bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Authors: Wilkinson Mark , Vandervalk Benjamin , McCarthy Luke 
Published: July 2019

Abstract
Background.
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.Description.SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.
Milk is for Children, Colostrum silage is for calves.
Authors: Leivas Leite Fábio , Helena Saalfeld Mara , Brayer Pereira Daniela , Krüguer Silveira Kathleen , Gularte Marcia , Valente Julia , Schramm Renata 
Published: July 2019

AbstractOne sixth of the world population is starving. In the meantime, producers from all over the world daily disdain billions of liters of bovine colostrum, which is seen as rich in nutrients, immunoglobulin and bioactive substances. The milk is the most expensive component in the final costs of calves breeding. Considering the impossibility of substituting the milk to feed the calf, different ways to use the colostrum have been studied however with controversial results. We have developed colostrum silage. This product is economical and possible to store in the environment for up to eighteen months. Being efficient for calf breeding, yielding income and profit to the dairy business. The colostrum silage keeps the necessary physicochemical characteristics for the development of the calves. Calves fed with this product had a significant higher weight gain comparing to the ones fed with milk. Then the milk can be used for human consumption.
Levy flights are not evolved behavior
Authors: Willis Jay , Merckelbach Lucas 
Published: July 2019

AbstractTracks of moving animals have many short moves interspersed with longer moves, and frequencies of all moves together often indicate Levy flights (a type of power law)^1^. The Levy flight foraging hypothesis suggests that, 'since Levy flights and walks can optimize search efficiencies, therefore natural selection should have led to adaptations for Levy flight foraging^1^ and it has been apparently supported by several studies of large numbers of tracks of marine animals^234^. We show that Levy flights are caused by marine animals attempting to move in simple ways and they are unlikely to be evolved behavior. We do this by analyzing the tracks of autonomous underwater gliders which conform to Levy flights while they were programmed to perform simple directed movement. Gliders are autonomous underwater vehicles (AUV), propelled by a buoyancy engine^5^.The principle of operation is that by alternating positive and negative buoyancy, the winged AUV glides through the ocean in an undulating path, resurfacing after a pre-programmed number of undulations. During the periods at the surface, which typically last 15 minutes, GPS is used for positioning before and after transmission of data via a satellite link, whereas underwater the trajectory is deadreckoned from measured heading, pitch and pressure rate. Thus they are potentially a good analogy to a navigating animal which may also attempt to make directed movements using the best available (and often intermittent^6^) navigational information.
A comparative study on the production of ethanol from lignocellulosic biomass by chemical and biological method
Authors: SM Shaheed , JP Rohit , R Madhan , K Selvakumar 
Published: July 2019

AbstractEthanol derived from non-edible biomass is renewable and a clean source of energy. It is independent of the food industry and it is economically feasible. The first generation biofuel or bioethanol is still not a very convenient source of energy as it prominently depends on the availability of grains. The main objective of this work is to develop an industrious efficient process to produce ethanol from lignocellulosic biomasses like wood and leaf in a lab scale. Two processes were compared. The first process involved an alkaline pre-treatment of the powdered biomass followed by dilute acid hydrolysis. The second process involved an alkaline treatment followed by direct hydrolysis of the biomass by use of a fungal species obtained from rotting wood. Following hydrolysis, fermentation was performed using Saccharomyces cerevisiae and ethanol produced was measured. The process methodologies performed here are liable to be scaled up easily. The final study determines factors such as temperature, strength of the reagents and retention time to maximize ethanol production.
Neural Basis of Motivation Lateralizes with Motor Control
Authors: Brookshire Geoffrey , Casasanto Daniel 
Published: July 2019

AbstractAccording to decades of research on affective motivation in the human brain, approach motivational states are subserved by the left hemisphere and avoidance states by the right hemisphere. Here we show that hemispheric specialization for motivation reverses with handedness. This covariation provides initial support for the Sword and Shield Hypothesis, according to which hemispheric laterality of affective motivation is causally linked to motor control for the dominant and non-dominant hands.
A potential cyanobacterial ancestor of Viridiplantae chloroplasts
Authors: Ghosh Wriddhiman , Haldar Prabir , Bhattacharya Sabyasachi , Chatterjee Jaideb , Pyne Prosenjit , Alam Masrure 
Published: July 2019

AbstractThe theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary complicated Chromalveolates [chromista (cryptophytes, haptophytes, and stramenopiles) and alveolata (dinoflagellates, apicomplexans, and ciliates)] are inexplicable in the light of a single endosymbiosis event, thereby necessitating the postulation of the secondary^4,5^ and tertiary^6^ endosymbiosis theories where a nonphotosynthetic protist supposedly engulfed a red or a green alga^7^ and an alga containing a secondary plastid itself was engulfed^8^ respectively. In the current state of understanding, however, there is no clue about the taxonomic identity of the cyanobacterial ancestor of chloroplasts, even though there is a wide consensus on a single primordial endosymbiosis event. During our metagenomic investigation of a photosynthetic geothermal microbial mat community we discovered a novel order-level lineage of Cyanobacteria that - in 16S rRNA gene sequence-based phylogeny - forms a robust monophyletic clade with chloroplast-derived sequences from diverse divisions of Viridiplantae. This cluster diverged deeply from the other major clade encompassing all hitherto known groups of Cyanobacteria plus the chloroplasts of Rhodophyta, Glaucocystophyceae and Chromalveolates. Since this fundamental dichotomy preceded the origin of all chloroplasts, it appears that two early-diverging cyanobacterial lineages had possibly given rise to two discrete chloroplast descents via two separate engulfment events.
Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm
Authors: Soam S.S. , Khan Feroz , Bhasker Bharat , Mishra B. N. 
Published: July 2019

AbstractThe identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class–II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming and cost intensive. Therefore, computational methods have been found helpful in classifying these peptides as binders or non-binders. We have applied negative selection algorithm, an artificial immune system approach to predict MHC class–II binders and non-binders. For the evaluation of the NSA algorithm, five fold cross validation has been used and six MHC class–II alleles have been taken. The average area under ROC curve for HLA-DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1501, DRB1*1301 have been found to be 0.75, 0.77, 0.71, 0.72, and 0.69, and 0.84 respectively indicating good predictive performance for the small training set.
NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents
Authors: Baianu I. , Guo Jun 
Published: July 2019

AbstractConventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer’s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry including meats, grains, and dairy products (Shadow, 1998).
Consortium Building For PEM MFC Using Synthetic Media As Substrate
Authors: Ayyappan Muralidharan , Parida Dimpal , Yadav Arti , Mohandass Ramya 
Published: July 2019

AbstractMicrobial production of electricity is an important form of bioenergy since Microbial Fuel cells (MFC) offer the possibility of extracting electric current from a wide range of organic wastes and renewable biomass. Factors affecting the MFC operational effectiveness are the MFC design and the bacterial metabolism and electron transfer. The purpose of this study is to identify species which are responsible for electricity generation so as to build a suitable consortium and to investigate the relative efficiencies between the microbial consortiums. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a MFC with synthetic media as a substrate increased the output from an initial level of 34 mA to a maximal level of 363 mA. Scanning electron microscope image indicated the enhanced microbial biofilm deposition over the electrode which were not initially detected in the community.
Pramipexole protective effect on rotenone induced neurotoxicity in mice
Authors: Gad-Elhak Seham , Salama Mohamed , El-Tantawy Dina , El-Dakroury Sahar , Abd-Elghaffar Hasan , El-Dosouky Sara , Ghanem Abdelaziz 
Published: July 2019

AbstractIntroduction:Pramipexole is a new dopaminergic drug which has been approved for PD treatment. However, we tried to find a new capacity for this drug rather than symptomatic effect.
Materials and Methods:
A chronic rotenone model with daily oral dose of 30mg/kg was induced in mice. Pramipexole was tried in a new approach where the treatment began in the middle of rotenone course with oral dose 1mg/kg/day of pramipexole.

Results:
Further analysis of behavioral tests and immunohistochemistry revealed success of pramipexole in improving the rotenone intoxicated mice.

Conclusion:
These results showed possible beneficial effects of pramipexole against rotenone-induced neurotoxicity.
The Olfactory Nervous System Of Terrestrial And Aquatic Vertebrates
Authors: Hussain Ashiq 
Published: July 2019

AbstractAnimals in their natural milieu are surrounded by odors. These odors are rich source of information, and are perceived by sophisticated olfactory systems, that have evolved over time. The sense of smell helps species to localize prey, evade predators, explore food and recognize viable mates. In humans, memoirs, thoughts, emotions, and associations are more readily reached through the sense of smell than through any other channel. This suggests that olfactory processing is imperative and may differ fundamentally from processing in other sensory modalities. The molecular age in olfaction initiated in 1991 with the significant discovery of a large, multigene family of olfactory receptors in rat by Linda Buck and Richard Axel (Buck and Axel, 1991). The first cloned olfactory receptors consisted of a diverse repertoire of G-protein coupled receptors (GPCRs) with seven-trans membrane topology, and they were sparsely expressed in the olfactory epithelium. This Nobel Prize worthy pioneering discovery, together with availability of modern techniques and numerous completely sequenced genomes opened the way to characterize the gene families of olfactory receptors through exhaustive computational data mining in different species genome as well as by in vitro biology. In this review, I will explain about the two main model organism of olfactory perceptions, zebrafish and mouse.
Finite Predation Rate: a Novel Parameter for the Quantitative Measurement of Predation Potential of Predator at Population Level
Authors: Farhadi Roya , Gholizadeh Majid , Chi Hsin , Mou De-Fen , Allahyari Hossein , Yu Jih-Zu , Huang Yu-Bing , Yang Ta-Chi 
Published: July 2019

AbstractDemography and population growth are the most important subjects of population ecology and economics. Finite and intrinsic growth rates have been used as standard parameters for describing and comparing growth potentials of populations. The predation potentials of predator populations or consumption potentials of consumer populations cannot be properly described using these growth rates alone. A standard parameter is needed for the description of the predation or consumption potential, as well as for the quantitative evaluation of a predator population in an ecosystem or biological control program. We show that the finite predation rate can be the standard parameter by linking the finite rate, the stable age-stage distribution, and the age-stage specific predation rate. The finite predation rate can be used to describe and compare the predation potentials of natural enemies used in biological control and in predicting the damage potential of different pest populations to crops.
Evolution signatures in genome network properties
Authors: Dalmolin Rodrigo , de Almeida Rita , Brunnet Leonardo , Rybarczyk-Filho José Luiz , Ferreira Ricardo , Moreira Jose Claudio , Castro Mauro 
Published: July 2019

AbstractGenomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome evolution, where genes in a network are either acquired de novo using a preferential attachment rule, or duplicated, with a duplication probability that linearly grows with gene degree and decreases with its clustering coefficient. The results show that topological distributions are better described than in previous genome evolution models. This model correctly predicts that, in order to produce protein-protein association networks with number of links and number of nodes in the observed range, it is necessary 90% of gene duplication and 10% of de novo gene acquisition. If this scenario is true, it implies a universal mechanism for genome evolution.
Distinct cytokine patterns in Occult Hepatitis C and Chronic Hepatitis C Virus Infection
Authors: Mousa Nasser , Abousamra Nashwa , Azza Abdel-Aziz Azza , Gad Yahia , Elhadidy Mona , Abd-elmaksoud Mohamed 
Published: July 2019

Abstract
Background & Aim:
The immunopathogenesis of chronic hepatitis C virus (HCV) infection is a matter of great controversy. The imbalance of T-helper lymphocyte cell cytokine production was believed to play an important pathogenic role in chronic viral hepatitis. Occult hepatitis C infection is regarded as a new entity that should be considered when diagnosing patients with a liver disease of unknown origin. The aim of this study was to determine serum T-helper 1 and T-helper 2 cytokine production in patients with occult HCV infection and its role in pathogenesis versus chronic viral hepatitis C infection.

Methods:
Serum levels of cytokines of T-helper 1 (IL-2, IFN-[gamma]) and T-helper 2 (IL-4) were measured in 27 patients with occult HCV infection and 50 patients with chronic hepatitis C infection.

Results:
The levels of the T-helper 1 cytokines, IL-2 and IFN-[gamma], were highly and significantly increased in patients with chronic HCV infection as compared with occult HCV infection (p<0.001). The T-helper 2 cytokine IL-4 was highly and significantly increased in occult HCV infection as compared with chronic HCV infection (p<0.001). Necroinflammation (P<0.001) fibrosis (P<0.001) and cirrhosis (P =0.03) were significantly increased in chronic HCV than occult HCV.

Conclusion:
Patients with occult HCV infection exhibited distinct immunoregulatory cytokine patterns, favoring viral persistence in the liver in spite of its absence from peripheral blood and explaining the less aggressive course of this disease entity than chronic hepatitis C virus infection.
A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices
Authors: Gelencser Andras , Prodromakis Themistoklis , Toumazou Christofer , Roska Tamas 
Published: July 2019

AbstractIn this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a memristor-based thresholding scheme for detecting the edges of grayscale images, while the proposed system is also evaluated for its adaptation and fault tolerance capacity against different light or noise conditions as well as distinct device yields.
Design of RNAi reagents for invertebrate model organisms and human disease vectors
Authors: Horn Thomas , Boutros Michael 
Published: July 2019

AbstractRNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters. Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and evaluate their predicted specificity and efficiency. Using a bioinformatics pipeline we also describe how to design a genome-wide RNAi library for Anopheles gambiae.
The Rise of Consortia
Authors: Caporaso Neil , Bennett Siiri 
Published: July 2019

AbstractWe provide some observations on the role of consortia in GWAS. We include 2 surveys (addressed to GWAS Investigators and to GWAS Consortia) sent to GWAS investigators in the spring of 2011. Tables and figures derived from the data are included. We also provide a summary table with some basic data on 110 consortia. We invite the community to visit the WikiGene site (http://www.wikigenes.org/GWAS/consortia.html) where this data may be further corrected and updated.
Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes
Authors: Adhyapak Srilakshmi , Parachuri V.Rao 
Published: July 2019

AbstractThe prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the ventricular equator, and hence its volume. However, the ventricular shape may still be spherical leading to suboptimal function. The aim in any therapy for heart failure should be therefore to achieve near normal left ventricular anatomy and physiology, with shape assessment as the surrogate marker of therapeutic success.