gebhart/patrepeval huggingface dataset:
Elevated Co-Silicide for sub-100nm High Performance and RF CMOS (2002)

In this paper we show that the ultimate limit of Cosilicide expected for 100nm CMOS technology node can be postponed to the next generation thanks to its elevation by selective epitaxy. We demonstrate that conventional Co-silicide combined with elevated S/D can be still compatible with the junctions representative for sub-50nm CMOS devices. Moreover, elevated silicide enables reducing sheet resistance without compromising the junction leakage and degrading transistor performance. Thanks to high drive current and reduced gate sheet resistance excellent RF characteristics were obtained. 70nm NMOS devices exhibit FT of 150GHz and Fmax of 70GHz.
Transcript Analysis of Genes Encoding a Family 61 Endoglucanase and a Putative Membrane-Anchored Family 9 Glycosyl Hydrolase from <i>Phanerochaete chrysosporium</i> (2002)

Phanerochaete chrysosporium cellulase genes were cloned and characterized. The cel61A product was structurally similar to fungal endoglucanases of glycoside hydrolase family 61, whereas the cel9A product revealed similarities to Thermobifida fusca Cel9A (E4), an enzyme with both endo- and exocellulase characteristics. The fungal Cel9A is apparently a membrane-bound protein, which is very unusual for microbial cellulases. Transcript levels of both genes were substantially higher in cellulose-grown cultures than in glucose-grown cultures. These results show that P. chrysosporium possesses a wide array of conventional and unconventional cellulase genes.
Multiple Factors Confer Specific Cdc42 and Rac Protein Activation by Dedicator of Cytokinesis (DOCK) Nucleotide Exchange Factors (2011)

DOCK (dedicator of cytokinesis) guanine nucleotide exchange factors (GEFs) activate the Rho-family GTPases Rac and Cdc42 to control cell migration, morphogenesis, and phagocytosis. The DOCK A and B subfamilies activate Rac, whereas the DOCK D subfamily activates Cdc42. Nucleotide exchange is catalyzed by a conserved DHR2 domain (DOCK(DHR2)). Although the molecular basis for DOCK(DHR2)-mediated GTPase activation has been elucidated through structures of a DOCK9(DHR2)-Cdc42 complex, the factors determining recognition of specific GTPases are unknown. To understand the molecular basis for DOCK-GTPase specificity, we have determined the crystal structure of DOCK2(DHR2) in complex with Rac1. DOCK2(DHR2) and DOCK9(DHR2) exhibit similar tertiary structures and homodimer interfaces and share a conserved GTPase-activating mechanism. Multiple structural differences between DOCK2(DHR2) and DOCK9(DHR2) account for their selectivity toward Rac1 and Cdc42. Key determinants of selectivity of Cdc42 and Rac for their cognate DOCK(DHR2) are a Phe or Trp residue within β3 (residue 56) and the ability of DOCK proteins to exploit differences in the GEF-induced conformational changes of switch 1 dependent on a divergent residue at position 27. DOCK proteins, therefore, differ from DH-PH GEFs that select their cognate GTPases through recognition of structural differences within the β2/β3 strands.
Chronic Vascular Inflammation in Patients With Type 2 Diabetes (2005)

Endothelial cells can be harvested during cardiac catheterization and can be characterized with respect to molecular phenotypes under the influence of both genetic and environmental factors. Induction of RAGE and MCP-1 transcripts in patients with diabetes supports a role of chronic vascular inflammation in macrovascular complications.
Variation-aware voltage island formation for power efficient near-threshold manycore architectures (2014)

The power-wall problem and its dual utilization-wall problem are considered among the main barriers to feasible/efficient scaling in the manycore era. Several researchers have proposed the usage of aggressive voltage scaling techniques at the near-threshold voltage region, promising significant improvements in power efficiency at the expense of reduced performance values and higher sensitivity to process parametric variations. In this paper, we introduce a variability-aware framework for exploring the potential power-efficiency of the Near Threshold Computing (NTC) under performance constraints. We propose and analyze the usage of fine-grained voltage islands to cope with the increased effect of variability problem in the NTC region. For the considered workloads, we found that the power impact of fine-grained voltage islands formation can be up to 35% for a 128-core chip operating at NTC region, while the adoption of a variability aware technique can bring to a power reduction of up to 43% with respect to a variability unaware technique. Finally, we show that voltage regulator's complexity, in terms of voltage quantization levels, has a very low effect on the power efficiency at NTC, making in that way the usage of voltage islands a feasible solution for copying with variability <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> .
Bcl-2 Modulation to Activate Apoptosis in Prostate Cancer (2009)

Apoptosis resistance is a hallmark of cancer linked to disease progression and treatment resistance, which has led to the development of anticancer therapeutics that restore apoptotic function. Antiapoptotic Bcl-2 is frequently overexpressed in refractory prostate cancer and increased following standard hormonal therapy and chemotherapy; however, the rationally designed Bcl-2 antagonist, ABT-737, has not shown single agent apoptosis-promoting activity against human prostate cancer cell lines. This is likely due to the coordinate expression of antiapoptotic, Bcl-2-related Mcl-1 that is not targeted by ABT-737. We developed a mouse model for prostate cancer in which apoptosis resistance and tumorigenesis were conferred by Bcl-2 expression. Combining ABT-737 with agents that target Mcl-1 sensitized prostate cancer cell lines with an apoptotic block to cell death in vitro. In mice in vivo, ABT-737 showed single agent efficacy in prostate tumor allografts in which tumor cells are under hypoxic stress. In human prostate cancer tissue, examined using a novel tumor explant system designated Tumor Tissue Assessment for Response to Chemotherapy, combination chemotherapy promoted efficient apoptosis. Thus, rational targeting of both the Bcl-2 and Mcl-1 mechanisms of apoptosis resistance may be therapeutically advantageous for advanced prostate cancer.
Warehouse inventory management system using IoT and open source framework (2018)

In general, warehouses are used to store goods or products. In the Warehouses, if the user wants to locate any product it is very difficult, because user have to do a detailed search manually in all the available stockrooms this requires a lot of effort. So to avoid this problem the warehouse inventory management system is very helpful because it maintains the detailed product information and tells us in which stockroom the product is present. The warehouse inventory management system is playing a significant aspect in many productions and goods based methodology. Though there are many wireless communication technologies the RFID suits the best for the warehouse inventory management system. The tag information is transferred from the transmitter section to open source hardware via a wireless link with the aid of internet. The warehouse inventory management system built on the architecture of the Internet of Things is developed to track the products attached to the tags with product information and their respective time stamps for further verification. The Raspberry Pi acts as a central server, monitoring all the information. The total system gives an archetype to correspond the information flow and material flow. The web page which is built in accordance to provide convenient and an interface to the user to track the products. The developed system results a very low cost system and works dynamically compared with the existing present warehouse inventory management systems. Keywords: IoT, RFID, Warehouse inventory management system, Wi-Fi module, Open source hardware
H.264 Intra Prediction Architecture Optimization (2007)

This paper proposes an optimized H.264 Intra Prediction arithmetic to reduce the time required to complete the intra prediction by saving ninety percent waste time during the process of intra prediction. Firstly, the 16×16 luminance prediction can be decomposed equally into 16 parts and inserted into the same macro-block's 4×4 luminance prediction to save the 16×16 luminance prediction time in one macro-block's luminance prediction. Then, by means of changing the computation sequence of 4×4 luminance prediction, a large amount of waiting time between 4×4 blocks' luminance predictions can be further removed. Almost all the waste time can be reused or eliminated by these optimizations. At the last part of this paper, an optimized hardware implementation aiming at fitting to the whole H.264 video coding system and a method to realize 16×16 luminance DC prediction on it are proposed.
Fast Iterative Graph Computation: A Path Centric Approach (2014)

Large scale graph processing represents an interesting challenge due to the lack of locality. This paper presents Path Graph for improving iterative graph computation on graphs with billions of edges. Our system design has three unique features: First, we model a large graph using a collection of tree-based partitions and use an path-centric computation rather than vertex-centric or edge-centric computation. Our parallel computation model significantly improves the memory and disk locality for performing iterative computation algorithms. Second, we design a compact storage that further maximize sequential access and minimize random access on storage media. Third, we implement the path-centric computation model by using a scatter/gather programming model, which parallels the iterative computation at partition tree level and performs sequential updates for vertices in each partition tree. The experimental results show that the path-centric approach outperforms vertex centric and edge-centric systems on a number of graph algorithms for both in-memory and out-of-core graphs.
A study of cross-bridge kelvin resistor structures for reliable measurement of low contact resistances (2008)

The parasitic factors that strongly influence the measurement accuracy of cross-bridge Kelvin Resistor (CBKR) structures for low specific contact resistances (p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> ) have been extensively discussed during last few decades and the minimum of the p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> value, which could be accurately extracted, was estimated. We fabricated a set of various metal-to-metal CBKR structures with different geometries, i.e., shapes and dimensions, to confirm this limit experimentally. As a result, a model was developed to account for the actual current flow and a method for reliable p <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> extraction was created. It was found that in our case of metal-to- metal contacts, the measured CBKR contact resistance was determined by the dimensions of the two-metal stack in the area of contact and sheet resistances of the metals used.
X-Ray Amplification from a Raman Free-Electron Laser (2012)

We demonstrate that a mm-scale free-electron laser can operate in the x-ray range, in the interaction between a moderately relativistic electron bunch, and a transverse high intensity optical lattice. The corrugated light-induced ponderomotive potential acts simultaneously as a guide and as a low-frequency wiggler, triggering stimulated Raman scattering. The gain law in the small signal regime is derived in a fluid approach, and confirmed from particle-in-cell simulations. We describe the nature of bunching, and discuss the saturation properties. The resulting all-optical Raman x-ray laser opens perspectives for ultracompact coherent light sources up to the hard x-ray range.
Spectral statistics and scattering resonances of complex primes arrays (2018)

We introduce a class of aperiodic arrays of electric dipoles generated from the distribution of prime numbers in complex quadratic fields (Eisenstein and Gaussian primes) as well as quaternion primes (Hurwitz and Lifschitz primes), and study the nature of their scattering resonances using the vectorial Green's matrix method. In these systems we demonstrate several distinctive spectral properties, such as the absence of level repulsion in the strongly scattering regime, critical statistics of level spacings, and the existence of critical modes, which are extended fractal modes with long lifetimes not supported by either random or periodic systems. Moreover, we show that one can predict important physical properties, such as the existence spectral gaps, by analyzing the eigenvalue distribution of the Green's matrix of the arrays in the complex plane. Our results unveil the importance of aperiodic correlations in prime number arrays for the engineering of gapped photonic media that support far richer mode localization and spectral properties compared to usual periodic and random media.
Integration and innovation in the nanoelectronics era (2005)

Demand for electronics continues to grow as new products combine and enhance computing, communications, and digital capabilities. Hardware and software are evolving to enable new applications and usage modes, by offering features such as multitasking, parallel processing, mobility and wireless connectivity. Integration at both component and product platform levels, and efficient use of power, will become more important. These call for holistic solutions involving systems, circuits, processes, devices, and packaging. Many techniques to improve power efficiency have been developed and more will emerge. Silicon technology and scaling remain keys to progress, with transistors and circuit elements already at nanoscale dimensions. Innovation will accelerate as nanotechnology further renews and extends silicon technology. Skillful integration of new materials, processes, and device structures will be essential. Successful nanoelectronics companies will excel in innovation and integration, extend Moore's law into and beyond the next decade, and drive the development of future growth opportunities.
Clustering Method Evaluation for Hidden Markov Model Based Real-Time Gesture Recognition (2009)

This paper deals with the development of high performance real-time system for complex dynamic gesture recognition. The various motion features are extracted from the video frames which are used by HMM classifier. We used several clustering techniques for performance evaluation of the classifier. Our system vectorises gestures into sequential symbols both for training and testing. We found very encouraging results and the proposed method has potential application in the field of human machine interaction.
Relative Abundance of<i>Bacteroides</i>spp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension (2008)

A molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominant Bacteroides spp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14 Bacteroides spp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species like B. vulgatus, B. thetaiotaomicron, B. caccae, B. uniformis, B. fragilis, B. eggerthii, and B. massiliensis could be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species like B. pyogenes, B. salyersiae, and B. nordii were detected only collectively using a primer that targeted the B. fragilis subgroup (corresponding to approximately 0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., most Bacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances of Bacteroides spp. predominant in fecal samples.
Analysis of the Interaction Between<i>Xanthomonas oryzae</i>pv.<i>oryzae</i>and the Rice Cultivars IR24 and IRBB21 (1994)

Xanthomonas oryzae pv. oryzae causes bacterial blight of rice, and interactions between this pathogen and its host occur in a gene-for-gene manner. In contrast to other resistance genes, the dominant locus Xa21 confers resistance to all Indian and Philippine races of X. o. oryzae that have been examined. In this study, multiplication of X. o. oryzae and subsequent disease development were comparable in cultivar IRBB21 possessing Xa-21 and in the susceptible rice cultivar IR24 when plants were inoculated prior to 21 days postemergence. Resistance conveyed by Xa-21 was evident in 21-day-old plants, and the level of resistance increased with plant maturity [...]
Applications of Chelating Agents in the Upstream Oil and Gas Industry: A Review (2020)

Chelating agents show very effective performance in different applications in the upstream oil and gas industry. This study presents a critical review of the application of chelating agents in acidizing, scale removal, filter cake removal, wettability alteration, enhanced oil recovery (EOR), and hydraulic fracturing treatments. The advantages and disadvantages of using several types of chelating agents for improving the well/reservoir productivity and enhancing the oil recovery from sandstone and carbonate reservoirs are discussed. Also, detailed comparisons between different chelating agents and their applications in many oil and gas areas are presented. Moreover, the combination of chelating agents with different chemicals to achieve better performance is addressed. Hydroxy amino carboxylic acids [such as ethylenediaminetetraacetic acid (EDTA) and glutamic acid diacetic acid (GLDA)] have replaced conventional acids, such as hydrochloric acid (HCl), hydrofluoric acid (HF), and organic acids, at high temperature and salinity conditions to stimulate carbonate and sandstone reservoirs without any side effects on the formation integrity. Furthermore, diethylenetriaminepentaacetic acid (DTPA) and GLDA are effective in removing different types of scales, such as carbonate, sulfate, and sulfides, without releasing hydrogen sulfide (H2S) and using corrosion inhibitors. Also, DTPA, EDTA, and GLDA are very active in dissolving filter cake layers formed by different drilling fluids. Aminopolycarboxylic groups can be injected into sandstone and carbonate reservoirs to adjust the wettability conditions and enhance oil recovery. Chelating agents, such as GLDA, EDTA, and DTPA, optimize the fracture conductivity and, meanwhile, minimize the number of additives in hydraulic fracturing, which significantly cut the cost of the operation. Overall, chelating agents are economically attractive chemicals for various upstream operations since produced, and seawater can be used without further treatment.
High-throughput bioinformatics and the rapid growth of human genomic datasets in research (2015)

These slides were presented at the "Open data and you" workshop held during International Open Access Week at ANU, 20 October 2015.
Immunosuppressive human anti‐lymphocyte autoantibodies specific for the type 1 sphingosine 1‐phosphate receptor (2009)

Anti-lymphocyte antibodies (Abs) that suppress T-cell chemotactic and other responses to sphingosine 1-phosphate (S1P), but not to chemokines, were found in a lymphopenic patient with recurrent infections. Lymphocyte type 1 S1P receptor (S1P(1)) that transduces S1P chemotactic stimulation was recognized by patient Abs in Western blots of T cells, S1P(1) transfectants, and S1P(1)-hemagglutinin purified by monoclonal anti-hemagglutinin Ab absorption. The amino terminus of S1P(1), but not any extracellular loop, prevented anti-S1P(1) Ab suppression of S1P(1) signaling and T-cell chemotaxis to S1P. Human purified anti-S1P(1) Abs decreased mouse blood lymphocyte levels by a mean of 72%, suppressed mouse T-cell chemotaxis to S1P in vivo, and significantly reduced the severity of dextran sodium sulfate-induced colitis in mice. Human Abs to the amino terminus of S1P(1) suppress T-cell trafficking sufficiently to impair host defense and provide therapeutic immunosuppression.
Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits (2010)

Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (<0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of brain regions in large animals such as non-human primates, but may also open up a clinical translational path for cell-specific optical control prosthetics, whose precision may enable improved treatment of intractable brain disorders. Finally, such devices as described here may facilitate precisely-timed fluidic delivery of other payloads, such as stem cells and pharmacological agents, to 3-dimensional structures, in an easily user-customizable fashion.