bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical efficiency analysis for the Iranian fishery in the Persian Gulf
Authors: Esmaeili Abdoulkarim 
Published: October 2006

Abstract
There are many fish landing areas in southern Iran, distributed all along the coastline, and despite gradually increasing effort, the total catch has fluctuated in recent years. This study examines the technical efficiency of the fishing industry, and identifies factors that could be causing inefficiency. A stochastic production function among fishery vessels is estimated. Technical efficiency measures the ability of firms to maximize output using a given set of inputs and technologies. The results indicate that technical efficiency in the fishery is relatively low, and that wooden vessels of medium size are more efficient than small fibreglass vessels. Both skippers' socio-economic drivers and vessel instrumentation have a significant impact on efficiency. Ownership of two-way radio and ownership of GPS are important considerations that influence fishing efficiency, and the skipper's level of education and experience are qualities that also affect it. Owner-operated vessels and younger skippers are more efficient than others. Understanding these constraints may contribute to increasing the efficiency of the Iranian fishery in the Persian Gulf.
Standard Right Atrial Ablation is Effective for Atrioventricular Nodal Reentry with Earliest Activation in the Coronary Sinus
Authors: CHEN JANE , ANSELME FRÉDÉRIC , SMITH TIMOTHY W. , ZIMETBAUM PETER , EPSTEIN LAURENCE M. , PAPAGEORGIOU PANOS , JOSEPHSON MARK E. 
Published: October 2006

Introduction: Reports suggest that coronary sinus (CS) or left atrial ablations may be necessary for treatment of AV nodal reentrant tachycardia (AVNRT) with earliest retrograde atrial activation in the CS. We assessed the efficacy of standard right atrial catheter ablation approaches in these tachycardias and determined the incidence of earliest activation in the CS in AVNRT. Methods and Results: We retrospectively evaluated intracardiac recordings from 225 consecutive patients who underwent electrophysiologic studies and radiofrequency (RF) ablation for AVNRT in two institutions. Atrial activation during AVNRT was evaluated using multiple catheters according to standard protocol used in our laboratories. RF ablations in the triangle of Koch were performed in all patients. Eighteen of 225 patients (8%) had earliest activation in one of the CS poles. The demographics and AVNRT characteristics of these 18 patients were similar to those of the other 207 patients who did not have CS as earliest activation site and included both typical and atypical AVNRT. Following RF ablation, none of the 18 patients had inducible AVNRT. Conclusion: Successful RF ablation can be performed at standard sites in the triangle of Koch regardless of earliest site of atrial activation. The incidence of CS as earliest retrograde atrial activation site in AVNRT is 8%. (J Cardiovasc Electrophysiol, Vol. 15, pp. 2‐7, January 2004)
Technique and Results of Pulmonary Vein Angiography in Patients Undergoing Catheter Ablation of Atrial Fibrillation
Authors: VASAMREDDY CHANDRASEKHAR R. , JAYAM VINOD , LICKFETT LARS , NASIR KHURRAM , BRADLEY DAVID J. , ELDADAH ZAYD , DICKFELD TIMM , DONAHUE KEVIN , HALPERIN HENRY R. , BERGER RONALD , CALKINS HUGH 
Published: October 2006

Introduction: Delineation of pulmonary vein (PV) anatomy is an integral part of the PV isolation procedure. The aims of the present study were to (1) describe the technique of selective PV angiography, (2) show the typical fluoroscopic locations and appearance of the PVs, and (3) compare the ostial diameters of PVs measured by angiography and magnetic resonance imaging (MRI). Methods and Results: Twenty consecutive patients undergoing a PV isolation procedure underwent selective PV angiography using a deflectable 8‐French lumened catheter (Naviport, Cardima). The left superior PV (LSPV) runs upward and away from the spine in the right anterior oblique (RAO) projection and upward and toward the spine in the left anterior oblique (LAO) projection. The opposite is true for the right superior PV (RSPV). The left inferior PV (LIPV) has a bull's‐eye appearance in the RAO projection, and the right inferior PV (RIPV) has a bull's‐eye appearance in the LAO projection due to their end‐on trajectories. The LIPV in the LAO projection and the RIPV in the RAO projection run horizontally toward the spine. An excellent correlation was noted in PV ostial size as assessed by angiography and MRI (r2 < 0.90, P < 0.0001). Conclusion: This study describes the technique and results of PV angiography and fluoroscopy. The study also demonstrates good correlation of PV ostial diameters by contrast venography and MRI. PV angiography can be used as an alternate to MRI or computed tomographic imaging, particularly when these tests are unavailable or are contraindicated in the patient. (J Cardiovasc Electrophysiol, Vol. 15, pp. 21‐26, January 2004)
Implications of Implantable Cardioverter Defibrillator Therapy in Congenital Heart Disease and Pediatrics
Authors: ALEXANDER MARK E. , CECCHIN FRANK , WALSH EDWARD P. , TRIEDMAN JOHN K. , BEVILACQUA LAURA M. , BERUL CHARLES I. 
Published: October 2006

Introduction: The incidence of appropriate and inappropriate discharges, indicators of system failure, and clinical implications of implantable cardioverter defibrillator (ICD) therapy in children and young adults with heart disease is poorly defined. Methods and Results: In a retrospective study at a single medical center, a total of 90 ICD procedures were performed in 76 patients younger than age 30 years (median 16 years, range 1–30): 42% with congenital heart disease, 33% with primary electrical disease, 17% with hypertrophic cardiomyopathy, and 8% with idiopathic dilated cardiomyopathy. Indications for ICD included arrest or sustained ventricular tachycardia (n = 27), and combinations of syncope (n = 32), palpitations (n = 17), spontaneous ventricular arrhythmia (n = 40), inducible ventricular tachycardia (n = 36), or severe hypertrophic cardiomyopathy. Transvenous dual‐chamber ICDs were implanted in 29 patients. Subcutaneous arrays or epicardial patches were used in 9 patients. Over a median 2‐year follow‐up, 28% of patients received appropriate shocks for ventricular tachycardia (median 13 months to first shock) and 25% experienced inappropriate shocks for multiple causes (median 16 months). With multivariate analysis, growth strongly correlated with lead failure (odds ratio 73, 3.5–1530, P = 0.006). Complications occurred in 29 patients, including lead failure in 16 (21%), ICD “storm” with sequential shocks in 5, and infection in 2 patients. No deaths were attributable to ICD placement or subsequent device failure. Conclusion: ICD therapy can effectively manage malignant arrhythmias in selected pediatric and congenital heart patients. Spurious shocks or ICD storm may increase morbidity and emphasize the need for concomitant medical and ablative therapy. ICD lead failure was relatively frequent in this population. (J Cardiovasc Electrophysiol, Vol. 15, pp. 72‐76, January 2004)
Survival analysis of longitudinal microarrays
Authors: Rajicic Natasa , Finkelstein Dianne M. , Schoenfeld David A. ,   the Inflammation Host Response to Injury Research Program Investigators
Published: October 2006

AbstractMotivation: The development of methods for linking gene expressions to various clinical and phenotypic characteristics is an active area of genomic research. Scientists hope that such analysis may, for example, describe relationships between gene function and clinical events such as death or recovery. Methods are available for relating gene expression to measurements that are categorized or continuous, but there is less work in relating expressions to an observed event time such as time to death, response or relapse. When gene expressions are measured over time, there are methods for differentiating temporal patterns. However, methods have not yet been proposed for the survival analysis of longitudinally collected microarrays.Results: We describe an approach for the survival analysis of longitudinal gene expression data. We construct a measure of association between the time to an event and gene expressions collected over time. Statistical significance is addressed using permutations and control of the false discovery rate. Our proposed method is illustrated on a dataset from a multi-center research study of inflammation and response to injury that aims to uncover the biological reasons why patients can have dramatically different outcomes after suffering a traumatic injury ().Contact: dfinkelstein@partners.org
Integration of gel-based proteome data with pProRep
Authors: Laukens Kris , Matthiesen Rune , Lemière Filip , Esmans Eddy , Onckelen Harry Van , Jensen Ole Nørregaard , Witters Erwin 
Published: October 2006

Abstract
Summary: pProRep is a web application integrating electrophoretic and mass spectral data from proteome analyses into a relational database. The graphical web-interface allows users to upload, analyse and share experimental proteome data. It offers researchers the possibility to query all previously analysed datasets and can visualize selected features, such as the presence of a certain set of ions in a peptide mass spectrum, on the level of the two-dimensional gel.
Availability: The pProRep package and instructions for its use can be downloaded from . The application requires a web server that runs PHP 5 () and MySQL. Some (non-essential) extensions need additional freely available libraries: details are described in the installation instructions.
Contact: kris.laukens@ua.ac.be
Evaluating the performance of microarray segmentation algorithms
Authors: Lehmussola Antti , Ruusuvuori Pekka , Yli-Harja Olli 
Published: October 2006

Abstract
Motivation: Although numerous algorithms have been developed for microarray segmentation, extensive comparisons between the algorithms have acquired far less attention. In this study, we evaluate the performance of nine microarray segmentation algorithms. Using both simulated and real microarray experiments, we overcome the challenges in performance evaluation, arising from the lack of ground-truth information. The usage of simulated experiments allows us to analyze the segmentation accuracy on a single pixel level as is commonly done in traditional image processing studies. With real experiments, we indirectly measure the segmentation performance, identify significant differences between the algorithms, and study the characteristics of the resulting gene expression data.
Results: Overall, our results show clear differences between the algorithms. The results demonstrate how the segmentation performance depends on the image quality, which algorithms operate on significantly different performance levels, and how the selection of a segmentation algorithm affects the identification of differentially expressed genes.
Availability: Supplementary results and the microarray images used in this study are available at the companion web site
Contact: antti.lehmussola@tut.fi
Proteomic Analysis of Seed Dormancy in Arabidopsis
Authors: Chibani Kamel , Ali-Rachedi Sonia , Job Claudette , Job Dominique , Jullien Marc , Grappin Philippe 
Published: October 2006

AbstractThe mechanisms controlling seed dormancy in Arabidopsis (Arabidopsis thaliana) have been characterized by proteomics using the dormant (D) accession Cvi originating from the Cape Verde Islands. Comparative studies carried out with freshly harvested dormant and after-ripened non-dormant (ND) seeds revealed a specific differential accumulation of 32 proteins. The data suggested that proteins associated with metabolic functions potentially involved in germination can accumulate during after-ripening in the dry state leading to dormancy release. Exogenous application of abscisic acid (ABA) to ND seeds strongly impeded their germination, which physiologically mimicked the behavior of D imbibed seeds. This application resulted in an alteration of the accumulation pattern of 71 proteins. There was a strong down-accumulation of a major part (90%) of these proteins, which were involved mainly in energetic and protein metabolisms. This feature suggested that exogenous ABA triggers proteolytic mechanisms in imbibed seeds. An analysis of de novo protein synthesis by two-dimensional gel electrophoresis in the presence of [35S]-methionine disclosed that exogenous ABA does not impede protein biosynthesis during imbibition. Furthermore, imbibed D seeds proved competent for de novo protein synthesis, demonstrating that impediment of protein translation was not the cause of the observed block of seed germination. However, the two-dimensional protein profiles were markedly different from those obtained with the ND seeds imbibed in ABA. Altogether, the data showed that the mechanisms blocking germination of the ND seeds by ABA application are different from those preventing germination of the D seeds imbibed in basal medium.
Molecular Interactions between the Specialist Herbivore Manduca sexta (Lepidoptera, Sphingidae) and Its Natural Host Nicotiana attenuata. VII. Changes in the Plant's Proteome
Authors: Giri Ashok P. , Wünsche Hendrik , Mitra Sirsha , Zavala Jorge A. , Muck Alexander , Svatoš Aleš , Baldwin Ian T. 
Published: October 2006

Abstract
When Manduca sexta attacks Nicotiana attenuata, fatty acid-amino acid conjugates (FACs) in the larvae's oral secretions (OS) are introduced into feeding wounds. These FACs trigger a transcriptional response that is similar to the response induced by insect damage. Using two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization-time of flight, and liquid chromatography-tandem mass spectrometry, we characterized the proteins in phenolic extracts and in a nuclear fraction of leaves elicited by larval attack, and/or in leaves wounded and treated with OS, FAC-free OS, and synthetic FACs. Phenolic extracts yielded approximately 600 protein spots, many of which were altered by elicitation, whereas nuclear protein fractions yielded approximately 100 spots, most of which were unchanged by elicitation. Reproducible elicitor-induced changes in 90 spots were characterized. In general, proteins that increased were involved in primary metabolism, defense, and transcriptional and translational regulation; those that decreased were involved in photosynthesis. Like the transcriptional defense responses, proteomic changes were strongly elicited by the FACs in OS. A semiquantitative reverse transcription-PCR approach based on peptide sequences was used to compare transcript and protein accumulation patterns for 17 candidate proteins. In six cases the patterns of elicited transcript accumulation were consistent with those of elicited protein accumulation. Functional analysis of one of the identified proteins involved in photosynthesis, RuBPCase activase, was accomplished by virus-induced gene silencing. Plants with decreased levels of RuBPCase activase protein had reduced photosynthetic rates and RuBPCase activity, and less biomass, responses consistent with those of herbivore-attacked plants. We conclude that the response of the plant's proteome to herbivore elicitation is complex, and integrated transcriptome-proteome-metabolome analysis is required to fully understand this ubiquitous ecological interaction.
A Posttranslationally Regulated Protease, VheA, Is Involved in the Liberation of Juveniles from Parental Spheroids inVolvox carteri
Authors: Fukada Kazutake , Inoue Tan , Shiraishi Hideaki 
Published: October 2006

AbstractThe lineage of volvocine algae includes unicellular Chlamydomonas and multicellular Volvox in addition to their colonial relatives intermediate in size and cell number. In an asexual life cycle, daughter cells of Chlamydomonas hatch from parental cell walls soon after cell division, while Volvox juveniles are released from parental spheroids after the completion of various developmental events required for the survival of multicellular juveniles. Thus, heterochronic change in the timing of hatching is considered to have played an important role in the evolution of multicellularity in volvocine algae. To study the hatching process in Volvox carteri, we purified a 125-kD Volvox hatching enzyme (VheA) from a culture medium with enzymatic activity to degrade the parental spheroids. The coding region of vheA contains a prodomain with a transmembrane segment, a subtilisin-like Ser protease domain, and a functionally unknown domain, although purified 125-kD VheA does not contain a prodomain. While 143-kD VheA with a prodomain is synthesized long before the hatching stage, 125-kD VheA is released into the culture medium during hatching due to cleavage processing at the site between the prodomain and the subtilisin-like Ser protease domain, indicating that posttranslational regulation is involved in the determination of the timing of hatching.
Bad nights or bad bars? Multi‐level analysis of environmental predictors of aggression in late‐night large‐capacity bars and clubs
Authors: Graham Kathryn , Bernards Sharon , Osgood D. Wayne , Wells Samantha 
Published: October 2006

ABSTRACTAims  To clarify environmental predictors of bar‐room aggression by differentiating relationships due to nightly variations versus across bar variations, frequency versus severity of aggression and patron versus staff aggression.Design, setting and participants  Male–female pairs of researcher–observers conducted 1334 observations in 118 large capacity (> 300) bars and clubs in Toronto, Canada.Measurements  Observers independently rated aspects of the environment (e.g. crowding) at every visit and wrote detailed narratives of each incident of aggression that occurred. Measures of severity of aggression for the visit were calculated by aggregating ratings for each person in aggressive incidents.Findings  Although bivariate analyses confirmed the significance of most environmental predictors of aggression identified in previous research, multivariate analyses identified the following key visit‐level predictors (controlling for bar‐level relationships): rowdiness/permissive environment and people hanging around after closing predicted both frequency and severity of aggression; sexual activity, contact and competition and people with two or more drinks at closing predicted frequency but not severity of aggression; lack of staff monitoring predicted more severe patron aggression, while having more and better coordinated staff predicted more severe staff aggression. Intoxication of patrons was significantly associated with more frequent and severe patron aggression at the bar level (but not at the visit level) in the multivariate analyses and negatively associated with severity of staff aggression at the visit level.Conclusions  The results demonstrate clearly the importance of the immediate environment (not just the type of bar or characteristics of usual patrons) and the importance of specific environmental factors, including staff behaviour, in predicting both frequency and severity of aggression.
Quantitative trait loci analysis of egg and meat production traits in a red junglefowl × White Leghorn cross
Authors: Wright D. , Kerje S. , Lundström K. , Babol J. , Schütz K. , Jensen P. , Andersson L. 
Published: October 2006

SummaryEgg and production traits are of considerable economic importance in chickens. Using a White Leghorn × red junglefowl F2 intercross, standard production measures of liver weight and colour, egg size, eggshell thickness, egg taste and meat quality were taken. A total of 160 markers covering 29 autosomes and the Z chromosome were genotyped on 175–243 individuals, depending on the trait under consideration. A total of nine significant quantitative trait loci (QTL) and three suggestive QTL were found on chicken chromosomes 1, 2, 4, 5, 7, 8, 10, 12, E47W24 and E22C19W28.
Increased prevalence of iron‐overload associated endocrinopathy in thalassaemia versus sickle‐cell disease
Authors: Fung Ellen B. , Harmatz Paul R. , Lee Phillip D.K. , Milet Meredith , Bellevue Rita , Jeng Michael R. , Kalinyak Karen A. , Hudes Mark , Bhatia Suruchi , Vichinsky Elliott P. ,   the Multi‐Centre Study of Iron Overload Research Group.
Published: October 2006

SummaryIron‐overload associated endocrinopathy is the most frequently reported complication of chronic transfusion therapy in patients with thalassaemia (Thal). This study compared iron‐overloaded subjects with Thal (n = 142; 54%M; age 25·8 ± 8·1 years) and transfused sickle‐cell disease (Tx‐SCD; n = 199; 43%M, 24·9 ± 13·2 years) to non‐transfused SCD subjects (non‐Tx‐SCD; n = 64, 50%M, 25·3 ± 11·3 years), to explore whether the underlying haemoglobinopathy influences the development of endocrinopathy. Subjects were recruited from 31 centres in the USA, Canada and the UK. Subjects with Thal had more evidence of diabetes (13% vs. 2%, P < 0·001), hypogonadism (40% vs. 4%, P < 0·001), hypothyroidism (10% vs. 2%, P = <0·001) and growth failure (33% vs. 7%, P < 0·001), versus Tx‐SCD. Fifty‐six per cent of Thal had more than one endocrinopathy compared with only 13% of Tx‐SCD (P < 0·001). In contrast, Tx‐SCD was not different from non‐Tx‐SCD. Multivariate analysis indicated that endocrinopathy was more likely in Thal than SCD [Odds Ratio (OR) = 9·4, P < 0·001], with duration of chronic transfusion a significant predictor (OR = 1·4 per 10 years of transfusion, P = 0·04). Despite iron overload, endocrinopathy was not increased in Tx‐SCD versus non‐Tx‐SCD, suggesting that the underlying disease may modulate iron‐related endocrine injury. However, because transfusion duration remained a significant predictor of endocrinopathy, these data should be confirmed in SCD subjects that have been chronically transfused for longer periods of time.
Down syndrome and acute lymphoblastic leukaemia
Authors: Whitlock James A. 
Published: October 2006

SummaryAcute lymphoblastic leukaemia in children with Down syndrome (ALL‐DS) is characterised by unique clinical and biological features. Notable among these are an absence of ALL in DS patients <1 year of age; a lower incidence of favourable and unfavourable chromosomal translocations; heightened sensitivity to methotrexate; and an increased propensity to infections. Although children with ALL‐DS have historically fared less well than their non‐DS counterparts (ALL‐NDS), recent data indicate that outcomes in ALL‐DS are now comparable with ALL‐NDS with risk‐adapted therapies, after adjusting for biological differences between the ALL‐DS and ALL‐NDS populations. Given the increased risk of ALL‐DS patients for treatment‐related toxicities, further intensification of therapy may not yield continued improvements in survival. Future investigations in the ALL‐DS population should focus on maintaining excellent outcomes while reducing treatment‐related complications through novel treatment strategies, such as the integration of targeted noncytotoxic agents.