bluuebunny/crossref_metadata_2025_split huggingface dataset:
­­Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq
Authors: Yin Qinyan , Strong Michael J , Zhuang Yan , Flemington Erik K , Kaminski Naftali , de Andrade Joao AM , Lasky Joseph A 
Published: August 2019

Abstract
Background

Numerous publications suggest an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports have employed immunohistochemistry, in situ hybridization and/or PCR, which are susceptible to specificity artifacts.

Methods

We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 age-matched controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K).

Results

We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs.

Conclusions

To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Proteomic identification and expression of oral apparatus constituents in cell regeneration of giant ciliate Stentor coeruleus (strain WHEL)
Authors: Xiong Jie , Wei Wei , Jiang Chuanqi , Yang Wentao , Miao Wei 
Published: August 2019

Abstract
Background
The giant ciliate Stentor coeruleus is a suitable model organism for studying morphogenesis and regeneration at the single-cell level. The anterior end of the cell is dominated by thousands of cilia organized into a ciliated band of membranelles, known as the oral apparatus (OA). This feeding organelle can be induced to shed by urea treatment. The OA then regenerates via a series of defined morphological events and the cell resumes normal feeding activity. These defined events provide an ideal opportunity to identify the protein constituents of OA and their expression patterns in OA regeneration.

Results
We identified OA constituents in S. coeruleus by mass spectrometry. A total of 882 OA-associated proteins were identified; the homologs of 181 of these are known OA constituents in other organisms. The expression pattern of OA-associated genes during regeneration was investigated using single-cell transcriptome sequencing. The expression of most OA-associated genes was high during regeneration, indicating their stable expression after OA shedding. We also identified OA-associated differentially expressed genes that may be involved in regulating OA reconstruction. This information enabled us to hypothesize the architecture of OA of S. coeruleus WHEL.

Conclusions
We have identified protein components of the OA and determined the temporal changes in their expression during OA regeneration in S. coeruleus WHEL. Although our results are preliminary, they form the basis of further studies into the molecular mechanisms of OA development in S. coeruleus. In addition, as S. coeruleus is an important model organism for studying morphogenesis, our findings may help to improve the understanding of OA formation in ciliates.
The Impact of HIV Knowledge and Attitudes on HIV Testing Acceptance among Patients in an Emergency Department in the Eastern Cape, South Africa
Authors: Ryan Sofia , Hahn Elizabeth , Rao Aditi , Mwinnyaa George , Black John , Maharaj Roshen , Mvandaba Nomzamo , Nyanisa Yandisa , Quinn Thomas C. , Hansoti Bhakti 
Published: August 2019

Abstract
Background: Transmission of HIV in South Africa continues to be high due to a large proportion of individuals living with undiagnosed HIV. Uptake of HIV testing is influenced by a multitude of factors including the patient’s knowledge and beliefs about HIV.
Methods: This study sought to quantify the impact of knowledge and attitudes on HIV testing acceptance in an emergency department by co-administering a validated HIV knowledge and attitudes survey to patients who were subsequently offered HIV testing.
Results: During the study period 223 patients were interviewed and offered HIV testing. Individuals reporting more negative overall attitudes (p = 0.006), higher levels of stigma to HIV testing (p<0.001), and individuals who believed their test was confidential (p<0.001) were more likely to accept an HIV test.
Conclusions: Interventions focused on improving patient perceptions around testing confidentiality will likely have the greatest impact on testing acceptance in the emergency department.
Later onset of hypertension increased the risk of dementia in Mild Cognitive Impairment in community
Authors: qin hongyun , Hu chengping , Zhao xudong , Zhu binggen , Cao Zhicheng , Wang ling , Guo yi 
Published: August 2019

Abstract
Objective
To investigate the effect of later onset of hypertension on the progression of MCI in community.
Methods
Participants are from The Study (NO.PKJ2010-Y26, 2011), a population-based longitudinal cognition survey of people aged 55+, sampled by probability proportional to size cluster. Hypertension onset age was estimated by self-reported information and medical insurance card records, then classified into two groups: the middle-age group (onset age < 65 years) and the old-age group (onset age ≥ 65 years). In order to study the effect of later onset of hypertension on dementia, the incidence of dementia was compared between the two groups.
Results
A total of 277 hypertensive mild cognitive impairment (MCI) participants without dementia were followed for 6 years. 56 MCI participants (20.22%) progressed to dementia (MCIp). The proportion of MCIp participants in the old-age onset hypertension group (≥ 65 years) was higher than that of middle-age onset one (27.0% vs 15.4%; X2 = 5.538, P = 0.019). And in the old-age onset hypertension group, the proportion of MCIp without diabetes mellitus was higher than those with diabetes mellitus (24.7% vs 12.6%; X2 = 5.321, P = 0.021), and the proportion of MCIp with increased pulse pressure was higher than those without increased pulse pressure (33.3% vs 15.4%; X2 = 3.902, P = 0.048). However, the multivariate logistic regression analysis showed that older age was the only risk for MCIp (OR=0.732, p=0.029).
Conclusions
These results suggest that, later onset hypertension was harmful to cognition even in cases where the level of blood pressure maintained at 130/80mmHg with antihypertensive management. It is necessary to expand the research sample and improve the experimental methods for further confirmation.
Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats
Authors: Zeng Hong , Yu Bao-fu , Liu Nan , Yang Yan-yan , Xing Hua-yi , Liu Xiao-xie , Zhou Mouwang 
Published: August 2019

Abstract
Abstract
Background
Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on transcriptional levels after SCI and to determine the mechanisms underlying α-Syn activity based on RNA-seq.
Result
The establishment of a rat model of lentiviral vector-mediated knockdown of α-Syn in Sprague-Dawley rats with T3 spinal cord contusion. The results of the RNA-SEQ analysis showed that there were 191 differentially expressed genes (DEGs) between the SCI group and the LV_SCI group, and 96 DEGs in the LV_SCI group compared with the sham operation group (CON group). The top 20 biological transition terms were identified by Gene ontology (GO) analysis. The Kyoto Gene and Genomic Encyclopedia (KEGG) analysis showed that the LV_SCI group significantly up-regulated the cholinergic synaptic pathway and the neuroactive ligand receptor interaction signaling pathway. Enriched chord analysis analyzes key genes. Further cluster analysis, gene and protein interaction network analysis showed that Chrm2 and Chrnb2 together observed the LV_SCI group to promote the proliferation of Chrm2 and Chrnb2 and the neurogenesis of the injury site by immunofluorescence. Further by subcellular localization, the LV_SCI group enhanced the expression of Chrnb2 at the cell membrane and cell junction.
Conclusion
Knockdown of α-synuclein after spinal cord injury enhance motor function and promote neurogenesis probably through enhancing cholinergic signaling pathways and neuroreceptor interactions. This study not only further clarifies the understanding of the mechanism of knockdown of α-synuclein on SCI but also helps to guide the treatment strategy for SCI.
Time to sputum culture conversion and its predictors among patients with multidrug resistant tuberculosis in Hangzhou, China: a retrospective cohort study
Authors: Li Qingchun , Lu Min , Hsieh Evelyn , Wu Limin , Wu Yifei , Wang Meng , Wang Le , Wang Ke , Zhao Gang , Xie Li , Qian Han-Zhu 
Published: August 2019

Abstract
Background To investigate the time to initial sputum culture conversion (SCC) and its predictors among multidrug-resistant tuberculosis (MDR-TB) patients in Hangzhou, China.Methods A retrospective cohort study was conducted among patients initiating treatment for MDR-TB from 2011-2015 in Hangzhou, China. Time to initial SCC was analyzed using the Kaplan-Meier method, and Cox proportional hazards regression was used to identify predictors of SCC.Results Among 384 patients enrolled with MDR-TB, 359 (93.5%) successfully achieved initial SCC after a median of 85 days (inter-quartile range, 40-112 days). A higher rate of SCC was observed in participants with successful treatment outcomes than those with poor treatment outcomes (P<0.01). Multivariate analysis showed that age 25-64 years (adjusted odds ratio [AOR], 0.7; 95% confidence interval [CI], 0.5-0.9; P<0.01), age ≥65 years (AOR, 0.5; 95%CI, 0.3-0.8; P<0.01) and household registration in Hangzhou (AOR, 1.3; 95%CI, 1.0-1.5; P<0.05) were found to be associated with SCC.Conclusions Although high SCC and treatment success rates were observed among MDR-TB patients in Hangzhou, the prolonged duration to initial SCC underscores the importance of emphasizing measures for infection control. A new policy of shifting outpatient treatment to inpatient treatment in China may reduce the risk of transmission from patients in the time window prior to SCC.
Diagnostic and prognostic value of interleukin-6, pentraxin 3, and procalcitonin levels among sepsis and septic shock patients: a prospective controlled study according to the Sepsis-3 definitions
Authors: Song Juhyun , Park Dae won , Moon Sungwoo , Cho Han-Jin , Park Jong Hak , Seok Hyeri , Choi Won Seok 
Published: August 2019

Abstract
Background This study investigated the clinical value of interleukin-6 (IL-6), pentraxin 3 (PTX3), and procalcitonin (PCT) in patients with sepsis and septic shock diagnosed according to the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3).Methods Serum levels of IL-6, PTX3, and PCT were measured in 143 enrolled subjects (51 with sepsis, 46 with septic shock, and 46 controls). Follow-up IL-6 and PTX3 levels were measured in patients with initial septic shock within 24 hours of hospital discharge. Optimal cut-off values were determined for sepsis and septic shock, and prognostic values were evaluated.Results Serum IL-6 levels could discriminate sepsis (area under the curve [AUC], 0.97–1.00, P < 0.001; cut-off value, 5.89 pg/mL, 97.0% sensitivity, 97.2% specificity) from controls and could distinguish septic shock (AUC, 0.85-0.95; cut-off value, 53.59 pg/mL, 91.8% sensitivity, 63.2% specificity) from both sepsis and controls. Twenty-eight-day mortality was significantly higher in the group with high IL-6 (≥ 53.59 pg/mL) than with low IL-6 (< 53.59 pg/mL) (P = 0.002). IL-6 was an independent risk factor for 28-day mortality among patients overall (hazard ratio, 1.0004; 95% confidence interval, 1.0003–1.0005; p = 0.024). In septic shock patients, both initial and follow-up PTX3 levels were consistently significantly higher in patients who died than in those who recovered (initial p = 0.004; follow-up P < 0.001).Conclusions The diagnostic and prognostic value of IL-6 was superior to those of PTX3 and PCT for sepsis and septic shock.
Diagnostic Accuracy of the Xpert MTB/Rif Ultra for tuberculosis adenitis
Authors: Antel Katherine , Oosthuizen Jenna , Malherbe Francois , Louw Vernon J , Nicol Mark P , Maartens Gary , Verburgh Estelle 
Published: August 2019

Abstract
Background The WHO recently recommended the new Xpert MTB/RIF Ultra assay (Ultra) instead of the Xpert MTB/RIF assay because Ultra has improved sensitivity. We report the diagnostic accuracy of Ultra for tuberculous adenitis in a tuberculosis and HIV endemic setting.Methods We obtained fine-needle aspirates (FNA) and lymph node tissue by core-needle biopsy in adult patients with peripheral lymphadenopathy of > 20 mm. Ultra and mycobacterial culture were performed on FNA and tissue specimens, with histological examination of tissue specimens. We assessed the diagnostic accuracy of Ultra against a composite reference standard (CRS) of ‘definite tuberculosis’ (presence of acid-fast bacilli (AFBs) or culture positive on FNA or lymph node tissue) or ‘probable tuberculosis’ (macroscopic caseation or granulomas on histology or tuberculosis proven from another site, and no other identified cause for lymphadenopathy).Results We prospectively evaluated 99 participants of whom 50 were HIV positive: 21 had ‘definite tuberculosis’, 15 ‘probable tuberculosis’ and 63 did not have tuberculosis (of whom 38% had lymphoma and 19% disseminated malignancy). Using the CRS, the sensitivity of Ultra on FNA was 70% (95% CI 51-85) and on tissue was 67% (95% CI 45-84); specificity on FNA was 100% (95% CI 92-100) and on tissue 96% (95% CI 88-99).Conclusions Ultra performed on FNA or tissue of a lymph node had reasonable sensitivity and high specificity. Ultra on FNA would be an appropriate initial investigation for lymphadenopathy in tuberculosis endemic areas.
Comprehensive transcriptomic analysis of Papillary Thyroid Cancer: potential biomarkers associated with tumor progression
Authors: Hosseinkhan Nazanin , Honardoost Maryam , Blighe Kevin , Moore C.B. Tara , Khamseh Mohammad Ebrahim 
Published: August 2019

Abstract
Background Identification of stage-specific prognostic/predictive biomarkers could lead to the more efficient clinical management in papillary thyroid carcinoma (PTC). The main objective of this study was to characterize the stage-specific deregulations in gene and miRNA expression in PTC and also to identify potential prognostic biomarkers.Methods 495 RNASeq and 499 miRNASeq PTC samples (stage I-IV) as well as, respectively, 56 and 57 normal samples were retrieved from The Cancer Genome Atlas (TCGA). DESeq2 was used to identify deregulation of genes and miRNAs between sequential stages of PTC. To identify the minority of patients who progress from stage I to higher stages, we additionally performed a clustering analysis focused on the stage I RNASeq data. Moreover a validation study was done on an independent PTC RNASeq study.Results Large amount of heterogeneity in gene expression patterns was observed in stage I PTC patients. LTF and PLA2R1 were identified as two promising biomarkers that exhibited down-regulation in a small subgroup of stage I (both in TCGA and in the validation data set) and in the majority of stage IV patients (in TCGA data set). hsa-miR-205, hsa-miR-509-2, hsa-miR-514-1 and hsa-miR-514-2 were also identified as up-regulated miRNAs in both PTC patients with stage I and stage III.Conclusion Common gene expression alterations in early and advanced stages of PTC, could be used for individualized risk stratification and personalized treatment approach.
Adolescents’ Perception Of Dietary Behaviour In A Public School In Chile
Authors: Vio Fernando , Olaya Marcela , Yañez Marisol , Montenegro Edith 
Published: August 2019

Abstract
Background: The objective was to assess dietary behavior among sixth to eighth-grade students to inform the delivery and content of nutrition education.
Methods: This is a qualitative study through focus groups. Subjects were 57 adolescents 10-14 years old, 30 males and 27 females distributed in six groups. To compare group responses, transcriptions were coded using the original question guide. The information was analyzed using the content analysis technique.
Results: The main findings showed that adolescents knew dietary guidelines recommendations, but they consumed non-healthy food. They liked to cook but preferred fast food preparations. They increased fast food consumption on weekends and with friends. In utilization of Information Communication Technologies, all students had access to technology trough mobile phones, tablets and computers and were open to have an interactive program with personal information about diet and behavior.
Conclusions: It is important to know adolescents’ dietary behavior to prevent obesity designing education intervention programs.
Keywords: adolescents, community health promotion, dietary behavior, qualitative methods, focus groups
Maternal and Fetal outcomes of Cesarean Delivery and factors associated with its unfavorable management outcomes; In Ayder Specialized Comprehensive Hospital, Mekelle, Tigray, Ethiopia, 2017.
Authors: mengesha Meresa Berwo , Adhanu Hadgay Hagos , weldegiwergis Desta Abraha , Assefa Natnael Etsay , werid Woldu mammo , weldemariam Mulu Gebretsadik , welay fissaha tekulu , Hidru Hagos Degefa , Gebru Tesfay tsegay 
Published: August 2019

Abstract
Objectives: The aim of this study was to determine the unfavorable outcomes and to assess factors contribute for the unfavorable management outcomes after caesarean deliveries in Ayder Specialized Comprehensive Hospital, Mekelle, Tigray, Ethiopia, 2017. Results: The unfavorable maternal management outcomes were Adhesion 28(8.3%), excessive blood loss and blood transfusion 19(5.6%), caesarean hysterectomy 10(3%), relaparotomy 5(1.5%), wound infection and wound dehiscence 23(6.8%).Unfavorable fetal outcomes were were still birth 9(2.6%), early neonatal death 8(2.4%), low birth weight 58(17.2%). Women’s who did not booked for Antenatal Care and having history of previous Caesarean delivery were found to be associated with unfavorable maternal outcomes and indications of Caesarean delivery as obstructed labor was associated with unfavorable fetal outcomes. Key words: caesarean delivery, fetal outcomes, maternal outcomes.
Impacts of conservative endodontic cavities on root canal therapy compare to traditional endodontic cavities in premolars
Authors: Juan Xia , weidong Wang , Zhengmao Li , Bingpeng Lin , Qian Zhang , Qianzhou Jiang , Yang xuechao 
Published: August 2019

Abstract
Background: This study aims to compare the percentage of dentin removed, instrumentation efficacy, root canal filling and load at fracture between contracted endodontic cavities and traditional endodontic cavities in premolars.
Methods: Forty extracted intact human first premolars were imaged with micro-CT and randomly assigned to CEC or TEC groups. Minimal CECs were prepared with the aid of 3D-printed guide template, canals were prepared with a 0.04 taper M-Two rotary instrument and cavities were restored with resin. The specimens were loaded to fracture in an Instron Universal Testing Machine after a fatigue phase. The data were analyzed by the independent samples T test and Mann-Whitney U test, appropriate post hoc tests.
Results: In the premolars tested in vitro, CECs conserved coronal dentin in premolars with two dental roots but no impact on the instrument efficacy, the root canal filling or the biomechanical responses compared with TECs.
Conclusion: The results of this study did not suggest that CEC could improve the fracture resistance of the endodontically treated premolars. The instrumentation efficacy and the percentage of filling material did not significantly differ between CECs and TECs in the premolars.
The Oral Microbiome and Salivary Proteins Influence Caries in Preschool Children
Authors: Chen Wang , Jiang Qian , Yan GuoWei , Yang DeQin 
Published: August 2019

Abstract
Background Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in preschool children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.Methods Children six to eight years old living in rural isolated areas with or without caries were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ)technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry(LC-MS/MS), respectively.Results A total of 328486 high-quality 16S rRNA sequences were obtained from 40 samples including 20 plaque and 20 saliva subjects, which was clustered into 14,076 OTUs, representing 18 phyla, 28 classes, 48 orders, 78 families,135 genera, and 410 species. We found the six most abundant phyla (Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria, and Candidate division TM7). The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between caries and caries-free children; differences in the bacterial community composition was analyzed by LEfSe. The core microbiome was defined as 18 predominant genera coming from the saliva and plaque of subjects. For the results of salivary proteome analysis, 9135 unique peptides and 1662 proteins group were identified from 20 salivary samples. 258 proteins were differentially expressed between the caries-free and caries-active group, which might be a potential proteinic biomarker of caries and health status.Conclusions Dental caries is a multifactorial disease affecting many children around the world. The result of our study revealed the complexities of the oral bacterial community and confirmed “ecological plaque hypothesis”. In addition, as an important host factor of caries the salivary proteins are different in healthy or carious status. Exploration on microbiological or protein biomarkers is of great significance to prevent dental caries.