bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolated Plexiform Neurofibroma: Treatment with Three‐Dimensional Conformal Radiotherapy
Authors: Robertson Thomas C. , Buck David A. , Schmidt‐Ullrich Rupert , Powers Celeste N. , Reiter Evan R.
Published: June 2004

Objectives: To present a case of an unusual benign tumor of the tongue treated successfully with radiotherapy.

Study Design: Case report.

Methods: Retrospective chart review.

Results: A 60‐year‐old man presented with a painful submucosal lesion of the tongue base. Computed tomography showed an infiltrative soft‐tissue mass involving the left base of the tongue. Operative biopsy revealed plexiform neurofibroma. Because of the patient's operative risk and the potential morbidity of surgical resection, he was treated with three‐dimensional conformal radiotherapy (3DCRT). His treatment was accomplished using a five‐field arrangement treating exclusively the mass lesion to a total tumor dose of 60 Gy. After treatment, the patient's tongue pain resolved, and he noted minimal transient xerostomia. Serial follow‐up radiographic examinations showed the base of tongue mass to be slightly smaller 4 months after treatment. The most recent follow‐up magnetic resonance image reveals a further decrease in size of the mass. The patient is now over 3 years out from treatment.

Conclusions: Solitary plexiform neurofibroma of the tongue base is a rare tumor. These benign neoplasms are usually treated with either observation or surgical excision. This case demonstrates that, when significant symptoms necessitate active management, these lesions may be successfully treated with minimal morbidity using 3DCRT. The ability of this technique to deliver a conformal radiation dose to the tumor volume while sparing the surrounding normal tissues may expand the application of radiotherapy in the treatment of these benign lesions of the head and neck.
The Canalith Repositioning Procedure for Benign Positional Vertigo: A Meta‐Analysis
Authors: Woodworth Bradford Alan , Gillespie M. Boyd , Lambert Paul R.
Published: June 2004

Objective: To review the effectiveness of the canalith repositioning procedure (CRP) in the treatment of benign paroxysmal positional vertigo (BPPV) with a critical review of the literature and meta‐analysis.

Study Design: Meta‐analysis.

Methods: Studies eligible for inclusion were randomized, controlled trials of the CRP performed on clearly defined cases of BPPV. A total of nine studies meeting inclusion criteria were identified by two independent literature searches of Medline. Treatment and control groups were compared for symptom resolution and elimination of a positive Dix‐Hallpike test.

Results: Patients treated with CRP were more likely to demonstrate symptom resolution (odds ratio [OR] 4.6; 95% confidence interval [CI] 2.8–7.6) and negative Dix‐Hallpike (OR 5.2; 95% CI 3.0–8.8) at the time of first follow‐up. The effect of CRP for symptom improvement was strongest within the first month after treatment (OR 4.1; 95% CI 3.1–5.2) with some decline thereafter (OR 2.8; 95% CI 1.7–3.9). Conversely, the ability of CRP to produce a negative Dix‐Hallpike strengthened between the first month after treatment (OR 3.0; 95% CI 1.8–4.0) and later follow‐up times (OR 5.0; 95% CI 3.9–6.1).

Conclusions: The CRP is more effective than control in resolving vertigo and positive Dix‐Hallpike associated with BPPV. This finding was consistent among a variety of studies using different study designs. Untreated patients may demonstrate symptom improvement with time; however, many will continue to have a positive Dix‐Hallpike when examined. Resolution of vertigo in untreated patients is therefore most likely because of avoidance of provocative positions.
Cidofovir Plasma Assays after Local Injection in Respiratory Papillomatosis
Authors: Naiman Ana Nusa , Roger Gilles , Gagnieu Marie‐Claude , Bordenave Joelle , Mathaut Savine , Ayari Sonia , Nicollas Richard , Bour Jean‐Baptiste , Garabedian Noel , Froehlich Patrick
Published: June 2004

Objective: To assess cidofovir plasma concentration after intralesional airway administration for recurrent respiratory papillomatosis.

Design: Prospective study.

Setting: Tertiary care teaching hospital.

Patients and Method: The study comprised 21 patients (10 children and 11 adults). Plasma samples were collected at 10 and 45 minutes (T10, T45) or at 10 and 60 minutes (T10, T60) after injection. The measurements of cidofovir were performed using a high‐performance liquid chromatographic method.

Results: Plasma samples were collected at T10 and T45 on 19 occasions from the children and on 17 from the adults. A linear relationship was found between plasma concentration and dose in children (mean dose 1.2 mg/kg; mean cidofovir plasma levels 0.91 and 0.81 μg/mL) but not in adults (mean dose 0.2 mg/kg; mean plasma levels 0.21 and 0.31 μg/mL). The same relationships were found between dose and area under the concentration/time curve (AUC). Four plasma samples were taken in children at T10 and T60: mean dose 1.2 mg/kg and mean plasma concentrations 1.11 and 1.24 μg/mL. Maximum plasma concentration averaged 34% (SD 11%) in children and 62% (SD 33%) in adults, with equivalent plasma level after intravenous infusion of the same dose.

Conclusions: The cidofovir plasma levels were below those leading to toxicity. The levels and the AUC were dose dependent in children but not in adults. Diffusion from the injected site was greatest in a few adults and unpredictable. Because of the great individual variation in diffusion in adults, cidofovir should be used at less than the recommended intravenous dose to prevent any risk of systemic toxicity.
Posttonsillectomy Taste Distortion: A Significant Complication
Authors: Goins Michael R. , Pitovski Dimitri Z.
Published: June 2004

Objective/Hypothesis: Tonsillectomy is among the most commonly performed procedures. As with any surgery, head and neck surgeons must be aware of possible complications and their potential affects. At our smell and taste center, we have been referred several patients in a 6‐month period with the complaint of taste distortion after tonsillectomy. We report in this article a patient that complains of taste distortion after a right tonsillectomy for unilateral tonsillar hypertrophy.

Study Design: A prospective study documenting taste distortion after tonsillectomy using clinical, subjective, and objective evaluation.

Methods: The clinical course of a patient with taste distortion after a tonsillectomy is described. The gustatory function was investigated by conducting electrogustometry and spatial taste testing. Threshold measurements were determined at three left‐ and three right‐side tongue regions: 1) the tongue tip region (innervated by the chorda tympani branch of the facial nerve), 2) the lateral margin of the tongue (anterior to the foliate papillae), and 3) the posterior tongue region (innervated by the lingual branch of the glossopharyngeal nerve).

Results: After a complete clinical evaluation and taste testing, it was found that the patient suffered an injury to the right lingual branch of the glossopharyngeal nerve. The close anatomic relationship between the palatine tonsil and lingual branch of the glossopharyngeal nerve makes the nerve vulnerable during tonsillectomy. This injury has caused the patient to suffer ageusia to the right posterior one third of the tongue, compensated by a contralateral phantogeusia (phantom taste) with clinical dysgeusia. The phantogeusia was abolished by application of anesthetic to the area where the phantom was perceived. We propose that the phantogeusia is the result of release‐of‐inhibition in the contralateral glossopharyngeal nerve.

Conclusion: Taste distortion (including, phantogeusia and dysgeusia) after tonsillectomy is rarely reported as a complication but has a significant impact on quality of life. This article examines the taste distortion presence as a complication after tonsillectomy to make head and neck surgeons aware of this serious complication and the pathophysiology of taste distortion.
Development and Evaluation of an Improved Cochlear Implant Electrode Design for Electric Acoustic Stimulation
Authors: Adunka Oliver , Kiefer Jan , Unkelbach Marc H. , Lehnert Thomas , Gstoettner Wolfgang
Published: June 2004

Objective: The objective of this study was to assess the intracochlear position and the extent of trauma to cochlear structures using a new prototype electrode carrier (Flex EAS). Special emphasis was placed on the practicality for combined electric and acoustic stimulation of the auditory system.

Study Design: Human temporal bones were evaluated histologically after insertion of the electrodes, and insertion forces were measured in an acrylic model of the scala tympani.

Methods: 1) Insertion forces with the regular C40+ array and the new electrode prototype were measured in an acrylic model of the scala tympani. 2) Ten human temporal bones were implanted using the same surgical procedure as in vivo. All bones underwent fixation methylmethacrylate embedding to allow cutting of the undecalcified bone with the electrode in situ. In addition, radiography of the implanted devices was performed and correlated to histologic results. Electrode positions and trauma to cochlear structures were then evaluated histologically.

Results: All insertions of the new electrode array were performed in the scala tympani of the cochlea. All insertions were atraumatic and covered one cochlear turn. The only effect on cochlear structures that could be observed was a slight lifting of the basilar membrane in the middle turn limited to the tip of the electrode. In three bones, basal trauma, which resulted from the cochleostomy itself, could be observed as well. All neural structures remained intact.

Conclusions: The new electrode prototype provides very good mechanical properties for safe and atraumatic implantation. All criteria for the use in hearing‐preservation cochlear implantation for electric and acoustic stimulation were fulfilled. Surgical measures to prevent basal trauma appear to be very important.
Increased Expression of Laminin‐5 and Its Prognostic Significance in Hypopharyngeal Cancer
Authors: Nakayama Meijin , Sato Yu‐ichi , Okamoto Makito , Hirohashi Setsuo
Published: June 2004

Objectives: We investigated the clinicopathologic significance of laminin‐5 γ2 chain (LNγ2) expression in 26 surgically removed hypopharyngeal cancers and compared the results with conventional prognostic factors elicited from hematoxylin‐eosin (H&E) stained whole‐mount laryngeal sections.

Study Design: Stainability of LNγ2 was mainly evaluated at the invasive front of the cancer nests. Scoring was performed on the basis of a semiquantitative scale defined according to the number of immunopositive cancer cells (score 3, 2, 1, and 0). Stainability of LNγ2 was also evaluated macroscopically at different tumor locations such as surface center, interstitial space, and invasive front. Status of cartilage and vascular invasion and patterns of tumor extension were evaluated from H&E stained sections. The results of LNγ2 expression correlated with the tumor stages, neck node status, pathologic differentiation, and prognoses.

Results: Among the 26 cases, 24 demonstrated positive LNγ2 expression. Of these cases, 1, 14, 9, and 0 showed scores of 3, 2, 1, and 0, respectively. Positive expression of LNγ2 at the invasive front was more prominent in the high‐expression group, and surface center was often positive in the cases of low‐expression group. Among the H&E stained prognostic factors, vascular invasion and infiltrative pattern demonstrated significant correlations with clinical outcome. Vascular invasion and infiltrative pattern were also closely related to positive LNγ2 expression. Five‐year survival rates of patients who showed high LNγ2 expression were significantly poorer than in patients with low expression.

Conclusion: Hypopharyngeal cancers positive for LNγ2 indicate a considerable risk for cancer progression and are closely related to prognosis. Increased LNγ2 expression might be a prognostic indicator for squamous cell carcinomas of the hypopharynx.
A Study of Moderately Differentiated Neuroendocrine Carcinomas of the Larynx and an Examination of Non‐Neoplastic Larynx Tissue for Neuroendocrine Cells
Authors: Chung Jin‐Haeng , Lee Seung‐Sook , Shim Yoon‐Sang , Kim Sang‐Yoon , Nam Soon‐Yuhl , Kim Dong‐Hoon , Cho Kyung‐Ja
Published: June 2004

Objectives/Hypothesis: To determine the most appropriate terminology for neuroendocrine carcinomas (NEC) of the larynx, successive clinicopathologic studies are encouraged. The typical location and immunophenotype of laryngeal NEC raise a question of whether any precursor cells exist.

Study Design: Six patients with laryngeal NEC were analyzed. Another 20 laryngectomy specimens were examined for the presence of non‐neoplastic neuroendocrine cells.

Methods: Tumor morphology and patient outcome were determined, and tumor tissue underwent immunohistochemical examination to identify cytokeratin, neuroendocrine markers (chromogranin, synaptophysin, CD56, calcitonin), S‐100 protein, and p53 protein. A neuroendocrine marker study was also performed on non‐neoplastic regions of another 20 laryngectomy specimens to identify any neuroendocrine cells.

Results: Laryngeal NEC, all submucosal, exhibited various morphology with or without histologic evidences of neuroendocrine differentiation. The tumors showed frequent (67%) calcitonin expression, calcitonin secretion in one case, and common (50%) p53 over‐expression. Three patients died within 3 years. In the non‐neoplastic larynx specimens, Kulchitsky cell‐like bipolar neuroendocrine cells were identified in the basal and middle layer of the respiratory epithelium of the ventricle and subglottis but none in the submucosal layer of the supraglottic region. The neuroendocrine cells did not express calcitonin.

Conclusions: Moderately differentiated or large‐cell NEC is a more favored term than atypical carcinoid until more refined classifications for upper respiratory tract NEC are agreed on. Despite the confirmed presence of neuroendocrine cells in the respiratory epithelium of the larynx, the origin of laryngeal NEC remains unknown. p53 mutation might be one of the major molecular steps in the pathogenesis of laryngeal NEC.
Granulomatous Inflammation and Nerve Necrosis in a Case of Apparent Idiopathic Vocal Fold Paralysis: Report of a Case
Authors: Torkian Behrooz A. , Crumley Roger L.
Published: June 2004

Objectives: We will present clinical and pathologic findings of the recurrent laryngeal nerve of a 54‐year‐old man with apparent idiopathic vocal fold paralysis and discuss clinical and scientific implications of these findings.

Study Design: Our design is in the format of a case report with emphasis on the clinical, intraoperative, histologic, and neuropathologic findings, followed by a discussion of contemporary theories of idiopathic unilateral vocal fold immobility and the implications of our findings.

Methods: A 54‐year‐old man presented with a 2‐year history of unilateral vocal fold motion impairment (VFMI) after an upper respiratory infection. Radiographic and laboratory data revealed no organic cause. The patient clinically appeared to have a classical unilateral vocal fold paralysis and had previously undergone collagen injection and medialization thyroplasty, each with only temporary improvement of voice. We performed ansa cervicalis‐recurrent laryngeal nerve anastomosis.

Results: Intraoperative dissection revealed an indurated and thickened section of nerve approximately 15 mm in length, located at the beginning of the intralaryngeal segment, near the cricothyroid joint. Segments of this nerve were submitted for histologic evaluation, revealing necrosis with granulomatous inflammation. Postoperative electromyography and videostrobolaryngoscopy were consistent with successful reinnervation from the ansa procedure.

Conclusions: The diagnosis of “idiopathic VFMI” likely represents a number of distinct pathologic entities. This case highlights our lack of understanding of idiopathic VFMI and raises many important questions regarding our current theories of this diagnosis. The clinical and pathologic implications are discussed, and continued investigation is recommended.
Ultrastructural and Electrophysiologic Changes of Rat Cochlea after Irradiation
Authors: Akmansu Halit , Eryilmaz Adil , Korkmaz Hakan , Sennaroğlu Gonca , Akmansu Müge , Göçer Celil , Tatar İlkan
Published: June 2004

Objective/Hypothesis: To determine the acute and subacute cochlear effects of sublethal total body irradiation.

Study Design: The study was designed prospectively as a Sprague‐Dawley (SD) rat model with otoacoustic emission measurement.

Methods and Materials: Ten rats and 20 ears were included in the study. Distortion product otoacoustic emission (DPOAE) measurements were performed under ketamine anesthesia before and 1 to 8 weeks after sublethal dose total body irradiation. Eight and six rats survived at the first and eighth week measurements, respectively. The frequency bandwidth was set to 1,067 Hz (referenced to f
1) – 9,512 Hz (referenced to f
2) (2f
1 − f
2 = 832 − 6,076 Hz) and eight points were sampled per octave, but low‐frequency (<2,549 Hz [referenced to 2f
1 − f
2]) results were not included in the analysis. Averages were obtained at each frequency, and statistical analysis was performed to compare the pre‐and postradiation values. Then, three of the rats were killed for transient electron microscopy (TEM) of the temporal bones.

Results: The posttreatment DPOAEs at almost all frequencies showed a trend toward decline at both the first and eighth weeks, but significant reduction was only detected at 3,600 and 3,961 Hz (referenced to 2f
1 − f
2) in the first week. TEM of the cochlea revealed ultrastructural changes in the outer hair cells (OHCs) and stria vascularis of the basal turn. The cochlear ganglion nuclei and cochlear nerve axons were unaffected.

Conclusion: Radiation can affect the cochlea in the acute phase at the mid to high frequencies; further prediction for long‐term effects requires longer follow‐ups.
Pseudocyst of the Auricle: A Histologic Perspective
Authors: Ming Lim Chwee , Hong Goh Yau , Shuen Chao Siew , Lim Lynne
Published: June 2004

Objective: The aim of the study is to describe the histologic spectrum in the pseudocyst of the auricle and to identify any consistent histologic features of this condition.

Study Design: A prospective study was performed in which the tissue specimen from patients with pseudocyst of the auricle treated at the Department of Otolaryngology, Singapore General Hospital during a 1‐year period was sent for histology.

Methods: Consecutive patients with pseudocyst of the auricle who were treated had their tissue specimen sent for histology. These specimens were independently reviewed by one consultant pathologist.

Results: All 16 specimens revealed an intracartilaginous cyst devoid of epithelial lining. Interestingly, there were consistent perivascular mononuclear infiltrates of lymphocytes evident in the connective tissue layer just superficial to the anterior segment of the cartilage.

Conclusion: Pseudocyst of the auricle is a benign condition predominantly affecting young Asian males. Histology characteristically reveals an intracartilaginous cyst devoid of epithelial lining, and there are no pathognomonic features. We postulate that an inflammatory response is crucial to the development of this condition on the basis of a consistent perivascular inflammatory response seen in all our specimens.
Vestibular Evoked Myogenic Potentials in Basilar Artery Migraine
Authors: Liao Lih‐Jen , Young Yi‐Ho
Published: June 2004

Objectives/Hypothesis: Because the sacculocollic reflex is a descending pathway passing through the territory of basilar artery, the aim of the study was to investigate whether hypoperfusion affects this pathway by applying vestibular evoked myogenic potential (VEMP) testing in patients with basilar artery migraine.

Study Design: A prospective study from May 2000 to April 2002.

Methods: Twenty patients were diagnosed as having basilar artery migraine according to the criteria of the International Headache Society and literature. Eight were male and 12 were female patients, and their ages ranged from 9 to 48 years (mean age, 40 y). Each patient underwent a battery of audio‐vestibular tests.

Results: Electronystagmography disclosed abnormal eye tracking test in six patients (30%), and there were abnormal optokinetic nystagmus test results in nine patients (45%). Caloric test revealed canal paresis in seven patients, directional preponderance in four patients, and normal responses in nine patients (45%). Vestibular evoked myogenic potential testing disclosed absent vestibular evoked myogenic potentials in seven patients and delayed vestibular evoked myogenic potentials in two patients, with one patient showing absent vestibular evoked myogenic potentials on one side and delayed vestibular evoked myogenic potentials on the other side. The remaining 10 patients (50%) had bilateral normal vestibular evoked myogenic potentials. Five patients had preserved both caloric and VEMP test responses, six patients displayed absent caloric and VEMP test responses, and the remaining nine patients had either abnormal caloric test responses or abnormal vestibular evoked myogenic potentials, exhibiting a nonsignificant relationship between caloric test responses and vestibular evoked myogenic potentials. Relief of headache and vertigo was achieved after 3 months of medication. Ten asymptomatic patients with either absent or delayed vestibular evoked myogenic potentials before treatment underwent follow‐up VEMP test, and nine patients (90%) displayed normal vestibular evoked myogenic potentials bilaterally.

Conclusion: Vestibular evoked myogenic potential testing evaluates the sacculocollic reflex, which descends through the lower brainstem. Some patients with basilar artery migraine have absent or delayed vestibular evoked myogenic potentials, presumably because the descending pathway from the saccule through the brainstem to cranial nerve XI is interrupted, which is attributed to hypoperfusion in the territory of the basilar artery. After 3 months of medication, recovery of normal vestibular evoked myogenic potentials in an asymptomatic patient indicates reversible ischemia in the territory of the basilar artery.
Unassisted refolding of urea‐denatured arginine kinase from shrimp Feneropenaeus chinensis: Evidence for two equilibrium intermediates in the refolding pathway
Authors: Pan Ji‐Cheng , Yu Zhenhang , Su Xiao‐Yang , Sun Ye‐Qing , Rao Xue‐Ming , Zhou Hai‐Meng
Published: June 2004

The refolding process and the equilibrium intermediates of urea‐denatured arginine kinase (AK) were investigated by 1‐anilino‐8‐naphthalenesulfonate (ANS) intrinsic fluorescence, far‐UV circular dichroism (CD), size‐exclusion chromatography (SEC), and enzymatic activity. In dilute denaturant, two equilibrium refolding intermediates (I and N′) were discovered, and a refolding scheme of urea‐denatured AK was proposed. During the refolding of urea‐denatured AK, the fluorescence intensity increased remarkably, accompanied by a significant blue shift of the emission maximum and a pronounced increase in molar ellipticity of CD at 222 nm. The first folding intermediate (I) was inactive in urea solution ranging between 2.4 and 3.0 M. The second (N′) existed between a 0.4‐ and 0.8‐M urea solution, with slightly increased activity. Neither the blue shift emission maximum nor the molar ellipticity of CD at 222 nm showed significant changes in these two regions. The two intermediates were characterized by monitoring the ANS binding ability in various residual urea solutions, and two peaks of the emission intensity were observed in urea solutions of 0.6 and 2.8 M, respectively. The SEC results indicated that a distribution coefficient (KD) platform existed in urea solutions ranging between 2.4 and 3.0 M urea, suggesting that there was a similarly apparent protein profile and size in the urea solution region. The refolding kinetics showed that the urea‐denatured AK was in two‐phase refolding. Proline isomerization occurred in the unfolding process of AK, which blocked the slow phase of refolding. These results suggested that the refolding process of urea‐denatured AK contained at the least two equilibrium refolding intermediates.
Database searching by flexible protein structure alignment
Authors: Ye Yuzhen , Godzik Adam
Published: June 2004

We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible structure alignment methods were applied in this task because of a lack of significance estimation of flexible alignments. In this paper, we developed an estimate of the statistical significance of FATCAT alignment score, allowing us to use it as a database‐searching tool. The results reported here show that (1) the distribution of the similarity score of FATCAT alignment between two unrelated protein structures follows the extreme value distribution (EVD), adding one more example to the current collection of EVDs of sequence and structure similarities; (2) introducing flexibility into structure comparison only slightly influences the sensitivity and specificity of identifying similar structures; and (3) the overall performance of FATCAT as a database searching tool is comparable to that of the widely used rigid‐body structure comparison programs DALI and CE. Two examples illustrating the advantages of using flexible structure alignments in database searching are also presented. The conformational flexibilities that were detected in the first example may be involved with substrate specificity, and the conformational flexibilities detected in the second example may reflect the evolution of structures by block building.
Best α‐helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
Authors: Viklund Håkan , Elofsson Arne
Published: June 2004

Methods that predict the topology of helical membrane proteins are standard tools when analyzing any proteome. Therefore, it is important to improve the performance of such methods. Here we introduce a novel method, PRODIV‐TMHMM, which is a profile‐based hidden Markov model (HMM) that also incorporates the best features of earlier HMM methods. In our tests, PRODIV‐TMHMM outperforms earlier methods both when evaluated on “low‐resolution” topology data and on high‐resolution 3D structures. The results presented here indicate that the topology could be correctly predicted for approximately two‐thirds of all membrane proteins using PRODIV‐TMHMM. The importance of evolutionary information for topology prediction is emphasized by the fact that compared with using single sequences, the performance of PRODIV‐TMHMM (as well as two other methods) is increased by approximately 10 percentage units by the use of homologous sequences. On a more general level, we also show that HMM‐based (or similar) methods perform superiorly to methods that focus mainly on identification of the membrane regions.
Determinants of quaternary association in legume lectins
Authors: Brinda K.V. , Mitra Nivedita , Surolia Avadhesha , Vishveshwara Saraswathi
Published: June 2004

It is well known that the sequence of amino acids in proteins code for its tertiary structure. It is also known that there exists a relationship between sequence and the quaternary structure of proteins. The question addressed here is whether the nature of quaternary association can be predicted from the sequence, similar to the three‐dimensional structure prediction from the sequence. The class of proteins called legume lectins is an interesting model system to investigate this problem, because they have very high sequence and tertiary structure homology, with diverse forms of quaternary association. Hence, we have used legume lectins as a probe in this paper to (1) gain novel insights about the relationship between sequence and quaternary structure; (2) identify the sequence motifs that are characteristic of a given type of quaternary association; and (3) predict the quaternary association from the sequence motif.
Protein simulations: The absorption spectrum of barnase point mutants
Authors: Somers Ken R.F. , Krüger Peter , Bucikiewicz Sylwia , De Maeyer Marc , Engelborghs Yves , Ceulemans Arnout
Published: June 2004

The near‐UV absorption spectra of barnase double‐point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared—Amber5.0, CHARMM‐c27b1, and GROMOS96—using indole as the fluorescent probe. It was found that calculated absorption spectra reproduce experimental values very well, provided detailed charge cloud descriptions are included. These calculations further sustain the hypothesis that different tryptophan rotamers can be present in proteins. Molecular dynamics calculations of the double‐point mutants also point to the structural effect of counter ions.
Structural conservation in the major facilitator superfamily as revealed by comparative modeling
Authors: Vardy Eyal , Arkin Isaiah T. , Gottschalk Kay E. , Kaback H. Ronald , Schuldiner Shimon
Published: June 2004

The structures of membrane transporters are still mostly unsolved. Only recently, the first two high‐resolution structures of transporters of the major facilitator superfamily (MFS) were published. Despite the low sequence similarity of the two proteins involved, lactose permease and glycerol‐3‐phosphate transporter, the reported structures are highly similar. This leads to the hypothesis that all members of the MFS share a similar structure, regardless of their low sequence identity. To test this hypothesis, we generated models of two other members of the MFS, the Tn10‐encoded metal‐tetracycline/H+ antiporter (TetAB) and the rat vesicular monoamine transporter (rVMAT2). The models are based on the two MFS structures and on experimental data. The models for both proteins are in good agreement with the data available and support the notion of a shared fold for all MFS proteins.
The progress of membrane protein structure determination
Authors: White Stephen H.
Published: June 2004

The rate of membrane protein (MP) structure determination has been examined for the 18‐year period following the publication of the first high‐resolution crystal structure. The growth is solidly exponential, but lags behind the rate for soluble proteins during the equivalent time period.
Seasonal pattern of antioxidant enzyme system in the roots of perennial forage grasses grown in alpine habitat, related to freezing tolerance
Authors: Zhou Ruilian , Zhao Halin
Published: June 2004

The relationship between active oxygen species (AOS) and membrane damage, and between antioxidant enzyme activity and chilling tolerance has been documented, but the mechanisms responsible for perennial forage grass to survive winter with temperatures at −30°C in temperate alpine regions is not well understood. In this study, the seasonal pattern of enzymatic antioxidant systems superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11) and lipid peroxidation in roots and leaves of alpine perennial grasses grown in their natural environment were investigated to understand the role of the enzymatic antioxidant system in freezing tolerance of perennial grasses. Four grasses, Poa sphyondylodes Trine., Bromus inermis Leyss., Bromus sinensis Keng. and Elymus nutans Griseb., were established in alpine conditions in 1993. The grasses were sampled at approximately semi‐monthly intervals in the autumn of 1995 and spring of 1996. The results showed that leaves were dead in the autumn and membrane damage seems to play a key role in the decline of this organ. Antioxidant enzyme activities of the roots strongly changed with declining temperature in the autumn and winter or increasing temperature in the spring. With the decrease in temperature in the autumn the antioxidant enzyme activities increased rapidly, reaching maximum values in early November and then slowly declining during the following winter period, although they were still higher than in September In the spring, antioxidant enzymes activities increased again in the roots with the rise of temperature from mid April to early May when the shoots began re‐growth. In contrast, thiobarbituric acid‐reactive substances content in the roots increased markedly in the autumn, reaching maximum values in early October and remaining constant with little fluctuation during the following winter. In the autumn when the roots experienced winter acclimation, the formation of freezing tolerance in the roots was correlated with the activities of the antioxidant enzyme, indicating that antioxidant activity systems in the roots played an important role in limiting the production of free radicals to protect membrane integrity. Freezing tolerance in alpine grasses correlated with an increased capacity to scavenge or detoxify activated AOS by the antioxidant enzymatic system. AOS accumulated with decreasing temperature in early cold acclimation may be an inducer in activating the antioxidant enzyme defence system for the formation of freezing tolerance in roots.
Genetic differences in seed longevity of various Arabidopsis mutants
Authors: Clerkx Emile J. M. , Blankestijn‐De Vries Hetty , Ruys Gerda J. , Groot Steven P. C. , Koornneef Maarten
Published: June 2004

Seeds gradually lose their viability during dry storage. The damage that occurs at the biochemical level can alter the seed physiological status and is affected by the storage conditions of the seeds. Although these environmental conditions controlling loss of viability have been investigated frequently, little information is available on the genetics of seed longevity. Using Arabidopsis mutants in defined developmental or biochemical pathways such as those affected in seed coat composition, seed dormancy, hormone function and control of oxidative stress, we tried to gain insight into the genes and mechanisms controlling viability of stored seeds. Mutations like abscisic acid insensitive3 (abi3) as well as abscisic acid deficient1 (aba1) show reduced longevity, which may be partially related to the seed dormancy phenotype of these mutants. Mutants with seed coat alterations, especially aberrant tests shape (ats), showed a stronger reduction in germination percentage after storage, indicating the importance of a ‘functional’ seed coat for seed longevity. A specific emphasis was placed on mutants affected in dealing with Reactive Oxygen Species (ROS). Because several pathways are involved in protection against ROS and because gene redundancy is a common feature in Arabidopsis, ‘double’ mutants were generated. These ‘double’ mutants and the corresponding single mutants were subjected to a controlled deterioration test (CDT) and a germination assay on hydrogen peroxide (H2O2) after prolonged storage at two relative humidities. CDT and germination on H2O2 affected all genotypes, although it appears that other effects like genetic background are more important than the deficiencies in the ROS scavenging pathway. Explanations for this limited effect of mutations affecting ROS scavenging are discussed.
Growth, nitrogen fixation and ammonium assimilation in common bean (Phaseolus vulgaris): effect of phosphorus
Authors: Olivera M. , Tejera N. , Iribarne C. , Ocaña A. , Lluch C.
Published: June 2004

The impact of phosphorous nutrition on plant growth, symbiotic N2 fixation, ammonium assimilation, carbohydrate and amino‐acid accumulation, as well as on nitrogen, phosphorus and ATP content in tissues in common bean (Phaseolus vulgaris) plants was investigated. Plants inoculated with Rhizobium tropici CIAT899 were grown in Leonard jars under controlled conditions, with P‐deficient (0 and 0.1 mM), P‐medium (0.5, 1 and 1.5 mM) and P‐high (2 mM) conditions in a N‐free nutrient solution. The P application, increased leaf area, whole plant DW (67%), nodule biomass (4‐fold), and shoot and root P content (4‐ and 6‐fold, respectively) in plant harvested at the onset of flowering (28‐days‐old). However, P treatments decreased the total soluble sugar and amino acid content in vegetative organs (leaf, root and nodules). The root growth proved less sensitive to P deficiency than did shoot growth, and the leaf area was significantly reduced at low P‐application. The absence of a relationship between shoot N content, and P levels in the growth medium could indicate that nitrogen fixation requires more P than does plant growth. The optimal amount for the P. vulgaris–R. tropici CIAT899 symbiosis was 1.5 mM P, this treatment augmented nodule‐ARA 20‐fold, and ARA per plant 70‐fold compared with plants without P application.
Molecular taxonomy and phylogeny of the ‘living fossil’ lineages Triops and Lepidurus (Branchiopoda: Notostraca)
Authors: Mantovani Barbara , Cesari Michele , Scanabissi Franca
Published: June 2004

Mantovani B. Cesari M. & Scanabissi F. (2004). Molecular taxonomy and phylogeny of the ‘living fossil’ lineages Triops and Lepidurus (Branchiopoda: Notostraca). —Zoologica Scripta, 33, 367–374.

European Triops cancriformis and Lepidurus apus were analysed for 12S and 16S mitochondrial genes and compared to North American and Japanese taxa. There are no cryptic species among European T. cancriformis populations, which are highly homogeneous in comparison to conspecific Japanese samples. T. cancriformis differs from congeneric taxa all over its range, which can be explained by its antiquity. In contrast, the parapatric subspecies L. apus apus and L. apus lubbocki are morphologically conserved and differ substantially at the mtDNA level. The genetic distance values between them are of the same order of magnitude as those observed between American Lepidurus species. Their subspecific status therefore requires further analysis. L. apus apus is more closely related to a L. arcticus sample from Iceland than to L. apus lubbocki. It is also related to a Canadian L. couesii population. Further analyses of populations from the whole range of L. arcticus and the European range of L. couesii are needed to understand the relationships among these notostracan taxa. When considering the two genera, it is clear that Lepidurus is a well supported monophyletic unit, while Triops is polyphyletic, embodying very divergent taxa.
GeneralizedMicrosporum canisdermatophytosis in six Yorkshire terrier dogs
Authors: CERUNDOLO ROSARIO
Published: June 2004

Abstract Six Yorkshire terrier dogs with generalized, chronic dermatophytosis caused byMicrosporum caniswere seen over a 3‐year period. Specific tests showed that they also had concurrent leishmaniosis (four cases), leishmaniosis and ehrlichiosis (one case) or diabetes mellitus (one case). Although specific therapy for these infectious diseases was instituted and the dogs were treated systemically and topically with appropriate antifungal drugs, only partial clinical resolution of the dermatophytosis was achieved.M. canisinfection resolved in the dog with diabetes mellitus after stabilizing the diabetes mellitus. Although immunological studies were not performed in these cases, it is theorized that the immune disregulation caused by leishmaniosis, ehrlichiosis or diabetes mellitus may have favoured generalization of the infection and prevented favourable responses to appropriate treatment of theM. canisinfection.
Suspected wood poisoning caused bySimarouba amara(marupá/caixeta) shavings in two dogs with erosive stomatitis and dermatitis
Authors: DECLERCQ JAN
Published: June 2004

Abstract Two male Labrador retrievers developed bleeding erosions/ulcerations involving the oral mucosa, mucocutaneous junctions of the lips, nose, prepuce and anus, ulcerated nodules on the chin, and crusting lesions on the elbows, hocks and scrotum. One of the dogs was anorexic and depressed, had haematological abnormalities consistent with damage to the liver and signs of neurological disease. As these dogs had recently been exposed to bedding containingSimarouba amarashavings and because of the striking similarities of clinical signs to those described for horses, a probable diagnosis of wood poisoning was made. This assumption was supported by the clinical course as healing of skin lesions occurred when the dogs were no longer exposed to the bedding.
Canine distemper virus infection of canine footpad epidermis
Authors: GRÖNE ANDREA , DOHERR MARCUS G. , ZURBRIGGEN ANDREAS
Published: June 2004

Abstract Infection of the footpad epidermis can occur in natural canine distemper virus (CDV) infection of dogs. Footpads from 19 dogs experimentally inoculated with virulent distemper strain A75/17 and from two nonexposed dogs were examined histopathologically and assessed for the presence of viral antigen and nucleoprotein mRNA, as well as number of inflammatory and apoptotic cells. Dogs were divided into four groups based on inoculation status and postmortem examination: inoculated dogs with severe distemper (group 1,n = 7); inoculated dogs with mild distemper (group 2,n = 4); inoculated dogs without distemper (group 3,n = 8); and noninoculated dogs (group 4,n = 2). Footpads from dogs of all groups had a comparably thick epidermis. Eosinophilic viral inclusions and syncytial cells were present in footpad epidermis of one dog of group 1. Footpads of group 1 dogs contained viral antigen and mRNA in the epidermis with strongest staining in a subcorneal location. Additionally, in these dogs footpad dermal structures including eccrine glands and vascular walls were positive for virus particles. No CDV antigen or mRNA was present in the footpad epidermis and dermis of any other dog. Group 1 dogs had more CD3‐positive cells and apoptotic cells within the basal layer of the epidermis when compared to the other groups. These findings demonstrate that in experimental infection CDV antigen and mRNA were colocalized in all layers of the infected canine footpad epidermis. The scarcity of overt pathological reactions with absence of keratinocyte degeneration indicates a noncytocidal persisting infection of footpad keratinocytes by CDV.
Does plant richness influence animal richness?: the mammals of Catalonia (NE Spain)
Authors: Hawkins Bradford A. , Pausas Juli G.
Published: June 2004

Although it has long been held that plant diversity must influence animal diversity, the nature of this relationship remains poorly understood at large spatial scales. We compare the species richness patterns of vascular plants and mammals in north‐eastern Spain using a 100‐km2 grain size to examine patterns of covariation. We found that the total mammal richness pattern, as well as those of herbivores and carnivores considered separately, only weakly corresponded to the pattern of plants. Rather, mammal richness was best described by climatic variables incorporating water inputs, and after adding these variables to multiple regression models, plant and mammal richness were virtually independent. We conclude that the observed association, although weak, is explained by shared responses of both groups to climate, and thus, plant richness has no influence on the richness pattern of Catalan mammals.
Density and species diversity of trees in four tropical forests of the Albertine rift, western Uganda
Authors: Eilu Gerald , Hafashimana David L. N. , Kasenene John M.
Published: June 2004

We assessed tree species density and diversity in 12 1‐ha plots in four forests of the Albertine rift, western Uganda. There were 5747 trees of diameter ≥ 10 cm in 53 families, 159 genera, and 212 species. Density ranged between 344 and 557 trees ha−1 (average 479 trees ha−1). Tree species diversity was highest in the Bwindi and Budongo forests. The Euphorbiaceae family was the most species rich (25 species) followed by Rubiaceae and Meliaceae with 16 species each. Canonical Correspondence Analysis (CCA) showed that major gradients in environmental variables influenced tree species distribution. Sample scores on ordination axes 1 and 2 were strongly correlated with pH and altitude, respectively. Correlated with rainfall and other soil factors, pH and altitude are presumed to be among the most important in influencing the distribution of tree species in the Albertine rift forests. Strategies that take account of variations in pH and elevation are required to conserve tree species in forests of the Albertine rift.
The fundamental and realized niche of the Monterey Pine aphid, Essigella californica (Essig) (Hemiptera: Aphididae): implications for managing softwood plantations in Australia
Authors: Wharton Trudi N. , Kriticos Darren J.
Published: June 2004

Essigella californica is a pine aphid native to western North America. In Australia, E. californica is considered an invasive pest that has the potential to cause severe economic loss to the Australian forestry industry. Two CLIMEX models were developed to predict the Australian and global distribution of E. californica under current climate conditions based upon the aphid's known North American distribution. The first model (model I) was fitted using the reasonably contiguous set of location records in North America that constituted the known range of E. californica, and excluded consideration of a single (reliable) location record of the aphid in southern Florida. The second model (model II) was fitted using all known records in North America. Model I indicated that the aphid would be climatically restricted to the temperate, Mediterranean and subtropical climatic regions of Australia. In northern Australia it would be limited by hot, wet conditions, while in more central areas of Australia it is limited by hot, dry conditions. Model II is more consistent with the current Australian distribution of E. californica. The contrast in geographical range and climatic conditions encompassed between the two models appears to represent the difference between the realized niche (model I) and fundamental niche (model II) of E. californica. The difference may represent the strength of biotic factors such as host limitation, competition and parasitism in limiting geographical spread in the native range. This paper provides a risk map for E. californica colonization in Australia and globally. E. californica is likely to remain a feature of the Australian pine plantations, and any feasibility studies into establishing coniferous plantations in lower rainfall areas should consider the likely impact of E. californica.
Reconstructing the Pleistocene geography of the Aphelocoma jays (Corvidae)
Authors: Peterson A. Townsend , Martínez‐Meyer Enrique , González‐Salazar Constantino
Published: June 2004

Understanding historical distributions of species and evolving lineages has been a topic of considerable interest, yet methods used to date have not provided detailed, quantitative distributional hypotheses. Here, we present a technique based on models of species’ ecological niches and Pleistocene climate reconstructions that provides such hypotheses, providing the example of reconstructions for the Aphelocoma jays. We demonstrate in general a greater degree than expected of stability in jay species’ distributional areas back through at least the most recent glaciation event, and that existing patterns of genetic differentiation may date to before the Late Pleistocene glaciations. More generally, the method offers the potential for reconstructing historical distributions of species or lineages, and providing a detailed geographic framework for addressing many biogeographic and systematic questions.