288 research outputs found
Mechanical Systems with Symmetry, Variational Principles, and Integration Algorithms
This paper studies variational principles for mechanical systems with symmetry and their applications to integration algorithms. We recall some general features of how to reduce variational principles in the presence of a symmetry group along with general features of integration algorithms for mechanical systems. Then we describe some integration algorithms based directly on variational principles using a
discretization technique of Veselov. The general idea for these variational integrators is to directly discretize Hamilton’s principle rather than the equations of motion in a way that preserves the original systems invariants, notably the symplectic form and, via a discrete version of Noether’s theorem, the momentum map. The resulting mechanical integrators are second-order accurate, implicit, symplectic-momentum algorithms. We apply these integrators to the rigid body and the double spherical pendulum to show that the techniques are competitive with existing integrators
Revisiting the Y=0 open spin chain at one loop
In 2005, Berenstein and Vazquez determined an open spin chain Hamiltonian
describing the one-loop anomalous dimensions of determinant-like operators
corresponding to open strings attached to Y=0 maximal giant gravitons. We
construct the transfer matrix (generating functional of conserved quantities)
containing this Hamiltonian, thereby directly proving its integrability. We
find the eigenvalues of this transfer matrix and the corresponding Bethe
equations, which we compare with proposed all-loop Bethe equations. We note
that the Bethe ansatz solution has a certain "gauge" freedom, and is not
completely unique.Comment: 16 page
Integrable boundaries in AdS/CFT: revisiting the Z=0 giant graviton and D7-brane
We consider the worldsheet boundary scattering and the corresponding boundary
algebras for the Z=0 giant graviton and the Z=0 D7-brane in the AdS/CFT
correspondence. We consider two approaches to the boundary scattering, the
usual one governed by the (generalized) twisted Yangians and the q-deformed
model of these boundaries governed by the quantum affine coideal subalgebras.
We show that the q-deformed approach leads to boundary algebras that are of a
more compact form than the corresponding twisted Yangians, and thus are
favourable to use for explicit calculations. We obtain the q-deformed
reflection matrices for both boundaries which in the q->1 limit specialize to
the ones obtained using twisted Yangians.Comment: 36 pages. v2: minor typos corrected, references updated; v3:
published versio
Expression of the 60 kDa and 71 kDa heat shock proteins and presence of antibodies against the 71 kDa heat shock protein in pediatric patients with immune thrombocytopenic purpura
BACKGROUND: Immune thrombocytopenic purpura (ITP) is an autoimmune disease characterized by platelet destruction resulting from autoantibodies against platelet proteins, particularly platelet glycoprotein IIb/IIIa. Heat shock proteins (Hsp) have been shown to be major antigenic determinants in some autoimmune diseases. Antibodies to Hsps have also been reported to be associated with a number of pathological states. METHODS: Using western blot, we measured the levels of the 60 kDa heat shock protein (Hsp60) and of the inducible 71 kDa member of the Hsp70 family (Hsp71) in lymphocytes and the presence of antibodies against these hsps in plasma of 29 pediatric patients with ITP before the treatment and in 6 other patients before and after treatment. RESULTS: Interestingly only one out of 29 patients showed detectable Hsp60 in lymphocytes while this heat shock protein was detected in the 30 control children. Hsp71 levels were slightly lower in lymphocytes of patients with ITP than in controls (1567.8 ± 753.2 via 1763.2 ± 641.8 integrated optical density (IOD) units). There was a small increase of Hsp71 after recovery from ITP. The titers of plasma antibodies against Hsp60 and Hsp71 were also examined. Antibodies against Hsp71 were more common in ITP patients (15/29) than in control children (5/30). The titer of anti-Hsp71 was also higher in children patients with ITP. The prevalence of ITP children with antibodies against Hsp71 (51.7%) was as high as those with antibodies against platelet membrane glycoproteins (58.3%). CONCLUSIONS: In summary, pediatric patients with ITP showed no detectable expression of Hsp60 in lymphocytes and a high prevalence of antibody against Hsp71 in plasma. These changes add to our understanding of the pathogenesis of ITP and may be important for the diagnosis, prognosis and treatment of ITP
Biological-effective versus conventional dose volume histograms correlated with late genitourinary and gastrointestinal toxicity after external beam radiotherapy for prostate cancer: a matched pair analysis
BACKGROUND: To determine whether the dose-volume histograms (DVH's) for the rectum and bladder constructed using biological-effective dose (BED-DVH's) better correlate with late gastrointestinal (GI) and genitourinary (GU) toxicity after treatment with external beam radiotherapy for prostate cancer than conventional DVH's (C-DVH's). METHODS: The charts of 190 patients treated with external beam radiotherapy with a minimum follow-up of 2 years were reviewed. Six patients (3.2%) were found to have RTOG grade 3 GI toxicity, and similarly 6 patients (3.2%) were found to have RTOG grade 3 GU toxicity. Average late C-DVH's and BED-DVH's of the bladder and rectum were computed for these patients as well as for matched-pair control patients. For each matched pair the following measures of normalized difference in the DVH's were computed: (a) δ(AUC )= (Area Under Curve [AUC] in grade 3 patient – AUC in grade 0 patient)/(AUC in grade 0 patient) and (b) δ(V60 )= (Percent volume receiving = 60 Gy [V60] in grade 3 patient – V60 in grade 0 patient)/(V60 in grade 0 patient). RESULTS: As expected, the grade 3 curve is to the right of and above the grade 0 curve for all four sets of average DVH's – suggesting that both the C-DVH and the BED-DVH can be used for predicting late toxicity. δ(AUC )was higher for the BED-DVH's than for the C-DVH's – 0.27 vs 0.23 (p = 0.036) for the rectum and 0.24 vs 0.20 (p = 0.065) for the bladder. δ(V60 )was also higher for the BED-DVH's than for the C-DVH's – 2.73 vs 1.49 for the rectum (p = 0.021) and 1.64 vs 0.71 (p = 0.021) for the bladder. CONCLUSIONS: When considering well-established dosimetric endpoints used in evaluating treatment plans, BED-DVH's for the rectum and bladder correlate better with late toxicity than C-DVH's and should be considered when attempting to minimize late GI and GU toxicity after external beam radiotherapy for prostate cancer
CCR2-V64I polymorphism is associated with increased risk of cervical cancer but not with HPV infection or pre-cancerous lesions in African women
<p>Abstract</p> <p>Background</p> <p>Cervical cancer, caused by specific oncogenic types of human papillomavirus (HPV), is the second most common cancer in women worldwide. A large number of young sexually active women get infected by HPV but only a small fraction of them have persistent infection and develop cervical cancer pointing to co- factors including host genetics that might play a role in outcome of the HPV infection. This study investigated the role of <it>CCR2-V64I </it>polymorphism in cervical cancer, pre-cancers and HPV infection in South African women resident in Western Cape. <it>CCR2-V64I </it>polymorphism has been previously reported to influence the progression to cervical cancer in some populations and has also been associated with decreased progression from HIV infection to AIDS.</p> <p>Methods</p> <p>Genotyping for <it>CCR2-V64I </it>was done by PCR-SSP in a case-control study of 446 women (106 black African and 340 mixed-ancestry) with histologically confirmed invasive cervical cancer and 1432 controls (322 black African and 1110 mixed-ancestry) group-matched (1:3) by age, ethnicity and domicile status. In the control women HPV was detected using the Digene Hybrid Capture II test and cervical disease was detected by cervical cytology.</p> <p>Results</p> <p>The <it>CCR2-64I </it>variant was significantly associated with cervical cancer when cases were compared to the control group (P = 0.001). Further analysis comparing selected groups within the controls showed that individuals with abnormal cytology and high grade squamous intraepitleial neoplasia (HSIL) did not have this association when compared to women with normal cytology. HPV infection also showed no association with <it>CCR2-64I </it>variant. Comparing SIL positive controls with the cases showed a significant association of <it>CCR2-64I </it>variant (P = 0.001) with cervical cancer.</p> <p>Conclusions</p> <p>This is the first study of the role of <it>CCR2-V64I </it>polymorphism in cervical cancer in an African population. Our results show that <it>CCR2-64I </it>variant is associated with the risk of cervical cancer but does not affect the susceptibility to HPV infection or HSIL in South African women of black and mixed-ancestry origin. This result implies that the role of CCR2 is important in invasive cancer of the cervix but not in HPV infection or in the development of pre-cancers.</p
Histidine-Rich Glycoprotein Protects from Systemic Candida Infection
Fungi, such as Candida spp., are commonly found on the skin and at mucosal surfaces. Yet, they rarely cause invasive infections in immunocompetent individuals, an observation reflecting the ability of our innate immune system to control potentially invasive microbes found at biological boundaries. Antimicrobial proteins and peptides are becoming increasingly recognized as important effectors of innate immunity. This is illustrated further by the present investigation, demonstrating a novel antifungal role of histidine-rich glycoprotein (HRG), an abundant and multimodular plasma protein. HRG bound to Candida cells, and induced breaks in the cell walls of the organisms. Correspondingly, HRG preferentially lysed ergosterol-containing liposomes but not cholesterol-containing ones, indicating a specificity for fungal versus other types of eukaryotic membranes. Both antifungal and membrane-rupturing activities of HRG were enhanced at low pH, and mapped to the histidine-rich region of the protein. Ex vivo, HRG-containing plasma as well as fibrin clots exerted antifungal effects. In vivo, Hrg−/− mice were susceptible to infection by C. albicans, in contrast to wild-type mice, which were highly resistant to infection. The results demonstrate a key and previously unknown antifungal role of HRG in innate immunity
Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
Inference of protein functions is one of the most important aims of modern
biology. To fully exploit the large volumes of genomic data typically produced
in modern-day genomic experiments, automated computational methods for protein
function prediction are urgently needed. Established methods use sequence or
structure similarity to infer functions but those types of data do not suffice
to determine the biological context in which proteins act. Current
high-throughput biological experiments produce large amounts of data on the
interactions between proteins. Such data can be used to infer interaction
networks and to predict the biological process that the protein is involved in.
Here, we develop a probabilistic approach for protein function prediction using
network data, such as protein-protein interaction measurements. We take a
Bayesian approach to an existing Markov Random Field method by performing
simultaneous estimation of the model parameters and prediction of protein
functions. We use an adaptive Markov Chain Monte Carlo algorithm that leads to
more accurate parameter estimates and consequently to improved prediction
performance compared to the standard Markov Random Fields method. We tested our
method using a high quality S.cereviciae validation network
with 1622 proteins against 90 Gene Ontology terms of different levels of
abstraction. Compared to three other protein function prediction methods, our
approach shows very good prediction performance. Our method can be directly
applied to protein-protein interaction or coexpression networks, but also can be
extended to use multiple data sources. We apply our method to physical protein
interaction data from S. cerevisiae and provide novel
predictions, using 340 Gene Ontology terms, for 1170 unannotated proteins and we
evaluate the predictions using the available literature
Development and psychometric testing of a scale assessing the sharing of medical information and interprofessional communication: the CSI scale
A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines
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