bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple secretoglobin 1A1 genes are differentially expressed in horses
Authors: Côté Olivier , Lillie Brandon N , Hayes Michael Anthony , Clark Mary Ellen , van den Bosch Laura , Katavolos Paula , Viel Laurent , Bienzle Dorothee 
Published: December 2012

Abstract

Background
Secretoglobin 1A1 (SCGB 1A1), also called Clara cell secretory protein, is the most abundantly secreted protein of the airway. The SCGB1A1 gene has been characterized in mammals as a single copy in the genome. However, analysis of the equine genome suggested that horses might have multiple SCGB1A1 gene copies. Non-ciliated lung epithelial cells produce SCGB 1A1 during inhalation of noxious substances to counter airway inflammation. Airway fluid and lung tissue of horses with recurrent airway obstruction (RAO), a chronic inflammatory lung disease affecting mature horses similar to environmentally induced asthma of humans, have reduced total SCGB 1A1 concentration. Herein, we investigated whether horses have distinct expressed SCGB1A1 genes; whether the transcripts are differentially expressed in tissues and in inflammatory lung disease; and whether there is cell specific protein expression in tissues.

Results
We identified three SCGB1A1 gene copies on equine chromosome 12, contained within a 512-kilobase region. Bioinformatic analysis showed that SCGB1A1 genes differ from each other by 8 to 10 nucleotides, and that they code for different proteins. Transcripts were detected for SCGB1A1 and SCGB1A1A, but not for SCGB1A1P. The SCGB1A1P gene had most inter-individual variability and contained a non-sense mutation in many animals, suggesting that SCGB1A1P has evolved into a pseudogene. Analysis of SCGB1A1 and SCGB1A1A sequences by endpoint-limiting dilution PCR identified a consistent difference affecting 3 bp within exon 2, which served as a gene-specific “signature”. Assessment of gene- and organ-specific expression by semiquantitative RT-PCR of 33 tissues showed strong expression of SCGB1A1 and SCGB1A1A in lung, uterus, Fallopian tube and mammary gland, which correlated with detection of SCGB 1A1 protein by immunohistochemistry. Significantly altered expression of the ratio of SCGB1A1A to SCGB1A1 was detected in RAO-affected animals compared to controls, suggesting different roles for SCGB 1A1 and SCGB 1A1A in this inflammatory condition.

Conclusions
This is the first report of three SCGB1A1 genes in a mammal. The two expressed genes code for proteins predicted to differ in function. Alterations in the gene expression ratio in RAO suggest cell and tissue specific regulation and functions. These findings may be important for understanding of lung and reproductive conditions.
Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
Authors: Ariza-Cosano Ana , Visel Axel , Pennacchio Len A , Fraser Hunter B , Gómez-Skarmeta José Luis , Irimia Manuel , Bessa José 
Published: December 2012

Abstract

Background
Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis- regulatory elements (cis- changes) or from changes in the expression pattern or function of transcription factors (trans- changes). While isolated examples of trans- changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear.

Results
Here, we attempt to examine the prevalence of trans- effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for trans- changes in the evolution of gene expression.

Conclusions
In total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the trans environment may play a significant role in the evolution of gene expression in vertebrates.
Translation and adaptation of an international questionnaire to measure usage of complementary and alternative medicine (I-CAM-G)
Authors: Re Meike Lo , Schmidt Stefan , Güthlin Corina 
Published: December 2012

Abstract

Background
The growing body of data on prevalence of complementary and alternative medicine (CAM) usage means there is a need to standardize measurement on an international level. An international team has published a questionnaire (I-CAM-Q), but no validation has yet been provided. The aim of the present study was to provide a German measurement instrument for CAM usage (I-CAM-G) which closely resembles the original English version, and to assess it’s performance in two potential samples for measuring CAM usage.

Methods
The English I-CAM-Q questionnaire was translated into German, and adapted slightly. The resulting I-CAM-G questionnaire was then pre-tested on 16 healthy volunteers, and 12 cognitive interviews were carried out. The questionnaire was employed in a sample of breast cancer patients (N = 92, paper and pencil), and a sample from the general population (N = 210, internet survey). Descriptive analyses of items and missing data, as well as results from the cognitive interviews, are presented in this paper.

Results
The translated questionnaire had to be adapted to be consistent with the German health care system. All items were comprehensible, whereby some items were unambiguous (e.g. CAM use yes/no, helpfulness), while others gave rise to ambiguous answers (e.g. reasons for CAM use), or high rates of missing data (e.g. number of times the CAM modality had been used during the last 3 months). 78% of the breast cancer patients and up to 85% of a sample of the general population had used some form of CAM.

Conclusions
Following methodologically sound and comprehensive translation, adaptation and assessment processes using recognized translation procedures, cognitive interviews, and studying the performance of the questionnaire in two samples, we arrived at a German questionnaire for measuring CAM use which is comparable with the international (English) version. The questionnaire appropriately measures CAM use, with some items being more appropriate than others. We recommend the development of a short version.
Mouse macrophage innate immune response to chikungunya virus infection
Authors: Kumar Shiril , Jaffar-Bandjee Marie-Christine , Giry Claude , Connen de Kerillis Léa , Merits Andres , Gasque Philippe , Hoarau Jean-Jacques 
Published: December 2012

Abstract

Background
Infection with Chikungunya alphavirus (CHIKV) can cause severe arthralgia and chronic arthritis in humans with persistence of the virus in perivascular macrophages of the synovial membrane by mechanisms largely ill-characterized.

Findings
We herein analysed the innate immune response (cytokine and programmed cell death) of RAW264.7 mouse macrophages following CHIKV infection. We found that the infection was restrained to a small percentage of cells and was not associated with a robust type I IFN innate immune response (IFN-α4 and ISG56). TNF-α, IL-6 and GM-CSF expression were upregulated while IFN-γ, IL-1α, IL-2, IL-4, IL-5, IL-10 or IL-17 expression could not be evidenced prior to and after CHIKV exposure. Although CHIKV is known to drive apoptosis in many cell types, we found no canonical signs of programmed cell death (cleaved caspase-3, -9) in infected RAW264.7 cells.

Conclusion
These data argue for the capacity of CHIKV to infect and drive a specific innate immune response in RAW264.7 macrophage cell which seems to be polarized to assist viral persistence through the control of apoptosis and IFN signalling.
Heritable alteration in salt-tolerance in rice induced by introgression from wild rice (Zizania latifolia)
Authors: Yang Chunwu , Zhang Tianyuan , Wang Huan , Zhao Na , Liu Bao 
Published: December 2012

Abstract

Background
Introgression as a means of generating phenotypic novelty, including altered stress tolerance, is increasingly being recognized as common. The underlying basis for de novo genesis of phenotypic variation in the introgression lines remains largely unexplored. In this investigation, we used a rice line (RZ35) derived from introgressive hybridization between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.), along with its rice parental line (cv. Matsumae) as the experimental materials. We compared effects of salt stress on growth, ion homeostasis, and relevant gene expression between RZ35 and Matsumae, to explore possible mechanisms of heritable alteration in stress tolerance induced by the introgression.

Results
Contrary to our expectation, the results showed that the inhibitory effect of salt stress on growth of RZ35 was significantly greater than that of Matsumae. We further found that a major underlying cause for this outcome is that the introgression process weakened the capacity in Na+ exclusion under the salt stress condition, and hence, escalated the injuries of Na+ and Cl- in shoots of RZ35. Accordingly, based on q-RT-PCR analysis, four genes known to be involved in the Na+ exclusion, i.e., OsHKT1;5, OsSOS1, OsCIPK24 and OsCBL4, were found to be significantly down-regulated in roots of RZ35 relative to its rice parental line under the salt stress condition, thus implicating a gene expression regulation-based molecular mechanism underlying the difference in salt stress-tolerance between the introgression line and its rice parental line.

Conclusions
We show that introgression represents a potent means for rapidly generating de novo heritable variations in physiological traits like stress tolerance in plants, although the direction of the alteration appears unpredictable.
Inflammatory Markers and Risk of Type 2 Diabetes
Authors: Wang Xia , Bao Wei , Liu Jun , OuYang Ying-Ying , Wang Di , Rong Shuang , Xiao Xiao , Shan Zhi-Lei , Zhang Yan , Yao Ping , Liu Lie-Gang 
Published: December 2012

OBJECTIVE
There has been growing evidence that inflammatory markers play a role in the development of type 2 diabetes. We aimed to systematically review prospective studies on the associations of elevated levels of interleukin-6 (IL-6) and C-reactive protein (CRP) with increased risk of type 2 diabetes by conducting a meta-analysis.

RESEARCH DESIGN AND METHODS
A systematic search of the PubMed, EMBASE, ISI Web of Knowledge, and Cochrane Library databases up until 10 February 2012 was conducted to retrieve prospective studies matched to search terms. We used generalized least-squares trend estimation to assess dose-response relationships. The summary risk estimates were pooled using either fixed-effects or random-effects models to incorporate between-study variation.

RESULTS
The meta-analysis, including 10 prospective studies, with a total of 19,709 participants and 4,480 cases, detected a significant dose-response association of IL-6 levels with type 2 diabetes risk (relative risk [RR] 1.31 [95% CI 1.17–1.46]). For CRP, the meta-analysis involving 22 cohorts, with a total of 40,735 participants and 5,753 cases, showed that elevated CRP levels were significantly associated with increased risk of type 2 diabetes (1.26 [1.16–1.37]), with the absence of publication bias. Sensitivity and subgroup analyses further supported the associations.

CONCLUSIONS
This meta-analysis provides further evidence that elevated levels of IL-6 and CRP are significantly associated with increased risk of type 2 diabetes.
Regroupement familial : l'exception algérienne (1962-1976)
Authors: Cohen Muriel 
Published: December 2012

Le décret de 1976 relatif aux conditions d’entrée et de séjour des familles d’étrangers résidant régulièrement en France ne fait qu’officialiser des procédures administratives apparues dans les années 1920 et qui se renforcent progressivement après-guerre. Mais ce cadre juridique ne s’applique pas aux familles algériennes qui, du fait de l’héritage colonial, bénéficient d’un régime dérogatoire censé les favoriser. Mais est-ce bien le cas ?
Outsourcing in Healthcare through Process Modularization – A Lean Perspective
Authors: Guimarães Cristina Machado , de Carvalho José Crespo 
Published: December 2012

Looking for efficiency, quality and profitability gains, healthcare organizations are adopting outsourcing solutions in the attempt of “doing more with less”. Seeking for cost reduction, risk mitigation, adapting to quick changes without compromising internal resources, these organizations also take big risks in control and flexibility variables. In order to understand how healthcare organizations find the best value equation combining internal and external resources in a modular service conception, a case study on a start-up Long-term Care unit with innovative format, great levels of customization and following an outsourcing strategy, was carried out. The main conclusion, among others, is that in ambitious start-ups, having speed of entrance as the conditioning factor, a process orientation and management approach may offer a clear view of the gains related with trade-off decisions regarding time and cost (agility) and cost and quality (Leanness) ie, decisions under the “leagile” paradigm. This study contributes for a wider understanding of the “leagile” concept associated to an outsourcing operational strategy. Additionally, it also provides new insights to the concept of modularity in services settings in a complex service as healthcare.
Concise Review: In Search of Unlimited Sources of Functional Human Pancreatic Beta Cells
Authors: Scharfmann Raphael , Rachdi Latif , Ravassard Philippe 
Published: December 2012

Abstract
It is well-established that insulin-producing pancreatic beta cells are central in diabetes. In type 1 diabetes, beta cells are destroyed by an autoimmune mechanism, whereas in type 2 diabetes, there is a decrease in functional beta-cell mass. In this context, studying beta cells is of major importance. Beta cells represent only 1% of total pancreatic cells and are found dispersed in the pancreatic gland. During the past decades, many tools and approaches have been developed to study rodent beta cells that efficiently pushed the field forward. However, rodent and human beta cells are not identical, and our knowledge of human beta cells has not progressed as quickly as our understanding of rodent beta cells. We believe that one of the reasons for this inefficient progress is the difficulty of accessing unlimited sources of functional human pancreatic beta cells. The main focus of this review concerns recent strategies to generate new sources of human pancreatic beta cells.
Dyes, Environmental Analysis ofUpdate based on the original article by J. Riu and D. Barceló,Encyclopedia of Analytical Chemistry, © 2000, John Wiley & Sons, Ltd
Authors: Pérez Sandra , Riu Josep , Barceló Damià 
Published: December 2012

AbstractAn overview of current analytical methodologies for the determination of dyes in environmental samples is presented. Analytical methods involving liquid chromatography (LC) and mass spectrometry (MS) are reviewed. The combination of capillary electrophoresis (CE) with MS as a new alternative for the analysis and confirmation of polar compounds (and particularly the sulfonated azo dyes) in environmental samples is also discussed. Finally, the extraction and preconcentration of dyes from water samples involving various solid‐phase extraction (SPE) protocols are presented. Recent findings in the occurrence of some dyes in the aquatic environment have also been included.
Clustering and Classification of Analytical DataUpdate based on the original article by Barry K. Lavine,Encyclopedia of Analytical Chemistry, © 2000, John Wiley & Sons, Ltd.
Authors: Lavine Barry K. , Mirjankar Nikhil 
Published: December 2012

AbstractClustering and classification are the major subdivisions of pattern recognition. Using these techniques, samples can be classified according to a specific property through measurements indirectly related to a property of interest (e.g. the type of fuel responsible for an underground spill). An empirical relationship or classification rule is developed from a set of samples for which the property of interest and the measurements are known. The classification rule can then be used to predict the property in samples that are not part of the original training set. The set of samples for which the property of interest and the measurements are known is called the training set. The set of measurements that describe each sample in the data set is called a pattern. The determination of the property of interest by assigning a sample to its respective category is called recognition, hence the term pattern recognition.For pattern recognition analysis, each sample is represented as a data vectorx = (x1,x2,x3,xj, …,xp), where componentxjis a measurement, e.g. the area of thejth peak in a chromatogram. Each sample is considered as a point in a p‐dimensional measurement space. The dimensionality of the space corresponds to the number of measurements that are available for each sample. A basic assumption is that distance between pairs of points in this measurement space is inversely related to the degree of similarity between the corresponding samples. Points representing samples from one class will cluster in a limited region of the measurement space distant from the points corresponding to the other class. Pattern recognition (i.e. clustering and classification) is a set of methods for investigating data represented in this manner, to assess its overall structure, which is defined as the overall relation of each sample to every other in the data set.
Chiral Separations by High‐Performance Liquid ChromatographyUpdate based on the original article by Timothy J. Ward and Tanya M. Oswald,Encyclopedia of Analytical Chemistry, © 2000, John Wiley & Sons, Ltd.
Authors: Ward Timothy J. , Ward Karen D. 
Published: December 2012

AbstractThe word ‘chiral’ is derived from the Greek word ‘cheir’, which means hand. Chiral molecules are molecules that are related to each other in the same way that a left hand is related to a right hand. These molecules are mirror images of each other and are nonsuperimposable. Chiral separations traditionally have been considered among the most difficult of all separations because enantiomers have identical chemical and physical properties in an achiral environment. In this article, we focus on techniques used in high‐performance liquid chromatography (HPLC). Most chiral separations by HPLC are accomplished via direct resolution using a chiral stationary phase (CSP). In this technique, a chiral resolving agent is bound or immobilized to an appropriate support to make a CSP, and the enantiomers are resolved by the formation of temporary diastereomeric complexes between the analyte and the CSP.Various types of CSPs have been developed, including polysaccharide‐based, cyclodextrin‐based, cyclofructan‐based, macrocyclic antibiotic‐based, protein‐based, Pirkle‐type, and ligand‐exchange CSPs. The most commercially common CSPs, polysaccharide‐based phases, consist of derivatized cellulose and amylose coated on silica gel and a new generation of polysaccharide‐based phases, which is immobilized through covalent bonding to a silica gel. Generally, analytes separated using the cyclodextrins require the formation of an inclusion complex between the analyte and the cyclodextrin. Separation is most favorable when the analyte also interacts with the mouth of the cyclodextrin molecule via hydrogen bonding to the functional groups present. The cyclofructan‐based CSPs are the newest development in chiral HPLC columns and are now available commercially. These bonded CSPs show excellent enantioselectivity toward all types of primary amines as well as other varieties of compounds. Numerous analytes have been separated using the macrocyclic antibiotic‐based CSPs, which can also be derivatized to alter their selectivity. Protein‐based CSPs comprise a number of commercially available columns. The protein‐based CSPs resemble the bonded macrocyclic antibiotic CSPs in many ways; however, the macrocyclic antibiotic CSPs are more stable and have greater capacities than the protein‐based CSPs. The Pirkle‐type CSPs typically use nonpolar organic mobile phases and often require derivatization of the analyte to add a π‐acid or π‐basic moiety, or both, to achieve separation. Ligand‐exchange phases are used with aqueous buffer mobile phases in which enantiomers are separated based on the differences in their charge and ionization constants. Limitations of ligand‐exchange separations are that only ionized analytes can be resolved using this technique and the copper‐salt‐containing mobile phases used absorb in the ultraviolet (UV) region, decreasing detection sensitivity.
Particle Size Determination for Process Analysis
Authors: Redman Terry P. 
Published: December 2012

AbstractParticles and droplets are critical in the determination of product quality and process efficiency in the manufacture of a wide range of chemical, pharmaceutical, and biological products. Processes such as crystallization and precipitation, homogenization and emulsification, polymerization, and fermentation are based on the detailed understanding, optimization, and control of particles, droplets, and bubbles.This article distinguishes between in situ particle system characterization (PSC) and traditional off‐line particle size analysis (PSA), and explains how the broader view of PSC is better suited to optimization and control of complex multiphase processes.PSC goes beyond traditional off‐line PSA, to provide real‐time, in‐process measurements of the rate and degree of change in particles and particle structures as they exist in the actual process environment. In situ process analytical methods can also significantly reduce measurement errors associated with off‐line sampling and sample preparation. This facilitates improved process development through direct real‐time monitoring of the particles and droplets as they exist and change in process. Process‐analytical‐based understanding contributes to faster methods of optimization and results in more consistent scale‐up. Real‐time monitoring and control of the particle system in the manufacturing environment is also used as a tool to help assure product quality.
Nanoparticles in Environmental Waters, Determination of
Authors: Sanchis Josep , Farre Marinella , Barcelo Damia 
Published: December 2012

AbstractNanomaterials of different chemical composition, physicochemical properties, and origins are emitted to the environment because of their wide use and incidental emission. Water suspended aggregates in the nanorange can be processed with conventional wastewater treatments, but their efficiency seems to vary according to the characteristics of the aggregates. Moreover, even in the best case scenario, certain amounts of nanomaterials are likely to be present in the effluent flows at trace concentrations. Sewage water disposal together with other processes, such as the atmospheric deposition and the direct spillage risk, make the water environment particularly susceptible to the introduction of these new compounds and carry ecological and health consequences that should be assessed.Studying the behavior of nanoparticles in water environments of ecological relevance is a crucial step toward a proper assessment of the ecotoxicological effects, distribution patterns, and persistence of nanomaterials in the water environment.