bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining the different mechanisms used by Pseudomonas species to cope with minimal inhibitory concentrations of zinc via comparative transcriptomic analyses
Authors: Lei Lei , Chen Jiahui , Liao Weifang , Liu Pulin 
Published: November 2020

Abstract
Pseudomonas is one of the most diverse bacterial genera identified in the environment. Genome sequence analysis has indicated that this genus can be clustered into three lineages and ten groups. Each group can adopt different mechanisms to thrive under zinc-depleted or high-zinc conditions, two environments that are frequently encountered during their environmental propagation. The response of three prominent Pseudomonas strains (Pseudomonas aeruginosa PAO1, Pseudomonas putida KT2440, and Pseudomonas fluorescens ATCC 13525T) to minimal inhibitory concentrations of zinc were compared using RNA-seq and ultra-performance liquid chromatography–tandem mass spectrometry analysis. Results demonstrated that the three strains shared only minimal similarity at the transcriptional level. Only four genes responsible for zinc efflux were commonly upregulated. P. aeruginosa PAO1 specifically downregulated the operons involved in siderophore synthesis and the genes that encode ribosomal protein, while upregulated the genes associated with antibiotic efflux and cell envelope biosynthesis. The membrane transporters in P. putida KT2440 were globally downregulated, indicating changes in cell permeability. Compared with P. aeruginosa PAO1 and P. putida KT2440, the most remarkable transcriptional variation in P. fluorescens ATCC 13525T is the significant downregulation of the type Ⅵ secretion system. Metabolite quantitative analysis showed that low concentrations of the metabolites involved in central carbon metabolism and amino acid synthesis were detected in the three strains. In summary, the cellular responses of the three strains under high-zinc condition is quite divergent. Although similar metal efflux systems were upregulated, the three strains employed different pathways to reduce zinc intrusion. In addition, zinc treatment can increase the difficulties of scavenging P. aeruginosa from its colonisation area, and reduce the competitiveness of P. fluorescens in microbiota.
Classification of Pharynx from MRI Using a Visual Analysis Tool to Study Obstructive Sleep Apnea
Authors: Shahid Muhammad Laiq Ur Rahman , Mir Junaid , Shaukat Furqan , Saleem Muhammad Khurram , Tariq Muhammad Atiq Ur Rehman , Nouman Ahmed 
Published: November 2020

Background:Obstructive sleep apnea (OSA) is a chronic sleeping disorder. The analysis of the pharynx and its surrounding tissues can play a vital role in understanding the pathogenesis of OSA. Classification of the pharynx is a crucial step in the analysis of OSA.Methods:A visual analysis-based classifier is developed to classify the pharynx from MRI datasets. The classification pipeline consists of different stages, including pre-processing to select the initial candidates, extraction of categorical and numerical features to form a multidimensional features space, and a supervised classifier trained by using visual analytics and silhouette coefficient to classify the pharynx.Results:The pharynx is classified automatically and gives an approximately 86% Jaccard coefficient by evaluating the classifier on different MRI datasets. The expert’s knowledge can be utilized to select the optimal features and their corresponding weights during the training phase of the classifier.Conclusion:The proposed classifier is accurate and more efficient in terms of computational cost. It provides additional insight to better understand the influence of different features individually and collectively. It finds its applications in epidemiological studies where large datasets need to be analyzed.
Experimental and Numerical Investigation of Old Masonry Wall Using a Macro-Modeling Approach
Authors: Kumar Ambareesh , Pallav Kumar 
Published: November 2020

Background:
A 3-D finite element model of the internal masonry wall of a 103-year-Old Senate hall, Allahabad University, has been modeled using macro-modeling approaches. The masonry wall is an excellent example of Indo-Saracenic style architecture used by Britishers during the late 19th Century, which is a unification of the Mughal and Colonial architecture.

Methods:
Non-destructive Test (NDT) has been conducted to estimate is compressive strength and Young’s modulus of the wall. Compressive strength of the brick masonry and stone arch was estimated in the range of 10.5-12.5 MPa and 18.6-21.2 MPa, respectively, whereas Young’s Modulus was estimated in the range of 1800-5000 MPa and 5500-8000 MPa (outlier not considered). Finite Element model was prepared using the macro-modeling approach.

Results:
The gravity load analysis shows that the wall is stable, and its geometrical configuration is safe with maximum Von-Mises stress of 5.38 MPa and deformation of 2.27 mm. The results of the first six modes are presented. Further, in the absence of a recorded ground motion for the Prayag city, synthetic ground motion is simulated for 25th April 2015 Nepal earthquake (Mw) using a stochastic finite fault model.

Conclusion:
Evaluated behaviour of the internal masonry wall is shown in the form of acceleration, deformation and stress response.
Fermentation of Sweet Sorghum Syrup Under Reduced Pressure for Bioethanol Production
Authors: Volodko Oleksii I. , Ivanova Tetiana S. , Kulichkova Ganna I. , Lukashevych Kostyantyn M. , Blume Yaroslav B. , Tsygankov Sergii P. 
Published: November 2020

Background:Production of bioethanol from sweet sorghum (Sorghum saccharatum) is a promising “green” energy source that can help to reduce energy dependence on petroleum products, to decrease greenhouse gas emissions, and fight environmental pollution. As an additional benefit, it can promote the exploitation of new uncultivated agricultural lands and favor establishing integrated agro-industrial energy independent enterprises. The alcoholic fermentation under reduced pressure may prevent the accumulation of high ethanol concentrations in the cultured broth and thus may create favorable conditions for the highest productivity of yeastSaccharomyces cerevisiae.Objective:Elaboration of optimal conditions for sweet sorghum syrup fermentation under reduced pressure.Aim:To determine the parameters of sweet sorghum syrup fermentation byS. cerevisiaeunder the conditions of constant and periodic reduced pressure for the highest bioethanol production efficiency.Methods:The sweet sorghum was grown in a temperate continental climate region of Northern Ukraine. The parameters of diluted stem syrup andS. cerevisiaefermentation under reduced and atmospheric pressure were established and controlled by chemical, biochemical and physicochemical methods. The yeast cells were dyed with methylene blue and counted using a microscope and a Neubauer counting chamber. The obtained data have been statistically analyzed.Results:It has been established that a periodic vacuum extraction with short-term heating of the medium to the boiling point is the most promising procedure for bioethanol production. Periodically reduced pressure fermentation of sweet sorghum diluted syrup resulted in 55% higher bioethanol productivity compared to atmospheric pressure fermentation. Such treatment enables to maintain the concentration of ethanol in the medium below 5.5% vol., which does not significantly inhibit the productivity of industrial yeast strains and allows adding a nutrient with the subsequent continuation of the cultivation process. The resulting distillate requires less energy for further dehydration.Conclusion:The sweet sorghum syrup does not contain substances that inhibit yeast cells although nitrogen and phosphorus supplements are required to support efficientS. cerevisiaegrowth. The optimal technology, elaborated in this research, consists of repeated cycles of fermentation under reduced pressure (to the level of vacuum) for boiling the cultured broth. This technology provides the highest bioethanol output, high efficiency, and productivity of the overall process.
Efficiency of Switchgrass (Panicum virgatum L.) Cultivation in the Ukrainian Forest-Steppe Zone and Development of Its New Lines
Authors: Rakhmetovа Svitlana O. , Vergun Olena M. , Kulyk Maksym I. , Blume Rostislav Y. , Bondarchuk Oleksandr P. , Blume Yaroslav B. , Rakhmetov Dzhamal B. 
Published: November 2020

Background:
Switchgrass (Panicum virgatum L.) is a promising C4-photosynthetising perennial grass and an important energy crop. It is resistant to drought, cold and winter frost, endures flooding and shows high performance at minimal energy consumption for cultivation.

Methods:
The purpose of the work was to develop and introduce high-yielding genotypes of switchgrass and develop effective cultivation technologies for the Forest-Steppe zone of Ukraine. The objective of the study was to evaluate the introduction potential of switchgrass, to establish biologically productive parameters and energy values of different genotypes and the effectiveness of cultivation techniques in the specific geo-climatic zone of Ukraine. To achieve the objectives, a wide range of introductory, biological-morphological, breeding-biotechnological, and agronomic methods have been used.

Results:
The gene pool of P. virgatum was collected (33 accessions), ten of which have been investigated, including both introduced genotypes and newly developed breeding lines. The bio-morphological, ecological features, the biochemical composition of plants have been evaluated. The productivity of the above-ground biomass and seeds, as well as the energy value of plants, has been evaluated. High-performance forms with specified yield parameters, biomass sugars, total energy and biofuel output per unit area have been determined.

Conclusion:
A new variety of P. virgatum (cv. Zoriane) has been introduced for cultivation. Among the accessions of newly developed genotypes, the most productive lines have been identified. New efficient technologies have been developed to increase the yield potential of switchgrass as a source of raw materials for biofuel production.
Potential of HIV Self-Sampling to Increase Testing Frequency Among Gay, Bisexual, and Other Men Who Have Sex With Men, and the Role of Online Result Communication: Online Cross-Sectional Study
Authors: Maté Tomás , Hoyos Juan , Guerras Juan Miguel , Agustí Cristina , Chanos Sophocles , Kuske Matthias , Fuertes Ricardo , Stefanescu Roxana , Pulido Jose , Sordo Luis , de la Fuente Luis , Belza María José ,   EURO HIV EDAT Group
Published: November 2020

BackgroundLate HIV diagnosis remains frequent among the gay, bisexual, and other men who have sex with men (GBMSM) population across Europe. HIV self-sampling could help remove barriers and facilitate access to testing for this high-risk population.ObjectiveWe assessed the capacity of HIV self-sampling to increase the testing frequency among GBMSM living in Denmark, Germany, Greece, Portugal, Romania, and Spain, and evaluated the role of new technologies in the result communication phase.MethodsWe analyzed a convenience sample of 5019 GBMSM with prior HIV testing experience who were recruited during 2016 through gay dating websites. We estimated the proportion of GBMSM who reported that the availability of self-sampling would result in an increase of their current testing frequency. We constructed a Poisson regression model for each country to calculate prevalence ratios and 95% CIs of factors associated with an increase of testing frequency as a result of self-sampling availability.ResultsOverall, 59% (between country range 54.2%-77.2%) of the participants considered that they would test more frequently for HIV if self-sampling was available in their country. In the multivariate analysis, the increase of testing frequency as a result of self-sampling availability was independently associated with reporting a higher number of unprotected anal intercourse events in all countries except for Greece. Independent associations were also observed among GBMSM who were not open about their sex life in Germany, Greece, Portugal, and Spain; those with a lower number of previous HIV tests in Denmark, Greece, Portugal, and Spain; and for those that took their last test more than 3 months previously in Germany, Portugal, Romania, and Spain. In addition, 58.4% (range 40.5%-73.6%) of the participants indicated a preference for learning their result through one-way interaction methods, mainly via email (25.6%, range 16.8%-35.2%) and through a secure website (20.3%, range 7.3%-23.7%). Almost two thirds (65%) of GBMSM indicated preferring one of these methods even if the result was reactive.ConclusionsAvailability of HIV self-sampling kits as an additional testing methodology would lead to a much-needed increase of testing frequency, especially for the hidden, high-risk, and undertested GBMSM population. Online-based technologies without any personal interaction were preferred for the communication of the results, even for reactive results.
Effective Use of Mobile Electronic Medical Records by Medical Interns in Real Clinical Settings: Mixed Methods Study
Authors: Kim SuJin , Ku Seulji , Kim Taerim , Cha Won Chul , Jung Kwang Yul 
Published: November 2020

Background
In South Korea, most graduated medical students undertake a 1-year internship before beginning residency and specialization. Interns usually work in a tertiary hospital and rotate between different, randomly assigned departments to be exposed to different medical specialties. Their jobs are mostly simple and repetitive but are still essential for the patient care process. However, owing to the lack of experience and overwhelming workload, interns at tertiary hospitals in South Korea are usually inefficient, often delaying the entire clinical process. Health care providers have widely adopted mobile electronic medical records (mEMRs) as they have been shown to improve workflow efficiency.

Objective
This study investigates the association between the frequency of mEMR usage and the clinical task completion interval time among interns in a tertiary hospital.

Methods
This mixed methods study was conducted at the Samsung Medical Center, Seoul, South Korea. Interns who worked at the Samsung Medical Center from March 2018 to February 2019 were included. The hospital electronic medical record (EMR) system known as DARWIN (Data Analysis and Research Window for Integrated kNowledge) was launched with PC and mobile. Both versions are actively used in hospitals by personnel in various positions. We collected the log data from the mEMR server and the intern clinical task time-series data from the EMR server. Interns can manage the process of identifying patients, assigning the clinical task, finishing the requested clinical intern tasks, etc, through the use of the mEMR system. We compared the clinical task completion interval among 4 groups of interns divided by the mEMR frequency quantile. Then, System Usability Score (SUS) questionnaires and semistructured interviews were conducted.

Results
The regular mEMR users were defined as those who logged in more than once a day on average and used the mEMR until the level after login. Among a total of 87 interns, 84 used the mEMR to verify the requested clinical tasks. The most frequently used item was “Intern task list.” Analysis of the 4 intern groups revealed an inverse relationship between the median time of the task completion interval and the frequency of mEMR use. Correlation analysis showed that the intern task completion time interval had a significant inverse relationship with the individual frequency of mEMR usage (coefficient=-0.27; 95% CI -0.46 to -0.04; P=.02). In the additional survey, the mean SUS value was 81.67, which supported the results of the data analysis.

Conclusions
Our findings suggest that frequent mEMR use is associated with improved work efficiency in hospital interns with good usability of the mEMR. Such finding supports the idea that the use of mEMR improves the effectiveness and workflow efficiency of interns working in hospitals and, more generally, in the context of health care.
Use of the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) for Processing Free Text in Health Care: Systematic Scoping Review
Authors: Gaudet-Blavignac Christophe , Foufi Vasiliki , Bjelogrlic Mina , Lovis Christian 
Published: November 2020

Background
Interoperability and secondary use of data is a challenge in health care. Specifically, the reuse of clinical free text remains an unresolved problem. The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) has become the universal language of health care and presents characteristics of a natural language. Its use to represent clinical free text could constitute a solution to improve interoperability.

Objective
Although the use of SNOMED and SNOMED CT has already been reviewed, its specific use in processing and representing unstructured data such as clinical free text has not. This review aims to better understand SNOMED CT's use for representing free text in medicine.

Methods
A scoping review was performed on the topic by searching MEDLINE, Embase, and Web of Science for publications featuring free-text processing and SNOMED CT. A recursive reference review was conducted to broaden the scope of research. The review covered the type of processed data, the targeted language, the goal of the terminology binding, the method used and, when appropriate, the specific software used.

Results
In total, 76 publications were selected for an extensive study. The language targeted by publications was 91% (n=69) English. The most frequent types of documents for which the terminology was used are complementary exam reports (n=18, 24%) and narrative notes (n=16, 21%). Mapping to SNOMED CT was the final goal of the research in 21% (n=16) of publications and a part of the final goal in 33% (n=25). The main objectives of mapping are information extraction (n=44, 39%), feature in a classification task (n=26, 23%), and data normalization (n=23, 20%). The method used was rule-based in 70% (n=53) of publications, hybrid in 11% (n=8), and machine learning in 5% (n=4). In total, 12 different software packages were used to map text to SNOMED CT concepts, the most frequent being Medtex, Mayo Clinic Vocabulary Server, and Medical Text Extraction Reasoning and Mapping System. Full terminology was used in 64% (n=49) of publications, whereas only a subset was used in 30% (n=23) of publications. Postcoordination was proposed in 17% (n=13) of publications, and only 5% (n=4) of publications specifically mentioned the use of the compositional grammar.

Conclusions
SNOMED CT has been largely used to represent free-text data, most frequently with rule-based approaches, in English. However, currently, there is no easy solution for mapping free text to this terminology and to perform automatic postcoordination. Most solutions conceive SNOMED CT as a simple terminology rather than as a compositional bag of ontologies. Since 2012, the number of publications on this subject per year has decreased. However, the need for formal semantic representation of free text in health care is high, and automatic encoding into a compositional ontology could be a solution.
The societal impact of a biologic treatment of ankylosing spondylitis: a case study based on secukinumab
Authors: Himmler Sebastian , Branner Jennifer C , Ostwald Dennis A 
Published: November 2020

Aim:
This study estimates the societal benefits of using biologics like secukinumab (SEC) instead of nonsteroidal anti-inflammatory drugs for treating patients with ankylosing spondylitis in Germany.
Materials & methods:
A Markov and a population model were used to predict the functional impairment of German ankylosing spondylitis patients using SEC or nonsteroidal anti-inflammatory drugs. This was translated into avoided productivity losses, which were valued according to gross value added.
Results:
The productivity impairment of SEC users was predicted to decrease by 20 percentage points, corresponding to 12.8 and 32.7 million hours in paid and unpaid work and a monetary value of €1.6 billion from 2016 to 2030. Accounting for economic spillover effects increases the societal value to € 3.3 billion.
Conclusion:
The improvements in functional impairment due to biologics could lead to sizable productivity effects.
Official Reporting of Religious Organizations as a Source of Empirical Data on the Activities of the Church: Some Questions of Theory and Practice of the Evangelical Lutheran Church of Sweden
Authors: Balabeikina O. A. , Mezhevich N. M. , Iankovskaia A. A. 
Published: November 2020

The relevance of any material offered to the scientific and expert community depends on many factors. Objectively, the presence of this or that issue in the center of public attention has a positive effect on the actualization of this or that article. However, there is an obvious danger. Academic approaches that accidentally find themselves in resonance with global trends can fall victim to political conjuncture. Relevance in this case can fall victim to the political moment. Moreover, this or that topic, being in the center of public discussion, negatively affects the academic understanding of the problem. All this fully relates to the question of the relationship between the state and the church in modern Europe and Russia.A few words about global trends. Their essence boils down to the growing confrontation between supporters of new ideological approaches and traditionalists, among whom are many adherents.The relationship between religion and the state testifies to the fact that states and societies have not yet learned to draw an effective line between their interests and those of adherents. This fact presupposes careful state and public participation in the affairs of the church. However, acknowledging this circumstance is not enough. The state must clearly know what, where and how is happening in the church sphere of the life of society in cases where church affairs can affect public and state security.It is also known that almost all the leading churches, to a greater or lesser extent, provide official reporting to the state. However, working with this reporting, its scientific analysis is not always representative.Objective. The presented article is aimed at a partial solution of the problem of increasing the effectiveness of academic research of the church` activities. Moreover, it is made based on official church statistics.The author’s position is the following. States and societies have no right to let go of this vital sphere of life. The functions of the state, in this case, are at least controlling. The ineffective execution of its functions by the state can be revealed in many countries of the world. The situation in France is nothing more than a reference case of a problem that, to one degree or another, exists in most of the countries of the world, which are distinguished by ethnic and confessional heterogeneity.