gebhart/patrepeval huggingface dataset:
Carbohydrate Bis-acetal-Based Substrates as Tunable Fluorescence-Quenched Probes for Monitoring <i>exo</i> -Glycosidase Activity (2017)

Tunable Förster resonance energy transfer (FRET)-quenched substrates are useful for monitoring the activity of various enzymes within their relevant physiological environments. Development of FRET-quenched substrates for exo-glycosidases, however, has been hindered by their constrained pocket-shaped active sites. Here we report the design of a new class of substrate that overcomes this problem. These Bis-Acetal-Based Substrates (BABS) bear a hemiacetal aglycon leaving group that tethers fluorochromes in close proximity, also positioning them distant from the active site pocket. Following cleavage of the glycosidic bond, the liberated hemiacetal spontaneously breaks down, leading to separation of the fluorophore and quencher. We detail the synthesis and characterization of GlcNAc-BABS, revealing a striking 99.9% quenching efficiency. These substrates are efficiently turned over by the human exo-glycosidase O-GlcNAcase (OGA). We find the hemiacetal leaving group rapidly breaks down, enabling quantitative monitoring of OGA activity. We expect this strategy to be broadly useful for the development of substrate probes for monitoring exo-glycosidases, as well as a range of other enzymes having constrained pocket-shaped active sites.
A survey of techniques for human detection from video (2006)

The heterojunction structure of the photocatalyst composite, which necessitates a robust interface and sufficient contact areas, holds the key to obtaining high charge carrier migration efficiency. Here, a novel composite, TiO<sub>2</sub> nanoparticles/Fe-doped hydroxyapatite (TONPs/FH_CS), is fabricated using a two-step synthetic technique, in which FH_CS is synthesized from artificial converter slag enriched with Fe and Ca. The unique nanorod@plate structure of FH_CS enables the uniform immobilization of TONPs onto FH_CS. Thereby, an n-n type heterojunction exhibits a highly intimate Ti-O-Fe heterointerface. Kelvin probe testing demonstrates the formation of an interfacial electric field oriented from FH_CS to TONPs, which serves as the driving force for interfacial electron transfer through the Ti-O-Fe channels. The photoacoustic signals provide information on electron trap levels and densities, indicating the formation of the electron transfer channels. •O<sub>2</sub><sup>-</sup> and •OH species are responsible for being the active species in this system. A photoexcited carrier transfer pathway exhibiting an S-scheme mechanism with high separation efficiency significantly enhances the utilization of charge carriers in each phase. Thus, improved xanthate degradation has been achieved using a heterojunction containing a photocatalyst derived from industrial solid waste. This work demonstrates the significant potential of steel-making byproduct utilization in industrial wastewater treatment.
Viral Genome Deep Classifier (2019)

The task of virus classification into subtypes is an important concern in many categorization studies, e.g., in virology or epidemiology. Therefore, the problem of virus subtyping has been a subject of considerable interest in the last decade. Although there exist several virus subtyping tools, they are often dedicated to a specific family of viruses. Even specialized methods, however, often fail to correctly subtype viruses, such as HIV or influenza. To address these shortcomings, we present a viral genome deep classifier (VGDC)-a tool for an automatic virus subtyping, which employs a deep convolutional neural network (CNN). The method is universal and can be applied for subtyping any virus, as confirmed by experiments on dengue, hepatitis B and C, HIV-1, and influenza A datasets. For all considered virus types, the obtained classification rates are very high with the corresponding values of the F1-score ranging from about 0.85 to 1.00 depending on the virus type and the considered number of subtypes. For HIV-1 and influenza A, the VGDC significantly outperforms the leading competitors, including CASTOR and COMET. The VGDC source code is freely available to facilitate easy usage and comparison with future approaches.
Organically Modified Transition Metal Alkoxides: Chemical Problems and Structural Issues on the Way to Materials Syntheses (2007)

Metal or semimetal alkoxides substituted with nonhydrolyzable organic groups are important precursors for inorganic-organic hybrid materials. Understanding the chemistry and structural issues of such precursors is a prerequisite for a rational materials design. Examples are given in this Account, mainly from the chemistry of titanium and zirconium alkoxides, which show that modified metal alkoxide precursors sometimes have an unexpected and unpredictable stuctural chemistry. Furthermore, chemical consequences of the Lewis acidity of the metal alkoxides are discussed, such as adduct formation, ligand exchange reactions, or organic side reactions.
Efficient new synthetic route to bidentate, monomeric cyclopentadienyl-amide complexes of Group 4 transition metals: synthesis and characterization of the zirconium and hafnium complexes [[.eta.5:.sigma.-C5H4(CH2)3NMe]MX2(NHMe2)] (X = Cl, I, M = Zr; X = I, M = Hf) and [[.eta.5:.sigma.-C5H4(CH2)3NMe]ZrX2] (X = NMe2, CH2Ph, CH2SiMe3, BH4) and molecular structure of [[.eta.5:.sigma.-C5H4(CH2)3NMe]ZrCl(CH2Ph)]2 (1993)

The synthesis of the amine-substituted cyclopentadiene C5H5CH2CH2CH2N(H)Me (2, HCpNH) is described. The reaction of 2 with M(NMe2)4 (M = Zr, Hf) gives the ring-closed species [M(η5:σ-C5H4CH2CH2CH2NMe)(NMe2)2] (M(CpN)(NMe2)2; M = Zr (3), Hf (4)) in high yields (60-95%). Aminolysis of 3 and 4 with 2 equiv of Me2NH·HX (X = Cl, I) provides a route to amine adducts of the dihalide complexes [M(CpN)X2(NHMe2)] (M = Zr, X = Cl (5), I (6); M = Hf, X = I (7)). Aminolysis of 3 with 1 equiv of Me2NH·HI gives the mixed amido-iodide [Zr(CpN)I(NMe2)] (8). The dichloride 5 is an excellent precursor to alkyl complexes; thus, reaction of 5 with C6H5CH2MgCl (2 equiv) gives [Zr(CpN)(CH2Ph)2] (9), that of 5 with Me3SiCH2Li gives [Zr(CpN)(CH2SiMe3)2] (10), and that of 5 with C6H5CH2MgCl (1 equiv) gives the mixed complex [Zr(CpN)(CH2Ph)Cl] (11). The 1H and 13C NMR data for 9 and 10 are discussed in terms of η2-benzyl (9) and agostic (10) interactions in these formally 14-valence-electron compounds. The reaction of 5 with LiBH4 gives [Zr(CpN)(η3-BH4)2] (13). Aminolysis of 3 with cyclopentadiene gives [Zr(CpN)(η-C5H5)(NMe2)] (14), while 3 also reacts with phenylacetylene to give the poorly stable bis(acetylide) [Zr(CpN)(CCPh)2] (15). Compound 11 has been characterized as a benzene-d6 solvate by X-ray crystallography: (C32H40Cl2N2Zr2)0.5(C6D6), Mr = 437.17, monoclinic, P21/c, a = 11.649(1) Å, b = 10.360(1) Å, c = 17.802(1) Å, βi = 106.750(4)°, V = 2057.3(3) Å3, Z = 4, Dx = 1.411 g cm-3, λ(Mo Kα) = 0.710 73 Å, μ = 6.6 cm-1, F(000) = 888, T = 295 K, and RF = 0.035 for 3691 unique observed reflections with I ≥ 2.5σ(I) and 260 parameters. The crystal structure consists of dimer molecules of 11, obeying symmetry 1 and coupled by two bridging Cl atoms, with two different Zr-Cl distances of 2.6288(8) and 2.6797(9) Å, respectively.
CW 7-W 900-nm-wide supercontinuum source by phosphosilicate fiber Raman laser and high-nonlinear fiber (2005)

High-power, continuous-wave (CW) supercontinuum spanning from 1200 to 2100 nm has been generated in an all-fiber configuration. The output of a CW 8-W phosphosilicate fiber Raman laser at 1556 nm was efficiently converted to the supercontinuum in the successive high-nonlinear dispersion-shift fiber with the zero-dispersion wavelength of 1539 nm. The fiber-length and input-power dependences were investigated, and both the spectral broadening and continuum power are found to be strongly affected by the 2220-nm absorption band in silica. An average power of 6.8 W and a 20-dB bandwidth of 900 nm were obtained from the optimal 150-m fiber length. Very flat spectral intensity of 10±1 mW/nm from 1640 to 2015 nm is also a noteworthy feature. Raman-assisted four-wave mixing driven by modulation instability is the most possible mechanism of the presented CW supercontinuum generation and well explains the spectral cutoffs.
Practical considerations in the selection of seed strength for prostate implants (2015)

There are advantages in using lower numbers of higher activity seeds for prostate seed implants. This work investigated the use of higher strength seeds for our manually optimized prostate implants. Following a planning study using a range of seeds strengths between 0.4 U and 0.7 U, a series of patients were implanted using seeds of strength ~ 0.7 U. Twenty consecutive patients were selected for this study; ten patients were implanted with 0.4 U seeds and the next ten patients implanted with 0.7 U seeds. Postimplant dosimetry for the target volume, urethra, and rectal wall was compared between the two groups. Our data showed a small and insignificant decrease in the total theatre time when implanting seeds of higher strength. The mean number of seeds required per implant decreased by over 30% for the 0.7 U implants, and the mean number of needles decreased by eight needles. The mean D90 (%) was marginally lower for the 0.7 U group, and spread over a wider range of values. Doses to the rectal wall were slightly higher for the 0.7 U group. At six years postimplant, the symptom scores for urinary and rectal toxicity and erectile function were similar to those reported before brachytherapy, with little differences between the 0.4 U and 0.7 U groups. Our experiences and practical advice in the selection of seed strength for prostate implants are reported in this paper.
Development of multidye UV filters for OPVs using luminescent materials (2016)

Luminescence down-shifting (LDS) is used in several photovoltaic technologies aiming to improve the photon conversion efficiency (PCE) of the devices through the increase of the light harvesting in the regions of the electromagnetic spectrum where the EQE of the solar cells is poor. The aim of this work was to produce films of mixtures (blends) of two luminescent materials, dispersed in a poly-methyl methacrylate (PMMA) matrix, hoping to improve their properties both as LDS layer and as UV filter when applied on the clear, external surface of P3HT:PC61BM photovoltaic devices. The best results led to an increment of 7.4% in the PCE of the devices, and a six fold enhancement in their half-life (T50%). This study indicates that multidye LDS layers with optimized optical properties can lead to an effective improvement in the performance and operational stability of OPVs.
Secure Role and Rights Management for Automotive Access and Feature Activation (2021)

The trend towards fully autonomous vehicles changes the concept of car ownership drastically. Purchasing a personal car becomes obsolete. Thus, business models related to feature activation are gaining even higher importance for car manufacturers in order to retain their customers. Various recent security incidents demonstrated however that vehicles are a valuable attack goal ranging from illegal access to car features to the theft of the whole vehicles.
Development of Informative Path Planning for Inspection of the Hanford Tank Farm (2019)

Traditional environmental and structural monitoring often uses static sensor networks deployed at predetermined locations or mobile robots that use a rastering technique for area coverage. These methods rely on the operators making assumptions about the nature of the unknown field that is being measured and are often time-consuming for localizing an area of interest. Here, we aim to quickly localize possible leaks within high-level nuclear waste tanks at the Hanford facility. The structure of these tanks precludes most sensor network approaches and raises many issues with robotic inspection, such as navigation within highly constrained environments. This work uses a Bayesian Optimization approach for guiding a mobile robot's search strategy and implements a utility function that allows for prior knowledge of the structure to be incorporated when selecting future search locations. Compared to traditional exhaustive approaches, our method quickly reduces RMSE error and shortens the distance the robot must travel.
The X-38 V-201 Flap Actuator Mechanism (2004)

The X-38 Crew Rescue Vehicle V-201 space flight test article was designed to achieve an aerodynamically controlled re-entry from orbit in part through the use of two body mounted flaps on the lower rear side. These flaps are actuated by an electromechanical system that is partially exposed to the re-entry environment. These actuators are of a novel configuration and are unique in their requirement to function while exposed to re-entry conditions. The authors are not aware of any other vehicle in which a major actuator system was required to function throughout the complete re-entry profile while parts of the actuator were directly exposed to the ambient environment.
Reduced cardiac hypertrophy in toll-like receptor 4-deficient mice following pressure overload (2005)

Our results demonstrate that TLR4 is a novel receptor contributing to the development of cardiac hypertrophy in vivo and that both the TLR4-mediated pathway and PI3K/Akt/mTOR signaling are involved in the development of cardiac hypertrophy in vivo.
Nightmare at test time (2006)

When constructing a classifier from labeled data, it is important not to assign too much weight to any single input feature, in order to increase the robustness of the classifier. This is particularly important in domains with nonstationary feature distributions or with input sensor failures. A common approach to achieving such robustness is to introduce regularization which spreads the weight more evenly between the features. However, this strategy is very generic, and cannot induce robustness specifically tailored to the classification task at hand. In this work, we introduce a new algorithm for avoiding single feature over-weighting by analyzing robustness using a game theoretic formalization. We develop classifiers which are optimally resilient to deletion of features in a minimax sense, and show how to construct such classifiers using quadratic programming. We illustrate the applicability of our methods on spam filtering and handwritten digit recognition tasks, where feature deletion is indeed a realistic noise model.
Different pathways leading to cutaneous leukocytoclastic vasculitis in mice (2001)

To investigate the pathomechanisms of leukocytoclastic vasculitis (LcV) we compared mouse models of LcV with non-vasculitic irritant contact dermatitis (ICD). Criteria for LcV as met by the immune complex-mediated Arthus reaction (Art-r) were also fulfilled by the localized Shwartzman reaction (Shw-r) and by cutaneous Loxoscelism (Lox) (injection of venom from Loxosceles reclusa containing sphingomyelinase D). After depletion of PMN (by gamma-irradiation) vessel damage could not be elicited in these models, distinguishing them from models of direct endothelial insult (necrotizing ICD). Depletion of complement could only delay, but not inhibit the Art-r, and did not change ICD, Lox or the Shw-r. The Shw-r exclusively revealed a sustained local expression of vascular adhesion molecules for 24 h in the preparatory phase (LPS s.c.), not observed in the Art-r, in Lox or ICD. Subsequent challenge with LPS i.p. was associated with upregulation of Mac-1 and ICAM-1 on PMN, but not of VLA-4 or LFA-1 (FACS analysis). Cytokines which were able to replace LPS in priming for LcV in the Shw-r (TNF-alpha and IL-1beta) also induced sustained expression of adhesion molecules, whereas IL-12 and IFN-gamma did neither. Neutralizing IL-12 or IFN-gamma also inhibited neither LcV nor sustained expression of adhesion molecules, whereas anti-TNF-alpha inhibited both. Anti-TNF-alpha had no marked inhibitory effects in the Art-r, in Lox or ICD. Combined (but not separate) neutralization of both E-selectin and VCAM-1 by antibodies suppressed LcV independent from reducing influx of PMN, proving that their sustained expression is decisive for the Shw-r and interferes with normal diapedesis. Since Loxosceles venom is known to dysregulate diapedesis and degranulation of PMN in vitro, since adherent immune complexes activate PMN at the vessel wall, and since adhesion molecules are dysregulated in the Shw-r, we suggest that LcV develops when activation of PMN coincides with vascular alterations which interfere with normal diapedesis.
An A* Curriculum Approach to Reinforcement Learning for RGBD Indoor Robot Navigation (2021)

Training robots to navigate diverse environments is a challenging problem as it involves the confluence of several different perception tasks such as mapping and localization, followed by optimal path-planning and control. Recently released photo-realistic simulators such as Habitat allow for the training of networks that output control actions directly from perception: agents use Deep Reinforcement Learning (DRL) to regress directly from the camera image to a control output in an end-to-end fashion. This is data-inefficient and can take several days to train on a GPU. Our paper tries to overcome this problem by separating the training of the perception and control neural nets and increasing the path complexity gradually using a curriculum approach. Specifically, a pre-trained twin Variational AutoEncoder (VAE) is used to compress RGBD (RGB & depth) sensing from an environment into a latent embedding, which is then used to train a DRL-based control policy. A*, a traditional path-planner is used as a guide for the policy and the distance between start and target locations is incrementally increased along the A* route, as training progresses. We demonstrate the efficacy of the proposed approach, both in terms of increased performance and decreased training times for the PointNav task in the Habitat simulation environment. This strategy of improving the training of direct-perception based DRL navigation policies is expected to hasten the deployment of robots of particular interest to industry such as co-bots on the factory floor and last-mile delivery robots.
TM-Coin: Trustworthy management of TCB measurements in IoT (2017)

Remote attestation is used to enable verifiers to check if an underlying Trusted Computing Base (TCB) of a device and data from the TCB are trustworthy. However, the current remote attestation has limitations to be deployed in IoT from the perspective of the management in a massive and diverse collection of TCB measurements and the redundant execution of remote attestation. To mitigate these limitations, we present a trustworthy management of TCB measurements called TM-Coin (TCB Measurement-Coin) using the blockchain and ARM TrustZone. The TM-Coin transactions and protocol are presented to manage the TCB measurements of IoT devices using the blockchain, a decentralized database. The trusted execution environment provided by ARM TrustZone is used as the TCB to generate the TM-Coin transactions securely. Based on TM-Coin, the verifiers launch remote attestation of sensed data from the devices using the TCB measurements published in the blockchain without attesting to the TCB. We implemented a prototype to evaluate the performance overhead caused by TM-Coin.
Melatonin Influences Human Balance (1999)

In order to evaluate a possible correlation between melatonin, the cerebellum and, consequently, human balance, a double-blind pilot study was performed in 5 subjects with random administration of different doses of melatonin. Before and 1 h after a single administration, a complete otoneurological examination was performed. This first pilot study revealed that melatonin had effects on human equilibrium although these effects were not dosage related and were different in individual subjects. On the basis of these results, a second study was performed. Fourteen healthy volunteers were investigated before and 1 h after administration of a single dose of 10 mg melatonin. The otoneurological examination was restricted to the evaluation of: horizontal saccades, horizontal sinusoidal smooth pursuit, eyes open, eyes closed and head retroflexed static posturography. All subjects showed a decrease in posturographic performances, especially in the simplest test (eyes open) and half of them (6 out of 13) showed also impairment of eye movements. These results confirm the role of melatonin in the control of sensorimotor performances, and the cerebellar receptors might be correlated with the control of human balance.
A predictive maintenance system for integral type faults based on support vector machines: An application to ion implantation (2013)

In semiconductor fabrication processes, effective management of maintenance operations is fundamental to decrease costs associated with failures and downtime. Predictive Maintenance (PdM) approaches, based on statistical methods and historical data, are becoming popular for their predictive capabilities and low (potentially zero) added costs. We present here a PdM module based on Support Vector Machines for prediction of integral type faults, that is, the kind of failures that happen due to machine usage and stress of equipment parts. The proposed module may also be employed as a health factor indicator. The module has been applied to a frequent maintenance problem in semiconductor manufacturing industry, namely the breaking of the filament in the ion-source of ion-implantation tools. The PdM has been tested on a real production dataset.
Structural requirements for transformation of substrates by the S-adenosyl-L-methionine:delta 24(25)-sterol methyltransferase. Inhibition by analogs of the transition state coordinate. (1992)

Microsomes from sunflower seedlings were used to investigate the transition state coordinate for the C-24 methylation reaction that mediates phytosterol biosynthesis. They were then used to study structurally related cationic and uncharged compounds of the natural sterol substrate, which were designed to interfere with the reaction progress. The hypothetical reaction course is described to proceed through an Sn2 formation of an activated complex involving the initial production of a covalent structure with a dative bond (methyl from AdoMet attacks si-face of the 24,25-double bond of the sterol) and the secondary production of a series of high energy intermediates, the stabilization of which determines the final C-24 methylated product. Derivatives of lanosterol and cholesterol with a methyl, hydrogen, oxygen, or bromine atom introduced into the side chain and/or at C-3 in place of the natural nucleophile were studied as inhibitors that interfere with the formation of the hypothetical tertiary isopropylcarbinyl cation intermediate in the conversion of cycloartenal to 24(28)-methylene cycloartanol. The data indicate the most potent inhibitor is a sterol with an aziridine group attached to C-24(25), which mimics the bridged C-24(25) carbenium ion generated in the transition state, and the methyltransferase possesses two strategic sites: one that recognizes the proximal end of the sterol acting as a proton donor and the other that recognizes the distal end that acts as a proton acceptor. The best fit (binding/catalysis) involves a flat sterol (including substrate and inhibitor) with intact unsubstituted nucleophilic centers at C-3 and C-24 and a freely rotating side chain that can assume the pseudocyclic conformation.