bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak
Authors: Zhang Xiaolan , Bao Qi , Jia Congjun , Li Chen , Chang Yongfang , Wu Xiaoyun , Liang Chunnian , Bao Pengjia , Yan Ping 
Published: September 2020

Abstract
Background: Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results: A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties.Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.
Classification Models using Circulating Neutrophil Transcripts Can Detect Unruptured Intracranial Aneurysm
Authors: Poppenberg Kerry E , Tutino Vincent M , Li Lu , Waqas Muhammad , June Armond , Chaves Lee , Jiang Kaiyu , Jarvis James N , Sun Yijun , Snyder Kenneth V , Levy Elad I , Siddiqui Adnan H , Kolega John , Meng Hui 
Published: September 2020

Abstract
Background: Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. Methods: Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n=94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n=40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. Results: Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC)=0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. Conclusions: We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.
Uganda’s Increasing Dependence On Development Partner’s Support For Immunization – A Five Year Resource Tracking Study (2012 – 2016)
Authors: Kamya Carol , Abewe Christabel , Waiswa Peter , Asiimwe Gilbert , Namugaya Faith , Opio Charles , Ampeire Immaculate , Lagony Stephen , Charlotte Muheki 
Published: September 2020

Abstract
Background: In Uganda, there are persistent weaknesses in obtaining accurate, reliable and complete data on local and external investments in immunization to guide planning, financing, and resource mobilization. This study aimed to measure and describe the financial envelope for immunization from 2012 to 2016 and analyze expenditures at sub-national level.Methods: The Systems of Health Accounts (SHA) 2011 methodology was used to quantify and map the resource envelope for immunization. Data was collected at national and sub-national level from public and external sources of immunization through key informant interviews coupled with document reviews. Data were coded using the SHA, categorized and disaggregated to detail the expenditure on immunization activities. Results: Over a five-year period, funding for immunization increased fourfold to US$ 85.6 million in 2016. The Ugandan government was the main contributor (55%) to immunization resources from 2012 to 2014. However, Gavi, the Vaccine Alliance contributed the majority (59%) of the resources to immunization in 2015 and 2016. Majority (66%) of the funds were managed by the National Medical Stores. Over the five-year period, 80% of the funds allocated to immunization activities were spent on facility based routine immunization (expenditure on human resources and outreaches). At sub-national level, districts allocated 15% of their total annual resources to immunization to support supervision to lower health centers (including distribution of vaccines). Health facilities spent 5.5% of their total annual resources on immunization to support outreaches.Conclusion: Development partner support has aided the improvement of vaccine coverage and increased access to vaccines. However, there is an increasing dependence on this support for a critical national program raising sustainability concerns alongside other challenges like being off budget and unpredictable. To ensure financial sustainability, there is need to operationalize the immunization fund, advocate and mobilize additional resources for immunization from the Government of Uganda and the private sector, increase the reliability of resources for immunization as well as leverage on health financing reforms like the National Health Insurance.
Access to and use of sexual and reproductive health services among street children in Uganda: Does migration matter?
Authors: Bwambale Mulekya Francis , Bukuluki Paul , Moyer Cheryl A. , Borne Bart H.W Van den 
Published: September 2020

Abstract
Background: While the nexus of migration and health outcomes is well acknowledged, the effect of rural-urban migration on use of sexual and reproductive health (SRH) services has received less attention. We assessed the effect of rural-rural migration on the use of SRH services while controlling for confounding and whether there is a difference in the use of SRH services among migrant and non-migrant street children and young adults.Methods: Data were collected among 513 street children and young adults aged 12 - 24 years using face‐to‐face interviews using venue-based time-space sampling (VBTS). Using STATA 16.00, multivariate logistic regression analysis was performed to identify factors associated with SRH services use, with rural-urban migration status as the main predictor. We defined migrants as street children and young adults aged 12 - 24 years who migrated from rural districts and settled in Kampala city for a period of not more than 24 months preceding the survey.Results: Overall, 18.13% of the street children and young adults had ever used contraception/family planning, 45.89% had ever tested for HIV and knew their status while 34.70% had ever been screened for sexually transmitted infections (STIs). Migrant street children and young adults had reduced odds of using SRH services (HIV testing, use of FP and screening for STIs compared to non-migrant street children and young adults (aOR=0.59, 95%CI 0.36 - 0.97). Other factors associated with use of SRH services among street children and young adults include age (aOR=4.51; 95%CI 2.78 - 7.33), schooling status (aOR=0.34; 95%CI - 1.830 0.15-0.76), knowledge of place of care (aOR=3.37,95%CI 2.04 - 5.34) and access to SRH information (aOR=2.7, 95%CI 1.67 - 4.53). Conclusion: Access to and use of SRH services is low among migrant street children and adults compared to the non-migrant street children and young adults and is independently associated with rural-urban migration status, age, schooling status, knowledge of place of SRH care and access to SRH information. Our findings call for the need to design and implement multi-dimensional interventions to increase use of SRH services among street children and young adults while taking into consideration their migration patterns.
Administration of Saccharomyces boulardii mafic-1701 improves feed conversion ratio, promotes antioxidant capacity, alleviates intestinal inflammation and modulates gut microbiota in weaned piglets
Authors: Zhang Wenxiu , Bao Chengling , Wang Jian , Zang Jianjun , Cao Yunhe 
Published: September 2020

Abstract
Background: Probiotics are used as a means to improve animal health and intestinal development. Saccharomyces boulardii is a well-known probiotic; however, few studies have examined the effects of S. boulardii on weaned piglet performance. Therefore, this 28-day study compared the effects of S. boulardii mafic-1701 and aureomycin in diets for weaned piglets on growth performance, antioxidant parameters, inflammation and intestinal microbiota. One hundred and eight piglets, weaned at 28 d of age (8.5 ± 1.1 kg), were randomly divided into the three dietary treatment groups with six pens and six piglets per pen (half male and half female). The dietary treatment groups were as follows: (1) basal diet (CON); (2) basal diet supplemented with 75 mg/kg aureomycin (ANT); (3) basal diet supplemented with 1 × 108 CFU/kg S. boulardii mafic-1701 (SB).Results: Compared to CON group, SB group had higher feed efficiency (P < 0.05) in the last 14 days and lower diarrhea rate (P < 0.05) over the entire 28 days. Total superoxide dismutase in serum was markedly increased in SB group (P < 0.05). Moreover, compared with CON group, SB group decreased the levels of pro-inflammatory cytokines interleukin-6 (P < 0.01) and Tumor necrosis factor-α (P < 0.05) in jejunum. Supplementation of S. boulardii mafic-1701 increased the abundance of Ruminococcaceae_UCG_009 and Turicibacter (P < 0.05), whereas the abundance of unclassified_Clostridiaceae_4 was decreased (P < 0.05). Furthermore, S. boulardii mafic-1701 administration increased cecal concentration of microbial metabolites, isobutyrate and valerate (P < 0.05).Conclusions: The improvement in feed conversion ratio, reduction in diarrhea rate in weaned piglets provided diets supplemented with S. boulardii mafic-1701 may be associated with enhanced antioxidant activity, anti-inflammatory responses and improved intestinal microbial ecology.
Enhanced PRL-1 expression in placenta-derived mesenchymal stem cells accelerates hepatic function via mitochondrial dynamics in a cirrhotic rat model
Authors: Kim Jae Yeon , Choi Jong Ho , Jun Ji Hye , Park Sohae , Jung Jieun , Bae Si Hyun , Kim Gi Jin 
Published: September 2020

Abstract
Background: Placenta-derived mesenchymal stem cells (PD-MSCs) have been highlighted as an alternative cell therapy agent that has become a next-generation stem cell treatment. Phosphatase of regenerating liver-1 (PRL-1), an immediate early gene, plays a critical role during liver regeneration. Here, we generated enhanced PRL-1 in PD-MSCs (PD-MSCsPRL-1, PRL-1+) using lentiviral and nonviral gene delivery systems and investigated mitochondrial functions by PD-MSCPRL-1 transplantation for hepatic functions in a rat bile duct ligation (BDL) model.Methods: PD-MSCsPRL-1 were generated by lentiviral and nonviral AMAXA gene delivery systems and analyzed for their characteristics and mitochondrial metabolic functions. Liver cirrhosis was induced in Sprague-Dawley (SD) rats using common BDL for 10 days. PKH67+ naïve and PD-MSCsPRL-1 were intravenously administered into cirrhotic rats using a nonviral system (2x106 cells/animal). The animals were sacrificed at 1, 2, 3, and 5 weeks after transplantation and engraftment of stem cells, and histopathological analysis and hepatic mitochondrial functions were performed.Results: PD-MSCsPRL-1 were successfully generated using lentiviral and nonviral AMAXA systems and maintained characteristics similar to those of naïve cells. Compared with naïve cells, PD-MSCsPRL-1 improved respirational metabolic states of mitochondria. In particular, mitochondria in PD-MSCsPRL-1 generated by the nonviral AMAXA system showed a significant increase in the respirational metabolic state, including ATP production and mitochondrial biogenesis (*p<0.05). Furthermore, transplantation of PD-MSCsPRL-1 using a nonviral AMAXA system promoted engraftment into injured target liver tissues of a rat BDL cirrhotic model and enhanced the metabolism of mitochondria via increased mtDNA and ATP production, thereby improving therapeutic efficacy.Conclusions: Our findings will further our understanding of the therapeutic mechanism of enhanced MSCs and provide useful data for the development of next-generation MSC-based cell therapy and therapeutic strategies for regenerative medicine in liver disease.
Illuminating the dark side of the human transcriptome with long read transcript sequencing
Authors: Kuo Richard , Cheng Yuanyuan , Zhang Runxuan , Brown John W.S. , Smith Jacqueline , Archibald Alan L. , Burt Dave W. 
Published: September 2020

Abstract
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide additional evidence for rare transcripts and genes such as mono-exonic and non-coding genes that were previously either undetectable or impossible to differentiate from sequencing noise. Results: We developed the Transcriptome Annotation by Modular Algorithms (TAMA) software to leverage the power of long read transcript sequencing and address the issues with current data processing pipelines. TAMA achieved high sensitivity and precision for gene and transcript model predictions in both reference guided and unguided approaches in our benchmark tests using simulated Pacific Biosciences (PacBio) and Nanopore sequencing data and real PacBio datasets. By analyzing PacBio Sequel II Iso-Seq sequencing data of the Universal Human Reference RNA (UHRR) using TAMA and other commonly used tools, we found that the convention of using alignment identity to measure error correction performance does not reflect actual gain in accuracy of predicted transcript models. In addition, inter-read error correction can cause major changes to read mapping, resulting in potentially over 6K erroneous gene model predictions in the Iso-Seq based human genome annotation. Using TAMA’s genome assembly based error correction and gene feature evidence, we predicted 2,566 putative novel non-coding genes and 1,557 putative novel protein coding gene models.Conclusions: Long read transcript sequencing data has the power to identify novel genes within the highly annotated human genome. The use of parameter tuning and extensive output information of the TAMA software package allows for in depth exploration of eukaryotic transcriptomes. We have found long read data based evidence for thousands of unannotated genes within the human genome. More development in sequencing library preparation and data processing are required for differentiating sequencing noise from real genes in long read RNA sequencing data.
Peritumoral ductular reaction can be a prognostic factor for intrahepaticcholangiocellular carcinoma
Authors: Shen Zhenyang , Xiao Jingbo , Wang Junjun , Lu Lungen , Wan Xinjian , Cai Xiaobo 
Published: September 2020

Abstract
Background: Peritumoral ductular reaction (DR) was reported to be related to the prognosis of combined hepatocellular-cholangiocarcinoma and hepatocellular carcinoma. Non-mucin-producing intrahepatic cholangiocarcinoma (ICC) which may be derived from small bile duct cells or liver progenitor cells (LPCs) was known to us. However, whether peritumoral DR is also related to non-mucin-producing ICCs remains to be investigated. Methods: Forty-seven patients with non-mucin-producing ICC were eventually included in the study and clinicopathological variables were collected. Immunohistochemical analysis and immunofluorescence staining for cytokeratin 19, proliferating cell nuclear antigen, and α-smooth muscle actin were performed in tumor and peritumor liver tissues.Results: A significant correlation existed between peritumoral DR and local inflammation and fibrosis. (r = 0.357, 95% CI, 0.037-0.557; P = 0.008 and r = 0.742, 95% CI, 0.580-0.849; P < 0.001, respectively). Patients with obvious peritumoral DR had high recurrence rate (81.8% vs 56.0%, P = 0.058) and poor overall and disease-free survival time (P = 0.01 and P = 0.03, respectively) comparing with mild peritumoral DR. Compared with the mild peritumoral DR group, the proliferation activity of LPCs/ cholangiocytes was higher in obvious peritumoral DR, which, however, was not statistically significant. (0.43±0.29 vs 0.28±0.31, P = 0.172). Furthermore, the correlation analysis showed that the DR grade was positively related to the portal/septalα-SMA level (r = 0.359, P = 0.001).Conclusions: Peritumoral DR was associated with local inflammation and fibrosis. Patients with non-mucin-producing ICC having obvious peritumoral DR had a poor prognosis. Peritumoral DR could be a prognostic factor for ICC. However, the mechanism should be further investigated.
Genome-wide small RNA profiling reveals tiller development in tall fescue (Festuca arundinacea Schreb.)
Authors: Hu Tao , Wang Tao , Li Huiying , Wassie Misganaw , Xu Huawei , Chen Liang 
Published: September 2020

Abstract
Background: Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes modules play critical roles in tiller development in plants. In this study, a genome-wide small RNA profiling was carried out in two tall fescue genotypes contrasting for tillering production (‘Ch-3’, high tiller production rate and ‘Ch-5’, low tiller production rate) and two types of tissue samples at different tillering development stage (Pre-tillering, grass before tillering; Tillering, grass after tillering). ‘Ch-3’, ‘Ch-5’, Pre-tillering, and Tillering samples were analyzed using high-throughput RNA sequencing. Results: A total of 222 million high-quality clean reads were generated and 208 miRNAs were discovered, including 148 known miRNAs belonging to 70 families and 60 novel ones. Furthermore, 18 miRNAs were involved in tall fescue tiller development process. Among them, 14 miRNAs displayed increased abundance in both Ch-3 and Tillering plants compared with that in Ch-5 and Pre-tillering plants and were positive with tillering, while another four miRNAs were negative with tiller development. Out of the three miRNAs osa-miR156a, zma-miR528a-3p and osa-miR444b.2, the rest of 15 miRNAs were newfound and associated with tiller development in plants. Based on our previous full-length transcriptome analysis in tall fescue, 2 8927 potential target genes were discovered for all identified miRNAs. Most of the 212 target genes of the 18 miRNAs were dominantly enriched into “ubiquitin-mediated proteolysis”, “phagosome”, “fatty acid biosynthesis”, “oxidative phosphorylation”, and “biosynthesis of unsaturated fatty acids” KEGG pathways. In addition, bdi-miR167e-3p targets two kinase proteins EIF2AK4 and IRAK4, and osa-miR397a targets auxin response factor 5, which may be the significant miRNA-genes controllers in tillering development. Conclusions: This is the first genome-wide miRNA profiles analysis to identify regulators involved in tiller development in cool-season turfgrass. Tillering related 18 miRNAs and their 212 target genes provide novel information for the understanding of the molecular mechanisms of miRNA-genes mediated tiller development in cool-season turfgrass.