Robo-AO M-dwarf Multiplicity Survey: Catalog

We analyze observations from Robo-AO's field M dwarf survey taken on the 2.1 m Kitt Peak telescope and perform a multiplicity comparison with Gaia DR2. Through its laser-guided, automated system, the Robo-AO instrument has yielded the largest adaptive optics M dwarf multiplicity survey to date. After developing an interface to visually identify and locate stellar companions, we selected 11 low-significance Robo-AO detections for follow-up on the Keck II telescope using NIRC2. In the Robo-AO survey we find 553 candidate companions within 4'' around 534 stars out of 5566 unique targets, most of which are new discoveries. Using a position cross-match with DR2 on all targets, we assess the binary recoverability of Gaia DR2 and compare the properties of multiples resolved by both Robo-AO and Gaia. The catalog of nearby M dwarf systems and their basic properties presented here can assist other surveys which observe these stars, such as the NASA TESS mission

Perception of soundscapes : an interdisciplinary approach

This paper takes an overall view of findings from the Positive Soundscape Project, a large inter-disciplinary soundscapes study. Qualitative fieldwork (soundwalks and focus groups) have found that soundscape perception is influenced by cognitive effects such as the meaning of a soundscape and its components, and how information is conveyed by a soundscape, for example on the behaviour of people within the soundscape. Three significant clusters were found in the language people use to describe soundscapes: sound sources, sound descriptors and soundscape descriptors. Results from listening tests and soundwalks have been integrated to show that the two principal dimensions of soundscape emotional response seem to be calmness and vibrancy. Further, vibrancy seems to have two aspects: organisation of sounds and changes over time. The possible application of the results to soundscape assessment and design are briefly discussed

Evidence of abundant stop codon readthrough in Drosophila and other Metazoa

While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop codon readthrough might be common in Drosophila. We return to this observation armed with deep RNA sequence data from the modENCODE project, an improved higher-resolution comparative genomics metric for detecting protein-coding regions, comparative sequence information from additional species, and directed experimental evidence. We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem–loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candidates in nematode and human, suggesting that functionally important translational stop codon readthrough is significantly more prevalent in Metazoa than previously recognized.National Institutes of Health (U.S.) (U54 HG00455-01)National Science Foundation (U.S.) (CAREER 0644282)Alfred P. Sloan Foundatio

Children’s Health after the Oil Spill: A Four-State Study Findings from the Gulf Coast Population Impact (GCPI) Project

In 2012, with funding from the Baton Rouge Area Foundation, the National Center for Disaster Preparedness (NCDP) at Columbia University, in partnership with the Children’s Health Fund, launched a four-state study in order (1) to identify communities of children in the coastal areas of Louisiana, Mississippi, Alabama and Florida who were adversely impacted by the Deepwater Horizon oil spill, (2) to explore the prevalence of physical and mental health effects among these children, and (3) to conduct a preliminary assessment of the health services available to these children and the potential for targeted interventions or health system enhancements. We identified fifteen communities with higher numbers of BP compensation claims submitted by individuals and by businesses, and which also had higher rates of oil washing up on their shores based upon monitoring data collected by the National Oceanic and Atmospheric Administration. Over a span of four and a half months, a field team of six interviewers and two field coordinators completed 1,437 face-to-face household surveys. The parents whom we interviewed reported considerable exposure to the oil spill as well as a number of physical and mental health problems among their children. Over half of the parents interviewed in these highly-impacted communities reported that their children had some type of oil spill-related exposure, whether it was through physical, environmental, or economic factors. One in every five parents said their children had direct contact with the oil; one in four reported smelling strong oil-related odors; and two of every five said their household had lost income or a job since the oil spill. A little over 40% of parents in these high-impact communities reported some type of health effect experienced by their children since the oil spill. 18.1% of the parents said their children had experienced breathing problems after the oil spill, 14.8% noted skin problems, 16.0% reported visual problems and 21.6% mentioned emotional or behavioral problems since the oil spill. In October 2012 our research team traveled to four communities to interview local officials and leaders and conduct in-depth parent focus groups. We selected the four communities based on the household data, where parents had reported significant health effects. Across the four communities, the team heard of significant issues related to children’s health and well-being

Notch ligand Delta-like 1 promotes in vivo vasculogenesis in human cord blood-derived endothelial colony forming cells

BACKGROUND AIMS: Human cord blood (CB) is enriched in circulating endothelial colony forming cells (ECFCs) that display high proliferative potential and in vivo vessel forming ability. Because Notch signaling is critical for embryonic blood vessel formation in utero, we hypothesized that Notch pathway activation may enhance cultured ECFC vasculogenic properties in vivo. METHODS: In vitro ECFC stimulation with an immobilized chimeric Notch ligand (Delta-like1(ext-IgG)) led to significant increases in the mRNA and protein levels of Notch regulated Hey2 and EphrinB2 that were blocked by treatment with γ-secretase inhibitor addition. However, Notch stimulated preconditioning in vitro failed to enhance ECFC vasculogenesis in vivo. In contrast, in vivo co-implantation of ECFCs with OP9-Delta-like 1 stromal cells that constitutively expressed the Notch ligand delta-like 1 resulted in enhanced Notch activated ECFC-derived increased vessel density and enlarged vessel area in vivo, an effect not induced by OP9 control stromal implantation. RESULTS: This Notch activation was associated with diminished apoptosis in the exposed ECFC. CONCLUSIONS: We conclude that Notch pathway activation in ECFC in vivo via co-implanted stromal cells expressing delta-like 1 promotes vasculogenesis and augments blood vessel formation via diminishing apoptosis of the implanted ECFC

From scaling up to sustainability in HIV: potential lessons for moving forward

Background: In 30 years of experience in responding to the HIV epidemic, critical decisions and program characteristics for successful scale-up have been studied. Now leaders face a new challenge: sustaining large-scale HIV prevention programs. Implementers, funders, and the communities served need to assess what strategies and practices of scaling up are also relevant for sustaining delivery at scale. Methods: We reviewed white and gray literature to identify domains central to scaling-up programs and reviewed HIV case studies to identify how these domains might relate to sustaining delivery at scale. Results: We found 10 domains identified as important for successfully scaling up programs that have potential relevance for sustaining delivery at scale: fiscal support; political support; community involvement, integration, buy-in, and depth; partnerships; balancing flexibility/adaptability and standardization; supportive policy, regulatory, and legal environment; building and sustaining strong organizational capacity; transferring ownership; decentralization; and ongoing focus on sustainability. We identified one additional potential domain important for programs sustaining delivery at scale: emphasizing equity. Conclusions: Today, the public and private sector are examining their ability to generate value for populations. All stakeholders are aiming to stem the tide of the HIV epidemic. Implementers need a framework to guide the evolution of their strategies and management practices. Greater research is needed to refine the domains for policy and program implementers working to sustain HIV program delivery at scale

How Americans Feel About Terrorism And Security: Two Years After 9/11

Understanding attitudes, concerns and reactions of individuals and families is critical to emergency planning efforts on all levels. In order to have effective implementation of a disaster plan, people need to be confident in (a) the reliability of information from official sources, (b) the capacity of government to perform effectively in a crisis and (c) the capability of response systems, particularly the health systems and first responders. Absence of confidence in response systems or leadership may undermine the best of crisis plans, leading to unnecessary panic and potential excess loss of life. In August 2003, The National Center for Disaster Preparedness at Columbia University's Mailman School of Public Health, in collaboration with The Children's Health Fund, commissioned the Marist Institute for Public Opinion to conduct a survey of adults nearly two years after the multiple terrorist attacks on New York, Washington, D.C. and Pennsylvania. The survey included both a national and a New York City representative sample of households contacted by telephone. Questions covered a wide range of issues including people's concern about potential new additional acts of terrorism in the U.S., the government's ability to protect citizens, and the health system's capacity to respond. Throughout, specific questions were asked of a subset of parents of children from four to eighteen years of age. To the extent possible, specific questions were replicated from four previous surveys commissioned by The Children's Health Fund since September 11, 2001 to identify trends in public attitudes and perceptions

The attitudes of police officers towards mental health services

The purpose of this study was to investigate the attitudes of police officers toward mental health services and the perceptions of police departments toward the promotion of dependable support systems and mandatory counseling in the work environment. Understanding the culture and norms within a law enforcement agency is critical to the well-being of officers and the communities they serve

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate – in the nearterm – probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories

Array-based sequencing of filaggrin gene for comprehensive detection of disease-associated variants

The filaggrin gene (FLG) is essential for skin differentiation and epidermal barrier formation. FLG loss-of-function (LoF) variants are associated with ichthyosis vulgaris and the major genetic risk factor for developing atopic dermatitis (AD).1, 2, 3 Genetic stratification of patients with AD according to FLG LoF risk is a common practice for both research and clinical studies; however, few studies comprehensively sequence the entire FLG coding region. Most studies that include FLG genotyping have screened for common predominant LoF variants to report allele frequencies after full Sanger sequencing of a smaller batch of test patient samples or previously published data. This strategy potentially results in underreporting of the genetic contribution especially in ethnicities where FLG LoF variants are highly diverse.4 Distinct LoF variants have been reported for most ethnicities studied to date. For example, 2 predominant sequence variants (p.R501X and c.2282del4) make up approximately 80% of the mutation burden in northern Europeans,5 whereas in East Asian ethnicities, a larger FLG LoF mutation spectrum is found with fewer predominating variants.6, 7 However, routinely Sanger sequencing the entire FLG coding region for large cohorts is not always feasible, although desirable as it is essential to correctly stratify patients. To address this, we developed a robust and cost-effective high-throughput PCR-based method for analyzing the entire coding region of FLG using Fluidigm microfluidics technology and next-generation sequencing (NGS). We have applied this method to fully resequence cohorts of Chinese, Malay, and Indian patients with AD from the Singaporean population.ASTAR (Agency for Sci., Tech. and Research, S’pore)Published versio