bluuebunny/crossref_metadata_2025_split huggingface dataset:
Querying and analyzing biological data with BioGraph
Authors: Messina Antonio , Fiannaca Antonino , La Paglia Laura , La Rosa Massimo , Urso Alfonso 
Published: January 2018

Nowadays, a huge amount of biomedical data of different biological entities is provided by many online databases and services, each with its own data model, user interface and query language. However, typical bioinformatics scenarios require the use of more than one resource. Therefore, the availability of a single bioinformatics platform that integrates many biological resources and services is a fundamental issue.
Some attempts to go beyond the drawbacks of a handcrafted combination of different resources have already been made. Regardless of focus and considered biological data sources, existing tools lack one or more high-level functional features, such as web interface availability, dynamic data visualization, custom queries support, analytics, and expandability.
Here, we present BioGraph, a web application that allows to query, visualize and analyze biological data belonging to several online available resources.
BioGraph is built on top of our previously developed graph database called BioGraphDB, which collects and integrates heterogeneous biological data and makes them available through a common structure and Gremlin as unique query language.
BioGraph makes use of state-of-the-art technologies and provides some pre-compiled bioinformatics scenarios, as well as the possibility to perform custom queries and obtaining an interactive and dynamic visualization of results.
Taphonomy and palaeoecology of the White Hunter Local Fauna
Authors: Myers Troy 
Published: January 2018

The White Hunter (WH) Local Fauna (LF) is one of the oldest assemblages from the Riversleigh World Heritage Area, belonging to Faunal Zone A and tentatively dated at approximately 24 Ma. The mammalian fauna has many plesiomorphic taxa and a wide range of body sizes are represented, although it is depauperate in medium to large arboreal mammals and over-represented by small to medium-sized macropodoids, vombatomorphians and carnivores. The non-mammalian vertebrate fauna also covers a wide body size range.
The palaeoenvironmental conditions at the time of deposition have been contentious, ranging from hypotheses of cold and dry woodland to warm, wet rainforest, and many climatic and vegetation combinations in between. The autecologies of various species provide only equivocal support for palaeoenvironmental conclusions.
Taphonomic and palaeoecologic data were tested herein to further illuminate palaeoenvironmental understanding. Mammalian post-cranial elements were examined for degree of weathering, abrasion, fragmentation, taxonomic bias and susceptibility to transport. No obvious bias against small vertebrates was observed. The fauna does not appear to represent a mixed-assemblage. Animals most likely died within close proximity to the site of deposition, although the absence of scavenger/carnivore damage militates against predation as the main source of accumulation. Trampling of elements may have been significant.
Results suggest that WH may have been a moderately large ephemeral water body, subject to periodic drying and fed by a slow-moving creek. The climate was cooler than the early Miocene, with a distinct wet and dry season. Surrounding vegetation may have been a type without modern analogue combining structural, but not floristic, equivalents of open dry forest and closed rainforest. There is no evidence for gradational wet open forest types, but this may represent a rapid move to closed forest. These results are reinforced by palaeocommunity analysis of Riversleigh LFs which unite WH LF with a suite of early Miocene Lfs as a similar palaeocommunity type, perhaps antecedent to them.
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
Authors: Guðbrandsson Jóhannes , Franzdóttir Sigríður Rut , Kristjánsson Bjarni Kristófer , Ahi Ehsan Pashay , Maier Valerie Helene , Snorrason Sigurður Sveinn , Jónsson Zophonías Oddur , Pálsson Arnar 
Published: January 2018

Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative developmental studies of closely related species or variable populations of the same species can help to elucidate the molecular mechanisms related to population divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ~10.000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during a timeframe in early development.
Expectedly, developmental time was the predominant explanatory variable. As the data were affected by RNA-degradation, an estimate of 3’-bias was the second most common explanatory variable. Morph, both as a independent variable and as interaction with developmental time, affected the expression of numerous transcripts. The majority of transcripts with significant morph effects separated the limnetic and the benthic morphs. However, gene ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as Arid4a and Tsn. The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.
Microsatellite markers developed in the stingless bee Melipona fasciculata by next-generation sequencing and an exploratory analysis of geographic genetic variation
Authors: Silva Geice R , Souza Isis G B , Souza Bruno A , Pereira Fábia M , Lopes Maria Teresa R , Bentzen Paul , Diniz Fabio Mendonça 
Published: January 2018

Background. Native meliponines are currently threatened by increased human impacts. The assessment of their genetic variation by microsatellite DNA markers can assist in the conservation of populations and help in the planning and establishment of efficient management strategies. Next generation sequencing has proven to be useful for identifying microsatellite loci from the large amounts of sequence data generated.
Methods. The purpose of this study was to develop the first set of microsatellite markers for Melipona fasciculata, selected from partial genome assembly of Illumina paired-end reads. Contigs were created from the resulting paired-end sequence data and these were analyzed with specialized software to extract those reads that contained microsatellite loci. Primer pairs were designed for each detected locus at their flanking regions. Bee samples were genotyped from two different locations for markers characterization and validation.
Results. A total of 17 microsatellite loci displayed polymorphism from two different populations of Northeastern Brazil. Mean HE and HO heterozygosities were 0.453 and 0.536, respectively. PIC across all loci ranged from 0.108 to 0.714. A genetic diversity analysis revealed high values for population differentiation estimates (FST = 0.194, RST = 0.230, and Dest = 0.162). PCoA and Bayesian clustering showed a separation of the species into two distinct clusters.
Discussion. The Illumina paired-end sequencing system provided a large number of microsatellite loci from the M. fasciculata genome. From the genotyped data this study was able to reveal high FST and RST estimates and suggest the existence of genetic structure. These microsatellite markers have demonstrated strong potential for population-level genetic studies and can be used effectively as a molecular tool. Moreover, the exploratory analysis of the genetic diversity in M. fasciculata provides provisional evidence of significant population differentiation between the two studied populations.
Protective effect of Rhus coriaria fruit extracts against hydrogen peroxide-induced oxidative stress in muscle progenitors and zebrafish embryos
Authors: Najjar Fadia , Rizk Francine , Carnac Gilles , Nassar Rim , Jabak Sara , Sobolev Anatoly Petrovich , Bou Saada Yara , El Sabban Marwan , Hamade Aline 
Published: January 2018

Background and purpose Oxidative stress is involved in normal and pathological functioning of skeletal muscle. Protection of myoblasts from oxidative stress may improve muscle contraction and delay aging. Here we studied the effect of R. coriaria sumac fruit extract on human myoblasts and zebrafish embryos in conditions of hydrogen peroxide-induced oxidative stress.
Study design and Methods Crude ethanolic 70 % extract (CE) and its fractions was obtained from sumac fruits. The composition of sumac ethyl acetate EtOAc fraction was studied by 1H NMR. The viability of human myoblasts treated with CE and the EtOAc fraction was determined by trypan blue exclusion test. Oxidative stress, cell cycle and adhesion were analyzed by flow cytometry and microscopy. Gene expression was analyzed by qPCR.
Results The EtOAc fraction (IC50 2.57 μg/mL) had the highest antioxidant activity and exhibited the best protective effect against hydrogen peroxide-induced oxidative stress. It also restored cell adhesion. This effect was mediated by superoxide dismutase 2 and catalase. Pre-treatment of zebrafish embryos with low concentrations of the EtOAc fraction protected them from hydrogen peroxide-induced death in vivo. 1H NMR analysis revealed the presence of gallic acid in this fraction.
Conclusion Rhus coriaria extracts inhibited or slowed down the progress of skeletal muscle atrophy by decreasing oxidative stress via superoxide dismutase 2 and catalase-dependent mechanisms.
Empirical model predictions and field measurements manifested divergent changes of SOC and SIC in calcareous soils in China
Authors: Wang Huimei , Wang Wenjie 
Published: January 2018

Background. Considerable amounts of calcareous soils exist in China and various management practices are used for improving their productivity; however, no holistic view is currently available of their effects on soil organic carbon (SOC) and soil inorganic carbon (SIC) pools. Our study aims to define co-current changes of SOC and SIC by using empirical model predictions and reviewing analysis of actual field data.
Methods. Three datasets were compiled for the present study; the first was obtained from 9 soil survey reports from China and included data for SOC and SIC concentrations and various soil fertility parameters of soil N and available N; soil P and available P; soil K and available K; and soil pH and cation exchange capacity (CEC). These data were used for empirical prediction of SIC and SOC changes with changes in other soil properties via regression analysis. The second dataset comprised 111 data points from concurrent measurements of SOC and SIC from long-term fixed sites and paired sampling sites (long-term fertilization, tillage treatment, paired land-uses, degraded farmland afforestation etc), which were used to confirm the empirical predication. The third dataset comprised separated measurements of rates of changes in SIC (36 data points) and SOC (74 data points), and frequent distribution and averages were analyzed for finding changing rate differences. These datasets were used to determine the relative magnitude of rates of changes in SIC and SOC to identify the importance of co-inclusion of the two components for soil carbon budget estimation.
Results. Empirical relationships between soil fertility parameters (total N and available N; total P and available P; total K and available K; and pH and CEC) and SOC were generally opposite to relationships between soil fertility parameters and SIC (p < 0.001), indicating that soil physicochemical changes as a result of management strategies may affect SOC and SIC in a divergent direction. A total of 111 concurrent measurements of SIC and SOC revealed that soil fertilization and tillage practices could increase SOC andlower SIC by 18% and 11%, respectively, compared to control practices. Similarly, the dataset comprising separated measurements showed that SOC changing rate averaged at 37.3 g m-2 yr-1(SOC accrual), and SIC changing rate averaged at -17.1 g m-2 yr-1(SIC loss), counteracting the SOC accumulation.
Discussion. Changes in SIC are more complicated than those of SOC. In a semiarid region with abundant CO 2 and Ca 2+ , pedogenic formation of SIC was observed, while in a moist region (such as a karst land region) with sufficient water supply, dissolution-induced SIC loss in surface soils was frequently observed. Our findings highlight that SOC and SIC should be simultaneously included in the computation of soil carbon budgets to avoid false estimation of carbon changes as a result of using either SOC or SIC alone.
Coccolith arrangement follows Eulerian mathematics in the coccolithophore Emiliania huxleyi
Authors: Xu Kai , Hutchins David , Gao Kunshan 
Published: January 2018

Background. The globally abundant coccolithophore, Emiliania huxleyi, plays an important ecological role in oceanic carbon biogeochemistry by forming a cellular covering of plate-like CaCO3 crystals (coccoliths) and fixing CO2. It is unknown how the cells arrange different sizes of coccoliths to maintain full coverage as the cell surface area changes due to growth and cell division.
Methods. We used Euler’s polyhedron formula and simulation software CaGe, validated with the geometries of coccoliths, to analyses the coccolith topology of coccosphere and the arrange mechanism.
Results. The cells arrange each of the coccoliths to interlock with 4–6 others to keep pace with cell growth and cell division.
Conclusions. This study represents an example of how natural selection has arrived at a solution based on Euler’s polyhedral formula in response to the challenge of maintaining a CaCO3 covering on coccolithophore cells as cell size changes.
Analysis of institutional competitiveness of junior high schools through the admission Test to High School Education
Authors: Armendáriz Joyzukey , Tarango Javier , Machin-Mastromatteo Juan Daniel 
Published: January 2018

Abstract
This descriptive and correlational research studies 15,658 students from 335 secondary schools in the state of Chihuahua, Mexico, through the results of the examination of admission to high school education (National High School Admission Test - EXANI I from the National Assessment Center for Education - CENEVAL) on logical-mathematical and verbal reasoning, mathematics and Spanish, comparing along the variables of sex, system (public or private), type of school of origin (there are seven types) and ranking of grades, with which, the main objective is to identify levels of institutional competitiveness. The main findings of the research were: (i) private schools, in comparison with public ones, showed percentages of more favorable grades (60.54 and 43.58 respectively); (ii) influence of the academic average of the students in the result of the examination of admission (correlation of .0403; (iii) greater competence in the area of verbal reasoning (56.47) compared to logical-mathematical reasoning (55.69); and (iv) the identification of a small number of secondary schools considered as having sufficient institutional competitiveness (11 schools, equivalent to 3.28% of the total).
Hillslope Topography Mediates Spatial Patterns of Ecosystem Sensitivity to Climate
Authors: Hoylman Zachary H. , Jencso Kelsey G. , Hu Jia , Martin Justin T. , Holden Zachary A. , Seielstad Carl A. , Rowell Eric M. 
Published: January 2018

AbstractUnderstanding how hillslope topography modulates ecosystem dynamics across topoclimatic gradients is critical for predicting future climate change impacts on vegetation function. We examined the influence of hillslope topography on ecosystem productivity, structure, and photosynthetic activity across a range of water and energy availability using three independent methods in a forested watershed (Montana, USA): 308 tree cores; light detection and ranging quantification of stem density, basal area, foliar biomass, and total biomass; and the enhanced vegetation index (EVI; 1984–2012). Multiple linear regression analysis across three conifer species revealed significant increases in measured basal area increment growth rates (from 56 to 2,058 mm2/yr) with increasing values of the topographic wetness index and decreases in the climatic water deficit. At the watershed scale, we observed strong gradients in total biomass (e.g., 52 to 75 Mg/ha), which increased from ridgelines to convergent hollows. The most predominant topographic organization of forest biomass occurred along locations of climatically driven water limitations. Similarly, an analysis of growing season EVI indicated enhanced photosynthetic activity and a prolonged growing season in convergent hillslope positions. Collectively, these analyses confirm that within water‐limited landscapes, meter‐scale differences in topographic position can mediate the effects of the local energy balance and contribute to large differences in local hydrometeorological processes that are a necessary consideration for quantifying spatial patterns of ecosystem productivity. Further, they suggest that local topography and its topology with regional climate may become increasingly important for understanding spatial patterns of ecosystem productivity, mortality, and resilience as regional climates become more arid.
Hodgkin–Huxley Artificial Synaptic Membrane Based on Protonic/Electronic Hybrid Neuromorphic Transistors
Authors: Fu Yang Ming , Wan Chang Jin , Zhu Li Qiang , Xiao Hui , Chen Xiao Dong , Wan Qing 
Published: January 2018

AbstractIontronics is a newly emerging interdisciplinary concept that bridges electronics and ionics. It provides new opportunities for biomimic information processing. Iontronic devices can act as building blocks for neuromorphic platforms. Here, a proof‐of‐principle Hodgkin–Huxley artificial synaptic membrane is proposed for the first time based on inorganic proton conductor. Phosphosilicate glass‐based proton conductor electrolyte demonstrates unique short‐term volatile charging behaviors, indicating potential short‐term synaptic plasticity applications. By using protonic/electronic hybrid oxide transistor configuration, dynamic synaptic membrane potential responses are triggered with gate current spikes. Typical resting potential, excitatory/inhibitory postsynaptic potential behaviors, and membrane depolarization/activation behaviors are mimicked on the proposed Hodgkin–Huxley artificial synaptic membrane. Moreover, proton‐related electrostatic coupling enables the device to possess short‐term synaptic plasticities with low power consumption. The proposed Hodgkin–Huxley artificial synaptic membrane provides a new prototype for neuromorphic system applications.
Magnetic Actuation of Multifunctional Nanorobotic Platforms to Induce Cancer Cell Death
Authors: Serrà Albert , Vázquez‐Mariño Gonzalo , García‐Torres José , Bosch Manel , Vallés Elisa 
Published: January 2018

AbstractSingle‐bath potentiostatic‐pulsed electrodeposition enables the synthesis of bicomponent (i.e., gold and nickel–nickel oxide) multi‐segmented magnetic nanowires that, with extraordinarily low cytotoxicity, are ideal three‐functional medical nanoplatforms because they can transport two types of functional molecules and be magnetically actuated for both controlled targeting and inducing cancer cell death. Alternated segments of Au and Ni–Ni oxide are selected to confer a magnetic character to the nanowires, prevent their dissolution in the cellular medium, and permit selective bio‐functionalization with thiol and porphyrin test molecules. The bi‐functionalized nanowires internalized in HeLa cancer cells, similar to other organelles, move inside the living cells. Applying the rotating magnetic fields cause them vibrate and increase their motion, although high viscosity and the presence of the cytoskeleton and other protein matrices preclude their rotation inside cells. Since no magneto‐mechanical destruction of the HeLa cells occurs on their membranes, organelles, or cytoskeletons programmed cancer cell death is likely induced by the vibration and translation of the nanowires, not by mechanical destruction.
Ferroelectricity in Polar Polymer‐Based FETs: A Hysteresis Analysis
Authors: Georgiou Vasileia , Veksler Dmitry , Campbell Jason P. , Shrestha Pragya R. , Ryan Jason T. , Ioannou Dimitris E. , Cheung Kin P. 
Published: January 2018

AbstractThere is an increasing number of reports on polar polymer‐based ferroelectric field effect transistors (FeFETs), where the hysteresis of the drain current–gate voltage (Id–Vg) curve is investigated as the result of the ferroelectric polarization effect. However, separating ferroelectric effect from many of the factors (such as charge injection/trapping and the presence of mobile ions in the polymer) that confound interpretation is still confusing and controversial. This work presents a methodology to reliably identify the confounding factors which obscure the polarization effect in FeFETs. Careful observation of the Id–Vg curves, as well as monitoring the Id–Vg hysteresis and flat band voltage shift as a function of temperature and sweep frequency, identifies the dominant mechanism. This methodology is demonstrated by using 15 nm thick high glass transition temperature polar polymer‐based FeFETs. In these devices, room temperature hysteresis is largely a consequence of charge trapping and mobile ions, while ferroelectric polarization is observed at elevated temperatures. This methodology can be used to unambiguously prove the effect of ferroelectric polarization in FeFETs.
New Strategy for Polysulfide Protection Based on Atomic Layer Deposition of TiO2 onto Ferroelectric‐Encapsulated Cathode: Toward Ultrastable Free‐Standing Room Temperature Sodium–Sulfur Batteries
Authors: Ma Dingtao , Li Yongliang , Yang Jingbo , Mi Hongwei , Luo Shan , Deng Libo , Yan Chaoyi , Rauf Muhammad , Zhang Peixin , Sun Xueliang , Ren Xiangzhong , Li Jianqing , Zhang Han 
Published: January 2018

AbstractThe room temperature (RT) sodium–sulfur batteries (Na–S) hold great promise for practical applications including energy storage and conversion due to high energy density, long lifespan, and low cost, as well based on the abundant reserves of both sodium metal and sulfur. Herein, freestanding (C/S/BaTiO3)@TiO2 (CSB@TiO2) electrode with only ≈3 wt% of BaTiO3 additive and ≈4 nm thickness of amorphous TiO2 atomic layer deposition protective layer is rational designed, and first used for RT Na–S batteries. Results show that such cathode material exhibits high rate capability and excellent durability compared with pure C/S and C/S/BaTiO3 electrodes. Notably, this CSB@TiO2 electrode performs a discharge capacity of 524.8 and 382 mA h g−1 after 1400 cycles at 1 A g−1 and 3000 cycles at 2 A g−1, respectively. Such superior electrochemical performance is mainly attributed from the “BaTiO3‐C‐TiO2” synergetic structure within the matrix, which enables effectively inhibiting the shuttle effect, restraining the volumetric variation and stabilizing the ionic transport interface.