bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brownian motion of polyphosphate complexes in yeast vacuoles: characterization by fluorescence microscopy with image analysis
Authors: Puchkov Evgeny O. 
Published: February 2010

AbstractIn the vacuoles of Saccharomyces cerevisiae yeast cells, vividly moving insoluble polyphosphate complexes (IPCs) <1 µm size, stainable by a fluorescent dye, 4′,6‐diamidino‐2‐phenylindole (DAPI), may appear under some growth conditions. The aim of this study was to quantitatively characterize the movement of the IPCs and to evaluate the viscosity in the vacuoles using the obtained data. Studies were conducted on S. cerevisiae cells stained by DAPI and fluorescein isothyocyanate‐labelled latex microspheres, using fluorescence microscopy combined with computer image analysis (ImageJ software, NIH, USA). IPC movement was photorecorded and shown to be Brownian motion. On latex microspheres, a methodology was developed for measuring a fluorescing particle's two‐dimensional (2D) displacements and its size. In four yeast cells, the 2D displacements and sizes of the IPCs were evaluated. Apparent viscosity values in the vacuoles of the cells, computed by the Einstein–Smoluchowski equation using the obtained data, were found to be 2.16 ± 0.60, 2.52 ± 0.63, 3.32 ± 0.9 and 11.3 ± 1.7 cP. The first three viscosity values correspond to 30–40% glycerol solutions. The viscosity value of 11.3 ± 1.7 cP was supposed to be an overestimation, caused by the peculiarities of the vacuole structure and/or volume in this particular cell. This conclusion was supported by the particular quality of the Brownian motion trajectories set in this cell as compared to the other three cells. Copyright © 2010 John Wiley & Sons, Ltd.
New applications of pHluorin—measuring intracellular pH of prototrophic yeasts and determining changes in the buffering capacity of strains with affected potassium homeostasis
Authors: Marešová Lydie , Hošková Barbora , Urbánková Eva , Chaloupka Roman , Sychrová Hana 
Published: February 2010

AbstractpHluorin is a pH‐sensitive variant of green fluorescent protein for measuring intracellular pH (pHin) in living cells. We constructed a new pHluorin plasmid with the dominant selection marker KanMX. This plasmid allows pH measurements in cells without auxotrophic mutations and/or grown in chemically indefinite media. We observed differing values of pHin for three prototrophic wild‐types. The new construct was also used to determine the pHin in strains differing in the activity of the plasma membrane Pma1 H+‐ATPase and the influence of glucose on pHin. We describe in detail pHluorin measurements performed in a microplate reader, which require much less hands‐on time and much lower cell culture volumes compared to standard cuvettes measurements. We also utilized pHluorin in a new method of measuring the buffering capacity of yeast cell cytosol in vivo, shown to be ca. 52 mM/pH for wild‐type yeast and moderately decreased in mutants with affected potassium transport. Copyright © 2010 John Wiley & Sons, Ltd.
Target validation and ligand development for a pathogenic fungal profilin, using a knock‐down strain of pathogenic yeast Candida glabrata and structure‐based ligand design
Authors: Ueno Keigo , Tamura Yutaka , Chibana Hiroji 
Published: February 2010

AbstractThe emergence of antifungal drug resistance is triggering vigorous searches for novel antifungal targets and lead compounds. In this study, we focused on fungal profilin, which is a small actin control protein sharing limited homology to human profilin. To validate its potentiality as a target, a profilin‐conditional mutant of the pathogenic yeast Candida glabrata was constructed, using a regulatable Tet promoter, and its growth was monitored in vitro. Repression of profilin expression led to severe growth defect, demonstrating the potential of this protein as a novel antifungal target. Next, novel peptides binding to the active interface of profilin were designed by computer simulation. ELISA analysis showed that these peptides did bind to the wild‐type profilin but bound less strongly to a profilin with amino acid substitutions at the active interface. Hence, we show here that profilin is a potential antifungal target and offer novel peptide ligands. Copyright © 2010 John Wiley & Sons, Ltd.
An International Perspective on Ultrasound Training and Use for Thyroid and Parathyroid Disease
Authors: Miller Barbra S. , Gauger Paul G. , Broome James T. , Burney Richard E. , Doherty Gerard M. 
Published: February 2010

AbstractBackgroundUse of ultrasound (USN) by endocrine surgeons has dramatically increased. Presently, optimal training and certification requirements have not been standardized at any level (resident/fellow/attending). We sought to define the types of USN training endocrine surgeons receive and how USN is employed in practice. We hypothesized that in more recent years fellowship‐trained endocrine surgeons were more likely to receive formal training in the use of USN during their endocrine surgery fellowship.MethodsA survey link was sent via email to a large group of endocrine surgeons around the world asking about the settings in which they received USN training, the type of instruction received, current use of USN, and other various questions. χ2 analysis was performed and P < 0.05 was considered significant.ResultsOne hundred twenty‐one surveys were collected from respondents in 27 countries. Median time from completion of residency to the present was 17 years (range = 2–49). Fifty‐nine percent of both fellowship‐ and nonfellowship‐trained endocrine surgeons currently use USN in their practice. Of those currently performing USN, 38% reported no USN training of any kind (47% international vs. 23% United States). USN experience among international and U.S. residents was not different (P = 0.27). Fifty‐nine percent of respondents reported completing an endocrine surgery fellowship; of those, 85% reported no formal USN training. Forty‐one percent reported not being comfortable performing USN at the completion of their endocrine surgery fellowships, requiring the presence of someone else to assist with the exam.ConclusionsUSN training among endocrine surgeons varies widely around the world. Despite an increase in the number of formal endocrine surgery fellowships offered, it does not appear that the number with formal USN training and certification has increased. Formal USN certification is achieved in only a minority of cases among practicing endocrine surgeons. It is currently unknown whether there is a difference in competency between endocrine surgeons with formal versus informal USN training.
HIV/Aids
Authors: Schafberger Armin 
Published: February 2010

Einleitung
Die antiretrovirale Therapie (ART) hat die Lebenserwartung von Menschen mit HIV deutlich erhöht. AIDS ist eine weitgehend vermeidbare Komplikation einer HIV-Infektion geworden und tritt vor allem noch bei zu später Diagnose oder zu spätem Therapiebeginn auf. Erkrankungen, die mit dem beschleunigten Alterungsprozess durch die HIV-Infektion oder mit den Langzeitnebenwirkungen von Medikamenten assoziiert sind, stellen neue Herausforderungen für die Therapie dar.
Pan-African metamorphic and magmatic rocks of the Khanka Massif, NE China: further evidence regarding their affinity
Authors: ZHOU JIAN-BO , WILDE SIMON A. , ZHAO GUO-CHUN , ZHANG XING-ZHOU , ZHENG CHANG-QING , WANG HU , ZENG WEI-SHUN 
Published: February 2010

AbstractThe Khanka Massif is a crustal block located along the eastern margin of the Central Asian Orogenic Belt (CAOB) and bordered to the east by Late Jurassic–Early Cretaceous circum-Pacific accretionary complexes of the Eastern Asian continental margin. It consists of graphite-, sillimanite- and cordierite-bearing gneisses, carbonates and felsic paragneisses, in association with various orthogneisses. Metamorphic zircons from a sillimanite gneiss from the Hutou complex yield a weighted mean206Pb/238U age of 490 ± 4 Ma, whereas detrital zircons from the same sample give ages from 934–610 Ma. Magmatic zircon cores in two garnet-bearing granite gneiss samples, also collected from the Hutou complex, yield weighted mean206Pb/238U ages of 522 ± 5 Ma and 515 ± 8 Ma, whereas their metamorphic rims record206Pb/238U ages of 510–500 Ma. These data indicate that the Hutou complex in the Khanka Massif records early Palaeozoic magmatic and metamorphic events, identical in age to those in the Mashan Complex of the Jiamusi Massif to the west. The older zircon populations in the sillimanite gneiss indicate derivation from Neoproterozoic sources, as do similar rocks in the Jiamusi Massif. These data confirm that the Khanka Massif has a close affinity with other major components of the CAOB to the west of the Dun-Mi Fault. Based on these results and previously published data, the Khanka Massif is therefore confirmed as having formed a single crustal entity with the Jiamusi (and possibly the Bureya) massif since Neoproterozoic time.
A serological study ofDirofilaria immitisin feral cats in Grenada, West Indies
Authors: Fernandez C. , Chikweto A. , Mofya S. , Lanum L. , Flynn P. , Burnett J.P. , Doherty D. , Sharma R.N. 
Published: February 2010

AbstractA study to determine the seroprevalence ofDirofilaria immitiswas carried out in feral cats in Grenada. Of the 137 feral cats tested for circulating antibodies (IgG; lateral-flow immunoassay) and circulating antigens (Ag; enzyme-linked immunosorbent assay), 8% (95% confidence interval (CI) 3.5–12.5%) were antibody positive and 5.1% (95% CI 1.4–8.8%) were antigen positive. No significant difference between cats aged>1 to 4 years and cats less than 1 year of age was found (P>0.05, χ2). There was also no significant difference (P>0.05, χ2) between male and female cats.Dirofilaria immitisprevalence is relatively high in the feral cat population of Grenada. Evidence ofD. immitisinfection in feral cats coupled with the endemic nature of heartworm disease in dogs in Grenada leads us to suggest the introduction of heartworm prophylaxis in cats. To the authors' knowledge, this serological evidence of heartworm infection in feral cats in Grenada is the first report from the Caribbean region.
Complete congenital third branchial fistula with left-sided, recurrent, suppurative thyroiditis
Authors: Madana J , Yolmo D , Gopalakrishnan S , K Saxena S 
Published: February 2010

AbstractObjective:We report an extremely rare case of a complete congenital third branchial arch fistula in a nine-year-old boy.Method:A case report and a review of the English literature concerning third branchial arch fistula of congenital origin are presented.Results:A nine-year-old boy presented with a history of a small opening in the middle third of the anterior neck since birth, with recurrent surrounding swelling. There was no history of surgical drainage or spontaneous rupture. Computed tomography with contrast injection into the external cervical opening revealed a patent tract from the neck skin to the base of the pyriform sinus. Complete excision of the tract up to the pyriform sinus with left hemithyroidectomy was performed. Follow up at 22 months showed no recurrence.Conclusion:To our knowledge, this case represents a very rare occurrence of the congenital variety of complete third branchial arch fistula at an unusual site. This case indicates that third branchial arch fistula can be complete, and may present in the anterior neck, an unusual site. In such cases, computed tomography fistulography and injection of dye into the pyriform sinus enables intra-operative delineation of the tract.
Nilpotent-by-abelian Lie algebras of type FPm
Authors: GROVES J. R. J. , KOCHLOUKOVA DESSISLAVA H. 
Published: February 2010

AbstractLet L be a finitely generated Lie algebra which is a split extension of a free nilpotent Lie algebra N by a finite dimensional abelian Lie algebra. Let V denote the quotient of N by its commutator subalgebra; we can regard V as a module for L/N. We discuss the relationship between the homological finiteness properties of V and those of L. In particular, we show that if L has type FPm and N has class c then V is 1 + c(m − 1)-tame (equivalently, the (1 + c(m − 1))th tensor power of V is finitely generated under the diagonal action of L/N).
Prevalence and clinical correlations of genetic subtypes ofGiardia lambliain an urban setting
Authors: BREATHNACH A. S. , McHUGH T. D. , BUTCHER P. D. 
Published: February 2010

SUMMARYThe clinical significance of different genetic subtypes or assemblages ofGiardia lambliais uncertain. Cases of giardiasis in south-west London between 1999 and 2005 were studied, comparing molecular-typing results with clinical and epidemiological findings from routine surveillance. We identified 819 cases, of whom 389 returned surveillance questionnaires. A subset of 267 faecal samples was submitted for typing by sequencing of the triose phosphate isomerase (tpi) and ribosomal RNA genes, and/or a separate duplex PCR of thetpigene. Typing was successful in 199 (75%) samples by at least one of the molecular methods. Assemblage A accounted for 48 (24%) samples and Assemblage B for 145 (73%); six (3%) were mixed. Both assemblages had similar seasonality, age distribution and association with travel. Clinical features were available for 59 successfully typed cases: both assemblages caused similar illness, but Assemblage A was significantly more frequently associated with fever than Assemblage B.
The use of a new virtual cohort study design to investigate an outbreak ofE. coliO157 linked to a supermarket delicatessen
Authors: McCARTNEY G. , COWDEN J. , MURRAY S. , AHMED S. 
Published: February 2010

SUMMARYIn outbreaks of foodborne disease associated with retail outlets, the outlet often closes as a precaution before the specific food vehicle has been identified. Suspect food vehicles may be named as part of general control measures. A conventional case-control study cannot be performed because both cases and potential controls are likely to be aware of the hypothesis and therefore potentially biased. Modern sales recording systems in many food retail outlets may provide a basis for constructing a virtual cohort and allow a statistical inference to be made about various possible vehicles of infection. In 2007, an outbreak ofE. coliO157 infection in Paisley, Scotland, was linked to cooked meat from a supermarket delicatessen using descriptive epidemiology. Construction of a virtual cohort allowed a relative risk and confidence interval to be estimated which supported the hypothesis of cooked beef topside being the vehicle of infection. This novel method could be valuable in the investigation of future outbreaks.
Trichinella infection in a hunting community in East Greenland
Authors: MØLLER L. N. , KOCH A. , PETERSEN E. , HJULER T. , KAPEL C. M. O. , ANDERSEN A. , MELBYE M. 
Published: February 2010

SUMMARYTrichinella nativa infection (trichinellosis) is highly prevalent in Arctic wildlife, but the human burden of trichinellosis in present-day Greenland is unknown. The study aimed to determine Trichinella seroprevalence in an eastern Greenlandic hunting community and to evaluate risk factors for seropositivity. Overall, 998 inhabitants aged ⩾10 years in the Ammassalik municipality were tested for Trichinella-specific IgG antibodies. Background information was obtained from questionnaires. Seropositivity was 1·4% in persons aged <40 years and increased to >12% in those aged ⩾60 years. Older age, occupation as hunter or fisherman, and consumption of polar bear meat significantly increased the risk of Trichinella seropositivity. The seropositivity age pattern probably reflects changes in dietary preferences, but could also reflect mandatory meat inspection since 1966. However, preventive measures against Trichinella infection should be strengthened in Greenland.
Counting Matchings and Tree-Like Walks in Regular Graphs
Authors: WANLESS IAN. M. 
Published: February 2010

The number of closed tree-like walks in a graph is closely related to the moments of the roots of the matching polynomial for the graph. Thus, by counting these walks up to a given length it is possible to find approximations for the matching polynomial. This approach has been used in two separate problems involving asymptotic enumerations of 1-factorizations of regular graphs. Nevertheless, a systematic way to count the required walks had not previously been found.In this paper we give an algorithm to count closed tree-like walks in a regular graph up to a given length. For smallm, this provides expressions for the number ofm-matchings in the graph in terms of the numbers of copies of certain small subgraphs that appear in the graph. The simplest of these expressions were already known, having been rediscovered by numerous authors usingad hocmethods. We offer the first general method for producing the expressions. We also find generating functions that isolate the contribution from the simplest kind of subgraph – namely a single cycle of arbitrary length.
Associations between being overweight, variability in heart rate, and well-being in the young men
Authors: Schmid Klaus , Schönlebe Jana , Drexler Hans , Mueck-Weymann Michael 
Published: February 2010

AbstractAbnormalities of the autonomic nervous system have been repeatedly shown in hypertension. We studied the associations between being overweight, blood pressure, cardiac vagal tone as measured by variability in heart rate, and well-being in a large cohort of young men. We hypothesised an inverse correlation between body mass index and the variability in heart rate. Further, we assessed systolic and diastolic blood pressure as traditional indicators of cardiovascular risk. Exclusion criteria were the use of drugs or pharmaceuticals. The following data from 786 men with a mean age of 19.4 years (standard deviation = 1.4, with a range from 16 to 24 years) were analysed in a cross-sectional study: body mass index, sleep duration, sporting activities, psychological well-being, blood pressure, heart rate, and variability in heart rate. Despite the young age of the men in this study, increased values for the body mass index were already associated with a shift in sympathovagal balance trending towards sympathetic dominance. There was also a significant positive correlation between body mass index and systolic and diastolic blood pressure. A multiple stepwise regression analysis showed that significant factors, which were associated with variability in heart rate, were body mass index and sporting activities. In addition, sporting activity and sleep duration had a significant positive impact on psychological well-being. Even in young men, being overweight is associated with increased cardiovascular risk, especially an increased sympathetic and/or lowered cardiovascular tone and increased blood pressure. Our study gives additional motivation for the early prevention and treatment of obesity in childhood and adolescence.
Continental Transform Basins: Why Are They Asymmetric?
Authors: Seeber Leonardo , Sorlien Christopher , Steckler Michael , Cormier Marie‐Helene 
Published: February 2010

Continental transforms constitute only a few of the world's plate boundaries and do not produce the largest earthquakes. Yet they are the tectonic underpinning of some of the most attractive and densely populated coastal environments. As a result, they have disproportionally contributed to catastrophic earthquakes. The most recent example is the M = 7.0 earthquake that struck Haiti on 12 January 2010, killing at least 100,000 people, by some reports.Because of concern for their earthquakes, continental transforms–particularly California's San Andreas Fault and Turkey's North Anatolian fault–have been intensely studied. Nonetheless, the link between the largest and most dangerous earthquakes and fault segments along transforms remains elusive. A better understanding of the structural singularities bounding these segments, particularly the subsurface nature of basins along transform faults, may clarify why some of them stop earthquake ruptures while others do not.
NO-γ emissions from streamer discharges: direct electron impact excitation versus resonant energy transfer
Authors: Liu Ningyu , Pasko Victor P 
Published: February 2010

It has been established that production of NO-γ emission in pulsed corona discharges is dominated by the energy transfer from
to the NO ground state NO(X
2Πr) while direct excitation by electron impact is negligible. However, recent studies suggest that the electron impact excitation plays a more important role. In this work, we report modelling results of NO-γ emission associated with streamer discharges using two cross section data sets available in the literature. The first set was originally reported by Mojarrabi et al (1996 Phys. Rev. A 54 2977–82) and later updated by Brunger et al (2000 J. Phys. B: At. Mol. Opt. Phys.
33 809–19); the second set was published by Hayashi (1990 Nonequilibrium Processes in Partially Ionized Gases (NATO Advanced Science Institutes Series, Series B, Physics vol 220) ed M Capitelli and J N Bardsley (New York: Plenum) pp 333–40). According to the results, the role played by the electron impact excitation in the production of NO-γ is drastically different when different cross sections are used. The results indicate that the first data set leads to better agreement with experimental measurements.
Microindel detection in short-read sequence data
Authors: Krawitz Peter , Rödelsperger Christian , Jäger Marten , Jostins Luke , Bauer Sebastian , Robinson Peter N. 
Published: February 2010

Abstract
Motivation: Several recent studies have demonstrated the effectiveness of resequencing and single nucleotide variant (SNV) detection by deep short-read sequencing platforms. While several reliable algorithms are available for automated SNV detection, the automated detection of microindels in deep short-read data presents a new bioinformatics challenge.
Results: We systematically analyzed how the short-read mapping tools MAQ, Bowtie, Burrows-Wheeler alignment tool (BWA), Novoalign and RazerS perform on simulated datasets that contain indels and evaluated how indels affect error rates in SNV detection. We implemented a simple algorithm to compute the equivalent indel region eir, which can be used to process the alignments produced by the mapping tools in order to perform indel calling. Using simulated data that contains indels, we demonstrate that indel detection works well on short-read data: the detection rate for microindels (&lt;4 bp) is &gt;90%. Our study provides insights into systematic errors in SNV detection that is based on ungapped short sequence read alignments. Gapped alignments of short sequence reads can be used to reduce this error and to detect microindels in simulated short-read data. A comparison with microindels automatically identified on the ABI Sanger and Roche 454 platform indicates that microindel detection from short sequence reads identifies both overlapping and distinct indels.
Contact: peter.krawitz@googlemail.com; peter.robinson@charite.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Phybase: an R package for species tree analysis
Authors: Liu Liang , Yu Lili 
Published: February 2010

Abstract
Motivation: Phybase is an R package for phylogenetic analysis using species trees. It provides functions to read, write, manipulate, simulate, estimate, summarize and plot species trees, which contain not only the topology and branch lengths but also population sizes.
Availability: The Phybase package is available at the R repository. The manual and supporting materials including source code, sample R code and sample data files for the species tree analysis are available at http://stat.osu.edu/∼liuliang/research/phybase.html
Contact: lliu@desu.edu