bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of cytotoxic T‐lymphocyte antigen 4 gene polymorphisms with type 1 autoimmune hepatitis in Japanese
Authors: Umemura Takeji , Ota Masao , Yoshizawa Kaname , Katsuyama Yoshihiko , Ichijo Tetsuya , Tanaka Eiji , Kiyosawa Kendo 
Published: March 2008

Aim:  Autoimmune hepatitis (AIH) is an organ‐specific autoimmune disease characterized by chronic inflammation of the liver. Although the HLA DR4 allele is associated with type 1 AIH in Japanese, the exact genetic etiology of AIH remains undefined. The cytotoxic T‐lymphocyte antigen 4 (CTLA4) is an inhibitory receptor expressed by T‐cells that acts largely as a negative regulator of T‐cell responses, and polymorphisms of CTLA4 have been reported to be associated with susceptibility to various autoimmune diseases. Therefore, we sought to clarify whether CTLA4 single‐nucleotide polymorphisms are associated with disease susceptibility in Japanese patients with type 1 AIH.Methods:  We genotyped 76 patients with AIH and 100 ethically matched controls for allelic determinants using TaqMan genotyping assays at four polymorphism sites: −1722 and −318 in the promoter; +49 in exon 1 and +6230 in the 3′ untranslated region.Results:  We observed no difference in the distribution of the alleles, genotypes, or haplotypes between patients and controls. Compared with −1722 C/C patients, −1722 T/T patients were younger (56 vs. 63 years; P = 0.01) and had significantly lower serum levels of aspartate aminotransferase (313 vs. 763 IU/L; P = 0.031) and bilirubin (1.1 vs. 8.6 mg/dL; P = 0.027). Analysis of allelic frequencies revealed no significant difference between patients with and without the HLA DR4 allele.Conclusion:  These data suggest that the CTLA4 polymorphism is not associated with susceptibility to type 1 AIH in the Japanese population.
Inhibition of hepatic stellate cell activation following Yinchenhao decoction administration to dimethylnitrosamine‐treated rats
Authors: Liu Cheng , Sun Mingyu , Yan Xiaofeng , Han Lin , Zhang Yan , Liu Chenghai , El‐Nezami Hani , Liu Ping 
Published: March 2008

Aim:  In an effort to investigate the mechanism by which Yinchenhao decoction (YCHD) acts on liver injury, we investigated the potential antifibrogenic effects of YCHD in an experimental liver fibrosis rat model, with special focus on the mechanisms inhibiting the activation and promoting apoptosis of hepatic stellate cells (HSC).Methods:  The rats were initially randomized into two groups: the control (n = 10) and dimethylnitrosamine‐treated (DMN; n = 30) groups. DMN (10 mg/kg body weight) was administered intraperitoneally to the DMN‐treated rats for three consecutive days each week. At the end of the second week, three rats from the control and six rats from the DMN‐treated groups were killed for the fibrosis development assessment. The remaining DMN rats were further randomized into two groups: the DMN–water group (n = 12) and the DMN–YCHD group (n = 12). Both groups continued to receive weekly DMN treatment for another 2 weeks in addition to daily administration of either water or YCHD, which were given intragastrically at a dose of 0.418 g/100 g body weight.Results:  Hepatic hydroxyproline content decreased and had improved histopathology in the DMN–YCHD rats. Compared to the DMN group, α‐smooth muscle actin (SMA) and CD68 expression in the DMN–YCHD group was reduced significantly; however, α‐SMA‐positive HSC apoptosis was not observed by confocal microscopy; Fibrogenic proteins (tissue inhibitor matrix proteinases‐1 and 2 and matrix metalloproteinase [MMP]‐2/14) and cytokines (tumor necrosis factor‐α and transforming growth factor‐β1) were decreased; MMP‐9 was significantly upregulated.Conclusion:  Yinchenhao administration attenuates liver fibrosis at least in part by inhibiting HSC activation directly, rather than promoting cell apoptosis of activated HSC, and the suppressive activation of Kupffer cells.
Polyclonal Population Structure of
Streptococcus pneumoniae
Isolates in Spain Carrying
mef
and
mef
plus
erm
(B)
Authors: de la Pedrosa Elia Gómez G. , Morosini María-Isabel , van der Linden Mark , Ruiz-Garbajosa Patricia , Galán Juan Carlos , Baquero Fernando , Reinert Ralf René , Cantón Rafael 
Published: March 2008

ABSTRACT

The population structure (serotypes, pulsed-field gel electrophoresis [PFGE] types, and multilocus sequencing types) of 45
mef
-positive
Streptococcus pneumoniae
isolates [carrying
mef
alone (
n
= 17) or with the
erm
(B) gene
n
= 28)] were studied. They were selected from among all erythromycin-resistant isolates (
n
= 244) obtained from a collection of 712 isolates recovered from different Spanish geographic locations in the prevaccination period from 1999 to 2003. The overall rates of resistance (according to the criteria of the CLSI) among the 45
mef
-positive isolates were as follows: penicillin G, 82.2%; cefotaxime, 22.2%; clindamycin, 62.2%; and tetracycline, 68.8% [mainly in isolates carrying
erm
(B) plus
mef
(E);
P
< 0.001]. No levofloxacin or telithromycin resistance was found. Macrolide resistance phenotypes (as determined by the disk diffusion approximation test) were 37.7% for macrolide resistance [with all but one due to
mef
(E)] and 62.2% for constitutive macrolide-lincosamide-streptogramin B resistance [cMLS
B
; with all due to
mef
(E) plus
erm
(B)]. Serotypes 14 (22.2%), 6B (17.7%), 19A (13.3%), and 19F (11.1%) were predominant. Twenty-five different DNA patterns (PFGE types) were observed. Our
mef
-positive isolates were grouped (by eBURST analysis) into four clonal complexes (
n
= 18) and 19 singleton clones (
n
= 27). With the exception of clone Spain
9V
-3, all clonal complexes (clonal complexes 6B, Spain
6B
-2, and Sweden
15A
-25) and 73.6% of singleton clones carried both the
erm
(B) and the
mef
(E) genes. The international multiresistant clones Spain
23F
-1 and Poland
6B
-20 were represented as singleton clones. A high proportion of
mef
-positive
S. pneumoniae
isolates presented the
erm
(B) gene, with all isolates expressing the cMLS
B
phenotype. A polyclonal population structure was demonstrated within our Spanish
mef
-positive
S. pneumoniae
isolates, with few clonal complexes overrepresented within this collection.
Immunization with a Single Dose of a Microencapsulated
Brucella melitensis
Mutant Enhances Protection against Wild-Type Challenge
Authors: Arenas-Gamboa Angela M. , Ficht Thomas A. , Kahl-McDonagh Melissa M. , Rice-Ficht Allison C. 
Published: March 2008

ABSTRACT

The development of safe and efficacious immunization systems to prevent brucellosis is needed to overcome the disadvantages of the currently licensed vaccine strains that restrict their use in humans. Alginate microspheres coated with a protein of the parasite
Fasciola hepatica
(vitelline protein B [VpB]) and containing live
Brucella melitensis
attenuated mutant
vjbR
::Tn
5
(BMEII1116) were evaluated for vaccine efficacy and immunogenicity in mice. A single immunization dose in BALB/c mice with the encapsulated
vjbR
mutant improved protection against wild-type
B. melitensis
16M challenge compared to the nonencapsulated vaccine strain (
P
< 0.05). The encapsulated mutant was also shown to induce a sustained elevation of Immunoglobulin G levels. Cytokine secretion from spleen cells of mice vaccinated with the encapsulated
vjbR
::Tn
5
revealed elevated secretion of gamma interferon and interleukin-12, but no interleukin-4, suggesting an induction of a T helper 1 response reflecting the enhanced immunity associated with microencapsulation. Together, these results suggest that microencapsulation of live attenuated organisms offers the ability to increase the efficacy of vaccine candidates.
Induction of Guanylate Binding Protein 5 by Gamma Interferon Increases Susceptibility toSalmonella entericaSerovar Typhimurium-Induced Pyroptosis in RAW 264.7 Cells
Authors: Rupper Adam C. , Cardelli James A. 
Published: March 2008

ABSTRACTThe regulation of caspase-1 activation in macrophages plays a central role in host defense against bacterial pathogens. The activation of caspase-1 by the detection of bacterial products through Nod-like receptors leads to the secretion of mature interleukin-1β (IL-1β) and IL-18 and the induction of rapid host cell death (pyroptosis). Here, we report that pyroptosis induced bySalmonella entericaserovar Typhimurium can be positively regulated by prior gamma interferon (IFN-γ) stimulation of RAW 264.7 cells. This increase in cell death is dependent on both caspase-1 activation and, in part,Salmonellapathogenicity island 1 (SPI-1) expression bySalmonella. Furthermore, the exogenous expression of the IFN-γ-induced protein guanylate binding protein 5 (GBP-5) is sufficient to induce a heightened susceptibility of RAW 264.7 cells toSalmonella-induced pyroptosis, and the endogenous expression of GBP-5 is important for this phenomenon. RAW 264.7 cells with decreased expression of GBP-5 mRNA (inhibited by short hairpin RNA against GBP-5) release twofold less lactate dehydrogenase (a marker of membrane permeability) upon infection by invasiveS. entericaserovar Typhimurium than do infected control cells. Importantly, 3× FLAG-tagged GBP-5 is localized to membrane ruffles, which contact invasiveSalmonella, and is found on the membranes of spacious phagosomes containingSalmonella(although it is also found in the cytoplasm and on other cellular membranes), placing 3× FLAG GBP-5 at the interface of secreted SPI-1 effectors and host protein machinery. The regulation of pyroptosis by the IFN-γ-induced protein GBP-5 may play an important role in the host defense againstSalmonella entericaserovar Typhimurium and perhaps other invasive bacterial pathogens.
Escherichia coliO157:H7 Colonization in Cattle following Systemic and Mucosal Immunization with Purified H7 Flagellin
Authors: McNeilly Tom N. , Naylor Stuart W. , Mahajan Arvind , Mitchell Mairi C. , McAteer Sean , Deane David , Smith David G. E. , Low J. Christopher , Gally David L. , Huntley John F. 
Published: March 2008

ABSTRACTEscherichia coliO157:H7 is an important pathogen of humans. Cattle are most frequently identified as the primary source of infection, and therefore, reduction inE. coliO157:H7 prevalence in cattle by vaccination represents an attractive strategy for reducing the incidence of human disease. H7 flagella have been implicated in intestinal-epithelial colonization ofE. coliO157:H7 and may represent a useful target for vaccination. In this study, calves were immunized either systemically with H7 flagellin by intramuscular injection or mucosally via the rectum with either H7 or H7 incorporated into poly(dl-lactide-co-glycolide) microparticles (PLG:H7). Systemic immunization resulted in high levels of flagellin-specific immunoglobulin G (IgG) and IgA in both serum and nasal secretions and detectable levels of both antibody isotypes in rectal secretions. Rectal administration of flagellin resulted in levels of rectal IgA similar to those by the intramuscular route but failed to induce any other antibody response, whereas rectal immunization with PLG:H7 failed to induce any H7-specific antibodies. Following subsequent oral challenge withE. coliO157:H7, reduced colonization rates and delayed peak bacterial shedding were observed in the intramuscularly immunized group compared to nonvaccinated calves, but no reduction in total bacterial shedding occurred. Rectal immunization with either H7 or PLG:H7 had no effect on subsequent bacterial colonization or shedding. Furthermore, purified H7-specific IgA and IgG from intramuscularly immunized calves were shown to reduce intestinal-epithelial binding in vitro. These results indicate that H7 flagellin may be a useful component in a systemic vaccine to reduceE. coliO157:H7 colonization in cattle.
Moraxella catarrhalis
Expresses an Unusual Hfq Protein
Authors: Attia Ahmed S. , Sedillo Jennifer L. , Wang Wei , Liu Wei , Brautigam Chad A. , Winkler Wade , Hansen Eric J. 
Published: March 2008

ABSTRACT

The Hfq protein is recognized as a global regulatory molecule that facilitates certain RNA-RNA interactions in bacteria. BLAST analysis identified a 630-nucleotide open reading frame in the genome of
Moraxella catarrhalis
ATCC 43617 that was highly conserved among
M. catarrhalis
strains and which encoded a predicted protein with significant homology to the Hfq protein of
Escherichia coli.
This protein, containing 210 amino acids, was more than twice as large as the Hfq proteins previously described for other bacteria. The C-terminal half of the
M. catarrhalis
Hfq protein was very hydrophilic and contained two different types of amino acid repeats. A mutation in the
M. catarrhalis hfq
gene affected both the growth rate of this organism and its sensitivity to at least two different types of stress in vitro. Provision of the wild-type
M. catarrhalis hfq
gene in
trans
eliminated these phenotypic differences in the
hfq
mutant. This
M. catarrhalis hfq
mutant exhibited altered expression of some cell envelope proteins relative to the wild-type parent strain and also had a growth advantage in a continuous flow biofilm system. The presence of the wild-type
M. catarrhalis hfq
gene in trans in an
E. coli hfq
mutant fully reversed the modest growth deficiency of this
E. coli
mutant and partially reversed the stress sensitivity of this
E. coli
mutant to methyl viologen. The use of an electrophoretic mobility shift assay showed that this
M. catarrhalis
Hfq protein could bind RNA derived from a gene whose expression was altered in the
M. catarrhalis hfq
mutant.
Mitochondrial monolysocardiolipin acyltransferase is elevated in the surviving population of H9c2 cardiac myoblast cells exposed to 2-deoxyglucose-induced apoptosis
Authors: Danos Maria , Taylor William A. , Hatch Grant M. 
Published: March 2008

Cardiolipin (CL) is a major mitochondrial membrane phospholipid in the mammalian heart and the remodeling of CL is essential to maintain its unique unsaturated fatty acyl composition. We examined CL de novo biosynthesis and remodeling in the surviving population of H9c2 cardiac myoblast cells exposed to 2-deoxyglucose (2-DG). H9c2 cells were incubated in the absence or presence of 2-DG for 16 h with [1,3-3H]glycerol or [1-14C]linoleic acid (bound to albumin in a 1:1 molar ratio). Dead cells were removed and radioactivity was incorporated into CL. Its pool size, fatty acid composition, and the activities of the CL biosynthesis and remodeling enzymes were determined. The CL pool size, its fatty acid composition, and [1,3-3H]glycerol or [1-14C]linoleic acid incorporated into CL were unaltered in the surviving population of 2-DG-treated cells compared with controls. In addition, the activities of the CL de novo biosynthetic enzymes were unaltered. Cleaved caspase-3 and poly(ADP–ribose) polymerase were slightly elevated in the surviving population of 2-DG-treated cells compared with controls, indicating that apoptosis induction was occurring in these cells. Mitochondrial phospholipase A2and monolysocardiolipin acyltransferase (MLCL AT) activities increased 33% (p < 0.05) and 63% (p < 0.05), respectively, in 2-deoxyglucose-treated cells compared with controls. In contrast, the activity of ALCAT1, an endoplasmic reticulum MLCL AT, decreased 77% (p < 0.05), but this was not due to a reduction in ALCAT1 mRNA expression. The mRNA expression of the Barth syndrome gene TAZ, encoding a mitochondrial CL transacylase, was unaltered in 2-DG treated cells. The increase in mitochondrial MLCL AT activity was due to an elevated expression in MLCL AT protein. Thus, an increase in MLCL AT activity and expression occurs to maintain the CL pool in the surviving population of H9c2 cells as a compensatory mechanism for the elevated phospholipase A2activity seen in 2-DG-induced apoptosis. We hypothesize that increased mitochondrial MLCL AT activity and its expression, and hence, elevated CL resynthesis, may be a protective mechanism against monolysocardiolipin-mediated apoptosis.
Real-time rendering of textures with feature curves
Authors: Parilov Evgueni , Zorin Denis 
Published: March 2008

The standard bilinear interpolation on normal maps results in visual artifacts along sharp features, which are common for surfaces with creases, wrinkles, and dents. In many cases, spatially varying features, like the normals near discontinuity curves, are best represented as functions of the distance to the curve and the position along the curve. For high-quality interactive rendering at arbitrary magnifications, one needs to interpolate the distance field preserving discontinuity curves exactly.
We present a real-time, GPU-based method for distance function and distance gradient interpolation which preserves discontinuity feature curves. The feature curves are represented by a set of quadratic Bezier curves, with minimal restrictions on their intersections. We demonstrate how this technique can be used for real-time rendering of complex feature patterns and blending normal maps with procedurally defined profiles near normal discontinuities.
Realistic rendering of birefringency in uniaxial crystals
Authors: Weidlich Andrea , Wilkie Alexander 
Published: March 2008

In this article we derive the complete set of formulas needed to generate physically plausible images of uniaxial crystals. So far no computer graphics publication contains all the formulas one needs to compute the interaction of light with such crystals in a form that is useable by a graphics application, especially if a polarization-aware rendering system is being used.
This paper contains the complete derivation of the Fresnel coefficients for birefringent transparent materials, as well as for the direction cosines of the extraordinary ray and the Mueller matrices necessary to describe polarization effects. The formulas we derive can be directly used in a ray based renderer, and we demonstrate these capabilities in test scenes.
Fault-tolerance in the borealis distributed stream processing system
Authors: Balazinska Magdalena , Balakrishnan Hari , Madden Samuel R. , Stonebraker Michael 
Published: March 2008

Over the past few years, Stream Processing Engines (SPEs) have emerged as a new class of software systems, enabling low latency processing of streams of data arriving at high rates. As SPEs mature and get used in monitoring applications that must continuously run (e.g., in network security monitoring), a significant challenge arises: SPEs must be able to handle various software and hardware faults that occur, masking them to provide high availability (HA). In this article, we develop, implement, and evaluate DPC (Delay, Process, and Correct), a protocol to handle crash failures of processing nodes and network failures in a distributed SPE.
Like previous approaches to HA, DPC uses replication and masks many types of node and network failures. In the presence of network partitions, the designer of any replication system faces a choice between providing availability or data consistency across the replicas. In DPC, this choice is made explicit: the user specifies an availability bound (no result should be delayed by more than a specified delay threshold even under failure if the corresponding input is available), and DPC attempts to minimize the resulting inconsistency between replicas (not all of which might have seen the input data) while meeting the given delay threshold. Although conceptually simple, the DPC protocol tolerates the occurrence of multiple simultaneous failures as well as any further failures that occur during recovery.
This article describes DPC and its implementation in the Borealis SPE. We show that DPC enables a distributed SPE to maintain low-latency processing at all times, while also achieving eventual consistency, where applications eventually receive the complete and correct output streams. Furthermore, we show that, independent of system size and failure location, it is possible to handle failures almost up-to the user-specified bound in a manner that meets the required availability without introducing any inconsistency.
A Framework for Identifying Compromised Nodes in Wireless Sensor Networks
Authors: Zhang Qing , Yu Ting , Ning Peng 
Published: March 2008

Sensor networks are often subject to physical attacks. Once a node's cryptographic key is compromised, an attacker may completely impersonate it and introduce arbitrary false information into the network. Basic cryptographic mechanisms are often not effective in this situation. Most techniques to address this problem focus on detecting and tolerating false information introduced by compromised nodes. They cannot pinpoint exactly where the false information is introduced and who is responsible for it.
In this article, we propose an application-independent framework for accurately identifying compromised sensor nodes. The framework provides an appropriate abstraction of application-specific detection mechanisms and models the unique properties of sensor networks. Based on the framework, we develop alert reasoning algorithms to identify compromised nodes. The algorithm assumes that compromised nodes may collude at will. We show that our algorithm is optimal in the sense that it identifies the largest number of compromised nodes without introducing false positives. We evaluate the effectiveness of the designed algorithm through comprehensive experiments.
Teaching cryptography with open-source software
Authors: McAndrew Alasdair 
Published: March 2008

Cryptography has become an important topic in undergraduate curricula in mathematics and computer science, not just for its intrinsic interest---``about the most fun you can have with mathematics''\cite{ferg04, but for its current standing as the basis for almost all computer security. From wireless networking to secure email to password protection, cryptographic methods are used to secure information, to protect users, and to protect data.
At Victoria University, cryptography has been taught as part of a mathematics and computer science degree for several years. The students all have had at least a year of tertiary mathematics, and some exposure to a computer algebra system (Maple). However, the cost of Maple, and the current licensing agreement, means that students are unable to experiment with the software away from the computer laboratories at the University. For this reason we have decided to investigate the use of open-source computer algebra systems Maxima and Axiom. Although not as full-featured and powerful as the commercial systems Maple and Mathematica, we show they are in fact admirably suited for a subject such as cryptography. In some ways Maxima and Axiom even surpass Maple and Mathematica. Student response to the introduction of these systems has been very positive.