bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limbal Stem Cell Deficiency After Treatment of Ocular Surface Squamous Neoplasia
Authors: Devebacak Ali , Yaman Banu , Palamar Melis 
Published: September 2024

Purpose:
To investigate limbal stem cell deficiency (LSCD) in patients surgically treated for ocular surface squamous neoplasia (OSSN).

Methods:
This retrospective case–control study investigated clinical and histological data from patients with OSSN surgically treated in a referral center.

Results:
The study included 98 patients (58 male, 40 female) with a mean age of 61.1 (23–86) years. Less than 3 clock hours were involved by OSSN in 48 eyes (49.0%), 3–6 clock hours in 32 eyes (32.7%), 6–9 clock hours in 12 eyes (12.2%), and more than 9 clock hours in 6 eyes (6.1%). Limbal stem cell deficiency was identified in 36 patients (36.7%) after surgery. The severity of LSCD was mild in 17 eyes, moderate in 11, and severe in 8. The prevalence of LSCD increased significantly in groups with 6 clock hours or more of OSSN involvement (p < 0.001). The affected limbal side (superior, inferior, nasal, or temporal) had no significant association with the prevalence of LSCD (p = 0.869). Patients with recurrent OSSN had a higher LSCD prevalence (p = 0.003). The higher the tumor stage, the more likely it was to develop LSCD (p < 0.001). Patients with corneal involvement were also more likely to develop LSCD (p = 0.021). The prevalence of LSCD was raised with increasing histopathological grade (p = 0.019). Furthermore, solely the number of clock hours affected by OSSN was an independent risk factor in multivariate analyses (p < 0.001).

Conclusions:
The size and severity of OSSN and the presence of recurrent OSSN are associated with an increased likelihood of developing LSCD. Furthermore, the extent of the limbal area involved by the OSSN is identified as an independent risk factor of the development of LSCD.
Sublingual hematoma as a rare complication of warfarin therapy in a patient with rheumatic heart disease: a case report
Authors: Idrees Muhammad , Jain Hritvik , Masood Abdullah , Usama Rana Muhammad , Odat Ramez M. , Bin Abid Hamza , Khalid Umair , Mahmood Armghan , Jain Jyoti , Hanifa Hamdah 
Published: September 2024

Introduction and importance:
Warfarin prevents thromboembolic events by acting as a vitamin-K antagonist. Close monitoring with an international normalized ratio (INR) is required to avoid bleeding-related complications. One of its rare complications is sublingual hematoma, with potentially life-threatening conditions such as severe airway obstruction. The authors present a rare case of sublingual hematoma after warfarin therapy in a patient with rheumatic heart disease (RHD).

Case presentation:
The authors report a case of a 44-year-old female with rheumatic heart disease who developed sublingual hematoma following warfarin therapy. She presented with difficulty swallowing and speaking due to pain and swelling under her tongue. Her INR was elevated. After discontinuing the drug, the patient received fresh frozen plasma and intravenous vitamin K. Her symptoms resolved within 24 h, and she was discharged without any complications. As per our understanding, this is the first case of sublingual hematoma secondary to warfarin therapy that has been reported in Pakistan.

Clinical discussion:
Warfarin remains a cornerstone anticoagulant in developing countries despite bleeding risks, with management of complications like sublingual hematoma involving INR normalization and conservative treatment. Timely intervention and monitoring of drug interactions are critical in preventing serious outcomes and reducing mortality associated with warfarin therapy.

Conclusion:
Warfarin is a commonly prescribed oral anticoagulant for a variety of conditions. Despite being rare, sublingual hematoma should be considered by the treating physician as a potential complication.
Giant ovarian mucinous cystadenoma complicating term pregnancy: a rare case report
Authors: Manh Thang Nguyen , Thi Huyen Anh Nguyen , Thanh Quang Huynh 
Published: September 2024

Introduction:
Adnexal masses in pregnancy are identified at a rate of 2 to 20 in 1000, which mostly are benign simple cysts. Although the majority of adnexal masses will resolve spontaneously by the beginning of the second trimester, some cases are persistent forms which can result in complications for both mother and fetus.

Presentation of case:
A 31-year-old pregnant woman was diagnosed with a left ovarian mucinous cystadenoma. The ovarian cyst was first detected in the 8th week of pregnancy, measured 5×5 cm and reached 40×30 cm at 38 weeks of gestation. The patient underwent an elective cesarean delivery along with a left salpingo-oophorectomy at term. An alive female baby of 3000 g was delivered with good APGAR scores at the first and fifth minutes. Histologic examination confirmed the diagnosis of a benign mucinous cystadenoma.

Dicussion:
The option of surgical intervention versus conservative management should be tailored to the patient’s physical symptoms, characteristics of the tumor, and gestational age. An elective cesarean section along with salpingo-oophorectomy can be adopted for a giant ovarian cyst complicating term pregnancy. There is a risk of recurrence after a removal of ovarian mucinous cystadenoma.

Conclusion:
Ovarian cysts coexisting with pregnancy should be followed up properly by routine ultrasound and regular antenatal care. The decision to postpone surgical management of a complex mass until the time of delivery must balance the risks and benefits for mother and fetus. After surgery, the patient needs to be provided an appropriate follow-up care to manage postoperative recurrence.
Characteristics of Patients Admitted to Vascular Surgery Service for a Major Lower Limb Amputation From 2017 to 2021 With Present on Admission Pressure Injuries
Authors: Ratliff Catherine R. , Rovnyak Virginia 
Published: September 2024

PURPOSE
The purpose of this study was to describe characteristics of patients admitted from 2017 to 2021 with peripheral arterial disease (PAD) who required a below knee amputation (BKA) or above knee amputation (AKA), including present on admission pressure injuries (POA-PIs).

DESIGN
Descriptive, cross-sectional retrospective research design.

SUBJECTS AND SETTING
The sample comprised 196 patients who underwent 258 major lower limb amputations. A majority (65.9 %n = 170) underwent BKAs and 88 (34.1 %) underwent AKAs. Coronary artery disease was present in 107 (54.6 %) and 143 (73.0%) had diabetes mellitus. The study site was a 670-bed level 1 trauma center in the Mid-Atlantic region of the United States.

METHODS
A retrospective chart review of patients undergoing major lower limb amputations using CPT codes 27880 BKA, and 27590 AKA was completed. Variables extracted included age, sex, race, and comorbid conditions such as smoking, cardiovascular disease, diabetes mellitus, end stage renal disease requiring dialysis, and POA-PI. Descriptive statistics (frequencies, percentages, and means) were used to describe the sample.

RESULTS
There were 25 (12.8%) individuals with POA-PI compared with 171 (87.2%) who did not have POA-PI. None of the characteristics reviewed significantly differed when patients with or without POA-PI were compared. Age was closest to statistical significance (P = .052). In addition, analysis revealed that 73% (n = 143) of individuals had diabetes mellitus in addition to having PAD.

CONCLUSION
Approximately 13% of a group of patients with PAD had POA-PI when admitted to hospital for major limb amputation. Analysis of multiple factors found that none significantly differed between patients with or without POA-PI. Age came nearest to statistical significance and we hypothesize that older age may increase the risk for POA-PI; additional research in samples with greater power to detect this effect are needed. Findings also indicate that diabetes mellitus is a common risk factor for major lower limb amputation. It is important to educate staff/patients/caregivers on the importance of PI prevention especially in the elderly vascular population who are at risk for undergoing major lower limb amputations.
Upregulation of Reward Mesolimbic Activity via fMRI-Neurofeedback Improves Vaccination Efficiency in Humans
Authors: Lubianiker Nitzan , Koren Tamar , Djerasi Meshi , Sirotkin Margarita , Singer Neomi , Jalon Itamar , Lerner Avigail , Sar-el Roi , Sharon Haggai , Azulay-Debby Hilla , Rolls Asya , Hendler Talma 
Published: September 2024

AbstractThe placebo response is associated with a positive expectation of recovery. Recent studies in mice uncovered a potential underlying mechanism of placebo effects, by demonstrating the involvement of the dopaminergic mesolimbic pathway, previously implicated in reward expectation, in immune modulation. Yet, it is not known whether an analogous brain-immune regulatory mechanism exists in humans, and whether it employs conscious positive expectations. Here, we employed fMRI-neurofeedback to train healthy participants to increase their reward mesolimbic activity by using self-chosen mental strategies, followed by Hepatitis B Virus (HBV) vaccination. We found that stronger Ventral Tegmental Area (VTA) activity, but not control regions activation, was associated with higher post-vaccination HBV antibody titer. Interestingly, higher VTA activity before vaccination was associated with mental strategies characterized by positive expectation. Thus, our results establish a relationship between reward system activity, positive expectation and immunity in humans and reveal a potential neuropsychological mechanism for non-invasive immune modulation.https://clinicaltrials.gov/study/NCT03951870.
Sex Differences in Home-Cage Ethanol Drinking and Operant Self-Administration in C57BL/6J Mice with Equivalent Regulation by Glutamate AMPAR Activity
Authors: Faccidomo Sara , Eastman Vallari R , Santanam Taruni S , Swaim Katarina S , Taylor Seth M , Hodge Clyde W 
Published: September 2024

AbstractIntroductionConsidering sex as a biological variable (SABV) in preclinical research can enhance understanding of the neurobiology of alcohol use disorder (AUD). However, the behavioral and neural mechanisms underlying sex-specific differences remain unclear. This study aims to elucidate SABV in ethanol (EtOH) consumption by evaluating its reinforcing effects and regulation by glutamate AMPA receptor activity in male and female mice.MethodsC57BL/6J mice (male and female) were assessed for EtOH intake under continuous and limited access conditions in the home cage. Acute sensitivity to EtOH sedation and blood clearance were evaluated as potential modifying factors. Motivation to consume EtOH was measured using operant self-administration procedures. Sex-specific differences in neural regulation of EtOH reinforcement were examined by testing the effects of a glutamate AMPA receptor antagonist on operant EtOH self-administration.ResultsFemale C57BL/6J mice exhibited a time-dependent escalation in EtOH intake under both continuous and limited access conditions. They were less sensitive to EtOH sedation and had lower blood levels post-EtOH administration (4 g/kg) despite similar clearance rates. Females also showed increased operant EtOH self-administration and progressive ratio performance over a 30-day baseline period compared to males. The AMPAR antagonist GYKI 52466 (0–10 mg/kg, IP) dose-dependently reduced EtOH-reinforced lever pressing in both sexes, with no differences in potency or efficacy.DiscussionThese findings confirm that female C57BL/6J mice consume more EtOH than males in home-cage conditions and exhibit reduced acute sedation, potentially contributing to higher EtOH intake. Females demonstrated increased operant EtOH self-administration and motivation, indicating higher reinforcing efficacy. The lack of sex differences in the relative effects of GYKI 52466 suggests that AMPAR activity is equally required for EtOH reinforcement in both sexes.
Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS
Authors: Xu Junyan , Zhu Kaiyuan , Cai Jieling , Kockan Can , Dokmai Natnatee , Cho Hyunghoon , Woodruff David P. , Sahinalp S. Cenk 
Published: September 2024

AbstractThe introduction of trusted execution environments (TEEs), such as secure enclaves provided by the Intel SGX technology has enabled secure and privacy-preserving computation on the cloud. The stringent resource limitations, such as memory constraints, required by some TEEs necessitates the development of computational approaches with reduced memory usage, such as sketching. One example is the SkSES method for GWAS on a cohort of case and control samples from multiple institutions, which identifies the most significant SNPs in a privacy-preserving manner without disclosing sensitive genotype information to other institutions or the cloud service provider. Here we show how to improve the performance of SkSES on large datasets by augmenting it with a learning-augmented approach. Specifically, we show how individual institutions can perform smaller scale GWAS on their own datasets and identify two sets of variants according to certain criteria, which are then used to guide the sketching process to more accurately identify significant variants over the collective dataset. The new method achieves up to 40% accuracy gain compared to the original SkSES method under the same memory constraints on datasets we tested on. The code is available athttps://github.com/alreadydone/sgx-genome-variants-search.Contactcenk.sahinalp@nih.gov
Characterizing trachoma elimination using serology
Authors: Kamau Everlyn , Ante-Testard Pearl Anne , Gwyn Sarah , Blumberg Seth , Abdalla Zeinab , Aiemjoy Kristen , Amza Abdou , Aragie Solomon , Arzika Ahmed M. , Awoussi Marcel S. , Bailey Robin L. , Butcher Robert , Callahan E. Kelly , Chaima David , Dawed Adisu Abebe , Saboyá Díaz Martha Idalí , Domingo Abou-Bakr Sidik , Drakeley Chris , Elshafie Belgesa E. , Emerson Paul M. , Fornace Kimberley , Gass Katherine , Goodhew E. Brook , Hammou Jaouad , Harding-Esch Emma M. , Hooper PJ , Kadri Boubacar , Kalua Khumbo , Kanyi Sarjo , Kasubi Mabula , Kello Amir B. , Ko Robert , Lammie Patrick J. , Lescano Andres G. , Maliki Ramatou , Masika Michael Peter , Migchelsen Stephanie J. , Nassirou Beido , Nesemann John M. , Parameswaran Nishanth , Pomat Willie , Renneker Kristen , Roberts Chrissy , Rymil Prudence , Sata Eshetu , Senyonjo Laura , Seife Fikre , Sillah Ansumana , Sokana Oliver , Srivathsan Ariktha , Tadesse Zerihun , Taleo Fasihah , Taylor Emma Michelle , Tekeraoi Rababe , Togbey Kwamy , West Sheila K. , Wickens Karana , William Timothy , Wittberg Dionna M. , Yeboah-Manu Dorothy , Youbi Mohammed , Zeru Taye , Keenan Jeremy D. , Lietman Thomas M. , Solomon Anthony W. , Nash Scott D. , Martin Diana L. , Arnold Benjamin F. 
Published: September 2024

AbstractTrachoma is targeted for global elimination as a public health problem by 2030. Measurement of IgG antibodies in children is being considered for surveillance and programmatic decision-making. There are currently no guidelines for applications of serology, which represents a generalizable problem in seroepidemiology and disease elimination. We collatedChlamydia trachomatisPgp3 and CT694 IgG measurements (63,911 children ages 1–9 years) from 48 serosurveys, including surveys across Africa, Latin America, and the Pacific Islands to estimate population-level seroconversion rates (SCR) along a gradient of trachoma endemicity. We propose a novel, generalizable approach to estimate the probability that populationC. trachomatistransmission is below levels requiring ongoing programmatic action, or conversely is above levels that indicate ongoing interventions are needed. We provide possible thresholds for SCR at a specified level of certainty and illustrate how the approach could be used to inform trachoma program decision-making using serology.
Functional impact of the hyperduplication genomophenotype in high copy number endometrial cancer
Authors: Florio Angela , Smadbeck James , Johnson Sarah H. , Lin Wan-Hsin , Sadeghian Dorsay , Sotiriou Sotiris , Salvatori Rebeca , Feathers Ryan W. , Berry Taylor , Kinsella Lindsey , Harris Faye R. , McCune Alexa F. , Murphy Stephen J. , Ali Mohamed F. , Pezeshki Abdulmohammad , Barrett Michael T. , Grcevich Leah , Capasso Ilaria , De Vitis Luigi Antonio , Schivardi Gabriella , Occhiali Tommaso , Larish Alyssa M. , Weroha John , Borad Mitesh J. , Cheville John , Anastasiadis Panos Z. , Mariani Andrea , Vasmatzis George 
Published: September 2024

SummaryHigh copy number endometrial cancers (HCNEC) are dominated by excessive duplications scattered across the genome, termed here as theHyperDuplicationGenomoPhenotype (HDGP). Although correlated with cancer progression, its biological significance and implications for therapy have not yet been established. We identified locations and sizes of duplications in 171 endometrial cancer cases and designated 71 HCNEC cases as HDGP. We also investigated the response to the pan-ERBB inhibitor afatinib in a subset of HDGP-EC cases withERBB2/ERBB3duplications using a patient-derived three-dimensional culture model. Our analysis demonstrates that beyond tandem duplications there is a more general pattern involving coordinated duplication of multiple distant regions of the genome, demonstrating preferential selectivity to over-expressed potential oncogenes within a broad network. This suggests that HDGP increases tumor fitness and resistance to therapy by perturbing important gene networks in concert rather than only driver genes, suggesting a mechanistic basis for the ineffectiveness of targeted drugs in these patients and highlighting the need for combination therapies in these highly aggressive cases.
Ectoine production through a marine methanotroph-microalgae culture allows complete biogas valorization
Authors: Ruiz-Ruiz Patricia , Mohedano-Caballero Patricia , De Vrieze Jo 
Published: September 2024

AbstractMethanotrophs have recently emerged as a promising platform for producing bio-based chemicals, like ectoine, from biogas, offering an economical alternative to glucose. However, most studies have focused solely on CH4consumption, often overlooking the CO2, which is both produced by methanotrophs and present in biogas, despite its potential as a carbon source for microorganisms, such as microalgae. In this study, marine methanotrophic-microalgal cultures were enriched from environmental samples collected at the North Sea coast to explore ectoine production from both CH4and CO2in biogas. The sediment-derived culture exhibited the highest CH4removal efficiency and CO2uptake, and was selected for further experiments. The culture was primarily composed ofMethylobacter marinus,Methylophaga marina, and the microalgaPicochlorum oklahomensis. Gas consumption, growth, and ectoine production were evaluated under varying salinity levels and osmotic stress. The NaCl concentrations above 6% negatively impacted CH4oxidation and inhibited ectoine synthesis, while osmotic shocks enhanced ectoine accumulation, with a maximum ectoine content of 51.3 mgectoinegVSS−1at 4.5% NaCl. This study is the first to report ectoine production from methanotroph-microalgal cultures, showing its potential for biogas valorization into high-value bio-based chemicals, like ectoine, marking a significant step toward sustainable biogas utilization.HighlightsMethanotroph-microalgae cultures can valorize CH4and CO2from biogas into ectoineNaCl concentrations above 6% reduced CH4uptake and inhibited ectoine synthesisOsmotic shock at 4.5% NaCl enhanced ectoine accumulationFirst report of ectoine production using methanotroph-microalgal cultures
Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets
Authors: Qi Guo-An , Zhang Qi-Xin , Kang Jingyu , Li Tianyuan , Xu Xiyun , Zhang Zhe , Fan Zhe , Liu Siyang , Chen Guo-Bo 
Published: September 2024

AbstractEstimation of heritability has been a routine in statistical genetics, in particular with the increasing sample size such as biobank-scale data and distributed datasets, the latter of which has increasing concerns of privacy. Recently a randomized Haseman-Elston regression (RHE-reg) has been proposed to estimate SNP-heritability, and given sufficient iteration (B) RHE-reg can tackle biobank-scale data, such as UK Biobank (UKB), very efficiently. In this study, we present an analytical solution that balances iterationBand RHE-reg estimation, which resolves the convergence of the proposed RHE-reg in high precision. We applied the method for 81 UKB quantitative traits and estimated their SNP-heritability and test statistics precisely. Furthermore, we extended RHE-reg into distributed datasets and demonstrated their utility in real data application and simulated data. The software for estimating SNP-heritability for biobank-scale data is released:https://github.com/gc5k/gear2.
Active segregation in binary mixtures under flow
Authors: Di Dio Giacomo , Colin Remy 
Published: September 2024

AbstractMany bacterial habitats, from the gut to the soil, feature narrow channels where confined flow is a key constraint that might influence the spatial organization, and thus the functioning, of the complex, phenotypically heterogeneous communities these microbes form. Here, we investigate how a model heterogeneous bacterial community of motile and non-motileEscherichia coliorganizes under confined Poiseuille flow. We discovered a new mode of active self-organization, where the motile bacteria induce the rapid sideways segregation of the non-motile cells to one side of the channel, eventually resulting in asymmetric biofilm formation. Our experiments and modeling elucidated the purely physical segregation mechanism: the rheotactic drift of the motile cells, which stems from shear acting on their chiral flagella, induces a conveyer-belt-like backflow advecting the non-motile cells. The latter then accumulate thanks to sedimentation countering flow incompressibility. This unexpected consequence of motility can affect the organization of complex bacteria communities colonizing environments under confined flow.
Evolutionary diversity of CXCL16-CXCR6: Convergent Substitutions and Recurrent Gene Loss in Sauropsids
Authors: Salve Buddhabhushan Girish , Sharma Sandhya , Vijay Nagarjun 
Published: September 2024

AbstractThe CXCL16-CXCR6 axis is crucial for regulating the persistence of CD8 tissue-resident memory T-cells (TRM). CXCR6 deficiency lowers TRMcell numbers in the lungs and depletes ILC3s in the lamina propria, impairing mucosal defence. This axis is linked to diseases like HIV/SIV, cancer, and COVID-19. Together, these highlight that the CXCL16-CXCR6 axis is pivotal in host immunity. Previous studies of the CXCL16-CXCR6 axis found genetic variation among species but were limited to primates and rodents. To understand the evolution and diversity of CXCL16-CXCR6 across vertebrates, we compared ∼400 1-to-1CXCR6orthologs spanning diverse vertebrates. The unique DRF motif ofCXCR6facilitates leukocyte adhesion by interacting with cell surface-expressedCXCL16and plays a key role in G-protein selectivity during receptor signalling; however, our findings show that this motif is not universal. The DRF motif is restricted to mammals, turtles, and frogs, while the DRY motif, typical in other CKRs, is found in snakes and lizards. Most birds exhibit the DRL motif. These substitutions at the DRF motif affect the receptor─Gi/oprotein interaction. We establish recurrentCXCR6gene loss in 10 out of 36 bird orders, including Galliformes and Passeriformes, Crocodilia, and Elapidae, attributed to segmental deletions and/or frame-disrupting changes. Notably, single-cell RNA sequencing of the lung shows a drop in TRMcells in species withCXCR6loss, suggesting a possible link. The concurrent loss ofITGAE, CXCL16andCXCR6in chickens may have altered CD8 TRMcell abundance, with implications for immunity against viral diseases and vaccines inducing CD8 TRMcells.