Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

Local Quantum Measurement and No-Signaling Imply Quantum Correlations

We show that, assuming that quantum mechanics holds locally, the finite speed of information is the principle that limits all possible correlations between distant parties to be quantum mechanical as well. Local quantum mechanics means that a Hilbert space is assigned to each party, and then all local positive-operator-valued measurements are (in principle) available; however, the joint system is not necessarily described by a Hilbert space. In particular, we do not assume the tensor product formalism between the joint systems. Our result shows that if any experiment would give nonlocal correlations beyond quantum mechanics, quantum theory would be invalidated even locally.Comment: Published version. 5 pages, 1 figure

Statistical Mechanics of Semi-Supervised Clustering in Sparse Graphs

We theoretically study semi-supervised clustering in sparse graphs in the presence of pairwise constraints on the cluster assignments of nodes. We focus on bi-cluster graphs, and study the impact of semi-supervision for varying constraint density and overlap between the clusters. Recent results for unsupervised clustering in sparse graphs indicate that there is a critical ratio of within-cluster and between-cluster connectivities below which clusters cannot be recovered with better than random accuracy. The goal of this paper is to examine the impact of pairwise constraints on the clustering accuracy. Our results suggests that the addition of constraints does not provide automatic improvement over the unsupervised case. When the density of the constraints is sufficiently small, their only impact is to shift the detection threshold while preserving the criticality. Conversely, if the density of (hard) constraints is above the percolation threshold, the criticality is suppressed and the detection threshold disappears.Comment: 8 pages, 4 figure

Coronary artery endothelial dysfunction is positively correlated with low density lipoprotein and inversely correlated with high density lipoprotein subclass particles measured by nuclear magnetic resonance spectroscopy.

OBJECTIVE: The association between cholesterol and endothelial dysfunction remains controversial. We tested the hypothesis that lipoprotein subclasses are associated with coronary endothelial dysfunction. METHODS AND RESULTS: Coronary endothelial function was assessed in 490 patients between November 1993 and February 2007. Fasting lipids and nuclear magnetic resonance (NMR) lipoprotein particle subclasses were measured. There were 325 females and 165 males with a mean age of 49.8+/-11.6 years. Coronary endothelial dysfunction (epicardial constriction>20% or increase in coronary blood flow<50% in response to intracoronary acetylcholine) was diagnosed in 273 patients, the majority of whom (64.5%) had microvascular dysfunction. Total cholesterol and LDL-C (low density lipoprotein cholesterol) were not associated with endothelial dysfunction. One-way analysis and multivariate methods adjusting for age, gender, diabetes, hypertension and lipid-lowering agent use were used to determine the correlation between lipoprotein subclasses and coronary endothelial dysfunction. Epicardial endothelial dysfunction was significantly correlated with total (p=0.03) and small LDLp (LDL particles) (p<0.01) and inversely correlated with total and large HDLp (high density lipoprotein particles) (p<0.01). CONCLUSIONS: Epicardial, but not microvascular, coronary endothelial dysfunction was associated directly with LDL particles and inversely with HDL particles, suggesting location-dependent impact of lipoprotein particles on the coronary circulation

Entanglement, recoherence and information flow in an accelerated detector - quantum field system: Implications for black hole information issue

We study an exactly solvable model where an uniformly accelerated detector is linearly coupled to a massless scalar field initially in the Minkowski vacuum. Using the exact correlation functions we show that as soon as the coupling is switched on one can see information flowing from the detector to the field and propagating with the radiation into null infinity. By expressing the reduced density matrix of the detector in terms of the two-point functions, we calculate the purity function in the detector and study the evolution of quantum entanglement between the detector and the field. Only in the ultraweak coupling regime could some degree of recoherence in the detector appear at late times, but never in full restoration. We explicitly show that under the most general conditions the detector never recovers its quantum coherence and the entanglement between the detector and the field remains large at late times. To the extent this model can be used as an analog to the system of a black hole interacting with a quantum field, our result seems to suggest in the prevalent non-Markovian regime, assuming unitarity for the combined system, that black hole information is not lost but transferred to the quantum field degrees of freedom. Our combined system will evolve into a highly entangled state between a remnant of large area (in Bekenstein's black hole atom analog) without any information of its initial state, and the quantum field, now imbued with complex information content not-so-easily retrievable by a local observer.Comment: 16 pages, 12 figures; minor change

Аналіз ефективності використання потенціалу матеріальних ресурсів підприємства

Метою даного дослідження виступає пошук аналітичних можливостей комплексної оцінки та аналізу використання потенціалу матеріальних ресурсів та визначення шляхів підвищення ефективності використання матеріальних ресурсів підприємства

The Academics Athletics Trade-off: Universities and Intercollegiate Athletics

This analysis focuses on several key issues in the Football Bowl Subdivision (FBS). The intrinsic benefits of athletic programs are discussed in the first section. Trends in graduation rates and academic performance among athletes and how they correlate with the general student body are discussed in the second section. Finally, an overview of the revenues and expenses of athletic department budgets are discussed in an effort to gain a better understanding of the allocation of funds to athletics. In spite of recent growth in revenues and expenses, the athletic department budget comprises on average only 5 percent of the entire university budget at an FBS school, though spending and revenues have increased dramatically in recent years. In the grand scheme of things, American higher education faces several other, arguably more pressing, areas of reform. However, athletics is a significant and growing dimension of higher education that warrants in-depth examination

A BRCA1 deficient-like signature is enriched in breast cancer brain metastases and predicts DNA damage-induced poly (ADP-ribose) polymerase inhibitor sensitivity

Introduction: There is an unmet clinical need for biomarkers to identify breast cancer patients at an increased risk of developing brain metastases. The objective is to identify gene signatures and biological pathways associated with human epidermal growth factor receptor 2-positive (HER2+) brain metastasis. Methods: We combined laser capture microdissection and gene expression microarrays to analyze malignant epithelium from HER2+ breast cancer brain metastases with that from HER2+ nonmetastatic primary tumors. Differential gene expression was performed including gene set enrichment analysis (GSEA) using publicly available breast cancer gene expression data sets. Results: In a cohort of HER2+ breast cancer brain metastases, we identified a gene expression signature that anti-correlates with overexpression of BRCA1. Sequence analysis of the HER2+ brain metastases revealed no pathogenic mutations of BRCA1, and therefore the aforementioned signature was designated BRCA1 Deficient-Like (BD-L). Evaluation of an independent cohort of breast cancer metastases demonstrated that BD-L values are significantly higher in brain metastases as compared to other metastatic sites. Although the BD-L signature is present in all subtypes of breast cancer, it is significantly higher in BRCA1 mutant primary tumors as compared with sporadic breast tumors. Additionally, BD-L signature values are significantly higher in HER2-/ER- primary tumors as compared with HER2+/ER + and HER2-/ER + tumors. The BD-L signature correlates with breast cancer cell line pharmacologic response to a combination of poly (ADP-ribose) polymerase (PARP) inhibitor and temozolomide, and the signature outperformed four published gene signatures of BRCA1/2 deficiency. Conclusions: A BD-L signature is enriched in HER2+ breast cancer brain metastases without pathogenic BRCA1 mutations. Unexpectedly, elevated BD-L values are found in a subset of primary tumors across all breast cancer subtypes. Evaluation of pharmacological sensitivity in breast cancer cell lines representing all breast cancer subtypes suggests the BD-L signature may serve as a biomarker to identify sporadic breast cancer patients who might benefit from a therapeutic combination of PARP inhibitor and temozolomide and may be indicative of a dysfunctional BRCA1-associated pathway