gebhart/patrepeval huggingface dataset:
Synthesis, Photophysical, Photochemical and Biological Properties of Caged GABA, 4-[[(2H-1-Benzopyran-2-one-7-amino-4-methoxy) carbonyl] amino] Butanoic Acid¶ (2005)

The photorelease of a caged neurotransmitter can be used to investigate the function of neuronal circuits in tissues. We have designed and synthesized a stable, caged gamma-aminobutyric acid (GABA) derivative, 4-[[(2H-1-benzopyran-2-one-7-amino-4-methoxy)carbonyl]amino] butanoic acid (BC204), that releases the neurotransmitter in physiological medium when irradiated with UV light at 300-400 nm in PBS at pH 7.4. The release of GABA occurs with the formation of the major photoproduct, 7-amino-4-(hydroxymethyl)-2H-1-benzopyran-2-one, via a solvolytic photodegradation mechanism of the coumarin moiety and was confirmed by electrospray mass spectrometry/mass spectrometry (ESI MS/MS). BC204 is chemically stable and shows no intrinsic activity after many hours under physiological dark conditions. These properties suggest that BC204 is an excellent form of caged GABA that is well suited for long-term biological studies.
Cloning and Characterization of the Glucooligosaccharide Catabolic Pathway β-Glucan Glucohydrolase and Cellobiose Phosphorylase in the Marine Hyperthermophile<i>Thermotoga neapolitana</i> (2000)

Characterization in Thermotoga neapolitana of a catabolic gene cluster encoding two glycosyl hydrolases, 1,4-beta-D-glucan glucohydrolase (GghA) and cellobiose phosphorylase (CbpA), and the apparent absence of a cellobiohydrolase (Cbh) suggest a nonconventional pathway for glucan utilization in Thermotogales. GghA purified from T. neapolitana is a 52.5-kDa family 1 glycosyl hydrolase with optimal activity at pH 6.5 and 95 degrees C. GghA releases glucose from soluble glucooligomers, with a preference for longer oligomers: k(cat)/K(m) values are 155.2, 76.0, and 9.9 mM(-1) s(-1) for cellotetraose, cellotriose, and cellobiose, respectively. GghA has broad substrate specificity, with specific activities of 236 U/mg towards cellobiose and 251 U/mg towards lactose. With p-nitrophenyl-beta-glucoside as the substrate, GghA exhibits biphasic kinetic behavior, involving both substrate- and end product-directed activation. Its capacity for transglycosylation is a factor in this activation. Cloning of gghA revealed a contiguous upstream gene (cbpA) encoding a 93.5-kDa cellobiose phosphorylase. Recombinant CbpA has optimal activity at pH 5.0 and 85 degrees C. It has specific activity of 11.8 U/mg and a K(m) of 1.42 mM for cellobiose, but shows no activity towards other disaccharides or cellotriose. With its single substrate specificity and low K(m) for cellobiose (compared to GghA's K(m) of 28.6 mM), CbpA may be the primary enzyme for attacking cellobiose in Thermotoga spp. By phosphorolysis of cellobiose, CbpA releases one activated glucosyl molecule while conserving one ATP molecule per disaccharide. CbpA is the first hyperthermophilic cellobiose phosphorylase to be characterized.
Terahertz generation with tilted-front laser pulses in a contact-grating scheme (2014)

We present a detailed analysis of terahertz generation with tilted-front optical pulses in a scheme, where the pulse-front tilt is introduced by transmitting the laser pulse through a diffraction grating placed on the boundary of an electro-optic crystal. The analysis accounts for a finite transverse size of the pump laser beam, initial chirp of the laser pulse, and distortion of the tilted-front pulse in the crystal due to angular and material dispersion. Two situations of practical interest are explored—LiNbO3 pumped at 0.8 μm wavelength and GaAs pumped at 1.8 μm. Recommendations on increasing the efficiency of the optical-to-terahertz conversion, optimizing the generated terahertz spectrum, and improving the quality of the terahertz beam are given.
Optimizing one-shot recognition with micro-set learning (2010)

For object category recognition to scale beyond a small number of classes, it is important that algorithms be able to learn from a small amount of labeled data per additional class. One-shot recognition aims to apply the knowledge gained from a set of categories with plentiful data to categories for which only a single exemplar is available for each. As with earlier efforts motivated by transfer learning, we seek an internal representation for the domain that generalizes across classes. However, in contrast to existing work, we formulate the problem in a fundamentally new manner by optimizing the internal representation for the one-shot task using the notion of micro-sets. A micro-set is a sample of data that contains only a single instance of each category, sampled from the pool of available data, which serves as a mechanism to force the learned representation to explicitly address the variability and noise inherent in the one-shot recognition task. We optimize our learned domain features so that they minimize an expected loss over micro-sets drawn from the training set and show that these features generalize effectively to previously unseen categories. We detail a discriminative approach for optimizing one-shot recognition using micro-sets and present experiments on the Animals with Attributes and Caltech-101 datasets that demonstrate the benefits of our formulation.
Immobilization of Penicillin G Acylase on Poly[(glycidyl methacrylate)‐<i>co</i>‐(glycerol monomethacrylate)]‐Grafted Magnetic Microspheres (2008)

Poly[(glycidyl methacrylate)-co-(glycerol monomethacrylate)]-grafted magnetic microspheres were prepared by graft random copolymerization via ATRP from polymer microspheres with dispersed Fe(3)O(4) nanoparticles. Penicillin G acylase (PGA) was immobilized onto the polymer brush-grafted magnetic microspheres. The immobilized PGA prepared with initial glycidyl methacrylate/glycerol monomethacrylate ratios of 40/60 to 60/40 possessed higher catalytic activity than that prepared with higher proportions of glycidyl methacrylate in the initial monomer mixture. The immobilized PGA showed high thermal stability and enhanced tolerability to the pH variance.
gp63 Homologues in<i>Trypanosoma cruzi</i>: Surface Antigens with Metalloprotease Activity and a Possible Role in Host Cell Infection (2003)

gp63 is a highly abundant glycosylphosphatidylinositol (GPI)-anchored membrane protein expressed predominantly in the promastigote but also in the amastigote stage of Leishmania species. In Leishmania spp., gp63 has been implicated in a number of steps in establishment of infection. Here we demonstrate that Trypanosoma cruzi, the etiological agent of Chagas' disease, has a family of gp63 genes composed of multiple groups. Two of these groups, Tcgp63-I and -II, are present as high-copy-number genes. The genomic organization and mRNA expression pattern were specific for each group. Tcgp63-I was widely expressed, while the Tcgp63-II group was scarcely detected in Northern blots, even though it is well represented in the T. cruzi genome. Western blots using sera directed against a synthetic peptide indicated that the Tcgp63-I group produced proteins of approximately 78 kDa, differentially expressed during the life cycle. Immunofluorescence staining and phosphatidylinositol-specific phospholipase C digestion confirmed that Tcgp63-I group members are surface proteins bound to the membrane by a GPI anchor. We also demonstrate the presence of metalloprotease activity which is attributable, at least in part, to Tcgp63-I group. Since antibodies against Tcgp63-I partially blocked infection of Vero cells by trypomastigotes, a possible role for this group in infection is suggested.
Protein secretion in Tetrahymena thermophila. Characterization of the major proteinaceous secretory proteins. (1986)

The contents of mucocysts of the ciliated protozoan Tetrahymena thermophila comprise about 12 proteins, ranging in relative mobility (Mr) from approximately 160,000 to 8,000. There are at least four families of sulfhydryl-linked mucocyst polypeptides. One of these families includes a prominent Mr 34,000 protein, as determined by one- and two-dimensional gel electrophoresis. The Mr 34,000 protein is resolved into two species in isoelectric focusing gels, with apparent pI values of 4.8 and 4.9; most of the other mucocyst proteins also exhibit acidic apparent isoelectric points. The identity of the major Mr 34,000 protein as a bona fide mucocyst component is substantiated by indirect immunofluorescent localization of this protein in a linear punctate pattern coincident with the localization of mucocysts in these cells; this pattern of localization can be abolished by stimulation of synchronous secretion and is absent in a mutant strain devoid of these secretory organelles (Maihle, N. J., and Satir, B. H. (1985a) J. Cell Sci. 78, 49-65.
An assistive robotic agent for pedestrian mobility (2001)

The goal of this project is to develop a pedestrian mobility aid for the elderly. In order for this type of assistive technology to be useful and accepted by its intended user community, it must enhance the abilities of users, not replace them. This leads to an agent architecture in which the agent must operate without hindering the user's ability to take direct action when they choose. In other words, the agent cannot simply be a proxy for the user's actions. The agent must select its own goals based on observations of its users actions. This is crucial not only because users may have diminished capacity to explain their actions to an agent, but because the ability of the agent to correctly interpret the user's goals is tied to its ability to act while still allowing the user to “feel in control”. We present a mobility aid, i. e. a wheeled walker, which varies its goals and level of activity based on an estimation of its user's intentions. The assistive agent often takes no action, allowing the user to be fully in control. When the ease or safety of the users travel is threatened, the agent attempts to influence the users motion based on its belief in the users goal. By varying the degree of autonomy, the walker can adjust to the user as their abilities change from day to day, or hour to hour. This prevents the walker from trying to do too much, allowing the user to feel as if they are in control and not being lead.
Structure and motion from line segments in multiple images (1995)

This paper presents a new method for recovering the three dimensional structure of a scene composed of straight line segments using the image data obtained from a moving camera. The recovery algorithm is formulated in terms of an objective function which measures the total squared distance in the image plane between the observed edge segments and the projections (perspective) of the reconstructed lines. This objective function is minimized with respect to the line parameters and the camera positions to obtain an estimate for the structure of the scene. The effectiveness of this approach is demonstrated quantitatively through extensive simulations and qualitatively with actual image sequences. The implementation is being made publicly available.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Replication of HIV-1 in Dendritic Cell-Derived Syncytia at the Mucosal Surface of the Adenoid (1996)

Human immunodeficiency virus-type 1 (HIV-1) replicates actively in infected individuals, yet cells with intracellular depots of viral protein are observed only infrequently. Many cells expressing the HIV-1 Gag protein were detected at the surface of the nasopharyngeal tonsil or adenoid. This infected mucosal surface contained T cells and dendritic cells, two cell types that together support HIV-1 replication in culture. The infected cells were multinucleated syncytia and expressed the S100 and p55 dendritic cell markers. Eleven of the 13 specimens analyzed were from donors who did not have symptoms of acquired immunodeficiency syndrome (AIDS). The interaction of dendritic cells and T cells in mucosa may support HIV-1 replication, even in subclinical stages of infection.
Speech recognition based on space diversity using distributed multi-microphone (2002)

This paper proposes space diversity speech recognition technique using distributed multi-microphones in a room, as a new paradigm of speech recognition. The key technology to realize the system is (1) distant-talking speech recognition and (2) the integration method of multiple inputs. In this paper, we propose the use of a distant speech model for distant-talking speech recognition, and feature-based and likelihood-based integration methods for multimicrophones distributed in the room. The distant speech model is a set of HMMs learned using speech data convolved with the impulse responses measured at several points in the room. The experimental results of simulated distant-talking speech recognition show that the proposed space diversity speech recognition system can attain about 80% in accuracy, while the performances of conventional HMMs using close-talking microphones are less than 50%. These results indicate that the space diversity approach is promising for robust speech recognition under a real acoustic environment.
Functional Analysis of CbpA, a DnaJ Homolog and Nucleoid-associated DNA-binding Protein (2006)

DnaK/Hsp70 proteins are universally conserved ATP-dependent molecular chaperones that help proteins adopt and maintain their native conformations. DnaJ/Hsp40 and GrpE are co-chaperones that assist DnaK. CbpA is an Escherichia coli DnaJ homolog. It acts as a multicopy suppressor for dnaJ mutations and functions in vitro in combination with DnaK and GrpE in protein remodeling reactions. CbpA binds nonspecifically to DNA with preference for curved DNA and is a nucleoid-associated protein. The DNA binding and co-chaperone activities of CbpA are modulated by CbpM, a small protein that binds specifically to CbpA. To identify the regions of CbpA involved in the interaction of CbpA with CbpM and those involved in DNA binding, we constructed and characterized deletion and substitution mutants of CbpA. We discovered that CbpA interacted with CbpM through its N-terminal J-domain. We found that the region C-terminal to the J-domain was required for DNA binding. Moreover, we found that the CbpM interaction, DNA binding, and co-chaperone activities were separable; some mutants were proficient in some functions and defective in others.
Scheduling for VoIP service in cdma2000 1x EV-DO (2004)

Recently cdma2000 1x EV-DO (HDR) system has begun to be deployed in some countries to support high data rate services in cellular networks. The system is originally designed to support data services, but now is expected to serve some real-time traffic including VoIP. For VoIP service with delay hound and low loss requirements, we propose a frame structure considering delay bound and a scheduling algorithm reflecting channel conditions. To schedule VoIP, we adopt the maximal rate algorithm and the proportionally fair algorithm. The proportionally fair algorithm (PF) was known to be appropriate for elastic-traffic, however, from simulation results, we conclude that the PF algorithm with the channel test is an appropriate scheduling scheme to provide QoS of VoIP. When the required slot portion of VoIP is 75%, the loss rate is about 1% on the average and 3% in the worse case. On the other hand, the maximal rate algorithm shows twice of the loss rate for the same delay bound and load. Additionally we propose a simple admission control scheme for VoIP service that controls the average portion of slots occupied by VoIP packets.
Exploring the Effects of H-Bonding in Synthetic Analogues of Nickel Superoxide Dismutase (Ni-SOD): Experimental and Theoretical Implications for Protection of the Ni−SCys Bond (2010)

Nickel superoxide dismutase (Ni-SOD) is a recently discovered SOD obtained from soil microbes and cyanobacteria that shares no structural or spectroscopic similarities with other isoforms of SOD. The enzyme is found in both the Ni(II) (Ni-SOD(red)) and Ni(III) (Ni-SOD(ox)) oxidation states in "as isolated" preparations of the enzyme from two separate and independently crystallized Streptomyces strains. Ni-SOD contains an unusual and unprecedented biological coordination sphere comprised of Cys-S and peptido-N donors. To understand the role of these donors, we have previously synthesized the monomeric Ni(II)N(2)S(2) complexes, (Et(4)N)[Ni(nmp)(SC(6)H(4)-p-Cl)] (2) and (Et(4)N)[Ni(nmp)(S(t)Bu)] (3) as Ni-SOD(red) models arising from the S,S-bridged precursor molecule, [Ni(2)(nmp)(2)] (1) (where nmp(2-) = doubly deprotonated form of N-2-(mercaptoethyl)picolinamide). In addition to 2 and 3, we report here three new complexes, (Et(4)N)[Ni(nmp)(S-o-babt)] (4), (Et(4)N)[Ni(nmp)(S-meb)] (5), and K[Ni(nmp)(S-NAc)] (6) (where (-)S-o-babt = thiolate of o-benzoylaminobenzene thiol; (-)S-meb = thiolate of N-(2-mercaptoethyl)benzamide; and (-)S-NAc = thiolate of N-acetyl-L-cysteine methyl ester), that provide a unique comparison as to the structural and reactivity effects imparted by H-bonding in square planar asymmetrically coordinated Ni(II)N(2)S(2) complexes. X-ray structural analysis in combination with cyclic voltammetry (CV), spectroscopic measurements, density functional theory (DFT) calculations, and reactivity studies with O(2) and various ROS were employed to gain insight into the role that H-bonding plays in NiN(2)S(2) complexes related to Ni-SOD. The experimental results coupled with theoretical analysis demonstrate that H-bonding to coordinated thiolates stabilizes S-based molecular orbitals relative to those arising from Ni(II), allowing for enhanced Ni contribution to the highest occupied molecular orbital (HOMO), which is predominantly of S-Ni pi* character. These studies provide a unique perspective on the role played by electronically different thiolates regarding the intimately coupled interplay and delicate balance of Ni- versus S-based reactivity in Ni-SOD model complexes. The reported results have offered new insight into the chemistry that H-bonding/thiolate protonation imparts upon the Ni-SOD active site during catalysis, in particular, as a protective mechanism against oxidative modification/degradation.
Importance of the Collagen Adhesin Ace in Pathogenesis and Protection against Enterococcus faecalis Experimental Endocarditis (2010)

Ace is an adhesin to collagen from Enterococcus faecalis expressed conditionally after growth in serum or in the presence of collagen. Here, we generated an ace deletion mutant and showed that it was significantly attenuated versus wild-type OG1RF in a mixed infection rat endocarditis model (P<0.0001), while no differences were observed in a peritonitis model. Complemented OG1RFDeltaace (pAT392::ace) enhanced early (4 h) heart valve colonization versus OG1RFDeltaace (pAT392) (P = 0.0418), suggesting that Ace expression is important for early attachment. By flow cytometry using specific anti-recombinant Ace (rAce) immunoglobulins (Igs), we showed in vivo expression of Ace by OG1RF cells obtained directly from infected vegetations, consistent with our previous finding of anti-Ace antibodies in E. faecalis endocarditis patient sera. Finally, rats actively immunized against rAce were less susceptible to infection by OG1RF than non-immunized (P = 0.0004) or sham-immunized (P = 0.0475) by CFU counts. Similarly, animals given specific anti-rAce Igs were less likely to develop E. faecalis endocarditis (P = 0.0001) and showed fewer CFU in vegetations (P = 0.0146). In conclusion, we have shown for the first time that Ace is involved in pathogenesis of, and is useful for protection against, E. faecalis experimental endocarditis.
BRIM-2: An open-label, multicenter phase II study of vemurafenib in previously treated patients with <i>BRAF</i> V600E mutation-positive metastatic melanoma. (2011)

8509 Background: Most agents tested in large phase II trials in patients (pts) with metastatic melanoma have response rates of 10-20%. Approximately 50% of melanomas harbor a V600E activating mutation in the BRAF gene, which can now be targeted with specific inhibitors. In a Phase I study, treatment with vemurafenib (V), an orally available inhibitor of mutant BRAF, led to a high incidence of tumor regressions in BRAF-mutant melanoma (Flaherty et al. NEJM 2010). Here we report the results of BRIM-2, a pivotal Phase II trial of V in previously treated pts with BRAF-mutant melanoma. Methods: The primary endpoint was best overall response rate (BORR), with a target of 30% and a lower boundary of the exact 95% CI of at least 20% by independent review committee (IRC). BRAF mutation status was determined using a PCR-based investigational, companion diagnostic assay (cobas 4800 BRAF V600 Mutation Test, Roche Molecular Systems). Pts without active CNS metastasis who had received at least one prior line of therapy for metastatic melanoma received V (960 mg po twice daily) until progressive disease, unacceptable toxicity, or death. Results: 132 pts were enrolled (Oct 2009-Mar 2010), median age 51.5 yr, 54% ECOG PS 1, 61% M1c, 49% elevated LDH, and 49% >1 line of prior therapy. At the time of analysis (Sept 27, 2010, median follow-up 7 mo), BORR was 52.3% (95% CI: 43–61%; 2.3% CR, 50% PR) by IRC, with 29.5% SD and only 13.6% PD. Median duration of response was 6.8 mo (95% CI: 5.6-NR), and median PFS was 6.2 mo (95% CI: 5.6–6.8%). Median OS had not been reached. Most common adverse events (AEs; ≥25% pts, mostly Grade 1-2) were arthralgia, rash, photosensitivity, fatigue, alopecia, pruritis, and skin papilloma. The most common Grade 3 AE was cutaneous squamous cell carcinoma (24.2%), the majority centrally reviewed as keratoacanthoma-type. AEs were generally reversible with dose modification or interruption. 42% of pts required dose reductions, most commonly for rash, arthralgia and LFT abnormalities. Conclusions: BRIM2 met its primary endpoint based on BORR, confirming that V is an active agent in pts with BRAF mutation-positive melanoma who have completed prior first-line therapy.
Accelerate the autonomous vehicles reliability testing in parallel paradigm (2017)

Autonomous vehicle testing is important. Testing tools are developed to carry out simulation or real field autonomous driving testing, which are both common used methods. However, real field on-road testing is with low efficiency and limited ability to test all critical scenarios due to safety and costs involved. How to accelerate the testing and achieve the full coverage is the goal of this research. Therefore, use the simulation methods to achieve the full coverage test, especial the corner cases, use the real field test methods to do the importance sampling verification, obtain the parameters estimate through iteration of testing data, and then the functional testing of Autonomous vehicle can be accomplished during the develop stage. This paper discusses the autonomous driving reliability accelerated testing in parallel paradigm and proves the importance of this method, which is an appropriate reference for autonomous vehicle testing.