A combined approach to data mining of textual and structured data to identify cancer-related targets

BACKGROUND: We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene/protein databases (UniProt, InterPro, NCBI Entrez), and state-of-the-art pathway knowledge bases (LSGraph and Ingenuity Pathway Analysis) was assembled to distinguish enzymes with hydrolytic activities that are expressed in the extracellular space of cancer cells. Proteins were identified with respect to six types of cancer occurring in the prostate, breast, lung, colon, ovary, and pancreas. RESULTS: The data mining method identified previously undetected targets. Our combined strategy applied to each cancer type identified a minimum of 375 proteins expressed within the extracellular space and/or attached to the plasma membrane. The method led to the recognition of human cancer-related hydrolases (on average, ~35 per cancer type), among which were prostatic acid phosphatase, prostate-specific antigen, and sulfatase 1. CONCLUSION: The combined data mining of several databases overcame many of the limitations of querying a single database and enabled the facile identification of gene products. In the case of cancer-related targets, it produced a list of putative extracellular, hydrolytic enzymes that merit additional study as candidates for cancer radioimaging and radiotherapy. The proposed data mining strategy is of a general nature and can be applied to other biological databases for understanding biological functions and diseases

Evidence for magnetic clusters in Ni1−x_{1-x}Vx_{x} close to the quantum critical concentration

The d-metal alloy Ni$_{1-x}$V$_{x}$ undergoes a quantum phase transition from a ferromagnetic ground state to a paramagnetic ground state as the vanadium concentration $x$ is increased. We present magnetization, ac-susceptibility and muon-spin relaxation data at several vanadium concentrations near the critical concentration $x_c \approx11.6$ at which the onset of ferromagnetic order is suppressed to zero temperature. Below $x_c$, the muon data reveal a broad magnetic field distribution indicative of long-range ordered ferromagnetic state with spatial disorder. We show evidence of magnetic clusters in the ferromagnetic phase and close to the phase boundary in this disordered itinerant system as an important generic ingredient of a disordered quantum phase transition. In contrast, the temperature dependence of the magnetic susceptibility above $x_c$ is best described in terms of a magnetic quantum Griffiths phase with a power-law distribution of fluctuation rates of dynamic magnetic clusters. At the lowest temperatures, the onset of a short-range ordered cluster-glass phase is recognized by an increase in the muon depolarization in transverse fields and maxima in ac-susceptibility.Comment: 6 pages, 5 figures, submitted to Proceedings of SCES 201

Trumpler 20 - an old and rich open cluster

We show that the open cluster Trumpler 20, contrary to the earlier findings, is actually an old Galactic open cluster. New CCD photometry and high-resolution spectroscopy are used to derive the main parameters of this cluster. At [Fe/H]=-0.11 for a single red giant star, the metallicity is slightly subsolar. The best fit to the color-magnitude diagrams is achieved using a 1.3 Gyr isochrone with convective overshoot. The cluster appears to have a significant reddening at E(B-V)=0.46 (for B0 spectral type), although for red giants this high reddening yields the color temperature exceeding the spectroscopic T_eff by about 200 K. Trumpler 20 is a very rich open cluster, containing at least 700 members brighter than M_V=+4. It may extend over the field-of-view available in our study at 20'x20'.Comment: 7 pages, 5 figures; accepted for publication in MNRA

Variable stars in the field of the old open cluster Melotte 66

We report the results of photometric monitoring of the Melotte 66 field in BVI filters. Ten variables were identified with nine being new discoveries. The sample includes eight eclipsing binaries of which four are W UMa type stars, one star is a candidate blue straggler. All four contact binaries are likely members of the cluster based on their estimated distances. Ten blue stars with U-B<-0.3 were detected inside a 14.8 x 22.8 arcmin^2 field centred on the cluster. Time series photometry for 7 of them showed no evidence for any variability. The brightest object in the sample of blue stars is a promising candidate for a hot subdwarf belonging to the cluster. We show that the anomalously wide main sequence of the cluster, reported in some earlier studies, results from a combination of two effects: variable reddening occuring across the cluster field and the presence of a rich population of binary stars in the cluster itself. The density profile of the cluster field is derived and the total number of member stars with 16<V<21 or 2.8<M_{V}<7.8 is estimated conservatively at about 1100.Comment: 8 pages, 12 figures, accepted to MNRAS - 29 June 200

Evidence for Magnetic Clusters in Ni₁₋ₓVₓ Close to the Quantum Critical Concentration

The d-metal alloy Ni1-xVx undergoes a quantum phase transition from a ferromagnetic ground state to a paramagnetic ground state as the vanadium concentration x is increased. We present magnetization, ac-susceptibility and muon-spin relaxation data at several vanadium concentrations near the critical concentration xc ~ 11.6 % at which the onset of ferromagnetic order is suppressed to zero temperature. Below xc, the muon data reveal a broad magnetic field distribution indicative of a long-range ordered ferromagnetic state with spatial disorder. We show evidence of magnetic clusters in the ferromagnetic phase and close to the phase boundary in this disordered itinerant system as an important generic ingredient of a disordered quantum phase transition. In contrast, the temperature dependence of the magnetic susceptibility above xc is best described in terms of a magnetic quantum Griffiths phase with a power-law distribution of fluctuation rates of dynamic magnetic clusters. At the lowest temperatures, the onset of a short-range ordered cluster-glass phase is recognized by an increase in the muon depolarization in transverse fields and maxima in ac-susceptibility

by M Sprenger Rapid communications HIV and AIDS in the European Union, 2009 4

D Tubin-Delic, on behalf of the outbreak control team Surveillance and outbreak reports Control of a multi-hospital outbreak of KPC-producing Klebsiella pneumonia

Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for <i>Elovl2</i> in glucose-induced insulin secretion.

In type 2 diabetes (T2D), pancreatic β cells become progressively dysfunctional, leading to a decline in insulin secretion over time. In this study, we aimed to identify key genes involved in pancreatic beta cell dysfunction by analyzing multiple mouse strains in parallel under metabolic stress. Male mice from six commonly used non-diabetic mouse strains were fed a high fat or regular chow diet for three months. Pancreatic islets were extracted and phenotypic measurements were recorded at 2 days, 10 days, 30 days, and 90 days to assess diabetes progression. RNA-Seq was performed on islet tissue at each time-point and integrated with the phenotypic data in a network-based analysis. A module of co-expressed genes was selected for further investigation as it showed the strongest correlation to insulin secretion and oral glucose tolerance phenotypes. One of the predicted network hub genes was &lt;i&gt;Elovl2&lt;/i&gt; , encoding Elongase of very long chain fatty acids 2. &lt;i&gt;Elovl2&lt;/i&gt; silencing decreased glucose-stimulated insulin secretion in mouse and human β cell lines. Our results suggest a role for &lt;i&gt;Elovl2&lt;/i&gt; in ensuring normal insulin secretory responses to glucose. Moreover, the large comprehensive dataset and integrative network-based approach provides a new resource to dissect the molecular etiology of β cell failure under metabolic stress