gebhart/patrepeval huggingface dataset:
Structure−Activity Relationship of Small-Sized HIV Protease Inhibitors Containing Allophenylnorstatine (1999)

We designed and synthesized a new class of peptidomimetic human immunodeficiency virus (HIV) protease inhibitors containing a unique unnatural amino acid, allophenylnorstatine [Apns; (2S, 3S)-3-amino-2-hydroxy-4-phenylbutyric acid], with a hydroxymethylcarbonyl (HMC) isostere as the active moiety. A systematic evaluation of structure-activity relationships for HIV protease inhibition, anti-HIV activities, and pharmacokinetic profiles has led to the delineation of a set of structural charateristics that appear to afford an orally available HIV protease inhibitor. Optimum structures, exemplified by 21f (JE-2147), incorporated 3-hydroxy-2-methylbenzoyl groups as the P2 ligand, (R)-5,5-dimethyl-1,3-thiazolidine-4-carbonyl (Dmt) residue at the P1' site, and 2-methylbenzylcarboxamide group as the P2' ligand. The present study demonstrated that JE-2147 has potent antiviral activities in vitro and exhibits good oral bioavailability and plasma pharmacokinetic profiles in two species of laboratory animals.
Dual-pump dual-broadband coherent anti-Stokes Raman scattering in reacting flows (2004)

A dual-pump, dual-broadband coherent anti-Stokes Raman scattering system for simultaneous measurements of temperature and concentrations of N2, O2, and CO2 in reacting flows is demonstrated. In this system pure rotational transitions of N2-O2 and rovibrational transitions of N2-CO2 are probed simultaneously with two narrowband pump beams, a broadband pump beam, and a broadband Stokes beam. The main advantage of this technique is that it permits accurate temperature measurements at both low and high temperatures as well as concentration measurements of three molecules.
A dynamic cepstrum incorporating time-frequency masking and its application to continuous speech recognition (1993)

A dynamic cepstrum parameter that incorporates the time-frequency characteristics of auditory forward masking is proposed. A masking model is derived from psychological experimental results. A novel operational method using a lifter array is derived to perform the time-frequency masking. The parameter simulates the effective input spectrum at the front-end of the auditory system and can enhance the spectral dynamics. The parameter represents both the instantaneous and transitional aspects of a spectral time series. Phoneme and continuous speech recognition experiments demonstrated that the dynamic cepstrum outperforms the conventional cepstrum individually and in various combinations with other spectral parameters. The phoneme recognition results were improved for ten male and ten female speakers. The masking lifter with a Gaussian window provided a better performance than that with a square window.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dopamine autoreceptor agonists as potential antipsychotics. 3. 6-Propyl-4,5,5a,6,7,8-hexahydrothiazolo[4,5-f]quinolin-2-amine (1991)

A series of rigid tricyclic analogues of the dopamine (DA) agonist PD 118440 [4-(1,2,5,6-tetrahydro-1-propyl-3-pyridinyl)-2-thiazolamine] was synthesized and evaluated for dopaminergic activity and DA autoreceptor selectivity. (R)-(+)-6-Propyl-4,5,5a,6,7,8-hexahydrothiazolo[4,5-f]quinolin+ ++-2-amine [+)-6) was identified as the most selective DA autoreceptor agonist from this group of compounds. It inhibited spontaneous locomotor activity (LMA) in rodents, reversed the gamma-butyrolactone (GBL) induced accumulation of rat striatal DOPA and inhibited brain DA neuronal firing, all suggestive of direct DA autoreceptor agonist activity. However, (+)-6 is not completely free of postsynaptic DA activity, as evidenced by its stimulation of LMA in rats at high doses and its ability to produce stereotypy. On the other hand, (-)-6 appears to be a weak partial DA agonist with some effects on brain DA synthesis only at high doses. Like other DA autoreceptor agonists and DA antagonists, (+)-6 inhibited Sidman conditioned avoidance in squirrel monkeys, a test predictive of clinical antipsychotic activity. However, unlike classical antipsychotics, (+)-6 did not induce dystonias in haloperidol-sensitized squirrel monkeys, suggesting a minimal propensity toward extrapyramidal side effects (EPS).
Intracellular temperature measurements with fluorescent polymeric thermometers (2017)

In 2003, we successfully created the first fluorescent polymeric thermometer by combining a thermo-responsive polymer and an environment-sensitive (polarity and hydrogen bonding-sensitive) fluorophore. Its high sensitivity to temperature variation and high hydrophilicity, even under conditions of high ionic strength, enabled intracellular temperature measurements. Along with the progress of our research projects, the development of new luminescent molecular thermometers and the establishment of novel methods for measuring intracellular temperature have matured in this field. In this Feature Article, we summarize the background and history of intracellular temperature measurements using fluorescent polymeric thermometers based on studies performed in our laboratory and the relationship between our methods and those of other eminent research groups. Future research directions regarding intracellular temperature measurements are also discussed.
Opportunistic interference alignment in cellular downlink (2012)

Interference alignment is known to be degrees of freedom optimal for the K-user interference channel. As a result, many alignment-based schemes have been developed in literature. However, most schemes are not easy to implement due to the requirements for a large number of dimensions and an extensive exchange of channel state information. This paper eliminates these requirements by combining interference alignment with the idea of opportunistic scheduling to facilitate alignment in the cellular downlink by opportunistically selecting users and harnessing the multi-user nature of cellular scheduling. Specifically, the opportunistic interference alignment scheme requires no channel state information at the base station transmitters. Simulation results show significant improvement in throughput of cell-edge users without any degradation in performance of other users.
<i>EyeVEIL</i> (2019)

Mixed reality headsets are being designed with integrated eye trackers: cameras that image the user's eye to infer gaze location and pupil diameter. While the intent is to improve the quality of experience, built-in eye trackers create a security vulnerability for hackers - high resolution images of the user's iris. Anyone stealing an iris image has effectively captured a gold standard biometric, relied on for secure authentication in applications such as banking and voting. We present a low cost solution to degrade iris authentication while still permitting the utility of gaze tracking with acceptable accuracy. By demonstrating this solution on a commodity eye tracker, this paper urges the community to think about iris based authentication as a byproduct of eye tracking, and create solutions that empower a user to control this biometric.
Gesture based 3D man-machine interaction using a single camera (2003)

This paper describes a new gesture based input interface system that allows users to control both 2D and 3D applications using simple hand gestures. Using a single camera attached to the computer, the system tracks the user's hand in three dimensions and computes up to four parameters in real-time (60 Hz). The system recognizes three gestures that can be interpreted as discrete commands to applications. This system is an off-shoot of an earlier system called Gesture VR that requires multiple cameras. Since the new system uses a single video source it can run readily on a standard home computer equipped with an inexpensive camera and is, therefore, accessible to most users. The system can be used with applications that require 2D and 2D interactions. Examples discussed in this paper include 3D virtual fly-throughs, graphical scene composers and video games.
Characterization of the <i>Moraxella catarrhalis uspA1</i> and <i>uspA2</i> Genes and Their Encoded Products (1999)

The uspA1 and uspA2 genes of M. catarrhalis O35E encode two different surface-exposed proteins which were previously shown to share a 140-amino-acid region with 93% identity (C. Aebi, I. Maciver, J. L. Latimer, L. D. Cope, M. K. Stevens, S. E. Thomas, G. H. McCracken, Jr., and E. J. Hansen, Infect. Immun. 65:4367-4377, 1997). The N-terminal amino acid sequences of the mature forms of both UspA1 and UspA2 from strain O35E were determined after enzymatic treatment to remove the N-terminal pyroglutamyl residue that had blocked Edman degradation. Mass spectrometric analysis indicated that the molecular mass of UspA1 from M. catarrhalis O35E was 83,500 +/- 116 Da. Nucleotide sequence analysis of the uspA1 and uspA2 genes from three other M. catarrhalis strains (TTA24, ATCC 25238, and V1171) revealed that the encoded protein products were very similar to those from strain O35E. Western blot analysis was used to confirm that each of these three strains of M. catarrhalis expressed both UspA1 and UspA2 proteins. Several different and repetitive amino acid motifs were present in both UspA1 and UspA2 from these four strains, and some of these were predicted to form coiled coils. Linear DNA templates were used in an in vitro transcription-translation system to determine the sizes of the monomeric forms of the UspA1 and UspA2 proteins from strains O35E and TTA24.
Head Tracking Stereoscopic Projection Display Technique (1990)

特殊な眼鏡を使用する従来の立体画像表示技術は, 観察者に不自然感, 不快感を与えるため, 眼鏡を使用しない表示技術の開発が望まれている.本検討では, レンティキュラスクリーンと2台の液晶プロジェクタ, および観察者の頭部位置を電子的に認識, 追跡する頭部認識追跡装置からなる新しいコンセプトの立体画像投写表示技術を提案し, 実験装置を試作した.レンティキュラスクリーンとしては, 縦1000mm, 横900mm, ピッチ0.5mmの反射タイプを試作した.液晶プロジェクタは, 横640画素, 縦440画素の画素からなる約6インチの単板液晶パネルをライトバルブとした装置を試作した.頭部認識追跡装置は, 観察者の頭部に装着した位置検出素子で観察者頭部の位置を検出し, その位置信号で液晶プロジェクタに入力する信号を制御する構成とした.実験検討の結果, 対角長44インチの立体表示が可能なこと, 頭部の認識追跡が可能なこと, 表示面から奥行き方向に約2100mmの位置で, 左右方向に約600mmの範囲で立体視が可能であることを確認した.
High temporal resolution and streak-free four-dimensional cone-beam computed tomography (2008)

Cone-beam computed tomography (CBCT) has been clinically used to verify patient position and to localize the target of treatment in image-guided radiation therapy (IGRT). However, when the chest and the upper abdomen are scanned, respiratory-induced motion blurring limits the utility of CBCT. In order to mitigate this blurring, respiratory-gated CBCT, i.e. 4D CBCT, was introduced. In 4D CBCT, the cone-beam projection data sets acquired during a gantry rotation are sorted into several respiratory phases. In these gated reconstructions, the number of projections for each respiratory phase is significantly reduced. Consequently, undersampling streaking artifacts are present in the reconstructed images, and the image contrast resolution is also significantly compromised. In this paper, we present a new method to simultaneously achieve both high temporal resolution ( approximately 100 ms) and streaking artifact-free image volumes in 4D CBCT. The enabling technique is a newly proposed image reconstruction method, i.e. prior image constrained compressed sensing (PICCS), which enables accurate image reconstruction using vastly undersampled cone-beam projections and a fully sampled prior image. Using PICCS, a streak-free image can be reconstructed from 10-20 cone-beam projections while the signal-to-noise ratio is determined by a denoising feature of the selected objective function and by the prior image, which is reconstructed using all of the acquired cone-beam projections. This feature of PICCS breaks the connection between the temporal resolution and streaking artifacts' level in 4D CBCT. Numerical simulations and experimental phantom studies have been conducted to validate the method.
Isolation and identification of a Giardia lamblia-specific stool antigen (GSA 65) useful in coprodiagnosis of giardiasis (1986)

A Giardia lamblia-specific antigen (GSA 65) was isolated from stools of G. lamblia-positive patients by crossed- and line-immunoelectrophoresis and counterimmunoelectrophoresis (CIE) in agarose by using rabbit antiserum prepared against G. lamblia cysts. CIE with rabbit anti-GSA 65 monospecific antiserum revealed that GSA 65 was present in aqueous stool eluates of giardiasis patients and in cysts and trophozoites of the parasite. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of immunoaffinity-purified antigen followed by Western blotting showed that the molecular weight of this molecule was about 65,000. GSA 65 was detectable by CIE in stool eluates of 36 of 40 giardiasis patients but not in eluates of 10 G. lamblia-negative asymptomatic controls. GSA 65 was detected in stool eluates of 2 of 18 individuals with chronic diarrhea who were negative for parasites by microscopic examination. Cross-specificity studies with other genera of parasitic protozoa performed by using CIE and immunofluorescence indicated that GSA 65 was present only in strains of G. lamblia. Based on these findings, GSA 65 may prove to have an important application in the design of sensitive diagnostic tests for giardiasis.
The Role of Interfaces in Damascene Phase-Change Memory (2007)

Phase change memory (PCM) research has largely focused on bulk properties to evaluate cell efficiency. Now both electrical and thermal interface resistances are characterized and shown to be critical for understanding power in a novel damascene-GST cell. Interfaces reduce reset power 20% and reset current 40% and allow reset current to scale faster than it would without interfaces.
Engineering of dual-functional hybrid glucanases (2012)

1,3-1,4-β-D-Glucanase (lichenase) and 1,3-β-D-glucanase (laminarinase) are fibrolytic enzymes which play an important role in the hydrolysis of polysaccharide components. Both of these glucanases have been employed in a number of industrial applications. This study aims to improve or combine the novel properties of both glucanases in an attempt to create desirable hybrid enzymes with economic benefits for industrial applications. A truncated and mutated 1,3-1,4-β-D-glucanase gene (TFs(W203F)) from Fibrobacter succinogenes, and a 1,3-β-D-glucanase gene (TmLam) from hyperthermophilic Thermotoga maritima were used as target enzymes. The substrate-binding domains (TmB₁ and TmB₂) and the catalytic domain (TmLam(CD)) of TmLam were ligated to the N- or C-terminus of TFsW203F to create four hybrid enzymes, TmB₁-TFs(W203F), TFs(W203F)-TmB₂, TmB₁-TFs(W203F)-TmB₂ and TFs(W203F)-TmLam(CD). The results obtained from kinetic studies show that increased specific activities and turnover rate for lichenan and laminarin were observed in TmB₁-TFs(W203F)-TmB₂ and TFs(W203F)-TmLam(CD), respectively. Furthermore, fluorescence and circular dichroism spectrometric analyses indicated that the hybrid TFs(W203F)-TmLam(CD) was structurally more stable than the parental TFs(W203F), which was attributed to an improved thermal tolerance of the hybrid enzyme. This study has been successful in creating bifunctional hybrid glucanases with dual substrate catalytic functions which warrant further evaluation of their possible use in industrial applications.
Molecular Interferometric Imaging Biosensor (2007)

We present molecular interferometric imaging (MI2) as a new sensing technique for direct detection of biomolecules that is easier and more sensitive than surface plasmon resonance and scalable to hundreds of assays per chip.
Ultrasonic Air Temperature Sensing for Automatic Climate Control - Sensor Development (2003)

Automatic climate control could be improved by measuring air temperature ultrasonically. Thermal comfort correlates better with bulk air temperature than with the temperature measured by the in-car sensor. The time of flight of an ultrasonic pulse through the air gives the bulk air temperature. In a proof-of-concept experiment, it is accurate to ′ 0.5 °C from -40 to +60 °C. Two operational modes are demonstrated: pulse-echo in which a single transducer creates a pulse and detects its return from a reflector, and single-pass in which a source transducer creates a pulse that travels directly to a separate transducer.
Demuxing Models in Joint Multilayer Restoration for Packet-over-Optical Networks (2003)

Given that packet grooming can only be performed in the packet network layer, there are three demuxing models proposed to handle the packet traffic demultiplexing in the novel joint multilayer restoration scheme. The essence of these alternative models is to compare different mechanisms and, therefore, find the best approach to de-multiplex the originally aggregated multiple packet streams when they are to be switched by the OXCs beneath the failed packet router. Our study concludes that the Upstream Router Demuxing Model performs the best among all the models proposed.
Dynamic peer-to-peer (P2P) solution to counter malicious higher Domain Name System (DNS) nameservers (2011)

The Domain Name System (DNS) is a critical service in the Internet infrastructure which provides user-friendly name to Internet IP address mapping. The absence of the DNS has a severe impact on several Internet services such as email. To avoid an intentional blocking from a malicious higher name server, a dynamic round-robin peer-to-peer (P2P) solution that is built over the Chord protocol is proposed as a secondary path to resolve the DNS queries. An evaluation of the proposed solution based on load balancing, failure, timeout, and number of hops is also conducted through simulation experiments.
High‐Throughput Proteomics Enabled by a Photocleavable Surfactant (2020)

Abstract Mass spectrometry (MS)‐based proteomics provides unprecedented opportunities for understanding the structure and function of proteins in complex biological systems; however, protein solubility and sample preparation before MS remain a bottleneck preventing high‐throughput proteomics. Herein, we report a high‐throughput bottom‐up proteomic method enabled by a newly developed MS‐compatible photocleavable surfactant, 4‐hexylphenylazosulfonate (Azo) that facilitates robust protein extraction, rapid enzymatic digestion (30 min compared to overnight), and subsequent MS‐analysis following UV degradation. Moreover, we developed an Azo‐aided bottom‐up method for analysis of integral membrane proteins, which are key drug targets and are generally underrepresented in global proteomic studies. Furthermore, we demonstrated the ability of Azo to serve as an “all‐in‐one” MS‐compatible surfactant for both top‐down and bottom‐up proteomics, with streamlined workflows for high‐throughput proteomics amenable to clinical applications.
A World-to-Chip Interface for Digital Microfluidics (2008)

Digital microfluidics (DMF) is a fluid handling technique that enables manipulation of discrete droplets on an array of electrodes. There is considerable enthusiasm for this method because of the potential for array-based screening applications. A limitation for DMF is nonspecific adsorption of reagents to device surfaces. If a given device is used to actuate multiple reagents, this phenomenon can cause undesirable cross-contamination. A second limitation for DMF (and all other microfluidic systems) is the "world-to-chip" interface; it is notoriously difficult to deliver reagents and samples to such systems without compromising the oft-hyped advantages of rapid analyses and reduced reagent consumption. We introduce a new strategy for digital microfluidics, in which a removable plastic "skin" is used to (a) eliminate cross-contamination and (b) bridge the world-to-chip interface. We demonstrated the utility of this format by implementing on-chip protein digestion on immobilized enzyme depots. This new method has the potential to transform DMF from being a curiosity for aficionados into a technology that is useful for biochemical applications at large.
Purification and In Vitro Activity of Mitochondria Targeted Nitrogenase Cofactor Maturase NifB (2017)

Active NifB is a milestone in the process of engineering nitrogen fixing plants. NifB is an extremely O<sub>2</sub>-sensitive <i>S</i>-adenosyl methionine (SAM)-radical enzyme that provides the key metal cluster intermediate (NifB-co) for the biosyntheses of the active-site cofactors of all three types of nitrogenases. NifB and NifB-co are unique to diazotrophic organisms. In this work, we have expressed synthetic codon-optimized versions of NifB from the γ-proteobacterium <i>Azotobacter vinelandii</i> and the thermophilic methanogen <i>Methanocaldococcus infernus</i> in <i>Saccharomyces cerevisiae</i> and in <i>Nicotiana benthamiana</i>. NifB proteins were targeted to the mitochondria, where O<sub>2</sub> consumption is high and bacterial-like [Fe-S] cluster assembly operates. In yeast, NifB proteins were co-expressed with NifU, NifS, and FdxN proteins that are involved in NifB [Fe-S] cluster assembly and activity. The synthetic version of thermophilic NifB accumulated in soluble form within the yeast cell, while the <i>A. vinelandii</i> version appeared to form aggregates. Similarly, NifB from <i>M. infernus</i> was expressed at higher levels in leaves of <i>Nicotiana benthamiana</i> and accumulated as a soluble protein while <i>A. vinelandii</i> NifB was mainly associated with the non-soluble cell fraction. Soluble <i>M. infernus</i> NifB was purified from aerobically grown yeast and biochemically characterized. The purified protein was functional in the <i>in vitro</i> FeMo-co synthesis assay. This work presents the first active NifB protein purified from a eukaryotic cell, and highlights the importance of screening <i>nif</i> genes from different organisms in order to sort the best candidates to assemble a functional plant nitrogenase.
SVP: scan-line video processor-general purpose video processor (2002)

The SVP achieved a fast processing rate exceeding standard DSPs by integrating 1024 PEs (Processing Elements). 50 MHz operation in each PE in the SIMD (Single Instruction Multiple Data) scheme is realized on two stage pipelines in the IG (Instruction Generator) and five stage pipelines in the PE CORE. With the realization of a 20 ns DRAM cycle in each PE and the system clock generated through a PLL, SVP enables full-spec-EDTV2 (the second generation Enhanced Definition Television in Japan).
New Estrogenic Prenylflavone from<i>Epimedium brevicornum</i>Inhibits the Growth of Breast Cancer Cells (2005)

Estrogens maintain female sexual health. The hormone also drives the growth of estrogen receptor (ER) positive breast tumors, and ER modulators, like tamoxifen, are used to reduce tumor recurrence. To identify phytoestrogens with possible health benefits, we screened several Traditional Chinese Medicines and encountered an extract from the leaves of Epimedium brevicornum (EB), with strong (EC50: 1.3 microg/mL) and specific ER-stimulatory activity. It increased estrogen-responsive human breast cancer cell proliferation at low doses, but paradoxically caused profound inhibition of growth at higher doses. Using bioassay-guided fractionation, we isolated and characterized a new prenylflavone, breviflavone B, which exerted biphasic stimulatory and inhibitory effects on breast cancer cell proliferation, mimicking the effects of EB. In contrast to estradiol and genistein, high doses (> 2 microM) of breviflavone B almost eliminated ERalpha protein; a process that may be mediated through increased proteasome degradation. Pre-clinical studies are needed to explore whether these prenylflavones are of value in estrogen-deficiency states and for prophylaxis of breast cancer.