bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct mapping and alignment of protein sequences onto genomic sequence
Authors: Gotoh Osamu 
Published: August 2008

Abstract
Motivation: Finding protein-coding genes in a newly determined genomic sequence is the first step toward understanding the content written in the genome. Sequences of transcripts of homologous genes, if available, can considerably improve accuracy of prediction of genes and their structures, compared with that without such knowledge. As protein sequences are generally better conserved than nucleotide sequences, remote homologs can be used as templates, extending the applicability of evidence-based gene recognition methods. However, no tool seems to have been developed so far to simultaneously map and align a number of protein sequences on mammalian-sized genomic sequence.
Results: We have extended our computer program Spaln to accept protein sequences, as well as cDNA sequences, as queries. When the query and the target sequences are reasonably similar, e.g. between mammalian orthologs, Spaln runs one to two orders of magnitude faster than conventional approaches that rely on Blast search followed by dynamic-programming-based spliced alignment. Exon-level and gene-level accuracies of Spaln are significantly higher than those obtained by the best available methods of the same type, particularly when the query and the target are distantly related.
Availability: Spaln is accessible online for a few species at http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user. The source code is available for free for academic users from the same site.
Contact: o.gotoh@i.kyoto-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Improving subcellular localization prediction using text classification and the gene ontology
Authors: Fyshe Alona , Liu Yifeng , Szafron Duane , Greiner Russ , Lu Paul 
Published: August 2008

Abstract
Motivation: Each protein performs its functions within some specific locations in a cell. This subcellular location is important for understanding protein function and for facilitating its purification. There are now many computational techniques for predicting location based on sequence analysis and database information from homologs. A few recent techniques use text from biological abstracts: our goal is to improve the prediction accuracy of such text-based techniques. We identify three techniques for improving text-based prediction: a rule for ambiguous abstract removal, a mechanism for using synonyms from the Gene Ontology (GO) and a mechanism for using the GO hierarchy to generalize terms. We show that these three techniques can significantly improve the accuracy of protein subcellular location predictors that use text extracted from PubMed abstracts whose references are recorded in Swiss-Prot.
Contact: duane@cs.ualberta.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Does Hyaluronic Acid Distribution in the Larynx Relate to the Newborn's Capacity for Crying?
Authors: Schweinfurth John M. , Thibeault Susan L. 
Published: August 2008

AbstractObjectives/Hypothesis: The newborn is heavily dependent on voice communication and therefore has relatively higher vocal demands and expenditures than the adult, the loudness output per mass performance exceeds that of the adult, and the newborn larynx exhibits significant histological and biochemical differences. The neonatal larynx is capable of sustaining relatively greater pitch and loudness than the adult over longer periods of time. This ability may be related to a more compact arrangement of collagen within the lamina propria, less interstitial space, and a uniform distribution of hyaluronic acid (HA). As HA is the primary determinant of vocal fold viscosity and water content, the distribution of HA in the superficial portion of the neonatal vocal fold is hypothesized to be related to newborn crying endurance. Our objective was to examine the histological structure and the quantity and arrangement of HA within the lamina propria of the pediatric larynx and review the relevant physiology of hyaluronic acid and its impact on voice production.Study Design: Histological and digital subtraction analysis.Methods: Intact, neonatal larynges were sourced from fresh cadaveric specimens. Trichrome stain was used to assess the collagen content and location in the tissues. HA was stained using a colloidal iron staining technique with and without incubation with bovine testicular hyaluronidase. Average optical density was calculated in tissue before and after treatment with hyaluronidase, and the stain intensity ratio was calculated.Results: A total of 14 larynges were suitable for examination, eight males and six females. Histological examination revealed a uniform appearance of the vocalfold without evidence of a distinct vocal ligament or layered structure. Colloidal iron staining revealed an even distribution of HA throughout the vocal fold with no significant difference between quadrants. Images of the colloidal iron‐stained tissue had a mean pixel intensity of 82 of 255. Slides of vocal fold tissue treated with hyaluronidase revealed a pixel intensity of 106 of 255 for a 22% mean difference in stain intensity (P < .01).Conclusions: The identification of the layered structure of the adult lamina propria has raised a number of questions as to the development and purpose of the human larynx. Based on histological observations from the current study, possible explanations for the physiological differences include differences in the distribution and tissue concentration of HA and consequently dynamic viscosity, oncotic affinity for water, and less intercellular space in the superficial lamina propria.
The Effect of Famciclovir on Delayed Facial Paralysis After Acoustic Tumor Resection
Authors: Brackmann Derald E. , Fisher Laurel M. , Hansen Marlan , Halim Andrea , Slattery William H. 
Published: August 2008

AbstractObjectives/Hypothesis: To determine the efficacy of prophylactic famciclovir to significantly reduce the percentage of patients experiencing postoperative delayed facial paresis.Study Design: Prospective evaluation of facial nerve grade for two groups (treated and untreated) with famciclovir before and after surgery. All procedures were conducted by the same group of experienced neurotologists.Methods: In a tertiary neurotologic private practice, the percentage of 1,023 patients with delayed facial paresis after undergoing microsurgical removal of unilateral acoustic tumor with no preoperative treatment was compared to the percentage of 530 patients with preoperative famciclovir treatment. Patients were prescribed famciclovir 500 mg BID for 3 days before surgery and 5 days postoperative. The House‐Brackmann Facial Nerve Grade was assessed prospectively at preoperative, immediate postoperative, and discharge from the hospital in both groups.Results: Twenty‐five percent of the no famciclovir group experienced delayed facial palsy compared to 20% in the famciclovir group, a statistically significant difference (P < .04). The famciclovir group undergoing translabyrinthine craniotomy showed a significantly greater decrease in percentage of patients with delayed facial palsy than those undergoing middle fossa craniotomies (P < .003).Conclusions: Famciclovir administered preoperatively and after craniotomies resulted in a smaller percentage of patients developing delayed facial weakness. We are continuing the routine use of famciclovir in perioperative acoustic tumor management and recommend that others do so.
Urocortin Expression in Mouse Cochlear Nucleus and Scarpa's Ganglion
Authors: Brawner James Travis , Thompson Ann 
Published: August 2008

AbstractObjectives/Hypothesis: Clinical and basic studies have correlated tinnitus with stress. Although the etiology of tinnitus is unknown, the cochlear nucleus (CN) appears to play a role. To better understand the potential impact of stress on tinnitus and modulation of the central auditory system in general, the goal of the current study was to examine the presence and distribution of axon terminals containing urocortin in the CN of the mouse.Study Design: Prospective description of histological findings.Methods: Three different forms of urocortin were labeled in brainstem sections collected from 10 wild‐type mice by immunohistochemistry. Immunoreactive terminal fibers in the CN were digitally photographed, as well as reconstructed in the CN under a drawing tube attached to a light microscope.Results: Specific staining was found in en passant type fibers scattered throughout the CN but situated mostly within the granule cell domains. Clusters of labeled fibers were observed in the nerve root. Labeled axons were observed in the three tracts known to carry olivocochlear fibers to the CN, as well as in the olivocochlear bundle itself. As the axons within the olivocochlear bundle departed the brainstem in the vestibular nerve, numerous labeled en passant fibers were observed among somata of the vestibular ganglion (Scarpa's). Centrally, labeled axons were followed from the CN to the lateral superior olive, an established source of urocortin‐positive efferents to the cochlea. These findings indicate that lateral olivocochlear efferents innervate the CN and Scarpa's ganglion, and also that urocortin is likely a neuromodulator in particular CN circuits.Conclusions: The current study supports innervation of specific regions of the mouse CN and Scarpa's ganglion by neurons expressing urocortin. The innervation may be one substrate by which stress modulates particular CN processes. Further studies are necessary to establish the role of urocortin in CN models of tinnitus.
Follicular Dendritic Cell Sarcoma of the Head and Neck: Case Report and Literature Review
Authors: Chera Bhishamjit S. , Orlando Christine , Villaret Douglas B. , Mendenhall William M. 
Published: August 2008

AbstractObjectives/Hypothesis: This article presents a case of a patient with follicular dendritic cell sarcoma (FDS), a rare neoplasm usually of the head and neck, and reviews the literature.Study Design: Literature review.Methods: A MEDLINE literature search was performed and the literature was reviewed.Results: Our patient presented with an FDS that had been excised from the upper neck and recurred in a level V node. He was treated with neck dissection and postoperative irradiation and remains disease free 5.25 years after salvage treatment. The literature search yielded 67 case reports on FDS of the head and/or neck. Most patients were treated with surgery (94%). Twenty‐eight percent of patients received adjuvant radiotherapy; 18% received adjuvant chemotherapy. Fifty percent of patients were alive with no evidence of disease at last follow‐up; 9% died from disease.Conclusions: We currently treat head and neck FDS with wide resection and postoperative radiotherapy.
Effect of Steroids, Acetyl‐cysteine and Calcium‐Activated Chloride Channel Inhibitors on Allergic Mucin Expression in Sinus Mucosa
Authors: Hauber Hans‐Peter , Steffen Armin , Goldmann Torsten , Vollmer Ekkehard , Hung Hsiao‐Ling , Wollenberg Barbara , Zabel Peter 
Published: August 2008

AbstractObjectives/Hypothesis: Allergic inflammation of the upper airways is commonly associated with mucus hypersecretion. At present, there is no specific mucus regulating drug available. Our goal was to investigate the effect of glucocorticosteroids, acetyl‐cysteine (ACC), and calcium‐activated chloride channel (CLCA) inhibitors in a model of Th2 type cytokine induced mucin expression in human airway mucosa.Study Design: Prospective.Methods: Explanted tissue from human sinus mucosa was stimulated with interleukin (IL)‐4, IL‐9, or IL‐13. Different concentrations of dexamethasone, ACC, or CLCA inhibitors [niflumic acid (NFA) or MSI‐2216] were added to stimulated tissue. Epithelial mucin expression was quantified using periodic acid‐Schiff staining.Results: IL‐4, IL‐9, and IL‐13 significantly increased epithelial mucin expression (P < .05). Dexamethasone reduced Th2 type cytokine induced mucin expression in a dose‐dependant manner being statistically significant at concentrations ≥4.0 μmol/L (IL‐4) and ≥40.0 μmol/L (IL‐9 and IL‐13) (P < .05). ACC had no significant effect on IL‐4 and IL‐13 induced mucin expression, whereas IL‐9 induced mucin expression was significantly decreased at concentrations ≥3.0 mmol/L (P < .05). NFA and MSI‐2216 decreased Th2 type cytokine induced mucin expression in a dose‐dependant manner. This effect was statistically significant at concentrations ≥100 μmol/L (NFA) and ≥50 μmol/L (MSI‐2216) (P < .05).Conclusions: Th2 type cytokines can induce mucin expression in a model of explanted human airway mucosa. Th2 type cytokine induced mucin expression can be effectively reduced by either glucocorticosteroids or CLCA inhibitors ex vivo. Besides glucocorticosteroids CLCA inhibitors may offer an alternative therapeutic approach to treat allergic mucus hypersecretion.
Steroids in Otolaryngology
Authors: Cope Daron , Bova Ronaldo 
Published: August 2008

AbstractSteroids are increasingly being used to treat a wide spectrum of otolaryngological disorders. It is important for ear‐nose‐throat surgeons to understand the short‐ and long‐term complications associated with steroid use. The aim of this study was to review the role of steroids in common ear‐nose‐throat disorders. Corticosteroid therapy has been shown to be effective in the management of idiopathic facial nerve palsy, allergic rhinitis, acute sinusitis, sinonasal inflammatory polyposis, and croup. The therapeutic efficacy of steroids in the management of Meniere's disease, sudden idiopathic sensorineural HL, chronic otitis media, and vestibular neuronitis remain controversial.
Topical Therapy in Anosmia: Relevance of Steroid‐Responsiveness
Authors: Stenner M , Vent J , Hüttenbrink K. ‐B. , Hummel T. , Damm M. 
Published: August 2008

AbstractObjectives/Hypothesis: The use of steroids either systemically or topically is known as a common therapy in patients with anosmia. Nevertheless, investigations giving proof for the benefit of a topical therapy are very rare, and no prognostic factors are known. In our study, we for the first time evaluated the additional effect of a topical therapy not only with steroids but also with antibiotics after conventional pretreatment with oral steroids and propose the steroid‐responsiveness of an anosmia as a prognostic factor.Study Design: Retrospective design.Methods: We analyzed the data of 299 patients with olfactory dysfunction. Eighty‐nine underwent initial pretreatment with systemic steroids and presented data over a sufficient follow‐up time. In a second step all these patients were given a topical treatment in a head down forward position, namely either budesonid alone or in combination with neomycin. Primary outcome parameter was the threshold, discrimination and identification (TDI) score.Results: Initial therapy with oral steroids changed the TDI from 15.5 to 18.7 in the means (P < .001). In general, leaving away systemic steroids while applying local therapy did not led to a reduction of the TDI (P < .001). Dividing up the patients into those suffering from a steroid‐responsive anosmia (SRA) and those without benefit from initial systemic steroids (non‐SRA), the topical treatment led to a significant difference between the two groups with benefit toward the non‐SRA group (P < .001). Regarding only the nonchronic rhinosinusitis anosmics, these findings became even more apparent. Furthermore, in non‐SRA patients we found even better results with steroids in combination with neomycin as a topical therapy. In this group, the combined topical therapy elevated the TDI for +2.1 points whereas topical steroids alone raised it only for +1.0 point.Conclusions: The steroid‐responsiveness of anosmia seems to be a relevant prognostic indicator for a significant benefit of a topical therapy in general. Within all patients, the effect of an initial systemic therapy could be maintained by the adjacent topical treatment whereas in non‐SRA patients a topical therapy has a significant greater impact. Furthermore, antibiotics even seem to have an additional effect in this group. Different reasons, first of all an overwhelmed steroid resistance by additional antiinflammatory effects of antibiotics, e.g., the inhibition of apoptosis might play a role and are discussed.
Adenoid Cystic Carcinoma of the External Auditory Canal
Authors: Dong Fei , Gidley Paul W. , Ho Tang , Luna Mario A. , Ginsberg Lawrence E. , Sturgis Erich M. 
Published: August 2008

AbstractObjective/Hypothesis: To describe the clinical history and outcome of patients with adenoid cystic carcinoma (ACC) of the external auditory canal (EAC).Study Design: Retrospective case series.Methods: A search of our institution's tumor registry identified 22 patients with ACC of the EAC. Both clinical histories and pathology slides, when available, were reviewed.Results: The mean age at diagnosis was 42 years (median, 38.5 years), and the most common presenting complaints were otalgia and ear canal mass. Nine patients (41%) developed recurrences at a mean of 8 years (median, 8 years) after initial diagnosis, six died of ACC, and three were living with distant metastases at their last follow‐up. The mean duration of symptoms at the time of diagnosis was 7.7 years (range, 2–30 years) for patients who developed a recurrence after treatment vs. 1.2 year (range, 0–2 years) for patients who remained disease‐free (P = .137). Every patient who had recurrent disease reported a duration of symptoms of ≥2 years (P = .013), and every patient with a duration of symptoms >2 years recurred (P = .002). There was a trend for more local recurrences after limited resection (P = .061).Conclusions: ACC of the EAC often recurs many years after definitive treatment. Although our sample size was too small to make definitive conclusions, we recommend aggressive local therapy with lateral temporal bone resection and adjuvant postoperative radiotherapy. In addition to successful local therapy, early diagnosis may be the only other effective means of preventing distant metastases.
Practice of venom immunotherapy in the United Kingdom: a national audit and review of literature
Authors: Diwakar L. , Noorani S. , Huissoon A. P. , Frew A. J. , Krishna M. T. 
Published: August 2008

SummaryBackground
Venom immunotherapy (VIT) is the only effective treatment for prevention of serious allergic reactions to bee and wasp stings in sensitized individuals. However, controversies exist relating to diagnosis, indications for treatment and treatment schedules. We audited current practice of VIT in the United Kingdom to evaluate adherence to international guidelines.Methods
An online questionnaire was sent to all clinicians practising immunotherapy identified on the British Society of Allergy and Clinical Immunology website. Eighty‐six questionnaires were sent and 53 responses (61.6%) were received. Of these, 48 (85%) carried out VIT at their centre.Results
Skin prick tests (SPT) and serum venom‐specific IgE (SSIgE) were equally preferred as first‐line investigation. Fifty percent of the respondents perform intradermal tests if both SPT and SSIgE are negative. While 8% of respondents commence VIT in patients with negative SSIgE and a history of severe reaction, 57% prefer to repeat the tests in 6–12 months if serum tryptase is elevated. If the insect responsible is uncertain and SSIgE is detected against bee and wasp venoms, 22% of the respondents will desensitize to both while 32% initiate treatment against the venom with the higher SSIgE. A protocol of weekly up‐dosing for 12 weeks is preferred for induction and only 25% of respondents have ever used rush or ultra‐rush protocols. Three years is thought to be optimum duration of VIT by most (56%). Eleven percent perform sting challenges at the end of treatment. Although 47% measure SSIgE at the end of treatment, only 3% use these results as a basis for discontinuing VIT.Conclusion
Currently there is considerable variation in the diagnosis and management of hymenoptera venom allergy in the United Kingdom. This audit has demonstrated that the current international guidelines for the diagnosis and management of hymenoptera venom allergy are not being followed by UK allergy practitioners.
Association of angiotensin I‐converting enzyme gene polymorphisms with aspirin intolerance in asthmatics
Authors: Kim T‐H. , Chang H‐S. , Park S‐M. , Nam B‐Y. , Park J‐S. , Rhim T. , Park H‐S. , Kim M‐K. , Choi I. S. , Cho S. H. , Chung I. Y. , Park B‐L. , Park C‐S. , Shin H‐D. 
Published: August 2008

SummaryBackgroundAspirin‐intolerant asthma (AIA) refers to the development of bronchoconstriction in asthmatic individuals following the ingestion of aspirin or other non‐steroidal anti‐inflammatory drugs (NSAIDs). Angiotensin I‐converting enzyme (ACE), a membrane‐bound peptidase present in the lung, plays a pivotal role in the metabolism of the endogenous peptides involved in the pathogenesis of asthma.MethodsWe screened a Korean asthma cohort (581 asthmatics including 81 aspirin‐intolerant asthmatics and 231 aspirin‐tolerant asthmatics, and 181 normal controls) for four single nucleotide polymorphisms (SNPs; −262 A>T and −115 T>C in the 5′‐flanking region and +5467 T>C [Pro450Pro] and+11860 A>G [Thr776Thr] in the coding region) and one ins/del (+21288 CT) in theACEgene.ResultsNone of the SNPs or haplotypes showed any association with the development of asthma, but they were significantly associated with the risk of AIA. Logistic regression indicated that the frequency of the rare alleles of −262 A>T and −115 T>C was higher in subjects with AIA than in subjects with aspirin‐tolerant asthma (ATA) (P=0.003–0.01,P corr=0.015–0.05). Subjects homozygous for the rare alleles of −262 A>T and −115 T>C showed a greater decline in forced expiratory volume in 1 s (FEV1) after aspirin provocation than those homozygous for the common alleles (P<0.05). A luciferase reporter assay indicated thatACEpromoters containing the rare −262 A>T allele possessed lower activity than did those containing the common allele (P=0.009). In addition,ACEpromoters bearing the rare −115 T>C allele had no luciferase activity. DNA–protein binding assays revealed a band containing theACEpromoter region (including −262 A) and a protein complex.ConclusionThe −262 A>T polymorphism in the promoter of theACEgene is associated with AIA, and the rare allele of −262 A>T may confer aspirin hypersensitivity via the down‐regulation ofACEexpression.