bluuebunny/crossref_metadata_2025_split huggingface dataset:
Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling
Authors: Zheng Hao , Powell J. Elijah , Steele Margaret I. , Dietrich Carsten , Moran Nancy A. 
Published: April 2017

SignificanceHoney bees are globally important plant pollinators. Guts of adult workers contain specialized bacteria not found outside bees. Experimental results show that gut bacteria increase weight gain in young adult bees, affect expression of genes governing insulin and vitellogenin levels, and increase sucrose sensitivity. Gut bacteria also shape the physicochemical conditions within the gut, lowering pH and oxygen levels. Peripheral resident bacteria consume oxygen, thus maintaining anoxia, as required for microbial activity. Additionally, gut bacteria produce short-chain fatty acids, with acetate and propionate as the major metabolites, as in guts of human and other animals. This study demonstrates how bacteria in the honey bee gut affect host weight gain and improves our understanding of how gut symbionts influence host health.
Introduction
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractThe use of graph theory to ‘visualize’ the relationship between sparsity patterns and Gaussian elimination is introduced. The potential of significant savings from the exploitation of sparsity is illustrated by one example. The effect of computer hardware on efficient computation is discussed. Realization of sparsity means more than faster solutions; it affects the formulation of mathematical models and the feasibility of solving them.
Gaussian elimination for dense matrices: numerical considerations
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractWe review of the impact of inexact computation (caused by data uncertainty and computer rounding error) on Gaussian elimination. We need to ensure that the algorithm produces answers that are consistent with the given data; that is, that the algorithm is stable. We want to know whether small changes to the original data lead to large changes in the solution; that is, whether the problem is ill-conditioned. We show how to control stability and measure conditioning. The concepts of pivoting, scaling, iterative refinement, and estimating condition numbers are introduced, which will be tools used while addressing sparsity issues in the rest of the book.
Reduction to block triangular form
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractWe consider algorithms for reducing a general sparse matrix to block triangular form. This form allows the corresponding set of linear equations to be solved as a sequence of subproblems. We discuss the assignment problem of placing entries on the diagonal as a part of the process of finding the block triangular form, though this problem is of interest in its own right. We also consider the extension of the block triangular form to rectangular and singular matrices.
Ordering sparse matrices for band solution
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractWe consider a different approach to reordering to preserve sparsity, with algorithms that take a global view of the problem. We now take a top-down approach to ordering as opposed to the local bottom-up approach considered in Chapter 7. In this chapter, we explore one global approach: ordering matrices for reduced bandwidth or profile (number of entries within the variable band). In this context, we also consider blocking and incorporating numerical pivoting. In Chapter 9, we introduce another approach to global orderings.
Orderings based on dissection
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractWe continue our discussion on orderings based on a global as opposed to a local approach. In this chapter, we study methods based on dissection. We discuss different ways of obtaining and refining a dissection ordering and compare the resulting ordering with that obtained by the minimum degree ordering. We also consider the extension of these methods to unsymmetric matrices.
Gaussian elimination using trees
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractWe first show how the frontal technique described in the previous chapter can be generalized. We then discuss a framework for implementing sparse Gaussian elimination following a symbolic choice of pivot sequence. Both the frontal technique and the framework involve trees and we discuss the relationship between them, how they can be constructed, their properties, and changes that can be made to improve the performance. We introduce the additional complexity of accommodating numerical pivoting which we will discuss more in Chapter 13.
Graphs for symmetric and unsymmetric matrices
Authors: Duff I. S. , Erisman A. M. , Reid J. K. 
Published: April 2017

AbstractFollowing on from the work of the previous chapter, we make extensive use of graphs for the efficient factorization of both symmetric and unsymmetric sparse matrices. It is in this area that most of the important recent developments concerning the factorization of large sparse matrices has occurred. We study the effect of numerical pivoting for stability, see how we can avoid it through static pivoting, and show how the pivoting is affected by scaling. We examine in some detail the factorization of matrices on parallel computers.
Evaluation of Water Content in Lumbar Intervertebral Discs and Facet Joints Before and After Physiological Loading Using T2 Mapping MRI
Authors: Yamabe Daisuke , Murakami Hideki , Chokan Kou , Endo Hirooki , Oikawa Ryosuke , Sawamura Shoitsu , Doita Minoru 
Published: April 2017

Study Design.
T2 mapping was used to quantify the water content of lumbar spine intervertebral discs (IVDs) and facet joints before and after physiological loading.

Objective.
The aim of this study was to clarify the interaction between lumbar spine IVD and facet joints as load-bearing structures by measuring the water content of their matrix after physiological loading using T2 mapping magnetic resonance imaging (MRI).

Summary of Background Data.
To date, few reports have functionally evaluated lumbar spine IVD and facet joints, and their interaction in vivo. T2 mapping may help detect changes in the water content of IVD and articular cartilage of facet joints before and after physiological loading, thereby enabling the evaluation of changes in interacted water retention between IVD and facet joints.

Methods.
Twenty asymptomatic volunteers (10 female and 10 male volunteers; mean age, 19.3 years; age range, 19–20 years) underwent MRI before and after physiological loading such as lumbar flexion, extension, and rotation. Each IVD from L1/2 to L5/S1 was sliced at center of the disc space, and the T2 value was measured at the nucleus pulposus (NP), anterior annulus fibrosus (AF), posterior AF, and bilateral facet joints.

Results.
In the NP, T2 values significantly decreased after exercise at every lumbar spinal level. In the anterior AF, there were no significant differences in T2 values at any level. In the posterior AF, T2 values significantly increased only at L4/5. In the bilateral facet joints, T2 values significantly decreased after exercise at every level.

Conclusion.
There was a significant decrease in the water content of facet joints and the NP at every lumbar spinal level after dynamic loading by physical lumbar exercise. These changes appear to play an important and interactional role in the maintenance of the interstitial matrix in the IVD NP and cartilage in the facet joint.

Level of Evidence: 3
Validity and Repeatability of a Novel Dynamic Visual Acuity System
Authors: Hirano Mariko , Hutchings Natalie , Simpson Trefford , Dalton Kristine 
Published: April 2017

ABSTRACT

Purpose
In many sports, athletes rely on visual information from the environment to perform. Some literature suggests athletes have superior visual abilities to non-athletes, particularly on tasks representative of the visual demands of their sport, such as dynamic acuity, eye movement accuracy and speed, and peripheral vision. Other literature suggests there is no difference between athletes and non-athletes, at least when standard clinical assessments are employed. A limitation of the literature is that almost none of the research has been conducted with standardized, validated tools. This is partly caused by a lack of readily available tools to measure tasks representative of the visual demands of sport, and available tests have typically not been validated against current clinical standards. The purpose of this study is to examine the validity and repeatability of a novel visual acuity system (moV&; V&MP Vision Suite) recently developed in the Vision & Motor Performance Lab (V&MP). moV& permits the measurement of many visual function parameters including dynamic visual acuity with predictable, random, and jittering target motion.

Methods
Twenty-five participants attended two study visits, separated by a minimum of 2 weeks. At each visit, static and dynamic visual acuity was measured using Snellen, ETDRS, and moV& charts. Static visual acuities were compared to determine the validity of moV&, and both static and dynamic visual acuities were compared between visits to determine the test–retest repeatability.

Results
moV& static visual acuities are clinically similar to visual acuities measured with the ETDRS chart (moV&, −0.09 ± 0.13; ETDRS, −0.03 ± 0.11, concordance correlation coefficient 0.726). Additionally, all static, dynamic, and jitter visual acuities demonstrate good test–retest repeatability (Lin’s concordance correlation coefficient range 0.451–0.953).

Conclusions
moV& provides good clinical measures of static visual acuity that are comparable to both Snellen and ETDRS measures. Dynamic visual acuity measures demonstrate good test–retest repeatability.
Environmental conditions and agronomic practices induce consistent global changes in DNA methylation patterns in grapevine (Vitis viniferacv Shiraz)
Authors: Xie Huahan , Konate Moumouni , Sai Na , Tesfamicael Kiflu Gebremicael , Cavagnaro Timothy , Gilliham Matthew , Breen James , Metcalfe Andrew , DeBei Roberta , Collins Cassandra , Rodriguez Lopez Carlos Marcelino 
Published: April 2017

AbstractFruit attributes that affect wine quality are thought to be largely driven by the interaction of grapevine’s genetic characteristics with environmental factors (i.e. climate, soil and topography) and vineyard management. All these variables, in conjunction with the wine making process, give a wine its distinctive character. Understanding how grapevines perceive and adapt to a changing environment will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant’s phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. Here we used Methylation Sensitive Amplified Polymorphisms to obtain global patterns of DNA methylation, and to identify the main drivers of epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six distinctive wine areas of a major wine zone, The Barossa, South Australia. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Furthermore, pairwise epigenetic distances between vineyards with similar management systems showed a significant correlation with geographic distance. Finally, methylation sensitive Genotyping By Sequencing identified 3,598 differentially methylated genes that were assigned to 1,144 unique GO terms of which 8.6% were associated with response to environmental stimulus. Taken together, our results indicate that the intensity and directionality of DNA methylation differentiation between vineyards and wine sub-regions within The Barossa are driven by management and local growing conditions. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
Predicting Protein Binding Affinity With Word Embeddings and Recurrent Neural Networks
Authors: Mazzaferro Carlo 
Published: April 2017

AbstractAt the core of our immunological system lies a group of proteins named Major Histocompatibility Complex (MHC), to which epitopes (also proteins sometimes named antigenic determinants), bind to eliciting a response. These responses are extremely varied and of widely different nature. For instance, Killer and Helper T cells are responsible for, respectively, counteracting viral pathogens and tumorous cells. Many other types exist, but their underlying structure can be very similar due to the fact that they all are proteins and bind to the MHC receptor in a similar fashion. With this framework in mind, being able to predict with precision the structure of a protein that will elicit a specific response in the human body represents a novel computational approach to drug discovery. Although many machine learning approaches have been used, no attempt to solve this problem using Recurrent Neural Networks (RNNs) exist. We extend the current efforts in the field by applying a variety of network architectures based on RNNs and word embeddings (WE). The code is freely available and under current development athttps://github.com/carlomazzaferro/mhcPreds
Nuclear microenvironments modulate transcription from low-affinity enhancers
Authors: Crocker Justin , Tsai Albert , Muthusamy Anand K. , Lavish Luke D. , Singer Robert H. , Stern David L. 
Published: April 2017

AbstractTranscription factors regulate gene expression by binding to DNA for short durations and by often binding to low-affinity DNA sequences. It is not clear how such temporally brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) functionally utilizes low-affinity binding sites in theDrosophila melanogaster shavenbaby(svb) locus in nuclear microenvironments of relatively high Ubx concentration. By manipulating the affinity ofsvbenhancers, we revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. A Ubx cofactor, Homothorax (Hth), was enriched together with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. These results suggest that low affinity sites overcome their kinetic inefficiency by utilizing microenvironments with high concentrations of transcription factors and cofactors. Mechanisms that generate these microenvironments are likely to be a general feature of eukaryotic transcriptional regulation.
Aging, mortality and the fast growth trade-off ofSchizosaccharomyces pombe
Authors: Nakaoka Hidenori , Wakamoto Yuichi 
Published: April 2017

AbstractReplicative aging has been demonstrated in asymmetrically dividing unicellular organisms, seemingly caused by unequal damage partitioning. Although asymmetric segregation and inheritance of potential aging factors also occurs in symmetrically dividing species, it nevertheless remains controversial whether this results in aging. Based on large-scale single-cell lineage data obtained by time-lapse microscopy with a microfluidic device, in this report, we demonstrate the absence of replicative aging in old-pole cell lineages ofSchizosaccharomyces pombecultured under constant favorable conditions. By monitoring more than 1,500 cell lineages in seven different culture conditions, we showed that both cell division and death rates are remarkably constant for at least 50–80 generations. Our measurements revealed that the death rate per cellular generation increases with division rate, pointing to a physiological trade-off with fast growth under balanced growth conditions. We also observed the formation and inheritance of Hsp104-associated protein aggregates, which are a potential aging factor in old-pole cell lineages, and found that these aggregates exhibited a tendency to preferentially remain at the old-poles for several generations. However, the aggregates were eventually segregated from old-pole cells upon cell division and probabilistically allocated to new-pole cells. The quantity and inheritance of protein aggregates increased neither cellular generation time nor cell death initiation rates. Furthermore, our results revealed that unusually large amounts of protein aggregates induced by oxidative stress exposure did not result in aging; old-pole cells resumed normal growth upon stress removal, despite the fact that most of them inherited significant quantities of aggregates. These results collectively indicate that protein aggregates are not a major determinant of cell fate inS. pombe, and thus cannot be an appropriate molecular marker or index for replicative aging under both favorable and stressful environmental conditions.
Relative electrical conductivity measurements of the rat frontal cortex and the influence on current source density
Authors: Yanovsky Yevgenij , Brankačk Jurij 
Published: April 2017

summaryThe relative electrical conductivity gradient with depth was estimated in the frontal cortex of anaesthetized rats. Current source density (CSD) approximations of field potentials evoked by ventromedial thalamic stimulations with an assumed homogeneous electrical conductivity of the neocortical tissue were compared to those with correction for the estimated conductivity gradient. In spite of the cellular heterogeneity the electrical conductivity of the frontal cortical tissue was found to be fairly homogeneous inside the superficial (layers I through IV) or deep layers (V- VI). The relative conductivity increased twofold at the transition between superficial and deep layers. Regardless of this changes CSD analysis of the field potentials evoked by ventromedial thalamic stimulation revealed negligible differences between estimations ignoring the conductivity and those taking the conductivity into account. No sinks or sources appeared or disappeared. Both CSD approximations revealed: 1) a strong sink in layer I representing most likely summed monosynaptic EPSPs of the ventromedial thalamic afferents; 2) a strong sink in layer VI, probably representing summed disynaptic EPSPs on dendrites of layer VI pyramidal cells, generated by axons of upper layer pyramidal cells; and 3) a sink in lower layer V representing probably threesynaptic summed EPSPs on dendrites of layer V pyramidal cells.
Modeling Zika Virus Congenital Eye Disease: Differential Susceptibility of Fetal Retinal Progenitor Cells and iPSC-Derived Retinal Stem Cells to Zika Virus Infection
Authors: Contreras Deisy , Jones Melissa Kaye , Martinez Laura E. , Gangalapudi Vineela , Tang Jie , Wu Ying , Zhao Jiagang J. , Chen Zhaohui , Wang Shaomei , Arumugaswami Vaithilingaraja 
Published: April 2017

SummaryZika virus (ZIKV) causes microcephaly and congenital eye disease that is characterized by macular pigment mottling, macular atrophy, and loss of foveal reflex. The cell and molecular basis of congenital ZIKV infection are not well understood. Here, we utilized a biologically relevant cell-based system on human fetal retinal pigment epithelial cells (FRPE) and iPSC-derived retinal stem cells (iRSCs) to model ZIKV-ocular cell injury processes. FRPEs were highly susceptible to ZIKV, resulting in apoptosis and decreased viability, whereas iRSCs showed reduced susceptibility. Transcriptomics and proteomics analyses of infected FRPE cells revealed the activation of innate immune and inflammatory response genes, and dysregulation of cell survival pathways, mitochondrial transmembrane potential, phagocytosis, and particle internalization. Nucleoside analogue drug treatment inhibited ZIKV replication and prevented apoptosis. In conclusion, ZIKV affects ocular cells of different developmental stages resulting in cellular injury and death, further providing molecular insight into the pathogenesis of congenital eye disease.
Measuring business sustainability in food service operations: a case study in the fast food industry
Authors: Vu Ha Minh , Chan Hing Kai , Lim Ming K. , Chiu Anthony S.F. 
Published: April 2017

Purpose
The purpose of this paper is to develop an approach to measure business sustainability in food service operations. The main objectives are to understand the concepts of business sustainability and, after constructing a framework based on a literature review, to assess the relation between the proposed framework and the empirical case study in a fast food retailer chain.

Design/methodology/approach
In order to examine the applicability of the proposed framework, focus group interview and face-to-face interviews were conducted. Additionally, some other secondary data such as official websites or company reports were also used to support the interview results.

Findings
Finding of the research result has shown most of the factors of business sustainability employed to measure sustainability food service operations are supported.

Originality/value
This study contributes to the literature by showing that environmental and social sustainability are significantly recognized in the corporation. More importantly, through the data analysis, a new factor of social sustainability, namely, community contribution has been found. The contribution of this paper is certainly applicable to other food service operations who wish to achieve a good degree of business sustainability.
A classification scheme for representing the variation in business and supply chain performance in Indian manufacturing industry
Authors: Soni Gunjan , Kodali Rambabu 
Published: April 2017

Purpose
The purpose of this paper is to identify a classification scheme which represents the variation in business and supply chain performance of supply chains in Indian manufacturing industry. Classification is done by presenting an empirical taxonomy of clusters representing supply chains in Indian manufacturing industry based on variation in supply chain excellence index (SCEI) and business performance index (BPI).

Design/methodology/approach
The clustering of supply chains in Indian manufacturing industry is done by considering BPI and SCEI as clustering variables, which were found by using survey responses and results of a prior empirical study which was carried out in Indian manufacturing industry. The cluster analysis is performed by using Ward’s agglomerative hierarchical clustering followed by using K-means clustering algorithm to establish final set of clusters.

Findings
It was found that supply chains in Indian manufacturing industries can be clustered in four major clusters which are named as strategic, celebrity, capable and undeveloped cluster. The characteristics of these clusters reveal some major characteristics of supply chains in Indian manufacturing industry.

Originality/value
The research work presented in this paper takes a novel way to introduce the clusters of supply chains in Indian manufacturing industry. The researchers who are seeking patterns in large data sets of manufacturing companies of Indian industry will be benefitted by using the proposed clusters. While practitioners who are seeking to move their supply chain one step ahead will also reap the benefits of the paper by seeking the characteristics of particular cluster.