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.

Pile Design and Tests for Integral Abutment Bridges, HR-273, 1987

Expansion joints increase both the initial cost and the maintenance cost of bridges. Integral abutment bridges provide an attractive design alternative because expansion joints are eliminated from the bridge itself. However, the piles in these bridges are subjected to horizontal movement as the bridge expands and contracts during temperature changes. The objective of this research was to develop a method of designing piles for these conditions. Separate field tests simulating a pile and a bridge girder were conducted for three loading cases: (1) vertical load only, (2) horizontal displacement of pile head only, and (3) combined horizontal displacement of pile head with subsequent vertical load. Both tests (1) and (3) reached the same ultimate vertical load, that is, the horizontal displacement had no effect on the vertical load capacity. Several model tests were conducted in sand with a scale factor of about 1:10. Experimental results from both the field and model tests were used to develop the vertical and horizontal load-displacement properties of the soil. These properties were input into the finite element computer program Integral Abutment Bridge Two-Dimensional (IAB2D), which was developed under a previous research contract. Experimental and analytical results compared well for the test cases. Two alternative design methods, both based upon the American Association of State Highway and Transportation Officials (AASHTO) Specification, were developed. Alternative One is quite conservative relative to IAB2D results and does not permit plastic redistribution of forces. Alternative Two is also conservative when compared to IAB2D, but plastic redistribution is permitted. To use Alternative Two, the pile cross section must have sufficient inelastic rotation capacity before local buckling occurs. A design example for a friction pile and an end-bearing pile illustrates both alternatives.

An Assessment ofFatigue Strength of Load Carrying Welded Joints with Lack of Penetration

On yleisesti tiedossa, että väsyttävän kuormituksen alaisena olevat hitsatut rakenteet rikkoutuvat juuri hitsausliitoksista. Täyden tunkeuman hitsausliitoksia sisältävien rakenteiden asiantunteva suunnittelu janykyaikaiset valmistusmenetelmät ovat lähes eliminoineet väsymisvauriot hitsatuissa rakenteissa. Väsymislujuuden parantaminen tiukalla täyden tunkeuman vaatimuksella on kuitenkin epätaloudellinen ratkaisu. Täyden tunkeuman hitsausliitoksille asetettavien laatuvaatimuksien on määriteltävä selkeät tarkastusohjeet ja hylkäämisperusteet. Tämän diplomityön tarkoituksena oli tutkia geometristen muuttujien vaikutusta kuormaa kantavien hitsausliitosten väsymislujuuteen. Huomio kiinnitettiin pääasiassa suunnittelumuuttujiin, joilla on vaikutusta väsymisvaurioiden syntymiseen hitsauksen juuren puolella. Nykyiset määräykset ja standardit, jotka perustuvat kokeellisiin tuloksiin; antavat melko yleisiä ohjeita hitsausliitosten väsymismitoituksesta. Tämän vuoksi muodostettiin kokonaan uudet parametriset yhtälöt sallitun nimellisen jännityksen kynnysarvon vaihteluvälin, ¿¿th, laskemiseksi, jotta vältettäisiin hitsausliitosten juuren puoleiset väsymisvauriot. Lisäksi, jokaiselle liitostyypille laskettiin hitsin juuren puolen väsymisluokat (FAT), joita verrattiin olemassa olevilla mitoitusohjeilla saavutettuihin tuloksiin. Täydentäviksi referensseiksi suoritettiin useita kolmiulotteisia (3D) analyysejä. Julkaistuja kokeellisiin tuloksiin perustuvia tietoja käytettiin apuna hitsausliitosten väsymiskäyttäytymisen ymmärtämiseksi ja materiaalivakioiden määrittämiseksi. Kuormaa kantavien vajaatunkeumaisten hitsausliitosten väsymislujuus määritettiin käyttämällä elementtimenetelmää. Suurimman pääjännityksen kriteeriä hyödynnettiin murtumiskäyttäytymisen ennakoimiseksi. Valitulle hitsatulle materiaalille ja koeolosuhteille murtumiskäyttäytymistä mallinnettiin särön kasvunopeudella da/dN ja jännitysintensiteettikertoimen vaihteluvälillä, 'K. Paris:n yhtälön numeerinen integrointi suoritettiin FRANC2D/L tietokoneohjelmalla. Saatujen tulosten perusteella voidaan laskea FAT tutkittavassa tapauksessa. ¿¿th laskettiin alkusärön jännitysintensiteettikertoimen vaihteluvälin ja kynnysjännitysintensiteettikertoimen, 'Kth, perusteella. ¿Kth arvoa pienemmällä vaihteluvälillä särö ei kasva. Analyyseissäoletuksena oli hitsattu jälkikäsittelemätön liitos, jossa oli valmis alkusärö hitsin juuressa. Analyysien tulokset ovat hyödyllisiä suunnittelijoille, jotka tekevät päätöksiä koskien geometrisiä parametreja, joilla on vaikutusta hitsausliitosten väsymislujuuteen.

La accesibilidad universal y el dise??o para todas las personas factor clave para la inclusi??n social desde el design thinking curricular

Resumen en ingl??s

Coxsackievirus B3-associated myocardial pathology and viral load reduced by recombinant soluble human decay-accelerating factor in mice

Coxsackievirus B3 (CVB3) infection can result in myocarditis, which in turn may lead to a protracted immune response and subsequent dilated cardiomyopathy. Human decay-accelerating factor (DAF), a binding receptor for CVB3, was synthesized as a soluble IgG1-Fc fusion protein (DAF-Fc). In vitro, DAF-Fc was able to inhibit complement activity and block infection by CVB3, although blockade of infection varied widely among strains of CVB3. To determine the effects of DAF-Fc in vivo, 40 adolescent A/J mice were infected with a myopathic strain of CVB3 and given DAF-Fc treatment 3 days before infection, during infection, or 3 days after infection; the mice were compared with virus alone and sham-infected animals. Sections of heart, spleen, kidney, pancreas, and liver were stained with hematoxylin and eosin and submitted to in situ hybridization for both positive-strand and negative-strand viral RNA to determine the extent of myocarditis and viral infection, respectively. Salient histopathologic features, including myocardial lesion area, cell death, calcification and inflammatory cell infiltration, pancreatitis, and hepatitis were scored without knowledge of the experimental groups. DAF-Fc treatment of mice either preceding or concurrent with CVB3 infection resulted in a significant decrease in myocardial lesion area and cell death and a reduction in the presence of viral RNA. All DAF-Fc treatment groups had reduced infectious CVB3 recoverable from the heart after infection. DAF-Fc may be a novel therapeutic agent for active myocarditis and acute dilated cardiomyopathy if given early in the infectious period, although more studies are needed to determine its mechanism and efficacy.

Finite element aided design evolution of composite leaf spring

This paper shows the process of the virtual production development of the mechanical connection between the top leaf of a dual composite leaf spring system to a shackle using finite element methods. The commercial FEA package MSC/MARC has been used for the analysis. In the original design the joint was based on a closed eye-end. Full scale testing results showed that this configuration achieved the vertical proof load of 150 kN and 1 million cycles of fatigue load. However, a problem with delamination occurred at the interface between the fibres going around the eye and the main leaf body. To overcome this problem, a second design was tried using transverse bandages of woven glass fibre reinforced tape to wrap the section that is prone to delaminate. In this case, the maximum interlaminar shear stress was reduced by a certain amount but it was still higher than the material’s shear strength. Based on the fact that, even with delamination, the top leaf spring still sustained the maximum static and fatigue loads required, the third design was proposed with an open eye-end, eliminating altogether the interface where the maximum shear stress occurs. The maximum shear stress predicted by FEA is reduced significantly and a safety factor of around 2 has been obtained. Thus, a successful and safe design has been achieved.

Fault Current Limiter Using YBCO Coated Conductor-The Limiting Factor and Its Recovery Time

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A novel single-phase ZCS-PWM high-power-factor boost rectifier

This paper presents a novel single-phase high-power-factor (HPF) pulsewidth-modulated (PWM) boost rectifier featuring soft commutation of the active switches at zero current (ZC), It incorporates the most desirable properties of conventional PWM and soft-switching resonant techniques.The input current shaping is achieved with average current mode control and continuous inductor current mode.This new PWM converter provides ZC turn on and turn off of the active switches, and it is suitable for high-power applications employing insulated gate bipolar transistors (IGBT's),The principle of operation, the theoretical analysis, a design example, and experimental results from a laboratory prototype rated at 1600 W with 400-Vdc output voltage are presented. The measured efficiency and the power factor were 96.2% and 0.99%, respectively, with an input current total harmonic distortion (THD) equal to 3.94%, for an input voltage with THD equal to 3.8%, at rated load.

Novel high-power-factor ZCS-PWM preregulators

This paper introduces novel zero-current-switching (ZCS) pulsewidth-modulated (PWM) preregulators based on a new soft-commutation cell, suitable for insulated gate bipolar transistor applications. The active switches in these proposed rectifiers turn on in zero current and turn off in zero current-zero voltage. In addition, the diodes turn on in zero voltage and their reverse-recovery effects over the active switches are negligible. Moreover, based on the proposed cell, an entire family of de-to-de ZCS-PWM converters can be generated, providing conditions to obtain naturally isolated converters, for example, derived buck-boost, Sepic. and Zeta converters. The novel ac-to-dc ZCS-PWM boost and Zeta preregulators are presented in order to verify the operation of this soft-commutation cell, In order to minimize the harmonic contents of the input current, increasing the ac power factor, the average-current-mode control is used, obtaining preregulators with ac power factor near unity and high efficiency at wide load range. The principle of operation, theoretical analysis, design example, and experimental results from test units for the novel preregulators are presented. The new boost preregulator was designed to nominal values of 1.6 kW output power, 220 V(rms) input voltage, 400 V(dc) output voltage, and operating at 20 kHz. The measured efficiency and power factor of the new ZCS-PWM boost preregulator were 96.7% and 0,99, respectively, with an input current total harmonic distortion (THD) equal to 3.42% for an input voltage with THD equal to 1.61%, at rated load, the new ZCS-PWM Zeta preregulator was designed to voltage step-down operation, and the experimental results were obtained from a laboratory prototype rated at 500 W, 220 V(rm), input voltage, 110 V(dc) output voltage, and operating at 50 kHz. The measured efficiency of the new ZCS-PWM Zeta preregulator is approximately 96.9% and the input power factor is 0.98, with an input current THD equal to 19.07% while the input voltage THD is equal to 1.96%, at rated load.

Analysis and design of constant-frequency peak-current-controlled high-power-factor boost rectifier with slope compensation

This paper presents the analysis and the design of a peak-current-controlled high-power-factor boost rectifier, with slope compensation, operating at constant frequency. The input current shaping is achieved, with continuous inductor current mode, with no multiplier to generate a current reference. The resulting overall circuitry is very simple, in comparison with the average-current-controlled boost rectifier. Experimental results are presented, taken from a laboratory prototype rated at 370 W and operating at 67 kHz. The measured power factor was 0.99, with a input current THD equal to 5.6%, for an input voltage THD equal to 2.26%.

Novel high-power-factor isolated electronic ballast for multiple tubular fluorescent lamps

This paper presents a novel isolated electronic ballast for multiple fluorescent lamps, featuring high power-factor, and high efficiency. Two stages compose this new electronic ballast, namely, a new voltage step-down isolated Sepic rectifier, and a classical resonant Half-Bridge inverter. The new isolated Sepic rectifier is obtained from a Zero-Current-Switching (ZCS) Pulse-Width-Modulated (PWM) soft-commutation cell. The average-current control technique is used in this preregulator stage in order to provide low phase displacement and low Total-Harmonic-Distortion (THD) at input current, resulting in high power-factor, and attending properly IEC 61000-3-2 standards. The resonant Half-Bridge inverter performs Zero-Voltage-Switching (ZVS), providing conditions for the obtaining of overall high efficiency. It is developed a design example for the new isolated electronic ballast rated at 200W output power, 220Vrms input voltage, 115Vdc dc link voltage, with rectifier and inverter stages operating at 50kHz. Finally, experimental results are presented in order to verify the developed analysis. The THD at input current is equal to 5.25%, for an input voltage THD equal to 1.63%, and the measured overall efficiency is about 88.25%, at rated load.

Orientation, building height and sky view factor as energy efficiency design parameters

The energy efficiency of buildings should be a goal at the pre-design phase, though the importance of the design variables is often neglected even during the design process. Highlighting the relevance of these design variables, this research studies the relationships of building location variables with the electrical energy consumption of residential units. The following building design parameters are considered: orientation, story height and sky view factor (SVF). The consideration of the SVF as a location variable contributes to the originality of this research. Data of electrical energy consumption and users' profiles were collected and several variables were considered for the development of an Artificial Neural Network model. This model allows the determination of the relative importance of each variable. The results show that the apartments' orientation is the most important design variable for the energy consumption, although the story height and the sky view factor play a fundamental role in that consumption too. We pointed out that building heights above twenty-four meters do not optimize the energy efficiency of the apartments and also that an increasing SVF can influence the energy consumption of an apartment according to their orientation.

Effect of microthread presence and restoration design (screw versus cemented) in dental implant reliability and failure modes

Objectives: This study evaluated the reliability and failure modes of implants with a microthreaded or smooth design at the crestal region, restored with screwed or cemented crowns. The postulated null hypothesis was that the presence of microthreads in the implant cervical region would not result in different reliability and strength to failure than smooth design, regardless of fixation method, when subjected to step-stress accelerated life-testing (SSALT) in water. Materials and methods: Eighty four dental implants (3.3 × 10 mm) were divided into four groups (n = 21) according to implant macrogeometric design at the crestal region and crown fixation method: Microthreads Screwed (MS); Smooth Screwed (SS); Microthreads Cemented (MC), and Smooth Cemented (SC). The abutments were torqued to the implants and standardized maxillary central incisor metallic crowns were cemented (MC, SC) or screwed (MS, SS) and subjected to SSALT in water. The probability of failure versus cycles (90% two-sided confidence intervals) was calculated and plotted using a power law relationship for damage accumulation. Reliability for a mission of 50,000 cycles at 150 N (90% 2-sided confidence intervals) was calculated. Differences between final failure loads during fatigue for each group were assessed by Kruskal-Wallis along with Benferroni's post hoc tests. Polarized-light and scanning electron microscopes were used for failure analyses. Results: The Beta (β) value (confidence interval range) derived from use level probability Weibull calculation of 1.30 (0.76-2.22), 1.17 (0.70-1.96), 1.12 (0.71-1.76), and 0.52 (0.30-0.89) for groups MC, SC, MS, and SS respectively, indicated that fatigue was an accelerating factor for all groups, except for SS. The calculated reliability was higher for SC (99%) compared to MC (87%). No difference was observed between screwed restorations (MS - 29%, SS - 43%). Failure involved abutment screw fracture for all groups. The cemented groups (MC, SC) presented more abutment and implant fractures. Significantly higher load to fracture values were observed for SC and MC relative to MS and SS (P < 0.001). Conclusion: Since reliability and strength to failure was higher for SC than for MC, our postulated null hypothesis was rejected. © 2012 John Wiley & Sons A/S.

Survival rate, load to fracture, and finite element analysis of incisors and canines restored with ceramic veneers having varied preparation design

Purpose: To evaluate the survival rate, success rate, load to fracture, and finite element analysis (FEA) of maxillary central incisors and canines restored using ceramic veneers and varying preparation designs.Methods and Materials: Thirty human maxillary central incisors and 30 canines were allocated to the following four groups (n=15) based on the preparation design and type of tooth: Gr1 = central incisor with a conservative preparation; Gr2 = central incisor with a conventional preparation with palatal chamfer; Gr3 = canine with a conservative preparation; Gr4 = canine with a conventional preparation with palatal chamfer. Ceramic veneers (lithium disilicate) were fabricated and adhesively cemented (Variolink Veneer). The specimens were subjected to 4 x 106 mechanical cycles and evaluated at every 500,000 cycles to detect failures. Specimens that survived were subjected to a load to fracture test. Bidimensional models were modeled (Rhinoceros 4.0) and evaluated (MSC.Patrans 2005r2 and MSC.Marc 2005r2) on the basis of their maximum principal stress (MPS) values. Survival rate values were analyzed using the Kaplan-Meier test (alpha = 0.05) and load to fracture values were analyzed using the Student t-test (alpha = 0.05).Results: All groups showed 100% survival rates. The Student t-test did not show any difference between the groups for load to fracture. FEA showed higher MPS values in the specimens restored using veneers with conventional preparation design with palatal chamfer.Conclusion: Preparation design did not affect the fracture load of canines and central incisors, but the veneers with conventional preparation design with palatal chamfer exhibited a tendency to generate higher MPS values.

The study of cardiovascular risk in adolescents - ERICA: rationale, design and sample characteristics of a national survey examining cardiovascular risk factor profile in Brazilian adolescents

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)