bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vestibular Evoked Myogenic Potentials in Basilar Artery Migraine
Authors: Liao Lih‐Jen , Young Yi‐Ho 
Published: June 2004

AbstractObjectives/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

AbstractThe 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

AbstractWe 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

AbstractMethods 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

AbstractIt 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

AbstractThe 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

AbstractThe 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.
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.
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

ABSTRACTAlthough 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

ABSTRACTWe 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

ABSTRACT 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

ABSTRACTUnderstanding 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.
The Proteolytic Cleavage of Protein Kinase C Isotypes, Which Generates Kinase and Regulatory Fragments, Correlates with Fas‐Mediated and 12‐O‐Tetradecanoyl‐Phorbol‐13‐Acetate‐Induced Apoptosis
Authors: Mizuno Keiko , Noda Kumi , Araki Tamao , Imaoka Tomomi , Kobayashi Yuko , Akita Yoshiko , Shimonaka Motoyuki , Kishi Shuji , Ohno Shigeo 
Published: June 2004

Protein kinase C (PKC) has been implicated in signaling induced by diverse sets of stimuli regulating growth, differentiation, and apoptosis. The present study focused on the fate of PKC isotype proteins during Fas‐mediated apoptosis of human leukemic cell lines. Among the PKC isotypes expressed in different cell types, such as Jurkat, HPB‐ALL, U937, and HL60, all the nPKC isotypes including nPKCδ, nPKCε, and nPKCθ, but not cPKCα and βII and aPKCζ (n, c, and a represent novel, conventional and atypical, respectively), showed limited proteolytic cleavage during Fas‐mediated apoptosis. The limited proteolysis of nPKC isotypes means the disappearance of the intact protein band concomitant with the appearance of two fragments, most likely containing the kinase and regulatory domains, in contrast to the so‐called down‐regulation known for both cPKC and nPKC isotypes following exposure to stimuli such as 12‐O‐tetradecanoyl‐phorbol 13‐acetate (TPA). The time course of Fas‐mediated apoptosis in Jurkat cells parallels that of the activation of a 32‐kDa cysteine protease (CPP32)‐like protease and also closely parallels the proteolytic cleavage of nPKC isotypes. A peptide inhibitor of the CPP32‐like protease, Ac‐DEVD‐CHO, blocked the proteolytic cleavage of nPKC isotypes as well as apoptosis mediated by Fas. Transfection of recombinant protein coding for the catalytic fragment of nPKCδ to COS1 cells resulted in the apoptotic morphology of cells and nuclei.The effect of TPA on apoptosis depends on the cell type. TPA significantly suppressed Fas‐mediated apoptosis in Jurkat, whereas TPA alone caused apoptosis in HPB‐ALL, U937, and HL60, only slight apoptosis in Jurkat. The proteolytic fragmentation of nPKC isotypes again closely correlated with the degree of apoptosis even in apoptosis induced by TPA. Separation of TPA‐treated cells into apoptotic and non‐apoptotic differentiating cells revealed that the proteolytic fragmentation of nPKC isotypes occurs only in apoptotic cells and, in adherent differentiating cells, nPKC isotypes as well as cPKCα were down‐regulated without the generation of nPKC fragments. These results are consistent with the idea that nPKC isotypes meet two different fates, down‐regulation and proteolytic cleavage generating kinase and regulatory fragments, and that the proteolytic cleavage of nPKC isotypes is a step in the signaling pathway involved in Fas‐mediated and TPA‐induced apoptosis.