Africa for Foresters

I sailed for Liberia, as the average American, with my head full of wild ideas that were equal in foundation to the Stork, Santa Claus, and Paul Bunyan. I was much comforted by seeing no bands of blacks in quest of a white man’s heart. They don’t even make it a practice of killing whites, let alone eating them. I awaited in trembling anticipation to see long, slimy serpents hanging from the many boughs that overhang the rivers-but not a one (I was sober). The terrible heat that is supposed to poach one’s brain and make life unbearable only affected the mercury to the extent of 93 degrees. The ferocious lion does not inhabit the deep jungle and the stealthy leopard, whose tail I nearly trod upon, ran like the family tabby that has been caught drinking out of the cream pitcher

New Year’s Eve in Equatorial Africa

It\u27s the same old game, eh Barney? Well, I hate to take the time to go into the sordid details of business, after not having seen you for about a year, but- Boy! Bring whiskey, this master got his feet wet. If you\u27ll sit real still and take notes, I\u27ll fill you up in a hurry

Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

<p>Abstract</p> <p>Background</p> <p>Transcriptional regulatory elements are central to development and interspecific phenotypic variation. Current regulatory element prediction tools rely heavily upon conservation for prediction of putative elements. Recent <it>in vitro </it>observations from the ENCODE project combined with <it>in vivo </it>analyses at the zebrafish <it>phox2b </it>locus suggests that a significant fraction of regulatory elements may fall below commonly applied metrics of conservation. We propose to explore these observations <it>in vivo </it>at the human <it>PHOX2B </it>locus, and also evaluate the potential evidence for genome-wide applicability of these observations through a novel analysis of extant data.</p> <p>Results</p> <p>Transposon-based transgenic analysis utilizing a tiling path proximal to human <it>PHOX2B </it>in zebrafish recapitulates the observations at the zebrafish <it>phox2b </it>locus of both conserved and non-conserved regulatory elements. Analysis of human sequences conserved with previously identified zebrafish <it>phox2b </it>regulatory elements demonstrates that the orthologous sequences exhibit overlapping regulatory control. Additionally, analysis of non-conserved sequences scattered over 135 kb 5' to <it>PHOX2B</it>, provides evidence of non-conserved regulatory elements positively biased with close proximity to the gene. Furthermore, we provide a novel analysis of data from the ENCODE project, finding a non-uniform distribution of regulatory elements consistent with our <it>in vivo </it>observations at <it>PHOX2B</it>. These observations remain largely unchanged when one accounts for the sequence repeat content of the assayed intervals, when the intervals are sub-classified by biological role (developmental versus non-developmental), or by gene density (gene desert versus non-gene desert).</p> <p>Conclusion</p> <p>While regulatory elements frequently display evidence of evolutionary conservation, a fraction appears to be undetected by current metrics of conservation. <it>In vivo </it>observations at the <it>PHOX2B </it>locus, supported by our analyses of <it>in vitro </it>data from the ENCODE project, suggest that the risk of excluding non-conserved sequences in a search for regulatory elements may decrease as distance from the gene increases. Our data combined with the ENCODE data suggests that this may represent a genome wide trend.</p

SIV-specific CD8+ T cells are clonotypically distinct across lymphoid and mucosal tissues

CD8+ T cell responses are necessary for immune control of simian immunodeficiency virus (SIV). However, the key parameters that dictate antiviral potency remain elusive, conceivably because most studies to date have been restricted to analyses of circulating CD8+ T cells. We conducted a detailed clonotypic, functional, and phenotypic survey of SIV-specific CD8+ T cells across multiple anatomical sites in chronically infected rhesus macaques with high (>10,000 copies/mL plasma) or low burdens of viral RNA (<10,000 copies/mL plasma). No significant differences in response magnitude were identified across anatomical compartments. Rhesus macaques with low viral loads (VLs) harbored higher frequencies of polyfunctional CXCR5+ SIV-specific CD8+ T cells in various lymphoid tissues and higher proportions of unique Gag-specific CD8+ T cell clonotypes in the mesenteric lymph nodes relative to rhesus macaques with high VLs. In addition, public Gag-specific CD8+ T cell clonotypes were more commonly shared across distinct anatomical sites than the corresponding private clonotypes, which tended to form tissue-specific repertoires, especially in the peripheral blood and the gastrointestinal tract. Collectively, these data suggest that functionality and tissue localization are important determinants of CD8+ T cell–mediated efficacy against SIV

The Current State of Performance Appraisal Research and Practice: Concerns, Directions, and Implications

On the surface, it is not readily apparent how some performance appraisal research issues inform performance appraisal practice. Because performance appraisal is an applied topic, it is useful to periodically consider the current state of performance research and its relation to performance appraisal practice. This review examines the performance appraisal literature published in both academic and practitioner outlets between 1985 and 1990, briefly discusses the current state of performance appraisal practice, highlights the juxtaposition of research and practice, and suggests directions for further research

Efficacy of tissue brushing as measured by the prosthodontic tissue index

This study was conducted to determine the efficacy of brushing the oral mucosa supporting complete dentures with a soft brush to see if this treatment would reduce inflammation. The oral mucosa health status of 60 patients was monitored for 120 days using the PTI to measure inflammation. For comparison the patients were divided into two groups, and every effort was made to balance the groups for those variables that may effect inflammation. The patients were also compared with themselves. The experiment consisted of three phases; Phase 1 established baseline data, and Phases 2 and 3 were information-gathering sessions. Each patient received brushing instructions at the start of the brushing test period and additional brushing instruction during a reinforcement session after 30 days. Tissue brushing did reduce the inflammation index of the oral mucosa examined.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74782/1/j.1754-4505.1984.tb00150.x.pd

Performance of the NOνA Data Acquisition and Trigger Systems for the full 14 kT Far Detector

The NOvA experiment uses a continuous, free-running, dead-timeless data acquisition system to collect data from the 14 kT far detector. The DAQ system readouts the more than 344,000 detector channels and assembles the information into an raw unfiltered high bandwidth data stream. The NOvA trigger systems operate in parallel to the readout and asynchronously to the primary DAQ readout/event building chain. The data driven triggering systems for NOvA are unique in that they examine long contiguous time windows of the high resolution readout data and enable the detector to be sensitive to a wide range of physics interactions from those with fast, nanosecond scale signals up to processes with long delayed coincidences between hits which occur at the tens of milliseconds time scale. The trigger system is able to achieve a true 100% live time for the detector, making it sensitive to both beam spill related and off-spill physics

A standard protocol to report discrete stage-structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compa dre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility