bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competence Assessment of Laparoscopic Operative and Cognitive Skills: Objective Structured Clinical Examination (OSCE) or Observational Clinical Human Reliability Assessment (OCHRA)
Authors: Tang B. , Hanna G. B. , Carter F. , Adamson G. D. , Martindale J. P. , Cuschieri A. 
Published: March 2006

AbstractBackgroundThere is no agreed system that is acknowledged as the ideal assessment of laparoscopic operative and cognitive skills. A new approach that combines Objective Structured Clinical Examination (OSCE) and Observational Clinical Human Reliability Assessment (OCHRA) was developed and used to assess trainees’ operative and cognitive skills during laparoscopic training courses.MethodsPerformance of 60 trainees participating in 3‐day essential laparoscopic skills training (cognitive and psychomotor) courses were assessed and scored using both OSCE and OCHRA.ResultsThe study showed significant inverse correlations between the number of technical errors identified by OCHRA and the scores obtained by OSCE for individual tasks performed either by electro‐surgical hook or laparoscopic scissors (r = −0.864 and r = −0.808, respectively). Significant differences between trainees were observed in relation to both overall OSCE scores and OCHRA parameters: execution time, total errors, and consequential errors (P < 0.001).ConclusionsOCHRA provides a discriminative feedback assessment of laparoscopic operative skills. OCHRA and OSCE are best regarded as complementary assessment tools for operative and cognitive skills. The present study has documented significant variance between surgical trainees in the acquisition of both cognitive and operative skills.
Civilian Duodenal Gunshot Wounds: Surgical Management Made Simpler
Authors: Talving Peep , Nicol Andrew J. , Navsaria Pradeep H. 
Published: March 2006

AbstractIntroductionLow‐velocity gunshot wounds cause most civilian duodenal injuries. The objective of this study was to describe a simplified surgical algorithm currently in use in a South African civilian trauma center and to verify its validity by measuring morbidity and mortality.MethodsA retrospective chart review of patients with duodenal gunshot injuries during the study period January 1999 to December 2003 was performed. Data points accrued included patient demographics, admission hemodynamic status and resuscitative measures, laparotomy damage control procedures, methods of surgical repair of the duodenal injury, associated injuries, length of intensive care and hospital stays, complications, and mortality.ResultsA total of 75 consecutive patients with gunshot injuries to the duodenum were reviewed. Primary repair was performed in 54 patients (87%), resection and reanastomosis in 7 (11%), and pancreatoduodenectomy in 1 (2%) during the initial phases. The overall morbidity and mortality were 58% and 28%, respectively. Duodenum‐related complications were recorded in nine (15%) patients: two duodenal fistulas, one duodenal obstruction, and six cases of suture‐line dehiscence. Overall and duodenum‐related morbidity rates in patients with combined pancreatoduodenal injuries were 83% and 17%, respectively. Duodenum‐related mortality occurred in three (4.8%) patients.ConclusionsMost civilian low‐velocity duodenal gunshot injuries treated with simple primary repair result in overall morbidity, mortality, and duodenum‐related complication rates comparable to those in reports where more complex surgical procedures were employed. Primary repair is also applicable for most combined pancreatic and duodenal gunshot injuries.
Diagnostic and Prognostic Value of Cell‐cycle Regulatory Genes in Malignant Thyroid Neoplasms
Authors: Kebebew Electron , Peng Miao , Reiff Emily , Duh Quan‐Yang , Clark Orlo H. , McMillan Alex 
Published: March 2006

AbstractBackgroundApproximately 30% of patients with thyroid nodules have indeterminate or suspicious fine‐needle aspiration (FNA) biopsy results. Because their risk of cancer is approximately 20%, these patients undergo thyroidectomy. We hypothesized that genes that regulate cell‐cycle progression would be differentially expressed in malignant versus benign thyroid nodules and could serve as diagnostic markers and markers of disease aggressiveness.MethodsWe used a cDNA array with 96 cell‐cycle regulatory genes to identify differentially expressed genes in pooled benign versus malignant thyroid neoplasms. Genes up‐ or down‐regulated by more than 2‐fold in malignant thyroid neoplasms were further evaluated by real‐time quantitative polymerase chain reaction (PCR) in 95 patients with hyperplastic nodules (n = 19), follicular adenoma (n = 19), follicular thyroid cancer (n = 19), the follicular variant of papillary thyroid cancer (n = 19), and papillary thyroid cancer (n = 19).ResultscDNA array analysis showed that cyclin B1, MCM5, MCM7, RAD9, ubiquitin C, CDK6, SKP2, and APAF1 were up‐regulated in malignant thyroid neoplasms. Real‐time quantitative PCR showed that MCM5, MCM7, and RAD9 mRNA expression were significantly higher in malignant than in benign thyroid neoplasms (≤0.0012). The combined use of MCM5, MCM7, and RAD9 mRNA expression had a sensitivity of 98.2% and a specificity of 65.7%. The level of MCM7 mRNA expression was higher in T4 than in T1, T2, and T3 differentiated thyroid cancers (P < 0.0127).ConclusionsMCM5, MCM7, and RAD9 are overexpressed in malignant thyroid neoplasms of follicular cell origin. These genes may be useful markers of malignant thyroid neoplasms as an adjunct to FNA biopsy. MCM7 mRNA expression is higher in locally invasive differentiated thyroid cancer.
Thyroidectomy Using Monitored Local or Conventional General Anesthesia: An Analysis of Outpatient Surgery, Outcome and Cost in 1,194 Consecutive Cases
Authors: Spanknebel Kathryn , Chabot John A. , DiGiorgi Mary , Cheung Kenneth , Curty James , Allendorf John , LoGerfo Paul 
Published: March 2006

AbstractBackgroundCritical appraisal of safety, feasibility, and economic impact of thyroidectomy procedures using local (LA) or general anesthesia (GA) is performed.MethodsConsecutive patients undergoing thyroidectomy procedures were selected from a prospective database from January 1996 to June 2003 of a single‐surgeon practice at a tertiary center. Statistical analyses determined differences in patient characteristics, outcomes, operative data, and length of stay (LOS) between groups. A cohort of consecutive patients treated in 2002–2003 by all endocrine surgeons at the institution was selected for cost analysis.ResultsA total of 1,194 patients underwent thyroidectomy, the majority using LA (n = 939) and outpatient surgery (65%). Female gender (76%), body mass index ≥30 kg/m2 (29%), median age (49 years), and cancer diagnosis (45%) were similar between groups. Extent of thyroidectomy (59% total) and concomitant parathyroidectomy (13%) were similarly performed. GA was more commonly utilized for patients with comorbidity [15% vs. 10%, Anesthesia Society of America (ASA) ≥3; P < 0.001], symptomatic goiter (13% vs. 7%; P = 0.004), reoperative cases (10% vs. 6%; P = 0.01), and concomitant lymphadenectomy procedures (15% vs. 3%; P < 0.001). GA was associated with significant increase in LOS ≥24 hours (17 % vs. 4%) or overnight observation (49 % vs. 14%), P < 0.001. Operative room utilization was significantly associated with type of anesthesia (180 min vs. 120 min, GA vs. LA, P <. 001) and impacted to a lesser degree by surgeon operative time (89 minutes vs. 76 minutes, GA vs. LA; P =. 089). Overall morbidity rates were similar between groups (GA 5.8 % vs. LA 3.2%). The actual total cost (ATC) per case for GA was 48% higher than for LA and 30% higher than the ATC for all procedures (P = 0.006), with the combined weighted average impacted by more LA cases (n = 217 vs. 85).ConclusionThese data from a large, unselected group of thyroidectomy patients suggest LA results in similar outcomes and morbidity rates to GA. It is likely that associated LA costs are lower.
Benign Peritoneal Cystic Mesothelioma
Authors: Søreide Jon Arne , Søreide Kjetil , Körner Hartwig , Søiland Håvard , Greve Ole Jacob , Gudlaugsson Einar 
Published: March 2006

AbstractBackgroundBenign peritoneal cystic mesothelioma (BPCM) is a rare tumor of unknown origin, most frequently encountered in women of reproductive age. Etiology is unknown; definitions and terminology are confusing, and preoperative diagnosis is difficult. Several differential diagnoses must be considered.MethodsBased on our own clinical experience and a review of the relevant literature, we address clinical challenges and controversies of importance.ResultsCurrent literature on BPCM is mostly based on small case reports. Complete surgical resection is recommended if possible. Nevertheless, recurrent disease is not uncommon. Clinical positive effects of various adjuvant medical treatments remain to be shown.ConclusionsLack of consistent definitions, various treatment approaches, and mostly short follow‐up times make it difficult to draw any firm conclusions from published reports. The natural history of this rare disease is less than well clarified. When possible, in an individual patient, surgical resection with curative intent seems to be the treatment of choice.
Does Resection Line Involvement Affect Prognosis in Early Gastric Cancer Patients? An Italian Multicentric Study
Authors: Morgagni Paolo , Garcea Domenico , Marrelli Daniele , de Manzoni Giovanni , Natalini Giovanni , Kurihara Hayato , Marchet Alberto , Vittimberga Giovanni , Saragoni Luca , Roviello Franco , Leo Alberto Di , De Santis Francesco , Panizza Valerio , Nitti Donato 
Published: March 2006

AbstractBackgroundResection line involvement has been indicated as an important prognostic factor for gastric cancer. Its late detection renders the choice of treatment difficult for surgeons.Materials and MethodsWe describe the multicenter experience of a group of 11 patients with early gastric carcinoma (EGC) and positive resection confirmed at histological examination who did not undergo surgical retreatment for reasons of associated disease, surgical considerations on duodenal stump, or patient refusal.ResultsThe gastric margin was involved in 4 patients, and 7 patients had duodenal resection line involvement. No surgical complications or postoperative deaths were observed. Five and 8‐year survival was 100% and 86%, respectively. The only patient who relapsed did not have lymph node involvement and died from liver metastases, without local recurrence.ConclusionsIt is sometimes difficult to accurately define the resection line in gastric cancer surgery, especially in the early stages of disease, but because of the strongly negative prognostic value of an infiltrated margin, frozen sections are recommended if neoplastic invasion is suspected and a new resection is always recommended if possible. Nevertheless, the good prognosis of resected EGC patients with resection line involvement must be considered before submitting patients with associated diseases to radical surgical retreatment.
Decomposing the process of species accumulation into area dependent and time dependent parts
Authors: Ulrich Werner 
Published: March 2006

AbstractIn 1960, Preston predicted that the process of species accumulation in time (species–time relationship, STR) should be similar to the species–area relationship (SAR) and follow a power function with a slope of about 0.26. Here these two conjectures are tested using data of the spatiotemporal species accumulation in a local community of beech forest Hymenoptera. A power function species–area–time model of the form S = S0 Az tτ gave better fits to observed species numbers than a simple power function SAR model, and was able to predict similar species turnover rates (about 9% per year) to those inferred by other methods. The STR was well fitted by a power function, although due the limited time span (8 years) a logarithmic STR pattern cannot be ruled out. STR slopes ranged between 0.01 and 0.23 and were lower than predicted by Preston. Temporal species turnover appeared to be negatively correlated to species densities and positively correlated to species body weights. Ecological guild and taxon membership did not significantly influence temporal species turnover.
Designing a “tailor‐made” ecological network using geographical information systems
Authors: Bona Francesca , Badino Guido , Isaia Marco 
Published: March 2006

AbstractDuring the last few years, geographical information systems (GIS) have spread as powerful tools for landscape analysis. The main purpose of this work was to use GIS to display an ecological network made up of core areas, key areas and ecological corridors. As an example of the application of this method we refer to the population of deer (Cervus elaphus) and roe deer (Capreolus capreolus) in an alpine area in northwestern Italy. The method provided an overall view of the ecological network of the area, highlighting how linear infrastructures can affect animal populations and consequently, their survival probability.
Analysis of internal loops within the RNA secondary structure in almost quadratic time
Authors: Ogurtsov Aleksey Y. , Shabalina Svetlana A. , Kondrashov Alexey S. , Roytberg Mikhail A. 
Published: March 2006

Abstract
Motivation: Evaluating all possible internal loops is one of the key steps in predicting the optimal secondary structure of an RNA molecule. The best algorithm available runs in time O(L3), L is the length of the RNA.
Results: We propose a new algorithm for evaluating internal loops, its run-time is O(M*log2L), M&lt;L2 is a number of possible nucleotide pairings. We created a software tool Afold which predicts the optimal secondary structure of RNA molecules of lengths up to 28 000 nt, using a computer with 2 Gb RAM. We also propose algorithms constructing sets of conditionally optimal multi-branch loop free (MLF) structures, e.g. the set that for every possible pairing (x, y) contains an optimal MLF structure in which nucleotides x and y form a pair. All the algorithms have run-time O(M*log2L).
Availability: Executables of Afold software tool, precompiled for Linux and Windows, are available at .
Contact: MRoytberg@impb.psn.ru
Supplementary information:
An effective structure learning method for constructing gene networks
Authors: Chen Xue-wen , Anantha Gopalakrishna , Wang Xinkun 
Published: March 2006

AbstractMotivation: Bayesian network methods have shown promise in gene regulatory network reconstruction because of their capability of capturing causal relationships between genes and handling data with noises found in biological experiments. The problem of learning network structures, however, is NP hard. Consequently, heuristic methods such as hill climbing are used for structure learning. For networks of a moderate size, hill climbing methods are not computationally efficient. Furthermore, relatively low accuracy of the learned structures may be observed. The purpose of this article is to present a novel structure learning method for gene network discovery.Results: In this paper, we present a novel structure learning method to reconstruct the underlying gene networks from the observational gene expression data. Unlike hill climbing approaches, the proposed method first constructs an undirected network based on mutual information between two nodes and then splits the structure into substructures. The directional orientations for the edges that connect two nodes are then obtained by optimizing a scoring function for each substructure. Our method is evaluated using two benchmark network datasets with known structures. The results show that the proposed method can identify networks that are close to the optimal structures. It outperforms hill climbing methods in terms of both computation time and predicted structure accuracy. We also apply the method to gene expression data measured during the yeast cycle and show the effectiveness of the proposed method for network reconstruction.Contact: xwchen@ku.edu
WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks
Authors: Lee Dong-Yup , Yun Choamun , Cho Ayoun , Hou Bo Kyeng , Park Sunwon , Lee Sang Yup 
Published: March 2006

Abstract
Summary: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.
Availability: WebCell is accessible at or .
Contact: leesy@kaist.ac.kr
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier
Authors: Yousef Malik , Nebozhyn Michael , Shatkay Hagit , Kanterakis Stathis , Showe Louise C. , Showe Michael K. 
Published: March 2006

Abstract
Motivation: Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we describe a new technique, which is applicable across several species, for predicting miRNA genes. This technique is based on machine learning, using the Naïve Bayes classifier. It automatically generates a model from the training data, which consists of sequence and structure information of known miRNAs from a variety of species.
Results: Our study shows that the application of machine learning techniques, along with the integration of data from multiple species is a useful and general approach for miRNA gene prediction. Based on our experiments, we believe that this new technique is applicable to an extensive range of eukaryotes' genomes. Specific structure and sequence features are first used to identify miRNAs followed by a comparative analysis to decrease the number of false positives (FPs). The resulting algorithm exhibits higher specificity and similar sensitivity compared to currently used algorithms that rely on conserved genomic regions to decrease the rate of FPs.
Availability: The BayesMiRNAfind program is available at
Contact: showe@wistar.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of viable circular permutants using a graph theoretic approach
Authors: Paszkiewicz Konrad H. , Sternberg Michael J. E. , Lappe Michael 
Published: March 2006

AbstractMotivation: In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting regions where a protein can be split to form a viable circular permutant. Circular permutants are a powerful experimental tool to probe folding mechanisms and more recently have been used to design split enzyme reporter proteins.Results: We test our method on an extensive set of experiments carried out on dihydrofolate reductase in which circular permutants were constructed for every amino acid position in the sequence, together with partial data from studies on other proteins. Results show that closeness is capable of correctly identifying significantly more residues which are suitable for circular permutation than solvent accessibility. This has potential implications for the design of successful split enzymes having particular importance for the development of protein–protein interaction screening methods and offers new perspectives on protein folding. More generally, the method illustrates the success with which graph-theoretic measures encapsulate the variety of long and short range interactions between residues during the folding process.Contact: konrad.paszkiewicz@imperial.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
CAFE: a computational tool for the study of gene family evolution
Authors: De Bie Tijl , Cristianini Nello , Demuth Jeffery P. , Hahn Matthew W. 
Published: March 2006

AbstractSummary: We present CAFE (Computational Analysis of gene Family Evolution), a tool for the statistical analysis of the evolution of the size of gene families. It uses a stochastic birth and death process to model the evolution of gene family sizes over a phylogeny. For a specified phylogenetic tree, and given the gene family sizes in the extant species, CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss (quantified by a p-value) and identify which branches cause the p-value to be small for significant families.Availability: Software is available fromContact: mwh@indiana.edu
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
Authors: Wainreb Gilad , Haspel Nurit , Wolfson Haim J. , Nussinov Ruth 
Published: March 2006

Abstract
Motivation: Secondary-Structure Guided Superposition tool (SSGS) is a permissive secondary structure-based algorithm for matching of protein structures and in particular their fragments. The algorithm was developed towards protein structure prediction via fragment assembly.
Results: In a fragment-based structural prediction scheme, a protein sequence is cut into building blocks (BBs). The BBs are assembled to predict their relative 3D arrangement. Finally, the assemblies are refined. To implement this prediction scheme, a clustered structural library representing sequence patterns for protein fragments is essential. To create a library, BBs generated by cutting proteins from the PDB are compared and structurally similar BBs are clustered. To allow structural comparison and clustering of the BBs, which are often relatively short with flexible loops, we have devised SSGS. SSGS maintains high similarity between cluster members and is highly efficient. When it comes to comparing BBs for clustering purposes, the algorithm obtains better results than other, non-secondary structure guided protein superimposition algorithms.
Availability: SSGS is available for download at
Contact: ruthn@ncifcrf.gov
Supplementary information: Supplementary data are available at Bioinformatics online.