bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying multiple alignment regions satisfying simple formulas and patterns
Authors: Stojanovic Nikola , Dewar Ken 
Published: March 2004

Abstract
Motivation: When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but researchers may also be interested in quantifying the frequency of occurrences of certain patterns.
Results: We have developed a program that applies simple formulas and pattern specifications to multiple alignments, reporting the positions and counts of conforming regions. As an example, we have navigated a 15-species alignment of the CAV2–CAV1 region and outlined some findings regarding PPARγ binding sites.
Availability: Our software and the accompanying documentation can be obtained at no charge by contacting the authors. It can also be accessed at http://ranger.uta.edu/~nick/compgen
Major Histocompatibility Gene Therapy: The Importance of Haplotype and β2‐Microglobulin
Authors: Salamone Frank N. , Gleich Lyon L. , Li Ya‐Qin , Stambrook Peter J. 
Published: March 2004

AbstractObjectives/Hypothesis Alloantigen gene therapy with the genes for the Class I major histocompatibility complex (MHC) HLA‐B7 and β2‐microglobulin in HLA‐B7–negative patients has potential efficacy in the treatment of head and neck cancer, although the mechanism of response is unclear. Whether tumor regression is due to a response to HLA‐B7 in HLA‐B7–negative patients (i.e., due to “foreign” antigen) or simply to MHC overexpression is unknown. Therefore, a mouse model was used to compare tumor growth following syngeneic MHC transfection to alloantigenic MHC transfection. The importance of the β2‐microglobulin gene was also evaluated.Study Design Prospective animal study.Methods The head and neck cancer cell line SCC‐VII that grows in immunocompetent C3H mice, which are MHC haplotype H2‐Kk, was used. Stable transfections were made with H2‐Kb, H2‐Kk, and β2‐microglobulin in the SCC‐VII cells. To test the importance of MHC “foreignness,” mice were injected with SCC‐VII cells, SCC‐VII plus H2‐Kb plus β2‐microglobulin transfected cells, and SCC‐VII plus H2‐Kk plus β2‐microglobulin transfected cells. To evaluate β2‐microglobulin, mice were injected with SCC‐VII cells, SCC‐VII plus H2‐Kb plus β2‐microglobulin transfected cells, SCC‐VII plusH2‐Kb transfected cells, and SCC‐VII plus β2‐microglobulin transfected cells. Tumor growth in all groups was compared statistically.Results Major histocompatibility complex foreignness was a part of the antitumor response. Foreign MHC routinely abrogated tumor growth, whereas syngeneic MHC only slowed tumor growth. β2‐microglobulin aided the MHC tumor inhibition but did not inhibit tumor without the MHC.Conclusion The antitumor response was greater when the MHC gene used was foreign. β2‐microglobulin increased the efficacy of MHC gene therapy. Both of these findings are important when designing clinical trials of immunologically based gene therapies for head and neck cancer.
Cochlear Changes in Chronic Otitis Media
Authors: Cureoglu Sebahattin , Schachern Patricia A. , Paparella Michael M. , Lindgren Bruce R. 
Published: March 2004

AbstractObjectives/Hypothesis The objective was to describe the morphological changes in the cochlea in chronic otitis media.Study Design Retrospective human temporal bone analysis.Methods Fifteen temporal bones with unilateral chronic otitis media were selected and compared with contralateral normal temporal bones. Standard cytocochleograms and spiral ganglion cell reconstructions were performed on all temporal bones. Spiral ligament was divided into four segments according to the locations of different types of fibrocytes. The average loss of fibrocytes in each segment was estimated. Morphometric measurements of areas of stria vascularis and spiral ligament were made in all turns of the cochlea on mid modiolar sections.Results Loss of outer and inner hair cells was common in the basal turn of the cochlea in temporal bones with chronic otitis media compared with control ears. There was no difference in the number of spiral ganglion cells in the chronic otitis media and contralateral ears. The areas of stria vascularis and spiral ligament in the basal turn decreased significantly in the ears with chronic otitis media compared with control ears. There were no significant differences between the ears with chronic otitis media and the contralateral ears for any of the regions characterized by the presence of types I–IV fibrocytes.Conclusion The results of the study are consistent with the hypothesis that chronic otitis media causes cochlear disease.
Chemokine RANTES Promoter Polymorphisms in Allergic Rhinitis
Authors: Kim Jeong Joong , Lee Jung Hun , Jang Chul Ho , Kim Yong Shin , Chae Soo Cheon , Chung Hun Taeg , Choi Tae Wook , Lee Jae Hoon 
Published: March 2004

AbstractObjectives/Hypothesis RANTES is one of the most widely studied of the chemokines linked to allergic diseases. Two polymorphisms of the RANTES promoter region (–403 G/A and –28 C/G) have been found. The authors investigated whether these RANTES promoter polymorphisms were associated with allergic rhinitis.Study Design Case‐control study.Methods Blood samples for genetic analysis were obtained from 151 individuals with allergic rhinitis and from 278 healthy individuals without atopic disease. Polymerase chain reaction–based assays for detection of the –403 G/A and –28 C/G polymorphisms of the RANTES gene were used for genotyping.Results The frequencies of both the RANTES –403A and –28G alleles were significantly higher in patients with allergic rhinitis than in control subjects (P < .05 for both).Conclusion The study results indicated that the –403 and –28 alleles in the RANTES promoter region belong to the predictor gene set for allergic rhinitis and could be used in genomic analysis.
Inner Ear Changes With Intracochlear Gentamicin Administration in Guinea Pigs
Authors: Okuda Takeshi , Sugahara Kazuma , Shimogori Hiroaki , Yamashita Hiroshi 
Published: March 2004

AbstractObjectives/Hypothesis Transtympanic administration of gentamicin is reported to be a useful treatment for vertigo in such conditions as Meniere's disease, and determining appropriate clinical dosage of gentamicin is difficult. The authors examined the relation between gentamicin dosages and inner ear function in guinea pigs.Study Design This study is a basic science project designed to examine cochlear and vestibular function in animal models.Methods Various concentrations of gentamicin solution were infused into the right inner ear of guinea pigs by osmotic pumps. Caloric nystagmus as a marker of vestibular function and the change in auditory brainstem response (ABR) threshold as a marker of cochlear function were observed.Results After 14 days of treatment, high gentamicin concentrations of 40 mg/mL caused canal paralysis and a rapid shift in ABR threshold. Animals exposed to low gentamicin concentrations of 4 mg/mL showed no obvious change in either vestibular or cochlear function. Animals exposed to moderate gentamicin concentrations of 12 mg/mL showed a moderate shift in ABR threshold and caloric malfunction. Histopathological examination revealed that after 14 days of treatment with 40 mg/mL gentamicin, severe cytoplasmic damage occurred in both vestibular and cochlear end organs. In animals treated with 12 mg/mL gentamicin, hair cells remained in the cochlear third turn and ampulla of the lateral semicircular canal.Conclusion The authors established an animal model that showed the moderate damage of inner ear with moderate‐dose gentamicin. The study results indicated that the appropriate administration of gentamicin could establish a stable effect on the inner ear. It may be important to select the protocol that delivers a stable dosage of gentamicin to treat patients with Meniere's disease safely and effectively.
p53‐Positive Tumor‐Distant Squamous Epithelia of the Head and Neck Reveal Selective Loss of Chromosome 17
Authors: Wolf Christina , Flechtenmacher Christa , Dietz Andreas , Weidauer Hagen , Abel Ulrich , Maier Heinz , Bosch Franz X. 
Published: March 2004

AbstractObjectives/Hypothesis The progression of clinically manifest premalignant lesions in the head and neck region to primary or second primary cancer is characterized by numerical and structural chromosomal aberrations. However, many tumors arise from histologically inconspicuous mucosal sites. The objective was to investigate whether chromosomal aberrations can be detected in tumor‐distant mucosa and whether they can help predict the risk of second primary malignancy.Study Design A retrospective series of 72 clinically healthy, arbitrarily taken mucosal samples from 53 patients with squamous cell carcinoma of the head and neck was studied. A previous analysis of the p53 protein status had revealed both p53‐positive and p53‐negative samples.Methods The samples were analyzed by fluorescence in situ hybridization (FISH) using centromeric probes specific for the chromosomes 1, 10, 17, and 18.Results Tumor‐distant mucosa generally showed increased numerical chromosomal aberrations, which consisted mainly of monosomies. In the group of patients with p53‐positive epithelia, all aberrations including gains of chromosomes (trisomies, tetrasomies) were more frequent. Monosomy for chromosome 17 was most significantly and selectively enhanced in this group (Wilcoxon Scores [rank sum] test, P = .0002).Conclusion Detectable chromosomal aberrations occur in clinically healthy epithelia in patients at risk for secondary head and neck cancer. Specifically, unbalanced chromosome 17 monosomy in conjunction with p53 protein overexpression may constitute a valuable biomarker for progressive “field cancerization.”
Therapy for Acute Nonpurulent Rhinosinusitis With Cineole: Results of a Double‐Blind, Randomized, Placebo‐Controlled Trial
Authors: Kehrl Wolfgang , Sonnemann Uwe , Dethlefsen Uwe 
Published: March 2004

AbstractObjectives/Hypothesis Nonpurulent rhinosinusitis can be treated successfully with cineole.Study Design Prospective, randomized, double‐blinded, placebo‐controlled study.Methods We compared efficacy and safety of cineole capsules with placebo capsules in 152 patients with acute rhinosinusitis (76 patients in each treatment group). The dosage of the active ingredient was two 100‐mg capsules of cineole three times daily. The primary end point was the reduction of a defined symptoms‐sum‐score based on symptoms and signs comparing baseline therapy difference from the beginning to the end of the 7‐day treatment.Results All randomly selected patients were assigned to the intention‐to‐treat‐population. At the beginning, the mean symptoms‐sum‐score was 15.6 in both treatment groups. The mean values for the symptoms‐sum‐scores in the cineole group were 6.9 ± 2.9 after 4 days and 3.0 ± 2.8 after 7 days, and in the placebo group, 12.2 ± 2.5 after 4 days and 9.2 ± 3.0 after 7 days. The differences between both groups were clinically relevant and statistically significant after 4 and 7 days. The result for the primary end point was validated by the amelioration of the following secondary end points: headache on bending, frontal headache, sensitivity of pressure points of trigeminal nerve, impairment of general condition, nasal obstruction, and rhinological secretion. Mild side effects, possibly associated with medication, were observed in two patients as heartburn and exanthema after treatment with cineole.Conclusion In patients with acute nonpurulent rhinosinusitis, timely treatment with cineole is effective and safe before antibiotics are indicated.
Mitomycin Does Not Prevent Laryngotracheal Repeat Stenosis After Endoscopic Dilation Surgery: An Animal Study
Authors: Eliashar Ron , Gross Menachem , Maly Bella , Sichel Jean‐Yves 
Published: March 2004

AbstractObjectives/Hypothesis Conflicting data exist in the literature regarding the role of mitomycin in the prevention and treatment of laryngotracheal stenosis. The purpose of the study was to assess the value of mitomycin in preventing repeat stenosis after endoscopic dilation surgery of well‐established stenoses.Study Design Prospective controlled animal study.Methods Laryngotracheal stenosis was induced in 16 dogs. After a period of 3 months the dogs underwent endoscopic dilation and were randomly divided into two groups. The control group received immediate topical application of normal saline. Dogs in the mitomycin group received immediate topical application of 0.5 mg mitomycin. The animals were then observed for 3 more months before euthanasia. The laryngeal lumens were measured endoscopically at baseline, before dilation, and before euthanasia. A comparison was made between the two study groups by means of the Wilcoxon rank‐sum test for change in the percentage of stenosis attained by the endoscopic dilation.Results Nine dogs were included in the control group, and seven in the mitomycin group. Group comparison for initial occlusion before endoscopic dilation using Wilcoxon rank‐sum test showed no difference between the two groups (z = 0.16 [P = .87]). Three months after endoscopic dilation, no difference was observed between the two groups regarding the change in the percentage of occlusion (z = −0.21 [P = .83]).Conclusion Mitomycin exerts a benefit equal to that of normal saline when applied to a well‐established laryngotracheal stenosis in dogs and does not prevent repeat stenosis after endoscopic dilation surgery.
Head and Neck Manifestations of Disseminated Coccidioidomycosis
Authors: Arnold Michelle G. , Arnold John C. , Bloom David C. , Brewster Douglas F. , Thiringer J. Kim 
Published: March 2004

AbstractObjectives/Hypothesis Coccidioidomycosis is a fungal disease endemic to semiarid regions in the southwestern United States, northern Mexico, and parts of South America. Although this is primarily a pulmonary disease, approximately 0.5% to 1.0% of infected individuals develop disseminated disease affecting skin, subcutaneous tissue, bone, joints, and meninges. The objectives of the study were to present three cases of head and neck manifestations of disseminated coccidioidomycosis and to review the literature of head and neck presentations, diagnosis, and treatment of this potentially life‐threatening disease.Study Design Case reports and literature review.Methods A Medline search was performed with the keyword “coccidioidomycosis.” Of 1719 articles in all, 47 were selected for their relevance to otolaryngology, diagnosis, or treatment.Results Virtually all head and neck manifestations in patients with disseminated coccidioidomycosis involved the skin, with a predilection for the central face. Systemic symptoms such as fever and cough are often subtle, making the diagnosis difficult. Infections of multiple sites of the head and neck have been reported, including life‐threatening airway lesions.Conclusion The incidence of patients with coccidioidomycosis has been steadily increasing since the late 1980s in endemic areas. Otolaryngologists are increasingly being called on to diagnose and manage the head and neck manifestations of the disease caused by Coccidioides immitis.
Auditory‐Perceptual Scaling and Quality of Life in Tracheoesophageal Speakers
Authors: Eadie Tanya L. , Doyle Philip C. 
Published: March 2004

AbstractObjectives/Hypothesis The purposes of the study were to determine listeners' auditory‐perceptual ratings of tracheoesophageal speakers, to determine quality of life in tracheoesophageal speakers, and to determine the potential relationship between listeners' ratings of speech and tracheoesophageal speakers' self‐rated quality of life.Study Design Twenty‐eight laryngectomized individuals who used tracheoesophageal speech as their primary mode of communication were studied. Fifteen naïve listeners provided auditory‐perceptual ratings.Methods Twenty‐eight tracheoesophageal speakers (22 men and 6 women) completed a general information form, in addition to the University of Michigan Head and Neck Quality of Life (HNQOL) instrument; speakers also provided connected speech samples of a standard passage. Fifteen naïve listeners evaluated the tracheoesophageal speech samples for overall speech severity, naturalness, acceptability, and pleasantness using direct magnitude estimation procedures.Results Listeners were able to discriminate among tracheoesophageal speech samples relative to the auditory‐perceptual dimensions. Male tracheoesophageal speakers were judged as having significantly better, more acceptable, and more pleasant voices than women. Scores on the HNQOL instrument were determined to be higher among the group of tracheoesophageal speakers in the present study than those reported in previous studies. No significant differences were found among men and women for quality of life scores. Quality of life domains and auditory‐perceptual judgments of tracheoesophageal speech were moderately correlated.Conclusion Women who use tracheoesophageal speech may be differentially penalized for dimensions related to voice quality. Limitations in voice did not necessarily translate into worse overall quality of life, indicating that auditory‐perceptual evaluation and quality of life questionnaires are evaluating different aspects of function after laryngectomy.
Hyaluronan Levels in Acute Vocal Fold Scar
Authors: Thibeault Susan L. , Rousseau Bernard , Welham Nathan V. , Hirano Shigeru , Bless Diane M. 
Published: March 2004

AbstractObjectives/Hypothesis The objective was to measure the level of hyaluronan during the first 15 days after vocal fold biopsy in a rabbit model.Study Design Experimental, nonrandomized prospective study.Methods Twenty‐eight rabbits underwent unilateral vocal fold biopsy. The contralateral vocal fold was preserved as a control sample. On days 3, 5, 10, and 15 after biopsy, hyaluronan levels in the injured and normal vocal folds were measured immunohistologically and with an ELISA assay.Results Hyaluronan levels in the injured vocal fold were lowest on day 3 and highest on day 5 after injury. Statistical analysis revealed that the injured vocal fold demonstrated significantly lower levels of hyaluronan on day 3 than on days 5, 10, and 15. On day 5, the injured vocal fold demonstrated significantly greater levels of hyaluronan than those observed on days 3, 10, and 15. Compared with the normal vocal fold, the injured vocal fold demonstrated significantly lower levels of hyaluronan on days 3, 10, and 15. No differences were observed between the injured and normal vocal fold on day 5, when the hyaluronan level was maximized in the injured vocal fold.Conclusion Maximizing hyaluronan levels in the early stages of wound repair may have therapeutic potential for decreasing the incidence of vocal fold scar. Decreased hyaluronan levels may provide a less than optimal environment for normal tissue regeneration and may contribute to the formation of scar tissue in vocal fold lamina propria.
Less inhibition of interferon‐γ to organism growth in host cells may contribute to the high susceptibility of C3H mice to Chlamydia trachomatis lung infection
Authors: Qiu Hongyu , Yang Jie , Bai Hong , Fan Yijun , Wang Shuhe , Han Xiaobing , Chen Lijun , Yang Xi 
Published: March 2004

SummaryT‐helper‐1‐like cytokine response and cell‐mediated immunity have been shown to be critical in host resistance to Chlamydia trachomatis infection. Using a murine pneumonia model, we compared the susceptibility of C3H/HeN (C3H) and C57BL/6 mice to C. trachomatis mouse pneumonitis (MoPn) infection. C3H mice exhibited significantly higher mortality, greater organism growth and much more severe pathological changes in the lung compared with C57BL/6 mice. However, the pattern of adaptive immune responses including organism‐specific delayed‐type hypersensitivity, antibody responses and cytokine [interferon‐γ (IFN‐γ), interleukin‐12 (IL‐12), IL‐4, IL‐10 and tumour necrosis factor α] production by spleen and local draining lymph node cells in these two strains of mice appeared comparable during the process of infection. Interestingly, MoPn growth in the cultured ex vivo macrophages from C3H mice was found to be significantly less inhibited by the exogenous IFN‐γ present in the culture compared to C57BL/6 mice. The lower inhibition of MoPn growth in C3H mice was associated with significantly lower nitric oxide production by the infected macrophages following IFN‐γ stimulation. The data suggest that the cellular events downstream of cytokine production in chlamydia host cells may be important in determining the different susceptibility of hosts to chlamydial infection.
High expression of myeloid‐related proteins 8 and 14 characterizes an inflammatorily active but ineffective response of macrophages during leprosy
Authors: Sunderkötter Cord H. , Tomimori‐Yamashita Jane , Nix Verena , Maeda Solange M. , Sindrilaru Anca , Mariano Mario , Sorg Clemens , Roth Johannes 
Published: March 2004

SummaryMacrophages are decisive cells for the course of leprosy as they phagocytose Mycobacterium leprae and have the potential to influence the specific immune response. Expression and release of the myeloid‐related protein (MRP) 8 and MRP14 (S100A8 and S100A9) characterize a proinflammatory subtype of macrophage that is prominent in, for example, murine infection with lack of a T helper 1 cell response and in certain highly active chronic inflammations of mice and humans. We investigated cutaneous biopsies of the different forms of leprosy (41 untreated patients) including leprosy reaction type 1 (reversal reaction) and type 2 (erythema nodosum leprosum) (n = 18) for expression of MRP8 and MRP14 by subtypes of macrophages. Concomitantly we determined serum levels of MRP8 and MRP14 by sandwich enzyme‐linked immunosorbent assay. Expression of MRP8 and MRP14 by CD68‐positive macrophages was low in tuberculoid leprosy and rose significantly in borderline tuberculoid leprosy and especially in multibacillary forms, there being expressed by mycobacteria‐loaded foam cells. A significant rise of MRP8 and MRP14 expression also occurred in lepra reactions compared to the corresponding non‐reactional forms. In type 2 reactions this additional increase was associated with a sigificant elevation of serum levels. In type 1 it was associated with expression of MRP8 and MRP14 by epitheloid and giant cells, which so far were considered not to express both proteins. In conclusion, we present evidence that the two prominent proteins MRP8 and MRP14 can be re‐expressed in vivo by tissue macrophages in chronic infection, that their increased expression is characteristic for a macrophage subtype associated with high inflammatory but low antimycobacterial activity in the absence of a T helper 1 response, and that their significant rise in serum during erythema nodosum leprosum bears diagnostic and pathophysiological relevance.