bluuebunny/crossref_metadata_2025_split huggingface dataset:
MSIGNET: a Metropolis sampling-based method for global optimal significant network identification
Authors: Chen Xi , Xuan Jianhua 
Published: February 2018

AbstractIn this paper, we propose a novel approach namely MSIGNET to identify subnetworks with significantly expressed genes by integrating context specific gene expression and protein-protein interaction (PPI) data. Specifically, we integrate differential expression of each gene and mutual information of gene pairs in a Bayesian framework and use Metropolis sampling to identify functional interactions. During the sampling process, a conditional probability is calculated given a randomly selected gene to control the network state transition. Our method provides global statistics of all genes and their interactions, and finally achieves a global optimal sub-network. We apply MSIGNET to simulated data and have demonstrated its superior performance over comparable network identification tools. Using a validated Parkinson data set we show that the network identified using MSIGNET is consistent to previously reported results but provides more biology meaningful interpretation of Parkinson’s disease. Finally, to study networks related to ovarian cancer recurrence, we investigate two patient data sets. Identified networks from independent data sets show functional consistence. And those common genes and interactions are well supported by current biological knowledge.
Inference of population structure from ancient DNA
Authors: Joseph Tyler A. , Pe’er Itsik 
Published: February 2018

AbstractMethods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.AvailabilityDystruct is implemented in C++, open-source, and available at https://github.com/tyjo/dystruct.
Focal adhesion kinase regulates early steps of myofibrillogenesis in cardiomyocytes
Authors: Taneja Nilay , Neininger Abigail C. , Bersi Matthew R. , Merryman W. David , Burnette Dylan T. 
Published: February 2018

AbstractForces generated by myofibrils within cardiomyocytes must be balanced by adhesion to the substrate and to other cardiomyocytes for proper heart function. Loss of this force balance results in cardiomyopathies that ultimately cause heart failure. How this force balance is first established during the assembly of myofibrils is poorly understood. Using human induced pluripotent stem cell derived cardiomyocytes, we show coupling of focal adhesions to myofibrils during early steps ofde novomyofibrillogenesis is essential for myofibril maturation. We also establish a key role for Focal adhesion kinase (FAK), a known regulator of adhesion dynamics in non-muscle cells, in regulating focal adhesion dynamics in cardiomyocytes. Specifically, FAK inhibition increased the stability of vinculin in focal adhesions, allowing greater substrate coupling of assembling myofibrils. Furthermore, this coupling is critical for regulating myofibril tension and viscosity. Taken together, our findings uncover a fundamental mechanism regulating the maturation of myofibrils in human cardiomyocytes.
Neural signatures of the processing of temporal patterns in sound
Authors: Herrmann Björn , Johnsrude Ingrid S. 
Published: February 2018

AbstractThe ability to detect regularities in sound (i.e., recurring structure) is critical for effective perception, enabling, for example, change detection and prediction. Two seemingly unconnected lines of research concern the neural operations involved in processing regularities: one investigates how neural activity synchronizes with temporal regularities (e.g., frequency modulation; FM) in sounds, whereas the other focuses on increases in sustained activity during stimulation with repeating tone-frequency patterns. In three electroencephalography studies with male and female human participants, we investigated whether neural synchronization and sustained neural activity are dissociable, or whether they are functionally interdependent. Experiment I demonstrated that neural activity synchronizes with temporal regularity (FM) in sounds, and that sustained activity increases concomitantly. In Experiment II, phase coherence of FM in sounds was parametrically varied. Although neural synchronization was more sensitive to changes in FM coherence, such changes led to a systematic modulation of both neural synchronization and sustained activity, with magnitude increasing as coherence increased. In Experiment III, participants either performed a duration categorization task on the sounds, or a visual object tracking task to distract attention. Neural synchronization was observed irrespective of task, whereas the sustained response was observed only when attention was on the auditory task, not under (visual) distraction. The results suggest that neural synchronization and sustained activity levels are functionally linked: both are sensitive to regularities in sounds. However, neural synchronization might reflect a more sensory-driven response to regularity, compared with sustained activity which may be influenced by attentional, contextual, or other experiential factors.Significance statementOptimal perception requires that the auditory system detects regularities in sounds. Synchronized neural activity and increases in sustained neural activity both appear to index the detection of a regularity, but the functional interrelation of these two neural signatures is unknown. In three electroencephalography experiments, we measured both signatures concomitantly while listeners were presented with sounds containing frequency modulations that differed in their regularity. We observed that both neural signatures are sensitive to temporal regularity in sounds, although they functionally decouple when a listener is distracted by a demanding visual task. Our data suggest that neural synchronization reflects a more automatic response to regularity, compared with sustained activity which may be influenced by attentional, contextual, or other experiential factors.
Prediction of the secundary structure at the tRNASer (UCN) ofLutzomyia longipalpis(Diptera: Psychodidae)
Authors: Hoyos-Lopez Richard 
Published: February 2018

AbstractLutzomyia longipalpisis the main vector ofLeishmania infantum, the etiological agent of visceral leishmaniasis in America and Colombia. Taxonomically belongs to the subgenusLutzomyia, which includes other vector species that exhibit high morphological similarity to the female species difficult to identify vectors in leishmaniasis foci and suggesting the search for molecular markers that facilitate this task, further researchs with mitochondrial genes, chromosome banding, reproductive isolation and pheromones evidence the existence of species complex. The aim of this study was to predict the secondary structure of mitochondrial transfer RNA serine (tRNASer) for UCN codon ofLutzomyia longipalpisas molecular marker for identify of this species. Sequences recorded in Genbank ofL. longipalpissequences were aligned with tRNA′s from previously described species and then tRNASer secondary structure was inferred by software tRNAscan-SE 1.21. The length of tRNASer was 67 base pairs (bp). Two haplotypes were detected in the five sequences analyzed. TheL. longipalpistRNASer showed 7 intrachain pairing in the acceptor arm, 3 in the DHU arm, 4 in the anticodon arm and 5 in the TψC. The size of the loops corresponded to 5 nucleotides in the DHU, 7 in the anticodon, 4 in the variable and 7 in the TψC.L. longipalpisis distinguished from other species at subgeneraLutzomyiaby the secondary structure and substitutions inferred tRNASer evidenced in the primary sequence.
Liquid co-substrates repower sewage microbiomes
Authors: Hardegen Justus , Latorre-Pérez Adriel , Vilanova Cristina , Günther Thomas , Simeonov Claudia , Porcar Manuel , Luschnig Olaf , Abendroth Christian 
Published: February 2018

AbstractA range of parameters are known to shape the methanogenic communities of biogas-producing digesters and to strongly influence the amount of biogas produced. In this work, liquid and solid fractions of grass biomass were used separately for semicontinuous batch methanation using sewage sludge as seed sludge. During 6 months of incubation, the amount of input COD was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based automated cell counting and full-length 16S rRNA high-throughput sequencing. In this sense, we prove for the first time the suitability of the ONT™MinION platform as a monitoring tool for anaerobic digestion systems. According to our results, solid-fed batches were highly unstable at higher COD input concentrations, and kept Methanosaeta spp. typically associated to sewage sludge-as the majoritary methanogenic archaea. In contrast, liquid-fed batches developed a more stable microbiome, proved enriched in Methanosarcina spp, and resulted in higher methanogenic yield. This work demonstrates the high repowering potential of microbiomes from sewage sludge digesters, and highlight the effectiveness of liquefied substrates for increasing biogas productivity in anaerobic digestions.
TreeCluster: Massively scalable transmission clustering using phylogenetic trees
Authors: Moshiri Niema 
Published: February 2018

AbstractBackgroundThe ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences.ResultsI present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multiple clustering optimization functions.ConclusionsTreeCluster is a freely-available cross-platform open source Python 3 tool for inferring transmission clusters from phylogenetic trees. Code, usage information, and in-depth descriptions of the implemented clustering modes are available publicly at the following repository:https://github.com/niemasd/TreeCluster
Cell type-specific variation of somatotopic precision across corticostriatal projections
Authors: Hooks Bryan M. , Papale Andrew E. , Paletzki Ronald , Feroze Muhammad , Eastwood Brian S. , Couey Jonathan J. , Winnubst Johan , Chandrashekar Jayaram , Gerfen Charles R. 
Published: February 2018

AbstractThe striatum shows general topographic organization and regional differences in behavioral functions. How corticostriatal topography differs across cortical areas and cell types to support these distinct functions is unclear. This study contrasted corticostriatal projections from two layer 5 cell types, intratelencephalic (IT-type) and pyramidal tract (PT-type) neurons, using viral vectors expressing fluorescent reporters in Cre-driver mice. Long-range corticostriatal projections from sensory and motor cortex are somatotopic, with a decreasing somatotopic specificity as injections move from sensory to motor and frontal areas. Somatotopic organization differs between IT-type and PT-type neurons, including injections in the same site, with IT-type neurons having higher somatotopic stereotypy than PT-type neurons. Furthermore, IT-type projections from interconnected cortical areas have stronger correlations in corticostriatal targeting than PT-type projections do. Thus, as predicted by a long-standing basal ganglia model, corticostriatal projections of interconnected cortical areas form parallel circuits in basal ganglia-thalamus-cortex loops.
Myosin Heavy Chain-embryonic is a crucial regulator of skeletal muscle development and differentiation
Authors: Sharma Akashi , Agarwal Megha , Kumar Amit , Kumar Pankaj , Saini Masum , Kardon Gabrielle , Mathew Sam J. 
Published: February 2018

SummaryMyosin heavy chains (MyHCs) are contractile proteins that are part of the thick filaments of the functional unit of the skeletal muscle, the sarcomere. In addition to MyHCs that are part of the adult muscle contractile network, two MyHCs - MyHC-embryonic and -perinatal are expressed during muscle development and are only transiently expressed in the adult during regeneration. The functions performed by these MyHCs has been a long-standing question and using a targeted mouse allele, we have characterized the role of MyHC-embryonic. Analysis of loss-of-function mice reveals that lack of MyHC-embryonic leads to mis-regulation of other MyHCs, alterations in fiber size, fiber number and fiber type at neonatal stages. We also find that loss of MyHC-embryonic leads to mis-regulation of genes involved in muscle differentiation. A broad theme from these studies is that loss of MyHC-embryonic has distinct effects on different muscles, possibly reflecting the unique fiber type composition of different muscles. Most significantly, our results indicate that MyHC-embryonic is required during embryonic and fetal myogenesis to regulate myogenic progenitor and myoblast differentiation in a non-cell autonomous manner via Mitogen Activated Protein Kinase (MAPKinase) and Fibroblast Growth Factor (FGF) signaling. Thus, our results signify that MyHC-embryonic is a key regulator of myogenic differentiation during embryonic, fetal and neonatal myogenesis.
Effect of rare earth lanthanum-cerium doping on corrosion behavior of zinc-aluminum-magnesium hot-dip galvanizing coatings used for transmission towers
Authors: Han Yu , Xia Yanqiu , Chen Xin , Sun Liang , Liu Dongyu , Ge Xiangyu 
Published: February 2018

Purpose
The purpose of this study is to improve the corrosion resistance of the transmission towers by Zinc-aluminum-magnesium (Zn-Al-Mg) coatings doped with rare earths lanthanum (La) and cerium (Ce) (denoted as Zn-Al-Mg-Re) in Q345 steel.

Design/methodology/approach
The phase structure of Zn-Al-Mg-Re composite coatings has been determined by X-ray diffraction, whereas their surface morphology and cross-sectional microstructure as well as cross-sectional elemental composition have been analyzed by scanning electron microscopy and energy-dispersive spectrometry. Moreover, the corrosion resistance of Zn-Al-Mg-Re composite coatings has been evaluated by acetic acid accelerated salt spray test of copper strip.

Findings
Experimental results show that doping with La and Ce favors to tune the composition (along with the generation of new phase, such as LaAl3 or Al11Ce3) and refine the microstructure of Zn-Al-Mg galvanizing coatings, thereby significantly improving the corrosion resistance of the coatings. Particularly, Zn-Al-Mg-Re with 0.15% (mass fraction) La exhibits the best corrosion resistance among the tested galvanizing coatings.

Originality/Value
Zinc-aluminum-magnesium (Zn-Al-Mg) coatings doped with rare earths lanthanum (La) and cerium (Ce) (denoted as Zn-Al-Mg-Re) have been prepared on Q345 steel substrate by hot-dip galvanizing so as to improve the corrosion resistance of the transmission towers, and to understand the corrosion inhibition of the Zn-Al-Mg-Re coating.
Co-production with young people to tackle alcohol misuse
Authors: Clark Jill , Laing Karen 
Published: February 2018

Purpose
The purpose of this paper is to present the learning gained from undertaking research activities in co-production with young people in order to tackle alcohol misuse in local communities.

Design/methodology/approach
The findings are drawn from an evaluation of an alcohol misuse change programme in which opportunities to learn about and conduct research were provided to young people through co-production. The evaluation was guided by a theory of change, and a portfolio of evidence collected which included feedback from the young people and project staff about their experiences.

Findings
This paper demonstrates that young people can be empowered to take on roles as agents of change in their own communities by learning more about research processes. However, the empowerment does not come from undertaking research training per se, but by being able to work co-productively with researchers on issues and questions that are of direct relevance to themselves and which are framed within a change agenda. Shared values, strong relationships and reciprocal knowledge exchange enabling flexible and relevant responses to real-world problems and questions are needed.

Originality/value
The paper suggests a reflexive and co-productive learning, design and delivery approach to involving young people in research. It challenges notions of young people as a problem in terms of alcohol misuse, and rather situates them as part of a solution that is aiming at longer-term transformational community change. This is significant in that much of the existing evidence concentrates on individual intervention.
The sources of house price changes in Malaysia
Authors: Kok Shiau Hui , Ismail Normaz Wana , Lee Chin 
Published: February 2018

Purpose
The purpose of this paper is to examine the house market in Malaysia from 2002 to 2015. Specifically, the macroeconomic determinants on the house price and house demand are investigated.

Design/methodology/approach
Structural Vector Autoregressive Regression was adopted to estimate the unexpected changes in both house demand (residential transaction volume) and prices based on economic theoretical reasoning that consider shock from macroeconomic determinants.

Findings
The transaction volume and real house prices respond to most of the macroeconomic shocks. While the impact of real gross domestic product (GDP) on house prices appears to be stronger and longer in comparison to other macroeconomic shocks, a 60 per cent change in house prices can be explained by real GDP regardless of whether it is in the short run or the long run. The studies also reveal that a positive effective exchange rate plays an important role when demonstrating the transaction volume. Moreover, monetary liquidity plays a major role in justifying the transaction volume. This implies that mortgage lending may have an impact on housing demand. Meanwhile, movements of house prices cannot be explained by the demand in quantity. This signifies that supply has a strong influence in determining the price.

Research limitations/implications
This study has implications on policymakers of which the interest rate as a cooling measure might not be effective in the short run. The interest rate has very little impact on housing prices. Furthermore, policymakers should address the concerns on speculations, as the results reveal that monetary liquidity and the exchange rate have a strong impact on the housing demand.

Originality/value
This study seeks to provide answers regarding the recent upsurge of Malaysian housing prices. Besides focusing on the house price changes, this study addresses the role of transaction volume while evaluating the house market, as housing prices are usually downwards rigid. Since the price and transaction volume are both related to the transaction activity, this study is significant and could be a good reflection on the actual demand behaviour in the residential market.
Notes on anthropogenic risks mitigation management and recovery of ancient theatres’ heritage
Authors: Haddad Naif Adel , Fakhoury Leen Adeeb , Akasheh Talal S. 
Published: February 2018

Purpose
Ancient theatres and odea are one of the most significant and creative socio-cultural edutainment centres of human history that are still in use. They stood and served as huge multi-functional structures for social, religious, propaganda and political meeting space. Meanwhile, ancient theatres’ sites have an intrinsic value for all people, and as a vital basis for cultural diversity, social and economic development, they should continue to be a source of information for future generations. Though, all places with ancient theatre heritage should be assessed as to their potential risk from any anthropogenic or natural process. The paper aims to discuss these issues.

Design/methodology/approach
The main paper’s objective is to discuss mainly the anthropogenic and technical risks, vulnerability and impact issues on the ancient classical theatres. While elaborating on relevant recent studies, where the authors were involved in ERATO and ATHENA European projects for ancient theatres and odea, this paper provides a brief overview of the main aspects of the anthropogenic qualitative risks and related issues for selected classical antiquity theatres. Some relevant cases are critically presented and investigated in order to examine and clarify the main risk mitigation issues as an essential prerequisite for theatre heritage preservation and its interface with heritage reuse.

Findings
Theatre risk mitigation is an ongoing and challenging task. By preventive conservation, theatre anthropogenic qualitative risks’ management can provide a framework for decision making. The needed related guidelines and recommendations that provide a systematic approach for sustainable management and planning in relation mainly to “ancient theatre compatible use” and “theatre technical risks” are analysed and presented. This is based on identification, classification and assessment of the theatre risk causes and contributing factors and their mitigation.

Originality/value
The paper also suggests a new methodological approach for the theatre anthropogenic qualitative risk assessment and mitigation management, and develop some recommendations that provide a systematic approach for theatre site managers and heritage experts to understand, assess, and mitigate risks mainly due to anthropogenic and technical threats.
Beyond metrics
Authors: Welch Amber N. , Wyatt-Baxter Krystal 
Published: February 2018

Purpose
The purpose of this paper is to describe an approach to developing a makerspace assessment plan. This approach focuses on connecting organizational and service point mission statements with outcome-based assessment plan goals, strategies, methods, and success measures.

Design/methodology/approach
This paper will outline the steps taken by an academic research library to design an outcomes-based assessment plan that monitors the human ecology of a makerspace. The paper includes a history of the space, the role of the library within the campus makerspace environment, the connection between mission statements and assessment plans, and how that connection can facilitate and drive space and service design.

Findings
Designing assessment plans that are centered on a makerspace mission statement can ensure that progress toward fulfilling the mission, values, and goals of the space is constantly monitored.

Originality/value
Academic library makerspace assessment literature is still in its infancy. This paper seeks to contribute to the literature on academic library makerspace management and stewardship.