bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid First- and Second-Line Drug Susceptibility Assay for
Mycobacterium tuberculosis
Isolates by Use of Quantitative PCR
Authors: Pholwat Suporn , Heysell Scott , Stroup Suzanne , Foongladda Suporn , Houpt Eric 
Published: November 2010

ABSTRACT

The slow turnaround time for
Mycobacterium tuberculosis
drug susceptibility results is a barrier to care. We developed a rapid quantitative PCR (qPCR)-based phenotypic antimicrobial susceptibility test that utilizes amplification of the
M. tuberculosis
16S rRNA gene after 3 days of incubation with antituberculosis drugs. To decrease background from killed organisms, we used propidium monoazide (PMA), a DNA-binding dye that penetrates damaged bacterial cells and renders DNA unamplifiable.
M. tuberculosis
was cultured in broth media containing PMA with or without drugs for 3 days prior to DNA extraction and real-time PCR amplification. 16S rRNA qPCR exhibited a significant decrease in threshold cycle (

C
T

) time values (

C
T

control −

C
T

drug treated) with drug-susceptible strains compared with resistant strains. Susceptibility data were reported as Δ
CT
or as 2
Δ

CT

and with appropriate cutoffs yielded an accuracy of 89 to 100% on 38 susceptible, multidrug-resistant, and extensively drug-resistant strains compared with conventional agar proportion susceptibility results for isoniazid, rifampin, ethambutol, streptomycin, amikacin, kanamycin, capreomycin, ofloxacin, moxifloxacin, ethionamide,
para
-aminosalicylic acid, linezolid, and cycloserine and compared with Bactec MGIT results for pyrazinamide. This PMA-qPCR assay is useful as a rapid 3-day first- and second-line drug susceptibility test for
M. tuberculosis
.
Catheter-Associated
Nocardia higoensis
Bacteremia in a Child with Acute Lymphocytic Leukemia
Authors: Watson Michael E. , Estabrook Michele M. , Burnham Carey-Ann D. 
Published: November 2010

ABSTRACT

A 23-month-old child with leukemia who was receiving chemotherapy developed fevers. Serial blood cultures from a central venous catheter and a peripheral venous site grew an organism identified by 16S rRNA gene sequencing and phenotypic analysis as
Nocardia higoensis
, an opportunistic organism isolated once previously from a pulmonary infection in Japan.
Early Events in Retrovirus XMRV Infection of the Wild-Derived MouseMus pahari
Authors: Sakuma Toshie , Tonne Jason M. , Squillace Karen A. , Ohmine Seiga , Thatava Tayaramma , Peng Kah-Whye , Barry Michael A. , Ikeda Yasuhiro 
Published: November 2010

ABSTRACTA novel gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), has been identified in patients with prostate cancer and in patients with chronic fatigue syndromes. StandardMus musculuslaboratory mice lack a functional XPR1 receptor for XMRV and are therefore not a suitable model for the virus. In contrast, Gairdner's shrew-mice (Mus pahari) do express functional XPR1. To determine whetherMus paharicould serve as a model for XMRV, primaryMus paharifibroblasts and mice were infected with cell-free XMRV. Infection of cellsin vitroresulted in XMRV Gag expression and the production of XMRV virions. After intraperitoneal injection of XMRV intoMus paharimice, XMRV proviral DNA could be detected in spleen, blood, and brain. Intravenous administration of a green fluorescent protein (GFP) vector pseudotyped with XMRV produced GFP+CD4+T cells and CD19+B cells. Mice mounted adaptive immune responses against XMRV, as evidenced by the production of neutralizing and Env- and Gag-specific antibodies. Prominent G-to-A hypermutations were also found in viral genomes isolated from the spleen, suggesting intracellular restriction of XMRV infection by APOBEC3in vivo. These data demonstrate infection ofMus pahariby XMRV, potential cell tropism of the virus, and immunological and intracellular restriction of virus infectionin vivo. These data support the use ofMus paharias a model for XMRV pathogenesis and as a platform for vaccine and drug development against this potential human pathogen.
Cloning of the Epstein-Barr Virus-Related Rhesus Lymphocryptovirus as a Bacterial Artificial Chromosome: a Loss-of-Function Mutation of the rhBARF1 Immune Evasion Gene
Authors: Ohashi Makoto , Orlova Nina , Quink Carol , Wang Fred 
Published: November 2010

ABSTRACT
Rhesus macaques are naturally infected with a gammaherpesvirus which is in the same lymphocryptovirus (LCV) genus as and closely related to Epstein-Barr virus (EBV). The rhesus macaque LCV (rhLCV) contains a repertoire of genes identical to that of EBV, and experimental rhLCV infection of naive rhesus macaques accurately models acute and persistent EBV infection of humans. We cloned the LCL8664 rhLCV strain as a bacterial artificial chromosome to create recombinant rhLCV for investigation in this animal model system. A recombinant rhLCV (clone 16 rhLCV) carrying a mutation in the putative immune evasion gene rhBARF1 was created along with a rescued wild-type (rWT) rhLCV in which the rhBARF1 open reading frame (ORF) was repaired. The rWT rhLCV molecular clone demonstrated viral replication and B-cell immortalization properties comparable to those of the naturally derived LCL8664 rhLCV. Qualitatively, clone 16 rhLCV carrying a mutated rhBARF1 was competent for viral replication and B-cell immortalization, but quantitative assays showed that clone 16 rhLCV immortalized B cells less efficiently than LCL8664 and rWT rhLCV. Functional studies showed that rhBARF1 could block CSF-1 cytokine signaling as well as EBV BARF1, whereas the truncated rhBARF1 from clone 16 rhLCV was a loss-of-function mutant. These recombinant rhLCV can be used in the rhesus macaque animal model system to better understand how a putative viral immune evasion gene contributes to the pathogenesis of acute and persistent EBV infection. The development of a genetic system for making recombinant rhLCV constitutes a major advance in the study of EBV pathogenesis in the rhesus macaque animal model.
Minor Oral Lesions Facilitate Transmission of Chronic Wasting Disease
Authors: Denkers Nathaniel D. , Telling Glenn C. , Hoover Edward A. 
Published: November 2010

ABSTRACT
While chronic wasting disease (CWD) prion transmission, entry, and trafficking remain incompletely elucidated, natural exposure of the oral and/or nasal mucous membranes seems certain. Cervids commonly sustain minor lesions on oral mucous membranes that could have an impact on susceptibility to prion infection. To explore this potential cofactor, we studied cohorts of cervid PrP transgenic mice with or without superficial abrasions on the lingual mucosa to determine whether minor oral mucosa lesions may enhance susceptibility to CWD infections. Results demonstrated that minor lingual abrasions substantially facilitate CWD transmission, revealing a cofactor that may be significant in cervids and perhaps other species.
Epitope Mapping of HIV-Specific CD8
+
T Cell Responses by Multiple Immunological Readouts Reveals Distinct Specificities Defined by Function
Authors: Richmond Meika , McKinnon Lyle R. , Kiazyk Sandra A. Koesters , Wachihi Charles , Kimani Makobu , Kimani Joshua , Plummer Francis A. , Ball T. Blake 
Published: November 2010

ABSTRACT

The limited success of HIV vaccine candidates to date highlights our need to better characterize protective cell-mediated immunity (CMI). While HIV-specific CD8
+
T cell responses have been defined largely by measuring gamma interferon (IFN-γ), these responses are not always protective, and it is unclear whether the same epitopes would predominate if other functional parameters were examined. Here, we assessed the epitope specificity of HIV-specific CD8
+
T cell responses by multiparametric flow cytometry, measuring five CD8
+
T cell functions (IFN-γ, macrophage inflammatory protein 1β [MIP-1β], tumor necrosis factor alpha [TNF-α], interleukin-2 [IL-2], and proliferative capacity) in 24 chronically HIV-infected individuals. Sixty-nine epitope-specific responses to 50 epitopes within p24 were measured. Surprisingly, most epitope-specific responses were IFN-γ negative (50/69 responses). Many responses had polyfunctional (33%) and proliferative (19%) components. An inverse association between IL-2 and proliferation responses was also observed, contrary to what was described previously. We confirm that long-term nonprogressors (LTNP) have more polyfunctional responses and also have higher-magnitude and broader p24-specific proliferation and higher levels of IL-2 and TNF-α production than do progressing controls. Together, these data suggest that the specificity of CD8
+
T cell responses differs depending on the immunological readout, with a 3.5-fold increase in breadth detected by including multiple parameters. Furthermore, the identification of epitopes that elicit polyfunctional responses reinforces the need for the comprehensive evaluation of HIV vaccine candidates, and these epitopes may represent novel targets for CMI-based vaccines.
Mapping the Landscape of Host-Pathogen Coevolution: HLA Class I Binding and Its Relationship with Evolutionary Conservation in Human and Viral Proteins
Authors: Hertz Tomer , Nolan David , James Ian , John Mina , Gaudieri Silvana , Phillips Elizabeth , Huang Jim C. , Riadi Gonzalo , Mallal Simon , Jojic Nebojsa 
Published: November 2010

ABSTRACTThe high diversity of HLA binding preferences has been driven by the sequence diversity of short segments of relevant pathogenic proteins presented by HLA molecules to the immune system. To identify possible commonalities in HLA binding preferences, we quantify these using a novel measure termed “targeting efficiency,” which captures the correlation between HLA-peptide binding affinities and the conservation of the targeted proteomic regions. Analysis of targeting efficiencies for 95 HLA class I alleles over thousands of human proteins and 52 human viruses indicates that HLA molecules preferentially target conserved regions in these proteomes, although the arboviralFlaviviridaeare a notable exception where nonconserved regions are preferentially targeted by most alleles. HLA-A alleles and several HLA-B alleles that have maintained close sequence identity with chimpanzee homologues target conserved human proteins and DNA viruses such asHerpesviridaeandAdenoviridaemost efficiently, while all HLA-B alleles studied efficiently target RNA viruses. These patterns of host and pathogen specialization are both consistent with coevolutionary selection and functionally relevant in specific cases; for example, preferential HLA targeting of conserved proteomic regions is associated with improved outcomes in HIV infection and with protection against dengue hemorrhagic fever. Efficiency analysis provides a novel perspective on the coevolutionary relationship between HLA class I molecular diversity, self-derived peptides that shape T-cell immunity through ontogeny, and the broad range of viruses that subsequently engage with the adaptive immune response.
Confirmation of Putative HIV-1 Group P in Cameroon
Authors: Vallari Ana , Holzmayer Vera , Harris Barbara , Yamaguchi Julie , Ngansop Charlotte , Makamche Florence , Mbanya Dora , Kaptué Lazare , Ndembi Nicaise , Gürtler Lutz , Devare Sushil , Brennan Catherine A. 
Published: November 2010

ABSTRACT
We report the second human immunodeficiency virus (HIV) belonging to the new HIV type 1 (HIV-1) group P lineage that is closely related to the simian immunodeficiency virus found in gorillas. This virus was identified in an HIV-seropositive male hospital patient in Cameroon, confirming that the group P virus is circulating in humans. Results from screening 1,736 HIV-seropositive specimens collected in Cameroon indicate that HIV-1 group P infections are rare, accounting for only 0.06% of HIV infections. Despite its rarity, group P shows evidence of adaptation to humans.
Medication use in relation to noise from aircraft and road traffic in six European countries: results of the HYENA study
Authors: Floud Sarah , Vigna-Taglianti Federica , Hansell Anna , Blangiardo Marta , Houthuijs Danny , Breugelmans Oscar , Cadum Ennio , Babisch Wolfgang , Selander Jenny , Pershagen Göran , Antoniotti Maria Chiara , Pisani Salvatore , Dimakopoulou Konstantina , Haralabidis Alexandros S , Velonakis Venetia , Jarup Lars 
Published: November 2010

ObjectivesStudies on the health effects of aircraft and road traffic noise exposure suggest excess risks of hypertension, cardiovascular disease and the use of sedatives and hypnotics. Our aim was to assess the use of medication in relation to noise from aircraft and road traffic.MethodsThis cross-sectional study measured the use of prescribed antihypertensives, antacids, anxiolytics, hypnotics, antidepressants and antasthmatics in 4,861 persons living near seven airports in six European countries (UK, Germany, the Netherlands, Sweden, Italy, and Greece). Exposure was assessed using models with 1dB resolution (5dB for UK road traffic noise) and spatial resolution of 250×250m for aircraft and 10×10m for road traffic noise. Data were analysed using multilevel logistic regression, adjusting for potential confounders.ResultsWe found marked differences between countries in the effect of aircraft noise on antihypertensive use; for night-time aircraft noise, a 10dB increase in exposure was associated with ORs of 1.34 (95% CI 1.14 to1.57) for the UK and 1.19 (1.02 to 1.38) for the Netherlands but no significant associations were found for other countries. For day-time aircraft noise, excess risks were found for the UK (OR 1.35; CI: 1.13 to 1.60) but a risk deficit for Italy (OR 0.82; CI: 0.71 to 0.96). There was an excess risk of taking anxiolytic medication in relation to aircraft noise (OR 1.28; CI: 1.04 to 1.57 for daytime and OR 1.27; CI: 1.01 to 1.59 for night-time) which held across countries. We also found an association between exposure to 24hr road traffic noise and the use of antacids by men (OR 1.39; CI 1.11 to 1.74).ConclusionOur results suggest an effect of aircraft noise on the use of antihypertensive medication, but this effect did not hold for all countries. Results were more consistent across countries for the increased use of anxiolytics in relation to aircraft noise.
DARK ENERGY IN PRACTICE
Authors: SAPONE DOMENICO 
Published: November 2010

In this paper we review a part of the approaches that have been considered to explain the extraordinary discovery of the late time acceleration of the Universe. We discuss the arguments that have led physicists and astronomers to accept dark energy as the current preferable candidate to explain the acceleration. We highlight the problems and the attempts to overcome the difficulties related to such a component. We also consider alternative theories capable of explaining the acceleration of the Universe, such as modification of gravity. We compare the two approaches and point out the observational consequences, reaching the sad but foresightful conclusion that we will not be able to distinguish between a Universe filled by dark energy or a Universe where gravity is different from General Relativity. We review the present observations and discuss the future experiments that will help us to learn more about our Universe. This is not intended to be a complete list of all the dark energy models but this paper should be seen as a review on the phenomena responsible for the acceleration. Moreover, in a landscape of hardly compelling theories, it is an important task to build simple measurable parameters useful for future experiments that will help us to understand more about the evolution of the Universe.
DISTAL RADIAL AND ULNAR LANDMARKS USED IN PERCUTANEOUS PIN FIXATION: ANATOMICAL RELATIONSHIP TO THE SUPERFICIAL RADIAL AND ULNAR NERVES
Authors: Tryfonidis M. , Charalambous C. P. , Mills S. P. , Jass G. K. , Jacob S. , Stanley J. K. , Hayton M. J. 
Published: November 2010

Background: The radial and ulnar styloids as well as Lister's tubercle are important surgical landmarks in the surgical treatment of distal forearm fractures. There have been limited studies assessing their relative safety in terms of their distance from superficial nerves which are in danger during surgical procedures. The aim of this cadaveric study was to assess and compare the distance of superficial nerves to these important surgical landmarks. Methods: Twenty embalmed cadaveric upper limbs were dissected exposing the nerves and tendons around the wrist. The radial styloid, Lister's tubercle, ulnar styloid and nerve branches were marked with pins. The distance of the nearest nerve branch to each landmark was measured with a digital calliper. Statistical analysis of the data was performed using SPSS for Windows 11.5 (SPSS Inc., Chicago, IL) using Friedman Tests and Wilcoxon Signed Ranks tests. Results: The median distance of the nearest nerve branch to the radial styloid was 5.42 mm, to the Lister's tubercle was 16.68 mm and to the ulnar styloid was 13.56 mm. There was unequal safety for these three surgical landmarks regarding proximity to nerve branches (p < 0.00001). Paired comparison using Wilcoxon Signed Ranks Test showed that the Lister's tubercle was safer than the radial styloid (p < 0.0001) and ulnar styloid (p = 0.04). In addition, the ulnar styloid was safer than the radial styloid (p < 0.001). Conclusions: There is a higher risk of injury to superficial nerves when operating near the radial styloid as it is significantly closer to nerve branches as compared to Lister's tubercle and ulnar styloid.
A WORKING CLASSIFICATION FOR THE MANAGEMENT OF SCAPHO-TRAPEZIUM-TRAPEZOIDOSTEO-ARTHRITIS
Authors: Westhuizen Johan van der , Mennen Ulrich 
Published: November 2010

Osteo-arthritis (OA) of the scapho-trapezium-trapezoid joint (STT) is the second most common involved joint after trapezium-metacarpal I OA in the wrist. The possible aetiology causing or contributing to the development of STT OA is shortly discussed. A working classification is then proposed, which assists in the management of STT OA.
HOW I DEVELOPED THE WORLD'S FIRST EVIDENCE-BASED ENDOSCOPIC MANAGEMENT OF CARPAL TUNNEL SYNDROME
Authors: Okutsu Ichiro 
Published: November 2010

Carpal tunnel syndrome has been surgically treated by release of the transverse carpal ligament (flexor retinaculum of the hand) using a blind procedure since 1930 or by an open procedure since 1946. The blind procedure has the possibility of unreliable results and ensuing complications, hence, the open procedure was developed. The open procedure, however, also resulted in various complications as reported in the 1970s. At the end of the 1970s, I had many questions regarding accepted surgical procedures for treatment of carpal tunnel syndrome. These included: "Why should any healthy tissue be injured?"; "How can I make operations as minimally invasive as possible?"; and "How can I shorten postoperative fixation periods that cause declines in activities of daily living?" This paper describes how I developed the world's first evidence-based endoscopic management procedure for carpal tunnel syndrome using local anaesthesia without a pneumatic tourniquet on an outpatient basis.
SIMULTANEOUS FRACTURE OF THE WAIST OF THE SCAPHOID AND THE HOOK OF THE HAMATE
Authors: Komura Shingo , Suzuki Yasushi , Ikehata Tatsuya 
Published: November 2010

A case of simultaneous fracture of the waist of the scaphoid and the hook of the hamate is presented. The scaphoid fracture was treated surgically with a headless compression screw, while the hook fracture was treated conservatively with cast immobilisation for eight weeks. Both fractures achieved bone union and the patient returned to work without any symptoms or complications. Only two cases of fractures of the scaphoid and hamate have been reported previously. However, both of them involved fracture of the body of the hamate. This is the first report of simultaneous fracture of the scaphoid and the hook of the hamate.
An assessment of steady-state scale-up for small-scale geological models
Authors: Pickup Gillian E. , Stephen Karl D. 
Published: November 2010

The calculation of pseudo-relative permeabilities can be speeded up considerably by using steady-state methods. The capillary equilibrium limit may be assumed at small scales (30 cm or less), when the flood rate is low. At high flow rates and larger distance scales, we may use a viscous-dominated steady-state method which assumes constant fractional flow. Steady-state pseudos may also be calculated at intermediate flow rates using fine-scale simulations, and allowing the flood to come into equilibrium at different fractional flow levels. The aim of this paper is to assess the accuracy of steady-state scale-up for small-scale sedimentary structures.
We have tested steady-state scale-up methods using a variety of small-scale geological models. The success of steady-state scale-up depends not only on the flow rate, but also on the nature of the heterogeneity. If high permeability zones are surrounded by low permeability ones (e.g. low permeability laminae or bed boundaries), oil trapping may occur in a water-wet system. In this case pseudo-oil-relative permeabilities are very sensitive to flow rate, and care must be taken to upscale using the correct viscous/capillary ratio. However, in permeability models, where phase trapping may not occur (unconnected low permeability regions), the pseudos are similar, whatever the viscous/capillary ratio.
The disadvantage of steady-state scale-up is that it cannot take account of numerical dispersion, in the manner in which dynamic methods can. However, we show examples of coarse-scale simulations with viscous-dominated steady-state pseudos which agree favourably with fine-scale simulations. Provided there are sufficient grid blocks in the coarse-scale model, the smearing of the flood front due to numerical effects is not serious.