bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the dynamics of Ebola epidemics
Authors: LEGRAND J. , GRAIS R. F. , BOELLE P. Y. , VALLERON A. J. , FLAHAULT A. 
Published: September 2006

SUMMARYEbola is a highly lethal virus, which has caused at least 14 confirmed outbreaks in Africa between 1976 and 2006. Using data from two epidemics [in Democratic Republic of Congo (DRC) in 1995 and in Uganda in 2000], we built a mathematical model for the spread of Ebola haemorrhagic fever epidemics taking into account transmission in different epidemiological settings. We estimated the basic reproduction number (R0) to be 2·7 (95% CI 1·9–2·8) for the 1995 epidemic in DRC, and 2·7 (95% CI 2·5–4·1) for the 2000 epidemic in Uganda. For each epidemic, we quantified transmission in different settings (illness in the community, hospitalization, and traditional burial) and simulated various epidemic scenarios to explore the impact of control interventions on a potential epidemic. A key parameter was the rapid institution of control measures. For both epidemic profiles identified, increasing hospitalization rate reduced the predicted epidemic size.
Analysis of clonal relationship amongShigella sonneiisolates circulating in Argentina
Authors: PICHEL M. , GONZÁLEZ FRAGA S. , TERRAGNO R. , MULKI J. , GENTILE A. , KREMER C. , MOLA A. M. , NOSEDA R. , BINSZTEIN N. 
Published: September 2006

SUMMARYThirty-five isolates ofShigella sonneifrom patients with diarrhoea in three geographic regions of Argentina were examined for genetic diversity by pulsed-field gel electrophoresis (PFGE) and plasmid profile. PFGE ofXbaI andBlnI DNA digests confirmed the occurrence of outbreaks in two regions caused by two separate predominant clones ofS. sonnei. The third region was characterized by three circulating clones, one of which was possibly associated with an outbreak. Similar plasmids were found in distinct clones and in one outbreak clone five different plasmid profiles were identified. Antimicrobial resistance of the isolates varied from fully susceptible to the agents tested, to resistance to cotrimoxazole, ampicillin and ciprofloxacin. Antibiotic resistance did not correlate with plasmid content. This information will form the basis for active surveillance of shigellosis in Argentina and elsewhere in the region through the PulseNet International Network.
PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
Authors: Xie Xudong , Wu Shuanhu , Lam Kin-Man , Yan Hong 
Published: September 2006

Abstract
Motivation: Promoter prediction is important for the analysis of gene regulations. Although a number of promoter prediction algorithms have been reported in literature, significant improvement in prediction accuracy remains a challenge. In this paper, an effective promoter identification algorithm, which is called PromoterExplorer, is proposed. In our approach, we analyze the different roles of various features, that is, local distribution of pentamers, positional CpG island features and digitized DNA sequence, and then combine them to build a high-dimensional input vector. A cascade AdaBoost-based learning procedure is adopted to select the most ‘informative’ or ‘discriminating’ features to build a sequence of weak classifiers, which are combined to form a strong classifier so as to achieve a better performance. The cascade structure used for identification can also reduce the false positive.
Results: PromoterExplorer is tested based on large-scale DNA sequences from different databases, including the EPD, DBTSS, GenBank and human chromosome 22. Experimental results show that consistent and promising performance can be achieved.
Contact: h.yan@cityu.edu.hk
GATHER: a systems approach to interpreting genomic signatures
Authors: Chang Jeffrey T. , Nevins Joseph R. 
Published: September 2006

Abstract
Motivation: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays.
Results: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses.
Availability: GATHER is available at
Contact: j.nevins@duke.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
Authors: Selivanov Vitaly A. , Marin Silvia , Lee Paul W. N. , Cascante Marta 
Published: September 2006

Abstract
Motivation: Metabolic flux analysis of biochemical reaction networks using isotope tracers requires software tools that can analyze the dynamics of isotopic isomer (isotopomer) accumulation in metabolites and reveal the underlying kinetic mechanisms of metabolism regulation. Since existing tools are restricted by the isotopic steady state and remain disconnected from the underlying kinetic mechanisms, we have recently developed a novel approach for the analysis of tracer-based metabolomic data that meets these requirements. The present contribution describes the last step of this development: implementation of (i) the algorithms for the determination of the kinetic parameters and respective metabolic fluxes consistent with the experimental data and (ii) statistical analysis of both fluxes and parameters, thereby lending it a practical application.
Results: The C++ applications package for dynamic isotopomer distribution data analysis was supplemented by (i) five distinct methods for resolving a large system of differential equations; (ii) the ‘simulated annealing’ algorithm adopted to estimate the set of parameters and metabolic fluxes, which corresponds to the global minimum of the difference between the computed and measured isotopomer distributions; and (iii) the algorithms for statistical analysis of the estimated parameters and fluxes, which use the covariance matrix evaluation, as well as Monte Carlo simulations.
An example of using this tool for the analysis of 13C distribution in the metabolites of glucose degradation pathways has demonstrated the evaluation of optimal set of parameters and fluxes consistent with the experimental pattern, their range and statistical significance, and also the advantages of using dynamic rather than the usual steady-state method of analysis.
Availability: Software is available free from
Contact: martacascante@ub.edu
A Paranasal Tumor Associated With Tumor‐Induced Osteomalacia
Authors: Inokuchi Go , Tanimoto Hitoshi , Ishida Haruhiko , Sugimoto Toshitsugu , Yamauchi Mika , Miyauchi Akimitsu , Nibu Ken‐ichi 
Published: September 2006

AbstractBackground: Tumor‐induced osteomalacia (TIO) is an extremely rare paraneoplastic syndrome associated with mesenchymal tumors in the craniofacial region.Methods: We treated a 24‐year‐old Japanese woman with paranasal sinus tumor and a low serum phosphate level who presented with nasal obstruction and systemic bone fractures. Serum fibroblast growth factor 23 (FGF‐23) was measured before and after surgery.Results: After surgery, her symptoms were resolved and the serum phosphate and FGF‐23 levels became normalized.Conclusion: FGF‐23 is thought to be a useful diagnostic marker in patients with craniofacial tumors associated with multiple systemic fractures.
Risk Acceptance in Laryngeal Transplantation
Authors: Reynolds Christopher C. , Martinez Serge A. , Furr Allen , Cunningham Michael , Bumpous Jeffrey M. , Lentsch Eric J. , Banis Joseph C. , Vasilic Dalibor , Storey Barckley , Wiggins Osborne , Maldonado Claudio , Perez‐Abadia Gustavo , Barker John H. 
Published: September 2006

AbstractPurpose: Advancements in the fields of head and neck surgery and immunology have paved the way for new quality of life‐improving procedures such as larynx transplantation. To quantitatively assess the risks versus benefits in larynx transplantation, we used a questionnaire‐based survey (Louisville Instrument For Transplantation [LIFT]) to measure the degree of risk individuals are willing to accept to receive different types of transplantation procedures.Methods: The LIFT contains 237 standardized questions incorporating standard gamble and time tradeoff outcome measures as well as questions assessing body image perception, depression, self‐esteem, optimism, socially desirable responding, and demographics. Respondents were questioned on the extent to which they would trade off specific numbers of life‐years, or sustain other costs, in exchange for receiving seven different types of transplant procedures. For this study, we questioned 243 individuals in three study populations with differing life experiences: healthy individuals, organ transplant recipients, and laryngectomees.Results: All populations questioned perceived risks differently based on their varied life experiences and would accept differing degrees of risk for the different transplant procedures. Organ transplant recipients were the most risk‐tolerant group, whereas laryngectomees were the least risk‐tolerant.Conclusions: By questioning individuals with life experiences directly relevant to the risks and benefits associated with larynx transplantation, this study provides an empiric basis for assessing risk versus benefit in this new quality of life‐improving procedure.
Fluorescent Retrograde Axonal Tracing of the Facial Nerve
Authors: O'Malley Matthew R. , Wittkopf Justin E. , Cutler Jeffrey L. , Labadie Robert F. , Hackett Troy A. , Haynes David S. 
Published: September 2006

AbstractObjective: The objective of this study was to investigate retrograde fluorescent axonal labeling of motor nerves as an aid to surgical dissection in otolaryngology–head and neck surgery.Methods: Cholera toxin B subunit conjugated to a fluorescent dye was injected into the facial musculature of New Zealand white rabbits. At variable time points after injection, the facial nerves were harvested and analyzed for fluorescence in the peripheral axon.Results: All injected animals demonstrated axonal fluorescence. No animal demonstrated facial weakness. Fluorescence was detected a maximum of 20 mm from the distal end of the nerve. Time periods greater than 48 hours did not substantially increase transport distance.Conclusions: Cholera toxin B subunit fluorescent conjugates, when administered intramuscularly, reliably label the distal portion of the facial nerve. In vivo labeling of a motor nerve may have significant potential for identifying a nerve in surgery. This work represents a preliminary investigation into the adaptation of in vivo fluorescence techniques as an aid to surgical dissection. Further research to refine this technique should be supported.
Surgical Treatment of Chronic Recurrent Rhinosinusitis: A Preliminary Report
Authors: Bhattacharyya Neil 
Published: September 2006

AbstractObjective: The objective of this study was to determine if endoscopic sinus surgery (ESS) is effective in the management of chronic recurrent rhinosinusitis (CRRS).Methods: A consecutive series of patients with CRRS diagnosed according to stringent criteria was prospectively examined before and at least 1 year after ESS. Paranasal sinus computed tomography scans were staged and ESS was performed targeting radiographic disease and the ostiomeatal complex. Preoperative and postoperative disease severities in terms of symptom scores, medicine utilization, and resource factors were assessed using the rhinosinusitis symptom inventory (RSI). Improvements in RSI symptom domains, medical and economic resource factors were determined using effect sizes and statistical comparison before and after ESS.Results: Nineteen patients (mean age, 42.3 years) completed the study with a mean follow up of 19.1 months. The mean Lund score was 3.42 (standard deviation, 4.09). Statistically significant decreases in nasal (−36.1), facial (−28.4), oropharyngeal (−34.6), systemic (−24.7), and total (−31.9) RSI symptom domain scores were observed (all P < .003) with effect sizes ranging from 0.87 to 1.63 (strong surgical effect). Statistically significant decreases in antihistamine use (−30%, P = .031), number of workdays missed as a result of CRRS (−1.9, P = .035), and number of acute infectious episodes (−2.5, P = .006) were also observed. However, declines in weeks of antibiotic use (−2.8 weeks, P = .293) and number of antibiotic courses (−1.7, P = .118) were not significant.Conclusions: Patients with CRRS may substantially benefit both symptomatically and medically from ESS. Although surgery should be used cautiously in treating CRRS, further trials of ESS for CRRS are warranted.
Useful Landmarks in Arytenoid Adduction and Laryngeal Reinnervation Surgery
Authors: Armin Bob B. , Head Christian , Berke Gerald S. , Chhetri Dinesh K. 
Published: September 2006

AbstractObjective: Knowledge of the location of the muscular process of the arytenoid cartilage and the recurrent laryngeal nerve is essential to performing a successful arytenoid adduction and laryngeal reinnervation surgery. We describe external landmarks useful in locating these structures.Study Design: Cadaveric laryngeal dissection.Methods: Posterior laryngeal dissection was performed in 16 human larynges. The position of the muscular process of the arytenoid was measured bilaterally relative to the inferior and superior borders of the thyroid lamina. The recurrent laryngeal nerve was followed distally from slightly below the level of the cricothyroid joint to its genu where its vertical course changes to an oblique intralaryngeal course.Results: The muscular process of the arytenoid was usually found halfway between the roots of the superior and inferior cornu of the thyroid lamina. The recurrent laryngeal nerve was found just deep to the cricothyroid joint and lateral to the posterior cricoarytenoid muscle. There were no other nerves in this area.Conclusions: This study finds that the superior and inferior borders of the thyroid lamina are useful intraoperative landmarks to locate the muscular process of the arytenoid. The cricothyroid joint provides a good starting point to locate the recurrent laryngeal nerve, which can be identified slightly deeper between it and the posterior cricoarytenoid muscle.
Analysis of the Long‐Term Hearing Results after the Surgical Repair of Aural Atresia
Authors: Chang Sun O. , Choi Byung Yoon , Hur Dong Gu 
Published: September 2006

AbstractObjectives: Careful surgical candidate selection guarantees a high probability of serviceable hearing postoperatively in congenital aural atresia (CAA) patients. The authors analyzed hearing results after CAA surgery with long‐term follow‐up (F/U) with respect to several clinical factors.Study Design: This was a retrospective study.Methods: The medical records of 93 CAA patients (100 ears) who underwent operations from January 1987 through December 2002 at Seoul National University Hospital were reviewed. Mean duration was 56.9 months. The authors evaluated the results of hearing after surgery over 3 year F/U with a view to clarifying the factors accounting for unsuccessful results.Results: Approximately 64% of patients treated surgically achieved a considerable hearing gain over long‐term F/U. Postoperative hearing remained relatively stable over the period from 6 months to 3 years postoperatively, yielding only 2.75 dB of aggravation. However, hearing results in revision cases deteriorated with time, which led to statistically higher air‐conduction thresholds than those of primary cases at the 1 and 3 year F/Us. Resultantly, only 26.6% of patients having achieved a poor hearing gain post first surgery benefited from revision audiologically. The severity of microtia was found to help predict poor long‐term hearing outcomes after CAA surgery.Conclusions: Nonrevision cases and cases with mild microtia appear to have acceptable and stable long‐term hearing results. Disappointing long‐term hearing results in revision, and severe microtia cases should lead to considerations of alternative options in these cases, such as bone‐anchored hearing aids, which offer reliable and stable results.
Chemopreventive Effect of Celecoxib in Oral Precancers and Cancers
Authors: Feng Lining , Wang Zhi 
Published: September 2006

AbstractObjectives: Oral cancer has become an important health care problem in many countries. Because this disease develops slowly, early detection and intervention can greatly affect ultimate outcome. Celecoxib is a cyclooxygenase‐2 inhibitor with significantly less toxicity. This study investigated the possibility of using it for chemoprevention of oral cancer at the early stages.Study Design: Randomized animal study.Methods: Dysplastic lesions were induced in the buccal pouches of 47 hamsters by a 5 week painting of 9,10‐dimethl‐1,2‐benzanthrancene (DMBA). Basal diets or diets containing 500 or 1,500 ppm of Celecoxib were orally given for 7 weeks. The T50 (50% incidence; i.e., the time to appearance of tumors in 50% of the hamsters) was observed, and volume of tumors was measured on day 1, 9, 19, 28, 35, and 48 with the Celecoxib treatment.Results: The T50 was 9, 19, and 28 days with the treatment in the control group, in the 500 ppm group, and in the 1,500 ppm group, respectively. It indicated that the Celecoxib treatment could delay progression of early lesion. The tumor measurement showed that this treatment was also effective in delaying tumor growth in both treatment groups. There was a difference in the treatment efficacy between the 500 ppm and 1,500 ppm of Celecoxib, indicating a dose‐dependent efficacy.Conclusions: Celecoxib is effective in delaying onset of early lesions induced by DMBA and in slowing growth of the tumors in hamster cheek pouches during the postinitiation stage. Its treatment efficacy appears to be dose dependent.
Age‐Dependent Degeneration of the Stria Vascularis in Human Cochleae
Authors: Suzuki Teruhisa , Nomoto Yukio , Nakagawa Takayuki , Kuwahata Naofumi , Ogawa Hiroshi , Suzuki Yukie , Ito Juichi , Omori Koichi 
Published: September 2006

AbstractObjective: Aging is a common cause of acquired hearing impairments. This study investigated age‐related morphologic changes in human cochleae, with a particular focus on degeneration of the stria vascularis (SV) and the spiral ganglion (SG).Study Design: Retrospective case review.Methods: The study group comprised 91 temporal bones from individuals aged 10 to 85 years who had no history or audiometric findings suggestive of specific causes of cochlear degeneration. We quantified the SV and SG atrophy at each cochlear turn using morphometric measurements. Correlations of the SV and SG atrophy with age, audiometric patterns of hearing loss, and auditory thresholds were statistically investigated.Result: The SV and the SG both showed a tendency for progressive atrophy to develop with age. However, statistically significant correlations were observed between aging and SV atrophy only in the apical and basal cochlear turns. These findings were consistent with those reported previously in gerbils. No significant correlations were detected between SV or SG atrophy and audiometric findings.Conclusion: SV atrophy appears to be the most prominent anatomic characteristic of aged human cochleae.
Sensorineural Hearing Loss in Vogt‐Koyanagi‐Harada Syndrome
Authors: Ondrey Frank G. , Moldestad Eric , Mastroianni Mary Ann , Pikus Anita , Sklare Daniel , Vernon Estelle , Nusenblatt Robert , Smith Janine 
Published: September 2006

AbstractBackground: Vogt‐Koyanagi‐Harada (VKH) syndrome is a systemic condition characterized by ocular inflammatory disease as well as skin, ear, and meningeal manifestations. Patients with VKH often report tinnitus and hearing loss, but these symptoms tend to be given secondary consideration because most undergo treatment with steroids to prevent blindness resulting from granulomatous uveitis, exudative retinal detachment, and optic nerve inflammation.Methods/Study Design: In the current retrospective review, 24 patients with this syndrome were screened for auditory system abnormalities. All patients denied history of noise exposure or ototoxic agent exposure. The age range of the patients was 13 to 42 years.Results: Three patients reported tinnitus and two patients reported sudden hearing loss. One patient experienced vertigo and aural fullness. Eight of 24 patients had pure‐tone thresholds greater than 25 dB hearing loss at two or more frequencies. Five of 24 of these patients experienced hearing loss outside of the 95% confidence interval for published age‐matched control populations. There was sloping sensorineural hearing loss at 4 kHz and above in five of 24 patients. All eight patients with hearing loss experienced some degree of hearing loss at 4 kHz or above. Three patients had mild to moderate low‐frequency sensorineural hearing loss. There were no tympanometric abnormalities suggestive of conductive involvement. Abnormal acoustic reflex decay was observed in one patient.Conclusions: We conclude that a significant number of patients with VKH experience sensorineural hearing loss and that every patient with VKH should undergo a review of systems for auditory abnormalities and referral for audiologic testing if symptomatic. It is possible that untreated patients may experience worse symptoms.
The Efficacy of Mitomycin‐C in the Treatment of Laryngotracheal Stenosis
Authors: Simpson C Blake , James Joshua C. 
Published: September 2006

AbstractObjective: The purpose of this study is to evaluate whether the addition of topical mitomycin‐C (MMC) application to the wound site after endoscopic treatment of laryngotracheal stenosis (LTS) resulted in measurable improvement in clinical outcomes.Study Design and Setting: A retrospective chart review of patients with LTS treated by the senior author over a 6‐year period was performed. The treatment groups were stratified into two main categories: 1) endoscopic treatment alone and 2) endoscopic treatment + topical MMC. The “symptom‐free” interval was determined (in months) for each subject using a two‐tailed t test for statistical analysis of the control/study groups.Results: Sixty‐seven procedures were performed in 36 patients with LTS with a mean of 1.86 surgical treatments per patient. The mean duration of the symptom‐free interval after endoscopic treatment for LTS was 4.9 months in the endoscopic‐only treatment group and 23.2 months in the endoscopic group receiving topical MMC. The symptom‐free interval observed in the MMC group was significantly longer than the control subjects (P = 1 × 10−11).Conclusions: The results of this study suggest that MMC is an effective adjuvant in the treatment of LTS. The results of this study provide strong supporting evidence that topical MMC is an effective adjuvant in the treatment of LTS.