bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peptide length-based prediction of peptide–MHC class II binding
Authors: Chang Stewart T. , Ghosh Debashis , Kirschner Denise E. , Linderman Jennifer J. 
Published: September 2006

Abstract
Motivation: Algorithms for predicting peptide–MHC class II binding are typically similar, if not identical, to methods for predicting peptide–MHC class I binding despite known differences between the two scenarios. We investigate whether representing one of these differences, the greater range of peptide lengths binding MHC class II, improves the performance of these algorithms.
Results: A non-linear relationship between peptide length and peptide–MHC class II binding affinity was identified in the data available for several MHC class II alleles. Peptide length was incorporated into existing prediction algorithms using one of several modifications: using regression to pre-process the data, using peptide length as an additional variable within the algorithm, or representing register shifting in longer peptides. For several datasets and at least two algorithms these modifications consistently improved prediction accuracy.
Availability:
Contact: linderma@umich.edu
Modelling interaction sites in protein domains with interaction profile hidden Markov models
Authors: Friedrich Torben , Pils Birgit , Dandekar Thomas , Schultz Jörg , Müller Tobias 
Published: September 2006

Abstract
Motivation: Due to the growing number of completely sequenced genomes, functional annotation of proteins becomes a more and more important issue. Here, we describe a method for the prediction of sites within protein domains, which are part of protein–ligand interactions. As recently demonstrated, these sites are not trivial to detect because of a varying degree of conservation of their location and type within a domain family.
Results: The developed method for the prediction of protein–ligand interaction sites is based on a newly defined interaction profile hidden Markov model (ipHMM) topology that takes structural and sequence data into account. It is based on a homology search via a posterior decoding algorithm that yields probabilities for interacting sequence positions and inherits the efficiency and the power of the profile hidden Markov model (pHMM) methodology. The algorithm enhances the quality of interaction site predictions and is a suitable tool for large scale studies, which was already demonstrated for pHMMs.
Availability: The MATLAB-files are available on request from the first author.
Contact: tobias.mueller@biozentrum.uni-wuerzburg.de
Supplementary information:
Incidence and Characteristics of Facial Nerve Stimulation in Children With Cochlear Implants
Authors: Cushing Sharon L. , Papsin Blake C. , Gordon Karen A. 
Published: September 2006

AbstractObjectives: Electrical stimulation from a cochlear implant can spread beyond the auditory nerve. The aims of this study were to accurately measure facial nerve stimulation in pediatric implant users and to determine the characteristics and incidence of this unwanted activity. Part A consisted of a prospective study of a randomized sample of 44 pediatric implant users. Part B consisted of a retrospective analysis of 121 children with previously recorded electrically evoked auditory brainstem responses (EABR).Study Design and Methods: Responses were evoked by 3 electrodes along the implant array in three groups of children: 1) postmeningitic, 2) abnormal cochlea, and 3) neither. Intraoperative measures were obtained under anesthesia; all other recordings were completed in awake children.Results: Intraoperative recordings revealed large nonauditory responses in a number of channels, including the midline EABR. Under paralysis, these responses disappeared, and clear EABRs were recorded. Similarly, prospective postoperative electromyographic (EMG) responses from the facial nerve were found in more than 59% (26 of 44) of experienced implant users (Nucleus 24): 31% of postmeningitic children (4 of 13), 80% of those with abnormal cochlea (8 of 10), and 66% of those with neither (14 of 21). Retrospective analysis of previously recorded postoperative EABRs demonstrated facial nerve stimulation in 35% (42 of 121). In most cases, facial nerve stimulation occurred when levels were perceptually loud but comfortable.Conclusions: 1) Facial nerve potentials can be recorded using EMG in a large proportion of cochlear implant users at high levels of stimulation. 2) The EABR can be obscured in the presence of facial nerve stimulation and care should be taken to distinguish it from the EMG response, particularly when auditory brainstem activity is in question. 3) Use of surface EMG provides an additional objective measure to ensure the safe and comfortable use of cochlear implants.
Quality of Life of Patients With Otitis Media and Caregivers: A Multicenter Study
Authors: Lee Jeanne , Witsell David L. , Dolor Rowena J. , Stinnett Sandra , Hannley Maureen 
Published: September 2006

AbstractObjective: The objective of this study was to determine the quality of life of otitis media (OM) patients and their caregivers.Study Design: A cross‐sectional study was conducted at 11 otolaryngology and five pediatric clinics in the United States between July 1998 and August 1999. All patients, regardless of primary complaint, completed a demographic survey, OM‐6 survey, and Child Health Questionaire‐PF28 survey by proxy. Physicians completed an International Classification of Diseases, 9th Revision diagnosis sheet for each patient.Methods: Analysis, including Spearman rank correlation, was restricted to study patients with active OM.Results: A total of 1,001 patients with active OM were identified: 503 OM with effusion, 267 acute OM, and 258 recurrent acute OM. Median patient age was 2 years (interquartile range, 1–5). Mean caretaker age was 32.6 years (standard deviation, 7.4). There was moderate correlation between OM frequency and physical suffering (r = 0.50; P < .001) and caregiver concerns (r = 0.45; P < .001). Moderate correlation was found between percentage of time with fluid in the ears and caregiver concerns (r = 0.46; P < .001) and physical suffering (r = 0.43; P < .001). OM patients over 5 years of age scored significantly worse than healthy children ages 5 to 7 years in almost all areas of global health, including physical functioning and impact on caretaker's personal time and emotions.Conclusion: The global quality of life of patients with OM over 5 years of age is worse than that of healthy children of similar age. Physical suffering and caregiver concerns are associated with frequent OM or effusion duration. Hopefully, these results will direct the focus of future outcomes studies.
Evaluation of Culture and Antibiotic Use in Patients With Pharyngitis
Authors: Rufener Justin B. , Yaremchuk Kathleen L. , Payne Spencer C. 
Published: September 2006

AbstractObjectives: The objectives of this study were to evaluate practice patterns for treatment of patients with pharyngitis with regard to testing for group A beta hemolytic streptococcal (GABHS) infection, frequency of antibiotic use, and appropriate choice of antibiotics.Study Design: The authors conducted a retrospective review of billing data for 10,482 office visits for pharyngitis.Methods: The 2004 billing database for a tertiary institution was queried for outpatient visits for pharyngitis or tonsillitis, group A Streptococcus tests (GAST), and antibiotic prescriptions filled after the visit. Patients were separated by age group and analyzed for the proportion of patients that received a GAST and proportion prescribed an antibiotic. Antibiotic prescriptions were also analyzed to determine whether they were appropriate for treatment of GABHS.Results: A total of 68.7% of all patients and 82.2% of pediatric patients were tested for GAST. A total of 47.1% of adult patients and 44.9% of pediatric patients received an antibiotic. For adult patients for whom GAST was obtained, 48.6% were prescribed an antibiotic versus 53.6% of those not tested. Streptococcus testing was a significant predictor of antibiotic use (P < .0001), whereas age was not (P = .22). A total of 82.1% of all antibiotics prescribed were recommended for treatment of GABHS.Conclusions: Most patients seen for pharyngitis were tested for GABHS, but pediatric patients were tested more frequently than adults. Patients who received a GAST were less likely to receive antibiotics. The rates experienced in our tertiary academic institution are higher than previously quoted for community practice. When antibiotics were prescribed, they were usually appropriate for the treatment of GABHS based on current recommendations.
Topical Pimecrolimus 1% for the Treatment of Pruritic External Auditory Canals
Authors: Djalilia Hamid R. , Memar Omid 
Published: September 2006

AbstractObjectives/Hypothesis: To understand the role and efficacy of topical pimecrolimus in the treatment of refractory pruritis of the external auditory canals (EACs).Study Design: Retrospective chart review.Methods: Thirty‐six patients with pruritic EACs who had failed conventional therapy with topical and systemic medications were treated with topical pimecrolimus 1% for a period of 3 months. Baseline and follow‐up evaluation of the degree of pruritis among other variables was performed. A control group of 19 patients was instructed on aural toilet alone and was not treated with topical pimecrolimus 1%.Results: Of the 36 patients who were treated with topical pimecrolimus for their pruritic EACs, 34 patients had resolution of their symptoms. There was evidence of return of cerumen production in 86% of patients. In the control group, 16% of patients had improvement of their symptoms with aural toilet. This difference was statistically significant (χ2, P < .0001).Conclusions: Topical pimecrolimus appears to be more efficacious than aural toilet in the treatment of pruritic ears for chronic use without side effects.
Delayed Extrusion of Hydroxyapatite after Transpetrosal Reconstruction
Authors: Krishnamoorthy Kumaresh , Pensa Myles L. , Samy Ravi N. 
Published: September 2006

AbstractObjectives:To review the long‐term results of hydroxyapatite closure of transpetrosal defects.Study Design:Retrospective chart review.Methods:One hundred seventy‐seven patients were followed for more than 5 years. After surgical management by way of transpetrosal routes, hydroxyapatite was placed after medial wound closure with abdominal fat and before a three‐layered lateral soft tissue closure.Results:Among this group of patients, three (1.7%) cerebrospinal fluid (CSF) leaks were encountered. None of these required re‐operation. Delayed extrusion of hydroxyapatite with concomitant superficial wound infections have occurred in seven (4%) patients. All required operative re‐intervention.Conclusions:Hydroxyapatite has proven to be an effective material in the closure of skull base defects. Nevertheless, delayed extrusion of this agent can occur, resulting in the potential for morbidity and the need for operative re‐intervention.
Clinical Evaluation of Parkinson's‐Related Dysphonia
Authors: Sewall Gregory K. , Jiang Jack , Ford Charles N. 
Published: September 2006

AbstractObjectives: Nearly one third of patients with idiopathic Parkinson's disease (IPD) cite dysphonia, characterized subjectively as causing a harsh and breathy voice, as their most debilitating deficit. Medical or behavioral treatments may lead to voice improvement. The purpose of this study was 1) to determine whether vocal fold injection of Cymetra (micronized form of collagen, elastin, proteoglycans; Lifecell Co.) is associated with changes in dysphonic voice characteristics in subjects with IPD, as judged perceptually using a standard instrument Consensus Auditory‐Perceptual Evaluation of Voice (CAPE‐V), and (2) which acoustic and aerodynamic measurements of voice are most reflective of any observed perceptual changes in voice.Study Design: Prospective clinical evaluation of patients with Parkinson's‐related dysphonia (PRD).Methods: Six patients with PRD were evaluated before treatment for the presence of dysphonia and glottal gap. All subjects underwent transoral vocal fold collagen injection using topical anesthesia in the otolaryngology clinic as part of their clinical care. At the initial clinic visit, and 10 to14 days after vocal fold collagen injection, patients were asked to complete the Voice Handicap Index (VHI), a questionnaire concerning voice‐related quality of life, and perceptual analyses of voice quality were performed. In addition, patients underwent acoustic (pitch/loudness range, maximum phonation time [MPT], and aerodynamic phonation threshold pressure [PTP]) voice analysis.Results: Five of six subjects had self‐perceived improvements in voice after treatment, as determined by the VHI (range, +8 to −24). All five subjects who completed testing demonstrated decreased PTP (range, −1.3 to −2.7, P = .002). Five of six subjects demonstrated statistically significant improvements in MPT (range, −2–16 s, P = .05). Five of six subjects had improved pitch range (−26–343 Hz), whereas all subjects had increased intensity range (0.6–23 db) after injection.Conclusions: Transoral collagen injection in patients with PRD is safe, well tolerated, and is an effective temporary method of subjectively improving voice and speech in selected patients with IPD. Reduction of glottal gap with collagen improves MPT and subglottal PTP. The resulting gain of vocal efficiency may reduce vocal fatigue and provide a useful adjunct to voice therapy for PRD.
Endoscopic Techniques in Resection of Anterior Skull Base/Paranasal Sinus Malignancies
Authors: Buchmann Luke , Larsen Christopher , Pollack Ania , Tawfik Ossama , Sykes Kevin , Hoover Larry A. 
Published: September 2006

AbstractObjective: The objective of this study was to examine the role of endoscopic approaches to the resection of anterior skull base and paranasal sinus malignancies at one tertiary care medical center.Study Design: The authors conducted a retrospective chart review over a period of 17 years.Methods: Patients undergoing anterior skull base resections for malignancies over a 17‐year period were reviewed. Data were collected on each patient with respect to the pathology of the tumor and approach used as well as demographic and follow‐up information.Results: A total of 78 patients were treated at a tertiary care medical center for malignancies of the paranasal sinuses and anterior skull base. The most common diagnosis was squamous cell carcinoma occurring in 33% of the cases. The remaining pathologies included esthesioneuroblastoma (23%), adenoid cystic carcinoma (15%), melanoma (3%), sinonasal undifferentiated carcinoma (3%), lymphoma (5%), nasopharyngeal carcinoma (4%), and other tumor types (14%). Endoscopic techniques were used extensively in this population of patients. Combined approaches using a sublabial/transmaxillary approach and coronal approaches were used when indicated and complemented the endoscopic approach. A majority of patients were without evidence of disease at the end of this review. Using endoscopic techniques allowed for acceptable cosmetic results and facial incisions were used minimally.Conclusion: With complete endoscopic surgical resection followed by radiation therapy, local recurrence, morbidity, and cosmetic deformity have been minimized. The microscopic view provided by endoscopic techniques, with or without complementary approaches, allows for complete tumor removal.
A New Generation Videokymography for Routine Clinical Vocal Fold Examination
Authors: Qiu Qingjun , Schutte Harm K. 
Published: September 2006

AbstractObjective: This study aims to introduce a new‐generation videokymographic system, which provides simultaneous laryngoscopic and kymographic image, for routine clinical vocal fold examination.Study Design: The authors explored a new imaging method for diagnosis and evaluation of voice disorders.Methods: The new‐generation videokymographic system includes two charge‐coupled device image sensors, a color area image sensor, and a monochromic high‐speed line‐scan image sensor. The high‐speed line‐scan image sensor is used to capture the kymogram, and the color area image sensor is used to obtain the laryngoscopic image. The two images can be displayed simultaneously on a video monitor or stored in a standard video recorder. Three subjects with nonpathologic voice were investigated in detail with the new videokymographic system.Results: The high‐quality laryngoscopic image and kymogram can be used directly for clinical purposes with no further postprocessing. The scan position of the kymogram is always indicated in the laryngoscopic image, which provides feedback for the operator to easily locate the expected scanning position. All varieties of vocal fold vibration, including irregular vibrations, phonation onset and offset, can be observed with the presented method. The continuous kymogram of the vocal fold vibration can be retrieved from a kymographic image sequence for quantitative analysis.Conclusions: The new‐generation videokymography provides a simple, quick means to investigate vocal fold vibration, especially for voice disorders. It can emerge as an important tool for routine clinical vocal fold examination.
Neck Management in Patients Undergoing Postradiotherapy Salvage Laryngeal Surgery for Recurrent/Persistent Laryngeal Cancer
Authors: Farrag Tarik Y. , Lin Frank R. , Cummings Charles W. , Koch Wayne M. , Flint Paul W. , Califano Joseph A. , Broussard Jennifer , Bajaj Gopal , Tufano Ralph P. 
Published: September 2006

AbstractObjective: To determine a plan for the management of cervical lymph nodes in patients undergoing salvage laryngeal surgery (SLS) for recurrent/persistent laryngeal cancer after primary radiotherapy (RT).Study Design: Retrospective chart review.Methods: Charts of 51 consecutive patients who had salvage total or supracricoid laryngectomy with or without neck dissection for recurrent/persistent laryngeal squamous cell carcinoma after primary RT from 1988 to 2005 in our institution were reviewed. No patients received concomitant or neo‐adjuvant chemotherapy. Thirty‐four patients underwent SLS along with unilateral or bilateral neck dissection, whereas 17 patients underwent the SLS without neck dissection. Reports of preRT and preSLS staging of the primary tumor and the neck, recorded using the TNM system, were reviewed. Reports of the final histopathologic examination for the excised laryngeal cancer and cervical lymph nodes were reviewed.Results: Thirty‐four patients underwent SLS with unilateral or bilateral neck dissection. The preRT staging of the primary tumor for those 34 patients showed that 32 (94%) were staged T‐1 (14) and T‐2 (18), whereas the preSLS staging of the primary tumor for those 34 patients showed that 29 (85%) were staged T‐3 and T‐4. The postSLS final histopathologic examination of the excised lymph nodes in those 34 patients demonstrated that 30 (88%) did not have any evidence of nodal metastasis. On comparing patients with and without nodal metastasis (on their postSLS final histopathology), we found that the preSLS neck staging, based on computed tomographic (CT) scanning of the neck, was significantly associated with the negative/positive postSLS status of nodal metastasis (P = .006). Of 29 patients staged preSLS as N‐0, 28 (97%) patients did not have nodal metastasis on their postSLS final pathology (negative predictive value = 97%, confidence interval, 82.2–99.9). PreRT neck staging, preRT and preSLS staging of the primary tumor, along with laryngeal subsite involvement (supraglottis, glottis, subglottis) did not significantly correlate with the status of neck metastasis on final postSLS histopathology (P = .68, 0.78, 0.49, and 0.42, respectively). None of the 34 patients had any neck tumor recurrence in the postSLS follow‐up period (median, 3 yr). In addition, all 17 patients who underwent SLS without neck dissection were staged N‐0 both before RT as well as preSLS, and none developed neck disease in the postSLS follow‐up period (median, 2.5 yr).Conclusion: Management of the neck in patients undergoing salvage total or supracricoid laryngectomy for laryngeal cancer recurrence/persistence after primary RT should be based on the preSLS CT staging of the neck. Patients staged N‐0 preSLS are not likely to harbor occult nodal metastasis and therefore may not require elective neck dissection.
Contour and Paired‐Point Registration in a Model for Image‐Guided Surgery
Authors: Knott P Daniel , Batra Pete S. , Butler Robert S. , Citardi Martin J. 
Published: September 2006

AbstractObjectives/Hypothesis: This study assesses target registration error (TRE) of contour‐based registration (CBR) and paired‐point registration (PPR) for endoscopic sinus surgery.Study Design: The experimental registration model consisted of a replica of a human head (Sawbones #1345‐27; Pacific Research Laboratories, Vashon, WA). Twelve surface fiducial markers were affixed to the simulated skin on the model, and titanium screws were placed in the regions of the anterior ethmoid (AE) and sphenoid face (SF). An axial computed tomography scan (1‐mm slice thickness) was then obtained.Methods: Registration was then performed on the InstaTrak 3500 Plus (GE Surgical Navigation & Visualization, Lawrence, MA) with the standard PPR protocol with 12 points and CBR protocol with 500, 250, 125, 50, and 4 points. TRE was then calculated at the AE and SF targets.Results: Target registration error was significantly lower for paired‐point registration compared with contour‐based registration (AE, 0.5 mm vs. 1.5 mm, P < .0001; SF, 0.8 mm vs. 1.5 mm, P < .0001). Among contour‐based registration protocols, target registration error at the sphenoid face was lowest with 50 points (1.5 mm, P < .02). At the anterior ethmoid, contour‐based registration with 50 points produced a lower target registration error than contour‐based registration with 125 points (1.5 vs. 1.8 mm, P < .01). Other target registration error values for CBR were similar at both regions. The target registration error interquartile range was lowest with CBR‐125 at both regions.Conclusions: Paired‐point registration provided significantly lower target registration error. Contour‐based registration with 125 points (and possibly as few as 50 points) produces clinically acceptable target registration error. This registration model elucidates important concepts about registration for surgical navigation for sinus surgery.