Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

High-throughput prioritization of cancer-causing mutations (drivers) is a key challenge of cancer genome projects, due to the number of somatic variants detected in tumors. One important step in this task is to assess the functional impact of tumor somatic mutations. A number of computational methods have been employed for that purpose, although most were originally developed to distinguish disease-related nonsynonymous single nucleotide variants (nsSNVs) from polymorphisms. Our new method, transformed Functional Impact score for Cancer (transFIC), improves the assessment of the functional impact of tumor nsSNVs by taking into account the baseline tolerance of genes to functional variants.

Road Use Tax Fund Efficiency Report Savings Status, December 31, 2014

Senate File 2355, 85th General Assembly, states the Iowa Department of Transportation shall submit annual reports regarding the implementation of efficiency measures identified in the “Road Use Tax Fund Efficiency Report,” January 2012. This report shall provide details of activities undertaken in the previous year relating to one-time and long-term program efficiencies and partnership efficiencies. Issues to be covered in the reports shall include but are not limited to savings realized from the implementation of particular efficiency measures; updates concerning measures that have not been implemented; efforts involving cities, counties, other jurisdictions, or stakeholder interest groups; any new efficiency measures identified or undertaken; and identification of any legislative action that may be required to achieve efficiencies.

Effects of plant population and nitrogen fertilizer on yield and efficiency of maize-bean intercropping

Nitrogen supply and plant population are basic parameters for cereal-legume intercropping. In order to study plant population and nitrogen fertilizer effects on yield and yield efficiency of maize-bean intercropping, a field experiment was established. Three bean plant populations and three nitrogen levels were used. Maize dry matter accumulation decreased with increases in bean plant population. Competitive effect of intercrop beans on maize yields was high at higher plant populations, being decreased by nitrogen fertilizer; application of 50 kg ha-1 N was very efficient in increasing maize cob yield. Intercropping significantly decreased harvest index of beans in all plant population and nitrogen fertilizer situations. The efficiency of intercropping, compared to sole cropping, was evidenced by the values obtained for Land Equivalent Ratio (LER) for biomass, cob and pod yields that increased with increases in bean plant populations and nitrogen fertilizer levels.

Guidance for Improving Foundation Layers to Increase Pavement Performance on Local Roads, TR-640, 2014

This document is the second of two deliverables for the project Optimizing Pavement Base, Subbase, and Subgrade Layers for Cost and Performance on Local Roads (TR-640). The first deliverable is the 454-page Final Field Data Report. The field data report describes test results and comparative analysis from 16 different portland cement concrete (PCC) pavement sites on local city and county roads in Iowa. At each site the surface conditions of the pavement (i.e., crack survey) and foundation layer strength, stiffness, and hydraulic conductivity properties were documented. The field test results were used to calculate in situ parameters used in pavement design methodologies for AASHTO (1993) and Iowa’s Statewide Urban Design and Specifications (SUDAS). Overall, the results of the study demonstrate how in situ and lab testing can be used to assess the support conditions and design values for pavement foundation layers and how the measurements compare to the assumed design values. This guide summarizes the study results and outlines general guidelines for applying them to optimize pavement bases, subbases, and subgrade layers of local roads with PCC pavements and thus their performance.

Efficiency of five biosolids to supply nitrogen and phosphorus to ryegrass

Biosolids have been considered satisfactory to supply crops and plant nutrients. The ideal biosolids application rate should result in high crop yields and nutrient uptake, and leave low concentrations of nutrients in soils to avoid environmental problems. The objective of this study was to estimate the capacity of five biosolids to supply N and P to ryegrass (Lolium perenne) after a single application of either fertilizers or biosolids to a Spodosol and an Oxisol. Results showed that 6% - 36% of N and 3% - 7% of P applied as biosolids were recovered in plants grown on the Spodosol, while the range on the Oxisol was 26%-75% for N and 1.2%-3.7% for phosphorus. Biosolids' efficiency on supplying N and P to plants was similar to fertilizer on the Spodosol, but on the Oxisol it refrained to 65%-67% fertilizer's efficiency. After a single application of biosolids followed by six consecutive harvests, 25%-94% of the N and 93%-99% of the P were not used by plants and remain in the soils.

Exercici terapèutic cognitiu en lesions cerebrals

Estudi experimental basat amb el mètode Perfetti realitzat per avaluar l’eficàcia i l’eficiència del tractament envers a les diferents afectacions cerebrals que pot tenir un pacient quan ha patit un AVC (Accident Vascular Cerebral). Farem un estudi quantitatiu, tenint en compte unes variables específiques que ens indicaran d’una forma molt més acurada l’evolució del pacient des de l’ inici fins a la fi del tractament. Hem de tenir en compte que al ser un estudi experimental ens podem trobar amb certes limitacions, implícites com trobar la idoneïtat de la mostra de pacients o que totes les afectacions cerebrals d’estudi siguin compatibles. Sempre tindrem en compte que no es seguirà un protocol sinó que és un tractament individualitzat i totalment personalitzat. La població en el nostre país cada cop envelleix més, per això millorar la qualitat de vida és imprescindible. El que volem és intentar que el pacient millori la seva qualitat de vida minvant la seva dependència i/o discapacitat, després de l’AVC. En conseqüència i ja que l’actual situació socioeconòmica no és favorable podrem afavorir la reducció de l’actual despesa sanitària,en aquest tipus de patologies en el nostre país.

Fast Approximation of Nonlinearities for improving inversion algorithms of PNL mixtures and Wiener systems

This paper proposes a very fast method for blindly approximating a nonlinear mapping which transforms a sum of random variables. The estimation is surprisingly good even when the basic assumption is not satisfied.We use the method for providing a good initialization for inverting post-nonlinear mixtures and Wiener systems. Experiments show that the algorithm speed is strongly improved and the asymptotic performance is preserved with a very low extra computational cost.

A high-efficiency HeLa cell nuclear transcription extract.

A HeLa cell nuclear transcription extract that is approximately 20 times more efficient than standard HeLa cell transcription extracts was developed. Transcription of the strong adenovirus II major late promoter by this extract results in the synthesis of 1.5-4 molecules of product RNA per molecule of template, indicating that the extract is capable of multiple rounds of initiation. Standard HeLa cell nuclear extracts transcribe closed circular and linear adenovirus major late promoter templates with equal efficiency. In contrast, the new extract exhibits an increase of approximately twofold on transcription of a closed circular, as opposed to a linear, major late promoter template.

Pollination efficiency of the stingless bee Melipona subnitida on greenhouse sweet pepper

The present study was carried out in Northeastern Region of Brazil, in order to investigate the use of stingless bee Melipona subnitida Ducke in the pollination of greenhouse sweet pepper (Capsicum annuum L.). Treatments of hand cross-pollination, hand self-pollination, pollination by bees and restricted pollination were performed. Results showed that despite sweet pepper flowers are considered autogamous, this crop benefits from pollination by M. subnitida, producing fruits significantly heavier and wider, containing a greater number of seeds and of better quality (lower percentage of malformed fruits) than self-pollinated sweet pepper. Thus, M. subnitida can be considered an efficient pollinator of greenhouse sweet pepper.

Growth components and zinc recovery efficiency of upland rice genotypes

The objective of this work was to evaluate Zn use efficiency by upland rice genotypes. The experiment was carried out in a greenhouse, with ten upland rice genotypes grown on an Oxisol (Typic Hapludox) with no application, and with application of 10 mg kg-1 Zn, applied as zinc sulfate. Shoot dry weight, grain yield, Zn harvest index, Zn concentration in shoot and in grain were significantly influenced by soil Zn levels and genotypes. However, panicle number and grain harvest index were significantly affected only by genotype. Genotypes CNA8557, CNA8540 and IR42 produced higher grain yield than other genotypes. Genotypes showed significant variability in Zn recovery efficiency. On average, 13% of the applied Zn was recovered by upland rice genotypes. Genotypes with high Zn recovery efficiency could be used in breeding of Zn efficient upland rice cultivars. Higher level of soil Zn (10 mg kg-1) increased significantly the concentrations of plant Cu and Mn. However, Fe concentrations in plant (shoot and grain) were not influenced by soil Zn levels.

Practical considerations for improving the productivity of mass spectrometry-based proteomics.

Mass spectrometry (MS) is currently the most sensitive and selective analytical technique for routine peptide and protein structure analysis. Top-down proteomics is based on tandem mass spectrometry (MS/ MS) of intact proteins, where multiply charged precursor ions are fragmented in the gas phase, typically by electron transfer or electron capture dissociation, to yield sequence-specific fragment ions. This approach is primarily used for the study of protein isoforms, including localization of post-translational modifications and identification of splice variants. Bottom-up proteomics is utilized for routine high-throughput protein identification and quantitation from complex biological samples. The proteins are first enzymatically digested into small (usually less than ca. 3 kDa) peptides, these are identified by MS or MS/MS, usually employing collisional activation techniques. To overcome the limitations of these approaches while combining their benefits, middle-down proteomics has recently emerged. Here, the proteins are digested into long (3-15 kDa) peptides via restricted proteolysis followed by the MS/MS analysis of the obtained digest. With advancements of high-resolution MS and allied techniques, routine implementation of the middle-down approach has been made possible. Herein, we present the liquid chromatography (LC)-MS/MS-based experimental design of our middle-down proteomic workflow coupled with post-LC supercharging.

Improving a leaves automatic recognition process using PCA

In this work we present a simulation of a recognition process with perimeter characterization of a simple plant leaves as a unique discriminating parameter. Data coding allowing for independence of leaves size and orientation may penalize performance recognition for some varieties. Border description sequences are then used, and Principal Component Analysis (PCA) is applied in order to study which is the best number of components for the classification task, implemented by means of a Support Vector Machine (SVM) System. Obtained results are satisfactory, and compared with [4] our system improves the recognition success, diminishing the variance at the same time.

Cellular immune responses against mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infection is known to have two main outcomes: latent infection (LTBI) where the pathogen is in a dormant form or active tuberculosis disease (TB), which is, most of the time, highly transmissible. Over one-third of the world's population asymptomatically harbours a latent form of Mtb with a 10% risk of disease reactivation. Efficient vaccine strategies remain unknown and the existing BCG vaccine is believed to protect against only some forms of TB (extra-pulmonary TB in children). Moreover, timely identification of TB remains complex with the actual diagnosis based on clinical observations associated to low efficient tests. Furthermore, current therapies are expensive, heavy and long for patients, and present lesser and lesser efficiency against new drug-resistant strains of Mtb. It is thus important to develop our knowledge on host -Mtb relationship to propose new vaccines, diagnosis tools and medications for the future. This thesis aims at improving our understanding of human immunology in the field of TB. All along this work, the same algorithm has been used and points towards the discovery of new correlates of protection through the comparison of T-cell immune responses in patients with LTBI or TB. We performed a comprehensive analysis of T-cell immune responses to Mtb using polychromatic flow cytometiy to study the functional profile of Μ/ό-specific CD4 Τ cells. We observed a polyfunctional profile in LTBI where CD4 Τ cells mainly co-produced IFN-γ, TNF-α and IL-2. In contrast, in TB, Mtó-specific CD4 Τ cells were mostly single TNF-a positive. Thus, analysis of the cytokine profiles was a strong immunological measure discriminating TB and LTBI. We next analyzed Thl7 cells. Mtò-specific Thl7 cells lacked immediate {i.e. ex vivo) IL-17A effector function in both LTBI and TB individuals. Moreover, they were also absent in bronchoalveolar lavages (BALs). Interestingly, we noticed that Mtb- specific Thl7 cells from LTBI but not from TB subjects acquired the ability to produce IL- 17A following Mtb-specific T-cell expansion. We finally performed a comprehensive characterization of Mfè-specific CD8 Τ cells that were detected in most (60%) TB patients and few (15%) LTBI subjects. We observed differences in the phenotype, the cytotoxicity and the proliferative capacities but not in the cytokine profile of Mtò-specific CD8 Τ cells between LTBI and TB. We concluded that the activity of Mtb infection (i.e. latent versus active) and the clinical presentation were associated to distinct profiles of Mtó-specific CD8 T-cell responses. To conclude, a multiparametric analysis including both CD4 and CD8 T-cell responses to Mtb lead to the development of a significantly improved diagnostic test discriminating between LTBI and TB. All together, these results provide new insights into the interaction between Mtb and the host immune response and expand upon our prior knowledge of tuberculosis. - L'infection par Mycobacterium tuberculosis peut résulter en une infection tuberculeuse latente et asymptomatique ou encore en une forme active et la plupart du temps contagieuse, la tuberculose. Un tiers de la population mondiale serait infectée de manière chronique avec 10 % de risques de développer la maladie durant la vie. Il n'existe actuellement aucun vaccin efficace, le BCG ne conférant qu'une protection partielle contre certaines formes extrapulmonaires de la maladie chez l'enfant. D'autre part, il n'existe pas de méthode diagnostique fiable et rapide, celle-ci se basant dans un premier temps sur l'analyse de la situation clinique des patients. Enfin, les thérapies actuelles sont couteuses et contraignantes pour les patients et tendent à ne plus être efficaces contre les souches émergentes de mycobactérie multi-résistantes. Aussi, il est important de bien comprendre la relation hôte-pathogène de manière à pouvoir proposer de nouveaux outils vaccinaux, diagnostiques et thérapeutiques. Ce manuscrit s'inscrit dans cette direction et vise à améliorer nos connaissances de la réponse immunitaire humaine dans le cadre de la tuberculose. Nous avons suivi un algorithme similaire tout au long des études proposées en comparant les réponses immunes des patients latents à celles des patients actifs, et ce, dans le but de mettre en évidence de potentiels corrélats de protection. Nous avons réalisé par cytométrie en flux une analyse du profil fonctionnel des cellules lymphocytaires CD4 dans la réponse au pathogène. Dans le cas de la tuberculose active, les cellules CD4 sécrètent majoritairement du TNF-α quand, au contraire, elles sécrètent à la fois du TNF-α, de l'IFN-γ et de l'IL-2 (poly-fonctionnalité) dans l'infection latente. Cette observation nous a permis de proposer un nouveau test diagnostique de la maladie active. Nous avons aussi étudié les cellules CD4 Thl7, impliquées dans la réponse immunitaire cellulaire contre les pathogènes extracellulaires et les champignons. Nous avons souligné une variation dans la production d'IL-17 entre infection latente et tuberculose active qui pourrait être impliquée dans la protection de l'individu contre le pathogène. D'autre part, ce manuscrit propose une caractérisation des cellules Τ CD8 dites cytotoxiques dans la tuberculose. Des divergences dans la fréquence des réponses observées, le phénotype mais aussi les capacités prolifératives et cytotoxiques ont pu être mises en évidence entre latence et tuberculose active. Ces observations soulignent le rôle important de ce groupe cellulaire dans l'évolution de la maladie et permettent de proposer une amélioration de l'outil diagnostic précédemment proposé et se basant à la fois sur le profil fonctionnel des cellules Τ CD4 ainsi que sur la présence potentielle d'une réponse CD8 spécifique au pathogène. Ces diverses études réalisées sur les cellules Τ humaines répondant spécifiquement à Mtb nous permettent de faire un pas supplémentaire dans la compréhension de notre réponse immunitaire face à ce pathogène particulièrement dangereux qui continue à l'heure actuelle à tuer chaque année des millions de personnes. - La tuberculose (TB) résulte d'une infection bactérienne par Mycobacterium tuberculosis (Mtb) et existe sous deux formes majeures: une forme latente, lorsque la bactérie est en phase de dormance ainsi qu'une forme active durant laquelle la bactérie se divise activement, entraînant les symptômes de la maladie. La personne infectée devient alors contagieuse dans la plupart des cas. Aujourd'hui des études épidémiologiques assument que plus d'un tiers de la population mondiale serait infectée par la forme latente de la bactérie et que 10% des cas réactiveront donnant lieu à diverses présentations de la maladie. Il n'existe actuellement aucun vaccin réellement efficace chez l'adulte. D'autre part, les traitements antibiotiques utilisés sont très lourds pour les patients et les cliniciens doivent faire face à l'émergence de nouvelles souches bactériennes multi-résistantes non affectées par les thérapies existantes. Les autorités sanitaires sont, d'autre part, confrontées à l'absence d'un outil diagnostique rapide, fiable et efficace. En effet, la méthode de référence reste la culture microbiologique du pathogène qui prend généralement plusieurs semaines, pendant lesquelles le patient pourra contaminer d'autres personnes. En résumé, la lutte contre la tuberculose doit passer par l'élaboration d'un vaccin efficace, de nouvelles thérapies, mais aussi par la mise en place de nouveaux tests diagnostics plus rapides afin d'éviter la dissémination de la maladie. Aussi, la relation hôte-bactérie qui n'est actuellement que peu comprise doit être investiguée. Ce travail de thèse a pour but d'étudier la réponse immunitaire chez l'homme infecté par Mtb et vise plus particulièrement l'étude d'une population clé de cellules immunitaires: les lymphocytes T. L'étude des cellules Τ CD4 nous a permis dans un premier temps de proposer un nouveau test diagnostic de la maladie active. Nous avons aussi analysé plus en détail une population spécifique des cellules Τ CD4 (les cellules Thl7), nous permettant d'associer leur fonction avec un possible état physiologique de protection contre le pathogène. En second lieu nous avons réalisé une caractérisation des cellules Τ CD8, à la fois chez les personnes avec des infections latentes et chez les personnes malades. Nous avons mis en évidence des différences fonctionnelles chez les deux groupes de patients, nous permettant ainsi une meilleure compréhension de l'immunité contre Mtb. Enfin, nous avons combiné les différents profils immunologiques obtenus pour développer un test diagnostic plus performant et sensible que celui proposé antérieurement. Ces diverses études réalisées sur les cellules Τ humaines nous permettent de faire un pas supplémentaire dans la compréhension de la réponse immunitaire face à ce pathogène particulièrement dangereux qui continue à tuer chaque année des millions de personnes.

Improving Traffic Safety Culture in Iowa, 2011

Vehicle crashes rank among the leading causes of death in the United States. In 2006, the AAA Foundation for Traffic Safety “made a long- term commitment to address the safety culture of the United States, as it relates to traffic safety, by launching a sustained research and educational outreach initiative.” An initiative to produce a culture of safety in Iowa includes the Iowa Comprehensive Highway Safety Plan (CHSP). The Iowa CHSP “engages diverse safety stakeholders and charts the course for the state, bringing to bear sound science and the power of shared community values to change the culture and achieve a standard of safer travel for our citizens.” Despite the state’s ongoing efforts toward highway safety, an average of 445 deaths and thousands of injuries occur on Iowa’s public roads each year. As such, a need exists to revisit the concept of safety culture from a diverse, multi-disciplinary perspective in an effort to improve traffic safety. This study summarizes the best practices and effective laws in improving safety culture in the United States and abroad. Additionally, this study solicited the opinions of experts in public health, education, law enforcement, public policy, social psychology, safety advocacy, and traffic safety engineering in a bid to assess the traffic safety culture initiatives in Iowa. Recommendations for improving traffic safety culture are offered in line with the top five Iowa CHSP safety policy strategies, which are young drivers, occupant protection, motorcycle safety, traffic safety enforcement and traffic safety improvement program, as well as the eight safety program strategies outlined in the CHSP. As a result of this study, eleven high-level goals were developed, each with specific actions to support its success. The goals are: improve emergency medical services response, toughen law enforcement and prosecution, increase safety belt use, reduce speeding-related crashes, reduce alcohol-related crashes, improve commercial vehicle safety, improve motorcycle safety, improve young driver education, improve older driver safety, strengthen teenage licensing process, and reduce distracted driving.

Improving Portland Cement Concrete Mix Consistency and Production Rate through Two-Stage Mixing, TR-505, 2007

A two-stage mixing process for concrete involves mixing a slurry of cementitious materials and water, then adding the slurry to coarse and fine aggregate to form concrete. Some research has indicated that this process might facilitate dispersion of cementitious materials and improve cement hydration, the characteristics of the interfacial transition zone (ITZ) between aggregate and paste, and concrete homogeneity. The goal of the study was to find optimal mixing procedures for production of a homogeneous and workable mixture and quality concrete using a two-stage mixing operation. The specific objectives of the study are as follows: (1) To achieve optimal mixing energy and time for a homogeneous cementitious material, (2) To characterize the homogeneity and flow property of the pastes, (3) To investigate effective methods for coating aggregate particles with cement slurry, (4) To study the effect of the two-stage mixing procedure on concrete properties, (5) To obtain the improved production rates. Parameters measured for Phase I included: heat of hydration, maturity, and rheology tests were performed on the fresh paste samples, and compressive strength, degree of hydration, and scanning electron microscope (SEM) imaging tests were conducted on the cured specimens. For Phases II and III tests included slump and air content on fresh concrete and compressive and tensile strengths, rapid air void analysis, and rapid chloride permeability on hardened concrete.