bluuebunny/crossref_metadata_2025_split huggingface dataset:
ProtBuD: a database of biological unit structures of protein families and superfamilies
Authors: Xu Qifang , Canutescu Adrian , Obradovic Zoran , Dunbrack Roland L. 
Published: October 2006

Abstract
Motivation: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs.
Results: ProtBuD is a database of BUs for all structures in the Protein Data Bank (PDB). We use both the PDBs BUs and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, the Structural Classification of Proteins (SCOP) designation or pairs of SCOP designations. The database provides the asymmetric and BU contents of related proteins in the PDB as identified in SCOP and Position-Specific Iterated BLAST (PSI–BLAST). The asymmetric unit is different from PDB and/or Protein Quaternary Server (PQS) BUs for 52% of X-ray structures, and the PDB and PQS BUs disagree on 18% of entries.
Availability: The database is provided as a standalone program and a web server from .
Contact: Roland.Dunbrack@fccc.edu
A Novel algorithm for identifying low-complexity regions in a protein sequence
Authors: Li Xuehui , Kahveci Tamer 
Published: October 2006

Abstract
Motivation: We consider the problem of identifying low-complexity regions (LCRs) in a protein sequence. LCRs are regions of biased composition, normally consisting of different kinds of repeats.
Results: We define new complexity measures to compute the complexity of a sequence based on a given scoring matrix, such as BLOSUM 62. Our complexity measures also consider the order of amino acids in the sequence and the sequence length. We develop a novel graph-based algorithm called GBA to identify LCRs in a protein sequence. In the graph constructed for the sequence, each vertex corresponds to a pair of similar amino acids. Each edge connects two pairs of amino acids that can be grouped together to form a longer repeat. GBA finds short subsequences as LCR candidates by traversing this graph. It then extends them to find longer subsequences that may contain full repeats with low complexities. Extended subsequences are then post-processed to refine repeats to LCRs. Our experiments on real data show that GBA has significantly higher recall compared to existing algorithms, including 0j.py, CARD, and SEG.
Availability: The program is available on request.
Contact: xli@cise.ufl.edu, tamer@cise.ufl.edu
Photoelastic Effects in Silicate Glasses
Authors: MATUSITA KAZUMASA , IHARA CHIKASHI , KOMATSU TAKAYUKI , YOKOTA RYOSUKE 
Published: October 2006

The photoelasticity of RnOmSiO2(RnOm=Li2O, Na2O, K2O, and ZnO), Li2O‐Al2O3‐SiO2, Na2O‐Al2O3‐SiO2, and Na2O‐ZnO‐SiO2 glasses was analyzed on the basis of the following equation relating the stress‐optical coefficient and the strain‐optical coefficient:
image

where C is the stress‐optical coefficient, n is the refractive index, G is the shear modulus, pI2and pI1are the Pockels strain‐optical coefticients, and p and q are the Neumann strain‐optical coefficients. No simple relation was found between the stress‐optical coefficient and the shear modulus, and the factor (p−q) was found to be an essential factor deter‐ mining the stress‐optical coefficient of silicate glasses. It was found that (p−q) decreases markedly with increasing content of modifier oxide, and that the change of (p − q) with composition is governed by the change of the atomic effect, while the lattice effect does not change as much. It is argued that the bridging oxygen with covalent bonds increases the atomic effect and the nonbridging oxygen with ionic bonds reduces the atomic effect.
Impacts of introduced brown and rainbow trout on benthic invertebrate communities in shallow New Zealand lakes
Authors: WISSINGER SCOTT A. , MCINTOSH ANGUS R. , GREIG HAMISH S. 
Published: October 2006

Summary1. Brown and rainbow trout have been introduced to many inland waters in New Zealand, but research on the impacts on native communities has focused mainly on streams. The purpose of this study was to compare the benthic communities of trout and troutless lakes. Based on previous studies in North America and Europe, we predicted that the benthic biomass, and especially the abundance of large invertebrates, would be lower in lakes with trout as compared to those without. We surveyed the invertebrate fauna of 43 shallow, high‐elevation lakes (26 with and 17 without trout) in four geographic clusters on the central South Island and then conducted a detailed quantitative study of invertebrate biomass and community structure in 12 of these lakes.2. Benthic community composition and diversity of lakes with and without trout were nearly identical and biomass was as high or higher in the lakes with as without trout. There was no evidence that trout have caused local extinctions of benthic invertebrates. Although the proportional abundance of large‐bodied aquatic was slightly lower in lakes with than without trout, the abundance of several groups of large‐bodied benthic taxa (dragonflies, caddisflies and water bugs) did not differ.3. Our findings are in contrast to those in North American and Europe where trout introductions into previously troutless lakes have led to declines in the abundance of benthic invertebrates, especially large‐bodied taxa. We propose that the modest effects of trout in New Zealand could be explained by (i) the high areal extent of submergent vegetation that acts as a benthic refuge, (ii) low intensity of trout predation on benthic communities and/or (iii) characteristics of the benthic invertebrates that make them relatively invulnerable to fish predation.4. Regardless of the relative importance of these hypotheses, our results emphasise that the same invertebrates occurred in all of the lakes, regardless of size, elevation and presence of trout, suggesting habitat generalists dominate the benthic fauna in shallow New Zealand lakes.
Eukaryotic diversity associated with carbonates and fluid–seawater interface in Lost City hydrothermal field
Authors: López‐García Purificación , Vereshchaka Alexander , Moreira David 
Published: October 2006

SummaryLost City is a unique off‐axis hydrothermal vent field characterized by highly alkaline and relatively low‐temperature fluids that harbours huge carbonate chimneys. We have carried out a molecular survey based on 18S rDNA sequences of the eukaryotic communities associated with fluid–seawater interfaces and with carbonates from venting areas and the chimney wall. Our study reveals a variety of lineages belonging to eight major taxa: Metazoa, Fungi, Heterokonta (Stramenopiles), Alveolata, Radiolaria, Cercozoa, Heterolobosea and Euglenozoa. We detected one fungal lineage that appears to be widespread in hydrothermal systems both submarine and continental. Alveolates were the most abundant and diverse group in Lost City samples, although their distribution was very different in carbonate, where ciliates dominated, and in fluid–seawater libraries, where dinoflagellates, Group I and Group II (Syndiniales) marine alveolates were profuse. Similarly, Euglenozoa also displayed a differential distribution, kinetoplastids being present on carbonates and a novel group of diplonemids so far exclusively observed in the deep sea being dominant in fluid–seawater libraries. Protist lineages identified in this ecosystem likely correspond to grazers, decomposers and parasites, playing key roles in the food web of the Lost City ecosystem.
Redefining the ‘Rural Question’: The New ‘Politics of the Rural’ and Social Policy
Authors: Woods Michael 
Published: October 2006

Abstract Politics in the countryside has undergone a significant shift in emphasis in recent decades, which may be characterized as a transition from ‘rural politics’ to ‘a politics of the rural’. Whereas ‘rural politics’ refers broadly to politics located in rural space, or relating to ‘rural issues’, the ‘politics of the rural’ is defined by the centrality of the meaning and regulation of rurality itself as the primary focus of conflict and debate. However, far from marginalizing social issues – as early work on the new rural conflicts by Mormont implied – the paper argues that the new politics of the rural has liberated rural social policy from the shadow of agricultural policy, providing a new language and context through which rural social issues can be placed on the political agenda. Three examples of this are discussed, drawing on illustrations from Britain, Australia, New Zealand and North America – conflicts over the rationalization of public and commercial services in rural communities; campaigns around the closure of rural schools and their symbolic place at the heart of rural communities; and issues of difference and discrimination in the countryside, including responses to travellers and asylum‐seekers.
Older People ‘on the Edge’ in the Countrysides of Europe
Authors: Giarchi George Giacinto 
Published: October 2006

Abstract Relatively few comparative studies have focused specifically upon the socio‐economic conditions affecting the welfare of older rural Europeans. Such publications as exist are usually confined to single studies. In presenting a European overview of their ‘life‐world’ this paper focuses upon the general conditions of older rural Europeans, living in different types of countryside within a centre–periphery framework. These conditions are largely dependent upon the interconnectivity (nexus) between regional urban centres and the older people's types of settlement. The extent of the global socio‐economic flows between urban centres and countrysides is critical, especially for those living in less accessible and remote European areas. Older people's positive and negative outcomes are seen to occur within four possible urban–rural parameters. The first consists of two‐way socio‐economic urban–rural flows that are more likely to be of benefit to significant numbers of older persons, especially in urban fringe and accessible countrysides. The second parameter arises when there is a long‐standing impasse, where the lack of communication between the rural locality and urban centre hampers socio‐economic urban–rural flows, isolating older people, particularly in less accessible and remote countrysides. The third occurs when regional and local urban centres block or cut back socio‐economic flows to the countryside. The fourth takes place when the rural communities resist socio‐economic urban flows that they regard as a threat to their rural idyll. Exemplars within each of the four urban–rural alternatives help to show the applicability and workability of this four‐way exploratory approach.
Treatment of Infantile Spasms: Results of a Population‐Based Study with Vigabatrin as the First Drug for Spasms
Authors: Granström Marja‐Liisa , Gaily Eija , Liukkonen Elina 
Published: October 2006

Summary: Purpose: The efficacy of a protocol consisting of vigabatrin (VGB) as the first and adrenocorticotropic hormone (ACTH) or valproate (VPA) as the second drug was studied in the treatment of newly diagnosed infantile spasms (IS) during 1994 to 1997 in a population‐based design. Methods: Only total disappearance of the spasms with a minimal duration of 1 month was accepted as a response. The treatment response was confirmed by video‐EEG study. All infants were studied by magnetic resonance imaging (MRI) or computed tomography (CT) for etiology. Results: Altogether 42 infants, 10 with cryptogenic and 32 with symptomatic etiology, were treated. Eleven (26%) responded to VGB, five (50%) with cryptogenic, and six (19%) with symptomatic etiology; 91% of infants responded to a dose of 50–100 mg/kg/day, and 82% of them within 1 week. ACTH was offered in combination with VGB to 22 and VPA to four infants for whom VGB failed. Eleven responded to ACTH and one to VPA. In total, 26 (62%) infants responded to the treatment protocol; all (100%) with cryptogenic etiology and 16 (50%) with symptomatic etiology. ACTH treatment was associated with more severe side effects than VGB or VPA. Only one infant relapsed after a spasm‐free period with VGB of >4 months, but none after ACTH was combined with VGB. Conclusions: We suggest VGB as a first drug to all infants with IS. After a treatment trial of 10–14 days with increasing dose from 50 to 150 mg/kg, ACTH should be considered.
Prothrombin and PIVKA‐II Levels in Cord Blood from Newborn Exposed to Anticonvulsants During Pregnancy
Authors: Howe A. M. , Oakes D. J. , Woodman P. D. C. , Webster W. S. 
Published: October 2006

Summary: Purpose: To determine whether anticonvulsant exposure during human pregnancy caused an increase of the abnormal form of prothrombin, known as PIVKA‐II (prothrombin induced by vitamin K absence for factor II), and a decrease in total prothrombin, in the blood of the newborn. Methods: Cord blood was collected from the placenta at the time of parturition from 12 women who had received anticonvulsant therapy during pregnancy and from 11 control women. Results: PIVKA‐II was present in cord blood from control mothers at low or nondetectable levels. In the same samples, total prothrombin concentrations were −50% of adult levels, but there was wide variation between individuals. Exposure to carbamazepine (CBZ) alone during pregnancy was associated with markedly increased PIVKA‐II levels in four of six samples and decreased total prothrombin levels for the whole group. High PIVKA‐II levels also were recorded in one cord blood sample from a mother who received phenytoin (PHT) and vigabatrin (VGB). Two cases of PHT alone and one of valproic acid (VPA) alone were not associated with increased PIVKA‐II levels. Conclusions: These results are consistent with the hypothesis that some anticonvulsants (particularly CBZ) interfere with vitamin K metabolism during pregnancy and may result in hematologic signs of vitamin K deficiency in the newborn.
Frontal lobe syndrome or adolescent‐onset schizophrenia? A case report
Authors: Ferrara M , Freda F. , Massa R. , Carratelli T. J. 
Published: October 2006

Objective:  To highlight the difficulties that abound in making a clinical distinction between early‐onset schizophrenia (EOS) and juvenile frontal dementia early in the course of illness.Method:  Clinical information and data from investigations in single case was collated and reviewed.Results:  A 15‐year‐old girl was admitted to our psychiatric unit because of cognitive decline and formal thought disorder with echopraxia, echolalia and palilalia, and a lack of flexibility in the use of cognitive and motor strategies that culminated in psychosis. A single photon emission computerized tomography scan showed marked frontal lobe hypoperfusion; however, on proton spectroscopy there was no differential in N‐acetyl aspartate levels.Conclusion:  Hypofrontality in EOS is well established and the association of frontal functional alterations, neuropsychological impairment and psychotic symptomatology is suggestive of frontal lobe prodrome that precedes the onset of psychosis.
Evolution as It Appears to the Paleontologist
Authors: Osborn Henry Fairfield 
Published: October 2006

The following facts are those which are put forth through paleontological observation, for verification by others:
1. That many origins of new characters are through some internal action in heredity.
2. That many important adaptive characters arise determinately, definitely, but by extremely slow stages.
3. That degrees of similarity in such origins correspond with degrees of kinship. 4. That degrees of kinship also affect to a certain extent, but not absolutely the time of appearance, or the time of the origin, or the rate of evolution.
5. That such origins find expression not spontaneously, or irrespective of conditions, or from purely internal mechanical causes, but through some entirely unknown and at present inconceivable relation to ontogeny (habit and use), to environment (external conditions), and to selection.
6. That if such origins do spring from internal hereditary principles, as they appear to do in many cases, slow origins (mutations of de Vries) may be simply due to the same law operating with a different velocity.
The Homologue ofhet-cofNeurospora crassaLacks Vegetative Compatibility Function inFusarium proliferatum
Authors: Kerényi Zoltán , Oláh Brigitta , Jeney Apor , Hornok László , Leslie John F. 
Published: October 2006

ABSTRACTFor two fungal strains to be vegetatively compatible and capable of forming a stable vegetative heterokaryon they must carry matching alleles at a series of loci variously termedhetorvicgenes. Clonedhet/vicgenes fromNeurospora crassaandPodospora anserinahave no obvious functional similarity and have various cellular functions. Our objective was to identify the homologue of theNeurospora het-cgene inFusarium proliferatumand to determine if this gene has a vegetative compatibility function in this economically important and widely dispersed fungal pathogen. InF. proliferatumand five other closely relatedFusariumspecies we found a few differences in the DNA sequence, but the changes were silent and did not alter the amino acid sequence of the resulting protein. Deleting the gene altered sexual fertility as the female parent, but it did not alter male fertility or existing vegetative compatibility interactions. Replacement of the allele-specific portion of the coding sequence with the sequence of an alternate allele inN. crassadid not result in a vegetative incompatibility response in transformed strains ofF. proliferatum. Thus, thefphchgene inFusariumappears unlikely to have the vegetative compatibility function associated with its homologue inN. crassa. These results suggest that the vegetative compatibility phenotype may result from convergent evolution. Thus, the genes involved in this process may need to be identified at the species level or at the level of a group of species and could prove to be attractive targets for the development of antifungal agents.
Molecular Comparisons of Freshwater and Marine Isolates of the Same Morphospecies of Heterotrophic Flagellates
Authors: Scheckenbach Frank , Wylezich Claudia , Mylnikov Alexander P. , Weitere Markus , Arndt Hartmut 
Published: October 2006

ABSTRACT

Heterotrophic flagellates are key components of all ecosystems. Understanding the patterns of biodiversity of these organisms is thus particularly important. Here we analyzed the intraspecific diversity of 10 morphospecies of heterotrophic flagellates comprising representatives of the Apusozoa (2 morphospecies) and Kinetoplastea (8 morphospecies), all belonging to the most common flagellates with worldwide distribution. Most morphospecies showed a mixing of lineages isolated from diverse habitats, indicating that some lineages of these morphospecies had been able to colonize different habitats several times. Furthermore, our results revealed remarkable levels of genetic divergence within most of the morphospecies studied, underlining the difficulty of correctly determining species by means of morphology alone. Many cryptic or pseudocryptic species seem to occur. Our results revealed clear divergence between marine and freshwater lineages of the morphospecies
Ancyromonas sigmoides
, showing that freshwater lineages have not been able to colonize marine environments and marine lineages have not been able to colonize freshwater environments for a long time.
Accuracy of Cefoxitin Disk Testing for Characterization of Oxacillin Resistance Mediated by Penicillin-Binding Protein 2a in Coagulase-Negative Staphylococci
Authors: Perazzi B. , Fermepin M. Rodríguez , Malimovka A. , García S. D. , Orgambide M. , Vay C. A. , de Torres R. , Famiglietti A. M. R. 
Published: October 2006

ABSTRACT

The Clinical and Laboratory Standards Institute (CLSI) proposed, beginning in 2004, the use of cefoxitin disks to predict resistance mediated by the
mecA
gene in all species of coagulase-negative staphylococci (CoNS). The aim of this work was to evaluate the efficiency of the cefoxitin disk and of oxacillin-salt agar screening (MHOX) to characterize the oxacillin resistance mediated by the
mecA
gene in CoNS. One hundred seven CoNS isolates from different clinical samples were studied. Detection of the
mecA
gene by PCR was considered the “gold standard.” The susceptibility to oxacillin and cefoxitin was detected by the disk diffusion and agar dilution tests, as described by the CLSI. MHOX was also performed with 6 μg/ml of oxacillin and 4% NaCl. The sensitivities of the oxacillin and cefoxitin disks for all CoNS species were 88% and 80%, respectively, whereas the specificities were 63% and 100%, respectively. The sensitivities of the agar dilution test for oxacillin and cefoxitin (for proposed breakpoints of ≥4 μg/ml for resistance and ≤2 μg/ml for susceptibility) were 90% and 85%, respectively, whereas the specificities were 76% and 98%, respectively. MHOX showed a sensitivity of 90% and a specificity of 95% for all CoNS species. Both the MHOX and the cefoxitin disk results indicate that these are appropriate methods for the evaluation of oxacillin resistance mediated by the
mecA
gene in all CoNS species.
Evaluation of Molecular-Beacon, TaqMan, and Fluorescence Resonance Energy Transfer Probes for Detection of Antibiotic Resistance-Conferring Single Nucleotide Polymorphisms in Mixed
Mycobacterium tuberculosis
DNA Extracts
Authors: Yesilkaya Hasan , Meacci Francesca , Niemann Stefan , Hillemann Doris , Rüsch-Gerdes Sabine ,   LONG DRUG Study Group, Barer Michael R. , Andrew Peter W. , Oggioni Marco R. 
Published: October 2006

ABSTRACT

The ability of fluorescence resonance energy transfer, molecular-beacon, and TaqMan probes to detect single nucleotide polymorphism (SNP) in the presence of a wild-type allele was evaluated using drug resistance-conferring SNPs in mixed
Mycobacterium tuberculosis
DNA. It was found that both the absolute quantity and the ratio of alleles determine the detection sensitivity of the probe systems.
Identification of
Borrelia burgdorferi
Ribosomal Protein L25 by the Phage Surface Display Method and Evaluation of the Protein's Value for Serodiagnosis
Authors: Mueller Markus , Bunk Sebastian , Diterich Isabel , Weichel Michael , Rauter Carolin , Hassler Dieter , Hermann Corinna , Crameri Reto , Hartung Thomas 
Published: October 2006

ABSTRACT

The phage surface display technique was used to identify
Borrelia burgdorferi
antigens. By affinity selection with immunoglobulin G from pooled sera of six Lyme borreliosis (LB) patients, the ribosomal protein L25 was identified. The diagnostic value of L25 was investigated by an enzyme-linked immunosorbent assay, using sera from 80 LB patients and 75 controls, and the use of the protein resulted in a specificity of 99% and a 23% sensitivity, which qualify L25 as a useful antigen when combined with others.
In Vitro Activities of Daptomycin, Ciprofloxacin, and Other Antimicrobial Agents against the Cells and Spores of Clinical Isolates of
Bacillus
Species
Authors: Citron Diane M. , Appleman Maria D. 
Published: October 2006

ABSTRACT

Daptomycin inhibited 67 of 70 clinical isolates of
Bacillus
species at ≤1 μg/ml and 100% of them at ≤2 μg/ml. It showed bactericidal activity similar to that of ciprofloxacin against vegetative cells but not against spores. For 2 strains, the ciprofloxacin MICs were >4 g/ml, and 10 strains were resistant to erythromycin.