bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unique and reliable fecal DNA extraction method for 16S rRNA gene and shotgun metagenomic sequencing in the analysis of the human gut microbiome
Authors: Elie Céline , Perret Magali , Louis Karen , Fritah-Lafont Asmaà , Leissner Philippe , Vachon Carole , Rostaing Hervé , Reynier Frédéric , Gervasi Gaspard , Saliou Adrien 
Published: August 2020

Abstract
Background: The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to select a unique and best performing DNA extraction protocol for both metagenomic sequencing methods. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) in order to facilitate DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and sequenced with both metagenomic methods. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates.Results: Independently of the sequencing methods used, SPD significantly improved efficiency of the four tested protocols compared with their commercial version, in terms of extracted DNA quality, accuracy of the predicted composition of the microbiota (notably for Gram-positive bacteria), sample alpha-diversity, and experimental repeatability. The best overall performance was obtained for the S-DQ protocol, SPD combined to the DNeasy PowerLyser PowerSoil protocol from QIAGEN.Conclusion: Based on this evaluation, we recommend to use the S-DQ protocol, to obtain standardized and high quality extracted DNA in the human gut microbiome studies.
Diagnostic and Prognostic Contribution of Cerebrospinal Fluid Analysis After Cardiac Arrest
Authors: Paul Marine , Benghanem sarah , Merceron sybille , bellut hugo , roche anne , Giabicani Mikhael , dumas florence , henry amandine , jaubert paul , bruneel fabrice , bedos jean pierre , cariou alain , legriel stephane 
Published: August 2020

Abstract
Background: Lumbar puncture is among the investigations used to determine the aetiology and prognosis of cardiac arrest, despite a dearth of data on its performance. We aimed to assess the diagnostic and prognostic performance of lumbar puncture after cardiac arrest. Methods: We retrospectively studied data from prospectively established databases of consecutive patients who were admitted to two French ICUs in 2007-2016 with sustained return of spontaneous circulation (ROSC) after cardiac arrest and who underwent lumbar puncture as an aetiological investigation. Results: Of 1984 patients with sustained ROSC, 65 (3.3%) underwent lumbar puncture and were included. Lumbar puncture identified a neurological cause of cardiac arrest in 6/65 (9%) patients, including 5 with neurologic prodromal symptoms before cardiac arrest and 4 with the lumbar puncture done post-mortem. Lumbar puncture performed before death showed nonspecific cerebrospinal fluid abnormalities in 37/53 (69.8%) patients. By univariate analysis, factors significantly associated with cerebrospinal fluid abnormalities were shorter no-flow time (0 min [0-3] versus 4 min [2-10], p=0.004) and post-resuscitation shock (26 [70%] versus 5 [31%], p<0.01). Presence of cerebrospinal fluid abnormalities was non significantly associated with poorer outcomes (CPC 3-4-5) (p=0.06). Conclusions: Lumbar puncture, although rarely performed, can contribute to the aetiological diagnosis of cardiac arrest. As a second-line investigation, it identified the cause in 9% of our patients. Nonspecific cerebrospinal fluid abnormalities are common after cardiac arrest, perhaps due to blood-brain barrier disruption, and may carry prognostic significance.
Providers' Definitions of Quality and Barriers to Providing Care: a Qualitative Study in Rural Mpumalanga Province, South Africa
Authors: West Rebecca L , Lippman Sheri A , Twine Rhian , Maritze Meriam , Kahn Kathleen , Leslie Hannah H 
Published: August 2020

Abstract
Background: Facing a quadruple burden of disease (infectious disease, non-communicable disease, maternal and child mortality, high levels of violence and injury), South Africa requires high-quality primary health care to retain patients and optimize outcomes. National health policy is focused on strengthening primary care. While prior research has identified implementation challenges within the primary health care system, there is less understanding of how providers define quality, their perceptions of barriers to providing quality care, and how they overcome these barriers. This study assesses provider views on quality at primary care clinics in a rural region of Mpumalanga Province. Methods: We conducted in-depth interviews with providers in Bushbuckridge sub-district in early 2019 on the value of quality metrics for providers and patients, what indicators they would use to assess clinic performance, and barriers and facilitators of delivering care. Interviews were conducted in Shangaan, audio-recorded, translated, and transcribed into English. A deductive approach was used to develop a provisional coding schema based on study questions, which was refined using an inductive approach in response to patterns and themes emerging from the data.Results: 23 providers were interviewed (83% female, 65% professional nurses). Definitions of quality were focused on clinic structure and resources. Few providers identified patient outcomes as indicators of quality. Providers linked deficiencies in infrastructure and support to deficits in care delivery, such as long wait times due to limited staffing, privacy breaches due to insufficient space, and a chronic lack of medication and equipment. Providers identified mitigating strategies including informal coordination across clinics to address medication shortages in individual facilities. Interwoven throughout the providers’ discussion was the poor communication between the district, PHC supervisors, and implementers at the facility level. Conclusion: Providers connected deficits in quality of care to inadequate infrastructure and insufficient support from district and provincial authorities; mitigating strategies across clinics could only partially address these deficits. The existence of a national quality measurement program was not broadly reflected in providers’ views on quality care. These findings underscore the need for effective district and national approaches to support individual facilities, accompanied by feedback methods designed with input from frontline service providers.
Compartmentalization Rather Than Host Tree Drives Truffle Microbiome
Authors: Liu Dong , Perez-Moreno Jesus , He Xinhua , Garibay-Orijel Roberto , Yu Fuqiang 
Published: August 2020

Abstract
Background: Truffles are some of the among the most expensive edible fungi worldwide whose value in international markets is worth billions of US dollars annually. They form ectomycorrhiza which is a symbiotic relationship with host trees and produce hypogeous ascomata. Their whole life-cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host trees are drivers for truffle microbiome is unclear.Methods: To identify and compare bacterial and fungal communities in four truffle-associated compartments (Tuber indicum bulk soil, adhering soil to peridium, peridium and gleba), associated to three host trees we sequenced their ITS (fungal) and 16S (bacterial) rDNA with Illumina MiSeq high throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Results: Tuber indicum microbiome composition was strongly driven by their associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacterial-dominated, and its bacterial community formed a substantially more complex interacting network compared with that of fungal community. Core fungal community changed from Basidiomycota-dominated (in bulk soil) to Rozellomycota-dominated (in interphase soil); while core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. At the truffle and soil interphase, an interphase-sieving process was confirmed by i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi and Planctomycetes) in gleba; ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon and Simpson indices); and iii) a substantial decrease in the complexity of the network from bulk soil, to soil-truffle interphase, to peridium and finally to gleba. The network analysis of microbiome showed a more complex and higher number of positive microbial interactions in truffle tissues than in both bulk soil and peridium-adhering soil. Cupriavidus, Bradyrhizobium, Aminobacter and Mesorhizobium were the keystone network hub genera associated to truffle gleba. Conclusion: This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing than they are more complex than previously thought.
Infected hip prosthesis in patient with suspected Covid-19 infection
Authors: Cosentino Andrea , Odorizzi Gianni , Berger Wilhelm 
Published: August 2020

Abstract
Background: Infections following arthroplasty are one of the major risks during this type of surgery.Case presentation: Four and half years after right hip arthroplasty surgery, the patient came back to our attention with pain at the same hip. The instrumental examinations showed signs of cup detachment and therefore, after carefully analyzing the case, we decided to perform a sterile aspiration of the hip in the operating room under C-arm fluoroscopy. Microbiological examinations showed positivity for E.Coli. The patient underwent to surgery to remove the prosthesis and implant a spacer. A therapy with Cefotaxim 2g 1-1-1 for 6 weeks was then set, after which a total arthroplasty was implanted. During this period, the Covid-19 pandemic occurred and therefore the patient performed two nasal-throat swabs, both negative. However, one week after the final surgery, respiratory conditions worsened and we performed a chest X-ray and CT scan, with suggestive images of ground-glass opacification patterns (GGO). Due to the clinic and the characteristic images of the instrumental examinations, the patient was transferred to the observation ward, waiting for the response of two additional swabs, also negative. The patient was then transferred to the ward for patients with typical symptoms of Covid-19 but with negative swabs for two weeks and subsequently discharged at home.Conclusion: Despite the concomitant Covid-19 pandemic, the guidelines in case of periprosthetic hip infection further confirm the correct management of the patient.
Incidences and risk factors of serious infections among different rheumatic patients: a retrospective cohort study
Authors: Ding Jin , Xiang Yang , Zhou Yujia , Zhu Cong , Hu Xinyue , Tao Cui , Xu Hua 
Published: August 2020

Abstract
Background

To compare the incidence and risk factors of serious infections among patients of seven common rheumatic diseases including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), polymyalgia rheumatica (PMR), Sjögren's syndrome (SS), systemic sclerosis (SSc), systemic vasculitis (VA), and other diffuse connective tissue diseases (oCTD).
Methods

In a retrospective cohort study using large Electronic Health Records (EHR) data, the infection rates of different rheumatic diseases in two years were calculated and variances on risk factors were analyzed using the multivariable Cox model.
Results

Among the overall 46,411 rheumatic patients, 8,308 presented serious hospitalized infections in the following two years (crude infection rates (IR) per 100 patient-years: 8.95, 8.76–9.14). SSc (10.89, 9.61–12.16), VA (10.82, 9.96–11.68), and SLE (10.13, 9.73–10.53) had relatively high IRs, while oCTD was with the lowest IR (7.71, 6.58–8.84). The Cox model identified previous infection (adjusted hazard ratio (HR):1.75, 1.62–1.88, p < 0.001), GCs usage (HR:1.64, 1.52–1.76, p < 0.001), nonbiologic DMARDs usage (HR:1.39, 1.32–1.45, p < 0.001) and congestive heart failure (CHF) (HR:1.42, 1.30–1.56, p < 0.001) as the top-ranked risk factors of infection in the overall population. While some of the variables were shared across subtypes of rheumatic diseases as highly associated risk factors, others varied significantly such as osteoporosis.
Conclusions

Infection rates and risk factors varied among cohorts of different rheumatic diseases. The analytical results may inform distinct strategies and influence clinical decision making to reduce the occurrence of infections.
The Early Start of Gonadotropin-releasing Hormone Antagonist Versus Flexible Antagonist Ovarian Stimulation Protocol in Poor Responders: A Randomized Clinical Trial
Authors: Esfidani Tayebeh , Moini Ashraf , Arabipoor Arezoo , Mojtahedi Maryam Farid , Mohiti Shima , Kashani Ladan 
Published: August 2020

Abstract
Background: Determining the initiation day of antagonist administration is an important and challenging issue and different results have been reported in the previous studies. The present study was designed to compare the controlled ovarian hyperstimulation (COH) cycles outcomes of the early start of gonadotropin-releasing hormone antagonist (GnRH-ant) protocol with conventional flexible GnRH-ant protocol in patients with poor ovarian response (POR) diagnosis. Methods: This randomized controlled trial was performed on infertile women who were diagnosed as poor ovarian responder in IVF/ICSI cycles at Arash Women’s Hospital affiliated to Tehran University of Medical Sciences between September 2019 and May 2020. POR was defined according to the Bologna criteria and the eligible women were randomly allocated into an experimental (early onset GnRH-ant) and control (flexible GnRH-ant) groups. The women in the experimental group received recombinant gonadotropins (150-225 IU) and GnRH-ant (0.25 mg) simultaneously on the second day of the cycle. In control group, the starting and dose of gonadotropins were similar but daily administration of GnRH-ant was initiated when the leading follicle diameter was ≥ 13 mm. The IVF/ICSI outcomes were compared between groups.Results: Totally, 116 women were randomly assigned to early start antagonist group (n=58) and control group (n=58). The analysis showed that the two groups did not have a statistically significant difference in terms of the ovarian stimulation duration and the total dose of used gonadotropins. Although, the total number of MII oocytes in early start of antagonist group was significantly higher than that of in control group (P=0.04). In the following, clinical and ongoing pregnancy rates per ET in early start of antagonist group were significantly higher than those of in control group (P=0.02 and P=0.03, respectively); however, the implantation and miscarriage rates were similar between group.Conclusion: The early onset of GnRH-ant protocol can improve the number of retrieved and MII oocytes rates and probably the pregnancy outcome after fresh embryo transfer in POR patients; however, larger randomized clinical trials are required to compare the pregnancy outcomes after this approach with other COH protocols with considering cost-effectiveness issue.Trial registration: IRCT, IRCT20110731007165N9. Registered 8 February 2020 – Registered while recruiting, https://www.irct.ir/trial/45024.
Multi-epitope peptide sequence in-silico construction from HGV genome
Authors: Sharp Kumar 
Published: August 2020

Abstract
In this study I have approached through in-silico method or reverse vaccinology taking advantage of the genome sequence of hepatitis G virus. It serves its benefit of identifying antigens seen by both conventional as well as discovering any novel antigen. This peptide candidate can serve a triple purpose of hepatitis C vaccine, hepatitis G vaccine and HIV management addition. 89.2% of the residues were in the favoured region of Ramachandran plot. These points make it favourable for in-vitro trials and further refinement. Because of the high similarity of hepatitis C genome to hepatitis G genome, it is highly probable that this peptide sequence might act as both hepatitis C and hepatitis G vaccine. Patients with past or current HGV infection have higher CD4+ lymphocyte counts and better AIDS-free survival rates. This peptide sequence might cause a breakthrough in the treatment of HIV without exposing them to develop hepatitis.
Concurrent cavitary pulmonary tuberculosisand COVID-19 pneumonia with in vitro immune cell anergy:a case report.
Authors: Musso Maria , Gennaro Francesco Di , Gualano Gina , Mosti Silvia , Cerva Carlotta , Fard Saeid Najafi , Libertone Raffaella , Bari Virginia Di , Cristofaro Massimo , Tonnarini Roberto , Goletti Delia , Palmieri Fabrizio 
Published: August 2020

Abstract
Tuberculosis (TB) is top infectious disease killer caused by a single organismresponsible for 1.5 million deaths in 2018. Both COVID 19 and the pandemic responseare risking to affect control measures for TB and continuity of essential services forpeople affected by this infection in western countries and even more in developingcountries. Knowledges about concomitant pulmonary TB and COVID-19 are extremelylimited. The double burden of these two diseases can have devastating effects. Herewe describe from both the clinical and the immunological point of view a case of apatient with in vitro immune cell anergy affected by bilateral cavitary pulmonary TB andsubsequent COVID-19-associated pneumonia with a worst outcome. COVID-19 can bea precipitating factor in TB respiratory failure and, during ongoing SARS COV 2 pandemic, clinicians must be aware of this possible coinfection in differential diagnosisof patients with active TB and new or worsening chest imaging
O Papel da Imunidade Inata na COVID-19
Authors: Silva de Sordi Luiz Henrique , Sales Oliveira Magalhães Isabela , Abreu Casselhas Daniela , Chaves Andrade Mariléia 
Published: August 2020

O sistema imune apresenta papel importante na pandemia da COVID-19, pois está envolvido na patogênese e agravamento da doença. O objetivo desta revisão é abordar os aspectos da imunidade inata na COVID-19, especialmente o papel dos neutrófilos. O sistema imune inato corresponde à primeira defesa do organismo, porém é necessário um equilíbrio para obter efetividade contra o invasor sem lesar excessivamente o hospedeiro. O desequilíbrio imune está relacionado com quadros mais graves e à ativação aberrante de neutrófilos, sendo a linfopenia e a neutrofilia preditores de pior prognóstico em pacientes com COVID-19. Especula-se que a neutrofilia seja uma importante fonte para formação excessiva de NET (Neutrophil Extracellular Traps), levando ao aumento da resposta inflamatória e evolução desfavorável da doença. As NET também estão associadas à tempestade de citocinas, outro mecanismo relacionado a gravidade da COVID-19. Portanto, estratégias que envolvam a imunomodulação podem ter um papel importante no controle da doença.
Motivations for Social Distancing and App Use as Complementary Measures to Combat the COVID-19 Pandemic: Quantitative Survey Study
Authors: Kaspar Kai 
Published: August 2020

Background
The current COVID-19 pandemic is showing negative effects on human health as well as on social and economic life. It is a critical and challenging task to revive public life while minimizing the risk of infection. Reducing interactions between people by social distancing is an effective and prevalent measure to reduce the risk of infection and spread of the virus within a community. Current developments in several countries show that this measure can be technologically accompanied by mobile apps; meanwhile, privacy concerns are being intensively discussed.

Objective
The aim of this study was to examine central cognitive variables that may constitute people’s motivations for social distancing, using an app, and providing health-related data requested by two apps that differ in their direct utility for the individual user. The results may increase our understanding of people’s concerns and convictions, which can then be specifically addressed by public-oriented communication strategies and appropriate political decisions.

Methods
This study refers to the protection motivation theory, which is adaptable to both health-related and technology-related motivations. The concept of social trust was added. The quantitative survey included answers from 406 German-speaking participants who provided assessments of data security issues, trust components, and the processes of threat and coping appraisal related to the prevention of SARS-CoV-2 infection by social distancing. With respect to apps, one central focus was on the difference between a contact tracing app and a data donation app.

Results
Multiple regression analyses showed that the present model could explain 55% of the interindividual variance in the participants’ motivation for social distancing, 46% for using a contact tracing app, 42% for providing their own infection status to a contact tracing app, and 34% for using a data donation app. Several cognitive components of threat and coping appraisal were related to motivation measurements. Trust in other people’s social distancing behavior and general trust in official app providers also played important roles; however, the participants’ age and gender did not. Motivations for using and accepting a contact tracing app were higher than those for using and accepting a data donation app.

Conclusions
This study revealed some important cognitive factors that constitute people’s motivation for social distancing and using apps to combat the COVID-19 pandemic. Concrete implications for future research, public-oriented communication strategies, and appropriate political decisions were identified and are discussed.
Apresentação: Religiões afro-brasileiras e a expansão das fronteiras: desafios interpretativos sobre a produção do sagrado e das identidades religiosas na contemporaneidade
Authors: Miranda Ana Paula Mendes de , Bahia Joana , Corrêa Roberta De Mello 
Published: August 2020

A organização deste dossiê foi motivada pelo interesse em analisar as especificidades que envolvem a expansão das religiões afro brasileiras em contextos sociopolíticos distintos, bem como os desafios teórico-metodológicos que surgem dessas pesquisas. Interessava-nos debater, a partir de pesquisas empíricas, como as formas de expressão afro-brasileiras são criativamente produzidas e transformadas e compreender suas consequências político-religiosas. Tal perspectiva é fundamental para uma controvérsia acerca de sua permanência e reprodução no cenário contemporâneo brasileiro de ataques e perseguições a essas tradições, bem como problematizar o debate sobre o que seriam essas novas misturas de religiões, com destaque para o papel dos atores religiosos e como suas crenças e comportamentos afetam os contextos sociais estudados.