Non-verbal behavioural patterns in trilogue play transitions and family alliances

This case study focuses on non-verbal behaviour in father-mother-infant triads. Analyses were done on transitional moments during which the partners exchanged an active role for a participant-observer role, or vice versa. Transitions are known to be crucial moments for revealing familial transactional mechanisms. Our sample was comprised of six non-clinical families, characterized by different types of functional or problematic alliances (which is the degree of coordination between the partners). Our methodology included micro-analysis of body and gaze formations, facial expressions, and so on. Data were analysed using the research package 'THEME' for the detection of hidden patterns. Different types of non-verbal patterns were found, which may be prototypes corresponding to the different types of alliance. The patterns of the families with high alliances had a more elaborate construction and were more efficient for the concluding of transitions than the patterns of families with low alliances, which were either elementary or laborious. (PsycINFO Database Record (c) 2006 APA, all rights reserved) (journal abstract)

Mynodbcsv: Lightweight Zero-Config Database Solution for Handling Very Large CSV Files.

Volumes of data used in science and industry are growing rapidly. When researchers face the challenge of analyzing them, their format is often the first obstacle. Lack of standardized ways of exploring different data layouts requires an effort each time to solve the problem from scratch. Possibility to access data in a rich, uniform manner, e.g. using Structured Query Language (SQL) would offer expressiveness and user-friendliness. Comma-separated values (CSV) are one of the most common data storage formats. Despite its simplicity, with growing file size handling it becomes non-trivial. Importing CSVs into existing databases is time-consuming and troublesome, or even impossible if its horizontal dimension reaches thousands of columns. Most databases are optimized for handling large number of rows rather than columns, therefore, performance for datasets with non-typical layouts is often unacceptable. Other challenges include schema creation, updates and repeated data imports. To address the above-mentioned problems, I present a system for accessing very large CSV-based datasets by means of SQL. It's characterized by: "no copy" approach - data stay mostly in the CSV files; "zero configuration" - no need to specify database schema; written in C++, with boost [1], SQLite [2] and Qt [3], doesn't require installation and has very small size; query rewriting, dynamic creation of indices for appropriate columns and static data retrieval directly from CSV files ensure efficient plan execution; effortless support for millions of columns; due to per-value typing, using mixed text/numbers data is easy; very simple network protocol provides efficient interface for MATLAB and reduces implementation time for other languages. The software is available as freeware along with educational videos on its website [4]. It doesn't need any prerequisites to run, as all of the libraries are included in the distribution package. I test it against existing database solutions using a battery of benchmarks and discuss the results.

Cis interactions of immunoreceptors with MHC and non-MHC ligands

The conventional wisdom is that cell-surface receptors interact with ligands expressed on other cells to mediate cell-to-cell communication (trans interactions). Unexpectedly, it has recently been found that two classes of receptors specific for MHC class I molecules not only interact with MHC class I molecules expressed on opposing cells, but also with those on the same cell. These cis interactions are a feature of immunoreceptors that inhibit, rather than activate, cellular functions. Here, we review situations in which cis interactions have been observed, the characteristics of receptors that bind in trans and cis, and the biological roles of cis recognition.

Objective assessment of image quality in conventional and digital mammography taking into account dynamic range.

The goal of this work is to develop a method to objectively compare the performance of a digital and a screen-film mammography system in terms of image quality. The method takes into account the dynamic range of the image detector, the detection of high and low contrast structures, the visualisation of the images and the observer response. A test object, designed to represent a compressed breast, was constructed from various tissue equivalent materials ranging from purely adipose to purely glandular composition. Different areas within the test object permitted the evaluation of low and high contrast detection, spatial resolution and image noise. All the images (digital and conventional) were captured using a CCD camera to include the visualisation process in the image quality assessment. A mathematical model observer (non-prewhitening matched filter), that calculates the detectability of high and low contrast structures using spatial resolution, noise and contrast, was used to compare the two technologies. Our results show that for a given patient dose, the detection of high and low contrast structures is significantly better for the digital system than for the conventional screen-film system studied. The method of using a test object with a large tissue composition range combined with a camera to compare conventional and digital imaging modalities can be applied to other radiological imaging techniques. In particular it could be used to optimise the process of radiographic reading of soft copy images.

Bonded, Thin-Lift, Non-Reinforced Portland Cement Concrete Resurfacing, MLR-77-2, 1977

A research project involving 2, 3, 4, and 5 in. (5.1, 7.6, 10.2, and 12.7 cm) of bonded portland cement concrete (PCC) overlay on a 1.3 mile (2.1 km) PCC pavement was conducted in Clayton County, Iowa, during September 1977, centering on the following objectives: (1) Determine the mixing and proportioning procedures required in using a conventional, central mix proportioning plant to produce a dense PCC mixture using standard mixes with super water reducing admixtures; (2) Determine the economics, longevity and maintenance performance of a bonded, thin-lift, non-reinforced PCC resurfacing course using conventional procedures, equipment and concrete paving mixtures both with and without super water reducing admixtures; and (3) Determine if an adequate bond between the existing pavement and an overlay of thin-lift, dense, non-reinforced PCC can be obtained with only special surface cleaning and no surface removal or grinding. The conclusions are as follows: (1) Normal mixing equipment and proportioning procedures could be used using a conventional central-mix proportioning plant. This was successful when used with super water reducing admixtures. Only minor changes need be made in procedures and timing. (2) The time has been too short since the completion of the project to determine how the new pavement will perform, however, initially it appears that the method is economical and no reason is seen at this time why the life of the pavement should not be comparable to an all new pavement. (3) The initial test results show that bond strength, regardless of which method of cleaning is used, scarifying, sand blasting or water blasting, far exceed what is considered the minimum bond strength of 200 psi (1379 kPa) except where the paint stripes were intentionally left, thus showing that the paint must be removed. (4) It appears that either cement and water grout or sand, cement and water grout may be used and still obtain the required bond.

Bonded, Thin-Lift, Non-Reinforced Portland Cement Concrete Resurfacing, HR-191, 1980

A Research Project involving two, three, four and five inches of bonded Portland Cement Concrete Overlay on a 1.3 mile Portland Cement Concrete pavement was conducted in Clayton County, Iowa, during September, 1977, centering on the following objectives: 1. Determine the mixing and proportioning procedures required in using a conventional, central mix proportioning plant to produce a dense Portland Cement Concrete mixture using standard mixes with super-water reducing admixtures; 2. Determine the economics, longevity and maintenance performance of a bonded, thin-lift, non-reinforced Portland Cement Concrete resurfacing course using conventional procedures, equipment and concrete paving mixtures both with and without super-water reducing admixtures; 3. Determine if an adequate bond between the existing pavement and an overlay of thin-lift, dense, non-reinforced Portland Cement Concrete can be obtained with only special surface cleaning and no surface removal or grinding.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS (http://genome.imim.es/datasets/abs2005/index.html) is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Exposure of the Swiss population by medical x-rays: 2008 review.

Nationwide surveys on radiation dose to the population from medical radiology are recommended in order to follow the trends in population exposure and ensure radiation protection. The last survey in Switzerland was conducted in 1998, and the annual effective dose from medical radiology was estimated to be 1 mSv y(-1) per capita. The purpose of this work was to follow the trends in diagnostic radiology between 1998 and 2008 in Switzerland and determine the contribution of different modalities and types of examinations to the collective effective dose from medical x-rays. For this reason, an online database (www.raddose.ch) was developed. All healthcare providers who hold a license to run an x-ray unit in the country were invited to participate in the survey. More than 225 examinations, covering eight radiological modalities, were included in the survey. The average effective dose for each examination was reassessed. Data from about 3,500 users were collected (42% response rate). The survey showed that the annual effective dose was 1.2 mSv/capita in 2008. The most frequent examinations are conventional and dental radiographies (88%). The contribution of computed tomography was only 6% in terms of examination frequency but 68% in terms of effective dose. The comparison with other countries showed that the effective dose per capita in Switzerland was in the same range as in other countries with similar healthcare systems, although the annual number of examinations performed in Switzerland was higher.

Roux-en-y Gastric Bypass is Superior to Gastric Banding in Non-superobese Patients. a Matched-case Study with Five-year Follow-up

Background: Roux-en-Y gastric bypass (RYGBP) and gastric banding (GB) are the two most popular bariatric procedures. Only few studies have compared their results and follow-up duration is usually limited to <3 years. Patients and Methods: Using our prospective bariatric database, we matched non-superobese GB to RYGBP patients for sex, age and BMI to RYGBP. Follow-up considered up to five years. Results: 442 patients were matched in 221 pairs. Mean age (38,6) and mean BMI (43) were identical. Overall operative morbidity was higher after RYGBP (17,2 versus 5,4 %, p<0,001), but major morbidity was similar (3,6 versus 2,2 %, p=0,57). More patients developed long-term complications after GB (43,9 % versus 19 %, p<0,001), and more required reoperations (24,4 % versus 12 %, p=0,001). After RYGBP, reoperations were mainly due to internal hernias (87 %), with no reversal, whereas 18,5 % of the GB patients required band removal. Even including only patients who retained their band, weight loss after RYGBP was better throughout the study period, with 5-year EBMIL of 77,6 % and 61,7 % (p<0,001) after RYGBP and GB respectively. RYGBP was associated with better food tolerance and greater improvement of the lipid profile. Conclusions: GB is associated with a smaller overall operative morbidity and similar major morbidity, but with more long-term complications, more reoperations, a significant number of reversal or conversion procedures, and reduced weight loss when compared with RYGBP. Five-year results of RYGBP are superior to GB and patients should be informed accordingly.

Protocol for a systematic review on the extent of non-publication of research studies and associated study characteristics.

BACKGROUND: Methodological research has found that non-published studies often have different results than those that are published, a phenomenon known as publication bias. When results are not published, or are published selectively based on the direction or the strength of the findings, healthcare professionals and consumers of healthcare cannot base their decision-making on the full body of current evidence. METHODS: As part of the OPEN project (http://www.open-project.eu) we will conduct a systematic review with the following objectives:1. To determine the proportion and/or rate of non-publication of studies by systematically reviewing methodological research projects that followed up a cohort of studies that a. received research ethics committee (REC) approval,b. were registered in trial registries, orc. were presented as abstracts at conferences.2. To assess the association of study characteristics (for example, direction and/or strength of findings) with likelihood of full publication.To identify reports of relevant methodological research projects we will conduct electronic database searches, check reference lists, and contact experts. Published and unpublished projects will be included. The inclusion criteria are as follows:a. RECs: methodological research projects that examined the subsequent proportion and/or rate of publication of studies that received approval from RECs;b. Trial registries: methodological research projects that examine the subsequent proportion and/or rate of publication of studies registered in trial registries;c. Conference abstracts: methodological research projects that examine the subsequent proportion and/or rate of full publication of studies which were initially presented at conferences as abstracts.Primary outcomes: Proportion/rate of published studies; time to full publication (mean/median; cumulative publication rate by time).Secondary outcomes: Association of study characteristics with full publication.The different questions (a, b, and c) will be investigated separately. Data synthesis will involve a combination of descriptive and statistical summaries of the included methodological research projects. DISCUSSION: Results are expected to be publicly available in mid 2013.

Fly Ash Soil Stabilization for Non-Uniform Subgrade Soils, Volume II: Influence of Subgrade Non-Uniformity on PCC Pavement Performance, TR-461, 2005

To provide insight into subgrade non-uniformity and its effects on pavement performance, this study investigated the influence of non-uniform subgrade support on pavement responses (stress and deflection) that affect pavement performance. Several reconstructed PCC pavement projects in Iowa were studied to document and evaluate the influence of subgrade/subbase non-uniformity on pavement performance. In situ field tests were performed at 12 sites to determine the subgrade/subbase engineering properties and develop a database of engineering parameter values for statistical and numerical analysis. Results of stiffness, moisture and density, strength, and soil classification were used to determine the spatial variability of a given property. Natural subgrade soils, fly ash-stabilized subgrade, reclaimed hydrated fly ash subbase, and granular subbase were studied. The influence of the spatial variability of subgrade/subbase on pavement performance was then evaluated by modeling the elastic properties of the pavement and subgrade using the ISLAB2000 finite element analysis program. A major conclusion from this study is that non-uniform subgrade/subbase stiffness increases localized deflections and causes principal stress concentrations in the pavement, which can lead to fatigue cracking and other types of pavement distresses. Field data show that hydrated fly ash, self-cementing fly ash-stabilized subgrade, and granular subbases exhibit lower variability than natural subgrade soils. Pavement life should be increased through the use of more uniform subgrade support. Subgrade/subbase construction in the future should consider uniformity as a key to long-term pavement performance.

Yield and fruit quality of apple from conventional and organic production systems

The objective of this study was to assess the yield and fruit quality of apple produced with a conventional and an organic production systems in Southern Brazil. The orchards consisted of alternate rows from 10 to 12-year old 'Royal Gala' and 'Fuji' apple trees on M.7 rootstocks, grown as slender spindles, on 4x6 m spacing. Eighteen apple trees of each cultivar and management system were randomly selected and assessed for nutrition, flowering, fruit set, yield, and fruit quality during two growing seasons (2002/2003 and 2003/2004). The organic management system resulted in lower concentrations of K, Mg, and N in leaves and fruits, and in smaller fruits for both cultivars, and lower fruit yield for 'Fuji' than from the conventional production system. For both cultivars, fruits from the organic orchard harvested at commercial maturity had a more yellowish skin background color, higher percentage of blush in the fruit skin, higher soluble solids content, higher density, higher flesh firmness, and higher severity of russet than fruits from the conventional orchard. Fruit from the organic orchard had lower titratable acidity in 'Royal Gala', and higher incidence of moldy core and lower incidence of watercore in 'Fuji', than fruit from the conventional orchard. A non-trained sensory panel detected no significant differences for fruit attributes of taste, flavor and texture between fruit from the production systems for either cultivar.

Development of Non-Petroleum-Based Binders for Use in Flexible Pavements – Phase II, TR-650, 2015

Bio-binders can be utilized as asphalt modifiers, extenders, and replacements for conventional asphalt in bituminous binders. From the rheology results of Phase I of this project, it was found that the bio-binders tested had good performance, similar to conventional asphalt, except at low temperatures. Phase II of this project addresses this shortcoming and evaluates the Superpave performance of laboratory mixes produced with the enhanced bio-binders. The main objective of this research was to develop a bio-binder capable of replacing conventional asphalt in flexible pavements by incorporating ground tire rubber (GTR) into bio-oil derived from fast pyrolysis of agriculture and forestry residues. The chemical compatibility of the new bio-binder with GTR was assessed, and the low-temperature performance of the bio-binders was enhanced by the use of GTR. The newly developed binder, which consisted of 80 percent conventional binder and 20 percent rubber-modified bio-oil (85 percent bio-oil with 15 percent GTR), was used to produce mixes at two different air void contents, 4 and 7 percent. The laboratory performance test results showed that the performance of the newly developed bio-binder mixes is as good as or better than conventional asphalt mixes for fatigue cracking, rutting resistance, moisture sensitivity, and low-temperature cracking. These results need to be validated in field projects in order to demonstrate adequate performance for this innovative and sustainable technology for flexible pavements.

Development of a cross-European virtual sample repository and HIV resistance database

BACKGROUND: Several European HIV observational data bases have, over the last decade, accumulated a substantial number of resistance test results and developed large sample repositories, There is a need to link these efforts together, We here describe the development of such a novel tool that allows to bind these data bases together in a distributed fashion for which the control and data remains with the cohorts rather than classic data mergers.METHODS: As proof-of-concept we entered two basic queries into the tool: available resistance tests and available samples. We asked for patients still alive after 1998-01-01, and between 180 and 195 cm of height, and how many samples or resistance tests there would be available for these patients, The queries were uploaded with the tool to a central web server from which each participating cohort downloaded the queries with the tool and ran them against their database, The numbers gathered were then submitted back to the server and we could accumulate the number of available samples and resistance tests.RESULTS: We obtained the following results from the cohorts on available samples/resistance test: EuResist: not availableI11,194; EuroSIDA: 20,71611,992; ICONA: 3,751/500; Rega: 302/302; SHCS: 53,78311,485, In total, 78,552 samples and 15,473 resistance tests were available amongst these five cohorts. Once these data items have been identified, it is trivial to generate lists of relevant samples that would be usefuI for ultra deep sequencing in addition to the already available resistance tests, Saon the tool will include small analysis packages that allow each cohort to pull a report on their cohort profile and also survey emerging resistance trends in their own cohort,CONCLUSIONS: We plan on providing this tool to all cohorts within the Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN) and will provide the tool free of charge to others for any non-commercial use, The potential of this tool is to ease collaborations, that is, in projects requiring data to speed up identification of novel resistance mutations by increasing the number of observations across multiple cohorts instead of awaiting single cohorts or studies to reach the critical number needed to address such issues.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.