bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services
Authors: Damkliang Kasikrit , Tandayya Pichaya , Sangket Unitsa , Pasomsub Ekawat 
Published: December 2017

SummaryAt the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow’s execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th
Feature Fusion Based SVM Classifier for Protein Subcellular Localization Prediction
Authors: Rahman Julia , Mondal Nazrul Islam , Islam Khaled Ben , Hasan Al Mehedi 
Published: December 2017

Summary For the importance of protein subcellular localization in different branch of life science and drug discovery, researchers have focused their attentions on protein subcellular localization prediction. Effective representation of features from protein sequences plays most vital role in protein subcellular localization prediction specially in case of machine learning technique. Single feature representation like pseudo amino acid composition (PseAAC), physiochemical property model (PPM), amino acid index distribution (AAID) contains insufficient information from protein sequences. To deal with such problem, we have proposed two feature fusion representations AAIDPAAC and PPMPAAC to work with Support Vector Machine classifier, which fused PseAAC with PPM and AAID accordingly. We have evaluated performance for both single and fused feature representation of Gram-negative bacterial dataset. We have got at least 3% more actual accuracy by AAIDPAAC and 2% more locative accuracy by PPMPAAC than single feature representation.
Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals
Authors: Babenko Vladimir N. , Bragin Anatoly O. , Spitsina Anastasia M. , Chadaeva Irina V. , Galieva Elvira R. , Orlova Galina V. , Medvedeva Irina V. , Orlov Yuriy L. 
Published: December 2017

Summary
Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.
Current Progress of High-Throughput MicroRNA Differential Expression Analysis and Random Forest Gene Selection for Model and Non-Model Systems: an R Implementation
Authors: Zhang Jing , Hadj-Moussa Hanane , Storey Kenneth B. 
Published: December 2017

SummaryMicroRNAs are short non-coding RNA transcripts that act as master cellular regulators with roles in orchestrating virtually all biological functions. The recent affordability and widespread use of high-throughput microRNA profiling technologies has grown along with the advancement of bioinformatics tools available for analysis of the mounting data flow. While there are many computational resources available for the management of data from genomesequenced animals, researchers are often faced with the challenge of identifying the biological implications of the daunting amount of data generated from these high-throughput technologies. In this article, we review the current state of highthroughput microRNA expression profiling platforms, data analysis processes, and computational tools in the context of comparative molecular physiology. We also present RBioMIR and RBioFS, our R package implementations for differential expression analysis and random forest-based gene selection. Detailed installation guides are available at kenstoreylab.com.
Satellite dependency of GNSS phase biases between receivers and between signals
Authors: Håkansson M. 
Published: December 2017

Abstract
The existence of hardware induced phase biases might influence the accuracy in precise positioning if not handled properly. This is extra problematic if the biases are dependent on the satellite tracked, as these biases no longer will be common between the satellites, and thus will not be absorbed by the receiver clock term of the positioning solution. In this paper, we carried out two studies to investigate whether there exists a satellite dependency of the relative phase biases. Even though small in size, satellite dependent variations were found in both cases. In the first case, relative receiver phase biases were studied, while relative phase biases between signals (e.g. between carrier phases from C/A-code and P-code tracking) were investigated in the second case. The biases in the first case had a size of 0.8 mm between the satellites with the largest and smallest values, and additionally showed temporal variations that were consistent over time. The corresponding sizes of the biases second case were 2 mm and 3.5 mm for GPS L1 and L2 respectively, and no temporal variations were found.
Fully populated VCM or the hidden parameter
Authors: Kermarrec G. , Schön S. 
Published: December 2017

Abstract
Least-squares estimates are trustworthy with minimal variance if the correct stochastic model is used. Due to computational burden, diagonal models that neglect correlations are preferred to describe the elevation dependency of the variance of GPS observations. In this contribution, an improved stochastic model based on a parametric function to take correlations between GPS phase observations into account is presented. Built on an adapted and flexible Mátern function accounting for spatiotemporal variabilities, its parameters can be fixed thanks to Maximum Likelihood Estimation or chosen apriori to model turbulent tropospheric refractivity fluctuations. In this contribution, we will show in which cases and under which conditions corresponding fully populated variance covariance matrices (VCM) replace the estimation of a tropospheric parameter. For this equivalence “augmented functional versus augmented stochastic model” to hold, the VCM should be made sufficiently largewhich corresponds to computing small batches of observations. A case study with observations from a medium baseline of 80 km divided into batches of 600 s shows improvement of up to 100 mm for the 3Drms when fully populated VCM are used compared with an elevation dependent diagonal model. It confirms the strong potential of such matrices to improve the least-squares solution, particularly when ambiguities are let float.
Requests for Help in a Multilingual Professional Environment Testimonies and Actantial Models
Authors: Lejot Eve 
Published: December 2017

AbstractProfessional multilingual environments using English as a lingua franca are prone to imbalances in communication, linguistic insecurity and rising tension. Non-native English speakers develop avoidance strategies in order to lessen their apprehension. To overcome these imbalances, this research aims to understand the relationships formed around languages focusing on the dynamics of integration and the requests for help. Guided by the actantial models of Greimas (1966), this qualitative study employs semiolinguistics and discourse analysis, including 19 narrative interviews with employees of Airbus and UNESCO in Hamburg, Germany in 2013. This methodology draws on actors connected through relationships of power and/or collaboration. The actantial models applied seek linguistic input through designational paradigms, shifters and modal occurrences. The actantial models illustrate how a good language competence provides a better understanding of one’s direct as well as passive environment. The learning process is shown to be a conduit to integration. The actantial model and discourse analysis shed light on the complex situation of multilingual communication settings by highlighting the influence of individuals’ linguistic skills. As a matter of fact, depending on the role of each individual in a given situation, lending a helping hand sometimes equates to upsetting the balance.
Anglophonic Influence in the Use of Sound Symbolism in Italian Disney Comics: A Corpus-based Analysis
Authors: Pischedda Pier Simone 
Published: December 2017

AbstractThis article will explore the linguistic implications of employing and creating sound symbolism (ideophones, onomatopoeia and interjections) in Italian Disney comics. It will endeavour to investigate the way sound symbolic forms in both imported Disney US comics and original Italian stories have profoundly influenced the development of Italian sound symbolism in the last century. The diachronic analysis is carried out thanks to the creation of a corpus of ideophones and interjections from 210 Disney stories published between 1932 and 2013. The corpus will allow the author to investigate how these forms have changed diachronically throughout the eighty years under investigation with the final aim of highlighting changes and patterns in both original and translated Italian stories. The unique status of ideophones, confirmed by language, sociological and neurological studies, has led to interesting experimentations but also to complicated dynamics. Certain linguistic settings seem to foster a better affinity towards the device- particularly if compared to Romance languages, such as Italian and Spanish, that often have to rely on Anglophone renditions. Anglicisation has indeed overshadowed previous original attempts. Nevertheless, recent creations, particularly from cartoonists, bear witness to a willingness to stretch language again in order to enhance language iconicity.
Covert Syncretism: The Reception of South Africa’s Sangoma Practise and Spirituality by “Double Faith” in the Contexts of Christianity and of Esotericism
Authors: Kleinhempel Ullrich Relebogilwe 
Published: December 2017

Abstract
South African Bantu mediumism (of “Sangoma” type) has moved from contexts in African Traditional Religion (ATR) and rural culture into South African Christianity, especially in the African Instituted Churches (AIC), which have adopted and transformed elements of mediumist practice and ritual. In recent years it has spread to urban culture and to white milieus in South Africa and Europe, where it is received in Esoteric contexts and beyond as a form of (alternative) “healing”. The spiritual aspects have been received as expressive of a “universal” spirituality, in particular by Jungian psychoanalysts. This reception involves reinterpretation in Jungian terms as by Ch. Bühler, which may be criticized as ambivalent. Although its concepts, phenomena and experiences exceed the Jungian or Esotericist frames of references, they are acknowledged by some, e.g., J.B.F. Laubscher. On an academic level this reception has been facilitated by approaches of anthropology of experience (V. Turner, W. Dilthey) in dissertations on the authors’ initiation and training as Sangomas, and by L-R.N. Mlisa and J.T. Wreford. In their itineraries of double spiritual or religious and therapeutic practice, epistemic repercussions on both sides and in their academic work are interesting, with observable transformations. Effects of “reductionism” can be observed where Sangomas in academia reframe their practice and its epistemic concepts in terms of Pragmatism or Positivitism or of Esotericism. However, the opposite can also be observed where cosmological and anthropological concepts encoded in Sangoma experience and practice have a transformative effect on the receiving milieus of Esoteric spirituality and Jungian psychoanalysis, and of wider audiences who participate through media of television and internet, literature as well as personal encounter and practice. Even this mediated “dual practice” provides avenues for reception and adaptation in both ways, leading to stimulating debate about cultural conditioning of perception and arcane realms of reality.
Monitoring Environmental Conditions with Low-Cost Single Board Computers
Authors: Maceli Monica , Cocciolo Anthony 
Published: December 2017

Abstract:Controlling environmental conditions is an important component in preserving archives and manuscripts, with building design and HVAC systems widely used to achieve the desired conditions. One tool used for monitoring HVAC systems is the datalogger, which stores data such as temperature and relative humidity. As such devices can be costly and inflexible, this work explores the creation of a do-it-yourself datalogger and compares its accuracy, reliability, extensibility, cost, and ease of use against a popular commercial device. Findings suggest that organizations with sufficiently technology-savvy staff can construct and employ a DIY monitor for approximately one-quarter the price of commercial options, although costs may rise over time for support and maintenance of such systems.
Fear of Discrimination: Net Neutrality and Product Differentiation on the Internet
Authors: Liu Xingyi 
Published: December 2017

AbstractWe study the impact of net neutrality on the content market with endogenous product differentiation. We show that when the Internet service provider is allowed to offer different connection qualities to content providers, it has incentives to favor contents that have a broader market feature. This biases content providers towards choosing those broader products, which may result in too little product differentiation in the content market. By eliminating the possibility of discrimination, net neutrality can reduce such distortion in the content market, and induce more efficient product choices. Net neutrality also raises social welfare if the extent of discrimination is relatively small compared to the extent of product differentiation.
Are the Aristotelian conversion rules easy for human thought?
Authors: López-Astorga Miguel 
Published: December 2017

AbstractDrawing on the theory of ‘mental models’, I have previously shown that the valid syllogisms in the Aristotelian logical system, including all of its figures and moods, are very easy for the human mind. Indeed, they can even be used to predict inferences that people can make with quantified sentences. In this paper, I further argue that, if mental models theory is correct, then also the Aristotelian conversion rules are not hard for the human mind. My account here again focuses on the distinction made by the mental models theory between canonical and noncanonical models.
Clinical and Economic Outcomes of New Oral Anticoagulants in Orthopaedics
Authors: Lakic Dragana , Travica Jovana , Odalovic Marina , Tadic Ivana 
Published: December 2017

Abstract
Venous thromboembolism, including pulmonary embolism and deep vein thrombosis, is a significant factor in morbidity and mortality of patients. New oral anticoagulants, such as apixaban, dabigatran, and rivaroxaban, have recently demonstrated their safety and efficacy in patients undergoing major orthopaedic surgery. Selection of the appropriate drug should be adjusted according to patient needs. Major bleeding is rare with new oral anticoagulants and is comparable with the bleeding rate associated with low-molecular-weight heparins. Clinical data indicate that therapy with apixaban and rivaroxaban was more effective compared to enoxaparin, while dabigatran has a similar efficacy to enoxaparin. Cost-effectiveness studies of new oral anticoagulants showed that these medicines offer higher efficacy with acceptable costs for the healthcare system, even saving costs in certain cases. Clinical practice in Serbia reflects considerably more frequent use of traditional anticoagulant medication therapy compared to new oral anticoagulants.
Fatigue Crack Growth Testing and Evaluation for Aluminum Alloys at Temperatures of 25°C and −70°C
Authors: Liu M. D. , Xiong J. J. 
Published: December 2017

Abstract
This paper seeks to measure and evaluate crack growth behaviors and residual lives of aluminum alloys (AAs) 2524-T3 and 7050-T7452 subjected to fatigue loading at temperatures of 25°C and −70°C. Fatigue crack growth tests were performed on AAs 2524-T3 and 7050-T7452 subjected to constant-amplitude and actual random-spectra loading histories at temperatures of about 25°C and −70°C, respectively, to determine the crack growth behaviors and residual lives. The interaction mechanisms between cryogenic temperature and the fatigue load were deduced on the basis of the results of fractographic analysis. The crack growth behaviors and residual lives were evaluated and compared at both temperatures of 25°C and −70°C. Good correlation was achieved between the predictions and actual experiments.
Evaluation of Bearing Capacity of Fly-Ash Highway Subgrade Based on Model Test
Authors: Cui Wei , Zheng Xiao , Zhang Qian-qing 
Published: December 2017

Abstract
Based on the mechanical properties of fly ash (FA) and the similarity theory, a small-scale geomechanical model was virtually built for evaluating the actual bearing capacity of FA embankments. The embankment model was divided into two sides: the right was covered by a concrete surface and the left was uncovered. The monitoring results of stress and displacement in different depths of the model embankment during the loading process were both presented. In the process of testing on the covered right side, both the additional stress and displacement of soil in different depths increased with an increasing load. There was a significant increase of displacement under large loading in different depths of the covered side, which suggested that plastic failure may happen and would gradually develop from bottom to top. The limit-bearing capacity of the FA embankment covered by concrete surface yield from the model test can be adopted as 419 kN that was assumed to fulfil the requirements of traffic load. As to the uncovered left side, plastic failure was very likely to occur in the soil beneath the bearing plate with a certain applied load, which caused a decrease of additional stress. Plastic failure gradually develops from top to bottom of the uncovered side. The limit-bearing capacity of the FA embankment without the concrete surface can be taken as 193 kN that may not meet the requirement for the overloading of vehicles.
Insulin-Like Growth Factor II Targets the mTOR Pathway to Reverse Autism-Like Phenotypes in Mice
Authors: Steinmetz Adam B. , Stern Sarah A. , Kohtz Amy S. , Descalzi Giannina , Alberini Cristina M. 
Published: December 2017

Autism spectrum disorder (ASD) is a developmental disability characterized by impairments in social interaction and repetitive behavior, and is also associated with cognitive deficits. There is no current treatment that can ameliorate most of the ASD symptomatology; thus, identifying novel therapies is urgently needed. We used male BTBRT+Itpr3tf/J (BTBR) mice, a model that reproduces most of the core behavioral phenotypes of ASD, to test the effects of systemic administration of insulin-like growth factor II (IGF-II), a polypeptide that crosses the blood–brain barrier and acts as a cognitive enhancer. We show that systemic IGF-II treatments reverse the typical defects in social interaction, cognitive/executive functions, and repetitive behaviors reflective of ASD-like phenotypes. In BTBR mice, IGF-II, via IGF-II receptor, but not via IGF-I receptor, reverses the abnormal levels of the AMPK-mTOR-S6K pathway and of active translation at synapses. Thus, IGF-II may represent a novel potential therapy for ASD.SIGNIFICANCE STATEMENTCurrently, there is no effective treatment for autism spectrum disorder (ASD), a developmental disability affecting a high number of children. Using a mouse model that expresses most of the key core as well as associated behavioral deficits of ASD, that are, social, cognitive, and repetitive behaviors, we report that a systemic administration of the polypeptide insulin-like growth factor II (IGF-II) reverses all these deficits. The effects of IGF-II occur via IGF-II receptors, and not IGF-I receptors, and target both basal and learning-dependent molecular abnormalities found in several ASD mice models, including those of identified genetic mutations. We suggest that IGF-II represents a potential novel therapeutic target for ASD.