gebhart/patrepeval huggingface dataset:
Metalated 2-Alkenylsulfoximides in Asymmetric Synthesis: Diastereoselective Preparation of Highly Substituted Pyrrolidine Derivatives (1998)

Thanks to a productive interaction between reagent and substrate control, 2-alkenylsulfoximides 1 react to provide highly substituted pyrrolidine derivatives 2 enantiomerically pure and with defined absolute configuration at the newly formed stereogenic centers. Tol=tolyl, BOC=tert-butoxycarbonyl.
ChemInform Abstract: Dendritic Architectures (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Vasa: A Simulator Infrastructure with Adjustable Fidelity (2005)

This article presents Vasa, a configurable high-performance multiprocessor simulation package for the Virtutech Simics full-system simulator. Vasa includes models of multilevel caches, store buffers, interconnects and memory controllers and can model complex out-of-order SMT/CMPprocessors in great detail. However, it can also be run in two less detailed simulation modes being up to 287 times faster on average. We compare the simulation results from a 16-way cache coherent multiprocessor system with four 4-way SMT/CMP processors in the three simulation modes. Our results indicate that for many architectural studies, it is justifiable to run the simulations in a faster less detailed mode as long as it is not the behavior of the processor itself or the first level caches that is being studied.
Effect of Glycosylation and Additional Domains on the Thermostability of a Family 10 Xylanase Produced by Thermopolyspora flexuosa (2009)

The effects of different structural features on the thermostability of Thermopolyspora flexuosa xylanase XYN10A were investigated. A C-terminal carbohydrate binding module had only a slight effect, whereas a polyhistidine tag increased the thermostability of XYN10A xylanase. In contrast, glycosylation at Asn26, located in an exposed loop, decreased the thermostability of the xylanase. The presence of a substrate increased stability mainly at low pH.
Generation of induced pluripotent stem cells from primary chronic myelogenous leukemia patient samples (2012)

Induced pluripotent stem cells (iPSCs) can be generated by the expression of defined transcription factors not only from normal tissue, but also from malignant cells. Cancer-derived iPSCs are expected to provide a novel experimental opportunity to establish the disease model. We generated iPSCs from imatinib-sensitive chronic myelogenous leukemia (CML) patient samples. Remarkably, the CML-iPSCs were resistant to imatinib although they consistently expressed BCR-ABL oncoprotein. In CML-iPSCs, the phosphorylation of ERK1/2, AKT, and JNK, which are essential for the maintenance of both BCR-ABL (+) leukemia cells and iPSCs, were unchanged after imatinib treatment, whereas the phosphorylation of signal transducer and activator of transcription (STAT)5 and CRKL was significantly decreased. These results suggest that the signaling for iPSCs maintenance compensates for the inhibition of BCR-ABL. CML-iPSC-derived hematopoietic cells recovered the sensitivity to imatinib although CD34(+)38(-)90(+)45(+) immature cells were resistant to imatinib, which recapitulated the pathophysiologic feature of the initial CML. CML-iPSCs provide us with a novel platform to investigate CML pathogenesis on the basis of patient-derived samples.
Registered Deposition of Nanoscale Ferroelectric Grains by Template‐Controlled Growth (2005)

Regular patterns of ferroelectric PbTiO3 nanostructures (see Figure) with lateral dimensions down to 30–60 nm have been grown onto platinized Si substrates by chemical solution deposition. The high registration of the grains is achieved by “top–down”-generated templates of TiO2 dots as seeds for their deposition. Ferroelectricity was verified by piezoresponse force microscopy.
Nanoporous Organosilicas as Preconcentration Materials for the Electrochemical Detection of Trinitrotoluene (2008)

We describe the use of nanoporous organosilicas for rapid preconcentration and extraction of trinitrotoluene (TNT) for electrochemical analysis and demonstrate the effect of template-directed molecular imprinting on TNT adsorption. The relative effects of the benzene (BENZ)- and diethylbenzene (DEB)-bridged organic-inorganic polymers, having narrow or broad pore size distributions, respectively, on electrochemical response and desorption behavior were examined. Sample volumes of 0.5-10 mL containing 5-1000 ppb TNT in a phosphate-buffered saline buffer were preconcentrated in-line before the detector using a microcolumn containing 10 mg of imprinted BENZ or DEB. Square-wave voltammetry was used to detect the first reduction peak of TNT in an electrochemical flow cell using a carbon working electrode and a Ag/AgCl reference electrode. Imprinted BENZ released TNT faster than imprinted DEB with considerably less peak tailing and displayed enhanced sensitivity and an improvement in the limit of detection (LOD) owing to more rapid elution of TNT from that material with increasing signal amplitude. For imprinted BENZ, the slope of signal versus concentration scaled linearly with increasing preconcentration volume, and for preconcentrating 10 mL of sample, the LOD for TNT was estimated to be 5 ppb. Template-directed molecularly imprinted DEB (TDMI-DEB) was 7-fold more efficient in adsorption of TNT from aqueous contaminated soil extract than nonimprinted DEB.
Quantitative evaluation of atrial radio frequency ablation using intracardiac shear‐wave elastography (2014)

Purpose: Radio frequency catheter ablation (RFCA) is a well‐established clinical procedure for the treatment of atrial fibrillation (AF) but suffers from a low single‐procedure success rate. Recurrence of AF is most likely attributable to discontinuous or nontransmural ablation lesions. Yet, despite this urgent clinical need, there is no clinically available imaging modality that can reliably map the lesion transmural extent in real time. In this study, the authors demonstrated the feasibility of shear‐wave elastography (SWE) to map quantitatively the stiffness of RFCA‐induced thermal lesions in cardiac tissues in vitro and in vivo using an intracardiac transducer array. Methods: SWE was first validated in ex vivo porcine ventricular samples ( N = 5). Both B‐mode imaging and SWE were performed on normal cardiac tissue before and after RFCA. Areas of the lesions were determined by tissue color change with gross pathology and compared against the SWE stiffness maps. SWE was then performed in vivo in three sheep ( N = 3). First, the stiffness of normal atrial tissues was assessed quantitatively as well as its variation during the cardiac cycle. SWE was then performed in atrial tissue after RFCA. Results: A large increase in stiffness was observed in ablated ex vivo regions (average shear modulus across samples in normal tissue: 22 ± 5 kPa, average shear‐wave speed ( c t ): 4.5 ± 0.4 m s −1 and in determined ablated zones: 99 ± 17 kPa, average c t : 9.0 ± 0.5 m s −1 for a mean shear modulus increase ratio of 4.5 ± 0.9). In vivo , a threefold increase of the shear modulus was measured in the ablated regions, and the lesion extension was clearly visible on the stiffness maps. Conclusions: By its quantitative and real‐time capabilities, Intracardiac SWE is a promising intraoperative imaging technique for the evaluation of thermal ablation during RFCA.
Purification and characterization of rat urinary esterase A, a plasminogen activator. (1983)

A plasminogen activator, previously designated as rat urinary esterase A (Nustad, K., and Pierce, J. V. (1974) Biochemistry 13, 2312-2319), was separated from kallikrein of rat urine and purified to homogeneity. In polyacrylamide slab gel electrophoresis, the purified enzyme showed three closely migrating protein bands which were labeled with [14C]diisopropylphosphorofluoridate and stained on a zymogram using the chromogenic substrate methionine-alpha-naphthyl ester. Two chains, heavy chain(s) (Mr approximately 15,800, 14,200) and light chain(s) (Mr approximately 8,850, 8,550), were separated in SDS-polyacrylamide gel under reducing conditions, while two bands (Mr approximately 24,500 and 23,000) were seen under nonreducing conditions. The active site of the enzyme was associated with the heavy chain. The purified enzyme was stained for carbohydrate by the periodic acid-Schiff reagent. Five bands were distinguished in slab gel electrofocusing with isoelectric points ranging from 5.05 to 5.45. The purified enzyme lysed fibrin clots containing plasminogen but not plasminogen-free fibrin. It hydrolyzed benzyloxylcarbonyl-Gly-Gly-Arg-amino-4-trifluoromethyl coumarin, and a Km of 53 microM and a Vmax of 63 mumol/min/mg of enzyme were obtained at pH 8.0 and 37 degrees C. The enzyme cleaved kininogen substrates to produce kinin which was measured by bioassay or radioimmunoassay. The enzyme was inhibited by soybean or lima bean trypsin inhibitor, aprotinin, alpha 1-antitrypsin, phenylmethanesulfonyl fluoride, D-Phe-Phe-ArgCH2Cl, antipain, leupeptin, benzamidine, and pentamidine. Its pH optimum was 8.5 to 9.0; it was unstable on dilution and on heating. On immunoelectrophoresis, an antiserum to the esterase formed precipitin arcs with rat plasma and this enzyme at identical positions, which in turn were different from those formed with kallikrein. This urinary enzyme belongs to the family of serine proteinases and is immunologically related to urinary kallikrein.
Serving datacube tuples from main memory (2002)

Existing datacube precomputation schemes materialize selected datacube tuples on disk, choosing the most beneficial cuboids (i.e., combinations of dimensions) to materialize given a space limit. However in the context of a data-warehouse receiving frequent "append" updates to the database, the cost of keeping these disk-resident cuboids up-to-date can be high. In this paper we propose a main memory based framework which provides rapid response to queries and requires considerably less maintenance cost than a disk based scheme in an append-only environment. For a given datacube query, we first look among a set of previously materialized tuples for a direct answer. If not found, we use a hash based scheme reminiscent of partial match retrieval to rapidly compute the answer to the query from the finest-level data stored in a special in-memory data structure. Our approach is limited to the important class of applications in which the finest granularity tuples of the datacube fit in main memory. We present analytical and experimental results demonstrating the benefits of our approach.
Plasma Lipopolysaccharide Concentrations in Cardiorenal Syndrome Type 1 (2019)

CRS type 1 patients present with an increased level of LPS and there is a direct correlation between LPS and renal parameters. This pilot research is the first study to explore the premise of LPS as novel pathophysiological factor in CRS type 1.
Pruning subsequence search with attention-based embedding (2016)

Searching a large database to find a sequence that is most similar to a query can be prohibitively expensive, particularly if individual sequence comparisons involve complex operations such as warping. To achieve scalability, "pruning" heuristics are typically employed to minimize the portion of the database that must be searched with more complex matching. We present an approximate pruning technique which involves embedding sequences in a Euclidean space. Sequences are embedded using a convolutional network with a form of attention that integrates over time, trained on matching and non-matching pairs of sequences. By using fixed-length embeddings, our pruning method effectively runs in constant time, making it many orders of magnitude faster than full dynamic time warping-based matching for large datasets. We demonstrate our approach on a large-scale musical score-to-audio recording retrieval task.
Optical Computing Research. (1986)

Abstract : The work covers several different areas of optical computing, as well as some work on digital processing of optically obtained images. The primary emphasis of the work is on the possible applications of optics to interconnections in integrated circuit technology. Other areas of effort include the diagonalization and inversion of circulant matrices using coherent optics, the division of complex wavefronts using four-wave mixing, and the suppression of speckle in coherently formed images. Publications during the last year arising out of work supported by the grant are also detailed.
Problems With Cementless Total Knee Arthroplasty at 11 Years Followup (2001)

One hundred two patients with 131 consecutive cementless total knee arthroplasties that retained the posterior cruciate ligament were followed up prospectively. The average age of the patients was 58 years (range, 32-75 years). The mean followup on the surviving knee arthroplasties was 11 years (range, 7-16 years). The patellar component was metal-backed in the first 112 (85%) knees, cementless all-polyethylene in the last 17 (13%) knees, and two knees had a prior patellectomy. Forty-four metal-backed patellar components (48%) were revised; nine were loose, and 35 had polyethylene wear through. Thirteen femoral components (12%) were revised because of femoral abrasion from a failed metal-backed patellar component. No other femoral component was revised, loose, or had osteolysis develop. Nine (8%) tibial components had failure of ingrowth; eight have been revised. Partial radiolucencies occurred in 53% of the tibias. Thirteen (12%) small osteolytic lesions developed, all around screws or screw holes in the tibial components. At an average of 11 years followup, cementless fixation yielded mixed results: cementless femoral fixation was excellent and metal-backed patellar components had a 48% patellar revision rate. Cementless tibial components had an 8% aseptic loosening rate and a 12% incidence of small osteolytic lesions. Based on these results, the authors have abandoned cementless fixation in total knee arthroplasty.
An absolute reflectometer for use with small samples in the visible and vacuum ultra-violet (1969)

This article describes an optical arrangement used to determine the absolute reflectivity of flat specular samples at near normal incidence. It employs two movable mirrors and has two possible light paths both equal in length. In one path, the radiation is focused at the sample, so that small samples may be studied. The arrangement is suitable for both visible and vacuum ultra-violet instruments.
Inherent Structure Energy is a Good Indicator of Molecular Mobility in\n Glasses (2016)

Glasses produced via physical vapor deposition can display greater kinetic\nstability and lower enthalpy than glasses prepared by liquid cooling. While the\nreduced enthalpy has often been used as a measure of the stability, it is not\nobvious whether dynamic measures of stability provide the same view. Here, we\nstudy dynamics in vapor-deposited and liquid-cooled glass films using molecular\nsimulations of a bead-spring polymer model as well as a Lennard-Jones binary\nmixture in two and three dimensions. We confirm that the dynamics in\nvapor-deposited glasses is indeed slower than in ordinary glasses. We further\nshow that the inherent structure energy is a good reporter of local dynamics,\nand that aged systems and glasses prepared by cooling at progressively slower\nrates exhibit the same behavior as vapor-deposited materials when they both\nhave the same inherent structure energy. These findings suggest that the\nstability inferred from measurements of the energy is also manifested in\ndynamic observables, and they strengthen the view that vapor deposition\nprocesses provide an effective strategy for creation of stable glasses.\n
Investigation of optimized high-density flip-chip interconnect design including micro Au bumps and underfill for ultrabroadband (DC-40GHz) applications (2012)

In this study, the high-speed signal transmission characteristics of high density flip-chip interconnect incorporating micro Au bumps were investigated. A TEG (test element group) device and substrate was designed and fabricated to measure the properties of the high density interconnect structure. The test chip and substrate had Cu wires patterned to create a controlled impedance CPW (coplanar waveguide) transmission line in order to test the high-speed signal transmission properties. The characteristic impedance and S-parameters (S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> ,S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> ) of the flip-chip bonded test chip and substrate was measured. 50 Ω CPWs were successfully fabricated both with and without underfill. The use of underfill was found not to have a significant effect on the transmission lines S-parameters. In this work we have presented a method for designing specific impedance and high frequency properties on Si substrates in the presence of underfill and flip-chip bonded circuits.
Discovery of a Potent Analgesic NOP and Opioid Receptor Agonist: Cebranopadol (2014)

In a previous communication, our efforts leading from 1 to the identification of spiro[cyclohexane-dihydropyrano[3,4-b]indole]-amine 2a as analgesic NOP and opioid receptor agonist were disclosed and their favorable in vitro and in vivo pharmacological properties revealed. We herein report our efforts to further optimize lead 2a, toward trans-6'-fluoro-4',9'-dihydro-N,N-dimethyl-4-phenyl-spiro[cyclohexane-1,1'(3'H)-pyrano[3,4-b]indol]-4-amine (cebranopadol, 3a), which is currently in clinical development for the treatment of severe chronic nociceptive and neuropathic pain.
Microsecond-switching liquid-crystal tunable optical filter (1993)

Chiral smectic liquid crystals (CSLCs) have microsecond response times due to a first order coupling between their macroscopic polarization and an applied electric field. With homeotropic alignment of the liquid crystal molecules direct analog phase modulation is obtained. [1] The significance of this device structure is that these materials can be fabricated in a Fabry-Perot (FP) cavity, making continuous optical wavelength tuning possible. This results in a low cost, microsecond tuning speed, narrow passband resolution, and potentially large tuning range optical filter for wavelength-divisionmultiplexing based lightwave networks, such as IBM Rainbow Network. [2] The proof-of-principle filter consists of two optical flats coated with mirrors (R= 97%) separated by metal films that operate as both a spacer (2 to 25 pm) and electrode. The cells were then heated up to 100° C and filled with CSLC in its isotropic phase by capillary action. Preliminary results suggest the tuning range is approximately 30 nm with a switching speed of a few psec at λ = 1.55 pm.
<title>Rare-earth-ions-doped graded-index single-mode polymer waveguide amplifier</title> (1994)

Recently, intense research on single-mode rare-earth doped fiber lasers and amplifiers[fl has led to the development of a range of active devices. The possibility of ion-doping of standard integrated-optic waveguides has recently allowed the demonstration of Nd- and Er-doped single-mode channel waveguide lasers in single crystal Ti:LiNbO3 waveguides[12] and various glass waveguides[35]. However, there are a number of intrinsic limitations associated with these material systems. First, glass waveguides have no electrooptic(EO) effect therefore, an active device cannot be made using these substrates. Second, LiNbO3 waveguides have significant walk-off between the refractive indices of microwave and optical waves. Consequently, the modulation speed of the EO modulator, which serves as the input signal generator for the waveguide amplifier, is limited to 4O GHz[6]. Third, the waveguide fabrication methods for LiNbO3 and glass substrates are not universal. They are not transferable to other substrates. For instance, Si and GaAs are the most frequently used substrates for optoelectronics. LiNbO3 and glass waveguide lasers cannot be implemented on these substrates as amplifiers without violating the monolithic integration preference. Photo lime gel-based polymer waveguide is an excellent guiding medium due to its wide transmission bandwidth(300nm to 2700nm). The GRIN characteristic of this material[7] allows the formation of high quality(loss &lt;0.1 dB/cm) single-mode passive and active devices on an array of substrate[81. In this paper, we report a graded index(GRIN) polymer waveguide amplifier working at 1 .O6im wavelength using Nd-doped photolime gel as the active medium. Fluorescent spectrums at 1 .32im (Nd3doped) and at 1.56 im (Er3-doped) were also observed and the results are shown in Figs.l and 2, respectively. The polymer introduced is soluble in water. As a result, the chemical compounds containing rare earth ions(REIs) can be mixed with the host polymer as long as they are hydrophilic. But the doping concentrations should be below the level of microscopic clustering[5] which quenches the active ions. There are other quenchers which shorten the lifetime of metastable states of active ions. The most serious quenchers are the admixed 0-H groups whose concentration must be less than 3-5x10'8/cm3 [4] for glass waveguide amplifier. The existence of 0-H groups generates a number of intermediate states between the transition states. Such states, primarily from water molecules, significantly reduce the lifetime of metastable states. The general rule of thumb is that the lifetime of the excited state will be temperature dependent if the gap is less than ten times the effective phonon frequency and completely quenched if less than four times[5I. Experiment results will be presented at the conference.
Enhanced enzyme kinetics of reverse transcriptase variants cloned from animals infected with SIVmac239 lacking viral protein X (2020)

HIV Type 1 (HIV-1) and simian immunodeficiency virus (SIV) display differential replication kinetics in macrophages. This is because high expression levels of the active host deoxynucleotide triphosphohydrolase sterile α motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) deplete intracellular dNTPs, which restrict HIV-1 reverse transcription, and result in a restrictive infection in this myeloid cell type. Some SIVs overcome SAMHD1 restriction using viral protein X (Vpx), a viral accessory protein that induces proteasomal degradation of SAMHD1, increasing cellular dNTP concentrations and enabling efficient proviral DNA synthesis. We previously reported that SAMHD1-noncounteracting lentiviruses may have evolved to harbor RT proteins that efficiently polymerize DNA, even at low dNTP concentrations, to circumvent SAMHD1 restriction. Here we investigated whether RTs from SIVmac239 virus lacking a Vpx protein evolve during <i>in vivo</i> infection to more efficiently synthesize DNA at the low dNTP concentrations found in macrophages. Sequence analysis of RTs cloned from Vpx (+) and Vpx (-) SIVmac239-infected animals revealed that Vpx (-) RTs contained more extensive mutations than Vpx (+) RTs. Although the amino acid substitutions were dispersed indiscriminately across the protein, steady-state and pre-steady-state analysis demonstrated that selected SIVmac239 Vpx (-) RTs are characterized by higher catalytic efficiency and incorporation efficiency values than RTs cloned from SIVmac239 Vpx (+) infections. Overall, this study supports the possibility that the loss of Vpx may generate <i>in vivo</i> SIVmac239 RT variants that can counteract the limited availability of dNTP substrate in macrophages.