bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification
Authors: Mancin Enrico , Tuliozi Beniamino , Pegolo Sara , Sartori Cristina , Mantovani Roberto 
Published: January 2022

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals’ life, a potentially important aspect in the study of the traits’ genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50–60 Mb), while the hotspot associated with CF and DP was on BTA18 (55–62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia
Authors: Cui Yang , Fan Baolian , Xu Xu , Sheng Shasha , Xu Yuhui , Wang Xiaoyun 
Published: January 2022

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.
Prevalence of Inflammatory Pathways Over Immuno-Tolerance in Peripheral Blood Mononuclear Cells of Recent-Onset Type 1 Diabetes
Authors: Santos Aritania Sousa , Cunha-Neto Edécio , Gonfinetti Nelson Vinicius , Bertonha Fernanda Bernardi , Brochet Pauline , Bergon Aurelie , Moreira-Filho Carlos Alberto , Chevillard Christophe , Silva Maria Elizabeth Rossi da 
Published: January 2022

BackgroundChanges in innate and adaptive immunity occurring in/around pancreatic islets had been observed in peripheral blood mononuclear cells (PBMC) of Caucasian T1D patients by some, but not all researchers. The aim of our study was to investigate whether gene expression patterns of PBMC of the highly admixed Brazilian population could add knowledge about T1D pathogenic mechanisms.MethodsWe assessed global gene expression in PBMC from two groups matched for age, sex and BMI: 20 patients with recent-onset T1D (≤ 6 months from diagnosis, in a time when the autoimmune process is still highly active), testing positive for one or more islet autoantibodies and 20 islet autoantibody-negative healthy controls.ResultsWe identified 474 differentially expressed genes between groups. The most expressed genes in T1D group favored host defense, inflammatory and anti-bacterial/antiviral effects (LFT, DEFA4, DEFA1, CTSG, KCNMA1) and cell cycle progression. Several of the downregulated genes in T1D target cellular repair, control of inflammation and immune tolerance. They were related to T helper 2 pathway, induction of FOXP3 expression (AREG) and immune tolerance (SMAD6). SMAD6 expression correlated negatively with islet ZnT8 antibody. The expression of PDE12, that offers resistance to viral pathogens was decreased and negatively related to ZnT8A and GADA levels. The increased expression of long non coding RNAs MALAT1 and NEAT1, related to inflammatory mediators, autoimmune diseases and innate immune response against viral infections reinforced these dataConclusionsOur analysis suggested the activation of cell development, anti-infectious and inflammatory pathways, indicating immune activation, whereas immune-regulatory pathways were downregulated in PBMC from recent-onset T1D patients with a differential genetic profile.
An Insight Into Systemic Immune Response in Leishmania donovani Mediated Atypical Cutaneous Leishmaniasis in the New Endemic State of Himachal Pradesh, India
Authors: Thakur Lovlesh , Madaan Priyanka , Jain Aklank , Shankar Vinay , Negi Ajeet , Chauhan Shashi Bhushan , Sundar Shyam , Singh Om Prakash , Jain Manju 
Published: January 2022

Leishmaniasis continues to afflict known and newer endemic sites despite global efforts towards its control and elimination. In this regard, the emergence of newer endemic sites with unusual disease formats is recognized wherein Leishmania donovani complex classically known to cause visceral disease is demonstrated to cause cutaneous manifestation. In this context, atypical cutaneous leishmaniasis (CL) cases caused by L. donovani genetic variants from the newer endemic state of Himachal Pradesh (HP) in India are beginning to be understood in terms of parasite determinants. The atypical CL manifestation further needs to be explored to define host immune correlates with a possible role in driving the unusual disease progression. In the given study, we performed comprehensive systemic-immune profiling of the atypical CL patients from the study area in HP, India, in comparison with the classical visceral leishmaniasis (VL) patients from the northeast region of India. The systemic immune response was studied using ELISA-based assessment of Th1, Th2, Th17, Treg, and Th22 specific plasma cytokine expression pattern and parasite-specific total serum IgG/IgG subclasses. The specified immune correlates are known to exhibit heterogeneous association with the different infecting parasite species, infection load, and co-lateral host immunopathology in classical CL and VL. In the atypical CL patient group, altered expression of IL-10 emerged as the key finding that could potentially fine-tune the Th1/Th17/Th22 effector cytokine axis towards a localized cutaneous manifestation. A reduced expression of IL-10 along with a high IFN-γ/IL-10 ratio as a readout of effective parasite killing defined atypical cutaneous outcome. In contrast, high circulatory IL-10 levels and a depressed IFN-γ/IL-10 ratio were seen in classical VL patients in line with an ineffective parasite-killing cytokine response. Overall, the study highlights new knowledge on host immune correlates in terms of cytokine expression pattern and IgG subclasses that underline atypical disease manifestation such that L. donovani, a generally visceralizing parasite species cause skin localized cutaneous lesions.
A New Risk Score for Patients With Acute Chest Pain and Normal High Sensitivity Troponin
Authors: Ma Chunpeng , Liu Xiaoli , Ma Lixiang 
Published: January 2022

Objective: To investigate a new risk score for patients who suffered from acute chest pain with normal high-sensitivity troponin I (hs-TnI) levels.Methods: In this study, patients with acute chest pain who were admitted to the emergency department (ED) of our hospital had been recruited. Hs-TnI was measured in serum samples drawn on admission to the ED. The end point was the occurrence of major adverse cardiac events (MACE) within 3 months. Predictor variables were selected by logistic regression analysis, and external validity was assessed in this study. Furthermore, validation was performed in an independent cohort, i.e., 352 patients (validation cohort).Results: A total of 724 patients were included in the derivation cohort. The results showed that four predictor variables were significant in the regression analysis—male, a history of chest pain, 60 years of age or older and with three or more coronary artery disease (CAD) risk factors. A total of 105 patients in the validation cohort had serious adverse cardiac events. The validation cohort showed a homogenous pattern with the derivation cohort when patients were stratified by score. The area under the curve (AUC) of the receiver operating characteristic (ROC) in the derivation cohort was 0.80 (95% CI: 0.76–0.83), while in the validation cohort, it was 0.79 (95% CI: 0.75–0.82).Conclusion: A new risk score was developed for acute chest pain patients without known CAD and ST-segment deviation and with normal hs-TnI and may aid MACE risk assessment and patient triage in the ED.
Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits
Authors: Xu Liangcai , Peng Bo , He Yuxiang , Cui Yujun , Hu Qinghua , Wu Yarong , Chen Hongbiao , Zhou Xiaofeng , Chen Lili , Jiang Min , Zuo Le , Chen Qiongcheng , Wu Shuang , Liu Yang , Qin Yanming , Shi Xiaolu 
Published: January 2022

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic.Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed.Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients’ samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple β-lactamase genes (blaB, blaGOB, and blaCME). The isolates displayed resistance to nitrofurans, penicillins, and most β-lactam drugs. The bacteria survived heating at 56°C for 30 min.Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.
Prognostic Value and Risk Factors of Treatment-Related Lymphopenia in Malignant Glioma Patients Treated With Chemoradiotherapy: A Systematic Review and Meta-Analysis
Authors: Zhang Yongchao , Chen Shichao , Chen Hualei , Chen Shanshan , Li Zhen , Feng Enshan , Li Wei 
Published: January 2022

Background: Immunotherapy has shown promising therapeutic efficacy in various cancers but not gliomas. Circulating lymphocytes play critical roles in cancer control and responses to immune checkpoint inhibitors. Treatment-related lymphopenia has been associated with poor survival in patients with various tumors. This meta-analysis evaluated the risk and impact of lymphopenia in patients with glioma.Methods: The PubMed, Embase, Web of Science, and Cochrane Library databases were comprehensively searched. Eligible studies were included if they reported the incidence and risk factors of lymphopenia and the impact of lymphopenia on survival. Stata 16.0 was used for this meta-analysis.Results: A total of 21 studies were included in the final systematic review and 20 were included in the quantitative analysis. The overall incidence of grade III/IV lymphopenia was 31.6% [95% confidence interval (CI), 22.3–40.8%]. Pooled results based on pathology of glioma revealed that the incidence in astrocytoma and astrocytoma oligodendroglioma patients was 20.2% (95% CI:5.9–34.4%), and the incidence in glioblastoma patients was 27.6% (95% CI:16.2–38.9%). Lymphopenia was associated with poor overall survival (hazard ratio, 1.99; 95% CI, 1.74–2.27; P&lt; 0.001) compared to no lymphopenia. Brain receiving radiation dose of 20 or 25 Gy, female sex, older age, lower baseline lymphocyte count, and dexamethasone dose &gt; 2 mg instead of baseline use were risk factors for lymphopenia.Conclusions: Treatment-related lymphopenia was associated with decreased survival in patients with glioma. Optimization of chemoradiation regimens, particularly in patients with concurrent risk factors, can reduce lymphopenia and potentially improve survival in the era of immunotherapy.
Intrinsic Brain Activity in Temporal Lobe Epilepsy With and Without Depression: Insights From EEG Microstates
Authors: Sun Yueqian , Ren Guoping , Ren Jiechuan , Wang Qun 
Published: January 2022

Background: Depression is the most common psychiatric comorbidity of temporal lobe epilepsy (TLE). In the recent years, studies have focused on the common pathogenesis of TLE and depression. However, few of the studies focused on the dynamic characteristics of TLE with depression. We tested the hypotheses that there exist abnormalities in microstates in patients with TLE with depression.Methods: Participants were classified into patients with TLE with depression (PDS) (n = 19) and patients with TLE without depression (nPDS) (n = 19) based upon the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-V). Microstate analysis was applied based on 256-channel electroencephalography (EEG) to detect the dynamic changes in whole brain. The coverage (proportion of time spent in each state), frequency of occurrence, and duration (average time of each state) were calculated.Results: Patients with PDS showed a shorter mean microstate duration with higher mean occurrence per second compared to patients with nPDS. There was no difference between the two groups in the coverage of microstate A–D.Conclusion: This is the first study to present the temporal fluctuations of EEG topography in comorbid depression in TLE using EEG microstate analysis. The temporal characteristics of the four canonical EEG microstates were significantly altered in patients with TLE suffer from comorbid depression.
Endovascular Treatment of Ruptured Very Small Intracranial Aneurysms: Complications, Recurrence Rate, and Clinical Outcomes
Authors: Qin Feiyun , Liu Jiaqiang , Zhao Xintong , Wu Degang , Lai Niansheng , Zhang Zihuan , Li Zhenbao 
Published: January 2022

Objective: The aim of this study was to evaluate the safety and efficacy of endovascular treatment for ruptured very small (≤3 mm) intracranial aneurysms (VSIAs).Methods: The clinical data and imaging results for 152 patients with VSIAs treated with coil embolization from August 2014 to June 2020 were retrospectively reviewed. The influential factors related to the preoperative complications, aneurysm recurrence, and clinical outcomes for these patients were analyzed.Results: Among 152 patients with ruptured VSIAs, 90 were treated with coil embolization alone, while 62 were treated with stent-assisted coil embolization. Eighteen patients experienced intra and/or postoperative complications (overall incidence = 11.8%). One person died of intraoperative aneurysm re-rupture and postoperative rebleeding (mortality rate = 0.65%). Twenty patients had various degrees of neurological dysfunction (morbidity rate = 13.1%). Statistical analysis showed that there was no independent risk factor associated with perioperative complications. The rate of complete aneurysm occlusion at discharge and follow-up was 76.3 and 86.2%, respectively. A total of 105 patients underwent digital subtraction angiography during follow-up, and 18 of them experienced postoperative recurrence (recurrence rate = 17.1%). Seven patients were retreated (retreatment rate = 6.7%). The use of stents was the only factor that affected the postoperative recurrence of aneurysm. The incidence of favorable clinical outcomes (Glasgow Outcome Scale score ≥ 4) at discharge and follow-up was 86.2 and 97.1%, respectively. Univariate analysis showed that the preoperative Hunt-Hess grade, CT Fisher grade, and perioperative complications were risk factors for poor clinical outcomes. Multiple logistic regression analysis showed that perioperative complication was the most significant risk factor for the clinical prognosis of patients with ruptured VSIAs.Conclusion: Endovascular treatment is a safe and efficient approach for ruptured VSIAs. Stent-assisted coiling reduced the recurrence rate of aneurysm without increasing the incidence of perioperative complications. The Hunt-Hess grade, CT Fisher grade, and perioperative complications were independent factors associated with the clinical outcomes of patients with ruptured VSIAs, and perioperative complication was the most significant risk factor for poor prognosis in patients.
High Flow Nasal Cannula Decreased Pulmonary Complications in Neurologically Critically Ill Patients
Authors: Wang Shuanglin , Yang Jingjing , Xu Yanli , Yin Huayun , Yang Bing , Zhao Yingying , Wei Zheng Zachory , Zhang Peng 
Published: January 2022

Objective: Pulmonary complications could badly affect the recovery of neurological function and neurological prognosis of neurological critically ill patients. This study evaluated the effect of high-flow nasal cannula (HFNC) therapy on decreasing pulmonary complications in neurologically critically ill patients.Patients and Methods: The patients admitted to the intensive care unit (ICU) with serious neurological disease and receiving oxygen therapy were retrospectively reviewed (Ethical No. IRB2021-YX-001). Patients were divided into the HFNC group and the conventional oxygen therapy (COT) group. We analyzed the data within these two groups, including patients’ baseline data, short-term outcomes of respiratory complications, general outcomes including hospital stay, ICU stay and mortality, and neurological functions. To analyze the relevant factors, we performed multivariable logistic regression analysis.Results: A total of 283 patients met the criteria, including 164 cases in the HFNC group and 119 cases in the COT group. The HFNC group had remarkably less mechanical ventilation requirement with lower phlegm viscosity. Even more, ICU stay and total hospital stay were significantly shortened in the HNFC group.Conclusion: HFNC decreased pulmonary complications in neurologically critically ill patients and improved recovery of neurological function and neurological prognosis.
Comparison of Comprehensive Morphological and Radiomics Features of Subsolid Pulmonary Nodules to Distinguish Minimally Invasive Adenocarcinomas and Invasive Adenocarcinomas in CT Scan
Authors: Qiu Lu , Zhang Xiuping , Mao Haixia , Fang Xiangming , Ding Wei , Zhao Lun , Chen Hongwei 
Published: January 2022

ObjectiveTo investigative the diagnostic performance of the morphological model, radiomics model, and combined model in differentiating invasive adenocarcinomas (IACs) from minimally invasive adenocarcinomas (MIAs).MethodsThis study retrospectively involved 307 patients who underwent chest computed tomography (CT) examination and presented as subsolid pulmonary nodules whose pathological findings were MIAs or IACs from January 2010 to May 2018. These patients were randomly assigned to training and validation groups in a ratio of 4:1 for 10 times. Eighteen categories of morphological features of pulmonary nodules including internal and surrounding structure were labeled. The following radiomics features are extracted: first-order features, shape-based features, gray-level co-occurrence matrix (GLCM) features, gray-level size zone matrix (GLSZM) features, gray-level run length matrix (GLRLM) features, and gray-level dependence matrix (GLDM) features. The chi-square test and F1 test selected morphology features, and LASSO selected radiomics features. Logistic regression was used to establish models. Receiver operating characteristic (ROC) curves evaluated the effectiveness, and Delong analysis compared ROC statistic difference among three models.ResultsIn validation cohorts, areas under the curve (AUC) of the morphological model, radiomics model, and combined model of distinguishing MIAs from IACs were 0.88, 0.87, and 0.89; the sensitivity (SE) was 0.68, 0.81, and 0.83; and the specificity (SP) was 0.93, 0.79, and 0.87. There was no statistically significant difference in AUC between three models (p &gt; 0.05).ConclusionThe morphological model, radiomics model, and combined model all have a high efficiency in the differentiation between MIAs and IACs and have potential to provide non-invasive assistant information for clinical decision-making.