bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome
Authors: Cui Jiawen , Shen Nan , Lu Zhaogeng , Xu Guolu , Wang Yuyao , Jin Biao 
Published: May 2020

Abstract
Background: The number of studies using third-generation sequencing using Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio sequencing, whereas ONT is rarely used. Therefore, in this study, we examined ONT RNA sequencing methods in plants. We performed a detailed evaluation of reads from PacBio, Nanopore direct cDNA (ONT Dc), and Nanopore PCR cDNA (ONT Pc) sequencing including characteristics of raw data and identification of transcripts. In addition, matched Illumina data were generated for comparison. Results: ONT Pc showed overall better raw data quality, whereas PacBio generated longer read lengths. In the transcriptome analysis, PacBio and ONT Pc performed similarly in transcript identification, simple sequence repeat analysis, and long non-coding RNA prediction. PacBio was superior in identifying alternative splicing events, whereas ONT Pc could estimate transcript expression levels. Conclusions: This paper made a comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome, the results indicate that ONT Pc is more cost-effective for generating extremely long reads and can characterise the transcriptome as well as quantify transcript expression. Therefore, ONT Pc is a new cost-effective and worthwhile method for full-length single-molecule transcriptome analysis in plants.
Dairy Cow Culling - Reasons and Risk Factors
Authors: Rilanto Triin , Reimus Kaari , Orro Toomas , Emanuelson Ulf , Viltrop Arvo , Mõtus Kerli 
Published: May 2020

Abstract
Background Culling is a major cost for dairy farms but also an essential part in managing herd productivity. This study aimed to identify the culling rates of Estonian dairy cows, identify the farmers’ stated reasons and risk factors for culling. This observational study used registry data of all cows from herds with ≥20 cow-years in 2013-2015. Cow lactation-level analyses included data of 86,373 primiparous cows from 409 herds and 177,561 lactations of 109,295 multiparous cows from 410 herds. Weibull proportional hazard regression models were used to identify risk factors for culling due to slaughter or death. Results The overall culling rate of Estonian dairy cows was 26.24 (95% CI 26.02; 26.46) per 100 cow-years. The most common reasons farmers stated for culling were feet/claw disorders (26.4%), udder disorders (22.6%), metabolic and digestive disorders (18.1%) and fertility problems (12.5%). Animal-level risk factors for culling were Holstein breed, older parity, lower milk yield breeding value, older age at first calving, longer previous calving interval, having assisted calving, stillbirth and birth of twins/triplets. Lower milk yield, somatic cell count over 200,000 cells/ml and fat/protein ratio over 1.5 at first test-milking after calving were associated with greater culling hazard during the lactation. Cows from larger herds, herds with decreasing size and higher milk yields had a higher culling probability. Conclusions This study emphasises the need for improved management of hoof health and prevention of mastitis and metabolic diseases. It is essential to ensure easy calving and good health of cows around calving in order to lower the culling hazard.
Exosomal microRNAs are novel circulating biomarkers in cigarette,waterpipe smokers, E-cigarette users and dual smokers
Authors: Singh Kameshwar P. , Maremanda Krishna P. , Li Dongmei , Rahman Irfan 
Published: May 2020

Abstract
Background: Electronic cigarettes (e-cigs) produce aerosolized substances by heating a liquid, which contains large number of chemicals. The aerosol generated by E-cig may produce adverse health effects. Cigarette smoke exposure causes various diseases including COPD, atherosclerosis, and lung cancer. Waterpipe tobacco smoking also causes various acute and chronic health effects including cardiopulmonary diseases. microRNAs are present in higher concentration in exosomes that play a major role in various physiological and pathological functions. We hypothesized that the non-coding RNAs transcript may serve as susceptibility to disease biomarkers by smoking and vaping. Results: Our data show the enrichment of various non-coding RNAs that include microRNAs, tRNAs, piRNAs, snoRNAs, snRNAs, Mt-tRNAs, and other biotypes in exosomes. A comprehensive differential expression analysis of microRNAs, tRNAs and piRNAs showed significant changes across different pairwise comparisons. The seven microRNAs that were common and differentially expressed of when all the smoking and vaping groups were compared with non-smokers (NS) are hsa-let-7a-5p, hsa-miR-21-5p, hsa-miR-29b-3p, hsa-let-7f-5p, hsa-miR-143-3p, hsa-miR-30a-5p and hsa-let-7i-5p. The e-cig vs. NS group has differentially expressed 5 microRNAs (hsa-miR-224-5p, hsa-miR-193b-3p, hsa-miR-30e-5p, hsa-miR-423-3p, hsa-miR-365a-3p, and hsa-miR-365b-3p) that is specific for this group and are not expressed in other three groups. Gene set enrichment analysis of microRNAs showed significant changes in the top six enriched functions that consisted of biological pathway, biological process, molecular function, cellular component, site of expression and transcription factor in all the groups. Further, the pairwise comparison of tRNAs and piRNA in all these groups revealed significant changes in their expressions. Conclusions: Plasma exosomes of cigarette smokers, waterpipe smokers, e-cig users and dual smokers have common differential expression of microRNAs which may serve to distinguish smoking and vaping subjects from NS. Among them has-let-7a-5p has high sensitivity and specificity to distinguish NS with the rest of the users, using ROC curve analysis. This study will pave the way for the utilizing the potential of exosomes/miRNAs as a novel theranostic agents in understanding the lung injury caused by tobacco smoking and vaping.
Functional production of human antibody by the filamentous fungus Aspergillus oryzae
Authors: Huynh Hung Hiep , Morita Naoki , Sakamoto Toshihiro , Katayama Takuya , Miyakawa Takuya , Tanokura Masaru , Chiba Yasunori , Shinkura Reiko , MARUYAMA Jun-ichi 
Published: May 2020

Abstract
Background: Monoclonal antibodies (mAbs) as biopharmaceuticals take a pivotal role in the current therapeutic applications. Generally mammalian cell lines, such as those derived from Chinese hamster ovaries (CHO), are used to produce the recombinant antibody. However, there are still concerns about the high cost and the risk of pathogenic contamination when using mammalian cells. Aspergillus oryzae, a filamentous fungus recognized as a GRAS (Generally Regarded As Safe) organism, has an ability to secrete a large amount of proteins into the culture supernatant, and thus the fungus has been used as one of the cost-effective microbial hosts for heterologous protein production. Pursuing this strategy the human anti-TNFα antibody adalimumab, one of the world’s best-selling antibodies for the treatment of immune-mediated inflammatory diseases including rheumatoid arthritis, was chosen to produce the full length of mAbs by A. oryzae. Generally, N-glycosylation of the antibody affects immune effector functions such as antibody-dependent cell-mediated cytotoxicity (ADCC) via binding to the Fc receptor (FcγR) on immune cells. The CRISPR/Cas9 system was used to first delete the Aooch1 gene encoding a key enzyme for the hyper-mannosylation process in fungi to investigate the binding ability of antibody with FcγRIIIa.Results: Adalimumab was expressed in A. oryzae by the fusion protein system with α-amylase AmyB. The full-length adalimumab consisting of two heavy and two light chains was successfully produced in the culture supernatants. Among the producing strains, the highest amount of antibody was obtained from the ten-protease deletion strain (39.7 mg/L). Two-step purifications by Protein A and size-exclusion chromatography were applied to obtain the high purity sample for further analysis. The antigen-binding and TNFα neutralizing activities of the adalimumab produced by A. oryzae were comparable with those of a commercial product Humira®. No apparent binding with the FcγRIIIa was detected with the recombinant adalimumab even by altering the N-glycan structure using the Aooch1 deletion strain, which suggests only a little additional activity of immune effector functions.Conclusion: These results demonstrated an alternative low-cost platform for human antibody production by using A. oryzae, possibly offering a reasonable expenditure for patient’s welfare.
Sex differences in the relationship between dietary pattern adherence and cognitive function among older adults: Findings from the NuAge study
Authors: D’Amico Danielle , Parrott Matthew D. , Greenwood Carol E. , Ferland Guylaine , Gaudreau Pierrette , Belleville Sylvie , Laurin Danielle , Anderson Nicole D. , Kergoat Marie-Jeanne , Morais Jose A. , Presse Nancy , Fiocco Alexandra J. 
Published: May 2020

Abstract
Background: Consumption of a prudent dietary pattern rich in healthy nutrients is associated with enhanced cognitive performance in older adulthood, while a Western dietary pattern low in healthy nutrients is associated with poor age-related cognitive function. Sex differences exist in dietary intake among older adults; however, there is a paucity of research examining the relationship between sex-specific dietary patterns and cognitive function in later life. Methods: The current study aimed to investigate sex differences in the relationship between sex-specific dietary pattern adherence and global cognitive function at baseline and over a 3-year follow-up in 1268 community-dwelling older adults (Mage=74 years, n = 664 women, n = 612 men) from the Quebec Longitudinal Study on Nutrition and Successful Aging (NuAge). A 78-item Food Frequency Questionnaire was used to estimate dietary intake over the previous year. Sex-specific dietary pattern scores were derived using principal component analysis. Global cognition was assessed using the Modified Mini-Mental State Examination (3MS). Results: Adjusted linear mixed effects models indicated that a healthy, prudent dietary pattern was not associated with baseline cognitive performance in men or women. No relationship was found between Western dietary pattern adherence and baseline cognitive function in women. Among men, adherence to an unhealthy, Western dietary pattern was associated with poorer baseline cognitive function (b = -0.652, p = 0.02, 95% CI [-1.22, -0.65]). No association was found between prudent or Western dietary patterns and cognitive change over time in men or women. Conclusions: These findings highlight the importance of conducting sex-based analyses in aging research and suggest that the relationship between dietary pattern adherence and cognitive function in late life may be sex-dependent.
Transitions in Adolescent Boys and Young Men’s High-Risk Sexual Behaviour in India
Authors: Sharma Santosh Kumar , Vishwakarma Deepanjali 
Published: May 2020

Abstract
Background: The sexual behaviour of adolescents is of importance due to the engagement in risky sexual activity at a too early age, which may be associated with the adverse outcomes. The study aims to understand the transitions in adolescent boys and young men’s high-risk sexual behaviour in India using two rounds of Indian demographic health survey, NFHS-3 (2005-06) and NFHS-4 (2015-16). Methods: A total of 25,538 in NFHS-3 (2005-06) and 35,112 in NFHS-4 (2015-16) men were considered for the analysis. Men have been divided into two age groups as 15-19 years (adolescent) and 20-24 (young men) for comparison purposes. Descriptive and multivariate statistics have been used. Results: Overall, high-risk sexual behaviour has increased among adolescent boys (64% to 70%) and young men (18% to 27%) from 2005-06 to 2015-16. The trend of live-in relationship has increased among adolescent boys of rural areas (0.6% to 6.0%) as well as in urban areas (3.1% to 10.9%) over the last ten years. Adolescent boys having 10th and above years of schooling (AOR=1.98; p<0.01), residing in urban areas (AOR=2.23; p<0.01), and belonging to the affluent class of households (AOR=1.41; p<0.05) were more likely to engage in high-risk sexual activity than the young men in India. The odds of high-risk sexual behaviour was higher among alcohol-using adolescent boys (AOR= 1.82; p<0.01) and young men (AOR=2.38; p<0.01) in 2015-16.Conclusions: The study concludes that early sexual debut, lower prevalence of condom use at first sexual experience, tendency of live-in-relationship, and alcohol consumption indicate the hazardous interconnection between such behaviours among adolescent boys over the last decade which put them at higher-risky sexual behaviour as compared to young men. Adolescent’ sexual behaviours have both short-term and long-term consequences, and interventions that focus on multiple domains of risk may be the most effective in helping to promote broad reproductive health among young adults.
Comparison of the clinicopathological characteristics and their impact on outcomes of resected colorectal liver metastases across time
Authors: Chen Lionel , Syn Nicholas L. , Goh Brian K. P. , Cheow Peng Chung , Raj Prema , Koh Yexin , Chung Alexander , Lee Ser Yee , Ooi London Lucien , Chan Chung Yip , Teo Jin Yao 
Published: May 2020

Abstract
Background Resection of colorectal liver metastases (CLM) has been established as the standard of care. This study aims to compare the change in clinicopathological characteristics of patients who underwent curative resection of CLM across two time periods – 2000 to 2010 (P1) and 2011 to 2016 (P2) and evaluate the prognostic impact of these characteristics on survival outcomes. Methods Patients who undergo liver resection for CLM at Singapore General Hospital from January 2000 to December 2016 were identified from a prospectively maintained database. The primary end point was overall survival. Results There were 183/318 (57.5%) patients and 135/318 (42.5%) patients in P1 and P2 respectively. There was a lower proportion of patients who had nodal metastases from primary colorectal cancer and clinical risk score (CRS) less than 3 in P2 when compared to P1. There was no difference in survival between both time periods. Independent predictors of survival for the cohort were CEA levels ≥200ng/ml, primary tumour grade and lymph nodal status. Independent predictors of poor survival in P1 were poorly differentiated colorectal cancer and nodal metastases while in P2, independent predictors of poor survival were multiple liver metastases and nodal metastases.Conclusion Nodal metastases from primary colorectal cancer is an independent predictor of poor survival across time for resectable CLM. Although there is no difference in survival between the two time periods, patients with multiple liver metastases should be carefully considered prior to surgery as it is also an independent predictor of overall survival.
Cerenkov luminescence imaging is an effective preclinical tool for assessing colorectal cancer PD-L1 levels in vivo
Authors: Zhao Sheng , Pan Wen-Bin , Jiang Hui-Jie , Zhang Rong-Jun , Jiang Hao , Liang Zong-Hui , Hu Hong-Bo 
Published: May 2020

Abstract
Background: Preclinical and clinical studies have demonstrated that immunotherapy has effectively delayed tumor progression, and the clinical outcomes of anti-PD-1/PD-L1 therapy were related to PD-L1 expression level in the tumors. A 131I-labeled anti-PD-L1 monoclonal antibody tracer, 131I-PD-L1-Mab, was developed to study the target ability of non-invasive Cerenkov luminescence imaging in colorectal cancer xenograft mice.Method: Anti-PD-L1 monoclonal antibody labeled with 131I (131I-PD-L1-Mab), and in vitro binding assays were used to evaluate the affinity of 131I-PD-L1-Mab to PD-L1 and their binding level to different colorectal cancer cells, and compared with flow cytometry, western blot analysis, and immunofluorescence staining. The clinical application value of 131I-PD-L1-Mab was evaluated through biodistribution and Cerenkov luminescence imaging, and different tumor-bearing models expressing PD-L1 were evaluated.Results: 131I-PD-L1-Mab showed high affinity to PD-L1, and the equilibrium dissociation constant was 1.069×10-9M. The competitive inhibition assay further confirmed the specific binding ability of 131I-PD-L1-Mab. In four different tumor-bearing models with different PD-L1 expression, the biodistribution and Cerenkov luminescence imaging showed that the RKO tumors demonstrated the highest uptake of the tracer 131I-PD-L1-Mab, with a maximum uptake of 1.613 ± 0.738%IA/g at 48 h.Conclusions: There is a great potential for 131I-PD-L1-Mab noninvasive Cerenkov luminescence imaging to assess the status of tumor PD-L1 expression and select patients for anti-PD-L1 targeted therapy.
Preoperative systemic immune-inflammation index predicts prognosis of patients with non-metastatic renal cell carcinoma: a propensity score-matched analysis
Authors: Hu Xu , Shao Yan-Xiang , Yang Zhi-Qiang , Dou Wei-Chao , Xiong San-Chao , Li Xiang 
Published: May 2020

Abstract
Background: A novel systemic immune-inflammation index (SII), based on the neutrophils, lymphocytes and platelet counts, is associated with the prognosis of several cancers. The present study evaluates the prognostic significance of SII in non-metastatic renal cell carcinoma (RCC).Method: The present study retrospectively reviewed the medical record of patients with non-metastatic RCC who underwent nephrectomy between 2010 and 2013. Receiver operating characteristic (ROC) curve analysis was performed to identify the optimal cut-off value. In addition, the propensity score matching (PSM) was performed with a matching ratio of 1:1. Univariate and multivariate Cox proportional hazards models were used to identify the prognostic factors. The results were reported by hazard ratio (HR) with 95% confidence interval (95% CI). Results: A total of 646 patients were included in the final analysis. High SII group (>529) was significantly associated with older age (P=0.014), larger tumor (P<0.001), higher pathological T stage (P<0.001), higher tumor grade (P<0.001) and more tumor necrosis (P<0.001). Multivariate Cox regression analysis demonstrated that the higher preoperative SII was significantly associated with worse overall survival (OS) (HR=2.26; 95%CI 1.44-3.54; P<0.001) and cancer-specific survival (CSS) (HR=2.17; 95%CI 1.33-3.55; P=0.002). After PSM, elevated preoperative SII was an independent predictor of poor OS (HR=1.78; 95%CI 1.1-2.87; P=0.018) and CSS (HR=1.8; 95%CI 1.07-3.03; P=0.027).Conclusion: In conclusion, preoperative SII is associated with adverse factors for RCC. Furthermore, higher preoperative SII is an independent predictor of poor OS and CSS in surgically treated patients with non-metastatic RCC. More prospective and large scale studies are warranted to validate our findings.
L-Carnitine Supplementation could improve Clinical Symptom but not effect on C- reactive Protein and Malondialdehyde in Obese Women with Knee Osteoarthritis: A Double Blind Randomized Controlled Trial
Authors: BAGHBAN FARNAZ , Hosseinzadeh Mahdieh , Mozaffari-Khosravi Hassan , Dehghan Ali , Fallahzadeh Hossein 
Published: May 2020

Abstract
Backgrounds:L-carnitine decreases oxidation and inflammation by reducing the fatty acid in plasma and using oxygen in ATP synthesis. So, knee osteoarthritis (KOA) can be improved by reducing apoptotic chondrocytes. The aim of this study was to compare the effect of L-carnitine supplementation along with low calorie diet and low calorie diet alone on improvement of KOA among obese women. In other words, we aimed to investigate the additional effect of L- carnitine on improvement of KOA among obese women who received low calorie diet.Methods76 obese women with KOA were randomly assigned into two low-calorie diet groups; the first one received the 1000 mg L-carnitine (LCG) and with the second group took the placebo (PLG) (n = 38). Anthropometry indices, body composition, lipid profile, C- reactive Protein (CRP), Malondialdehyde (MDA), and the Western Ontario and McMaster Universities Arthritis Index (WOMAC) WOMAC index were assessed at the baseline and after 12 weeks. Results: At the end of the study, the LCG showed significant improvements compared with the PLG in the total WOMAC scores (17.41 ± 9.81 compared with 23.50 ± 12.02 (P = 0.024)); physical function (11.15 ± 6. 56 compared with 15.61 ± 8.17 (P = 0.014)); BMI (-1.21 ± 0.84 kg/m2 compared with − 0.79 ± 0.70 kg/m2 (P = 0.027)). However, MDA, total cholesterol, fat and visceral fat mass decreased only in LCG significantly, but not in the PLG. Other variables did not have any significant changes. Conclusion: Oral administration of 1000 mg L-carnitine in 12 weeks could improve WOMAC score and BMI, but not affect CRP, MDA, and lipid profile. Further trials with higher doses and longer durations, are required to verify our results. IRCT registration number: IRCT2017011932026N2. Registration date: 2017-04-27.
90 Days Impacts of Remote Ischemic Preconditioning on Patients Undergoing Open Total Aortic Arch Replacement: A Post-Hoc Analysis of a Previous Trial
Authors: Chen Yimeng , Wang Guyan , Zhou Hui , Yang Lijing , Zhang Congya , Yang Xiying , Lei Guiyu 
Published: May 2020

Abstract
Background: In the previous randomized controlled trial by our research group, we evaluated the effect of remote ischemic preconditioning (RIPC) in 130 patients (65 per arm) on acute kidney injury (AKI) within 7 days of open total aortic arch replacement. Significantly fewer RIPC-treated patients than sham-treated patients developed postoperative AKI, and, epically, RIPC significantly reduced serious AKI (stage II–III). However, the long-term effect of RIPC in patients undergoing open total aortic arch replacement is unclear. Methods: This study was a post-hoc analysis. We aimed to assess the roles of RIPC in major adverse kidney events (MAKE), defined as consisting persistent renal dysfunction, renal replacement therapy and mortality, within 90 days after surgery in patients receiving open total aortic arch replacement.Results: In this 90-day follow-up study, data were available for all study participants. We found that RIPC failed to improve the presence of MAKE within 90 days after surgery (RIPC: 7 of 65[10.8%]) vs sham: 15 of 65[23.1%]; P=0.061). In those patients who developed AKI after surgery, we found that the rate of MAKE within 90 days after surgery differed between the RIPC group and the sham group (RIPC: 4 of 36[11.2%]; sham: 14 of 48[29.2%]; P=0.046).Conclusions: At 90 days after open total aortic arch replacement, we failed to find a difference between the renoprotective effects of RIPC and sham treatment. The effectiveness or ineffectiveness of RIPC should be further investigated in a large randomized sham-controlled trial.Trial registration: This study was approved by the Ethics Committee of Fuwai Hospital (No. 2016–835) and our previous study was registered at clinicaltrials.gov before patient enrollment (NCT03141385; principal investigator: G.W.; date of registration: March 5, 2017).