bluuebunny/crossref_metadata_2025_split huggingface dataset:
Summer microhabitat partitioning by different size classes of masu salmon (Oncorhynchus masou) in habitats formed by installed large wood in a large lowland river
Authors: Nagayama Shigeya , Kawaguchi Yôichi , Nakano Daisuke , Nakamura Futoshi 
Published: January 2009

Different size classes of masu salmon ( Oncorhynchus masou ) were partitioned in three-dimensional space in habitats created by artificially installed large wood (LW) structures in a large river. Fish >300 mm in size (L-sized) returning from the ocean distinctly occurred in sheltered areas near the riverbed, which had a moderate current velocity and contained large root wads or tree trunks; 140–200 mm (M-sized) and 100–120 mm (S-sized) fish selected deep areas of high velocity current adjacent to LW structures; ≤80 mm fish (SS-sized) were most common in the lower depth layers throughout all LW habitats, including shallow areas with moderate currents where LW structures blocked the fast currents. Some SS-sized fish used cover areas provided by branches and leaves. Masu salmon abundance in all size classes combined was greater in habitats with LW structures than in habitats without them. Our study suggests that the natural recruitment of whole trees from the riparian zone or artificial placement of whole trees will have a profound effect on creating salmonid habitats in large rivers.
Ages and growth rates of some deep-sea gorgonian and antipatharian corals of Newfoundland and Labrador
Authors: Sherwood Owen A. , Edinger Evan N. 
Published: January 2009

Using bomb-14C dating and growth ring counting methods, we calculate life spans and growth rates of six species of deep-sea corals collected at depths of between 400 and 900 m from the continental slope of Newfoundland and Labrador. Bamboo corals ( Acanella arbuscula , Keratoisis ornata ) and antipatharians ( Stauropathes arctica ) secrete concentric growth rings in their axial skeletons, which were proven to form annually for K. ornata and S. arctica. These species had the lowest radial growth rates of 33 ± 11 to 75 ± 11 μm·year–1. Primnoa resedaeformis and Paramuricea spp. had higher radial growth rates of 83 ± 6 to 215 ± 37 μm·year–1. Paragorgia arborea had the highest radial growth rate of 830 ± 120 μm·year–1. Axial growth rates ranged from 0.56 ± 0.05 cm·year–1 for a specimen of Paramuricea spp. to 2.61 ± 0.45 cm·year–1 for a specimen of Primnoa resedaeformis . Life spans ranged from 18 ± 4 years for a live-collected P. resedaeformis to 200 ± 30 years for a subfossil specimen of K. ornata. Because all of the corals were from heavily fished areas, it is likely that age distributions are biased towards smaller and younger colonies. Recovery of deep-sea corals from fishing-induced damage will take decades to centuries.
ON SIMULATING THE GENERATION OF MOSAICISM DURING MAMMALIAN CEREBRAL CORTICAL DEVELOPMENT
Authors: CASE MICHAEL A. , MACMILLAN HUGH R. 
Published: January 2009

Renewed calls for a systems biology reflect the hope hat enduring biological questions at single-cell and cell-population scales will be resolved as modern molecular biology, with its reductionist program, approaches a nearly-complete characterization of the molecular mechanisms of specific cellular processes. Due to the confounding complexity of biological organization across these scales, computational science is sought to complement the intuition of experimentalists. However, with respect to the molecular basis of cellular processes during development and disease, a gulf between feasible simulations and realistic biology persists. Formidable are the mathematical and computational challenges to conducting and validating cell population-scale simulations, drawn from single-cell level and molecular level details. Nonetheless, in some biological contexts, a focus on core processes crafted by evolution can yield coarse-grained mathematical models that retain explanatory potential despite drastic simplification of known biochemical kinetics.In this article, we bring this modeling philosophy to bear on the nature of neural progenitor cell decision making during mammalian cerebral cortical development. Specifically, we present the computational component to a research program addressing developmental links between (i) the cellular response to endogenous DNA damage, (ii) primary mechanisms of neuronal genetic heterogeneity, or mosaicism, and (iii) the cell fate decision making that defines the population kinetics of neurogenesis.
Randomized, Double-Blinded, Placebo Controlled Study of Neuroprotection With Lidocaine in Cardiac Surgery
Authors: Mathew Joseph P. , Mackensen G. Burkhard , Phillips-Bute Barbara , Grocott Hilary P. , Glower Donald D. , Laskowitz Daniel T. , Blumenthal James A. , Newman Mark F. 
Published: January 2009

Background and Purpose—Cognitive decline after cardiac surgery remains common and diminishes patients’ quality of life. Based on experimental and clinical evidence, this study assessed the potential of intravenously administered lidocaine to reduce postoperative cognitive dysfunction after cardiac surgery using cardiopulmonary bypass.Methods—After IRB approval, 277 patients undergoing cardiac surgery were enrolled into this prospective, randomized, double-blinded placebo controlled clinical trial. Subjects were randomized to receive: (1) Lidocaine as a 1 mg/kg bolus followed by a continuous infusion through 48 hours postoperatively, or (2) Placebo bolus and infusion. Cognitive function was assessed preoperatively and again at 6 weeks and 1 year postoperatively. The effect of lidocaine on postoperative cognition was tested using multivariable regression modeling;P<0.05 was considered significant.Results—Among the 241 allocated subjects (Lidocaine: n=114; Placebo: n=127), the incidence of cognitive deficit in the lidocaine group was 45.5% versus 45.7% in the placebo group (P=0.97). Multivariable analysis revealed a significant interaction between treatment group and diabetes, such that diabetic subjects receiving lidocaine were more likely to suffer cognitive decline (P=0.004). Secondary analysis identified total lidocaine dose (mg/kg) as a significant predictor of cognitive decline and also revealed a protective effect of lower dose lidocaine in nondiabetic subjects.Conclusions—Lidocaine administered during and after cardiac surgery does not reduce the high rate of postoperative cognitive dysfunction. Higher doses of lidocaine and diabetic status were independent predictors of cognitive decline. Protective effects of lower dose lidocaine in nondiabetic subjects need to be further evaluated.
Roles of Glia Limitans Astrocytes and Carbon Monoxide in Adenosine Diphosphate-Induced Pial Arteriolar Dilation in Newborn Pigs
Authors: Kanu Alie , Leffler Charles W. 
Published: January 2009

Background and Purpose—Astrocytes, neurons, and microvessels together form a neurovascular unit allowing blood flow to match neuronal activity. Adenosine diphosphate (ADP) is an important signaling molecule in the brain, and dilation in response to ADP is astrocyte-dependent in rats and newborn pigs. Carbon monoxide (CO), produced endogenously by catabolism of heme to CO, iron, and biliverdin via heme oxygenase, is an important cell-signaling molecule in the neonatal cerebral circulation. We hypothesize ADP stimulates CO production by glia limitans astrocytes and that this CO causes pial arteriolar dilation.Methods—Experiments were performed using anesthetized piglet with closed cranial windows, and freshly isolated piglet astrocytes and microvessels. Astrocyte injury was caused by topical application of L-2-alpha aminoadipic acid (2 mmol/L, 5 hours). Cerebrospinal fluid was collected from under the cranial windows for measurement of ADP-stimulated CO production. CO was measured by gas chromatography-mass spectroscopy analysis.Results—Before, but not after, astrocyte injury in vivo, topical ADP stimulated both CO production and dilation of pial arterioles. Astrocyte injury did not block dilation to isoproterenol or bradykinin. Chromium mesoporphyrin, an inhibitor of heme oxygenase, also prevented the ADP-induced increase in cerebrospinal fluid CO and pial arteriolar dilation caused by ADP, but not dilation to sodium nitroprusside. ADP also increased CO production by freshly isolated piglet astrocytes and cerebral microvessels, although the increase was smaller in the microvessels.Conclusions—These data suggest that glia limitans astrocytes use CO as a gasotransmitter to cause pial arteriolar dilation in response to ADP.
When the Hegemony Studies the Minority—An Israeli Jewish Researcher Studies Druze Women
Authors: Weiner-Levy Naomi 
Published: January 2009

This study describes the positionality and power relations revealed during research on women in Israel's Druze minority, conducted by a Jewish woman in the country's hegemonic society. Although the researcher's position and power appear obvious, changes took place constantly, reflecting her unstable position as a stranger, “outsider” or “insider,” as well as shifts in power relations. The researcher's positionality is believed to be affected primarily by formal aspects, such as culture, ethnicity, social hierarchies, and the like, that intrude and affect encounters. The study demonstrates that such considerations do not always exert a dominant effect on research, nor is their influence invariably predictable. They involve many complex and intricate factors that impact the encounter, overriding the well-known and much-debated issue of whether the researcher is an insider or an outsider. By focusing on the intricate relations formed with participants from a different culture, the study shatters widely accepted notions regarding researchers' positionalities.
Numerical Study of the Thermal Efficiency of a School Building with Complex Topology for Different Orientations
Authors: Conceição Eusébio Z.E. , Lúcio Ma Manuela J.R. 
Published: January 2009

In this work a numerical model that simulates the thermal behavior of a building with complex topology and evaluates the indoor thermal and air quality, in transient conditions, is used for a school building thermal project. The program calculates the building surfaces solar radiation field, the building's temperatures, the internal environmental variables, and the occupant's comfort levels. Initially, after the numerical model is validated, the software is used to evaluate the school building's thermal response for four different orientations, either in winter or summer conditions. The work then aims to identify uncomfortable spaces in order to propose, as an example, several solutions that could be introduced for each orientation, that would improve the thermal comfort and air quality levels to which the occupants are subjected, and decrease the building's energy consumption levels. The information obtained from this study could be used to help a designer choose which thermal systems and solutions function best for a preferred school building orientation.
A novel in vivo siRNA delivery system specifically targeting dendritic cells and silencing CD40 genes for immunomodulation
Authors: Zheng Xiufen , Vladau Costin , Zhang Xusheng , Suzuki Motohiko , Ichim Thomas E. , Zhang Zhu-Xu , Li Mu , Carrier Ewa , Garcia Bertha , Jevnikar Anthony M. , Min Wei-Ping 
Published: January 2009

Abstract
Translation of small interfering RNA (siRNA)–based approaches into practical therapeutics is limited because of lack of an effective and cell-specific delivery system. Herein, we present a new method of selectively delivering siRNA to dendritic cells (DCs) in vivo using CD40 siRNA-containing immunoliposomes (siILs) that were decorated with DC-specific DEC-205 mAb. Administration of CD40 siILs resulted in DC-specific cell targeting in vitro and in vivo. On treatment with CD40 siILs, the expression of CD40 in DCs, as well allostimulatory activity was inhibited. In vivo administration resulted in selective siRNA uptake into immune organs and functional immune modulation as assessed using a model antigen. In conclusion, this is the first demonstration of DC-specific siRNA delivery and gene silencing in vivo, which highlights the potential of DC-mediated immune modulation and the feasibility of siRNA-based clinical therapy.
PKCβ is essential for the development of chronic lymphocytic leukemia in the TCL1 transgenic mouse model: validation of PKCβ as a therapeutic target in chronic lymphocytic leukemia
Authors: Holler Claudia , Piñón Josefina D. , Denk Ursula , Heyder Christoph , Hofbauer Sebastian , Greil Richard , Egle Alexander 
Published: January 2009

Abstract
The development and the propagation of chronic lymphocytic leukemia (CLL) has been linked to signaling via the B-cell receptor (BCR). Protein kinase C β (PKCβ) is an essential signaling element of the BCR and was recently shown to be overexpressed in human CLL. We used the TCL1 transgenic mouse model to directly target PKCβ in the development of murine CLL. TCL1 overexpression did restore the CD5+ B-cell population that is absent in PKCβ-deficient mice. However, PKCβ-deleted TCL1 transgenic mice did not develop a CLL disease, suggesting a role of PKCβ in the establishment of the malignant clone. Moreover, targeting of PKCβ with the specific inhibitor enzastaurin led to killing of human CLL samples in vitro. We thus propose that PKCβ may be a relevant target for the treatment of CLL.
Gene expression profile of the third pharyngeal pouch reveals role of mesenchymal MafB in embryonic thymus development
Authors: Sultana Dil Afroz , Tomita Shuhei , Hamada Michito , Iwanaga Yasuyuki , Kitahama Yuki , Van Khang Nguyen , Hirai Shuichi , Ohigashi Izumi , Nitta Sachiko , Amagai Takashi , Takahashi Satoru , Takahama Yousuke 
Published: January 2009

AbstractThe thymus provides a microenvironment that induces the differentiation of T-progenitor cells into functional T cells and that establishes a diverse yet self-tolerant T-cell repertoire. However, the mechanisms that lead to the development of the thymus are incompletely understood. We report herein the results of screening for genes that are expressed in the third pharyngeal pouch, which contains thymic primordium. Polymerase chain reaction (PCR)–based cDNA subtraction screening for genes expressed in microdissected tissues of the third pharyngeal pouch rather than the second pharyngeal arch yielded one transcription factor, MafB, which was predominantly expressed in CD45−IA−PDGFRα+ mesenchymal cells and was detectable even in the third pharyngeal pouch of FoxN1-deficient nude mice. Interestingly, the number of CD45+ cells that initially accumulated in the embryonic thymus was significantly decreased in MafB-deficient mice. Alterations of gene expression in the embryonic thymi of MafB-deficient mice included the reduced expression of Wnt3 and BMP4 in mesenchymal cells and of CCL21 and CCL25 in epithelial cells. These results suggest that MafB expressed in third pharyngeal pouch mesenchymal cells critically regulates lymphocyte accumulation in the embryonic thymus.
Inhibition of activation-induced death of dendritic cells and enhancement of vaccine efficacy via blockade of MINOR
Authors: Wang Tianhong , Jiang Qiong , Chan Camie , Gorski Kevin S. , McCadden Erin , Kardian David , Pardoll Drew , Whartenby Katharine A. 
Published: January 2009

AbstractActivation of dendritic cells (DCs) leads to cell maturation, which is accompanied by a regulated pattern of gene expression changes. Two significant and contradictory consequences of DC activation are that, although activation is necessary for maximal T-cell stimulation, it also leads to the initiation of gene expression that results ultimately in cell death. We have identified a gene, MINOR (mitogen-inducible nuclear orphan receptor), that becomes highly up-regulated on activation and whose expression leads to apoptosis in mature DCs. MINOR is a member of the Nur77 family of nuclear orphan receptors, which includes Nur77 and Nurr1. Although Nur77 and Nurr1 are expressed in macrophages and DCs, their expression levels do not change on DC activation. We thus tested the hypothesis that induction of MINOR would lead to an activation-induced cell death in DCs and that its inhibition would increase the lifespan of DCs and improve their vaccine efficacy. To block natural expression of MINOR by DCs, we generated a lentiviral vector that expresses a small interfering RNA. Our results indicate that blockade of MINOR expression dramatically decreases apoptosis in DCs and suggest that this approach may be a novel means to improve the potency of ex vivo–generated DC vaccines.
Rate of progression of lung function impairment in α1-antitrypsin deficiency
Authors: Dawkins P. A. , Dawkins C. L. , Wood A. M. , Nightingale P. G. , Stockley J. A. , Stockley R. A. 
Published: January 2009

The aim of the present study was to identify α1-antitrypsin (α1-AT)-deficient patients who had rapidly progressive disease.PiZ patients (n = 101) underwent annual lung function measurements over a 3-yr period, and the results were related to factors that may influence decline.The mean annual decline in forced expiratory volume in 1 s (FEV1) was 49.9 mL. The greatest FEV1decline occurred in the moderate severity group (FEV150–80% of the predicted value), with a mean annual decline of 90.1 mL, compared with 8.1 mL in the very severe group (FEV1<30% pred). However, annual decline in transfer coefficient of the lung for carbon monoxide (KCO) was greatest in the severe and very severe groups. When the whole group was divided into tertiles of FEV1decline, the fast tertile compared with the slow tertile had more patients with bronchodilator reversibility (BDR) (73versus41%; p = 0.010), more males (79versus56%; p = 0.048) and lower body mass index (BMI) (24.0versus26.1; p = 0.042). Logistic regression analyses confirmed that FEV1decline was independently associated with BMI, BDR, exacerbation rate and high physical component 36-item short-form health survey scores.In PiZ α1-AT-deficient patients, FEV1decline was greatest in moderate disease, unlikeKCOdecline, which was greatest in severe disease. The FEV1decline showed associations with BDR, BMI, sex and exacerbation rate.
Effect of breastfeeding on asthma, lung function and bronchial hyperreactivity in ISAAC Phase II
Authors: Nagel G. , Büchele G. , Weinmayr G. , Björkstén B. , Chen Y-Z. , Wang H. , Nystad W. , Saraclar Y. , Bråbäck L. , Batlles-Garrido J. , Garcia-Hernandez G. , Weiland S. K. ,   the ISAAC Phase II Study Group
Published: January 2009

The association between breastfeeding and wheezing, lung function and atopy was evaluated in the International Study of Asthma and Allergy in Childhood (ISAAC) Phase II.Cross-sectional studies were performed in 27 centres in 20 countries. Information on disease and exposure factors was collected by parental questionnaires. Data from 54,000 randomly selected school children (aged 8–12 yrs, 31,759 with skin prick testing) and a stratified subsample (n = 4,888) were used for testing the correlation of breastfeeding with bronchial hyperreactivity and lung function. Random effect models for meta-analysis were applied to calculate combined odds ratios (ORs).Any breastfeeding was associated with less wheeze both in affluent (adjusted OR (ORadj) 0.87, 95% confidence interval (CI) 0.78–0.97) and nonaffluent countries (ORadj0.80, 95% CI 0.68–0.94). Further analyses revealed that this was true only for nonatopic wheeze in nonaffluent countries (ORadj0.69, 95% CI 0.53–0.90). Breastfeeding was not associated with atopic wheeze and objective measures of allergy in both affluent and nonaffluent countries. In contrast, breastfeeding was associated with higher predicted forced expiratory volume in one second in affluent countries only (mean ratio 1.11, 95% CI 1.02–1.20).Breastfeeding is associated with protection against nonatopic wheeze, which becomes particularly evident in nonaffluent countries. Overall, breastfeeding was not related to any measure of allergy. These findings may explain some of the controversy regarding breastfeeding, since the direction of the association with breastfeeding depends on the predominating wheeze phenotype (e.g.atopic, nonatopic).
Erythropoietin inhibits respiratory epithelial cell apoptosis in a model of acute lung injury
Authors: MacRedmond R. , Singhera G. K. , Dorscheid D. R. 
Published: January 2009

Fas-mediated apoptosis of the alveolar epithelium is important in the pathogenesis of acute respiratory distress syndrome. Erythropoietin (EPO) has cytoprotective properties in other organ systems, and is relatively deficient in critical illness. This study investigates a potential role for EPO in reducing apoptosis in a model of acute lung injury.Apoptosis was induced in human alveolar epithelial (A549) cells or normal human bronchial epithelial (NHBE) cells by Fas activation with CH-11 Fas-crosslinking antibody or by co-culture with polymorphonuclear neutrophils in a transwell system. The effect of recombinant human (rh)EPO on apoptosis was measured by poly(ADP-ribose) polymerase cleavage and cell death detection assay. The specific EPO–EPO receptor (EPOR)-mediated effect was determined using an EPO-blocking antibody or EPOR small interfering RNA.Expression of EPOR was demonstrated in A549, NHBE and normal human alveolar epithelium. Fas- and neutrophil-mediated apoptosis of A549 and NHBE cells was inhibited by rhEPO by a specific EPO–EPOR-mediated mechanism. This anti-apoptotic effect was associated with induction of a pro-apoptotic Bcl-xL/Bax ratio.EPO has cytoprotective properties in respiratory epithelium in anin vitromodel, which may indicate a potential therapeutic role in acute lung injury.
Validation of the COPD severity score for use in primary care: the NEREA study
Authors: Miravitlles M. , Llor C. , de Castellar R. , Izquierdo I. , Baró E. , Donado E. 
Published: January 2009

Spirometry is underused for the assessment of severity of chronic obstructive pulmonary disease (COPD) in primary care (PC). Therefore, simple assessment tools are required in this setting. The aim of the present study was to validate the COPD severity score (COPDSS) for use in PC.A multicentric study was carried out in stable COPD patients in PC. The concurrent validity of the COPDSS was evaluated by examining the association between COPDSS, COPD clinical indicators and the London Chest Activity of Daily Living (LCADL) scale, European quality of life (EuroQOL) questionnaires and Charlson comorbidity index.A total of 837 patients with COPD were analysed (males 84.3%; mean±sdage 68±11 yrs; forced expiratory volume in one second 54.6±17.7% of the predicted value). A strong correlation was found between COPDSS and dyspnoea level and a moderate correlation between COPDSS and exacerbation number. The COPDSS discriminated between patients with varying degrees of dyspnoea (area under receiver operating characteristic (ROC) curve 0.837), and according to number of exacerbations in the last year (area under ROC curve 0.773). Higher COPDSS scores were significantly associated with lower EuroQOL scores, lower EuroQOL visual analogue scale scores and higher LCADL scores.The present results indicate that the chronic obstructive pulmonary disease severity score is a useful and reliable tool for assessing the severity of chronic obstructive pulmonary disease in primary care.