IN-SITU TEM PLASMA CHIP NANOFABRICATION AND CHARACTERIZATION

A silicon-based microcell was fabricated with the potential for use in in-situ transmission electron microscopy (TEM) of materials under plasma processing. The microcell consisted of 50 nm-thick film of silicon nitride observation window with 60μm distance between two electrodes. E-beam scattering Mont Carlo simulation showed that the silicon nitride thin film would have very low scattering effect on TEM primary electron beam accelerated at 200 keV. Only 4.7% of primary electrons were scattered by silicon nitride thin film and the Ar gas (60 μm thick at 1 atm pressure) filling the space between silicon nitride films. Theoretical calculation also showed low absorption of high-energy e-beam electrons. Because the plasma cell needs to survive the high vacuum TEM chamber while holding 1 atm internal pressure, a finite element analysis was performed to find the maximum stress the low-stress silicon nitride thin film experienced under pressure. Considering the maximum burst stress of low-stress silicon nitride thin film, the simulation results showed that the 50 nm silicon nitride thin film can be used in TEM under 1 atm pressure as the observation window. Ex-situ plasma generation experiment demonstrated that air plasma can be ignited at DC voltage of 570. A Scanning electron microscopy (SEM) analysis showed that etching and deposition occurred during the plasma process and larger dendrites formed on the positive electrode.

Influence of hormone replacement therapy on proteomic pattern in serum of postmenopausal women

OBJECTIVES: Proteomics approaches to cardiovascular biology and disease hold the promise of identifying specific proteins and peptides or modification thereof to assist in the identification of novel biomarkers. METHOD: By using surface-enhanced laser desorption and ionization time of flight mass spectroscopy (SELDI-TOF-MS) serum peptide and protein patterns were detected enabling to discriminate between postmenopausal women with and without hormone replacement therapy (HRT). RESULTS: Serum of 13 HRT and 27 control subjects was analyzed and 42 peptides and proteins could be tentatively identified based on their molecular weight and binding characteristics on the chip surface. By using decision tree-based Biomarker Patternstrade mark Software classification and regression analysis a discriminatory function was developed allowing to distinguish between HRT women and controls correctly and, thus, yielding a sensitivity of 100% and a specificity of 100%. The results show that peptide and protein patterns have the potential to deliver novel biomarkers as well as pinpointing targets for improved treatment. The biomarkers obtained represent a promising tool to discriminate between HRT users and non-users. CONCLUSION: According to a tentative identification of the markers by their molecular weight and binding characteristics, most of them appear to be part of the inflammation induced acute-phase response

Cell force measurements in 3D microfabricated environments based on compliant cantilevers.

We report the fabrication, functionalization and testing of microdevices for cell culture and cell traction force measurements in three-dimensions (3D). The devices are composed of bent cantilevers patterned with cell-adhesive spots not lying on the same plane, and thus suspending cells in 3D. The cantilevers are soft enough to undergo micrometric deflections when cells pull on them, allowing cell forces to be measured by means of optical microscopy. Since individual cantilevers are mechanically independent of each other, cell traction forces are determined directly from cantilever deflections. This proves the potential of these new devices as a tool for the quantification of cell mechanics in a system with well-defined 3D geometry and mechanical properties.

Wattles in goats are associated with the FMN1/GREM1 region on chromosome 10.

The presence of congenital appendages (wattles) on the throat of goats is supposed to be under genetic control with a dominant mode of inheritance. Wattles contain a cartilaginous core covered with normal skin resembling early stages of extremities. To map the dominant caprine wattles (W) locus, we collected samples of 174 goats with wattles and 167 goats without wattles from nine different Swiss goat breeds. The samples were genotyped with the 53k goat SNP chip for a subsequent genome-wide association study. We obtained a single strong association signal on chromosome 10 in a region containing functional candidate genes for limb development and outgrowth. We sequenced the whole genomes of an informative family trio containing an offspring without wattles and its heterozygous parents with wattles. In the associated goat chromosome 10 region, a total of 1055 SNPs and short indels perfectly co-segregate with the W allele. None of the variants were perfectly associated with the phenotype after analyzing the genome sequences of eight additional goats. We speculate that the causative mutation is located in one of the numerous gaps in the current version of the goat reference sequence and/or represents a larger structural variant which influences the expression of the FMN1 and/or GREM1 genes. Also, we cannot rule out possible genetic or allelic heterogeneity. Our genetic findings support earlier assumptions that wattles are rudimentary developed extremities.

Genome-wide association studies based on sequence-derived genotypes reveal new QTL associated with conformation and performance traits in the Franches-Montagnes horse breed

To identify novel quantitative trait loci (QTL) within horses, we performed genome-wide association studies (GWAS) based on sequence-level genotypes for conformation and performance traits in the Franches-Montagnes (FM) horse breed. Sequence-level genotypes of FM horses were derived by re-sequencing 30 key founders and imputing 50K data of genotyped horses. In total, we included 1077 FM horses genotyped for ~4 million SNPs and their respective de-regressed breeding values of the traits in the analysis. Based on this dataset, we identified a total of 14 QTL associated with 18 conformation traits and one performance trait. Therefore, our results suggest that the application of sequence-derived genotypes increases the power to identify novel QTL which were not identified previously based on 50K SNP chip data.

Memory performance of and-parallel prolog on shared-memory architectures

The goal of the RAP-WAM AND-parallel Prolog abstract architecture is to provide inference speeds significantly beyond those of sequential systems, while supporting Prolog semantics and preserving sequential performance and storage efficiency. This paper presents simulation results supporting these claims with special emphasis on memory performance on a two-level sharedmemory multiprocessor organization. Several solutions to the cache coherency problem are analyzed. It is shown that RAP-WAM offers good locality and storage efficiency and that it can effectively take advantage of broadcast caches. It is argued that speeds in excess of 2 ML IPS on real applications exhibiting medium parallelism can be attained with current technology.

Integrated luminescent chemical microsensors based on GaN LEDs for security applications using smartphones

Development of PCB-integrateable microsensors for monitoring chemical species is a goal in areas such as lab-on-a-chip analytical devices, diagnostics medicine and electronics for hand-held instruments where the device size is a major issue. Cellular phones have pervaded the world inhabitants and their usefulness has dramatically increased with the introduction of smartphones due to a combination of amazing processing power in a confined space, geolocalization and manifold telecommunication features. Therefore, a number of physical and chemical sensors that add value to the terminal for health monitoring, personal safety (at home, at work) and, eventually, national security have started to be developed, capitalizing also on the huge number of circulating cell phones. The chemical sensor-enabled “super” smartphone provides a unique (bio)sensing platform for monitoring airborne or waterborne hazardous chemicals or microorganisms for both single user and crowdsourcing security applications. Some of the latest ones are illustrated by a few examples. Moreover, we have recently achieved for the first time (covalent) functionalization of p- and n-GaN semiconductor surfaces with tuneable luminescent indicator dyes of the Ru-polypyridyl family, as a key step in the development of innovative microsensors for smartphone applications. Chemical “sensoring” of GaN-based blue LED chips with those indicators has also been achieved by plasma treatment of their surface, and the micrometer-sized devices have been tested to monitor O2 in the gas phase to show their full functionality. Novel strategies to enhance the sensor sensitivity such as changing the length and nature of the siloxane buffer layer are discussed in this paper.

Methodologies for implement video decoders over multiprocessor platforms

The latest video coding standards developed, like HEVC (High Efficiency Video Coding, approved in January 2013), require for their implementation the use of devices able to support a high computational load. Considering that currently it is not enough the usage of one unique Digital Signal Processor (DSP), multicore devices have appeared recently in the market. However, due to its novelty, the working methodology that allows produce solutions for these configurations is in a very initial state, since currently the most part of the work needs to be performed manually. In consequence, the objective set consists on finding methodologies that ease this process. The study has been focused on extend a methodology, under development, for the generation of solutions for PCs and embedded systems. During this study, the standards RVC (Reconfigurable Video Coding) and HEVC have been employed, as well as DSPs of the Texas Instruments company. In its development, it has been tried to address all the factors that influence both the development and deployment of these new implementations of video decoders, ranging from tools up to aspects of the partitioning of algorithms, without this can cause a drop in application performance. The results of this study are the description of the employed methodology, the characterization of the software migration process and performance measurements for the HEVC standard in an RVC-based implementation. RESUMEN Los estándares de codificación de vídeo desarrollados más recientemente, como HEVC (High Efficiency Video Coding, aprobado en enero de 2013), requieren para su implementación el uso de dispositivos capaces de soportar una elevada carga computacional. Teniendo en cuenta que actualmente no es suficiente con utilizar un único Procesador Digital de Señal (DSP), han aparecido recientemente dispositivos multinúcleo en el mercado. Sin embargo, debido a su novedad, la metodología de trabajo que permite elaborar soluciones para tales configuraciones se encuentra en un estado muy inicial, ya que actualmente la mayor parte del trabajo debe realizarse manualmente. En consecuencia, el objetivo marcado consiste en encontrar metodologías que faciliten este proceso. El estudio se ha centrado en extender una metodología, en desarrollo, para la generación de soluciones para PC y sistemas empotrados. Durante dicho estudio se han empleado los estándares RVC (Reconfigurable Video Coding) y HEVC, así como DSPs de la compañía Texas Instruments. En su desarrollo se ha tratado de atender a todos los factores que influyen tanto en el desarrollo como en la puesta en marcha de estas nuevas implementaciones de descodificadores de vídeo; abarcando desde las herramientas a utilizar hasta aspectos del particionado de los algoritmos, sin que por ello se produzca una reducción en el rendimiento de las aplicaciones. Los resultados de este estudio son una descripción de la metodología empleada, la caracterización del proceso de migración de software, y medidas de rendimiento para el estándar HEVC en una implementación basada en RVC.

A self-adaptive image processing application based on evolvable and scalable hardware

Evolvable Hardware (EH) is a technique that consists of using reconfigurable hardware devices whose configuration is controlled by an Evolutionary Algorithm (EA). Our system consists of a fully-FPGA implemented scalable EH platform, where the Reconfigurable processing Core (RC) can adaptively increase or decrease in size. Figure 1 shows the architecture of the proposed System-on-Programmable-Chip (SoPC), consisting of a MicroBlaze processor responsible of controlling the whole system operation, a Reconfiguration Engine (RE), and a Reconfigurable processing Core which is able to change its size in both height and width. This system is used to implement image filters, which are generated autonomously thanks to the evolutionary process. The system is complemented with a camera that enables the usage of the platform for real time applications.

Development of a versatile biotinylated material based on SU-8

The negative epoxy-based SU-8 photoresist has a wide variety of applications within the semiconductor industry, photonics and lab-on-a-chip devices, and it is emerging as an alternative to silicon-based devices for sensing purposes. In the present work, biotinylation of the SU-8 polymer surface promoted by light is reported. As a result, a novel, efective, and low-cost material, focusing on the immobilization of bioreceptors and consequent biosensing, is developed. This material allows the spatial discrimination depending on the irradiation of desired areas. The most salient feature is that the photobiotin may be directly incorporated into the SU-8 curing process, consequently reducing time and cost. The potential use of this substrate is demonstrated by the immunoanalytical detection of the synthetic steroid gestrinone, showing excellent performances. Moreover, the naked eye biodetection due to the transparent SU-8 substrate, and simple instrumental quantication are additional advantages.

Automated parallel DNA sequencing on multiple channel microchips

We report automated DNA sequencing in 16-channel microchips. A microchip prefilled with sieving matrix is aligned on a heating plate affixed to a movable platform. Samples are loaded into sample reservoirs by using an eight-tip pipetting device, and the chip is docked with an array of electrodes in the focal plane of a four-color scanning detection system. Under computer control, high voltage is applied to the appropriate reservoirs in a programmed sequence that injects and separates the DNA samples. An integrated four-color confocal fluorescent detector automatically scans all 16 channels. The system routinely yields more than 450 bases in 15 min in all 16 channels. In the best case using an automated base-calling program, 543 bases have been called at an accuracy of >99%. Separations, including automated chip loading and sample injection, normally are completed in less than 18 min. The advantages of DNA sequencing on capillary electrophoresis chips include uniform signal intensity and tolerance of high DNA template concentration. To understand the fundamentals of these unique features we developed a theoretical treatment of cross-channel chip injection that we call the differential concentration effect. We present experimental evidence consistent with the predictions of the theory.

Effects of receptor dimerization on the interaction between the class I major histocompatibility complex-related Fc receptor and IgG.

The neonatal Fc receptor (FcRn) transports maternal IgG from ingested milk in the gut to the bloodstream of newborn mammals. An FcRn dimer was observed in crystals of the receptor alone and of an FcRn-Fc complex, but its biological relevance was unknown. Here we use surface plasmon resonance-based biosensor assays to assess the role of FcRn dimerization in IgG binding. We find high-affinity IgG binding when FcRn is immobilized on a biosensor chip in an orientation facilitating dimerization but not when its orientation disrupts dimerization. This result supports a model in which IgG-induced dimerization of FcRn is relevant for signaling the cell to initiate endocytosis of the IgG-FcRn complex.

Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides.

The challenge of the Human Genome Project is to increase the rate of DNA sequence acquisition by two orders of magnitude to complete sequencing of the human genome by the year 2000. The present work describes a rapid detection method using a two-dimensional optical wave guide that allows measurement of real-time binding or melting of a light-scattering label on a DNA array. A particulate label on the target DNA acts as a light-scattering source when illuminated by the evanescent wave of the wave guide and only the label bound to the surface generates a signal. Imaging/visual examination of the scattered light permits interrogation of the entire array simultaneously. Hybridization specificity is equivalent to that obtained with a conventional system using autoradiography. Wave guide melting curves are consistent with those obtained in the liquid phase and single-base discrimination is facile. Dilution experiments showed an apparent lower limit of detection at 0.4 nM oligonucleotide. This performance is comparable to the best currently known fluorescence-based systems. In addition, wave guide detection allows manipulation of hybridization stringency during detection and thereby reduces DNA chip complexity. It is anticipated that this methodology will provide a powerful tool for diagnostic applications that require rapid cost-effective detection of variations from known sequences.

"Chip's" dogs : a collection of humorous drawings /

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