gebhart/patrepeval huggingface dataset:
Epothilones as Lead Structures for the Synthesis-Based Discovery of New Chemotypes for Microtubule Stabilization (2007)

Epothilones are macrocyclic bacterial natural products with potent microtubule-stabilizing and antiproliferative activity. They have served as successful lead structures for the development of several clinical candidates for anticancer therapy. However, the structural diversity of this group of clinical compounds is rather limited, as their structures show little divergence from the original natural product leads. Our own research has explored the question of whether epothilones can serve as a basis for the development of new structural scaffolds, or chemotypes, for microtubule stabilization that might serve as a basis for the discovery of new generations of anticancer drugs. We have elaborated a series of epothilone-derived macrolactones whose overall structural features significantly deviate from those of the natural epothilone scaffold and thus define new structural families of microtubule-stabilizing agents. Key elements of our hypermodification strategy are the change of the natural epoxide geometry from cis to trans, the incorporation of a conformationally constrained side chain, the removal of the C3-hydroxyl group, and the replacement of C12 with nitrogen. So far, this approach has yielded analogs 30 and 40 that are the most advanced, the most rigorously modified, structures, both of which are potent antiproliferative agents with low nanomolar activity against several human cancer cell lines in vitro. The synthesis was achieved through a macrolactone-based strategy or a high-yielding RCM reaction. The 12-aza-epothilone ("azathilone" 40) may be considered a "non-natural" natural product that still retains most of the overall structural characteristics of a true natural product but is structurally unique, because it lies outside of the general scope of Nature's biosynthetic machinery for polyketide synthesis. Like natural epothilones, both 30 and 40 promote tubulin polymerization in vitro and at the cellular level induce cell cycle arrest in mitosis. These facts indicate that cancer cell growth inhibition by these compounds is based on the same mechanistic underpinnings as those for natural epothilones. Interestingly, the 9,10-dehydro analog of 40 is significantly less active than the saturated parent compound, which is contrary to observations for natural epothilones B or D. This may point to differences in the bioactive conformations of N-acyl-12-aza-epothilones like 40 and natural epothilones. In light of their distinct structural features, combined with an epothilone-like (and taxol-like) in vitro biological profile, 30 and 40 can be considered as representative examples of new chemotypes for microtubule stabilization. As such, they may offer the same potential for pharmacological differentiation from the original epothilone leads as various newly discovered microtubule-stabilizing natural products with macrolactone structures, such as laulimalide, peloruside, or dictyostatin.
Bend Tunable Coupling in Dual-Hollow-Core Photonic Bandgap Fiber (2012)

We demonstrate the first measured dual-hollow-core photonic bandgap silica fiber. We examine its bend-induced coupling characteristics both theoretically and experimentally. Varying the bend diameter of the fiber allows control of the resonant coupling wavelength.
Influence of Excimer Laser Beam Shape on Poly-Si Crystallisation (2004)

Excimer laser crystallization is the currently preferred technique for the fabrication of high performance poly-Si thin film transistors for use in active matrix displays with integrated drive circuits. One of the issues with this process is the trade-off between increased throughput, by reducing the number of laser shots per unit area, and the range of laser energies over which this can be reliably implemented. The fundamental aspects of the crystallization process are analysed, and it is demonstrated that the size of the laser process window has a complex dependence on beam shape and shot number. Experimental results are presented, which show good consistency with a simple analytical model, and the optimum beam shape, and the limits to its application, are discussed.
고차원 공간에서 최근접 질의를 효과적으로 처리하기 위한 새로운 인덱싱 기법 (2000)

최근접 질의(nearest neighbor query)는 멀티미디어 데이터베이스에서 주어진 질의 객체와 가장 유사한 객체를 찾기 위한 매우 중요한 연산으로 사용된다. 대부분의 최근접 질의 처리 기법들은 객체의 효과적인 인덱싱을 위하여 다차원 인덱스(multidimensional index)를 사용한다. 그러나 N차원 사각형 혹은 원을 사용하여 객체 클러스터의 캡슐을 표현하는 기존의 다차원 인덱스들은 차원 수가 높아짐에 따라 검색 성능이 크게 떨어진다. 본 논문에서는 이러한 문제를 해결하는 새로운 인덱스 구조를 제시하고, 이를 이용하는 최근접 질의 처리 방안을 제안한다. 또한, 다양한 실험에 의한 성능 평가를 통하여 제안된 기법의 우수성을 검증한다.
A codebook of articulatory shapes (1987)

The acoustical properties of a vocal tract depend on its shape which, at frequencies below about 4 kHz, is adequately described by the area function (i.e., cross-sectional area as a function of position from glottis to lips). Obtaining even this simplified description of the tract is a difficult problem. The solution that is proposed is to construct a linked codebook of area functions and corresponding LPC vectors. Then, a given LPC vector is transformed to an area function by finding the closest LPC vector in the codebook and accessing the linked area function. The authors have constructed just such a codebook (to our knowledge, the first). At present, it has about 1500 shapes clustered from a training set of about 10 000 shapes generated by a vocal tract model [P. Mermelstein, J. Acoust. Soc. Am. 53, 1070–1082 (1973)]. Distance between area functions is defined as the Itakura distance between the corresponding LPC vectars. Handling the unique problems arising from this definition of distance and from the large size of the training set will be described. The plan for refining and enlarging the codebook will also be discussed.
Direct assessment of confinement effect in zeolite-encapsulated subnanometric metal species (2022)

Subnanometric metal species confined inside the microporous channels/cavities of zeolites have been demonstrated as stable and efficient catalysts. The confinement interaction between the metal species and zeolite framework has been proposed to play the key role for stabilization, though the confinement interaction is elusive to be identified and measured. By combining theoretical calculations, imaging simulation and experimental measurements based on the scanning transmission electron microscopy-integrated differential phase contrast imaging technique, we have studied the location and coordination environment of isolated iridium atoms and clusters confined in zeolite. The image analysis results indicate that the local strain is intimately related to the strength of metal-zeolite interaction and a good correlation is found between the zeolite deformation energy, the charge state of the iridium species and the local absolute strain. The direct observation of confinement with subnanometric metal species encapsulated in zeolites provides insights to understand their structural features and catalytic consequences.
Supplementary Figure 1 from <i>PIK3CA</i> Mutations and Copy Number Gains in Human Lung Cancers (2023)

Supplementary Figure 1 from &lt;i&gt;PIK3CA&lt;/i&gt; Mutations and Copy Number Gains in Human Lung Cancers
Continuous supercritical route for quantum-confined GaN nanoparticles (2015)

GaN quantum dots (QDs) are prepared in a one-step continuous process using anhydrous solvents at supercritical conditions (and temperatures below 450 °C) in short residence times, typically less than 25 s.
Metalens for distance estimation (Conference Presentation) (2018)

Metalenses have great ability in light focusing and can be tailored to exhibit varied functionalities for ultrathin optical applications. Here, we demonstrate a GaN metalens array which can be regarded as a light shaping generator for the structured light generation. The metalens array consists of 60 x 60 metalenses which can project a 42 cm x 42 cm light spots area at the distance of 1.5 M. The distance can be estimated by identifying the deformation of light spot distribution. The advantages of this metadevice is light weight, small, ultrathin, durable and easy to compact with other devices. Our design provides a new avenue for the structured light applications such as distance sensing and 3D environmental construction.
Polyoxometalate HIV-1 Protease Inhibitors. A New Mode of Protease Inhibition (2001)

Nb-containing polyoxometalates (POMs) of the Wells-Dawson class inhibit HIV-1 protease (HIV-1P) by a new mode based on kinetics, binding, and molecular modeling studies. Reaction of alpha(1)-K(9)Li[P(2)W(17)O(61)] or alpha(2)-K(10)[P(2)W(17)O(61)] with aqueous H(2)O(2) solutions of K(7)H[Nb(6)O(19)] followed by treatment with HCl and KCl and then crystallization affords the complexes alpha(1)-K(7)[P(2)W(17)(NbO(2))O(61)] (alpha(1)()1) and alpha(2)-K(7)[P(2)W(17)(NbO(2))O(61)] (alpha(2)()1) in 63 and 86% isolated yields, respectively. Thermolysis of the crude peroxoniobium compounds (72-96 h in refluxing H(2)O) prior to treatment with KCl converts the peroxoniobium compounds to the corresponding polyoxometalates (POMs), alpha(1)-K(7)[P(2)W(17)NbO(62)] (alpha(1)()2) and alpha(2)-K(7)[P(2)W(17)NbO(62)] (alpha(2)()2), in moderate yields (66 and 52%, respectively). The identity and high purity of all four compounds were confirmed by (31)P NMR and (183)W NMR. The acid-induced dimerization of the oxo complexes differentiates sterically between the cap (alpha(2)) site and the belt (alpha(1)) site in the Wells-Dawson structure (alpha(2)()2 dimerizes in high yield; alpha(1)()2 does not). All four POMs exhibit high activity in cell culture against HIV-1 (EC(50) values of 0.17-0.83 microM), are minimally toxic (IC(50) values of 50 to >100 microM), and selectively inhibit purified HIV-1 protease (HIV-1P) (IC(50) values for alpha(1)()1, alpha(2)()1, alpha(1)()2, and alpha(2)()2 of 2.0, 1.2, 1.5, and 1.8 microM, respectively). Thus, theoretical, binding, and kinetics studies of the POM/HIV-1P interaction(s) were conducted. Parameters for [P(2)W(17)NbO(62)](7)(-) were determined for the Kollman all-atom (KAA) force field in Sybyl 6.2. Charges for the POM were obtained from natural population analysis (NPA) at the HF/LANL2DZ level of theory. AutoDock 2.2 was used to explore possible binding locations for the POM with HIV-1P. These computational studies strongly suggest that the POMs function not by binding to the active site of HIV-1P, the mode of inhibition of all other HIV-1P protease inhibitors, but by binding to a cationic pocket on the "hinge" region of the flaps covering the active site (2 POMs and cationic pockets per active homodimer of HIV-1P). The kinetics and binding studies, conducted after the molecular modeling, are both in remarkable agreement with the modeling results: 2 POMs bind per HIV-1P homodimer with high affinities (K(i) = 1.1 +/- 0.5 and 4.1 +/- 1.8 nM in 0.1 and 1.0 M NaCl, respectively) and inhibition is noncompetitive (k(cat) but not K(m) is affected by the POM concentration).
Hole mobilities in sol-gel materials (2000)

New silylated precursors with hole transporting units are prepared by modification of different active molecules (carbazole, oxadiazole and tetraphenylphenylenediamine derivatives) using sol-gel precursors. Absorption and photoluminescence spectra show that the electronic structures are not significantly modified by the functionalization. Field dependence of the hole mobility of the different sol-gel layers is measured using the time-of-flight technique. The highest hole mobility is observed for the layer having tetraphenylphenylenediamine units: 5.7 × 10—5 cm2.V—1.s—1 at a field strength of E = 5 × 105 V.cm—1. For the best carbazole compound, the mobility is found to be about twentyfold lower at the same field. Further experiments are required to test these new materials as hole transporting layers in photorefractive and electroluminescent devices. Copyright © 2000 John Wiley & Sons, Ltd.
SNAP: Efficient Extraction of Private Properties with Poisoning (2022)

Property inference attacks allow an adversary to extract global properties of the training dataset from a machine learning model. Such attacks have privacy implications for data owners sharing their datasets to train machine learning models. Several existing approaches for property inference attacks against deep neural networks have been proposed, but they all rely on the attacker training a large number of shadow models, which induces a large computational overhead. In this paper, we consider the setting of property inference attacks in which the attacker can poison a subset of the training dataset and query the trained target model. Motivated by our theoretical analysis of model confidences under poisoning, we design an efficient property inference attack, SNAP, which obtains higher attack success and requires lower amounts of poisoning than the state-of-the-art poisoning-based property inference attack by Mahloujifar et al. For example, on the Census dataset, SNAP achieves 34% higher success rate than Mahloujifar et al. while being 56.5x faster. We also extend our attack to infer whether a certain property was present at all during training and estimate the exact proportion of a property of interest efficiently. We evaluate our attack on several properties of varying proportions from four datasets and demonstrate SNAP's generality and effectiveness. An open-source implementation of SNAP can be found at https://github.com/johnmath/snap-sp23.
A verilog RTL synthesis tool for heterogeneous FPGAs (2005)

Modern heterogeneous FPGAs contain "hard" specific-purpose structures such as blocks of memory and multipliers in addition to the completely flexible "soft" programmable logic and routing. These hard structures provide major benefits, yet raise interesting questions in FPGA CAD and architecture. To develop high-quality CAD mapping algorithms for these structures, and indeed to measure the quality of proposed new structures in the architectural domain, it is essential to have a flexible tool at the RTL synthesis level that permits heterogeneous FPGA CAD and architecture experimentation. In this paper we present a synthesis tool, called Odin, and an algorithm that permits flexible targeting of hard structures in FPGAs. Odin maps Verilog designs to two different FPGA CAD flows: Altera's Quartus, and the academic VPR CAD flow. We have expended significant effort to make the quality of this tool comparable to an industrial front-end synthesis tool, and we present mapping results for our benchmarks that show the quality of our results.
Observation of two discrete conductivity states in quinone-oligo(phenylene vinylene) (2010)

The single-molecule conductivity of quinone-oligo(phenylene vinylene) (Q-OPV) attached to a gold substrate was studied using electrochemical scanning tunnelling microscopy. The results show that the molecule has two discrete conductivity states: a low-conductivity state, when it is oxidized, and a high-conductivity state, when reduced. The electron transport through the molecule in both states occurs via coherent tunnelling. The molecular conductivity in either oxidation state is independent from the electrochemical gate potential; however, the gate potential can be used to switch the oxidation state of the molecule. Numerical calculations suggest that the highest occupied molecular orbital (HOMO) of Q-OPV controls tunnelling through the molecule and that the independence of conductivity from the electrochemical gate in either oxidation state originates from strong penetration of HOMO into the substrate. In addition, the greater delocalization of HOMO in the reduced state than in the oxidized state explains the greater conductivity of Q-OPV in the former than in the latter.
The GaAs/AlGaAs optical neurochip with variable synaptic interconnections (1991)

Our paper examines the optical learning chip which acquires knowledge from the external circumstances in real time. The key to its success is to develop a variable sensitivity photodiode (VSPD) with the combined functions of the analogue spatial light modulator and the photodiode.
GaN-based high-electron-mobility transistor structures with homogeneous lattice-matched InAlN barriers grown by plasma-assisted molecular beam epitaxy (2014)

Metal-polar In0.17Al0.83N barriers, lattice-matched to GaN, were grown under N-rich conditions by plasma-assisted molecular beam epitaxy. The compositional homogeneity of these barriers was confirmed by plan-view high-angle annular dark-field scanning transmission electron microscopy and atom probe tomography. Metal-polar In0.17Al0.83N/(GaN)/(AlN)/GaN structures were grown with a range of AlN and GaN interlayer (IL) thicknesses to determine the optimal structure for achieving a low two-dimensional electron gas (2DEG) sheet resistance. It was determined that the presence of a GaN IL was necessary to yield a 2DEG sheet density above 2 × 1013 cm−2. By including AlN and GaN ILs with thicknesses of 3 nm and 2 nm, respectively, a metal-polar In0.17Al0.83N/GaN/AlN/GaN structure regrown on a GaN-on-sapphire template yielded a room temperature (RT) 2DEG sheet resistance of 163 Ω/□. This structure had a threading dislocation density (TDD) of ∼5 × 108 cm−2. Through regrowth on a free-standing GaN template with low TDD (∼5 × 107 cm−2), an optimized metal-polar In0.17Al0.83N/GaN/AlN/GaN structure achieved a RT 2DEG sheet resistance of 145 Ω/□ and mobility of 1822 cm2 V−1 s−1. High-electron-mobility transistors with output current densities above 1 A mm−1 were also demonstrated on the low-TDD structure.
Les instruments d'action publique mis en théorie : introduction (2011)

L'approche de l'action publique sous l'angle de ses instruments s'est developpee a partir des annees 70 dans une perspective fonctionnaliste et de management public qui recherchait la meilleure adequation entre les finalites des programmes d'intervention publique et les techniques de regulation utilisees. Depuis les annees 90 la reflexion sur les technologies de gouvernement s'est amplement diversifiee. Le projet initial est poursuivi plus ou moins explicitement et s'inscrit aujourd'hui dans reflexion sur les « nouveaux modes de gouvernance ». Mais, cette perspective n'est plus hegemonique, elle est amplement concurrencee par un ensemble de travaux de type historique et/ou sociologique bases sur l'etude des organisations et de la bureaucratie, celle des innovations scientifiques et techniques, celles des systemes cognitifs, mais aussi sur celle des rapports de pouvoir et des modes de domination induits et equipes par les Instruments. Il serait absurde de pretendre a « Une Ecole de l'Instrumentation Politique ». D'ailleurs, personne n'y pretend. Ce champ de recherche est manifestement pluriel et c'est la que reside aujourd'hui sa principale richesse scientifique. Tout en travaillant dans le cadre de paradigmes tres differents, les auteurs qui introduisent a un moment donne de leur recherche un angle de reflexion sur les instruments se rejoignent pour en faire surtout une entree methodologique. Envisager, a un moment une activite de regulation sous l'angle de son instrumentation c'est : * d'une part, un moyen de deplacer le regard scientifique en prenant une distance vis-a-vis des categories d'analyse traditionnelles (les acteurs, leurs interets et leurs croyances, les institutions formelles) ; * c'est d'autre part, recourir a un analyseur qui met souvent en evidence des dynamiques et des mobilisations peu visibles et des effets inattendus.
Variability of Creatine Metabolism Genes in Children with Autism Spectrum Disorder (2017)

Creatine deficiency syndrome (CDS) comprises three separate enzyme deficiencies with overlapping clinical presentations: arginine:glycine amidinotransferase (<i>GATM</i> gene, glycine amidinotransferase), guanidinoacetate methyltransferase (<i>GAMT</i> gene), and creatine transporter deficiency (<i>SLC6A8</i> gene, solute carrier family 6 member 8). CDS presents with developmental delays/regression, intellectual disability, speech and language impairment, autistic behaviour, epileptic seizures, treatment-refractory epilepsy, and extrapyramidal movement disorders; symptoms that are also evident in children with autism. The objective of the study was to test the hypothesis that genetic variability in creatine metabolism genes is associated with autism. We sequenced <i>GATM</i>, <i>GAMT</i> and <i>SLC6A8</i> genes in 166 patients with autism (coding sequence, introns and adjacent untranslated regions). A total of 29, 16 and 25 variants were identified in each gene, respectively. Four variants were novel in <i>GATM</i>, and 5 in <i>SLC6A8</i> (not present in the 1000 Genomes, Exome Sequencing Project (ESP) or Exome Aggregation Consortium (ExAC) databases). A single variant in each gene was identified as non-synonymous, and computationally predicted to be potentially damaging. Nine variants in <i>GATM</i> were shown to have a lower minor allele frequency (MAF) in the autism population than in the 1000 Genomes database, specifically in the East Asian population (Fisher's exact test). Two variants also had lower MAFs in the European population. In summary, there were no apparent associations of variants in <i>GAMT</i> and <i>SLC6A8</i> genes with autism. The data implying there could be a lower association of some specific <i>GATM</i> gene variants with autism is an observation that would need to be corroborated in a larger group of autism patients, and with sub-populations of Asian ethnicities. Overall, our findings suggest that the genetic variability of creatine synthesis/transport is unlikely to play a part in the pathogenesis of autism spectrum disorder (ASD) in children.
Discrepancies between clinicians and rural healthcare workers regarding referral procedures based on blood pressure measurements (2013)

Fig. 1. Range, mean, and standard deviation of systolic and diastolic thresholds reported by healthcare participants. A. Systolic and diastolic thresholds reported by healthcare participant group. B. Systolic and diastolic thresholds reported by healthcare center. Range is indicated by the whiskers, standard deviation by the rectangles, and mean by the solid lines within the rectangles.
The Inhibitive Effect of Sebacate-Modified LDH on Concrete Steel Reinforcement Corrosion (2022)

In recent decades, layered double hydroxides (LDH) have been proposed as innovative corrosion inhibitors for reinforced concrete. Their protective action is based on the ability to intercalate specific anions in the interlayer and on their ability to exchange the intercalated anion. In the present study, an organically charged LDH, with sebacate anions in the interlayer (LDH-S), is proposed as a water-repellent additive for mortar. The waterproofing efficiency of LDH-S and the associated corrosion inhibition ability has been evaluated in reinforced mortar samples. A 42% decrease in the water capillary absorption coefficient has been estimated when 3% LHD-S is added to a mortar. Both the passivation processes of the steel rebars during the curing period and the initiation of corrosion due to chloride exposure have been studied by electrochemical measurements. Three different mortars have been evaluated: reference mortar (REF), mortar with Mg-Al LDH (LDH), and mortar with LDH-sebacate (LDH-S). The latter has shown an important protective capacity for preventing the initiation of corrosion by chloride penetration, with an inhibitory efficiency of 74%. The presence of LDHs without sebacate in the interlayer also improved the performance of the mortar against rebar corrosion, but with lower efficiency (23% inhibitory efficiency). However, this protection is lost after continued chloride exposure over time, and corrosion initiates similarly to the reference mortar. The low corrosion current density values registered when LDH-S is added to the mortar may be related to the increased electrical resistance recorded in this mortar.