bluuebunny/crossref_metadata_2025_split huggingface dataset:
BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA
Authors: Hidalgo Juan Saez , Oróstica Karen Y , Sanchez–Daza Anamaria , Olivera–Nappa Álvaro 
Published: September 2020

Abstract

Motivation
BRENDA is the largest enzyme functional database, containing information of 84 000 experimentally characterized enzyme entries. This database is an invaluable resource for researchers in the biological field, which classifies enzyme-related information in categories that are very useful to obtain specific functional and protein engineering information for enzyme families. However, the BRENDA web interface, the most used by researchers with a non-informatic background, does not allow the user to cross-reference data from different categories or sub-categories in the database. Obtaining information in an easy and fast way, in a friendly web interface, without the necessity to have a deep informatics knowledge, will facilitate and improve research in the enzymology and protein engineering field.

Results
We developed the Brenda Easy Search Tool (BEST), an interactive Shiny/R application that enables querying the BRENDA database for complex cross-tabulated characteristics, and retrieving enzyme-related parameters and information readily and efficiently, which can be used for the study of enzyme function or as an input for other bioinformatics tools.

Availability and implementation
BEST and its tutorial are freely available from https://pesb2.cl/best/.

Supplementary information
Supplementary data are available at Bioinformatics online.
On order determination by predictor augmentation
Authors: Luo Wei , Li Bing 
Published: September 2020

Summary
In many dimension reduction problems in statistics and machine learning, such as in principal component analysis, canonical correlation analysis, independent component analysis and sufficient dimension reduction, it is important to determine the dimension of the reduced predictor, which often amounts to estimating the rank of a matrix. This problem is called order determination. In this article, we propose a novel and highly effective order-determination method based on the idea of predictor augmentation. We show that if the predictor is augmented by an artificially generated random vector, then the parts of the eigenvectors of the matrix induced by the augmentation display a pattern that reveals information about the order to be determined. This information, when combined with the information provided by the eigenvalues of the matrix, greatly enhances the accuracy of order determination.
Mapping Progressive Gray Matter Alterations in Early Childhood Autistic Brain
Authors: Guo Xiaonan , Duan Xujun , Suckling John , Wang Jia , Kang Xiaodong , Chen Heng , Biswal Bharat B , Cao Jing , He Changchun , Xiao Jinming , Huang Xinyue , Wang Runshi , Han Shaoqiang , Fan Yun-Shuang , Guo Jing , Zhao Jingping , Wu Lijie , Chen Huafu 
Published: September 2020

Abstract
Autism spectrum disorder is an early-onset neurodevelopmental condition. This study aimed to investigate the progressive structural alterations in the autistic brain during early childhood. Structural magnetic resonance imaging scans were examined in a cross-sectional sample of 67 autistic children and 63 demographically matched typically developing (TD) children, aged 2–7 years. Voxel-based morphometry and a general linear model were used to ascertain the effects of diagnosis, age, and a diagnosis-by-age interaction on the gray matter volume. Causal structural covariance network analysis was performed to map the interregional influences of brain structural alterations with increasing age. The autism group showed spatially distributed increases in gray matter volume when controlling for age-related effects, compared with TD children. A significant diagnosis-by-age interaction effect was observed in the fusiform face area (FFA, Fpeak = 13.57) and cerebellum/vermis (Fpeak = 12.73). Compared with TD children, the gray matter development of the FFA in autism displayed altered influences on that of the social brain network regions (false discovery rate corrected, P &lt; 0.05). Our findings indicate the atypical neurodevelopment of the FFA in the autistic brain during early childhood and highlight altered developmental effects of this region on the social brain network.
National Immunization Campaigns With Oral Polio Vaccine May Reduce All-cause Mortality: An Analysis of 13 Years of Demographic Surveillance Data From an Urban African Area
Authors: Andersen Andreas , Fisker Ane Bærent , Nielsen Sebastian , Rodrigues Amabelia , Benn Christine Stabell , Aaby Peter 
Published: September 2020

Abstract

Background
Between 2002 and 2014, Guinea-Bissau had 17 national campaigns with oral polio vaccine (OPV) as well as campaigns with vitamin A supplementation (VAS), measles vaccine (MV), and H1N1 influenza vaccine. We examined the impact of these campaigns on child survival.

Methods
We examined the mortality rate between 1 day and 3 years of age of all children in the study area. We used Cox models with age as underlying time to calculate adjusted mortality rate ratios (MRRs) between “after-campaign” mortality and “before-campaign” mortality, adjusted for temporal change in mortality and stratified for season at risk.

Results
Mortality was lower after OPV-only campaigns than before, with an MRR for after-campaign vs before-campaign being 0.75 (95% confidence interval [CI], .67–.85). Other campaigns did not have similar effects, the MRR being 1.22 (95% CI, 1.04–1.44) for OPV + VAS campaigns, 1.39 (95% CI, 1.20–1.61) for VAS-only campaigns, 1.32 (95% CI, 1.09–1.60) for MV + VAS campaigns, and 1.13 (95% CI, .86–1.49) for the H1N1 campaign. Thus, all other campaigns differed significantly from the effect of OPV-only campaigns. Effects did not differ for trivalent, bivalent, or monovalent strains of OPV. With each additional campaign of OPV only, the mortality rate declined further (MRR, 0.86 [95% CI, .81–.92] per campaign). With follow-up to 3 years of age, the number needed to treat to save 1 life with the OPV-only campaign was 50 neonates.

Conclusions
OPV campaigns can have a much larger effect on child survival than otherwise assumed. Stopping OPV campaigns in low-income countries as part of the endgame for polio infection may increase child mortality.
RBX7455, a Non-frozen, Orally Administered Investigational Live Biotherapeutic, Is Safe, Effective, and Shifts Patients’ Microbiomes in a Phase 1 Study for Recurrent Clostridioides difficile Infections
Authors: Khanna Sahil , Pardi Darrell S , Jones Courtney , Shannon William D , Gonzalez Carlos , Blount Ken 
Published: September 2020

Abstract

Background
Recurrent Clostridioides difficile infections (rCDI) are a global public health threat. To reduce rCDI, microbiota-restoring therapies are needed, particularly standardized, easy-to-administer formulations.

Methods
This phase I open-label trial assessed the safety, efficacy in preventing rCDI recurrence, and intestinal microbiome effects of RBX7455, a room temperature-stable, orally administered investigational live biotherapeutic. Adult participants with 1 or more prior episodes of rCDI received: 4 RBX7455 capsules twice daily for 4 days (group 1); 4 RBX7455 capsules twice daily for 2 days (group 2); or 2 RBX7455 capsules twice daily for 2 days (group 3). For all groups, the first dose was administered in clinic, with remaining doses self-administered at home. Adverse events were monitored during and for 6 months after treatment. Treatment success was defined as rCDI prevention through 8 weeks after treatment. Participants’ microbiome composition was assessed prior to and for 6 months after treatment.

Results
Nine of 10 group 1 patients (90%), 8 of 10 group 2 patients (80%), and 10 of 10 group 3 patients (100%) were recurrence-free at the 8-week endpoint with durability to 6 months. Seventy-five treatment-emergent adverse events were observed in 27 participants with no serious investigational product-related events. Prior to treatment, participants’ microbiomes were dissimilar from the RBX7455 composition with decreased Bacteroidia- and Clostridia-class bacteria, whereas after treatment, responders’ microbiomes showed increased Bacteroidia and Clostridia.

Conclusions
Three dosing regimens of RBX7455 were safe and effective at preventing rCDI. Responders’ microbiomes converged toward the composition of RBX7455. These results support its continued clinical evaluation.

Clinical Trials Registration
NCT02981316.
Identifying female phenotypes that promote behavioral isolation in a sexually dimorphic species of fishEtheostoma zonale
Authors: Roberts Natalie S , Mendelson Tamra C 
Published: September 2020

AbstractIn sexually dimorphic species characterized by exaggerated male ornamentation, behavioral isolation is often attributed to female preferences for conspecific male signals. Yet, in a number of sexually dimorphic species, male mate choice also results in behavioral isolation. In many of these cases, the female traits that mediate species boundaries are unclear. Females in sexually dimorphic species typically lack many of the elaborate traits that are present in males and that are often used for taxonomic classification of species. In a diverse and largely sexually dimorphic group of fishes called darters (Percidae: Etheostoma), male mate choice contributes to behavioral isolation between a number of species; however, studies addressing which female traits males prefer are lacking. In this study, we identified the dominant female pattern for two sympatric species, Etheostoma zonale and Etheostoma barrenense, using pattern energy analysis, and we used discriminate function analysis to identify which aspects of female patterning can reliably classify species. We then tested the role of female features in male mate choice for E. zonale, by measuring male preference for computer animations displaying the identified (species-specific) conspecific features. We found that the region above the lateral line is important in mediating male mate preferences, with males spending a significantly greater proportion of time with animations exhibiting conspecific female patterning in this region than with animations exhibiting heterospecific female patterning. Our results suggest that the aspects of female phenotypes that are the target of male mate choice are different from the conspicuous male phenotypes that traditionally characterize species.
Exaggerated postprandial GLP-1 secretion following esophagectomy is not associated with gastric emptying and intestinal transit
Authors: Murphy C F , Elliott J A , Docherty N G , Mohamed A A , Vincent R P , Ravi N , Reynolds J V , le Roux C W 
Published: September 2020

SummaryEsophagectomy causes postprandial symptoms associated with an exaggerated postprandial gut hormone response. This study aimed to compare the gastrointestinal transit time of patients 1 year after esophagectomy with unoperated controls, including its relation to satiety gut hormone release. In this cross-sectional study, consecutive, disease-free patients after esophagectomy with pyloroplasty were compared with unoperated control subjects to assess gastric emptying (GE) and cecal arrival time (CAT). Serial plasma samples were collected before, and for 300 minutes after, a mixed-meal challenge. Body composition was assessed, and symptom scores were calculated. Eleven patients 1 year post-esophagectomy (age: 62.6 ± 9.8, male: 82%) did not show a significantly different GE pattern compared with 10 control subjects (P = 0.245). Rather, patients could be categorized bimodally as exhibiting either rapid or slow GE relative to controls. Those with rapid GE trended toward a higher postprandial symptom burden (P = 0.084) without higher postprandial glucagon-like peptide-1 (GLP-1) secretion (P = 0.931). CAT was significantly shorter after esophagectomy (P = 0.043) but was not significantly associated with GE, GLP-1 secretion, or symptom burden. Neither early nutrient delivery to the proximal small intestine nor to the colon explains the exaggerated postprandial GLP-1 response after esophagectomy. GE varies significantly in these patients despite consistent pyloric management.
Anastomotic stricture indexes for endoscopic balloon dilation after esophageal atresia repair: a single-center study
Authors: Huang Jinshi , Liao Junmin , Yang Shen , Zhang Yanan , Zhao Yong , Gu Yichao , Hua Kaiyun , Li Shuangshuang , Xia Leizhen , Cai Siyu 
Published: September 2020

Summary
We investigated changes in anastomotic stricture indexes (SIs) and stricture diameter (SD) between before and 6 months after the first dilatation in children with anastomotic stricture after esophageal atresia (EA) repair and identified predictors of medium-term dilatation success (success for at least 3 months). We retrospectively reviewed the records and measurement indexes of patients who underwent post-EA repair endoscopic balloon dilatation between November 2017 and August 2019 in our hospital. We identified diagnostic and performance indicators that predicted medium-term dilatation success by univariate and multivariate analyses and receiver operator characteristic (ROC) curve analysis. Sixty patients (34 boys and 26 girls) showed post-EA repair anastomotic stricture. Paired sample t-tests showed that SD (P &lt; 0.001), upper pouch SI (U-SI, P &lt; 0.001), lower pouch SI (L-SI, P &lt; 0.001), upper pouch esophageal anastomotic SI (U-EASI, P &lt; 0.001) and lower pouch EASI (L-EASI, P &lt; 0.001) were significantly better at 6 months after than before the first dilatation. Logistic regression analysis showed that dilatation number (P = 0.002) and U-SI at 6 months after the first dilatation (P = 0.019) significantly predicted medium-term dilatation success. ROC curve analysis revealed that combining U-SI (cut-off value = 55.6%) and dilatation number (cut-off value = 10) had good accuracy in predicting medium-term dilatation success 6 months after the first dilatation (area under the curve-ROC: 0.95). In conclusion, endoscopic balloon dilatation significantly improved SD and SIs in children with post-EA repair anastomotic stricture. Dilatation number and U-SI at 6 months after the first dilatation were useful in predicting medium-term dilatation success and could represent a supplementary method to improve judgment regarding whether further dilatation is needed 6 months after the first dilatation.
Revealing the Diet of Generalist Insect Predators in Strawberry Fields: Not Only Pests, But Other Predators Beware
Authors: Krey K L , Cooper W R , Renkema J M 
Published: September 2020

AbstractGeneralist invertebrate predators contribute to pest management in agriculture, providing an important ecosystem service, particularly in organically managed fields. DNA-based methods to study food webs and feeding interactions in unrestricted field conditions have transformed dietary analysis of generalist predators. In this study, we used MiSeq next-generation sequencing (NGS) technology and universal arthropod primers to investigate the diet of several generalist insect predators collected in commercial organic Florida strawberry fields from November 2017 to March 2018. Of 12 predator insect taxa, Geocoris spp. (Say) (Hemiptera: Geocoridae) was the most abundant early in the growing season (November) and was collected consistently until the end of the season (early March). DNA sequences from 105 predator samples were matched to 44 arthropod families, and of these, 17 were categorized as pest families, 10 as nonpest or nonpredator families, and 17 as predator families. Drosophilidae was the most detected pest family, and Dolichopodidae was the most detected predator family. Prey diversity differed among the predators. Chrysoperla spp. (Neuroptera: Chrysopidae) consumed more prey earlier in the season than did other predators, whereas the other predators consumed a greater diversity of other predators regardless of month. Our results showed a high amount of intraguild predation, but also that predators are contributing to pest suppression in organic strawberries and providing an important biological control service in Florida organic strawberries.
Surgical repair of tetralogy of Fallot using autologous right atrial appendages: short- to mid-term results
Authors: Amirghofran Ahmadali , Edraki Fatemeh , Edraki Mohammadreza , Ajami Gholamhossein , Amoozgar Hamid , Mohammadi Hamid , Emaminia Abbas , Ghasemzadeh Bahram , Borzuee Mohammad , Peiravian Farah , Kheirandish Zahra , Mehdizadegan Nima , Sabri Mohammadreza , Cheriki Sirus , Arabi Hamid 
Published: September 2020

Abstract

OBJECTIVES
The prevention of pulmonary insufficiency (PI) is a crucial part of the tetralogy of Fallot repair. Many techniques have been introduced to construct valves from different materials for the right ventricular outflow tract, including the most commonly constructed monocusp valves. We are introducing a new bicuspid valve made intraoperatively using the autologous right atrial appendage (RAA) to prevent PI in these patients.

METHODS
The RAA valve was constructed and used in 21 patients with tetralogy of Fallot. The effective preservation of the native valve was impossible in all patients because of either a severe valve deformity or a small annulus. The RAA valve was created after ventricular septal defect closure and right ventricular outflow tract myectomy and was covered with a bovine transannular pericardial patch. The perioperative data were evaluated, and the echocardiography results were assessed immediately after operations and in follow-up with a median of 10.5 months. The data were retrospectively compared with 10 other patients with similar demographic data but with only transannular patches.

RESULTS
The mean age of the patients was 13.3 months. No mortality or related morbidity occurred after repair using the RAA valve. The PI severity early after the operation was trivial or no PI in 18 patients, and mild PI was observed in 3 patients, which progressed to moderate PI in one of them in the mean 12-month follow-up period. Fifteen patients had mild or no pulmonary stenosis, while moderate pulmonary stenosis was observed in 6 others. Compared with the other 10 patients with only transannular patches, the RAA valve patients had prolonged operative and clamping times, but no difference in postoperative course and shorter hospital stays. The degree of PI was, of course, significantly less in the RAA valve patients, but pulmonary stenosis was the same.

CONCLUSIONS
The RAA valve construction is a safe and effective technique to prevent PI after the tetralogy of Fallot repair, at least in terms of short- and mid-term results. A longer follow-up period is needed to confirm if this new valve can eliminate or significantly delay the need for pulmonary valve replacement in these patients.
Fungi and viruses as important players in microbial mats
Authors: Carreira Cátia , Lønborg Christian , Kühl Michael , Lillebø Ana I , Sandaa Ruth-Anne , Villanueva Laura , Cruz Sónia 
Published: September 2020

ABSTRACTMicrobial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.
Influence of hydrothermal alteration on the elastic behaviour and failure of heat-treated andesite from Guadeloupe
Authors: Nicolas A , Lévy L , Sissmann O , Li Z , Fortin J , Gibert B , Sigmundsson F 
Published: September 2020

SUMMARYStudies on the mechanical behaviour of rocks, including volcanic rocks, usually seek for unaltered and simple material: rocks without macroscopic defects. However, volcanic rocks are often naturally altered due to the circulation of hydrothermal fluids. This alteration may influence mechanical and physical properties. Here, we study the effect of hydrothermal alteration on the elasticity and failure properties of andesite. A homogeneous block of natural andesite was retrieved from a quarry. Three samples were first heat-treated and then artificially altered at different temperatures by soaking them in a brine for one month at a pressure of 20 MPa and temperatures of 80, 180 and 280 °C. Heat-treated unaltered and altered samples were hydrostatically loaded up to 50 MPa and unloaded, while strains and elastic wave velocities were recorded. Samples were also triaxially deformed to failure at a constant strain rate and a confining pressure of 15 MPa. At ambient pressure, increased alteration temperature resulted in increased wave propagation velocity, thus increased dynamic elastic moduli. During hydrostatic loading, volumetric deformation at a given effective pressure decreased with alteration temperature denoting increased static elastic moduli. During triaxial loading, the degree of alteration decreased elastic compaction and peak stress at failure. These observations are interpreted as the result of microcracks in-filling by alteration minerals, and in particular smectite, a swelling-clay mineral with a low friction coefficient. The mechanical behaviour of a volcanic rock subjected to triaxial loading was modelled with a damage model based on crack propagation from pre-existing flaws. A decreasing friction coefficient within the flanks of the cracks leads to a decrease of the peak stress and explains the experimental observations.
The Rotavirus Vaccine Story: From Discovery to the Eventual Control of Rotavirus Disease
Authors: Glass Roger I , Tate Jacqueline E , Jiang Baoming , Parashar Umesh 
Published: September 2020

Abstract
Worldwide, rotavirus is the leading pathogen causing severe diarrhea in children and a major cause of under 5 years mortality. In 1998, the first rotavirus vaccine, RotaShield, was licensed in the United States but a rare adverse event, intussusception, led to its withdrawal. Seven years passed before the next generation of vaccines became available, Rotarix (GSK) and Rotateq (Merck), and 11 years later, 2 additional vaccines from India, Rotavac (Bharat) and Rotasiil (Serum Institute), were recommended by World Health Organization for all children. Today, these vaccines are used in more than 100 countries and have contributed to marked decreases in hospitalizations and deaths from diarrhea. However, these live oral vaccines are less effective in low-income countries with high under 5 years mortality for reasons that are not understood. Efforts to develop new vaccines that avoid the oral route are in progress and will likely be needed to ultimately control rotavirus disease.