bluuebunny/crossref_metadata_2025_split huggingface dataset:
Newly identified c-di-GMP pathway putative EAL domain gene STM0343 regulates stress resistance and virulence in Salmonella enterica serovar Typhimurium
Authors: Chen Kaifeng , Li Lili , Wang Nanwei , Zhou Zhouping , Pan Peng , Xu Chenggang , Sun Dage , Li Jiayi , Dai Changzhi , Kuang Dai , Liao Ming , Zhang Jianmin 
Published: January 2025

Abstract

S. Typhimurium is a significant zoonotic pathogen, and its survival and transmission rely on stress resistance and virulence factors. Therefore, identifying key regulatory elements is crucial for preventing and controlling S. Typhimurium. We performed transcriptomic analysis and screened for a c-di-GMP pathway key gene STM0343, a putative EAL domain protein with an unknown function. Our findings revealed that the deletion of this gene (269ΔSTM0343) led to a 29.85% increase in c-di-GMP. In terms of stress resistance, the strain 269ΔSTM0343 showed significant improvements compared to the wild strain WT269. Specifically, it exhibited increases of 95.74% in extracellular protein and 35.96% in exopolysaccharide production by upregulating the expression of relevant genes. As a result, the biofilm formation ability of 269ΔSTM0343 was enhanced by 21.54%, accompanied by a more pronounced red, dry, and rough colony morphology. 269ΔSTM0343 also showed a 19.03% decrease in motility due to the downregulation of flhD expression. As a result, 269ΔSTM0343 increased resistance to various antibiotics, as well as to acidic conditions, oxidative stress, and disinfectants. In terms of virulence, compared to WT269, the adhesion and invasive ability of 269ΔSTM0343 to HeLa cells was enhanced by onefold and 25.67%, respectively. In in vivo experiments, mice challenged with 269ΔSTM0343 experienced greater weight loss, and the bacterial loads in the spleen, liver, and intestines were elevated by fivefold, 30-fold, and 21-fold, respectively, accompanied by more severe pathological damage. Mechanistic studies revealed that the adhesion and invasion capacities of 269ΔSTM0343ΔCsgB decreased by 29.41% and 68.58%, respectively, compared to 269ΔSTM0343. Additionally, LacZ gene reporting indicated that STM0343 inhibited the expression of CsgB. This suggests that STM0343 suppresses virulence by downregulating CsgB expression. This study provides insights into the regulatory mechanisms by which STM0343 reduces the stress resistance and pathogenicity of S. Typhimurium.
Protein palmitoylation is involved in regulating mouse sperm motility via the signals of calcium, protein tyrosine phosphorylation and reactive oxygen species
Authors: Xiong Yuping , Yi Chenchen , Zheng Haixia , Ni Ya , Xue Yamei , Li Kun 
Published: January 2025

Abstract

Background
Protein palmitoylation, a critical posttranslational modification, plays an indispensable role in various cellular processes, including the regulation of protein stability, mediation of membrane fusion, facilitation of intracellular protein trafficking, and participation in cellular signaling pathways. It is also implicated in the pathogenesis of diseases, such as cancer, neurological disorders, inflammation, metabolic disorders, infections, and neurodegenerative diseases. However, its regulatory effects on sperm physiology, particularly motility, remain unclear. This study aimed to elucidate the mechanism by which protein palmitoylation governs sperm motility.

Methods
Protein palmitoylation in situ in mouse sperm was observed using innovative click chemistry. Sperm motility and motion parameters were evaluated using a computer-assisted sperm analyzer (CASA) after treatment with 2-bromopalmitic acid (2BP), a specific inhibitor of protein palmitoylation. Protein palmitoylation levels were confirmed by the acyl-biotin exchange (ABE) method. The interplay between protein palmitoylation, protein tyrosine phosphorylation, and intracellular calcium was investigated using Western blotting, ABE method, and fluorescent probes. The regulation of reactive oxygen species was also examined using fluorescent probes.

Results
Localized patterns and dynamics of protein palmitoylation in distinct sperm regions were revealed, including the midpiece, post-acrosomal region, acrosome, and head. Alterations in protein palmitoylation in sperm were observed under in vitro physiological conditions. Treatment with 2BP significantly affected sperm motility and motion parameters. The study revealed interactions between protein palmitoylation, including heat shock protein 90, and protein kinase A/protein kinase C-associated protein tyrosine phosphorylation and intracellular calcium. Additionally, protein palmitoylation was found to be involved in reactive oxygen species regulation.

Conclusions
Protein palmitoylation regulates sperm motility through calcium signaling, protein tyrosine phosphorylation, and reactive oxygen species. This study revealed the characteristics of protein palmitoylation in sperm and its role in regulating sperm motility, thereby providing novel insights into the causes of asthenozoospermia associated with sperm motility in humans.
Microfinance for change: how financial innovation enables structural transformation
Authors: Ghimire Shankar , Thapa Bharat Singh , Zheng Rong 
Published: January 2025

Abstract
This study examines the influence of microfinance institutions’ (MFIs) financial innovation on structural transformation. For this purpose, we considered a household survey from Nepal. The survey collected data on various individual and household characteristics, borrowing patterns, and occupations over the years. The key question focused on occupations before and after borrowing, a categorical response variable indicating 1 for occupational change after borrowing and 0 otherwise. Therefore, we use logistic regression to estimate the probability of occupational change, given two measures of financial innovation: loan purpose and size. The results show that the number of households involved in agriculture significantly decreased, with the majority switching to businesses and convenience stores, indicating a shift to the manufacturing and service sectors. These findings suggest that MFIs contribute to local-level structural transformation by enabling borrowers to move away from traditional employment. This study has important implications for policymakers, development practitioners, and academics interested in promoting economic development through microfinancing in low-income countries.
Primary cutaneous gamma–delta T cell lymphoma presenting as a leg ulcer in a kidney transplant recipient on hemodialysis: a case report with a literature review
Authors: Oba Yuki , Mizuno Hiroki , Kurihara Shigekazu , Ikuma Daisuke , Yamanouchi Masayuki , Suwabe Tatsuya , Miki Katsuyuki , Kono Kei , Ohashi Kennichi , Nishida Aya , Wake Atsushi , Nakamura Yuki , Ubara Yoshifumi , Sawa Naoki 
Published: January 2025

Abstract

Background
Kidney transplantation has long been associated with the incidence of lymphoma. These lymphomas are typically Epstein–Barr virus-associated B cell lymphomas. However, T cell lymphomas occur rarely.

Case presentation
We present the case of a 57-year-old Japanese man. He underwent a living kidney transplantation twice at age 43 and 46 years. However, the kidney function abolished after 9 years, and he restarted hemodialysis at age 55. After 2 years, an ulcer appeared on his right lower leg. It was not ameliorated but enlarged and became too painful to walk. Skin biopsy diagnosed with primary cutaneous gamma–delta (γδ) T cell lymphoma (PCGD-TCL) on his right leg. PCGD-TCL is one of the highly aggressive lymphomas that express gamma–delta T cell receptor gene arrangement and is difficult to diagnose and treat. He underwent cyclophosphamide 350 mg/m2(50% dose), hydroxydaunorubisin 50 mg/m2, vincristine 1.4 mg/m2, and prednisolone 100 mg/body (CHOP) therapy four times, but these were not effective and caused many complications such as septic febrile neutropenia. Although he decided to undergo amputation of his right leg finally, he died following postoperative cytomegalovirus meningitis.

Conclusions
This is the first case of PCGD-TCL after kidney transplantation. It shows that the transplanted kidney can lead to lymphoma development, even after the functional loss of the transplanted kidney, and that it is crucial to consider performing the biopsy aggressively for untreatable leg ulcers in hemodialysis patients.
Neurobrucellosis: a retrospective cohort of 106 patients
Authors: Arazi Fatemeh , Haddad Mahboubeh , Sheybani Fereshte , Farzadfard Mohammad Taghi , Rezaeian Majid Khadem 
Published: January 2025

Abstract

Background
Neurobrucellosis, a serious central nervous system infection caused by Brucella species, presents significant challenges due to its diverse clinical manifestations and the risk of long-term complications and poor outcomes. Identifying predictors of adverse outcomes is critical for improving patient management and overall prognosis.

Objectives
This study aimed to evaluate the long-term morbidity and mortality associated with neurobrucellosis and to identify key predictors of adverse outcomes.

Methods
We performed a retrospective cohort study of 106 neurobrucellosis patients treated at two major referral centers in Mashhad, Iran, from March 21, 2011, to March 20, 2022. We analyzed clinical, neuroimaging, and laboratory data, and estimated survival probabilities using Kaplan–Meier analysis. Long-term morbidity was evaluated using the Glasgow Outcome Scale.

Results
The median age of the cohort was 30 years (IQR: 21.8–46.3). The median length of hospital stay was 11 days (IQR: 7–19.8), with an in-hospital mortality rate of 4.7% (n = 5). Survival probabilities were 92.2% (SE = 0.027) at 1 month and 90.1% (SE = 0.030) at 6 months. The median follow-up duration was 52 months (IQR: 35–77). At follow-up, 23.5% (n = 20) of patients had an unfavorable outcome based on the Glasgow Outcome Scale. Predictors of mortality included older age, altered level of consciousness, seizures, elevated body temperature on admission, and white matter changes on neuroimaging.

Conclusion
Neurobrucellosis is associated with significant long-term morbidity and mortality. Key predictors of mortality include older age, altered level of consciousness, seizures, elevated body temperature on admission, and white matter changes. Identifying these predictors can help in targeting therapeutic strategies and improving patient outcomes through early intervention and close monitoring.
Optimal allocation of antenatal and young child nutrition interventions: an individual-based global burden of disease calibrated microsimulation
Authors: Bowman Alison , Lutze Sylvia , Albright James , Blair-Stahn Nathaniel , Jafari Hussain , Kaur Simar , Kinuthia Caroline , Mudambi Rajan , Nast Patrick , Pletcher Alix , Flaxman Abraham 
Published: January 2025

Abstract

Background
Undernutrition remains a global crisis and is a focus of Sustainable Development Goals. While there are multiple known, effective interventions, complex interactions between prevention and treatment and resource constraints can lead to difficulties in allocating funding. Simulation studies that use in silico simulation can help illuminate the interactions between interventions and provide insight into the cost-effectiveness of alternative packages of options.

Methods
We developed an individual-based microsimulation model based on the Global Burden of Disease (GBD) 2021 study data to test a range of nutrition interventions, including antenatal interventions (iron and folic acid, multiple micronutrients, and balanced energy protein supplementation) and child interventions (treatment for severe acute malnutrition, treatment for moderate acute malnutrition, and wasting prevention with small-quantity lipid-based nutrient supplements). We also developed an analytic approach to process the results of the microsimulation and identify the optimal intervention funding allocation for a given budget size. We use Ethiopia as an example in this paper.

Results
In our illustrative example of Ethiopia, the reallocation of the baseline budget to minimize disability-adjusted life years (DALYs) resulted in first funding the antenatal multiple micronutrients to their maximum coverage and then funding treatment for severe child acute malnutrition. Relative to the baseline allocation, the reallocation optimized to minimizing DALYs resulted in 592,000 fewer annual DALYs, constituting an 8.3% reduction in total DALYs in Ethiopia.
For budgets larger than the baseline, our model recommended funding first targeted moderate acute malnutrition treatment, second universal moderate acute malnutrition treatment, third wasting prevention with small-quantity lipid-based nutrient supplements, and fourth balanced energy protein supplementation.

Conclusions
Our simulation is a novel model for estimating optimal allocation of spending on antenatal and child health nutrition interventions which accounts for the interaction between preventive and therapeutic approaches. Our illustrative results show that an optimized reallocation of current spending can substantially improve pregnancy-related and child health without additional funding. We hope this model can add validity and confidence to prior results to aid stakeholders in funding decisions.
Sex-Based Bias in Industry Payments to Medical Oncologists
Authors: Jan Imraan , De Brian , Kwon Young Suk , Freeman Robert , Larkin Kelsey , Subramanian Shyamala , Pandu Prathyusha , Song Amy , Young Meredith , Sayan Mutlay , Beier Matthew , Ludmir Ethan B. , Vapiwala Neha , Haffty Bruce G. , Mattes Malcolm D. 
Published: January 2025

PURPOSE
Industry payments are common among oncology researchers and can reflect professional stature and achievement; however, whether such payments differ on the basis of the sex of the recipient is unclear.

METHODS
To investigate potential differences in industry payments to male and female medical oncologists from 2016 through 2020, industry payment information was sourced from the Open Payments database and Centers for Medicare and Medicaid Services website. Covariate details including h-index, academic rank, institution National Institutes of Health (NIH) funding rank, sex, and practice location, were sourced from SCOPUS, Doximity, NIH RePORTER, National Plan and Provider Enumeration system, and institutional websites. Medical oncologists who received at least one industry research payment from 2016 through 2020 were included (n = 7,285).

RESULTS
No significant sex differences were observed in research payments; however, male medical oncologists received significantly more general payments than did female medical oncologists in several domains, including speaker fees (+194%), consulting (+204%), travel and lodging (+162%), and food and beverage (+114%).

CONCLUSION
Although we found no discernible sex-based differences in research funding among medical oncologists, female medical oncologists received significantly lower general payments than male medical oncologists. Efforts to improve transparency and interventions to address these discrepancies are important to ensure gender equity in oncology.
Comparison of Cumulative Live Birth Rates Between Progestin and GnRH Analogues in Preimplantation Genetic Testing Cycles
Authors: Zhou Ruiqiong , Dong Mei , Huang Li , Wang Songlu , Wang Zhaoyi , Xu Liqing , Zhang Xiqian , Liu Fenghua 
Published: January 2025

Abstract

Context
Progestins have recently been used as an alternative for gonadotropin-releasing hormone (GnRH) analogues to prevent premature luteinizing hormone surge due to the application of vitrification technology. However, the long-term efficacy and safety of a progestin-primed ovarian stimulation (PPOS) regimen, including oocyte competence, cumulative live birth rate (LBR), and offspring outcomes, remain to be investigated.

Objective
To compare cumulative LBR of preimplantation genetic testing (PGT) cycles between a PPOS regimen and GnRH analogues.

Methods
This was a retrospective cohort study at a tertiary academic medical center. A total of 967 patients with good prognosis were categorized into 3 groups: 478 patients received a long GnRH agonist, 248 patients received a GnRH antagonist, and 250 received a PPOS regimen. Medroxyprogesterone 17-acetate was the only progestin used in the PPOS regimen. The primary outcome was cumulative LBR. Secondary outcomes included time to live birth, cumulative rates of biochemical and clinical pregnancy and pregnancy loss, and perinatal outcomes.

Results
The PPOS regimen was negatively associated with cumulative LBR compared with GnRH antagonists and GnRH agonists (28.4% vs 40.7% and 42.7%). The average time to live birth was significantly shorter with GnRH antagonists than with the PPOS regimen. The cumulative biochemical and clinical pregnancy rates were also lower in the PPOS regimen than GnRH analogues, while cumulative pregnancy loss rates were similar across groups. Furthermore, the number and ratio of good-quality blastocysts were significantly reduced in the PPOS regimen compared with GnRH analogues. In addition, perinatal outcomes were comparable across 3 groups.

Conclusion
A PPOS regimen may adversely affect cumulative LBR and blastocyst quality in women with good prognosis compared with GnRH analogues in PGT cycles.
Phenotypes Linked to Duplication Upstream of SOX9: New Insights Into Presentation and Diagnosis
Authors: Unal Edip , Tekmenuray-Unal Aysel , Cayir Atilla , Papatya Cakir Esra Deniz , Beyazit Nurcan , Kolbasi Baris , Gurpinar Tosun Busra , Yigit Gokhan , Zibat Arne , Wollnik Bernd , Demirbilek Huseyin , Guran Tulay 
Published: January 2025

Abstract

Context
Duplications occurring upstream of the SOX9 gene have been identified in a limited subset of patients with 46,XX testicular/ovotesticular differences/disorders of sex development (DSD). However, comprehensive understanding regarding their clinical presentation and diagnosis is limited.

Objective
To gain further insight into the diagnosis of a large cohort of 46,XX individuals with duplications upstream of SOX9.

Methods
We retrospectively analyzed data of 46,XX/SRY-negative individuals with SOX9 upstream duplications. Clinical data were recorded, and genetic etiologies were investigated using karyotyping, fluorescence in situ hybridization (FISH) for SRY analysis, microarray analysis, multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing panels including whole genome sequencing.

Results
We analyzed 12 individuals with 46,XX karyotype who had heterozygous duplications upstream of SOX9, ranging from 107 to 941 kb. Ages at diagnosis ranged from 0.1 to 55 years. Seven (58%) had testicular/ovotesticular DSD, while 5 (41%) were asymptomatic carriers detected through family screening. There was no significant correlation between duplication size and genital/gonadal phenotype. The duplication was inherited from the father (n = 3) or an asymptomatic mother (n = 2). In one family, a duplication missed by the 300K microarray was detected by MLPA and confirmed with 750K microarray.

Conclusion
46,XX individuals with SOX9 upstream duplications may exhibit no symptoms, but thorough family screening is crucial due to the potential inheritance and testicular/ovotesticular DSD risk in subsequent generations. We emphasize the effectiveness of high-resolution microarray analysis (&gt;500K) as the primary diagnostic tool for 46,XX/SRY-negative testicular/ovotesticular DSD individuals, enabling thorough genome-wide assessment of copy number variations and detecting small alterations.
Construction of a Simplified Bone Age Assessment Model in Chinese Children Aged 3 to 18 Years
Authors: Wu Hua-hong , Zhang Ya-qin , Yu Cheng-dong , Li Yang , Shu Wen , Li Tao , Huang Gui-min , Hou Dong-qing , Chen Fang-fang , Liu Jun-ting , Li Shao-li , Zong Xin-nan 
Published: January 2025

Abstract

Context
Bone age assessment (BAA) is critical for pediatric endocrinology. Traditional methods are complex and time-consuming, and current computer-aided systems have made progress but still lacking in robustness.

Objective
Develop simplified BAA methods to aid pediatricians in quick clinical assessments.

Design
Overall, 5551 left-hand X-ray images were collected from a cross-sectional survey in 2022 and 2023. Bone age (BA) was assessed using the Tanner-Whitehouse 3-China/radius-ulna-short bone method. The linear regression models were constructed with BA as the dependent variable and 13 radius-ulna-short bone bones' grades as independent variables.

Setting
A cross-sectional survey in Beijing, China.

Participants
A total of 5551 children aged 3 to 18 years.

Main Outcome Measures
Model accuracy was evaluated by R², residuals, and root mean square error, and BA with an error margin ≤0.5 years.

Results
When bone grades were consistent, a single or few bones may serve as proxies for BA, such as metacarpals and phalanges reaching grade 6, the BA for boys and girls were 13.0 to 13.5 years and 10.9 to 11.5 years, respectively. When bone grades were inconsistent, regression models were needed. Comparatively, the 3-bone models have advantages and are proposed for clinically simplified BAA. The simplified 3-bone model (radius, ulna, and metacarpal I) yielded an R² &gt; 0.94 and a root mean square error &lt; 0.5 years. When considering puberty stages, specific bone combination models can further improve assessment accuracy.

Conclusion
These 3-bone models could be useful for rapid BAA, with improved accuracy when puberty stages is included. Further validation is warranted to test their robustness across populations and scenarios.
Interaction of Linguistic and Literary Aspects in the Context of the Cultural Diversity of the Turkic Peoples of Central Asia
Authors: Omorov Aitmamat , Chokoeva Dilbar , Kalchakeyev Kubanychbek , Sheripbayev Amangeldi , Kochorova Gulumkan 
Published: January 2025

Abstract
The purpose of the study was to investigate the linguistic and literary components within the framework of the cultural diversity of Central Asian peoples of the Turkic ethnic group. The study analysed the linguistic features of the Turkic languages and their mutual influence through literary texts and oral traditions, with an emphasis on the processes of borrowing and adaptation of linguistic elements in a multilingual environment. The study examined scientific sources on linguistics and ethnolinguistics, and compared phonetic, morphological, and syntactic features of the Kazakh, Uzbek, Turkmen, and Kyrgyz languages in a historical context. The analysis of borrowings from Persian, Arabic, and Russian languages, content analysis of literary texts and folklore works, and an assessment of the role of mass media and the Internet in popularising Turkic languages were also included in the study. The results showed that the Turkic languages have gone through a difficult path of evolution under the influence of various cultural and political factors, such as the Mongol conquests and Russification in the Soviet period. The languages were significantly enriched with borrowings from Persian, Arabic, and Russian, which affected their vocabulary and grammar.