bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alterations of Oropharyngeal Microbiome Reflected Disease Severity and Long-Term Dysbiosis in Patients With COVID-19
Authors: Zhou Yongzhao , Lu Sifen , Li Mengjiao , Wang Minjin , Ma Jinmin , Mao Yuanchen , Zhu Zhongyi , Min Jiumeng , Xiao Jun , Qiu Rong , Deng Taibing , Jiang Li , Zhu Jing , Zeng Yilan , Liu Dan , li weimin , Ying Binwu 
Published: May 2021

Abstract
Background: Recent evidences have shown that gut microbiome of patients with COVID-19 significantly changes and can reflect the severity of the disease. And gut microbiota richness was not restored to normal levels after 6-month recovery. However, SARS-CoV-2 primarily infects the respiratory tract, few studies investigate whether the alterations of oropharyngeal microbiome is associated with disease severity in patients with COVID-19, and whether interferences in microbiome composition, if any, eliminate with clearance of the SARS-CoV-2 virus. We employed metatranscriptomic sequencing to analyse oropharyngeal swabs collected within a week of diagnosis COVID-19 (period of disease group: PDG) and two months after clearance of the SARS-CoV-2 virus (convalescent group: CG) from 47 patients with COVID-19. Meanwhile, oropharyngeal swabs from 40 healthy subjects were analyzed as healthy control group (HCG). Results: Oropharyngeal microbial composition was significantly altered in patients with COVID-19 compared with healthy controls even two months after clearance of the SARS-CoV-2 virus. Little changes in α-diversity among HCG, PDG and CG ( P ＞0.05), but obviously changes in β-diversity among them. Notably, Prevotella increased significantly in PDG than that in HCG (Wilcoxon rank-sum test, P ＜0.001) and increased gradually along with the severity of patients with COVID-19 aggravated. There was a positive correlation between Prevotella and the elevation of Neutrophil percentage (R = 0.301, P = 0.040). Similarly, SARS-CoV-2 and Aspergillus increased remarkably in critical Patients with COVID-19. There was a negative correlation between SARS-CoV-2 viral load and platelet counts (R = −0.330, P = 0.022). Conclusions: The oropharyngeal microbiome in patients with COVID-19 present persistent dysbiosis even two months after clearance of the SARS-CoV-2 virus. Furthermore, alterations in oropharyngeal microbial composition reflected the severity of disease in patients with COVID-19. Our findings underscore that there is an urgent need to understand the specific roles of oropharyngeal microorganisms in COVID-19 disease progression and rehabilitation.
Molecular Epidemiologic Factors Contributing to Guinolone Resistance in Clinical Multidrug-resistant Klebsiella Pneumoniae Isolates from Shanghai, China
Authors: Wang Yan , Cai Guoping , Zhang Jinan , Xu Xiaogang , Lu Hongzhou 
Published: May 2021

Abstract
Background : The soaring quinolone-resistance rate of Klebsiella pneumoniae , a common pathogen in immunocompromised individuals, has seriously undermined the wide applications of antimicrobials of this class. This study aimed to investigate the emerging key contributors to quinolone resistance in multidrug resistant K. pneumoniae (MDR-KP) isolates from a clinical setting with continuing point-source infection outbreaks. Methods : A total of 34 K. pneumoniae isolates, including 30 carbapenem-resistant K. pneumoniae (CRKP) isolates were randomly selected from a teaching hospital participating in an ongoing Bacterial Resistance Surveillance Project in Shanghai, China. Investigations included antimicrobial susceptibility tests, MLST and wzi -genotyping, PCR and DNA sequencing for identification of resistance determinants, sequence analyses using MEGA7.0 software, and clinical information retrieving through electronic medical records. Results : Two predominant high-risk resistant clones, ST11- wzi 64 and ST15- wzi 19/ wzi 24, from 30 CRKP isolates caused three point-source nosocomial outbreaks in intensive care unit and neurosurgery department potentially by respiratory-route, promoting the co-selection and evolution of multidrug resistant determinants. Multiple quinolone resistance-determining region (QRDR) mutations occurred in isolates of ST15 (S83F, D87A; S80I), ST11 (S83I, D87G; S80I), and ST218 (D87A; S80I). Plasmid-mediated quinolone resistance determinants, qnrS1 , aac(6’)-Ib-cr , oqxAB , were detected in 32 (94.1%) isolates alone or in combination, accompanied with β-lactamases, 16S rRNA methylases, and putrescine ABC permeases. AcrR, AcrAB transcriptional repressor, was insertion-inactivated by IS5-transposase in isolates of ST11. Thirteen ompK36 variants associated with specific ST (n=7) and wzi -allele (n=9) clustered into 10 (sub)lineages in the phylogenetic tree possibly affecting the MDR phenotype and infection outcome of isolates. Isolates of ST11, ST15, and ST218 had frameshift disruptions in OmpK35 coupled with specific GD-insertion at position 134-135 in OmpK36, all showing distinct microevolution clusters of ompK36 genotypes. Seven quinolone-susceptible isolates kept the porin genes integral, including two each CRKPs of ST13- wzi74 (carbapenemase KPC-2 and NDM-1-coproducers) and ST65- wzi72 . Conclusions : Under multiple selective pressures, accumulation of mutations of three types (QRDR, AcrR, OmpK36/OmpK35) and acquisition of resistance-conferring genes contribute to quinolone-resistance in clinical MDR-KP isolates, reinforcing the importance of continued epidemiologic surveillance on the evolution and transmission of these isolates. Our findings provided detailed mechanistic analyses and epidemiologic implications for further infection control and antibiotic stewardship initiatives.
Performance and Utility of More Highly Sensitive Malaria Rapid Diagnostic Tests
Authors: Slater Hannah C , Ding Xavier C , Knudson Sophia , Bridges Daniel J , Moonga Hawela , Saad Neil J. , De Smet Martin , Bennett Adam F , Dittrich Sabine , Slutsker Laurence , Domingo Gonzalo J 
Published: May 2021

Abstract
BackgroundA new more highly sensitive rapid diagnostic test (HS-RDT) for Plasmodium falciparum malaria (Alere™/Abbott Malaria Ag P.f RDT [05FK140], now called NxTek™ Eliminate Malaria Ag Pf) was launched in 2017. The test has already been used in many research studies in a wide range of geographies and use cases. MethodsIn this study, we collate all published and available unpublished studies that use the HS-RDT and assess its performance in (i) prevalence surveys, (ii) clinical diagnosis, (iii) screening pregnant women, and (iv) active case detection. Two individual-level data sets from asymptomatic populations are used to fit logistic regression models to estimate the probability of HS-RDT positivity based on histidine-rich protein 2 (HRP2) concentration and parasite density. The performance of the HS-RDT in prevalence surveys is estimated by calculating the sensitivity and positive proportion in comparison to polymerase chain reaction (PCR) and conventional malaria RDTs. ResultsWe find that across 18 studies, in prevalence surveys, the mean sensitivity of the HS-RDT is estimated to be 56.1% (95% confidence interval [CI] 46.9%–65.4%) compared to 44.3% (95% CI 32.6%–56.0%) for a conventional RDT (co-RDT) when using nucleic acid amplification techniques as the reference standard. For use in clinical diagnosis, the HS-RDT was not significantly more sensitive than a co-RDT; however, it did detect more polymerase chain reaction (PCR)–positive individuals presenting with fever in both studies that investigated this use case. Similarly, for screening pregnant women, the HS-RDT was more sensitive than a co-RDT in all but one study; however, this improvement was only statistically significant in one study where data were aggregated across all stages of pregnancy. ConclusionsOverall, the evidence presented here suggests that the HS-RDT is more sensitive in asymptomatic populations and could provide a marginal improvement in clinical diagnosis and screening pregnant women. Although the HS-RDT has limited temperature stability and shelf-life claims compared to co-RDTs, there is no evidence to suggest, given this test has the same cost as current RDTs, it would have any negative impacts if it were widely used in all use cases explored here.
A Re-assessment of 4CMenB Vaccine Effectiveness Against Serogroup B Invasive Meningococcal Disease in England based on an Incidence Model
Authors: Argante Lorenzo , Abbing-Karahagopian Victoria , Vadivelu Kumaran , Rappuoli Rino , Medini Duccio 
Published: May 2021

Abstract
Background: The four-component serogroup B meningococcal 4CMenB vaccine (Bexsero, GSK) has been routinely given to all infants in the United Kingdom at 2, 4 and 12 months of age since September 2015. After three years, Public Health England (PHE) reported a 75% [95% confidence interval: 64%; 81%] reduction in the incidence of serogroup B invasive meningococcal disease (IMD) in age groups eligible to be fully vaccinated. In contrast, vaccine effectiveness (VE) evaluated in the same immunization program applying the screening method was not statistically significant. We re-analyzed the data using an incidence model and obtained more precise VE estimates. Methods: Aggregate data stratified by age, year and doses received were provided by PHE: serogroup B IMD case counts for the entire population of England (years 2011-2018) and 4CMenB vaccine uptake in infants. We combined uptake with national population estimates to obtain counts of vaccinated and unvaccinated person-time by age and time. We re-estimated VE comparing incidence rates in vaccinated and non-vaccinated using a Bayesian Poisson model for case counts with person-time data as an offset. The model was adjusted for age, time and number of doses received. Results: The incidence model showed that cases decreased until 2013-2014, followed by an increasing trend that continued in the non-vaccinated population during the immunization program. VE in fully vaccinated (three doses) was 80.1% [95% Bayesian credible interval (BCI): 70.3%; 86.7%]. After a single dose, VE was 33.5% [12.4%; 49.7%]95%BCI, and, after two doses, 78.7% [71.5%; 84.5%]95%BCI. We estimated that vaccination has averted 312 cases [252; 368]95%BCI between 2015 and 2018. VE was in line with the previously reported incidence reduction. Conclusions: Our estimates of VE had higher precision than previous estimates based on the screening method, that were not statistically significant. When disease incidence is low and vaccine uptake is high, the screening method applied to cases exclusively from the population eligible to vaccination may not be enough precise and produce misleading point-estimates. Precise and accurate VE estimates are fundamental for informing public health decision making. VE assessment can be enhanced using models that leverage data on subjects not eligible for vaccination.
Clinical Case Report: Recurrence of CASTLE Thyroid Tumor
Authors: Van Dang Nguyen , Le Xuan Son , Nguyen Thi Thanh Hong , Nguyen Thi Thu Nhung , Ngo Thanh Tung , Le Van Quang 
Published: May 2021

Abstract
Background: CASTLE (Carcinoma showing thymus-like differentiation) in thyroid gland is a rare disease with favorable prognosis. Treating with surgery and adjuvant radiation therapy has been reported to be able to improve local controlling and long – term survival rates. In this report, we give an account of a clinical case of thyroid gland CASTLE and include relevant literature review in diagnosis and treatment of this disease.Case presentation: A 60-year-old female patient diagnosed with Castle in 2015, had a total thyroidectomy and hormone maintenance. After 5 years, the patient was diagnosed with recurrence, late stage and incapable of surgery. Due to the refusal of radiation therapy, the patient is followed and is currently stable after 15 months.Conclusions: CASTLE is a rare disease, diagnosis is based on postoperative pathology and immunohistochemistry analysis, especially upon CD5 marker. In the case of relapse, treatment includes surgery and radiation therapy. In some cases, follow-up is also an acceptable option for the patient.
Cluster Randomised Trials - Ivermectin Repurposing For COVID-19 Treatment Of Outpatients With Mild Disease In Primary Health Care Centers
Authors: Chahla Rossana Elena , Ruiz Luis Medina , Mena Teresa , Brepe Yolanda , Terranova Paola , Ortega Eugenia Silvana , Barrenechea Guillermo , Goroso Daniel Gustavo , de Bruno María de los Ángeles Peral 
Published: May 2021

Abstract
Background The emergency of COVID-19, along with the current difficulties in responding to the high demand for vaccines, requests to the scientific community to find alternative treatments based on reuse of drugs as a strategy to prevent the progression of the disease in patients infected with SARS COV 2. This study aims to evaluate the use of ivermectin in mild-stage patients to increase outpatient discharge and prevent the progression to moderate or severe stages of the disease.Methods Cluster Randomised Trials in outpatients care, n = 254. The subjects were divided into experimental (EG: n = 110) and control groups (CG: n = 144). The EG received ivermectin orally 4 tablets of 6 mg = 24 mg every 7 days for 4 weeks. All participants were diagnosed by positive RT-PCR for COVID-19 and were evaluated by clinical examination, at the beginning and the end of protocol. Data analyzed using proportion, bivariate and logistic regression. P-value was considered significant at the p < 0·05 threshold. This study was registered at ClinicalTrials.gov Identifier NCT04784481.Findings Both groups were similar in age, sex, and comorbidities (EG: median age = 40·0, range: 18·0–75·0, 42·11% Female; CG: median age = 36, range: 18·0–71·0, 57·89% Female). A significant reduction in the percentage of participants with symptoms (PPS) was observed in the EG and CG when the clinical evaluation of symptoms was performed from 5th to 9th (p = 0·0005). When the clinical evaluation was performed from 10th to 14th day there was no significant difference. A higher proportion of outpatient discharge was observed in EG (98·2%) vs. CG (86·1%) (p-Value = 0·0007). EG showed 8 times more chance of receiving discharge than CG (8·71 CI = [1·99, 38·12]; p = 0·004). The treatment effect with ivermectin to obtain discharge from outpatient care was analyzed by the logistic regression. Then, the chance to obtain outpatient discharge was independent of variables sex, age, and comorbidities.Interpretation Treatment with ivermectin in outpatients care with mild disease of COVID-19 managed to slightly reduce PPS. Also, this treatment improved the clinical state to obtain outpatient discharge, even in the presence of comorbidities. The treatment with ivermectin could significantly prevent the evolution to serious stages since the EG did not present any patient with referral to critical hospitalization.
Fitting Problems: Evaluating Model Fit in Behavior Genetic Models
Authors: Garrison S. Mason , Rodgers Joseph Lee 
Published: May 2021

Abstract
In behavior genetics, like many fields, researchers must decide whether their models adequately explain their data – whether their models “fit” at some satisfactory level. Well-fitting models are compelling, whereas poorly-fitting models are not (Rodgers & Rowe, 2002). Oftentimes, researchers evaluate model fit by employing “universal” rules of thumb (e.g., Hu and Bentler, 1999). However, these rules are not universal, and should be treated as model specific (Kang et al., 2016). Accordingly, we focused on developing fit criteria emulating Hu and Bentler (1999) for classic univariate models (ACE; CE; AE) by fitting simulated twin data with correctly- and incorrectly-specified models. Ideal criteria should consistently accept correct models and reject incorrect models. Classic ACE models were indistinguishable and virtually all fit indices were non-informative because (or especially when) they were obtained in saturated models. For non-ACE models, criteria were informative. Nevertheless, every fit metric employed, except TLI, differed markedly across models and/or conditions. Universal solutions remain elusive, but promising and valid approaches include nested model comparisons, increasing degrees of freedom, and ruthless skepticism.
Seawater Reverse Osmosis Desalination: Assessment and Pre-treatment of Fouling and Scaling
Authors: Salinas-Rodríguez Sergio G. , Schippers Jan C. , Amy Gary L. , Kim In S. , Kennedy Maria D. 
Published: May 2021

This book can of interest to undergraduate and graduate engineering students and researchers, academics, plant operators, consultants, professionals and practitioners in the water sector. The book is not necessarily intended to be read from cover to cover, but consulted as the need arises.
The content of this book deals with: Membrane-based desalinationBasic principles of reverse osmosisFouling and pre-treatmentParticulate foulingOrganic and biological foulingAlgal bloom eventsInorganic foulingScalingProcess designRecent advances and emerging processes
This book forms part of the Master of Science curriculum in Water Supply Engineering and of the Master of Science Programme in Water and Sustainable Development at IHE Delft Institute for Water Education.
ISBN: 9781780409856 (Hardback)
ISBN: 9781780409863 (eBook)
Soil phosphorus composition, loss risk and contribution to the aquatic environment in a typical agricultural area
Authors: Ma Tianhai , Bai Ying , Ruan Xiaohong 
Published: May 2021

Abstract
River eutrophication risk increased significantly in agricultural areas. In this paper, spatial variability of soil phosphorus (P) and loss risk in the Jialu River Basin, China, were analyzed using a geostatistical approach. The correlation between soil and river sediment P was analyzed to identify the main aquatic P source. The results showed that inorganic phosphorus (IP) was the main form of soil TP (82.13%), but the ratio of apatite phosphorus (AP) and non-apatite phosphorus (NAIP) varied between different soil types. AP was the primary form of IP in fluvo-aquic cinnamon soil, while NAIP dominated in meadow aeolian sandy soil. Calculated soil total dissolvable P (TDP, 94–622 mg/kg) exceeded the environmental threshold. High TDP (&gt;400 mg/kg) in mixed soil and sandy soil indicated a high P loss risk. The spatial variability of soil P was moderate to weak, indicating a low heterogeneity. In sediment, IP and AP showed a significant correlation with total organic carbon (p &lt; 0.05), indicating a P source of soil erosion. Sediment AP had a significant positive correlation with soil AP (p &lt; 0.05), confirming soil as the main source of sediment P. Furthermore, an accumulation of sediment P along the Jialu River and its consistency with water TP was revealed.
Metodologias utilizadas para pesquisas em turismo de bicicleta
Authors: De Almeida Teixeira Camila , Edra Fátima Priscila Morela 
Published: May 2021

Este artigo buscou analisar quais os métodos científicos e os assuntos e temas mais utilizados por pesquisadores em pesquisas sobre o turismo de bicicleta. Para alcançar o objetivo deste trabalho, primeiramente, realizou-se pesquisa em três plataformas de busca, utilizando as palavras-chave cycle tourism, bicycle tourism, bike lane, turismo de bicicleta. Em uma segunda etapa desta seleção foram descartados os artigos que não apresentavam relação com a infraestrutura cicloviária ou relação ao uso da bicicleta como atividade turística. E, no terceiro momento, os artigos foram analisados em relação a sua metodologia. O resultado deste levantamento foi sendo apresentado juntamente com o referencial teórico, seção em que foi explicado de maneira sucinta os tipos de coleta de dados e os tipos de análise de dados utilizados nos artigos selecionados. Posteriormente, pode-se fazer uma reflexão sobre as metodologias encontradas neste lavamento a respeito do turismo de bicicleta e da infraestrutura cicloviária. Esta análise mostrou a existência de diversas metodologias que podem ser utilizadas de diferentes perspectivas sobre um determinado assunto.
Palavras-chave: Análise Metodológica. Infraestrutura Cicloviária. Cicloturismo. Cicloviagens.
A mulher negra viajante: experiências e estratégias de combate à sua (in)visibilidade no turismo
Authors: Dos Santos Joice , Silva Coimbra de Sá Natália 
Published: May 2021

Este artigo tem como objetivo evidenciar a presença de mulheres negras viajantes no turismo como estratégia de combate ao racismo. Essa discussão é relevante no contexto da representatividade, pois questiona sobre a invisibilidade das mulheres viajantes e seu impacto no imaginário do que é ser turista e como esta categoria é vista socialmente, buscando desmistificar a imagem do turista branco como o único tipo de consumidor do turismo. Foi utilizada a metodologia de caráter qualitativo, descritivo e exploratório, pautada em pesquisa bibliográfica, documental e com levantamento de dados online, identificando os casos para análise por meio de redes sociais; sites oficiais de empresas de afroturismo e/ou turismo afrocentrado, assim como iniciativas voltadas para mulheres negras viajantes; e plataformas de turismo reconhecidas pelo trade turístico e turistas como referências para busca de serviços de hospitalidade. Por fim, a partir da discussão teórica e da reflexão sobre os casos observados, chegou-se à conclusão de que é necessário um turismo antirracista, que reconheça e valorize as pessoas negras, em especial as mulheres, por serem o grupo mais invisibilizado pelo racismo, destacando seu papel como gestoras da atividade turística, empreendedoras e também como turistas. E que isso seja um compromisso de todos os atores que compõem o trade turístico, em especial aqueles responsáveis pelo marketing e pelo planejamento da atividade, pautados em políticas públicas que promovam a igualdade, a inclusão e o respeito no turismo.
Palavras-chave: Mulher Negra. Viajante. Turismo. Invisibilidade.
THE FEATURES OF INDIAN DIASPORA AND THEIR IDENTITY IN JUMPHA LAHIRI’S SHORT STORY “UNACCUSTOMED EARTH”
Authors: Sugiarto Tri 
Published: May 2021

(Title: The Features of Indian Diaspora and Their Identity in Jumpha Lahiri’s Short Story “Unaccustomed Earth”). America is a multicultural country. It results from the immigration of various ethnic backgrounds from Asia, Africa, and Europe since the beginning of the 19th century. As one of the ethnic communities in the US, the Indian diaspora encounters many experiences in their life. This article explores the feature and identity of Indian diaspora represented in Lahiri's “Unaccustomed Earth”. It aims to reveal some of the Indian diaspora’s features in the US and concludes their current cultural identity through analytical reading of the short story. This is a qualitative content analysis. It applies a theory of diaspora to dig the underlying information from the data. The study shows that Indian diaspora experience several features that include having trouble at their first interaction in the country, recalling the tradition of the homeland, associating with the people from the same ethnic background, and processing the idea of going home to the homeland. In the short story, it is found that the characters embody a hybrid identity. Keywords: Indian, diaspora, identity, hybrid, America