bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of flow injection analysis electrospray mass spectrometry and tandem mass spectrometry and electrospray high‐field asymmetric waveform ion mobility mass spectrometry and tandem mass spectrometry for the determination of underivatized amino acids
Authors: McCooeye Margaret , Mester Zoltán 
Published: May 2006

AbstractTwenty proteinogenic amino acids (AAs) were determined without derivatization using flow injection analysis followed by electrospray ionization mass spectrometry and tandem mass spectrometry (ESI‐MS and ESI‐MS/MS) and electrospray ionization high‐field asymmetric waveform ion mobility mass spectrometry and tandem mass spectrometry (ESI‐FAIMS‐MS and ESI‐FAIMS‐MS/MS), in positive and negative ionization modes. Three separate sets of ESI‐FAIMS conditions were used for the separation and detection of the 20 AAs. Typically ESI‐FAIMS‐MS showed somewhat improved sensitivity and significantly better signal‐to‐noise ratios than ESI‐MS mainly due to the elimination of background noise. However, the difference between ESI‐FAIMS‐MS and ESI‐MS/MS was significantly less. ESI‐FAIMS was able to partially or completely resolve all the isobaric amino acid overlaps such as leucine, isoleucine and hydroxyproline or lysine and glutamine. Detection limits for the amino acids in ESI‐FAIMS‐MS mode ranged from 2 ng/mL for proline to 200 ng/mL for aspartic acid. Overall, ESI‐FAIMS‐MS is the preferred method for the quantitative analysis of AAs in a hydrolyzed yeast matrix. Copyright © 2006 Crown in the right of Canada. Published by John Wiley & Sons, Ltd.
Contribution of the mu loop to the structure and function of rat glutathione transferase M1‐1
Authors: Hearne Jennifer L. , Colman Roberta F. 
Published: May 2006

AbstractThe “mu loop,” an 11‐residue loop spanning amino acid residues 33–43, is a characteristic structural feature of the mu class of glutathione transferases. To assess the contribution of the mu loop to the structure and function of rat GST M1‐1, amino acid residues 35–44 (35GDAPDYDRSQ44) were excised by deletion mutagenesis, resulting in the “Deletion Enzyme.” Kinetic studies reveal that the Km values of the Deletion Enzyme are markedly increased compared with those of the wild‐type enzyme: 32‐fold for 1‐chloro‐2,4‐dinitrobenzene, 99‐fold for glutathione, and 880‐fold for monobromobimane, while the Vmax value for each substrate is increased only modestly. Results from experiments probing the structure of the Deletion Enzyme, in comparison with that of the wild‐type enzyme, suggest that the secondary and quaternary structures have not been appreciably perturbed. Thermostability studies indicate that the Deletion Enzyme is as stable as the wild‐type enzyme at 4°C and 10°C, but it rapidly loses activity at 25°C, unlike the wild‐type enzyme. In the temperature range of 4°C through 25°C, the loss of activity of the Deletion Enzyme is not the result of a change in its structure, as determined by circular dichroism spectroscopy and sedimentation equilibrium centrifugation. Collectively, these results indicate that the mu loop is not essential for GST M1‐1 to maintain its structure nor is it required for the enzyme to retain some catalytic activity. However, it is an important determinant of the enzyme's affinity for its substrates.
Crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 reveals a new protein family with an RNA recognition motif‐like domain
Authors: Ebihara Akio , Yao Min , Masui Ryoji , Tanaka Isao , Yokoyama Shigeyuki , Kuramitsu Seiki 
Published: May 2006

AbstractWe have determined the crystal structure of hypothetical protein TTHB192 from Thermus thermophilus HB8 at 1.9 Å resolution. This protein is a member of the Escherichia coli ygcH sequence family, which contains ∼15 sequence homologs of bacterial origin. These homologs have a high isoelectric point. The crystal structure reveals that TTHB192 consists of two independently folded domains, and that each domain exhibits a ferredoxin‐like fold with a four‐stranded antiparallel β‐sheet packed on one side by α‐helices. These two tandem domains face each other to generate a β‐sheet platform. TTHB192 displays overall structural similarity to Sex‐lethal protein and poly(A)‐binding protein fragments. These proteins have RNA binding activity which is supported by a β‐sheet platform formed by two tandem repeats of an RNA recognition motif domain with signature sequence motifs on the β‐sheet surface. Although TTHB192 does not have the same signature sequence motif as the RNA recognition motif domain, the presence of an evolutionarily conserved basic patch on the β‐sheet platform could be functionally relevant for nucleic acid‐binding. This report shows that TTHB192 and its sequence homologs adopt an RNA recognition motif‐like domain and provides the first testable functional hypothesis for this protein family.
A categorization approach to automated ontological function annotation
Authors: Verspoor Karin , Cohn Judith , Mniszewski Susan , Joslyn Cliff 
Published: May 2006

AbstractAutomated function prediction (AFP) methods increasingly use knowledge discovery algorithms to map sequence, structure, literature, and/or pathway information about proteins whose functions are unknown into functional ontologies, typically (a portion of) the Gene Ontology (GO). While there are a growing number of methods within this paradigm, the general problem of assessing the accuracy of such prediction algorithms has not been seriously addressed. We present first an application for function prediction from protein sequences using the POSet Ontology Categorizer (POSOC) to produce new annotations by analyzing collections of GO nodes derived from annotations of protein BLAST neighborhoods. We then also present hierarchical precision and hierarchical recall as new evaluation metrics for assessing the accuracy of any predictions in hierarchical ontologies, and discuss results on a test set of protein sequences. We show that our method provides substantially improved hierarchical precision (measure of predictions made that are correct) when applied to the nearest BLAST neighbors of target proteins, as compared with simply imputing that neighborhood's annotations to the target. Moreover, when our method is applied to a broader BLAST neighborhood, hierarchical precision is enhanced even further. In all cases, such increased hierarchical precision performance is purchased at a modest expense of hierarchical recall (measure of all annotations that get predicted at all).
Functional annotation prediction: All for one and one for all
Authors: Sasson Ori , Kaplan Noam , Linial Michal 
Published: May 2006

AbstractIn an era of rapid genome sequencing and high‐throughput technology, automatic function prediction for a novel sequence is of utter importance in bioinformatics. While automatic annotation methods based on local alignment searches can be simple and straightforward, they suffer from several drawbacks, including relatively low sensitivity and assignment of incorrect annotations that are not associated with the region of similarity. ProtoNet is a hierarchical organization of the protein sequences in the UniProt database. Although the hierarchy is constructed in an unsupervised automatic manner, it has been shown to be coherent with several biological data sources. We extend the ProtoNet system in order to assign functional annotations automatically. By leveraging on the scaffold of the hierarchical classification, the method is able to overcome some frequent annotation pitfalls.
The effect of exercise in reducing desire to smoke and cigarette withdrawal symptoms is not caused by distraction
Authors: Daniel James Z. , Cropley Mark , Fife‐Schaw Chris 
Published: May 2006

ABSTRACTAims and design  Moderate‐intensity exercise has been shown to reduce common smoking withdrawal symptoms and desire to smoke in acutely abstinent smokers. The aim of the present study was to determine if this was caused by distraction. A secondary aim was to determine whether exercise‐related changes in affect were related to a reduction in symptoms.Methods  Forty ‘sedentary’ participants who had smoked at least 10 or more cigarettes per day for at least 3 years were assigned randomly to one of two groups. They completed either 10 minutes of moderate‐intensity exercise on a stationary bicycle ergometer or 10 minutes of a cognitive distraction task (paced visual serial addition task, PVSAT) after 11–15 hours of smoking abstinence. Participants rated smoking withdrawal symptoms and desire to smoke using standard scales at 10, 5 and 0 minutes before the experimental intervention, then at 5 and 10 minutes after the start of the intervention and 5 and 10 minutes after its completion.Findings  Significant group × time interactions were observed for ratings of desire to smoke and several withdrawal symptoms (irritability, depression, restlessness, difficulty concentrating and stress). There was a reduction in ratings during and immediately following exercise that was not observed with cognitive distraction. Also it was found the effects were not mediated by changes in affect observed in the exercise condition.Conclusions  A brief bout of moderate‐intensity exercise can lead to a rapid reduction in desire to smoke and withdrawal discomfort, which is not due to the distracting effect of exercise or the effects of mood. These findings support recommendations to smokers to use exercise as a means of helping cope with the difficulties encountered when they try to stop.
Communication skills in blind children: a preliminary investigation
Authors: James D. M. , Stojanovik V. 
Published: May 2006

AbstractBackground  There are anecdotal reports that blind children sometimes use language inappropriately, but there has been no recent systematic investigation of the communication skills of children with congenital blindness. The aim of the present study was to conduct a preliminary investigation of the communication skills of a group of children with congenital blindness.Methods  The parents of eight congenitally blind children completed the Children’s Communication Checklist‐2.Results  The checklist ratings showed that the communication profiles of a large proportion of the group warranted clinical investigation or were indicative of a communication disorder.Conclusions  The results from this preliminary investigation support the need for a larger study on the communication skills of children with congenital blindness.
The influence of volume, type of irrigant and flushing method on removing artificially placed dentine debris from the apical root canal during passive ultrasonic irrigation
Authors: Van Der Sluis L. W. M. , Gambarini G. , Wu M. K. , Wesselink P. R. 
Published: May 2006

AbstractAim  To determine the influence of volume, irrigant and method of flushing on the removal of artificially‐placed dentine debris from the apical part of root canals during passive ultrasonic irrigation.Methodology  Access cavities were prepared in 15 canine teeth and their root canals instrumented to size 20, 0.10 taper. Each root was split longitudinally, forming two halves. A groove was cut in the canal wall 2–6 mm from the apex in each half which was then filled with dentine debris prior to the roots being reassembled. All canals were ultrasonically irrigated, using a size 15, 0.02 taper smooth wire to a length of 21 mm that was placed in the canal to the apical foramen. In group 1 the canal was flushed with a continuous flow of 50 mL 2% sodium hypochlorite (NaOCl). In group 2 the continuous flow was not used but the canal was flushed with 12 mL 2% NaOCl, at a rate of 2 mL 30 s−1 using a syringe. Group 3 was treated in the same way as group 2 but the canal was flushed with 6 mL 2% NaOCl, at a rate of 2 mL min−1. Group 4 was treated in the same way as group 1 but water was used as the irrigant. Before and after irrigation, images of the grooves were captured and stored. The quantity of dentine debris in the groove was evaluated. The differences in debris scores between the experimental groups were analysed with the Kruskal–Wallis test and the Mann–Whitney U‐test. The level of significance was set at P = 0.05.Results  The difference between all groups was statistically significant (K–W test P < 0.001).Groups 1, 2 and 3 differed significantly from group 4 (P < 0.001); there was no significant difference between groups 1, 2 and 3 (P = 0.550).Conclusions  Syringe delivery of 2% NaOCl (6 and 12 mL) was as effective as a continuous flow of 2% NaOCl (50 mL). Water was not effective in removing dentine debris from grooves in the apical portion of root canals.
In vivo drafting of single‐chain antibodies for regulatory duty on the σ54‐promoter Pu of the TOL plasmid
Authors: Jurado Paola , Fernández Luis Angel , De Lorenzo Víctor 
Published: May 2006

SummaryThe identification of single‐chain antibodies (scFvs) that interfere in vivo with the building of the complex that activate the prokaryotic, σ54‐dependent promoter Pu of the catabolic TOL plasmid pWW0 is reported. To this end, a phage M13 library of scFvs was raised against the cognate prokaryotic enhancer‐binding activator, XylR. The scFv pool was then expressed intracellularly in a reporter Pu–lacZ strain of Escherichia coli designed to permit formation of intramolecular disulphide bonds in cytoplasmic proteins. This strain allowed the assembly of functional scFvs and the direct testing of their activity on the Pu promoter in vivo. Specifically, genetic screening for lacZ‐minus colonies yielded a number of scFvs able to downregulate transcriptional output in live cells. Two antibody clones were purified and shown to inhibit the activity of the same promoter in vitro as well. These scFvs targeted the DNA‐binding domain of XylR and its ATP binding site respectively. This work provides a proof of principle that mimetic regulatory factors can be derived from an antibody repertoire that specifically interact with given transcriptional activators. As assembly of initiation complexes is stimulated or inhibited by regulatory proteins we argue that anti‐XylR scFvs operate as bona fide transcriptional inhibitors of the Pu promoter.
(p)ppGpp regulates type 1 fimbriation of Escherichia coli by modulating the expression of the site‐specific recombinase FimB
Authors: Åberg Anna , Shingler Victoria , Balsalobre Carlos 
Published: May 2006

SummaryIn this report we have examined the role of the regulatory alarmone (p)ppGpp on expression of virulence determinants of uropathogenic Escherichia coli strains. The ability to form biofilms is shown to be markedly diminished in (p)ppGpp‐deficient strains. We present evidence (i) that (p)ppGpp tightly regulates expression of the type 1 fimbriae in both commensal and pathogenic E. coli isolates by increasing the subpopulation of cells that express the type 1 fimbriae; and (ii) that the effect of (p)ppGpp on the number of fimbrial expressing cells can ultimately be traced to its role in transcription of the fimB recombinase gene, whose product mediates inversion of the fim promoter to the productive (ON) orientation. Primer extension analysis suggests that the effect of (p)ppGpp on transcription of fimB occurs by altering the activity of only one of the two fimB promoters. Furthermore, spontaneous mutants with properties characteristic of ppGpp0 suppressors restore fimB transcription and consequent downstream effects in the absence of (p)ppGpp. Consistently, the rpoB3770 allele also fully restores transcription of fimB in a ppGpp0 strain and artificially elevated levels of FimB bypass the need for (p)ppGpp for type 1 fimbriation. Our findings suggest that the (p)ppGpp‐stimulated expression of type 1 fimbriae may be relevant during the interaction of pathogenic E. coli with the host.
Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism
Authors: Cadman Cassandra S.C. , Toorop Peter E. , Hilhorst Henk W.M. , Finch‐Savage William E. 
Published: May 2006

SummaryPhysiologically dormant seeds, like those of Arabidopsis, will cycle through dormant states as seasons change until the environment is favourable for seedling establishment. This phenomenon is widespread in the plant kingdom, but has not been studied at the molecular level. Full‐genome microarrays were used for a global transcript analysis ofArabidopsis thaliana(accession Cvi) seeds in a range of dormant and dry after‐ripened states during cycling. Principal component analysis of the expression patterns observed showed that they differed in newly imbibed primary dormant seeds, as commonly used in experimental studies, compared with those in the maintained primary and secondary dormant states that exist during cycling. Dormant and after‐ripened seeds appear to have equally active although distinct gene expression programmes, dormant seeds having greatly reduced gene expression associated with protein synthesis, potentially controlling the completion of germination. A core set of 442 genes were identified that had higher expression in all dormant states compared with after‐ripened states. Abscisic acid (ABA) responsive elements were significantly over‐represented in this set of genes the expression of which was enhanced when multiple copies of the elements were present. ABA regulation of dormancy was further supported by expression patterns of key genes in ABA synthesis/catabolism, and dormancy loss in the presence of fluridone. The data support an ABA–gibberelic acid hormone balance mechanism controlling cycling through dormant states that depends on synthetic and catabolic pathways of both hormones. Many of the most highly expressed genes in dormant states were stress‐related even in the absence of abiotic stress, indicating that ABA, stress and dormancy responses overlap significantly at the transcriptome level.
Evaluation of three different histamine concentrations in intradermal testing of normal cats and attempted determination of ‘irritant’ threshold concentrations for 48 allergens
Authors: Austel Michaela , Hensel Patrick , Jackson Dawn , Vidyashankar Anand , Zhao Ying , Medleau Linda 
Published: May 2006

AbstractThe purpose of this study was to determine the optimal histamine concentration and ‘irritant’ allergen threshold concentrations in intradermal testing (IDT) in normal cats. Thirty healthy cats were tested with three different histamine concentrations and four different concentrations of each allergen. The optimal histamine concentration was determined to be 1: 50 000 w/v (0.05 mg mL−1). Using this histamine concentration, the ‘irritant’ threshold concentration for most allergens was above the highest concentrations tested (4000 PNU mL−1 for 41 allergens and 700 PNU mL−1 for human dander). The ‘irritant’ threshold concentration for flea antigen was determined to be 1:750 w/v. More than 10% of the tested cats showed positive reactions to Dermatophagoides farinae, Dermatophagoides pteronyssinus, housefly, mosquito and moth at every allergen concentration, which suggests that the ‘irritant’ threshold concentration for these allergens is below 1000 PNU mL−1, the lowest allergen concentration tested. Our results confirm previous studies in indicating that allergen and histamine concentrations used in feline IDT may need to be revised.
Spatial and temporal patterns of Lolium rigidum–Avena sterilis mixed populations in a cereal field
Authors: BLANCO‐MORENO J M , CHAMORRO L , SANS F X 
Published: May 2006

SummaryThrough a detailed case study of a two‐species (Lolium rigidum and Avena sterilis) weed community at contrasting scales, this paper examined factors that affect weed distribution across space and time in a commercial wheat field in north‐east Spain. A. sterilis showed relatively stable spatial distribution and spatial structure of its population over time at large scale, with well‐defined patches, although weed density rose quickly. L. rigidum showed poorly defined patches that were not stable across time. Interaction between species could explain to some degree the spatial distribution at large scale: a negative relationship was detected between the spatial structures of both weed populations. At fine scale, both species showed a clear interaction effect from primary dispersal (more important in A. sterilis) and secondary dispersal from combine harvesting (more important in L. rigidum).
Practical experiences with a system for site‐specific weed control in arable crops using real‐time image analysis and GPS‐controlled patch spraying
Authors: GERHARDS R , OEBEL H 
Published: May 2006

SummaryInformation on temporal and spatial variation in weed seedling populations within agricultural fields is very important for weed population assessment and management. Primarily, spatial information allows a potential reduction in herbicide use, when post‐emergent herbicides are only applied to field sections with high weed infestation levels. This paper presents a system for site‐specific weed control in sugar beet, maize, winter wheat, winter barley, winter rape and spring barley. The system includes on‐line weed detection using digital image analysis, computer‐based decision making and Global Positioning System‐controlled patch spraying. In a 2‐year study, herbicide use with this map‐based approach was reduced in winter cereals by 6–81% for herbicides against broad leaved weeds and 20–79% for grass weed herbicides. Highest savings were achieved in cereals followed by sugar beet, maize and winter rape. The efficacy of weed control varied from 85% to 98%, indicating that site‐specific weed management will not result in higher infestation levels in the following crops.
Clinical behavior of multiple sclerosis is modulated by the MHC class I‐chain‐related gene A
Authors: Fdez‐Morera J. L. , Tunon A. , Rodriguez‐Rodero S. , Rodrigo L. , Martinez‐Borra J. , Gonzalez S. , Lopez‐Vazquez A. , Lahoz C. H. , Lopez‐Larrea C. 
Published: May 2006

AbstractIt is well known that certain HLA class II alleles confer an increased risk for developing multiple sclerosis (MS). Recent studies have suggested HLA class I as a region that may also contribute to the development of MS. In this study, we investigated the association between HLA‐DR, HLA‐B alleles, and major histocompatibility complex (MHC) class I‐chain‐related gene A (MICA) transmembrane (MICA‐TM) polymorphisms and disease progression in 104 MS patients and 116 healthy controls. DR1 was found to be decreased in patients when compared with controls (pc = 0.012). Neither HLA‐B nor HLA‐DR alleles were found to be associated with MS susceptibility. Furthermore, the prevalence of MICA‐A5 in patients with relapsing MS was 9% while the prevalence in progressive forms was 42% (pc = 0.0015). The extended haplotypes related to MICA‐TM5 that were found in our population were DR7‐MICA5‐B64 (EH 64.1, Δs = 0.38), DR4‐MICA5‐B62 (EH 62.1, Δs = 0.28), and DR11‐MICA5‐B35 (EH35.1, Δs = 0.10), but none of them were found to be associated to MS susceptibility or disease progression. Our data could indicate a possible role of MICA‐TM in MS prognosis.