bluuebunny/crossref_metadata_2025_split huggingface dataset:
Designing robot grippers: optimal edge contacts for part alignment
Authors: Zhang Mike Tao , Goldberg Ken 
Published: November 2006

SUMMARYAlthough parallel-jaw grippers play a vital role in automated manufacturing, gripper surfaces are still designed by trial-and-error. This paper presents an algorithmic approach to designing gripper jaws that mechanically align parts in the vertical (gravitational) plane. We consider optimal edge contacts, based on modular trapezoidal segments that maximize contact between the gripper and the part at its desired final orientation. Given then-sided 2D projection of an extruded convex polygonal part, mechanical properties such as friction and center of mass, and initial and desired final orientations, we present anO(n3logn) numerical algorithm to design optimal gripper jaws. We also present anO(nlogn) algorithm to compute tolerance classes for these jaws, and report on an online implemented version of the algorithm and physical experiments with the jaws it designed. This paper extends earlier results that generated optimal point contacts [M. T. Zhang and K. Goldberg, “Gripper point contacts for part alignment,”IEEE Trans. Robot. Autom.18(6), 902–910 (2002)].
Survey on the occurrence ofBrachyspiraspecies andLawsonia intracellularisin children living on pig farms
Authors: JACOBSON M. , RÅSBÄCK T. , FLÖISTRUP H. , BENZ M. , BRAUN-FAHRLÄNDER C. , RIEDLER J. , SCHRAM-BIJKERK D. , FELLSTRÖM C. 
Published: November 2006

SUMMARYThe occurrence ofBrachyspiraspecies andLawsonia intracellulariswas investigated by PCR analyses of faeces from 60 children living on European pig farms. In addition, 60 other children were included as controls. Two samples were positive forB. aalborgibutB. pilosicoliandL. intracellulariswere not demonstrated.
An observer study: comparison of computed radiography to electronic and film portal imaging
Authors: Roberts N. , Stanley S. 
Published: November 2006

Introduction: Computed radiography (CR) is an imaging facility that does not require the use of hard copy film, digital images are obtained with a photostimulable phosphor plate, which replaces film, in a cassette. As the first UK radiotherapy site to trial CR, we are collecting data to assess the feasibility of using CR in radiotherapy treatment verification.Method: From 30 patients undergoing radical radiotherapy, 10 were consecutively accrued to three sites: pelvis, thorax and head and neck. Treatment verification images were taken using current protocols, but substituting standard imaging for CR images on one fraction. Four independent observers were used: two clinical oncologists and two therapy radiographers. Observers rated CR, electronic portal imaging (EPI) and enhanced contrast (EC) films of the three sites for both landmark visibility and ease of verification decision, using a numerical scoring system.Results: Ratings for visibility of landmarks and for verification decision were similar for CR and film/EPI images for most landmarks. However, CR images rated poorly compared to EC film in the head and neck region with landmarks such as thyroid cartilage and cricoid cartilage rating as ‘not clear’. CR images rated better than EPI images for both visibility and verification decision on the majority of landmarks in the pelvis region.Conclusion: Results gathered from a relatively small sample size have provided the following conclusion. The visibility of landmarks in CR images is comparable to that in film and EPI. Verification of treatment images based on CR is comparable to that of the current imaging media in the department.
PharmGKB: Capturing knowledge to catalyze pharmacogenomics research
Authors: Altman Russ 
Published: November 2006

AbstractThis is a powerpoint presentation made initially at the Cold Spring Harbor meeting on Pharmacogenomics, November 2006. It discusses the PharmGKB (http://www.pharmgkb.org/) and how we are building a pipeline for annotation of knowledge. In particular, we are focusing on pathway knowledge, "Very important Pharmacogene" annotations, and curation of the pharmacogenomics literature. We are building an ontology-based system to capture and aggregate knowledge, for use by our curators.
Magnetic resonance imaging and radiographic findings of seal finger
Authors: Marjelund S. , Tikkakoski T. , Isokangas M. , Räisänen S. 
Published: November 2006

Purpose: To describe the magnetic resonance imaging (MRI) and radiographic findings of five patients with seal finger. Material and Methods: The MR images and radiographs of five patients with seal finger were retrospectively evaluated. MRI was performed on four patients in the subacute phase, and follow-up imaging was done on one of them at 5 months. One patient had MRI only at a later stage 5 years after onset. Radiographs were taken three times in the subacute phase and once at a later stage. One patient had had seal finger in another finger previously. Results: Short-tau inversion-recovery (STIR) sequence showed extensive subcutaneous soft tissue edema in all four patients in the subacute phase and tenosynovitis of the flexion tendons in two cases. Three patients had edema in 2–3 phalanges, and effusion in the distal interphalangeal (DIP) joint was seen in one case. At the later stage, no signal pathology in soft tissues or bones was seen in STIR images. In the subacute phase, radiographs showed digital soft-tissue swelling in three patients, and one patient had a narrowed DIP joint, periarticular osteoporosis, and a periosteal reaction. At the later stage, flexion contracture of the finger was seen. Conclusion: In addition to soft-tissue infection, seal finger causes bone marrow edema, tenosynovitis, and effusion in the interphalangeal joints visible as increased signal intensity in STIR images. Radiographs reveal periarticular osteoporosis with loss of cartilage in the subacute phase and flexion contracture at the later stage. MRI (STIR) allows more precise delineation of the inflammatory process compared to radiography.
Percutaneous transluminal cutting-balloon angioplasty for hemodialysis access stenoses resistant to conventional balloon angioplasty
Authors: Kariya S. , Tanigawa N. , Kojima H. , Komemushi A. , Shomura Y. , Shiraishi T. , Kawanaka T. , Sawada S. 
Published: November 2006

Purpose: To examine the value of cutting-balloon percutaneous transluminal angioplasty (PTA) for hemodialysis access with residual stenosis after conventional balloon PTA. Material and Methods: Angioplasty with conventional balloons was performed on 48 hemodialysis access stenoses in 28 patients. If the balloon waist still remained at the rated burst pressure, the balloon was reinflated up to three times. Fifteen of 48 stenoses had residual stenoses of more than 30% after conventional balloon PTA. In these 15 stenoses, additional cutting-balloon PTA was performed. Results: The mean residual percent diameter stenoses before and after conventional balloon PTA were 77.6±3.4% and 48.6±8.5%, respectively. Additional cutting-balloon PTA decreased the mean residual percent diameter to 27.9±10.0%, and the cutting balloon was completely inflated without complication. In 12 patients, the 6-month primary patency rate (±SE) was 90.0% (9.5), and the 1-year primary patency rate (±SE) was 25.0% (14.8). Conclusion: Additional cutting-balloon PTA was found useful for reducing residual stenosis.
O-(2-[18F]fluoroethyl)-l-tyrosine (18F-FET) uptake in mouse thymoma cells, and its biodistribution in mice and human volunteers
Authors: Abe K. , Hayashi K. , Sasaki M. , Koga H. , Kaneko K. , Sawamoto H. , Himuro K. , Honda H. 
Published: November 2006

Purpose: To evaluate O-(2-[18F]fluoroethyl)-l-tyrosine (18F-FET) uptake in mouse malignant thymoma (EL4), and its biodistribution in mice and humans. Material and Methods: First, 18F-FET uptake in EL4 cells was examined in an in vitro study. Second, the kinetics of 18F-FET uptake and its biodistribution were examined in mice after subcutaneous injection of EL4 cells and complete Freund's adjuvant. Finally, the kinetics of 18F-FET uptake and its biodistribution in healthy human volunteers were examined. Results: In an in vitro study, 18F-FET was extensively incorporated in EL4 cells. In an animal study, 18F-FET accumulation in normal organs peaked within 30 min postinjection. The mean ratios of 18F-FET uptake in tumors and in inflammatory lesions to that in muscle tissue at 60 min postadministration were 2.18 (range 2.00–2.29) and 1.04 (range 0.95–1.14), respectively. In a human study, static images were taken 60 min after 18F-FET administration. Mean standardized uptake values (SUVs) of the liver (1.52, range 1.38–1.71) and kidneys (1.90, range 1.74–2.24) were nearly equal or slightly higher than that of muscle tissue (1.19, range 0.99–1.33). Conclusion: This study demonstrates that 18F-FET accumulation in thymoma is significantly higher than in normal organs. 18F-FET could be a useful tracer for tumor imaging.
Coverage Strategies in Wireless Sensor Networks
Authors: Commuri Sesh , Watfa Mohamed K. 
Published: November 2006

An energy efficient cover of a region using Wireless Sensor Networks (WSNs) is addressed in this paper. Sensor nodes in a WSN are characterized by limited power and computational capabilities, and are expected to function for extended periods of time with minimal human intervention. The life span of such networks depends on the efficient use of the available power for sensing and communication. In this paper, the coverage problem in a three dimensional space is rigorously analyzed and the minimum number of sensor nodes and their placement for complete coverage is determined. Also, given a random distribution of sensor nodes, the problem of selecting a minimum subset of sensor nodes for complete coverage is addressed. A computationally efficient algorithm is developed and implemented in a distributed fashion. Numerical simulations show that the optimized sensor network has better energy efficiency compared to the standard random deployment of sensor nodes. It is demonstrated that the optimized WSN continues to offer better coverage of the region even when the sensor nodes start to fail over time. A localized “self healing” algorithm is implemented that wakes up the inactive neighbors of a failing sensor node. Using the “flooding algorithm” for querying the network, it is shown that the optimized WSN with integrated self healing far outweighs the performance that is obtained by standard random deployment. For the first time, a “measure of optimality” is defined that will enable the comparison of different implementations of a WSN from an energy efficiency stand point.
Tightly Clustered Outbreak of Group A Streptococcal Disease at a Long-Term Care Facility
Authors: Arnold Kathryn E. , Schweitzer Jody L. , Wallace Barbara , Salter Monique , Neeman Ruth , Hlady W. Gary , Beall Bernard 
Published: November 2006

Objective.To describe investigation of a tightly clustered outbreak of invasive group A streptococcal (GAS) disease associated with a high mortality rate in a long-term care facility (LTCF).Design.Cross-sectional carriage survey and epidemiologic investigation of LTCF resident and employee cohorts.Setting.A 104-bed community LTCF between March 1 and April 7, 2004.Patients.A cohort of LTCF residents with assigned beds at the time of the outbreak.Interventions.Reinforcement of standard infection control measures and receipt of chemoprophylaxis by GAS carriers.Results.Four confirmed and 2 probable GAS cases occurred between March 16 and April 1, 2004. Four case patients died. The final case occurred during the investigation, before the patient was determined to be a GAS carrier. No case occurred during the 6 months after the intervention. Disease was caused by type emm3 GAS; 16.5% of residents and 2.4% of employees carried the outbreak strain. Disease was clustered in 1 quadrant of the LTCF and associated with nonintact skin. GAS disease or carriage was associated with having frequent personal visitors.Conclusions.Widespread carriage of a virulent GAS strain likely resulted from inadequate infection control measures. Enhanced infection control and targeted prophylaxis for GAS carriers appeared to end the outbreak. In addition to employees, regular visitors to LTCFs should be trained in hand hygiene and infection control because of the potential for extended relationships over time, leading to interaction with multiple residents, and disease transmission in such residential settings. Specific attention to prevention of skin breaks and proper wound care may prevent disease. The occurrence of a sixth case during the investigation suggests urgency in addressing severe, large, or tightly clustered outbreaks of GAS infection in LTCFs.
A Prospective Study of Outcomes, Healthcare Resource Utilization, and Costs Associated With Postoperative Nosocomial Infections
Authors: Herwaldt Loreen A. , Cullen Joseph J. , Scholz David , French Pamela , Zimmerman M. Bridget , Pfaller Michael A. , Wenzel Richard P. , Perl Trish M 
Published: November 2006

Objective.We evaluated 4 important outcomes associated with postoperative nosocomial infection: costs, mortality, excess length of stay, and utilization of healthcare resources.Design.The outcomes for patients who underwent general, cardiothoracic, and neurosurgical operations were recorded during a previous clinical trial. Multivariable analyses including significant covariates were conducted to determine whether nosocomial infection significantly affected the outcomes.Setting.A large tertiary care medical center and an affiliated Veterans Affairs Medical Center.Patients.A total of 3,864 surgical patients.Results.The overall nosocomial infection rate was 11.3%. Important covariates included age, Karnofsky score, McCabe and Jackson classification of the severity of underlying disease, National Nosocomial Infection Surveillance system risk index, and number of comorbidities. After accounting for covariates, nosocomial infection was associated with increased postoperative length of stay, increased costs, increased hospital readmission rate, and increased use of antimicrobial agents in the outpatient setting. Nosocomial infection was not associated independently with a significantly increased risk of death in this surgical population.Conclusion.Postoperative nosocomial infection was associated with increased costs of care and with increased utilization of medical resources. To accurately assess the effects of nosocomial infections, one must take into account important covariates. Surgeons seeking to decrease the cost of care and resource utilization must identify ways to decrease the rate of postoperative nosocomial infection.
Excess Length of Stay Attributable to Surgical Site Infection Following Hip Replacement: A Nested Case-Control Study
Authors: Jodra Vicente Monge , Soler Lourdes Sainz de los Terreros , Pérez Cristina Díaz-Agero , Requejo Carmen María Saa , Farrás Nieves Plana 
Published: November 2006

Objective.We estimated the impact of hip replacement-associated surgical site infection (SSI) on morbidity and length of stay.Methods.This was a pairwise matched (1 : 1) case-control study nested in a cohort. All patients who underwent hip replacement from January 1, 2000, to June 30, 2004, were prospectively enrolled for the nested case-control design analysis and were monitored from the time of surgery until hospital discharge, including any patients readmitted because of infection.Results.Among the 1,260 hip replacements performed, 28 SSIs were detected, yielding a crude SSI rate of 2.2%. The median excess length of stay attributable to SSI was 32.5 days (P< .001), whereas the median prolonged postoperative stay due to SSI was 31 days (P< .001). Deep-wound SSI was the type that prolonged hospital stay the most (up to 49 days). Of the patients who developed an SSI, 4 required revision surgery, for an SSI-related morbidity rate of 14.3%.Conclusion.SSI prolongs hospital stay; however, although hospital stay is a rough indicator of the cost of this complication, to accurately estimate the costs of SSI, we would need to consider individual costs in a linear regression model adjusted for all possible confounding factors.
Impact of Postdischarge Surveillance on the Rate of Surgical Site Infection After Orthopedic Surgery
Authors: Huotari Kaisa , Lyytikäinen Outi ,   Hospital Infection Surveillance Team
Published: November 2006

Objective.To evaluate the impact of postdischarge surveillance on surgical site infection (SSI) rates after orthopedic surgery.Setting.Nine hospitals participating in the Finnish Hospital Infection Program.Patients.All patients who underwent hip or knee arthroplasty or open reduction of a femur fracture during 1999-2002.Results.The date of discharge was available for 11,812 procedures (90%). The median length of hospital stay was 8 days (range per hospital, 6-9 days). The overall SSI rate was 3.3% (range, 0.8%-6.4%). Of 384 SSIs detected, 216 (56%; range, 28%-90%) were detected after discharge: 93 (43%) were detected on readmission to the hospital, 73 (34%) at completion of a postdischarge questionnaire, and 23 (11%) at a follow-up visit. For 27 postdischarge SSIs (13%), the location of detection was unknown. Altogether, 32 (86%) of 37 of organ/space SSIs, 57 (80%) of 71 deep incisional SSIs, and 127 (46%) of 276 superficial incisional SSIs were detected after discharge. Most SSIs (70%) detected on readmission were severe (organ/space or deep incisional), whereas most SSIs (86%) detected at follow-up visits or at completion of a postdischarge questionnaire were superficial. Of all SSIs, 78% (range, 48%-100%) were microbiologically confirmed. Microbiologic confirmation was less common after discharge than during postoperative hospital stay (66% vs 93%; P< .001).Conclusions.Postdischarge surveillance had a large impact on the rate of SSI detected after orthopedic surgery. However, postdischarge surveillance conducted by means of a questionnaire detected only a minority of deep incisional and organ/space SSIs.
Improved Risk Adjustment for Comparison of Surgical Site Infection Rates
Authors: Geubbels Eveline L. P. E. , Grobbee Diederick E. , Vandenbroucke-Grauls Christina M. J. E. , Wille Jan C. , Boer Annette S. de 
Published: November 2006

Objective.To develop prognostic models for improved risk adjustment in surgical site infection surveillance for 5 surgical procedures and to compare these models with the National Nosocomial Infection Surveillance system (NNIS) risk index.Design.In a multicenter cohort study, prospective assessment of surgical site infection and risk factors was performed from 1996 to 2000. In addition, risk factors abstracted from patient files, available in a national medical register, were used. The c-index was used to measure the ability of procedure-specific logistic regression models to predict surgical site infection and to compare these models with models based on the NNIS risk index. A c-index of 0.5 indicates no predictive power, and 1.0 indicates perfect predictive power.Setting.Sixty-two acute care hospitals in the Dutch national surveillance network for nosocomial infections.Participants.Patients who underwent 1 of 5 procedures for which the predictive ability of the NNIS risk index was moderate: reconstruction of the aorta (n= 875), femoropopliteal or femorotibial bypass (n= 641), colectomy (n= 1,142), primarytotal hip prosthesis (n= 13,770), and cesarean section (n= 2,962).Results.The predictive power of the new model versus the NNIS index was 0.75 versus 0.62 for reconstruction of the aorta (P< .01), 0.78 versus 0.58 for femoropopliteal or femorotibial bypass (P< .001), 0.69 versus 0.62 for colectomy (P< .001), 0.64 versus 0.56 for primary total hip prosthesis arthroplasty (P< .001), and 0.70 versus 0.54 for cesarean section (P< .001).Conclusion.Data available from hospital information systems can be used to develop models that are better at predicting the risk of surgical site infection than the NNIS risk index. Additional data collection may be indicated for certain procedures–for example, total hip prosthesis arthroplasty.
QSCOP—SCOP quantified by structural relationships
Authors: Suhrer Stefan J. , Wiederstein Markus , Sippl Manfred J. 
Published: November 2006

AbstractSummary: The database SCOP (Structural Classification Of Proteins) has become a major resource in bioinformatics and protein science. A particular strength of SCOP is the flexibility of its rules enabling the preservation of the many details spotted by experts in the classification process. Here we endow classic SCOP Families with quantified structural information and comment on the structural diversity found in the SCOP hierarchy.Availability: Quantified SCOP (QSCOP) is available as a public WEB service.Contact: sippl@came.sbg.ac.at
Integrating transcription factor binding site information with gene expression datasets
Authors: Jeffery Ian B. , Madden Stephen F. , McGettigan Paul A. , Perrière Guy , Culhane Aedín C. , Higgins Desmond G. 
Published: November 2006

AbstractMotivation: Microarrays are widely used to measure gene expression differences between sets of biological samples. Many of these differences will be due to differences in the activities of transcription factors. In principle, these differences can be detected by associating motifs in promoters with differences in gene expression levels between the groups. In practice, this is hard to do.Results: We combine correspondence analysis, between group analysis and co-inertia analysis to determine which motifs, from a database of promoter motifs, are strongly associated with differences in gene expression levels. Given a database of motifs and gene expression levels from a set of arrays, the method produces a ranked list of motifs associated with any specified split in the arrays. We give an example using the Gene Atlas compendium of gene expression levels for human tissues where we search for motifs that are associated with expression in central nervous system (CNS) or muscle tissues. Most of the motifs that we find are known from previous work to be strongly associated with expression in CNS or muscle. We give a second example using a published prostate cancer dataset where we can simply and clearly find which transcriptional pathways are associated with differences between benign and metastatic samples.Availability: The source code is freely available upon request from the authors.Contact: Ian.Jeffery@ucd.ie
Extensions to gene set enrichment
Authors: Jiang Zhen , Gentleman Robert 
Published: November 2006

AbstractMotivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene sets with correlated expression. We also address issues that arise when gene sets overlap.Results: Our proposals extend the range of applicability of GSEA and allow for adjustments based on other covariates. We have provided a well-defined procedure to address interpretation issues that can raise when gene sets have substantial overlap. We have shown how standard dimension reduction methods, such as PCA, can be used to help further interpret GSEA.Contact: zjiang@fhcrc.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Mosclust: a software library for discovering significant structures in bio-molecular data
Authors: Valentini Giorgio 
Published: November 2006

AbstractSummary: The R package mosclust (model order selection for clustering problems) implements algorithms based on the concept of stability for discovering significant structures in bio-molecular data. The software library provides stability indices obtained through different data perturbations methods (resampling, random projections, noise injection), as well as statistical tests to assess the significance of multi-level structures singled out from the data.Availability: Contact: valentini@dsi.unimi.itSupplementary information: