Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Surgical site infections in colon surgery: the patient, the procedure, the hospital, and the surgeon.

Objective: To determine the role of the surgeon in the occurrence of surgical site infection (SSI) following colon surgery, with respect to his or her adherence to guidelines and his or her experience.Design, Setting, and Patients: Prospective cohort study of 2393 patients who underwent colon surgery performed by 31 surgeons in 9 secondary and tertiary care public Swiss hospitals, recruited from a surveillance program for SSI between March 1, 1998, and December 31, 2008, and followed up for 1 month after their operation.Main Outcome Measures: Risk factors for SSI were identified in univariate and multivariate analyses that included the patients' and procedures' characteristics, the hospitals, and the surgeons as candidate covariates. Correlations were sought between surgeons' individual adjusted risks, their self-reported adherence to guidelines, and the delay since their board certification.Results: A total of 428 SSIs (17.9%) were identified, with hospital rates varying from 4.0% to 25.2% and individual surgeon rates varying from 3.7% to 36.1%. Features of the patients and procedures associated with SSI in univariate analyses were male sex, age, American Society of Anesthesiologists score, contamination class, operation duration, and emergency procedure. Correctly timed antibiotic prophylaxis and laparoscopic approach were protective. Multivariate analyses adjusting for these features and for the hospitals found 4 surgeons with higher risk of SSI (odds ratio [OR] = 2.37, 95% confidence interval [CI], 1.51-3.70; OR = 2.19, 95% CI, 1.41-3.39; OR = 2.15, 95% CI, 1.02-4.53; and OR = 1.97, 95% CI, 1.18-3.30) and 2 surgeons with lower risk of SSI (OR = 0.43, 95% CI, 0.19-0.94; and OR = 0.19, 95% CI, 0.04-0.81). No correlation was found between surgeons' individual adjusted risks and their adherence to guidelines or their experience.Conclusion: For reasons beyond adherence to guidelines or experience, the surgeon may constitute an independent risk factor for SSI after colon surgery.

Transapical aortic 'valve-in-valve' procedure for degenerated stented bioprosthesis.

Standard surgical aortic valve replacement with a biological prosthesis remains the treatment of choice for low- and mid-risk elderly patients (traditionally >65 years of age) suffering from severe symptomatic aortic valve stenosis or insufficiency, and for young patients with formal contraindications to long-lasting anticoagulation. Unfortunately, despite the fact that several technical improvements have noticeably improved the resistance of pericardial and bovine bioprostheses to leaflet calcifications and ruptures, the risk of early valve failure with rapid degeneration still exists, especially for patients under haemodialysis and for patients <60 years of age at the time of surgery. Until now, redo open heart surgery under cardiopulmonary bypass and on cardioplegic arrest was the only available therapeutic option in case of bioprosthesis degeneration, but it carried a higher surgical risk when elderly patients with severe concomitant comorbidities were concerned. Since a few years, the advent of new transcatheter aortic valve procedures has opened new horizons in cardiac surgery and, in particular, the possibility of implanting stented valves within the degenerated stented bioprosthesis, the so-called 'valve-in-valve' (VinV) concept, has become a clinical practice in experienced cardiac centres. The VinV procedure represents a minimally invasive approach dedicated to high-risk redo patients, and published preliminary reports have shown a success rate of 100% with absence of significant valvular leaks, acceptable transvalvular gradients and low complication rate. However, this procedure is not riskless and the most important concerns are about the size mismatch and the right positioning within the degenerated bioprosthesis. In this article, we review the limited available literature about VinV procedures, underline important technical details for the positioning and provide guidelines to prevent valve-prosthesis mismatch comparing the three sizes of the only commercially available transapical device, the Edwards Sapien, with the inner diameter of three of the most commonly used stented bioprostheses.

Design Manual for Low Water Stream Crossings, October 1983

The purpose of this manual is to provide design guidelines for low water stream crossings (LWSCs). Rigid criteria for determining the applicability of a LWSC to a given site are not established since each site is unique in terms of physical, social, economic, and political factors. Because conditions vary from county to county, it is not the intent to provide a "cook-book" procedure for designing a LWSC. Rather, engineering judgment must be applied to the guidelines contained in this manual.

Computer-aided procedure for optimization of layer thickness uniformity in thermal evaporation physical vapor deposition chambers for lens coating

A computer-aided method to improve the thickness uniformity attainable when coating multiple substrates inside a thermal evaporation physical vapor deposition unit is presented. The study is developed for the classical spherical (dome-shaped) calotte and also for a plane sector reversible holder setup. This second arrangement is very useful for coating both sides of the substrate, such as antireflection multilayers on lenses. The design of static correcting shutters for both kinds of configurations is also discussed. Some results of using the method are presented as an illustration.

Subclass problem-dependent design for error-correcting output codes

A common way to model multiclass classification problems is by means of Error-Correcting Output Codes (ECOCs). Given a multiclass problem, the ECOC technique designs a code word for each class, where each position of the code identifies the membership of the class for a given binary problem. A classification decision is obtained by assigning the label of the class with the closest code. One of the main requirements of the ECOC design is that the base classifier is capable of splitting each subgroup of classes from each binary problem. However, we cannot guarantee that a linear classifier model convex regions. Furthermore, nonlinear classifiers also fail to manage some type of surfaces. In this paper, we present a novel strategy to model multiclass classification problems using subclass information in the ECOC framework. Complex problems are solved by splitting the original set of classes into subclasses and embedding the binary problems in a problem-dependent ECOC design. Experimental results show that the proposed splitting procedure yields a better performance when the class overlap or the distribution of the training objects conceal the decision boundaries for the base classifier. The results are even more significant when one has a sufficiently large training size.

Automatic selection of tidal volume, respiratory frequency and minute ventilation in intubated ICU patients as start up procedure for closed-loop controlled ventilation.

OBJECTIVE: Before a patient can be connected to a mechanical ventilator, the controls of the apparatus need to be set up appropriately. Today, this is done by the intensive care professional. With the advent of closed loop controlled mechanical ventilation, methods will be needed to select appropriate start up settings automatically. The objective of our study was to test such a computerized method which could eventually be used as a start-up procedure (first 5-10 minutes of ventilation) for closed-loop controlled ventilation. DESIGN: Prospective Study. SETTINGS: ICU's in two adult and one children's hospital. PATIENTS: 25 critically ill adult patients (age > or = 15 y) and 17 critically ill children selected at random were studied. INTERVENTIONS: To stimulate 'initial connection', the patients were disconnected from their ventilator and transiently connected to a modified Hamilton AMADEUS ventilator for maximally one minute. During that time they were ventilated with a fixed and standardized breath pattern (Test Breaths) based on pressure controlled synchronized intermittent mandatory ventilation (PCSIMV). MEASUREMENTS AND MAIN RESULTS: Measurements of airway flow, airway pressure and instantaneous CO2 concentration using a mainstream CO2 analyzer were made at the mouth during application of the Test-Breaths. Test-Breaths were analyzed in terms of tidal volume, expiratory time constant and series dead space. Using this data an initial ventilation pattern consisting of respiratory frequency and tidal volume was calculated. This ventilation pattern was compared to the one measured prior to the onset of the study using a two-tailed paired t-test. Additionally, it was compared to a conventional method for setting up ventilators. The computer-proposed ventilation pattern did not differ significantly from the actual pattern (p > 0.05), while the conventional method did. However the scatter was large and in 6 cases deviations in the minute ventilation of more than 50% were observed. CONCLUSIONS: The analysis of standardized Test Breaths allows automatic determination of an initial ventilation pattern for intubated ICU patients. While this pattern does not seem to be superior to the one chosen by the conventional method, it is derived fully automatically and without need for manual patient data entry such as weight or height. This makes the method potentially useful as a start up procedure for closed-loop controlled ventilation.

Development of Performance Properties of Ternary Mixtures and Concrete Pavement Mixture Design and Analysis (MDA): Effect of Paste Quality on Fresh and Hardened Properties of Ternary Mixtures, TPF-5(117), 2012

The purpose of this study was to investigate the effect of cement paste quality on the concrete performance, particularly fresh properties, by changing the water-to-cementitious materials ratio (w/cm), type and dosage of supplementary cementitious materials (SCM), and airvoid system in binary and ternary mixtures. In this experimental program, a total matrix of 54 mixtures with w/cm of 0.40 and 0.45; target air content of 2%, 4%, and 8%; a fixed cementitious content of 600 pounds per cubic yard (pcy), and the incorporation of three types of SCMs at different dosages was prepared. The fine aggregate-to- total aggregate ratio was fixed at 0.42. Workability, rheology, air-void system, setting time, strength, Wenner Probe surface resistivity, and shrinkage were determined. The effects of paste variables on workability are more marked at the higher w/cm. The compressive strength is strongly influenced by the paste quality, dominated by w/cm and air content. Surface resistivity is improved by inclusion of Class F fly ash and slag cement, especially at later ages. Ternary mixtures performed in accordance with their ingredients. The data collected will be used to develop models that will be part of an innovative mix proportioning procedure.

MEPDG Work Plan Task No. 8: Validation of Pavement Performance Curves for the Mechanistic-Empirical Pavement Design Guide, 2009

The objective of this research is to determine whether the nationally calibrated performance models used in the Mechanistic-Empirical Pavement Design Guide (MEPDG) provide a reasonable prediction of actual field performance, and if the desired accuracy or correspondence exists between predicted and monitored performance for Iowa conditions. A comprehensive literature review was conducted to identify the MEPDG input parameters and the MEPDG verification/calibration process. Sensitivities of MEPDG input parameters to predictions were studied using different versions of the MEPDG software. Based on literature review and sensitivity analysis, a detailed verification procedure was developed. A total of sixteen different types of pavement sections across Iowa, not used for national calibration in NCHRP 1-47A, were selected. A database of MEPDG inputs and the actual pavement performance measures for the selected pavement sites were prepared for verification. The accuracy of the MEPDG performance models for Iowa conditions was statistically evaluated. The verification testing showed promising results in terms of MEPDG’s performance prediction accuracy for Iowa conditions. Recalibrating the MEPDG performance models for Iowa conditions is recommended to improve the accuracy of predictions. ****************** Large File**************************

Estimating Design-Flood Discharges for Streams in Iowa Using Drainage-Basin and Channel-Geometry Characteristics, HR-322, 1993

Drainage-basin and channel-geometry multiple-regression equations are presented for estimating design-flood discharges having recurrence intervals of 2, 5, 10, 25, 50, and 100 years at stream sites on rural, unregulated streams in Iowa. Design-flood discharge estimates determined by Pearson Type-III analyses using data collected through the 1990 water year are reported for the 188 streamflow-gaging stations used in either the drainage-basin or channel-geometry regression analyses. Ordinary least-squares multiple-regression techniques were used to identify selected drainage-basin and channel-geometry regions. Weighted least-squares multiple-regression techniques, which account for differences in the variance of flows at different gaging stations and for variable lengths in station records, were used to estimate the regression parameters. Statewide drainage-basin equations were developed from analyses of 164 streamflow-gaging stations. Drainage-basin characteristics were quantified using a geographic-information-system (GIS) procedure to process topographic maps and digital cartographic data. The significant characteristics identified for the drainage-basin equations included contributing drainage area, relative relief, drainage frequency, and 2-year, 24-hour precipitation intensity. The average standard errors of prediction for the drainage-basin equations ranged from 38.6% to 50.2%. The GIS procedure expanded the capability to quantitatively relate drainage-basin characteristics to the magnitude and frequency of floods for stream sites in Iowa and provides a flood-estimation method that is independent of hydrologic regionalization. Statewide and regional channel-geometry regression equations were developed from analyses of 157 streamflow-gaging stations. Channel-geometry characteristics were measured on site and on topographic maps. Statewide and regional channel-geometry regression equations that are dependent on whether a stream has been channelized were developed on the basis of bankfull and active-channel characteristics. The significant channel-geometry characteristics identified for the statewide and regional regression equations included bankfull width and bankfull depth for natural channels unaffected by channelization, and active-channel width for stabilized channels affected by channelization. The average standard errors of prediction ranged from 41.0% to 68.4% for the statewide channel-geometry equations and from 30.3% to 70.0% for the regional channel-geometry equations. Procedures provided for applying the drainage-basin and channel-geometry regression equations depend on whether the design-flood discharge estimate is for a site on an ungaged stream, an ungaged site on a gaged stream, or a gaged site. When both a drainage-basin and a channel-geometry regression-equation estimate are available for a stream site, a procedure is presented for determining a weighted average of the two flood estimates.

Design Manual for Strengthening of Continuous-Span Composite Bridges, HR-333, 1993

The need for upgrading a large number of understrength bridges in the United States has been well documented in the literature. This manual presents two methods for strengthening continuous-span composite bridges: post-tensioning of the positive moment regions of the bridge stringers and the addition of superimposed trusses at the piers. The use of these two systems is an efficient method of reducing flexural overstresses in undercapacity bridges. Before strengthening a given bridge however, other deficiencies (inadequate shear connection, fatigue problems, extensive corrosion) should be addressed. Since continuous-span composite bridges are indeterminant structures, there is longitudinal and transverse distribution of the strengthening axial forces and moments. This manual basically provides the engineer with a procedure for determining the distribution of strengthening forces and moments throughout the bridge. As a result of the longitudinal and transverse force distribution, the design methodology presented in this manual for continuous-span composite bridges is extremely complex. To simplify the procedure, a spreadsheet has been developed for use by practicing engineers. This design aid greatly simplifies the design of a strengthening system for a given bridge in that it eliminates numerous tedious hand calculations, computes the required force and moment fractions, and performs the necessary iterations for determining the required strengthening forces. The force and moment distribution fraction formulas developed in this manual are primarily for the Iowa DOT V12 and V14 three-span four-stringer bridges. These formulas may be used on other bridges if they are within the limits stated in this manual. Use of the distribution fraction formulas for bridges not within the stated limits is not recommended.

A Multi-Project Scheduling Procedure for Transportation Projects, Part II, HR-339, 1994

The Iowa Department of Transportation (IDOT) has been requiring Critical Path Method (CPM) schedules on some larger or more schedule sensitive projects. The Office of Construction's expectations for enhanced project control and improved communication of project objectives have not been fully met by the use of CPM. Recognizing that the current procedures might not be adequate for all projects, IDOT sponsored a research project to explore the state-of-the-art in transportation scheduling and identify opportunities for improvement. The first phase of this project identified a technique known as the Linear Scheduling Method (LSM) as an alternative to CPM on certain highway construction projects. LSM graphically displays the construction process with respect to the location and the time in which each activity occurs. The current phase of this project was implemented to allow the research team the opportunity to evaluate LSM on all small groups of diverse projects. Unlike the first phase of the project, the research team was closely involved in the project from early in the planning phase throughout the completion of the projects. The research strongly suggests that the linear scheduling technique has great potential as a project management tool for both contractors and IDOT personnel. However, before this technique can become a viable weapon in the project management arsenal, a software application needs to be developed. This application should bring to linear scheduling a degree of functionality as rich and as comprehensive as that found in microcomputer based CPM software on the market today. The research team recommends that the IDOT extend this research effort to include the development of a linear scheduling application.

Development of Preliminary Load and Resistance Factor Design of Drilled Shafts in Iowa, RB03-012, 2014

The Federal Highway Administration (FHWA) mandated utilizing the Load and Resistance Factor Design (LRFD) approach for all new bridges initiated in the United States after October 1, 2007. To achieve part of this goal, a database for Drilled Shaft Foundation Testing (DSHAFT) was developed and reported on by Garder, Ng, Sritharan, and Roling in 2012. DSHAFT is aimed at assimilating high-quality drilled shaft test data from Iowa and the surrounding regions. DSHAFT is currently housed on a project website (http://srg.cce.iastate.edu/dshaft) and contains data for 41 drilled shaft tests. The objective of this research was to utilize the DSHAFT database and develop a regional LRFD procedure for drilled shafts in Iowa with preliminary resistance factors using a probability-based reliability theory. This was done by examining current design and construction practices used by the Iowa Department of Transportation (DOT) as well as recommendations given in the American Association of State Highway and Transportation Officials (AASHTO) LRFD Bridge Design Specifications and the FHWA drilled shaft guidelines. Various analytical methods were used to estimate side resistance and end bearing of drilled shafts in clay, sand, intermediate geomaterial (IGM), and rock. Since most of the load test results obtained from O-cell do not pass the 1-in. top displacement criterion used by the Iowa DOT and the 5% of shaft diameter for top displacement criterion recommended by AASHTO, three improved procedures are proposed to generate and extend equivalent top load-displacement curves that enable the quantification of measured resistances corresponding to the displacement criteria. Using the estimated and measured resistances, regional resistance factors were calibrated following the AASHTO LRFD framework and adjusted to resolve any anomalies observed among the factors. To illustrate the potential and successful use of drilled shafts in Iowa, the design procedures of drilled shaft foundations were demonstrated and the advantages of drilled shafts over driven piles were addressed in two case studies.

Evaluation of Gap-Graded Asphalt Concrete Mixtures Part II: Statistical Design and Analysis, HR-157, 1973

This report presents the results of a comparative laboratory study between well- and gap-graded aggregates used in asphalt concrete paving mixtures. A total of 424 batches of asphalt concrete mixtures and 3, 960 Marshall and Hveem specimens were examined. The main thrust of the statistical analysis conducted in this experiment was in the calibration study and in Part I of the experiment. In the former study, the compaction procedure between the Iowa State University Lab and the Iowa Highway Commission Lab was calibrated. By an analysis of the errors associated with the measurements we were able to separate the "preparation" and "determination" errors for both laboratories as well as develop the calibration curve which describes the relationship between the compaction procedures at the two labs. In Part I, the use of a fractional factorial design in a split plot experiment in measuring the effect of several factors on asphalt concrete strength and weight was exhibited. Also, the use of half normal plotting techniques for indicating significant factors and interactions and for estimating errors in experiments with only a limited number of observations was outlined,

Design Methodology for Corrugated Metal Pipe Tiedowns, HR-362, Phase II, 1995

This investigation is the final phase of a three part study whose overall objectives were to determine if a restraining force is required to prevent inlet uplift failures in corrugated metal pipe (CMP) installations, and to develop a procedure for calculating the required force when restraint is required. In the initial phase of the study (HR-306), the extent of the uplift problem in Iowa was determined and the forces acting on a CMP were quantified. In the second phase of the study (HR- 332), laboratory and field tests were conducted. Laboratory tests measured the longitudinal stiffness ofCMP and a full scale field test on a 3.05 m (10 ft) diameter CMP with 0.612 m (2 ft) of cover determined the soil-structure interaction in response to uplift forces. Reported herein are the tasks that were completed in the final phase of the study. In this phase, a buried 2.44 m (8 ft) CMP was tested with and without end-restraint and with various configurations of soil at the inlet end of the pipe. A total of four different soil configurations were tested; in all tests the soil cover was constant at 0.61 m (2 ft). Data from these tests were used to verify the finite element analysis model (FEA) that was developed in this phase of the research. Both experiments and analyses indicate that the primary soil contribution to uplift resistance occurs in the foreslope and that depth of soil cover does not affect the required tiedown force. Using the FEA, design charts were developed with which engineers can determine for a given situation if restraint force is required to prevent an uplift failure. If an engineer determines restraint is needed, the design charts provide the magnitude of the required force. The design charts are applicable to six gages of CMP for four flow conditions and two types of soil.