Increasing Written Language Skills Utilizing Writing Software and Traditional Methods

A grid based computer program, Clicker5, appeared to have many features that logically may assist struggling writers. It utilizes pictures, sound, speech synthesis, word banks and a spelling checker. Karemaker et al. (2008) examined the use of Clicker5 and observed increased attention and focus during reading, and greater gains in word recognition and rhyme awareness. Scattered research exists on some of the multimedia features that Clicker5 utilizes (e.g. auditory and visual instruction, specific feedback, student specific examples, Wissick & Gardner, 2000; composition processes and revision facilitation, MacArthur 2000; spell checkers with strategy instruction, and speech synthesis to increase error detection and correction, Borgh & Dickson, 1992). However, no research exists on writing outcomes utilizing Clicker5. The purpose of this study was to evaluate the effectiveness of individual Clicker instruction on classroom hand-written products and individually generated computer-assisted written products for children with speech-language deficits who were identified as weak writers by their teachers. A single subject multiple baseline across subjects design was utilized to investigate the research question. The participants included 2 matched pairs of second grade students from two second grade classrooms demonstrating speech-language deficits and difficulty with writing. They were identified by teachers and the speech-language pathologist (SLP) at the Shelbyville elementary school as being at risk for reading difficulty. In the regular classroom, the Daily 6-Trait Writing program was utilized for writing instruction, and consisted of five days of instruction over a 25 week period. The students in the regular classroom filled in a graphic organizer to a writing prompt on the fourth day, and responded to the prompt on the fifth day. The intervention was conducted with one student from each matched pair in two phases, one in the fall and one in the spring, and included three 20 minute sessions each week for four weeks. Each Friday, the subjects responded to the writing prompt in the regular classroom, and then responded to it utilizing Clicker5 independently. These responses were scored on measures of form and content including total number of words, number of different words (NDW), mean length of utterance (MLU), spelling and grammatical accuracy, and local and global coherence. Results indicated good growth in a relatively short treatment period. The phase 1 intervention subject demonstrated an increase from the initial to final writing samples in the classroom and using Clicker5 on measures of total number of words, NDW and MLU. The phase 2 intervention subject demonstrated gains on the same measures when using Clicker5 to respond to the writing prompt. Overall, spelling accuracy was higher when the subjects used Clicker5 to respond to the writing prompts. The intervention subjects also scored highest on total number of words and NDW when using Clicker5 across subjects and samples. Clinical implications include that the subjects demonstrated motivation and enjoyment when using the software program. Some limitations may be that the independent response was conducted in the presence of the primary investigator, and there was inconsistency in the classroom instruction from week to week. Future directions include a multiple baseline across subjects design and a longer treatment period with more participants

Morphological development of a small-scale beach nourishment in a non-tidal area

Combining hard and soft costal protection solutions can be an appropriate measure to enhance structure lifetime. This study aims to quantify the morphological evolution of the nourished stretch and adjacent coastlines. A small-scale beach nourishment has been performed in front of a rock revetment at site in Faxe Ladeplads in Zealand, Denmark. The overall objective is to learn more about the dynamics of small-scale nourishments in low energy environments. Monitoring techniques include repeated topographic (Trimble RTK-GPS, drone surveying) and bathymetric (single beam) measurements. To measure the hydrodynamic conditions two surface acceleration buoys deployed at -4 and -7 m water depth were used. Sediment volumes from nourishments of size 70,000 m3 and 20,000 m3 redistributed relatively quickly. The nourished material built up the cross-shore profile and a longshore bar in this area, and distributed sediments in the direction of the dominant littoral drift (SW). Results suggest that the morphological evolution of the nourishment is dependent on local hydrodynamic conditions and local geomorphology. These findings have implications for the main objectives of preventing wave overtopping onto an adjacent coastal road during extreme events and restoring a beach for recreation

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Microbiology 20 (2018): 769–784, doi:10.1111/1462-2920.14011.At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013 to 2015 at three different vents: Anemone, Marker 33, and Marker 113. Results showed that individual vent sites maintained microbial communities and specific populations over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription profiles. The geochemistry and physical structure of each vent both played important roles in shaping the dominant organisms and metabolisms present at each site. Genomic binning identified key populations of SUP05, Aquificales and methanogenic archaea carrying out important transformations of carbon, sulfur, hydrogen, and nitrogen, with groups that appear unique to individual sites. This work highlights the connection between microbial metabolic processes, fluid chemistry, and microbial population dynamics at and below the seafloor and increases understanding of the role of hydrothermal vent microbial communities in deep ocean biogeochemical cycles.Gordon and Betty Moore Foundation Grant Number: GBMF3297; NSF Center for Dark Energy Biosphere Investigations Grant Number: OCE—0939564; Schmidt Ocean Institut

Addition of Inflammatory Biomarkers Did Not Improve Diabetes Prediction in the Community: The Framingham Heart Study

Background: Prior studies have reported conflicting findings with regard to the association of biomarkers in the prediction of incident type 2 diabetes. We evaluated 12 biomarkers as possible diabetes predictors in the Framingham Heart Study. Methods and results: Biomarkers representing inflammation (C-reactive protein, interleukin-6, monocyte chemoattractant protein-1, tumor necrosis factor receptor 2, osteoprotegerin, and fibrinogen), endothelial dysfunction (intercellular adhesion molecule-1), vascular damage (CD40-ligand, P-selectin, and lipoprotein-associated phospholipase A2 mass and activity), and oxidative stress (urinary isoprostanes) were measured in participants without diabetes attending the Offspring seventh (n=2499) or multiethnic Omni second (n=189) examination (1998–2001). Biomarkers were loge transformed and standardized. Multivariable logistic regression tested each biomarker in association with incident diabetes at a follow-up examination (the Offspring eighth and Omni third examination; mean 6.6 years later), with adjustment for age, sex, cohort, body mass index, fasting glucose, systolic blood pressure, high-density lipoprotein cholesterol, triglycerides, and smoking. C statistics were evaluated with and without inflammatory markers. In 2638 participants (56% women, mean age 59 years), 162 (6.1%) developed type 2 diabetes. All biomarkers, excluding osteoprotegerin, were associated with the outcome with adjustment for age, sex, and cohort; however, none remained significant after multivariable adjustment (all P>0.05). The c statistic from the model including only clinical covariates (0.89) did not statistically significantly improve after addition of biomarkers (all P>0.10). Conclusions: Biomarkers representing different inflammatory pathways are associated with incident diabetes but do not remain statistically significant after adjustment for established clinical covariates. Inflammatory biomarkers might not be an effective resource to predict type 2 diabetes in community-based samples

Adiposity, Cardiometabolic Risk, and Vitamin D Status: The Framingham Heart Study

OBJECTIVE: Because vitamin D deficiency is associated with a variety of chronic diseases, understanding the characteristics that promote vitamin D deficiency in otherwise healthy adults could have important clinical implications. Few studies relating vitamin D deficiency to obesity have included direct measures of adiposity. Furthermore, the degree to which vitamin D is associated with metabolic traits after adjusting for adiposity measures is unclear. RESEARCH DESIGN AND METHODS: We investigated the relations of serum 25-hydroxyvitamin D (25[OH]D) concentrations with indexes of cardiometabolic risk in 3,890 nondiabetic individuals; 1,882 had subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) volumes measured by multidetector computed tomography (CT). RESULTS: In multivariable-adjusted regression models, 25(OH)D was inversely associated with winter season, waist circumference, and serum insulin (P < 0.005 for all). In models further adjusted for CT measures, 25(OH)D was inversely related to SAT (−1.1 ng/ml per SD increment in SAT, P = 0.016) and VAT (−2.3 ng/ml per SD, P < 0.0001). The association of 25(OH)D with insulin resistance measures became nonsignificant after adjustment for VAT. Higher adiposity volumes were correlated with lower 25(OH)D across different categories of BMI, including in lean individuals (BMI <25 kg/m2). The prevalence of vitamin D deficiency (25[OH]D <20 ng/ml) was threefold higher in those with high SAT and high VAT than in those with low SAT and low VAT (P < 0.0001). CONCLUSIONS: Vitamin D status is strongly associated with variation in subcutaneous and especially visceral adiposity. The mechanisms by which adiposity promotes vitamin D deficiency warrant further study.National Institutes of Health's National Heart, Lung, and Blood Institute (N01-HC-25195, R01-DK-80739): American Heart Associatio

Engineering a detect and destroy skin probiotic to combat methicillin-resistant Staphylococcus aureus.

The prevalence and virulence of pathogens such as methicillin-resistant Staphylococcus (S.) aureus (MRSA), which can cause recurrent skin infections, are of significant clinical concern. Prolonged antibiotic exposure to treat or decolonize S. aureus contributes to development of antibiotic resistance, as well as depletion of the microbiome, and its numerous beneficial functions. We hypothesized an engineered skin probiotic with the ability to selectively deliver antimicrobials only in the presence of the target organism could provide local bioremediation of pathogen colonization. We constructed a biosensing S. epidermidis capable of detecting the presence of S. aureus quorum sensing autoinducer peptide and producing lysostaphin in response. Here, we demonstrate in vitro activity of this biosensor and present and discuss challenges to deployment of this and other engineered topical skin probiotics

Stormfloder - en kunskapsöversikt av metoder för att identifiera och kvantifiera extrema havsvattenstånd

Stormfloder är tillfälligt förhöjda vattennivåer orsakade av meteorologiska fenomen som kan ge upphov till översvämningar utmed kusten. När havsnivån stiger till följd av klimatförändringarna och befolkningen utmed kusten ökar, leder det till en ökad översvämningsrisk. Risk kan beskrivas som en kombination av sannolikhet och konsekvens. För att kunna bestämma var som är säkert att bygga och hur befintlig bebyggelse kan skyddas behövs kunskap om hur höga vattenstånd som kan uppstå, hur stora vågorna kan bli och hur länge en storm varar. Vanligtvis utgår man från en sannolikhetsnivå, till exempel att ett område kan tillåtas att översvämmas i genomsnitt vart hundrade år, och bestämmer sedan vilken vattennivå det motsvarar genom extremvärdesanalys av tillgängliga mätdata. För att göra en så säker förutsägelse som möjligt behövs en lång tidserie (i förhållande till den beräknade frekvensen). Det är även viktigt att veta om observationerna är representativa även för framtida förhållanden. Vid stadsplanering och dimensionering av kustskydd är planeringshorisonten i storleksordningen 25 – 200 år, och känsliga byggnader, till exempel vattenverk, kärnkraftverk, och sjukhus dimensioneras för långa återkomsttider, i storleksordningen 200 – 10 000 år. I dagsläget är det svårt att med rimlig säkerhet bedöma konsekvenserna av så ovanliga händelser och hur de kommer att utvecklas i framtiden. Problemet är att mätserierna av stormfloder ofta är för korta för att göra en robust analys. I den här rapporten undersöks hur analyser av stormfloder kan förbättras genom att ta hänsyn till händelser som inträffade innan vattenståndsmätningarna började samt hur de påverkas av klimatvariationer och klimatförändringar.Genom en internationell litteraturstudie undersöks vilka metoder som kan användas för att utöka dataserierna genom att studera historiska dokument, geologiska undersökningar, samt hydrodynamisk modellering. Vidare studeras hur olika statistiska modeller kan användas för att inkludera dessa faktorer i extremvärdesanalys. En fördjupad studie görs av utvalda länder runt Nordsjön och Östersjön (Danmark, England, Schleswig-Holstein och Nederländerna). Analysen visar på stora skillnader, både mellan de studerade länderna och i jämförelse med Sverige, avseende dimensionerande händelser, metoder för extremvärdesanalys, samt hur historiska stormfloder beaktas i riskanalyser.Om översvämningsrisker underskattas, föreligger risk för stora materiella skador och i värsta fall människors liv och hälsa. Om översvämningsrisker å andra sidan överskattas innebär det en suboptimal markanvändning i kustnära områden och att översvämningsskydd överdimensioneras med negativa samhällsekonomiska och miljömässiga effekter till följd. För att möjliggöra en hållbar utveckling av kustnära områden är därför korrekta bedömningar av översvämningsrisken en nyckelfaktor. Metoderna som presenteras i den här studien kan appliceras på Sveriges kuster för öka kunskapsunderlaget om stormfloder och möjliggöra mer robusta riskanalyser och dimensioneringsunderlag för kustskydd

Using Family-Based Imputation in Genome-Wide Association Studies with Large Complex Pedigrees: The Framingham Heart Study

Imputation has been widely used in genome-wide association studies (GWAS) to infer genotypes of un-genotyped variants based on the linkage disequilibrium in external reference panels such as the HapMap and 1000 Genomes. However, imputation has only rarely been performed based on family relationships to infer genotypes of un-genotyped individuals. Using 8998 Framingham Heart Study (FHS) participants genotyped with Affymetrix 550K SNPs, we imputed genotypes of same set of SNPs for additional 3121 participants, most of whom were never genotyped due to lack of DNA sample. Prior to imputation, 122 pedigrees were too large to be handled by the imputation software Merlin. Therefore, we developed a novel pedigree splitting algorithm that can maximize the number of genotyped relatives for imputing each un-genotyped individual, while keeping new sub-pedigrees under a pre-specified size. In GWAS of four phenotypes available in FHS (Alzheimer disease, circulating levels of fibrinogen, high-density lipoprotein cholesterol, and uric acid), we compared results using genotyped individuals only with results using both genotyped and imputed individuals. We studied the impact of applying different imputation quality filtering thresholds on the association results and did not found a universal threshold that always resulted in a more significant p-value for previously identified loci. However most of these loci had a lower p-value when we only included imputed genotypes with with ≥60% SNP- and ≥50% person-specific imputation certainty. In summary, we developed a novel algorithm for splitting large pedigrees for imputation and found a plausible imputation quality filtering threshold based on FHS. Further examination may be required to generalize this threshold to other studies

A three-stage approach for genome-wide association studies with family data for quantitative traits

Background: Genome-wide association (GWA) studies that use population-based association approaches may identify spurious associations in the presence of population admixture. In this paper, we propose a novel three-stage approach that is computationally efficient and robust to population admixture and more powerful than the family-based association test (FBAT) for GWA studies with family data. We propose a three-stage approach for GWA studies with family data. The first stage is to perform linear regression ignoring phenotypic correlations among family members. SNPs with a first stage p-value below a liberal cut-off (e.g. 0.1) are then analyzed in the second stage that employs a linear mixed effects (LME) model that accounts for within family correlations. Next, SNPs that reach genome-wide significance (e.g. $10^{-6}$ for 34,625 genotyped SNPs in this paper) are analyzed in the third stage using FBAT, with correction of multiple testing only for SNPs that enter the third stage. Simulations are performed to evaluate type I error and power of the proposed method compared to LME adjusting for 10 principal components (PC) of the genotype data. We also apply the three-stage approach to the GWA analyses of uric acid in Framingham Heart Study's SNP Health Association Resource (SHARe) project. Results: Our simulations show that whether or not population admixture is present, the three-stage approach has no inflated type I error. In terms of power, using LME adjusting PC is only slightly more powerful than the three-stage approach. When applied to the GWA analyses of uric acid in the SHARe project of FHS, the three-stage approach successfully identified and confirmed three SNPs previously reported as genome-wide significant signals. Conclusions: For GWA analyses of quantitative traits with family data, our three-stage approach provides another appealing solution to population admixture, in addition to LME adjusting for genetic PC

Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents

The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20–40 °C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29–33 h. Only 1011 methanogenic cells occupying 1.8–18 m3 of ocean crust per m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities