bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partial direct contact transmission in ferrets of a mallard H7N3 influenza virus with typical avian-like receptor specificity
Authors: Song Haichen , Wan Hongquan , Araya Yonas , Perez Daniel R 
Published: August 2009

Abstract

Background
Avian influenza viruses of the H7 subtype have caused multiple outbreaks in domestic poultry and represent a significant threat to public health due to their propensity to occasionally transmit directly from birds to humans. In order to better understand the cross species transmission potential of H7 viruses in nature, we performed biological and molecular characterizations of an H7N3 virus isolated from mallards in Canada in 2001.

Results
Sequence analysis that the HA gene of the mallard H7N3 virus shares 97% identity with the highly pathogenic avian influenza (HPAI) H7N3 virus isolated from a human case in British Columbia, Canada in 2004. The mallard H7N3 virus was able to replicate in quail and chickens, and transmitted efficiently in quail but not in chickens. Interestingly, although this virus showed preferential binding to analogs of avian-like receptors with sialic acid (SA) linked to galactose in an α2–3 linkage (SAα2–3Gal), it replicated to high titers in cultures of primary human airway epithelial (HAE) cells, comparable to an avian H9N2 influenza virus with human-like α2–6 linkage receptors (SAα2–6Gal). In addition, the virus replicated in mice and ferrets without prior adaptation and was able to transmit partially among ferrets.

Conclusion
Our findings highlight the importance and need for systematic in vitro and in vivo analysis of avian influenza viruses isolated from the natural reservoir in order to define their zoonotic potential.
Efficacy of prescribed injectable diacetylmorphine in the Andalusian trial: Bayesian analysis of responders and non-responders according to a multi domain outcome index
Authors: Perea-Milla Emilio , Ayçaguer Luis Carlos Silva , Cerdà Joan Carles March , Saiz Francisco González , Rivas-Ruiz Francisco , Danet Alina , Vallecillo Manuel Romero , Oviedo-Joekes Eugenia 
Published: August 2009

Abstract

Background
The objective of this research was to evaluate data from a randomized clinical trial that tested injectable diacetylmorphine (DAM) and oral methadone (MMT) for substitution treatment, using a multi-domain dichotomous index, with a Bayesian approach.

Methods
Sixty two long-term, socially-excluded heroin injectors, not benefiting from available treatments were randomized to receive either DAM or MMT for 9 months in Granada, Spain. Completers were 44 and data at the end of the study period was obtained for 50. Participants were determined to be responders or non responders using a multi-domain outcome index accounting for their physical and mental health and psychosocial integration, used in a previous trial. Data was analyzed with Bayesian methods, using information from a similar study conducted in The Netherlands to select a priori distributions. On adding the data from the present study to update the a priori information, the distribution of the difference in response rates were obtained and used to build credibility intervals and relevant probability computations.

Results
In the experimental group (n = 27), the rate of responders to treatment was 70.4% (95% CI 53.2-87.6), and in the control group (n = 23), it was 34.8% (95% CI 15.3-54.3). The probability of success in the experimental group using the a posteriori distributions was higher after a proper sensitivity analysis. Almost the whole distribution of the rates difference (the one for diacetylmorphine minus methadone) was located to the right of the zero, indicating the superiority of the experimental treatment.

Conclusion
The present analysis suggests a clinical superiority of injectable diacetylmorphine compared to oral methadone in the treatment of severely affected heroin injectors not benefiting sufficiently from the available treatments.

Trial Registration
Current Controlled Trials ISRCTN52023186
The Ras guanine nucleotide exchange factor RasGRF1 promotes matrix metalloproteinase-3 production in rheumatoid arthritis synovial tissue
Authors: Abreu Joana RF , de Launay Daphne , Sanders Marjolein E , Grabiec Aleksander M , Sande Marleen G van de , Tak Paul P , Reedquist Kris A 
Published: August 2009

Abstract
Introduction
Fibroblast-like synoviocytes (FLS) from rheumatoid arthritis (RA) patients share many similarities with transformed cancer cells, including spontaneous production of matrix metalloproteinases (MMPs). Altered or chronic activation of proto-oncogenic Ras family GTPases is thought to contribute to inflammation and joint destruction in RA, and abrogation of Ras family signaling is therapeutic in animal models of RA. Recently, expression and post-translational modification of Ras guanine nucleotide releasing factor 1 (RasGRF1) was found to contribute to spontaneous MMP production in melanoma cancer cells. Here, we examine the potential relationship between RasGRF1 expression and MMP production in RA, reactive arthritis, and inflammatory osteoarthritis synovial tissue and FLS.

Methods
Expression of RasGRF1, MMP-1, MMP-3, and IL-6 was detected in synovial tissue by immunohistochemistry and stained sections were evaluated by digital image analysis. Expression of RasGRF1 in FLS and synovial tissue was also assessed by immunoblotting. Double staining was performed to detect proteins in specific cell populations, and cells producing MMP-1 and MMP-3. RasGRF1 expression was manipulated in RA FLS by cDNA transfection and gene silencing, and effects on MMP-1, TIMP-1, MMP-3, IL-6, and IL-8 production measured by ELISA.

Results
Expression of RasGRF1 was significantly enhanced in RA synovial tissue, and detected in FLS and synovial macrophages in situ. In cultured FLS and synovial biopsies, RasGRF1 was detected by immunoblotting as a truncated fragment lacking its negative regulatory domain. Production of MMP-1 and MMP-3 in RA but not non-RA synovial tissue positively correlated with expression of RasGRF1 and co-localized in cells expressing RasGRF1. RasGRF1 overexpression in FLS induced production of MMP-3, and RasGRF1 silencing inhibited spontaneous MMP-3 production.

Conclusions
Enhanced expression and post-translational modification of RasGRF1 contributes to MMP-3 production in RA synovial tissue and the semi-transformed phenotype of RA FLS.
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
Authors: Kircher Martin , Stenzel Udo , Kelso Janet 
Published: August 2009

AbstractThe Illumina Genome Analyzer generates millions of short sequencing reads. We present Ibis (Improved base identification system), an accurate, fast and easy-to-use base caller that significantly reduces the error rate and increases the output of usable reads. Ibis is faster and more robust with respect to chemistry and technology than other publicly available packages. Ibis is freely available under the GPL from http://bioinf.eva.mpg.de/Ibis/.
MouseCyc: a curated biochemical pathways database for the laboratory mouse
Authors: Evsikov Alexei V , Dolan Mary E , Genrich Michael P , Patek Emily , Bult Carol J 
Published: August 2009

AbstractLinking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc http://mousecyc.jax.org. MouseCyc has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.
Kinematics, hydrodynamics and force production of pleopods suggest jet-assisted walking in the American lobster (Homarus americanus)
Authors: Lim Jeanette L. , DeMont M. Edwin 
Published: August 2009

SUMMARYThe American lobster (Homarus americanus) displays a diverse set of locomotory behaviours that includes tail flips, walking and paddling. Paddling is carried out by the four pairs of paddle-shaped pleopods on the ventral abdomen. Although it is recognized that pleopod-generated fluid flows have some locomotory role in adults, reports on their relative importance in locomotion are inconsistent. This paper integrates experimental kinematics and hydrodynamics of lobster pleopod beating to determine the mechanism and magnitude of pleopod force production. A kinematic analysis of pleopod beating in live lobsters showed that the pleopods execute an adlocomotory metachronal beating pattern. We modelled in vivo pleopod kinematics with a set of simple trigonometric functions, and used these functions to program a mechanical lobster model consisting of motor-driven pleopods on a lobster abdomen exoskeleton. Based on flow visualizations obtained from applying particle image velocimetry to the lobster model, we propose that the unsteady metachronal kinematics of the pleopods can maximize thrust by exploiting forces arising from individual pleopod activity and interactions among adjacent pairs. The pleopods continuously entrain fluid surrounding the lobster and create a caudally directed fluid jet oriented parallel to the substratum. Inputting wake morphology and velocity data into a simplified model for steady jet thrust showed that the pleopods of the lobster model produced 27–54 mN of thrust, which is comparable to the propulsive forces generated by other proficient swimmers. These results suggest that lobster pleopods are capable of producing forces of a magnitude that could assist the walking legs in forward propulsion.
Sugar feedingviatrehalose haemolymph concentration affects sex pheromone production in matedHeliothis virescensmoths
Authors: Foster Stephen 
Published: August 2009

SUMMARYLong-distance, female-produced sex pheromones are widespread among moths. Larval feeding provides most of the nutrients for development of these insects but is not thought to influence the de novo production of the fatty-acid derived compounds used as pheromones by most species. Feeding on plant nectar (sugar) by adult moths is important for increasing female fitness and also for the pollination of many plant species. In this paper, I show that feeding on sucrose solution, as opposed to water, increases sex pheromone titre in mated, but not virgin, female Heliothis virescens. Mating caused a rapid decrease in haemolymph trehalose concentration, which was restored to near-virgin levels by sugar ingestion. When isolated mated female abdomens were cultured with different concentrations of trehalose, pheromone titre increased with increasing trehalose concentration. This effect was not observed when abdomens were cultured on saline containing the sugar rhamnose,which insects cannot metabolise to glucose. Virgins injected with the juvenile hormone (JH) analogue, methoprene, showed the same effects as mated females with respect to pheromone titre and haemolymph trehalose concentration. Thus,following mating increases in JH titre increase demand for, and lowering of,blood sugar to develop oocytes, which can be compensated for by sugar ingestion. Haemolymph trehalose concentration probably influences glycolysis in gland cells and, consequently, levels of cytosolic citrate and acetyl-CoA for pheromone biosynthesis. This increase in pheromone titre in sugar-fed,mated females may facilitate further mating and increased fecundity. Thus,exogenous sugar feeding is behaviourally and physiologically integrated with endogenous JH titre to maximise female fitness.
Changes in thyroid hormone reception precede SWS1 opsin downregulation in trout retina
Authors: Raine J. C. , Hawryshyn C. W. 
Published: August 2009

SUMMARY
Rainbow trout undergo natural cone degeneration and thus are interesting models for examining mechanisms of neural degeneration. They have ultraviolet-sensitive (UVS) cones that are lost over most of the retina during development; only a small functional population remains in the dorsal retina. How this spatial distribution of UVS cones is maintained is unclear. Thyroxine(T4) induces UVS cone loss, and local thyroid hormone regulation was hypothesized to control UVS cone distribution. Thyroid hormone receptor alpha(TRα), thyroid hormone receptor beta (TRβ) and Type 2 deiodinase(D2) regulate thyroid hormone exposure to target cells. Regional retinal expression of these genes was investigated during exogenous T4 treatment and natural smoltification of rainbow trout. Each retina from dark-adapted parr,T4-treated parr and natural smolts was divided into four quadrants, and total RNA was isolated. Quantitative real-time RT-PCR analysis demonstrated that all retinal quadrants had increased accumulation of TRβ transcripts 2 days post-T4 treatment, corresponding to initiation of SWS1 opsin downregulation. Smolts exhibited decreased accumulation of TRαand TRβ transcripts in all quadrants, but this effect was most pronounced in the dorso-temporal (DT) retinal quadrant where UVS cones persist. By contrast, in 2 day T4-treated parr, the DT quadrant showed increased expression of TRα and TRβ. Furthermore, D2 transcripts decreased in the DT quadrant of T4-treated parr but increased in the DT quadrant of smolts. These results suggest that T4 upregulates TRβ expression to initiate SWS1 opsin downregulation, while TRα and TRβ downregulation occurs to prevent natural loss of UVS cones from the DT retina.
A comparative study of cellulase and hemicellulase activities of brackish water clam Corbicula japonica with those of other marine Veneroida bivalves
Authors: Sakamoto Kentaro , Toyohara Haruhiko 
Published: August 2009

SUMMARY
Corbicula japonica is a typical brackish water bivalve species belonging to the order Veneroida, and it is the most important inland fishery resource in Japan. Corbicula japonica has been suggested to assimilate organic matter from terrestrial plants, unlike Ruditapes philippinarum and Mactra veneriformis, which selectively assimilate organic matter of marine origin. This led us to hypothesize that C. japonica, despite being a suspension feeder, could assimilate cellulosic materials derived from terrestrial plants. In the present study, we measured cellulase and hemicellulase activities in the crystalline styles of C. japonica and other commercially important Veneroida bivalve species in Japan: Ruditapes philippinarum, Meretrix lamarckii and Meretrix lusoria. Corbicula japonica demonstrated notably higher cellulase, xylanase and β-mannanase activities than the other marine bivalves, suggesting that this species possesses a far greater biochemical capacity to break down the structural polysaccharides of plant cell walls than the other species. In contrast, the β-1,3-glucanase and pectinase activities of C. japonica were similar to or even lower than those of the others. This is possibly due to the presence of these polysaccharides in the cell walls of diatoms, a principal food of most marine bivalves. Although direct evidence is lacking, the high cellulase, xylanase and β-mannanase activities of C. japonica may result from adaptation to an upstream estuarine environment where phytoplankton and diatoms are scarce, but plant-derived substances are abundant.
Cold acclimation in Peromyscus: individual variation and sex effects in maximum and daily metabolism, organ mass and body composition
Authors: Rezende Enrico L. , Hammond Kimberly A. , Chappell Mark A. 
Published: August 2009

SUMMARY
We studied metabolic and organ mass responses to thermal acclimation (7 weeks at 5°C or 23°C) in deer mice, Peromyscus maniculatus. Cold acclimation resulted in significantly higher maximal oxygen consumption in thermogenesis (V̇O2max)and daily mean oxygen consumption(V̇O2mean), an increase in the mass of most visceral organs, a lower absolute body fat and a marginally significant increase in hematocrit. The mass of digestive organs and body fat content differed significantly between sexes. Acclimation effects on fat content were more pronounced in females. Variation in heart and lung mass was positively correlated with V̇O2max and V̇O2mean, while body fat content was negatively correlated with both traits. Nonetheless, a large fraction of the metabolic difference between cold- and warm-acclimated groups remained unexplained. Associations between traits at lower levels of biological organization measured here and whole-organism energetics remained consistent across acclimation temperatures, except for the correlation between kidney mass and V̇O2mean,which was positive and significant in cold acclimation and negligible following warm acclimation. We conclude that: (1)V̇O2max and V̇O2mean share a common physiological basis that remains overall the same across acclimation regimes;(2) changes in these traits are associated primarily with changes in heart mass; and (3) male and female deer mice respond differently to thermal acclimation, possibly due to differences in reproductive allocation.
Selectivity of Co and Ni by K-depleted micas
Authors: Cho Yunchul , Komarneni Sridhar , Choi Sang-il 
Published: August 2009

AbstractContamination of the environment with heavy metals, including cationic radionuclides, is a serious problem which has yet to be fully overcome. A class of potentially effective cation exchangers for sequestering heavy metals which has received little attention is K-depleted mica. The purpose of this study was to investigate the heavy-metal cation exchange properties of K-depleted phlogopite and biotite, which were prepared from a natural phlogopite and biotite, respectively, using sodium tetraphenylborate (NaTPB). The X-ray diffraction (XRD) patterns showed that interlayer K+ ions were completely replaced with exchangeable Na+ ions, resulting in the expansion of the d001 spacing of both K-depleted phlogopite and K-depleted biotite. In order to investigate the cation exchange selectivity of K-depleted phlogopite and biotite for Co2+ and Ni2+, cation exchange isotherms and Kielland plots were constructed. The isotherms and Kielland plots indicated that both K-depleted phlogopite and biotite are highly selective for Co2+ as well as Ni2+. The XRD patterns after both 2Na+ → Co2+ and Ni2+ exchange reactions suggest that double sheets of interlayer water are present in the interlayer. These K-depleted micas are potential cation exchange materials for removal of some heavy metals such as Ni and radioactive species such as 60Co from solution.
Simple synthesis and characterization of nanoporous materials from talc
Authors: Du Chunfang , Yang Huaming 
Published: August 2009

AbstractSynthetic siliceous mesoporous materials are of great value in many different applications, including nanotechnology, biotechnology, information technology, and medical fields, but historically the resource materials used in their synthesis have been expensive. Recent efforts have focused on indirect synthesis methods which utilize less expensive silicate minerals as a resource material. The purpose of the present study was to investigate talc, a natural silicate mineral, as one such resource. It was used as raw material to prepare two advanced materials: porous silica (PS) and ordered mesoporous silica (MCM-41). The PS, with a specific surface area of 260 m2/g and bimodal pore-size distribution of 1.2 nm and 3.7 nm, was prepared by grinding and subsequent acid leaching. The MCM-41, with a large surface area of 974 m2/g and a narrow pore-size distribution of 2.8 nm, was obtained using a surfactant, cetyltrimethylammonium bromide (CTAB), by hydrothermal treatment using the as-prepared PS as a source of Si. The two resultant materials were characterized by small angle X-ray diffraction (SAXRD) and wide-angle X-ray diffraction (WAXRD), high-resolution transmission electron microscopy (HRTEM), solid-state magic-angle-spinning nuclear magnetic resonance (MAS NMR), Fourier transform infrared spectroscopy (FTIR), and N2 adsorption-desorption measurements. Based on these measurements, possible processes of transformation of PS from talc, upon acid treatment, and the formation of MCM-41 were investigated systemically. Acid leaching induced the transformation of a rigid layered structure to a nearly amorphous one, with micropores formed by a residual layered structure and mesopores formed from a condensed framework. The MCM-41 was a mixture of silanol groups (Si(SiO)3(OH)) and a condensed Q4 framework structure (Si(SiO)4), with a small amount of remaining Q3 layered structure (Si(SiO)3OMg). The increased Q4/Q3 value confirmed greater polymerization of MCM-41 than of PS. At the low CTAB concentration used (2 wt.%), the highly charged silicate species controlled the surfactant geometry. Charge-density matching, together with the degree of polymerization of the silicates, determined the resultant mesophase.
The occurrence and origin of the söğüt kaolinite deposits in the Paleozoic Saricakaya granite-granodiorite complexes and overlying Neogene sediments (Bilecik, northwestern Turkey)
Authors: Kadir Selahattin , Kart Firdevs 
Published: August 2009

AbstractThe Söğüt kaolinite deposits at Çaltı, İnhisar, and Küre, Turkey, are an important source of raw materials for the ceramics industry of that country, but no detailed mineralogical or geochemical characterizations of these economically important materials have been carried out to date. The purpose of this study was to fill this gap by performing mineralogical, geochemical, and isotopic characterizations of these kaolinite deposits which occur within Paleozoic granite-granodiorite complexes that are crosscut by aplite and pegmatite dikes, and overlain by Neogene sedimentary units. These units are dominated by quartz veins and networks of subvertical fractures and weak zones that were invaded by hydrothermal fluids, resulting in their kaolinization and silicification. Altered units and related host rocks were examined using polarized-light microscopy, X-ray diffractometry, scanning electron microscopy, infrared spectroscopy, and chemical and isotopic methods. Feldspar crystals are either sericitized or kaolinized, and mica exhibits partial chloritization; Fe-Ti-Mn oxides occur within fractures. Kaolinite crystals occur in authigenic vermiform or plate-like stacked forms, having contacts with resorbed feldspar crystals which locally exhibit thick, platy, and subparallel orientations relative to microfractures, the pathways for hydrothermal-fluid injection. Altered feldspar relicts are associated mainly with kaolinite, smectite, quartz crystals, and illite/mica. Increase in (Al+Fe)/Si in the kaolinized units (relative to host-rock granite and granodiorite complexes and silicification), depletion of Ba+Rb, and a negative Eu anomaly reveal that the alteration of feldspar by hydrothermal fluid, the character of which was determined from O- and H-isotopic values, resulted in the precipitation of kaolinite. Thus, the Söğüt kaolinite deposit possibly formed by hydrothermal alteration and a feldspar dissolution-precipitation mechanism in both the granite-granodiorites complexes and related overlying sedimentary units under acidic environmental conditions, which developed via depletion of the soluble elements Na and Ca.