Changes in Social Structure, Class, and Stratification: The Polish Panel Survey (POLPAN)

We present an overview of the intellectual foundations and some major research questions and topics of the Polish Panel Survey (POLPAN). Carried out since 1988 in 5-year intervals, with the latest in 2013, POLPAN is the longest continuously run panel survey on changes in social structure, class and stratification in Central and Eastern Europe. The 2018 round is in planning. POLPAN is strongly anchored in recent theoretical innovations surrounding analyses of social structure and its change, as well as in the most up-to-date survey methodology. As such, POLPAN has major substantive and methodological contributions. Substantively, POLPAN constitutes a breakthrough that stems from taking into account individuals' life courses in a long time span. Methodologically, POLPAN enhances knowledge about how to conduct long-term panel studies and how to assess the quality of this type of data. Social scientists interested in the dynamics of social structure, class, and stratification, as well as political attitudes and behaviors, have a wealth of data with which to address timeless and timely research questions from a variety of perspectives and fields

Ranked prediction of p53 targets using hidden variable dynamic modeling

Full exploitation of microarray data requires hidden information that cannot be extracted using current analysis methodologies. We present a new approach, hidden variable dynamic modeling (HVDM), which derives the hidden profile of a transcription factor from time series microarray data, and generates a ranked list of predicted targets. We applied HVDM to the p53 network, validating predictions experimentally using small interfering RNA. HVDM can be applied in many systems biology contexts to predict regulation of gene activity quantitatively

Randomly Broken Nuclei and Disordered Systems

Similarities between models of fragmenting nuclei and disordered systems in condensed matter suggest corresponding methods. Several theoretical models of fragmentation investigated in this fashion show marked differences, indicating possible new methods for distinguishing models using yield data. Applying nuclear methods to disordered systems also yields interesting results.Comment: 10 pages, 4 figure

CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells

The persistence of HIV reservoirs, including latently infected, resting CD4+ T cells, is the major obstacle to cure HIV infection. CD32a expression was recently reported to mark CD4+ T cells harboring a replication-competent HIV reservoir during antiretroviral therapy (ART) suppression. We aimed to determine whether CD32 expression marks HIV latently or transcriptionally active infected CD4+ T cells. Using peripheral blood and lymphoid tissue of ART-treated HIV+ or SIV+ subjects, we found that most of the circulating memory CD32+ CD4+ T cells expressed markers of activation, including CD69, HLA-DR, CD25, CD38, and Ki67, and bore a TH2 phenotype as defined by CXCR3, CCR4, and CCR6. CD32 expression did not selectively enrich for HIV- or SIV-infected CD4+ T cells in peripheral blood or lymphoid tissue; isolated CD32+ resting CD4+ T cells accounted for less than 3% of the total HIV DNA in CD4+ T cells. Cell-associated HIV DNA and RNA loads in CD4+ T cells positively correlated with the frequency of CD32+ CD69+ CD4+ T cells but not with CD32 expression on resting CD4+ T cells. Using RNA fluorescence in situ hybridization, CD32 coexpression with HIV RNA or p24 was detected after in vitro HIV infection (peripheral blood mononuclear cell and tissue) and in vivo within lymph node tissue from HIV-infected individuals. Together, these results indicate that CD32 is not a marker of resting CD4+ T cells or of enriched HIV DNA–positive cells after ART; rather, CD32 is predominately expressed on a subset of activated CD4+ T cells enriched for transcriptionally active HIV after long-term ART

Vascularization of the Selaginella rhizophore: anatomical fingerprints of polar auxin transport with implications for the deep fossil record

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138403/1/nph14478_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138403/2/nph14478-sup-0005-Legends.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138403/3/nph14478.pd

The role of paleontological data in bryophyte systematics

Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products-phenotypes and genotypes-to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils-age, phenotypes, and systematic affinities-and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology. Unlocking the severely underutilized potential of the bryophyte fossil record for illuminating phylogeny, systematics, and evolution will require, aside from continued exploration, development of extensive morphological matrices and trained specialists.Peer reviewe