bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Differential mRNA and lncRNA Expression in AcMNPV- Infected Sf9 Cells
Authors: Zhao Tiejun , Deng Riqiang , Chen Mengqiu , Wang Xunzhang 
Published: August 2020

Abstract
Autographa californica multiple Nucleopolyhedrovirus (AcMNPV) is the archetypal species of the alphabaculovirus. Sf9 are the ovarian cells of their host—Spodoptera frugiperda. In this study, a total of 3,463 pieces of time-series differentially expressed RNA are identified, including 1,200 mRNA and 2,263 lncRNA, with high-throughput sequencing technology using samples collected from Sf9 cells at different time points after AcMNPV infection. The result could provide a reference for the further study of the interaction and regulatory mechanism between the virus and the host.
Surgical Treatment for Brachiocephalic Artery Aneurysm with Takayasu Arteritis Using Isolated Cerebral Perfusion
Authors: Sugiyama Kayo , Watanuki Hirotaka , Futamura Yasuhiro , Okada Masaho , Makino Satoshi , Matsuyama Katsuhiko 
Published: August 2020

Abstract
Background: Takayasu arteritis (TA) is a chronic inflammatory disease that induces stenosis, occlusion, or aneurysmal degeneration of the aorta and its major branches. In the surgical treatment of TA, anastomotic aneurysm can be problematic. Furthermore, atherosclerotic complications should be considered in surgical treatment for elderly TA patients. Case presentation: Here, we report a case of brachiocephalic artery (BCA) aneurysm with TA for which surgical treatment was successful. For avoidance of anastomotic aneurysm, both distal and proximal anastomosis were reinforced with Teflon felt strips. Preoperative computed tomography detected severe atherosclerotic changes in the arch vessels. The patient underwent partial arch replacement using isolated cerebral perfusion (ICP) for brain protection and recovered without any neurological deficits.Conclusions: In avoidance with anastomotic aneurysm, reinforcement of the anastomosis was introduced. ICP was effective for brain protection in case with severe atherosclerotic changes.
ITRAQ-Based quantitative proteomics reveals the proteome profiles of MDBK cells infected with bovine viral diarrhea virus
Authors: Li Yaxin , Guo Tao , Wang Xiaokui , Ni Wei , Hu Ruirui , Cui Yuying , Mi Taotao , Hu Shengwei 
Published: August 2020

Abstract
Background

Bovine viral diarrhea (BVD) which is caused by Bovine viral diarrhea virus (BVDV), is an acute, contagious disease. In spite of the use of vaccines and elimination projects, BVDV is still found to cause severe financial losses to the cattle industry for the past years. The current study presents a preliminary analysis of the pathogenic mechanisms from the perspective of protein expression levels in infected host cells at different points in time to elucidate the infection process associated with BVDV.
Methods

We used the isobaric tags for relative and absolute quantitation (iTRAQ) technology coupled with liquid chromatography-tandem mass spectrometric (LC-MS/MS) approach for a quantitative proteomics comparison of BVDV NADL-infected MDBK cells and non-infected cells. The functions of the proteins were deduced by functional annotation and their involvement in metabolic processes explored by KEGG pathway analysis to identify their interactions.
Results

There were 357 (47.6% downregulated, 52.4% upregulated infected vs. control), 101 (52.5% downregulated, 47.5% upregulated infected vs. control), and 66 (21.2% downregulated, 78.8% upregulated infected vs. control) proteins were differentially expressed (fold change > 1.5 or < 0.67) in the BVDV NADL-infected MDBK cells at 12, 24, and 48 h after infection. GO analysis showed that the differentially expressed proteins (DEPs) are mainly involved in metabolic processes, biological regulation and localization. KEGG enrichment analysis showed that some signaling pathways that involved in the regulation of BVDV NADL-infection and host resistance are significantly (P < 0.05) enriched at different stages of the BVDV NADL-infection, such as Endocytosis signaling pathway, FoxO signaling pathway, Homologous recombination signaling pathway and Lysosome pathway.
Conclusions

These results revealed that the DEPs in BVDV NADL-infected MDBK cells have a wide range of regulatory effects; in addition, they provide a lot of resources for the study of host cell proteomics after BVDV infection.
Prevalence of Depression, Anxiety, Delirium, and Post-traumatic Stress Disorder Among COVID-19 Patients: Protocol for a Living Systematic Review
Authors: Shi Jiyuan , Zhao Liang , Li Yuanyuan , Yan Meili , Mingming Niu , Chen Yamin , Song Ziwei , Gao Ya , Zhang Ruixing , Tian Jinhui 
Published: August 2020

Abstract
BackgroundPrevious studies on the impact of COVID-19 on the mental health of the patients has been limited by the lack of relevant data. With the rapid and sustained growth of the publications on COVID-19 research, we will perform a living systematic review (LSR) to provide comprehensive and continuously updated data to explore the prevalence of depression, anxiety, delirium, and post-traumatic stress disorder (PTSD) among COVID-19 patients.MethodsWe will perform a comprehensive search of the following databases: Cochrane library, PubMed, Web of Science, Embase, and Chinese Biomedicine Literature to identify relevant studies. We will utilize different tools to examine the bias risks (quality) regarding studies of varying design types, such as the Newcastle-Ottawa Scale (NOS) for cohort and case-control studies, etc. Study inclusion, data extraction, and risk of bias assessments will be performed independently by two reviewers. The literature searches would be updated every three months. We will perform meta-analysis if any new eligible studies or data are obtained and resubmit an updated systematic review if any change in outcomes and heterogeneity is determined after the addition of the new studies. DiscussionThis LSR would provide an in-depth and up-to-date summary of the psychological impact of COVID-19 diagnosis and treatment on the patients. Systematic review registrationPROSPERO CRD42020196610
Combined IFN-γ and IL-2 Release Assay for Detect Active Pulmonary Tuberculosis: A Prospective Multicentre Diagnostic Study in China
Authors: Tan Yaoju , Tan Yunhong , Li Junlian , Hu Pengnan , Guan Ping , Kuang Haobin , Liang Qide , Yu Yanyan , Chen Zhongnan , Wang Quan , Yang Zhenping , AiKeReMu DiLiNaZi , Pang Yu , Liu Jianxiong 
Published: August 2020

Abstract
Background: We performed a prospective multicenter diagnostic study to evaluate combined interferon-γ (IFN-γ) and interleukin-2 (IL-2) release assays for detecting active pulmonary tuberculosis (TB) in China. Methods: Adult patients presenting with symptoms suggestive of pulmonary TB were consecutively enrolled in three TB-specialized hospitals. Sputum specimens and blood samples were collected from each participant at enrollment. In vitro measurements of IFN-γ and IL-2 release from Mycobacterium tuberculosis (MTB)-specific antigen-stimulated patient peripheral blood mononuclear cells were conducted using enzyme-linked immunosorbent assays (ELISAs).Results: Between July 2017 and December 2018, a total of 3,245 patients with symptoms suggestive of pulmonary TB were included in the final analysis. Of these patients, 2,536 were diagnosed with active TB, including 1,092 definite and 1,444 clinically diagnosed cases. Overall sensitivity and specificity rates of the IFN-γ release assay were 83.8% and 81.5%, respectively, as compared to IL-2 assay rates yielding greater specificity (94.3%) but lower sensitivity (72.6%). Notably, a parallel-type combination test for IFN-γ/IL-2 provided greatest overall sensitivity (87.9%) but relatively low specificity (79.8%). Meanwhile, a series-type combination test had an overall sensitivity rate of 68.5% that, when stratified by case subgroup, yielded sensitivity rates of 72.1% and 65.8% for definite and clinically diagnosed TB cases, respectively.Conclusion: We developed a new immunological method to differentiate between active TB and other pulmonary diseases. Our data demonstrated that both series-type and parallel-type IFN-γ/IL-2 combination tests may improve diagnosis of active TB cases in different settings. Additionally, the diagnostic accuracy of the series-type combination assay correlated with disease severity in our patient cohort.
Hyponatremia is Associated with Poor Outcome in COVID-19
Authors: DE CARVALHO Hugo , LETELLIER Thibault , KARAKACHOFF Matilde , DESVAUX Geoffrey , CAILLON Hélène , PAPUCHON Emmanuelle , BENTOUMI-LOAEC Maxime , BENAOUICHA Nesrine , CANET Emmanuel , CHAPELET Guillaume , TURNIER Paul LE , MONTASSIER Emmanuel , ROUHANI Armine , GOFFINET Nicolas , FIGUERES Lucile 
Published: August 2020

Abstract
Background
Hyponatremia has been described in severe acute respiratory syndrome. Our objective was to describe the impact of hyponatremia on COVID-19 patients’ outcome (intensive care unit [ICU] admission, mechanic ventilation or death).
Methods
According to natremia at admission, two groups were retrospectively screened: hyponatremic (< 135 mM, n = 101) or normonatremic (natremia ≥ 135 mM, n = 222) patients. Pearson’s chi-2 (qualitative variables) and Student tests (quantitative variables) were used to compare the two groups. A multiple logistic regression model was used to assess the association of outcome and patients’ data.
Results
Hyponatremia was generally mild. There were more male patients in the hyponatremic group (p = 0.005). Pulmonary lesions on the first thoracic CT-scanner performed during the hospitalization were significantly more extended in the hyponatremic group (p = 0.03). ICU admission, mechanic ventilation or death were significantly higher in hyponatremic compared to normonatremic patients (34 versus 14%; p < 0.001; 16% versus 5%; p = 0.002; 19 versus 9%, p = 0.021, respectively). Hyponatremia was an independent predictor of poor outcome (adjusted Odds-ratio: 2.49 [1.18–5.33, p = 0.017]).
Conclusions
Our study showed an independent relationship between hyponatremia at admission and transfer to ICU, use of mechanic ventilation or death in COVID-19. Hyponatremia may reflect the potential severity of underlying pulmonary lesions. Our results support the use of natremia as a simple bedside screening tool for early identification of SARS-CoV-2 infected patients at high risk of poor outcome.
Microbial Genes Involved in the Aromatic Compound Degradation Deciphered Through Metagenomics Analysis of Industrial Wastewater.
Authors: Pandit Priti , Kumar Raghawendra , Kumar Dinesh , Patel Zarna , Pandya Labdhi , Joshi Chaitanya 
Published: August 2020

Abstract
Background: Understanding microbial and functional diversity from different stages of common effluent treatment plant (CETP) plays an important role to enhance the treatment performs of wastewater systems. However, unraveling microbial interactions as well as utilization of substrate involved in complex microbial communities is a challenging task. Hence, we demonstrate an integrated approach of shotgun metagenomics and whole genome sequencing to identify the microbial diversity and genes involved in degradation of benzoate, 1,2-dichloroethane and phenylalanine metabolism and degradation pathways from CETP microbiome.Results: The taxonomy profile was annotated using the Ribosomal Database Project (RDP) database in the MG-RAST server. The results showed that, bacteria accounted for 98.46% was the most abundant domain, followed by Eukaryota (0.10%) and Archea 0.02%. At Phylum level, Proteobacteria (28.8%) were dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%) and Fusobacteria (6.9%). The most dominated species were Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibris vulgaris, Clostridium sticklandii, and Escherichia coli. The Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, revealed the presence of the genes responsible for the metabolism and degradation of aromatic compounds. This information was validated with the whole genome analysis of the bacteria isolated from the CETP.Conclusion: The two type of integrated meta omics analyses revealed that the metabolic and degradation capability at both community wide and individual bacterial levels. In addition, we demonstrated that microbial diversity changes with the treatment process in which inlet of CETP effluent shows higher dominancy of Proteobacteria whereas in textile industry outlet the high abundance of Firmicutes was observed. We foresee this approach would contribute in designing the bioremediation strategies for the industrial treatment process.
Reducing posttraumatic stress in parents of patients with a rare inherited metabolic disorder using eye movement desensitization and reprocessing therapy: a case study
Authors: Conijn Thirsa , Haverman Lotte , Wijburg Frits A , de Roos Carlijn 
Published: August 2020

Abstract
Background
Parents of children with severe inborn errors of metabolism (IEMs) frequently face stressful events related to the disease of their child and are consequently at high risk for developing parental posttraumatic stress disorder (PTSD). Assessment and treatment of posttraumatic stress disorder (PTSD) in these parents is however not yet common in clinical practice. PTSD can be effectively treated by Eye Movement Desensitization and Reprocessing (EMDR), mostly offered in multiple weekly sessions which may preclude participation as parents are generally overburdened by the ongoing and intensive care for their child. We offered time-limited EMDR therapy with a maximum of four sessions over two subsequent days to two parents (from different families) of mucopolysaccharidosis type III (MPS III) patients to explore the potential effect of this approach in reducing post-traumatic stress symptoms and comorbid psychological distress.
Methods
Both qualitative and quantitative outcomes were used. The case conceptualisation, EMDR sessions and the effects reported by parents are described. The change in the severity of post-traumatic stress symptoms and comorbid psychological distress were evaluated with the Reliable Change Index (RCI).
Results
All traumatic memories and catastrophic fears of the future reported by parents were successfully processed and neutralized. Parents felt more competent to face future difficulties related to the disease of their child, and no adverse effects were reported. Quantitative outcomes showed a clinically significant decrease in post-traumatic stress symptoms and comorbid psychological distress from pre- to post treatment, and these beneficial effects were maintained at follow-up.
Conclusion
Time-limited EMDR might be a successful treatment for traumatized parents of children with mucopolysaccharidosis type III, and we suggest that this approach may have a wider application including parents of children with other severe IEMs. More awareness in clinical practice of the need for assessment and treatment of PTSD in parents of children with IEMs is essential to improve the psychosocial wellbeing of both parent and child.
Application of Cryopreservation Technique in the Preservation of Rat Limbs
Authors: Tian Yu , Li Nan , Wang Wei , Li Na 
Published: August 2020

Abstract
Objective: This study aims to observe the physiological and pathological changes of severed fingers (limbs) under different storage conditions through animal experiments, and to screen out the best preservation conditions. Medthods: Sixty healthy adult male Sprague-Dawley rats were selected and evenly divided into 4 preservation groups, including conventional low-temperature dry (CLTD), the university of wisconsin (UW) solution, cryopreservation and cryopreservation + UW solution preservation group. After harvesting the limbs, were preservated for 72 h and 7 days, respectively. Then the limbs were thawed and replanted in situ. Sciatic nerves were collected for hematoxylin and eosin (HE) staining, and observed the changes in tissue morphology. Results: Replantation was successful in 11 out of 15 rats (73%) in cryopreservation + UW group, and the walking function of the 9 (82%) rats in cryopreservation + UW group were significantly better than that of the cryopreservation preservation group. In addition, the HE staining results shown that the CLTD group nerve bundles were morphologically damaged, and there were more acellular structures and tissue fragments; the UW group nerve bundles were less injured and the perineurium was more complete and orderly; The nerve bundles in the cryopreservation group and cryopreservation + UW group are tightly arranged and the tissue morphology is regular; Compared with the cryopreservation + UW group, the complete of the cryopreservation group is not well. Conclusions: The cryopreservation technology combined with UW solution is a new and effective method for the severed limbs preserving.
Morbidity and Mortality in the Antiretroviral Era in Sub-saharan Africa: A Systematic Review Protocol
Authors: Ghislain Manimani Riziki , Mushebenge Aganze Gloire-Aime , Magula Nombulelo 
Published: August 2020

Abstract
Background: Worldwide, Human Immunodeficiency Virus / Acquired Immunodeficiency Syndrome (HIV/AIDS) remains a public health concern. The prevalence of HIV in Sub-Saharan Africa is one of the uppermost in the world. This study aims to identify the determinants of morbidity and specific causes of mortality in the antiretroviral treatment (ART) era in Sub-Saharan Africa.Method/design: Observational studies will be systematically reviewed reporting on morbidity and mortality in the antiretroviral therapy (ART) era in Sub-Saharan Africa. We will search for relevant studies from Google Scholar, PubMed, and CINAHL databases. Two review authors will independently screen titles, abstracts and full-text articles in duplicate, extract data and assess the bias. Discrepancies will be resolved by discussion or arbitration of a third review author. The study will use the Preferred Reporting Item of Systematic Review (PRISMA 2015) guideline. We will use R software to analyze and synthesize the data, the information will be captured into a spreadsheet regarding the most causes of hospitalization and death related to HIV in the antiretroviral treatment, Graphic displays will be used to visually compare the prevalence of comorbidities across the study region. This will also enable to provide any form of patterns in the comorbidities.Discussion: This review will summarize the determinants of morbidity and causes of mortality in the antiretroviral era in Sub-Saharan Africa. The findings of this study will help to improve opportunistic infection’s prevention and clinical outcomes in the ART era.Systematic review registration: PROSPERO CDR42019141933
MALAT1 Promotes Epithelial-Mesenchymal Transition of Pancreatic Cancer Cells Through miR-141-5p/ TGFBR1 / TGFBR2 Axis
Authors: Lu Huimin , Li Mao , Ye Jun , Zhang Ling , Lu Shan , Yang Dujiang , Li Zhenlu , Yue Chao , Hu Weiming 
Published: August 2020

Abstract
The authors have requested that this preprint be removed from Research Square.
The effect of opioid-free anesthesia on the quality of recovery after gynecological laparoscopy: study protocol for a prospective randomized controlled trial
Authors: Song Jae Yen , Choi Hoon , Chae Minsuk , Ko Jemin , Moon Youg Eun 
Published: August 2020

Abstract
Background: Because of the indiscriminate use of opioids during the perioperative period, opioid-free anesthesia (OFA) has been increasingly required. Nevertheless, the studies on the detailed techniques and effects of OFA are not sufficient. The Quality of Recovery-40 (QoR-40) questionnaire is a validated assessment tool for measuring recovery from general anesthesia. However, no study has used the QoR-40 to determine if OFA leads to better recovery than standard general anesthesia. Therefore, we aim to perform this study to determine the effects of OFA using dexmedetomidine and lidocaine on the quality of recovery as well as the various postoperative outcomes. Methods: The patients (n=78) will be allocated to one of the two groups; Study group will receive bolus and infusion of dexmedetomidine and lidocaine and Control group will receive remifentanil infusion during general anesthesia for gynecological laparoscopy. The other processes including anesthetic and postoperative care will be performed similarly in two groups. Intraoperative hemodynamic, anesthetic, and nociceptive variables will be recorded. Postoperative outcomes such as QoR-40, pain severity, opioid-related side effects will be assessed. Additionally, ancillary cytokine study (inflammatory cytokine, stress hormone, and reactive oxygen species) will be performed during study period. Discussion: This will be the first study to determine the effect of OFA, using the combination of dexmedetomidine and lidocaine, on the quality of recovery after gynecological laparoscopy compared with standard general anesthesia using remifentanil. The findings from this study will provide scientific and clinical evidence on the efficacy of OFA.
Ankara City Hospital COVID-19 Severity Score (ACCSES):A Calculation Tool in the Prediction of Severe Illness Requiring Intensive Care Follow-up
Authors: Guner Rahmet , Kayaaslan Bircan , Hasanoglu Imran , Aypak Adalet , Bodur Hurrem , Ates Ihsan , Akinci Esragul , Erdem Deniz , Eser Fatma , Izdes Seval , Kalem Ayse Kaya , Bastug Aliye , Karalezli Aysegul , Surel Aziz , Ayhan Muge , Karaahmetoglu Selma , Ozkocak Isil , Arguder Emine , Ozdemir Burcu , Mutlu Mehmet Nevzat , Bilir Yesim Aybar , Saricaoglu Elif Mukime , Gokcinar Derya , Gunay Sibel , Dinc Bedia , Gemcioglu Emin , Bilmez Ruveyda , Aydos Omer , Asilturk Dilek , Inan Osman , Buzgan Turan 
Published: August 2020

Abstract
Aim: The aim of this study is to develop and explain an easy-to-use severity score calculation tool to predict severe COVID-19 cases that would need intensive care unit (ICU) follow-up.Material method: The study was carried out in patients with laboratory-confirmed COVID-19 hospitalized in Ankara City Hospital between March 15, 2020, and June 15, 2020. The outcome was severe illness that required ICU follow-up. Univariate and binary logistic regression were used to create a prediction model by using potential predictive parameters obtained on the day of hospitalization. Youden’s J index was calculated with receiver-operator characteristic curves analysis in order to evaluate cut-off points, and predicted probability was calculated. The accuracy of the prediction model was tested by calculating the area under curve (AUC). Results: Of the total of 1022 patients, 152 had a severe illness and required ICU follow-up. Among 68 variables, 20 parameters met the potential predictive factor condition for severe illness and were included in the development process for ANKARA CITY HOSPITAL COVID-19 SEVERITY SCORE (ACCSES). The ACCSES calculation tool was created by the final 9 parameters (sex, oxygen saturation, hemoglobin, platelet count, glomerular filtration rate, aspartate transaminase, procalcitonin, ferritin, and D-dimer). AUC was 0.96 (95% CI, 0.95-0.98).Conclusion: We developed a simple, accessible, easy to use calculation tool, ACCSES, with good distinctive power for a severe illness that required ICU follow-up. The clinician can easily predict the course of COVID-19 and decide the procedure and facility of further follow-up simply using available clinical and laboratory values of patients upon admission.