De senaste decennierna har en miniatyriseringstrend inom ingenjörsvetenskaperna blivit allt större. Komplexa maskiner eller processer skalas ner till en allt mindre skala. Det kan vara motorer som inte är större än 500 μm eller kemiska analyser som vanligtvis görs på en större laboratorieutrustning som nu går att utföra på en yta på ca 2x4 cm. En sådan utrustning som kan utföra kemiska analyser kallas ofta för ”Lab-on-a-Chip” (LoC) och innehåller kemiska kretsar som hanterar mikroflöden av analysvätskor. En del av dagens forskning för att ta fram nya LoC handlar om att möta ett behov av portabel, billig och snabb analysutrustning i utvecklingsländer. Dock finns ett problem med att få ut produkter på marknaden. De flesta LoC som presenteras i forskningsrapporter idag är tillverkade av polydimetylsiloxan (PDMS). Det är en elastomer som lämpar sig väl för småskalig prototypframställning, men är svår att producera i stor skala, dessutom krävs ofta extern utrustning för att vätskeflöde skall uppstå. Det finns även LoC i papper, vilkas porösa struktur möjliggör för spontan vätsketransport, wicking, utan extern utrustning. Dessa är billiga och har nått större framgång. Exempelvis är vanliga graviditetstest som går att köpa på apoteket ofta LoC i papper. Textiliers fukt- och vätskehantering är relevant för komfort, och för många beredningsprocesser. Exempelvis är wicking ett välstuderat område som det finns djup kunskap om i den textila sektorn. Denna kunskap kan utnyttjas för att skapa ett textilt LoC. Att använda textila tekniker innebär möjligheter att styra vätskeflödet med hjälp av garn med och utan wickingförmåga. Denna studie undersöker hur en vävs naturliga X-Y-system av varp- och väftgarner kan utnyttjas för att skapa en kontrollerad vätskestyrning, en textil kemisk krets. Arbetet har utgått från frågan om hur en väv kan konstrueras för att leda en vätska från ett varpgarn till ett väftgarn utan läckage i oönskad del av väven. Två olika garner valdes: ett monofilament av polyeten för de områden där vätskeledning ej var önskvärd och ett multifilament av Coolmax® polyester med god wickingförmåga där vätskan vara avsedd att transporteras. Tre parametrar testades; bindningen i de delar av väven som var avsedd för vätsketransport (önskad väg); bindningen där vätskan skulle övergå från ett varpgarn till ett väftgarn (vägskälet); och antalet wickande trådar (trådigheten). Åtta olika kombinationer avseende dessa parametrar testade. Samtliga parametrar hade signifikant inverkan på läckaget. Den konstruktion med minst läckage in i oönskad väg var den med bindning över två trådar i önskad väg, flotteringar i vägskälet och var tvåtrådig. Den framtagna vävens möjlighet att användas i en biosensor undersöktes genom ett försök att konstruera en elektrokemisk glukosmätare. Som elektroder valdes en silverbelagd polyamid. Vid preparering av elektroderna skedde en oväntad reaktion mellan det silverbelagda garnet och en av de ingående kemikalierna, prussian blue. Därför kunde ingen detektion av glukos ske. Det noterades även att den textila kemiska kretsens wickingförmåga försämrades då den utsattes för våta prepareringsprocesserna av elektroderna. Från experimentet med att konstruera en textil glukosmätare drogs slutsatsen att preparering av elektroderna bör ske innan invävning i den textila kemiska kretsen.

The healthy development of a living cell requires precise spatial-temporal gene expression. The code that dictates when and where genes are expressed is stored in a pattern of specific sequence motifs, which can be recognised by transcription factors. Understanding the interaction between these DNA sequence motifs and transcription factors will help to elucidate how genomic sequences build transcriptional control networks. However, the DNA-binding specificities of ~1400 human transcription factors are largely unknown. The in vivo DNA-binding events of transcription factors involve great subtlety, because most transcription factors recognise degenerate sequence motifs and related transcription factors often prefer similar or even identical sequences. Forkhead transcription factors exemplify these challenges. To understand how members within the Forkhead transcription factor family gain their binding and functional specificities, we used chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) to interrogate the genome-wide chromatin binding events of three Forkhead transcription factors: FOXM1, FOXO3 and FOXK2. We find that FOXM1 specifically binds to the promoters of a large array of genes whose activities peak at the G2 and M phases of the cell cycle. The canonical Forkhead consensus GTAAACA is not enriched within the FOXM1 cistrome. It gains its own specific binding events and biological functions by interacting and cooperating with the MMB complex. FOXO3 and FOXK2 are recruited to chromatin by the canonical Forkhead consensus GTAAACA, and they bind both shared and specific regions in the genome. FOXO3 mostly binds to the regions which are also bound by FOXK2, but no competitive or assisted binding between FOXO3 and FOXK2 is detected within those regions. Overall, these results help explain how individual members of the Forkhead transcription factor family gain binding specificity within the genome yet raises new questions of how functional specificity is achieved by other family members.

Particleboard (PB) is a widely used panel material because of its physical properties and low cost. Unfortunately, cutting can degrade its surface creating rejects and increasing manufacturing costs. A major challenge is PB’s internal variability. Different particle and glue bond strength combinations can sometimes create high quality surfaces in one area and defects such as edge chipping in nearby areas. This research examines methods of improving surface quality by examining PB characteristics and their interactions with the cutting tool. It also develops an analytical model and software tool that allows the effects of these factors to be simulated, thereby giving practical guidance and reducing the need for costly experiments. When PB is cut and the glue bond strength is weaker than the particle strength, particles are pulled out, leading to surface defects. When instead the glue bond strength is stronger than the particle strength, particles are smoothly cut, leading to a high quality surface. PB is modeled as a matrix of particles each with stochastically assigned material and glue bond strengths. The PB model is layered allowing particles to be misaligned. Voids are modeled as missing particles. PB cutting is modeled in three zones. In the finished material and tool tip zones, particles are compressed elastically and then crushed at constant stress. After failure, chip formation occurs in the chip formation zone. At large rake angles, the chip is modeled as a transversely loaded beam that can fail by cleavage at its base or tensile failure on its surface. At small rake angles, the chip is modeled as the resultant force acting on the plane from the tool tip through to the panel surface. Experimental and simulation results show that cutting forces increase with depth of cut, glue content and particle strength. They decrease with rake angle. Glue bond strength can be increased to the equivalent particle strength through the selection of particle geometry and the subsequent increased glue bond efficiency, which increases the cut surface quality without the need for additional glue. Minimizing the size and frequency of voids and using larger rake angles can also increase surface quality. / Applied Science, Faculty of / Mechanical Engineering, Department of / Graduate

FPGA clock frequencies are slow enough that only a fraction of the interconnect’s bandwidth is used. By exploiting this bandwidth, the transfer of large amounts of data can be greatly accelerated. Alternatively, it may also be possible to save area on fixed-bandwidth links by using on-chip serial signaling. For datapath-intensive designs which operate on words instead of bits, this can reduce wiring congestion as well. This thesis proposes relatively simple circuit-level modifications to FPGA interconnect to enable high-bandwidth communication. High-level area estimates indicate a potential interconnect area savings of 10 to 60% when serial links are used. Two interconnect pipelining techniques, wave pipelining and surfing, are adapted to FPGAs and compared against each other and against regular FPGA interconnect in terms of throughput, reliability, area, power, and latency. Source-synchronous signaling is used to achieve high data rates with simple receiver design. Statistical models for high-frequency power supply noise are developed and used to estimate the probability of error of wave pipelined and surfing links as a function of link length and operating speed. Surfing is generally found to be more reliable and less sensitive to noise than wave pipelining. Simulation results in a 65nm process demonstrate a throughput of 3Gbps per wire across a 50-stage, 25mm link. / Applied Science, Faculty of / Electrical and Computer Engineering, Department of / Graduate

In the past decade, fast advancements have been made in the sequencing, digitalization and collection of the biological data. However the bottleneck remains at the point of analysis and extraction of patterns from the data. We have developed a method that is aimed at widening this bottleneck by automating the knowledge extraction from the biological data. Our approach is aimed at discovering patterns in a set of DNA sequences based on the location of transcription factor binding sites or any other biological markers with the emphasis of discovering relationships. A variety of statistical and computational methods exists to analyze such data. However, they either require an initial hypothesis, which is later tested, or classify the data based on its attributes. Our approach does not require an initial hypothesis and the classification it produces is based on the relationships between attributes. The value of such approach is that is is able to uncover new knowledge about the data by inducing a general theory based on basic known rules. The core of our approach lies in an inductive logic programming engine, which, based on positive and negative examples as well as background knowledge, is able to induce a descriptive, human-readable theory, describing the data. An application provides an end-to-end analysis of DNA sequences. A simple to use Web interface accepts a set of related sequences to be analyzed, set of negative example sequences to contrast the main set (optional), and a set of possible genetic markers as position-specific scoring matrices. A Java-based backend formats the sequences, determines the location of the genetic markers inside them and passes the information to the ILP engine, which induces the theory. The model, assumed in our background knowledge, is a set of basic interactions between biological markers in any DNA sequence. This makes our approach applicable to analyze a wide variety of biological problems, including detection of cis-regulatory modules and analysis of ChIP-Sequencing experiments. We have evaluated our method in the context of such applications on two real world datasets as well as a number of specially designed synthetic datasets. The approach has shown to have merit even in situations when no significant classification could be determined.

Adult skeletal muscles can regenerate after injury due to the presence of satellite cells, a quiescent population of myogenic progenitor cells characterized by expressing the transcription factor Pax7. Once activated, satellite cells repair the muscle damage and replenish the stem cell niche due to the coordinated function of several transcription factors including Pax7 and the myogenic regulatory factors (MRFs). MRFs are skeletal muscle-specific transcription factors that can convert non-muscle cells into the myogenic lineage. MRFs are known to cooperate with other transcription factors in regulating the complex transcriptional network driving myogenic differentiation of muscle progenitors. The Six4 transcription factor emerges as a strong candidate for cooperating with MRFs. Six4 is expressed in skeletal muscles; the lack of a muscle development phenotype in Six4-null mice has been attributed to compensation by other Six family members. However, this did not exclude a critical role for Six4 during muscle development as Six1;Six4 double mutant mice show a more severe muscle phenotype than Six1 mutant mice. Nevertheless, the role of Six4 during adult muscle regeneration has never been addressed. I combined a partial loss-of-function of Six4 with high-throughput approaches to address the role of Six4 during adult skeletal muscle regeneration. I observed an important function of Six4 during muscle regeneration in vivo and in in vitro cell models. Using RNA interference assays against Six4 in tibialis anterior muscle regeneration after cardiotoxin-induced muscle damage, I observed for the first time that Six4 plays a role in proper muscle regeneration. The ability of the MRF MyoD, a central regulator of skeletal myogenesis, to convert a non-muscle cell model into the myogenic lineage was impaired with attenuated Six4 expression. I employed genome-wide approaches by combining ChIP-sequencing with gene expression profiling and identified a set of muscle genes coordinately regulated by both Six4 and MyoD. Throughout the genome, the cooperation between Six4 and MyoD was associated with binding of the H3K27me3 demethylase Utx and depletion of the H3K27me3 repressive chromatin mark. Together, these results reveal an important role for Six4 during adult muscle regeneration, and suggest a widespread mechanism of cooperation between Six4 and MyoD that correlates with modifying the epigenetic landscape of the regulatory regions of a large set of genes needed for efficient myogenesis.

Hernández Luz, C. (2012). Addressing Manufacturing Challenges in NoC-based ULSI Designs [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/16694 / Palancia

Las actuales arquitecturas de m�ltiples n�cleos como los chip multiprocesadores (CMP) y soluciones multiprocesador para sistemas dentro del chip (MPSoCs) han adoptado a las redes dentro del chip (NoC) como elemento -ptimo para la inter-conexi-n de los diversos elementos de dichos sistemas. En este sentido, fabricantes de CMPs y MPSoCs han adoptado NoCs sencillas, generalmente con una topolog'a en malla o anillo, ya que son suficientes para satisfacer las necesidades de los sistemas actuales. Sin embargo a medida que los requerimientos del sistema -- baja latencia y alto rendimiento -- se hacen m�s exigentes, estas redes tan simples dejan de ser una soluci-n real. As', la comunidad investigadora ha propuesto y analizado NoCs m�s complejas. No obstante, estas soluciones son m�s dif'ciles de implementar -- especialmente los enlaces largos -- haciendo que este tipo de topolog'as complejas sean demasiado costosas o incluso inviables. En esta tesis, presentamos una metodolog'a de dise-o que minimiza la p�rdida de prestaciones de la red debido a su implementaci-n real. Los principales problemas que se encuentran al implementar una NoC son los conmutadores y los enlaces largos. En esta tesis, el conmutador se ha hecho modular, es decir, formado como uni-n de m-dulos m�s peque-os. En nuestro caso, los m-dulos son id�nticos, donde cada m-dulo es capaz de arbitrar, conmutar, y almacenar los mensajes que le llegan. Posteriormente, flexibilizamos la colocaci-n de estos m-dulos en el chip, permitiendo que m-dulos de un mismo conmutador est�n distribuidos por el chip. Esta metodolog'a de dise-o la hemos aplicado a diferentes escenarios. Primeramente, hemos introducido nuestro conmutador modular en NoCs con topolog'as conocidas como la malla 2D. Los resultados muestran como la modularidad y la distribuci-n del conmutador reducen la latencia y el consumo de potencia de la red. En segundo lugar, hemos utilizado nuestra metodolog'a de dise-o para implementar un crossbar distribuid / Roca Pérez, A. (2012). Floorplan-Aware High Performance NoC Design [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/17844 / Palancia

90% de la mortalité par cancer provient de tumeurs disséminées, ou métastases. Ces métastases se forment à partir de cellules tumorales qui s'échappent d'une tumeur primaire, circulent dans le sang, puis quittent les vaisseaux sanguins pour enfin aller nicher dans des organes distants et former des tumeurs secondaires. Les processus par lesquels ces cellules circulantes envahissent les organes distants, remodèlent leur environnement pour créer une «niche micrométastatique», prolifèrent pour produire des métastases macroscopiques, sont mal connus, principalement en raison d'un manque de modèles expérimentaux. En effet ces événements sont rares, se produisent à une échelle microscopique et à des localisations à priori inconnues. La perte d'adhérence cellulaire des cellules tumorales se détachant des tissus tumoraux primaires est associée à un phénomène de transformation connu sous le nom de transition épithéliale-mésenchymateuse (EMT) conduisant à la perte des caractéristiques épithéliales. Dans ce travail, nous avons souhaité aborder la question du processus métastatiques par l'étude de l'influence de l'étape de circulation dans le flux sanguin sur différentes caractéristiques de cellules tumorales. Pour cela, des modèles microfluidiques contenant des constrictions mécaniques afin d'imiter la microcirculation sanguine ont été conçus et fabriqués. Nous avons soumis des cellules provenant de tumeurs primaires du sein dans des situations de confinement périodiques à l'intérieur de ces canaux microfluidiques en utilisant un système de contrôle de flux. Nous avons étudiés l'impact des déformations induites par les constrictions des canaux microfluidiques sur l'expression génétique des marqueurs EMT, la morphologie ainsi que la dynamique des changements morphologiques. Nous montrons que ces paramètres cellulaires sont touchés par la déformation mécanique imposée sous flux, suggérant que l'étape de circulation des cellules tumorales dans le sang a un rôle important dans la capacité de celles-ci à produire des métastases. / 90% of cancer mortality arises from metastases, due to cells that escape from a primary tumor, circulate in the blood as circulating tumor cells (CTCs), leave blood vessels and nest in distant organs. The processes by which CTCs invade distant organs, remodel their environment to create a “micrometastatic niche”, the eventual triggering of a proliferation leading to a macroscopic metastases, are poorly known, mostly because of a lack of experimental models. These events are rare; occur in the body at unknown places and on a microscopic scale. The loss of cell adhesion of tumor cells detaching from the primary tumor tissues will undergo a transformation phenomenon known as epithelial-to mesenchymal transition (EMT) leading to the loss of epithelial characteristics with different expression patterns of EMT markers (E-cadherin, N-cadherin, Vimentin, Snail1/2, Twist1/2, ZEB1/2). The changes in mechanical and physical properties of interacting cells during morphological and malignant transformation are investigated and their quantifications measured. Here, microfluidic models containing mechanical constrictions in order to mimic the blood microcirculation have been designed and fabricated. Metastatic breast cancer cells are subjected and confined to the microfluidic channels using a flow control system. These cells are circulated under optimal culture conditions, and monitored in the channels for the observance of biophysical occurrences from continuous mechanical cellular deformations. The biophysical effects of circulation and confinement on tumor cell morphogenesis will be investigated.

Thesis advisor: Thomas C. Chiles / Rapid diagnosis of infectious disease at the site of the patient is critical for preventing the escalation of an outbreak into an epidemic. This is particularly true for cholera, a disease known to spread swiftly within resource-limited populations. A device suited to point-of- care (POC) diagnosis of cholera must not only demonstrate laboratory levels of sensitivity and specificity, but it must do so in a highly portable, low-cost manner, with a simplistic readout. Here, we report novel proof-of-concept lab-on-a-chip (LOC) electrochemical immunosensors for the detection of cholera toxin subunit B (CTX), based on two nanostructured architectures: the gold dendritic array, and the extended core coax (ECC). The dendritic array has an ~18x greater surface area than a planar gold counterpart, per electrochemical measurements, allowing for a higher level of diagnostic sensitivity. An electrochemical enzyme-linked immunosorbant assay (ELISA) for CTX performed via differential pulse voltammetry (DPV) on the dendritic sensor demonstrated a limit-of detection of 1 ng/mL, per a signal-to-noise ratio of 2.6, which was more sensitive than a simple planar gold electrode (100 ng/mL). This sensitivity also matches a currently available diagnostic standard, the optical ELISA, but on a miniaturized platform with simple electrical readout. The ECC was optimized and explored, undergoing several changes in design to facilitate sensitive LOC electrochemical detection. The ECC matched the off-chip sensitivity towards CTX demonstrated by a previous non-extended core coaxial iteration, which was comparable to a standard optical ELISA. In contrast to the previous coaxial architecture, the ECC is amenable to functionalization of the gold core, allowing for LOC detection. ECCs were functionalized using a thiolated protein G, and CTX was detected via an electrochemical ELISA. While this work is ongoing, the ECC shows promise as a platform for LOC electrochemical ELISA. The ability to potentially meet POC demands makes biofunctionalized gold dendrites and ECCs promising architectures for further development as LOC sensors for the detection of infectious disease biomarkers. / Thesis (PhD) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.