bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching medical microbiology during the COVID-19 pandemic: perceptions of medical undergraduates and the effects of online learning
Authors: Papan Cihan , Schmitt Monika , Becker Sören L. 
Published: May 2021

Abstract
Background:The coronavirus disease 2019 (COVID-19) pandemic has imposed unprecedented hurdles to health care systems and medical faculties alike. Lecturers of practical courses at medical schools have been confronted with the challenge to transfer knowledge distantly. We sought to evaluate the effects of an online learning alternative to the traditional medical microbiology course.Methods: During the summer term 2020, medical students at the University of Saarland, Germany, participated in an online-only course in medical microbiology. Teaching content comprised clinical scenarios, theoretical knowledge and instructive videos on microbiological techniques. Test performances, failure rates, and student evaluation, including open-response items, of the course during the summer term 2020 were compared to the summer term 2019.Results:Student performance was comparable between both the online-only group and the comparator for both the written (average grades 7.6 vs. 7.3; p=0.1985) and the oral exam (33.6 vs. 33.4, p=0.7749). Failure rate did not significantly differ between the online-only group and the comparator group (2.4% vs. 3.3%). While lecturer expertise was graded similarly high from students of both groups, students from the summer term 2020 gave lower grades for interdisciplinarity, possibilities for interaction, and the extent to which the educational objectives were defined. Main critiques formulated within the open-response items concerned organizational deficits.Conclusions:Online-only courses in medical microbiology are a feasible teaching option, especially in the setting of a pandemic, leading to similar test performances in comparison to traditional courses. The lack of interaction and sustainability of acquired manual skills warrant further research.
Use of a Community of Practice for the Implementation of Evidence-based Practices for Heart Failure Within the United States Department of Veterans Affairs
Authors: Sahay Anju , Mittman Brian S , Gholami Parisa , Lin Shoutzu , Heidenreich Paul A 
Published: May 2021

Abstract
Communities of Practice (CoPs) are a promising approach to facilitate the implementation of evidence-based practices (EBPs) to improve care for chronic conditions like heart failure (HF). COPs involve a complex process of acquiring and converting both explicit and tacit knowledge into clinical activities.Formation: In July 2006, a CoP called the Heart Failure Provider Network (HF Network) was established in the United States (US) Department of Veterans Affairs (VA) with the overarching goal of improving the quality of care for HF patients. The CoP has involved a total of 1,341 multidisciplinary and multilevel members at all 144 VA Health Care Systems (sites). Examples of CoP activities include discussions of interventions to decrease hospitalization rates and to empower patients and caregivers for self-management. Goals of the CoP include networking facilitation, information dissemination and exchange, collaboration and implementation of EBPs.Assessment: We conceptualized the assessment (formative evaluation) of the HF Network in terms of its various activities (inputs) and proximal impacts (mediators) at the individual-level, and its distal and ultimate impacts (outcomes) at the site-level leading to an improved culture of implementation of new/improved EBPs at the system-wide level.The HF Network membership grew steadily over the nine years. Most members were practicing clinicians (n=891, 66.4%), followed by administrators (n=342, 25.5%), researchers (n=70, 5.2%), and others (n=38, 2.8%). Participation was “active” for 70.9% versus “passive” for 29.4% of members. The distribution of active members (clinicians 64.7%, administrators 21.6%) was similar to the distribution of overall membership.Survey respondents perceived the HF Network as useful in terms of its varied activities and resources relevant for patient care. Members, particularly those that consider themselves influential in improving quality of care, noted multiple benefits of membership. These included confirmation of one’s own clinical practices, evidence-based changes to their practice and help in understanding facilitators and barriers in setting up or running HF clinics and other programs.
A Novel Potential Diagnostic and Prognostic Biomarker for Esophageal Cancer
Authors: Miao Fei , Xie Fucun , Xu Xin , Liu Zhisong 
Published: May 2021

Abstract
Background: Esophageal cancer (EC) is a lethal malignancy of the digestive tract with high morbidity and mortality rates, lacking molecular biomarkers for EC diagnosis and prognosis with high specificity and sensitivity.Methods: Downloaded from the Cancer Genome Atlas (TCGA), the high-throughput transcriptome sequencing mRNA data was normalized, after which dysregulated genes were identified via limma package. Weight gene coexpression network analysis (WGCNA) was performed to select diagnostic modules and candidate genes. Later, Hub genes were screened through functional enrichment, LASSO Cox regression and survival analysis. Furthermore, we performed comparation with other biomarkers and investigated the association between our target gene and immune microenvironment.Results: Esophageal adenocarcinoma subtype and esophageal squamous cell carcinoma subtype displayed similar expression patterns in terms of differentially expressed genes, which indicates the existence of consensus biomarkers. After a series of analyses, including weighted gene coexpression network analysis, Gene Ontology enrichment analysis and Cox regression analysis, CMA1 was identified as an abnormally upregulated biomarker with highest diagnostic and prognostic potential. Moreover, CMA1 might exert its effect by influencing the immune microenvironment. Conclusion: CMA1 is a potential biomarker for EC in not only diagnosis but also prognosis. Future prospective clinic trials are expected to evaluate its performance in clinical practice.
Pipelines and Systems for Threshold Avoiding Quantification of LC-MS/MS data
Authors: Brotons Alejandro Sánchez , Eriksson Jonatan , Kwiatkowski Marcel , Wolters Justina , Kema Ido , Barcaru Andrei , Kuipers Folkert , Bakker Stephan , Bischoff Rainer , Suits Frank , Horvatovich Peter 
Published: May 2021

Abstract
The accurate processing of complex LC-MS/MS data from biological samples is a major challenge for metabolomics, proteomics and related approaches. Here we present the Pipelines and Systems for Threshold Avoiding Quantification (PASTAQ) LC-MS/MS pre-processing toolset, which allows highly accurate quantification of data-dependent acquisition (DDA) LC-MS/MS datasets. PASTAQ performs compound quantification using single-stage (MS1) data and implements novel algorithms for high-performance and accurate quantification, retention time alignment, feature detection, and linking annotations frommultiple identification engines. PASTAQ offers straightforward parametrization and automatic generation of quality control plots for data and pre-processing assessment. This design results in smaller variance when analyzing replicates of proteomes mixed with known ratios, and allows the detection of peptides over a larger dynamic concentration range compared to widely used proteomics preprocessing tools. The performance of the pipeline is also demonstrated in a biological human serum dataset for the identification of gender related proteins.
Effect of acupoint with moxa cone on 1H-MRS of hippocampus and posterior cingulate gyrus in patients with mild cognitive impairment
Authors: Mai Wei , Tang Liying , Wei Yichen , Zhou Lu , Zou Zhuocheng , Teng Jinlong , Su Jiahui , Nong Xiucheng , Yu Bihan , Li Chong , Shao Lijuan , Duan Gaoxiong , Zhao Lihua , Deng Demao , Chen Shangjie 
Published: May 2021

Abstract
Background: Mild cognitive impairment (MCI) is often the prodromal stage to Alzheimer's disease (AD). Most patients with MCI harbor the pathologic changes of AD and experience progressive brain metabolites change. We investigated the changes of metabolites in bilateral hippocampus (HIP) and posterior cingulate gyrus (PCG) in MCI patients, and observed the effects of moxa cone moxibustion on the metabolites of bilateral hippocampus and posterior cingulate gyrus in patients with MCI.Methods: Sixty-nine patients with MCI and sixty-seven cases of age-matched normal controls (NC) were enrolled in this study.MCI patients were randomly divided into drug group(Drug, n=24),sham acupoint group(Sham, n=20) and acupoint group(Acupoint, n=25).All subjects received proton magnetic resonance spectroscopy (1H-MRS) for measurement of NAA/tCr and Cho/tCr ratios in bilateral hippocampus and posterior cingulate gyrus before and after treatment. Mini-Mental Status Examination(MMSE) and Montreal Cognitive Assessment(MoCA) were used to evaluate cognitive function.Results: MCI patients were characterized by lower NAA/tCr in bilateral hippocampus and posterior cingulate gyrus and Cho/tCr in right hippocampus compared to those in NC group(P < 0.05). After two months treatment, NAA/tCr in bilateral hippocampus and posterior cingulate gyrus and Cho/tCr in right hippocampus were increased in the three treatment groups, and there was no significant difference compared to NC group(P > 0.05).NAA/tCr in right hippocampus and Cho/tCr of right posterior cingulate gyrus of acupoint group was significantly higher than those in sham acupoint group(P < 0.05) and NC group(P < 0.05).The scores of MMSE and MOCA in the acupoint group and sham acupoint group were better than those in the drug group, especially in the long-term efficacy.Conclusions: Moxa cone moxibustion may improve the cognitive function of MCI patients by regulating the abnormal metabolites of bilateral hippocampus and posterior cingulate gyrus. MRS can provide objective imaging basis for moxibustion prevention and treatment of MCI.Trial Registration: ChiCTR-IPR-16009144 (Retroactively registered on 26 AUG 2016)
Bioaugmentation mitigates ammonia and hydrogen sulfide emissions during the mixture compost of dewatered sewage sludge and reed straw
Authors: Cheng Qingli , Zhang Longlong , Wang Dawei , Niu Bochao 
Published: May 2021

Abstract
This study investigated the effectiveness of bio-augmenting aerobic cell culture to mitigate ammonia and hydrogen sulfide emission in sewage sludge composting amended with reed straw (with the weight ratio of 1:0.3–0.4). During the 20-day aerated lab-scale composting, adding 200 mL culture (56.80 NTU) reduced ammonia and hydrogen sulfide emissions by 38.00 % and 54.32 %, and conserved total nitrogen and sulfate by 39.42 % and 70.75 %, respectively. Organic matters degradation was quick started 1 day ahead. Comparing to the control, nitrate content increased 38.75 % at the end of the compost. Bioaugmentation evened the distributions of bacterial communities in the thermophilic phase. The shift was mainly due to 22.97 % of relative abundance of Proteobacteria depressed and 157.16 % of Bacteroidetes increased, which were benefit for nitrogen conservation and glycan breakdown, respectively. In summary, the results demonstrated that bioaugmentation addition could be an effective strategy for enhanced sludge composting.
Numerical Analysis of The Ti6Al4V Behavior Based on the Definition of a New Phenomenological Model
Authors: YAICH Mariem , Ayed Yessine , Germain Guenael , Bouaziz Zoubeir 
Published: May 2021

Abstract
The finite element modeling is significantly depended on the accurate prediction of the thermomechanical material behavior. In order to increase the accuracy of numerical simulations, a new phenomenological model is proposed in this study. Its mathematical formulation allows accurate predictions of the Ti6Al4V sensitivity to the strain rate and the temperature, while maintaining a low identification cost of its constitutive coefficients. Its implementation in the Abaqus® software is carried out based on the developed VUMAT. The subroutine robustness is investigated in the case of the modeling of uniaxial tensile and impact tests. A 3D numerical analysis of the Ti6Al4V machining is set up based on the definition of the rheological Johnson-Cook model and the proposed one. Experimental orthogonal machining tests are also established for several cutting conditions. An important sensitivity of the chip serration, segments geometry and the cutting forces to the feed rate is pointed out. Comparisons of the numerical results obtained with both models are carried out. Interesting agreements with the experimental results are guaranteed with the new phenomenological model, which is not the case of the Johnson-Cook empirical law. In addition, intuitive insights about the effect of the cutting conditions on the material flow towards the workpiece edges and the side burr geometry are provided with the 3D numerical modeling. The results presented in this study point out the inability of the 2D numerical simulations to accurately predict the phenomena induced during the machining process, even in the case of an orthogonal machining.
Analysis of sputum microbial diversity in patients with different histological types of lung cancer
Authors: Ran Zhuonan , Liu Jiexing , Xin Caiyan , Wang Fen , Zeng Shan , Xiao Hua , Shen Xiang , Xiong Bin , Song Zhangyong 
Published: May 2021

Abstract
Background: The respiratory microbiome of lung cancer patients is different from healthy people. Finding the characteristics of microorganisms is conducive to exploring new directions for the assist in distinguishing different histological types of lung cancer. Methods: 16S rRNA sequencing and internal transcribed spacer sequencing were performed respectively on sputum samples from 8 adenocarcinomas, 10 squamous cell carcinomas, 5 small cell lung cancers, and 3 combined-small cell lung cancer patients. And then, bioinformatics analysis of their bacterial microbiome and fungal mycobiome were conducted. And the correlation between respiratory microorganisms and clinical characteristics was further analyzed.Results: The difference in species diversity of the respiratory tract microorganisms of different histological types of lung cancer is statistically significant. Moreover, smoking can increase the diversity of respiratory bacteria. Nevertheless, quitting smoking is beneficial to the transformation of the respiratory tract flora to a non-smoking state. Spearman’s correlation further showed that Fusarium was positively related to Streptococcus, Neisseria, Prevotella-7, and Veillonella, and Penicillium was positively related to Neisseria. Conclusions: Based on the differences of microorganisms among different histological types of lung cancer, deep composition characterization of lung cancer-related microorganisms and their clinical characteristics is an important advancement in understanding the role of microorganisms in lung cancer development.
Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B
Authors: Sistigu Antonella , Musella Martina , Galassi Claudia , Guarracino Andrea , Manic Gwenola , Manduca Nicoletta , Pietrosanto Marco , Helmer-Citterich Manuela , Pallocca Matteo , Fanciulli Maurizio , Benedetto Anna Di , Ercolani Cristiana , Pescarmona Edoardo , Pizzuti Laura , Sperati Francesca , Signore Michele , Vitale Sara , Schiavoni Giovanna , Mattei Fabrizio , De Ninno Adele , Businaro Luca , Lucarini Valeria , Bracci Laura , Aricò Eleonora , Ziccheddu Giovanna , Facchiano Francesco , Rossi Stefania , Sanchez Massimo , Boe Alessandra , Biffoni Mauro , De Maria Ruggero , Vitale Ilio 
Published: May 2021

Abstract
Cancer stem cells (CSCs) are immature, immortal cells within tumors, adept at resisting therapeutic pressure and responsible for local and distant disease recurrence. Non-genetic mechanisms of acquired resistance are increasingly being described, however molecular insights into this evolutionary process still lack. Here, we showed that Type I interferons (IFNs-I) act as molecular hubs of resistance during immunogenic chemotherapy, as they trigger the epigenetic regulator KDM1B, responsible for an adaptive, yet reversible, transcriptional rewiring of cancer cells towards stemness and immune escape. Accordingly, KDM1B pharmacological inhibition antagonizes the appearance of IFN-I-adapted CSCs, both in vitro and in vivo. Notably, IFN-I-adapted CSCs are heterogeneous in terms of multidrug resistance, plasticity, invasiveness and immunogenicity. Moreover, in breast cancer patients receiving anthracycline-based chemotherapy, IFN-I and KDM1B signatures positively correlate with CSC and immune evasion markers. Our study identifies IFN-I→KDM1B axis as a potent engine of cancer cell reprogramming and recommends KDM1B targeting an attractive adjunctive to immunogenic drugs to prevent CSC expansion and increase the long-term benefit of therapy.
Geochemical characterization of groundwater and water quality assessment for sustainable management of hard rock aquifer in South India
Authors: Madasamy Senthilkumar , Rajendiran Thilagavathi , Nagappan Ganesh , Sabarathinam Chidambaram , Panda Banajarani , Elumalai Vetrimurugan , Ghai Meenu , Singh Dhiraj kr. 
Published: May 2021

Abstract
Hydrogeochemical investigation was carried out in groundwater of Virudhunagar district, Tamil Nadu, India. Geologically the study area is occupied with Archaean, Charnockite, Unclassified Genesis and Pleistocene Laterite formations. A total of 72 groundwater samples were collected spatially during North East Monsoon (NEM) in 2019 based upon the coverage of geological formations. The collected samples were studied for different physio-chemical parameters like pH, TDS and EC, major cations (Ca, Mg, Na, K) and major anions (Cl, HCO3, SO4, PO4). EC and TDS ranges from 273 to 5869 mg/L and 194 to 4159 mg/L. The ionic dominance of the hydrochemical parameters follows in the order of Na > Ca > Mg > K and Cl > HCO3 > SO3 > PO4. The data represents two major hydrogeochemical facies of Ca-HCO3 and mixed Ca-Mg-Cl in the study region. The USSL classifications of samples signifies low alkali hazard and high to very high salinity hazard. The higher concentration of TDS and EC in the samples reflects the unsuitability of groundwater. According to the WHO drinking water quality standards and the value of SAR, RSC, Na% reflects the groundwater in the study region is more suitable for irrigation than drinking purpose. The statistical method also adopted to understand the major factors influencing the variation in hydrochemistry of the region. Weathering, leaching of salts and anthropogenic activities were identified to be the key governing factor in the varied groundwater chemistry of this region.
Iraqi bentonite as a natural pozzolan for sustainable concrete
Authors: Al-Hammood Amer Abbas , Frayyeh Qais J. , Abbas Waleed A. 
Published: May 2021

Abstract
Iraqi high-calcium bentonite was used for the first time to prepare natural pozzolan. Twenty-four calcination programs were studied. The optimum calcination program is 800°C for 90min. The calcined bentonite meets the requirements of the Iraqi specification of pozzolanic materials. The incorporation of calcined bentonite as a part of cementitious binder extends both initial and final setting time in proportion to the percentage of calcined bentonite. In concrete, the calcined bentonite reduces workability and early strength in proportion to the percentage of Portland cement replacement, while promotes the later strength at 5–15% replacement. The retardation effect of calcined bentonite makes it suitable for concrete production in hot climate territories and for mass concrete. Moreover, the relatively low embodied energy and low carbon dioxide emission of calcined bentonite enhance the sustainability of concrete.
Rechallenge with Previously Administered Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in EGFR-Mutated Non-Small Cell Lung Cancer with Leptomeningeal Metastasis
Authors: Miyawaki Taichi , Kenmotsu Hirotsugu , Yabe Michitoshi , Kodama Hiroaki , Nishioka Naoya , Miyawaki Eriko , Mamesaya Nobuaki , Kobayashi Haruki , Omori Shota , Wakuda Kazushige , Ono Akira , Deguchi Shoichi , Mitsuya Koichi , Naito Tateaki , Murakami Haruyasu , Mori Keita , Harada Hideyuki , Hayashi Nakamasa , Takahashi Kazuhisa , Takahashi Toshiaki 
Published: May 2021

Abstract
Objectives: In EGFR-mutated non-small cell lung cancer (NSCLC) patients, approximately 80–90% of leptomeningeal metastasis (LM) develops after failed initial epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (EGFR-TKI) treatment. However, the efficacy of rechallenging previously administered EGFR-TKIs in patients with EGFR-mutated NSCLC and LM that develops after EGFR-TKI treatment failure remains unknown.Materials and Methods: We retrospectively reviewed the medical records of patients with EGFR-mutated NSCLC and LM from November 2011 to August 2019. Patients were classified into two groups according to LM treatment type: switched to previously unadministered EGFR-TKIs (Switch-TKI) and rechallenge with previously administered EGFR-TKIs (Rechallenge-TKI).Results: In total, 50 patients treated with EGFR-TKI after LM diagnosis were included; 35 were treated with Switch-TKI, and 15 with Rechallenge-TKI. The median overall survival (OS) from the time of LM diagnosis was 6.2 months in all study patients. According to the treatment type, the median OS from the time of LM diagnosis was 6.9 months in Switch-TKI patients and 4.9 months in Rechallenge-TKI patients. There was no significant difference in the OS between the Switch-TKI and Rechallenge-TKI groups (P = 0.864). Thirty-five patients were treated with erlotinib and 15 with osimertinib; Regardless of the type for EGFR-TKI, there was no significant difference in OS between patients treated with Switch-TKI and those treated with Rechallenge-TKI. Conclusion: Our findings suggest that rechallenge of previously administered EGFR-TKIs may be a therapeutic option for LM development after EGFR-TKI treatment failure in patients with EGFR-mutated NSCLC, not only switching to previously unadministered EGFR-TKIs.
Research on Laser Ultrasonic Testing of 316l Stainless Steel Mean Grain Size Based on Wavelet Threshold Denoising
Authors: Yuan Shu-Xian , Wu Jin-Feng , Chen Huai-Dong , Liu Shu-Hong , Zhu Zhen-Ge , Yu Hui-Hui , Yin Anmin 
Published: May 2021

Abstract
This paper investigated a mean grain size characterization method base on laser ultrasonic. The 316L stainless steel samples with different mean grain size were conducted with different heat treatments and times, and each sample was observed by SEM and tested by laser ultrasonic. Due to the state of the sample surface, complexity of equipment and environment, the ultrasonic signal contain a lot of noise. Proposes a method to calculate the ultrasonic attenuation coefficient based on the signal after wavelet threshold denoising. Using db3 as the wavelet basis function, the signal is decomposed and denoised 5 times and then recombined. The attenuation coefficients of the amplitudes in the time domain and frequency domain of the original signal and the denoised signal are calculated. The results show that wavelet threshold denoising can improve the signal-to-noise ratio of the signal and the calculation accuracy of the average grain size.