bluuebunny/crossref_metadata_2025_split huggingface dataset:
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates
Authors: D’Mello Adonis , Ahearn Christian P. , Murphy Timothy F. , Tettelin Hervé 
Published: December 2019

Abstract
Background
Reverse vaccinology accelerates the discovery of potential vaccine candidates (PVCs) prior to experimental validation. Current programs typically use one bacterial proteome to identify PVCs through a filtering architecture using feature prediction programs or a machine learning approach. Filtering approaches may eliminate potential antigens based on limitations in the accuracy of prediction tools used. Machine learning approaches are heavily dependent on the selection of training datasets with experimentally validated antigens (positive control) and non-protective-antigens (negative control). The use of one or few bacterial proteomes does not assess PVC conservation among strains, an important feature of vaccine antigens.

Results
We present ReVac, which implements both a panoply of feature prediction programs without filtering out proteins, and scoring of candidates based on predictions made on curated positive and negative control PVCs datasets. ReVac surveys several genomes assessing protein conservation, as well as DNA and protein repeats, which may result in variable expression of PVCs. ReVac’s orthologous clustering of conserved genes, identifies core and dispensable genome components. This is useful for determining the degree of conservation of PVCs among the population of isolates for a given pathogen. Potential vaccine candidates are then prioritized based on conservation and overall feature-based scoring. We present the application of ReVac, applied to 69 Moraxella catarrhalis and 270 non-typeable Haemophilus influenzae genomes, prioritizing 64 and 29 proteins as PVCs, respectively.

Conclusion
ReVac’s use of a scoring scheme ranks PVCs for subsequent experimental testing. It employs a redundancy-based approach in its predictions of features using several prediction tools. The protein’s features are collated, and each protein is ranked based on the scoring scheme. Multi-genome analyses performed in ReVac allow for a comprehensive overview of PVCs from a pan-genome perspective, as an essential pre-requisite for any bacterial subunit vaccine design. ReVac prioritized PVCs of two human respiratory pathogens, identifying both novel and previously validated PVCs.
Ectopic expression of Medicago truncatula homeodomain finger protein, MtPHD6, enhances drought tolerance in Arabidopsis
Authors: Quan Wenli , Liu Xun , Wang Lihua , Yin Mingzhu , Yang Li , Chan Zhulong 
Published: December 2019

Abstract
Background
The plant homeodomain (PHD) finger is a Cys4HisCys3-type zinc finger which promotes protein-protein interactions and binds to the cis-acting elements in the promoter regions of target genes. In Medicago truncatula, five PHD homologues with full-length sequence were identified. However, the detailed function of PHD genes was not fully addressed.

Results
In this study, we characterized the function of MtPHD6 during plant responses to drought stress. MtPHD6 was highly induced by drought stress. Ectopic expression of MtPHD6 in Arabidopsis enhanced tolerance to osmotic and drought stresses. MtPHD6 transgenic plants exhibited decreased water loss rate, MDA and ROS contents, and increased leaf water content and antioxidant enzyme activities under drought condition. Global transcriptomic analysis revealed that MtPHD6 reprogramed transcriptional networks in transgenic plants. Expression levels of ABA receptor PYR/PYLs, ZINC FINGER, AP2/EREBP and WRKY transcription factors were mainly up-regulated after transformation of MtPHD6. Interaction network analysis showed that ZINC FINGER, AP2/EREBP and WRKY interacted with each other and downstream stress induced proteins.

Conclusions
We proposed that ZINC FINGER, AP2/EREBP and WRKY transcription factors were activated through ABA dependent and independent pathways to increase drought tolerance of MtPHD6 transgenic plants.
The efficacy of lyticase and β-glucosidase enzymes on biofilm degradation of Pseudomonas aeruginosa strains with different gene profiles
Authors: Banar Maryam , Emaneini Mohammad , Beigverdi Reza , Fanaei Pirlar Rima , Node Farahani Narges , van Leeuwen Willem B. , Jabalameli Fereshteh 
Published: December 2019

Abstract
Background
Pseudomonas aeruginosa is a nosocomial pathogen that causes severe infections in immunocompromised patients. Biofilm plays a significant role in the resistance of this bacterium and complicates the treatment of its infections. In this study, the effect of lyticase and β-glucosidase enzymes on the degradation of biofilms of P. aeruginosa strains isolated from cystic fibrosis and burn wound infections were assessed. Moreover, the decrease of ceftazidime minimum biofilm eliminating concentrations (MBEC) after enzymatic treatment was evaluated.

Results
This study demonstrated the effectiveness of both enzymes in degrading the biofilms of P. aeruginosa. In contrast to the lyticase enzyme, β-glucosidase reduced the ceftazidime MBECs significantly (P < 0.05). Both enzymes had no cytotoxic effect on the A-549 human lung carcinoma epithelial cell lines and A-431 human epidermoid carcinoma cell lines.

Conclusion
Considering the characteristics of the β-glucosidase enzyme, which includes the notable degradation of P. aeruginosa biofilms and a significant decrease in the ceftazidime MBECs and non-toxicity for eukaryotic cells, this enzyme can be a promising therapeutic candidate for degradation of biofilms in burn wound patients, but further studies are needed.
Comparative study on the effects of different feeding habits and diets on intestinal microbiota in Acipenser baeri Brandt and Huso huso
Authors: Xu Guanling , Xing Wei , Li Tieliang , Xue Min , Ma Zhihong , Jiang Na , Luo Lin 
Published: December 2019

Abstract
Background
Siberian sturgeon (Acipenser baeri Brandt) and Beluga sturgeon (Huso huso) are two important commercial fish in China, and the feeding habits of them are very different. Diets and feeding habits are two significant factors to affect the gastrointestinal microbiota in fish. The intestinal microbiota has been reported to play a key role in nutrition and immunity. However, it is rarely reported about the relationship between the intestinal microbiota and feeding habits/diets on different Acipenseridae fish. This study is to comparative analysis of gut microbial community in Siberian sturgeon and Beluga sturgeon fed with the same diet/Beluga sturgeon fed with different diets in order to determine the effects of different feeding habits/diets on the fish intestinal microbiota.

Results
According to the experimental objectives, BL and BH groups were Beluga sturgeon (Huso huso) fed with low fishmeal diet and high fishmeal diet, respectively. SH group represented Siberian sturgeon (Acipenser baeri Brandt) fed with the same diet as BH group. After 16 weeks feeding trial, the intestinal microbiota was examined by 16S rRNA high-throughput sequencing technology. On the phylum level, Proteobacteria and Bacteroidetes were significantly higher in BL group than BH group, and Cyanobacteria showed the opposite trend. Compared with BH group, Proteobacteria and Firmicutes were significantly increased in SH group, whereas Cyanobacteria were clearly decreased. At the genus level, Pseudomonas and Citrobacter in BL group were significantly higher comparing with BH group, while Bacillus, Luteibacter, Staphylococcus and Oceanobacillus was lower in BH group than SH group.

Conclusions
Alpha and beta diversities indicated that the intestinal microflora were significant difference between Siberian sturgeon and Beluga sturgeon when they fed with the same diet. Meanwhile, Beluga sturgeon fed with low fishmeal diet can increase the species diversity of intestinal microbiota than it fed high fishmeal diet. Therefore, feeding habits clearly affected the gastrointestinal microbiota of sturgeons. Moreover, the impact of changes in food on the gut microbiota of sturgeons should be taken into consideration during the process of sturgeon aquaculture.
Comparison of sciatic nerve block quality achieved using the anterior and posterior approaches: a randomised trial
Authors: Yektaş Abdulkadir , Balkan Bedih 
Published: December 2019

AbstractBackgroundThe co-administration of sciatic and femoral nerve blocks can provide anaesthesia and analgesia in patients undergoing lower extremity surgeries. Several approaches to achieve sciatic nerve block have been described, including anterior and posterior approaches.MethodsIn total, 58 study patients were randomly assigned to receive either anterior (group A, n = 29) or posterior (group P,n = 29) sciatic nerve block. Thereafter, the following parameters were determined: sensory and motor block start and end times, time to first fentanyl requirement after blockade but before the start of the operation, time to first fentanyl requirement after the start of the operation, mean fentanyl dose administered after blockade but before the start of the operation, mean fentanyl dose after the start of the operation, time to first diclofenac sodium dose, and total dose of diclofenac sodium required. The trial was retrospectively registered on 11 July 2018.ResultsThe time to initiation of sensory block was significantly shorter in group P than in group A (7.70 ± 2.05 min and 12.88 ± 4.87 min, respectively;p = 0.01). Group P also had a significantly shorter time to first fentanyl requirement after block but before the start of the operation (00.00 ± 00.00 min for group P and 4.05 ± 7.47 min for group A;p < 0.01), significantly higher mean fentanyl dose per patient after block but before the start of the operation (44.03 ± 23.78 μg for group P and 31.20 ± 27.79 μg for group A), significantly longer time to first fentanyl requirement after the start of the operation (16.24 ± 7.13 min for group P and 00.00 ± 00.00 min for group A;p = 0.01), and significantly lower mean fentanyl dose per patient after the start of the operation (11.51 ± 2.87 μg for group P and 147.75 ± 22.30 μg for group A). Patient satisfaction (p < 0.01), anaesthesia quality (p = 0.006), and surgical quality (p = 0.047) were significantly higher in group P.ConclusionsAnterior and posterior approaches can be used to achieve sciatic nerve block in patients undergoing surgery for malleolar fractures. However, better anaesthesia and pain control results can be obtained if analgesia is administered preoperatively in patients with a posterior approach block and after the start of the operation in patients with an anterior approach block.
The association between carotid intima-media thickness and new-onset hypertension in a Chinese community-based population
Authors: Zhang Long , Fan Fangfang , Qi Litong , Jia Jia , Yang Ying , Li Jianping , Zhang Yan 
Published: December 2019

Abstract
Background
Hypertension and arterial vasculopathy may be mutual causes and effects. It is unknown whether carotid intima-media thickness (cIMT) is reliably predictive of the presence of newly developed hypertension in the Chinese population. This study evaluated the impacts of cIMT on new-onset hypertension in a community-based population without hypertension at baseline in China.

Methods
A total of 672 Chinese subjects who had complete data for demographics, baseline and follow-up blood pressure measurements, and cIMT measurements at baseline were included in our study. Baseline cIMT was obtained under standardized procedures using the GE Vivid 7 ultrasound system equipped with an 8-MHz linear array vascular probe (GE Medical Systems, Milwaukee, Wl, USA). The outcome was the incidence of hypertension at follow-up. Multivariate regression models were used to access the association between baseline cIMT and the risk of new-onset hypertension.

Results
Subjects were 51.5 ± 4.7 years old, and 32.0% were male. The mean baseline systolic blood pressure (SBP) was 122.5 ± 10.0 mmHg. The mean baseline diastolic blood pressure (DBP) was 72.4 ± 7.5 mmHg. The number of subjects with thickened cIMT (maximum ≥0.9 mm) at baseline was 198 (29.5%). After 2.3 years of follow-up, the rate of new-onset hypertension was 12.6%. The incidence rates of hypertension in the groups with thickened cIMT and normal cIMT were 19.2 and 9.9%, respectively. In the multivariable logistic regression analyses, both the average (OR = 1.69, 95% CI: 1.30–2.19, P = 0.0001) and maximum (OR = 1.55, 95% CI: 1.23–1.95, P = 0.0002) cIMT were significantly associated with new-onset hypertension after adjustment for various confounders. The group with thickened cIMT showed a higher risk for the incidence of hypertension, with an OR of 1.82 (95% CI: 1.07–3.10, P = 0.0270), compared to the normal group.

Conclusion
Thickened cIMT has a strong association with incident hypertension risk in a community-based population without hypertension at baseline in China.
Simulation and minimization: technical advances for factorial experiments designed to optimize clinical interventions
Authors: Kuhn Jocelyn , Sheldrick Radley Christopher , Broder-Fingert Sarabeth , Chu Andrea , Fortuna Lisa , Jordan Megan , Rubin Dana , Feinberg Emily 
Published: December 2019

Abstract
Background
The Multiphase Optimization Strategy (MOST) is designed to maximize the impact of clinical healthcare interventions, which are typically multicomponent and increasingly complex. MOST often relies on factorial experiments to identify which components of an intervention are most effective, efficient, and scalable. When assigning participants to conditions in factorial experiments, researchers must be careful to select the assignment procedure that will result in balanced sample sizes and equivalence of covariates across conditions while maintaining unpredictability.

Methods
In the context of a MOST optimization trial with a 2x2x2x2 factorial design, we used computer simulation to empirically test five subject allocation procedures: simple randomization, stratified randomization with permuted blocks, maximum tolerated imbalance (MTI), minimal sufficient balance (MSB), and minimization. We compared these methods across the 16 study cells with respect to sample size balance, equivalence on key covariates, and unpredictability. Leveraging an existing dataset to compare these procedures, we conducted 250 computerized simulations using bootstrap samples of 304 participants.

Results
Simple randomization, the most unpredictable procedure, generated poor sample balance and equivalence of covariates across the 16 study cells. Stratified randomization with permuted blocks performed well on stratified variables but resulted in poor equivalence on other covariates and poor balance. MTI, MSB, and minimization had higher complexity and cost. MTI resulted in balance close to pre-specified thresholds and a higher degree of unpredictability, but poor equivalence of covariates. MSB had 19.7% deterministic allocations, poor sample balance and improved equivalence on only a few covariates. Minimization was most successful in achieving balanced sample sizes and equivalence across a large number of covariates, but resulted in 34% deterministic allocations. Small differences in proportion of correct guesses were found across the procedures.

Conclusions
Based on the computer simulation results and priorities within the study context, minimization with a random element was selected for the planned research study. Minimization with a random element, as well as computer simulation to make an informed randomization procedure choice, are utilized infrequently in randomized experiments but represent important technical advances that researchers implementing multi-arm and factorial studies should consider.
Clinic and patient variation in intermediate clinical outcomes for type 2 diabetes: a multilevel analysis
Authors: Lim Yvonne Mei Fong , Ang Swee Hung , Nasir Nazrila Hairizan , Ismail Fatanah , Ismail Siti Aminah , Sivasampu Sheamini 
Published: December 2019

Abstract
Background
Variation at different levels of diabetes care has not yet been quantified for low- and middle-income countries. Understanding this variation and its magnitude is important to guide policy makers in designing effective interventions. This study aims to quantify the variation in the control of glycated haemoglobin (HbA1c), systolic blood pressure (SBP) and low-density lipoprotein cholesterol (LDL-C) for type 2 diabetes (T2D) patients at the clinic and patient level and determine patient and clinic factors associated with control of these outcomes in T2D.

Methods
This is a cross-sectional study within the baseline data from the impact evaluation of the Enhanced Primary Health Care (EnPHC) intervention on 40 public clinics in Malaysia. Patients aged 30 and above, diagnosed with T2D, had a clinic visit for T2D between 01 Nov 2016 and 30 April 2017 and had at least one HbA1c, SBP and LDL-C measurement within 1 year from the date of visit were included for analysis. Multilevel linear regression adjusting for patient and clinic characteristics was used to quantify variation at the clinic and patient levels for each outcome.

Results
Variation in intermediate clinical outcomes in T2D lies predominantly (93% and above) at the patient level. The strongest predictors for poor disease control in T2D were the proxy measures for disease severity including duration of diabetes, presence of microvascular complications, being on insulin therapy and number of antihypertensives. Among the three outcomes, HbA1c and LDL-C results provide greatest opportunity for improvement.

Conclusion
Clinic variation in HbA1c, SBP and LDL-C accounts for a small percentage from total variation. Findings from this study suggest that standardised interventions need to be applied across all clinics, with a focus on customizing therapy based on individual patient characteristics.
Adverse events associated with colonoscopy; an examination of online concerns
Authors: Yom-Tov Elad , Lebwohl Benjamin 
Published: December 2019

Abstract
Background
Colonoscopy as a screening and diagnostic tool is generally safe and well-tolerated, and significant complications are rare. The rate of more mild adverse effects is difficult to estimate, particularly when such effects do not result in hospital admission. We aimed to identify the rate and timing of adverse effects as reported by users querying symptoms on an internet search engine.

Methods
We identified queries made to Bing originating from users in the United States containing the word “colonoscopy” during a 12-month period and identified those queries in which the timing of colonoscopy could be estimated. We then identified queries from those same users for medical symptoms during the time span from 5 days before through 30 days after the colonoscopy date.

Results
Of 641,223 users mentioning colonoscopy, 7013 (1.1%) had a query that enabled identification of their colonoscopy date. The majority of queries about colonoscopy preceded the procedure, and concerned diet. 28% of colonoscopy-related queries were made afterwards, and included queries about diarrhea and cramps, with 2.6% of users querying respiratory symptoms after the procedure, including cough (1.2%) and pneumonia (0.6%). Respiratory symptoms rose significantly at days 7–10 after the colonoscopy.

Conclusions
Internet search queries for respiratory symptoms rose approximately one week after queries relating to colonoscopy, raising the possibility that such symptoms are an under-reported late adverse effect of the procedure. Given the widespread use of colonoscopy as a screening modality and the rise of anesthesia-assisted colonoscopy in the United States in recent years, this signal is of potential public health concern.
Appraisal of the faecal haemoglobin, age and sex test (FAST) score in assessment of patients with lower bowel symptoms: an observational study
Authors: Digby Jayne , Strachan Judith A. , Mowat Craig , Steele Robert J. C. , Fraser Callum G. 
Published: December 2019

Abstract
Background
Many patients present in primary care with lower bowel symptoms, but significant bowel disease (SBD), comprising colorectal cancer (CRC), advanced adenoma (AA), or inflammatory bowel disease (IBD), is uncommon. Quantitative faecal immunochemical tests for haemoglobin (FIT), which examine faecal haemoglobin concentrations (f-Hb), assist in deciding who would benefit from colonoscopy. Incorporation of additional variables in an individual risk-score might improve this approach. We investigated if the published f-Hb, age and sex test score (FAST score) added value.

Methods
Data from the first year of routine use of FIT in primary care in one NHS Board in Scotland were examined: f-Hb was estimated using one HM-JACKarc FIT system (Kyowa Medex Co., Ltd., Tokyo, Japan) with a cut-off for positivity ≥10 μg Hb/g faeces. 5660 specimens were received for analysis in the first year. 4072 patients were referred to secondary care: 2881 (70.6%) of these had returned a FIT specimen. Of those referred, 1447 had colonoscopy data as well as the f-Hb result (group A): 2521 patients, also with f-Hb, were not immediately referred (group B). The FAST score was assessed in both groups.

Results
1196 (41.7%) of patients who returned a specimen for FIT analysis had f-Hb ≥10 μg Hb/g faeces. In group A, 252 of 296 (85.1%) with SBD had f-Hb > 10 μg Hb/g faeces, as did 528 of 1151 (45.8%) without SBD. Using a FAST score > 2.12, which gives high clinical sensitivity for CRC, only 1143 would have been referred for colonoscopy (21.0% reduction in demand): 286 of 296 (96.6%) with SBD had a positive FAST score, as did 857 of 1151 (74.5%) without SBD. However, one CRC, five AA and four IBD would have been missed. In group B, although 95.2% had f-Hb < 10 μg Hb/g faeces, 1371 (53.7%) had FAST score ≥ 2.12: clinical rationale led to only 122 of group B completing subsequent bowel investigations: a FAST score > 2.12 was found in 13 of 15 (86.7%) with SBD.

Conclusions
The performance characteristics of the FAST score did not seem to enhance the utility of f-Hb alone. Locally-derived formulae might confer desired benefits.