bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Odorant Binding Protein Gene Family from the Genome of Silkworm, Bombyx mori
Authors: Gong Da-Ping , Zhang Hui-Jie , Zhao Ping , Xia Qing-You , Xiang Zhong-Huai 
Published: July 2009

AbstractBackgroundChemosensory systems play key roles in the survival and reproductive success of insects. Insect chemoreception is mediated by two large and diverse gene superfamilies, chemoreceptors and odorant binding proteins (OBPs). OBPs are believed to transport hydrophobic odorants from the environment to the olfactory receptors.ResultsWe identified a family of OBP-like genes in the silkworm genome and characterized their expression using oligonucleotide microarrays. A total of forty-four OBP genes were annotated, a number comparable to the 57 OBPs known fromAnopheles gambiaeand 51 fromDrosophila melanogaster. As seen in other fully sequenced insect genomes, most silkworm OBP genes are present in large clusters. We defined six subfamilies of OBPs, each of which shows lineage-specific expansion and diversification. EST data and OBP expression profiles from multiple larvae tissues of day three fifth instars demonstrated that many OBPs are expressed in chemosensory-specific tissues although some OBPs are expressed ubiquitously and others exclusively in non-chemosensory tissues. Some atypical OBPs are expressed throughout development. These results reveal that, although many OBPs are chemosensory-specific, others may have more general physiological roles.ConclusionSilkworms possess a number of OBPs genes similar to other insects. Their expression profiles suggest that many OBPs may be involved in olfaction and gustation as well as general carriers of hydrophobic molecules. The expansion of OBP gene subfamilies and sequence divergence indicate that the silkworm OBP family acquired functional diversity concurrently with functional constraints. Further investigation of the OBPs of the silkworm could give insights in the roles of OBPs in chemoreception.
DNA binding by Corynebacterium glutamicum TetR-type transcription regulator AmtR
Authors: Muhl Daniela , Jeßberger Nadja , Hasselt Kristin , Jardin Christophe , Sticht Heinrich , Burkovski Andreas 
Published: July 2009

Abstract

Background
The TetR family member AmtR is the central regulator of nitrogen starvation response in Corynebacterium glutamicum. While the AmtR regulon was physiologically characterized in great detail up to now, mechanistic questions of AmtR binding were not addressed. This study presents a characterization of functionally important amino acids in the DNA binding domain of AmtR and of crucial nucleotides in the AmtR recognition motif.

Results
Site-directed mutagenesis, the characterization of corresponding mutant proteins by gel retardation assays and surface plasmon resonance and molecular modelling revealed several amino acids, which are directly involved in DNA binding, while others have more structural function. Furthermore, we could show that the spacing of the binding motif half sites is crucial for repression of transcription by AmtR.

Conclusion
Although the DNA binding domain of TetR-type repressors is highly conserved and a core binding motif was identified for AmtR and TetR(D), the AmtR binding domain shows individual properties compared to other TetR proteins. Besides by distinct amino acids of AmtR, DNA binding is influenced by nucleotides not only of the conserved binding motif but also by spacing nucleotides in C. glutamicum.
Inappropriate medication use and risk of falls – A prospective study in a large community-dwelling elderly cohort
Authors: Berdot Sarah , Bertrand Marion , Dartigues Jean-François , Fourrier Annie , Tavernier Béatrice , Ritchie Karen , Alpérovitch Annick 
Published: July 2009

Abstract

Background
Explicit criteria for determining potentially inappropriate medication consumption in elderly were elaborated by Beers et al. These lists have been used worldwide to evaluate medical prescriptions but there is little epidemiologic evidence demonstrating negative consequences of inappropriate medication use. It has been reported that some drugs could increase the risk of falls, which are a frequent and serious problem in elderly population. We aimed to evaluate the association between the use of potentially inappropriate medications and the risk of falls.

Methods
The 3C Study is a multicentre prospective cohort study conducted in France with 4 years of follow-up. Non-institutionalized men and women aged 65 years or over (N = 6343) were randomly selected from electoral rolls. Data on socio-demographic, medical characteristics and medication use (based on self-reports and data from the national healthcare insurance) were collected. Use of inappropriate medication for elderly was defined from established criteria. Data about falls were collected at the two follow-up examinations (2 years and 4 years after baseline). The association between the exposure to inappropriate medications and the risk of falls was evaluated using multivariate models (Cox model and logistic regression).

Results
32% of subjects reported inappropriate medication use at baseline and 29% at least two of the three examinations; 22% had fallen 2 times or more during follow-up. Overall, inappropriate medication users had an increased risk of falling. This increase was mainly due to the use of long-acting benzodiazepines (adjusted odds ratio (OR) = 1.4, 95% confidence interval: [1.1–1.8], in both occasional and regular users), other inappropriate psychotropics (adjusted OR = 1.7 [1.7–2.7] in regular users), or medication with anticholinergic properties (adjusted OR = 1.6 [1.2–2.1] in regular users). Neither occasional, nor regular use of short- or intermediate-acting benzodiazepines was associated with an increased risk of falling. Further analysis in long-acting benzodiazepines users did not show any dose-effect relation between the number of prescriptions filled over a 3-year period and the risk of falling.

Conclusion
Our study showed that use of inappropriate medications was associated with an increased risk of falling in elderly persons. This increase was mainly due to long-acting benzodiazepines and other inappropriate psychotropics, and to medications with anticholinergic properties.
DAS-28-based EULAR response and HAQ improvement in rheumatoid arthritis patients switching between TNF antagonists
Authors: Navarro-Sarabia Federico , Ruiz-Montesinos Dolores , Hernandez Blanca , Navarro-Compán Victoria , Marsal Sara , Barcelo Mireia , Perez-Pampín Eva , Gómez-Reino Juan J 
Published: July 2009

Abstract

Introduction
No definitive data are available regarding the value of switching to an alternative TNF antagonist in rheumatoid arthritis patients who fail to respond to the first one. The aim of this study was to evaluate treatment response in a clinical setting based on HAQ improvement and EULAR response criteria in RA patients who were switched to a second or a third TNF antagonist due to failure with the first one.

Methods
This was an observational, prospective study of a cohort of 417 RA patients treated with TNF antagonists in three university hospitals in Spain between January 1999 and December 2005. A database was created at the participating centres, with well-defined operational instructions. The main outcome variables were analyzed using parametric or non-parametric tests depending on the level of measurement and distribution of each variable.

Results
Mean (± SD) DAS-28 on starting the first, second and third TNF antagonist was 5.9 (± 2.0), 5.1 (± 1.5) and 6.1 (± 1.1). At the end of follow-up, it decreased to 3.3 (± 1.6; Δ = -2.6; p > 0.0001), 4.2 (± 1.5; Δ = -1.1; p = 0.0001) and 5.4 (± 1.7; Δ = -0.7; p = 0.06). For the first TNF antagonist, DAS-28-based EULAR response level was good in 42% and moderate in 33% of patients. The second TNF antagonist yielded a good response in 20% and no response in 53% of patients, while the third one yielded a good response in 28% and no response in 72%. Mean baseline HAQ on starting the first, second and third TNF antagonist was 1.61, 1.52 and 1.87, respectively. At the end of follow-up, it decreased to 1.12 (Δ = -0.49; p < 0.0001), 1.31 (Δ = -0.21, p = 0.004) and 1.75 (Δ = -0.12; p = 0.1), respectively. Sixty four percent of patients had a clinically important improvement in HAQ (defined as ≥ -0.22) with the first TNF antagonist and 46% with the second.

Conclusion
A clinically significant effect size was seen in less than half of RA patients cycling to a second TNF antagonist.
Acute ingestion of a novel whey-derived peptide improves vascular endothelial responses in healthy individuals: a randomized, placebo controlled trial
Authors: Ballard Kevin D , Bruno Richard S , Seip Richard L , Quann Erin E , Volk Brittanie M , Freidenreich Daniel J , Kawiecki Diana M , Kupchak Brian R , Chung Min-Yu , Kraemer William J , Volek Jeff S 
Published: July 2009

Abstract

Background
Whey protein is a potential source of bioactive peptides. Based on findings from in vitro experiments indicating a novel whey derived peptide (NOP-47) increased endothelial nitric oxide synthesis, we tested its effects on vascular function in humans.

Methods
A randomized, placebo-controlled, crossover study design was used. Healthy men (n = 10) and women (n = 10) (25 ± 5 y, BMI = 24.3 ± 2.3 kg/m2) participated in two vascular testing days each preceded by 2 wk of supplementation with a single dose of 5 g/day of a novel whey-derived peptide (NOP-47) or placebo. There was a 2 wk washout period between trials. After 2 wk of supplementation, vascular function in the forearm and circulating oxidative stress and inflammatory related biomarkers were measured serially for 2 h after ingestion of 5 g of NOP-47 or placebo. Macrovascular and microvascular function were assessed using brachial artery flow mediated dilation (FMD) and venous occlusion strain gauge plethysmography.

Results
Baseline peak FMD was not different for Placebo (7.7%) and NOP-47 (7.8%). Placebo had no effect on FMD at 30, 60, and 90 min post-ingestion (7.5%, 7.2%, and 7.6%, respectively) whereas NOP-47 significantly improved FMD responses at these respective postprandial time points compared to baseline (8.9%, 9.9%, and 9.0%; P < 0.0001 for time × trial interaction). Baseline reactive hyperemia forearm blood flow was not different for placebo (27.2 ± 7.2%/min) and NOP-47 (27.3 ± 7.6%/min). Hyperemia blood flow measured 120 min post-ingestion (27.2 ± 7.8%/min) was unaffected by placebo whereas NOP-47 significantly increased hyperemia compared to baseline (29.9 ± 7.8%/min; P = 0.008 for time × trial interaction). Plasma myeloperoxidase was increased transiently by both NOP-47 and placebo, but there were no changes in markers inflammation. Plasma total nitrites/nitrates significantly decreased over the 2 hr post-ingestion period and were lower at 120 min after placebo (-25%) compared to NOP-47 (-18%).

Conclusion
These findings indicate that supplementation with a novel whey-derived peptide in healthy individuals improves vascular function.
Ovarian steroids regulate tachykinin and tachykinin receptor gene expression in the mouse uterus
Authors: Pinto Francisco M , Pintado C Oscar , Pennefather Jocelyn N , Patak Eva , Candenas Luz 
Published: July 2009

AbstractBackgroundIn the mouse uterus, pregnancy is accompanied by changes in tachykinin and tachykinin receptor gene expression and in the uterotonic effects of endogenous tachykinins. In this study we have investigated whether changes in tachykinin expression and responses are a result of changes in ovarian steroid levels.MethodsWe quantified the mRNAs of tachykinins and tachykinin receptors in uteri from ovariectomized mice and studied their regulation in response to estrogen and progesterone using real-time quantitative RT-PCR. Early (3 h) and late (24 h) responses to estrogen were evaluated and the participation of the estrogen receptors (ER), ERalpha and ERbeta, was analyzed by treating mice with propylpyrazole triol, a selective ERalpha agonist, or diarylpropionitrile, a selective agonist of ERbeta.ResultsAll genes encoding tachykinins (Tac1, Tac2 and Tac4) and tachykinin receptors (Tacr1, Tacr2 and Tacr3) were expressed in uteri from ovariectomized mice. Estrogen increased Tac1 and Tacr1 mRNA after 3 h and decreased Tac1 and Tac4 expression after 24 h. Tac2 and Tacr3 mRNA levels were decreased by estrogen at both 3 and 24 h. Most effects of estrogen were also observed in animals treated with propylpyrazole triol. Progesterone treatment increased the levels of Tac2.ConclusionThese results show that the expression of tachykinins and their receptors in the mouse uterus is tightly and differentially regulated by ovarian steroids. Estrogen effects are mainly mediated by ERalpha supporting an essential role for this estrogen receptor in the regulation of the tachykinergic system in the mouse uterus.
Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes
Authors: Hui Jerome HL , Raible Florian , Korchagina Natalia , Dray Nicolas , Samain Sylvie , Magdelenat Ghislaine , Jubin Claire , Segurens Béatrice , Balavoine Guillaume , Arendt Detlev , Ferrier David EK 
Published: July 2009

Abstract

Background

The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the more recently discovered ParaHox cluster. ParaHox gene clustering, and its relationship to expression, has only been described in deuterostomes. Conventional protostome models (Drosophila melanogaster and Caenorhabditis elegans) are secondarily derived with respect to ParaHox genes, suffering gene loss and cluster break-up.

Results

We provide the first evidence for ParaHox gene clustering from a less-derived protostome animal, the annelid Platynereis dumerilii. Clustering of these genes is thus not a sole preserve of the deuterostome lineage within Bilateria. This protostome ParaHox cluster is not entirely intact however, with Pdu-Cdx being on the opposite end of the same chromosome arm from Pdu-Gsx and Pdu-Xlox. From the genomic sequence around the P. dumerilii ParaHox genes the neighbouring genes are identified, compared with other taxa, and the ancestral arrangement deduced.

Conclusion

We relate the organisation of the ParaHox genes to their expression, and from comparisons with other taxa hypothesise that a relatively complex pattern of ParaHox gene expression existed in the protostome-deuterostome ancestor, which was secondarily simplified along several invertebrate lineages. Detailed comparisons of the gene content around the ParaHox genes enables the reconstruction of the genome surrounding the ParaHox cluster of the protostome-deuterostome ancestor, which existed over 550 million years ago.
Human rheumatoid arthritis tissue production of IL-17A drives matrix and cartilage degradation: synergy with tumour necrosis factor-α, Oncostatin M and response to biologic therapies
Authors: Moran Ellen M , Mullan Ronan , McCormick Jennifer , Connolly Mary , Sullivan Owen , FitzGerald Oliver , Bresnihan Barry , Veale Douglas J , Fearon Ursula 
Published: July 2009

Abstract
Introduction
The aim of this study was to examine IL-17A in patients, following anti-TNF-α therapy and the effect of IL-17A on matrix turnover and cartilage degradation.

Methods
IL-17A expression was examined by ELISA and immunohistology in the rheumatoid arthritis (RA) joints. RA whole synovial tissue explant (RA ST), primary synovial fibroblasts (RASFC), human cartilage and chondrocyte cultures were stimulated with IL-17A +/- TNF-α and Oncostatin M (OSM). Matrix metalloproteinase (MMP) and tissue inhibitor (TIMP-1) were assessed by ELISA and zymography. Cartilage proteoglycan release was assessed histologically by Safranin-O staining. Clinical parameters, IL-17A, MMP/TIMP were assessed in patients pre/post biologic therapy.

Results
IL-17A levels were higher in RA vs osteoarthritis (OA)/normal joints (P < 0.05). IL-17A up-regulated MMP-1, -2, -9, and -13 in RA ST, RASFC, cartilage and chondrocyte cultures (P < 0.05). In combination with TNF-α and OSM, IL-17A shifted the MMP:TIMP-1 ratio in favor of matrix degradation (all P < 0.05). Cartilage proteoglycan depletion in response to IL-17A was mild; however, in combination with TNF-α or OSM showed almost complete proteoglycan depletion. Serum IL-17A was detected in 28% of patients commencing biologic therapy. IL-17A negative patients demonstrated reductions post therapy in serum MMP1/TIMP4, MMP3/TIMP1 and MMP3/TIMP4 ratios and an increase in CS846 (all P < 0.05). No significant changes were observed in IL-17A positive patients.

Conclusions
IL-17A is produced locally in the inflamed RA joint. IL-17A promotes matrix turnover and cartilage destruction, especially in the presence of other cytokines, mimicking the joint environment. IL-17A levels are modulated in vivo, following anti-TNF therapy, and may reflect changes in matrix turnover.
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
Authors: MacArthur Stewart , Li Xiao-Yong , Li Jingyi , Brown James B , Chu Hou Cheng , Zeng Lucy , Grondona Brandi P , Hechmer Aaron , Simirenko Lisa , Keränen Soile VE , Knowles David W , Stapleton Mark , Bickel Peter , Biggin Mark D , Eisen Michael B 
Published: July 2009

Abstract
Background
We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional.

Results
Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors.

Conclusions
It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.
Fatigue Crack Growth Rates in Pipeline Steels Using Curved M(T) Specimens
Authors: Darcis Ph. P. , Treinen J. M. , McColskey J. D. 
Published: July 2009

Abstract
This study presents fatigue data for two different ferrite-pearlite pipeline steels. A fatigue crack growth test for full-thickness curved pipeline samples was developed using a middle tension (M(T)) specimen. Also, finite element analyses (FEAs) were carried out to show the M(T) curvature effects on the fatigue crack growth results. The two steels showed similar fatigue crack growth rate (da/dN) behavior. However, the ferrite-pearlite steel without banding had slightly better fatigue properties than the ferrite-pearlite banded steel. Uncertainty in the fatigue crack growth rates was analyzed by attributing all the fatigue scatter to the Paris law parameter C. The FEA based simulations, based on curved geometries, of the compliance relationship more accurately predicted both fatigue crack growth data and true crack lengths. Nevertheless, the ASTM E647-05 compliance relationship accurately predicted the crack length for the M(T) geometry, although its use leads to slightly conservative fatigue crack growth trends and a slight overestimation of the true final crack length.
Application of Computed Tomography in Manufacturing MetrologyAnwendung der Computer-Tomographie in der Fertigungsmesstechnik
Authors: Weckenmann Albert , Krämer Philipp 
Published: July 2009

Abstract
Since the development of X-ray Computed Tomography (CT) and its rapid acceptance in medical diagnostics, it became not only a powerful tool for non-destructive testing but was also adopted in manufacturing metrology in the last decade. CT offers new possibilities for coordinate measurements as it is possible to acquire a volumetric model of the entire workpiece with a single measurement at which analyses known from coordinate metrology such as estimation of geometric features or nominal/actual value comparisons can be performed. But with data sets generated by tomographic measurements it is as well possible to analyze the entire volume of the workpiece, so detection and analysis of conventionally not accessible features like defects (flaws, blow holes, bubbles) or wall thickness analyses with uncertainties in the micrometer range are possible.
High Speed 3-D Surface Profilometry using HSI Color Model and Trapezoidal Phase-Shifting MethodHochgeschwindigkeits-3D-Oberflächenprofilometrie mit HSI-Farbmodell und Trapez-Phasenverschiebungsmethode
Authors: Chen Liang-Chia , Nguyen Xuan-Loc , Shu Yao-Sheng 
Published: July 2009

Abstract
To achieve high-speed profilometry and avoid in-field vibration disturbances, high-speed 3-D surface profilometry using an innovative HSI color model and trapezoidal phase-shifting method has been developed to detect the morphology of measured objects at a high speed. By employing novel phase-shifting trapezoidal color fringe patterns, the method can reconstruct precise 3-D surface models by single one-shot image. Some industrial measurements were conducted to confirm that the measurement accuracy reached to 2.5% of the overall measurement range and the repeatability of 3.0% within ±3σ was achieved.
Process-Integrated Measurement of Aspherical SurfacesProzessintegrierte Vermessung asphärischer Oberflächen
Authors: Garbusi Eugenio , Pruss Christof , Osten Wolfgang 
Published: July 2009

Abstract
Aspheric lenses have become a synonym for high-performance optics. With an aspherical surface it is possible to correct a great number of aberrations in an optical system that otherwise would require a combination of several spherical ones. However the production of aspherical elements is substantially more complex as in the case of spherical ones because they require different production and measurement procedures. A flexible solution to the aspheric metrology problem without the use of additional compensation optics is presented.
Separability criteria via wavelet transform on homogenous spaces and projective representations
Authors: Karamati Mahdi , Rezapour Mohammad 
Published: July 2009

Abstract
The intimate connection between the Banach space wavelet reconstruction method for each unitary representation of a given group and homogenous space, and the quantum entanglement description using group theory were both studied in our previous articles. Here, we present a universal description of quantum entanglement using group theory and non-commutative characteristic functions for homogenous space and projective representation of compact groups on Banach spaces for some well known examples, such as: Moyal representation for a spin; Dihedral and Permutation groups.