bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhizosphere mycobiome diversity in four declining Mediterranean tree species
Authors: Diez-Hermano Sergio , Poveda Jorge , Niño-Sanchez Jonatan , Bocos-Asenjo Irene Teresa , Peix Álvaro , Martín-Pinto Pablo , Diez Julio Javier 
Published: October 2023

IntroductionForests in the Mediterranean basin are currently in decline. Their resilience has been eroded as a result of climate change and anthropogenic impacts, making them vulnerable to increasingly frequent episodes of drought, fire and the spread of pests and diseases. The impact of these natural and anthropogenic events on soil biodiversity is of particular concern, as the soil fungal community plays a key role in ecosystem homeostasis.Objectives and methodsIn order to analyse the relationship between soil health status and fungal diversity, soil samples were collected from declining Mediterranean forests of Castanea sativa (chestnut), Quercus ilex (holm oak), Quercus suber (cork oak) and Quercus pyrenaica (Pyrenean oak). A metabarcoding study was carried out by sequencing the ITS genomic region.ResultsA total of 674 fungal genera were found. It has not been possible to explain the differences in health status from the fungal genera found exclusively on declining forest soils, as none of them have been described as pathogenic. Healthy chestnut soils were characterized by a high alpha diversity and a higher abundance of the genus Metarhizium. No differentially abundant genera were found in any of the other forest species tested. Declining chestnut soils harbored more abundance of ectomycorrhizae and soil saprotrophs than healthy samples. Ectomycorrhizae were the dominant lifestyle in all oak species regardless of health status, whereas arbuscular mycorrhizae were preferentially found in declining cork oak soils.DiscussionThis work highlights the resilience of fungal communities of soil against decline and highlights the need to further investigate its relationship with the forest’s ability to cope with the challenges of climate change.
Learning the kernel for rare variant genetic association test
Authors: Falk Isak , Zhao Millie , Nait Saada Juba , Guo Qi 
Published: October 2023

Introduction: Compared to Genome-Wide Association Studies (GWAS) for common variants, single-marker association analysis for rare variants is underpowered. Set-based association analyses for rare variants are powerful tools that capture some of the missing heritability in trait association studies.Methods: We extend the convex-optimized SKAT (cSKAT) test set procedure which learns from data the optimal convex combination of kernels, to the full Generalised Linear Model (GLM) setting with arbitrary non-genetic covariates. We call this extended cSKAT (ecSKAT) and show that the resulting optimization problem is a quadratic programming problem that can be solved with no additional cost compared to cSKAT.Results: We show that a modified objective is related to an upper bound for the p-value through a decreasing exponential term in the objective function, indicating that optimizing this objective function is a principled way of learning the combination of kernels. We evaluate the performance of the proposed method on continuous and binary traits using simulation studies and illustrate its application using UK Biobank Whole Exome Sequencing data on hand grip strength and systemic lupus erythematosus rare variant association analysis.Discussion: Our proposed ecSKAT method enables correcting for important confounders in association studies such as age, sex or population structure for both quantitative and binary traits. Simulation studies showed that ecSKAT can recover sensible weights and achieve higher power across different sample sizes and misspecification settings. Compared to the burden test and SKAT method, ecSKAT gives a lower p-value for the genes tested in both quantitative and binary traits in the UKBiobank cohort.
Osteonecrosis is associated with APOL1 variants in African Americans with systemic lupus erythematosus
Authors: Yip Kevin , Akerman Meredith , Fernandez Ruiz Ruth , Leung Nicole , Algasas Huda , Qian Yingzhi , Buyon Jill P. , Divers Jasmin , Izmirly Peter , Belmont Michael , Blazer Ashira D. 
Published: October 2023

Background/purposeAfrican Americans (AA) with systemic lupus erythematosus (SLE) are at higher risk for both kidney disease and Osteonecrosis (ON). Two Apolipoprotein L1 (APOL1) risk variants (RV), G1 and G2, have been associated with chronic kidney disease (CKD), hypertension, and microvascular disease in AAs, which are independent risk factors for ON. Accordingly, we investigated the association between carriers of the APOL1 risk variants and the prevalence of ON in AA SLE patients.MethodsA cohort of 121 adult participants of self-reported AA ancestry and meeting at least four of the American College of Rheumatology (ACR) revised criteria for SLE were recruited from a high volume urban SLE clinical site. PCR/sequencing was used to stratify participants by APOL1 genotype. Medical records, including clinical notes and imaging reports, were retrospectively reviewed for documentation of ON. Association between the number of APOL1 risk variants with time to first ON was tested.ResultsIn our cohort, 18 individuals developed ON; across the APOL1 genotype groups, 2/37 0RV, 11/59 1RV, and 5/15 2RV participants were affected. The mean time to ON was 27 years, 22 years, and 18 years in 0RV, 1RV, and 2RV carriers, respectively. An adjusted Cox regression model showed that carrying the APOL1 risk variants associated with shorter ON free survival with hazard ratios (HR) of 3.1 (95% CI: 1.6–6.2) and 9.6 (95% CI 2.4–37.8) for 1RV and 2RV carriers, respectively. 2RV carriers more often exhibited multiple and bilateral joint sites affected by ON. Disease duration was longer in ON-affected participants at 20.5 years compared to 9.0 years in those unaffected (p &lt; 0.001). In individuals who had received glucocorticoids, median cumulative prednisone equivalent dose was higher in ON-affected participants, though this did not reach statistical significance (18.7 g vs. 9.0 g; p-value = 0.3).ConclusionOur analysis suggests a higher risk of osteonecrosis among African American SLE patients who carry the APOL1 risk variants. In addition, disease duration increased the rate of ON. Given the high frequency of the APOL1 risk variants in African Americans, APOL1 high-risk genotype carriers may represent an ON-vulnerable subgroup within the AA population. Further work is necessary to uncover the mechanism of this association.
Cultural adaptation and validation of the Arabic version of the short 12-item stroke-specific quality of life scale
Authors: Sakr Fouad , Dabbous Mariam , Akel Marwan , Salameh Pascale , Hosseini Hassan 
Published: October 2023

BackgroundGiven the excessive length and inconsistent validity of the existing long stroke-specific quality of life (SS-QOL) scales, there is a need to validate a shorter measuring tool. The aim of this study was to validate the Arabic version of the short 12-item SS-QOL (SS-QOL-12-AR) and examine its validity measures and psychometric properties. Additionally, the study aimed to assess the QOL after stroke and identify the sociodemographic and clinical factors that influence it in Lebanon.MethodsA cross-sectional study was conducted. The SS-QOL-12-AR structure was validated, and its reliability and internal consistency were assessed. The scale’s specificity and sensitivity were evaluated and then compared with those of other SS-QOL scales. The correlation between each item and the overall scale were examined, and its convergent validity was evaluated.ResultsA total of 172 stroke survivors were included. The SS-QOL-12-AR structure was validated with a solution of two factors, with a Kaiser-Meyer-Olkin measure of sampling adequacy of 0.850 and a significant Bartlett’s test of sphericity (p &lt; 0.001). The Cronbach’s alpha of the scale was 0.917. According to ROC curve analysis, the optimal cut-off point for distinguishing between lower and better QOL was 32.50. At this cut-off, the sensitivity and specificity were 70.0% and 71.2%, respectively. The area under the curve was 0.779 (95% CI 0.704–0.855, p &lt; 0.001). The SS-QOL-12-AR demonstrated a strong and highly significant correlation with existing versions of the SS-QOL, confirming its convergent validity. 61.6% of stroke survivors had a lower QOL, which was significantly associated with poor stroke prognosis, increased physical dependence, current smoking, and alcohol abstinence.ConclusionThe SS-QOL-12-AR exhibits strong validity and reliability, demonstrating excellent psychometric properties. The scale holds potential for application in clinical practice and research settings, enabling the measurement of stroke-related consequences and evaluation of management outcomes.
Optimal target blood pressure for the primary prevention of hemorrhagic stroke: a nationwide observational study
Authors: Shim Hwan Seok , Park Jeong-Mee , Lee Yong Jae , Kim Young-Deok , Kim Tackeun , Ban Seung Pil , Bang Jae Seung , Kwon O-Ki , Oh Chang Wan , Lee Si Un 
Published: October 2023

BackgroundThere are few reports on the preventative value of intensive blood pressure (BP) management for stroke, especially hemorrhagic stroke (HS), after new criteria for hypertension (HTN) were announced by the American College of Cardiology/American Heart Association in 2017.AimsThis study aimed to identify the optimal BP for the primary prevention of HS in a healthy population aged between 20 and 65 years.MethodsWe conducted a 10-year observational study on the risk of HS, subclassified as intracerebral hemorrhage (ICH) and subarachnoid hemorrhage (SAH) according to BP categories (e.g., low normal BP, high normal BP, elevated BP, stage 1 HTN, and stage 2 HTN) using the National Health Insurance Service Database.ResultsOut of 8,327,751 participants who underwent a health checkup in 2008, 949,550 were included in this study and observed from 2009 to 2018. The risk of ICH was significantly increased in men with stage 2 HTN {adjusted hazard ratio [aHR] 2.002 [95% confidence interval (CI) 1.203–3.332]} and in women with stage 1 HTN [aHR 2.021 (95% CI, 1.251–3.263)]. The risk of SAH was significantly increased in both men [aHR 1.637 (95% CI, 1.066–2.514)] and women [aHR 4.217 (95% CI, 2.648–6.715)] with stage 1 HTN. Additionally, the risk of HS was significantly increased in men with stage 2 HTN [aHR 3.034 (95% CI, 2.161–4.260)] and in women with stage 1 HTN [aHR 2.976 (95% CI, 2.222–3.986)].ConclusionTo prevent primary HS, including ICH and SAH, BP management is recommended for adults under the age of 65 years with stage 1 HTN.
Top 100 cited classical articles in sentinel lymph nodes biopsy for breast cancer
Authors: Liang Xinrui , Wang Yu , Fu Guanghua , Fan Pingmig , Ma Ke , Cao Xu-Chen , Lin Guang-Xun , Zheng Wu-ping , Lyu Peng-fei 
Published: October 2023

BackgroundThe sentinel lymph node biopsy (SLNB) takes on a critical significance in breast cancer surgery since it is the gold standard for assessing axillary lymph node (ALN) metastasis and determining whether to perform axillary lymph node dissection (ALND). A bibliometric analysis is beneficial to visualize characteristics and hotspots in the field of sentinel lymph nodes (SLNs), and it is conducive to summarizing the important themes in the field to provide more insights into SLNs and facilitate the management of SLNs.Materials and methodsSearch terms relating to SLNs were aggregated and searched in the Web of Science core collection database to identify the top 100 most cited articles. Bibliometric tools were employed to identify and analyze publications for annual article volume, authors, countries, institutions, keywords, as well as hotspot topics.ResultsThe period was from 1998 to 2018. The total number of citations ranged from 160 to 1925. LANCET ONCOLOGY and JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION were the top two journals in which the above articles were published. Giuliano, AE was the author with the highest number of articles in this field with 15. EUROPEAN INST ONCOL is the institution with the highest number of publications, with 35 articles. Hotspots include the following 4 topics, false-negative SLNs after neoadjuvant chemotherapy; prediction of metastatic SLNs; quality of life and postoperative complications; and lymphography of SLNs.ConclusionThis study applies bibliometric tools to analyze the most influential literature, the top 100 cited articles in the field of SLNB, to provide researchers and physicians with research priorities and hotspots.
Endocrine treatment near the end of life among older women with metastatic breast cancer: a nationwide cohort study
Authors: Szilcz Máté , Wastesson Jonas W. , Calderón-Larrañaga Amaia , Morin Lucas , Lindman Henrik , Johnell Kristina 
Published: October 2023

BackgroundThe appropriate time to discontinue chemotherapy at the end of life has been widely discussed. In contrast, few studies have investigated the patterns of endocrine treatment near death. In this study, we aimed to investigate the end-of-life endocrine treatment patterns of older women with metastatic breast cancer and explore characteristics associated with treatment.MethodsA retrospective cohort study of all older women (age ≥65 years) with hormone receptor-positive breast cancer who died in Sweden, 2016 − 2020. We used routinely collected administrative and health data with national coverage. Treatment initiation was defined as dispensing during the last three months of life with a nine-month washout period, while continuation and discontinuation were assessed by previous use during the same period. We used log-binomial models to explore factors associated with the continuation and initiation of endocrine treatments.ResultsWe included 3098 deceased older women with hormone receptor-positive breast cancer (median age 78). Overall, endocrine treatment was continued by 39% and initiated by 5% and of women during their last three months of life, while 31% discontinued and 24% did not use endocrine treatment during their last year of life. Endocrine treatment continuation was more likely among older and less educated women, and among women who had multi-dose drug dispensing, chemotherapy, and CDK4/6 use. Only treatment-related factors were associated with treatment initiation.ConclusionMore than a third of women with metastatic breast cancer continue endocrine treatments potentially past the point of benefit, whereas late initiation is less frequent. Further research is warranted to determine whether our results reflect overtreatment at the end of life once patients’ preferences and survival prognosis are considered.
Prevalence and risk factors for high-risk human papillomavirus infection among women from three southern geopolitical zones of Nigeria
Authors: Onwuamah Chika Kingsley , Feng Ning , Momoh Abidemi Esther , Uwandu Mabel , Ahmed Rahaman Ademolu , Idigbe Ifeoma , Vincent Grace Deborah , Ogbu Chinenye Angela , Okonkwo Nkem , Sokei Judith , Abimbola Bowofoluwa Sharon , Ojopagogo Temiloluwa , Okoli Leona Chika , Adesina Mary , Ezemelue Priscilla Ngozi , Sowunmi Omowunmi , Okwuzu Jane , Labo−Popoola Olaoniye Habeebat , Shaibu Joseph Ojonugwa , Ohihoin Greg Aigbe , Nzeribe Emily , David Agatha , Olaleye Olufemi , Ofotokun Ighovwerha , Dong Xiao−ping , Ezechi Oliver Chukwujekwu 
Published: October 2023

IntroductionHuman Papillomavirus (HPV) infection is a risk factor for cervical cancer, the fourth most common cancer among women globally. Its burden is the highest in sub-Saharan Africa, with over 90% mortality. Interventions may fail without evidence-based data on stratified prevalence and risk factors among most at-risk women across Nigeria.MethodsA cross-sectional comparative study, with participants recruited from the Nigerian Institute of Medical Research’s Clinics, NGO outreaches, a cancer screening centre and a university teaching hospital. Questionnaires were self-administered. Trained medics performed sampling at healthcare facilities, and self-sampling was used at outreaches.ResultsNine hundred eighty-five study participants were recruited. About 37% and 27% of the women knew about HPV and its vaccines, respectively, but only 6% confirmed vaccination with HPV vaccines. HPV prevalence was highest among women with unknown marital status (35.9%), single women (33.8%), widowed/divorced/separated women (30.3%), and married/cohabiting women (19.6%). HPV infection was significantly higher among women who take alcohol (odds=1.7 [95% CI: 1.2-2.4]) and women who smoke (odds=2.6 [95% CI: 1.4 - 4.6]. HPV strains detected included HPV16 (1.3%), HPV18 (1.5%), Low Risk (0.2%) and Other High-Risk groups (19.7%).ConclusionThe inverse relationship between prevalence and education suggests interventions improving awareness and prevention would be impactful. Such interventions could also target HIV-positive women, women presenting with sexually-transmitted infections, who smoke and frequently drink alcohol.
Assessing real-world safety concerns of Sacituzumab govitecan: a disproportionality analysis using spontaneous reports in the FDA adverse event reporting system
Authors: Gui Xiujuan , Zhao Jianli , Ding Linxiaoxiao , Chai Jie , Lai Hongna , Cai Yangyang , Luo Simin , Zeng Yinduo , Wu Wenjing , Chen Haizhu , Yao Herui , Wang Ying 
Published: October 2023

AimThe aim of this study was to identify potential safety concerns associated with Sacituzumab Govitecan (SG), an antibody-drug conjugate targeting trophoblastic cell-surface antigen-2, by analyzing real-world safety data from the largest publicly available worldwide pharmacovigilance database.MethodsAll data obtained from the FDA Adverse Event Reporting System (FAERS) database from the second quarter of 2020 to the fourth quarter of 2022 underwent disproportionality analysis and Bayesian analysis to detect and assess the adverse event signals of SG, considering statistical significance when the lower limit of the 95% CI &gt;1, based on at least 3 reports.ResultsTotal of 1072 cases were included. The main safety signals were blood and lymphatic system disorders [ROR(95CI)=7.23 (6.43-8.14)], gastrointestinal disorders [ROR(95CI)=2.01 (1.81-2.22)], and relative infection adverse events, such as neutropenic sepsis [ROR(95CI)=46.02 (27.15-77.99)] and neutropenic colitis [ROR(95CI)=188.02 (120.09-294.37)]. We also noted unexpected serious safety signals, including large intestine perforation [ROR(95CI)=10.77 (3.47-33.45)] and hepatic failure [ROR(95CI)=3.87 (1.45-10.31)], as well as a high signal for pneumonitis [ROR(95CI)=9.93 (5.75-17.12)]. Additionally, age sub-group analysis revealed that geriatric patients (&gt;65 years old) were at an increased risk of neutropenic colitis [ROR(95CI)=282.05 (116.36-683.66)], neutropenic sepsis [ROR(95CI)=101.11 (41.83-244.43)], acute kidney injury [ROR(95CI)=3.29 (1.36-7.94)], and atrial fibrillation [ROR(95CI)=6.91 (2.86-16.69)].ConclusionThis study provides crucial real-world safety data on SG, complementing existing clinical trial information. Practitioners should identify contributing factors, employ monitoring and intervention strategies, and focus on adverse events like neutropenic sepsis, large intestine perforation, and hepatic failure. Further prospective studies are needed to address these safety concerns for a comprehensive understanding and effective management of associated risks.
Single cell transcriptomics identifies distinct choroid cell populations involved in visually guided eye growth
Authors: Summers Jody A. , Jones Kenneth L. 
Published: October 2023

IntroductionPostnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. The choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refraction.MethodsTo elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations when the eye is undergoing emmetropization. Emmetropization was modeled by inducing form deprivation myopia in 3 -4 day old chicks via application of translucent occluders to one eye for a period of 10 days followed by 24 hrs of unrestricted vision (by removing the occluder). Numerous studies have previously shown that visual form deprivation stimulates axial elongation and myopia, and upon removal of the occluder, the myopic chick eye rapidly slows its rate of axial elongation to recover from the induced myopia and regain emmetropia. The contralateral, untreated eyes served as controls.ResultsUMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of gene expression changes were relatively small (&lt; 2 fold). The greatest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This population expressed neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive.DiscussionOur results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization and provide insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.
Clinical outcomes of nephrocalcinosis in preschool-age children: association between nephrocalcinosis improvement and long-term kidney function
Authors: Woo Hyun Ah , Lee Hyeonju , Choi Young Hun , Min Jeesu , Kang Hee Gyung , Ahn Yo Han , Lee Hyun Kyung 
Published: October 2023

BackgroundWe evaluated the long-term clinical outcomes of nephrocalcinosis (NC) according to etiology and grade in preschool-age children with NC.MethodsWe retrospectively analyzed the clinical outcomes and disease grade of children with NC classified into three groups according to etiology: prematurity, tubular disorders, and others.ResultsOverall, 67 children were diagnosed with NC [median age, 0.76 years; interquartile range (IQR) 0.46–2.14 years]. The etiologies of NC included prematurity (28.4%), tubular disorders (25.4%), and others (46.3%). Moreover, 56 (83.6%) children were asymptomatic and diagnosed accidentally through kidney ultrasonography. Newly diagnosed underlying diseases were greater in the tubular disorders group than in the other two groups (P = 0.001). Significantly more newly diagnosed NCs were grade 3 than grade 1 (P = 0.003). The median estimated glomerular filtration rate (eGFR) changed from 96.1 (IQR 68.8–119.2) ml/min/1.72 m2 at diagnosis to 90.9 (IQR 76.4–106.4) ml/min/1.72 m2 at the last follow-up, without a significant difference (P = 0.096). Changes in the kidney function did not differ according to etiology. However, patients without improvement in NC grade showed a decrease in eGFR from 98.1 (IQR 71.1–132.9) to 87.4 (IQR 74.0–104.1) ml/min/1.73 m2 (P = 0.023), while patients with improved NC grade did not show any change in the kidney function.ConclusionsEarly recognition, especially in NC grade 3, can help uncover further diagnoses, such as tubular disorders. Long-term kidney function depends on whether the NC grade improves.