bluuebunny/crossref_metadata_2025_split huggingface dataset:
OmicsNet: Integration of Multi-Omics Data using Path Analysis in Multilayer Networks
Authors: Akhmedov Murodzhon , Arribas Alberto , Montemanni Roberto , Bertoni Francesco , Kwee Ivo 
Published: December 2017

ABSTRACTIntegrative analysis of heterogeneous omics data is essential to obtain a comprehensive overview of otherwise fragmented information and to better understand dysregulated biological pathways leading to a specific condition. One of the major challenges in systems biology is to develop computational methods for proper integration of multi-omics datasets. We propose OmicsNet that uses a multilayer network for the integration and analysis of multi-omics data of heterogeneous types. Each layer of the multilayer network represents a certain data type: input layers correspond to genotype features and nodes in the output layer correspond to phenotypes, while intermediate layers may represent genesets or biological concepts to facilitate functional interpretation of the data. OmicsNet then calculates the highest coefficient paths in multilayer network from each genomic feature to the phenotype by computing an integrated score along the paths. These paths may indicate the most plausible signalling cascade caused by perturbed genotype features leading to a particular phenotype response. With example applications, we illustrate the potential power of OmicsNet in the functional analysis, biomarker discovery and drug response prediction in personalized medicine using multi-omics data.
The bovine alveolar macrophage DNA methylome is resilient to infection withMycobacterium bovis
Authors: O’Doherty Alan Mark , Rue-Albrecht Kevin , Magee David Andrew , Ahting Simone , Irwin Rachelle Elizabeth , Hall Thomas Johnathan , Browne John Arthur , Nalpas Nicolas Claude , Walsh Colum Patrick , Gordon Stephen Vincent , Wojewodzic Marcin Wlodzimierz , MacHugh David Evan 
Published: December 2017

AbstractDNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due toMycobacterium bovis(M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect ofM. bovisinfection on the bAM DNA methylome. The methylomes of bAM infected withM. boviswere compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33–66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Leukemia Development
Authors: Rockne Russell C. , Branciamore Sergio , Qi Jing , Frankhouser David , O’Meally Denis , Hua Wei-Kai , Cook Guerry J. , Carnahan Emily , Zhang Lianjun , Marom Ayelet , Wu Herman , Maestrini Davide , Wu Xiwei , Yuan Yate-Ching , Liu Zheng , Wang Leo D. , Forman Stephen J. , Carlesso Nadia , Kuo Ya-Huei , Marcucci Guido 
Published: December 2017

AbstractTemporal dynamics of gene expression are informative of changes associated with disease development and evolution. Given the complexity of high-dimensional temporal datasets, an analytical framework guided by a robust theory is needed to interpret time-sequential changes and to predict system dynamics. Herein, we use acute myeloid leukemia as a proof-of-principle to model gene expression dynamics in a transcriptome state-space constructed based on time-sequential RNA-sequencing data. We describe the construction of a state-transition model to identify state-transition critical points which accurately predicts leukemia development. We show an analytical approach based on state-transition critical points identified step-wise transcriptomic perturbations driving leukemia progression. Furthermore, the gene(s) trajectory and geometry of the transcriptome state-space provides biologically-relevant gene expression signals that are not synchronized in time, and allows quantification of gene(s) contribution to leukemia development. Therefore, our state-transition model can synthesize information, identify critical points to guide interpretation of transcriptome trajectories and predict disease development.Graphical AbstractIn briefThe theory of state-transition is applied to acute myeloid leukemia (AML) to model transcriptome dynamics and trajectories in a state-space, and is used to identify critical points corresponding to critical transcriptomic perturbations that predict leukemia development.HighlightsLeukemia transcriptome dynamics are modeled as movement in transcriptome state-spaceState-transition model and critical points accurately predicts leukemia developmentCritical point-based approach identifies step-wise transcriptome events in leukemiaState-based geometric analysis provides quantification of leukemogenic contribution
The PTPRT pseudo-phosphatase domain is a denitrase
Authors: Zhao Yiqing , Zhao Shuliang , Hao Yujun , Wang Benlian , Zhang Peng , Feng Xiujing , Chen Yicheng , Song Jing , Mieyal John , Markowitz Sanford , Ewing Rob M. , Conlon Ronald A. , Miyagi Masaru , Wang Zhenghe 
Published: December 2017

AbstractProtein tyrosine nitration occurs under both physiological and pathological conditions1. However, enzymes that remove this protein modification have not yet been identified. Here we report that the pseudo-phosphatase domain of protein tyrosine receptor T (PTPRT) is a denitrase that removes nitro-groups from tyrosine residues in paxillin. PTPRT normally functions as a tumor suppressor and is frequently mutated in a variety of human cancers including colorectal cancer2,3. We demonstrate that some of the tumor-derived mutations located in the pseudophosphatase domain impair the denitrase activity. Moreover, PTPRT mutant mice that inactivate the denitrase activity are susceptible to carcinogen-induced colon tumor formation. This study uncovers a novel enzymatic activity that is involved in tumor suppression.
Handling Multiplicity in Neuroimaging through Bayesian Lenses with Multilevel Modeling
Authors: Chen Gang , Xiao Yaqiong , Taylor Paul A. , Rajendra Justin K. , Riggins Tracy , Geng Fengji , Redcay Elizabeth , Cox Robert W. 
Published: December 2017

AbstractHere we address the current issues of inefficiency and over-penalization in the massively univariate approach followed by the correction for multiple testing, and propose a more efficient model that pools and shares information among brain regions. Using Bayesian multilevel (BML) modeling, we control two types of error that are more relevant than the conventional false positive rate (FPR): incorrect sign (type S) and incorrect magnitude (type M). BML also aims to achieve two goals: 1) improving modeling efficiency by having one integrative model and thereby dissolving the multiple testing issue, and 2) turning the focus of conventional null hypothesis significant testing (NHST) on FPR into quality control by calibrating type S errors while maintaining a reasonable level of inference efficiency The performance and validity of this approach are demonstrated through an application at the region of interest (ROI) level, with all the regions on an equal footing: unlike the current approaches under NHST, small regions are not disadvantaged simply because of their physical size. In addition, compared to the massively univariate approach, BML may simultaneously achieve increased spatial specificity and inference efficiency, and promote results reporting in totality and transparency. The benefits of BML are illustrated in performance and quality checking using an experimental dataset. The methodology also avoids the current practice of sharp and arbitrary thresholding in thep-value funnel to which the multidimensional data are reduced. The BML approach with its auxiliary tools is available as part of the AFNI suite for general use.
Case report of Schöpf–Schulz–Passarge syndrome resulting from a missense mutation, p.Arg104Cys, in WNT10A
Authors: Hsu Tzu‐Chien , Lee Julia Yu‐Yun , Hsu Mark Ming‐Long , Chao Sheau‐Chiou 
Published: December 2017

AbstractSchöpf–Schulz–Passarge syndrome (SSPS) is a rare ectodermal dysplasia characterized by cysts of the eyelids, hypodontia, hypotrichosis, palmoplantar keratosis and onychodystrophy, and it is not common in Asia according to the published work. This autosomal recessive disorder was believed to result from mutations in the WNT10A gene. We report a 54‐year‐old Taiwanese man with SSPS resulted from a homozygous mutation (p.Arg104Cys) in WNT10A. This mutation has not been reported in odonto‐onycho‐dermal dysplasia but was demonstrated to link with dental abnormalities. This report implies the significance of WNT10A gene mutation in ectodermal dysplasia and highlights the clinical features of SSPS.
Ecological context and the probability of mistakes underlie speed choice
Authors: Wheatley Rebecca , Niehaus Amanda C. , Fisher Diana O. , Wilson Robbie S. 
Published: December 2017

Abstract

Movement is fundamental to the ecology of animals, and an animal's choice of movement speed determines the duration, energetic costs, and probability of success of any given activity. It is often assumed that animals should use maximum speeds when escaping from predators, but an increasing number of studies find animals rarely move as fast as they can in nature because faster speeds come with a greater chance of mistakes. Mathematical modelling suggests that, when escaping predators, prey animals should optimise speeds to simultaneously outrun their pursuer and minimise their probability of slipping. This can be particularly important when running along narrow structures like branches. When foraging, however, animals should avoid moving at high speeds, which are often energetically costly and decrease the ability to detect food or predators.

In this study, we examined how trade‐offs between speed and probability of slipping influenced the speed choice of wild antechinus (Antechinus mysticus) during escaping and foraging behaviours. We also examined how this trade‐off affected foraging behaviour.

Antechinus ran significantly faster when escaping (1.207 ± 0.033 m/s) than foraging (0.145 ± 0.002 m/s), and slipped 37% more often during escapes. However, foraging antechinus still slipped frequently on narrow branches, despite running an order of magnitude more slowly than they did on wide branches. Furthermore, antechinus slipped at lower speeds when foraging than they did when escaping, suggesting that avoiding mistakes is less highly prioritized when foraging.

Antechinus visited the feeding station accessed by a wide branch more frequently (and ate more while there) compared with feeding stations accessed by narrow branches, even when those branches were 33% or 67% shorter. This suggests that foraging decisions may be based on potential limitations to speed and the probability of slipping over distance to cover.

Though activities such as running can be fundamental to animals’ fitness, a general framework to understand how animals select speeds in nature is still being developed. We test the assumption that animals choose running speeds to minimise their motor mistakes, and demonstrate the cost of mistakes is likely to be different across ecological and behavioural contexts.

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Anti‐angiogenesis effect of β‐D‐mannuronic acid (M2000) as a novel NSAID with immunosuppressive properties under experimental model
Authors: Rastegari‐Pouyani Mohsen , Mostafaie Ali , Mansouri Kamran , Mortazavi‐Jahromi Seyed Shahabeddin , Mohammadi‐Motlagh Hamid‐Reza , Mirshafiey Abbas 
Published: December 2017

SummaryAngiogenesis is a process through which new capillaries are formed from pre‐existing ones, which contributes significantly to the pathogenesis of numerous diseases, such as cancer and chronic inflammatory disorders. The β‐D‐mannuronic acid (M2000) is a novel non‐steroidal anti‐inflammatory drug (NSAID) with immunosuppressive effects and is a matrix metalloproteinase (MMP) inhibitor. This research aimed to study the anti‐angiogenesis effects of M2000 under in vitro and in vivo models. The cytotoxic and anti‐proliferative effects of M2000 were examined using the trypan blue method and the MTT assay, respectively. The 3D collagen‐cytodex model and the chick chorioallantoic membrane (CAM) assay were then used to evaluate the anti‐angiogenesis property of M2000. Cytotoxicity assay revealed that M2000 (at concentrations of less than 100 μg/mL) had no cytotoxic effect on human umbilical vein endothelial cells (HUVECs). It was also illustrated that M2000 had little or no anti‐proliferative effect on HUVECs. In addition, the anti‐angiogenesis effects of M2000 were shown to be marginal in the in vitro model and both significant and dose‐dependent in the in vivo status. This study showed that M2000 could be considered as an anti‐angiogenic molecule which more likely exerts its activity mainly via indirect effects on endothelial cells and its anti‐inflammatory effects may partly be attributable to its anti‐angiogenic activity. Therefore, it could be recommended as a candidate for prevention and treatment of cancer, chronic inflammatory diseases, and other angiogenesis‐related disorders.
Are the Greens ‘Neither Left nor Right but Out in Front’? What the Carbon Pollution Reduction Scheme Debate Reveals About Ideological Divisions Between Labor and the Greens
Authors: Edwards Lindy 
Published: December 2017

AbstractIn 2009, the Rudd Labor Government proposed a Carbon Pollution Reduction Scheme (CPRS) but was unable to secure support from the Australian Greens. This paper uses this case study to examine ideological divisions that may hamper policy making within Australia's left in the future. It finds the Greens saw the issue through a classic left schema that constructed the environmental crisis as having been created by the powerful exploiting the vulnerable. In contrast, Labor saw the issue through a liberal schema that constructed the crisis as a product of a morally neutral market failure. These different framings led to very different views on the appropriateness of the polluting industries’ compensation package. It concludes that co‐operation between the parties in the future is likely to centre on issues they both view through the left schema.
Incentives, Resources and Combinations of Innovation Radicalness and Innovation Speed
Authors: Behrens Judith , Patzelt Holger 
Published: December 2017

AbstractAlthough scholars have independently explored the antecedents of innovation radicalness and innovation speed, this study's focus on combinations of radicalness and speed offers a number of new insights. Drawing on a comparative case study approach of ten innovation departments of large organizations, the authors’ findings provide evidence that intrinsic rewards trigger innovation radicalness, but the simultaneous presence of extrinsic rewards diminishes innovation speed. Further, the authors show that the availability of high levels of non‐financial resources increases innovation radicalness, but the additional provision of high levels of financial resources leads to a slower process of developing these radical innovations to market. The analysis also uncovers the mechanisms by which extrinsic rewards and financial resources slow down the development of radical innovations. The authors discuss the implications of these findings for the literature on innovation management and managerial practice.
New insights into diet breadth of polyphagous and oligophagous aphids on two Arabidopsis ecotypes
Authors: Wattier Christopher , Turbant Amélie , Sargos‐Vallade Lisa , Pelloux Jérôme , Rustérucci Christine , Cherqui Anas 
Published: December 2017

AbstractWe investigated whether plant ecotype might affect aphid performance and behavior. The probing behaviors of the polyphagous aphid Myzus persicae and the oligophagous aphid Brevicoryne brassicae on two ecotypes of Arabidopsis thaliana, WS and Col‐0 were recorded using the direct current electrical penetration graph method (DC‐EPG). Myzus persicae displayed a significant preference for the WS ecotype but was not greatly disturbed on Col‐0, while B. brassicae discriminated between the two A. thaliana ecotypes, feeding less on WS than on Col‐0. A Principal Component Analysis of aphid probing behavior data recorded on Col‐0 and WS ecotypes showed that the one of M. persicae was positively correlated with the phloem ingestion phases while the one of B. brassicae was more related to nonfeeding phase. The survival of the aphid species was followed during early larval stages on the two ecotypes and a significantly higher mortality was observed of B. brassicae neonates compared to M. persicae, both reared on WS. Moreover, transcriptomic analysis of noninfested plant leaves from both ecotypes was monitored and underlined constitutive differences between Col‐0 and WS gene expression that might explain the different aphid behaviors. Among a unigene set comprising 39 042 sequences for A. thaliana, 6% were differently expressed affecting, for example, the secondary metabolites and cell wall pathways: two third upregulated in WS and one third upregulated in Col‐0. Thus, the “ecotype” variable should be taken into account when setting up a plant–insect experimental research.
Seed vigour contributes to yield improvement in dry direct‐seeded rainfed lowland rice
Authors: Yamane K. , Garcia R. , Imayoshi K. , Mabesa‐Telosa R.C. , Banayo N.P.M.C. , Vergara G. , Yamauchi A. , Sta. Cruz P. , Kato Y. 
Published: December 2017

AbstractDry direct‐seeded rice (DSR) cultivation is widely spreading in tropical Asia, but drought and nutrient deficiency stresses often cause crop failure in rainfed lowlands. The objective of this study was to dissect the physio‐morphological characteristics associated with crop establishment and early vigour of DSR under drought and P deficiency conditions in the Philippines. It was found that new drought‐resistant cultivars bred for DSR (Rc348 and Rc192) had faster germination and sprout growth than popular irrigated rice cultivars (Rc222 and Rc10) under soil water deficit due to rapid moisture acquisition by the germinating seeds from drying soils. There was a significant correlation between seed moisture content and the reduction in seed dry weight, and between reduction in seed dry weight and shoot elongation under both control and drought stress treatments at the germination stage. At the seedling stage, the root growth of Rc348 under drought tended to be more vigorous with its higher root‐to‐shoot ratio compared to Rc222 and Rc10. The seedling vigour of Rc348 under P deficiency was also greater than that of Rc222 due to its greater root growth and P uptake. The yields of Rc348 and Rc192 grown under rainfed condition at the target drought‐prone site where a dry spell of 13 days occurred during crop establishment were higher (4.0–4.1 t ha−1) than the yield of Rc10 (3.0 t ha−1). These results suggest that quick germination and seedling vigour with quick root anchorage and great nutrient uptake capacity, even with limitations of soil moisture and nutrients, would be important traits for DSR in rainfed lowlands.
POST‐PRIVATIZATION OWNERSHIP AND FIRM PERFORMANCE: A LARGE META‐ANALYSIS OF THE TRANSITION LITERATURE
Authors: IWASAKI Ichiro , MIZOBATA Satoshi 
Published: December 2017

ABSTRACTThis paper aims to perform a large‐scale meta‐analysis of the relationship between post‐privatization ownership and firm performance in Central and Eastern Europe and the former Soviet Union. Baseline estimation of a meta‐regression model that employs a total of 2,894 estimates drawn from 121 previous studies indicated the superior impact of foreign ownership on firm performance in comparison with state and domestic private entities. Furthermore, the estimation of an extended meta‐regression model that explicitly controls for the idiosyncrasies of transition economies and privatization policies strongly suggested that differences between countries in location, privatization method, and speed of policy implementation strongly influence the link between post‐privatization ownership structure and firm performance. We also found that these factors not only cause a remarkable gap between countries in terms of ex post improvement in firm performance but also significantly affect the interrelationship between foreign investors, domestic outsider owners, and firm managers, and the relative superiority of various domestic outsiders. Conclusive evidence of the harm caused to ex post firm performance by voucher privatization is one of the most noteworthy empirical findings in this paper.
Oseltamivir and indomethacin reduce the oxidative stress in brain and stomach of infected rats
Authors: Guzmán David Calderón , Herrera Maribel Ortiz , Brizuela Norma Osnaya , Mejía Gerardo Barragán , García Ernestina Hernández , Olguín Hugo Juárez , Ruíz Norma Labra , Peraza Armando Valenzuela 
Published: December 2017

The aim of this study was to determine the effect of oseltamivir and indomethacin on lipid peroxidation (LP), GABA levels, and ATPase activity in brain and stomach of normal and infected rats (IR), as novel inflammation model. Female Sprague Dawley rats grouped five each, either in the absence or presence of a live culture of Salmonella typhimurium (S. typh), were treated as follows: group 1 (control), PBS buffer; group 2, oseltamivir (100 mg/kg); group 3, indomethacin (67 μg/rat); group 4, oseltamivir (100 mg/kg) + indomethacin (67 μg/rat). All drugs were given intraperitoneally for 5 days. IR received the same treatments and the brain and stomach of the rats were removed in order to measure levels of GABA, LP, and total ATPase, using validated methods. Levels of GABA increased in stomach and cortex of IR with oseltamivir, but decreased in striatum and cerebellum/medulla oblongata of IR with indomethacin. LP decreased in the three brain regions of IR with oseltamivir. ATPase increased in stomach of IR and non‐IR with oseltamivir and in striatum and cerebellum/medulla oblongata of IR with indomethacin. Results suggest that the effect of free radicals produced in an infection and inflammatory condition caused by S. typh could be less toxic by a combination of oseltamivir and indomethacin.
Editorial: rifaximin—a kick in the gut for spontaneous bacterial peritonitis?
Authors: Woodhouse C. , Shawcross D. L. 
Published: December 2017

Linked ContentThis article is linked to Goel et al and Goel and Nguyen papers. To view these articles visit https://doi.org/10.1111/apt.14361 and https://doi.org/10.1111/apt.14450.
Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD—Authors’ reply
Authors: Lang B. M. , Beerenwinkel N. , Misselwitz B. 
Published: December 2017

Linked ContentThis article is linked to Adams et al and Lang et al papers. To view these articles visit https://doi.org/10.1111/apt.14334 and https://doi.org/10.1111/apt.14378.
Editorial: rifaximin—a kick in the gut for spontaneous bacterial peritonitis? Authors’ reply
Authors: Goel A. , Nguyen M. H. 
Published: December 2017

Linked ContentThis article is linked to Goel et al and Woodhouse and Shawcross papers. To view these articles visit https://doi.org/10.1111/apt.14361 and https://doi.org/10.1111/apt.14406.