bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of Subchondral Cysts on the Outcomes of Surgical Treatment for Osteochondral Lesions of the Talus: A Systematic Review and Meta-analysis
Authors: Zhang Jiayao , Zheng Kaiwen , Cai Wufeng , Huang Xihao , Li Qi 
Published: February 2024

Background: Limited literature is available regarding the effect of subchondral cysts on the surgical outcomes for treatment of osteochondral lesion of the talus (OLT). Purpose: To conduct a systematic review and meta-analysis of studies comparing surgical outcomes between OLTs with and without cysts. Study Design: Systematic review; Level of evidence, 4. Methods: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, the authors searched PubMed, Embase, Web of Science, and the Cochrane Library for relevant studies published up to January 7, 2023. The 4375 retrieved studies were screened, and 9 articles (level of evidence, 2-4) were included, which comprised 165 patients with OLT and subchondral cysts (cyst group) and 223 without cysts (noncyst group). After data extraction, mean differences in outcome scores (American Orthopaedic Foot and Ankle Society [AOFAS] Ankle Hindfoot Scale, visual analog scale [VAS] score for pain) and adverse events were compared between the groups. Results: Functional scores improved after surgery in both groups, with the cyst group having a significantly higher AOFAS score than the noncyst group ( P = .005; I2 = 0%); subgroup analysis revealed that this difference was attributable to the size of the osteochondral lesion and the type of surgical procedure. No significant difference was found between the cyst and noncyst groups in VAS pain scores ( P = .77; I2 = 0%) or postoperative adverse events ( P = .35; I2 = 0%). Conclusion: The results of this review indicated that patients with subchondral cysts improved with surgical treatment of OLT. A relatively low level of evidence was available to indicate that surgical treatment for small OLTs with subchondral cysts will result in better clinical outcomes compared with OLTs without cysts.
Experiences of an Online Palliative Rehabilitation Programme for Spousal Caregivers of People With Amyotrophic Lateral Sclerosis and Cognitive and/or Behavioural Impairments: A Qualitative Interpretive Study
Authors: Olesen Lene Klem , la Cour Karen , Nimmon Laura , With Heidi , Handberg Charlotte 
Published: February 2024

Purpose: The purpose of this study was to understand how spousal caregivers of people with amyotrophic lateral sclerosis and cognitive and/or behavioural impairments felt about the EMBRACE intervention. Materials and methods: A qualitative interpretive study, using individual semi-structured interviews pre- and post-participation in a palliative rehabilitation blended learning programme, was applied. In total, 13 spousal caregivers were interviewed pre-intervention and 10 of them post-intervention. Results: Three overarching themes were identified: Striving to Obtain Control in Everyday Life, Peer support Across the Illness Trajectory and The Complexity of Relations. Information provided in targeted videos and sharing experiences with peers in virtual group meetings were beneficial to comprehend, manage and find meaning in everyday challenges related to being a caregiver. Conclusion: The EMBRACE intervention helped spousal caregivers cope with everyday needs and challenges related to being a caregiver. EMBRACE was found to support and strengthen the participants in gaining more control in everyday life, creating a sense of coherence. Through targeted videos and discussions with peers, the participants felt prepared for the illness trajectory of their relative. Peer support promoted resilient functioning and reduced their feelings of loneliness. Clinical trial registration: This study was registered on clinicaltrials.gov under the name: A Complex Intervention Study on a Palliative Rehabilitation Blended Learning Programme to Support Relatives and Health Care Providers of People with ALS and Cognitive Impairments in Coping with Challenges. ID no. NCT04638608. URL: https://clinicaltrials.gov/ct2/results?cond=&term=NCT04638608&cntry=&state=&city=&dist= .
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction
Authors: Zhuang Yongwen , Kim Na Yeon , Fritsche Lars G. , Mukherjee Bhramar , Lee Seunggeun 
Published: February 2024

Abstract
Background
Genetic variants can contribute differently to trait heritability by their functional categories, and recent studies have shown that incorporating functional annotation can improve the predictive performance of polygenic risk scores (PRSs). In addition, when only a small proportion of variants are causal variants, PRS methods that employ a Bayesian framework with shrinkage can account for such sparsity. It is possible that the annotation group level effect is also sparse. However, the number of PRS methods that incorporate both annotation information and shrinkage on effect sizes is limited. We propose a PRS method, PRSbils, which utilizes the functional annotation information with a bilevel continuous shrinkage prior to accommodate the varying genetic architectures both on the variant-specific level and on the functional annotation level.

Results
We conducted simulation studies and investigated the predictive performance in settings with different genetic architectures. Results indicated that when there was a relatively large variability of group-wise heritability contribution, the gain in prediction performance from the proposed method was on average 8.0% higher AUC compared to the benchmark method PRS-CS. The proposed method also yielded higher predictive performance compared to PRS-CS in settings with different overlapping patterns of annotation groups and obtained on average 6.4% higher AUC. We applied PRSbils to binary and quantitative traits in three real world data sources (the UK Biobank, the Michigan Genomics Initiative (MGI), and the Korean Genome and Epidemiology Study (KoGES)), and two sources of annotations: ANNOVAR, and pathway information from the Kyoto Encyclopedia of Genes and Genomes (KEGG), and demonstrated that the proposed method holds the potential for improving predictive performance by incorporating functional annotations.

Conclusions
By utilizing a bilevel shrinkage framework, PRSbils enables the incorporation of both overlapping and non-overlapping annotations into PRS construction to improve the performance of genetic risk prediction. The software is available at https://github.com/styvon/PRSbils.
A juvenile bird with possible crown-group affinities from a dinosaur-rich Cretaceous ecosystem in North America
Authors: Brownstein Chase Doran 
Published: February 2024

Abstract
Background
Living birds comprise the most speciose and anatomically diverse clade of flying vertebrates, but their poor early fossil record and the lack of resolution around the relationships of the major clades have greatly obscured extant avian origins.

Results
Here, I describe a Late Cretaceous bird from North America based on a fragmentary skeleton that includes cranial material and portions of the forelimb, hindlimb, and foot and is identified as a juvenile based on bone surface texture. Several features unite this specimen with crown Aves, but its juvenile status precludes the recognition of a distinct taxon. The North American provenance of the specimen supports a cosmopolitan distribution of early crown birds, clashes with the hypothesized southern hemisphere origins of living birds, and demonstrates that crown birds and their closest relatives coexisted with non-avian dinosaurs that independently converged on avian skeletal anatomy, such as the alvarezsaurids and dromaeosaurids.

Conclusions
By revealing the ecological and biogeographic context of Cretaceous birds within or near the crown clade, the Lance Formation specimen provides new insights into the contingent nature of crown avian survival through the Cretaceous-Paleogene mass extinction and the subsequent origins of living bird diversity.
Identification of genomic characteristics and selective signals in Guizhou black goat
Authors: Chang Lingle , Zheng Yundi , Li Sheng , Niu Xi , Huang Shihui , Long Qingmeng , Ran Xueqin , Wang Jiafu 
Published: February 2024

Abstract
Background
Guizhou black goat is one of the indigenous black goat breeds in the southwest region of Guizhou, China, which is an ordinary goat for mutton production. They are characterized by moderate body size, black coat, favorite meat quality with tender meat and lower odor, and tolerance for cold and crude feed. However, little is known about the genetic characteristics or variations underlying their important economic traits.

Results
Here, we resequenced the whole genome of Guizhou black goat from 30 unrelated individuals breeding in the five core farms. A total of 9,835,610 SNPs were detected, and 2,178,818 SNPs were identified specifically in this breed. The population structure analysis revealed that Guizhou black goat shared a common ancestry with Shaanbei white cashmere goat (0.146), Yunshang black goat (0.103), Iran indigenous goat (0.054), and Moroccan goat (0.002). However, Guizhou black goat showed relatively higher genetic diversity and a lower level of linkage disequilibrium than the other seven goat breeds by the analysis of the nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity. Based on FST and θπ values, we identified 645, 813, and 804 selected regions between Guizhou black goat and Yunshang black goat, Iran indigenous goat, and cashmere goats. Combined with the results of XP-EHH, there were 286, 322, and 359 candidate genes, respectively. Functional annotation analysis revealed that these genes are potentially responsible for the immune response (e.g., CD28, CD274, IL1A, TLR2, and SLC25A31), humility-cold resistance (e.g., HBEGF, SOSTDC1, ARNT, COL4A1/2, and EP300), meat quality traits (e.g., CHUK, GAB2, PLAAT3, and EP300), growth (e.g., GAB2, DPYD, and CSF1), fertility (e.g., METTL15 and MEI1), and visual function (e.g., PANK2 and NMNAT2) in Guizhou black goat.

Conclusion
Our results indicated that Guizhou black goat had a high level of genomic diversity and a low level of linkage disequilibrium in the whole genome. Selection signatures were detected in the genomic regions that were mainly related to growth and development, meat quality, reproduction, disease resistance, and humidity-cold resistance in Guizhou black goat. These results would provide a basis for further resource protection and breeding improvement of this very local breed.
Hyperactivation and enhanced cytotoxicity of reduced CD8+ gamma delta T cells in the intestine of patients with Crohn’s disease correlates with disease activity
Authors: Zhu Tao , Zhu Linlin , Sheng Caixia , Wu Danju , Gu Qianru , Jiang Zhinong , Xu Jiaqi , Fu Guoxiang , Jiang Yujie 
Published: February 2024

Abstract
Background and aims
We aimed to investigate the immune characteristics of intestinal CD8+ gamma delta T (CD8+ γδ T) cells in Crohn’s disease (CD) and their correlation with disease activity.

Methods
The study cohorts included 21 CD patients and 21 healthy individuals. CD8+ γδ T cells were isolated from human ileal mucosa for detection by flow cytometry. The activation or inhibition status of cells was detected by detecting the expression of activation marker HLA-DR and the immunosuppressive molecule PD-1 on cells. The cytotoxicity of cells was assessed by detecting the expression of cytotoxic molecules (Perforin, Granzyme B, and TRAIL) in cells. Ratios of investigated cells were calculated as prediction factors by receiver operating characteristic curve (ROC) analysis.

Results
The study revealed a reduction in intestinal CD8+ γδT cells among active CD patients, with a more pronounced reduction observed in moderately active patients compared to mildly active patients. Moreover, active CD patients exhibited heightened activation levels in their intestinal CD8+ γδT cells, whereas the activation was comparatively weakened in moderately active patients compared with mildly active patients. Additionally, the cytotoxicity of intestinal CD8+ γδT cells was enhanced solely in mildly active patients, while it was impaired in moderately active patients compared with mildly active patients. Furthermore, HLA-DR+ CD8+ γδT cell ratio, CD8+ γδT ratio, and CD8+ γδT count were identified as indicators in the diagnosis of active CD. Meanwhile, the ratios of Granzyme B+ CD8+ γδT cell and Perforin+ CD8+ γδT cell were identified as indicators that distinguish mildly moderately active CD cases.

Conclusions
Intestinal CD8+ γδT was reduced in active CD patients, but their activation and cytotoxicity were enhanced. However, with increased disease activity, intestinal CD8+ γδ T cells became dysfunctional. CD-specific perturbations observed in various phenotypic markers in CD8+ γδ T cells can be used as indicators to assist in diagnosing CD patients.
Facultative mycorrhization in a fern (Struthiopteris spicant L. Weiss) is bound to light intensity
Authors: Guillen-Otero Thais , Lee Soon-Jae , Hertel Dietrich , Kessler Michael 
Published: February 2024

Abstract
Background
The establishment of mycorrhizal relationships between a fungus and a plant typically enhances nutrient and water uptake for the latter while securing a carbon source for the fungus. However, under a particular set of environmental conditions, such as low availability of light and abundant nutrients in the soil, the resources invested in the maintenance of the fungi surpass the benefits obtained by the host. In those cases, facultative mycorrhizal plants are capable of surviving without symbiosis. Facultative mycorrhization in ferns has been overlooked until now. The present study measured the response of Struthiopteris spicant L. Weiss, and its root-associated fungi to different levels of light and nutrient availability in terms of growth, mycorrhizal presence, and leaf nutrient content. This fern species exhibits a great tolerance to variable light, nutrient, and pH conditions, and it has been found with and without mycorrhizae. We conducted a greenhouse experiment with 80 specimens of S. spicant and three factors (Light, Phosphorus, and Nitrogen) resulting in eight treatments.

Results
We found a significant influence of the factor light on fungal community composition, plant biomass, and nutrient accumulation. Departing from a lack of colonization at the initial stage, plants showed a remarkable increment of more than 80% in the arbuscular mycorrhizal fungi (AMF) richness and abundance in their roots when grown under high light conditions, compared with the ones in low light. We also observed an upward trend of C:P and C:N ratios and the above- and belowground biomass production when AMF abundance increased. Furthermore, the compositional analysis of the whole fungal communities associated with S. spicant roots revealed clear differences among low-light and high-light treatments.

Conclusions
This study is the first to investigate the importance of light and nutrient availability in determining fern-AMF relationships. We confirmed that Struthiopteris spicant is a facultative mycorrhizal plant. The composition and diversity of AMF found in the roots of this fern are strongly influenced by light and less by nutrient conditions. Our study shows that ferns respond very sensitively to changes in environmental factors, leading to shifts in the associated mycorrhizal communities.
Carbon monoxide is involved in melatonin-enhanced drought resistance in tomato seedlings by enhancing chlorophyll synthesis pathway
Authors: Liu Yunzhi , Xu Junrong , Lu Xuefang , Huang Mengxiao , Mao Yuanzhi , Li Chuanghao , Yu Wenjin , Li Changxia 
Published: February 2024

Abstract
Background
Drought is thought to be a major abiotic stress that dramatically limits tomato growth and production. As signal molecule, melatonin (MT) and carbon monoxide (CO) can enhance plant stress resistance. However, the effect and underlying mechanism of CO involving MT-mediated drought resistance in seedling growth remains unknown. In this study, tomato (Solanum lycopersicum L. ‘Micro-Tom’) seedlings were used to investigate the interaction and mechanism of MT and CO in response to drought stress.

Results
The growth of tomato seedlings was inhibited significantly under drought stress. Exogenous MT or CO mitigated the drought-induced impairment in a dose-dependent manner, with the greatest efficiency provided by 100 and 500 µM, respectively. But application of hemoglobin (Hb, a CO scavenger) restrained the positive effects of MT on the growth of tomato seedlings under drought stress. MT and CO treatment promoted chlorophyll a (Chl a) and chlorophyll a (Chl b) accumulations. Under drought stress, the intermediate products of chlorophyll biosynthesis such as protoporphyrin IX (Proto IX), Mg-protoporphyrin IX (Mg-Proto IX), potochlorophyllide (Pchlide) and heme were increased by MT or CO, but uroporphyrinogen III (Uro III) content decreased in MT-treated or CO-treated tomato seedlings. Meanwhile, MT or CO up-regulated the expression of chlorophyll and heme synthetic-related genes SlUROD, SlPPOX, SlMGMT, SlFECH, SlPOR, SlChlS, and SlCAO. However, the effects of MT on chlorophyll biosynthesis were almost reversed by Hb.

Conclusion
The results suggested that MT and CO can alleviate drought stress and facilitate the synthesis of Chl and heme in tomato seedlings. CO played an essential role in MT-enhanced drought resistance via facilitating chlorophyll biosynthesis pathway.
Rare and common coding variants in lipid metabolism-related genes and their association with coronary artery disease
Authors: Li Wei , Wang Yongyi , Huang Ritai , Lian Feng , Xu Genxing , Wang Weijun , Xue Song 
Published: February 2024

Abstract
Background
Coronary artery disease (CAD) is a complex disease that is influenced by environmental and genetic factors. In this study, we aimed to investigate the relationship between coding variants in lipid metabolism-related genes and CAD in a Chinese Han population.

Methods
A total of 252 individuals were recruited for this study, including 120 CAD patients and 132 healthy control individuals. Rare and common coding variants in 12 lipid metabolism-related genes (ANGPTL3, ANGPTL4, APOA1, APOA5, APOC1, APOC3, CETP, LDLR, LIPC, LPL, PCSK9 and SCARB1) were detected via next-generation sequencing (NGS)-based targeted sequencing. Associations between common variants and CAD were evaluated by Fisher’s exact test. A gene-based association test of rare variants was performed by the sequence kernel association test-optimal (SKAT-O test).

Results
We found 51 rare variants and 17 common variants in this study. One common missense variant, LIPC rs6083, was significantly associated with CAD after Bonferroni correction (OR = 0.47, 95% CI = 0.29–0.76, p = 1.9 × 10− 3). Thirty-three nonsynonymous rare variants were identified, including two novel variants located in the ANGPTL4 (p.Gly47Glu) and SCARB1 (p.Leu233Phe) genes. We did not find a significant association between rare variants and CAD via gene-based analysis via the SKAT-O test.

Conclusions
Targeted sequencing is a powerful tool for identifying rare and common variants in CAD. The common missense variant LIPC rs6083 confers protection against CAD. The clinical relevance of rare variants in CAD aetiology needs to be investigated in larger sample sizes in the future.
Diagnostic performance of coronary computed tomography angiography stenosis score for coronary stenosis
Authors: Xiong Qing-feng , Fu Xiao-rong , Ku Lei-zhi , Zhou Di , Guo Sheng-peng , Zhang Wen-sheng 
Published: February 2024

Abstract
Background
Coronary computed tomography angiography stenosis score (CCTA-SS) is a proposed diagnosis score that considers the plaque characteristics, myocardial function, and the diameter reduction rate of the lesions. This study aimed to evaluate the diagnostic performance of the CCTA-SS in seeking coronary artery disease (CAD).

Methods
The 228 patients with suspected CAD who underwent CCTA and invasive coronary angiography (ICA) procedures were under examination. The diagnostic performance was evaluated with the receiver operating curve (ROC) for CCTA-SS in detecting CAD (defined as a diameter reduction of ≥ 50%) and severe CAD (defined as a diameter reduction of ≥ 70%).

Results
The area under ROC (AUC) of CCTA-SS was 0.909 (95% CI: 0.864–0.943), which was significantly higher than that of CCTA (AUC: 0.826; 95% CI: 0.771–0.873; P = 0.0352) in diagnosing of CAD with a threshold of 50%. The optimal cutoff point of CCTA-SS was 51% with a sensitivity of 90.66%, specificity of 95.65%, positive predictive value of 98.80%, negative predictive value of 72.13%, and accuracy of 91.67%, whereas the optimal cutoff point of CCTA was 55%, and the corresponding values were 87.36%, 93.48%, 98.15%, 65.15%, and 88.60%, respectively. With a threshold of 70%, the performance of CCTA-SS with an AUC of 0.927 (95% CI: 0.885–0.957) was significantly higher than that of CCTA with an AUC of 0.521 (95% CI: 0.454–0.587) (P < 0.0001).

Conclusions
CCTA-SS significantly improved the diagnostic accuracy of coronary stenosis, including CAD and severe CAD, compared with CCTA.
Quality-of-life measures and their psychometric properties used in African chronic kidney disease populations: a systematic review using COSMIN methodology
Authors: Faye Moustapha , Manneville Florian , Faye Adama , Frimat Luc , Guillemin Francis 
Published: February 2024

Abstract
Background
If any benefit is to be derived from the use of the health-related quality of life (HRQoL) questionnaires in chronic kidney disease (CKD) patients, they should be validated and culturally adapted to the target population. We aimed to critically appraise the psychometric properties of HRQoL questionnaires used in African populations with CKD.

Methods
Web of Science, Embase, PubMed and PsycINFO databases were searched. Psychometric validation studies of HRQoL questionnaires reporting at least one psychometric property of the COSMIN checklist in CKD African population, published up to October 16, 2023 were included and independently assessed for methodological quality and level of measurement properties by using the COSMIN methodology.

Results
From 1163 articles, 5 full-text were included. Only the Kidney Disease Quality-of-Life questionnaire was translated and cross-culturally adapted for studies of patients with CKD. Internal consistency was of doubtful quality in 4 studies and very good in 1. Its measurement was sufficient in 1 study and insufficient in 4. Test–retest reliability was of doubtful quality in 4 studies. Its measurement was sufficient in 3 studies and insufficient in 1. Structural validity was of inadequate quality in 1 study and very good quality in 1. Its measurement was sufficient in both. Construct validity was of inadequate quality in all studies. Their measurement was insufficient in 4 studies and sufficient in 1.

Conclusions
This review highlighted that only one HRQoL questionnaire used in studies of African populations with CKD underwent a small number of cultural adaptations and psychometric validations, generally of poor methodological quality. HRQoL validation studies in African CKD populations are needed to better take advantage of the benefits in patient care, population health management, and research.