bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibacterial activity of biogenic silver and gold nanoparticles synthesized from Salvia africana-lutea and Sutherlandia frutescens
Authors: Dube Phumuzile , Meyer Samantha , Madiehe Abram , Meyer Mervin 
Published: October 2020

Abstract
Nanoparticles (NPs) synthesized using various chemical and physical methods are often cytotoxic which restricts their use in biomedical applications. In contrast, metallic biogenic NPs synthesized using biological systems such as plant extracts are said to be safer and their production more cost effective. NPs synthesized from plants with known medicinal properties can potentially have similar bioactivities as these plants. It has been shown that Salvia africana-lutea (SAL) and Sutherlandia frutescens (SF) have antibacterial activities. This study used water extracts of SAL and SF to produce biogenic silver NPs (AgNPs) and gold NPs (AuNPs). The antibacterial activity of AgNPs and AuNPs was tested against two pathogens (Staphylococcus epidermidis and P. aeruginosa). NP synthesis was optimized by varying the synthesis conditions which include synthesis time and temperature, plant extract concentration, silver nitrate (AgNO3) concentration and sodium tetrachloroaurate (III) dihydrate (NaAuCl4 · 2H2O) concentration. The NPs were characterized using Ultraviolet-visible (UV–vis) spectroscopy, dynamic light scattering, high-resolution transmission electron microscopy (HR-TEM), and Fourier transform infrared (FT-IR) spectroscopy. SAL was able to synthesize both Ag (SAL AgNP) and Au (SAL AuNP) nanoparticles, whilst SF synthesized Ag (SF AgNP) nanoparticles only. The absorbance spectra revealed the characteristic surface plasmon resonance peak between 400–500 nm and 500–600 nm for AgNP and AuNP, respectively. HR-TEM displayed the presence of spherical and polygon shaped nanoparticles with varying sizes whilst the Energy Dispersive x-ray spectra and selected area diffraction pattern confirmed the successful synthesis of the AgNPs and AuNPs by displaying the characteristic crystalline nature, optical adsorption peaks and lattice fringes. FT-IR spectroscopy was employed to identify the functional groups involved in the NP synthesis. The microtitre plate method was employed to determine the minimum inhibitory concentration (MIC) of the NPs and the extracts. The water extracts and SAL AuNP did not have significant antibacterial activity, while SAL AgNP and SF AgNP displayed high antibacterial activity. In conclusion, the data generated suggests that SAL and SF could be used for the efficient synthesis of antibacterial biogenic nanoparticles.
In silico design, building and gas adsorption of nano-porous graphene scaffolds
Authors: Bellucci Luca , Delfino Francesco , Tozzini Valentina 
Published: October 2020

Abstract
Graphene-based nano-porous materials (GNM) are potentially useful for all those applications needing a large specific surface area (SSA), typical of the bidimensional graphene, yet realized in the bulk dimensionality. Such applications include for instance gas storage and sorting, catalysis and electrochemical energy storage. While a reasonable control of the structure is achieved in micro-porous materials by using nano-micro particles as templates, the controlled production or even characterization of GNMs with porosity strictly at the nano-scale still raises issues. These are usually produced using dispersion of nano-flakes as precursors resulting in little control on the final structure, which in turn reflects in problems in the structural model building for computer simulations. In this work, we describe a strategy to build models for these materials with predetermined structural properties (SSA, density, porosity), which exploits molecular dynamics simulations, Monte Carlo methods and machine learning algorithms. Our strategy is inspired by the real synthesis process: starting from randomly distributed flakes, we include defects, perforation, structure deformation and edge saturation on the fly, and, after structural refinement, we obtain realistic models, with given structural features. We find relationships between the structural characteristics and size distributions of the starting flake suspension and the final structure, which can give indications for more efficient synthesis routes. We subsequently give a full characterization of the models versus H2 adsorption, from which we extract quantitative relationship between the structural parameters and the gravimetric density. Our results quantitatively clarify the role of surfaces and edges relative amount in determining the H2 adsorption, and suggest strategies to overcome the inherent physical limitations of these materials as adsorbers. We implemented the model building and analysis procedures in software tools, freely available upon request.
Magnetite nanoparticle anchored graphene cathode enhances microbial electrosynthesis of polyhydroxybutyrate by Rhodopseudomonas palustris TIE-1
Authors: Rengasamy Karthikeyan , Ranaivoarisoa Tahina , Bai Wei , Bose Arpita 
Published: October 2020

Abstract
Microbial electrosynthesis (MES) is an emerging technology that can convert carbon dioxide (CO2) into value-added organic carbon compounds using electrons supplied from a cathode. However, MES is affected by low product formation due to limited extracellular electron uptake by microbes. Herein, a novel cathode was developed from chemically synthesized magnetite nanoparticles and reduced graphene oxide nanocomposite (rGO-MNPs). This nanocomposite was electrochemically deposited on carbon felt (CF/rGO-MNPs), and the modified material was used as a cathode for MES production. The bioplastic, polyhydroxybutyrate (PHB) produced by Rhodopseudomonas palustris TIE-1 (TIE-1), was measured from reactors with modified and unmodified cathodes. Results demonstrate that the magnetite nanoparticle anchored graphene cathode (CF/rGO-MNPs) exhibited higher PHB production (91.31 ± 0.9 mg l−1). This is ∼4.2 times higher than unmodified carbon felt (CF), and 20 times higher than previously reported using graphite. This modified cathode enhanced electron uptake to −11.7 ± 0.1 μA cm−2, ∼5 times higher than CF cathode (−2.3 ± 0.08 μA cm−2). The faradaic efficiency of the modified cathode was ∼2 times higher than the unmodified cathode. Electrochemical analysis and scanning electron microscopy suggest that rGO-MNPs facilitated electron uptake and improved PHB production by TIE-1. Overall, the nanocomposite (rGO-MNPs) cathode modification enhances MES efficiency.
Ion temperature measurements in a tokamak using active neutral particle analyzers diagnostics
Authors: Bakharev N N , Chernyshev F V , Gusev V K , Kiselev E O , Kurskiev G S , Larionova M M , Melnik A D , Minaev V B , Mironov M I , Miroshnikov I V , Petrov Yu V , Sakharov N V , Shchegolev P B , Skrekel O M , Telnova A Yu , Tukhmeneva E A , Varfolomeev V I 
Published: October 2020

Abstract
Active ion temperature measurement in the core plasma of a tokamak using active neutral particle analyzers (NPA) diagnostics is considered. Two approaches for local ion temperature reconstruction are reviewed: semi-analytical and iterative. A semi-analytical approach allows the calculation of ion temperature using simple expression, while a more complex iterative approach provides more flexibility. Problems associated with active NPA measurements and their possible solutions are discussed. An example of the core ion temperature profile reconstruction in the compact spherical tokamak Globus-M2 using both approaches is shown. Problems associated with active ion temperature measurements in a compact reactor and possible solutions are considered.
A gravity model and network analysis of household food sharing in Zambia
Authors: von Gnechten Rachel , Wang Junren , Konar Megan , Baylis Kathy , Anderson Patrese , Giroux Stacey , Jackson Nicole D , Evans Thomas 
Published: October 2020

Abstract
Food sharing is an important part of smallholder food systems and can help households to buffer food security shocks. Household food sharing is the smallest scale food exchange system, yet we do not understand how it compares with food exchange networks at other spatial scales. To this end, we collect information on bilateral household food sharing in two villages in Zambia with approximately 50 households each. We observed seasonal fluctuations for the density of the food sharing. To our knowledge, we are the first to show that the gravity model of trade is applicable to household food sharing. Additionally, sharing networks exhibit the same statistical properties as food exchanges in other locations and at different spatial scales. Specifically, maize exchanges (in mass) follow the Gamma distribution and the relationship between household mass flux and connectivity follows a power law distribution. This work sheds light on household food sharing in rainfed agricultural systems and suggests common underlying mechanisms of food exchange systems across spatial scales and geographies.
Comparative study on cutting performance of plain and coated carbide inserts in CNC turning of EN9 steel
Authors: Chauhan Sachin , Kumar Rajeev 
Published: October 2020

Abstract
The present work deals with comparative study on cutting performance of plain carbide and coated carbide inserts in turning of EN9 steel. The design of experiments (DOE) was done using response surface methodology (RSM) technique. The cutting parameters were spindle speed, feed and depth of cut (DOC). The combined interactions of cutting parameters on surface roughness, flank wear and crater wear were analyzed. The crater and flank wear were observed using machine vision system. This work is concentrated on building up a mathematical relation between cutting parameters and output responses. Analysis of variance (ANOVA) was used for checking the adequacy of the model. The relation between input factors and the response parameters are determined using a cubic regression model. The optimization was done using desirability ramp plots. The main motive behind this research is to compare the performance of plain and coated carbide tool and analyzing which tool performs better and to optimize the cutting parameters for high quality and cost reduction. It was concluded from this research that at optimized speed, feed and DOC the coated carbide tool is suitable for turning of EN9 steel. The tool wear observed on coated carbide tool was less than plain carbide tool. The coated carbide tool showed a slight improvement in results as compared to the plain carbide tool.
Changes in the Price of Alcohol and Effect on Youth Drinking and in Different Socio-Economic Groups
Authors: Trolldal Björn , Landberg Jonas , Ramstedt Mats 
Published: October 2020

Abstract

Aims
Many studies have shown that changes in alcohol prices have a significant effect on total sales. However, few studies have focused on youth, particularly in different socioeconomic groups. This study examined the effect of changes in the price of alcohol on consumption levels and binge drinking among 15 to 16 year old students in Sweden, both overall, among boys and girls, as well as within different socioeconomic groups.

Methods
Data on consumption were retrieved from a representative survey of students aged 15-16, conducted annually between 1989 and 2017. Time series analysis employed an autoregressive integrated moving average model (ARIMA). Two types of price data were used: the official price at the retail stores, and the mean price of the ten cheapest beverages in each category. The mean aggregate annual income per Swedish household was included as a control variable.
The variable used to measure the socioeconomic status was the proportion of the ninth-grade students at each school, who had at least one parent with an education higher than upper secondary school.

Results
The students' alcohol consumption levels and binge drinking were not significantly affected by price changes during the study period; this was true both for the group as a whole, and among subgroups of boys or girls or of different socioeconomic status. Results were similar regardless of which type of price data variable was used in the analyses.

Conclusion
Neither average nor minimum price of alcohol had a significant impact on the development of youth drinking in Sweden during the study period.
Context-dependent trait covariances: how plasticity shapes behavioral syndromes
Authors: Mitchell David J , Houslay Thomas M 
Published: October 2020

Abstract
The study of behavioral syndromes aims to understand among-individual correlations of behavior, yielding insights into the ecological factors and proximate constraints that shape behavior. In parallel, interest has been growing in behavioral plasticity, with results commonly showing that animals vary in their behavioral response to environmental change. These two phenomena are inextricably linked—behavioral syndromes describe cross-trait or cross-context correlations, while variation in behavioral plasticity describes variation in response to changing context. However, they are often discussed separately, with plasticity analyses typically considering a single trait (univariate) across environments, while behavioral trait correlations are studied as multiple traits (multivariate) under one environmental context. Here, we argue that such separation represents a missed opportunity to integrate these concepts. Through observations of multiple traits while manipulating environmental conditions, we can quantify how the environment shapes behavioral correlations, thus quantifying how phenotypes are differentially constrained or integrated under different environmental conditions. Two analytical options exist which enable us to evaluate the context dependence of behavioral syndromes—multivariate reaction norms and character state models. These models are largely two sides of the same coin, but through careful interpretation we can use either to shift our focus to test how the contextual environment shapes trait covariances.
Supervised clustering of high-dimensional data using regularized mixture modeling
Authors: Chang Wennan , Wan Changlin , Zang Yong , Zhang Chi , Cao Sha 
Published: October 2020

AbstractIdentifying relationships between genetic variations and their clinical presentations has been challenged by the heterogeneous causes of a disease. It is imperative to unveil the relationship between the high-dimensional genetic manifestations and the clinical presentations, while taking into account the possible heterogeneity of the study subjects.We proposed a novel supervised clustering algorithm using penalized mixture regression model, called component-wise sparse mixture regression (CSMR), to deal with the challenges in studying the heterogeneous relationships between high-dimensional genetic features and a phenotype. The algorithm was adapted from the classification expectation maximization algorithm, which offers a novel supervised solution to the clustering problem, with substantial improvement on both the computational efficiency and biological interpretability. Experimental evaluation on simulated benchmark datasets demonstrated that the CSMR can accurately identify the subspaces on which subset of features are explanatory to the response variables, and it outperformed the baseline methods. Application of CSMR on a drug sensitivity dataset again demonstrated the superior performance of CSMR over the others, where CSMR is powerful in recapitulating the distinct subgroups hidden in the pool of cell lines with regards to their coping mechanisms to different drugs. CSMR represents a big data analysis tool with the potential to resolve the complexity of translating the clinical representations of the disease to the real causes underpinning it. We believe that it will bring new understanding to the molecular basis of a disease and could be of special relevance in the growing field of personalized medicine.
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
Authors: Rodríguez-Pérez Héctor , Ciuffreda Laura , Flores Carlos 
Published: October 2020

Abstract

Summary
NanoCLUST is an analysis pipeline for the classification of amplicon-based full-length 16S rRNA nanopore reads. It is characterized by an unsupervised read clustering step, based on Uniform Manifold Approximation and Projection (UMAP), followed by the construction of a polished read and subsequent Blast classification. Here, we demonstrate that NanoCLUST performs better than other state-of-the-art software in the characterization of two commercial mock communities, enabling accurate bacterial identification and abundance profile estimation at species-level resolution.

Availability and implementation
Source code, test data and documentation of NanoCLUST are freely available at https://github.com/genomicsITER/NanoCLUST under MIT License.

Supplementary information
Supplementary data are available at Bioinformatics online.
Only males care about their environment: sex-biased dispersal in the asp viper (Vipera aspis)
Authors: Zwahlen Valerie , Nanni-Geser Silvia , Kaiser Laura , Golay Joaquim , Dubey Sylvain , Ursenbacher Sylvain 
Published: October 2020

AbstractSex-biased dispersal is common among vertebrates and numerous studies have documented a tendency towards male-biased dispersal in mammals and female-biased dispersal in birds. A few studies have demonstrated that male-biased dispersal seems to be prevalent in reptiles. However, most of these studies considered only a single study site without taking into account possible local variability. We investigated sex-biased dispersal in Vipera aspis in four study sites in Switzerland using microsatellite markers and we predicted a higher dispersal in males than females. In two study sites, females were more spatially autocorrelated and showed a stronger isolation by distance compared with males, which suggests male-biased dispersal. In the other two study sites, the absence of sex-biased dispersal could have been the result of habitat fragmentation. Surprisingly, the dispersal ability of females was similar in the four sites, regardless of habitat fragmentation. This finding suggests a limited impact of habitat on female dispersal and the opposite for male dispersal. Our study demonstrates the importance of inferring sex-biased dispersal in different habitats, because local barriers can affect the outcome of such studies. Hence, general conclusions about patterns of sex-biased dispersal should be drawn with caution when studies are conducted at a single study site.
Comment on: Low Health Literacy Exists in the Inflammatory Bowel Disease Population and Is Disproportionately Prevalent in Older African Americans
Authors: Languido Lauren S , Salwen-Deremer Jessica K 
Published: October 2020

Lay Summary
Dos Santos Margues and colleagues found that African Americans with IBD may have more difficulty with understanding and making decisions about health information. We discuss their work and give suggestions on how to create a supportive clinic environment.
The physiological and pathological functions of VEGFR3 in cardiac and lymphatic development and related diseases
Authors: Monaghan Richard M , Page Donna J , Ostergaard Pia , Keavney Bernard D 
Published: October 2020

Abstract
Vascular endothelial growth factor receptors (VEGFRs) are part of the evolutionarily conserved VEGF signalling pathways that regulate the development and maintenance of the body’s cardiovascular and lymphovascular systems. VEGFR3, encoded by the FLT4 gene, has an indispensable and well-characterized function in development and establishment of the lymphatic system. Autosomal dominant VEGFR3 mutations, that prevent the receptor functioning as a homodimer, cause one of the major forms of hereditary primary lymphoedema; Milroy disease. Recently, we and others have shown that FLT4 variants, distinct to those observed in Milroy disease cases, predispose individuals to Tetralogy of Fallot, the most common cyanotic congenital heart disease, demonstrating a novel function for VEGFR3 in early cardiac development. Here, we examine the familiar and emerging roles of VEGFR3 in the development of both lymphovascular and cardiovascular systems, respectively, compare how distinct genetic variants in FLT4 lead to two disparate human conditions, and highlight the research still required to fully understand this multifaceted receptor.
Quantitative fluorescence-guided perfusion assessment of the gastric conduit to predict anastomotic complications after esophagectomy
Authors: Slooter M D , de Bruin D M , Eshuis W J , Veelo D P , van Dieren S , Gisbertz S S , van Berge Henegouwen M I 
Published: October 2020

Summary
Background: Fluorescence angiography (FA) assesses anastomotic perfusion during esophagectomy with gastric conduit reconstruction, but its interpretation is subjective. This study evaluated time to fluorescent enhancement in the gastric conduit, with the aim to determine a threshold to predict postoperative anastomotic complications.
Methods: In a prospective cohort study, all consecutive patients undergoing esophagectomy with gastric conduit reconstruction from July 2018 to October 2019 were included. FA was performed before anastomotic reconstruction following injection of indocyanine green (ICG). During FA, the following time points were recorded: ICG injection, first fluorescent enhancement in the lung, at the base of the gastric conduit, at the planned anastomotic site, and at ICG watershed or in the tip of the gastric conduit. Anastomotic complications including anastomotic leakage and clinically relevant strictures were documented.
Results: Eighty-four patients were included, the majority (67 out of 84, 80%) of which underwent an Ivor Lewis procedure. After a median follow-up of 297 days, anastomotic leakage was observed in 12 out of 84 (14.3%) and anastomotic stricture in 12 out of 82 (14.6%). Time between ICG injection and enhancement in the tip was predictive for anastomotic leakage (P = 0.174, area under the curve = 0.731), and a cut-off value of 98 seconds was derived (specificity: 98%). All times to enhancement at the planned anastomotic site and ICG watershed were significantly predictive for the occurrence of a stricture, however area under the curves were &lt;0.7.
Conclusions: The identified fluorescent threshold can be used for intraoperative decision making or to identify potentially high-risk patients for anastomotic leakage after esophagectomy with gastric conduit reconstruction.