bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinicians’ Experience of Providing Care: A Rapid Review
Authors: Iqbal Maha Pervaz , Manias Elizabeth , Mimmo Laurel , Mears Stephen , Jack Briony , Hay Liz , Harrison Reema 
Published: October 2020

Abstract
BackgroundHealth care services internationally are refocussing care delivery towards patient centred, integrated care that utilises effective, efficient and innovative models of care to optimise patient outcomes and system sustainability. Whilst significant efforts have been made to examine and enhance patient experience, to date little has progressed in relation to provider experience. This review aims to explore this knowledge gap by capturing evidence of clinician experience, and how this experience is defined and measured in the context of health system change and innovation.Methods:A rapid review of published and grey literature review was conducted utilising a rapid evidence assessment methodology. 79 studies retrieved from the literature were included in the review. 14 articles were identified from the grey literature search and one article obtained via hand searching. In total, 94 articles were included in the review. This study was commissioned by and co-designed with the New South Wales, Ministry of Health.Results:Clinician experience of delivering health care is inconsistently defined in the literature, with identified articles lacking clarity regarding distinctions between experience, engagement and work-related outcomes such as job satisfaction. Clinician experience was commonly explored using qualitative research that focused on experiences of discrete health care activities or events in which a change was occurring. Such research enabled exploration of complex experiences. In these contexts, clinician experience was captured in terms of self-reported information that clinicians provided about the health care activity or event, their perceptions of its value, the lived impacts they experienced, and the specific behaviours they displayed in relation to the activity or event. Moreover, clinician’s experience has been identified to have a paucity of measurement tools. Conclusion:Literature to date has not examined clinician experience in a holistic sense. In order to achieve the goals identified in relation to value-based care, further work is needed to conceptualise clinician experience and understand the nature of measurement tools required to assess this. In health system application, a broader ‘clinician pulse’ style assessment may be valuable to understand the experience of clinical work on a continuum rather than in the context of episodes of change/care.
Virtual Screening on Indonesian Herbal Compounds as COVID-19 Supportive Therapy: Machine Learning and Pharmacophore Modelling Approaches
Authors: Erlina Linda , Paramita Rafika Indah , Kusuma Wisnu Ananta , Fadilah Fadilah , Tedjo Aryo , Pratomo Irandi Putra , Ramadhanti Nabila Sekar , Nasution Ahmad Kamal , Surado Fadhlal Khaliq , Fitriawan Aries , Istiadi Khaerunissa Anbar , Yanuar Arry 
Published: October 2020

Abstract
Background: The latest development of COVID-19 spread in Indonesia has reached 311,176 cases, with 11,374 patients died, updated on October 6, 2020. Unfortunately, these numbers continue to overgrow, and no drug has yet been approved for effective treatment. This study aims to determine the potential candidate compounds in Indonesian herbal medicine as a COVID-19 supportive therapy using a machine learning and pharmacophore modelling approach.Methods: For the machine learning approach, we used three classification methods that have different ways in decision making, such as Support Vector Machine (SVM), Multilayer Perceptron (MLP), and Random Forest (RF). Moreover, for the pharmacophore modelling approach, we performed a structure-based method on the 3D structure of the main protease SARS-CoV-2 (3CLPro) and used the SARS, MERS, and SARS-CoV-2 repurposing drugs known from the literature as data sets on the ligand-based method. Finally, we used molecular docking to analyse the interactions between the 3CLpro protein (main protease) and 14 hit compounds from the Indonesian Herbal Database (HerbalDB) and Lopinavir as a positive control.Results: The machine learning approach with SVM, RF, and MLP methods and pharmacophore modelling approach were used for screening in herbal compounds obtained from HerbalDB. Based on the screening on HerbalDB using these two prediction approaches, we got 14 hit compounds. We then performed molecular docking to determine the interaction of these compounds with the main protease SARS-CoV-2 as an inhibiting agent. From the molecular docking analysis, it was found that six potential compounds as the main proteases of the SARS-CoV-2 inhibitor, i.e. Hesperidin, Kaempferol-3,4'-di-O-methyl ether (Ermanin); Myricetin-3-glucoside, Peonidine 3-(4’-arabinosylglucoside); Quercetin 3-(2G-rhamnosylrutinoside); and Rhamnetin 3-mannosyl-(1-2)-alloside.Conclusions: We used layered virtual screening with machine learning and pharmacophore modelling approaches that could provide more objective and optimal virtual screening and avoid subjective decision making on research results. Herbal compounds from various plants have potential as antiviral candidates for SARS-CoV-2. Based on our research and literature study, one of Indonesia's potential commodity crops is Psidium guajava (guava), and people can use it directly as a preventive effort.
Investigation of early and lifetime clinical features and comorbidities for the risk of developing treatment-resistant depression in a 13-year nationwide cohort study&nbsp;
Authors: Huang Shiau-Shian , Chen Hsi-Han , Wang Jui , Chen Wei J. , Chen Hsi-Chung , Kuo Po-Hsiu 
Published: October 2020

Abstract
Background: To investigate the risk of treatment-resistant depression (TRD) in patients with depression by examining their clinical features, early prescription patterns, and early and lifetime comorbidities. Methods: In total, 31,422 depressive inpatients were followed-up from diagnostic onset for more than 10-years. Patients were diagnosed with TRD if their antidepressant treatment regimen was altered ≥two times or if they were admitted after at least two different antidepressant treatments. Multiple Cox regression model were used to determine whether physical and psychiatric comorbidities, psychosis, and prescription patterns increased the risk of TRD by controlling for relevant demographic covariates. Survival analyses were performed for important TRD-associated clinical variables. Results: Females with depression (21.24%) were more likely to suffer from TRD than males (14.02%). Early anxiety disorders were more commonly observed in the TRD group than in the non-TRD group (81.48 vs. 58.96%, p<0.0001). Lifetime anxiety disorders had the highest population attributable fraction (42.87%). Seventy percent of patients with multiple psychiatric comorbidities developed TRD during follow-up. Cox regression analysis further identified that functional gastrointestinal disorders significantly increased TRD risk (aHR=1.19). Higher doses of antidepressants and benzodiazepines and Z drugs in the early course of major depressive disorder increased TRD risk (p<0.0001). Conclusion: Our findings indicate the need to monitor early comorbidities and polypharmacy patterns in patients with depression associated with elevated TRD risk.
Per-Protocol Analysis of The ZINC Trial for HIV Disease Among Alcohol Users
Authors: Lodi Sara , Freiberg Matthew , Gnatienko Natalia , Blokhina Elena , Yaroslavtseva Tatiana , Krupitsky Evgeny , Murray Eleanor , Samet Jeffrey H. , Cheng Debbie M. 
Published: October 2020

Abstract
Background. The ZINC trial randomized HIV-positive heavy drinkers to either daily zinc supplementation or placebo. The primary outcome was change in VACS index, a predictor of mortality, between baseline and 18 months. Because adherence and follow-up were suboptimal, the intention-to-treat analysis, which was not statistically significant, may have underestimated the effect of the zinc supplementation. Objective. We estimated the per-protocol effect of zinc versus placebo in the ZINC trial (i.e., the effect that would have been observed if all participants had had high adherence and none were lost to follow-up).Methods. Adherence was measured as the self-reported percentage of pills taken in the previous 6 weeks and assessed at all post-baseline visits. We used inverse probability weighting to estimate and compare the change in VACS index at 18 months in the zinc and placebo groups had all the trial participants had high adherence (i.e., cumulative adherence ≥80% at 18 months). To examine trends by level of adherence, we rerun the analyses using thresholds for high-adherence of 70% and 90% of average self-reported pill coverage.Results. The estimated (95% confidence interval) change in VACS index was –2.16 (-8.07, 3.59) and 5.84 (0.73, 11.80) under high adherence and no loss to follow-up in the zinc and placebo groups, respectively. The per-protocol effect estimate of the mean difference in change between the zinc and placebo group was -8.01 (-16.42, 0.01), somewhat larger than the intention-to-treat effect difference in change (-4.68 (-9.62, 0.25)), but it was still not statistically significant. The mean difference in change between individuals in the zinc and placebo group was -4.07 (-11.5,2.75) and -12.34 (-20.14,-4.14) for high adherence defined as 70% and 90% of pill-coverage, respectively. Conclusions. Overall, high adherence to zinc was associated with lower VACS score, but confidence intervals were wide and crossed 0. Further studies with larger sample size are needed to quantify the benefits of zinc supplementation in this population.Trial Registration. ClinicalTrials.gov Identifier: NCT01934803, August 30, 2013
Metastasis to lateral lymph nodes with no mesenteric lymph node involvement in low rectal cancer: a retrospective case series
Authors: Li Peng , Zhang Zhichun , Zhou Yuanda , Zeng Qingsheng , Zhang Xipeng , Sun Yi 
Published: October 2020

Abstract
Purpose The aim of this study is to examine the pattern of lymph node metastasis (lateral vs. mesenteric lymph nodes) in low rectal cancer.Methods This retrospective analysis included all patients undergoing laparoscopic total mesorectal excision plus lateral lymph node dissection for advanced low rectal cancer (up to 8 cm from the anal verge) during a period from July 1, 2017 to August 31, 2019 at the Department of Colorectal Surgery, Tianjin Union Medical Center. The decision to conduct lateral lymph node dissection was based on positive findings in preoperative imaging assessments.Results A total of 42 patients were included in data analysis. Surgery was successfully completed as planned, without conversion to open surgery in any case. A minimum of 10 mesenteric lymph nodes and 1 lateral lymph node on each side were dissected in all patients. Pathologic examination of resected specimens showed no metastasis to either mesenteric or lateral lymph nodes in 7 (16.7%) case, metastasis to both mesenteric and lateral lymph nodes in 26 (61.9%) cases, metastasis to mesenteric but not lateral lymph nodes in 4 (9.5%) cases, and metastasis to lateral but not mesenteric lymph nodes in 5 (11.9%) cases (n=2 in the obturator region; n=3 in the iliac artery region).Conclusion A clinically significant proportion of low rectal cancer patients have metastasis to lateral lymph nodes without involvement of mesenteric lymph nodes. More carefully planned prospective studies are needed to verify this preliminary finding.
Cytokine Profile During Occult Hepatitis B Virus Infection in Chronic Hepatitis C Patients
Authors: Ribeiro Camilla Rodrigues de Almeida , de Almeida Nathalia Alves Araújo , Martinelli Katrini Guidolini , Pires Marcia Amendola , Mello Carlos Eduardo Brandao , Barros José J. , De Paula Vanessa Salete 
Published: October 2020

Abstract
Background: The hepatitis B virus (HBV) is one of the leading causes of acute, chronic and occult hepatitis (OBI) representing a serious public health threat. Cytokines are known to be important chemical mediators that regulate the differentiation, proliferation and function of immune cells. Accumulating evidence indicate that the inadequate immune responses are responsible for HBV persistency. The aim of this study were to investigate the cytokines IFN-γ, TNF-α, IL-2, IL-4, IL-6, IL-10 and IL-17A in patients with OBI and verify if there is an association between the levels of these cytokines with the determination of clinical courses during HBV occult infection. Methods: 114 patients with chronic hepatitis C were investigated through serological and molecular tests, the OBI coinfected patients were subjected to the test for cytokines using the commercial human CBA kit. As controls, ten healthy donors with no history of liver disease and 10 chronic HBV monoinfected patients of similar age to OBI patients were selected. Results: Among 114 HCV patients investigated, 11 individuals had occult hepatitis B. The levels of cytokines were heterogeneous between the groups, most of the cytokines showed higher levels of production detection among OBI/HCV individuals when compared to control group and HBV monoinfected pacients. We found a high level of IL-17A in the HBV monoinfected group, high levels of TNF-α, IL-10, IL-6, IL-4 and IL-2 in OBI/HCV patients.Conclusion: These cytokines could be involved in the persistence of HBV DNA in hepatocytes triggers a constant immune response, inducing continuous liver inflammation, which can accelerate liver damage and favor the development of liver cirrhosis in other chronic liver diseases.
IRLnc: A novel functional noncoding RNA contributes to intramuscular fat deposition
Authors: Wang Ligang , Zhou Zhong-Yin , Zhang Tian , Zhang Longchao , Hou Xinhua , Yan Hua , Wang Lixian 
Published: October 2020

Abstract
Background Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. ResultsA total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (<10 kb) in pig and humans. Real-time quantitative polymerase chain reaction (RT-qPCR) validation study indicated that nuclear receptor subfamily 4 group A member 3 (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3.ConclusionsIn conclusion, a novel functional noncoding variation named IRLnc has been found contribute to IMF by regulating the expression of NR4A3. These findings suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.
Novel immune-related genes in the tumor microenvironment with prognostic value in breast cancer
Authors: Tan Wen , Liu Maomao , Wang Liangshan , Guo Yang , Wei Changsheng , Zhang Shuqi , Luo Chengyu , Liu Nan 
Published: October 2020

Abstract
Background: Breast cancer is one of the most frequently diagnosed cancers among women worldwide. Alterations in the tumor microenvironment (TME) have been increasingly recognized as key in the development and progression of breast cancer in recent years. To deeply comprehend the gene expression profiling of the TME and identify immunological targets, as well as determine the relationship between gene expression and different prognoses is highly critical. Results: The stromal/immune scores of breast cancer patients from The Cancer Genome Atlas were employed to comprehensively evaluate the TME. Although the TME did not correlate with the stages of breast cancer, it was closely associated with the subtypes of breast cancer and gene mutations (CDH1, TP53 and PTEN), and had immunological characteristics. Based on Gene Ontology (GO) functional enrichment analysis, the upregulated genes from the high vs low immune score groups were mainly involved in T cell activation, the external side of the plasma membrane, and receptor ligand activity. We further analyzed and screened the overlapping genes of the top 3 GO terms and upregulated differentially expressed genes (DEGs). Overall survival, time-dependent receiver operating characteristic (ROC), and protein-protein interaction (PPI) network analyses revealed that the genes of the top GO terms of the upregulated DEGs from the high vs low immune score groups exhibited better prognosis in breast cancer; 15 of them were related to good prognosis in breast cancer, especially CD226 and KLRC4-KLRK1.Conclusions: High CD226 and KLRC4-KLRK1 expression levels were identified and validated to correlate with better overall survival in specific stages or subtypes of breast cancer. CD226, KLRC4-KLRK1 and other new targets seem to be promising avenues for promoting antitumor targeted immunotherapy in breast cancer.
Integrated transcriptome and proteome analysis reveals potential mechanisms for differential abdominal fat deposition between divergently selected chicken lines
Authors: Wang Lijian , Leng Li , Ding Ran , Gong Pengfei , Liu Chang , Wang Ning , Li Hui , Du Zhi-Qiang , Cheng Bohan 
Published: October 2020

Abstract
Background: Genetic selection for meat production performance of broilers concomitantly causes excessive abdominal fat deposition, accompanied by several adverse effects, such as the reduction of feed conversion efficiency and reproduction performance. Our previous studies have identified important genes regulating chicken fat deposition, using the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) as an animal model. However, the molecular mechanism underlying fat deposition differences between fat and lean broilers remains largely unknown.Results: Here, we integrated the transcriptome (RNA-Seq) and quantitative proteome (isobaric tags for relative and absolute quantitation, iTRAQ) profiling analyses on abdominal fat tissues from NEAUHLF chicken lines. Differentially expressed genes (466 DEGs) and proteins (231 DEPs) were identified, and enriched in pathways related to fatty acid metabolism, fatty acid biosynthesis, glycerophospholipid metabolism, and PPAR signaling, and in pathways mainly involved in protein processing, endocytosis and lipid metabolism, respectively. Moreover, several key DEGs and DEPs involved in long-chain fatty acid uptake, in situ lipogenesis (fatty acid and cholesterol synthesis), and lipid droplets accumulation were discovered, and most of them were up-regulated in the fat line, after integrated transcriptome and proteome analysis.Conclusions: Together, our findings provided a novel insight into abdominal fat content discrepancy between the fat and lean chicken lines.
Allogeneic Administration of Human Umbilical Cord-derived Mesenchymal Stem/Stromal Cells for Bronchopulmonary Dysplasia: Preliminary Outcomes in Four Vietnamese Infants.
Authors: Thanh Liem Nguyen , Trieu Thai T.H. , Bui Hue T.H. , Hoang Van T. , Nguyen Anh T.T , Trinh Nhung T.H. , Nguyen Kien T. , Hoang Duc M. 
Published: October 2020

Abstract
Background: Bronchopulmonary dysplasia (BPD) is a severe condition in premature infants that compromises lung function and necessitates oxygen support. Despite major improvements in perinatal care minimizing the devastating effects, BPD remains the most frequent complication of extreme preterm birth. Our study reports the safety of the allogeneic administration of umbilical cord-derived mesenchymal stem/stromal cells (allo-UC-MSCs) and the progression of lung development in four infants with established BPD. Methods : UC tissue was collected from a healthy donor, followed by propagation at the Stem Cell Core Facility at Vinmec Research Institute of Stem Cell and Gene Technology. UC-MSC culture was conducted under xeno- and serum-free conditions. Four patients with established BPD were enrolled in this study between May 25, 2018, and December 31, 2018. All four patients received two intravenous doses of allo-UC-MSCs (1 million cells/kg patient body weight (PBW) per dose) with an intervening interval of 7 days. Safety and patient conditions were evaluated during hospitalization and at 7 days and 1, 6 and 12 months postdischarge. Results: No intervention-associated severe adverse events or prespecified adverse events were observed in the four patients throughout the study period. At the time of this report, all patients had recovered from BPD and were weaned off of oxygen support. Chest X-rays and CT scans confirmed the progressive reductions in fibrosis. Conclusions: Allo-UC-MSC administration is safe in preterm infants with established BPD. Trial registration : This preliminary study was approved by the Vinmec International Hospital Ethics Board (approval number: 88/2019/QĐ-VMEC; retrospectively registered March 12, 2019).
Characterization of the Serum Levels of Meteorin-like in Patients with Inflammatory Bowel Disease and its Association with Inflammatory Cytokines&nbsp;
Authors: Gholamrezayi Afsane , Mohamadinarab Maryam , Rahbarinejad Pegah , Fallah Soudabeh , Barez Shekufe Rezghi , Setayesh Leila , Moradi Nariman , Fadaei Reza , Chamani Elham , Tavakoli Tahmine 
Published: October 2020

Abstract
Background: Meteorin-like (Metrnl) is an adipokine with insulin sensitizing and anti-inflammatory properties that has been discovered recently. The relation among Metrnl, Inflammatory Bowel Disease (IBD), and obesity has been unexplored yet. Methods: The present study was conducted on 54 healthy control, 42 Ulcerative Colitis (UC), and 43 Crohn's disease (CD) patients who were diagnosed by pathological examination. In all participants, serum levels of adiponectin, Metrnl, interleukin (IL)-6, and Tumor necrosis factor (TNF-α) were measured using ELISA kits.Results: Metrnl concentration was considerably lower in both UC (85.25±36.55 pg/mL) and CD (76.93±27.92 pg/mL) patients in comparison to control (107.52 ± 35.33 pg/mL). In addition, it was seen that both patient groups have a decreased level of adiponectin compared to the controls. Besides that, the level of IL-6 and TNF-α were significantly greater in the patient groups. Moreover, the result showed that the level of Metrnl is inversely correlated with body mass index (BMI) in the controls and the patients. Metrnl levels are also inversely associated with IL-6, and TNF-α in both of the patient groups.Conclusions: The current study is the first one reporting the decreased levels of Metrnl in serum among patients with IBD, which is inversely related with BMI, TNF-α, and IL-6. These results suggested a possible relation of Metrnl with the pathogenesis of IBD, particularly through inflammatory process, although further studies are warranted to dissect the possible mechanism.