gebhart/patrepeval huggingface dataset:
Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance (2010)

Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type protease ranging from 58 nM to 0.8 pM was chosen for crystallographic analysis. The inhibitor-protease complexes revealed that tightly binding inhibitors (at the picomolar level of affinity) appear to "lock" into the protease active site by forming hydrogen bonds to particular active-site residues. Both this hydrogen bonding pattern and subtle variations in protein-ligand van der Waals interactions distinguish nanomolar from picomolar inhibitors. In general, inhibitors that fit within the substrate envelope, regardless of whether they are picomolar or nanomolar, have flatter profiles with respect to drug-resistant protease variants than inhibitors that protrude beyond the substrate envelope; this provides a strong rationale for incorporating substrate-envelope constraints into structure-based design strategies to develop new HIV-1 protease inhibitors.
P2E-2 Acoustic Radiation Force Impulse Imaging of Excised Human Prostates (2006)

We present initial results in acoustic radiation force impulse (ARFI) imaging of excised human prostates. Prostates were obtained from four patients undergoing prostatectomy for prostate cancer. All men had positive biopsy prior to surgery and had consented to allowing elastographic imaging of the excised tissue. The prostates were obtained immediately after surgery and immersed and scanned in an isotonic saline bath at room temperature. Scanning was performed with a Siemens Antares scanner using a VF10-5 linear array. Tissue displacement was induced with pushing pulses of 30 mus duration at 6.67 MHz and an Isppa of < 1 kW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Pushing beams were focused at 2 cm with an F/# of 3.5. RF data were collected and processed off-line using cross correlation methods to obtain displacement estimates. Low-resolution displacement images were obtained in near-real time (~3 seconds/frame) to guide image acquisition. The saved RF data were later processed to produce displacement images with improved SNR. Prostates were scanned free-hand, looking for interesting b-mode or ARFI targets. Peak displacements in healthy tissue were in the range of 6-12 mum. Cancerous lesions were stiffer and showed smaller displacements
Automatic multi-atlas segmentation using dual registrations (2013)

Atlas-based segmentation is widely used in medical image analysis. In multi-atlas segmentation, segmentations of multiple atlas images are propagated to a target image through image registration and the results are combined to obtain a final segmentation for the target image. However, registration does not always perfectly work between the target and each atlas image. Furthermore, the preparation of large number of atlases is also not easy. In this paper, we utilized two different characterized registration methods for deforming each atlas in multi-atlas segmentation. Since deformed atlases are voxel-wise candidates for a final segmentation mask, the proposed method has a similar effect to having more atlas sets, from which we could improve segmentation accuracy and reliability.
Characterization of microRNA Profile in the Blood of Patients with Marfan Syndrome (2017)

Background: Marfan syndrome (MFS) is an autosomal dominant inheritance disorder with a 1/5,000 live-birth prevalence. It is characterized by a wide range of clinical manifestations with more than 3000 mutations identified in the FBN1 gene. In this study we aimed to determine whether specific patterns of circulating microRNAs (miRNAs) are associated with MFS, and whether the abundance of miRNA levels in individuals with MFS versus healthy volunteers (HVs) controls could be used as a biomarker for accurate diagnosis of MFS.
AzTEC observations of 1.1 mm emission from the Orion Nebula (2007)

We present a map of the OMC-1 region in the 1.1 mm emission observed with the AzTEC, a new large-format array composed of 144 silicon-nitride micromesh bolometers currently in use at the James Clerk Maxwell Telescope (JCMT). The Orion A molecular cloud is known to be the most important high-mass star-forming region in the Milky Way, and the OMC-1, located in the middle of the Orion A cloud, is especially important to structure the environment. The AzTEC observations of the OMC-1 at 1.1 mm reveal dozens of cloud cores and a tail of filaments in a manner almost identical to the submillimeter continuum emission at 450 and 850 mum of the entire OMC-1 region and coincide with the filaments of ammonia gas. The implication is that the direction of flow is likely to be away from the core of OMC-1 and the dust-clump structures correspond to Jean's length, i.e. thermal fragmentation of the dense filamentary material. With physical properties of the cores in the clumped structures in conjunction with the Spitzer images of the OMC-1, we will discuss new young core candidates which could harbor embedded young stellar objects. This research was supported in part by Korea Science &amp; Engineering Foundation (KOSEF) under a cooperative agreement with the Astrophysical Research Center of the Structure and Evolution of the Cosmos (ARCSEC).
Multi-core holey fibers for ultra large capacity wide-band transmission (2008)

Multi-core holey fibers for the ultra large capacity transmission were investigated numerically and experimentally. Each core can realize the ultra wide band transmission over 550-1700 nm.
Synthesis of tritium labelled (R) and (S)-3-aminoquinuclidine: A ubiquitous component of serotonin receptor ligands, part II (1996)

(S)-3-Aminoquinuclidine-3H 10c-S having a specific activity of 66 Ci/mmol was prepared in eight steps from Isonicotinic acid (2). Reduction of 2 with carrier free tritium gas over PtO2 in DMF gave isonipecotic acid-3H 3c. Conversion to α-bromo ketone 5c followed by cyclization afforded 3-quinuclidone-3H 6c. Racemic 3-aminoquinuclidine-3H 8c was prepared by conversion of 6c to oxime 7c followed by reduction with NaBH4/NiCl2·6H2O. Racemic 8c was resolved with (R)-methylbenzyl isocyanate. Hydrolysis of 9c-S.R afforded (S)-3-aminoquinuclidine-3H 10c-S. The enantiopurity was >99.5% (S).
Effect of Number of Phases on Losses in Conducting Sleeves of Surface PM Machine Rotors Equipped With Fractional-Slot Concentrated Windings (2008)

High-speed machines with a solid rotor or a high- strength retaining sleeve could offer design and performance advantages. For a specific application, if the use of a high-strength nonmagnetic metallic retaining sleeve is more advantageous than a nonmetallic (e.g., carbon fiber) one, one needs to evaluate the eddy-current losses due to armature reaction space and time harmonics and/or tooth ripple, as they can be significant. This problem is aggravated furthermore in fractional-slot concentrated-winding machines due to their inherent sub- and super nonsynchronous MMF harmonic components. In this paper, the impact of the number of phases is quantified to help design a lower eddy loss rotor sleeve for a high-speed surface-mounted permanent-magnet rotor machine with fractional-slot concentrated armature winding, FSPCW-SPM. The goal of this paper is to provide a general method for laying out preferred FSPCW configurations. Also, a general method for screening and choosing the optimal slot/pole combinations is presented.
A hardware prototype for integration, test and validation of avionic networks (2013)

Based on the current state-of-the-art in avionics, the adoption of new networking technologies and their integration into complex systems requires important efforts to guarantee the respect of system level requirements. This sets a need for a more effective and systematic approach to validate new technological choices and their integration process. In this paper, we propose a hardware prototyping platform for validating the design of an avionic transducers network in an early development stage. The specific implementation reported in this paper targets two boards based on a Spartan-6 LX45T Xilinx FPGA. Both boards were configured to validate a custom transducers network architecture proposed by the authors. The resulting prototype is configured to maintain a throughput of at least 1 Mbit/s and to guarantee a deterministic traffic on the field bus to conform to actual avionic constraints. This paper covers the methodology involved in the design of our prototyping platform and highlights some of the advantages it offers.
Optimal Discrete Finite Preview Problems (Why and How Is Future Information Important?) (1975)

The preview control problem is one in which a controller can use future as well as present and past information to determine the control. In the optimal discrete finite preview problem studied in this paper, the controller is assumed to make use of preview information with respect to command signal (desired trajectory) from the present time i up to Nla time units in the future. Nla is called the preview time, and is usually shorter than N, the problem duration. To make the solution applicable to a broad class of problems, measurement time delay, observation noise and driving noise are included in formulating the problem. The solution shows how to utilize the local future information obtained by finite preview (Nla) to minimize an optimality criterion evaluated over the problem duration (N). An illustrative example is given to show that preview drastically improves the performance of a system relative to non-preview optimal performance, and that there is a critical preview length essential for such an improvement.
HydraJet Testing under Deep Well Conditions Defines New Requirements for Hard-Rock Perforating (2009)

Abstract The use of hydrajetting for perforating wells has been common since the sixties. During those early years, wells were relatively shallow and jetting success was consistently demonstrated. However, as wells were drilled to depths where rock formations were harder, performance of hydrajetting became less dependable because subsequent stimulation failures occurred more often from the lack of fracture initiation. To help prevent this situation, a series of tests were performed to define new best practices for hydrajet perforating of rock under high ambient pressure. Various rocks were subjected to the tests that were conducted using different jetting pressures and abrasives. To better understand the jetting behavior, the mechanical characteristics (such as Young's Moduli, Poisson's Ratios, and compressive strengths) and chemical structures were also evaluated. This paper discusses various tests results, and new constraints for jetting are defined and presented.
Mid-infrared astrophotonics: study of ultrafast laser induced index change in compatible materials (2017)

The mid-infrared wavelength regime 3:5 􀀀 4:1 m, known as the astronomical L’&#13;\nband is of special interest for exoplanet hunting. Mid-IR compatible photonic technologies are&#13;\nan enabling platform for a range of critical observational science using compact instruments&#13;\non the next generation of Extremely Large Telescopes. Pupil remapping interferometry is a&#13;\ntechnique in which subapertures of the telescope pupil (2D) are reformatted into a 1D linear&#13;\narray. This can be done efficiently using 3D photonics. One of the most important techniques to&#13;\nfabricate 3D photonic devices in glass is ultrafast laser inscription. However, common silicate&#13;\nglasses are opaque above 2-2.2 m and therefore not useful for the fabrication of waveguides at&#13;\nmid-infrared wavelengths. Here we present a study of mid-infrared transparent materials that are&#13;\ncompatible with the ultrafast laser inscription technique. This study will inform the development&#13;\nof mid-infrared photonic devices for future exoplanetary discovery.
Metal organic chemical vapor deposition of ZnO from β‐ketoiminates (2012)

ZnO is a high‐mobility electron conductor being considered for high‐throughput electronics in flexible and transparent formats. We demonstrated the Zn β‐ketoiminate system, based on acetylacetimine with N ‐propyl, isopropyl, and butyl groups, as a vehicle for preparing ZnO thin films for electronic applications. Surface carbon was a primary impurity, and the precursors studied afforded films with the lowest surface carbon contamination at deposition temperatures near 400°C. Thermal annealing of the films reduced the surface carbon content and afforded semiconducting materials. Annealing also gave larger‐grained, better connected films. Thinner films were associated with semiconducting as opposed to ohmic behavior; such films will be adaptable for transparent logic circuits. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Do We Need Binary Features for 3D Reconstruction? (2016)

Binary features have been incrementally popular in the past few years due to their low memory footprints and the efficient computation of Hamming distance between binary descriptors. They have been shown with promising results on some real time applications, e.g., SLAM, where the matching operations are relative few. However, in computer vision, there are many applications such as 3D reconstruction requiring lots of matching operations between local features. Therefore, a natural question is that is the binary feature still a promising solution to this kind of applications? To get the answer, this paper conducts a comparative study of binary features and their matching methods on the context of 3D reconstruction in a recently proposed large scale mutliview stereo dataset. Our evaluations reveal that not all binary features are capable of this task. Most of them are inferior to the classical SIFT based method in terms of reconstruction accuracy and completeness with a not significant better computational performance.
Ultrastructural organization of dentin in mice lacking dentin sialo-phosphoprotein (2014)

Dentin Sialophosphoprotein (DSPP) is the major non-collagenous protein of dentin and plays a significant role in dentin mineralization. Recently, animal models lacking DSPP have been developed and the DSPP KO phenotype has been characterized at the histological level. Little is known, however, about the DSPP KO dentin at nano- and meso-scale. Dentin is a hierarchical material spanning from nano- to macroscale, hence information on the effects of DSPP deficiency at the submicron scale is essential for understanding of its role in dentin biomineralization. To bridge this gap, we have conducted ultrastructural studies of dentin from DSPP KO animals. Transmission electron microscopy (TEM) studies of DSPP KO dentin revealed that although the overall ultrastructural organization was similar to the WT, the mineral particles were less organized. Scanning electron microscopy in the back-scattered mode (BS-SEM) of the DSPP KO dentin revealed that circumpulpal dentin comprises large areas of non-mineralized matrix, with numerous spherulitic mineralized inclusions, while the mantle dentin appeared largely unaffected. Analysis of the mineral distribution in the circumpulpal dentin of the DSPP KO mice suggests a reduction in the number of mineral nucleation sites and an increase in the nucleation barrier in DSPP KO dentin. These preliminary results indicate that in addition to the reduction of mineralized and total dentin volume in DSPP KO animals significant changes in the ultrastructural organization exist. These changes are likely related to the role of DSPP in the regulation of mineral formation and organization in dentin.
Deep CG2Real: Synthetic-to-Real Translation via Image Disentanglement (2019)

We present a method to improve the visual realism of low-quality, synthetic images, e.g. OpenGL renderings. Training an unpaired synthetic-to-real translation network in image space is severely under-constrained and produces visible artifacts. Instead, we propose a semi-supervised approach that operates on the disentangled shading and albedo layers of the image. Our two-stage pipeline first learns to predict accurate shading in a supervised fashion using physically-based renderings as targets, and further increases the realism of the textures and shading with an improved CycleGAN network. Extensive evaluations on the SUNCG indoor scene dataset demonstrate that our approach yields more realistic images compared to other state-of-the-art approaches. Furthermore, networks trained on our generated ``real'' images predict more accurate depth and normals than domain adaptation approaches, suggesting that improving the visual realism of the images can be more effective than imposing task-specific losses.
Hydroformylation of Glycals Using a Rhodium(I)(acac)(CO)2 Catalyst. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Analysis of resolution limits of VTI anisotropy with full waveform inversion (2015)

Summary Here we analyze the resolution limits of multiparameter inversion and describe correlations between the parameters depending on their spatial resolution. The analysis is based on the singular value decomposition of the far-field linearized inversion operator in the wavenumber domain. We show principle limitations of P-P and P-SV scattering data inversion such as decrease of sensitivity of finite-frequency data at low and high wavenumbers. The theoretical predictions are in a good agreement with the numerical results obtained in spatial domain.
Newell's program, like Hilbert's, is dead; let's move on (2003)

We draw an analogy between Hilbert's program (HP) for mathematics and Newell's program (NP) for cognitive modeling. The analogy reveals that NP, like HP before it, is fundamentally flawed. The only alternative is a program anchored by an admission that cognition is more than computation.
Coronary Embolization and Myocardial Microinfarction: MR Imaging and Histopathologic Characterization (2016)

Magnetic resonance imaging (MRI) has been proven to reliably assess regional perfusion and left ventricular (LV) function of microembolized myocardium. The visibility of microinfarct on delayed enhancement MRI (DE-MRI) is limited and dependent on technical and biological issues. Furthermore, MRI underestimates total microinfarct size compared with microscopy. MRI studies revealed that the presence of microemboli in pre-existing acute infarct delays infarct healing and magnifies LV remodeling. Discrimination of acute from chronic microinfarct is based on presence of inflammatory cells, edema and scar tissue, respectively. These noninvasive findings highlight the importance of prognostic utility of MRI and warrant larger clinical studies or registries to evaluate the significance of presence of focal microinfarct. Serial microscopic studies revealed that intravascular microemboli migrate into the extravascular space and this migration process is a function of time. This phenomenon may limit the use of microemboli therapy in occluding hemorrhagic blood vessels or treating tumors. Despite current standard of care, existing methods and therapies do not prevent coronary embolization nor reverse their deleterious effects.
Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection (2014)

These data collectively suggest that HIV-1 infection induces fully glycosylated HERV-K (HML-2) envelope TM protein to which antibodies are induced. These anti-HERV-K (HML-2) TM antibodies are a potential marker of HIV-1 infection, and are at higher titer in elite controllers. HERV-K (HML-2) envelope TM protein may be a new therapeutic target in HIV-1 infection.
Production of monocyte chemotactic protein–1 in human type B synoviocytes. synergistic effect of tumor necrosis factor α and interferon‐γ (1993)

These studies demonstrate that the MCP-1 gene is regulated by TNF alpha and IFN gamma in type B synoviocytes and indicate that these cells may play an important role in the recruitment of inflammatory cells to the rheumatoid synovial environment, via the production of novel chemotactic cytokines such as MCP-1.
Identification of mutations associated with acquired resistance to sunitinib in renal cell cancer (2019)

Sunitinib is one of the most widely used targeted therapeutics for renal cell carcinoma (RCC), but acquired resistance against targeted therapies remains a major clinical challenge. To dissect mechanisms of acquired resistance and unravel reliable predictive biomarkers for sunitinib in RCC, we sequenced the exons of 409 tumor-suppressor genes and oncogenes in paired tumor samples from an RCC patient, obtained at baseline and after development of acquired resistance to sunitinib. From newly arising mutations, we selected, using in silico prediction models, six predicted to be deleterious, located in G6PD, LRP1B, SETD2, TET2, SYNE1, and DCC. Consistently, immunoblotting analysis of lysates derived from sunitinib-desensitized RCC cells and their parental counterparts showed marked differences in the levels and expression pattern of the proteins encoded by these genes. Our further analysis demonstrates essential roles for these proteins in mediating sunitinib cytotoxicity and shows that their loss of function renders tumor cells resistant to sunitinib in vitro and in vivo. Finally, sunitinib resistance induced by continuous exposure or by inhibition of the six proteins was overcome by treatment with cabozantinib or a low-dose combination of lenvatinib and everolimus. Collectively, our results unravel novel markers of acquired resistance to sunitinib and clinically relevant approaches for overcoming this resistance in RCC.
New unidirectional high-efficiency three-level single-phase bridgeless PFC rectifier (2013)

This work presents a new multilevel unidirectional single-phase PFC rectifier topology well-suited for applications targeting for high efficiency and/or high power density. The characteristics of this rectifier topology, including the principles of operation, modulation strategy, feedback control scheme, and dimensioning equations are described in this paper. Finally, a 3 kW laboratory prototype is constructed and used in order to verify the characteristics of the new converter.
A review: the utilization of mesoporous materials in wastewater treatment (2019)

A review about the use of fabricated mesoporous materials with emphasis on silica in water treatment is presented. The problem of water supply is a well-known global problem because many areas around the world are suffering due to the lack of water, and therefore, the treatment and reuse of wastewater is crucial. Mesoporous materials have some unique features, such as a high surface area, which is normally associated with wide pore volume in addition to good thermal and mechanical stability. These properties have attracted researchers to study the use of mesoporous materials in water treatment. The first section of the current review is focused on traditional materials that are used for water purification from different pollutants, in addition to the different techniques that are using for the preparation of the mesoporous materials. The second section discusses the several functionalization tactics of mesoporous materials and their role in the efficiency enhancement towards pollutant removal from water. Finally, the third section presents the use of mesoporous materials in two of the most popular applications in water treatment: adsorption and photocatalysis techniques.