bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance Assessment of the GenoType MTBDR
sl
Test and DNA Sequencing for Detection of Second-Line and Ethambutol Drug Resistance among Patients Infected with Multidrug-Resistant Mycobacterium tuberculosis
Authors: Huang Wei-Lun , Chi Ting-Lin , Wu Mei-Hua , Jou Ruwen 
Published: May 2011

ABSTRACT

The GenoType MTBDR
sl
test and DNA sequencing were used to rapidly detect second-line drug- and ethambutol (EMB)-resistant
Mycobacterium tuberculosis
. The ability of these two assays to detect the presence of mutations associated with resistance to fluoroquinolones (FLQ), aminoglycosides/cyclic peptide (AG/CP), and EMB in the
gyrA
,
rrs
, and
embB
genes (for the GenoType MTBDR
sl
test) and
gyrA
,
gyrB
,
rrs
,
eis
,
embC
,
embA
,
embB
, and
embR
genes (for DNA sequencing) was compared to that of conventional agar proportion drug susceptibility testing (DST). We evaluated 234 multidrug-resistant (MDR)
M. tuberculosis
isolates. The two molecular methods had high levels of specificity (95.8 to 100%). The sensitivities for FLQ resistance detection for both methods were 85.1%. For AG (kanamycin [KM] and amikacin [AM]) and CP (capreomycin CAP]), the sensitivities of resistance detection using the GenoType MTBDR
sl
test were 43.2%, 84.2%, and 71.4%, respectively, while with the inclusion of an extra gene,
eis
, in sequencing, the sensitivity reached 70.3% for detection of KM resistance. The sensitivities of EMB resistance detection were 56.2% and 90.7% with the GenoType MTBDR
sl
test and sequencing, respectively. We found that the GenoType MTBDR
sl
test can rapidly detect resistance to FLQ, CAP, and AM. The accuracy of the GenoType MTBDR
sl
test for the detection of FLQ and AM resistance was comparable to that of conventional DST; however, the test was less accurate for the detection of KM and EMB resistance and demonstrated a poor predictive value for CAP resistance. We recommend including new alleles consisting of the
eis
promoter and
embB
genes in molecular analysis. However, conventional DST is necessary to rule out false-negative results from molecular assays.
Curtobacterium flaccumfaciens Septic Arthritis following Puncture with a Coxspur Hawthorn Thorn
Authors: Francis Michelle J. , Doherty Richard R. , Patel Minoo , Hamblin John F. , Ojaimi Samar , Korman Tony M. 
Published: May 2011

ABSTRACT

Curtobacterium
species are recognized plant pathogens. We report the first well-documented case of
Curtobacterium
human infection, a child with septic arthritis following puncture with a Coxspur Hawthorn plant thorn. The organism isolated from synovial tissue and the plant thorn was identified as
Curtobacterium flaccumfaciens
by 16S rRNA gene sequence analysis.
Isolation of Mycobacterium tuberculosis Strains with a Silent Mutation in
rpoB
Leading to Potential Misassignment of Resistance Category
Authors: Alonso María , Palacios Juan José , Herranz Marta , Penedo Ana , Menéndez Ángela , Bouza Emilio , García de Viedma Darío 
Published: May 2011

ABSTRACT

Our study provides an alert regarding the transmission of rifampin-susceptible strains of
Mycobacterium tuberculosis
with a silent substitution in codon 514 of
rpoB
. Among 1,450 cases, we identified 12 isolates sharing this mutation and related restriction fragment length polymorphism (RFLP) types. The mutation impaired hybridization with the wild-type probes in three independent commercial assays, which could lead to misassignment of resistance.
Genetic Diversity among Korean Candida albicans Bloodstream Isolates: Assessment by Multilocus Sequence Typing and Restriction Endonuclease Analysis of Genomic DNA by Use of BssHII
Authors: Shin Jong Hee , Bougnoux Marie-Elisabeth , d'Enfert Christophe , Kim Soo Hyun , Moon Chang-Jin , Joo Min Young , Lee Kyungwon , Kim Mi-Na , Lee Hye Soo , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook 
Published: May 2011

ABSTRACT

Multilocus sequence typing (MLST) has been successfully applied to the epidemiology of
Candida albicans
isolates not only within the hospital setting but also in multiple locations nationwide. We performed MLST to investigate the genetic relatedness among bloodstream infection (BSI) isolates of
C. albicans
recovered from 10 Korean hospitals over a 12-month period. The 156 isolates yielded 112 unique diploid sequence types (DSTs). While 95 DSTs were each derived from a single isolate, 17 DSTs were shared by 61 isolates (39.1%). Interestingly, 111 (71.1%) isolates clustered within previously known clades, and 29 (18.6%) clustered within a new clade that includes strains of Asian origin previously typed as singletons. This MLST study was complemented by restriction endonuclease analysis of genomic DNA using BssHII (REAG-B) in order to evaluate whether strains with identical DSTs and originating from the same hospital corresponded to nosocomial clusters. Importantly, only those isolates with a strong epidemiological relationship showed ≥95% identical REAG-B types. Our results indicate that REAG-B typing can be complementary to MLST but should be limited to the investigation of isolates of identical DSTs and when interhuman transmission is suspected.
Substitution of Specific Cysteine Residues in the E1 Glycoprotein of Classical Swine Fever Virus Strain Brescia Affects Formation of E1-E2 Heterodimers and Alters Virulence in Swine
Authors: Fernández-Sainz I. , Holinka L. G. , Gladue D. , O'Donnell V. , Lu Z. , Gavrilov B. K. , Risatti G. R. , Borca M. V. 
Published: May 2011

ABSTRACT

E1, along with E
rns
and E2, is one of the three envelope glycoproteins of classical swine fever virus (CSFV). E1 and E2 are anchored to the virus envelope at their carboxyl termini, and E
rns
loosely associates with the viral envelope. In infected cells, E2 forms homodimers and heterodimers with E1 mediated by disulfide bridges between cysteine residues. The E1 protein of CSFV strain Brescia contains six cysteine residues at positions 5, 20, 24, 94, 123, and 171. The role of these residues in the formation of E1-E2 heterodimers and their effect on CSFV viability
in vitro
and
in vivo
remain unclear. Here we observed that recombinant viruses harboring individual cysteine-to-serine substitutions within the E1 envelope protein still have formation of E1-E2 heterodimers which are functional in terms of allowing efficient virus progeny yields in infected primary swine cells. Additionally, these single cysteine mutant viruses were virulent in infected swine. However, a double mutant harboring Cys24Ser and Cys94Ser substitutions within the E1 protein altered formation of E1-E2 heterodimers in infected cells. This recombinant virus, E1ΔCys24/94v, showed delayed growth kinetics in primary swine macrophage cultures and was attenuated in swine. Furthermore, despite the observed diminished growth
in vitro
, infection with E1ΔCys24/94v protected swine from challenge with virulent CSFV strain Brescia at 3 and 28 days postinfection.
Diverse Peptide Presentation of Rhesus Macaque Major Histocompatibility Complex Class I Mamu-A*02 Revealed by Two Peptide Complex Structures and Insights into Immune Escape of Simian Immunodeficiency Virus
Authors: Liu Jun , Dai Lianpan , Qi Jianxun , Gao Feng , Feng Youjun , Liu Wenjun , Yan Jinghua , Gao George F. 
Published: May 2011

ABSTRACT

Major histocompatibility complex class I (MHC I)-restricted CD8
+
T-cell responses play a pivotal role in anti-human immunodeficiency virus (HIV) immunity and the control of viremia. The rhesus macaque is an important animal model for HIV-related research. Among the MHC I alleles of the rhesus macaque, Mamu-A*02 is prevalent, presenting in ≥20% of macaques. In this study, we determined the crystal structure of Mamu-A*02, the second structure-determined MHC I from the rhesus macaque after Mamu-A*01. The peptide presentation characteristics of Mamu-A*02 are exhibited in complex structures with two typical Mamu-A*02-restricted CD8
+
T-cell epitopes, YY9 (Nef159 to -167; YTSGPGIRY) and GY9 (Gag71 to -79; GSENLKSLY), derived from simian immunodeficiency virus (SIV). These two peptides utilize similar primary anchor residues (Ser or Thr) at position 2 and Tyr at position 9. However, the central region of YY9 is different from that of GY9, a difference that may correlate with the immunogenic variance of these peptides. Further analysis indicated that the distinct conformations of these two peptides are modulated by four flexible residues in the Mamu-A*02 peptide-binding groove. The rare combination of these four residues in Mamu-A*02 leads to a variant presentation for peptides with different residues in their central regions. Additionally, in the two structures of the Mamu-A*02 complex, we compared the binding of rhesus and human β
2
microglobulin (β
2
m) to Mamu-A*02. We found that the peptide presentation of Mamu-A*02 is not affected by the interspecies interaction with human β
2
m. Our work broadens the understanding of CD8
+
T-cell-specific immunity against SIV in the rhesus macaque.
An imbalance of COX level is not related to placental abruption
Authors: Avagliano Laura , Falleni Monica , Marconi Anna Maria , Bulfoni Camilla , Prada Arianna , Barbera Antonino F , Doi Patrizia , Bulfamante Gaetano P 
Published: May 2011

AimsMuscularised basal plate arteries (MA) or chorioamnionitis (CA) are often present in placental abruption. The aim of this study was to evaluate the placental expression of COX 1 and COX 2 in cases of placental abruption with MA or CA hypothesising that an imbalance in COX placental expression might be implicated in its pathogenesis.MethodsCOX 1 and COX 2 placental immunostaining was analysed in 16 placentas with abruption (nine with MA, seven with CA), in 26 normal placentas and in 10 gestational age-matched MA or CA cases without abruption.ResultsCOX 1 and COX 2 protein expression was observed in all cases, both in placental abruption and in normal placentas. No differences in distribution of immunoreactivity were observed either between cases and controls or between MA and CA. The mean COX 1 ratio between COX-positive cells and all stromal cells was significantly lower in placental abruption with MA (0.14±0.05) when compared with cases with CA (0.35±0.06) and normal placenta (0.23±0.02; p<0.001). The mean COX 2 ratio was lower in placental abruption with MA than in normal placenta (0.09±0.06 vs 0.18±0.05: p<0.001). In contrast, no difference in COX 1 and COX 2 ratio was observed between MA cases with or without abruption and between CA cases with or without abruption.ConclusionsIt is hypothesised that an imbalance of normal COX level may be present in cases with MA and CA but it is not related to placental abruption.
EGFR Signaling Regulates Tumor Cell Migration in Craniopharyngiomas
Authors: Hölsken Annett , Gebhardt Matthias , Buchfelder Michael , Fahlbusch Rudolf , Blümcke Ingmar , Buslei Rolf 
Published: May 2011

Abstract
Purpose: Constitutive Wnt signaling caused by mutations in the β-catenin gene is a molecular hallmark of adamantinomatous craniopharyngiomas (adaCP) and promotes infiltration into adjacent brain tissue. Herein, we studied the pathogenic role of epidermal growth factor receptor (EGFR) activation in adaCP and whether tumor cell migration can be inhibited by the tyrosine kinase inhibitor gefitinib.
Experimental Design: EGFR expression and activation [phosphorylated EGFR (EGFR-P)] was examined in a cohort of 25 surgical adaCP samples by PCR and Western blotting. Regional and cellular localization patterns of EGFR-P, β-catenin, and its target gene product Fascin were determined by immunofluorescence microscopy. Mutation analysis and gene copy number assay were carried out to examine genetic alterations in the EGFR gene. The impact of EGFR signaling on tumor cell migration was studied in vitro by using 11 primary human adaCP cultures treated with the EGFR ligand EGF and its inhibitor gefitinib.
Results: Neither mutations nor amplifications in the EGFR gene were detected in our adaCP series. However, EGFR-P was detectable in tumor cell clusters located at the brain infiltration border and colocalized with nuclear β-catenin and Fascin. Activated EGFR significantly promoted tumor cell migration in vitro, whereas gefitinib reduced both tumor cell motility and Fascin expression.
Conclusion: Our data suggest EGFR signaling to play a role in cell migration and brain infiltration of adaCP. Targeting the EGFR signaling pathway by gefitinib may present a promising pharmacologic option in the treatment of this challenging tumor disease. Clin Cancer Res; 17(13); 4367–77. ©2011 AACR.
Some Regions within Broca's Area Do Respond More Strongly to Sentences than to Linguistically Degraded Stimuli: A Comment on Rogalsky and Hickok ()
Authors: Fedorenko Evelina , Kanwisher Nancy 
Published: May 2011

Abstract
On the basis of their review of the literature, Rogalsky and Hickok [Rogalsky, C., & Hickok, G. The role of Broca's area in sentence comprehension. Journal of Cognitive Neuroscience, 23, 1664–1680, 2011] conclude that there is currently no strong evidence for the existence of “sentence-specific processing regions within Broca's area” (p. 1664). Their argument is based, in part, on the observation that many previous studies have failed to detect an effect in the left inferior frontal regions for contrasts between sentences and linguistically degraded control conditions (e.g., lists of unconnected words, lists of nonwords, or acoustically degraded sentence stimuli). Our data largely replicate this lack of activation in inferior frontal regions when traditional random-effects group analyses are conducted but crucially show robust activations in the same data for the same contrasts in almost every subject individually. Thus, it is the use of group analyses in studies of language processing, not the idea that sentences robustly activate frontal regions, that needs to be reconsidered. This reconsideration has important methodological and theoretical implications.
Dopamine and the Management of Attentional Resources: Genetic Markers of Striatal D2 Dopamine Predict Individual Differences in the Attentional Blink
Authors: Colzato Lorenza S. , Slagter Heleen A. , de Rover Mischa , Hommel Bernhard 
Published: May 2011

Abstract
The attentional blink (AB)—a deficit in reporting the second of two target stimuli presented in close succession in a rapid sequence of distracters—has been related to processing limitations in working memory. Given that dopamine (DA) plays a crucial role working memory, the present study tested whether individual differences in the size of the AB can be predicted by differences in genetic predisposition related to the efficiency of dopaminergic pathways. Polymorphisms related to mesocortical and nigrostriatal dopaminergic pathways were considered, as well as polymorphisms related to norepinephrine (NE), a transmitter system that has also been suspected to play a role in the AB. In a sample of 157 healthy adults, we studied the dependency of the individual magnitude of the AB and the C957T polymorphism at the DRD2 gene (associated with striatal DA/D2 receptors), the DARPP32 polymorphism (associated with striatal DA/D1), the COMT Val158Met polymorphism (associated with frontal DA), DBH444 g/a and DBH5′-ins/del polymorphisms (polymorphisms strongly correlated with DA beta hydroxylase, the enzyme catalyzing the DA–NE conversion) and NET T-182C (a polymorphism related to the NE transporter). DRD2 C957T T/T homozygotes showed a significantly smaller AB, whereas polymorphisms associated with frontal DA and NE were unrelated to performance. This outcome pattern suggests a crucial role of the nigrostriatal dopaminergic pathway and of nigrostriatal D2 receptors, in particular, in the management of attentional resources.
On the Wave Spectrum Generated by Tropical Heating
Authors: Ortland David A. , Alexander M. Joan , Grimsdell Alison W. 
Published: May 2011

Abstract
Convective heating profiles are computed from one month of rainfall rate and cloud-top height measurements using global Tropical Rainfall Measuring Mission and infrared cloud-top products. Estimates of the tropical wave response to this heating and the mean flow forcing by the waves are calculated using linear and nonlinear models. With a spectral resolution up to zonal wavenumber 80 and frequency up to 4 cpd, the model produces 50%–70% of the zonal wind acceleration required to drive a quasi-biennial oscillation (QBO). The sensitivity of the wave spectrum to the assumed shape of the heating profile, to the mean wind and temperature structure of the tropical troposphere, and to the type of model used is also examined. The redness of the heating spectrum implies that the heating strongly projects onto Hough modes with small equivalent depth. Nonlinear models produce wave flux significantly smaller than linear models due to what appear to be dynamical processes that limit the wave amplitude. Both nonlinearity and mean winds in the lower stratosphere are effective in reducing the Rossby wave response to heating relative to the response in a linear model for a mean state at rest.
Climate Change Effects on Spatiotemporal Patterns of Hydroclimatological Summer Droughts in Norway
Authors: Wong Wai Kwok , Beldring Stein , Engen-Skaugen Torill , Haddeland Ingjerd , Hisdal Hege 
Published: May 2011

AbstractThis study examines the impact of climate change on droughts in Norway. A spatially distributed (1 × 1 km2) version of the Hydrologiska Byråns Vattenbalansavdelning (HBV) precipitation-runoff model was used to provide hydrological data for the analyses. Downscaled daily temperature and precipitation derived from two atmosphere–ocean general circulation models with two future emission scenarios were applied as input to the HBV model. The differences in hydroclimatological drought characteristics in the summer season between the periods 1961–90 and 2071–2100 were studied. The threshold level method was adopted to select drought events for both present and future climates. Changes in both the duration and spatial extent of precipitation, soil moisture, runoff, and groundwater droughts were identified. Despite small changes in future meteorological drought characteristics, substantial increases in hydrological drought duration and drought affected areas are expected, especially in the southern and northernmost parts of the country. Reduced summer precipitation is a major factor that affects changes in drought characteristics in the south while temperature increases play a more dominant role for the rest of the country.
Downscaling Ensemble Weather Predictions for Improved Week-2 Hydrologic Forecasting
Authors: Liu Xiaoli , Coulibaly Paulin 
Published: May 2011

AbstractThis study investigates the use of large-scale ensemble weather predictions provided by the National Centers for Environmental Prediction (NCEP) Global Forecast System [GFS; formerly known as Medium-Range Forecast (MRF)] for improving week-2 hydrologic forecasting. The ensemble weather predictor variables are used to downscale daily precipitation and temperature series at two meteorological stations in the Saguenay watershed in northeastern Canada. Three data-driven methods—namely, the statistical downscaling model (SDSM), the time-lagged feed-forward neural network (TLFN), and evolutionary polynomial regression (EPR)—are used as comparative downscaling models. The downscaled results of the best models are used as additional inputs in two hydrological models, namely Hydrologiska Byråns Vattenbalansavdelning (HBV2005) and a Bayesian neural network (BNN)-based hydrologic model, for up to 14-day-ahead reservoir inflow and river flow forecasting. The performance of the two hydrologic models is compared, the ultimate objective being to improve week-2 (7–14-day ahead) forecasts. To identify a suitable approach for using the ensemble weather data in the downscaling experiments, six scenarios are evaluated. It is found that the best approach to downscaling the ensemble weather predictions is to use the means of the predictor members derived from the two grid points closest to the local meteorological station of interest. The downscaling results show that all three models have a relatively good performance in downscaling daily temperature series, but the results are in general less accurate for daily precipitation. The TLFN and EPR models have quite close performance in most cases, and they both perform better than SDSM. The hydrologic forecasting results show that for both reservoir inflow and river flow, the HBV model has better performance when downscaled meteorological predictions are included, while there is no significant improvement for the BNN model. For the week-2 forecast, an improvement of about 18% on average is obtained for both streamflow and reservoir inflow forecasts. However, for the spring season where accurate peak flow forecast is of main concern, an improvement of about 26% on average is achieved. It is also shown that using only downscaled temperature in spring reservoir inflow forecasting, the improvements for week 2 range from 16% to 24%. Overall, the forecast results show that large-scale ensemble weather predictions can be effectively exploited through statistical downscaling tools for improved week-2 hydrologic forecasts. The forecast results also indicate that even imperfect medium-range (week 2) weather predictions can be very useful for producing significantly improved week-2 hydrologic forecasts.
Lateral Friction in Reduced-Gravity Models: Parameterizations Consistent with Energy Dissipation and Conservation of Angular Momentum
Authors: Ochoa José , Sheinbaum Julio , Jiménez Aleph 
Published: May 2011

AbstractThe f-plane reduced-gravity model has been extended with the parameterization of lateral friction in the momentum equations. The parameterization should preferably fulfill some requisites. One of them is that in the absence of external torques the change in angular momentum should be determined by boundary conditions alone. Internal torques should balance in the angular momentum budget. This requirement is fulfilled when the parameterization in the vertically integrated momentum equations is the divergence of a symmetric stress tensor. These equations solve for the mean transport, which includes implicitly the eddy-induced contribution. Another requirement on the parameterization of lateral stress follows from considering that it should imply kinetic energy dissipation. Both requirements fail with a commonly used parameterization and are fulfilled with the one proposed by C. Schär and R. B. Smith, which also is in near agreement with derivations of the shallow-water equations via vertical integrations of the Navier–Stokes equations. Here, the authors show two other parameterizations that are consistent with the angular momentum and energy requirements. One of the parameterizations follows from the symmetric component of a stress tensor in agreement with the parameterization shown by P. R. Gent to be energetically consistent. The other parameterization is related to the so-called biharmonic dissipation. In general, the difficulty for friction parameterizations is on the energy dissipation requirement, because the one on angular momentum is easily fulfilled.