bluuebunny/crossref_metadata_2025_split huggingface dataset:
FORTE: a profile–profile comparison tool for protein fold recognition
Authors: Tomii Kentaro , Akiyama Yutaka 
Published: February 2004

Abstract
Summary: We present FORTE, a profile–profile comparison tool for protein fold recognition. Users can submit a protein sequence to explore the possibilities of structural similarity existing in known structures. Results are reported via email in the form of pairwise alignments.
Availability: The server is available at http://www.cbrc.jp/forte/
GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures
Authors: Yabuki Yukimitsu , Mukai Yuri , Swindells Mark B. , Suwa Makiko 
Published: February 2004

Abstract
Summary: GENIUS II is an automated database system in which open reading frames (ORFs) in complete genomes are assigned to known protein three-dimensional (3D) structures. The system uses the multiple intermediate sequence search method in which query and target sequences are linked by intermediate sequences gathered by PSI-BLAST search. By applying the system to 129 complete genomes, 43.8% on average of the ORFs in the genomes were assigned to known 3D structures and the results are available for free at GENIUS II web site.
Availability: http://genius.cbrc.jp
Supplementary information: http://genius.cbrc.jp/summary_linking.html
Dysregulation of Hypoxia Inducible Factor‐1α in Head and Neck Squamous Cell Carcinoma Cell Lines Correlates With Invasive Potential
Authors: Cohen Noam A. , Lai Stephen Y. , Ziober Amy F. , Ziober Barry L. 
Published: February 2004

AbstractObjectives/Hypothesis Tumor hypoxia appears to be closely associated with tumor propagation, malignant progression, and resistance to radiotherapy. Hypoxia inducible factor‐1α (HIF‐1α) is a transcription factor that is upregulated under hypoxic conditions and activates hypoxic adaptation pathways which include neovascularization, erythropoiesis, and glycolysis. Hypoxia inducible factor‐1α is under tight regulation with undetectable levels of expression in normoxia and robust expression in hypoxia. Mutations that activate oncogenes or inactivate tumor suppressor genes increase the expression of HIF‐1α. Furthermore, it has been demonstrated that HIF‐1α is overexpressed in head and neck squamous cell carcinoma and that the degree of expression has predictive and prognostic significance for patients undergoing radiotherapy. The study investigated whether overexpression of HIF‐1α in head and neck squamous cell carcinoma results from a physiological response to local hypoxia or from oncogenic mutational progression.Study Design Expression of HIF‐1α under normoxic and hypoxic conditions was evaluated in cell lines derived from head and neck squamous cell carcinoma. Cell lines that were used displayed varying degrees of in vitro invasiveness.Methods Hypoxia inducible factor‐1α expression was detected by Western blot analysis. Cells were treated for 3 hours in 1% oxygen, then re‐exposed to normoxia for varying times before lysis and detection of HIF‐1α.Results Under normoxic conditions, HIF‐1α expression was upregulated in invasive cells compared with noninvasive cells, and the degradation of HIF‐1α following a hypoxic stimulus was blunted in invasive cells as compared with noninvasive cells.Conclusion The authors presented evidence that dysregulation of HIF‐1α may play a role in the malignant progression of head and neck squamous cell carcinoma. It is likely that dysregulated expression of the transcription factor HIF‐1α contributes to the invasive properties associated with hypoxia and advanced head and neck squamous cell carcinoma.
Utility of Image Guided Surgery in the Diagnosis of Pterygopalatine Fossa Lesions
Authors: Aronsohn Michael S. , Stringer Scott P. , Brown Heather M. 
Published: February 2004

AbstractObjectives To describe the utility of image guided surgery in the diagnosis of pterygopalatine fossa lesions and to discuss the varied pathologic diagnoses from this area.Study Design Case series presentation.Methods Three cases of pterygopalatine fossa lesions were accessed and biopsied by way of a middle meatus antrostomy approach into the pterygopalatine fossa under image guidance for rapid localization.Results The diagnoses of melanoma, squamous cell carcinoma, and schwannoma were obtained with minimal morbidity with image guidance. More extensive external approaches were avoided, and appropriate treatment was started without delay. The utility of the image guided approach will be discussed along with the varied pathologies encountered in the pterygopalatine fossa.Conclusions 1) One must recognize the diverse, yet related, symptoms of patients presenting with pterygopalatine fossa lesions. Early recognition as well as skull‐base imaging is crucial. 2) Biopsy, in addition to imaging, is necessary for diagnosis and may be achieved with little morbidity and increased accuracy using the image guided surgery middle meatus antrostomy approach to the pterygopalatine fossa. 3) The origin of lesions that involve the pterygopalatine fossa may be difficult to identify. Involvement of the pterygopalatine fossa by malignancy may be by contiguous spread, by way of metastasis, or by perineural invasion.
Uvulopalatoplasty (UP2): A Modified Technique for Selected Patients
Authors: Friedman Michael , Ibrahim Hani , Lowenthal Sarah , Ramakrishnan Vidyasagar , Joseph Ninos J. 
Published: February 2004

AbstractObjectivesThe goal of uvulopalatopharyngoplasty (UP3) in the treatment of obstructive sleep apnea–hypopnea syndrome (OSAHS) is to reduce obstruction by eliminating redundant tissue in three areas: the soft palate, tonsils, and pharynx. However, some OSAHS patients may present with tonsil hypertrophy and elongated soft palate without redundant pharyngeal folds. We treated this group of patients with tonsil reduction using radiofrequency coblation combined with uvulopalatoplasty (UP2) using a palatal flap technique without pharyngoplasty. Morbidity and outcome was then compared with a group of patients who underwent classic UP3.Study DesignA retrospective, nonrandomized study comparing morbidity and outcomes of the modified technique (UP2) with patients who underwent standard UP3.MethodsPatients were all staged according to the previously described Friedman staging system. Those with redundant pharyngeal folds were treated with UP3 (n = 33), and those without redundant pharyngeal folds were treated with tonsil coblation and UP2 (n = 30). Charts of patients undergoing UP2 and UP3 between July 1, 2001 and July 1, 2002 were reviewed. Thirty‐three consecutive patients who underwent UP3 were selected for study as well as 30 consecutive patients who underwent UP2. Pre‐ and postoperative quality of life questionnaires and patient questionnaires focusing on diet, pain, and return to activity were reviewed to assess subjective morbidity and elimination of symptoms. Objective measurements include preoperative and postoperative (6–18 months) polysomnography (PSG).ResultsSymptom elimination and objective PSG results were compared. There was no statistical difference in results between the UP3 group and the UP2 group. Morbidity, however, was significantly more prominent, and recovery was more prolonged, in the UP3 group. Patients undergoing UP2 had fewer pain days, less narcotic use, quicker return to solid diet, and less long‐term complaints of globus sensation.ConclusionsUP2 with tonsil coblation offers some reduction in postoperative morbidity without affecting outcome for selected patients with OSAHS. Pain levels, however, are still very significant.
Incidence of Serious Complications After Uvulopalatopharyngoplasty
Authors: Kezirian Eric J. , Weaver Edward M. , Yueh Bevan , Deyo Richard A. , Khuri Shukri F. , Daley Jennifer , Henderson William 
Published: February 2004

AbstractObjectives Uvulopalatopharyngoplasty (UPPP) is the most common surgical treatment for obstructive sleep apnea (OSA). Anatomic and physiologic abnormalities associated with OSA can make perioperative management difficult. Only single‐site case series provide current estimates of the incidence of perioperative complications, with a pooled crude serious complication rate of 3.5% and a crude mortality rate of 0.4%. The primary objective of this study was to calculate the incidence of perioperative morbidity and mortality in a large, multisite cohort of UPPP patients.Study Design Prospective cohort study of adults undergoing inpatient UPPP with or without other concurrent proceduresMethods The serious complication and 30‐day mortality rates were calculated from the Department of Veterans Affairs (VA) National Surgical Quality Improvement Program database of prospectively collected outcomes of all VA inpatient surgeries nationally 1991 to 2001. Serious complications were defined by 15 specific life‐threatening complications. Deaths were captured whether the patient was in the hospital or discharged.Results Veteran patients (n = 3130) had a mean age of 50 years and were predominantly male (97%). The serious nonfatal complication rate was 1.5% (47/3,130) (95% confidence interval [CI] 1.1%, 1.9%). The 30‐day mortality rate was 0.2% (7/3130) (95% CI 0.1%, 0.4%). There was no significant effect of year of surgery or patient age on the risk of serious complication or death.Conclusion The incidence of serious nonfatal complications and 30‐day mortality after UPPP are 1.5% and 0.2%, respectively, in a large cohort of UPPP patients at veteran hospitals.
Quantitative Analysis of Fungal DNA in Chronic Rhinosinusitis
Authors: Scheuller Michael C. , Murr Andrew H. , Goldberg Andrew N. , Mhatre Anand N. , Lalwani Anil K. 
Published: February 2004

AbstractObjectives/Hypothesis Fungi have been recognized as important pathogens in sinusitis; however, they are equally present in patients with and without sinusitis. The authors postulated that the quantity of fungal DNA in the nose is determinant of disease, is greater in patients with chronic rhinosinusitis, and is directly correlated to their quality of life.Study Design Prospective recruitment of patients with chronic rhinosinusitis.Methods Objective quality of life data were collected using three validated questionnaires: the Sinonasal Outcomes Test (SNOT‐20), Medical Outcomes Short‐Form 36 Survey (SF‐36), and Guy Marks Asthma Questionnaire (GMAQ). Endoscopically guided middle meatus mucosal samples were collected from patients with chronic rhinosinusitis and normal control subjects. Fungal‐specific polymerase chain reaction was performed on each sample. Every fungal‐positive sample underwent fungal‐specific quantitative polymerase chain reaction analysis. Statistical analysis was used to correlate fungal DNA quantities with outcomes indices between groups.Results Patients with chronic rhinosinusitis had a mean SNOT‐20 index of 32.0 as compared with a SNOT‐20 index of 17.3 (P < .01) in the normal control subjects. There were no statistical differences between the groups' indices for the SF‐36 or GMAQ outcomes questionnaires. Four of 19 (21.1%) patients with chronic rhinosinusitis and 7 of 19 (36.8%) normal control subjects had positive findings for fungal DNA using polymerase chain reaction. The median relative quantity of fungal DNA to human DNA for chronic rhinosinusitis and control samples was identical (0.13) using quantitative polymerase chain reaction.Conclusion The quantity of fungal DNA in the middle meatus did not differ in patients with and without chronic rhinosinusitis and was not correlated with quality of life outcomes. Therefore, the quantity of fungi does not explain pathogenicity in patients with chronic rhinosinusitis. However, because of small sample size, the study must be replicated in a larger patient population.
Long‐Term Results of Armstrong Beveled Grommet Tympanostomy Tubes in Children
Authors: Lindstrom D. Richard , Reuben Brian , Jacobson Ken , Flanary Valerie A. , Kerschner Joseph E. 
Published: February 2004

AbstractObjective Many different tympanostomy tubes have been developed with different sizes, shapes, compositions, and coatings. Despite the frequency of ventilation tube placement, very few large studies have examined the outcomes of patients receiving this procedure. An ideal tube would be easy to insert and would extrude at a predictable interval without complications. This study was performed to assess outcome measures and complication rates of the Armstrong beveled grommet tube.Design A retrospective case series of patients who had Armstrong beveled grommet tympanostomy tubes placed over a 3 year period by two Children's Hospital of Wisconsin pediatric Otolaryngology staff.Main Outcome Measures Patient age, diagnosis, operative findings, and time to tube extrusion were reviewed. Otorrhea, perforation, and cholesteatoma rates were also assessed.Results Five hundred seven consecutive patients who had Armstrong tubes placed were reviewed. One thousand ninety‐six Armstrong tubes were placed in these patients. Follow‐up to extrusion rates were available for 756 tubes. The mean patient age at tube placement was 33.3 months, and the median age was 23 months. Mean and median times to extrusion were 16.5 and 15.5 months. One hundred sixty episodes of otorrhea were noted in 148 patients. Four patients had histories of cholesteatoma, none of which developed in conjunction with Armstrong tubes. Ten (1.32%) perforations that have not resolved over time were noted after Armstrong tube placement.Conclusions Armstrong beveled grommet tympanostomy tubes have complication rates comparable with those reported for Armstrong or other short‐acting tubes in smaller series.
High‐Frequency Pulsed Electromagnetic Energy in Tinnitus Treatment
Authors: Ghossaini Soha N. , Spitzer Jaclyn B. , Mackins Cynthia C. , Zschommler Anne , Diamond Beverly E. , Wazen Jack J. 
Published: February 2004

AbstractObjectives/Hypothesis Electromagnetic therapy has been used with reported success in multiple clinical settings, including the treatment of seizure disorders, brain edema, migraine headaches, revascularization of burn wounds, and diabetic ulcers. The purpose of the study was to investigate the effect of pulsed high‐frequency electromagnetic therapy on chronic tinnitus.Study Design A randomized, prospective, double‐blind, placebo‐controlled pilot study was conducted to evaluate the effectiveness of high‐frequency pulsed electromagnetic energy using the Diapulse device in the treatment of chronic tinnitus. Thirty‐seven adult patients with chronic tinnitus of at least 6 months' duration were recruited and randomly assigned to either a treatment or a placebo group.Methods Patients received 30‐minute treatments with the Diapulse device three times a week for 1 month. The unit was set to deliver electromagnetic energy at a frequency of 27.12 MHz at a repetition rate of 600 pulses per second. All subjects had pretreatment and post‐treatment audiological testing, including tinnitus frequency and intensity matching. They responded to a tinnitus rating questionnaire and the Tinnitus Handicap Inventory before and after treatment.Results There was no significant change in the pretreatment and post‐treatment audiometric thresholds in either group. There were no significant differences between the pretreatment and post‐treatment Tinnitus Handicap Inventory scores or the tinnitus rating scores in either subject group (Student t test). No diagnosis‐specific differences were identified.Conclusion High‐frequency pulsed electromagnetic energy (Diapulse) at the settings used in the study showed no role in the therapy of patients with chronic tinnitus.
Impact of Mastoidectomy on Simple Tympanic Membrane Perforation Repair
Authors: McGrew Benjamin M. , Jackson C. Gary , Glasscock Michael E. 
Published: February 2004

AbstractObjectives/Hypothesis Mastoidectomy has long been identified as an effective method of treatment for chronic ear infection. The effect of mastoidectomy on patients without evidence of active infectious disease remains highly debated and unproven. The objective in the study was to examine the impact of mastoidectomy on the repair of uncomplicated tympanic membrane perforations.Study Design Retrospective study of patients at tertiary referral center.Methods Four hundred eighty‐four patients who underwent surgical repair of simple tympanic membrane perforations were identified and reviewed in a retrospective manner. Simple tympanic membrane perforations were defined as tympanic membrane perforations of any size and location without any of the following confounding variables: 1) active infection (active otorrhea, abnormal middle ear mucosa, or granulations tissue); 2) ossicular abnormalities (ossicular fixation, ossicular discontinuity, ossicular malformation, or ossicular absence); 3) cholesteatoma; or 4) prior attempt at tympanic membrane repair (prior tympanoplasty or mastoidectomy). Surgical outcome and clinical course were assessed to compare results of tympanic membrane perforation repair with and without canal wall up mastoidectomy.Results Tympanic membrane repair was equally effective in both groups at 91%. Hearing results were comparable. Development of persistent ipsilateral otological disease requiring a subsequent ipsilateral procedure was approximately twice as common in the tympanoplasty group. In the tympanoplasty group, 14.1% of patients underwent subsequent ipsilateral otological procedures, and 6.1% of patients in the tympanoplasty with mastoidectomy intact canal wall group underwent subsequent ipsilateral procedures (P < .05). The most common subsequent ipsilateral procedures were tympanoplasty, tympanostomy tube placement, tympanoplasty with mastoidectomy canal wall up, and tympanoplasty with mastoidectomy canal wall down, in that order. After including untreated tympanic membrane perforations as subsequent procedures, the adjusted rate of subsequent procedures was 15.5% in the tympanoplasty group and 12.2% in the tympanoplasty with mastoidectomy group (P > .05).Conclusion Mastoidectomy was not necessary for successful repair of simple tympanic membrane perforations. However, mastoidectomy impacted the clinical course in patients by reducing the number of patients requiring future procedures and by decreasing disease progression. This suggests that even in the absence of active evidence of infection, mastoidectomy improved the underlying disease process. Combining mastoidectomy with tympanoplasty during repair of simple perforations in patients with no active evidence of infection remains an appropriate option and may be valuable in reducing the need for future surgery.
Carbon Dioxide Laser Endoscopic Diverticulotomy Versus Open Diverticulectomy for Zenker's Diverticulum
Authors: Chang C. W. David , Burkey Brian B. , Netterville James L. , Courey Mark S. , Garrett C. Gaelyn , Bayles Stephen W. 
Published: February 2004

AbstractObjectives/Hypothesis To compare open and CO2 laser–assisted endoscopic surgical management of Zenker's diverticulum.Study Design A retrospective review of 49 consecutive surgically treated patients with Zenker's diverticulum was conducted.Methods Patients' records were reviewed and analyzed for patient age and sex, size of diverticulum, incision time (time recorded from start of incision to surgical completion of case), length of hospital stay, complications, and follow‐up management. A postoperative questionnaire inquiring about swallow function was conducted by mail or telephone. Swallow function was assessed on a four‐point scale.Results Various procedures performed included endoscopic CO2 laser–assisted diverticulotomy (n = 24) and open diverticulectomy with cricopharyngeal myotomy (n = 28). The average incision time of laser endoscopic cases (47 min) was significantly shorter (P < .001) than that of open diverticulectomy cases (170 min). Length of hospital stay did not significantly vary between the two groups. Five patients (21%) initially treated with laser endoscopic diverticulotomy demonstrated symptomatic persistent Zenker's diverticulum; three underwent repeat operation. No open cases required repeat operation. One endoscopic case was aborted secondary to esophageal injury from placement of the endoscope. Postoperative fever was seen in two (8%) endoscopic cases and four (14%) open approach cases. No major complications (recurrent laryngeal nerve paralysis, mediastinitis, or death) were encountered. More than 90% of respondents in each treatment group reported normal or near‐normal swallow function.Conclusion Laser endoscopic management is a reasonable and safe method for surgical treatment of Zenker's diverticulum in comparison with the open technique. Employment of the endoscopic approach reduces operative time and the complexity of postoperative care. Practitioners should be aware that the endoscopic approach may result in a higher failure rate.
Endoscopic Transnasal Transpterygopalatine Fossa Approach to the Lateral Recess of the Sphenoid Sinus
Authors: Al‐Nashar Ismail S. , Carrau Ricardo L. , Herrera Alfredo , Snyderman Carl H. 
Published: February 2004

AbstractObjectives Lesions affecting the lateral recess of the sphenoid sinus are rarely discussed in the literature as a separate entity. This region is difficult to visualize and manipulate through the transnasal routes, especially when extensive pneumatization is present. External approaches to this area involve extensive surgery and are associated with significant morbidity. The objectives of this study are to present our experience with the endoscopic transpterygopalatine fossa approach as a method for exposing and manipulating lesions of the lateral recess of the sphenoid and to illustrate the detailed surgical steps of the procedure.Study Design Retrospective review.Methods Clinical charts of patients who had lesions originating from or extending into the lateral recess of the sphenoid sinus and who were treated at our institutions from September 1995 to June 2002 were retrospectively reviewed. All these patients were managed by the endoscopic transpterygopalatine fossa approach.Results Twelve patients (7 males and 5 females) were included in the study. Lesions included seven cerebrospinal fluid (CSF) leaks and five tumors. One patient with squamous cell carcinoma (SCC) of the sphenoid died of his disease. All CSF leaks were successfully repaired, and benign tumors were removed with good local control through the follow‐up period.Conclusion The endoscopic transpterygopalatine fossa approach is an excellent approach for dealing with lesions of the sphenoid lateral recess.