensus was that HIC studies must not be restricted to high income settings if they are to be relevant to LMIC populations. This report summarises the work presented at the HIC-Vac annual meeting, highlighting current and future challenge models, challenge agent manufacture, public engagement, ethics, and industry perspectives.
Factors Associated With the Transmission of the Delta Severe Acute Respiratory Syndrome Coronavirus 2 Variant in Households: The Israeli COVID-19 Family Study (ICoFS)
Authors: Cortier Thomas , Gilboa Mayan , Layan Maylis , Joseph Gili , Meltzer Lilac , Amit Sharon , Rubin Carmit , Lustig Yaniv , Alroy-Preis Sharon , Kreiss Yitshak , Cauchemez Simon , Regev-Yochay Gili 
Published: February 2025

Abstract
Understanding how interpersonal interactions and immunological factors shape severe acute respiratory syndrome coronavirus 2 transmission in households is crucial for designing control measures. We developed a Bayesian data augmentation transmission model to evaluate the effects of isolation, parental care, and vaccine-induced immunity on Delta variant transmission from the follow-up of 1093 Israeli households (July–August 2021). Among the 2883 household contacts, 1096 (38%) were infected. Children were 38% (95% Credibleconfidence interval [CrI], 7%–81%) more likely to be infected than adults. Isolation measures reduced transmission by 52% (95% CrI, 46%–57%). Transmission was 39% (95% CrI, 11%–76%) higher between children and female adults than between children and male adults. Vaccine effectiveness was 78% (95% CrI, 54%–90%), 85% (95% CrI, 70%–94%), and 73% (95% CrI, 49%–88%), respectively, for 1, 2, and 3 recent vaccine doses (within ≤90 days) but dropped to 18% (95% 95% CrI, −6% to 36%) for 2 doses administered &gt;90 days earlier. Household member interactions significantly shaped transmission, and isolation measures effectively reduced transmission.
The TET-TDG axis in T cells and biological processes
Authors: Suzuki Kazumasa , Rao Anjana , Onodera Atsushi 
Published: February 2025

Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). All three epigenetic modifications are intermediates in DNA demethylation. In the “passive” (replication-dependent) DNA demethylation pathway, sequential oxidation reactions by TETs are essential and modified cytosines (C) are diluted at each cycle of DNA replication. In the “active” (replication-independent) DNA demethylation pathway, both thymine DNA glycosylase (TDG) and TETs play important roles. TDG removes 5fC and 5caC from 5fC:G and 5caC:G base pairs and these modified bases are replaced by unmodified C via base excision repair. Through epigenetic regulation of DNA demethylation, TETs and TDG are involved in cell development, differentiation, and homeostasis. The interplay between TDG and TETs is involved in embryo development, stem cell differentiation, neural development, immune responses, and tumorigenesis. Loss-of-function mutations of TET proteins in immune cells are associated with a variety of abnormalities, including inflammation, cancer, and clonal hematopoiesis, a condition related to aging. Loss of TETs also has a significant impact on the plasticity and differentiation of T cells, which contributes to inflammation and cancer. In this review, we describe recent findings in function of TETs in T cell plasticity and differentiation and the TET-TDG axis in selected biological processes.
Correlation of Interferons and Autoimmune Aspects in Long COVID-19 Patients
Authors: Hattori Fumiyuki , Nishiyama Junji , Hasuo Hideaki 
Published: February 2025

Abstract
Long COVID, or post-acute sequelae of COVID-19 (PASC), represents a major global health challenge, with its underlying mechanisms remaining poorly understood despite substantial research and clinical trials. This study investigates the role of the interferon (IFN) axis in the pathogenesis of PASC, drawing parallels to systemic lupus erythematosus (SLE). The potential pathogenic role of IFNs was detected by meta-analyses of mRNA sequencing data comparing PASC patients to healthy controls. We analyzed serum samples from 39 PASC patients and found significant correlations among multiple IFN subtypes, including IFN alpha-2, beta, gamma, lambda-1, and lambda-2/3. The biological activity of IFNs in the serum was positively correlated with levels of both total and type III IFNs. Notably, we detected the widespread presence of anti-double-stranded DNA (anti-dsDNA) and anti-Smith (anti-Sm) antibodies in these patients, with anti-dsDNA levels showing a strong correlation with IFN activity. Based on these findings, we propose a hypothetical autoimmune pathogenesis for PASC highlighting the crucial role of IFN signaling.