gebhart/patrepeval huggingface dataset:
In Silico Profiling of Clinical Phenotypes for Human Targets Using Adverse Event Data (2018)

We present a novel approach for the molecular transformation and analysis of patient clinical phenotypes. Building on the fact that drugs perturb the function of targets/genes, we integrated data from 8.2 million clinical reports detailing drug-induced side effects with the molecular world of drug-target information. Using this dataset, we extracted 1.8 million associations of clinical phenotypes to 770 human drug-targets. This collection is perhaps the largest phenotypic profiling reference of human targets to-date, and unique in that it enables rapid development of testable molecular hypotheses directly from human-specific information. We also present validation results demonstrating analytical utilities of the approach, including drug safety prediction, and the design of novel combination therapies. Challenging the long-standing notion that molecular perturbation studies cannot be performed in humans, our data allows researchers to capitalize on the vast tomes of clinical information available throughout the healthcare system.
An ultra-fast floating-body/gate cell for embedded DRAM (2013)

Floating-body DRAM cells (FBCs) on SOI are of interest because of integration problems associated with the large storage capacitor of nanoscale conventional 1T/ 1C DRAM. However, limitations on FBC speed, due to relatively slow write times governed by the usual impact-ionization or tunneling body-charging processes, preclude the application of most interest - embedded DRAM. We recently proposed a novel 2T (T1 and T2) FBC, i.e., a floating-body/gate cell (FBGC) , which enables design flexibility for optimizing performance. We present herein a new 2T design concept (FBGC4) that gives ultra-fast write times, in addition to good current-signal margin and long retention times, and thus enables the embedded-DRAM application. Further, low power and good reliability are implied because of low-voltage operation afforded by FBGC4.
A VLSI Design Flow for Secure Side-Channel Attack Resistant ICs (2005)

The paper presents a digital VLSI design flow to create secure, side-channel attack (SCA) resistant integrated circuits. The design flow starts from a normal design in a hardware description language, such as VHDL or Verilog, and provides a direct path to an SCA resistant layout. Instead of a full custom layout or an iterative design process with extensive simulations, a few key modifications are incorporated in a regular synchronous CMOS standard cell design flow. We discuss the basis for side-channel attack resistance and adjust the library databases and constraints files of the synthesis and place-and-route procedures accordingly. Experimental results show that a DPA (differential power analysis) attack on a regular single ended CMOS standard cell implementation of a module of the DES algorithm discloses the secret key after 200 measurements. The same attack on a secure version still does not disclose the secret key after more than 2000 measurements.
Inverse model of the glass pH sensor (2008)

Introduction The concentration of ion H (pH) in solution plays very important role in chemical, biological and physical processes. Since Cremer (1906) first reported the pH response of oxide glasses, many theoretical researches about the glass electrode and its applications have been carried out. The glass electrode is stable mechanically and chemically and can be used in the wide range of solvents. In spite of new developments of semiconductor sensors and optical sensors for pH measurements (Bakker, 1998), the glass electrode is still of great practical importance. The glass electrode is relatively fast and can be applied effectively in on-line measurements. However, for some applications such as identification tanks (Sung et al., 1995; Obut and Ozgen, 2008), end-point estimations and auto-titrators, faster responses will be preferable. The detailed mechanism of glass electrode is still questionable. Roughly, the dynamic response of glass electrode consists of quick response to a quasi-equilibrium and slow drift due to ion permeation through the glass membrane (Kohler et al., 2005). The former, response to the quasi-equilibrium, can be explained through the equivalent circuit having a very high internal resistance and a capacitance (Buck, 1968). Time constant of the glass electrode is the time that the capacitance is charged through the very large internal resistance. Here a measuring method that reduces this time by an order of magnitude is proposed. External voltage is introduced to charge the capacitance. It is compared and controlled to trace the glass pH electrode voltage by the integral controller.
Automatic Reconfiguration of Distributed Storage (2015)

The configuration of a distributed storage system with multiple data replicas typically includes the set of servers and their roles in the replication protocol. The configuration can usually be changed manually, but in most cases, system administrators have to determine a good configuration by trial and error. We describe a new workload-driven optimization framework that dynamically determines the optimal configuration at run time. Applying the framework to a large-scale distributed storage system used internally in Google resulted in halving the operation latency in 17% of the tested databases, and reducing it by more than 90% in some cases.
Polarization Entanglement Converted from Spatially Correlated Photon Pairs (2007)

We propose and demonstrate a novel scheme for the generation of polarization entanglement from spatially correlated photon pairs generated by parametric down-conversion. Using the state, we also demonstrate the violation of Bell's inequality.
Fuel composition and method for its preparation. [fuel theory of SRC and fuel oils] (1981)

A stable, uniform solvent refined coal (SRC)-oil dispersion is prepared by grinding 15 to 55% by weight of SRC particles in the absence of free oxygen in a medium consisting essentially of gas oil and/or a heavier petroleum fraction. Grinding is continued until the size of the majority of the particles is reduced to a value in the range 1 to 10 micron. Preferably the src is uniformly dispersed in the gas oil and/or heavier petroleum fraction prior to grinding.
Rubber-Thermoplastic Compositions. Part I. EPDM-Polypropylene Thermoplastic Vulcanizates (1980)

Abstract Thermoplastic elastomers are rubbery materials which can be fabricated by techniques usually associated with thermoplastic resins. Classical elastomers rely upon the crosslinked network, developed during vulcanization, to provide the retractive forces of rubber type elasticity. Thermoplastic elastomers contain rubber domains and resinous thermoplastic domains. The thermoplasticity results from the melting characteristics of the hard thermoplastic phase, while the rubber properties arise from the rubbery domains. Thermoplastic elastomers are, therefore, almost by definition, heterogeneous in their phase morphology. Such materials can be blends or block polymers. In the case of block polymers, the rubbery phase is not crosslinked chemically. However, hard or resinous phase domains occur as the hard segments of the block polymer which separate from the composition by agglomeration during cooling from the molten state. These domains act both as well-bonded reinforcing filler particles and as crosslinks. This is, of course, because the hard blocks are connected to the soft or rubbery segments by primary chemical bonds. In the case of the blend compositions, the hard and soft domains are separate polymeric species. However, there must be some form of interaction between the domains if useful properties are to be realized. Recently, uncured or partially cured EPDM rubber has been blended with polyolefin resin to make thermoplastic elastomer-like compositions. However, these compositions suffer deficiencies in performance as well as in certain aspects of fabricability. Only poor to fair performance at temperatures above 70°C in air or in oil has been achieved with the uncured to partially cured compositions. More recently, it has been found in our laboratories that fully cured EPDM compositions which are fabricable as thermoplastics can be prepared. Such compositions, referred to here as thermoplastic vulcanizates, have superior strength, high-temperature mechanical properties, hot oil and solvent resistance, better compression set, etc. This report outlines critical parameters associated with these unique materials.
New Trends with Cochlear Implants and Atraumaticity Demonstrated by Deep Electrode Insertion and Hearing Preservation (2012)

Cochlear implantation (CI) combined with residual hearing preservation is a fascinating concept which is possible due to recent improvements in surgical technique and advanced electrode design. Current candidacy includes adults and children with significant residual hearing. Residual hearing must be maximally protected during cochlear implantation, since preservation of cochlear sensorineural structures contribute to a better outcome with electrical stimulation. Further pharmacological therapies for paediatric patients also necessitate maximum functionality of intracochlear structures to be effective. Results obtained in several implantation centres over the world with soft, standard size Med-El electrodes demonstrate that full electrode insertion (around 28 mm) is possible without compromising residual hearing. Such an approach provides the benefit of complete cochlear coverage for electrical stimulation combined with low-frequency acoustic hearing. The use of such soft electrodes in atraumatic surgery can therefore improve sound perception in difficult hearing conditions.
Design and Fabrication of FlexConnects: A Cost-Effective Implementation of Compliant Chip-to-Substrate Interconnects (2008)

Compliant free-standing structures can be used as chip-to-substrate interconnects. Such ldquocompliant interconnectsrdquo are a potential solution to the requirements that will be imposed on chip-to-substrate interconnects over the next decade. However, cost of implementation and electrical performance limit compliant interconnects. This paper presents two concepts to address this. First, an innovative, cost-effective fabrication process to realize compliant interconnects is proposed. Sequential lithography and electroplating processes with up to two masking steps are utilized. Such an approach potentially reduces the cost of fabricating compliant interconnects. Second, an innovative approach to designing compliant interconnects is proposed to improve electrical performance without compromising on mechanical reliability. The new approach uses parallel/multiple electrical paths as part of the compliant interconnect design. These concepts are integrated to realize a new compliant interconnect technology called FlexConnects. Utilizing the proposed fabrication process parallel-path FlexConnects are realized at a 100- <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mu</i> m pitch. Numerical simulations are used to demonstrate that the electrical performance of parallel-path FlexConnects (self inductance of ~ 37 pH) is enhanced without compromising on mechanical performance, validating the use of parallel/multiple electrical paths in the interconnect design.
Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography (2008)

Electron tomography is currently the highest resolution imaging modality available to study the 3D structures of pleomorphic macromolecular assemblies, viruses, organelles and cells. Unfortunately, the resolution is currently limited to 3-5nm by several factors including the dose tolerance of biological specimens and the inaccessibility of certain tilt angles. Here we report the first experimental demonstration of equally-sloped tomography (EST) to alleviate these problems. As a proof of principle, we applied EST to reconstructing frozen-hydrated keyhole limpet hemocyanin molecules from a tilt-series taken with constant slope increments. In comparison with weighted back-projection (WBP), the algebraic reconstruction technique (ART) and the simultaneous algebraic reconstruction technique (SART), EST reconstructions exhibited higher contrast, less peripheral noise, more easily detectable molecular boundaries and reduced missing wedge effects. More importantly, EST reconstructions including only two-thirds the original images appeared to have the same resolution as full WBP reconstructions, suggesting that EST can either reduce the dose required to reach a given resolution or allow higher resolutions to be achieved with a given dose. EST was also applied to reconstructing a frozen-hydrated bacterial cell from a tilt-series taken with constant angular increments. The results confirmed similar benefits when standard tilts are utilized.
Advanced Speech Enhancement With Partial Speech Reconstruction (2013)

Publication in the conference proceedings of EUSIPCO, Marrakech, Morocco, 2013
Estimating energy consumption of a PHEV using vehicle and on-board navigation data (2015)

This paper presents a novel approach for predicting the energy consumption of a plug-in hybrid electric vehicle (PHEV). We propose to estimate energy consumption strategy from data via regression applied to trip recordings. Descriptors of the trip elements are obtained from both recordings and statistics provided by a GPS navigation system. Trips are then split into elementary units corresponding to an homogeneous driving context. For each trip element, the optimal energy consumption strategy is computed via (expensive) dynamic programming simulations. Here, data analysis is used so as to identify descriptors of this trip element that are relevant to predict the energy consumption. Then, a polynomial model is fit to the data so as to estimate, for each new trip element, the optimal energy consumption strategy from the expected driving condition, rather than using dynamic programming. Our approach distinguishes itself by the fact that road context, driver style, road slope and auxiliary electrical power are taken into account to estimate the energy consumption of a PHEV. The accuracy of the prediction process is evaluated over test data, and demonstrates the interest of our approach in predicting energy consumption.
Phase‐resolved fluorescence lifetime measurements for flow cytometry (1993)

A flow cytometer capable of measuring fluorescence lifetimes by the phase shift method has been built and evaluated. Under optimal conditions, the resolution of the fluorescence lifetime measurement is shown to be under 200 picoseconds. Pulse intensity variations are normalized using limiting amplifiers and electronic filtering. Normalization of signal intensities provides a lifetime measurement that is independent of fluorescence intensity over at least a 50-fold (17 dB) range in fluorescence intensity. The fluorescence lifetimes of unbound dye, fluorescent beads, cells stained with ethidium bromide, propidium iodide, and phycoerythrin-conjugated monoclonal antibodies have been measured. The fluorescence lifetimes measured for these particles are well correlated with lifetime measurements made using a standard fluorimeter. Cells stained with ethidium bromide and propidium iodide at various nucleotide-to-dye ratios are shown to exhibit similar behavior to static cuvette measurements. The fluorescence lifetime parameter is also shown to resolve phycoerthyrin fluorescence from propidium iodide fluorescence.
Isolation and characterization of Lactococcus lactis subsp. lactis promoters (1991)

DNA fragments with promoter activity were isolated from the chromosome of Lactococcus lactis subsp. lactis. For the isolation, a promoter probe vector based on the cat gene was constructed, which allowed direct selection with chloramphenicol in Bacillus subtilis and L. lactis. Four of the putative promoters (P1, P2, P10, and P21) were analyzed further by sequencing, mapping of the 5' end of the mRNA, Northern (RNA blot) hybridization, and chloramphenicol acetyltransferase activity measurements. From these fragments, -10 and -35 regions resembling the consensus Escherichia coli sigma 70 and B. subtilis sigma 43 promoters were identified. Another set of promoters, together with a signal sequence, were also isolated from the same organism. These fragments promoted secretion of TEM beta-lactamase from L. lactis. When the two sets of promoters were compared, it was found that the ones isolated with the cat vector were more efficient (produced more mRNA). By changing the promoter part of the promoter-signal sequence fragment giving the best TEM beta-lactamase secretion into a more efficient one (P2), a 10-fold increase in enzyme production was obtained.
Polyimide—Nylon 6 Copolymers: Single-Component Molecular Composites (1996)

Novel polyimide-g-nylon 6 and nylon 6-b-polyimide-b-nylon 6 copolymers were synthesized by polycondensation and subsequent anionic, ring-opening polymerization methods. The graft copolymers were prepared by initially incorporating an N-acylated caprolactam ring in a diamine monomer, i.e., 3,5-bis(4-aminophenoxy)benzoyl caprolactam The diamine was polymerized with dianhydrides to produce polyimides containing pendant acylated caprolactam moieties. The triblock copolymers were prepared by initially synthesizing N-acylated caprolactam end-capped polyimides. These multi- and difunctionalized polyimides were then used as polymeric activators for the subsequent anionic, ring-opening polymerization of ε-caprolactam. Thus, they were dissolved in molten ε-caprolactam at 140°C and treated with phenylmagnesium bromide. Nylon 6 chains grew from the activated sites on the polyimide chains to form well-defined graft and block copolymer structures. No nylon 6 homopolymer was produced. The effective reinforcement of the nylon 6 by only a small amount, i.e., 5%, of the polyimide components was demonstrated by the dramatic improvements in thermal and mechanical properties.
Molecular Cloning and Expression of <i>cor</i> (<i>Co</i>ld-<i>R</i>egulated) Genes in <i>Arabidopsis thaliana</i> (1990)

We have previously shown that changes in gene expression occur in Arabidopsis thaliana. L. (Heyn) during cold acclimation (SJ Gilmour, RK Hajela, MF Thomashow [1988] Plant Physiol 87: 745-750). Here we report the isolation of cDNA clones of four cold-regulated (cor) genes from Arabidopsis and examine their expression in response to low temperature, abscisic acid (ABA), water stress, and heat shock. The results of Northern analysis indicated that the transcript levels for the four cor genes, represented by clones pHH7.2, pHH28, pHH29, and pHH67, increased markedly between 1 and 4 hours of cold treatment, reached a maximum at about 8 to 12 hours, and remained at elevated levels for as long as the plants were kept in the cold (up to 2 weeks). Returning cold acclimated plants to control temperature resulted in the levels of the cor transcripts falling rapidly to those found in nonacclimated plants; this occurred within 4 hours for the transcripts represented by pHH7.2 and pHH28, and 8 hours for those represented by pHH29 and pHH67. Nuclear run-on transcription assays indicated that the temperature-regulated expression of the cor genes represented by pHH7.2, pHH28, and pHH29 was controlled primarily at the posttranscriptional level while the cor gene represented by pHH67 was regulated largely at the transcriptional level. Northern analysis also indicated that the levels of cor gene transcripts increased in response to both ABA application and water stress, but not to heat shock. The possible significance of cor genes being regulated by both low temperature and water stress is discussed.
Multistep Convergent Solution-Phase Combinatorial Synthesis and Deletion Synthesis Deconvolution (1998)

A solution-phase convergent versus linear, divergent solid-phase synthesis of chemical libraries is illustrated enlisting the 2-fold dimerization of iminodiacetic acid diamides ultimately incorporating eight variable groups. The first dimerization is conducted with ω-alkene carboxamide derivatives of iminodiacetic acid which sets up the second dimerization conducted with the olefin metathesis reaction. This latter reaction randomizes the linking tether length adding a ninth degree of diversification suitable for the discovery of receptor dimerization antagonists and their linkage into potential receptor dimerization agonists. Unlike the divergent synthesis of libraries which is amendable to solid-phase synthesis techniques, such convergent syntheses are especially suited for solution-phase synthesis and are precluded by conventional solid-phase techniques since the combining components typically would be on mutually exclusive phases. Two mixture libraries of 476 775 and 114 783 975 compounds were prepared in five steps from four ω-alkene carboxamides and 10 or 20 amines, respectively. Deconvolution of the library mixtures by positional scanning or a complementary technique we introduce as deletion synthesis can be conducted up front for depository libraries subjected to multiple assays. For convergent dimerizations such as that illustrated herein, only deletion deconvolution can provide information on all components of the mixture including the unsymmetrical combinations.
Alteration of epitope recognition pattern in Ag85B and ESAT‐6 has a profound influence on vaccine‐induced protection against <i>Mycobacterium tuberculosis</i> (2006)

To analyze the effect of vaccine delivery systems on antigen recognition and vaccine efficacy, we compared immune responses in mice immunized either with an adenovirus vector expressing a fusion of Ag85B and ESAT-6 or with the recombinant fusion protein in a liposomal adjuvant. Both vaccines induced high levels of antigen-specific IFN-gamma production. The adjuvanted protein vaccine induced primarily a CD4 T cell response directed to the epitope Ag85B(241-255) and gave efficient protection against subsequent Mycobacterium tuberculosis infection. In contrast, the adenoviral construct induced a strong CD8 response predominantly targeted to the epitope ESAT-6(15-29) and no significant protection against infection. Vaccination with the protein vaccine resulted in highly accelerated recall of Ag85B(241-255)-specific T cells immediately post M. tuberculosis challenge whereas the ESAT-6(15-29) epitope was barely recognized during infection. Delivery of the viral construct in cationic liposomes switched the immune response to a protective one dominated by CD4 T cells targeted to the Ag85B(241-255) epitope. These data demonstrate that the nature of the T cell response to a vaccine antigen is more important than its magnitude with respect to protective efficacy and that vaccine-mediated changes in immunodominance can result in T cell responses of limited relevance during the natural infection.
Frequency stabilization for mobile satellite terminals via LORAN (1990)

Digital satellite communication systems require careful management of frequency stability. Historically, frequency stability has been accomplished by continuously powered, high cost, high performance reference oscillators. Today's low cost mobile satellite communication equipment must operate under wide ranging environmental conditions, stabilize quickly after application of power, and provide adequate performance margin to overcome RF link impairments unique to the land mobile environment. Methods for frequency stabilization in land mobile applications must meet these objectives without incurring excessive performance degradation. A frequency stabilization scheme utilizing the LORAN (Long Range Navigation) system is presented.