bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection of Reference Genes for Transcription Studies on Adventitious Root Induction in Olive (Olea Europaea L.) Microshoots Considering Co-expression and Average Transcriptional Stability
Authors: Noceda Carlos , Peixe Augusto , Arnholdt-Schmitt Birgit 
Published: August 2020

Abstract
BackgroungSelection of reference genes (RGs) for normalization of PCR-gene expression data includes two crucial steps: determination of the among-sample transcriptionally more stable genes and subsequent choosing of the most suitable genes as internal controls. Both steps can be carried-out through generally accepted strategies each having different strengths and weaknesses. The present study proposes to reinforce normalization of gene expression data by integrating and adding analytical revision at critical steps of those accepted procedures. Especially crucial is to counterbalance a higher representative number of RGs with a correspondent increase in their average transcriptional instability or a generalised co-expression trend among the samples. This methodological study used in vitro olive adventitious rooting as an experimental system, since the underlying morphogenetic process -wich is common to diverse species- is still not completely understood.ResultsFirstly, RG candidates were ranked according to transcriptional stability following a simple statistical method that reduces biasing effects of concomitant, systematic biological variations associated to experimental conditions, such as the variations caused by gene co-regulation. Those types of systematic co-variation are unconsidered by several popular ad hoc informatics programmes. To select the adequate genes among those already ranked, an algorithm of one of the ad hoc informatics programmes (GeNorm) was adapted to allow partial automatization of RG selection for any strategy of transcriptional-gene stability ordering. In order to delve into the resulting possible RG sets suitability for inter-assay comparisons and technical-error compensation, separate statistics were formulated. The achieved results were compared with those obtained by standard stability ranking methods. Finally, a double evaluation was performed to accurately contrast two choice RG sets. The whole strategy was applied to a panel considering several independent factors, but the suitability of the obtained putative RG sets was tested for cases restricted to fewer variables. H2B, OUB and ACT are valid for normalization in transcriptional studies on olive microshoot rooting when comparing treatments, time points and assays.ConclusionsThe set of genes identified as internal reference is now available for wider expression studies on any target gene in similar biological systems. The overall methodology aims to constitute a guide for general application.
Follistatin-like 1 (FSTL1) is a Prognostic Biomarker and Correlated with Immune Cell Infiltration in Gastric Cancer
Authors: Li Li , Huang Shanshan , Yao Yangyang , Chen Jun , Li Junhe , Xiang Xiaojun , Deng Jun , Xiong Jianping 
Published: August 2020

Abstract
Background: Follistatin-like 1 (FSTL1) plays a central role in the progression of tumor and tumor immunity. However, the effect of FSTL1 on the prognosis and immune infiltration of gastric cancer (GC) remains to be elucidated.Method: The expression of FSTL1 data was analyzed in Oncomine and TIMER databases. Analyses of clinical parameters and survival data were conducted by Kaplan-Meier plotter and immunohistochemistry. Western blot assay and real‐time quantitative PCR (RT-qPCR) was using to analyzed protein and mRNA expression, respectively. The correlations between FSTL1 and cancer immune infiltrates was analyzed by Tumor Immune Estimation Resource (TIME), Gene Expression Profiling Interactive Analysis (GEPIA) and LinkedOmics database.Results: The expression of FSTL1 was significantly higher in GC tissues than in normal tissues, and bioinformatic analysis and Immunohistochemistry (IHC) indicated that high FSTL1 expression significantly correlated with poor prognosis in GC. Moreover, FSTL1 was predicted as an independent prognostic factor in GC patients. Bioinformatics analysis results suggested that FSTL1 mainly involved in tumor progression and tumor immunity. And significant correlations were found between FSTL1 expression and immune cell infiltration in GC.Conclusion: The study effectively revealed useful information about FSTL1 expression, prognostic values, potential functional networks and impact of tumor immune infiltration in GC. In summary, FSTL1 can be used as a biomarker for prognosis and evaluating immune cell infiltration in GC.
Maternal Dietary Linoleic Acid Altered Intestinal Barrier Function in Domestic Pigeons (Columba Livia)
Authors: Xu Qianqian , Zou Xiaoting , Dong Xinyang 
Published: August 2020

Abstract
BackgroundLinoleic acid (LA) is predominantly essential for poultry. Deficiency of LA in poultry were manifested in various aspects such as retarded growth and reduced resistance to disease. The effects of LA on intestinal health in vitro and in mammals has been studied, whereas research related to the effects of LA on intestine health in poultry was scanty. Intestinal health and immune function play an important role in pigeon squab growth. Considering squabs are fed by their parents, the purpose of this study was to explore the effects of maternal dietary LA on intestinal barrier function in squabs by determining intestinal morphology, gene expression of tight junction protein, immune cytokines, and microbial flora.ResultsA completely randomized design with a control group, 1% dietary LA supplementation group, 2% dietary LA supplementation group, and 4% dietary LA supplementation group was used. Six squabs from each treatment were randomly sampled at 21 posthatch. Results indicated that LA supplementation improved intestinal morphology as reflected by increased villus height, villus area and the ratio of villus to crypt, and the promotion at dosage of 1% was most significant. Besides, 1% LA supplementation elevated distribution density of goblet cell in intestine, and strengthened tight junction between enterocytes by up-regulating claudin3 and occludin gene expression, but down-regulating claudin2 gene expression. Moreover, 1% LA supplementation reduced secretion of pro-inflammation cytokines and increased anti-inflammation cytokines partly. The diversity index Chao1 of intestinal microbiota in 1% LA supplementation group was higher than other groups. And Butyrivibrio as beneficial bacteria was the biomarker of LA1%. However, excessive (4%) LA supplementation led to adverse impact on intestinal immunity and microbiota.ConclusionsMaternal dietary LA in three levels all could improve intestinal morphology in squabs. Therein, appropriate dosage (1%) supplementation might enhance mucosal protection and epithelium barrieer in squabs, and furthermore consolidated intestine immunity and luminal microbial environment. However, excessive (4%) LA supplementation might lead to adverse impact on immunity and microbiota. Maternal dietary LA might alter intestinal barrier function in pigeon squabs in a dose-dependent manner.
Using Behavioral Insights to Design Implementation Strategies in Public Mental Health Settings: a Qualitative Study of Clinical Decision-Making
Authors: Last Briana S , Schriger Simone H , Timon Carter E. , Frank Hannah E , Buttenheim Alison M. , Rudd Brittany N , Fernandez-Marcote Sara , Comeau Carrie , Shoyinka Sosunmolu , Beidas Rinad S. 
Published: August 2020

Abstract
Background: Trauma focused-cognitive behavioral therapy (TF-CBT) is an evidence-based intervention for youth with posttraumatic stress disorder. An important component of TF-CBT is the trauma narrative (TN), a phase in the intervention in which youth are guided to process the memories, thoughts, and feelings associated with their traumatic experience(s). Previous work has shown that only half of TF-CBT clinicians complete the TN with their clients. Drawing from the behavioral insights literature—an interdisciplinary field studying judgment and decision-making—the present study seeks to understand what determines clinician use of the TN and to generate strategies that target these determinants. Methods: Through semi-structured qualitative interviews, we sought the perspectives of trained TF-CBT clinicians working in public mental health settings across the city of Philadelphia (n=17) to understand their decisions to use the TN with clients. We analyzed the qualitative data using a coding approach informed by the behavioral insights literature. We used an iterative process of structured hypothesis generation, aided by a behavioral insights guide, and rapid validation informed by behavioral insights to uncover the determinants of TN use. We then generated implementation strategies that targeted these determinants using the “Easy Attractive Social Timely” framework, a behavioral insights design approach. Results: We generated and validated three broad themes about what determines clinician implementation of the TN: decision complexity, clinician affective experience, and agency norms. We hypothesized the behavioral insights that underlie these implementation determinants and generated a list of nine behavioral insights strategies that theoretically may facilitate TN implementation. Conclusions: Our study investigated why an effective component of an evidence-based intervention is often neglected. We leveraged robust scientific theories and empirical regularities from the behavioral insights literature to understand clinician perspectives on TN implementation. These factors were theoretically linked to implementation strategies. Our work revealed the potential for using behavioral insights in the diagnosis of evidence-based intervention determinants and the design of implementation strategies.
Spectrum of Movement Disorders in GNAO1 Encephalopathy: in-depth Phenotyping and Literature Review
Authors: Kim Soo Yeon , Shim YoungKyu , Ko Young Joon , Park Soojin , Jang Se Song , Lim Byung Chan , Kim Ki Joong , Chae Jong-Hee 
Published: August 2020

Abstract
Background
GNAO1 encephalopathy is a rare neurodevelopmental disorder characterized by distinct movement presentations and early onset epileptic encephalopathy. Here, we report the in-depth phenotyping of genetically confirmed patients with GNAO1 encephalopathy, focusing on movement presentations.
Results
Six patients who participated in Korean Undiagnosed Disease Program were diagnosed to have pathogenic or likely pathogenic variants in GNAO1 using whole exome sequencing. All medical records and personal video clips were analyzed with a literature review. Three of the 6 patients were male. Mean follow-up duration was 39 months (range, 7–78 months) and age at last examination was 8.0 years (range, 3.3–16.9 years). Initial complaints were hypotonia or developmental delay in 5 and right-hand clumsiness in 1 patient, which were noticed at 20 months of age on average (range, 0–75 months). All patients showed global developmental delay and 4 had severely retarded development. Five patients (5/6, 83.3%) had many different movement symptoms with various onset and progression. The symptoms included stereotyped hands movement, non-epileptic myoclonus, dyskinesia, dystonia and choreoathetosis. Whole exome sequencing identified 6 different variants in GNAO1. Three were novel de novo variants and atypical presentation was noted in a patient. One variant turned out to be inherited from patient’s mother who had mosaic variant. Distinct phenotypes in patients with variant p.Glu246Lys and p.Arg209His were elucidated by in-depth phenotyping and literature review.
Conclusions
We reported 6 patients with GNAO1 encephalopathy showing an extremely diverse clinical spectrum on video. Some characteristic movement features identified by careful inspection may also provide important diagnostic insight and practice guidelines.
Network Analysis, and Experimental Validation to Uncover the Mechanism of the Four Compounds in Artemisia Annua (Qing Hao) Antimalarial
Authors: zhao yuping , Zhang Xiao-bo , Xu Hai-yu , Wang Ling , Huang Lu-qi 
Published: August 2020

Abstract
Background

Artemisinin is widely used to treat malaria, but the antimalarial mechanism and coordinative interactions governing the actions of artemisinin, scopoletin, arteannuin B and artemisinic acid have not been elucidated.
Methods

Based on the existence of antimalarial drugs, the antimalaria targets of artemisinin, scopoletin, arteannuin B and artemisinic acid were investigated by molecular docking using the similarity theory of chemical structure, and the antimalaria mechanism of scopoletin and its coordinative antimalaria interactions with the other three ingredients of the mixture were subsequently explored.
Results

Using the text information excavation method, the relevant proteins involved in the antimalarial effect of artemisinin were determined to be IL-6, ACHE, PC3, IPOB, CYC, TNF-α, UGT1A9, CASP3, XDH, IL-1β, VEGF, CAT, CREB, AMPK, UGT1A6, ADR, MAPK, COX2, LB24AB and CYP450. Meanwhile, the relevant proteins involved in the antimalarial effect of scopoletin were TNF-α, PI3K, IL-8, IL- 6, VEGF, IL-1β, MAPK, CD4, SP2, CTNNB, CASP3, PRO1400, IgE, IL-4, ICAM1, p38, STAT3, TLR4 and API4. However, arteannuin B and artemisinic acid had little relevance to the abovementioned proteins. The interaction property between TNF-α and Artemisia annua was that the effect of the mixture of artemisinin, scopoletin, arteannuin B and artemisinic acid was greater than that of artemisinin, and the synergistic effect of the four elements was considered to be beneficial to the progress of antimalarial treatment.
Conclusion

Antimalarial targets of Artemisia annua ingredients were explored with data mining methods, and the antimalarial effect of scopoletin may be related to TNF. Combined application of the four elements could achieve the same antimalarial effect and reduce the clinical usage of artemisinin and scopoletin.
Clinical deployment and validation of a radiology artificial intelligence system for COVID-19
Authors: Hashemian Behrooz , Manchanda Aman , Li Matthew D. , Farzam Parisa , Dash Suma D. , Ihsan Alvin , Guan Jiahui , Haukioja Risto , Arun Nishanth Thumbavanam , Naidu Ram , Schultz Thomas , Andriole Katherine P. , Kalpathy-Cramer Jayashree , Dreyer Keith J. 
Published: August 2020

Abstract
The global COVID-19 pandemic has disrupted patient care delivery in healthcare systems world-wide. For healthcare providers to better allocate their resources and improve the care for patients with severe disease, it is valuable to be able to identify those patients with COVID-19 who are at higher risk for clinical complications. This may help to optimize clinical workflow and more efficiently allocate scarce medical resources. To this end, medical imaging shows great potential and artificial intelligence (AI) algorithms have been developed to assist in diagnosing and risk stratifying COVID-19 patients. However, despite the rapid development of numerous AI models, these models cannot be clinically useful unless they can be deployed in real-world environments in real-time on clinical data. Here, we propose an end-to-end AI hospital-deployment architecture for COVID-19 medical imaging algorithms in hospitals. We have successfully implemented this system at our institution and it has been used in prospective clinical validation of a deep learning algorithm potentially useful for triaging of patients with COVID-19. We demonstrate that many orchestration processes are required before AI inference can be performed on a radiology studies in real-time with the AI model being just one of the components that make up the AI deployment system. We also highlight that failure of any one of these processes can adversely affect the model's performance.
Impact of the COVID-19 pandemic on healthcare workers risk of infection and outcomes in a large, integrated health system.
Authors: Misra-Hebert Anita D , Jehi Lara , Ji Xinge , Nowacki Amy S. , Gordon Steven , Terpeluk Paul , Chung Mina K. , Mehra Reena , Dell Katherine M. , Pennell Nathan , Hamilton Aaron , Milinovich Alex , Kattan Michael W. , Young James B. 
Published: August 2020

Abstract
Background: Understanding the impact of the COVID-19 pandemic on healthcare workers (HCW) is crucial.Objective: Utilizing a health system COVID-19 research registry, we assessed HCW risk for COVID-19 infection, hospitalization and intensive care unit (ICU) admission.Design: Retrospective cohort study with overlap propensity score weighting.Participants: Individuals tested for SARS-CoV-2 infection in a large academic healthcare system (N=72,909) from March 8-June 9 2020 stratified by HCW and patient-facing status. Main Measures: SARS-CoV-2 test result, hospitalization, and ICU admission for COVID-19 infection. Key Results: Of 72,909 individuals tested, 9.0% (551) of 6,145 HCW tested positive for SARS-CoV-2 compared to 6.5% (4353) of 66,764 non-HCW. The HCW were younger than non-HCW (median age 39.7 vs. 57.5, p<0.001) with more females (proportion of males 21.5 vs. 44.9%, p<0.001), higher reporting of COVID-19 exposure (72 vs. 17 %, p<0.001) and fewer comorbidities. However, the overlap propensity score weighted proportions were 8.9 vs. 7.7 for HCW vs. non-HCW having a positive test with weighted odds ratio (OR) 1.17, 95% confidence interval (CI) 0.99-1.38. Among those testing positive, weighted proportions for hospitalization were 7.4 vs.15.9 for HCW vs. non-HCW with OR of 0.42 (CI 0.26-0.66) and for ICU admission: 2.2 vs.4.5 for HCW vs. non-HCW with OR of 0.48 (CI 0.20 -1.04). Those HCW identified as patient-facing compared to not had increased odds of a positive SARS-CoV-2 test (OR 1.60, CI 1.08-2.39, proportions 8.6 vs. 5.5), but no statistically significant increase in hospitalization (OR 0.88, CI 0.20-3.66, proportions 10.2 vs. 11.4) and ICU admission (OR 0.34, CI 0.01-3.97, proportions 1.8 vs. 5.2).Conclusions: In a large healthcare system, HCW had similar odds for testing SARS-CoV-2 positive, but lower odds of hospitalization compared to non-HCW. Patient-facing HCW had higher odds of a positive test. These results are key to understanding HCW risk mitigation during the COVID-19 pandemic.
A concomitant Guillain-Barre Syndrome with COVID-19: a first case-report in Colombia
Authors: Mackenzie Nuvia , Lopez-Coronel Eva , Dau Alberto , Maloof Dieb , Mattar Salvador , Garcia Jesus Tapia , Fontecha Briyis , Lanata Cristina , Guillen-Burgos Hernan Felipe 
Published: August 2020

Abstract
Background: During the COVID-19 pandemic, different neurological manifestations have been published. However, few cases of Guillain-Barre Syndrome and COVID-19 have been reported. We describe a concomitant Guillain-Barre Syndrome and COVID-19 patient.Case presentation: a 39 years old woman was admitted in a teaching hospital in Barranquilla, Colombia with a history of progressive general weakness with lower limb dominance. A previous symptom as ageusia, anosmia and intense headache was reported. On admission, facial diplegia, quadriparesis with lower limbs predominance and Medical Research Council Scale 2/5 in lower limbs and 4/5 in upper limbs was reported. During clinical evolution, due to general areflexia, hypertensive emergency and progressive diaphragmatic weakness, the patient was admitted to intensive care unit. Cerebrospinal Serum Fluid revealed protein-cytologic dissociation and electromyography test were compatible with Guillain-Barre Syndrome. By symptoms before hospitalization, SARS-CoV2 diagnostic testing was performed with positive result in second test. Management to COVID-19 and Guillain Barre Syndrome was performed and patient was discharged after 20 days of hospitalization with clinical improvement.Conclusions: Few cases have been published reporting COVID-19 and Guillain-Barre Syndrome. We report the first confirmed case of COVID-19 with concomitant Guillain-Barre Syndrome in Colombia. In patients with Guillain-Barre Syndrome, several viral and bacterial pathogens have been found in case-control studies but there are do not clarity in what triggers the immune-mediated destruction of nerves. More studies are needed to determine possible association among COVID-19 exposure and Guillain-Barre Syndrome.
Sex and age differences in COVID-19 mortality in Europe&nbsp;
Authors: Ahrenfeldt Linda Juel , Otavova Martina , Christensen Kaare , Lindahl-Jacobsen Rune 
Published: August 2020

Abstract
Aim: To examine the magnitude of sex differences in survival from the Coronavirus Disease 2019 (COVID-19) in Europe across age and countries. We hypothesise that men have higher mortality than women at any given age, but that sex differences will decrease with age as only the strongest men survive to older ages.Methods: We used population data from Institut National D’Études Démographiques on cumulative deaths due to COVID-19 from February to June 2020 in 10 European countries: Denmark, Norway, Sweden, The Netherlands, England & Wales, France, Germany, Italy, Spain and Portugal. For each country, we calculated cumulative mortality rates stratified by age and sex and corresponding relative risks for men vs. women.Results: The relative risk of dying from COVID-19 was higher for men than for women in almost all age groups in all countries. The overall relative risk ranged from 1.11 (95% CI 1.01-1.23) in Portugal to 1.54 (95% CI 1.49-1.58) in France. In most countries, sex differences increased until ages 60-69 years, but decreased thereafter with the smallest sex difference at ages 80+.Conclusions: Despite variability in data collection and time coverage among countries, we illustrate an overall similar pattern of sex differences in COVID-19 mortality in Europe.
The involvement of Central Nervous System and sequence variability of Severe Adult Respiratory Syndrome – Coronavirus-2 revealed in autopsy tissue samples: a case report.
Authors: Marbjerg Lis Høy , Jacobsen Christina , Fonager Jannik , Bøgelund Claus , Rasmussen Morten , Fomsgaard Anders , Banner Jytte , Jensen Veronika Vorobieva Solholm 
Published: August 2020

Abstract
Background: The case presented here illustrates that interdisciplinary teamwork can be essential for the understanding of the COVID-19 disease presentation and enlightening of the pathophysiology. Case presentation: A 60-years-old overweight woman without any comorbidities was found dead in her apartment after 14 days of home isolation due to suspicion on the Coronavirus disease 2019 (COVID-19). She had reported symptoms of tachycardia, fever, and increasing respiratory difficulty one day before her death. Due to the Danish legal act on sudden deaths a forensic autopsy was performed including a thorough examination and biosampling. The results of the forensic autopsy displayed sever densified, almost airless, firm lungs, and an unspecific reactive minimal focal perivascular inflammation consisting of macrophages of the brain tissue. The final diagnosis, COVID-19 with involvement of the central nervous system was established by use of the RT-RNA analysis on cerebrospinal fluid, as well as by serologic detection of the specific antibodies for SARS-CoV-2 in cerebrospinal fluid and serum. The genetic analysis displayed a 2 % variation between SARS-CoV-2 isolates recovered from the tracheal sample, cerebrospinal fluid, and tissues from both lungs.Conclusion: The combination of all available results revealed that the cause of death was COVID-19 with severe pulmonary disease and neuroinvasion, as well as renal affection resulting in hyponatremia. To our knowledge, it was not shown previously that neuroinvasion could be confirmed by the detection of specific antibodies for SARS-CoV-2 and SARS-CoV-2 specific RNA in cerebrospinal fluid. This case supports hypotheses that SARS-CoV-2 may cause central nervous system infection. The genetic distinction between SARS-CoV-2 isolates was done by whole-genome sequencing, where the isolate recovered from the cerebrospinal fluid was the most different.