bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction and analysis of skin cancer progression using genomics profiles of patients
Authors: Bhalla Sherry , Kaur Harpreet , Dhall Anjali , Raghava Gajendra P. S. 
Published: August 2018

AbstractMetastatic state of the Skin Cutaneous Melanoma (SKCM) has led to high mortality rate worldwide. Previously, various studies have revealed the association of the metastatic melanoma with the diminished survival rate in comparison to primary tumors. Thus, prediction of melanoma at primary tumor state is crucial to employ optimal therapeutic strategy for prolonged survival of patients. The RNA, miRNA and methylation data of The Cancer Genome Atlas (TCGA) cohort of SKCM is comprehensively analysed to recognize key genomic features that can categorize various states of metastatic tumors from primary tumors with high precision. Subsequently, various prediction models were developed using filtered genomic features implementing various machine learning techniques to classify these primary tumors from metastatic tumors. The SVC model (with class weight and RBF kernel) developed using 17 mRNA features achieved maximum MCC 0.73 with sensitivity, specificity and accuracy 89.19%, 90.48% and 89.47% respectively on independent validation dataset. Our study reveals that gene expression based features performs better than features obtained from miRNA profiling and epigenomic profiling. Our analysis shows that the expression of genesC7, MMP3, KRT14, KRT17, MASP1, and miRNA hsa-mir-205 and hsa-mir-203a are among the key genomic features that may substantially contribute to the oncogenesis of melanoma even on the basis of simple expression threshold. The major prediction models and analysis modules to predict metastatic and primary tumor samples of SKCM are available from a webserver, CancerSPP (http://webs.iiitd.edu.in/raghava/cancerspp/).
Tendon Structure Quantified using Ultrasound Imaging Differs Based on Location and Training Type
Authors: Hagan Kenton L. , Hullfish Todd , Casey Ellen , Baxter Josh R. 
Published: August 2018

AbstractAchilles tendinopathy is ten-times more common amongst running athletes compared to age-matched peers. Load induced tendon remodeling and its progression in an at-risk population of developing symptomatic tendinopathy is not well understood. The purpose of this study was to prospectively characterize Achilles and patellar tendon structure in competitive collegiate distance runners over different competitive seasons using quantitative ultrasound imaging. Twenty-two collegiate cross country runners and eleven controls were examined for this study. Longitudinal and cross-sectional ultrasound images of bilateral Achilles and patellar tendons were obtained at the one week prior to start of formal collegiate cross country practices, one week after the conclusion of cross country season, and one week prior to outdoor track and field championships. Collagen organization, mean echogenicity, tendon thickness, and neovascularity were determined using well established image processing techniques. We found that Achilles and patellar tendons respond differently to high-volume running and transitions from one sport season to another, suggesting that tendon structure is sensitive to differences in tendon loading biomechanics. Our findings indicate that Achilles tendon structure in trained runners differ structurally to control tendons but is stable throughout training while patellar tendon structure changes in response to the transition in training volume between cross country and track seasons. These findings expand upon prior reports that some degree of tendon remodeling may act as a protective adaptation for sport specific loading.News and NoteworthyIn this study we prospectively examined the Achilles and patellar tendon structure of distance runners to determine if continued training through multiple seasons elicits tendon remodeling or pathology. We found that Achilles and patellar tendons respond uniquely to the changing loads required during each season. Achilles tendon collagen alignment is mostly stable throughout the competitive cycle, but the patellar tendon undergoes structural changes following the transition from cross-country to track season.
A quantitative genetics approach to the evolution of phenotypic (co)variance under limited dispersal, with an application to socially synergistic traits
Authors: Mullon Charles , Lehmann Laurent 
Published: August 2018

AbstractDarwinian evolution consists of the gradual transformation of heritable quantitative traits due to natural selection and the input of random variation by mutation. Here, we use a quantitative genetics approach to investigate the coevolution of multiple traits under selection, mutation, and limited dispersal. We track the dynamics of trait means and variance-covariances between traits that experience frequency-dependent selection. Assuming a multivariate-normal trait distribution, we recover classical dynamics of quantitative genetics, as well as stability and evolutionary branching conditions of invasion analyses, except that due to limited dispersal, selection depends on indirect fitness effects and relatedness. In particular, correlational selection that associates different traitswithin-individuals depends on the fitness effects of such associationsbetween-individuals. These kin selection effects can be as relevant as pleiotropy for correlation between traits. We illustrate this with an example of the coevolution of two social traits whose association within-individual is costly but synergistically beneficial between-individuals. As dispersal becomes limited and relatedness increases, associations between-traits between-individuals become increasingly targeted by correlational selection. Consequently, the trait distribution goes from being bimodal with a negative correlation under panmixia to unimodal with a positive correlation under limited dispersal. More broadly, our approach can help understand the evolution of intra-specific variation.
Consequences of PCA graphs, SNP codings, and PCA variants for elucidating population structure
Authors: Gauch Hugh G. , Qian Sheng , Piepho Hans-Peter , Zhou Linda , Chen Rui 
Published: August 2018

AbstractSNP datasets are high-dimensional, often with thousands to millions of SNPs and hundreds to thousands of samples or individuals. Accordingly, PCA graphs are frequently used to provide a low-dimensional visualization in order to display and discover patterns in SNP data from humans, animals, plants, and microbes—especially to elucidate population structure. Given the popularity of PCA, one might expect that PCA is understood well and applied effectively. However, our literature survey of 125 representative articles that apply PCA to SNP data shows that three choices have usually been made poorly: PCA graph, SNP coding, and PCA variant. Our main three recommendations are simple and easily implemented: Use PCA biplots, SNP coding 1 for the rare allele and 0 for the common allele, and double-centered PCA (or AMMI1 if main effects are of interest). The ultimate benefit from informed and optimal choices of PCA graph, SNP coding, and PCA variant, is expected to be discovery of more biology, and thereby acceleration of medical, agricultural, and other vital applications.
Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
Authors: Mateus Ivan D. , Masclaux Frédéric G. , Aletti Consolée , Rojas Edward C. , Savary Romain , Dupuis Cindy , Sanders Ian R. 
Published: August 2018

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.
Cooperativity and Avidity in Membrane Binding by C2AB Tandem Domains of Synaptotagmins 1 and 7
Authors: Tran H. , Anderson L. , Knight J. 
Published: August 2018

AbstractSynaptotagmin-1 (Syt-1) and synaptotagmin-7 (Syt-7) contain analogous tandem C2 domains, C2A and C2B, which together serve as a Ca2+ sensor to bind membranes and promote the stabilization of exocytotic fusion pores. Functionally, Syt-1 triggers fast release of neurotransmitters, while Syt-7 is involved in lower-Ca2+ processes such as hormone secretion. Evidence suggests that Syt-1 C2 domains bind membranes cooperatively, penetrating farther into membranes as the C2AB tandem than as individual C2 domains. In contrast, we previously reported that the two C2 domains of Syt-7 bind membranes independently, based in part on measurements of their liposome dissociation kinetics. Here, we have investigated the effects of C2A-C2B interdomain cooperativity with Syt-1 and Syt-7 using directly comparable measurements. We report Ca2+ sensitivities, dissociation kinetics, and membrane insertion using liposomes approximating physiological lipid compositions. Equilibrium Ca2+ titrations confirm that the Syt-7 C2AB tandem has a greater Ca2+ sensitivity of membrane binding than either of its individual domains. Stopped-flow fluorescence kinetic measurements show that Syt-1 C2AB dissociates from liposome membranes much more slowly than either of its isolated C2 domains, suggesting that the two C2 domains of Syt-1 bind membranes cooperatively. In contrast, the dominant population of Syt-7 C2AB has a dissociation rate comparable to its C2A domain, indicating a lack of cooperativity, while only a small subpopulation dissociates at a slower rate. Measurements using an environment-sensitive fluorescent probe indicate that the Syt-7 C2B domain inserts more deeply into membranes as part of the C2AB tandem, similarly to Syt-1. Overall, these measurements are consistent with a model in which the structural linkage of C2A and C2B impacts the membrane-binding geometry of synaptotagmin C2B domains, but imparts little or no cooperativity to Syt-7 membrane binding and dissociation events that are dominated by its C2A domain.
Higher order assembling of the mycobacterial essential polar growth factor DivIVA/Wag31
Authors: Choukate Komal , Gupta Aanchal , Basu Brohmomoy , Virk Karman , Ganguli Munia , Chaudhuri Barnali 
Published: August 2018

AbstractHow proteins localize at the pole remains an enigma. DivIVA/Wag31, which is an essential pole organizing protein in mycobacteria, can assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. A single-site phosphorylation in Wag31 is linked to the regulation of peptidoglycan biosynthesis for optimal mycobacterial growth. The structural organization of polar scaffold formed by coiled-coil rich Wag31, which is a target for anti-tubercular agent amino-pyrimidine sulfonamide, remains to be determined. Here, we report biophysical characterizations of a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of mycobacterial Wag31 using circular dichroism, small angle solution X-ray scattering and atomic force microscopy. While data obtained from both variants of Wag31 in solution states suggested formation of alpha-helical, large, elongated particles, their structural organizations were different. Atomic force microscopic images of Wag31 indicate polymer formation, with occasional curving, sharp bending and branching. Observed structural features in this first view of the polymeric forms of Wag31 suggest a basis for higher order network scaffold formation for polar protein localization.
Extensive Secondary Contact Among Three Glacial Lineages of Arctic Char (Salvelinus alpinus) in Newfoundland and Labrador
Authors: Salisbury Sarah J. , McCracken Gregory R. , Keefe Donald , Perry Robert , Ruzzante Daniel E. 
Published: August 2018

ABSTRACTWe sequenced a portion of the D-loop region in over 1000 Arctic char (Salvelinus alpinus) samples from 67 locations across Newfoundland and Labrador to assess the extent of secondary contact among the Arctic, Atlantic, and Acadian glacial lineages in Newfoundland and Labrador. Within Labrador, the Arctic and Atlantic lineages were widespread. Two locations (one landlocked and one with access to the sea) also contained individuals of the Acadian lineage, constituting the first record of this lineage in Labrador. Atlantic and Acadian lineage individuals were found in both eastern and western Newfoundland. Multiple sampling locations in Newfoundland and Labrador contained fish of two or more different glacial lineages, implying their introgression. Glacial lineage did not appear to dictate contemporary genetic divergence between the pale and dark morph of char present in Gander Lake, Newfoundland. Both were predominately of the Atlantic lineage, suggesting the potential for their divergence in sympatry. This study reveals Newfoundland and Labrador to be a unique junction of three glacial lineages which have likely hybridized extensively in this region.
Genome Analyses of a New Mycoplasma Species From the scorpion Centruroides vittatus
Authors: Yamashita Tsunemi , Rhoads Douglas D. , Pummill Jeff 
Published: August 2018

ABSTRACTArthropod Mycoplasma are little known endosymbionts in insects, primarily known as plant disease vectors. Mycoplasma in other arthropods such as arachnids are unknown. We report the first complete Mycoplasma genome sequenced, identified, and annotated from a scorpion, Centruroides vittatus, and designate it as Mycoplasma vittatus. We find the genome is at least a 683,827 bp single circular chromosome with a GC content of 43.7% and with 1,010 protein-coding genes. The putative virulence determinants include 20 genes associated with the virulence operon associated with protein synthesis (SSU ribosomal proteins) and nine genes with fluoroquinolone resistance. Comparative analysis revealed that the M. vittatus genome is smaller than other Mycoplasma genomes and exhibits a higher GC content. Phylogenetic analysis shows M. vittatus as part of the Hominis group of Mycoplasma. As arthropod genomes accumulate, further novel Mycoplasma genomes may be identified and characterized.
Sae2/CtIP prevents R-loop accumulation in eukaryotic cells
Authors: Makharashvili Nodar , Arora Sucheta , Yin Yizhi , Fu Qiong , Leung Justin W. C. , Miller Kyle M. , Paull Tanya T. 
Published: August 2018

AbstractThe Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5’ flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.
Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer’s disease
Authors: Whitesell Jennifer D. , Buckley Alex R. , Knox Joseph E. , Kuan Leonard , Graddis Nile , Pelos Andrew , Mukora Alice , Wakeman Wayne , Bohn Phillip , Ho Anh , Hirokawa Karla E. , Harris Julie A. 
Published: August 2018

AbstractA variety of Alzheimer’s disease (AD) mouse models overexpress mutant forms of human amyloid precursor protein (APP), producing high levels of amyloid β (Aβ) and forming plaques However, the degree to which these models mimic spatiotemporal patterns of Aβ deposition in brains of AD patients is unknown. Here, we mapped the spatial distribution of Aβ plaques across ages in three APP-overexpression mouse lines (APP/PS1, Tg2576, hAPP-J20) using in vivo labeling with methoxy-X04, high throughput whole brain imaging, and an automated informatics pipeline. Images were acquired with high resolution serial 2-photon tomography and labeled plaques were detected using custom-built segmentation algorithms. Image series were registered to the Allen Mouse Brain Common Coordinate Framework, a 3D reference atlas, enabling automated brain-wide quantification of plaque density, number, and location. In both APP/PS1 and Tg2576 mice, plaques were identified first in isocortex, followed by olfactory, hippocampal, and cortical subplate areas. In hAPP-J20 mice, plaque density was highest in hippocampal areas, followed by isocortex, with little to no involvement of olfactory or cortical subplate areas. Within the major brain divisions, distinct regions were identified with high (or low) plaque accumulation; e.g., the lateral visual area within the isocortex of APP/PS1 mice had relatively higher plaque density compared with other cortical areas, while in hAPP-J20 mice, plaques were densest in the ventral retrosplenial cortex. In summary, we show how whole brain imaging of amyloid pathology in mice reveals the extent to which a given model recapitulates the regional Aβ deposition patterns described in AD.
Adaptive efficiency of the Mexican Stock Exchange
Authors: Brito-Cervantes Esmeralda , Coronado Semei , Morales-García Manuel , Rojas Omar 
Published: August 2018

Purpose
The purpose of this paper is to analyse the adaptive market efficiency in the price–volume (P–V) relationship of the stocks listed in the Mexican Stock Exchange. The period under study goes from 1982 to 2015. In order to detect causality and, thus, determine adaptive efficiency in the market, one linear and two non-linear tests are applied. There are few papers in the literature that study the P–V relationship in Latin American markets; as such, this paper may be of interest and importance to financial academics and practitioners alike.

Design/methodology/approach
The Diks and Panchenko (DP) non-parametric Granger causality and the Brooks and Hinich (BH) cross-bicorrelation tests are applied.

Findings
Derived from the DP test, the findings show that there exists bi-directional non-linear Granger causality in 25.71 per cent of the firms studied, compared to 8 per cent when applying the linear Granger causality test. Therefore, there is evidence of weak-form efficiency in the market. From the BH test, evidence is shown of the adaptive market efficiency, since 71.42 per cent of firms exhibited some form of non-linear dependence in certain periods of time. With these results, the information process should be better studied for a greater comprehension of regulatory policies in the market and better decision-making tools for the investors.

Originality/value
This paper complements studies on the P–V relationship and efficiency in a Latin American market.
BIM adoption model for small and medium construction organisations in Australia
Authors: Hong Ying , Hammad Ahmed W.A. , Sepasgozar Samad , Akbarnezhad Ali 
Published: August 2018

Purpose
The purpose of this paper is to present a model for building information modelling (BIM) implementation at small and medium-sized construction contractor organisations (SMOs). The proposed BIM adoption model assesses BIM implementation benefits, costs and challenges faced by SMOs. Correlation between BIM adoption in SMOs and the associated impacting factors, including knowledge support and BIM adoption motivation, is captured through the model.

Design/methodology/approach
A literature review of BIM adoption in construction was first presented. Research data, collected from 80 SMOs in Australia through a conducted survey, are then analysed. Descriptive analysis and structural equation modelling were used to investigate SMOs’ understanding of BIM, and to qualify the correlations among the proposed latent variables impacting BIM implementation at SMOs, respectively. Additionally, this study used χ2 test to compare differences between BIM users and non-BIM users regarding BIM understanding, interested applications and attitudes towards implementation benefits and challenges.

Findings
Potential benefits associated with BIM implementation are a major motivation factor when it comes to BIM adoption at SMOs. In addition, existing staff’s capability in using BIM tools positively affects the establishment of an organisational knowledge-support system, which determines the decision of adopting BIM eventually. Ultimately, there is a need for further emphasis on staff engagement in the implementation process.

Research limitations/implications
The results presented in this paper are applicable to SMOs in the building sector of construction. BIM implementation at organisations involved in non-building activities, including civil works and infrastructure, needs to be assessed in the future.

Practical implications
The results indicate that rather than placing the focus mainly on benefits of BIM implementation, successful implementation of BIM in practice requires adequate effort to assess implementation problems, establish knowledge support and engage staff in using BIM.

Originality/value
Results of this study provide an insight into the adoption challenges of BIM in SMOs, given that the focus of previous studies has been mostly placed on BIM adoption in architectural firms and large contractors.