Behavioral Communities and the Atomic Structure of Networks

We develop a theory of `behavioral communities' and the `atomic structure' of networks. We define atoms to be groups of agents whose behaviors always match each other in a set of coordination games played on the network. This provides a microfoundation for a method of detecting communities in social and economic networks. We provide theoretical results characterizing such behavior-based communities and atomic structures and discussing their properties in large random networks. We also provide an algorithm for identifying behavioral communities. We discuss applications including: a method of estimating underlying preferences by observing behavioral conventions in data, and optimally seeding diffusion processes when there are peer interactions and homophily. We illustrate the techniques with applications to high school friendship networks and rural village networks

Lost: The Crisis Of Jobless and Out Of School Teens and Young Adults In Chicago, Illinois and the U.S.

This report contains compilations and calculations of various employment data for males and females 16 to 24 years old by race/ethnicity from 2005 to 2014, comparing Chicago, Illinois, the U.S. and in some instances, adding Los Angeles and New York. Besides an array of figures and tables, the report contains GIS generated maps that illustrate the relationship between employment data and population distribution by race/ethnicity. A significant contribution of this report is its demonstration that low rates of employment are spatially concentrated in neighborhoods that are also racially segregated. This report clearly highlights that youth employment rates are tied to conditions in neighborhoods and cannot be seen as distinct from what is happening in the neighborhoods themselves. The devastation of unemployment in turn, wreaks havoc on the neighborhood

HIV versus the Terminator: Drug resistance of HIV reverse transcriptase with mutations at the connection subdomain

Abstract only availableAntiretroviral drug therapy can prolong the life of an HIV-infected individual, but this treatment also promotes drug-resistance mutations. The replicative enzyme of HIV, reverse transcriptase (RT), is a primary target for anti-HIV drug therapy because it is responsible for converting the single stranded RNA genome of HIV into double stranded DNA for integration into the host genome. Many current anti-HIV drugs belong to two classes of inhibitors that target RT: nucleoside reverse transcriptase inhibitors (NRTIs) incorporate into and chain-terminate nascent transcription products of RT, whereas non-nucleoside reverse transcriptase inhibitors (NNRTIs) alter enzyme-nucleic acid interactions, thereby affecting the efficiency of DNA polymerization. Here, we focus on NRTI resistance mutations that are located at the connection subdomain of the enzyme in the presence and absence of thymidine analog associated mutations (TAMs). TAMs cause resistance to the commonly prescribed chain terminator 3'-azido-3'-deoxythymidine (AZT) through excision of the incorporated AZT-monophosphate. Mutations in the connection domain, such as N348I, confer resistance to NRTIs and NNRTIs and augment AZT resistance when present in combination with TAMs. Although the underlying mechanism of N348I resistance remains elusive, it has been suggested that the mutation compromises ribonuclease (RNase) H activity, which is responsible for cleaving the viral genomic RNA of the RNA/DNA heterodimeric intermediate. Changes in RNase H cleavage affect the availability of AZT-terminated primers to be excised, thereby increasing the unblocking of template/primer and NRTI resistance. Our investigation attempts to determine if AZT-resistance mutations affect resistance to other commonly prescribed NRTIs, as well as to competitive substrate inhibitors currently in development, through changes in template/primer processing. In addition, we are examining the effects of NRTI and NNRTI cocktails on the RNase H activity of RT possessing connection domain mutations. Our findings should provide insight for screening novel inhibitors for their efficacy against emergent strains of drug-resistant HIV.Life Sciences Undergraduate Research Opportunity Progra

Racial/Ethnic Differences in Bone Mineral Density of Young Adults

An estimated 1.5 million people suffer a bone disease-related fracture every year. Most work investigating bone mineral density (BMD) focuses on post-menopausal females but a report from the Surgeon General in 2004 stated that of particular concern are men, racial and ethnic minorities, poor individuals, individuals with disabilities, and individuals living in rural areas. The purpose of this study was to examine the racial/ethnic differences in bone mineral density of young adults and to investigate any correlations with variables suggested to influence BMD. BMD was assessed at a younger age than most studies based on the assumption that osteoporosis is a pediatric disorder that manifests in old age. Whole-body BMD, percent body fat (BF), fat mass (FM), and lean mass (LM) of 103 college-aged Blacks, Whites, and Hispanics (18 – 34 years of age) were measured using a Lunar Prodigy Dual Energy X-ray Absorptiometry (DEXA). Blacks and Whites were taller than Hispanics. Blacks had higher BMD than Whites and Hispanics. Blacks and Whites had higher t-scores than Hispanics. Weight and LM correlated with BMD for all three groups. Height correlated with BMD for Blacks only. FM correlated with BMD for Hispanics only. In conclusion, BMD is suggested to be higher in Blacks than Whites and Hispanics. LM is suggested to be an important component of bone health. It is important to stress resistance training for building and maintaining bone health throughout life

Contact-less measurements of Shubnikov-de Haas oscillations in the magnetically ordered state of CeAgSb2_2 and SmAgSb2_2 single crystals

Shubnikov - de Haas oscillations were measured in single crystals of highly metallic antiferromagnetic SmAgSb$_{2}$ and ferromagnetic CeAgSb$_{2}$ using a tunnel diode resonator. Resistivity oscillations as a function of applied magnetic field were observed via measurements of skin depth variation. The effective resolution of $\Delta\rho\simeq20$ p$\Omega$ allows a detailed study of the SdH spectra as a function of temperature. The effects of the Sm long - range magnetic ordering as well as its electronic structure ($4f$-electrons) on the Fermi surface topology is discussed

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (<it>Acipenser fulvescens</it>) gonads.</p> <p>Results</p> <p>Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (~19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type.</p> <p>Conclusion</p> <p>Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.</p

Effect of Xpcl1 Activation and p27Kip1 Loss on Gene Expression in Murine Lymphoma

Mice lacking the p27Kip1 Cdk inhibitor (Cdkn1b) exhibit increased susceptibility to lymphomas from the Maloney murine leukemia virus (M-MuLV), and exhibit a high frequency of viral integrations at Xpcl1 (Kis2), a locus on the X-chromosome. Xpcl1 encodes miR-106a∼363, a cluster of microRNAs that are expressed in response to adjacent retroviral integrations. We report the first large-scale profile of microRNA expression in MuLV-induced lymphomas, in combination with microarray gene expression analysis. The source material was T-cell lymphomas induced by M-MuLV in p27Kip1 knockout mice and normal thymus. Surprisingly, the overall levels of miRNA expression were equivalent in lymphomas and normal thymus. Nonetheless, the expression of specific microRNAs was altered in tumors. The miR-106a∼363 miRNA were over-expressed in lymphomas, particularly those with viral integrations at the Xpcl1 locus. In contrast, p27Kip1 deletion itself was associated with a different pattern of microRNA expression. Gene expression was dramatically altered in lymphomas, yet paralleled data from T-cell lymphomas induced by other mechanisms. Genes with altered expression in association with the p27Kip1 null genotype were of similar functional classes to those associated with Xpcl1 integration, but with the opposite pattern of expression. Thus, the effect of p27Kip1 deletion may be to oppose an anti-oncogenic effect of Xpcl1 rather than enhancing its oncogenic functions. A subset of miR-106a∼363 target genes was consistently reduced in lymphomas with Xpcl1 integrations, particularly genes with cell cycle and immune functions. We identify four predicted target genes of miR-106a∼363 miRNA, including N-Myc (Mycn), and the TGF-beta receptor (Tgfbr2) using 3'UTR reporter assays. Still, bioinformatic miRNA target predictions were poor predictors of altered gene expression in lymphomas with Xpcl1 integration. Confirmation of miR-106a∼363 gene targeting relevant to the tumor phenotype requires in vivo validation, because only a subset of predicted targets are consistently reduced in tumors that overexpress miR-106a∼363

Inflammation mobilizes copper metabolism to promote colon tumorigenesis via an IL-17-STEAP4-XIAP axis.

Copper levels are known to be elevated in inflamed and malignant tissues. But the mechanism underlying this selective enrichment has been elusive. In this study, we report a axis by which inflammatory cytokines, such as IL-17, drive cellular copper uptake via the induction of a metalloreductase, STEAP4. IL-17-induced elevated intracellular copper level leads to the activation of an E3-ligase, XIAP, which potentiates IL-17-induced NFκB activation and suppresses the caspase 3 activity. Importantly, this IL-17-induced STEAP4-dependent cellular copper uptake is critical for colon tumor formation in a murine model of colitis-associated tumorigenesis and STEAP4 expression correlates with IL-17 level and XIAP activation in human colon cancer. In summary, this study reveals a IL-17-STEAP4-XIAP axis through which the inflammatory response induces copper uptake, promoting colon tumorigenesis

Globally elevated titanium, tantalum, and niobium (TITAN) in ocean island basalts with high 3He/4He

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 9 (2008): Q04027, doi:10.1029/2007GC001876.We report evidence for a global Ti, Ta, and Nb (TITAN) enriched reservoir sampled by ocean island basalts (OIBs) with high 3He/4He ratios, an isotopic signature associated with the deep mantle. Excesses of Ti (and to a lesser degree Nb and Ta) correlate remarkably well with 3He/4He in a data set of global OIBs, demonstrating that a major element signature is associated with the high 3He/4He mantle. Additionally, we find that OIBs with high 3He/4He ratios have moderately radiogenic 187Os/188Os (>0.135). The TITAN enrichment and radiogenic 187Os/188Os in high 3He/4He OIBs indicate that they are melts of a mantle domain that hosts a nonprimitive (nonchondritic) component. The observation of TITAN enrichment in the high 3He/4He mantle may be important in balancing the Earth's budget for the TITAN elements. Understanding the origin of the TITAN enrichment is important for constraining the evolution of the enigmatic high 3He/4He mantle domain.Funds for helium measurements were provided by NSF-OCE to M.D.K. Funds for major and trace element analyses were provided by NSF-EAR 0509891 to S.R.H