bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can we have our steak and eat it: The impact of breeding for lowered environmental impact on yield and meat quality in sheep
Authors: Rowe S. J. , Hickey S. M. , Bain W. E. , Greer G. J. , Johnson P. L. , Elmes S. , Pinares-Patiño C. S. , Young E. A. , Dodds K. G. , Knowler K. , Pickering N. K. , Jonker A. , McEwan J. C. 
Published: September 2022

Global agreements in place to reduce methane emissions in livestock are a potential threat to food security. Successful but independent breeding strategies for improved production and lower methane are in place. The unanswered questions are whether these strategies can be combined and how they impact one another, physically and economically. The New Zealand economy is largely dependent on pastoral agriculture from grazing ruminants. The sheep industry produces ∼20 million lamb carcasses for export each year primarily from grass. Methane emitted from the fermentation of forage by grazing ruminants accounts for one-third of all New Zealand’s greenhouse gas emissions. Here, we use sheep selection lines bred for divergent methane production and large numbers of their relatives to determine the genetic and phenotypic correlations between enteric methane emissions, carcass yield, and meat quality. The primary objectives were to determine whether previously shown physiological differences between methane selection lines (differing by ∼12% in methane) result in a negative impact on meat production and quality by measuring close relatives. The results show no negative effects of breeding for lowered methane on meat and carcass quality. Gross methane emissions were highly correlated with liveweight and measures of carcass weight and negatively correlated with dressing-out percentage and fat yield (GR). Trends were similar but not significant for methane yield (g CH4/kg DMI). Preliminary evidence, to date, shows that breeding for low methane may result in animals with higher lean yields that are economically favorable even before carbon costs and environmental benefits are taken into account. These benefits were seen in animals measured for methane on fixed intakes and require validation on intakes that are allowed to vary.
Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance
Authors: Singh Kaushal Pratap , Kumari Preetesh , Yadava Devendra Kumar 
Published: September 2022

Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba+B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n= 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used forde-novoassembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies.
A risk signature based on necroptotic-process-related genes predicts prognosis and immune therapy response in kidney cell carcinoma
Authors: Li Jingxian , Liu Xun , Qi Yuanjiong , Liu Yang , Du E. , Zhang Zhihong 
Published: September 2022

Necroptosis is a regulated form of cell necroptotic process, playing a pivotal role in tumors. In renal cell cancer (RCC), inhibiting necroptosis could promote the proliferation of tumor cells. However, the molecular mechanisms and prognosis prediction of necroptotic-process-related genes in RCC are still unclear. In this study, we first identified the necroptotic process prognosis-related genes (NPRGss) by analyzing the kidney renal clear cell carcinoma (KIRC) data in The Cancer Genome Atlas (TCGA, n=607). We systematically analyzed the expression alteration, clinical relevance, and molecular mechanisms of NPRGss in renal clear cell carcinoma. We constructed an NPRGs risk signature utilizing the least absolute shrinkage and selection operator (LASSO) Cox regression analysis on the basis of the expression of seven NPRGss. We discovered that the overall survival (OS) of KIRC patients differed significantly in high- or low-NPRGs-risk groups. The univariate/multivariate Cox regression revealed that the NPRGs risk signature was an independent prognosis factor in RCC. The gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to explore the molecular mechanisms of NPRGss. Immune-/metabolism-related pathways showed differential enrichment in high-/low-NPRGs-risk groups. The E-MTAB-1980, TCGA-KIRP, GSE78220, the cohort of Alexandra et al., and IMvigor210 cohort datasets were respectively used as independent validation cohorts of NPRGs risk signature. The patients in high- or low-NPRGs-risk groups showed different drug sensitivity, immune checkpoint expression, and immune therapy response. Finally, we established a nomogram based on the NPRGs risk signature, stage, grade, and age for eventual clinical translation; the nomogram possesses an accurate and stable prediction effect. The signature could predict patients’ prognosis and therapy response, which provides the foundation for further clinical therapeutic strategies for RCC patients.
Comprehensive analysis of cellular senescence-related genes in the prognosis, tumor microenvironment, and immunotherapy/chemotherapy of clear cell renal cell carcinoma
Authors: Lu Caibao , Wang Yiqin , Nie Ling , Chen Liping , Li Moqi , Qing Huimin , Li Sisi , Wu Shuang , Wang Zhe 
Published: September 2022

BackgroundThe transcriptome public database and advances in biological discoveries contributed to significant progresses in identifying the drivers of cancer progression. Cellular senescence (CS) is considered as a leading factor resulting in cancer development. The purpose of this study was to explore the significance of CS-related genes in the molecular classification and survival outcome of clear cell renal cell carcinoma (ccRCC).MethodsCS-related genes were obtained from the CellAge database, and patients from TCGA-KIRC dataset and ICGC dataset were clustered by ConsesusClusterPlus. The characteristics of overall survival (OS), genomic variation, and tumor microenvironment (TME) of each cluster were analyzed. Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis was conducted to develop a CS-related risk model to score ccRCC patients and assess the risk scores in predicting patients’ response to immunotherapy and chemotherapy. A nomogram based on the risk model was established to improve the risk stratification of patients.ResultsCcRCC was divided into three molecular subtypes based on CS-related genes. The three molecular phenotypes showed different OS and clinical manifestations, mutation patterns, and TME states. Five genes were obtained from nine differentially expressed CS-related genes in the three molecular subtypes to develop a risk model. Patients with ccRCC were divided into high- and low-risk subgroups. The former showed an unfavorable OS, with a significantly higher genomic variation rate, TME score, and numerous immune checkpoint expressions when compared to the low-risk subgroup. Risk score reflected the response of patients to axitinib, bortezomib, sorafenib, sunitinib, and temsirolimus.ConclusionsIn general, CS-related genes divided ccRCC into three molecular subtypes with distinct OS, mutation patterns, and TME states. The risk model based on the five CS-related genes can predict the prognosis and therapeutic outcome of ccRCC patients, providing a theoretical basis for further study on the molecular mechanism of CS-related ccRCC.
Bioinformatics and systems biology approach to identify the pathogenetic link of Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome
Authors: Lv Yongbiao , Zhang Tian , Cai Junxiang , Huang Chushuan , Zhan Shaofeng , Liu Jianbo 
Published: September 2022

BackgroundThe COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global crisis. Although many people recover from COVID-19 infection, they are likely to develop persistent symptoms similar to those of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) after discharge. Those constellations of symptoms persist for months after infection, called Long COVID, which may lead to considerable financial burden and healthcare challenges. However, the mechanisms underlying Long COVID and ME/CFS remain unclear.MethodsWe collected the genes associated with Long COVID and ME/CFS in databases by restricted screening conditions and clinical sample datasets with limited filters. The common genes for Long COVID and ME/CFS were finally obtained by taking the intersection. We performed several advanced bioinformatics analyses based on common genes, including gene ontology and pathway enrichment analyses, protein–protein interaction (PPI) analysis, transcription factor (TF)–gene interaction network analysis, transcription factor–miRNA co-regulatory network analysis, and candidate drug analysis prediction.ResultsWe found nine common genes between Long COVID and ME/CFS and gained a piece of detailed information on their biological functions and signaling pathways through enrichment analysis. Five hub proteins (IL-6, IL-1B, CD8A, TP53, and CXCL8) were collected by the PPI network. The TF–gene and TF–miRNA coregulatory networks were demonstrated by NetworkAnalyst. In the end, 10 potential chemical compounds were predicted.ConclusionThis study revealed common gene interaction networks of Long COVID and ME/CFS and predicted potential therapeutic drugs for clinical practice. Our findings help to identify the potential biological mechanism between Long COVID and ME/CFS. However, more laboratory and multicenter evidence is required to explore greater mechanistic insight before clinical application in the future.
Peritumoral tertiary lymphoid structure and tumor stroma percentage predict the prognosis of patients with non-metastatic colorectal cancer
Authors: Wang Qianyu , Shen Xiaofei , An Ran , Bai Junchao , Dong Junhua , Cai Huiyun , Zhu Hongyan , Zhong Wentao , Chen Wenliang , Liu Aijun , Du Junfeng 
Published: September 2022

BackgroundTertiary lymphoid structures (TLSs) are crucial in promoting and maintaining positive anti-tumor immune responses. The tumor stroma has a powerful immunosuppressive function that could exclude tumor-infiltrating lymphocytes from the tumor beds and lead to a “cold” phenotype. TLSs and tumor stroma percentage (TSP) are significantly associated with the prognosis of patients with certain cancers. However, the exact roles of TLSs and TSP and their intrinsic relationship are still largely unknown in colorectal cancer (CRC).MethodsTLSs and TSP were assessed using hematoxylin-eosin (H&amp;E) and/or immunohistochemistry (IHC) staining from 114 CRC patients in the training set and 60 CRC patients in the external validation set. The correlation between TILs, TLS and clinicopathological characteristics and their prognostic values were assessed. Finally, we plotted a Nomogram including the TLS, TSP and tumor-node-metastasis (TNM) stage to predict the probability of recurrence-free survival (RFS) at 2- and 5-years in non-metastatic colorectal cancer (nmCRC) patients.ResultsPeritumoral TLS (P-TLS), intratumoral TLS (In-TLS) and high TSP (H-TSP, &gt;50%) were present in 99.1%, 26.3% and 41.2% patients, respectively. H-TSP tumor tends to be associated with lower P-TLS density (P =0.0205). The low P-TLS density (&lt; 0.098/mm2) was significantly associated with reduced RFS (HR=6.597 95% CI: 2.882-15.103, P &lt;0.001) and reduced overall survival (OS) (HR=6.628 95% CI: 2.893-15.183, P &lt; 0.001) of nmCRC patients. In-TLS was not of significance in evaluating the clinical outcomes of nmCRC patients. H-TSP was significantly associated with reduced RFS (HR=0.126 95% CI: 0.048-0.333, P &lt;0.001) and reduced OS (HR=0.125 95% CI: 0.047-0.332, P &lt;0.001) of nmCRC patients. The 5-year RFS of the high P-TLS, low-TLS, H-TSP, and L-TSP groups were 89.7%, 47.2%, 53.2%, and 92.5%, respectively. The P-TLS density, TSP and TNM stage were independent prognosis factors of nmCRC patients. The Nomogram, including the P-TLS density, TSP and TNM stage, outperformed the TNM stage.ConclusionsHigh P-TLS density and low TSP (L-TSP) were independent and favorable prognostic factors of nmCRC patients, which might provide new directions for targeted therapy in the CRC tumor microenvironment, especially the tumor immune microenvironment.
The short-term and long-term effects of intranasal mesenchymal stem cell administration to noninflamed mice lung
Authors: Tynecka Marlena , Janucik Adrian , Niemira Magdalena , Zbikowski Arkadiusz , Stocker Nino , Tarasik Agnieszka , Starosz Aleksandra , Grubczak Kamil , Szalkowska Anna , Korotko Urszula , Reszec Joanna , Kwasniewski Miroslaw , Kretowski Adam , Akdis Cezmi , Sokolowska Milena , Moniuszko Marcin , Eljaszewicz Andrzej 
Published: September 2022

Mesenchymal stem cells (mesenchymal stromal cells; MSC)-based therapies remain a promising approach to treat degenerative and inflammatory diseases. Their beneficial effects were confirmed in numerous experimental models and clinical trials. However, safety issues concerning MSCs’ stability and their long-term effects limit their implementation in clinical practice, including treatment of respiratory diseases such as asthma, chronic obstructive pulmonary disease, and COVID-19. Here, we aimed to investigate the safety of intranasal application of human adipose tissue-derived MSCs in a preclinical experimental mice model and elucidate their effects on the lungs. We assessed short-term (two days) and long-term (nine days) effects of MSCs administration on lung morphology, immune responses, epithelial barrier function, and transcriptomic profiles. We observed an increased frequency of IFNγ- producing T cells and a decrease in occludin and claudin 3 as a long-term effect of MSCs administration. We also found changes in the lung transcriptomic profiles, reflecting redox imbalance and hypoxia signaling pathway. Additionally, we found dysregulation in genes clustered in pattern recognition receptors, macrophage activation, oxidative stress, and phagocytosis. Our results suggest that i.n. MSCs administration to noninflamed healthy lungs induces, in the late stages, low-grade inflammatory responses aiming at the clearance of MSCs graft.
Rapid visual detection of Enterocytozoon hepatopenaei by recombinase polymerase amplification combined with lateral flow dipstick
Authors: Pang Jianhu , Zhao Caiyuan , Su Hualong , Liu Zhongcheng , Lu Qiang , He Xinyi , Weng Shaoping , He Jianguo 
Published: September 2022

Enterocytozoon hepatopenaei (EHP) is a high-impact pathogen in shrimp farming, causing huge economic losses to the global shrimp farming industry every year. However, current EHP detection methods are primarily based on the development of polymerase chain reaction (PCR) techniques that rely on sophisticated and expensive instruments. Consequently, a rapid, practical, and sensitive protocol for the detection of EHP is necessary. Recombinase polymerase amplification combined with a lateral flow dipstick (LFD-RPA) assay was developed using a pair of primers and nfo-probe targeting the conserved region of the spore wall protein gene. Under optimized reaction conditions, the LFD-RPA assay can detect 10 copies/μL of standard plasmid within 20 min at 40°C. Furthermore, the specificity of the LFD-RPA was also verified with other common pathogens of shrimp. Thirty-nine samples of Litopenaeus vannamei were collected in shrimp farms and detected using LFD-RPA and nested PCR. Thirty-two positive samples were detected by LFD-RPA. Compared with those of nested PCR, the diagnostic sensitivity and specificity of LFD-RPA were 100% and 100%, respectively. These results indicated the great application potential of the newly developed LFD-RPA assay for point-of-care diagnosis, epidemic surveillance, and epidemiological investigation of EHP.
Corneal characteristics in Down syndrome patients with normal and keratoconic cornea
Authors: Hashemi Hassan , Asgari Soheila 
Published: September 2022

PurposeTo determine the reference range of corneal indices in Down syndrome patients with normal corneas (DS-N) and to compare it with the corneal indices in Down syndrome patients with keratoconic corneas (DS-KC).MethodsA study was conducted using the data of 154 eyes of 154 DS-N and 25 eyes of 25 DS-KC patients. Eighteen indices related to thickness, anterior chamber, keratometry, elevation, and aberrations routinely used for KC diagnosis were extracted from the Pentacam.ResultsThe mean age of the participants in DS-N and DS-KC groups was 16.73 ± 4.70 and 16.56 ± 4.22 years (P = 0.852). In the DS-N group, 95% CI were 511.65–520.31 for minimum corneal thickness, 2.97–3.07 for anterior chamber depth (ACD), 46.83–47.37 for maximum keratometry (Kmax), 46.13–46.62 for zonal Kmax at 3 mm, 0.35–0.58 for inferior-superior asymmetry (I-S value), 1.56–1.88 for Belin/Ambrósio display-total deviation, 8.65–10.79 for best-fit-sphere posterior elevation at the thinnest point, and 0.18–0.22 for corneal vertical coma. The age-related change in I-S value and corneal spherical aberration (SA) was significant (both P &lt; 0.05). There were significant inter-gender differences in 11 indices; the female DS patients had shallower, steeper, more elevated, and more aberrated corneas (all P &lt; 0.05). There were significant differences in all indices except for ACD (P = 0.372) and corneal SA (P = 0.169) between DS-N and DS-KC groups.ConclusionIn DS patients aged 10–30 years, the reference ranges of corneal indices are different from the range reported for non-DS subjects and are close to values reported for mild KC non-DS cases. The normal values are different between DS male and female; hence, sex-specific ranges should be considered for diagnosis of corneal abnormality in DS patients.
Osteoporosis is associated with elevated baseline cerebrospinal fluid biomarkers and accelerated brain structural atrophy among older people
Authors: Pan Hao , Cao Jiali , Wu Congcong , Huang Furong , Wu Peng , Lang Junzhe , Liu Yangbo 
Published: September 2022

ObjectiveThe aim of this study was to examine whether osteoporosis (OP) is associated with Alzheimer’s disease-related cerebrospinal fluid (CSF) biomarkers and brain structures among older people.MethodsFrom the Alzheimer’s disease Neuroimaging Initiative database, we grouped participants according to the OP status (OP+/OP−) and compared the Alzheimer’s disease (AD)-related CSF biomarker levels and the regional brain structural volumes between the two groups using multivariable models. These models were adjusted for covariates including age, education, gender, diagnosis of Alzheimer’s disease, and apolipoprotein E4 carrier status.ResultsIn the cross-sectional analyses at baseline, OP was related to higher CSF t-tau (total tau) and p-tau181 (tau phosphorylated at threonine-181) but not to CSF amyloid-beta (1–42) or the volumes of entorhinal cortex and hippocampus. In the longitudinal analyses, OP was not associated with the change in the three CSF biomarkers over time but was linked to a faster decline in the size of the entorhinal cortex and hippocampus.ConclusionOP was associated with elevated levels of CSF t-tau and p-tau181 at baseline, and accelerated entorhinal cortex and hippocampal atrophies over time among older people.
Opium abuse and stroke in Iran: A systematic review and meta-analysis
Authors: Mardi Parham 
Published: September 2022

IntroductionOpium dependence is a significant health concern in low and middle-income countries, leading to a considerable number of deaths annually. Opium has several detrimental effects on its consumers. Data regarding the impact of opium on stroke are controversial. The objective of this study is to evaluate the association between opium dependence and stroke.MethodsI conducted a systematic search based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to evaluate the association between opium dependence and stroke. Following the extraction of qualitative findings from included studies, a meta-analysis was performed to assess the pooled estimate of odds ratios (ORs).ResultsEight and four studies were included in qualitative and quantitative synthesis, respectively. Opium dependence increases the hazard of stroke mortality. Also, opium increases the odds of ischemic stroke by 127% (pooled OR = 2.27, 95% CI: 1.47–3.07).ConclusionOpium not only merely increases the odds of being diagnosed with ischemic stroke but also leads to a notable increase in the mortality rate following stroke.
Diffusion-weighted imaging hyperintensities during the chronic stage of intracerebral hemorrhage with surgery: A new clinical situation or post-surgery artifact?
Authors: Chen Xiaoyan , Li Ying , Guo Shengli , Han Xun , Liu Ruozhuo , Tian Chenglin , Cui Rongtai , Dong Zhao , Yu Shengyuan 
Published: September 2022

Background and objectiveDiffusion-weighted imaging (DWI) hyperintensities were occasionally seen at previous hematoma in patients several months after intracerebral hemorrhage with surgery. Whether they are newly occurred clinical situations or post-surgery changes is unknown. This study aims to investigate the prevalence and possible mechanisms for this phenomenon.MethodsWe retrospectively reviewed the MRI database for intracerebral hemorrhage with surgery after 3 months of disease onset in our hospital. We also prospectively performed repeated multimodal MRI scans for two patients at the chronic stage after surgery for intracerebral hemorrhage.ResultsWe found that 14 out of 23 patients (60.9%) had DWI hyperintensities at the site of previous hematoma 3 months after intracerebral hemorrhage with surgery. All the DWI lesions were hyperintense on T1- and T2-weighted imaging, most of which appeared long and narrow in shape. The DWI lesions were usually located adjacent to the thin wall of the previous hematoma cavity close to the lateral ventricle. They were more associated with the basal ganglia hemorrhage than with the lobar hemorrhage (P = 0.02) and were more frequently seen for those with intraventricular hemorrhage than without (P = 0.02). Prospectively repeated MRI exams of two patients revealed unchanged DWI hyperintensity during the 18- and 2-month follow-up, respectively.ConclusionThe DWI lesions at previous hematoma were commonly seen in patients after surgery for intracerebral hemorrhage at the chronic stage which would persist for years. We hypothesized a possible mechanism by which extracellular methemoglobin “islands” are formed with delayed or no absorption by macrophages from adjacent thin residual brain tissue. Unnecessary further examinations and treatment would be avoided by realizing this imaging phenomenon.