bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of incidence of tuberculosis infection in health-care workers using repeated interferon-γ assays
Authors: YOSHIYAMA T. , HARADA N. , HIGUCHI K. , NAKAJIMA Y. , OGATA H. 
Published: May 2009

SUMMARYThe aim was to estimate the incidence of Mycobacterium tuberculosis (Mtb) infection in health-care workers (HCWs) in Japan. We repeated cross-sectional surveys of HCWs with QuantiFERON®-TB Gold (QFT-G) in 2003, 2005 and 2007 at a hospital with tuberculosis (TB) wards, and 311 HCWs who underwent QFT-G testing two or three times were included in the study. Five HCWs (1·8%) converted from negative to positive. Incidence of new TB infection was estimated to be 0·6/100 person-years by the CDC's definition. Thirteen positive persons (41%) reverted from positive to negative. Multivariable logistic regression analysis identified a significant association between QFT-G conversion and working in TB wards. The IFN-γ levels of all but two subjects with reverting or converting QFT-G results were close to the test's cut-off. The incidence of Mtb infection in HCWs at our hospital was higher than that estimated for the general population in Japan. Criteria for defining QFT-G conversion and reversion need further investigation considering the high proportion of reversion, as the incidence of infection would have changed if we had applied other definitions.
Endothelium‐dependent Vasodilation in Myogenically Active Mouse Skeletal Muscle Arterioles: Role of EDH and K+ Channels
Authors: POTOCNIK SIMON J. , MCSHERRY IAIN , DING HONG , MURPHY TIMOTHY V. , KOTECHA NEELA , DORA KIM A. , YUILL KATHRYN H. , TRIGGLE CHRIS R. , HILL MICHAEL A. 
Published: May 2009

ABSTRACTAs smooth muscle cell (SMC) membrane potential (Em) is critical for vascular responsiveness, and arteriolar SMCs are depolarized at physiological intraluminal pressures, we hypothesized that myogenic tone impacts on dilation mediated by endothelium‐derived hyperpolarization (EDH). Studies were performed on cannulated mouse cremaster arterioles [diameter, 33±2 μm (n=23) at 60 mmHg; SMC Em ‐34.6±1.2 mV (n=7)]. Myogenic activity was assessed as tone developed in response to intraluminal pressure. Functional observations were related to mRNA, protein expression, and anatomy. Acetylcholine concentration‐response curves showed a modest shift following indomethacin (10 μM) and L‐NAME (100 μM), although maximal vasodilation was achieved. Residual dilation was removed by apamin (1 μM) in combination with TRAM‐34 (1 μM) or charybotoxin (0.1 μM), indicating the requirement of small (S) and intermediate (I) calcium‐activated potassium channels (KCa). Charybdotoxin, but not TRAM‐34, caused vasoconstriction, presumably through the inhibition of SMC BKCa. Expression of SK3 and IK1 was confirmed by immunohistochemistry and polymerase chain reaction, while myoendothelial junctions were common, suggesting a high degree of cell coupling. Also consistent with a role for endothelial KCa channels, acetylcholine increased endothelium [Ca2+]i. Apamin and TRAM‐34 similarly blocked EDH‐mediated dilation at intraluminal pressures of 30 and 90 mmHg, suggesting that in mouse arterioles, SKCa ‐ and IKCa ‐ mediated mechanisms predominate and operate independently of physiological levels of myogenic activation.
Threatened and stressed mountain lakes of Europe: Assessment and progress
Authors: Battarbee Richard W. , Kernan Martin , Rose Neil 
Published: May 2009

Mountain regions are cold environments that are hostile to human occupation and widely regarded as places where the air is clean, water is pure and ecosystems are pristine. Yet many mountain regions, especially in Europe, are far from pristine. In the 1980s, research showed that mountain lakes were especially vulnerable to acid deposition and sediment core studies at many sites demonstrated that some mountain lakes had become acidified over the course of the last century. Since then, studies of the water chemistry, biology and history of lakes across the different European mountain regions have increased our understanding of the processes within these systems, their ecological condition and the threats facing them. These studies have demonstrated that: i) gradients of sulphur, nitrogen, metals and persistent organic pollutant deposition occur from relatively uncontaminated regions in Spain and Central Norway to regions of heavy pollution loading in central and eastern Europe;ii) nitrate and sulphate concentrations in lake water reflect the gradients in atmospheric deposition;iii) concentrations of mercury, lead and cadmium in fish tissue show marked regional differences;iv) the spatial pattern of organochlorine concentrations in fish and in sediments follow the pattern for other pollutants, although there is also good evidence for the selective cold trapping of some compounds both at high latitudes and at high altitudes;v) fish suffer physiological stress in mountain lake-water of low ionic strength;vi) climate change over the last century is likely to have induced significant changes in lake ice-cover and water column stratification and mixing in some regions and these have in turn influenced the structure and productivity of biological communities;
This paper provides a review of the research undertaken on European mountain lakes over the past 30 years. In particular, it highlights the stresses faced by these vulnerable systems and the effects these have had, continue to have, and are likely to have on mountain lake ecosystems in future.
Use of predictive models and rapid methods to nowcast bacteria levels at coastal beaches
Authors: Francy Donna S. 
Published: May 2009

The need for rapid assessments of recreational water quality to better protect public health is well accepted throughout the research and regulatory communities. Rapid analytical methods, such as quantitative polymerase chain reaction (qPCR) and immunomagnetic separation/adenosine triphosphate (ATP) analysis, are being tested but are not yet ready for widespread use.
Another solution is the use of predictive models, wherein variable(s) that are easily and quickly measured are surrogates for concentrations of fecal-indicator bacteria. Rainfall-based alerts, the simplest type of model, have been used by several communities for a number of years. Deterministic models use mathematical representations of the processes that affect bacteria concentrations; this type of model is being used for beach-closure decisions at one location in the USA. Multivariable statistical models are being developed and tested in many areas of the USA; however, they are only used in three areas of the Great Lakes to aid in notifications of beach advisories or closings. These “operational” statistical models can result in more accurate assessments of recreational water quality than use of the previous day's Escherichia coli (E. coli) concentration as determined by traditional culture methods. The Ohio Nowcast, at Huntington Beach, Bay Village, Ohio, is described in this paper as an example of an operational statistical model. Because predictive modeling is a dynamic process, water-resource managers continue to collect additional data to improve the predictive ability of the nowcast and expand the nowcast to other Ohio beaches and a recreational river. Although predictive models have been shown to work well at some beaches and are becoming more widely accepted, implementation in many areas is limited by funding, lack of coordinated technical leadership, and lack of supporting epidemiological data.
Bathing water signage and predictive water quality models in Scotland
Authors: McPhail Calum D. , Stidson Ruth T. 
Published: May 2009

The Scottish Environment Protection Agency (SEPA) has developed, and runs, real-time bathing water quality predictions at ten sites throughout Scotland since 2004. Daily bathing water quality predictions are posted on electronic variable message signs at 10 beach locations networked to a central communication centre and updates are simultaneously made on the SEPA website, phone and text message service.
Antecedent rainfall and subsequent river flow can significantly increase the concentrations of faecal indicator organisms in bathing waters. The SEPA signage prediction tool, an Excel spreadsheet based model, was developed and used to set site-specific criteria for rainfall and river flow to predict bathing water quality based on historical data. Real-time predictions against the current EU Bathing Water Directive were correct or precautionary on 99% of days and correct for 82% of compliance samples during 2007, and 81% of compliance samples during the 2008 season.
The revised 2006 Directive sets out more stringent bathing water quality standards which require increased model performance. New predictive models are now being trailed using decision tree statistical software and are intended to replace the existing prediction tool by 2012.
FlexServ: an integrated tool for the analysis of protein flexibility
Authors: Camps Jordi , Carrillo Oliver , Emperador Agustí , Orellana Laura , Hospital Adam , Rueda Manuel , Cicin-Sain Damjan , D'Abramo Marco , Gelpí Josep Lluís , Orozco Modesto 
Published: May 2009

Abstract
Summary: FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics.
Availability: http://mmb.pcb.ub.es/FlexServ; http://www.inab.org
Contact: modesto@mmb.pcb.ub.es or gelpi@mmb.pcb.ub.es
Supplementary information: Additional information and methodology details can be found at http://mmb.pcb.ub.es/FlexServ/help.
MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining
Authors: DeLuca David S. , Beisswanger Elena , Wermter Joachim , Horn Peter A. , Hahn Udo , Blasczyk Rainer 
Published: May 2009

AbstractMotivation: The high level of polymorphism associated with the major histocompatibility complex (MHC) poses a challenge to organizing associated bioinformatic data, particularly in the area of hematopoietic stem cell transplantation. Thus, this area of research has great potential to profit from the ongoing development of biomedical ontologies, which offer structure and definition to MHC-data related communication and portability issues.Results: We introduce the design considerations, methodological foundations and implementational issues underlying MaHCO, an ontology which represents the alleles and encoded molecules of the major histocompatibility complex. Importantly for human immunogenetics, it includes a detailed level of human leukocyte antigen (HLA) classification. We then present an ontology browser, search interfaces for immunogenetic fact and document retrieval, and the specification of an annotation language for semantic metadata, based on MaHCO. These use cases are intended to demonstrate the utility of ontology-driven bioinformatics in the field of immunogenetics.Availability and Implementation: The MaHCO Ontology is available via the BioPortal: http://www.bioontology.org/tools/portal/bioportal.html, and at: http://purl.org/stemnet/Contact: david_deluca@dfci.harvard.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Measuring herring densities with one real and several phantom research vessels
Authors: Patel Ruben , Ona Egil 
Published: May 2009

AbstractPatel, R., and Ona, E. 2009. Measuring herring densities with one real and several phantom research vessels. – ICES Journal of Marine Science 66: 1264–1269. Vessel-induced avoidance can potentially cause a large bias in acoustic estimates of schooling, pelagic-fish biomass. This paper presents a method for quantifying this uncertainty. Volume-backscattering strength (Sv) from a horizontally projecting, multibeam sonar (Simrad MS70) is resampled to form synthetic, vertical, echosounder beams to the side of the survey vessel. These data are analysed as if they were collected from phantom vessels surveying parallel transects at fixed ranges from the real vessel. The nautical-area-backscattering coefficients (sA) from the synthetic echograms are compared with those measured by conventional 70 and 120 kHz echosounders (Simrad EK60) on the real vessel. Data collected in 2006 from schools of Norwegian spring-spawning herring are used to illustrate the method and explore its limitations. Potential effects of vessel-induced avoidance are evaluated by comparing the mean sA values observed from the phantom vessels with those observed from the real vessel. The technique also allows direct estimates of the mean lateral-aspect target strength of in situ herring.
Zooplankton spatial distribution along the South African coast studied by multifrequency acoustics, and its relationships with environmental parameters and anchovy distribution
Authors: Lebourges-Dhaussy Anne , Coetzee Janet , Hutchings Larry , Roudaut Gildas , Nieuwenhuys Cornelia 
Published: May 2009

Abstract
Lebourges-Dhaussy, A., Coetzee, J., Hutchings, L., Roudaut, G., and Nieuwenhuys, C. 2009. Zooplankton spatial distribution along the South African coast studied by multifrequency acoustics, and its relationships with environmental parameters and anchovy distribution. – ICES Journal of Marine Science, 66: 1055–1062. The Central Agulhas Bank (CAB) is an important component of the southern Benguela ecosystem. Despite relatively low primary production, secondary production supports large populations of mid-trophic-level pelagic fish. Exhaustive sampling of the Agulhas Bank ecosystem was performed during a routine acoustic biomass survey in November 2006. A TAPS-6 was deployed with near-simultaneous, plankton-net sampling. Concurrent collections of fish-school and environmental data permitted a detailed study of the water column. Zooplankton was classified by equivalent spherical diameter (ESD; mm): 0.0–0.35 (Class I), 0.35–0.8 (Class II), 0.8–2 (Class III), and >2.0 mm (Class IV). Clear relationships with environmental parameters were only evident at night on the CAB (west of 23°E) for Classes II and III. Class III exhibited pronounced diel vertical migrations, whereas Class I exhibited a reverse pattern. Also observed were the effects of anchovy predation on small zooplankton aggregated in areas of high chlorophyll a.
Collar Rot on Italian Alder Trees in California Caused by Phytophthora siskiyouensis
Authors: Rooney-Latham Suzanne , Blomquist Cheryl L. , Pastalka Tomas , Costello Laurence 
Published: May 2009

In November 2006, trees of Italian alder (Alnus cordata) were observed declining in association with bleeding trunk cankers in a commercial landscape in Foster City, CA. A species of Phytophthora was isolated on PARP selective medium from the leading edge of the cankers. The Phytophthora species was homothallic with primarily paragynous antheridia and had oospores that were mostly globose and aplerotic. Sporangia were produced from mycelia on plugs of carrot piece agar in soil extraction solution and were semi-papillate and ovoid to ellipsoid in shape. The intergenic transcribed spacer region of rDNA from an alder isolate matched with 100% identity to isolates in GenBank of Phytophthora siskiyouensis, a recently described species associated with tanoak and found in the soil and waterways of coastal Oregon. Pathogenicity was tested on young alder trees growing in pots. Pathogenicity was confirmed on Italian alder trees and potential pathogenicity was demonstrated on red and white alder trees. Accepted for publication 11 March 2009. Published 13 April 2009.
A Redox-Mediated Modulation of Stem Bolting in TransgenicNicotiana sylvestrisDifferentially Expressing the External Mitochondrial NADPH Dehydrogenase
Authors: Liu Yun-Jun , Nunes-Nesi Adriano , Wallström Sabá V. , Lager Ida , Michalecka Agnieszka M. , Norberg Fredrik E.B. , Widell Susanne , Fredlund Kenneth M. , Fernie Alisdair R. , Rasmusson Allan G. 
Published: May 2009

AbstractCytosolic NADPH can be directly oxidized by a calcium-dependent NADPH dehydrogenase, NDB1, present in the plant mitochondrial electron transport chain. However, little is known regarding the impact of modified cytosolic NADPH reduction levels on growth and metabolism. Nicotiana sylvestris plants overexpressing potato (Solanum tuberosum) NDB1 displayed early bolting, whereas sense suppression of the same gene led to delayed bolting, with consequential changes in flowering time. The phenotype was dependent on light irradiance but not linked to any change in biomass accumulation. Whereas the leaf NADPH/NADP+ ratio was unaffected, the stem NADPH/NADP+ ratio was altered following the genetic modification and strongly correlated with the bolting phenotype. Metabolic profiling of the stem showed that the NADP(H) change affected relatively few, albeit central, metabolites, including 2-oxoglutarate, glutamate, ascorbate, sugars, and hexose-phosphates. Consistent with the phenotype, the modified NDB1 level also affected the expression of putative floral meristem identity genes of the SQUAMOSA and LEAFY types. Further evidence for involvement of the NADPH redox in stem development was seen in the distinct decrease in the stem apex NADPH/NADP+ ratio during bolting. Additionally, the potato NDB1 protein was specifically detected in mitochondria, and a survey of its abundance in major organs revealed that the highest levels are found in green stems. These results thus strongly suggest that NDB1 in the mitochondrial electron transport chain can, by modifying cell redox levels, specifically affect developmental processes.
FRIGIDA Delays Flowering in Arabidopsis via a Cotranscriptional Mechanism Involving Direct Interaction with the Nuclear Cap-Binding Complex
Authors: Geraldo Nuno , Bäurle Isabel , Kidou Shin-ichiro , Hu Xiangyang , Dean Caroline 
Published: May 2009

AbstractA major determinant of flowering time in natural Arabidopsis (Arabidopsis thaliana) variants is FRIGIDA (FRI). FRI up-regulates expression of the floral repressor FLOWERING LOCUS C (FLC), thereby conferring a vernalization requirement and a winter annual habit. FRI encodes a novel nuclear protein with no conserved domains except for two coiled-coil regions. A mutation in the large subunit of the nuclear cap-binding complex (CBC) suppresses FRI activity, so we have explored the connection between FRI and the nuclear CBC in order to gain further insight into FRI biochemical activity. Mutations in the small subunit of the CBC (CBP20) also suppress FRI up-regulation of FLC. CBP20 interacted directly with FRI in yeast and in planta, and this association of FRI with the 5′ cap was reinforced by an RNA ligase-mediated rapid amplification of cDNA ends assay that showed FRI decreased the proportion of FLC transcripts lacking a 5′ cap. Loss of CBP20 resulted in very low FLC mRNA levels and an increased proportion of unspliced FLC transcripts. FRI compensated for CBP20 loss, partially restoring FLC levels and normalizing the unspliced-spliced transcript ratio. Our data suggest that FRI up-regulates FLC expression through a cotranscriptional mechanism involving direct physical interaction with the nuclear CBC with concomitant effects on FLC transcription and splicing.
Site-Specific Integration of Transgenes in Soybean via Recombinase-Mediated DNA Cassette Exchange
Authors: Li Zhongsen , Xing Aiqiu , Moon Bryan P. , McCardell Richard P. , Mills Kelly , Falco S. Carl 
Published: May 2009

Abstract
A targeting method to insert genes at a previously characterized genetic locus to make plant transformation and transgene expression predictable is highly desirable for plant biotechnology. We report the successful targeting of transgenes to predefined soybean (Glycine max) genome sites using the yeast FLP-FRT recombination system. First, a target DNA containing a pair of incompatible FRT sites flanking a selection gene was introduced in soybean by standard biolistic transformation. Transgenic events containing a single copy of the target were retransformed with a donor DNA, which contained the same pair of FRT sites flanking a different selection gene, and a FLP expression DNA. Precise DNA cassette exchange was achieved between the target and donor DNA via recombinase-mediated cassette exchange, so that the donor DNA was introduced at the locus previously occupied by the target DNA. The introduced donor genes expressed normally and segregated according to Mendelian laws.
A Visual Reporter System for Virus-Induced Gene Silencing in Tomato Fruit Based on Anthocyanin Accumulation
Authors: Orzaez Diego , Medina Aurora , Torre Sara , Fernández-Moreno Josefina Patricia , Rambla José Luis , Fernández-del-Carmen Asun , Butelli Eugenio , Martin Cathie , Granell Antonio 
Published: May 2009

AbstractVirus-induced gene silencing (VIGS) is a powerful tool for reverse genetics in tomato (Solanum lycopersicum). However, the irregular distribution of the effects of VIGS hampers the identification and quantification of nonvisual phenotypes. To overcome this limitation, a visually traceable VIGS system was developed for fruit, comprising two elements: (1) a transgenic tomato line (Del/Ros1) expressing Antirrhinum majus Delila and Rosea1 transcription factors under the control of the fruit-specific E8 promoter, showing a purple-fruited, anthocyanin-rich phenotype; and (2) a modified tobacco rattle virus VIGS vector incorporating partial Rosea1 and Delila sequences, which was shown to restore the red-fruited phenotype upon agroinjection in Del/Ros1 plants. Dissection of silenced areas for subsequent chemometric analysis successfully identified the relevant metabolites underlying gene function for three tomato genes, phytoene desaturase, TomloxC, and SlODO1, used for proof of concept. The C-6 aldehydes derived from lipid 13-hydroperoxidation were found to be the volatile compounds most severely affected by TomloxC silencing, whereas geranial and 6-methyl-5-hepten-2-one were identified as the volatiles most severely reduced by phytoene desaturase silencing in ripening fruit. In a third example, silencing of SlODO1, a tomato homolog of the ODORANT1 gene encoding a myb transcription factor, which regulates benzenoid metabolism in petunia (Petunia hybrida) flowers, resulted in a sharp accumulation of benzaldehyde in tomato fruit. Together, these results indicate that fruit VIGS, enhanced by anthocyanin monitoring, can be a powerful tool for reverse genetics in the study of the metabolic networks operating during fruit ripening.