bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peripheral NKT Cells in Simian Immunodeficiency Virus-Infected Macaques
Authors: Fernandez Caroline S. , Chan Angela C. , Kyparissoudis Konstantinos , De Rose Robert , Godfrey Dale I. , Kent Stephen J. 
Published: December 2008

ABSTRACTNKT cells are a specialized population of T lymphocytes that have an increasingly recognized role in immunoregulation, including controlling the response to viral infections. The characteristics of NKT cells in the peripheral blood of macaques during simian immunodeficiency virus (SIV) or chimeric simian/human immunodeficiency virus (HIV) (SHIV) infection were assessed. NKT cells comprised a mean of 0.19% of peripheral blood lymphocytes across the 64 uninfected macaques studied. Although the range in the percentages of NKT cells was large (0 to 2.2%), levels were stable over time within individual macaques without SIV/SHIV infection. The majority of NKT cells in macaques were CD4+(on average 67%) with smaller populations being CD8+(21%) and CD4/CD8 double positive (13%). A precipitous decline in CD4+NKT cells occurred in all six macaques infected with CXCR4-tropic SHIVmn229early after infection, with a concomitant rise in CD8+NKT cells in some animals. The depletion of CD4+NKT cells was tightly correlated with the depletion of total CD4+T cells. R5-tropic SIVmac251infection of macaques resulted in a slower and more variable decline in CD4+NKT cells, with animals that were able to control SIV virus levels maintaining higher levels of CD4+NKT cells. An inverse correlation between the depletion of total and CD4+NKT cells and SIV viral load during chronic infection was observed. Our results demonstrate the infection-driven depletion of peripheral CD4+NKT cells during both SHIV and SIV infection of macaques. Further studies of the implications of the loss of NKT cell subsets in the pathogenesis of HIV disease are needed.
COMPUTED TOMOGRAPHIC IMAGING SPECTROMETER (CTIS) AND A SNAPSHOT HYPERSPECTRAL IMAGER AND POLARIMETER
Authors: HARTKE JOHN , HAGAN NATHAN , KINDER BRIAN A. , DERENIAK EUSTACE L. 
Published: December 2008

A Computed Tomographic Imagining Spectrometer (CTIS) is an imaging spectrometer system that acquires all the information required to reconstruct the data cube in a single integration time. This is compared to conventional systems such as whiskbroom systems, pushbroom systems, and filter wheel systems that requiring scanning in one or more coordinate direction. CTIS systems have been designed and tested in several different singular spectral bands as well as a dual band system. In addition to hyperspectral imaging spectrometers, CTIS systems have been used as an imaging spectropolarimeter and as a ranging imaging spectrometer. An imaging spectropolarimeter not only reconstructs the spectral content at every point in the scene of interest, but also provides the Stokes parameters at every point. So instead of just one data cube, we get four data cubes, one for each element of the Stokes vector. The ranging CTIS incorporates a LADAR system with the CTIS to provide the range information to targets in scene as well as the reconstructed data cube. The physical principles behind the CTIS system are presented as well as some of representative data from single band systems, the dual band proof of concept, the spectropolarimeter, and the ranging imaging spectrometer.
Are disks the dominant contributor for storage failures?
Authors: Jiang Weihang , Hu Chongfeng , Zhou Yuanyuan , Kanevsky Arkady 
Published: December 2008

Building reliable storage systems becomes increasingly challenging as the complexity of modern storage systems continues to grow. Understanding storage failure characteristics is crucially important for designing and building a reliable storage system. While several recent studies have been conducted on understanding storage failures, almost all of them focus on the failure characteristics of one component—disks—and do not study other storage component failures.This article analyzes the failure characteristics of storage subsystems. More specifically, we analyzed the storage logs collected from about 39,000 storage systems commercially deployed at various customer sites. The dataset covers a period of 44 months and includes about 1,800,000 disks hosted in about 155,000 storage-shelf enclosures. Our study reveals many interesting findings, providing useful guidelines for designing reliable storage systems. Some of our major findings include: (1) In addition to disk failures that contribute to 20--55% of storage subsystem failures, other components such as physical interconnects and protocol stacks also account for a significant percentage of storage subsystem failures. (2) Each individual storage subsystem failure type, and storage subsystem failure as a whole, exhibits strong self-correlations. In addition, these failures exhibit “bursty” patterns. (3) Storage subsystems configured with redundant interconnects experience 30--40% lower failure rates than those with a single interconnect. (4) Spanning disks of a RAID group across multiple shelves provides a more resilient solution for storage subsystems than within a single shelf.
BAX and BAK proteins are required for cyclin-dependent kinase inhibitory drugs to cause apoptosis
Authors: Garrofé-Ochoa Xènia , Melero-Fernández de Mera Raquel M. , Fernández-Gómez Franciso J. , Ribas Judit , Jordán Joaquín , Boix Jacint 
Published: December 2008

AbstractIn previous reports, we have shown in SH-SY5 cells that olomoucine and roscovitine, two inhibitory drugs of cyclin-dependent kinases, caused apoptosis independent of the extrinsic pathway. In this experimental paradigm, apoptosis was refractory to the protective effects of either Bcl-2 or Bcl-XL overexpression. We are now reporting that the failure of Bcl-XL to prevent dell death was consistent with no effect on the kinetics of caspase activation and cytochrome c release. To further characterize this issue, we have discarded a direct effect of either olomoucine or roscovitine on mitochondrial permeability transition. Moreover, we have evidence that an intrinsic pathway took place in SH-SY5Y cells by showing the mitochondrial translocation of a GFP-Bax construct on transfection and treatment with cyclin-dependent kinase inhibitory drugs. Finally, we tested the effect of olomoucine and roscovitine on wild-type, bax−/−, bak−/−, and double bax−/−bak−/− mouse embryonic fibroblasts (MEF). In wild-type MEFs, both drugs induced cell death by apoptosis in a dose-dependent manner. In bax−/−, bak−/−, and, particularly, double bax−/−bak−/− MEFs, we observed the inhibition of apoptosis. In conclusion, olomoucine and roscovitine caused apoptosis through an intrinsic pathway, with Bax and Bak proteins being involved. [Mol Cancer Ther 2008;7(12):3800–6]
IFN-β sensitizes neuroblastoma to the antitumor activity of temozolomide by modulating O6-methylguanine DNA methyltransferase expression
Authors: Rosati Shannon F. , Williams Regan F. , Nunnally Lindsey C. , McGee Mackenzie C. , Sims Thomas L. , Tracey Lorraine , Zhou Junfang , Fan Meiyun , Ng Catherine Y. , Nathwani Amit C. , Stewart Clinton F. , Pfeffer Lawrence M. , Davidoff Andrew M. 
Published: December 2008

Abstract
Although temozolomide has shown clinical activity against neuroblastoma, this activity is likely limited by the DNA repair enzyme O6-methylguanine DNA methyltransferase (MGMT). We hypothesized that IFN-β could sensitize neuroblastoma cells to the cytotoxic effects of temozolomide through its ability to down-regulate MGMT expression. In vitro proliferation of three neuroblastoma cell lines treated with IFN-β and temozolomide alone or in combination was examined. Antitumor activity was assessed in both localized and disseminated neuroblastoma xenografts using single-agent and combination therapy, with continuous delivery of IFN-β being established by a liver-targeted adeno-associated virus-mediated approach. Two neuroblastoma cell lines (NB-1691 and SK-N-AS) were found to have high baseline levels of MGMT expression, whereas a third cell line (CHLA-255) had low levels. Temozolomide had little effect on in vitro proliferation of the neuroblastoma cell lines with high MGMT expression, but pretreatment with IFN-β significantly decreased MGMT expression and cell counts (NB-1691: 36 ± 3% of control, P = 0.0008; SK-N-AS: 54 ± 7% control, P = 0.003). In vivo, NB-1691 tumors in CB17-SCID mice treated with the combination of IFN-β and temozolomide had lower MGMT expression and a significantly reduced tumor burden, both localized [percent initial tumor volume: 2,516 ± 680% (control) versus 1,272 ± 330% (temozolomide), P = 0.01; 1,348 ± 220%, P = 0.03 (IFN-β); 352 ± 110%, P = 0.0001 (combo)] and disseminated [bioluminescent signal: control (1.32e10 ± 6.5e9) versus IFN-β (2.78e8 ± 3.09e8), P = 0.025, versus temozolomide (2.06e9 ± 1.55e9), P = 0.1, versus combination (2.13e7 ± 7.67e6), P = 0.009]. IFN-β appears to sensitize neuroblastoma cells to the cytotoxic effects of temozolomide through attenuation of MGMT expression. Thus, IFN-β and temozolomide may be a useful combination for treating children with this difficult disease. [Mol Cancer Ther 2008;7(12):3852–8]
Relationship Between Noninvasively Measured Endothelial Function and Peripheral Arterial Disease
Authors: Medina Maldonado Francisco José , de Haro Miralles Joaquín , Martínez Aguilar Esther , Florez Gonzalez Aurora , March García Jose Ramón , Acín García Francisco 
Published: December 2008

Objectives: To determine the relationship between endothelial function by means of brachial artery flow-mediated dilation (BAFMD) and the clinical severity of peripheral arterial disease (PAD). Methods and Results: We examined the brachial artery diameter by ultrasound, before and after ischemia of the arm in 3 groups of participants— group A: healthy individuals under 30 years, without cardiovascular risk factors (n = 30); group B: patients with PAD and ischemic claudication (n = 30); and group C: patients with critical leg ischemia (n = 20). There were no differences between groups B and C, in regard to age, sex, and main cardiovascular risk factor. The BAFMD was 9.9% in group A compared with 5.5% in the pooled patients group (B + C; P < .001). Significant differences were absent between groups B and C (P > .05). Correlation coefficient of ankle-brachial index/BAFMD was r = .1; P = .49. Conclusions: Patients with PAD present endothelial dysfunction, but this does not seem to determine the severity of the disease.
An early decrease in Notch activation is required for human TCR-αβ lineage differentiation at the expense of TCR-γδ T cells
Authors: Van de Walle Inge , De Smet Greet , De Smedt Magda , Vandekerckhove Bart , Leclercq Georges , Plum Jean , Taghon Tom 
Published: December 2008

AbstractAlthough well characterized in the mouse, the role of Notch signaling in the human T-cell receptor αβ (TCR-αβ) versus TCR-γδ lineage decision is still unclear. Although it is clear in the mouse that TCR-γδ development is less Notch dependent compared with TCR-αβ differentiation, retroviral overexpression studies in human have suggested an opposing role for Notch during human T-cell development. Using the OP9-coculture system, we demonstrate that changes in Notch activation are differentially required during human T-cell development. High Notch activation promotes the generation of T-lineage precursors and γδ T cells but inhibits differentiation toward the αβ lineage. Reducing the amount of Notch activation rescues αβ-lineage differentiation, also at the single-cell level. Gene expression analysis suggests that this is mediated by differential sensitivities of Notch target genes in response to changes in Notch activation. High Notch activity increases DTX1, NRARP, and RUNX3 expression, genes that are down-regulated during αβ-lineage differentiation. Furthermore, increased interleukin-7 levels cannot compensate for the Notch dependent TCR-γδ development. Our results reveal stage-dependent molecular changes in Notch signaling that are critical for normal human T-cell development and reveal fundamental molecular differences between mouse and human.
Evolution of the parasitic wasp subfamily Rogadinae (Braconidae): phylogeny and evolution of lepidopteran host ranges and mummy characteristics
Authors: Zaldívar-Riverón Alejandro , Shaw Mark R , Sáez Alberto G , Mori Miharu , Belokoblylskij Sergey A , Shaw Scott R , Quicke Donald LJ 
Published: December 2008

AbstractBackgroundThe braconid subfamily Rogadinae is a large, cosmopolitan group of endoparasitoid wasps characterised by 'mummifying' their lepidopteran host larvae, from which the adult subsequently emerges. Rogadines attack a variety of both macro- and microlepidopteran taxa, although the speciose genusAleiodesalmost exclusively attacks macrolepidopterans. Here, we investigate the phylogenetic history of the Rogadinae, revise their higher-level classification and assess the evolution of their host ranges and mummy types. We also assess the divergence times within the subfamily and discuss the reasons for the extraordinary evolutionary diversification ofAleiodes.ResultsOur Bayesian analyses weakly support the monophyly of the subfamily. A clade comprising allAleiodesspecies and some other taxa is not nested within the tribe Rogadini as previously supposed, but instead is recovered as sister to the Yeliconini, with the remaining Rogadini genera being recovered as sister to the Stiropiini. The Rogadinae is estimated to have originated during the mid to late Eocene, 36.1–51.62 MYA. Molecular dating gives a more recent origin for theAleiodesclade (17.98–41.76 MYA) compared to the origins proposed for two of its principal lepidopteran host groups (Noctuidae: 60.7–113.4 MYA; Geometridae 48–62 MYA). The Bayesian ancestral reconstruction of the emergence habits from the mummified hosts weakly recovered an anterior emergence as the ancestral condition for the subfamily. Producing a hard mummy has evolved at various times independently, though most of the species with this biology belong to theAleiodesclade.ConclusionBased on our results, we erect the tribe Aleiodininov.to includeAleiodesandHeterogamusstat. rev.Cordylorhogas,PholichoraandHemigyroneuronare synonymised withAleiodes. The molecular dating of clades and the ancestral reconstruction of host ranges support the hypothesis that radiation withinAleiodes s. s.was due to host recruitment leading to host range expansion followed by speciation, and not to parasitoid-host coevolution. Within the Rogadinae, variation in the site of emergence from the mummified host probably evolved as a consequence of the mummy's site and mode of formation, and the extent of mummy tanning/hardness to the degree of protection needed in relation to the cost of providing it.
A globally occurring indel polymorphism in the promoter of the IFNA2 gene is not associated with severity of malaria but with the positivity rate of HCV
Authors: Tena-Tomás Cristina , de Messias-Reason Iara , Song Le H , Tomiuk Jürgen , Kemsner Peter G , Kun Jürgen FJ 
Published: December 2008

Abstract

Background
Type I Interferons (IFNs) are well known cytokines which exert antiviral activity, antitumor activity and immunomodulatory effects. Single-nucleotide polymorphisms (SNP) and deletions in the gene coding for IFNA2 have been shown to influence the level of expression in vitro. The indel polymorphism -305_-300delAACTTT showed the strongest effect in vitro. To analyse the worldwide distribution of this polymorphism we analyzed five different populations (586 Vietnamese, 199 Central Africans, 265 Brazilians, 108 Kaingang and 98 Guarani). To investigate a possible association with susceptibility to infectious diseases we determined the polymorphism in malaria patients suffering either mild or severe malaria and in a cohort of hepatitis C virus infected individuals.

Results
We could detect the indel polymorphism in all populations analysed. There was no association with this polymorphism and the outcome of malaria but we found an increase of this indel polymorphism in hepatitis C virus positive individuals compared to healthy controls (p = 0.014).

Conclusion
Polymorphisms in genes involved in the interferon pathway have been implicated in the resistance or susceptibility against cerebral malaria and HBV. Here we show that an indel polymorphism, which mediates a disadvantageous effect in HBV patients, may also play a disadvantageous role in HCV infections stressing the importance of a fully functional interferon pathway.
SNP discovery in swine by reduced representation and high throughput pyrosequencing
Authors: Wiedmann Ralph T , Smith Timothy PL , Nonneman Dan J 
Published: December 2008

Abstract

Background
Relatively little information is available for sequence variation in the pig. We previously used a combination of short read (25 base pair) high-throughput sequencing and reduced genomic representation to discover > 60,000 single nucleotide polymorphisms (SNP) in cattle, but the current lack of complete genome sequence limits this approach in swine. Longer-read pyrosequencing-based technologies have the potential to overcome this limitation by providing sufficient flanking sequence information for assay design. Swine SNP were discovered in the present study using a reduced representation of 450 base pair (bp) porcine genomic fragments (approximately 4% of the swine genome) prepared from a pool of 26 animals relevant to current pork production, and a GS-FLX instrument producing 240 bp reads.

Results
Approximately 5 million sequence reads were collected and assembled into contigs having an overall observed depth of 7.65-fold coverage. The approximate minor allele frequency was estimated from the number of observations of the alternate alleles. The average coverage at the SNPs was 12.6-fold. This approach identified 115,572 SNPs in 47,830 contigs. Comparison to partial swine genome draft sequence indicated 49,879 SNP (43%) and 22,045 contigs (46%) mapped to a position on a sequenced pig chromosome and the distribution was essentially random. A sample of 176 putative SNPs was examined and 168 (95.5%) were confirmed to have segregating alleles; the correlation of the observed minor allele frequency (MAF) to that predicted from the sequence data was 0.58.

Conclusion
The process was an efficient means to identify a large number of porcine SNP having high validation rate to be used in an ongoing international collaboration to produce a highly parallel genotyping assay for swine. By using a conservative approach, a robust group of SNPs were detected with greater confidence and relatively high MAF that should be suitable for genotyping in a wide variety of commercial populations.
Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction
Authors: Prins Theo W , van Dijk Jeroen P , Beenen Henriek G , Van Hoef AM Angeline , Voorhuijzen Marleen M , Schoen Cor D , Aarts Henk JM , Kok Esther J 
Published: December 2008

Abstract

Background
To maintain EU GMO regulations, producers of new GM crop varieties need to supply an event-specific method for the new variety. As a result methods are nowadays available for EU-authorised genetically modified organisms (GMOs), but only to a limited extent for EU-non-authorised GMOs (NAGs). In the last decade the diversity of genetically modified (GM) ingredients in food and feed has increased significantly. As a result of this increase GMO laboratories currently need to apply many different methods to establish to potential presence of NAGs in raw materials and complex derived products.

Results
In this paper we present an innovative method for detecting (approved) GMOs as well as the potential presence of NAGs in complex DNA samples containing different crop species. An optimised protocol has been developed for padlock probe ligation in combination with microarray detection (PPLMD) that can easily be scaled up. Linear padlock probes targeted against GMO-events, -elements and -species have been developed that can hybridise to their genomic target DNA and are visualised using microarray hybridisation.
In a tenplex PPLMD experiment, different genomic targets in Roundup-Ready soya, MON1445 cotton and Bt176 maize were detected down to at least 1%. In single experiments, the targets were detected down to 0.1%, i.e. comparable to standard qPCR.

Conclusion
Compared to currently available methods this is a significant step forward towards multiplex detection in complex raw materials and derived products. It is shown that the PPLMD approach is suitable for large-scale detection of GMOs in real-life samples and provides the possibility to detect and/or identify NAGs that would otherwise remain undetected.
Therapeutic potential of resveratrol in Alzheimer's disease
Authors: Vingtdeux Valérie , Dreses-Werringloer Ute , Zhao Haitian , Davies Peter , Marambaud Philippe 
Published: December 2008

Abstract
Several epidemiological studies indicate that moderate consumption of red wine is associated with a lower incidence of dementia and Alzheimer's disease. Red wine is enriched in antioxidant polyphenols with potential neuroprotective activities. Despite scepticism concerning the bioavailability of these polyphenols, in vivo data have clearly demonstrated the neuroprotective properties of the naturally occurring polyphenol resveratrol in rodent models for stress and diseases. Furthermore, recent work in cell cultures and animal models has shed light on the molecular mechanisms potentially involved in the beneficial effects of resveratrol intake against the neurodegenerative process in Alzheimer's disease.