gebhart/patrepeval huggingface dataset:
Suppression of autolysis and cell wall turnover in heterogeneous Tn551 mutants of a methicillin-resistant Staphylococcus aureus strain (1991)

Isogenic Tn551 mutants of a highly and uniformly methicillin-resistant strain of Staphylococcus aureus were tested for their rates of autolysis and cell wall degradation in buffer and for cell wall turnover during growth. The normal (relatively fast) autolysis and turnover rates of the parent strain were retained in a Tn551 mutant in which the insert was located within the mec gene and which produced undetectable levels of penicillin-binding protein 2A. On the other hand, autolysis and cell wall turnover rates were greatly reduced in auxiliary mutants, i.e., mutants in which the transposon caused conversion of the high-level and uniform resistance of the parent strain to a variety of distinct heterogeneous expression types and greatly decreased resistance levels. All of these mutants contained an intact mec gene and produced normal amounts of penicillin-binding protein 2A, and one of the mutations was located in the femA region of the staphylococcal chromosome (B. Berger-Bachi, L. Barberis-Maino, A. Strassle, and F. H. Kayser, Mol. Gen. Genet. 219:263-269, 1989). Autolysis rates were related to the degree of residual methicillin resistance and to the sites of Tn551 insertion. Fast cell wall turnover may help expression of high-level methicillin resistance by providing a mechanism for the excision of abnormal (and potentially lethal) structural elements of the cell wall synthesized by the bacteria in the presence of methicillin.
Optimization for multiport VNA vector error correction (2007)

Multiport vector error correction leverages the techniques that apply to two-port error correction. In some testset configurations the load match at any particular port may take on multiple distinct values that must be characterized. As the number of ports increases it becomes important to find ways to minimize the number of connections required to calibrate the VNA. This paper presents techniques for optimizing the calibration both from the point of view of minimizing the number of calibration steps as well as utilizing TRL, Unknown Thru and QSOLT calibration without requiring dual reflectometers at each testport.
3D Reconstruction and Analysis of the Vertebral Body Line (2002)

Quantitative analysis of 3D spinal deformities includes measurements related to individual vertebrae and measurements related to the overall shape of the spine. For the latter aspect, we propose to build a 3D model of the line that connects all vertebrae centres. We present two methods that allow reconstructing this vertebral body line in a quick and easy way. Various new descriptors of the spinal shape can be automatically computed. A study is under way to assess their clinical relevance and reliability.
From Declarative Languages to Declarative Processing in Computer Games (2009)

Recent work has shown that we can dramatically improve the performance of computer games and simulations through declarative processing: Character AI can be written in an imperative scripting language which is then compiled to relational algebra and executed by a special games engine with features similar to a main memory database system. In this paper we lay out a challenging research agenda built on these ideas. We discuss several research ideas for novel language features to support atomic actions and reactive programming. We also explore challenges for main-memory query processing in games and simulations including adaptive query plan selection, support for parallel architectures, debugging simulation scripts, and extensions for multi-player games and virtual worlds. We believe that these research challenges will result in a dramatic change in the design of game engines over the next decade.
Integrated Lithium Niobate Platform for Nonlinear Optics and Electro-Optic Applications (2017)

We demonstrate an integrated lithium niobate platform with sub-wavelength light confinement and low propagation loss (3dB/cm). We show efficient second harmonic generation in phase-matched waveguides (41% W−1cm−2), as well as high-speed electro-optic modulation (40 Gbps).
Challenges in the development of antimalarial drugs with causal prophylactic activity (1998)

Introduction There is a continuing need for improved drugs for treatment and prevention of malaria. Drugs with causal prophylactic activity are especially useful for prevention of malaria in individuals with a limited duration of exposure in a malaria-endemic area. In this paper I compare the requirements for causal prophylaxis of relapsing and non-relapsing malarias and review some of the challenges to the development of new prophylactic antimalarial drugs.
Symbolic QED Pre-silicon Verification for Automotive Microcontroller Cores: Industrial Case Study (2019)

We present an industrial case study that demonstrates the practicality and effectiveness of Symbolic Quick Error Detection (Symbolic QED) in detecting logic design flaws (logic bugs) during pre-silicon verification. Our study focuses on several microcontroller core designs (~1,800 flip-flops, ~70,000 logic gates) that have been extensively verified using an industrial verification flow and used for various commercial automotive products. The results of our study are as follows: 1. Symbolic QED detected all logic bugs in the designs that were detected by the industrial verification flow (which includes various flavors of simulation-based verification and formal verification). 2. Symbolic QED detected additional logic bugs that were not recorded as detected by the industrial verification flow. (These additional bugs were also perhaps detected by the industrial verification flow.)3.Symbolic QED enables significant design productivity improvements: (a) 8X improved (i.e., reduced) verification effort for a new design (8 person-weeks for Symbolic QED vs. 17 person-months using the industrial verification flow). (b) 60X improved verification effort for subsequent designs (2 person-days for Symbolic QED vs. 4-7 person-months using the industrial verification flow). (c) Quick bug detection (runtime of 20 seconds or less), together with short counterexamples (10 or fewer instructions) for quick debug, using Symbolic QED.
DNase Protection Analysis of Retrovirus Integrase at the Viral DNA Ends for Full-Site Integration In Vitro (2001)

Retrovirus intasomes purified from virus-infected cells contain the linear viral DNA genome and integrase (IN). Intasomes are capable of integrating the DNA termini in a concerted fashion into exogenous target DNA (full site), mimicking integration in vivo. Molecular insights into the organization of avian myeloblastosis virus IN at the viral DNA ends were gained by reconstituting nucleoprotein complexes possessing intasome characteristics. Assembly of IN-4.5-kbp donor complexes capable of efficient full-site integration appears cooperative and is dependent on time, temperature, and protein concentration. DNase I footprint analysis of assembled IN-donor complexes capable of full-site integration shows that wild-type U3 and other donors containing gain-of-function attachment site sequences are specifically protected by IN at low concentrations (<20 nM) with a defined outer boundary mapping ~20 nucleotides from the ends. A donor containing mutations in the attachment site simultaneously eliminated full-site integration and DNase I protection by IN. Coupling of wild-type U5 ends with wild-type U3 ends for full-site integration shows binding by IN at low concentrations probably occurs only at the very terminal nucleotides (<10 bp) on U5. The results suggest that assembly requires a defined number of avian IN subunits at each viral DNA end. Among several possibilities, IN may bind asymmetrically to the U3 and U5 ends for full-site integration in vitro.
Development and applications of a beta-catenin oligonucleotide microarray: beta-catenin mutations are dominantly found in the proximal colon cancers with microsatellite instability. (2003)

beta-catenin mutations have been identified in a variety of human malignancies; most of these are missense mutations restricted at hot-spot areas in exon 3. beta-catenin mutations are known to be highly associated with colorectal cancers with microsatellite instability (MSI). More than 70 beta-catenin mutations have been reported in colorectal cancers, and approximately 90% of beta-catenin mutations have been found in 11 codons (codons 29, 31, 32, 33, 34, 35, 37, 38, 41, 45, and 48) as missense mutations or in-frame deletions. We have developed an oligonucleotide microarray for detecting beta-catenin mutations at these 11 codons. The developed oligonucleotide microarray can detect a total of 110 types of beta-catenin mutations, including the 60 mutations reported previously. Nine beta-catenin mutations were identified in this study by five different methods, i.e., PCR- single-strand conformational polymorphism, denaturing high performance liquid chromatography, direct sequencing, cloning-sequencing, and with an oligonucleotide microarray. All nine of the mutations were identified by denaturing high performance liquid chromatography, cloning-sequencing, and by the oligonucleotide microarray. However, PCR-single-strand conformational polymorphism missed 1 beta-catenin mutation and direct sequencing missed 2. Five beta-catenin mutations from 74 colorectal carcinomas (34 proximal colon cancers and 40 distal colorectal cancers) and 4 beta-catenin mutations from 31 colorectal cancer cell lines (7 from the proximal colon, 6 from the distal colorectum, and 18 unknown) were identified. In colorectal carcinomas, all 5 of the beta-catenin mutations were found in proximal colon tumors. In colorectal cancer cell lines, 2 of 4 cell lines with beta-catenin mutations originated from the proximal colon, and the remaining 2 cell lines were simply described as having originated from the colon. Considering the relationships among beta-catenin mutations, MSI, and tumor location, the frequency of beta-catenin mutations was found to be meaningfully higher in colorectal carcinomas with MSI than in those with microsatellite stability (P < 0.001); moreover, MSI was found to be more frequent in proximal colon tumors (P < 0.01). In addition, beta-catenin mutations were also found to be associated with proximal colon cancer (P = 0.017).
Developing a Device for Measuring and Regulating the Rope Tension of Elevators. (1997)

We describes a tension measurement and regulation method for an elevator rope. The rope tension imbalance causes the rope life to be shortened and the sheave groove to become worn in the early stage, and the elevator car riding comfort is decreased. Usually, rope tension measurement is done manually and regulation is carried out by trial and error based on experience. These procedures require much manual labor and corresponding time. Thus, we have developed a rope tension estimation algorithm based on the reciprocating time of the rope acceleration wave generated by hand excitation. Second, we have formulated the relationship between the tension adjustment value and the rope vibration wave reciprocating time. The results of our experiments indicate that the proposed method is able to adjust the tension easily and the accuracy is sufficient for even super highspeed elevators. Lastly, we developed a device for measuring and regulating rope tension. The device is small enough to be carried by hand.
Rewriting Flash Memories by Message Passing (2015)

This paper constructs WOM codes that combine rewriting and error correction for mitigating the reliability and the endurance problems in flash memory. We consider a rewriting model that is of practical interest to flash applications where only the second write uses WOM codes. Our WOM code construction is based on binary erasure quantization with LDGM codes, where the rewriting uses message passing and has potential to share the efficient hardware implementations with LDPC codes in practice. We show that the coding scheme achieves the capacity of the rewriting model. Extensive simulations show that the rewriting performance of our scheme compares favorably with that of polar WOM code in the rate region where high rewriting success probability is desired. We further augment our coding schemes with error correction capability. By drawing a connection to the conjugate code pairs studied in the context of quantum error correction, we develop a general framework for constructing error-correction WOM codes. Under this framework, we give an explicit construction of WOM codes whose codewords are contained in BCH codes.
Automatic creation of both the topology and parameters for a robust controller by means of genetic programming (1999)

The paper describes a general automated method for synthesizing the design of both the topology and parameter values for controllers. The automated method automatically makes decisions concerning the total number of processing blocks to be employed in the controller, the type of each block, the topological interconnections between the blocks, the values of all parameters for the blocks, and the existence, if any, of internal feedback between the blocks of the overall controller. Incorporation of time-domain, frequency-domain, and other constraints on the control or state variables (often analytically intractable using conventional methods) can be readily accommodated. The automatic method described in the paper (genetic programming) is applied to a problem of synthesizing the design of a robust controller for a plant with a second-order lag. A textbook PID compensator preceded by a lowpass pre-filter delivers credible performance on this problem. However, the automatically created controller employs a second derivative processing block (in addition to proportional, integrative, and derivative blocks and a pre-filter). It is better than twice as effective as the textbook controller as measured by the integral of the time-weighted absolute error, has only two-thirds of the rise time in response to the reference (command) input, and is 10 times better in terms of suppressing the effects of disturbance at the plant input.
Identification of antigens and antibodies specific for <i>Pneumocystis carinii</i> . (1988)

To increase understanding of Pneumocystis carinii and its interaction with its hosts, Ag specific for rodent and human P. carinii were identified by the immunoblot method after PAGE of P. carinii organism extracts. The m.w. of the major Ag of rat P. carinii were 45,000, 110,000, and a broad band of 49,000 to 64,000, and of human P. carinii were 22,000, 24,000, and a broad band of 35,000 to 45,000 daltons. Human and rat pneumocystis were not antigenically identical. Specific antibodies against rat P. carinii Ag were found in 18 of 79 rats by the immunoblot method. Specific antibodies against human P. carinii Ag were found in 32 of 33 adult human sera, but in only 1 of 8 sera from infants and children. Specific antibodies were found in sera of 13 of the 14 adults with no history of P. carinii pneumonia, and all 19 patients with recently diagnosed P. carinii pneumonia, including 9 patients with P. carinii pneumonia associated with AIDS. The results of this study support previous suggestions that a large proportion of adults have been exposed to P. carinii and provide a basis for the further investigations of host-P. carinii interactions.
Fast and Transparent Adaptive Lens Based on Plasmonic Heating (2015)

In the current trend toward miniaturization, integrated micro-optical elements play a central role in the development of various applications including high-density data storage and imaging. In these operations, fine alignment and focus adjustment are usually performed mechanically, thus, limiting the accuracy, size and speed of devices. Here, we propose a novel reconfigurable microlens based on the engineering of the temperature distribution induced by a patterned plasmonic surface shined with a resonant near-infrared light. The refractive index change generated in a surrounding thermo-optical material acts as an effective lens whose parameters are remotely adjusted by the control near-infrared light. We demonstrate focal distance tunability of tens of microns with subnanometer accuracy along with time-responses down to 200 μs. The applicability of this photothermal lens is proved in the framework of optical microscopy and adaptive optics.
Simultaneous passive and active detection and localization of humpback whales using data recorded on a towed horizontal receiving array. (2010)

A large number of marine mammal vocalizations, most likely from humpback whales, were passively recorded by a towed horizontal receiver array during the ocean acoustic waveguide remote sensing (OAWRS) Gulf of Maine 2006 Experiment. Spectral analyzes show that most of the vocalizations were random broadband signals with short time duration, typically lasting 1–2 s in the 300–600-Hz frequency range. The array invariant method [Lee and Makris, J. Acoust. Soc. Am. (2006)] is applied to localize the whales in bearing and range after conventional plane-wave beamforming and matched filtering of passively recorded vocalizations on the array. The source levels of a sequence of whale calls in a 110-min time period, belonging to a number of individuals, are estimated based on the localization results. The estimation results are consistent with previous studies. We also examine the feasibility of actively detecting and localizing whales with OAWRS at low-to-mid frequencies in a random range-dependent ocean waveguide. A full-field waveguide scattering model is applied to determine the scattered field level from whales, as a function of range and depth location of the whale, and compared to environmental reverberation measured in the Gulf of Maine. The dominant source of scattering from whales at these frequencies is their air-filled lungs.
Polyamine‐Tethered Porous Polymer Networks for Carbon Dioxide Capture from Flue Gas (2012)

Gas guzzler: The introduction of polyamines in porous polymer networks results in significant enhancement of CO2-uptake capacities at low pressures. The best substituted network was found to exhibit high adsorption enthalpies for CO2 and the largest selectivity (see graph) of any porous material reported to date. It also had outstanding physicochemical stability and could be regenerated under mild conditions. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Linear constellation-precoding for OFDM with maximum multipath diversity and coding gains (2001)

This paper introduces linear constellation precoding (LCP) for OFDM transmissions over frequency-selective fading channels. Exploiting the correlation structure of OFDM subchannels, and choosing system parameters properly, we first perform optimal subcarrier grouping to divide the set of correlated subchannels into subsets. Within each subset, a non-redundant constellation-specific unitary precoder is then designed to achieve maximum multipath diversity and coding gains. While greatly reducing the decoding complexity and simplifying the LCP design, subcarrier grouping offers optimal performance by maximizing multipath diversity and coding gains. In addition, the proposed system does not sacrifice the transmission rate. Analytic evaluation and corroborating simulations reveal its performance merits.
Polymer thermoelectric modules screen-printed on paper (2014)

Screen-printed polymer thermoelectric devices provided sufficient power to illuminate light-emitting diodes.
Expression of Parathyroid Hypertensive Factor in Hypertensive Primary Hyperparathyroid Patients (1993)

Hypertension is frequently associated with primary hyperparathyroidism, yet the mechanism of such hypertension is unknown. Parathyroid hypertensive factor (PHF) is a circulating hypertensive factor found in a proportion of human essential hypertensive patients as well as in spontaneously hypertensive rats (SHR). In the latter case, PHF has been shown to be secreted by the parathyroid gland. The purpose of this study was to determine if PHF expression might be responsible for the hypertension seen in primary hyperparathyroidism. Ten hypertensive and 10 normotensive primary hyperparathyroid patients underwent measurement of blood pressure and PHF pre- and post-parathyroidectomy. Cases reported are those of parathyroid adenomas. There were no significant differences between the hypertensive and normotensive groups preoperatively except that 9 out of 10 of the hypertensive group had significant PHF levels (mean 11 +/- 2 mm Hg vs 0.6 +/- 2 mm Hg, respectively, p = 0.003). Post-operative change in mean arterial pressure could be predicted by pre-operative PHF level, with all PHF-positive patients showing a fall in blood pressure (r = -0.73, p < 0.01). Post-operatively, PHF was undetectable in PHF-positive patients. These results suggest that the parathyroid gland can express PHF in humans and that such expression may be responsible for a proportion of the high reported incidence of hypertension in primary hyperparathyroidism.
A Blockchain-Assisted Hash-Based Signature Scheme. (2019)

We present a server-supported, hash-based digital signature scheme. To achieve greater efficiency than current state of the art, we relax the security model somewhat. We postulate a set of design requirements, discuss some approaches and their practicality, and finally reach a forward-secure scheme with only modest trust assumptions, achieved by employing the concepts of authenticated data structures and blockchains. The concepts of blockchain authenticated data structures and the presented blockchain design could have independent value and are worth further research.
Use of interfering RNAs targeted against feline herpesvirus 1 glycoprotein D for inhibition of feline herpesvirus 1 infection of feline kidney cells (2009)

2 chemically produced siRNAs that targeted the glycoprotein D gene significantly reduced FHV-1 titers in treated cells, suggesting that glycoprotein D is necessary for production of infective virions. This gene is a potential target for RNA interference as a means of inhibition of FHV-1 infection of feline cells.