gebhart/patrepeval huggingface dataset:
Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration (2016)

Tissue repair and regenerative medicine address the important medical needs to replace damaged tissue with functional tissue. Most regenerative medicine strategies have focused on delivering biomaterials and cells, yet there is the untapped potential for drug-induced regeneration with good specificity and safety profiles. The Hippo pathway is a key regulator of organ size and regeneration by inhibiting cell proliferation and promoting apoptosis. Kinases MST1 and MST2 (MST1/2), the mammalian Hippo orthologs, are central components of this pathway and are, therefore, strong target candidates for pharmacologically induced tissue regeneration. We report the discovery of a reversible and selective MST1/2 inhibitor, 4-((5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino)benzenesulfonamide (XMU-MP-1), using an enzyme-linked immunosorbent assay-based high-throughput biochemical assay. The cocrystal structure and the structure-activity relationship confirmed that XMU-MP-1 is on-target to MST1/2. XMU-MP-1 blocked MST1/2 kinase activities, thereby activating the downstream effector Yes-associated protein and promoting cell growth. XMU-MP-1 displayed excellent in vivo pharmacokinetics and was able to augment mouse intestinal repair, as well as liver repair and regeneration, in both acute and chronic liver injury mouse models at a dose of 1 to 3 mg/kg via intraperitoneal injection. XMU-MP-1 treatment exhibited substantially greater repopulation rate of human hepatocytes in the Fah-deficient mouse model than in the vehicle-treated control, indicating that XMU-MP-1 treatment might facilitate human liver regeneration. Thus, the pharmacological modulation of MST1/2 kinase activities provides a novel approach to potentiate tissue repair and regeneration, with XMU-MP-1 as the first lead for the development of targeted regenerative therapeutics.
A Lateral Electric Field charge Modulator with Bipolar-gates for Time-resolved Imaging (2017)

This paper reports high time-resolved imaging technique using a lateral electric field charge modulator with bipolar-gates. The proposed pixel structure achieved high time-resolved signal detection by using negative bias effect by work function difference between the p-type gate and p-substrate. The test chip fabricated in 0.11 um CIS technology demonstrates the high-speed charge modulation, and the modulation contrast is measured to be 97%.
Dataset for Optical Anapole Metamaterial (2018)

Raw data for the paper: Wu, PC et al (2018) 'Optical Anapole Metamaterial' in ACS Nano.See ReadMe file for more information.
VeriStrat predicts survival in patients with non-small cell lung cancer (NSCLC) treated with erlotinib and bevacizumab (2008)

8008 Background: We previously developed a serum Matrix-Assisted Laser Desorption/Ionization- Time of Flight Mass Spectrometry (MALDI-TOF MS) proteomic algorithm (VeriStrat) that can reliably predict survival outcome in patients treated with erlotinib or gefitinib (Taguchi, JNCI 2007). We wanted to determine if the VeriStrat model could also also identify those patients with improved time to progression and overall survival in a separate data set of NSCLC patients treated with the combination of erlotinib plus bevacizumab on a Phase I/II multicenter study (Herbst, et al JCO 2005). Methods: Pretreatment serum was available for 35 of 40 patients with advanced NSCLC treated with bevacizumab and erlotinib. MALDI-TOF mass spectra were obtained with a Voyager-DE STR instrument (PerSeptive Biosystems) and the raw spectra were calibrated, corrected for baseline, and normalized prior to analysis. Results: The reproducibility and variability were tested in total of 276 spectra from 35 patient samples. Of these, 26 patients were classified as having a “good” outcome and 9 were classified as “bad”. We found that VeriStrat accurately predicts both OS and PFS when applied in a blinded fashion to this cohort of patients using the log-rank test (p=0.004 and p=0.003, respectively). Conclusions: MALDI-TOF MS proteomic analysis of pretreatment serum was able to identify protein/peptide expression patterns that independently predicted survival in patients treated with erlotinib with or without bevacizumab, confirming our the previously published results and extending them to patients treated with erlotinib and bevacizumab. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Biodesix Biodesix Biodesix
Validity of the Red Reflex Exam in the Newborn Eye Screening Test Cohort (2018)

This study demonstrates the ability of wide-angle fundus imaging to detect fundus abnormalities not otherwise identified by standard newborn red reflex screening prior to hospital discharge. [Ophthalmic Surg Lasers Imaging Retina. 2018;49:103-110.].
ATTRITION RESISTANT IRON-BASED FISCHER-TROPSCH CATALYSTS (1999)

The Fischer-Tropsch (F-T) reaction provides a way of converting coal-derived synthesis gas (CO+H{sub 2}) to liquid fuels. Since the reaction is highly exothermic, one of the major problems in control of the reaction is heat removal. Recent work has shown that the use of slurry bubble column reactors (SBCRs) can largely solve this problem. Iron-based (Fe) catalysts are preferred catalysts for F-T when using low CO/H2 ratio synthesis gases derived from modern coal gasifiers. This is because in addition to reasonable F-T activity, the F-T catalysts also possess high water gas shift (WGS) activity. However, a serious problem with the use of Fe catalysts in a SBCR is their tendency to undergo attrition. This can cause fouling/plugging of downstream filters and equipment, making the separation of catalyst from the oil/wax product very difficult if not impossible, and results in a steady loss of catalyst from the reactor. The objectives of this research are to develop a better understanding of the parameters affecting attrition resistance of Fe F-T catalysts suitable for use in SBCRs and to incorporate this understanding into the design of novel Fe catalysts having superior attrition resistance. Catalyst preparations will be based on the use of spray drying and will be scalable using commercially available equipment. The research will employ among other measurements, attrition testing and F-T synthesis, including long duration slurry reactor runs in order to ascertain the degree of success of the various preparations. The goal is to develop an Fe catalyst which can be used in a SBCR having only an internal filter for separation of the catalyst from the liquid product, without sacrificing F-T activity and selectivity. The effect of silica addition via coprecipitation and as a binder to a doubly promoted Fischer-Tropsch synthesis iron catalyst (100 Fe/5 Cu/4.2 K) was studied. The catalysts were prepared by coprecipitation, followed by binder addition and drying in a 1 m diameter, 2 m tall spray dryer. The binder silica content was varied from 0 to 20 wt %. A catalyst with 12 wt % binder silica was found to have the highest attrition resistance. F-T reaction studies over 100 hours in a fixed-bed reactor showed that this catalyst maintained around 95 % CO conversion with a methane selectivity of less than 7 wt % and a C5 + selectivity of greater than 73 wt %. The effect of adding precipitated silica from 0 to 20 parts by weight to this catalyst (containing 12 wt % binder silica) was also studied. Addition of precipitated silica was found to be detrimental to attrition resistance and resulted in increased methane and reduced wax formation. An HPR series of proprietary catalysts was prepared to further improve the attrition resistance. Based on the experience gained, a proprietary HPR-43 catalyst has been successfully spray dried in 500 g quantity. This catalyst showed 95 % CO conversion over 125 h and had less than 4 % methane selectivity. Its attrition resistance was one of the highest among the catalyst tested.
Wireless Broadcast with Network Coding: A Connected Dominating Sets Approach (2008)

We study network coding for multi-hop wireless networks. We focus the case of broadcasting, where one source transmits information to all the nodes in the network. Our goal is energy-efficient broadcasting, in other words, to minimize the number of transmissions for broadcasting to the entire network. To achieve this goal, we propose a family of methods that combine the use of network coding and connected dominating sets. They consists in rate selections using connected dominated sets (RAUDS: Rate Adjustment Using Dominating Sets, and an generalized version, MARAUDS). The main insight behind these methods is that their use of connected dominating sets, allows near-optimality in the core of the network, while they efficiently handle borders and non-uniformity. The main contribution is a formal proof of the performance of these families of algorithms. One main result is the comparison of performance between routing and these methods (and in general, network coding).
Boron Carbon Nitride Thin Films: From Disordered to Ordered Conjugated Ternary Materials (2020)

We present an innovative method for the synthesis of boron carbon nitride thin film materials in a simple furnace setup, using commonly available solid precursors and relatively low temperature compared to previous attempts. The as-prepared structural and optical properties of thin films are tuned via the precursor content, leading to a sp<sup>2</sup>-conjugated boron nitride-carbon nitride mixed material, instead of the commonly reported boron nitride-graphene phase segregation, with tunable optical properties such as band gap and fluorescence.
Identification of Redox Partners of the Thiol-Disulfide Oxidoreductase SdbA in Streptococcus gordonii (2019)

We previously identified a novel thiol-disulfide oxidoreductase, SdbA, in <i>Streptococcus gordonii</i> that formed disulfide bonds in substrate proteins and played a role in multiple phenotypes. In this study, we used mutational, phenotypic, and biochemical approaches to identify and characterize the redox partners of SdbA. Unexpectedly, the results showed that SdbA has multiple redox partners, forming a complex oxidative protein-folding pathway. The primary redox partners of SdbA that maintain its active site in an oxidized state are a surface-exposed thioredoxin family lipoprotein called SdbB (Sgo_1171) and an integral membrane protein annotated as CcdA2. Inactivation of <i>sdbB</i> and <i>ccdA2</i> simultaneously, but not individually, recapitulated the <i>sdbA</i> mutant phenotype. The <i>sdbB-ccdA2</i> mutant had defects in a range of cellular processes, including autolysis, bacteriocin production, genetic competence, and extracellular DNA (eDNA) release. AtlS, the natural substrate of SdbA produced by the <i>sdbB-ccdA2</i> mutant lacked activity and an intramolecular disulfide bond. The redox state of SdbA in the <i>sdbB-ccdA2</i> mutant was found to be in a reduced form and was restored when <i>sdbB</i> and <i>ccdA2</i> were knocked back into the mutant. In addition, we showed that SdbB formed a disulfide-linked complex with SdbA in the cell. Recombinant SdbB and CcdA2 exhibited oxidase activity and reoxidized reduced SdbA <i>in vitro</i> Collectively, our results demonstrate that <i>S. gordonii</i> uses multiple redox partners for oxidative protein folding.<b>IMPORTANCE</b><i>Streptococcus gordonii</i> is a commensal bacterium of the human dental plaque. Previously, we identified an enzyme, SdbA, that forms disulfide bonds in substrate proteins and plays a role in a number of cellular processes in <i>S. gordonii</i> Here, we identified the redox partners of SdbA. We showed that SdbA has multiple redox partners, SdbB and CcdA2, forming a complex oxidative protein-folding pathway. This pathway is essential for autolysis, bacteriocin production, genetic competence, and extracellular DNA (eDNA) release in <i>S. gordonii</i> These cellular processes are considered to be important for the success of <i>S. gordonii</i> as a dental plaque organism. This is the first example of an oxidative protein-folding pathway in Gram-positive bacteria that consists of an enzyme that uses multiple redox partners to function.
Numerical and Experimental Investigations on the Defect Tolerance of Brazed Steel Joints (2012)

Abstract Based on the combination of FE-calculations and experimental results a defect assessment procedure for brazed steel joints was developed in the present work, which reliably takes into account the effect of different steel heat treatments and defined artificial defects in the braze layer. Tensile tests with defect free joints consisting of X3CrNiMo13-4 as substrate material and of Au-18wt.-%Ni as filler metal serve as a basis to simulate the elastic-plastic material behaviour. By correlating experimental and numerical methods, failure criteria could be derived which indicate and predict failure of brazed components. These failure criteria were also presumed to calculate the maximum tolerable loads for specimens containing different defects. The results show that the simulations correlate very well with the experimental results. Furthermore, they provide a possibility to analyze the failure behaviour for different defect types and the influence of different heat treatments on the joint strength.
XPS Analysis on the Surface of CdZnTe Annealed in Ar and H_2 Atmosphere (2014)

CZT crystals were annealed in Ar and H2 atmosphere under the same temperature conditions.XPS analysis with sputter depth profiling was employed to analyze the surface composition and valence states after annealing. Based on the above results,the possible surface structure and composition of CZT crystals were determined before and after annealing. In contrast to the Ar atmosphere annealing,TeO2 and Te-rich layer had a significant reduction owing to chemical reaction with H2 during the H2 atmosphere annealing. Because of the elimination of TeO2 and Te-rich layer,the contact area between H and CZT was increased to promote further reaction of H with CZT.
Three‐dimensional conductive constructs for nerve regeneration (2008)

The unique electrochemical properties of conductive polymers can be utilized to form stand-alone polymeric tubes and arrays of tubes that are suitable for guides to promote peripheral nerve regeneration. Noncomposite, polypyrrole (PPy) tubes ranging in inner diameter from 25 microm to 1.6 mm as well as multichannel tubes were fabricated by electrodeposition. While oxidation of the pyrrole monomer causes growth of the film, brief subsequent reduction allowed mechanical dissociation from the electrode mold, creating a stand-alone, conductive PPy tube. Conductive polymer nerve guides made in this manner were placed in transected rat sciatic nerves and shown to support nerve regeneration over an 8-week time period.
Carrier lifetime in argon-implanted silicon (1984)

The effects of argon-ion implantation upon the carrier lifetime in lightly phosphorus-doped silicon (ρ=600 Ω cm) are deduced by an analysis of the shape of the photoconductivity transients induced in the material by irradiation with picosecond laser pulses. The results obtained for samples subjected to 250-keV ion doses in the range 1013 −1015 cm−2, show that the carrier lifetime is reduced within a region which is considerably greater than the volume affected directly by the ions. Furthermore, deep-level transient spectroscopy measurements at the depths 2 and 3 μm reveal the creation of at least two new recombination centers in the band gap at the energy levels Ec −0.46 eV and Ev +0.44 eV, respectively. These levels are attributed to dislocations. Finally, other measurements show that, next to the surface, n-doped material can be converted into p type by this kind of implantation.
On aggregating binary relations using 0-1 integer linear programming (2014)

This paper is concerned with the general problem of aggregating many binary relations in order to find out a consensus. The theoretical background we rely on is the Relational Analysis (RA) approach. The latter method represents binary relations (BRs) as adjacency matrices, models relational properties as linear equa-tions and finds a consensus by maximizing a majority-based criterion using 0-1 integer linear programming. Our contribution consists in a generalization of the the-oretical results obtained in this framework. First, with regards to classical BRs on a single set, we provide new linear equations that correspond to relational properties that have not been covered yet such as semi-transitivity, quasi-transitivity or Ferrers relation. Second, we extend the BR aggregation problem to the case of maps or func-tions which are interpreted as BRs on two different sets. These results allow the RA approach to be a more gen-eral framework for dealing with BR aggregation prob-lems. We also analyze the relationships between dif-ferent BR aggregation problems and several tasks ad-dressed in the artificial intelligence and machine learn-ing fields. In that case, preference aggregation, cluster-ing, and bi-clustering tasks are studied and we thus em-phasize the underlying theoretical foundations of such problems from the point of view of BRs and their ag-gregations. 1
FindIt: Generalized Localization with Natural Language Queries (2022)

We propose FindIt, a simple and versatile framework that unifies a variety of visual grounding and localization tasks including referring expression comprehension, text-based localization, and object detection. Key to our architecture is an efficient multi-scale fusion module that unifies the disparate localization requirements across the tasks. In addition, we discover that a standard object detector is surprisingly effective in unifying these tasks without a need for task-specific design, losses, or pre-computed detections. Our end-to-end trainable framework responds flexibly and accurately to a wide range of referring expression, localization or detection queries for zero, one, or multiple objects. Jointly trained on these tasks, FindIt outperforms the state of the art on both referring expression and text-based localization, and shows competitive performance on object detection. Finally, FindIt generalizes better to out-of-distribution data and novel categories compared to strong single-task baselines. All of these are accomplished by a single, unified and efficient model. The code will be released.
Thermal imaging of buried heterostructure quantum cascade lasers (QCLs) and QCL arrays using CCD-based thermoreflectance microscopy (2019)

Thermal profiles of a single-element quantum cascade laser (QCL) and a five-element QCL array at different bias currents, under quasi-continuous-wave (QCW) conditions, are obtained using the charge-coupled device (CCD)-based thermoreflectance imaging technique. Peak temperature changes of 55 K and 105 K are measured on the single-element QCL (operating at 1.2 A) and the central element of the QCL array (operating at 4.2 A), respectively. The average facet temperature of the single QCL device shows a linear relationship with the dissipated power, indicating an effective thermal resistance of Rth = 3.0 ± 0.2 K/W (7%) for the device. The thermal transient behavior of the single QCL device, in response to a 35 μs-wide heating pulse, is also measured. From the transient curve, an effective thermal time constant of τth = 9.5 ± 0.4 μs (4%) is obtained. Experimental results are compared to the results obtained from heat-transfer models for both the single-element and array devices. Thermal profiles show a thermal lensing effect at the facet of the single-element QCL. In the array device, a more pronounced heating is observed at the center of the device while the temperature gradually decreases away from the central element.
Synthesis of a Protected Phosphoamino Acid, Nα-tert-Butyloxycarbonyl-O-Diethylphosphoro-L-Serine (1982)

Abstract Phosphoproteins are known to play metabolic and structural roles in many biological processes. In such proteins, serine is the most commonly phosphorylated amino acid and is usually flanked by a cluster of acidic or basic residues. In our studies of the structure and reactivity of the phosphorylated segments of the caseins, we have been concerned with the development of a synthetic methodology suitable for the rapid synthesis in gram quantities of phosphopeptides.
Design and characterization of an RF pulse train generator for large-signal analysis (2008)

In this paper an RF pulse train signal is introduced that can serve as a reference signal for the phase calibration of the large-signal network analyser (LSNA) under modulated excitations. Hence, the pulse train generator is specifically designed to fulfil the requirements of such a calibration signal. The design and characterization of the RF signal generator are discussed in this work.
Point defect–dislocation interactions in BEOL-compatible Ge-on-Si epitaxy (2023)

Reduced thermal budget is required for back-end-of-line (BEOL) integration of application specific functionality into the multilevel metal stack of a processor “substrate.” We report 400 °C BEOL-compatible Ge-on-Si growth (LT Ge) that is epitaxial and single crystalline with a defect density similar to high temperature growth and a small 0.05% tensile strain. Room temperature methanol–iodine passivation is employed pre-growth in lieu of the typical 800 °C oxide removal step. Undoped LT Ge exhibits p-type conductivity initially and n-type conductivity conversion upon annealing. Hall effect measurements following post growth heat treatment between 400 and 600 °C reveal an acceptor removal reaction that follows first-order kinetics with an activation energy of 1.7 ± 0.5 eV and a pre-exponential factor of 2.3×107 s−1 consistent with a point defect, diffusion limited process. We also observe that 90° sessile dislocations identified via transmission electron microscopy are annihilated in the same temperature regime, which is evidence for point defect-mediated climb. Ensuring high-quality epitaxy by characterizing defect reactions in a BEOL-compatible Ge-on-Si process flow is key to enabling vertical integration of optical interconnects.
DNN-Assisted Particle-Based Bayesian Joint Synchronization and Localization (2022)

In this work, we propose a Deep neural network-assisted Particle Filter-based (DePF) approach to address the Mobile User (MU) joint synchronization and localization (sync&loc) problem in ultra-dense networks. In particular, DePF deploys an asymmetric time-stamp exchange mechanism between the MUs and the Access Points (APs), which, traditionally, provides us with information about the MUs’ clock offset and skew. However, information about the distance between an AP and an MU is also intrinsic to the propagation delay experienced by the exchanged time-stamps. In addition, to estimate the angle of arrival of the received synchronization packets, DePF draws on the multiple signal classification algorithm that is fed with the Channel Impulse Response (CIR) experienced by the sync packets. The CIR is also leveraged to determine the link condition, i.e. Line-of-Sight (LoS) or Non-LoS. Finally, to perform joint sync&loc, DePF capitalizes on particle Gaussian mixtures that allow for a hybrid particle-based and parametric Bayesian Recursive Filtering (BRF) fusion of the aforementioned pieces of information and, thus, jointly estimates the position and clock parameters of the MUs. The simulation results verify the superiority of the proposed algorithm over the state-of-the-art schemes, especially that of the extended Kalman filter- and linearized BRF-based joint sync&loc. In particular, only drawing on the synchronization time-stamp exchange and CIRs from a single AP, for 90% of the cases, the absolute position and clock offset estimation error remain below 1 meter and 2 nanoseconds, respectively.