bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgeon Quality Control and Standardization of D2 Lymphadenectomy for Gastric Cancer
Authors: Han Sang-Uk , Hur Hoon , Lee Hyuk-Joon , Cho Gyu Seok , Kim Min-Chan , Park Young Kyu , Kim Wook , Hyung Woo Jin 
Published: May 2020

Objective:
To qualify surgeons to participate in a randomized trial comparing laparoscopic and open distal D2 gastrectomy for advanced gastric cancer.

Summary of Background Data:
No studies have sought to qualify surgeons for a randomized trial comparing laparoscopic and open D2 gastrectomy for advanced gastric cancer.

Methods:
We conducted a multicenter prospective observational study evaluating unedited videos of laparoscopic and open D2 gastrectomy performed by 27 surgeons. Surgeons performed 3 of each laparoscopic and open distal gastrectomies with D2 lymphadenectomy for gastric cancer. Five peers reviewed each unedited video using a video assessment form. Based on experts’ review of videos, a separate review committee decided surgeons as “Qualified” or “Not-qualified.”

Results:
Twelve surgeons (44.4%) were qualified on initial evaluation whereas the other 15 surgeons were not. Another 9 surgeons were finally qualified after re-evaluation. The median score for Qualified was significantly higher than Not-qualified (P < 0.001).
Significant differences between Qualified and Not-qualified were noted both in operation type and in all evaluation area of surgical skill, perigastric, and extra-perigastric lymphadenectomy, although the inter-rater variability of the assessment score was low (kappa = 0.285). However, Not-qualified surgeons’ scores improved upon re-evaluation of resubmitted videos.
When compared laparoscopy with open surgery, median scores were similar between the 2 groups (P = 0.680). However, open gastrectomy scores for surgical skills were significantly higher than for laparoscopic surgery (P = 0.016).

Conclusions:
Our surgeon quality control study for gastrectomy represents a milestone in surgical standardization for surgical clinical trials. Our methods could also serve as a system for educating surgeons and assessing surgical proficiency.
Safety and Efficacy of Bariatric Surgery in Cirrhosis Patients With Extreme Obesity
Authors: Vuppalanchi Raj , McCabe Marshall E. , Tandra Sweta R. , Parcha Siva P. , Ghafoor Adil , Schuh Leslie , Inman Margaret M. , Selzer Don J. , Stefanidis Dimitrios , Chalasani Naga 
Published: May 2020

Objective:
To assess the safety and efficacy of bariatric surgery in patients with cirrhosis.

Summary Background Data:
Bariatric surgery may be a viable option for patients with cirrhosis and extreme obesity. However, the risk of liver decompensation after surgery is not thoroughly investigated.

Methods:
We conducted a case-controlled study with 106 obese patients with cirrhosis (cases) and 317 age, sex, body mass index-, and type of surgery-matched obese patients without cirrhosis (controls) who underwent bariatric surgery.

Results:
Patients with cirrhosis were predominantly Child-Pugh class A (97%) with the diagnosis established prior to surgery in only 46%. In the cirrhosis group, there was no death in the first 30 days compared with 1 patient in the control group. At 90 days there was 1 death in the cirrhosis group but no additional deaths in the control group. In total, 12 months after the surgery, there were 3 deaths in the cirrhosis group and 1 in the control group (2.8% vs 0.6%, P = 0.056). The surgery-related length of stay was significantly longer in patients with cirrhosis (3.7 ± 4.0 vs 2.6 ± 2.4 d, P = 0.001), but the 30-day readmission rate was lower (7.5% vs 11.9%, P = 0.001). The percent of total weight loss at 30 and 90-days was not significantly different between the groups and remained that way even at 1 year (29.1 ± 10.9 vs 31.2 ± 9.4%, P = 0.096).

Conclusions:
Bariatric surgery in obese cirrhotic patients is not associated with excessive mortality compared with noncirrhotic obese patients.
Implementation Strategies and the Uptake of the World Health Organization Surgical Safety Checklist in Low and Middle Income Countries
Authors: White Michelle C. , Peven Kimberly , Clancy Olivia , Okonkwo Ijeoma , Bakolis Ioannis , Russ Stephanie , Leather Andrew J. M. , Sevdalis Nick 
Published: May 2020

Objectives:
To identify the implementation strategies used in World Health Organization Surgical Safety Checklist (SSC) uptake in low- and middle-income countries (LMICs); examine any association of implementation strategies with implementation effectiveness; and to assess the clinical impact.

Background:
The SSC is associated with improved surgical outcomes but effective implementation strategies are poorly understood.

Methods:
We searched the Cochrane library, MEDLINE, EMBASE and PsycINFO from June 2008 to February 2019 and included primary studies on SSC use in LMICs. Coprimary objectives were identification of implementation strategies used and evaluation of associations between strategies and implementation effectiveness. To assess the clinical impact of the SSC, we estimated overall pooled relative risks for mortality and morbidity. The study was registered on PROSPERO (CRD42018100034).

Results:
We screened 1562 citations and included 47 papers. Median number of discrete implementation strategies used per study was 4 (IQR: 1–14, range 0–28). No strategies were identified in 12 studies. SSC implementation occurred with high penetration (81%, SD 20%) and fidelity (85%, SD 13%), but we did not detect an association between implementation strategies and implementation outcomes. SSC use was associated with a reduction in mortality (RR 0.77; 95% CI 0.67–0.89), all complications (RR 0.56; 95% CI 0.45–0.71) and infectious complications (RR 0.44; 95% CI 0.37–0.52).

Conclusions:
The SSC is used with high fidelity and penetration is associated with improved clinical outcomes in LMICs. Implementation appears well supported by a small number of tailored strategies. Further application of implementation science methodology is required among the global surgical community.
Quantitative SARS-CoV-2 antibody screening of healthcare workers in the southern part of Kyoto city during the COVID-19 peri-pandemic period
Authors: Fujita Kohei , Kada Shinpei , Kanai Osamu , Hata Hiroaki , Odagaki Takao , Satoh-Asahara Noriko , Tagami Tetsuya , Yasoda Akihiro 
Published: May 2020

AbstractBackgroundThe coronavirus disease-2019 (COVID-19) pandemic is associated with a heavy burden on the mental and physical health of patients, regional healthcare resources, and global economic activity. While our understanding of the incidence and case-fatality rates increases, data on seroprevalence of antibodies against the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) in healthcare workers during the peri-pandemic period is insufficient. This study quantitatively evaluated seroprevalence of SARS-CoV-2 antibody in healthcare workers in the southern part of Kyoto city, Japan.MethodsWe prospectively recruited healthcare workers from a single hospital between April 10 and April 20, 2020. We collected serum samples from these participants and quantitatively evaluated SARS-CoV-2 IgG antibody levels by enzyme-linked immunosorbent assay.ResultsFive (5.4%), 15 (16.3%), and 72 (78.3%) participants showed positive, borderline, and negative serum SARS-CoV-2 IgG antibody status, respectively. We found the mean titer associated with each antibody status (overall, positive, borderline, and negative) was clearly differentiated. Participants working at the otolaryngology department and/or having a history of seasonal common cold symptoms had a significantly higher titer of SARS-CoV-2 IgG antibody (p=0.046, p=0.046, respectively).ConclusionsFive (5.4%) and 15 (16.3%) participants tested positive and borderline, respectively, for SARS-CoV-2 IgG antibody during the COVID-19 peri-pandemic period. These rates were higher than expected based on government situation reports. The present findings suggest that COVID-19 was already spread in the southern part of Kyoto city at the early stage of pandemic.
Silent Disease and Loss of Taste and Smell are Common Manifestations of SARS-COV-2 Infection in a Quarantine Facility: Saudi Arabia
Authors: Alshami Alanoud , Alattas Rabab , Anan Hadeel , Qahtani Hadi Al , Alahilm Abdulbari , Mulhim Mobarak Al , Alfaraj Ahmed 
Published: May 2020

AbstractBACKGROUNDThe Coronavirus disease 2019 (COVID-19) outbreak in Saudi Arabia was first identified in a traveler from Al Qatif city, on March 2nd, 2020. The disease has quickly spread and reached multiple cities within a few weeks. In an attempt to limit the spread of COVID-19 in Saudi Arabia, the government has implemented strict regulations. Starting March 15th, all travelers coming back to the kingdom were tested for COVID-19 and were quarantined in a government-designated facility. The same rule was applied to all positive cases identified by contact tracing. In this study, we aimed to assess the prevalence of asymptomatic carriers, epidemiological characteristics, clinical presentations, and viral clearance of SARS-COV-2 positive quarantined individuals in a quarantine facility in the eastern province.METHODSWe conducted a cross-sectional study on 128 laboratory-confirmed COVID-19 subjects who were quarantined in a government-designated facility. The study period was from March 16th – till April 18th, 2020. We collected data on demographics and on clinical symptoms. Also, samples for PCR tests were collected upon admission and were repeated every 72 hours if they were still positive. All negative samples were repeated within 24 hours for confirmation.RESULTSSixty-nine of the 128 residents (54%) were completely asymptomatic until the end of the study. The remaining 59 residents (46%) had only mild symptoms. The most common symptom was a sudden loss of smell and taste, accounting for 47.5%. The median time to virus clearance was significantly different between the two groups. Symptomatic residents cleared the virus at a median of 17 days (95% CI,12.4-21.6) from the first positive PCR vs. 11days (95% CI, 8.7-13.3) in the asymptomatic group (P=0.011). False-negative test results occurred in 18.8% of the total residents and false positive results in 3%.CONCLUSIONThe prevalence of asymptomatic carriers is high in our study. Testing, and isolating travelers and contacts of laboratory-confirmed cases, regardless of symptoms, were very effective measures for early disease identification and containment. Loss of taste and smell was the most common presentation in our mild symptomatic residents, and it might be predictive of mild disease. The persistent positive PCR beyond 14 days observed in the mild symptomatic residents despite being symptoms free, warrant further studies to determine its implications on disease spread and control.
Clinical characteristics and early outcomes in patients with COVID-19 treated with tocilizumab at a United States academic center
Authors: Rimland Casey A. , Morgan Camille E. , Bell Griffin J. , Kim Min K. , Hedrick Tanner , Marx Ashley , Bramson Brian , Swygard Heidi , Napravnik Sonia , Schmitz John L. , Carson Shannon S. , Fischer William A. , Eron Joseph J. , Gay Cynthia L. , Parr Jonathan B. 
Published: May 2020

AbstractWe describe early outcomes in 11 COVID-19 patients treated with the IL-6 receptor inhibitor tocilizumab. While C-reactive protein decreased, neither clinical improvement nor reduced temperature or oxygen requirements was observed in most patients. Our findings contrast with prior reports and raise questions about tocilizumab use in severe COVID-19.
Magnesium maintains length of circadian period inArabidopsis thaliana
Authors: de Melo J. Romário F. , Gutsch Annelie , De Caluwé Joëlle , Leloup Jean-Christophe , Gonze Didier , Hermans Christian , Webb Alex A.R. , Verbruggen Nathalie 
Published: May 2020

AbstractThe circadian clock coordinates the physiological response of a biological system to day and night rhythms through complex loops of transcriptional/ translational regulation. It can respond to external stimuli and adjust generated circadian oscillations accordingly to keep an endogenous period close to 24 h. To date, the interaction between nutritional status and circadian rhythms in plants is poorly understood. Magnesium (Mg) is essential for numerous biological processes in plants and its homeostasis is crucial to maintain optimal development and growth. Magnesium deficiency in youngArabidopsis thalianaseedlings increased the circadian period ofpCCA1:LUCoscillations and dampened its amplitude in constant light in a dose-dependent manner. Although circadian period increase by Mg deficiency was light dependent, it did not depend on active photosynthesis. Mathematical modelling of the Mg input to the circadian clock reproduced the experimental increase of the circadian period and suggested that Mg is likely to affect global transcription/translation levels rather than a single component of the circadian oscillator. The model prediction was supported by a synergistic interaction between Mg deficiency and cyclohexamide, an inhibitor of translation. These findings suggest that proper Mg supply is required to support proper timekeeping in plants.One sentence summaryMagnesium maintains the circadian period in Arabidopsis seedlings and interferes with the circadian oscillator most likely through translational mechanisms.
Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms
Authors: Huffer Katherine E. , Aleksandrova Antoniya A. , Jara-Oseguera Andrés , Forrest Lucy R. , Swartz Kenton J. 
Published: May 2020

AbstractThe recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters towards the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.
Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population
Authors: Butsashvili Maia , Gulbiani Lasha , Kanchelashvili George , Kochlamazashvili Marika , Nioradze George , kamkamidze George 
Published: May 2020

AbstractIntroductionGeorgia confirmed its first case of SARS-COV-2 infection on February 26, 2020. Despite the government’s proactive measures during the early stages of the epidemic, number of new infections of SARS-COV-2 is increasing and by March 31, a total of 110 cases have been reported. Limited understanding about epidemics can lead to panic and disrupt public health efforts to contain transmission. Thus, it is very important to understand the perceptions of the population regarding the disease and perceived level of government preparedness to fight against the spread of infection. This study reports results of a survey designed to understand attitudes and knowledge regarding SARS-COV-2 virus among Georgian population, including health care workers (HCWs).Materials and methodsThe online survey was conducted using a Facebook advertisement. The target was the whole country and the language used was Georgian. We collected information on demographic data, knowledge of symptoms and transmission modes of coronavirus, perceived differences between coronavirus and influenza, availability of antiviral medication and vaccination. We also included questions to capture the Georgian population’s perceptions about government preparedness to combat the new coronavirus.ResultsThe survey was open for three days (March 2–4, 2020). 5228 participants completed the survey. Of these, 40.3% were 25–45 years old and 58.2% were female. 20.7% of respondents had university degree and 10.3% were HCWs. For 25.8% of respondents, COVID-19 and influenza are the same diseases; 10.9% did not know if they are different. The majority correctly identified the transmission route and symptoms (96.9% and 98.0%, respectively). Regarding physical distancing, 13.2% indicated they would attend public events if needed even if they had COVID-19 symptoms. 19.1% think that Georgia is ready for COVID 19 epidemic, while according to 55% the county is not ready, but HCWs are trying hard to respond to this challenge properly. For 18% response is inadequate. There was no difference in knowledge between HCWs, non-HCWs and unemployed. 20% of HCWs as well as other study subjects believe that SARS-COV-2 vaccine and medications do exist but are simply not available in Georgia.ConclusionOne in five Georgians believe that there is a vaccine and medication to treat coronavirus, but that it is not available in the country. Given that information regarding coronavirus is changing very rapidly, the need to reach people with time-sensitive educational messages as well as prevention strategies is vital.
Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys
Authors: Vemuri Ravichandra , Sherrill Chrissy , Davis Matthew , Kavanagh Kylie 
Published: May 2020

AbstractRecent evidence suggests that gut microbiome changes that occur with age impact the health of the host. While it is known that the gut microbiome and physiological systems interact, the relationship between the microbiome in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation and the mucosal microbiome in young and old female vervet monkeys. Ascending colon mucosal biopsies and blood samples from healthy young and old monkeys were collected for 16S rRNA gene sequencing and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma MCP-1 and CRP in old monkeys, which are indicative of higher systemic inflammation. Microbiome analysis revealed increases in abundance of opportunistic pathobionts such as members of the Proteobacteria phylum in old monkeys. At the family level, abundances ofPrevotellaceaeandHelicobacteraceaewere higher in old monkeys than in young. We also found significantly lower Firmicutes to Bacteroidetes ratio (P= 0.03) and lower abundance of butyrate-producing microbes in old monkeys, consistent with a less healthy profile. Microbial community co-occurrence analysis revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provided novel insights into systemic inflammation and gut microbial interactions, highlights the importance of the mucosal niche changes with age, and may facilitate further understanding of the decline in the stability of the microbial community with aging.
Resolving complex structures at oncovirus integration loci with conjugate graph
Authors: Jia Wenlong , Xu Chang , Li Shuai Cheng 
Published: May 2020

AbstractOncovirus integrations cause copy number variations (CNVs) and complex structural variations (SVs) on host genomes. However, the understanding of how inserted viral DNA impacts the local genome remains limited. The linear structure of the oncovirus integrated local genomic map (LGM) will lay the foundations to understand how oncovirus integrations emerge and compromise the host genome’ s functioning. We propose a conjugate graph model to reconstruct the rearranged local genomic map at integrated loci. Simulation tests prove the reliability and credibility of the algorithm. Applications of the algorithm to whole-genome sequencing data of Human papillomavirus (HPV) and hepatitis B virus (HBV)-infected cancer samples gained biological insights on oncovirus integrations. We observed five affection patterns of oncovirus integrations from the HPV and HBV-integrated cancer samples, including the exon loss, promoter gain, hyper-amplification of tumor gene, the viral cis-regulation inserted at the single intron and at the intergenic region. We found that the focal duplicates and host SVs are frequent in the HPV-integrated LGMs, while the focal deletions and complex virus SVs are prevalent in HBV-integrated LGMs. Furthermore, with the results yields from our method, we found the enhanced microhomology-mediated end joining (MMEJ) might lead to both HPV and HBV integrations, and conjectured that the HPV integrations might mainly occur during the DNA replication process. The conjugate graph algorithm code and LGM construction pipeline, available athttps://github.com/deepomicslab/FuseSV.Key pointsConjugate graph model resolves complex local genomic strcuture at oncovirus integration loci.Local genome maps reveal five affection patterns of oncovirus integrations.Microhomology bases and small insertions are enriched at the junctions of structural variations and virus integrations.HPV and HBV integrations may be induced by the enhanced microhomology-meditated mechanism.
Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones
Authors: Sarthy Jay F. , Meers Michael P. , Janssens Derek H. , Henikoff Jorja G. , Feldman Heather , Paddison Patrick J. , Lockwood Christina M. , Vitanza Nicholas A. , Olson James M. , Ahmad Kami , Henikoff Steven 
Published: May 2020

AbstractLysine 27-to-methionine (K27M) mutations in the H3.1 or H3.3 histone genes are characteristic of pediatric diffuse midline gliomas (DMGs). These oncohistone mutations dominantly inhibit histone H3K27 trimethylation and silencing, but it is unknown how oncohistone type affects gliomagenesis. We show that the genomic distributions of H3.1 and H3.3 oncohistones in human patient-derived DMG cells are consistent with the DNA replication-coupled deposition of histone H3.1 and the predominant replication-independent deposition of histone H3.3. Although H3K27 trimethylation is reduced for both oncohistone types, H3.3K27M-bearing cells retain some domains, and only H3.1K27M-bearing cells lack H3K27 trimethylation. Neither oncohistone interferes with PRC2 binding. Using Drosophila as a model, we demonstrate that inhibition of H3K27 trimethylation occurs only when H3K27M oncohistones are deposited into chromatin and only when expressed in cycling cells. We propose that oncohistones inhibit the H3K27 methyltransferase as chromatin patterns are being duplicated in proliferating cells, predisposing them to tumorigenesis.