EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA

In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data manipulations, referred to as preprocessing, can influence the quality of the ultimate measurements. In the last few years, the high-throughput measurement of gene expression is the most popular application of microarray technology. For this application, various groups have demonstrated that the use of modern statistical methodology can substantially improve accuracy and precision of gene expression measurements, relative to ad-hoc procedures introduced by designers and manufacturers of the technology. Currently, other applications of microarrays are becoming more and more popular. In this paper we describe a preprocessing methodology for a technology designed for the identification of DNA sequence variants in specific genes or regions of the human genome that are associated with phenotypes of interest such as disease. In particular we describe methodology useful for preprocessing Affymetrix SNP chips and obtaining genotype calls with the preprocessed data. We demonstrate how our procedure improves existing approaches using data from three relatively large studies including one in which large number independent calls are available. Software implementing these ideas are avialble from the Bioconductor oligo package.

Effect of two different bioabsorbable collagen membranes on guided bone regeneration: a comparative histomorphometric study in the dog mandible

BACKGROUND: This study compared bone regeneration following guided bone regeneration with two bioabsorbable collagen membranes in saddle-type bone defects in dog mandibles. METHODS: Three standardized defects were created, filled with bone chips and deproteinized bovine bone mineral (DBBM), and covered by three different methods: control = no membrane; test 1 = collagen membrane; and test 2 = cross-linked collagen membrane (CCM). Each side of the mandible was allocated to one of two healing periods (8 or 16 weeks). The histomorphometric analysis assessed the percentage of bone, soft tissue, and DBBM in the regenerate; the absolute area in square millimeters of the bone regenerate; and the distance in millimeters from the bottom of the defect to the highest point of the regenerate. RESULTS: In the 8-week healing group, two dehiscences occurred with CCM. After 8 weeks, all treatment modalities showed no significant differences in the percentage of bone regenerate. After 16 weeks, the percentage of bone had increased for all treatment modalities without significant differences. For all groups, the defect fill height increased between weeks 8 and 16. The CCM group showed a statistically significant (P = 0.0202) increase over time and the highest value of all treatment modalities after 16 weeks of healing, CONCLUSIONS: The CCM showed a limited beneficial effect on bone regeneration in membrane-protected defects in dog mandibles when healing was uneventful. The observed premature membrane exposures resulted in severely compromised amounts of bone regenerate. This increased complication rate with CCM requires a more detailed preclinical and clinical examination before any clinical recommendations can be made.

Evaluation of a novel biphasic calcium phosphate in standardized bone defects: a histologic and histomorphometric study in the mandibles of minipigs

OBJECTIVE: A novel biphasic calcium phosphate (CaP) granulate consisting of hydroxyapatite (HA) and beta-tricalciumphosphate (TCP) was compared with pure HA and pure TCP and with autograft as positive control. MATERIALS AND METHODS: Four standardized bone defects were prepared in both mandibular angles of 16 minipigs and grafted with autogenous bone chips, HA, HA/TCP (60% : 40%), or TCP. Histologic and histomorphometric analysis of bone formation and graft degradation followed healing periods of 2, 4, 8, and 24 weeks. RESULTS: 2 weeks: more bone formation in defects filled with autograft than with the three CaP materials (P<0.05). 4 weeks: bone formation differed significantly (P<0.05) between all four materials (autograft>TCP>HA/TCP>HA). 8 weeks: more bone formation in defects with autograft and TCP than with HA/TCP (P<0.05), and HA/TCP had more bone formation than HA (P<0.05). 24 weeks: no difference in bone formation between the groups. Autograft and TCP resorbed quickly and almost completely over 8 weeks, whereas HA/TCP and HA showed limited degradation over 24 weeks. CONCLUSION: All defects healed with mature lamellar bone and intimate contact between bone and the remaining graft material. The rate of bone formation corresponded to the content of TCP in the CaP materials.

Performance of dental implants after staged sinus floor elevation procedures: 5-year results of a prospective study in partially edentulous patients

OBJECTIVES: The aim of this prospective study was to evaluate the 5-year performance and success rate of titanium screw-type implants with the titanium plasma spray (TPS) or the sand-blasted, large grit, acid-etched (SLA) surface inserted in a two-stage sinus floor elevation (SFE) procedure in the posterior maxilla. MATERIAL AND METHODS: A total of 59 delayed SFEs were performed in 56 patients between January 1997 and December 2001, using a composite graft with autogenous bone chips combined with deproteinized bovine bone mineral (DBBM) or synthetic porous beta-tricalcium phosphate (beta-TCP). After a healing period averaging 7.75 months, 111 dental implants were inserted. After an additional 8-14-week healing period, all implants were functionally loaded with cemented crowns or fixed partial dentures. The patients were recalled at 12 and 60 months for clinical and radiographic examination. RESULTS: One patient developed an acute infection in the right maxillary sinus after SFE and did not undergo implant therapy. Two of the 111 inserted implants had to be removed because of a developing atypical facial pain, and 11 implants were lost to follow-up and were considered drop-outs. The remaining 98 implants showed favorable clinical and radiographic findings at the 5-year examination. The peri-implant soft tissues were stable over time; the mean probing depths and mean attachment levels did not change during the follow-up period. The measurement of the bone crest levels (DIB values) indicated stability as well. Based on strict success criteria, all 98 implants were considered successfully integrated, resulting in a 5-year success rate of 98% (for TPS implants 89%, for SLA implants 100%). CONCLUSION: This prospective study assessing the performance of dental implants inserted after SFE demonstrated that titanium implants can achieve and maintain successful tissue integration with high predictability for at least 5 years of follow-up in carefully selected patients.

Early implant placement following single-tooth extraction in the esthetic zone: biologic rationale and surgical procedures

Early implant placement is one treatment option for implant therapy following single-tooth extraction in the anterior maxilla. The surgical technique presented here is characterized by tooth extraction without flap elevation, a 4- to 8-week soft tissue healing period, implant placement in a correct three-dimensional position, simultaneous contour augmentation on the facial aspect with guided bone regeneration using a bioabsorbable collagen membrane combined with autogenous bone chips and a low-substitution bone filler, and tension-free primary wound closure. The surgical step-by-step procedure is presented with a case report. In addition, the biologic rationale is discussed.

HIGH PERFORMANCE, LOW COST SUBSPACE DECOMPOSITION AND POLYNOMIAL ROOTING FOR REAL TIME DIRECTION OF ARRIVAL ESTIMATION: ANALYSIS AND IMPLEMENTATION

This thesis develops high performance real-time signal processing modules for direction of arrival (DOA) estimation for localization systems. It proposes highly parallel algorithms for performing subspace decomposition and polynomial rooting, which are otherwise traditionally implemented using sequential algorithms. The proposed algorithms address the emerging need for real-time localization for a wide range of applications. As the antenna array size increases, the complexity of signal processing algorithms increases, making it increasingly difficult to satisfy the real-time constraints. This thesis addresses real-time implementation by proposing parallel algorithms, that maintain considerable improvement over traditional algorithms, especially for systems with larger number of antenna array elements. Singular value decomposition (SVD) and polynomial rooting are two computationally complex steps and act as the bottleneck to achieving real-time performance. The proposed algorithms are suitable for implementation on field programmable gated arrays (FPGAs), single instruction multiple data (SIMD) hardware or application specific integrated chips (ASICs), which offer large number of processing elements that can be exploited for parallel processing. The designs proposed in this thesis are modular, easily expandable and easy to implement. Firstly, this thesis proposes a fast converging SVD algorithm. The proposed method reduces the number of iterations it takes to converge to correct singular values, thus achieving closer to real-time performance. A general algorithm and a modular system design are provided making it easy for designers to replicate and extend the design to larger matrix sizes. Moreover, the method is highly parallel, which can be exploited in various hardware platforms mentioned earlier. A fixed point implementation of proposed SVD algorithm is presented. The FPGA design is pipelined to the maximum extent to increase the maximum achievable frequency of operation. The system was developed with the objective of achieving high throughput. Various modern cores available in FPGAs were used to maximize the performance and details of these modules are presented in detail. Finally, a parallel polynomial rooting technique based on Newton’s method applicable exclusively to root-MUSIC polynomials is proposed. Unique characteristics of root-MUSIC polynomial’s complex dynamics were exploited to derive this polynomial rooting method. The technique exhibits parallelism and converges to the desired root within fixed number of iterations, making this suitable for polynomial rooting of large degree polynomials. We believe this is the first time that complex dynamics of root-MUSIC polynomial were analyzed to propose an algorithm. In all, the thesis addresses two major bottlenecks in a direction of arrival estimation system, by providing simple, high throughput, parallel algorithms.

Experimental investigation of regular fluids and nanofluids during flow boiling in a single microchannel at different heat fluxes and mass fluxes

The dissipation of high heat flux from integrated circuit chips and the maintenance of acceptable junction temperatures in high powered electronics require advanced cooling technologies. One such technology is two-phase cooling in microchannels under confined flow boiling conditions. In macroscale flow boiling bubbles will nucleate on the channel walls, grow, and depart from the surface. In microscale flow boiling bubbles can fill the channel diameter before the liquid drag force has a chance to sweep them off the channel wall. As a confined bubble elongates in a microchannel, it traps thin liquid films between the heated wall and the vapor core that are subject to large temperature gradients. The thin films evaporate rapidly, sometimes faster than the incoming mass flux can replenish bulk fluid in the microchannel. When the local vapor pressure spike exceeds the inlet pressure, it forces the upstream interface to travel back into the inlet plenum and create flow boiling instabilities. Flow boiling instabilities reduce the temperature at which critical heat flux occurs and create channel dryout. Dryout causes high surface temperatures that can destroy the electronic circuits that use two-phase micro heat exchangers for cooling. Flow boiling instability is characterized by periodic oscillation of flow regimes which induce oscillations in fluid temperature, wall temperatures, pressure drop, and mass flux. When nanofluids are used in flow boiling, the nanoparticles become deposited on the heated surface and change its thermal conductivity, roughness, capillarity, wettability, and nucleation site density. It also affects heat transfer by changing bubble departure diameter, bubble departure frequency, and the evaporation of the micro and macrolayer beneath the growing bubbles. Flow boiling was investigated in this study using degassed, deionized water, and 0.001 vol% aluminum oxide nanofluids in a single rectangular brass microchannel with a hydraulic diameter of 229 µm for one inlet fluid temperature of 63°C and two constant flow rates of 0.41 ml/min and 0.82 ml/min. The power input was adjusted for two average surface temperatures of 103°C and 119°C at each flow rate. High speed images were taken periodically for water and nanofluid flow boiling after durations of 25, 75, and 125 minutes from the start of flow. The change in regime timing revealed the effect of nanoparticle suspension and deposition on the Onset of Nucelate Boiling (ONB) and the Onset of Bubble Elongation (OBE). Cycle duration and bubble frequencies are reported for different nanofluid flow boiling durations. The addition of nanoparticles was found to stabilize bubble nucleation and growth and limit the recession rate of the upstream and downstream interfaces, mitigating the spreading of dry spots and elongating the thin film regions to increase thin film evaporation.

A STUDY ON THE FEASIBILITY OF UNIVERSAL CHIP CONTROL IN MACHINING

A novel solution to the long standing issue of chip entanglement and breakage in metal cutting is presented in this dissertation. Through this work, an attempt is made to achieve universal chip control in machining by using chip guidance and subsequent breakage by backward bending (tensile loading of the chip's rough top surface) to effectively control long continuous chips into small segments. One big limitation of using chip breaker geometries in disposable carbide inserts is that the application range is limited to a narrow band depending on cutting conditions. Even within a recommended operating range, chip breakers do not function effectively as designed due to the inherent variations of the cutting process. Moreover, for a particular process, matching the chip breaker geometry with the right cutting conditions to achieve effective chip control is a very iterative process. The existence of a large variety of proprietary chip breaker designs further exacerbates the problem of easily implementing a robust and comprehensive chip control technique. To address the need for a robust and universal chip control technique, a new method is proposed in this work. By using a single tool top form geometry coupled with a tooling system for inducing chip breaking by backward bending, the proposed method achieves comprehensive chip control over a wide range of cutting conditions. A geometry based model is developed to predict a variable edge inclination angle that guides the chip flow to a predetermined target location. Chip kinematics for the new tool geometry is examined via photographic evidence from experimental cutting trials. Both qualitative and quantitative methods are used to characterize the chip kinematics. Results from the chip characterization studies indicate that the chip flow and final form show a remarkable consistency across multiple levels of workpiece and tool configurations as well as cutting conditions. A new tooling system is then designed to comprehensively break the chip by backward bending. Test results with the new tooling system prove that by utilizing the chip guidance and backward bending mechanism, long continuous chips can be more consistently broken into smaller segments that are generally deemed acceptable or good chips. It is found that the proposed tool can be applied effectively over a wider range of cutting conditions than present chip breakers thus taking possibly the first step towards achieving universal chip control in machining.

PROOF OF CONCEPT PROTOTYPE FOR A RAILROAD PEDESTRIAN WARNING SYSTEM USING WIRELESS SENSOR NETWORKS

Wireless sensor network is an emerging research topic due to its vast and ever-growing applications. Wireless sensor networks are made up of small nodes whose main goal is to monitor, compute and transmit data. The nodes are basically made up of low powered microcontrollers, wireless transceiver chips, sensors to monitor their environment and a power source. The applications of wireless sensor networks range from basic household applications, such as health monitoring, appliance control and security to military application, such as intruder detection. The wide spread application of wireless sensor networks has brought to light many research issues such as battery efficiency, unreliable routing protocols due to node failures, localization issues and security vulnerabilities. This report will describe the hardware development of a fault tolerant routing protocol for railroad pedestrian warning system. The protocol implemented is a peer to peer multi-hop TDMA based protocol for nodes arranged in a linear zigzag chain arrangement. The basic working of the protocol was derived from Wireless Architecture for Hard Real-Time Embedded Networks (WAHREN).

DEVELOPMENT OF CONFOCAL IMAGING TECHNIQUES FOR PROBING INTERFACIAL DYNAMICS IN MICROSCALE, GAS-LIQUID, TWO-PHASE FLOW

Micro-scale, two-phase flow is found in a variety of devices such as Lab-on-a-chip, bio-chips, micro-heat exchangers, and fuel cells. Knowledge of the fluid behavior near the dynamic gas-liquid interface is required for developing accurate predictive models. Light is distorted near a curved gas-liquid interface preventing accurate measurement of interfacial shape and internal liquid velocities. This research focused on the development of experimental methods designed to isolate and probe dynamic liquid films and measure velocity fields near a moving gas-liquid interface. A high-speed, reflectance, swept-field confocal (RSFC) imaging system was developed for imaging near curved surfaces. Experimental studies of dynamic gas-liquid interface of micro-scale, two-phase flow were conducted in three phases. Dynamic liquid film thicknesses of segmented, two-phase flow were measured using the RSFC and compared to a classic film thickness deposition model. Flow fields near a steadily moving meniscus were measured using RSFC and particle tracking velocimetry. The RSFC provided high speed imaging near the menisci without distortion caused the gas-liquid interface. Finally, interfacial morphology for internal two-phase flow and droplet evaporation were measured using interferograms produced by the RSFC imaging technique. Each technique can be used independently or simultaneously when.

A feasibility study evaluating an in situ formed synthetic biodegradable membrane for guided bone regeneration in dogs

PURPOSE: The aim was (1) to evaluate the soft-tissue reaction of a synthetic polyethylene glycol (PEG) hydrogel used as a barrier membrane for guided bone regeneration (GBR) compared with a collagen membrane and (2) to test whether or not the application of this in situ formed membrane will result in a similar amount of bone regeneration as the use of a collagen membrane. MATERIAL AND METHODS: Tooth extraction and preparation of osseous defects were performed in the mandibles of 11 beagle dogs. After 3 months, 44 cylindrical implants were placed within healed dehiscence-type bone defects resulting in approximately 6 mm exposed implant surface. The following four treatment modalities were randomly allocated: PEG+autogenous bone chips, PEG+hydroxyapatite (HA)/tricalcium phosphate (TCP) granules, bioresorbable collagen membrane+autogenous bone chips and autogenous bone chips without a membrane. After 2 and 6 months, six and five dogs were sacrificed, respectively. A semi-quantitative evaluation of the local tolerance and a histomorphometric analysis were performed. For statistical analysis, repeated measures analysis of variance (ANOVA) and subsequent pairwise Student's t-test were applied (P<0.05). RESULTS: No local adverse effects in association with the PEG compared with the collagen membrane was observed clinically and histologically at any time-point. Healing was uneventful and all implants were histologically integrated. Four out of 22 PEG membrane sites revealed a soft-tissue dehiscence after 1-2 weeks that subsequently healed uneventful. Histomorphometric measurement of the vertical bone gain showed after 2 months values between 31% and 45% and after 6 months between 31% and 38%. Bone-to-implant contact (BIC) within the former defect area was similarly high in all groups ranging from 71% to 82% after 2 months and 49% to 91% after 6 months. However, with regard to all evaluated parameters, the PEG and the collagen membranes did not show any statistically significant difference compared with sites treated with autogenous bone without a membrane. CONCLUSION: The in situ forming synthetic membrane made of PEG was safely used in the present study, revealing no biologically significant abnormal soft-tissue reaction and demonstrated similar amounts of newly formed bone for defects treated with the PEG membrane compared with defects treated with a standard collagen membrane.

Contribution of genome-wide significant single-nucleotide polymorphisms and antiretroviral therapy to dyslipidemia in HIV-infected individuals: a longitudinal study

BACKGROUND: HIV-infected individuals have an increased risk of myocardial infarction. Antiretroviral therapy (ART) is regarded as a major determinant of dyslipidemia in HIV-infected individuals. Previous genetic studies have been limited by the validity of the single-nucleotide polymorphisms (SNPs) interrogated and by cross-sectional design. Recent genome-wide association studies have reliably associated common SNPs to dyslipidemia in the general population. METHODS AND RESULTS: We validated the contribution of 42 SNPs (33 identified in genome-wide association studies and 9 previously reported SNPs not included in genome-wide association study chips) and of longitudinally measured key nongenetic variables (ART, underlying conditions, sex, age, ethnicity, and HIV disease parameters) to dyslipidemia in 745 HIV-infected study participants (n=34 565 lipid measurements; median follow-up, 7.6 years). The relative impact of SNPs and ART to lipid variation in the study population and their cumulative influence on sustained dyslipidemia at the level of the individual were calculated. SNPs were associated with lipid changes consistent with genome-wide association study estimates. SNPs explained up to 7.6% (non-high-density lipoprotein cholesterol), 6.2% (high-density lipoprotein cholesterol), and 6.8% (triglycerides) of lipid variation; ART explained 3.9% (non-high-density lipoprotein cholesterol), 1.5% (high-density lipoprotein cholesterol), and 6.2% (triglycerides). An individual with the most dyslipidemic antiretroviral and genetic background had an approximately 3- to 5-fold increased risk of sustained dyslipidemia compared with an individual with the least dyslipidemic therapy and genetic background. CONCLUSIONS: In the HIV-infected population treated with ART, the weight of the contribution of common SNPs and ART to dyslipidemia was similar. When selecting an ART regimen, genetic information should be considered in addition to the dyslipidemic effects of ART agents.

Generative Serienproduktion von Mikrokomponenten

Stetig steigende Funktionalitäten, intelligente Materialien, eine möglichst geringe Leistungsaufnahme verbunden mit kleinem Volumen und geringem Gewicht sind die zentralen Anforderungen u.a. der Medizintechnik und der Telekommunikation. Um diesen Bedarf mit industriellen Fertigungsverfahren abzudecken, startete das Unternehmen nach seiner Gründung in Rumeln bereits 1996 mit dem Aufbau der RMPD® Technologiefamilie. Heute sichern diese Technologien, mit denen die direkte Serienproduktion auf Basis der CAD Kontruktionsdaten für Mikrosysteme und –komponenten werkzeuglos erfolgt, einem internationalen Kundenkreis Markterfolge mit dem Einsatz patentierter Fertigungssysteme. microTEC ist an zwei Standorten als Auftragsproduzent für Unternehmen u.a. aus den Bereichen Sensorik, Telekommunikation, Medizintechnik und Biotechnologie tätig. Mit den RMPD® Technologien profitieren die Kunden auch durch die schnelle Anpassungsfähigkeit an sich ändernde Marktbedingungen und Verbraucherwünsche. Über 300 Kunststoffe mit den unterschiedlichsten Eigenschaften stehen für mikroelektronische Packaging-Dienstleistungen und Auftragsfertigung von Mikrosystemen zur Verfügung, zu den Produkten gehören z.B. Mikrogetriebe mit selbstschmierenden Zahnrädern und Lab-on-a-Chipsysteme, die mit dem Einsatz hydrophiler Kunststoffe die Kapillarwirkung auch in 3D nutzen. Die beiden Geschäftsführer Dipl. Ing. Reiner Götzen und Andrea Reinhardt, sowie der Prokurist Dr. Ing. Helge Bohlmann stehen für eine konzernunabhängige, kundenorientierte Strategie und verfügen über langjährige Erfahrung als mittelständische Unternehmer. Dies bildet zusammen mit der internationalen Marktorientierung, dem branchenübergreifenden Technologie Know-how und den inhouse verfügbaren Produktionsanlagen die Basis für den weiteren Standortausbau im 8. Jahr des Unternehmens.

Bone-Conditioned Medium Inhibits Osteogenic and Adipogenic Differentiation of Mesenchymal Cells In Vitro

BACKGROUND AND PURPOSE Autografts are used for bone reconstruction in regenerative medicine including oral and maxillofacial surgery. Bone grafts release paracrine signals that can reach mesenchymal cells at defect sites. The impact of the paracrine signals on osteogenic, adipogenic, and chondrogenic differentiation of mesenchymal cells has remained unclear. MATERIAL AND METHODS Osteogenesis, adipogenesis, and chondrogenesis were studied with murine ST2 osteoblast progenitors, 3T3-L1 preadipocytes, and ATDC5 prechondrogenic cells, respectively. Primary periodontal fibroblasts from the gingiva, from the periodontal ligament, and from bone were also included in the analysis. Cells were exposed to bone-conditioned medium (BCM) that was prepared from porcine cortical bone chips. RESULTS BCM inhibited osteogenic and adipogenic differentiation of ST2 and 3T3-L1 cells, respectively, as shown by histological staining and gene expression. No substantial changes in the expression of chondrogenic genes were observed in ATDC5 cells. Primary periodontal fibroblasts also showed a robust decrease in alkaline phosphatase and peroxisome proliferator-activated receptor gamma (PPARγ) expression when exposed to BCM. BCM also increased collagen type 10 expression. Pharmacologic blocking of transforming growth factor (TGF)-β receptor type I kinase with SB431542 and the smad-3 inhibitor SIS3 at least partially reversed the effect of BCM on PPARγ and collagen type 10 expression. In support of BCM having TGF-β activity, the respective target genes were increasingly expressed in periodontal fibroblasts. CONCLUSIONS The present work is a pioneer study on the paracrine activity of bone grafts. The findings suggest that cortical bone chips release soluble signals that can modulate differentiation of mesenchymal cells in vitro at least partially involving TGF-β signaling.

Nanomaterials and the human lung: what is known and what must be deciphered to realise their potential advantages?

Due to the constant expansion within the nanotechnology industry in the last decade, nanomaterials are omnipresent in society today. Nanotechnology-based products have numerous different applications ranging from electronic (e.g., advanced memory chips) to industrial (e.g., coatings or composites) to biomedical (e.g., drug delivery systems, diagnostics). Although these new nanomaterials can be found in many "everyday" products, their effects on the human body have still to be investigated in order to identify not only their risk, but also their potential benefits towards human health. Since the lung is commonly thought to be the main portal of entry into the human body for nanomaterials released within the environment, this review will attempt to summarise the current knowledge and understanding of how nanomaterials interact with the respiratory tract. Furthermore, the advantages and disadvantages of different experimental model systems that are commonly used to study this exposure route to the human body will be discussed.