bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical quantitation of immune signature in follicular lymphoma by RT-PCR–based gene expression profiling
Authors: Byers Richard J. , Sakhinia Ebrahim , Joseph Preethi , Glennie Caroline , Hoyland Judith A. , Menasce Lia P. , Radford John A. , Illidge Timothy 
Published: January 2008

Abstract
Microarray gene expression profiling studies have demonstrated immune response gene signatures that appear predictive of outcome in follicular lymphoma (FL). However, measurement of these marker genes in routine practice remains difficult. We have therefore investigated the immune response in FL using real-time polymerase chain reaction (PCR) to measure expression levels of 35 candidate Indicator genes, selected from microarray studies, to polyA cDNAs prepared from 60 archived human frozen lymph nodes, in parallel with immunohistochemical analysis for CD3, CD4, CD7, CD8, CD10, CD20, CD21, and CD68. High levels of CCR1, a marker of monocyte activation, were associated with a shorter survival interval, and high levels of CD3 with better survival, while immunohistochemistry demonstrated association of high numbers of CD68+ macrophages with a shorter survival interval and of high numbers of CD7+ T cells with a longer survival interval. The results confirm the role of the host immune response in outcome in FL and identify CCR1 as a prognostic indicator and marker of an immune switch between macrophages and a T cell–dominant response. They demonstrate the utility of polyA DNA and real-time PCR for measurement of gene signatures and the applicability of using this type of “molecular block” in clinical practice.
Maximum likelihood estimates of two-locus recombination fractions under some natural inequality restrictions
Authors: Zhou Ying , Shi Ning-Zhong , Fung Wing-Kam , Guo Jianhua 
Published: January 2008

AbstractBackgroundThe goal of linkage analysis is to determine the chromosomal location of the gene(s) for a trait of interest such as a common disease. Three-locus linkage analysis is an important case of multi-locus problems. Solutions can be found analytically for the case of triple backcross mating. However, in the present study of linkage analysis and gene mapping some natural inequality restrictions on parameters have not been considered sufficiently, when the maximum likelihood estimates (MLEs) of the two-locus recombination fractions are calculated.ResultsIn this paper, we present a study of estimating the two-locus recombination fractions for the phase-unknown triple backcross with two offspring in each family in the framework of some natural and necessary parameter restrictions. A restricted expectation-maximization (EM) algorithm, called REM is developed. We also consider some extensions in which the proposed REM can be taken as a unified method.ConclusionOur simulation work suggests that the REM performs well in the estimation of recombination fractions and outperforms current method. We apply the proposed method to a published data set of mouse backcross families.
Open access for the non-English-speaking world: overcoming the language barrier
Authors: Fung Isaac CH 
Published: January 2008

AbstractThis editorial highlights the problem of language barrier in scientific communication in spite of the recent success of Open Access Movement. Four options for English-language journals to overcome the language barrier are suggested: 1) abstracts in alternative languages provided by authors, 2) Wiki open translation, 3) international board of translator-editors, and 4) alternative language version of the journal. The Emerging Themes in Epidemiology announces that with immediate effect, it will accept translations of abstracts or full texts by authors as Additional files.Editorial note:In an effort towards overcoming the language barrier in scientific publication, ETE will accept translations of abstracts or the full text of published articles. Each translation should be submitted separately as an Additional File in PDF format. ETE will only peer review English-language versions. Therefore, translations will not be scrutinized in the review-process and the responsibility for accurate translation rests with the authors.
Resveratrol amelioratesSerratia marcescens-induced acute pneumonia in rats
Authors: Lu Chia-Chen , Lai Hsin-Chih , Hsieh Shang-Chen , Chen Jan-Kan 
Published: January 2008

AbstractSerratia marcescens is an important nosocomial pathogen, which has been especially problematic as a cause of hospital-acquired pneumonia in the past two decades. Treatment of S. marcescens-related infections has been limited by emergence of multiple drug-resistant strains. Thus, the development of alternative agents for the prevention and treatment of Serratia infection is urgently needed. Resveratrol (RSV) is a compound with diverse biological effects including anti-cancer, anti-inflammation, anti-diabetes, and cancer chemoprevention. Whether RSV has in vivo prophylactic or therapeutic potential against infection remains uncharacterized. In the present study, we used a murine acute pneumonia model initiated by intratracheal application of S. marcescens to evaluate whether RSV possesses anti-infection properties. We showed that pretreatment with RSV for 3 days markedly increased alveolar macrophage infiltration, elevated NK cell activity, and decreased bacterial burden in the infected lung with a subsequent decrease in mortality. These effects were associated with significantly less-severe inflammatory phenotypes in lung tissue and bronchoalveolar lavage fluid, including reduced neutrophil infiltration of the lungs, reduced phagocytosis activity, and reduced secretion of cytokines such as TNF-α, IL-1β, and IL-6. To further characterize the underlying mechanism responsible for these effects of RSV, LPS derived from S. marcescens was used to induce acute pneumonia in rats, with or without RSV pretreatment. RSV was shown to ameliorate acute pneumonia via inhibition of the NF-κB signaling pathway, including inhibition of IκBα phosphorylation and subsequent NF-κB activation. These findings suggest that RSV might be beneficial as a prophylactic treatment in patients at risk of an episode of S. marcescens-induced acute pneumonia.
Assessment of mental capacity: who can do it?
Authors: Singhal Ankush , Kumar Alok , Belgamwar Ravindra B. , Hodgson Richard E. 
Published: December 2007

Aims and MethodsTo determine the point prevalence of mental incapacity and the ‘Bournewood gap’ in general adult and old age mental health in-patients. The correlation of mental capacity assessment between doctors and nurses was investigated. Data were gathered on one census day for all general adult and old age psychiatric in-patients at three hospital sites.ResultsHalf the sample lacked capacity and one third fell into the ‘Bournewood gap’. The capacity assessment by nurses and doctors correlated highly (κ=0.719, P=0.0001).Clinical Implications‘Bournewood gap’ patients should have their needs assessed in order to identify and protect their rights. Appropriately trained mental health nursing staff can undertake this assessment.
Cryopreservation and Methanol Effects on Burbot Sperm Motility and Egg Fertilization
Authors: Jensen N R , Zuccarelli M D , Patton S J , Williams S R , Ireland S C , Cain K D 
Published: January 2008

Abstract
Cryopreservation of semen from North American burbot Lota lota maculosa was investigated and optimal methanol concentrations were determined for a conservation breeding program. Methods were modified from those reported for Eurasian burbot L. lota lota. The permeable cryoprotectant (methanol) concentration in the semen extender was varied to provide final methanol concentrations of 5, 10, and 20%. Semen motility was evaluated at 80 and 363 d postfreeze (dpf). Fertilization was determined at 340 and 367 dpf. Methanol concentration in the extender significantly (P &lt; 0.05) affected sperm motility and egg fertilization percentages. Motility and fertilization were lowest when 5% methanol was used. Motility of semen at 80 dpf was not significantly different between 10% and 20% methanol, but semen at 363 dpf had significantly higher motility when stored in 20% methanol than in 10% methanol. Egg fertilization was highest when semen was stored in extenders containing 10% or 20% methanol. Results suggest that good motility and fertilization can be achieved by cryopreserving burbot semen with 10% or 20% methanol in the extender instead of 5% methanol. This study demonstrates the potential to utilize cryopreserved burbot semen in the development of germplasm repositories for imperiled fish stocks.
A Simple Apparatus for Maintaining Gas-Supersaturated Seawater in the Laboratory for Experimental Purposes
Authors: Smiley Jeffrey E , Drawbridge Mark A 
Published: January 2008

Abstract
Gas bubble disease caused by supersaturated conditions is generally well understood for commercially important freshwater species, such as salmon and trout, but very little is known about impacts to marine finfish culture. We developed a relatively simple, low-cost apparatus to expose juvenile white seabass Atractoscion nobilis and striped bass Morone saxatilis to multiple gas saturation levels simultaneously. We found that the system was capable of operating under different temperatures and accommodating a range of juvenile fish sizes. Gas saturation treatments were maintained by mixing a supersaturated seawater source with a saturated one. The supersaturated seawater source was created by reducing pressure of an air- or oxygen-equilibrated water source maintained at a pressure of 623.2 mm Hg. The saturated seawater source was achieved by degassing seawater using a packed column. By mixing these two water sources manually by use of needle valves, differential gas pressures (ΔP) ranging from 0.0 to 167.2 mm Hg were maintained. The control treatment level ranged from −35.7 to 0 mm Hg and was maintained using a vacuum degasser. Oxygen-nitrogen (O2:N2) ratios ranged from 0.83 to 1.41. Temperature within the experiment was computer controlled. The supersaturation apparatus operated very effectively and delivered treatment levels that were stable and significantly different from one another throughout all trials.
Corn Gluten Meal Partially Replaces Dietary Fish Meal without Compromising Growth or Fatty Acid Composition of Sunshine Bass
Authors: Lewis Heidi A , Kohler Christopher C 
Published: January 2008

Abstract
A 7-week feed trial was conducted to determine the minimum dietary level of menhaden (Brevoortia spp.) meal (MM) needed to maintain growth, fillet quality, and health in sunshine bass (female white bass Morone chrysops × male striped bass M. saxatilis). Sunshine bass were stocked at 10 fish/tank (group weight per tank: Mean ± SD = 182.0 ± 2.0 g) into each of 28 tanks and were fed seven experimental diets (4 randomly assigned tanks/diet). Experimental treatments ranged from 0% to 24% MM; corn gluten meal (CGM) was used as the dietary protein replacement. The isonitrogenous diets contained 41% crude protein and 14% crude lipid, and fish were fed to apparent satiation twice daily. Sunshine bass given diets with less than 20% MM had significantly lower (P &lt; 0.05) weight gain than fish in other treatments; however, specific growth rates and feed conversion ratios remained constant in fish fed diets with as little as 16% and 12% MM, respectively. Total n-3 fatty acids and 20:5(n-3) content of the fillets were similar between the 20% and 24% MM treatments; however, these fatty acids declined as more MM was replaced. Highly unsaturated fatty acid concentrations in the fillet were similar among diets of at least 16% MM. Collectively, our data provide evidence that MM can be substituted with CGM in diets fed to sunshine bass without adversely affecting growth and fillet quality; however, complete replacement of MM adversely affected growth, lipid metabolism, and oxidative stability in the liver. More effective usage of menhaden resources will enable the industry to create economically and environmentally sustainable diet formulations for sunshine bass.
Using the Support Immersion Endoscope for Socket Assessment
Authors: Juodzbalys Gintaras , Bojarskas Stasys , Kubilius Ricardas , Wang Hom‐Lay 
Published: December 2007

Background: The purpose of this study was to determine the indications, efficacy, and advantages of the support immersion endoscope (SIE) method for extraction socket assessment.Methods: Twelve patients (four women and eight men; mean age: 28 years) in need of extraction with implant placement participated in the study. The teeth extracted included eight upper central incisors and six upper lateral incisors. Extraction sockets were evaluated with a conventional extraction site evaluation (CESE) method alone or with CESE + SIE. CESE includes: visual evaluation; periodontal probing; ridge mapping with calipers, dental mirror, and orthopantomogram; and diagnostic wax‐up.Results: CESE + SIE had significantly better accuracy in examining extraction socket labial plate vertical position, labial plate thickness, and bone quality compared to CESE alone. The results obtained from CESE assessment were inconsistent because of poor visualization.Conclusion: The SIE can be used as an adjunct tool in assessing extraction socket morphology and bone conditions without flap elevation.
Intravitreal Triamcinolone Acetonide Inhibits Breakdown of the Blood-Retinal Barrier Through Differential Regulation of VEGF-A and Its Receptors in Early Diabetic Rat Retinas
Authors: Zhang Xinyuan , Bao Shisan , Lai Donna , Rapkins Robert W. , Gillies Mark C. 
Published: January 2008

OBJECTIVE
To elucidate the mechanism of the unique beneficial effect of intravitreal steroid therapy on diabetic macular edema, we investigated the effect of locally administered triamcinolone acetonide (TA) on the expression of vascular endothelial growth factor (VEGF)-A and its receptors in retinas of rats with streptozotocin (STZ)-induced diabetes. We then correlated the expression of these proteins with breakdown of the blood-retinal barrier (BRB).

RESEARCH DESIGN AND METHODS
Thirty-two eyes of 16 diabetic and nondiabetic rats were divided into four groups. TA was injected into the vitreous of the right eye, and saline was injected into the left eye (control) 3.5 weeks after induction of diabetes. Retinas were harvested 48 h following treatment. mRNA and protein expression of VEGF-A, VEGF-A receptor 1 (fms-like tyrosine kinase [FLT]-1), and VEGF-A receptor 2 (fetal liver kinase [FLK]-1) were determined by real-time RT-PCR and immunohistochemistry. BRB permeability was quantitated by measuring extravasated endogenous albumin and retinal thickness.

RESULTS
Diabetes-induced retinal thickness and albumin extravasation were significantly reduced in TA-treated diabetic retinas to a level similar to that in sham-treated nondiabetic eyes. A close correlation between albumin leakage and increased expression of both Vegf-a and Flk-1 was noted in the diabetic retinas. TA downregulated the expression of Vegf-a and Flk-1 but upregulated the expression of Flt-1. TA did not alter the expression of these genes in nondiabetic retinas.

CONCLUSIONS
Intravitreal injection of TA stabilizes the BRB in association with regulation of Vegf-a, Flk-1, and Flt-1 expression in retinas in the early stages of diabetes.
Quantifying acceptable levels of visitor use on Red Sea reef flats
Authors: Leujak Wera , Ormond Rupert F.G. 
Published: December 2007

Abstract
The effects of trampling by visitors walking over the reef flat to snorkel or swim along the reef edge were studied at Ras Um Sidd, a popular fringing reef site at Sharm El Sheikh, and in the Ras Mohammed National Park, South Sinai, Egypt. Twelve stations showed a sequence of events linked to increased frequency and extent of trampling, with the intensities of trampling ranging from 0.1 to 324 tramplers m−2 yr−1.
Heavily trampled stations had a reduced coral cover (in particular branching corals), higher amounts of coral damage, less old dead coral, less obligate corallivorous fishes and more herbivores.
Wave exposure was crucial in determining the susceptibility of coral communities to trampling. Exposed communities were dominated by branching corals and were mechanically more resistant, since wave stress had favoured stockier growth forms.
The applicability of the ‘carrying capacity concept’ was investigated as a management tool for determining how much use is sustainable. Examination of the relationship between hard coral cover and intensity of trampling suggested that carrying capacity could be set at approximately 50 tramplers m−2 yr−1. The actual amount of damage caused by trampling showed a linear increase with increasing trampling intensities, so that the carrying capacity concept, as defined in this study, was not applicable to the relationship since no threshold existed. Instead, the ‘limits of acceptable change’ approach would be more practicable, with managers deciding what amount of coral damage they permit before limiting access. To establish meaningful limits of change, more knowledge is required about ecological as well as social consequences (e.g. visitor satisfaction) of such limits.
Copyright © 2007 John Wiley & Sons, Ltd.
Response of a gorgonian (Paramuricea clavata) population to mortality events: recovery or loss?
Authors: Cupido R. , Cocito S. , Sgorbini S. , Bordone A. , Santangelo G. 
Published: December 2007

Abstract
During late summer 1999 and 2003 two mass mortality events affected the population of the slow growing, long‐lived Mediterranean gorgonian Paramuricea clavata living in the Gulf of La Spezia (Italy).
The population was monitored for three years after the mortality events. Availability of pre‐event data (1998) allowed comparison of population density and population size structure of the healthy population with those recorded in the three years following the mortality events.
In 1998, before the two mass mortality events, mean colony density was 33.3 ± 3.7 colonies m−2 and had fallen to 6.7 ± 1.9 colonies m−2 in 2004.
In the post‐event period the population size structure changed and the modal class of colonies shifted from 16–21 cm to 6–15 cm height.
In 2004 mortality affected 75 ± 6.4% of colonies. A significant, positive correlation between the extent of damage and colony size was found throughout the monitoring period.
In the three years following the two mortality events, a small increase in density of recruits and of older undamaged colonies was recorded suggesting that the population was slowly recovering.
The bathymetric distribution of P. clavata straddles the summer thermocline making this population particularly sensitive to temperature increases. The lack of deeper colonies (less exposed to warming) and the geographical isolation of this population is likely to prevent any substantial external larval supply.
An increased frequency of mass mortality events associated with ever increasingly high temperature events represent a considerable threat to the persistence of a P. clavata population in the Gulf of La Spezia.
Copyright © 2007 John Wiley & Sons, Ltd.
A bioluminescent HL‐60 cell line to assay anti‐leukaemia therapeutics under physiological conditions
Authors: Isaza Maria P. , Chau Jennie T. , Le Amy , Balashova Nataliya V. , Patel Jigna K. , Salerno Erica , Crosby Juan A. , O'Connor Anna , Kachlany Scott C. 
Published: December 2007

AbstractScreens for compounds and proteins with anti‐cancer activity employ viability assays using relevant cancer cell lines. For leukaemia studies, the human leukaemia cell line, HL‐60, is often used as a model system. To facilitate the discovery and investigation of anti‐leukaemia therapeutics under physiological conditions, we have engineered HL‐60 cells that stably express firefly luciferase and produce light that can be detected using an in vivo imaging system (IVIS). Bioluminescent HL‐60luc cells could be rapidly detected in whole blood with a sensitivity of approximately 1000 viable cells/200 µl blood. Treatment of HL‐60luc cells with the drug chlorambucil revealed that the bioluminescent viability assay is able to detect cell death earlier than the Trypan blue dye exclusion assay. HL‐60luc cells administered intraperitoneally (i.p.) or intravenously (i.v.) were visualized in living mice. The rapidity and ease of detecting HL‐60luc cells in biological fluid indicates that this cell line could be used in high‐throughput screens for the identification of drugs with anti‐leukaemia activity under physiological conditions. Copyright © 2007 John Wiley & Sons, Ltd.
A novel homogeneous bioluminescence resonance energy transfer element for biomolecular detection with CCD camera or CMOS device
Authors: Filanoski Brian , Rastogi Shiva K. , Cameron Eric , Mishra Nirankar N. , Maki Wusi , Maki Gary 
Published: December 2007

AbstractA novel optical signal element based on homogeneous bioluminescence resonance energy transfer (BRET) was developed for biomolecular detection. A fluorescent dye and alkaline phosphatase (AP) conjugate was used as a reporter and light‐generation element for imaging detection platforms that use a CCD camera or CMOS chip‐based devices. In the presence of a luminescence substrate, the energy from the first light emission of a bioluminescence enzymatic reaction was transferred to fluorescent dyes which were conjugated to an enzyme. This resulted in a second light emission with a shorter wavelength. The second light was localized at the position of target molecules without the diffusion problems present in current technology. To optimize energy transfer efficiency, the ratio of enzyme to fluorophore in the conjugates, the fluorescent dyes used in the conjugates and the luminescence substrates used for BRET were investigated. BRET was demonstrated by using both a CCD camera and a CMOS imaging device. Image spatial resolution was greatly improved compared with conventional chemiluminescence detection. This new signal element opens a door for the direct measurement of fluorescent signals on an imaging chip without an external light source and portable instrumentation normally required for the fluorescent detection of biomolecules. Copyright © 2007 John Wiley & Sons, Ltd.
Gene expression analysis on sections of zebrafish regenerating fins reveals limitations in the whole‐mount in situ hybridization method
Authors: Smith A. , Zhang J. , Guay D. , Quint E. , Johnson A. , Akimenko M.A. 
Published: December 2007

AbstractThe caudal fin of adult zebrafish is used to study the molecular mechanisms that govern regeneration processes. Most reports of gene expression in regenerating caudal fins rely on in situ hybridization (ISH) on whole‐mount samples followed by sectioning of the samples. In such reports, expression is mostly confined to cells other than those located between the dense collagenous structures that are the actinotrichia and lepidotrichia. Here, we re‐examined the expression of genes by performing ISH directly on cryo‐sections of regenerates. We detected expression of some of these genes in cell types that appeared to be non‐expressing when ISH was performed on whole‐mount samples. These results demonstrate that ISH reagents have a limited capacity to penetrate between the regenerating skeletal matrices and suggest that ISH performed directly on fin sections is a preferable method to study gene expression in fin regenerates. Developmental Dynamics 237:417–425, 2008. © 2007 Wiley‐Liss, Inc.