bluuebunny/crossref_metadata_2025_split huggingface dataset:
The informational and signaling impacts of labels: experimental evidence from India on GM foods
Authors: Bansal Sangeeta , Chakravarty Sujoy , Ramaswami Bharat 
Published: July 2013

AbstractMuch of the debate between the European and US positions about the labeling of genetically modified (GM) foods has been whether consumers perceive labels as a source of information or as a signal to change behavior. In this paper we provide an experimental framework for examining these roles of information and signaling. While previous studies have focused on the impact of labels on consumer behavior, our interest is also in what happens prior to the expression of aversion to GM-labeled foods. In particular, the experiment design allows the researcher to estimate a lower bound of the informational impact of labels on GM food aversion. The other novel feature of this paper is that, unlike earlier studies, it uses subjects from a developing country.
Targeting cancer stem cells expressing an embryonic signature with anti-proteases to decrease their tumor potential
Authors: Darini C Y , Martin P , Azoulay S , Drici M-D , Hofman P , Obba S , Dani C , Ladoux A 
Published: July 2013

AbstractCancer stem cells (CSCs) are a specific subset of cancer cells that sustain tumor growth and dissemination. They might represent a significant treatment target to reduce malignant progression and prevent tumor recurrence. In solid tumors, several hierarchically organized CSC clones coexist, even within a single tumor. Among them, CSCs displaying an embryonic stem cell ‘stemness’ signature, based on the expression of Oct-4, Nanog and Sox2, are present in distinct high-grade tumor types associated with poor prognosis. We previously designed a model to isolate pure populations of these CSCs from distinct solid tumors and used it to screen for molecules showing selective toxicity for this type of CSC. Here we show that human immunodeficiency virus (HIV)-protease inhibitors (HIV-PIs) specifically target CSCs expressing an embryonic signature derived from tumors with distinct origins. They reduced proliferation in a dose-dependent manner with a higher specificity as compared with the total population of cancer cells and/or healthy stem cells, and they were efficient in inducing cell death. Lopinavir was the most effective HIV-PI among those tested. It reduced self-renewal and induced apoptosis of CSCs, subsequently impairing in vivo CSC-induced allograft formation. Two key pharmacophores in the LPV structure were also identified. They are responsible for the specificity of CSC targeting and also for the overall antitumoral activity. These results contribute to the identification of molecules presenting selective toxicity for CSCs expressing an embryonic stemness signature. This paves the way to promising therapeutic opportunities for patients suffering from solid cancer tumors of poor prognosis.
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
Authors: Barnard Romain L , Osborne Catherine A , Firestone Mary K 
Published: July 2013

Abstract
The microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil CO2 pulse upon rewetting, an important component of the ecosystem carbon budget. In three California annual grasslands, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced, and the abundances of these genes and transcripts were measured. Although bacterial community composition differed among sites, all sites shared a similar response pattern of the present and potentially active bacterial community to dry-down and wet-up. In contrast, the fungal community was not detectably different among sites, and was largely unaffected by dry-down, showing marked resistance to dessication. The potentially active bacterial community changed significantly as summer dry-down progressed, then returned to pre-dry-down composition within several hours of rewetting, displaying spectacular resilience. Upon rewetting, transcript copies of bacterial rpoB genes increased consistently, reflecting rapid activity resumption. Acidobacteria and Actinobacteria were the most abundant phyla present and potentially active, and showed the largest changes in relative abundance. The relative increase (Actinobacteria) and decrease (Acidobacteria) with dry-down, and the reverse responses to rewetting reflected a differential response, which was conserved at the phylum level and consistent across sites. These contrasting desiccation-related bacterial life-strategies suggest that predicted changes in precipitation patterns may affect soil nutrient and carbon cycling by differentially impacting activity patterns of microbial communities.
You are what you talk: quorum sensing induces individual morphologies and cell division modes in Dinoroseobacter shibae
Authors: Patzelt Diana , Wang Hui , Buchholz Ina , Rohde Manfred , Gröbe Lothar , Pradella Silke , Neumann Alexander , Schulz Stefan , Heyber Steffi , Münch Karin , Münch Richard , Jahn Dieter , Wagner-Döbler Irene , Tomasch Jürgen 
Published: July 2013

Abstract
Dinoroseobacter shibae, a member of the Roseobacter clade abundant in marine environments, is characterized by a pronounced pleomorphism. Cell shapes range from variable-sized ovoid rods to long filaments with a high copy number of chromosomes. Time-lapse microscopy shows cells dividing either by binary fission or by budding from the cell poles. Here we demonstrate that this morphological heterogeneity is induced by quorum sensing (QS). D. shibae utilizes three acylated homoserine lactone (AHL) synthases (luxI1–3) to produce AHLs with unsaturated C18 side chains. A ΔluxI1-knockout strain completely lacking AHL biosynthesis was uniform in morphology and divided by binary fission only. Transcriptome analysis revealed that expression of genes responsible for control of cell division was reduced in this strain, providing the link between QS and the observed phenotype. In addition, flagellar biosynthesis and type IV secretion system (T4SS) were downregulated. The wild-type phenotype and gene expression could be restored through addition of synthetic C18-AHLs. Their effectiveness was dependent on the number of double bonds in the acyl side chain and the regulated trait. The wild-type expression level of T4SS genes was fully restored even by an AHL with a saturated C18 side chain that has not been detected in D. shibae. QS induces phenotypic individualization of D. shibae cells rather than coordinating the population. This strategy might be beneficial in unpredictably changing environments, for example, during algal blooms when resource competition and grazing exert fluctuating selective pressures. A specific response towards non-native AHLs might provide D. shibae with the capacity for complex interspecies communication.
Negative regulation of bacterial quorum sensing tunes public goods cooperation
Authors: Gupta Rashmi , Schuster Martin 
Published: July 2013

Abstract
Bacterial quorum sensing (QS) often coordinates the expression of other, generally more costly public goods involved in virulence and nutrient acquisition. In many Proteobacteria, the basic QS circuitry consists of a synthase that produces a diffusible acyl-homoserine lactone and a cognate receptor that activates public goods expression. In some species, the circuitry also contains negative regulators that have the potential to modulate the timing and magnitude of activation. In this study, we experimentally investigated the contribution of this regulatory function to the evolutionary stability of public goods cooperation in the opportunistic pathogen Pseudomonas aeruginosa. We compared fitness and public goods expression rates of strains lacking either qteE or qscR, each encoding a distinct negative regulator, with those of the wild-type parent and a signal-blind receptor mutant under defined growth conditions. We found that (1) qteE and qscR mutations behave virtually identically and have a stronger effect on the magnitude than on the timing of expression, (2) high expression in qteE and qscR mutants imposes a metabolic burden under nutrient conditions that advance induction and (3) high expression in qteE and qscR mutants increases population growth when QS is required, but also permits invasion by both wild-type and receptor mutant strains. Our data indicate that negative regulation of QS balances the costs and benefits of public goods by attenuating expression after transition to the induced state. As the cells cannot accurately assess the amount of cooperation needed, such bet-hedging would be advantageous in changing parasitic and nonparasitic environments.
Oxypnictide SmFeAs(O,F) superconductor: a candidate for high–field magnet applications
Authors: Iida Kazumasa , Hänisch Jens , Tarantini Chiara , Kurth Fritz , Jaroszynski Jan , Ueda Shinya , Naito Michio , Ichinose Ataru , Tsukada Ichiro , Reich Elke , Grinenko Vadim , Schultz Ludwig , Holzapfel Bernhard 
Published: July 2013

AbstractThe recently discovered oxypnictide superconductor SmFeAs(O,F) is the most attractive material among the Fe-based superconductors due to its highest transition temperature of 56 K and potential for high-field performance. In order to exploit this new material for superconducting applications, the knowledge and understanding of its electro-magnetic properties are needed. Recent success in fabricating epitaxial SmFeAs(O,F) thin films opens a great opportunity to explore their transport properties. Here we report on a high critical current density of over 105 A/cm2 at 45 T and 4.2 K for both main field orientations, feature favourable for high-field magnet applications. Additionally, by investigating the pinning properties, we observed a dimensional crossover between the superconducting coherence length and the FeAs interlayer distance at 30–40 K, indicative of a possible intrinsic Josephson junction in SmFeAs(O,F) at low temperatures that can be employed in electronics applications such as a terahertz radiation source and a superconducting Qubit.
No exacerbation but impaired anti-viral mechanisms in a rhinovirus-chronic allergic asthma mouse model
Authors: Rochlitzer Sabine , Hoymann Heinz-Gerd , Müller Meike , Braun Armin 
Published: July 2013

Severe asthma and viral-induced asthma exacerbations represent a high unmet medical need as no therapy is currently available for these patients. HRV (human rhinovirus) is prominently associated with asthma exacerbations in humans. The aim of the present study was to establish a mouse model of severe asthma with additional rhinovirus infection to investigate the interplay between chronic allergic airway inflammation and acute respiratory viral infection. Balb/c mice were sensitized with HDM (house dust mite) extract (25 μg in 50 μl of saline) by i.n. (intranasal) delivery to the lung over 7 weeks. HRV1B (HRV serotype 1B) inoculation was performed i.n. on the last 3 days. Therapeutic treatment with FP (fluticasone propionate) was performed to assess steroid efficacy. Lung resistance was measured invasively to assess AHR (airway hyper-responsiveness). BAL (bronchoalveolar lavage) differential cell count, cytokines, lung histology and the proliferative and cytokine response of MLN (mediastinal lymph node) cells upon in vitro restimulation were analysed. Chronic HDM application induced a strong Th2-skewed eosinophilic airway inflammation and AHR, which was not exacerbated by superimposed HRV1B infection. Therapeutic steroid intervention in the chronic HDM model reduced BAL eosinophil cell counts, cytokine levels and AHR, while neutrophil numbers were unaffected. Steroid efficacy against inflammatory readouts was maintained during additional HRV1B infection. Animals with chronic allergic airway inflammation exhibited a diminished immune response towards superimposed HRV1B infection compared with HRV1B alone, as induction of the anti-viral and pro-inflammatory cytokines IFN (interferon)-α, IFN-γ and IL (interleukin)-12 were suppressed. Although superimposed HRV1B infection did not provoke asthma exacerbation in this severe model, a deficient anti-viral immune response to HRV1B was present under chronic allergic airway inflammatory conditions. Thus, this model is able to reflect some aspects of the complex interplay of respiratory virus infection in chronic allergic asthma.
Evaluating Salmon Spawning Habitat Capacity Using Redd Survey Data
Authors: Groves Phillip A. , Chandler James A. , Alcorn Brad , Richter Tracy J. , Connor William P. , Garcia Aaron P. , Bradbury Steven M. 
Published: July 2013

Abstract
Management and recovery goals for fish populations often rely on estimating the number of fish that can be supported by finite habitats. In the absence of direct measures of carrying capacity, management decisions are commonly informed by results of habitat models. However, the shortcomings and spatially explicit nature of most habitat models result in making assumptions, often preclude inclusion of important variables, and are rarely validated at the reach level. We analyze long-term, redd-count data for a population of Chinook Salmon Oncorhynchus tshawytscha to evaluate spawning habitat capacity of a major river. Adult escapement generally increased during the years 1994–2012; consequently site use and total redd counts also increased. Together, the annual use of spawning sites and the redd counts (as functions of adult escapement) provided evidence for density-dependent changes in the availability and capacity of spawning sites. Redd counts exceeded one recovery criterion specific to one spawning aggregate of the population during 11 years of our survey data, supporting the conclusion that adequate spawning habitat is available to attain a management goal set for this aggregate.
Received May 31, 2012; accepted March 27, 2013
CellMix: a comprehensive toolbox for gene expression deconvolution
Authors: Gaujoux Renaud , Seoighe Cathal 
Published: July 2013

Abstract
Summary: Gene expression data are typically generated from heterogeneous biological samples that are composed of multiple cell or tissue types, in varying proportions, each contributing to global gene expression. This heterogeneity is a major confounder in standard analysis such as differential expression analysis, where differences in the relative proportions of the constituent cells may prevent or bias the detection of cell-specific differences. Computational deconvolution of global gene expression is an appealing alternative to costly physical sample separation techniques and enables a more detailed analysis of the underlying biological processes at the cell-type level. To facilitate and popularize the application of such methods, we developed CellMix, an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.
Availability and Implementation: The CellMix package builds on R/BioConductor and is available from http://web.cbio.uct.ac.za/∼renaud/CRAN/web/CellMix. It is currently being submitted to BioConductor. The package’s vignettes notably contain additional information, examples and references.
Contact: renaud@cbio.uct.ac.za
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data
Authors: Yang Wen-Yun , Hormozdiari Farhad , Wang Zhanyong , He Dan , Pasaniuc Bogdan , Eskin Eleazar 
Published: July 2013

Abstract
Motivation: Haplotypes, defined as the sequence of alleles on one chromosome, are crucial for many genetic analyses. As experimental determination of haplotypes is extremely expensive, haplotypes are traditionally inferred using computational approaches from genotype data, i.e. the mixture of the genetic information from both haplotypes. Best performing approaches for haplotype inference rely on Hidden Markov Models, with the underlying assumption that the haplotypes of a given individual can be represented as a mosaic of segments from other haplotypes in the same population. Such algorithms use this model to predict the most likely haplotypes that explain the observed genotype data conditional on reference panel of haplotypes. With rapid advances in short read sequencing technologies, sequencing is quickly establishing as a powerful approach for collecting genetic variation information. As opposed to traditional genotyping-array technologies that independently call genotypes at polymorphic sites, short read sequencing often collects haplotypic information; a read spanning more than one polymorphic locus (multi-single nucleotide polymorphic read) contains information on the haplotype from which the read originates. However, this information is generally ignored in existing approaches for haplotype phasing and genotype-calling from short read data.
Results: In this article, we propose a novel framework for haplotype inference from short read sequencing that leverages multi-single nucleotide polymorphic reads together with a reference panel of haplotypes. The basis of our approach is a new probabilistic model that finds the most likely haplotype segments from the reference panel to explain the short read sequencing data for a given individual. We devised an efficient sampling method within a probabilistic model to achieve superior performance than existing methods. Using simulated sequencing reads from real individual genotypes in the HapMap data and the 1000 Genomes projects, we show that our method is highly accurate and computationally efficient. Our haplotype predictions improve accuracy over the basic haplotype copying model by ∼20% with comparable computational time, and over another recently proposed approach Hap-SeqX by ∼10% with significantly reduced computational time and memory usage.
Availability: Publicly available software is available at http://genetics.cs.ucla.edu/harsh
Contact: bpasaniuc@mednet.ucla.edu or eeskin@cs.ucla.edu
Magnetic Resonance Imaging Evaluation of the Effects of Surgical Invasiveness on Paravertebral Muscles After Muscle-preserving Interlaminar Decompression (MILD)
Authors: Tonomura Hitoshi , Hatta Yoichiro , Mikami Yasuo , Ikeda Takumi , Harada Tomohisa , Nagae Masateru , Koike Hironori , Hase Hitoshi , Kubo Toshikazu 
Published: July 2013

Study Design:
This is a retrospective study.

Objectives:
The aim of this study was to determine the extent of damage to the paravertebral muscles after muscle-preserving interlaminar decompression (MILD) using magnetic resonance imaging to evaluate changes in the multifidus muscle (MF).

Summary of Background Data:
Short-term surgical outcomes of MILD for lumbar spinal canal stenosis (LSCS) are satisfactory; however, the extent of damage to the paravertebral muscles after MILD remains unclear.

Methods:
Thirty-four patients (18 men/16 women; mean age: 72.6 y) who had LSCS treated with MILD were retrospectively investigated. A total of 61 decompressed disk levels [L2/3(5); L3/4(21); L4/5(30); L5/S(5)] and 34 nondecompressed levels (L1/2) were assessed. There was 1 decompressed disk level in 12 cases, 2 in 17 cases, and 3 in 5 cases. Magnetic resonance imaging scans were obtained before surgery and at 3 and 12–18 months after surgery, using the same scanner. The rate of paravertebral muscle atrophy was evaluated to compare the area of the MF in the T2-weighted axial plane (intervertebral disk level) preoperatively and postoperatively, using OsiriX Medical Imaging Software. Changes in muscle signal intensity were also recorded. Statistical analysis was performed using 3-way analysis of variance with the post hoc Fisher PSLD test.

Results:
The rate of MF atrophy was 4.0% at the decompressed levels and 2.1% at the nondecompressed levels. There were no changes of signal intensity in the MF between the preoperative and postoperative periods. In decompressed levels, muscle atrophy and signal intensity were significantly improved from 3 months to 12–18 months after surgery. The number and level of the decompressed disks did not affect the extent of muscle injury.

Conclusions:
The extent of paravertebral muscle injury after MILD is satisfactory. The midline interlaminar approach used in this technique may prevent local denervation and irreversible damage to the paravertebral muscles. These results indicate that MILD is useful to treat LSCS less invasively.
Smart space technology innovations
Authors: Chen Mu‐Yen , Lughofer Edwin David 
Published: July 2013

PurposeThe purpose of this paper is to introduce the theme issue on “Smart space technology innovations”.Design/methodology/approachThis editorial discusses the innovation concepts and advantages of smart space. The technologies of smart space and its application also are discussed. The editorial surveys the latest literature and research papers submitted to this special issue about smart space and technology in Library Hi Tech.FindingsSmart space has novel design and implementation perspectives for traditional information systems. Smart space depends not only on ambient intelligence and context‐aware computing techniques, but also on overall information architecture. Therefore, smart space innovation may have wide implications for academic and practice of library and information systems.Research limitations/implicationsThe paper discusses opportunities and challenges that smart space will bring. Its discusses the research of the papers submitted to this special issue on these topics.Originality/valueThe research issues of smart space are occurring at international conferences and in journal papers. The focal point on the techniques and applications for library and information systems is primary original and novel.
Facets of digital data dissemination: value addition through “imprints collection”
Authors: Meera B.M. , Manjunath M. , Kaddipujar Manjunath 
Published: July 2013

PurposeFacets of digital data dissemination, namely RRI Digital repository and Imprints collection, are two methods in which science communication can happen in the digital world. The purpose of this paper is to discuss the design, novelty and functionality of these facets as an archive, comprising a collage of profiles and publications of RRIians whose imprints on the sands of time have been culled and collated for posterity.Design/methodology/approachRRI Digital repository makes use of DSpace to preserve and showcase the research papers in text format, audio/video of lectures and images. Imprints collection is designed using Dreamweaver software. Images are uploaded using Jalbum.net software.FindingsDSpace, an open source software meant for managing digital assets can be used as a platform to develop a modern genre of data dissemination. An example to this end is the Imprints collection, a bio‐bibliographic database with many valuable additions showcasing the digital scholarship of an institute with archival value.Practical implicationsPractical implications of both RRI digital repository and imprints collection is to act as support service to enhance the creativity and collaboration among scientists of the institute within and across different research institutes in the country and across the world. Further, ResearcherID embedded in the profile pages of scientists helps scientometricians in citation analysis.Originality/valueNovelty associated with imprints collection in science communication using DSpace data is the strength of this tool. This is a unique style of digital data dissemination with supporting links between authors, their persona, their papers, lectures and photographs.