bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties
Authors: Khatri Indu , Sharma Gaurav , Subramanian Srikrishna 
Published: October 2019

Abstract
Background: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.
Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina ® and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor higher heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens S. aureus and S. epidermidis , were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in Bacillus clausii and other probiotics.
Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains and industrially relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections.
Explaining the successes and failures of tuberculosis treatment programs; a tale of two regions in rural Eastern Uganda
Authors: Izudi Jonathan , Tamwesigire Imelda K , Bajunirwe Francis 
Published: October 2019

Abstract
Background Well performing tuberculosis (TB) programs are characterized by treatment success rate (TSR) of at least 90%. In rural eastern Uganda, and elsewhere in sub Saharan Africa, TSR varies considerably across district TB programs and the reasons for the differences are unclear. This study explored factors that explain the low and high TSR across four districts in rural eastern Uganda.Methods We interviewed District TB and Leprosy Supervisors (DTLS), Laboratory focal persons (LFPs) and TB focal persons (TBFPs) from four districts in Eastern Uganda as key informants. Interviews were audio recorded, transcribed verbatim, and imported into ATLAs.ti where thematic content analysis was performed and results were summarized into themes.Results The emerging themes were categorized as either facilitators of or barriers to treatment success. The emerging facilitators prevailing in the districts with high rates of treatment success were using data to make decisions and design interventions, continuous quality improvement, capacity building, and considered TB as a priority disease. The barriers that were common in districts with low rates of treatment success included lack of motivated and dedicated TB focal persons, scarce or no funding for implementing TB activities, and a poor implementation of community-based directly observed therapy short course.Conclusion This study shows several factors account for the differing rates of treatment success in rural eastern Uganda. These factors should be the focus for TB control programs in Uganda and similar settings in order to improve rates of treatment success.
COMMENCE Trial – Comparing hypOtherMic teMperaturEs duriNg hemiarCh surgEry A Randomized Controlled Trial of Mild vs Moderate Hypothermia on Patient Outcomes in Aortic Hemiarch Surgery with Anterograde Cerebral Perfusion
Authors: Jabagi Habib , Wells George , Boodhwani Munir 
Published: October 2019

Abstract
Background: Aortic arch surgery remains the only viable life-saving treatment for aortic arch disease. However, the necessity for cessation of systemic blood flow with hypothermic cardiac arrest carries substantial risk of morbidity and mortality, including poor neurological outcomes and kidney failure. While uncontrolled studies have suggested the safety of operating at warmer temperatures, significant variables remain un-investigated supporting the need for a randomized clinical trial (RCT) to produce evidence-based guidelines for perfusion strategies in aortic surgery. This study proposes a multi-centre RCT, in order to compare outcomes of warmer hypothermic strategies during aortic hemiarch surgery on a composite endpoint of neurologic and acute kidney injury (AKI).
Methods: This is a prospective multi-centre, single-blind two-arm RCT comparing mild (32°C) versus moderate (26°C) hypothermic cardiac arrest in patients (n=282) undergoing hemiarch surgery with antegrade cerebral perfusion (ACP). The primary endpoint is a composite of neurological injury (incidence of transient ischemic attack and/or stroke) and Kidney Disease Improving Global Outcomes (KDIGO) stage 1 or higher AKI. Secondary outcomes include death, cardiopulmonary bypass time, bleeding, transfusion rates, prolonged mechanical ventilation, myocardial infarction, length of stay, and quality of life measures. Patients will undergo 1:1 block randomization to each treatment arm on day of surgery. Sequence of operation will be at the surgeon's discretion with mandatory guidelines for temperature and ACP administration. Perioperative management will occur as per enrolling centre standard of care. Neurocognitive function will be assessed for neurological injury using validated neurological screening tests: NIHSS, MOCA, BI, and MRS throughout patient follow-up. Diagnosis and classification of AKI will be based on rising creatinine values as per the KDIGO criteria. Study duration for each patient will be 60±14 days.
Discussion: It is hoped that performing hemiarch surgery using mild hypothermia (32°C) and selective ACP will result in a 15% absolute risk reduction in the composite outcomes. The potential of this risk reduction will translate into improved patient outcomes, survival, and long-term financial savings to the Health Care system. In addition, the results of this trial will be used to create the first-ever guidelines for temperature management strategy during aortic surgery.
Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity
Authors: Bin Liu , Yin Zhiqiu , Yuan Chao , Du Yuhui , Yang Pan , Qian Chengqian , Wei Yi , Zhang Si , Huang Di 
Published: October 2019

Abstract
Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.
Effect of short-term blood pressure variability on functional outcome after intra-arterial treatment in acute stroke patients with large-vessel occlusion
Authors: Zhang Tianli , Wang Xiaolong , Wen Chao , Zhou Feng , Gao Shengwei , Zhang Xiaodong , Lin Shiqin , Shi Jing , Li Weirong 
Published: October 2019

Abstract
Background : Endovascular treatment (EVT) is advocated for acute ischaemic stroke with large-vessel occlusion (LVO), but perioperative periods are challenging. This study investigated the relationship between post-EVT short-term blood pressure variability (BPV) and early outcomes in LVO patients.
Methods : We retrospectively reviewed 72 LVO patients undergoing EVT between June 2015 and June 2018. Hourly systolic and diastolic blood pressures (SBP and DBP, respectively) were recorded in the first 24 hours post-EVT. BPV were evaluated as standard deviation (SD), coefficient of variation (CV), and successive variation (SV) separately for SBP and DBP. Functional independence at 3 months was defined as a modified Rankin Scale (mRS) score of 0-2.
Results : For 58.3% patients with favorable outcomes, the median National Institutes of Health Stroke Scale and Alberta Stroke Program Early CT scores on admission were 14 and 8, respectively. The maximum SBP ([154.3±16.8] vs. [163.5±15.6], P=0.02), systolic CV ([8. 8%±2.0%] vs. [11.0%±1.8%], P<0.001), SV ([11.4±2.3] vs. [14.6±2.0], P<0.001), and SD ([10.5±2.4] vs. [13.8±3.9], P<0.001) were lower in patients with favorable outcomes. On multivariable logistic regression analysis, systolic SV (OR: 4.273, 95% CI: 1.030 to 17.727, P=0.045) independently predicted unfavorable prognosis. The area under the curve was 0.868 (95% CI: 0.781 to 0.955, P<0.001), and sensitivity and specificity were 93.3% and 73.8%, respectively, showing excellent predictive value for 3-month poor-outcomes.
Conclusions : Decreased systolic SV following intra-arterial therapies result in favorable outcomes at 3 months. Systolic SV may be a novel predictor of functional prognosis in LVO patients.
Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina
Authors: Fachet Melanie , Witte Carina , Flassig Robert J , Rihko-Struckmann Liisa K. , McKie-Krisberg Zaid , Polle Juergen EW , Sundmacher Kai 
Published: October 2019

Abstract
Background The green microalga Dunaliella salina accumulates a high proportion of beta-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, this work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the recently published. Results The reconstruction resulted in a network model with 221 reactions and 212 metabolites within three compartments: cytosol, chloroplast and mitochondrion. The network was implemented in the MATLAB toolbox CellNetAnalyzer and checked for feasibility. Furthermore, a flux balance analysis was carried out for different light and nutrient uptake rates. The comparison of the experimental knowledge with the model prediction revealed that the results of the stoichiometric network analysis are plausible and in good agreement with the observed behavior. Accordingly, our model provides an excellent new tool to interrogate and better understand the carbon core metabolism of D. salina. Conclusions The reconstructed metabolic network of D. salina presented in this work is able to predict the biological behavior under light and nutrient stress and will lead to an improved process understanding for the optimized production of high-value products in microalgae.
Fire needle acupuncture or moxibustion for chronic plaque psoriasis: study protocol for a randomized controlled trial
Authors: Chen Zhaoxia , Zhou Dongmei , Wang Yan , Lan Haibing , Duan Xingwu , Li Bohua , Zhao Jingxia , Li Wei , Liu Zhengrong , Di Tingting , Guo Xinwei , Zhang Jinchao , Li Bo , Feng Shuo , Li Ping 
Published: October 2019

Abstract
Background: Psoriasis is a chronic, immune-mediated disorder with chronic plaque psoriasis during remission stage. Patients often have a slow course and long history of the disease. The refractory type of psoriasis is a stubborn rash that does not subside easily. We designed this randomized controlled trial to compare the effectiveness and relapse rates of plaque psoriasis in patients treated with either acupuncture, moxibustion or calcipotriol ointment. The ultimate aim of the study is to select an effective traditional Chinese medicine (TCM) therapy for patients with plaque psoriasis.
Methods: The study will be a multi-center, prospective randomized controlled trial (RCT), which compares the effectiveness of fire needle therapy, moxibustion and calcipotriol ointment. 160 plaque psoriasis patients who meet the inclusion criteria will be recruited from three hospitals in Beijing, and then randomly assigned to receive either fire needle therapy (group A1), moxibustion (group A2) or calcipotriol ointment (group B). All participants will receive a 8-week treatment and then be followed up for another 24 weeks, with the time point of the 12th and 24th week after treatment complete. The primary outcomes measured are relapse rates and Psoriasis area and severity index (PASI) score of the target lesions. In addition, the target lesion onset time, dermatology life quality index (DLQI), Traditional Chinese Medicine (TCM) syndrome score, and the relapse interval of the target lesion will be measured. Adverse events will be recorded for safety assessment.
Discussion: This study is to determine whether fire needle therapy or moxibustion could improve the clinical effectiveness of psoriasis lesions and reduce the relapse rate. Once completed, it will provide information regarding therapeutic evaluation on fire needle therapy or moxibustion for plaque psoriasis, which will assist clinicians select the most effective treatment options for patients.
Trial registration: ChiCTR1800019588; Pre-results; Registered on 19 November 2018; International Clinical Trials Registry Platform (ICTRP). URL: http://apps.who.int/trialsearch/Trial2.aspx?TrialID=ChiCTR1800019588
Keywords: Fire needle therapy, Moxibustion, Plaque Psoriasis, Clinical effectiveness, Relapse rate
Teachers’ attitude to the use electronic devices in technology lessons, educating pupils with special educational needs
Authors: Vaitkevičienė Asta , Širiakovienė Asta 
Published: October 2019

Abilities of pupils with moderate, severe and profound intellectual disabilities are developed in activities. One of such activities is technology lessons with its essential feature – practical orientation. The most important achievements of SEN pupils in the technology subject is formation of practical daily life skills. As provided in The Recommendations on Adaptation of Basic Education General Curricula for Education of Special Needs Pupils with Low and Very Low Intellectual Abilities (2010), technology education consists of such parts as nutrition, textiles, structural materials and electronics. Properly organized electronics lessons prepare special needs pupils for life, form their practical skills, and help them to get familiar with new technologies. It was relevant to find out the attitudes of teachers of special education institutions to the use of electronic devices in the lessons of technology, because previous research did not deal with learning resources of special education institutions, teachers’ attitude to new technologies, and possibilities of using electronic devices.
PO4 adsorption on the calcite surface modulates calcite formation and crystal size
Authors: Sugiura Yuki , Ishikawa Kunio , Onuma Kazuo , Makita Yoji 
Published: October 2019

AbstractCalcium carbonate (CaCO3) and particularly its stable phase, calcite, is of great geological significance in the deep carbon cycle since CaCO3 from biomineralized shells and corals form sedimentary rocks. Calcite also attracts attention in medical science and pharmacy as a primary or intermediate component in biomaterials because it possesses excellent biocompatibility along with suitable physicochemical properties. Calcite blocks have already been used during surgical procedures as a bone substitute for reconstructing bone defects formed by diseases and injury. When producing CaCO3 biomaterials and bioceramics, in particular, in vivo control of the size and polymorphic nature of CaCO3 is required. In this study, we investigated the effects of PO4 on calcite formation during the phase conversion of calcium sulfate anhydrate (CaSO4, CSA), which is sometimes used as a starting material for bone substitutes because of its suitable setting ability. CSA powder was immersed in 2 mol/L Na2CO3 solution containing a range of PO4 concentrations (0–60 mmol/L) at 40 °C for 3 days. The treated samples were investigated by X-ray diffraction, Fourier-transform infrared spectroscopy, X-ray fluorescence spectroscopy, and thermal analysis. In addition, the fine structures of the treated samples were observed by field-emission scanning electron microscopy, and the specific surface area was measured. We found that PO4, which is universally present in vivo, can modulate the calcite crystal size during calcite formation. A fluorescence study and calcite crystal growth experiments indicated that PO4 adsorbs tightly onto the surface of calcite, inhibiting crystal growth. In the presence of high PO4 concentrations, vaterite is formed along with calcite, and the appearance and stability of the CaCO3 polymorphs can be controlled by adjusting the PO4 concentration. These findings have implications for medical science and pharmacology, along with mineralogy and geochemistry.
Determination of the corresponding roughness height in a WDS model containing old rough pipes
Authors: Annus Ivar , Vassiljev Anatoli , Kändler Nils , Kaur Katrin 
Published: October 2019

Abstract
The aim of the paper was to determine the influence of irregular pipe wall roughness on the flow velocity in a water distribution system (WDS) containing old pipes. Field studies have shown that due to pipe wall build-up, the shape of the inner pipe surface can vary temporally and spatially. This will lead to unrealistic pipe roughness values when calibrating the WDS model using nominal pipe diameters. Therefore, in this study, three types of pipe wall build-up were investigated using EPANET2 and computational fluid dynamics (CFD) to estimate the velocity correction coefficients for EPANET2 calculations. It was shown that in old rough pipes, the mean velocities are higher than expected, indicating that in water quality estimation in a WDS, actual pipe diameters with reasonable roughness need to be defined.
Machine learning models for the estimation of monthly mean daily reference evapotranspiration based on cross-station and synthetic data
Authors: Wu Lifeng , Peng Youwen , Fan Junliang , Wang Yicheng 
Published: October 2019

AbstractThe estimation of reference evapotranspiration (ET0) is important in hydrology research, irrigation scheduling design and water resources management. This study explored the capability of eight machine learning models, i.e., Artificial Neuron Network (ANN), Random Forest (RF), Gradient Boosting Decision Tree (GBDT), Extreme Gradient Boosting (XGBoost), Multivariate Adaptive Regression Spline (MARS), Support Vector Machine (SVM), Extreme Learning Machine and a novel Kernel-based Nonlinear Extension of Arps Decline (KNEA) Model, for modeling monthly mean daily ET0 using only temperature data from local or cross stations. These machine learning models were also compared with the temperature-based Hargreaves–Samani equation. The results indicated that the estimation accuracy of these machine learning models differed in various scenarios. The tree-based models (RF, GBDT and XGBoost) exhibited higher estimation accuracy than the other models in the local application. When the station has only temperature data, the MARS and SVM models were slightly superior to the other models, while the ANN and HS models performed worse than the others. When there was no temperature data at the target station and the data from adjacent stations were used instead, MARS, SVM and KNEA were the suitable models. The results can provide a solution for ET0 estimation in the absence of complete meteorological data.
Underrepresented groups in WaSH – the overlooked role of chemical toxicants in water and health
Authors: Kearns Joshua P. , Bentley Matthew J. , Mokashi Poorva , Redmon Jennifer H. , Levine Keith 
Published: October 2019

AbstractThe anthropogenic release of chemicals from industry, agriculture and the breakdown of consumer wastes constitute a major threat to water resources and public health. Pollution is severe and increasing in the developing world where chemical substances are produced, used, and disposed of in an unregulated manner. The global public health consequences of chemical pollution are comparable to or greater than those of widespread infectious diseases such as HIV/AIDS, tuberculosis, and malaria. However, chemicals have so far been neglected by the WaSH sector. Here, we report the results of a systematic review of the Journal of Water, Sanitation, and Hygiene for Development (2011–2018) and oral/poster presentations given at the UNC Water & Health Conference (2010–2018). The review enumerated studies that focused on water quality and treatment from a chemical perspective, highlighting in particular organic contaminants of emerging concern. Organic chemicals were addressed in only 2% of journal articles and fewer than 0.7% of conference presentations. Geogenic contaminants arsenic and fluoride were only addressed in 2–3% of articles and presentations. The review concludes that a rapid, major effort to address toxic chemicals in WaSH is necessary to meet UN Sustainable Development Goals for universal access to safe and affordable drinking water by 2030.