gebhart/patrepeval huggingface dataset:
The Rechargeability of Silicon-Air Batteries (2012)

Abstract : This project aimed to investigate silicon-air batteries as a rechargeable power source of high energy density. Si-air batteries are an attractive possibility due to high charge capacity (approximately 4 times higher than conventional Zn-air, and nearly that of Li-air) with less safety and environmental concerns. Studies of Si-air electrochemical cells using both liquid room-temperature ionic liquid as electrolyte and a gel polymer electrolyte (formed by incorporating an ionic liquid electrolyte into polymeric matrix) were undertaken. Research challenges included overcoming the SiO2 reaction product from clogging the porous carbon-air electrode, reducing the SiO2 byproduct during recharging and redepositing the Si ions in a manner to permit continued operation without loss of energy density, and avoiding the build-up of water byproduct in the electrolyte during reduction during recharge phase. This last issue was seen as a critical roadblock for the continued development at this time, although production of H2O during operation could make an Si-air electrochemical cell a source of water for other applications.
Hypermethylation of the <i>GABRE∼miR-452∼miR-224</i> Promoter in Prostate Cancer Predicts Biochemical Recurrence after Radical Prostatectomy (2014)

The GABRE∼miR-452∼miR-224 locus is downregulated and hypermethylated in prostate cancer and is a new promising epigenetic candidate biomarker for prostate cancer diagnosis and prognosis. Tumor-suppressive functions of the intronic miR-224 and miR-452 were demonstrated in two prostate cancer cell lines, suggesting that epigenetic silencing of GABRE∼miR-452∼miR-224 may be selected for in prostate cancer.
Potential benefits and risks of clinical xenotransplantation (2012)

Abstract: The transplantation of organs and cells from pigs into humans could overcome the critical and continuing problem of the lack of availability of deceased human organs and cells for clinical transplantation. Developments in the genetic engineering of pigs have enabled considerable progress to be made in the experimental laboratory in overcoming the immune barriers to successful xenotransplantation. With regard to pig organ xenotransplantation, antibody- and cell-mediated rejection have largely been overcome, and the current major barrier is the development of coagulation dysregulation. This is believed to be due to a combination of immune activation of the vascular endothelial cells of the graft and molecular incompatibilities between the pig and primate coagulation–anticoagulation systems. Pigs with new genetic modifications specifically directed to this problem are now becoming available. With regard to less complex tissues, such as islets (for the treatment of diabetes), neuronal cells (for the treatment of Parkinson's disease), and corneas, the remaining barriers are less problematic, and graft survival in nonhuman primate models extends for >1 year in all three cases. In planning the initial clinical trials, consideration will be concentrated on the risk–benefit ratio, based to a large extent on the results of preclinical studies in nonhuman primates. If the benefit to the patient is anticipated to be high, eg, insulin-independent control of glycemia, and the potential risks low, eg, minimal risk of transfer of a porcine infectious agent, then a clinical trial would be justified. Keywords: infection, pigs, genetically-engineered, xenotransplantation, islets, xenotransplantation, organs
Variable-Orifice Oxygen-Flow Regulator (1992)

Variable-orifice flow-control valve switchable between fully and partially opened positions. Straight-through flow patch minimizes high-speed impacts of entrained particles, reducing erosion and accidental ignition. Designed for use with oxygen, also used with variety of liquids and gases.
PSA-activated proaerolysin as a prostate specific cancer therapy (2006)

2178 Native proaerolysin is a channel-forming bacterial protoxin that is activated upon cleavage by host proteases such as furin. PRX302 is an engineered form of proaerolysin in which the furin cleavage site has been replaced with a sequence known to be preferred by the protease, prostate specific antigen (PSA). The goal of this study was to examine the suitability of PRX302 for use as a therapeutic agent in prostate cancer and benign prostatic hyperplasia as assessed by comparing proteolytic activation of PRX302 and native proaerolysin and their cytotoxicity towards PSA-producing and non-producing cell lines. Modification of native proaerolysin to PRX302 markedly altered the activity of each of the proteases (chymotrypsin, trypsin, furin, and thrombin) tested toward this protein. Activity toward proaerolysin was decreased 10-100 fold for each of the proteases tested except PSA, which showed a 4-fold increase in activity against the modified protein. Of all enzymes tested, only PSA cleaved more PRX302 than proaerolysin. Indeed the ratio of PRX302 to proaerolysin cleavage by PSA was more than 40 times that of any other protease tested. As expected, native proaerolysin was effectively cytotoxic at low pM concentrations in all cells tested (LNCaP, DU145, CWR22Rvi, PC3, PrEC, and RWPE2-W99). However, PRX302 was cytotoxic at low pM concentration only in normal (PrEC) and papilloma- transfected (RWPE2-W99) prostate cells, both of which produce active PSA. In conclusion, PRX302 appears to be preferentially activated by PSA and selectively kills PSA producing cells. PRX302 deserves further study for possible treatment of prostate cancer and benign prostatic hyperplasia.
On-chip repair and an ATE independent fusing methodology (2003)

This paper describes a novel on chip repair system designed for ATE independent application on many unique very dense ASIC devices in a high turnover environment. During test, the system controls on chip built-in self-test (BIST) engines, collects and compresses repair data, programs fuses and finally decompresses and reloads the repair data for post fuse testing. In end use applications this system decompresses and loads the repair data at power-up or at the request of the system.
Preclinical development of an oral anti- <i>Wolbachia</i> macrolide drug for the treatment of lymphatic filariasis and onchocerciasis (2019)

There is an urgent global need for a safe macrofilaricide drug to accelerate elimination of the neglected tropical diseases onchocerciasis and lymphatic filariasis. From an anti-infective compound library, the macrolide veterinary antibiotic, tylosin A, was identified as a hit against <i>Wolbachia</i> This bacterial endosymbiont is required for filarial worm viability and fertility and is a validated target for macrofilaricidal drugs. Medicinal chemistry was undertaken to develop tylosin A analogs with improved oral bioavailability. Two analogs, A-1535469 and A-1574083, were selected. Their efficacy was tested against the gold-standard second-generation tetracycline antibiotics, doxycycline and minocycline, in mouse and gerbil infection models of lymphatic filariasis (<i>Brugia malayi</i> and <i>Litomosoides sigmodontis</i>) and onchocerciasis (<i>Onchocerca ochengi</i>). A 1- or 2-week course of oral A-1535469 or A-1574083 provided >90% <i>Wolbachia</i> depletion from nematodes in infected animals, resulting in a block in embryogenesis and depletion of microfilarial worm loads. The two analogs delivered comparative or superior efficacy compared to a 3- to 4-week course of doxycycline or minocycline. A-1574083 (now called ABBV-4083) was selected for further preclinical testing. Cardiovascular studies in dogs and toxicology studies in rats and dogs revealed no adverse effects at doses (50 mg/kg) that achieved plasma concentrations >10-fold above the efficacious concentration. A-1574083 (ABBV-4083) shows potential as an anti-<i>Wolbachia</i> macrolide with an efficacy, pharmacology, and safety profile that is compatible with a short-term oral drug course for treating lymphatic filariasis and onchocerciasis.
Dye-Sensitized TiO<sub>2</sub> Nanotube Solar Cells with Markedly Enhanced Performance via Rational Surface Engineering (2009)

Highly ordered anodic TiO2 nanotube arrays fabricated by electrochemical anodization were sensitized with ruthenium dye N-719 to yield dye-sensitized TiO2 nanotube solar cells. Rational surface treatments on photoanode TiO2 nanotubes markedly improved the device performance. With TiCl4 treatment, in conjunction with oxygen plasma exposure under optimized conditions, dye-sensitized TiO2 nanotube solar cells produced using 14-μm-thick TiO2 nanotube arrays in backside illumination mode subjected to simulated AM 1.5 G irradiation of 100 mW/cm2 exhibited a pronounced power conversion efficiency (PCE) of 7.37%.
Microactuators of thin film shape memory alloy on silicon (1992)

Microns-thick sputtered films of TiNi shape memory alloy deposited on silicon substrates have been capable of forceful electrical actuation. Present devices are made to millimeter scale. Research under way concentrates on reducing component size to hundreds of microns. Combined with springs, orifices, and ports, these devices made miniature valves for pneumatic and fluid control. Design, fabrication, and flow characteristics of a valve of 0.25 cm3 in size are discussed. Other applications for this technology will also be addressed, including microswitches and movable micromirrors.
Micromechanical IBARs: Tunable High-$Q$ Resonators for Temperature-Compensated Reference Oscillators (2010)

This paper presents a unique capacitive micromechanical resonator and oscillator architecture for temperature-compensated frequency references. The I-shaped bulk acoustic resonator (IBAR) is designed to have excellent electrical tunability for temperature compensation (TC) and dynamic frequency control. High quality factor and low motional resistance are also achieved. The applicable range of frequencies is 1-30 MHz, in which quality factors exceeding 100 000 have been measured. Resonator metrics, including the electrostatic tuning coefficient, normalized dynamic stiffness, and relative dynamic compliance, are introduced. A small-signal resistance in the resonator is reported and explained. This unexpected resistance is beneficial for oscillator functionality over a large temperature range. The interface IC, inclusive of all blocks for sustaining oscillations and TC, is also presented. A two-chip 6-MHz oscillator with a temperature stability of 39 ppm over 100°C is demonstrated. The interface IC consumes 1.9 mW.
Folate receptor-β constitutes a marker for human proinflammatory monocytes (2014)

Activated macrophages are commonly involved in the pathogenesis of inflammatory and autoimmune diseases and have been frequently reported to overexpress FR-β. Although FR-targeted therapies aimed at eliminating activated macrophages have shown promise for treating inflammatory diseases, little work has been performed to evaluate whether other hematopoietic cells might also express FR-β. Analysis of peripheral blood cells with a mAb to human FR-β reveals that only monocytes express FR-β. Molecular characterization of these circulating monocytes further demonstrates that solely the classic/proinflammatory subset (CD14(high)CD16(-)) expresses the FR and that only CD14(high)CD16(-) FR-β(+) monocytes also display the ability to bind folate-linked molecules. Confirmation that this subset of monocytes indeed constitutes the proinflammatory subpopulation was obtained by demonstrating coexpression of FR-β with other proinflammatory markers, including CCR2 and HLA-DR. Synovial monocytes from the joints of patients with RA were also shown to express FR-β. As inhibition of the chemotaxis of proinflammatory monocytes into sites of inflammation has been explored frequently as a means of controlling autoimmune diseases, demonstration that FR-β is uniquely expressed on this proinflammatory subpopulation offers a new strategy to suppress migration of inflammatory monocytes into sites of inflammation.
Accelerating Big Data analytics with Collaborative Planning in Teradata Aster 6 (2015)

The volume, velocity, and variety of Big Data necessitate the development of new and innovative data processing software. A multitude of SQL implementations on distributed systems have emerged in recent years to enable large-scale data analysis. User-Defined Table operators (written in procedural languages) embedded in these SQL implementations are a powerful mechanism to succinctly express and perform analytic operations typical in Big Data discovery workloads. Table operators can be easily customized to implement different processing models such as map, reduce and graph execution. Despite an inherently parallel execution model, the performance and scalability of these table operators is greatly restricted as they appear as a black box to a typical SQL query optimizer. The optimizer is not able to infer even the basic properties of table operators, prohibiting the application of optimization rules and strategies. In this paper, we introduce an innovative concept of “Collaborative Planning”, which results in the removal of redundant operations and a more optimal rearrangement of query plan operators. The optimization of the query proceeds through a collaborative exchange between the planner and the table operator. Plan properties and context information of surrounding query plan operations are exchanged between the optimizer and the table operator. Knowing these properties also allows the author of the table operator to optimize its embedded logic. Our main contribution in this paper is the design and implementation of Collaborative Planning in the Teradata Aster 6 system. Using real-world workloads, we show that Collaborative Planning reduces query execution times as much as 90.0% in common use cases, resulting in a 24x speedup.
Integrated Heat Assisted Magnetic Recording Head: Design and Recording Demonstration (2007)

Scaling the areal density, while maintaining a proper balance between media signal-to-noise ratio, thermal stability, and writability, will soon require an alternative recording technology. Heat assisted magnetic recording (HAMR) can achieve this balance by allowing high anisotropy media to be written by heating the media during the writing process (e.g., by laser light) to temporarily lower the anisotropy. Three major challenges of designing a HAMR head that tightly focuses light and collocates it with the magnetic field are discussed: 1) magnetic field delivery; 2) optical delivery; and 3) magnetic and optical field delivery integration. Thousands of these HAMR heads were built into sliders and head-gimbal assemblies, and optical and scanning electron micrograph images are shown. Scanning near-field optical microscopy (SNOM) characterization of the HAMR head shows that the predicted ~ lambda/4 full-width half-maximum (FWHM) spot size can be achieved using 488 nm light (124 nm was achieved). SNOM images also show that wafer level fabricated apertures were able to effectively eliminate sidelobes from the focused spot intensity profile. A magnetic force microscopy image of HAMR media shows that non-HAMR (laser power off) was not able to write transitions in the HAMR specific media even at very high write currents, but transitions could be written using HAMR (laser power on), even at lower write currents. A cross-track profile is shown for a fully integrated HAMR head where the magnetic pole physical width is ~350 nm, but the written track is ~200 nm, which demonstrates HAMR. A HAMR optimization contour shows that there is an optimum write current and laser power and that simply going to the highest write current and laser power does not lead to the best recording. Lastly, some prospects for advancing HAMR are given and a few key problems to be solved are mentioned.
4-D shock-sensing for hard-disk drives (1999)

There is a need for reliable and low-cost shock-sensing in magnetic hard-disk drives to maintain data integrity when a drive is subjected to external shocks. This paper describes a novel method that is both reliable and low-cost, using only the existing head preamp and data channel.
Learning a Generative Model of Images by Factoring Appearance and Shape (2010)

Computer vision has grown tremendously in the past two decades. Despite all efforts, existing attempts at matching parts of the human visual system's extraordinary ability to understand visual scenes lack either scope or power. By combining the advantages of general low-level generative models and powerful layer-based and hierarchical models, this work aims at being a first step toward richer, more flexible models of images. After comparing various types of restricted Boltzmann machines (RBMs) able to model continuous-valued data, we introduce our basic model, the masked RBM, which explicitly models occlusion boundaries in image patches by factoring the appearance of any patch region from its shape. We then propose a generative model of larger images using a field of such RBMs. Finally, we discuss how masked RBMs could be stacked to form a deep model able to generate more complicated structures and suitable for various tasks such as segmentation or object recognition.
A cupredoxin derived peptide inhibits angiogenesis and mammary end bud transformation in vitro. (2006)

A217 The cupredoxins are a family of small, single domain, copper containing redox proteins present in bacteria and plants. We have previously reported that azurin, a cupredoxin isolated from Pseudomonas arugenosum , preferentially penetrates cancer cells, alters cell cycle and induces apoptosis in several human cancer cell lines (Yamada et. al., Proc Natl Acad Sci U S A. 99:14098, 2002), including the human breast cancer cell line, MCF-7, in vitro and in vivo (Punj et. al. Oncogene. 23(:2367, 2004). A 28aa fragment of azurin (aa 50-77; p28) also inhibits tumor proliferation. Like azurin, p28 appears to exert its anti-proliferative activity through the tumor suppressor gene, p53. As p53 appears responsible for regulating a number of cellular processes, including differentiation, we explored whether azurin and could alter additional p53 mediated process i.e . cellular transformation, in mouse mammary organ culture (MMOC), an established model of cellular transformation and angiogenesis in a human umbilical vascular endothelial cell model. Azurin and p28 reproducibly induced a dose related inhibition in the incidence and multiplicity of mammary alveolar and ductal precancerous lesions. Confocal microscopy and FAC showed that azurin and p28 entered normal murine mammary epithelial cells (MM3MG) and mammary cancer cells (4T1). P28 also entered human umbilical vein endothelial cells (HUVEC) in a temperature, time and concentration dependent manner and induced a does related inhibition of capillary tube formation of HUVEC plated on Matrigel®. At 75uM, tube formation was completely inhibited. Cell migration was also inhibited (40-50%) in cell migration scratch and electro- wound assays in vitro The anti-angiogenic and anti-migratory effects of p28 were also evident in the presence of VEGF and FGF. Taken together, these observations suggest that azurin and p28 not only inhibit the proliferation of breast cancer cells, but angiogenesis and the transformation of relatively undifferentiated mammary gland structures believed to be involved in the genesis of mammary cancer. As such, these peptides appear to offer a unique approach to treating breast cancer.
Area Efficient Hardware Implementation of Elliptic Curve Cryptography by Iteratively Applying Karatsuba's Method (2007)

Securing communication channels is especially needed in wireless environments. But applying cipher mechanisms in software is limited by the calculation and energy resources of the mobile devices. If hardware is applied to realize cryptographic operations cost becomes an issue. In this paper we describe an approach which tackles all these three points. We implemented a hardware accelerator for polynomial multiplication in extended Galois fields (GF) applying Karatsuba's method iteratively. With this approach the area consumption is reduced to 2.1 mm^2 in comparison to. 6.2 mm^2 for the standard application of Karatsuba's method i.e. for recursive application. Our approach also reduces the energy consumption to 60 per cent of the original approach. The price we have to pay for these achievement is the increased execution time. In our implementation a polynomial multiplication takes 3 clock cycles whereas the recurisve Karatsuba approach needs only one clock cycle. But considering area, energy and calculation speed we are convinced that the benefits of our approach outweigh its drawback.
Exploring the Effectiveness of Various Patterns in an Extended Pattern Search Layout Algorithm (2004)

Automated synthesis of product layout has the potential of substantially reducing design cycle time while allowing for quick check of interference, clearance, scale and fit prior to the building of physical prototypes. The search for optimal positions and orientations of parts in the layout typically requires a huge number of iterations. An extended pattern search layout algorithm based on coordinate search was introduced in an earlier paper and shown quite effective over the previous state-of-the-art. Coordinate search is a simple and straightforward way of implementing the extended pattern search method in the layout problem. However, it is not taking advantage of the wide variety of heuristics admissible in pattern search methods for identifying promising search directions. By introducing various search patterns and exploring their effectiveness in the layout problem, the question of whether complex tactics can do better than the basic coordinate pattern search is addressed. This paper presents four different heuristics for generating pattern directions in the extended pattern search layout algorithm: the conjugate direction method, the modified gradient method, the rank ordering method, and the simplex method. These heuristics are utilized to identify promising search directions and update the set of pattern directions used in the algorithm over iterations. The performance of the different heuristics is compared to that of the basic coordinate extended pattern search layout approach.
Gradient Profile Prior and Its Applications in Image Super-Resolution and Enhancement (2010)

In this paper, we propose a novel generic image prior-gradient profile prior, which implies the prior knowledge of natural image gradients. In this prior, the image gradients are represented by gradient profiles, which are 1-D profiles of gradient magnitudes perpendicular to image structures. We model the gradient profiles by a parametric gradient profile model. Using this model, the prior knowledge of the gradient profiles are learned from a large collection of natural images, which are called gradient profile prior. Based on this prior, we propose a gradient field transformation to constrain the gradient fields of the high resolution image and the enhanced image when performing single image super-resolution and sharpness enhancement. With this simple but very effective approach, we are able to produce state-of-the-art results. The reconstructed high resolution images or the enhanced images are sharp while have rare ringing or jaggy artifacts.
Double clicking for site-specific coupling of multiple enzymes (2015)

A method to site-specifically couple multiple enzymes is reported. The approach is based on the site-specific incorporation of a clickable non-natural amino acid into enzymes and two compatible click reactions. The multi-enzyme reaction system exhibited enhanced catalytic efficiency over the respective free enzymes.