bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Organization of the Inverted Repeats of IS30
Authors: Szabó Mónika , Kiss János , Olasz Ferenc 
Published: April 2010

ABSTRACTThe mobile element IS30has 26-bp imperfect terminal inverted repeats (IRs) that are indispensable for transposition. We have analyzed the effects of IR mutations on both major transposition steps, the circle formation and integration of the abutted ends, characteristic for IS30. Several mutants show strikingly different phenotypes if the mutations are present at one or both ends and differentially influence the transposition steps. The two IRs are equivalent in the recombination reactions and contain several functional regions. We have determined that positions 20 to 26 are responsible for binding of the N-terminal domain of the transposase and the formation of a correct 2-bp spacer between the abutted ends. However, integration is efficient without this region, suggesting that a second binding site for the transposase may exist, possibly within the region from 4 to 11 bp. Several mutations at this part of the IRs, which are highly conserved in the IS30family, considerably affected both major transposition steps. In addition, positions 16 and 17 seem to be responsible for distinguishing the IRs of related insertion sequences by providing specificity for the transposase to recognize its cognate ends. Finally, we show bothin vivoandin vitrothat position 3 has a determining role in the donor function of the ends, especially in DNA cleavage adjacent to the IRs. Taken together, the present work provides evidence for a more complex organization of the IS30IRs than was previously suggested.
Vp1659 Is a
Vibrio parahaemolyticus
Type III Secretion System 1 Protein That Contributes to Translocation of Effector Proteins Needed To Induce Cytolysis, Autophagy, and Disruption of Actin Structure in HeLa Cells
Authors: Zhou Xiaohui , Konkel Michael E. , Call Douglas R. 
Published: April 2010

ABSTRACT

Vibrio parahaemolyticus
harbors two type III secretion systems (T3SSs; T3SS1 and T3SS2), of which T3SS1 is involved in host cell cytotoxicity. T3SS1 expression is positively regulated by ExsA, and it is negatively regulated by ExsD. We compared the secretion profiles of a wild-type strain (NY-4) of
V. parahaemolyticus
with those of an ExsD deletion mutant (Δ
exsD
) and with a strain of NY-4 that overexpresses T3SS1 (NY-4:p
exsA
). From this comparison, we detected a previously uncharacterized protein, Vp1659, which shares some sequence homology with LcrV from
Yersinia
. We show that
vp1659
expression is positively regulated by ExsA and is negatively regulated by ExsD. Vp1659 is specifically secreted by T3SS1 of
V. parahaemolyticus
, and Vp1659 is not required for the successful extracellular secretion of another T3SS1 protein, Vp1656. Mechanical fractionation showed that Vp1659 is translocated into HeLa cells in a T3SS1-dependent manner and that deletion of Vp1659 does not prevent VopS from being translocated into HeLa cells during infection. Deletion of
vp1659
significantly reduces cytotoxicity when HeLa cells are infected by
V. parahaemolyticus
, while complementation of the Δ
vp1659
strain restores cytotoxicity. Differential staining showed that Vp1659 is required to induce membrane permeability in HeLa cells. We also show evidence that Vp1659 is required for actin rearrangement and the induction of autophagy. On the basis of these data, we conclude that Vp1659 is a T3SS1-associated protein that is a component of the secretion apparatus and that it is necessary for the efficient translocation of effector proteins into epithelial cells.
Isolation of the Fungus
Geosmithia argillacea
in Sputum of People with Cystic Fibrosis
Authors: Barton R. C. , Borman A. M. , Johnson E. M. , Houbraken J. , Hobson R. P. , Denton M. , Conway S. P. , Brownlee K. G. , Peckham D. , Lee T. W. R. 
Published: April 2010

ABSTRACT

We report the repeated isolation of the fungus
Geosmithia argillacea
from sputum samples of people with cystic fibrosis. Identification was based on morphology and DNA sequence analysis. Isolation of
G. argillacea
did not appear to be associated with clinical deterioration. The pathogenic potential of
G. argillacea
is discussed.
Does Bleach Processing Increase the Accuracy of Sputum Smear Microscopy for Diagnosing Pulmonary Tuberculosis?
Authors: Cattamanchi A. , Davis J. L. , Pai M. , Huang L. , Hopewell P. C. , Steingart K. R. 
Published: April 2010

ABSTRACT

Bleach digestion of sputum prior to smear preparation has been reported to increase the yield of microscopy for diagnosing pulmonary tuberculosis, even in high-HIV-prevalence settings. To determine the diagnostic accuracy of bleach microscopy, we updated a systematic review published in 2006 and applied the Grading of Recommendations Assessment, Development, and Evaluation framework to rate the overall quality of the evidence. We searched multiple databases (as of January 2009) for primary studies in all languages comparing bleach and direct microscopy. We assessed study quality using a validated tool and heterogeneity by standard methods. We used hierarchical summary receiver operating characteristic (HSROC) analysis to calculate summary estimates of diagnostic accuracy and random-effects meta-analysis to pool sensitivity and specificity differences. Of 14 studies (11 papers) included, 9 evaluated bleach centrifugation and 5 evaluated bleach sedimentation. Overall, examination of bleach-processed versus direct smears led to small increases in sensitivity (for bleach centrifugation, 6% [95% confidence interval {CI} = 3 to 10%,
P
= 0.001]; for bleach sedimentation, 9% [95% CI = 4 to 14%,
P
= 0.001]) and small decreases in specificity (for bleach centrifugation, −3% [95% CI = −4% to −1%,
P
= 0.004]; for bleach sedimentation, −2% [95% CI = −5% to 0%,
P
= 0.05]). Similarly, analysis of HSROC curves suggested little or no improvement in diagnostic accuracy. The quality of evidence was rated very low for both bleach centrifugation and bleach sedimentation. This updated systematic review suggests that the benefits of bleach processing are less than those described previously. Further research should focus on alternative approaches to optimizing smear microscopy, such as light-emitting diode fluorescence microscopy and same-day sputum collection strategies.
Development and Evaluation of a Simple Assay for Marburg Virus Detection Using a Reverse Transcription-Loop-Mediated Isothermal Amplification Method
Authors: Kurosaki Yohei , Grolla Allen , Fukuma Aiko , Feldmann Heinz , Yasuda Jiro 
Published: April 2010

ABSTRACT

Marburg virus (MARV) causes a severe hemorrhagic fever in humans with a high mortality rate. The rapid and accurate identification of the virus is required to appropriately provide infection control and outbreak management. Here, we developed and evaluated a one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and simple detection of MARV. By combining two sets of primers specific for the Musoke and Ravn genetic lineages, a multiple RT-LAMP assay detected MARV strains of both lineages, and no cross-reactivity with other hemorrhagic fever viruses (Ebola virus and Lassa virus) was observed. The assay could detect 10
2
copies of the viral RNA per tube within 40 min by real-time monitoring of the turbidities of the reaction mixtures. The assay was further evaluated using viral RNA extracted from clinical specimens collected in the 2005 Marburg hemorrhagic fever outbreak in Angola and yielded positive results for samples containing MARV at greater than 10
4
50% tissue culture infective doses/ml, exhibiting 78% (14 of 18 samples positive) consistency with the results of a reverse transcription-PCR assay carried out in the field laboratory. The results obtained by both agarose gel electrophoresis and naked-eye judgment indicated that the RT-LAMP assay developed in this study is an effective tool for the molecular detection of MARV. Furthermore, it seems suitable for use for field diagnostics or in laboratories in areas where MARV is endemic.
Mupirocin Resistance Related to Increasing Mupirocin Use in Clinical Isolates of Methicillin-Resistant
Staphylococcus aureus
in a Pediatric Population
Authors: Hogue Jacob S. , Buttke Patricia , Braun LoRanee E. , Fairchok Mary P. 
Published: April 2010

ABSTRACT

We investigated the proportion of methicillin-resistant
Staphylococcus aureus
(MRSA) isolates from pediatric patients demonstrating mupirocin resistance related to mupirocin use at our institution. No mupirocin resistance was found in 98% of isolates, whereas mupirocin prescriptions increased by 110%. Resistance rates remained low despite the increasing use of mupirocin.
Simple PCR-Based DNA Microarray System To Identify Human Pathogenic Fungi in Skin
Authors: Sato Tomotaka , Takayanagi Atsushi , Nagao Keisuke , Tomatsu Nobuhiro , Fukui Toshifumi , Kawaguchi Masahiro , Kudoh Jun , Amagai Masayuki , Yamamoto Nobuko , Shimizu Nobuyoshi 
Published: April 2010

ABSTRACT
Fungal diseases in immunocompromised hosts pose significant threats to their prognoses. An accurate diagnosis and identification of the fungal pathogens causing the infection are critical to determine the proper therapeutic interventions, but these are often not achieved, due to difficulties with isolation and morphological identification. In an effort to ultimately carry out the simultaneous detection of all human pathogenic microbes, we developed a simple system to identify 26 clinically important fungi by using a combination of PCR amplification and DNA microarray assay (designated PCR-DM), in which PCR-amplified DNA from the internal transcribed spacer region of the rRNA gene was hybridized to a DNA microarray fabricated with species-specific probes sets using the Bubble Jet technology. PCR-DM reliably identified all 26 reference strains; hence, we applied it to cases of onychomycosis, taking advantage of the accessibility of tissue from skin. PCR-DM detected fungal DNA and identified pathogens in 92% of 106 microscopy-confirmed onychomycosis specimens. In contrast, culture was successful for only 36 specimens (34%), 3 of which had results inconsistent with the results of PCR-DM, but sequence analysis of the isolates proved that the PCR-DM result was correct. Thus, PCR-DM provides a powerful method to identify pathogenic fungi with high sensitivity and speed directly from tissue specimens, and this concept could be applied to other fungal or nonfungal infectious human diseases in less accessible anatomical sites.
HER-2/NEU overexpression in vulvar Paget disease: the Yale experience
Authors: Richter Christine E , Hui Pei , Buza Natalia , Silasi Dan-Arin , Azodi Masoud , Santin Alessandro D , Schwartz Peter E , Rutherford Thomas J 
Published: April 2010

AimsTo determine the level of HER-2/neu overexpression in vulvar Paget disease (PD) in order to assess the possibility of using HER-2/neu as a target for the treatment of Paget disease.MethodsA medical record search identified 39 patients with a histologically confirmed diagnosis of vulvar PD between 1986 and 2009. A tissue microarray containing all 39 tumour samples was created, and corresponding sections were stained immunohistochemically with an anti-HER-2/neu-antibody (HercepTest). Staining results were reported on a scale from 0 to 3+. 2+ and 3+ were considered as HER-2/neu overexpression. The HER-2/neu expression was correlated with clinical, pathological and outcome data.ResultsNegative staining for HER-2/neu was noticed in four patients (12%), 1+ in 10 patients (30%), 2+ in 11 patients (33%) and 3+ in eight patients (25%), resulting in 19 patients with HER-2/neu overexpression (2+ and 3+, 58%) and 14 patients without HER-2/neu overexpression (0 and 1+, 42%). The proportion of HER-2/neu overexpression was higher in the patients with invasive than with non-invasive PD (71%, n=5/7 invasive PD vs 54%, n=14/26 non-invasive PD). There was no significant correlation between HER-2/neu staining results and clinical, pathological or outcome data.ConclusionsSurgical treatment of vulvar Paget disease is associated with a high recurrence rate and extensive reconstructive procedures. In this study, over 50% of the patients with vulvar Paget disease overexpress HER-2/neu. Anti-HER-2/neu-antibodies like trastuzumab may therefore be an interesting treatment option for HER-2/neu-positive vulvar Paget disease. Clinical trials are needed to evaluate the efficacy of trastuzumab in this disease.
Optimal distance bounds for fast search on compressed time-series query logs
Authors: Vlachos Michail , Kozat Suleyman S. , Yu Philip S. 
Published: April 2010

Consider a database of time-series, where each datapoint in the series records the total number of users who asked for a specific query at an internet search engine. Storage and analysis of such logs can be very beneficial for a search company from multiple perspectives. First, from a data organization perspective, because query Weblogs capture important trends and statistics, they can help enhance and optimize the search experience (keyword recommendation, discovery of news events). Second, Weblog data can provide an important polling mechanism for the microeconomic aspects of a search engine, since they can facilitate and promote the advertising facet of the search engine (understand what users request and when they request it).
Due to the sheer amount of time-series Weblogs, manipulation of the logs in a compressed form is an impeding necessity for fast data processing and compact storage requirements. Here, we explicate how to compute the lower and upper distance bounds on the time-series logs when working directly on their compressed form. Optimal distance estimation means tighter bounds, leading to better candidate selection/elimination and ultimately faster search performance. Our derivation of the optimal distance bounds is based on the careful analysis of the problem using optimization principles. The experimental evaluation suggests a clear performance advantage of the proposed method, compared to previous compression/search techniques. The presented method results in a 10--30% improvement on distance estimations, which in turn leads to 25--80% improvement on the search performance.
A case for the accountable cloud
Authors: Haeberlen Andreas 
Published: April 2010

For many companies, clouds are becoming an interesting alternative to a dedicated IT infrastructure. However, cloud computing also carries certain risks for both the customer and the cloud provider. The customer places his computation and data on machines he cannot directly control; the provider agrees to run a service whose details he does not know. If something goes wrong - for example, data leaks to a competitor, or the computation returns incorrect results - it can be difficult for customer and provider to determinewhich of themhas caused the problem, and, in the absence of solid evidence, it is nearly impossible for them to hold each other responsible for the problem if a dispute arises.
In this paper, we propose that the cloud should be made accountable to both the customer and the provider. Both parties should be able to check whether the cloud is running the service as agreed. If a problem appears, they should be able to determine which of them is responsible, and to prove the presence of the problem to a third party, such as an arbitrator or a judge. We outline the technical requirements for an accountable cloud, and we describe several challenges that are not yet met by current accountability techniques.
Marcion’s Antitheses and the Isagogic Genre
Authors: Scherbenske Eric W. 
Published: April 2010

AbstractAccording to early Christian heresiologists, the Antitheses articulated Marcion’s fundamental convictions based on the separation of the God of the Hebrew Bible from the God of the Christ. While scholars have long stressed the importance of this separation for Marcion’s theology, the genre of the Antitheses, the primary vehicle for this belief, remains problematic. This article proposes that Marcion’s Antitheses ought to be categorized as isagogic, a genre utilized primarily for preliminary instruction. A survey of the salient characteristics of isagogic texts reveals that in form, content, audience, and function, the Antitheses (as described by Marcion’s opponents) align nicely with this genre. Identifying the Antitheses as an isagogic text offers insight into Marcion’s composition and deployment of this work for his evangelic campaign; by leading the reader into a Marcionite interpretation of the scriptures, the Antitheses fostered the catechetical indoctrination and continual growth in the rudiments of his faith.
Spatial Predictions of Extreme Wind Speeds over Switzerland Using Generalized Additive Models
Authors: Etienne Christophe , Lehmann Anthony , Goyette Stéphane , Lopez-Moreno Juan-Ignacio , Beniston Martin 
Published: April 2010

AbstractThe purpose of this work is to present a methodology aimed at predicting extreme wind speeds over Switzerland. Generalized additive models are used to regionalize wind statistics for Swiss weather stations using a number of variables that describe the main physiographical features of the country. This procedure enables one to present the results for Switzerland in the form of a map that provides the 98th percentiles of daily maximum wind speeds (W98) at a 10-m anemometer height for cells with a 50-m grid interval. This investigation comprises three major steps. First, meteorological data recorded by the weather stations was gathered to build local wind statistics at each station. Then, data describing the topographic and landscape characteristics of the country were prepared using geographic information systems (GIS). Third, appropriate regression models were selected to make spatially explicit predictions of extreme wind speeds in Switzerland. The predictions undertaken in this study provide realistic values of the W98. The effects of topography on the results are particularly conspicuous. Wind speeds increase with altitude and are greatest on mountain peaks in the Alps, as would be intuitively expected. Relative errors between observations and model results calculated for the meteorological stations do not exceed 30%, and only 12 out of 70 stations exhibit errors that exceed 20%. The combination of GIS techniques and statistical models used to predict a highly uncertain variable, such as extreme wind speed, yields interesting results that can be extended to other fields, such as the assessment of storm damage on infrastructures.
Investigating the Influence of Carbon Dioxide and the Stratosphere on the Long-Term Tropospheric Temperature Monitoring from HIRS
Authors: Chung Eui-Seok , Soden Brian J. 
Published: April 2010

Abstract
Contrary to a midtropospheric warming trend detected from Microwave Sounding Unit (MSU) measurements, High-Resolution Infrared Radiation Sounder (HIRS) temperature (15 μm) channels, sensitive to the thermal emission from the troposphere, produce distinct cooling trends for the period 1980–99. This apparent discrepancy in the tropospheric temperature trend is investigated through radiative transfer simulations using Geophysical Fluid Dynamics Laboratory climate model output and the profiles of the standard model atmospheres. Radiative simulations with time-invariant carbon dioxide concentration throughout the entire analysis period produce trends that are qualitatively similar to that obtained from the MSU observations, implying that the observed cooling trends of the HIRS temperature channels are attributable to increased carbon dioxide concentration over the 20-yr period. Additional simulations with the observed time-varying concentration of carbon dioxide confirm this basic result. Whereas temperature fluctuations dominate variability on monthly to interannual time scales, carbon dioxide changes dominate the decadal trends in both the observations and model simulations. Further simulations examined the sensitivity of the brightness temperature change with respect to the changes in tropospheric and stratospheric temperature. These calculations indicate that the influences of stratospheric temperature on the measured radiances are greater for the HIRS temperature channels relative to the MSU midtropospheric channel. These results highlight the contributions of time-varying carbon dioxide concentrations and stratospheric temperature to the HIRS 15-μm (temperature channel) radiance record and underscore the importance of accurately accounting for these changes when using HIRS measurements for long-term monitoring.
A Nonlinear Impedance Relation for the Surface Winds in Pressure Disturbances
Authors: Coleman Timothy A. , Knupp Kevin R. 
Published: April 2010

Abstract
The “impedance relation” between the wind perturbation within an ageostrophic atmospheric disturbance and its pressure perturbation and intrinsic propagation speed has been in use for decades. The correlation between wind and pressure perturbation was established through this relation. However, a simple Lagrangian model of an air parcel traversing an idealized sinusoidal wave in the pressure field indicates that the impedance relation produces significant errors. Examination of the nonlinearized horizontal momentum equation with a sinusoidal disturbance in pressure reveals an additional nonlinear term in the impedance relation, not previously included.
In this paper, the impedance relation is rederived, with the solution being the original equation with the addition of the nonlinear term. The new equation is then evaluated against the Lagrangian model of an air parcel traversing an idealized gravity wave, as well as three observed cases. It is shown that the new impedance relation is indeed more accurate in predicting wind perturbations in disturbances based on pressure perturbations and intrinsic speed than the accepted equation. Implications for determination of the intrinsic phase speed of a disturbance when pressure and wind perturbations are known (another widely used application of the impedance relation) are also discussed.
Clinical determinants of migraine preventive treatment: Contribution of SMILE, an observational survey of primary care migraine management in France
Authors: Valade D , Lantéri-Minet M , Radat F , Mekies C , Lucas C , Vivès E , Joubert JM , Géraud G 
Published: April 2010

Methods: SMILE was an observational study carried out in France among office-based general practitioners (GPs) and neurologists from November 2005 to July 2006 to assess the determinants of prescription of migraine preventive therapy in primary care medicine. A total of 1467 GPs and 83 neurologists were included, treating 5417 and 248 migraine sufferers, respectively. Results: The main factors leading physicians to deem a patient eligible for preventive treatment were perceived medication overuse and frequency of headaches, and secondarily, severity of headaches and functional impact. On the other hand, patient satisfaction with the acute treatment of attacks and triptan use, and secondarily, a long migraine history were found to influence patient eligibility negatively. Discussion/conclusion: Noticeably, psychiatric disorders (anxiety, stress) did not appear, aside from somatic factors, among the determinants that significantly influence physicians' judgment about the option of establishing a preventive treatment. However, they are important features of migraine condition and should be listed among the factors guiding choices about migraine preventive therapy.