New York City School Survey 2008-2010: Assessing the Reliability and Validity of a Progress Report Measure

A growing number of cities and states are using surveys to collect vital information about school climate from students, teachers and parents. The New York City Department of Education's (DOE) annual survey of parents, students, and teachers is the largest of its kind in the United States. Since 2010, the Research Alliance has been working with the DOE to assess the reliability and validity of the survey's measures. This technical report provides an account of our statistical exploration of the School Survey

Estimating spillovers using imprecisely measured networks

In many experimental contexts, whether and how network interactions impact the outcome of interest for both treated and untreated individuals are key concerns. Networks data is often assumed to perfectly represent these possible interactions. This paper considers the problem of estimating treatment effects when measured connections are, instead, a noisy representation of the true spillover pathways. We show that existing methods, using the potential outcomes framework, yield biased estimators in the presence of this mismeasurement. We develop a new method, using a class of mixture models, that can account for missing connections and discuss its estimation via the Expectation-Maximization algorithm. We check our method's performance by simulating experiments on real network data from 43 villages in India. Finally, we use data from a previously published study to show that estimates using our method are more robust to the choice of network measure

Investigations into Xpat, a novel gene expressed in the germ plasm and primordial germ cells of Xenopus laevis

To determine the expression pattern of XPAT (Xenopus primordial germ cell associated transcript) protein in Xenopus oocytes, XPAT-GFP fusion proteins were generated. When XPAT was amino-terminally tagged with GFP it became localised to the nuclei of stage VI Xenopus oocytes. However, when carboxy-terminally tagged with GFP, XPAT also translocated to the vegetal pole of stage VI oocytes. XPAT-GFP formed particles (1 to 2.5mm in diameter) which aggregated into large (10 to 50mm) granular structures at the vegetal pole. These particles looked exactly like those seen after in situ hybridisation to germ plasm RNAs. The granules of XPAT-GFP were larger than endogenous germ plasm granules seen in stage VI oocytes; they were more consistent with those observed in 2-cell embryos during germ plasm aggregation. Studies involving the use of the anticytoskeletal drugs colcemid, nocodazole and cytochalasin D and the microtubule stabilising agent taxol indicated that microtubular transport was important in the location of XPAT-GFP. Several attempts were made to raise antibodies to XPAT peptides, but at present the endogenous expression pattern of XPAT protein is unresolved. To investigate possible domain structure of XPAT, one carboxy-terminal and three amino-terminal deletion variants of XPAT-GFP were constructed. An N-terminal deletion protein lacking the first 61 amino acids of XPAT was able to form small particles, but none of the deletion proteins exhibited vegetal localisation or formed large aggregates in Xenopus oocytes. The N-terminal deletion proteins all became predominantly localised to the nucleus; protein motif analysis revealed that XPAT contains a putative bipartite NLS in its carboxy-terminal region. The C-terminal deletion protein, which lacked the putative NLS, was evenly distributed throughout the nucleus and cytoplasm of Xenopus oocytes. XPAT was shown to be able to bind to homopolymeric RNAs in vitro. When Xpat mRNA was depleted from stage VI Xenopus oocytes (by injection of an antisense oligo) levels of DEADSouth and XVLG1 mRNAs decreased substantially

Age-related Changes in miR-143-3p:Igfbp5 Interactions Affect Muscle Regeneration

A common characteristic of aging is defective regeneration of skeletal muscle. The molecular pathways underlying age-related decline in muscle regenerative potential remain elusive. microRNAs are novel gene regulators controlling development and homeostasis and the regeneration of most tissues, including skeletal muscle. Here, we use satellite cells and primary myoblasts from mice and humans and an in vitro regeneration model, to show that disrupted expression of microRNA-143-3p and its target gene, Igfbp5, plays an important role in muscle regeneration in vitro. We identified miR-143 as a regulator of the insulin growth factor-binding protein 5 (Igfbp5) in primary myoblasts and show that the expression of miR-143 and its target gene is disrupted in satellite cells from old mice. Moreover, we show that downregulation of miR-143 during aging may act as a compensatory mechanism aiming at improving myogenesis efficiency; however, concomitant upregulation of miR-143 target gene, Igfbp5, is associated with increased cell senescence, thus affecting myogenesis. Our data demonstrate that dysregulation of miR-143-3p:Igfbp5 interactions in satellite cells with age may be responsible for age-related changes in satellite cell function

The British Geological Survey Rock Classification Scheme, its representation as linked data, and a comparison with some other lithology vocabularies

Controlled vocabularies are critical to constructing FAIR (findable, accessible, interoperable, re-useable) data. One of the most widely required, yet complex, vocabularies in earth science is for rock and sediment type, or ‘lithology’. Since 1999 the British Geological Survey has used its own Rock Classification Scheme in many of its workflows and products including the national digital geological map. This scheme pre-dates others that have been published, and is deeply embedded in BGS’ processes. By publishing this classification scheme now as a Simple Knowledge Organisation System (SKOS) machine-readable informal ontology, we make it available for ourselves and third parties to use in modern semantic applications, and we open the future possibility of using the tools SKOS provides to align our scheme with other published schemes. These include the IUGS-CGI Simple Lithology Scheme, the European Commission INSPIRE Lithology Code List, the Queensland Geological Survey Lithotype Scheme, the USGS Lithologic Classification of Geologic Map Units, and Mindat.org. The BGS lithology classification was initially based on four narrative reports that can be downloaded from the BGS website, although it has been added to subsequently. The classification is almost entirely mono-hierarchical in nature and includes 3454 currently valid concepts in a classification 11 levels deep. It includes igneous rocks and sediments, metamorphic rocks, sediments and sedimentary rocks, and superficial deposits including anthropogenic deposits. The SKOS informal ontology built on it is stored in a triplestore and the triples are updated nightly by extracting from a relational database where the ontology is maintained. Bulk downloads and version history are available on github. The RCS concepts themselves are used in other BGS linked data, namely the Lexicon of Named Rock Units and the linked data representation of the 1:625 000 scale geological map of the UK. Comparing the RCS with the other published lithology schemes, all are broadly similar but show characteristics that reveal the interests and requirements of the groups that developed them, in terms of their level of detail both overall and in constituent parts. It should be possible to align the RCS with the other classifications, and future work will focus on automated mechanisms to do this, and possibly on constructing a formal ontology for the RCS

A Single Dose TMV-HA Vaccine Protects Mice from H5N1 Influenza Challenge

Recombinant subunit vaccines are an efficient strategy to meet the demands of a possible influenza pandemic, because of rapid and scalable production. However, vaccines made from recombinant Hemagglutinin (HA) subunit protein are often of low potency, requiring repeated boosting to generate a sustained immune response. Previously, we demonstrated improved immunogenicity of a plant-made H1 Hemagglutinin (HA) vaccine by chemical conjugation to the surface of the Tobacco Mosaic Virus (TMV) which is non infectious in mammals. Antigen coated TMV is taken up by mammalian dendritic cells and is a highly effective antigen carrier for subunit protein vaccines. In this work, we tested the effectiveness of a TMV-H5 HA conjugate vaccine. We compared the TMV-H5 immunogenicity in mice, with and without an oil-in water squalene adjuvant, to H5N1 virus or HA protein alone, as measured by anti-H5 IgG titers and Hemagglutination Inhibition (HAI). We then evaluated the efficacy of the TMV-H5 vaccine by lethal H5N1 virus challenge in mice. Our results show that a single dose of the TMV-H5 conjugate vaccine is sufficient to generate 40% survival, similar to H5 protein given with adjuvant, or 100% survival after vaccination with adjuvant, similar to H5N1 virus vaccination

Disability Around the World: Study Abroad in Diverse Cultural Contexts

During a short-term study abroad program undergraduates and instructors from the U.S. explored disability issues in diverse cultural contexts: Ghana, UAE, Nepal, and Thailand. Through qualitative analyses of personal narratives, student interviews, journals, and other products, student- and faculty-researchers learned that participating students developed more critical perspectives on the importance of culture in shaping disability experiences in the U.S. and abroad

Effect of tart cherry juice on recovery and next day performance in well-trained Water Polo players

Background: Tart Montmorency cherries contain high concentrations of phytochemicals and anthocyanins, which have recently been linked to improved athletic recovery and subsequent performance. To date however, previous work reporting promising results has focused on land-based endurance sports, with any potential benefits to team sports remaining unknown. As such, this investigation set-out to examine the effect of supplemental tart cherry juice (CJ) on recovery and next day athletic performance in highly-trained water-based team sport athletes over seven days. Methods: In a randomised, double-blind, repeated measures, crossover design, nine male Water Polo athletes were supplemented with CJ or a placebo equivalent (PLA) for six consecutive days. Prior to, and at the completion of the supplementation period, water-based performance testing was conducted. On day 6, participants also undertook a fatiguing simulated team game activity. Venous blood samples were collected (Pre-exercise: day 1, 6 and 7; Post-exercise: day 6) to investigate markers of inflammation [Interleukin-6 (IL-6); C-reactive protein (CRP)] and oxidative stress [Uric Acid (UA); F2-Isoprostane (F2-IsoP)]. A daily diary was also completed (total quality of recovery, delayed onset muscle soreness) as a measure of perceptual recovery. Results: In both conditions, day 6 post-exercise IL-6 was significantly higher than pre-exercise and day 7 (p<0.05); CRP was greater on day 7 as compared to day 6 pre- and post-exercise (p<0.05); F2-IsoP was significantly lower on day 7 as compared to day 1 and day 6 (p<0.05); UA remained unchanged (p>0.05). No differences were found for any performance or recovery measures. Conclusions: The lack of difference observed in the blood markers between groups may reflect the intermittent, non-weight bearing demands of Water Polo, with such activity possibly unable to create a substantial inflammatory response or oxidative stress (over 7 days) to impede performance; thereby negating any potential beneficial effects associated with CJ supplementation. Trial registration: This trial was registered with the Australian and New Zealand Clinical Trials Registry (ANZCTR). Registration number: ACTRN12616001080415. Date registered: 11/08/2016, retrospectively registered. © 2016 The Author(s)