bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Mixture Copula Bayesian Network Model for Multimodal Genomic Data
Authors: Zhang Qingyang , Shi Xuan 
Published: February 2017

AbstractGaussian Bayesian networks have become a widely used framework to estimate directed associations between joint Gaussian variables, where the network structure encodes decomposition of multivariate normal density into local terms. However, the resulting estimates can be inaccurate when normality assumption is moderately or severely violated, making it unsuitable to deal with recent genomic data such as the Cancer Genome Atlas data. In the present paper, we propose a mixture copula Bayesian network model which provides great flexibility in modeling non-Gaussian and multimodal data for causal inference. The parameters in mixture copula functions can be efficiently estimated by a routine Expectation-Maximization algorithm. A heuristic search algorithm based on Bayesian information criterion is developed to estimate the network structure, and prediction can be further improved by the best-scoring network out of multiple predictions from random initial values. Our method outperforms Gaussian Bayesian networks and regular copula Bayesian networks in terms of modeling flexibility and prediction accuracy, as demonstrated using a cell signaling dataset. We apply the proposed methods to the Cancer Genome Atlas data to study the genetic and epigenetic pathways that underlie serous ovarian cancer.
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
Authors: Zhu Xun , Wolfgruber Thomas , Tasato Austin , Garmire David G. , Garmire Lana X 
Published: February 2017

AbstractBackgroundSingle-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level.Computational methods to process scRNA-Seq have limited accessibility to bench scientists as they require significant amounts of bioinformatics skills.ResultsWe have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene filtering, geneexpression normalization, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein-networ interaction visualization, and pseudo-time cell series construction.ConclusionsGranatum enables broad adoption of scRNA-Seq technology by empowering the bench scientists with an easy-to-use graphical interface for scRNA-Seq data analysis. The package is freely available for research use athttp://garmiregroup.org/granatum/app
An attempt to replicate a dissociation between syntax and semantics during sentence comprehension reported by Dapretto & Bookheimer (1999,Neuron)
Authors: Siegelman Matthew , Mineroff Zachary , Blank Idan , Fedorenko Evelina 
Published: February 2017

AbstractDoes processing the meanings of individual wordsvs. assembling words into phrases and sentences rely on distinct pools of cognitive and neural resources? Many have argued for such a dissociation, although the field is lacking a consensus on which brain region(s) support lexico-semanticvs. syntactic processing. Although some have also argued against such a dissociation, the dominant view in the field remains that distinct brain regions support these two fundamental components of language. One of the earlier and most cited pieces of evidence in favor of this dissociation comes from a paper by Dapretto & Bookheimer (1999, Neuron; DB). Using a sentence meaning comparison task, DB observed two distinct peaks within the left inferior frontal gyrus (LIFG): one more active when comparisons relied on lexico-semantic cues, and another – when they instead relied on syntactic cues. Although the paper has been highly cited over the years, no attempt has been made, to our knowledge, to replicate the original finding. We here report an fMRI study that attempts to do so. Using a combination of three approaches – whole-brain, group-level ROIs, and individual functional ROIs – we fail to replicate the originally reported dissociation. In particular, parts of the LIFG respond reliably more strongly during lexico-semantic than syntactic processing, but no part of the LIFG (including in the region defined around the peak reported by DB) shows the opposite response pattern. We hypothesize that the original result was a false positive, possibly driven by one participant or item given the use of a fixed-effects analysis and a small number of items (8 per condition) and participants (n=8).
Simulating heterogeneous populations using Boolean models
Authors: Ross Brian C. , Boguslav Mayla , Weeks Holly , Costello James 
Published: February 2017

AbstractCertain biological processes such as cancer development and immune activation are controlled by rare cellular events that are difficult to capture computationally through simulations of individual cells. Here we show that when cellular states are described using a Boolean network model, one can exactly simulate the dynamics of non-interacting, highly heterogeneous populations directly, without having to model the various subpopulations. This strategy captures even the rarest outcomes of the model with no sampling error. Our method can incorporate heterogeneity in both cell state and, by augmenting the model, the underlying rules of the network as well (i.e. mutations). We demonstrate our method by using it to simulate a heterogeneous population of Boolean networks modeling the T-cell receptor, spanning ~ 1020distinct cellular states and mutational profiles.
The evolution of queen control over worker reproduction in the social Hymenoptera
Authors: Olejarz Jason , Veller Carl , Nowak Martin A. 
Published: February 2017

AbstractA trademark of eusocial insect species is reproductive division of labor, in which workers forego their own reproduction while the queen produces almost all offspring. The presence of the queen is key for maintaining social harmony, but the specific role of the queen in the evolution of eusociality remains unclear. A long-discussed scenario is that a queen either behaviorally or chemically sterilizes her workers. However, the demographic and ecological conditions that enable such manipulation are unknown. Accordingly, we propose a simple model of evolutionary dynamics that is based on haplodiploid genetics. We consider a mutation that acts in a queen, causing her to control the reproductive behavior of her workers. Our mathematical analysis yields precise conditions for the evolutionary emergence and stability of queen-induced worker sterility. These conditions do not depend on the queen's mating frequency. Moreover, we find that queen control is always established if it increases colony reproductive efficiency and can evolve even if it decreases colony efficiency. We further outline the conditions under which queen control is evolutionarily stable against invasion by mutant, reproductive workers.
What is in it for me: firms strategizing for public-private innovation
Authors: Munksgaard Kristin B. , Evald Majbritt Rostgaard , Højbjerg Clarke Ann , Damgaard Torben Munk 
Published: February 2017

Purpose
Public-private innovation (PPI) is often claimed to contribute to societal welfare, to bring positive effects to the public sector and to open new markets to private firms. Engaging in public-private relationships for innovation is, however, also recognised as challenging and problematic. The purpose of this paper is to discuss the managerial and strategic challenges faced by private firms when engaging in public-private relationships for innovation.

Design/methodology/approach
This qualitative study presents ten firms’ engagement in public-private relationships. Half of them are experienced in innovation in public-private relationship, the other half are engaging in public-private relationships for the first time. Cross-case analysis brings insight into how these different types of firms strategize for handling relationships with public partners.

Findings
Contrary to non-experienced firms, experienced firms deliberately build a long-term strategy for engaging in PPI in expectation of outcome from more than a single project. They not only engage in building an understanding of the public using setting, but also seek to bridge with the public developing and producing setting to a greater extent than less experienced firms. The experienced firms utilise relationships with actors in the wider public network as a device and an asset for overcoming challenges and for reaping benefits from their engagement.

Originality/value
The study outlines the characteristics of strategizing among the most experienced firms and their special ability to embrace the complexity of the public sector network while working simultaneously on developing innovation for specific public counterparts.
Developing attributes for evaluating construction project-based performance
Authors: Willar Debby 
Published: February 2017

Purpose
The Indonesian construction industry has to considerably rise due to the issues of quality product, organisational performance and global competitiveness faced today, along with settling several national challenges that continue to plague the construction industry. Delivering high-quality construction products and services is non-negotiable when competing for contracts with international constructors. Developing such an assessment system to evaluate the performance of Indonesian construction companies is an urgent need in order to encourage and motivate the construction companies to continually improve their performance in the execution of construction works. The purpose of this paper is to empirically test the key attributes related to the evaluation of quality and performance in the construction project-based case of Indonesia.

Design/methodology/approach
A survey was conducted in the five provinces in Indonesia involving 216 construction practitioners from medium and large qualifications of construction companies.

Findings
On the basis of the data analysis results, the study develops the 39 key attributes that can be a basis for the development of Indonesian building construction project performance assessment system. The attributes cover construction companies’ performance during project implementation, in delivering final project results and in implementing quality procedures for building construction works.

Originality/value
The outcome of this study is considered significant to provide a tool for the government to assess the quality performance of contractors in delivering projects against specified standards, and a guideline for the contractors to improve their competitiveness by implementing continuous quality improvement. The confirmed attributes developed from this study is an initial step towards developing an Indonesian construction comprehensive quality performance assessment system.
Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir
Authors: Freedman Adam J.E. , Tan BoonFei , Thompson Janelle R. 
Published: February 2017

SummaryMicroorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling.
The Effect of Body Mass on Outdoor Adult Human Decomposition
Authors: Roberts Lindsey G. , Spencer Jessica R. , Dabbs Gretchen R. 
Published: February 2017

AbstractForensic taphonomy explores factors impacting human decomposition. This study investigated the effect of body mass on the rate and pattern of adult human decomposition. Nine males and three females aged 49–95 years ranging in mass from 73 to 159 kg who were donated to the Complex for Forensic Anthropology Research between December 2012 and September 2015 were included in this study. Kelvin accumulated degree days (KADD) were used to assess the thermal energy required for subjects to reach several total body score (TBS) thresholds: early decomposition (TBS≥6.0),TBS≥12.5, advanced decomposition (TBS≥19.0),TBS≥23.0, and skeletonization (TBS≥27.0). Results indicate no significant correlation between body mass andKADDat anyTBSthreshold. Body mass accounted for up to 24.0% of variation in decomposition rate depending on stage, and minor differences in decomposition pattern were observed. Body mass likely has a minimal impact on postmortem interval estimation.
Evaluation of Skin Surface as an Alternative Source of ReferenceDNASamples: A Pilot Study
Authors: Albujja Mohammed H. , Bin Dukhyil Abdul Aziz , Chaudhary Abdul Rauf , Kassab Ahmed Ch. , Refaat Ahmed M. , Babu Saranya Ramesh , Okla Mohammad K. , Kumar Sachil 
Published: February 2017

AbstractAn acceptable area for collectingDNAreference sample is a part of the forensicDNAanalysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of referenceDNAsample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. GenomicDNAwas extracted and quantified then genotyped using standard techniques. The highestDNAconcentration ofSSCsamples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities ofDNAthan swabs moistened with salicylic acid, and it gave the highest percentage of fullSTRprofiles (97%). This study supports the use ofSSCas a noninvasive sampling technique and as a extremely useful source ofDNAreference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable.
Condition‐dependence and sexual ornamentation: Effects of immune challenges on a highly sexually dimorphic grasshopper
Authors: Valverde J. Pablo , Eggert Hendrik , Kurtz Joachim , Schielzeth Holger 
Published: February 2017

AbstractSexual ornaments contribute substantially to phenotypic diversity and it is particularly relevant to understand their evolution. Ornaments can assume the function of signals‐of‐quality that the choosy sex uses to evaluate potential mating partners. Often there are no obvious direct benefits and investment into mate choice is primarily rewarded by beneficial alleles that are inherited to the offspring. Inter‐sexual communication via sexual ornaments requires honesty of the sexual signal, yet the question of what maintains honesty remains only partially solved. One solution is that honesty is maintained by trait expression being dependent on individual condition, since condition‐dependent trait expression offers an effectively inexhaustible source of genetic variability. Here we test in the highly sexually dimorphic club‐legged grasshopper Gomphocerus sibiricus if putative sexual ornaments, in particular the striking front‐leg clubs, are more strongly affected by a lipopolysaccharide (LPS) immune challenge than putatively not sexually selected traits. Our results show overall little condition‐dependent expression of morphological and song traits, with sexually selected traits exhibiting effects comparable to nonsexually selected traits (with the possible exception of stridulatory file length and syllable‐to‐pause ratio in advertisement songs). Interestingly, field observations of individuals of lethally parasitized individuals suggest that a very strong environmental challenge can specifically affect the expression of the front‐leg clubs. The presence of 1% of males in natural populations with missing or heavily deformed clubs plus 5% with minor club deformations furthermore indicate that there are risks associated with club development during final ecdysis and this might act as a filter against deleterious alleles.
Understanding the linkages between migration and household food security in India
Authors: Choithani Chetan 
Published: February 2017

AbstractThis paper argues for the need to integrate migration in future food policy research and practice and, in doing so, examines the role of internal migration as a livelihood strategy in influencing food security among rural households. Migration has become a key component of livelihood strategies for an increasing number of rural households across the developing world. Importantly, there is emerging consensus among academics and policy makers on migration's potentially positive effects in reducing poverty and promoting sustainable human development. Concurrently, the significance of the catch‐cry ‘food security for all’ as an important development objective has been growing, particularly since the 2007–08 global food crisis. However, academic and policy discussions on these two issues have tended to proceed largely in silos, with little attention devoted to the relationship they bear with each other. Using primary survey data collected from 392 rural households from a district in western Bihar in India, this paper seeks to fill this gap in relational dynamics. It first reviews plausible reasons for this disconnect between migration and food security in the wider developing countries' context, and then draws on a primary survey of rural Indian households to provide empirical household‐level insights on the linkages between people's movements and households' capacity to secure food. In particular, the paper focuses on the often‐overlooked role of migrants' remittances for food security of rural households at points of origin. The findings show that, by equipping households with improved purchasing power and enabling investment in agriculture, remittances contribute positively to household food security.
Bilateral thalamic lesions: A pictorial review
Authors: Özgür Anıl , Esen Kaan , Kaleağası Hakan , Yılmaz Arda , Kara Engin , Yıldız Altan 
Published: February 2017

SummaryBithalamic lesions are uncommon, however, both focal and systemic disorders may present bilateral abnormalities in the thalamus in different acute and chronic clinical situations. Neuroimaging, in particular magnetic resonance imaging, plays an essential role in diagnostic approach. Imaging features such as signal alterations, diffusion restriction or contrast enhancement are helpful in characterization of these abnormalities. The location of the lesions may provide key information because some pathologies typically involve a certain part of the thalamus. In addition to thalamic findings, neuroimaging findings in other parts of the brain associated with the clinical and laboratory information should be taken into account to make a correct diagnosis.
Skin prick tests and specific IgE in 10‐year‐old children: Agreement and association with allergic diseases
Authors: Chauveau A. , Dalphin M.‐L. , Mauny F. , Kaulek V. , Schmausser‐Hechfellner E. , Renz H. , Riedler J. , Pekkanen J. , Karvonen A. M. , Lauener R. , Roduit C. , Vuitton D. A. , von Mutius E. , Dalphin J.‐C. ,   the PASTURE Study Group
Published: February 2017

AbstractBackgroundAccurate assessment of atopic sensitization is pivotal to clinical practice and research. Skin prick test (SPT) and specific IgE (sIgE) are often used interchangeably. Some studies have suggested a disagreement between these two methods, and little is known about their association with allergic diseases. The aims of our study were to evaluate agreement between SPT and sIgE, and to compare their association with allergic diseases in 10‐year‐old children.MethodsSkin prick test, sIgE measurements, and assessment of allergic diseases were performed in children aged 10 years in the Protection against Allergy: STUdy in Rural Environments (PASTURE) cohort. The agreement between SPT and sIgE was assessed by Cohen's kappa coefficient with different cutoff values.ResultsSkin prick tests and sIgE were performed in 529 children. The highest agreement (κ=.44) was found with a cutoff value of 3 and 5 mm for SPT, and 3.5 IU/mL for sIgE. The area under the curve (AUC) obtained with SPT was not significantly different from that obtained with sIgE. For asthma and hay fever, SPT (cutoff value at 3 mm) had a significantly higher specificity (P<.0001) than sIgE (cutoff value at 0.35 IU/mL) and the specificity was not different between both tests (P=.1088).ConclusionSkin prick test and sIgE display moderate agreement, but have a similar AUC for allergic diseases. At the cutoff value of 3 mm for SPT and 0.35 IU/mL for sIgE, SPT has a higher specificity for asthma and hay fever than sIgE without difference for sensitivity.
Most children who took part in a comprehensive malnutrition programme in Madagascar reached and maintained the recovery threshold
Authors: Magnin Margot , Stoll Beat , Voahangy Rajaobelina , Jeannot Emilien 
Published: February 2017

AbstractAimThe benefits of including nutritional education in programmes that tackle moderate and severe acute malnutrition remain poorly documented. This study in Madagascar evaluated the nutritional status of children who took part in an innovative programme that included maternal education, on completion and after a year.MethodsEach year, this outpatient programme admits 2400 malnourished children from six months to 59 months in the lower districts of Antananarivo, Madagascar. Children were drawn by lots, and their anthropometric data were measured. A descriptive retrospective longitudinal study was conducted on 573 children who took part between 2010 and 2013.ResultsThe programme lasted an average of 38 days and, on completion, 82.2% had reached the recovery threshold, and 16.2% had moved up to mild malnutrition. This was achieved with food supplements of 720 kcal per day, despite the Malagasy Public Health recommendation of 1000–1500 kcal per day. After one year, 79.1% were still above the recovery threshold, and 15% had mild malnutrition. The recovery rate was higher for children under 24 months of age (odds ratio 2.9, 95% confidence interval 1.93–4.59).ConclusionMost children who attended this malnutrition programme with maternal education in Madagascar reached the recovery threshold on completion and had maintained it after one year.