gebhart/patrepeval huggingface dataset:
A New Potent HIV-1 Reverse Transcriptase Inhibitor (1999)

The biologically relevant and active forms of human immunodeficiency viruses type 1 and 2 reverse transcriptase found in infectious virions are heterodimers produced in a two-step dimerization process. Dimerization involves first the rapid association of the two subunits, followed by a slow conformational change yielding a fully active form. We have shown that the dimeric nature of reverse transcriptase represents a important target for the design of a new class of antiviral agents. In this work, we propose a new strategy for its inhibition by targeting protein/protein interactions during viral formation in infected cells. From the screening of peptides derived from the tryptophan cluster at the interface of the connection subdomain, we have designed a short peptide (10 residues) corresponding to residues 395-404, which can block dimerization of reverse transcriptase in vitro and in infected cells. This peptide is highly efficient in abolishing the production of viral particles, without any adverse toxic side effects, when transduced into human immunodeficiency virus type 1-infected cells together with a new peptide carrier.
Area, Power, and Pin Efficient Bus Transceiver Using Multi-Bit-Differential Signaling (2005)

This paper describes a new low-power, area and pin efficient alternative to differential encoding for high performance chip-to-chip and backplane signaling. The technique, called multi-bit-differential-signaling (MBDS), consists of a new design for the driver and link termination network coupled with a novel coding system based on N choose M (nCm) codes. In an nCm coded MBDS channel, there are n physical interconnections over which all code symbols carry exactly m 1-bits. This property gives MBDS links signal-to-noise and transmission characteristics comparable to pair-wise differential links such as low-voltage differential signaling (LVDS). Moreover, MBDS is compatible with commercial LVDS receivers in point-to-point and multi-point bus topologies. However, because MBDS channels have a higher information density, they use up to 45% less power and up to 45% fewer I/O pads than equivalent differentially encoded buses.
Analysis of controlled coherence conversion in a double rephasing scheme of photon echoes for quantum memories (2016)

A controlled double rephasing (CDR) photon echo is analyzed for inversion-free photon echoes using controlled coherence conversion (CCC), where an optical Rabi flopping between an excited and an auxiliary ground states is used for atom phase control for emissive photon echoes. Unlike the rephasing mechanism in photon echoes, the CCC induces coherence inversion to the intrinsic absorptive echoes in a double rephasing scheme. Thus, the CDR echo protocol can be vastly applied for modified photon-echo quantum memories.
Synthetic Jet Cooling Technology for Electronics Thermal Management—A Critical Review (2021)

Effective removal of excess heat from electronics equipment is the key to its intended functionality. A Defense Advanced Research Projects Agency (DARPA) hard problem is proposed in microtechnologies for the air-cooled heat exchangers (MACE) program that posed challenges to reduce the heat sink size fourfold while using only 50% of the current power budget. While numerous heat removal techniques have been proposed over the last several decades, synthetic jet actuator (SJA) is one of the leading candidates to create a game-changing cooling performance. This is due to its inherent advantages, such as size, low power consumption, ease of use, and affordability. This review article looks at different actuation methods (electromagnetic, piston cylinder, piezoelectric, and so on) to generate synthetic jet cooling. The performances of these approaches vary and need a procedure to unify the predictive capability. The performances are evaluated based on actuation (stroke length, operating frequency, and jet-to-heater spacing) and geometric parameters (shape and size of the cavity and the orifice). The flow characteristics and jet formation criterion are also discussed methods, and a critical commentary is added to normalize previous findings. Available correlations for predicting Nu numbers are evaluated and summarized through data sets for a possible unification. Finally, an empirical correlation is proposed based on available data using nonlinear regression via computational tools. To conclude, the challenges and research gaps are enumerated covering the fundamental and applied aspects of those jets for the implementation in electronics thermal management.
A Bi-Directional, Zero-Latency Adaptive Clocking Circuit in a 28-nm Wide AVFS System (2019)

Resilient circuits based on in situ timing monitoring adaptive voltage-frequency scaling (AVFS) eliminate excess time margins caused by process, voltage, and temperature (PVT) variations but suffer from 50% throughput loss during error recovery when operating at a half frequency. We propose a bi-directional adaptive clocking circuit to provide fine frequency tuning with zero latency for AVFS system. It can either stretch the clock cycle when there are timing errors to ensure correct function or compress the cycle when there are excess timing margins. To support a wide frequency range, we generate multiple phase clocks based on two delay lines and select one appropriate phase clock to obtain a stretched output clock, where balanced clock paths are obtained by a time-to-digital converter and dynamic-OR gates. Applied to a wide-operating-range AVFS system of an SHA-256 accelerator with transition detector (TD) latches, the whole AVFS system is able to respond to errors in one clock cycle, with dynamic-OR gates collecting all the errors in half a cycle and adaptive clocking circuit stretching at the current cycle. Fabricated in 28-nm CMOS, chip measurement shows that it achieves 38.6%-69.4% power gains at near threshold while reducing throughput loss during error recovery.
Dispersion in holey optical fibers (1999)

Holey fibers are described using an efficient new technique based on decompo-sitions of the electric field and fiber profile. Unique and interesting dispersion properties are predicted, including dispersion flattening and anomalous dispersion below 1:3μm.
An Energy-Efficient and Bandwidth-Scalable DWDM Heterogeneous Silicon Photonics Integration Platform (2022)

Heterogeneous III-V-on-silicon photonic integration has proved to be an attractive and volume manufacturable solution that marries the merits of III-V compounds and silicon technology for various photonic integrated circuit (PIC) applications. The current main-stream Ethernet trends for larger bandwidth are pushing higher modulation baudrate or employing advanced modulation format for datacom applications. However, neither solution is likely able to significantly drive overall solution cost and energy efficiency to the best sweet spot, nor to unfold the full potential of heterogeneous integration. Here we review our innovations on a special heterogeneous III-V-on-silicon platform, and the development of a dense wavelength division multiplexed (DWDM) transceiver. A 40-channel DWDM architecture and platform fabrication are discussed first, followed by experimental demonstration of each high-quality building block. InAs/GaAs quantum dot material is the choice for building robust multi-wavelength lasers, amplifiers, and high-speed avalanche photodetectors (APDs) which complements the more mature SiGe APDs. A metal-oxide-semiconductor capacitor phase shifter is a mission critical structure to provide athermal and efficient tuning for deinterleavers and microring resonators, and high-speed modulation. A successful 8 × 25 Gb/s link demonstration paves the way for the world's first fully-integrated DWDM PIC on Si with Terabit/s aggregated bandwidth and energy efficiency likely to ∼100 fJ/bit.
S2FA (2018)

Big data analytics using the JVM-based MapReduce framework has become a popular approach to address the explosive growth of data sizes. Adopting FPGAs in datacenters as accelerators to improve performance and energy efficiency also attracts increasing attention. However, the integration of FPGAs into such JVM-based frameworks raises the challenge of poor programmability. Programmers must not only rewrite Java/Scala programs to C/C++ or OpenCL, but, to achieve high performance, they must also take into consideration the intricacies of FPGAs. To address this challenge, we present S2FA (Spark-to-FPGA-Accelerator), an automation framework that generates FPGA accelerator designs from Apache Spark programs written in Scala. S2FA bridges the semantic gap between object-oriented languages and HLS C while achieving high performance using learning-based design space exploration. Evaluation results show that our generated FPGA designs achieve up to 49.9× performance improvement for several machine learning applications compared to their corresponding implementations on the JVM.
Timing model extraction of hierarchical blocks by graph reduction (2002)

Timing model extractor builds a timing model of a digital circuit for use with a static timing analyzer. This paper proposes a novel method of generating a gray box timing model from gate-level netlist by reducing a timing graph. Previous methods of generating timing models sacrificed accuracy and/or did not scale well with design size. The proposed method is simple, yet it provides model accuracy including arbitrary levels of latch time borrowing and capability to support timing constraints that span multiple blocks. Also, cpu and memory resources required to generate the model scale well with size of the circuit. The generated model can provide a capacity improvement in timing verification by more than two orders of magnitude.
Short undeniable signatures : design, analysis, and applications (2006)

Digital signatures are one of the main achievements of public-key cryptography and constitute a fundamental tool to ensure data authentication. Although their universal verifiability has the advantage to facilitate their verification by the recipient, this property may have undesirable consequences when dealing with sensitive and private information. Motivated by such considerations, undeniable signatures, whose verification requires the cooperation of the signer in an interactive way, were invented. This thesis is mainly devoted to the design and analysis of short undeniable signatures. Exploiting their online property, we can achieve signatures with a fully scalable size depending on the security requirements. To this end, we develop a general framework based on the interpolation of group elements by a group homomorphism, leading to the design of a generic undeniable signature scheme. On the one hand, this paradigm allows to consider some previous undeniable signature schemes in a unified setting. On the other hand, by selecting group homomorphisms with a small group range, we obtain very short signatures. After providing theoretical results related to the interpolation of group homomorphisms, we develop some interactive proofs in which the prover convinces a verifier of the interpolation (resp. non-interpolation) of some given points by a group homomorphism which he keeps secret. Based on these protocols, we devise our new undeniable signature scheme and prove its security in a formal way. We theoretically analyze the special class of group characters on Z*n. After studying algorithmic aspects of the homomorphism evaluation, we compare the efficiency of different homomorphisms and show that the Legendre symbol leads to the fastest signature generation. We investigate potential applications based on the specific properties of our signature scheme. Finally, in a topic closely related to undeniable signatures, we revisit the designated confirmer signature of Chaum and formally prove the security of a generalized version.
Subdivision surfaces: a new paradigm for thin-shell finite-element analysis (2000)

We develop a new paradigm for thin-shell finite-element analysis based on the use of subdivision surfaces for (i) describing the geometry of the shell in its undeformed configuration, and (ii) generating smooth interpolated displacement fields possessing bounded energy within the strict framework of the Kirchhoff–Love theory of thin shells. The particular subdivision strategy adopted here is Loop's scheme, with extensions such as required to account for creases and displacement boundary conditions. The displacement fields obtained by subdivision are H2 and, consequently, have a finite Kirchhoff–Love energy. The resulting finite elements contain three nodes and element integrals are computed by a one-point quadrature. The displacement field of the shell is interpolated from nodal displacements only. In particular, no nodal rotations are used in the interpolation. The interpolation scheme induced by subdivision is non-local, i.e. the displacement field over one element depend on the nodal displacements of the element nodes and all nodes of immediately neighbouring elements. However, the use of subdivision surfaces ensures that all the local displacement fields thus constructed combine conformingly to define one single limit surface. Numerical tests, including the Belytschko et al. [10] obstacle course of benchmark problems, demonstrate the high accuracy and optimal convergence of the method. Copyright © 2000 John Wiley & Sons, Ltd.
Using rf impedance probe measurements to determine plasma potential and the electron energy distribution (2010)

Earlier work has demonstrated the usefulness of a network analyzer in plasma diagnostics using spherical probes in the thin sheath limit. The rf signal applied to the probe by the network analyzer is small in magnitude compared to probe bias voltages, and the instrument returns both real and imaginary parts of the complex plasma impedance as a function of frequency for given bias voltages. This information can be used to determine sheath resistance, sheath density profiles, and a technique for measuring electron temperature. The present work outlines a method for finding plasma potential and the electron energy distribution within a limited energy range. The results are compared to those using conventional Langmuir probe techniques. The rf method has general application to diverse areas of plasma investigations when the plasma is uniform and probe dimensions are much less than the size of the plasma. These applications include laboratory and space environments.
Use of venom coagglutinin and lyophilized platelets in testing for platelet-aggregating von Willebrand factor (1980)

Previous procedures for measuring von Willebrand factor (vWF) in human plasma have usually utilized ristocetin and platelet-rich plasma or washed platelets. In this study, we describe a new approach for determination of vWF utilizing two new reagents. One is venom coagglutinin, a recently recognized component of Bothrops and other venoms, which aggregates platelets in the presence of vWF. The other is lyophilized fixed human platelets. The rate of platelet aggregation was found to be a function of both plasma vWF and venom coagglutinin concentration. By keeping the venom factor constant, simple and reliable test procedures for vWF were devised. Both a macroscopic test procedure and aggregometry were used for measuring platelet aggregation, with similar findings. Results obtained with the venom coagglutinin reagent were compared with those obtained with ristocetin. With the venom factor, normal plasmas from 20 subjects had a range of 70%–133% vWF and a mean of 96% of a reference plasma, while with ristocetin, the values were 63%–131%, mean 101%. Plasmas from seven von Willebrand disease patients gave comparable reduced values for vWF with venom factor and with ristocetin. The venom coagglutinin and dried platelet reagents appear to provide the basis for simple and reliable procedures for determination of plasma vWF.
Leveraging Pre-trained Language Model for Speech Sentiment Analysis (2021)

In this paper, we explore the use of pre-trained language models to learn sentiment information of written texts for speech sentiment analysis. First, we investigate how useful a pre-trained language model would be in a 2-step pipeline approach employing Automatic Speech Recognition (ASR) and transcripts-based sentiment analysis separately. Second, we propose a pseudo label-based semi-supervised training strategy using a language model on an end-to-end speech sentiment approach to take advantage of a large, but unlabeled speech dataset for training. Although spoken and written texts have different linguistic characteristics, they can complement each other in understanding sentiment. Therefore, the proposed system can not only model acoustic characteristics to bear sentiment-specific information in speech signals, but learn latent information to carry sentiments in the text representation. In these experiments, we demonstrate the proposed approaches improve F1 scores consistently compared to systems without a language model. Moreover, we also show that the proposed framework can reduce 65% of human supervision by leveraging a large amount of data without human sentiment annotation and boost performance in a low-resource condition where the human sentiment annotation is not available enough.
Parallelism of double divide and conquer algorithm for singular value decomposition (2007)

This paper presents some numerical evaluations of parallel double Divide and Conquer for singular value decomposition. For eigenvalue decomposition and singular value decomposition, double Divide and Conquer was recently proposed. It first computes eigen/singular values by a compact version of Divide and Conquer. The corresponding eigen/singular vectors are then computed by twisted factorization. The speed and accuracy of double Divide and Conquer are as good or even better than standard algorithms such as QR and the original Divide and Conquer. In addition, it is expected that double Divide and Conquer has great parallelism because each step is theoretically parallel and heavy communication is not required. This paper numerically evaluates a parallel implementation of dDC with MPI on some large scale problems using a distributed memory architecture and a massively parallel super computer, especially in terms of parallelism. It shows high scalability and super linear speed-up is observed in some cases.
A NEW APPROACH TO OLIGONUCLEOTIDE N3′⇉P5′ PHOSPHORAMIDATE BUILDING BLOCKS (2005)

A new synthetic approach to 5-phosphoramidites of 3'-aminonucleosides was developed. The methodology relies upon the use of 3'-amino-2',3'-dideoxy nucleosides as the key starting materials. The final phosphoramidite products were obtained with high yields via 2-3-step efficient chemical transformations using selective introduction of orthogonal protective groups to the 3'-aminonucleoside sugar and base moieties.
Semisynthetic Derivatives of Purpuromycin as Potential Topical Agents for Vaginal Infections (1997)

Purpuromycin (1) is an antibiotic with a broad spectrum of antimicrobial activity, encompassing bacteria, fungi, and protozoa, particularly those involved in vaginal infections. With the aim of enhancing the solubility and reducing the serum binding, a chemical program of modifications was undertaken on the natural compound, and a new interesting series of derivatives at the naphthoquinone system was synthesized and evaluated as potential topical agents for vaginal infections. In particular three semisynthetic derivatives, 7'-amino (8a), 7'-methylamino (8b), 7'-ethylamino (8c), of 7'-demethoxypurpuromycin seemed to be the most promising. They were tested for in vitro activity against three of the most important vaginal pathogens and showed activity similar to that of purpuromycin against Candida isolates while they were significantly more active against Trichomonas vaginalis and Gardnerella vaginalis, which are cultured in media containing blood or serum. This is probably due to the fact that the activity of the derivatives is less antagonized by these supplements than that of purpuromycin.
Mining alarm clusters to improve alarm handling efficiency (2005)

It is a well-known problem that intrusion detection systems overload their human operators by triggering thousands of alarms per day. As a matter of fact, IBM Research's Zurich Research Laboratory has been asked by one of our service divisions to help them deal with this problem. This paper presents the results of our research, validated thanks to a large set of operational data. We show that alarms should be managed by identifying and resolving their root causes. Alarm clustering is introduced as a method that supports the discovery of root causes. The general alarm clustering problem is proved to be NP-complete, an approximation algorithm is proposed, and experiments are presented.
Induction of superovulation using inhibin antiserum and competence of embryo development in wild large Japanese field mice (<i>Apodemus speciosus</i>) (2019)

Seasonally, bred wild mice provide a unique bioresource, with high genetic diversity that differs from wild-derived mice and laboratory mice. This study aimed to establish an alternative superovulation method using wild large Japanese field mice (Apodemus speciosus) as the model species. Specifically, we investigated how the application of inhibin antiserum and equine chorionic gonadotropin (IASe) during both the reproductive and non-reproductive seasons impact the ovulation rate and competence of embryo development after in vitro fertilization (IVF) with fresh and cryopreserved sperm. When the wild mice were superovulated by injecting eCG followed by human chorionic gonadotropin (hCG), few oocytes were collected during the reproductive and non-reproductive seasons. In comparison, the number of ovulated oocytes was dramatically enhanced by the administration of IASe, followed by isolation of ovulated oocytes 24 hr after 30 IU hCG administration. The IVF oocytes that were in vitro cultured (IVC) with medium containing serum further developed to the 2- and/or 4-cell stage using both fresh and frozen-thawed sperm. In conclusion, we successfully established an alternative protocol for collecting ovulated oocytes from wild large Japanese field mice by administering IASe and hCG during both the reproductive and non-reproductive seasons. This study is the first to develop IVF-IVC wild large Japanese field mice beyond the 2- and/or 4-cell stage in vitro using fresh and cryopreserved sperm. This approach could be used in other species of wild or endangered mice to reduce the number of animals used for experiments, or in maintaining stocks of germ cells or embryos.
Optical diffraction tomography for high resolution live cell imaging (2009)

We report the experimental implementation of optical diffraction tomography for quantitative 3D mapping of refractive index in live biological cells. Using a heterodyne Mach-Zehnder interferometer, we record complex field images of light transmitted through a sample with varying directions of illumination. To quantitatively reconstruct the 3D map of complex refractive index in live cells, we apply optical diffraction tomography based on the Rytov approximation. In this way, the effect of diffraction is taken into account in the reconstruction process and diffraction-free high resolution 3D images are obtained throughout the entire sample volume. The quantitative refractive index map can potentially serve as an intrinsic assay to provide the molecular concentrations without the addition of exogenous agents and also to provide a method for studying the light scattering properties of single cells.