bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid, High-Throughput Detection of Rifampin Resistance and Heteroresistance in Mycobacterium tuberculosis by Use of Sloppy Molecular Beacon Melting Temperature Coding
Authors: Chakravorty Soumitesh , Kothari Harsheel , Aladegbami Bola , Cho Eun Jin , Lee Jong Seok , Roh Sandy S. , Kim Hyunchul , Kwak Hyungkyung , Lee Eun Gae , Hwang Soo Hee , Banada Padmapriya P. , Safi Hassan , Via Laura E. , Cho Sang-Nae , Barry Clifton E. , Alland David 
Published: April 2012

ABSTRACT

Rifampin resistance in
Mycobacterium tuberculosis
is largely determined by mutations in an 80-bp rifampin resistance determining region (RRDR) of the
rpoB
gene. We developed a rapid single-well PCR assay to identify RRDR mutations. The assay uses sloppy molecular beacons to probe an asymmetric PCR of the
M. tuberculosis
RRDR by melting temperature (

T
m

) analysis. A three-point

T
m

code is generated which distinguishes wild-type from mutant RRDR DNA sequences in approximately 2 h. The assay was validated on synthetic oligonucleotide targets containing the 44 most common RRDR mutations. It was then tested on a panel of DNA extracted from 589 geographically diverse clinical
M. tuberculosis
cultures, including isolates with wild-type RRDR sequences and 25 different RRDR mutations. The assay detected 236/236 RRDR mutant sequences as mutant (sensitivity, 100%; 95% confidence interval [CI], 98 to 100%) and 353/353 RRDR wild-type sequences as wild type (specificity, 100%; 95% CI, 98.7 to 100%). The assay identified 222/225 rifampin-resistant isolates as rifampin resistant (sensitivity, 98.7%; 95% CI, 95.8 to 99.6%) and 335/336 rifampin-susceptible isolates as rifampin susceptible (specificity, 99.7%; 95% CI, 95.8 to 99.6%). All mutations were either individually identified or clustered into small mutation groups using the triple

T
m

code. The assay accurately identified mixed (heteroresistant) samples and was shown analytically to detect RRDR mutations when present in at least 40% of the total
M. tuberculosis
DNA. This was at least as accurate as Sanger DNA sequencing. The assay was easy to use and well suited for high-throughput applications. This new sloppy molecular beacon assay should greatly simplify rifampin resistance testing in clinical laboratories.
The 2010 Global Proficiency Study of Human Papillomavirus Genotyping in Vaccinology
Authors: Eklund Carina , Forslund Ola , Wallin Keng-Ling , Zhou Tiequn , Dillner Joakim 
Published: April 2012

ABSTRACTAccurate and internationally comparable human papillomavirus (HPV) DNA genotyping is essential both for evaluation of HPV vaccines and for effective monitoring and implementation of vaccination programs. The World Health Organization (WHO) HPV Laboratory Network (LabNet) regularly issues international proficiency studies. The 2010 HPV genotyping proficiency panel for HPV vaccinology contained 43 coded samples composed of purified plasmids of 16 HPV types (HPV types 6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68a and 68b) and 3 coded extraction controls. Proficient typing was defined as detection in both single and multiple infections of 50 international units (IU) of HPV type 16 (HPV-16) and HPV-18 DNA and 500 genome equivalents (GE) for the other 14 HPV types. Ninety-eight laboratories worldwide submitted a total of 132 data sets. Twenty-four different HPV genotyping assay methods were used, with Linear Array being the most commonly used. Other major assays used were a line blot assay (Inno-LiPa), CLART, type-specific real-time PCR, PCR Luminex, and different microarray assays. Altogether, 72 data sets were proficient for detection of more than 1 type, and only 26 data sets proficiently detected all 16 HPV types. The major oncogenic HPV types, 16 and 18, were proficiently detected in 95.0% (114/120) and 87.0% (94/108) of data sets, respectively. Forty-six data sets reported multiple false-positive results and were considered nonproficient. A trend toward increased sensitivity of assays was seen for the 41 laboratories that participated in both 2008 and 2010. In conclusion, continued global proficiency studies will be required for establishing comparable and reliable HPV genotyping services for vaccinology worldwide.
Survival of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococcus spp. for an Extended Period of Transport
Authors: Robinson Gwen L. , Harris Anthony D. , Morgan Daniel J. , Pineles Lisa , Belton Beverly M. , Johnson J. Kristie ,   the Benefits of Universal Gloving and Gowning (BUGG) Study Group
Published: April 2012

ABSTRACT

This study determined the survivability of methicillin-resistant
Staphylococcus aureus
(MRSA) and vancomycin-resistant enterococci (VRE) for extended periods of time and temperatures using a standard swab for assessment. Our study showed that transportation in Liquid Amies medium could be performed at room temperature or 4°C for up to 14 days without a decrease in recovery of MRSA or VRE.
Replication of Herpes Simplex Virus: Egress of Progeny Virus at Specialized Cell Membrane Sites
Authors: Mingo Rebecca M. , Han Jun , Newcomb William W. , Brown Jay C. 
Published: April 2012

ABSTRACT

In the final stages of the herpes simplex virus 1 (HSV-1) life cycle, a viral nucleocapsid buds into a vesicle of
trans
-Golgi network (TGN)/endosome origin, acquiring an envelope and an outer vesicular membrane. The virus-containing vesicle then traffics to the plasma membrane where it fuses, exposing a mature virion. Although the process of directed egress has been studied in polarized epithelial cell lines, less work has been done in nonpolarized cell types. In this report, we describe a study of HSV-1 egress as it occurs in nonpolarized cells. The examination of infected Vero cells by electron, confocal, and total internal reflection fluorescence (TIRF) microscopy revealed that HSV-1 was released at specific pocket-like areas of the plasma membrane that were found along the substrate-adherent surface and cell-cell-adherent contacts. Both the membrane composition and cytoskeletal structure of egress sites were found to be modified by infection. The plasma membrane at virion release sites was heavily enriched in viral glycoproteins. Small glycoprotein patches formed early in infection, and virus became associated with these areas as they expanded. Glycoprotein-rich areas formed independently from virion trafficking as confirmed by the use of a UL25 mutant with a defect in capsid nuclear egress. The depolymerization of the cytoskeleton indicated that microtubules were important for the trafficking of virions and glycoproteins to release sites. In addition, the actin cytoskeleton was found to be necessary for maintaining the integrity of egress sites. When actin was depolymerized, the glycoprotein concentrations dispersed across the membrane, as did the surface-associated virus. Lastly, viral glycoprotein E appeared to function in a different manner in nonpolarized cells compared to previous studies of egress in polarized epithelial cells; the total amount of virus released at egress sites was slightly increased in infected Vero cells when gE was absent. However, gE was important for egress site formation, as Vero cells infected with gE deletion mutants formed glycoprotein patches that were significantly reduced in size. The results of this study are interpreted to indicate that the egress of HSV-1 in Vero cells is directed to virally induced, specialized egress sites that form along specific areas of the cell membrane.
Implication of Inflammatory Macrophages, Nuclear Receptors, and Interferon Regulatory Factors in Increased Virulence of Pandemic 2009 H1N1 Influenza A Virus after Host Adaptation
Authors: Josset Laurence , Belser Jessica A. , Pantin-Jackwood Mary J. , Chang Jean H. , Chang Stewart T. , Belisle Sarah E. , Tumpey Terrence M. , Katze Michael G. 
Published: April 2012

ABSTRACT

While pandemic 2009 H1N1 influenza A viruses were responsible for numerous severe infections in humans, these viruses do not typically cause corresponding severe disease in mammalian models. However, the generation of a virulent 2009 H1N1 virus following serial lung passage in mice has allowed for the modeling of human lung pathology in this species. Genetic determinants of mouse-adapted 2009 H1N1 viral pathogenicity have been identified, but the molecular and signaling characteristics of the host response following infection with this adapted virus have not been described. Here we compared the gene expression response following infection of mice with A/CA/04/2009 (CA/04) or the virulent mouse-adapted strain (MA-CA/04). Microarray analysis revealed that increased pathogenicity of MA-CA/04 was associated with the following: (i) an early and sustained inflammatory and interferon response that could be driven in part by interferon regulatory factors (IRFs) and increased NF-κB activation, as well as inhibition of the negative regulator TRIM24, (ii) early and persistent infiltration of immune cells, including inflammatory macrophages, and (iii) the absence of activation of lipid metabolism later in infection, which may be mediated by inhibition of nuclear receptors, including PPARG and HNF1A and -4A, with proinflammatory consequences. Further investigation of these signatures in the host response to other H1N1 viruses of various pathogenicities confirmed their general relevance for virulence of influenza virus and suggested that lung response to MA-CA/04 virus was similar to that following infection with lethal H1N1 r1918 influenza virus. This study links differential activation of IRFs, nuclear receptors, and macrophage infiltration with influenza virulence
in vivo
.
Kaposi's Sarcoma-Associated Herpesvirus Inhibits Expression and Function of Endothelial Cell Major Histocompatibility Complex Class II via Suppressor of Cytokine Signaling 3
Authors: Butler L. M. , Jeffery H. C. , Wheat R. L. , Long H. M. , Rae P. C. , Nash G. B. , Blackbourn D. J. 
Published: April 2012

ABSTRACTEndothelial cells (EC) can present antigen to either CD8+T lymphocytes through constitutively expressed major histocompatibility complex class I (MHC-I) or CD4+T lymphocytes through gamma interferon (IFN-γ)-induced MHC-II. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), an EC neoplasm characterized by dysregulated angiogenesis and a substantial inflammatory infiltrate. KSHV is understood to have evolved strategies to inhibit MHC-I expression on EC and MHC-II expression on primary effusion lymphoma cells, but its effects on EC MHC-II expression are unknown. Here, we report that the KSHV infection of human primary EC inhibits IFN-γ-induced expression of the MHC-II molecule HLA-DR at the transcriptional level. The effect is functionally significant, since recognition by an HLA-DR-restricted CD4+T-cell clone in response to cognate antigen presented by KSHV-infected EC was attenuated. Inhibition of HLA-DR expression was also achieved by exposing EC to supernatant from KSHV-inoculated EC before IFN-γ treatment, revealing a role for soluble mediators. IFN-γ-induced phosphorylation of STAT-1 and transcription ofCIITAwere suppressed in KSHV-inoculated EC via a mechanism involving SOCS3 (suppressor of cytokine signaling 3). Thus, KSHV infection resulted in transcriptional upregulation of SOCS3, and treatment with RNA interference against SOCS3 relieved virus-induced inhibition of IFN-γ-induced STAT-1 phosphorylation. Since cell surface MHC-II molecules present peptide antigens to CD4+T lymphocytes that can function either as direct cytolytic effectors or to initiate and regulate adaptive immune responses, inhibition of this antigen-presenting pathway would provide a survival advantage to the virus.
Social and geographical factors affecting access to treatment of colorectal cancer: a cancer registry study
Authors: Crawford S Michael , Sauerzapf Violet , Haynes Robin , Forman David , Jones Andrew P 
Published: April 2012

ObjectiveCancer outcomes vary between and within countries with patients from deprived backgrounds known to have inferior survival. The authors set out to explore the effect of deprivation in relation to the accessibility of hospitals offering diagnostic and therapeutic services on stage at presentation and receipt of treatment.DesignAnalysis of a Cancer Registry Database. Data included stage and treatment details from the first 6 months. The socioeconomic status of the immediate area of residence and the travel time from home to hospital was derived from the postcode.SettingPopulation-based study of patients resident in a large area in the north of England.Participants39 619 patients with colorectal cancer diagnosed between 1994 and 2002.Outcomes measuredStage of diagnosis and receipt of treatment in relation to deprivation and distance from hospital.ResultsPatients in the most deprived quartile were significantly more likely to be diagnosed at stage 4 for rectal cancer (OR 1.516, p<0.05) but less so for colonic cancer. There was a trend for both sites for patients in the most deprived quartile to be less likely to receive chemotherapy for stage 4 disease. Patients with colonic cancer were very significantly less likely to receive any treatment if they came from any but the most affluent area (ORs 0.639, 0.603 and 0.544 in increasingly deprived quartiles), this may have been exacerbated if the hospital was distant from their residence (OR for forth quartile for both travel and deprivation 0.731, not significant). The effect was less for rectal cancer and no effect of distance was seen.ConclusionsResiding in a deprived area is associated with tendencies to higher stage at diagnosis and especially in the case of colonic cancer to reduced receipt of treatment. These observations are consistent with other findings and indicate that access to diagnosis requires further investigation.
Resonance classification of mixed assemblages of fish with swimbladders using a modified commercial broadband acoustic echosounder at 1–6 kHz
Authors: Stanton Timothy K. , Sellers Cynthia J. , Jech J. Michael 
Published: April 2012

Recently developed broadband acoustic methods were used to study mixed assemblages of fish spanning a wide range of lengths and species. Through a combination of resonance classification and pulse-compression signal processing, which provides for high-range resolution, a modified commercial broadband echosounder was demonstrated to provide quantitative information on the spatial distribution of the individual size classes within an assemblage. In essence, this system spectrally resolves the different size classes of fish that are otherwise not resolved spatially. This method reveals new insights into biological processes, such as predator–prey interactions, that are not obtainable through the use of a conventional narrowband high-frequency echosounder or previous broadband systems. A recent study at sea with this system revealed aggregations containing bladdered fish 15–30 cm in length (Atlantic herring ( Clupea harengus ) and silver hake ( Merluccius bilinearis )) and a variety of species of smaller fish 2–5 cm in length. These observations infer that the smaller 2–5 cm fish can be colocated in the same aggregations as their predator, the larger silver hake, as well as pre-spawning herring. While this technological advancement provides more information, there remain challenges in interpreting the echo spectra in terms of meaningful biological quantities such as size distribution and species composition.
Environmental factors correlate with hybridization in stocked brook charr (Salvelinus fontinalis)
Authors: Marie Amandine D. , Bernatchez Louis , Garant Dany 
Published: April 2012

Stocking is a common practice throughout the world that may increase hybridization between wild and domesticated populations. Stocking intensity alone does not always fully explain the observed patterns of hybridization, suggesting that the intensity of hybridization may be modulated by environmental factors. Using brook charr (i.e., brook trout, Salvelinus fontinalis ) as a model, the objective of this study was to assess the relative effect of environmental factors and stocking intensity on the level of hybridization observed within brook charr from 15 lacustrine populations of two wildlife reserves in Quebec, Canada. The level of hybridization significantly increased with (i) the number of stocking events, (ii) a reduction in both surface area and maximum depth of lakes, and (iii) a reduction in dissolved oxygen and an increase in temperature and pH. These results suggest that levels of hybridization were affected by the availability and quality of lacustrine habitats as well as by the extent of propagule pressure. Our study provides the first demonstration that knowledge of environmental features may help predict the effects of stocking on the genetic integrity of wild populations.
Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka)
Authors: Gomez-Uchida Daniel , Seeb James E. , Habicht Christopher , Seeb Lisa W. 
Published: April 2012

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.
Predicting the interactions between “ecologically equivalent” indigenous and nonindigenous brachyurans
Authors: Breen Erin , Metaxas Anna 
Published: April 2012

Predictive models used to determine the impacts of nonindigenous brachyurans on their “ecological equivalents” in marine ecosystems are sorely lacking. Determining the spatial and temporal extent and magnitude of such impacts by nonindigenous species is difficult because of the broad range of qualitative and quantitative criteria currently used to describe their effects. Forecasting potential impacts requires the development of predictive models that incorporate the effects of interspecific interactions and the mechanisms that give rise to these interactions. Successful validation of such models requires improved techniques for measuring and estimating the functional responses on bioenergetic processes across species compositions, abundances, and environmental conditions. Species-specific information used to support predictive modeling of nonindigenous brachyurans is currently heavily biased towards (i) estimating per capita consumption and growth rates in laboratory conditions and (ii) incorporating the effects of abiotic and biotic factors on these measures. Robust predictive models require repetitive experimentation that advances the understanding of species’ interactions (beyond consumption alone) across variable densities and considers their effects across different spatial and temporal scales.
A detrimental soil disturbance prediction model for ground-based timber harvesting
Authors: Reeves Derrick A. , Reeves Matthew C. , Abbott Ann M. , Page-Dumroese Deborah S. , Coleman Mark D. 
Published: April 2012

Soil properties and forest productivity can be affected during ground-based harvest operations and site preparation. The degree of impact varies widely depending on topographic features and soil properties. Forest managers who understand site-specific limits to ground-based harvesting can alter harvest method or season to limit soil disturbance. To determine the potential areal extent of detrimental (potentially plant growth limiting) soil disturbance based on site characteristics and season of harvest, we developed a predictive model based on soil monitoring data collected from 167 ground-based harvest units. Data collected included dominant site parameters (e.g., slope, aspect, soil texture, and landtype), harvest season, harvest type (intermediate or regeneration), and the machine(s) used during ground-based harvest operations. Aspect (p = 0.0217), slope (p = 0.0738), landtype (p = 0.0002), and the interaction of harvest season × landtype (p = 0.0002) were the key variables controlling the areal extent and magnitude of detrimental soil disturbance. For example, harvesting during non-winter months on gently rolling topography resulted in greater soil disturbance than similar harvest operations on landscapes that are highly dissected. This is likely due to the ease with which equipment can move off designated trails. A geospatially explicit predictive model was developed using general linear model variables found to significantly influence the areal extent of detrimental soil disturbance on nine defined landtypes. This tool provides a framework that, with local calibration, can be used on other forest lands as a decision support tool to geospatially depict landtypes susceptible to detrimental soil disturbance during ground-based harvest operations.
Impact of competition from coppicing stumps on the growth of retained trees differs in thinned Eucalyptus globulus and Eucalyptus tricarpa plantations in southeastern Australia
Authors: Forrester David I. , Bertram Courtney A. , Murphy Simon 
Published: April 2012

Coppice growth on cut stumps in thinned Eucalyptus plantations has the potential to compete with and reduce the growth of retained sawlog crop trees (SCTs). This study examined to what extent SCT growth was reduced by coppice in two stands in southeastern Australia: (i) a Eucalyptus globulus Labill. plantation thinned at age 10 years and (ii) a slower growing Eucalyptus tricarpa L.A.S. Johnson & K. Hill (syn. Eucalyptus sideroxylon subsp. tricarpa L.A.S. Johnson) plantation thinned at age 62 years. After 5 years, thinning E. globulus from 850 to 400 trees·ha–1 increased the basal area of the largest diameter 200 SCTs·ha–1 (SCT200) by 11% when coppice was removed. There was no significant thinning response by SCT200 when coppice was retained. After 10 years, thinning E. tricarpa from about 600 to 100 trees·ha–1 increased the basal area of the largest diameter 100 SCTs trees·ha–1 (SCT100) by about 10% whether coppice was removed or not. At the time of measurement, coppice contributed 17% and 36% of stand sapwood area in thinned E. globulus and E. tricarpa treatments, respectively, and possibly competed with SCTs for water. This study shows the significant competitive effect that coppice can have in thinned eucalypt plantations and the importance of coppice management to the growth of retained trees.