bluuebunny/crossref_metadata_2025_split huggingface dataset:
A linear memory algorithm for Baum-Welch training
Authors: Miklós István , Meyer Irmtraud M 
Published: September 2005

AbstractBackground:Baum-Welch training is an expectation-maximisation algorithm for training the emission and transition probabilities of hidden Markov models in a fully automated way. It can be employed as long as a training set of annotated sequences is known, and provides a rigorous way to derive parameter values which are guaranteed to be at least locally optimal. For complex hidden Markov models such as pair hidden Markov models and very long training sequences, even the most efficient algorithms for Baum-Welch training are currently too memory-consuming. This has so far effectively prevented the automatic parameter training of hidden Markov models that are currently used for biological sequence analyses.Results:We introduce the first linear space algorithm for Baum-Welch training. For a hidden Markov model withMstates,Tfree transition andEfree emission parameters, and an input sequence of lengthL, our new algorithm requiresO(M) memory andO(LMTmax(T + E)) time for one Baum-Welch iteration, whereTmaxis the maximum number of states that any state is connected to. The most memory efficient algorithm until now was the checkpointing algorithm withO(log(L)M) memory andO(log(L)LMTmax) time requirement. Our novel algorithm thus renders the memory requirement completely independent of the length of the training sequences. More generally, for an n-hidden Markov model and n input sequences of lengthL, the memory requirement ofO(log(L)Ln-1M) is reduced toO(Ln-1M) memory while the running time is changed fromO(log(L)LnMTmax+Ln(T+E)) toO(LnMTmax(T+E)).An added advantage of our new algorithm is that a reduced time requirement can be traded for an increased memory requirement andvice versa, such that for anyc∈ {1, ..., (T+E)}, a time requirement ofLnMTmaxcincurs a memory requirement ofLn-1M(T+E-c).ConclusionFor the large class of hidden Markov models used for example in gene prediction, whose number of states does not scale with the length of the input sequence, our novel algorithm can thus be both faster and more memory-efficient than any of the existing algorithms.
Genome annotation of Anopheles gambiae using mass spectrometry-derived data
Authors: Kalume Dário E , Peri Suraj , Reddy Raghunath , Zhong Jun , Okulate Mobolaji , Kumar Nirbhay , Pandey Akhilesh 
Published: September 2005

Abstract

Background
A large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still remains a problematic task. Availability of protein sequence data allows direct confirmation of protein-coding genes. Mass spectrometry has recently emerged as a powerful tool for proteomic studies. Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts. This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified.

Results
We searched 3,967 mass spectra from 16 LC-MS/MS runs of Anopheles gambiae salivary gland homogenates against the Anopheles gambiae genome database. This allowed us to validate 23 known transcripts and 50 novel transcripts. In addition, a novel gene was identified on the basis of peptides that matched a genomic region where no gene was known and no transcript had been predicted. The amino termini of proteins encoded by two predicted transcripts were confirmed based on N-terminally acetylated peptides sequenced by tandem mass spectrometry. Finally, six sequence polymorphisms could be annotated based on experimentally obtained peptide sequences.

Conclusion
The peptide sequences from this study were mapped onto the genomic sequence using the distributed annotation system available at Ensembl and can be visualized in the context of all other existing annotations. The strategy described in this paper can be used to correct and confirm genome annotations and permit discovery of novel proteins in a high-throughput manner by mass spectrometry.
Effect of dataset selection on the topological interpretation of protein interaction networks
Authors: Hakes Luke , Robertson David L , Oliver Stephen G 
Published: September 2005

Abstract

Background
Studies of the yeast protein interaction network have revealed distinct correlations between the connectivity of individual proteins within the network and the average connectivity of their neighbours. Although a number of biological mechanisms have been proposed to account for these findings, the significance and influence of the specific datasets included in these studies has not been appreciated adequately.

Results
We show how the use of different interaction data sets, such as those resulting from high-throughput or small-scale studies, and different modelling methodologies for the derivation pair-wise protein interactions, can dramatically change the topology of these networks. Furthermore, we show that some of the previously reported features identified in these networks may simply be the result of experimental or methodological errors and biases.

Conclusion
When performing network-based studies, it is essential to define what is meant by the term "interaction" and this must be taken into account when interpreting the topologies of the networks generated. Consideration must be given to the type of data included and appropriate controls that take into account the idiosyncrasies of the data must be selected
Characteristic wave detection in ECG signal using morphological transform
Authors: Sun Yan , Chan Kap Luk , Krishnan Shankar Muthu 
Published: September 2005

Abstract

Background
Detection of characteristic waves, such as QRS complex, P wave and T wave, is one of the essential tasks in the cardiovascular arrhythmia recognition from Electrocardiogram (ECG).

Methods
A multiscale morphological derivative (MMD) transform-based singularity detector, is developed for the detection of fiducial points in ECG signal, where these points are related to the characteristic waves such as the QRS complex, P wave and T wave. The MMD detector is constructed by substituting the conventional derivative with a multiscale morphological derivative.

Results
We demonstrated through experiments that the Q wave, R peak, S wave, the onsets and offsets of the P wave and T wave could be reliably detected in the multiscale space by the MMD detector. Compared with the results obtained via with wavelet transform-based and adaptive thresholding-based techniques, an overall better performance by the MMD method was observed.

Conclusion
The developed MMD method exhibits good potentials for automated ECG signal analysis and cardiovascular arrhythmia recognition.
Generation of human antibody fragments recognizing distinct epitopes of the nucleocapsid (N) SARS-CoV protein using a phage display approach
Authors: Flego Michela , Di Bonito Paola , Ascione Alessandro , Zamboni Silvia , Carattoli Alessandra , Grasso Felicia , Cassone Antonio , Cianfriglia Maurizio 
Published: September 2005

Abstract

Background
Severe acute respiratory syndrome (SARS)-CoV is a newly emerging virus that causes SARS with high mortality rate in infected people. Successful control of the global SARS epidemic will require rapid and sensitive diagnostic tests to monitor its spread, as well as, the development of vaccines and new antiviral compounds including neutralizing antibodies that effectively prevent or treat this disease.

Methods
The human synthetic single-chain fragment variable (scFv) ETH-2 phage antibody library was used for the isolation of scFvs against the nucleocapsid (N) protein of SARS-CoV using a bio panning-based strategy. The selected scFvs were characterized under genetics-molecular aspects and for SARS-CoV N protein detection in ELISA, western blotting and immunocytochemistry.

Results
Human scFv antibodies to N protein of SARS-CoV can be easily isolated by selecting the ETH-2 phage library on immunotubes coated with antigen. These in vitro selected human scFvs specifically recognize in ELISA and western blotting studies distinct epitopes in N protein domains and detect in immunohistochemistry investigations SARS-CoV particles in infected Vero cells.

Conclusion
The human scFv antibodies isolated and described in this study represent useful reagents for rapid detection of N SARS-CoV protein and SARS virus particles in infected target cells.
Comparison of plasma endothelin levels between osteoporotic, osteopenic and normal subjects
Authors: Muratli Hasan Hilmi , Çelebi Levent , Hapa Onur , Biçimoğlu Ali 
Published: September 2005

Abstract

Background
It has been demonstrated that endothelins (ET) have significant roles in bone remodeling, metabolism and physiopathology of several bone diseases. We aimed to investigate if there was any difference between the plasma ET levels of osteoporotic patients and normals.

Methods
86 patients (70 women and 16 men) with a mean age of 62.6 (ranges: 51–90) years were included in this study. Patients were divided into groups of osteoporosis, osteopenia and normal regarding reported T scores of DEXA evaluation according to the suggestions of World Health Organization. According to these criteria 19, 43 and 24 were normal, osteopenic and osteoporotic respectively. Then total plasma level of ET was measured in all patients with monoclonal antibody based sandwich immunoassay (EIA) method. One-way analysis of variance test was used to compare endothelin values between normals, osteopenics and osteoporotics.

Results
Endothelin total plasma level in patients was a mean of 98.36 ± 63.96, 100.92 ± 47.2 and 99.56 ± 56.6 pg/ml in osteoporotic, osteopenic and normal groups respectively. The difference between groups was not significant (p > 0.05).

Conclusion
No significant differences in plasma ET levels among three groups of study participants could be detected in this study.
Aerobic exercise and its impact on musculoskeletal pain in older adults: a 14 year prospective, longitudinal study
Authors: Bruce Bonnie , Fries James F , Lubeck Deborah P 
Published: September 2005

AbstractWe studied the long term impact of running and other aerobic exercise on musculoskeletal pain in a cohort of healthy aging male and female seniors who had been followed for 14 years. We conducted a prospective, longitudinal study in 866 Runners' Association members (n = 492) and community controls (n = 374). Subjects were also categorized as Ever-Runners (n = 565) and Never-Runners (n = 301) to include runners who had stopped running. Pain was the primary outcome measure and was assessed in annual surveys on a double-anchored visual analogue scale (0 to 100; 0 = no pain). Baseline differences between Runners' Association members and community controls and between Ever-Runners versus Never-Runners were compared using chi-square and t-tests. Statistical adjustments for age, body mass index (BMI), gender, health behaviors, history of arthritis and comorbid conditions were performed using generalized estimating equations. Runner's Association members were younger (62 versus 65 years, p < 0.05), had a lower BMI (22.9 versus 24.2, p < 0.05), and less arthritis (35% versus 41%, p > 0.05) than community controls. Runners' Association members averaged far more exercise minutes per week (314 versus 123, p < 0.05) and miles run per week (26 versus 2, p < 0.05) and tended to report more fractures (53% versus 47%, p > 0.05) than controls. Ever-Runners were younger (62 versus 66 years, p < 0.05), had lower BMI (23.0 versus 24.3, p < 0.05), and less arthritis (35% versus 43%, p < 0.05) than Never-Runners. Ever-Runners averaged more exercise minutes per week (291 versus 120, p < 0.05) and miles run per week (23 versus 1, p < 0.05) and reported a few more fractures (52% versus 48%, p > 0.05) than Never-Runners. Exercise was associated with significantly lower pain scores over time in the Runners' Association group after adjusting for gender, baseline BMI, and study attrition (p < 0.01). Similar differences were observed for Ever-Runners versus Never-Runners. Consistent exercise patterns over the long term in physically active seniors are associated with about 25% less musculoskeletal pain than reported by more sedentary controls, either by calendar year or by cumulative area-under-the-curve pain over average ages of 62 to 76 years.
Searching for differentially expressed gene combinations
Authors: Dettling Marcel , Gabrielson Edward , Parmigiani Giovanni 
Published: September 2005

AbstractWe propose 'CorScor', a novel approach for identifying gene pairs with joint differential expression. This is defined as a situation with good phenotype discrimination in the bivariate, but not in the two marginal distributions. CorScor can be used to detect phenotype-related dependencies and interactions among genes. Our easily interpretable approach is scalable to current microarray dimensions and yields promising results on several cancer-gene-expression datasets.
Design guidance for naturally ventilated theatres
Authors: Short CA , Cook MJ 
Published: September 2005

This paper considers the reconstruction and redesign for natural ventilation of the UK’s stock of performing arts buildings from the 1960s and 1970s * / many of which are regarded as barely fit for service because of poorly maintained and noisy mechanical ventilation systems. The paper reviews interventions by the lead author into three such buildings, intended, in part, to reduce their dependence on mechanical systems and improve their thermal and aural comfort. It reports on the ventilation and control strategies devised, the difficulties encountered during design development and the performance achieved. Design issues deriving specifically from the application of natural ventilation principles to the three theatres are identified. The paper provides design guidance for intervention in this building type distilled from the authors’ practical experience. Practical application: This paper catalogues a series of naturally ventilated auditoria built by the lead author, records their key physical characteristics and gives an indication of their performance. Practitioners can use the guidance contained in this paper in the formulation of their own draft schemes. Natural ventilation is peculiarly suited to performing arts spaces due to its almost silent operation. Actors and artistic directors appear to prefer working in nonmechanically-conditioned environments. Furthermore, operating costs are particularly important to revenue-poor arts organizations.
Evaluation of coated oxygenators in cardiopulmonary bypass systems and their impact on neurocognitive function
Authors: Khosravi Amir , Skrabal Christian A , Westphal Bernd , Kundt Guenther , Greim Brigitte , Kunesch Erwin , Liebold Andreas , Steinhoff Gustav 
Published: September 2005

Introduction: Coronary artery bypass graft surgery (CABG) using cardiopulmonary bypass (CPB) is assumed to be associated with a decline of neurocognitive functions. This study was designed to analyse the neurocognitive function of patients with coronary heart disease before and after CABG and to determine possible protective effects of oxygenator surface coating on neurological outcome. Methods: Forty patients scheduled for selective CABG were prospectively randomized into two groups of 20 patients each according to the type of hollow-fibre membrane oxygenator used. Non-coated oxygenators (Group A) were compared to phosphorylcholine (PC)- coated oxygenators (Group B). A battery of six neurological tests was administered preoperatively, 7 - 10 days and 4 - 6 months after surgery. Results: One patient of Group A suffered from a perioperative stroke and died on postoperative day 3, presumably because of sudden heart failure. Two patients of Group A (10%) developed a symptomatic transitory delirious psychotic syndrome (STPT) on postoperative days 3 and 5. None of the patients of Group B had perioperative complications. The test analysis revealed a trend of declined neurocognitive function early after CABG, but did not show any difference in neurocognitive outcome between the two groups. Discussion: PC coating of the oxygenators did not show any significant benefit on neurocognitive function after CABG using CPB.
Are we doing everything we can to conserve blood during bypass? A national survey
Authors: Belway D , Rubens F D , Wozny D , Henley B , Nathan H J 
Published: September 2005

Introduction: Despite major advances in biomaterial research and blood conservation, bleeding is still a common complication after cardiopulmonary bypass and cardiac surgery remains a major consumer of blood products. Although the underlying mechanisms for these effects are not fully established, two proposed major etiologies are the hemodilution associated with the use of the heart-lung machine and the impact of reinfusion of shed cardiotomy blood. Therapeutic strategies that primarily encompass the use of devices or technologies to overcome these effects may result in improved clinical outcomes. Objective: To determine the extent to which 1) lipid/leukocyte filtration and centrifugal processing of cardiotomy blood, and 2) modified ultrafiltration (MUF) are currently applied in adult cardiac surgery in Canada. Methods: A questionnaire was mailed to the chief perfusionist at all adult cardiac surgical centers in Canada, addressing details regarding the frequency of use of cardiotomy blood processing and MUF. Results: All questionnaires (36, 100%) were completed and returned. With regards to cardiotomy blood management, in 21 centers (58%), no specific processing steps were utilized exclusive of the integrated cardiotomy reservoir filter. Of the remaining centers, two (6%) reported using lipid/leukocyte filtration and 15 (42%) reported washing their cardiotomy blood. Three centers (8%) reported using MUF at the end of CPB. Conclusions: Despite growing concern about the potential detrimental effects of cardiotomy blood, few centers in Canada routinely manage this blood with additional filtration and/or centrifugal processing prior to reinfusion. Similarly, MUF, demonstrated to be effective in the pediatric population, has not seen popular application in adult cardiac surgical practice.
Evidence for a significant myocardial contribution to total metabolic burden during hypothermic cardiopulmonary bypass: a study of continuously measured oxygen consumption and arterial lactate levels in pigs
Authors: Li Jia , Stokoe Jacqueline , Konstantinov Igor E , Kharbanda Rajesh K , Redington Andrew N 
Published: September 2005

Objective: We assessed the causes of imbalance of oxygen transport by continuously measuring oxygen consumption (VO2) during hypothermic cardiopulmonary bypass (CPB) in pigs. Methods: Six pigs (17.2±1.6 kg) underwent hypothermic (328C) CPB for 180 min with 120 min of aortic crossclamping (ACC). An AMIS 2000 mass spectrometer was adapted for the on-line measurement of VO2. Arterial lactate was measured at the beginning of CPB, the end of hypothermia, before and 10 min after ACC release, 20 min later, and at the end of CPB. Results: Arterial lactate increased from 1.8±0.7 to 5.1±1.8 mmol/L during CPB. Hypothermia reduced VO2by 0.63±0.29 ml/min/kg per 8C, but lactate increased to 4.2±1.5 mmol/L ( p <0.05). The most rapid rise of VO2and lactate occurred during the first 10 min after ACC removal, accounting for 26% and 68%, respectively, of the total rise during rewarming. Conclusions: Inadequate tissue oxygenation persists throughout hypothermic CPB. The rise in systemic VO2 and lactate immediately after ACC release may reflect inadequate oxygen transport within the myocardium during ischemia and manifest on reperfusion. This simple technique may be used to provide important information regarding the dynamic balance of systemic and myocardial oxygen transport during ischemia - reperfusion.
Antineoplastic agent workplace contamination study: the Alberta Cancer Board Pharmacy perspective
Authors: Schulz Heidi , Bigelow Susan , Dobish Roxanne , Chambers Carole R 
Published: September 2005

Study objective. To investigate the feasibility of routine monitoring for workplace antineoplastic agent contamination in the Alberta Cancer Board (ACB) pharmacy practice environment. Setting. The ACB in the Canadian province of Alberta, which includes two public tertiary centres and 17 associated community satellite sites based around the province in existing hospitals. Methods. Obtained organizational support and input prior to launching the feasibility study (Phase I). Samples were analysed for a common cytotoxic agent - cyclophosphamide. Surfaces chosen were within the biological safety cabinets, workplace counter tops and on external surfaces of vials provided by manufacturers. Blank samples and known contaminated controls were included in Phase I to reconfirm the methodology in a previously published study.1 Feasibility aspects of logistics and financial expenses were examined. A second phase (Phase II) was completed to test other areas of the pharmacy and vials, with blank samples included to reconfirm previously mentioned methodology. Results. The results determined that the samples tested were below acceptable detection limits with the exception of the known contaminated sample (Phase I) and exterior surfaces of vials (Phase II). Conclusion. This project has increased staff awareness of the sources for antineoplastic agent workplace contamination. Some practice changes were instituted during the project itself. Logistics and expenses were realistic for routine monitoring to be adopted.
Strategies for management of the peritoneal surface component of cancer: cytoreductive surgery plus perioperative intraperitoneal chemotherapy
Authors: Sugarbaker Paul H , Stuart O. Anthony , Yoo Dal 
Published: September 2005

Background. A prominent part of treatment failure of gastrointestinal and gynecologic malignancy is dissemination to peritoneal surfaces. This has been associated with a limited survival and no reliable treatment strategies. Methods. A review of the natural history of carcinomatosis was performed and a rationale for intraperitoneal chemotherapy was sought. The pharmacology of chemotherapy administration into the peritoneal cavity was reviewed. Results. The technology of perioperative intraperitoneal chemotherapy requires the administration of drugs along with moderate hyperthermia in the operating room as a planned part of the surgical procedure. The solution in which the chemotherapy is diluted has an effect upon the drug clearance from the peritoneal cavity. Also, the volume of the carrier solution affects the exposure of cancer nodules on peritoneal surfaces. Conclusions. New combinations of intraperitoneal chemotherapy administration when combined with optimal surgical technology for maximal chemotherapy effects should result in benefit to patients with peritoneal surface dissemination of gastrointestinal and gynecologic malignancy.