bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational modeling of immune system of the fish for a more effective vaccination in aquaculture
Authors: Madonia Alice , Melchiorri Cristiano , Bonamano Simone , Marcelli Marco , Bulfon Chiara , Castiglione Filippo , Galeotti Marco , Volpatti Donatella , Mosca Francesco , Tiscar Pietro-Giorgio , Romano Nicla 
Published: May 2017

Abstract

Motivation
A computational model equipped with the main immunological features of the sea bass (Dicentrarchus labrax L.) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae.

Results
Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen. The model has shown a good ability to be used in sea bass and could be implemented for different routes of vaccine administration even with more than two pathogens. The model confirms the suitability of in silico methods to optimize vaccine doses and the immune response to them. This model could be applied to other species to optimize the design of new vaccination treatments of fish in aquaculture.

Availability and implementation
The method is available at http://www.iac.cnr.it/∼filippo/c-immsim/

Supplementary information
Supplementary data are available at Bioinformatics online.
Remnant lipoproteins
Authors: Varbo Anette , Nordestgaard Børge G. 
Published: May 2017

Purpose of review
To review recent advances in the field of remnant lipoproteins and remnant cholesterol with a focus on cardiovascular disease risk.

Recent findings
In line with previous years’ research, current observational, genetic, and mechanistic studies find remnant lipoproteins (defined in different ways) to be involved in atherosclerosis development and cardiovascular disease risk. High concentrations of remnant cholesterol could explain some of the residual risk of cardiovascular disease seen after LDL cholesterol lowering. This will be increasingly important as populations worldwide become more obese and more have diabetes, both of which elevate remnant cholesterol concentrations. Many smaller scale studies and post hoc analyses show that remnant cholesterol can be lowered by different types of drugs; however, results from large scale studies with the primary aim of reducing cardiovascular disease risk through lowering of remnant cholesterol in individuals with elevated concentrations are still missing, although some are under way.

Summary
Remnant cholesterol is a risk factor for cardiovascular disease, and can be lowered by different types of drugs; however, large scale studies of cardiovascular disease risk reduction through remnant lipoprotein lowering are under way.
Zygomaticomaxillary complex fractures: diagnosis and treatment
Authors: Peretti Nicholas , MacLeod Stephen 
Published: May 2017

Purpose of review
To provide an overview of zygomaticomaxillary complex (ZMC) fractures and their treatment. Aspects of anatomy, diagnosis, and treatment objectives of these common fractures will be reviewed including recent literature.

Recent findings
Advances in technology such as guided surgery have allowed for better outcomes and a reduction in surgeon variability with regard to postoperative results. The use of titanium and bioresorbable mini screws and plates have expanded the ability to achieve stable and predictable results. There are many different challenges and techniques that are acceptable to treat zygoma fractures. Surgeon preference and training dictate these methods that vary among specialties.

Summary
ZMC fractures are commonly encountered in the trauma setting. Although there is a multitude of treatment methods available, the ultimate goal for any surgeon should be to reproduce premorbid form and function. The availability of techniques such as 3D navigation, contralateral mirroring, and advances in fixation technology have shown promise for better outcomes, particularly in severely comminuted or displaced fractures.
Data for Community Health Assessment in Rural Colorado: A Comparison of Electronic Health Records to Public Health Surveys to Describe Childhood Obesity
Authors: Gutilla Margaret J. , Davidson Arthur J. , Daley Matthew F. , Anderson G. Brooke , Marshall Julie A. , Magzamen Sheryl 
Published: May 2017

Context:
Community-level data are necessary to inform community health assessments and to plan for appropriate interventions. However, data derived from public health surveys may be limited or unavailable in rural locations.

Objective:
We compared 2 sources of data for community health assessment in rural Colorado, electronic health records (EHRs) and routine public health surveys.

Design:
Comparison of cross-sectional measures of childhood/youth obesity prevalence and data quality.

Setting:
Two rural Colorado counties, La Plata and Prowers.

Participants:
The EHR cohort comprised patients 2 to 19 years of age who underwent a visit with the largest health care provider in each county. These data included sex, age, weight, height, race, ethnicity, and insurance status. Public health survey data were obtained from 2 surveys, the Colorado Child Health Survey (2-14 years of age) and the Healthy Kids Colorado Survey (15-19 years of age) and included caregiver and self-reported height and weight estimates.

Main Outcome Measures:
We calculated body mass index percentile for each patient and survey respondent and determined overweight/obesity prevalence by county. We evaluated data source quality indicators according to a rubric developed for this analysis.

Results:
The EHR sample captured approximately 35% (n = 3965) and 70% (n = 2219) of all children living in La Plata and Prowers Counties, respectively. The EHR prevalence estimates of overweight/obesity were greater in precision than survey data in both counties among children 2 to 14 years of age. In addition, the EHR data were more timely and geographically representative than survey data and provided directly measured height and weight. Conversely, survey data were easier to access and more demographically representative of the overall population.

Conclusions:
Electronic health records describing the prevalence of obesity among children/youth living in rural Colorado may complement public health survey data for community health assessment and health improvement planning.
Bilateral Optic Disc Pits With Posterior Pituitary Ectopia
Authors: Horton Jonathan C. , Barkovich A. James 
Published: May 2017

Abstract:
Posterior pituitary ectopia has been reported previously in association with optic nerve hypoplasia, as a variant of septo-optic dysplasia. We describe a 14-year-old boy with posterior pituitary ectopia and bilateral optic disc pits. He had hypopituitarism and a reduction in visual acuity to 20/40 in each eye, owing to loss of foveal ganglion cells. Optic pits and posterior pituitary ectopia may have occurred together in the same subject by chance, but the rarity of both conditions suggests a possible association.
Comparative Huntington and Parkinson Disease mRNA Analysis Reveals Common Inflammatory Processes
Authors: Labadorf Adam , Choi Seung Hoan , Myers Richard H 
Published: May 2017

ABSTRACTHuntington’s and Parkinson’s Diseases (HD and PD) are neurodegenerative disorders that share some pathological features but are disparate in others. For example, while both diseases are marked by aberrant protein aggregation in the brain, the specific proteins that aggregate and types of neurons affected differ. A better understanding of the molecular similarities and differences between these two diseases may lead to a more complete mechanistic picture of both the individual diseases and the neurodegenerative process in general. We sought to characterize the common transcriptional signature of HD and PD as well as genes uniquely implicated in each of these diseases using mRNA-Seq data from post mortem human brains in comparison to neuropathologically normal controls. The enriched biological pathways implicated by HD differentially expressed genes show remarkable consistency with those for PD differentially expressed genes and implicate the common biological processes of neuroinflammation, apoptosis, transcriptional dysregulation, and neuron-associated functions. Comparison of the differentially expressed (DE) genes highlights a set of consistently altered genes that span both diseases. In particular, processes involving nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB) and transcription factor cAMP response element-binding protein (CREB) are the most prominent among the genes common to HD and PD. When the combined HD and PD data are compared to controls, relatively few additional biological processes emerge as significantly enriched suggesting that most pathways are independently seen within each disorder. Despite showing comparable numbers of DE genes, DE genes unique to HD are enriched in far more coherent biological processes than the DE genes unique to PD, suggesting that PD may represent a more heterogeneous disorder.
General environmental heterogeneity as the explanation of sexuality? Comparative study shows that ancient asexual taxa are associated with both biotically and abiotically homogeneous environments
Authors: Toman Jan , Flegr Jaroslav 
Published: May 2017

AbstractEcological theories of sexual reproduction assume that sexuality is advantageous in certain conditions, for example, in biotically or abiotically more heterogeneous environments. Such theories thus could be tested by comparative studies. However, the published results of these studies are rather unconvincing. Here we present the results of a new comparative study based solely on the ancient asexual clades. The association with biotically or abiotically homogeneous environments in these asexual clades was compared with the same association in their sister, or closely related, sexual clades. Using the conservative definition of ancient asexuals (i.e. age > 1 million years), we found six pairs for which relevant ecological data are available. The difference between the homogeneity type of environment associated with the sexual and asexual species was then compared in an exact binomial test. Based on available literature, the results showed that the vast majority of ancient asexual clades tend to be associated with biotically or abiotically, biotically, and abiotically more homogeneous environments than their sexual controls. In the exploratory part of the study, we found that the ancient asexuals often have durable resting stages, enabling life in subjectively homogeneous environments, live in the absence of intense biotic interactions, and are very often sedentary, inhabiting benthos and soil. The consequences of these findings for the ecological theories of sexual reproduction are discussed.
Building applications for interactive data exploration in systems biology
Authors: Fjukstad Bjørn , Dumeaux Vanessa , Olsen Karina Standahl , Hallet Michael , Lund Eiliv , Bongo Lars Ailo 
Published: May 2017

AbstractAs the systems biology community generates and collects data at an unprecedented rate, there is a growing need for interactive data exploration tools to explore the datasets. These tools need to combine advanced statistical analyses, relevant knowledge from biological databases, and interactive visualizations in an application with clear user interfaces. To answer specific research questions tools must provide specialized user interfaces and visualizations. While these are application-specific, the underlying components of a data analysis tool can be shared and reused later. Application developers can therefore compose applications of reusable services rather than implementing a single monolithic application from the ground up for each project.Our approach for developing data exploration applications in systems biology builds on the microservice architecture. Microservice architectures separates an application into smaller components that communicate using language-agnostic protocols. We show that this design is suitable in bioinformatics applications where applications often use different tools, written in different languages, by different research groups. Packaging each service in a software container enables re-use and sharing of key components between applications, reducing development, deployment, and maintenance time.We demonstrate the viability of our approach through a web application, MIxT blood-tumor, for exploring and comparing transcriptional profiles from blood and tumor samples in breast cancer patients. The application integrates advanced statistical software, up-to-date information from biological databases, and modern data visualization libraries.The web application for exploring transcriptional profiles, MIxT, is online atmixt-blood-tumor.bci.mcgill.caand open-sourced atgithub.com/fjukstad/mixt. Packages to build the supporting microservices are open-sourced as a part of Kvik atgithub.com/fjukstad/kvik.
Serial Crystallography with Multi-stage Merging of 1000s of Images
Authors: Soares Alexei S , Yamada Yusuke , Jakoncic Jean , McSweeney Sean , Sweet Robert M , Skinner John , Foadi James , Fuchs Martin R. , Schneider Dieter K. , Shi Wuxian , Andi Babak , Andrews Lawrence C , Bernstein Herbert J 
Published: May 2017

AbstractKAMO and Blend provide particularly effective tools to manage automatically the merging of large numbers of datasets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending Blend to support additional clustering options such as use of more accurate cell distance metrics and use of reflection-intensity correlation coefficients to infer “distances” among sets of reflec- tions. This increases the sensitivity to differences in unit cell parameters and allows for clustering to assemble nearly complete datasets on the basis of intensity or ampli- tude differences. If datasets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. If starting from incomplete datasets, one applies KAMO twice, first using cell parameters. In this step we use either the simple cell vector distance of the original Blend, or we use the more sensi- tive NCDist. This step tends to find clusters of sufficient size so that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between the reflections having a common hkl to merge clusters in a way sensitive to structural differences that may not have perturbed the cell parameters sufficiently to make meaningful clusters.Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into cate- gories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent from one another, it should be possible to greatly improve the efficacy of data clustering software by using a multi-stage partitioning strategy. Here, we have demonstrated one possible approach to multi-stage data clustering. Our strategy is to use unit-cell clustering until merged data is sufficiently complete then to use intensity-based clustering. We have demonstrated that, using this strategy, we are able to accurately cluster datasets from crystals that have subtle differences.
The nucleoid occlusion protein SlmA is a direct transcriptional activator of chitobiose utilization inVibrio cholerae
Authors: Klancher Catherine A. , Hayes Chelsea A. , Dalia Ankur B. 
Published: May 2017

ABSTRACTChitin utilization by the cholera pathogenVibrio choleraeis required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by thechboperon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of thechboperon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of thechboperon. SlmA has not previously been implicated in gene regulation. Also, SlmA is a member of the TetR family of proteins, which are generally transcriptional repressors.In vitro, we find that SlmA binds directly to thechboperon promoter, andin vivo, we show that this interaction is, surprisingly, required for transcriptional activation of this locus and for chitobiose utilization. Using point mutations that disrupt distinct functions of SlmA, we find that DNA-binding, but not nucleoid occlusion, is critical for transcriptional activation. This study identifies a novel role for SlmA as a transcriptional regulator inV. choleraein addition to its established role as a cell division licensing factor.AUTHOR SUMMARYThe cholera pathogenVibrio choleraeis a natural resident of the aquatic environment and causes disease when ingested in the form of contaminated food or drinking water. In the aquatic environment, the shells of marine zooplankton, which are primarily composed of chitin, serve as an important food source for this pathogen. The genes required for the utilization of chitin are tightly regulated inV. cholerae, however, the exact mechanism underlying this regulation is currently unclear. Here, we uncover that a protein involved in regulating cell division is also important for regulating the genes involved in chitin utilization. This is a newly identified property for this cell division protein and the significance of a common regulator for these two disparate activities remains to be understood.
Drift-induced selection between male and female heterogamety
Authors: Veller Carl , Muralidhar Pavitra , Constable George W. A. , Nowak Martin A. 
Published: May 2017

AbstractEvolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes and in those creating a new pair. In fact, substitution rates are strongly biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of ‘drift-induced selection’ operating at every point along the equilibrium paths: stochastic jumps off the paths return, on average, with a directional bias in favor of the dominant segregating sex chromosome. Our results offer novel explanations for the ubiquity of transitions between male and female heterogamety and the preponderance of dominant major sex determining genes.
Influence of innovation competence on firm level competitiveness: an exploratory study
Authors: Srivastava Saurabh , Sultan Abid , Chashti Nasreen 
Published: May 2017

PurposeThe dynamics of the competitive performance of the small medium firms is an evolving field of research in the developing countries like India. The influence of the innovation on the competitive performance of the firms is still an evolving area in India. This paper aims to explore the influence of the innovation on the competitive performance. The study is based upon the agro-food processing industry of the Jammu and Kashmir state of India.Design/methodology/approachThe paper is based upon the exploratory design. It uses quantitative as well as qualitative method for the firm level analysis of competitiveness. The aggregate index method has been used to construct the innovation competence and total competitive performance index. The regression analysis is used for describing the model based upon the primary data.FindingsThe results of the study provide for a significant relationship between the innovation competence and firm level competitiveness. It describes the position of the agro-food processing firms under study with respect to the innovation competence index score and total competitiveness performance index.Research limitations/implicationsThe paper provides for the managerial implications of strategically incubating the innovation-based competence for the firms in specific geographical areas. The policy implications in terms of developing specific clusters and incubators for incremental and radical innovations can be derived, in regional economies.Originality/valueThe paper discusses the issue of interaction of innovation competence and firm level competitiveness of the agro-food processing industry, which is dynamic, specifically in the developing states. The paper discussed unique methodology of using aggregate index method for defining the innovation competence and competitiveness for the firms where the consistency of data is a major issue for such a complex phenomenon.
Research on Chinese school of modern GUANLI science
Authors: Liu Ren-huai , Sun Kai , Sun Dongchuan 
Published: May 2017

Purpose
The purpose of this article is to put forward China’s Hanyu Pinyin word guanli as an academic basic term to the world.

Design/methodology/approach
GUANLI as an academic basic term, which holds multiple meanings of several English words, such as management, administration, governance, etc. As a basic term, GUANLI, derived several words, such as GUANLIOLOGY, GUANLIST/GUANLIER and GUANLIWORK/GUANLIJOB, to precisely and exactly convey the Chinese GUANLI ideas. It is the historical mission and opportunity for the authors to research and establish the Chinese School of Modern GUANLI Science (CSMGS).

Findings
It is inevitably necessary to build the combined Chinese–Western discourse system of GUANLI science (CCWDSGS). Some other research results of CSMGS are also presented in this paper.

Research limitations/implications
It is needless to say that there are still lots of problems in China, including in the GUANLI field. These problems will gradually be solved in China’s reform and development that takes place continuously. New problems will come up while old problems are being solved and settled; problems producing in a loop, problems solving in a loop, this is the dialectics. The authors have full confidence in solving problems, as well as in China’s development and future.

Originality/value
Practice comes first and then it is followed by theory. The authors first have the “China Model”, followed by the “Chinese School” consequently. The “China Model” has already been there, and the “Chinese School” relies on the author’s proactive research and innovation. It is just the right time for the authors to study and create the CSMGS. This is the historical mission and opportunity awaited by contemporary Chinese.