bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evaluation of noise- and threshold-induced bias in the integration of single-fish echoes
Authors: Bethke Eckhard 
Published: April 2004

Abstract
The echo integration of single-fish echoes shows that characteristically the received-signal energy of single targets is small compared with the echo energy of schooled fish. The measuring error is minimized by the application of an integration threshold. The echo energy, however, is often only slightly larger than the noise and reverberation level making the determination of the optimal integration threshold difficult. During the evaluation of data from the echo-integration surveys on redfish in the Irminger Sea it was observed that the integration value of single fish increased steadily with decreasing integration threshold. There is no way to determine the integration threshold by eye as for schooled fish.
The approach taken in all past publications for the estimation of the influence of the integration threshold on the integration result has been based on the computation of an equivalent beam angle. The influence of “environment noise” was not considered. Here a model is presented, which considers both influences on the integration result during the integration of single-fish echoes. It is assumed that the targets are distributed evenly in the observed volume and that in each pulse volume of the beam only one target is present. The starting point of the computations is the equation for signal processing implemented in the EK500. The echo signal power received is converted pixel-by-pixel into the appropriate volume-backscattering coefficients, sv and stored as echograms. These echograms are available for post-processing in the Bergen Integrator BI500. To exclude noise and reverberation from the subsequent processing a threshold was introduced.
We assume that the fish echoes are always larger than the noise and reverberation. This is a very common situation and the largest part of the energy of noise and reverberation can be eliminated in this way. When a fish echo is received outside the centre of the beam it is attenuated by the beam pattern of the transducer and may therefore lie below the threshold and could be cut off. This leads to the reduction of the measured values and a measuring error. An opposite error arises when the signal crosses the threshold. In practice the signal received always consists of noise and echo signals and has more power than it should have. The measured value is larger and this is another error of the measurement process per se.
The object of this paper is to calculate the influence of the threshold level on the result of measurement and to derive a practicable rule for the determination of the threshold level. The noise is modelled as a constant input power. The computations are carried out with model functions of the transducer beam and the received-echo pulse. General statements can be met by defining a signal-to-noise ratio and a signal-to-threshold ratio. The results of the theoretical investigations are applied on acoustic data obtained during redfish survey WH229 in the Irminger Sea and adjacent waters.
Dynamics of fisheries, and the flexibility of vessel activity in Denmark between 1989 and 2001
Authors: Ulrich Clara , Andersen Bo Sølgaard 
Published: April 2004

Abstract
Danish fishing vessels can be characterized by their diversity of fishing practice in terms of fishing gear and target species, and by their operational flexibility in respect of these fishing practices throughout the year. We describe the temporal fluctuations in this flexibility by following the activity of individual fishing vessels between 1989 and 2001. Initially, a typology of fisheries (classification of fishing trips) and vessel groups (classification of fishing vessels) was established through multivariate analyses of catch and effort data for 1999. In all, 54 fisheries and 25 vessel groups were identified. These typologies were then applied to all data for the whole time period, and the dynamics of fisheries and vessel groups investigated. The dynamics of vessels groups are studied both within groups (main and secondary fisheries, changes in activity patterns) and between groups (tracking of vessels shifting between groups). Results show average stability of vessel activity in terms of the main fishery, along with a great diversity of secondary fisheries and some possibilities for shifting between gears and areas. We conclude that the level of technical interactions is high, and that separation into distinct management units is difficult.
First Human Chronic Experience with Cardiac Contractility Modulation by Nonexcitatory Electrical Currents for Treating Systolic Heart Failure:
Authors: PAPPONE CARLO , AUGELLO GIUSEPPE , ROSANIO SALVATORE , VICEDOMINI GABRIELE , SANTINELLI VINCENZO , ROMANO MASSIMO , AGRICOLA EUSTACHIO , MAGGI FRANCESCO , BUCHMAYR GERHARD , MORETTI GIOVANNI , MIKA YUVAL , BEN‐HAIM SHLOMO A. , WOLZT MICHAEL , STIX GUENTER , SCHMIDINGER HERWIG 
Published: April 2004

Introduction: Conventional electrical therapies for heart failure (HF) encompass defibrillation and ventricular resynchronization for patients at high risk for lethal arrhythmias and/or with inhomogeneous ventricular contraction. Cardiac contractility modulation (CCM) by means of nonexcitatory electrical currents delivered during the action potential plateau has been shown to acutely enhance systolic function in humans with HF. The aim of this multicenter study was to assess the chronic safety and preliminary efficacy of an implantable device delivering this novel form of electrical therapy. Methods and Results: Thirteen patients with drug‐resistant HF (New York Heart Association [NYHA] class III) were consecutively implanted with a device (OPTIMIZER™ II) delivering CCM biphasic square‐wave pulses (20 ms, 5.8–7.7 V, 30 ms after detection of local activation) through two right ventricular leads screwed into the right aspect of the interventricular septum. CCM signals were delivered 3 hours daily over 8 weeks (3‐hour phase) and 7 hours daily over the next 24 weeks (7‐hour phase). Safety and feasibility of this novel therapy were regarded as primary endpoints. Preliminary clinical efficacy, ‐as expressed by changes in ejection fraction (EF), NYHA class, 6‐minute walking test (6‐MWT), peak O2 uptake (peak VO2), and Minnesota Living with HF Questionnaire (MLWHFQ), was assessed at baseline and at the end of each phase. At the end of follow‐up (8.8 ± 0.2 months), all patients were alive, without heart transplantation or need for left ventricular assist device. Serial 24‐hour Holter analysis revealed no proarrhythmic effect. No devices malfunctioned or failed for any reason other than end‐of‐battery life. Throughout the two study phases, EF improved from 22.7 ± 7% to 28.7 ± 7% and 37 ± 13% (P = 0.004), 6‐MWT from 418 ± 99 m to 477 ± 96 m and 510 ± 107 m (P = 0.002), MLWHFQ from 36 ± 21 to 18 ± 12 and 7 ± 6 (P = 0.002), peak VO2 from 13.7 ± 1.1 to 14.9 ± 1.9 to 16.2 ± 2.4 (P = 0.037), and NYHA class from 3 to 1.8 ± 0.4 to 1.5 ± 0.7 (P < 0.001). Conclusion: CCM therapy appears to be safe and feasible. Proarrhythmic effects of this novel therapy seem unlikely. Preliminary data indicate that CCM gradually and significantly improves systolic performance, symptoms, and functional status. CCM therapy for 7 hours per day is associated with greater dispersion near the mean, emphasizing the need to individually tailor CCM delivery duration. The technique appears to be attractive as an additive treatment for severe HF. Controlled randomized studies are needed to validate this novel concept. (J Cardiovasc Electrophysiol, Vol. 15, pp. 418‐427, April 2004)
Occult Cervical Metastases: Immunoperoxidase Analysis of the Pathologically Negative Neck
Authors: Enepekides Danny J. , Sultanem Khaleil , Nguyen Cam , Shenouda George , Black Martin J. , Rochon Louise 
Published: April 2004

OBJECTIVESThe purpose of this study is to better estimate the true incidence of occult regional metastases associated with stage I and II squamous cell carcinoma of the oral cavity. The clinical and prognostic significance of micrometastatic disease discovered by cytokeratin immunoperoxidase reactivity in the previously pathologically N0 neck is also evaluated.METHODSForty patients treated between 1985 and 1996 with T1 or T2 squamous cell carcinoma of the lip and oral cavity were studied. All had primary surgical treatment including functional neck dissection. No metastases were demonstrated on hematoxylin and eosin microscopy. All specimens were reexamined with immunoperoxidase staining for cytokeratin.RESULTSFive percent of patients had micrometastatic disease. Retrospective analysis of patients with a minimum follow‐up of 2 years has failed to show a statistically significant association between a positive cytokeratin analysis and poor locoregional control or overall survival.CONCLUSIONSResults suggest that the true incidence of occult metastases with carcinoma of the oral cavity is significantly higher than previously documented. However, the prognostic significance of these findings remains unclear.
High‐Risk Human Papillomavirus Types and Squamous Cell Carcinoma in Patients with Respiratory Papillomas
Authors: Moore Charles E. , Wiatrak Brian J. , Mcclatchey Kenneth D. , Koopmann Charles F. , Thomas Giovanna R. , Bradford Carol R. , Carey Thomas E. 
Published: April 2004

Respiratory papillomas (RPs) are benign, virally induced tumors of the larynx and respiratory epithelium that may obstruct the airway and tend to recur frequently. RPs are thought to be the result of infection with the human papillomaviruses (HPVs) types 6 and 11. We surveyed archival RP specimens to determine whether there were correlations of HPV type with patient characteristics or clinical course. Paraffin‐embedded papilloma specimens of 45 different patients were analyzed. We assessed HPV types using the polymerase chain reaction with E6 consensus primers, hybrid capture assays (high or low risk), and dot blot hybridization of generic E6 PCR products with E6 type‐specific oligonucleotide probes. The presence and type of HPV were correlated with patient data from a retrospective chart review. We found that RPs may have either low‐ or high‐risk HPV types and some contain multiple HPV types. Respiratory infection with high‐risk HPV apparently introduces a long‐term risk of squamous cell carcinoma development, even in the absence of conventional cofactors. Low‐risk HPV infection may also act in association with these cofactors to promote carcinogenesis. Our data also show a racial imbalance in RP that may indicate a difference in genetic resistance and/or susceptibility to HPV infection and the development of RP.
Network-based regulatory pathways analysis
Authors: Xiong Momiao , Zhao Jinying , Xiong Hao 
Published: April 2004

Abstract
Motivation: A useful approach to unraveling and understanding complex biological networks is to decompose networks into basic functional and structural units. Recent application of convex analysis to metabolic networks leads to the development of network-based metabolic pathway analysis and the decomposition of metabolic networks into metabolic extreme pathways that are true functional units of metabolic systems. Metabolic extreme pathways are derived from limited knowledge of the metabolic networks, but provide an integrated predictive description of metabolic networks. It is important to extend the concept of network-based metabolic pathways to genetic networks and develop mathematical procedures for network-based regulatory pathway analysis.
Results: We have established Kirchhoff's first law in genetic networks and introduced a concept of gene flows using matrix decomposition method. The Kirchhoff's first law provides the theoretical foundations for mathematical framework for development defining network-based regulatory pathways, and applying convex analysis in decomposing the genetic networks into regulatory extreme pathways. We presented a new approach to characterize the extreme pathway and developed a new algorithm for identifying a set of extreme pathways. Convex analysis and extreme pathway structure provide a unified framework for functional and structural analysis of metabolic and genetic networks, which will increase our ability to analyze, interpret and predict the function of metabolic and genetic networks. The proposed models for network-based regulatory pathway analysis have been applied to apoptosis regulatory network.
Probabilistic nucleotide assembling method for sequencing by hybridization
Authors: Endo Takaho A. 
Published: April 2004

Abstract
Motivation: Developing a new method of assembling small sequences based on sequencing by hybridization with many positive and negative faults. First, an interpretation of a generic traveling salesman problem is provided (i.e. finding the shortest route for visiting many cities), using genetic algorithms. Second, positive errors are excluded before assembly by a sanitization process.
Results: The present method outperforms those described in previous studies, in terms of both time and accuracy.
Availability: http://kamit.med.u-tokai.ac.jp/~takaho/sbh/index.html
Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families
Authors: Miguel Ricardo Núñez 
Published: April 2004

Abstract
Motivation: Most proteins have evolved to perform specific functions that are dependent on the adoption of well-defined three-dimensional (3D) structures. Specific patterns of conserved residues in amino acid sequences of divergently evolved proteins are frequently observed; these may reflect evolutionary restraints arising both from the need to maintain tertiary structure and the requirement to conserve residues more directly involved in function. Databases of such sequence patterns are valuable in identifying distant homologues, in predicting function and in the study of evolution.
Results: A fully automated database of protein sequence patterns, Functional Protein Sequence Pattern Database (FPSPD), has been derived from the analysis of the conserved residues that are predicted to be functional in structurally aligned homologous families in the HOMSTRAD database. Environment-dependent substitution tables, evolutionary trace analysis, solvent accessibility calculations and 3D-structures were used to obtain the FPSPD. The method yielded 3584 patterns that are considered functional and 3049 patterns that are probably functional. FPSPD could be useful for assigning a protein to a homologous superfamily and thereby providing clues about function.
Availability: FPSPD is available at http://www-cryst.bioc.cam.ac.uk/~fpspd/
GEPIS—quantitative gene expression profiling in normal and cancer tissues
Authors: Zhang Yan , Eberhard David A. , Frantz Gretchen D. , Dowd Patrick , Wu Thomas D. , Zhou Yan , Watanabe Colin , Luoh Shiuh-Ming , Polakis Paul , Hillan Kenneth J. , Wood William I. , Zhang Zemin 
Published: April 2004

Abstract
Motivation: Expression profiling in diverse tissues is fundamental to understanding gene function as well as therapeutic target identification. The vast collection of expressed sequence tags (ESTs) and the associated tissue source information provides an attractive opportunity for studying gene expression.
Results: To facilitate EST-based expression analysis, we developed GEPIS (gene expression profiling in silico), a tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples. We found EST-based expression patterns to be consistent with published papers as well as our own experimental results. We also built a GEPIS Regional Atlas that depicts expression characteristics of all genes in a selected genomic region. This program can be adapted for large-scale screening for genes with desirable expression patterns, as illustrated by our large-scale mining for tissue- and tumor-specific genes.
Availability: The email server version of the GEPIS application is freely available at http://share.gene.com/share/gepis. An interactive version of GEPIS will soon be freely available at http://www.cgl.ucsf.edu/Research/genentech/gepis/. The source code, modules, data and gene lists can be downloaded at http://share.gene.com/share/gepis
Supplementary information: Supplementary tables and figures are available at http://www.cgl.ucsf.edu/Research/genentech/gepis/
Shorter side chains optimize helix–helix packing
Authors: Jiang Sulin , Vakser Ilya A. 
Published: April 2004

AbstractA systematic study of helix–helix packing in a comprehensive database of protein structures revealed that the side chains inside helix–helix interfaces on average are shorter than those in the noninterface parts of the helices. The study follows our earlier study of this effect in transmembrane helices. The results obtained on the entire database of protein structures are consistent with those obtained on the transmembrane helices. The difference in the length of interface and noninterface side chains is small but statistically significant. It indicates that helices, if viewed along their main axis, statistically are not circular, but have a flattened interface. This effect brings the helices closer to each other and creates a tighter structural packing. The results provide an interesting insight into the aspects of protein structure and folding.
Orange County Bankruptcy: Financial Contagion in the Municipal Bond and Bank Equity Markets
Authors: Halstead John M. , Hegde Shantaram , Klein Linda Schmid 
Published: April 2004

AbstractWe examine the spillover wealth effects of the Orange County, California bankruptcy announcement in December 1994 on municipal bonds, municipal bond funds, and bank stocks. This bankruptcy is prominent because of unprecedented losses and because it was caused by a highly leveraged derivatives strategy rather than a shortage of tax revenues and excess spending. We find contagion in the bond market with significantly negative abnormal returns for municipal bond funds without direct exposure to Orange County and for non‐Orange County municipal bonds. In addition, our findings suggest the contagion spills over to the common stocks of investment and commercial banks that deal in or use derivatives; however, the equities of banks unexposed to derivatives are not affected.
Intensive care nurses' experiences of assessing and dealing with patients' psychological needs
Authors: Price Ann M 
Published: April 2004

Summary• Several authors have highlighted the short‐ and long‐term psychological effects of an intensive care unit (ICU) stay• Few authors have discussed the nurses' perceptions of psychological care• In this research, 12 nurses, who currently work in ICU, were interviewed using a semi‐structured technique• Six categories were developed about issues in psychological care• Implications for practice included the important role of the family, need for improved communication and improved staff awareness of issues
Can nurses in cardiology areas prepare patients for implantable cardioverter defibrillator implant and life at home?
Authors: Tagney Jenny 
Published: April 2004

Summary• This study explored nurses' confidence and competence in preparing patients for having an implantable cardioverter defibrillator implanted and for life at home after discharge• Whilst research has identified various physical and psychosocial effects to patients and their partners associated with device implant and subsequent lifestyle adjustments, no research has explored nurses' knowledge of the device or these effects• A survey was designed using a purposive sample of 152 nurses from cardiology areas in four large teaching hospitals and a 28‐point postal questionnaire to explore knowledge of the device and its impact• Most subjects were not confident in their abilities to prepare patients for implant or life at home after implant• Knowledge of the device and its effects appeared poorly understood by all nurses, irrespective of additional qualifications, length of time since qualifying or area of work• Many participants were aware of the poor knowledge level of nurses and identified it as a weakness in current care practices• Lack of understanding may impair preparation of patients for implantation of or for living with an implantable cardioverter defibrillator, and feasible strategies to change this situation will require careful consideration and further investment
Introducing an early warning scoring system in a district general hospital
Authors: Sharpley Julie T , Holden Janet C 
Published: April 2004

Summary• One of the critical care outreach service's aims in this local hospital was to develop an assessment tool to help identify patients in danger of deterioration• This paper describes the introduction of an early warning scoring system between April 2001 and March 2002 to the surgical unit of a district general hospital• The informal and gradual approach used to optimize the effectiveness of introducing the early warning scoring system is highlighted• Explanations are given of the training processes undertaken, the pilot evaluation and lessons learned from the process• Using the experiences of the outreach service in introducing the early warning scoring system, this paper aims to provide thought for others considering a similar initiative in their area
Absorption of the cholic acid‐conjugated peptide hormone cholylsecretin from the rat ileum in vivo
Authors: McHarg S. , Morton J. S. , McGinn B. J. , Yasin M. , Morrison J. D. 
Published: April 2004

AbstractAims:  Previously, we demonstrated that gastrin peptides as long as 34 amino acids were absorbed from the ileum of rat after conjugation to the C24 position of cholic acid and that these peptides retained full biological activity. As absorption was specific to the ileum, it was inferred that the conjugated hormone was taken up by the bile salt transporters. We have now extended these experiments to a member of a different family of hormones, viz. secretin, a 27‐amino acid hormone that stimulates serous secretions from the exocrine pancreas.Methods:  After conjugation to cholic acid, the degree of cholylsecretin absorption from the ileum of anaesthetized rats was assessed from the increase in pancreatic secretions.Results:  A complication to the study was that intra‐ileal infusion of native secretin caused a transient increase in the levels of pancreatic secretions. This was in contrast to the effects of intra‐ileal infusion of cholylsecretin which did not cause this transient increase but, instead, gave rise to a delayed increase in pancreatic secretions which was sustained over several hours during which cholylsecretin was detected in plasma in high concentration by mass spectrometry. The pancreatic response to cholylsecretin was abolished by co‐infusion of 50 mm taurocholate, employed to compete with the bile salt transporters, although a transient increase in pancreatic secretions similar to that caused by secretin was now generated. This was shown to arise from an action of taurocholate per se causing the release of endogenous secretin which is present in rat ileum.Conclusions:  We, therefore, concluded that cholylsecretin had been absorbed from the rat ileum by uptake by bile salt transporters.