gebhart/patrepeval huggingface dataset:
An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules (2005)

The DNA of functional cis-regulatory modules displays extensive sequence conservation in comparisons of genomes from modestly distant species. Patches of sequence that are several hundred base pairs in length within these modules are often seen to be 80-95% identical, although the flanking sequence cannot even be aligned. However, it is unlikely that base pairs located between the transcription factor target sites of cis-regulatory modules have sequence-dependent function, and the mechanism that constrains evolutionary change within cis-regulatory modules is incompletely understood. We chose five functionally characterized cis-regulatory modules from the Strongylocentrotus purpuratus (sea urchin) genome and obtained orthologous regulatory and flanking sequences from a bacterial artificial chromosome genome library of a congener, Strongylocentrotus franciscanus. As expected, single-nucleotide substitutions and small indels occur freely at many positions within the regulatory modules of these two species, as they do outside the regulatory modules. However, large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence. The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA.
Mechanical imaging in medical applications (2009)

Mechanical Imaging (MI), a.k.a. tactile imaging or stress imaging, is a branch of Elasticity Imaging, a medical diagnostic technique based on the visualization of tissue internal structures in terms of their elasticity modulus. During the last decade, numerous methods and devices have been developed implementing MI technology in various medical applications, such as the visualization and evaluation of prostate conditions, breast cancer screening, the differentiation of benign and malignant lesions, and the characterization of vaginal wall elasticity. This paper presents an overview of MI technology and its applications, strengths and limitations. Results of laboratory and clinical studies clearly indicate that Mechanical Imaging devices have the potential to be used as a cost effective means for cancer screening as well as diagnostics of various diseases accompanied by changes of mechanical properties of soft tissues.
TensorFuzz: Debugging Neural Networks with Coverage-Guided Fuzzing (2018)

Machine learning models are notoriously difficult to interpret and debug. This is particularly true of neural networks. In this work, we introduce automated software testing techniques for neural networks that are well-suited to discovering errors which occur only for rare inputs. Specifically, we develop coverage-guided fuzzing (CGF) methods for neural networks. In CGF, random mutations of inputs to a neural network are guided by a coverage metric toward the goal of satisfying user-specified constraints. We describe how fast approximate nearest neighbor algorithms can provide this coverage metric. We then discuss the application of CGF to the following goals: finding numerical errors in trained neural networks, generating disagreements between neural networks and quantized versions of those networks, and surfacing undesirable behavior in character level language models. Finally, we release an open source library called TensorFuzz that implements the described techniques.
A New Wireless Communication Paradigm through Software-controlled Metasurfaces (2018)

Electromagnetic waves undergo multiple uncontrollable alterations as they propagate within a wireless environment. Free space path loss, signal absorption, as well as reflections, refractions and diffractions caused by physical objects within the environment highly affect the performance of wireless communications. Currently, such effects are intractable to account for and are treated as probabilistic factors. The paper proposes a radically different approach, enabling deterministic, programmable control over the behavior of the wireless environments. The key-enabler is the so-called HyperSurface tile, a novel class of planar meta-materials which can interact with impinging electromagnetic waves in a controlled manner. The HyperSurface tiles can effectively re-engineer electromagnetic waves, including steering towards any desired direction, full absorption, polarization manipulation and more. Multiple tiles are employed to coat objects such as walls, furniture, overall, any objects in the indoor and outdoor environments. An external software service calculates and deploys the optimal interaction types per tile, to best fit the needs of communicating devices. Evaluation via simulations highlights the potential of the new concept.
Fiber Bragg grating interrogation and multiplexing with a 3/spl times/3 coupler and a scanning filter (2000)

We present a new technique for fiber Bragg grating (FBG) sensor interrogation and multiplexing. The technique combines a scanning bandpass filter used to multiplex by wavelength multiple gratings in a single fiber, and an unbalanced Mach-Zehnder fiber interferometer made with a 3/spl times/3 coupler to detect strain-induced wavelength shifts. A demonstration system interrogates four gratings in a single fiber at a sampling rate up to 20 kHz, with a noise floor measured at less than 10 n/spl epsiv///spl radic/(Hz) above 0.1 Hz.
Design of a Security System to Defeat Abnormal IPSec Traffic in IPv6 Networks (2006)

The IPSec is a basic security mechanism of the IPv6 protocol, which can guarantee an integrity and confidentiality of data that transmit between two corresponding hosts. Also, both data and communication subjects can be authenticated using the IPSec mechanism. However, it is difficult that the IPSec mechanism protects major important network from attacks which transmit mass abnormal IPSec traffic in session-configuration or communication phases. In this paper, we present a design of the security system that can effectively detect and defeat abnormal IPSec traffic, which is encrypted by the ESP extension header, using the IPSec Session and Configuration table without any decryption. This security system is closely based on a multi-tier attack mitigation mechanism which is based on network bandwidth management and aims to counteract DDoS attacks and DoS effects of worm activity.
Direct Determination of Carbohydrates, Amino Acids, and Antibiotics by Microchip Electrophoresis with Pulsed Amperometric Detection (2003)

The separation and detection of underivatized carbohydrates, amino acids, and sulfur-containing antibiotics in an electrophoretic microchip with pulsed amperometric detection (PAD) is described. This report also describes the development of a new chip configuration for microchip electrophoresis with PAD. The configuration consists of a layer of poly(dimethylsiloxane) that contains the microfluidic channels, reservoirs, and a gold microwire, sealed to a second layer of poly(dimethylsiloxane). Example separations of carbohydrates, amino acids, and sulfur-containing antibiotics are shown. The effect of the separation and injection potentials, buffer pH and composition, injection time, and PAD parameters were studied in an effort to optimize separations and detection. Detection limits ranging from 6 fmol (5 microM) for penicillin and ampicillin to 455 fmol (350 microM) for histidine were obtained.
Site-specific methylated reporter constructs for functional analysis of DNA methylation (2013)

Methods to experimentally alter and functionally evaluate cytosine methylation in a site-specific manner have proven elusive. We describe a site-specific DNA methylation method, using synthetically methylated primers and high fidelity PCR coupled with ligation of reporter constructs. We applied this method to introduce methylated cytosines into fragments of the respective DAPK and RASSF1A promoters that had been cloned into luciferase reporters. We found that methylation of 3-7 residue CpG clusters that were 5' adjacent to the transcription start site (TSS) of the DAPK gene produced up to a 54% decrease in promoter activity (p<0.01). Similarly, for RASSF1A promoter reporter constructs, the methylation of either of two clusters of four CpGs each, but not an intervening cluster, produced a 63% decrease in promoter activity (p<0.01), suggesting that precise mCpG position is crucial, and factors other than simple proximity to the TSS are at play. Chromatin immunoprecipitation analysis of these reporter constructs demonstrated that transcription factor Oct-1 and Sp1 preferentially bound the unmethylated vs. methylated DAPK or RASSF1A promoter reporter constructs at the functional CpG sites. Histone H1, hnRNP1, and MeCP2 showed preferential binding to methylated sequence at functional sites in these reporter constructs, as well as highly preferential (> 8-80-fold) binding to native methylated vs. unmethylated chromatin. These results suggest that: (1) site-specific, precision DNA methylation of a reporter construct can be used for functional analysis of commonly observed gene promoter methylation patterns; (2) the reporter system contains key elements of the endogenous chromatin machinery.
Immunologic efficacy of E39 & E39' vaccination in a phase I/IIa trial in ovarian and endometrial cancer patients. (2018)

75 Background: The treatment options for cancer are ever-evolving & now include vaccines targeting tumor-specific immunogenic peptides to induce tumor cytolysis. Folate binding protein (FBP) is a tumor-associated antigen (TAA) highly expressed in most endometrial & ovarian cancers (Ca), shielded from the normal immune system. The most promising FBP peptides are E39 & an attenuated form, E39' (aka J65). In our most recent phase I/IIa trial we evaluated an E39+GM-CSF inoculation series at 3 doses (VG) vs controls (CG) as well as booster vaccination with E39 or E39' after the initial inoculation series. Here we present the immunologic data from this phase I/IIa trial. Methods: Patients (pts) with ovarian or endometrial Ca who were disease-free after standard of care therapy but at risk for recurrence were enrolled. HLA-A2+ pts were vaccinated in a 3+3 dose escalation of 100mcg, 500mcg, & 1000mcg. The remaining pts received 1000mcg inoculations. Vaccine was given every 3-4 weeks for a total of 6 inoculums. Pts were then offered to participate in booster vaccination with 9 pts randomized to receive E39 & 9 pts E39'. FBP expression level was measured on the resected disease. Overall immunologic response & by subgroups was measured by delayed type hypersensitivity (DTH) & ELISPOT in the VG. Results: A total of 29 pts were vaccinated. Mean DTH prior to the initial dose of E39 was 5.74mm & after final dose was 10.33mm (p = 0.018). Mean overall ELISPOT change over time through 18 months was +69.1 when compared to baseline (p = 0.675). At 18 months, mean ELISPOT increased by 97.1 in 1000mcg vs -57.0 in < 1000mcg dosed pts (p = 0.047) & by +255.33 in pts with > average initial DTH vs -0.75 in < average initial DTH (p = 0.004) when compared to baseline. Immunological analyses were not significantly different between FBP hi/lo expression or E39 vs E39’ booster (p > 0.05). Conclusions: E39 demonstrated significant overall immunogenicity on in vivo testing as measured by DTH. Ex vivo analysis (ELISPOT) suggests that E39 is more immunogenically efficacious in pts with > average initial DTH & those who are optimally dosed (1000mcg). FBP expression level & E39 vs E39’ use in booster inoculations did not significantly impact in vivo or ex vivo immunogenicity. Clinical trial information: NCT01580696.
Pareto optimal spectrally selective emitters for thermophotovoltaics via weak absorber critical coupling (Conference Presentation) (2018)

Tailoring the emission spectra of a thermophotovoltaic emitter away from that of a blackbody has the potential to minimize transmission and thermalization loss in a photovoltaic receiver. Selective thermophotovoltaic emitters could lead to solar energy conversion with efficiency greater than the Shockley-Queisser limit and could facilitate the generation of useful energy from waste heat. We introduce a new design to radically tune thermal emission that leverages the interplay between two resonant phenomena in a simple planar structure – absorption in weakly-absorbing thin films and reflection in multi-layer dielectric stacks. We will discuss a virtual screening approach based on Pareto optimality to identify a small number of promising structures for a selective thermal emitter from a search space of millions, several of which approach the ideal values of a step-function selective thermal emitter. We will also discuss the experimental realization of several simple and optimal structures, estimates of their device-level performance, and ongoing efforts to close the gap between theoretical estimates and experimentally-realized performance of these structures.
Transient tip-sample interactions in high-speed AFM imaging of 3D nano structures (2015)

The maximum amount of repulsive force applied to the surface plays a very important role in damage of tip or sample in Atomic Force Microscopy(AFM). So far, many investigations have focused on peak repulsive forces in tapping mode AFM in steady state conditions. However, it is known that AFM could be more damaging in transient conditions. In high-speed scanning, and in presence of 3D nano structures (such as FinFET), the changes in topography appear in time intervals shorter than the response time of the cantilever. In this case, the tip may crush into the sample by exerting much higher forces than for the same cantilever-sample distance in steady state situations. In this study the effects of steep upward steps in topography on the tip-sample interactions have been investigated, and it has been found that the order(s) of magnitude higher forces can be applied. The information on the worst case scenario obtained by this method can be used for selection of operation parameters and probe design to minimize damage in high-speed imaging. The numerically obtained results have been verified with the previous works in steady state regime. Based on this investigation the maximum safe scanning speed has been obtained for a case study.
Recent progress of fiber optic gyroscopes and applications at JAE (2003)

This paper describes the recent progress in production and research for interferometer fiber optic gyroscopes at Japan Aviation Electronics (JAE), and applications of the I-FOGs are also described.
GMRAM: giant magneto-resistance random-access memory (2002)

Giant Magneto-resistance Random-Access Memory (GMRAM) is a nonvolatile random access memory that uses magnetic multi-layers made of thin layers of common ferromagnetic materials to write digital data and the giant magneto-resistance (GMR) effect to read stored data. The direction of magnetization in the storage layer of the magnetic multi-layer is used to store a bit of information. The GMR material is magneto-resistive and changes resistance when the magnetization of the layers is changed by a magnetic field. The GMR effect produces a signal that distinguishes between a "1" and "0." GMRAM is a chip that integrates magnetic and semiconductor devices in an architecture. Attributes for GMRAM make it desirable as a nonvolatile memory.
135 A Novel Therapy for Premature Ejaculation: Transcutaneous Functional Electrical Stimulation-results of a Pioneer Study (2018)

To evaluate the safety and efficacy of Transcutaneous functional electrical stimulation (TFES) for the treatment of Premature Ejaculation (PE). Our preliminary safety study (n=19) demonstrated that applying TFES to the perineal region is safe. In the present study, we included 23 men aged 20-60 that complained of PE. On the first visit of this prospective, single-blinded, self-controlled study, we alternately delivered either TFES or sham treatment to the perineum, based on the enrollment order. For stimulation, we used a commercial neuro-muscular electrical stimulation device. The alternating second treatment was given to the same subject after a minimal period of one week. In order to determine the intensity threshold for muscle contraction, we gradually increased TFES intensity. Patients were instructed to inform the investigator upon first sensation of a convenient muscle contraction in the stimulated area, after which we applied this individual intensity-threshold during the study. The patients were left alone in a silent room to masturbate and, using a stopwatch, to measure their Masturbation Ejaculatory Latency Time (MELT), measured between full erection and ejaculation. Patients filled-out safety questionnaires after each visit and on each of the three following days.
Preparation of Aluminum Fluoride Film with Graphite Fluoride (1984)

Abstract An aluminum fluoride film covered by graphite fluoride on metallic aluminum was prepared by reaction in the ternary system of aluminum, graphite and fluorine gas at 450–550 °C. The film consisted of a large amount of aluminum fluoride covered by thin graphite fluoride layers. The contact angle of a water drop on the film was around 120°, which decreased to 85–95° during 45 d probably due to reaction with moisture and/or water drop. Almost no oxygen was detected in the film. The film formation would be based on the reduction of oxide layer on aluminum by carbon radical produced by thermal decomposition of graphite fluoride.
Wear Mechanisms of Chromia Refractories in Slagging Gasifiers (2007)

The hot‐face refractory lining is a key component of gasification systems. The refractory liner protects the gasification system from the high‐temperature corrosive gaseous and from the molten slag environment associated with the conversion of carbon feedstocks. This paper will discuss the effect of gasifier operating conditions and carbon feedstock slag/ash chemistry on the refractory service life. Particular attention is focused on the wear mechanism of chromia refractories, determined through postmortem analysis of spent refractory bricks from service in gasifiers. Also presented is the behavior of a phosphate‐containing chromia refractory with improved resistance to structural spalling.
(Invited) Designer Ionic Liquids for Improved Magnesium Anode Behavior (2016)

Our group has been involved in studies of the complexation and speciation of Mg 2+ in ionic liquids as a means to understand the influence of coordination environment on Mg anode electrochemical behavior. 1 In this presentation we will focus on the complexation of Mg 2+ by bis(trifluoromethylsulfonyl)imide ionic anion (TFSI - ), borohydride anion, glyme-based (i.e. PEGylated) solvents and chelating ionic liquids bearing polyethylene glycol-like chelating groups, and on the influence of such complexation on the reversibility of Mg electrodeposition/dissolution. 1,2 Complexation is predominantly studied by Raman spectroscopy, which allows facile differentiation of complexed and free species. We show that the lessons learned from such studies of Mg 2+ complexation allow the design of new chelating ionic liquids that show markedly improved Mg 2+ /Mg 0 electrochemical behavior compared to the parent TFSI-based ionic liquids. Specifically, we describe reasonable coulombic efficiency (ca. 90%) and current densities (>1 mA/cm 2 ) that are achievable through judicious choice of the complexation environment and other chemical features of the electrolyte system. We also discuss more generally the factors that act to suppress facile Mg electrodeposition/dissolution. We provide experimental verification of some of the means by which these various factors influence both chemical and electrochemical reversibility of Mg anode behavior. These results represent the first demonstration of reversible electrochemical deposition/dissolution of Mg in an ionic liquid specifically designed with this task in mind. Acknowledgment: We acknowledge support from the Army Research Office grant number W911NF-11-1-0432. References: “Determination of Mg 2+ Speciation in a TFSI - -Based Ionic Liquid With and Without Chelating Ethers Using Raman Spectroscopy”, Watkins, T., Buttry, D. A.; J. Phys. Chem. B , 2015 , 119(23) , 7003-7014. (DOI: 10.1021/acs.jpcb.5b00339) “Designer Ionic Liquids for Reversible Electrochemical Deposition/Dissolution of Magnesium”, Watkins, T.; Kumar, A.; Buttry, D.A.; J. Am. Chem. Soc., 2016 , 138(2) , 641-650 (DOI: 10.1021/jacs.5b11031)
Distributed feedback quantum cascade lasers (1997)

Continuously tunable, pulsed single-mode operation of distributed feedback quantum cascade lasers is reported above room temperature within the wavelength range from 5.2µm to 11.6µm. Peak optical powers of 60mW at 300K and 5.4µm are obtained.
Direct kernel biased discriminant analysis: a new content-based image retrieval relevance feedback algorithm (2006)

In recent years, a variety of relevance feedback (RF) schemes have been developed to improve the performance of content-based image retrieval (CBIR). Given user feedback information, the key to a RF scheme is how to select a subset of image features to construct a suitable dissimilarity measure. Among various RF schemes, biased discriminant analysis (BDA) based RF is one of the most promising. It is based on the observation that all positive samples are alike, while in general each negative sample is negative in its own way. However, to use BDA, the small sample size (SSS) problem is a big challenge, as users tend to give a small number of feedback samples. To explore solutions to this issue, this paper proposes a direct kernel BDA (DKBDA), which is less sensitive to SSS. An incremental DKBDA (IDKBDA) is also developed to speed up the analysis. Experimental results are reported on a real-world image collection to demonstrate that the proposed methods outperform the traditional kernel BDA (KBDA) and the support vector machine (SVM) based RF algorithms.
Liquid chromatography-mass spectrometry. II—continuous monitoring (1974)

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