The Thermal Electrical Conductivity Probe (TECP) for Phoenix

The Thermal and Electrical Conductivity Probe (TECP) is a component of the Microscopy, Electrochemistry, and Conductivity Analyzer (MECA) payload on the Phoenix Lander. TECP will measure the temperature, thermal conductivity and volumetric heat capacity of the regolith. It will also detect and quantify the population of mobile H2O molecules in the regolith, if any, throughout the polar summer, by measuring the electrical conductivity of the regolith, as well as the dielectric permittivity. In the vapor phase, TECP is capable of measuring the atmospheric H2O vapor abundance, as well as augment the wind velocity measurements from the meteorology instrumentation. TECP is mounted near the end of the 2.3 m Robotic Arm, and can be placed either in the regolith material or held aloft in the atmosphere. This paper describes the development and calibration of the TECP. In addition, substantial characterization of the instrument has been conducted to identify behavioral characteristics that might affect landed surface operations. The greatest potential issue identified in characterization tests is the extraordinary sensitivity of the TECP to placement. Small gaps alter the contact between the TECP and regolith, complicating data interpretation. Testing with the Phoenix Robotic Arm identified mitigation techniques that will be implemented during flight. A flight model of the instrument was also field tested in the Antarctic Dry Valleys during the 2007-2008 International Polar year.

Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Chemical exchange saturation transfer MRI in central nervous system tumours on a 1.5 T MR-Linac

Purpose: To describe the implementation and initial results of using Chemical Exchange Saturation Transfer (CEST) for monitoring patients with central nervous system (CNS) tumours treated using a 1.5 tesla MR-guided radiotherapy system. Methods: CNS patients were treated with up to 30 fractions (total dose up to 60 Gy) using a 1.5 T Elekta Unity MR-Linac. CEST scans were obtained in 54 subjects at one or more time points during treatment. CEST metrics, including the amide magnetization transfer ratio (MTRAmide), nuclear Overhauser effect (NOE) MTR (MTRNOE) and asymmetry, were quantified in phantoms and CNS patients. The signal was investigated between tumour and white matter, across time, and across disease categories including high- and low-grade tumours. Results: The gross tumour volume (GTV) exhibited lower MTRAmide and MTRNOE and higher asymmetry compared to contralateral normal appearing white matter. Signal changes in the GTV during fractionated radiotherapy were observed. There were differences between high- and low-grade tumours, with higher CEST asymmetry associated with higher grade disease. Conclusion: CEST MRI using a 1.5 T MR-Linac was demonstrated to be feasible for in vivo imaging of CNS tumours. CEST images showed tumour/white-matter contrast, temporal CEST signal changes, and associations with tumour grade. These results show promise for the eventual goal of using metabolic imaging to inform the design of adaptive radiotherapy protocols

The intracellular chloride ion channel protein CLIC1 undergoes a redox-controlled structural transition.

Most proteins adopt a well defined three-dimensional structure; however, it is increasingly recognized that some proteins can exist with at least two stable conformations. Recently, a class of intracellular chloride ion channel proteins (CLICs) has been shown to exist in both soluble and integral membrane forms. The structure of the soluble form of CLIC1 is typical of a soluble glutathione S-transferase superfamily protein but contains a glutaredoxin-like active site. In this study we show that on oxidation CLIC1 undergoes a reversible transition from a monomeric to a non-covalent dimeric state due to the formation of an intramolecular disulfide bond (Cys-24-Cys-59). We have determined the crystal structure of this oxidized state and show that a major structural transition has occurred, exposing a large hydrophobic surface, which forms the dimer interface. The oxidized CLIC1 dimer maintains its ability to form chloride ion channels in artificial bilayers and vesicles, whereas a reducing environment prevents the formation of ion channels by CLIC1. Mutational studies show that both Cys-24 and Cys-59 are required for channel activity

Genetic Determinants of Circulating Sphingolipid Concentrations in European Populations

Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08 x 10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases

Taking Ownership: Our Pledge to Educate All of Detroit's Children

Excellent Schools Detroit represents a broad and diverse cross section of Detroit's education, government, civic and community, parent, organized labor, and philanthropic leaders who are committed to ensuring that all Detroit children receive the great education they deserve. This citywide education plan reflects months of discussions and deliberations by coalition members, as well as a series of six community meetings in November and December, youth focus groups, small group discussions with multiple stakeholders, and other outreach efforts. We appreciate the thoughtful recommendations from the many Detroiters who are as passionate as we are about the need to prepare all students for college, careers, and life in the 21st century

Lessons learned from shallow subglacial bedrock drilling campaigns in Antarctica

We review successes and challenges from five recent subglacial bedrock drilling campaigns intended to find evidence for Antarctic Ice Sheet retreat during warm periods in the geologic past. Insights into times when the polar ice sheets were smaller than present serve as guiding information for modeling efforts that aim to predict the rate and magnitude of future sea level rise that would accompany major retreat of the Antarctic Ice Sheet. One method to provide direct evidence for the timing of deglaciations and minimum extent of prior ice sheets is to extract subglacial bedrock cores for cosmogenic nuclide analysis from beneath the modern ice sheet surface. Here we summarize the lessons learned from five field seasons tasked with obtaining bedrock cores from shallow depths (<120 m beneath ice surface) across West Antarctica since 2016. We focus our findings on drilling efforts and technology and geophysical surveys with ground-penetrating radar. Shallow subglacial drilling provides a high risk, high reward means to test for past instabilities of the Antarctic Ice Sheet, and we highlight key challenges and solutions to increase the likelihood of success for future subglacial drilling efforts in polar regions

Review article: Existing and potential evidence for Holocene grounding line retreat and readvance in Antarctica

Widespread existing geological records from above the modern ice sheet surface and outboard of the current ice margin show that the Antarctic Ice Sheet (AIS) was much more extensive at the Last Glacial Maximum (∼ 20 ka) than at present. However, whether it was ever smaller than present during the last few millennia, and (if so) by how much, is known only for a few locations because direct evidence lies within or beneath the ice sheet, which is challenging to access. Here, we describe how retreat and readvance (henceforth “readvance”) of AIS grounding lines during the Holocene could be detected and quantified using subglacial bedrock, subglacial sediments, marine sediment cores, relative sea-level (RSL) records, geodetic observations, radar data, and ice cores. Of these, only subglacial bedrock and subglacial sediments can provide direct evidence for readvance. Marine archives are of limited utility because readvance commonly covers evidence of earlier retreat. Nevertheless, stratigraphic transitions documenting change in environment may provide support for direct evidence from subglacial records, as can the presence of transgressions in RSL records, and isostatic subsidence. With independent age control, ice structure revealed by radar can be used to infer past changes in ice flow and geometry, and therefore potential readvance. Since ice cores capture changes in surface mass balance, elevation, and atmospheric and oceanic circulation that are known to drive grounding line migration, they also have potential for identifying readvance. A multidisciplinary approach is likely to provide the strongest evidence for or against a smaller-than-present AIS in the Holocene

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Abstract Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website ( http://www.phylotastic.org ), and a server image. Conclusions Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.http://deepblue.lib.umich.edu/bitstream/2027.42/112888/1/12859_2013_Article_5897.pd