The automation of protein crystal presentation for X ray diffraction experiments using standing acoustic waves in a microfluidic chip environment

As the pressure continues to grow on Diamond and the world's synchrotrons for higher throughput of diffraction experiments, new and novel techniques are required for presenting micron dimension crystals to the X ray beam. Currently this task is both labour intensive and primarily a serial process. Diffraction measurements typically take milliseconds but sample preparation and presentation can reduce throughput down to 4 measurements an hour. With beamline waiting times as long as two years it is of key importance for researchers to capitalize on available beam time, generating as much data as possible. Other approaches detailed in the literature [1] [2] [3] are very much skewed towards automating, with robotics, the actions of a human protocols. The work detailed here is the development and discussion of a bottom up approach relying on SSAW self assembly, including material selection, microfluidic integration and tuning of the acoustic cavity to order the protein crystals.

Development and reliability of a direct access sensor using flip chip on flex technology with anisotropic conductive adhesive

Technological developments in biomedical microsystems are opening up new opportunities to improve healthcare procedures. Swallowable diagnostic sensing capsules are an example of these. In none of the diagnostic sensing capsules, is the sensor’s first level packaging achieved via Flip Chip Over Hole (FCOH) method using Anisotropic Conductive Adhesive (ACA). In a capsule application with direct access sensor (DAS), ACA not only provides the electrical interconnection but simultaneously seals the interconnect area and the underlying electronics. The development showed that the ACA FCOH was a viable option for the DAS interconnection. Adequate adhesive formed a strong joint that withstood a shear stress of 120N/mm2 and a compressive stress of 6N required to secure the final sensor assembly in place before encapsulation. Electrical characterization of the ACA joint in a fluid environment showed that the ACA was saturated with moisture and that the ions in the solution actively contributed to the leakage current, characterized by the varying rate of change of conductance. Long term hygrothermal aging of the ACA joint showed that a thermal strain of 0.004 and a hygroscopic strain of 0.0052 were present and resulted in a fatigue like process. In-vitro tests showed that high temperature and acidity had a deleterious effect of the ACA and its joint. It also showed that the ACA contact joints positioned at around or over 1mm would survive the gastrointestinal (GI) fluids and would be able to provide a reliable contact during the entire 72hr of the GI transit time. A final capsule demonstrator was achieved by successfully integrating the DAS, the battery and the final foldable circuitry into a glycerine capsule. Final capsule soak tests suggested that the silicone encapsulated system could survive the 72hr gut transition.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

A parametric study of flip-chip reliability via computer simulation

Abstract not available

Large scale parallel simulations for the assembly of a flip-chip component to a printed circuit

Abstract not available

Dynamic Workload Parallelization and System Calibration on Single-Chip Cloud Computer

Many-core systems are emerging from the need of more computational power and power efficiency. However there are many issues which still revolve around the many-core systems. These systems need specialized software before they can be fully utilized and the hardware itself may differ from the conventional computational systems. To gain efficiency from many-core system, programs need to be parallelized. In many-core systems the cores are small and less powerful than cores used in traditional computing, so running a conventional program is not an efficient option. Also in Network-on-Chip based processors the network might get congested and the cores might work at different speeds. In this thesis is, a dynamic load balancing method is proposed and tested on Intel 48-core Single-Chip Cloud Computer by parallelizing a fault simulator. The maximum speedup is difficult to obtain due to severe bottlenecks in the system. In order to exploit all the available parallelism of the Single-Chip Cloud Computer, a runtime approach capable of dynamically balancing the load during the fault simulation process is used. The proposed dynamic fault simulation approach on the Single-Chip Cloud Computer shows up to 45X speedup compared to a serial fault simulation approach. Many-core systems can draw enormous amounts of power, and if this power is not controlled properly, the system might get damaged. One way to manage power is to set power budget for the system. But if this power is drawn by just few cores of the many, these few cores get extremely hot and might get damaged. Due to increase in power density multiple thermal sensors are deployed on the chip area to provide realtime temperature feedback for thermal management techniques. Thermal sensor accuracy is extremely prone to intra-die process variation and aging phenomena. These factors lead to a situation where thermal sensor values drift from the nominal values. This necessitates efficient calibration techniques to be applied before the sensor values are used. In addition, in modern many-core systems cores have support for dynamic voltage and frequency scaling. Thermal sensors located on cores are sensitive to the core's current voltage level, meaning that dedicated calibration is needed for each voltage level. In this thesis a general-purpose software-based auto-calibration approach is also proposed for thermal sensors to calibrate thermal sensors on different range of voltages.

A functional specification and validation model for networks on chip in the ACL2 logic

International audience

Optimisation tools for flip-chip design

Abstract not available

TAXONOMY, MORPHOLOGY, AND RNA-SEQ TRANSCRIPTOMICS OF THE CUBOZOAN ALATINA ALATA, AN EMERGING MODEL CNIDARIAN

Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.

mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Background The Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis. Results A database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed. Conclusions This study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Portable “lab-on-chip” platform for bovine mastitis diagnosis in raw milk

Tese de Doutoramento em Ciências Veterinárias, Especialidade de Ciências Biológicas e Biomédicas

Structural determination and gynecological tumor diagnosis using antibody chip captured proteins

Purpose: To identify markers for gynecological tumor diagnosis using antibody chip capture. Methods: Marker proteins, including cancer antigen 153 (CA153), CA125, and carcinoembryonic antigen (CEA), were analyzed using antibody chip capture of serum samples. Fifteen agglutinin types that specifically recognized five common glycans (fucose, sialic acid, mannose, N - acetylgalactosamine, and N-acetylglucosamine) were used to detect marker protein glycan levels. The levels of CA153, CA125, and CEA from 49 healthy control samples, 31 breast cancer samples, 24 cervical cancer samples, and 19 ovarian cancer samples were used to measure the glycan levels of these marker proteins. Results: In breast cancer samples, CA153 and CA125 were down-regulated (p < 0.01), while differences in ovarian cancer samples were not statistically significant (p > 0.01). The total accuracy was 85.1 %, with 96.8 % accuracy for breast cancer, 75 % in cervical cancer, and 78.9 % in ovarian cancer. Cross-validation analyses showed that breast cancer had 93.5 % accuracy, cervical cancer was 66.7 %, and ovarian cancer was 68.4 %, leading to 78.4 % total accuracy (58/74). Conclusions: The results indicate that better clinical diagnosis of gynecological tumors can be obtained by monitoring changes in glycan levels of serum proteins and types of proteoglycan changes.

Citrus HLB x Potato "Zebra Chip" in Brazil: Attempting to transmit citrus Candidatus liberibacter spp (asiaticus and americanus) to potato plants.

2009

Strategic Optimization Techniques For FRTU Deployment and Chip Physical Design

Combinatorial optimization is a complex engineering subject. Although formulation often depends on the nature of problems that differs from their setup, design, constraints, and implications, establishing a unifying framework is essential. This dissertation investigates the unique features of three important optimization problems that can span from small-scale design automation to large-scale power system planning: (1) Feeder remote terminal unit (FRTU) planning strategy by considering the cybersecurity of secondary distribution network in electrical distribution grid, (2) physical-level synthesis for microfluidic lab-on-a-chip, and (3) discrete gate sizing in very-large-scale integration (VLSI) circuit. First, an optimization technique by cross entropy is proposed to handle FRTU deployment in primary network considering cybersecurity of secondary distribution network. While it is constrained by monetary budget on the number of deployed FRTUs, the proposed algorithm identi?es pivotal locations of a distribution feeder to install the FRTUs in different time horizons. Then, multi-scale optimization techniques are proposed for digital micro?uidic lab-on-a-chip physical level synthesis. The proposed techniques handle the variation-aware lab-on-a-chip placement and routing co-design while satisfying all constraints, and considering contamination and defect. Last, the first fully polynomial time approximation scheme (FPTAS) is proposed for the delay driven discrete gate sizing problem, which explores the theoretical view since the existing works are heuristics with no performance guarantee. The intellectual contribution of the proposed methods establishes a novel paradigm bridging the gaps between professional communities.