gebhart/patrepeval huggingface dataset:
New Insights into the Design of Inhibitors of Human <i>S</i>-Adenosylmethionine Decarboxylase: Studies of Adenine C<sup>8</sup> Substitution in Structural Analogues of <i>S</i>-Adenosylmethionine (2009)

S-adenosylmethionine decarboxylase (AdoMetDC) is a critical enzyme in the polyamine biosynthetic pathway and depends on a pyruvoyl group for the decarboxylation process. The crystal structures of the enzyme with various inhibitors at the active site have shown that the adenine base of the ligands adopts an unusual syn conformation when bound to the enzyme. To determine whether compounds that favor the syn conformation in solution would be more potent AdoMetDC inhibitors, several series of AdoMet substrate analogues with a variety of substituents at the 8-position of adenine were synthesized and analyzed for their ability to inhibit hAdoMetDC. The biochemical analysis indicated that an 8-methyl substituent resulted in more potent inhibitors, yet most other 8-substitutions provided no benefit over the parent compound. To understand these results, we used computational modeling and X-ray crystallography to study C(8)-substituted adenine analogues bound in the active site.
HIGH-IMPACT, ENERGY-ABSORBING VEHICLE BARRIER SYSTEM : United States Patent 7,410,320 B2 (2008)

A high-impact, energy-absorbing vehicle barrier system generally includes a substantially rigid outer containment wall coupled via strap assemblies with an energy-absorbing inner impact wall, and energy-absorbing cartridges strategically positioned between the impact wall and containment wall. The impact wall is constructed of a number of tubes coupled with one another to present a substantially smooth, unifonn surface to passing vehicles. The energy-absorbing cartridges generally consist of a foam member or a number of foam sheets which compress and crush between the containment wall and impact wall to absorb energy from an errant vehicle striking the face of the impact wall, while the deflection and deformation of the impact wall tubes dissipates additional energy to reduce peak decelerations and mitigate the severity of high-energy vehicular impacts. Internal splice units and the strap assemblies provide for relatively easy and quick replacement of damaged impact wall sections and energyabsorbing cartridges
Abstract 10829: Biological and Pharmacological Properties of the Protease Proprotein Convertase Subtilisin-Like Kexin Type 9 Antagonists (Best of Basic Science Abstract) (2015)

Protease proprotein convertase subtilisin-like kexin type 9 (PCSK9) is a new important target for the treatment of hypercholesterolemia. Currently, several pharmaceutical companies are racing to develop new drugs against PCSK9, which could be the newest weapon against heart disease since the introduction of statins in the 80’s. However, those companies have focused primarily on the development of mAbs, not small molecules, as drugs. PCSK9 is a serine protease that is synthesized as a zymogen that undergoes autocatalytic processing and secretion. Secreted PCSK9 binds to the LDL-receptor (LDLR) and chaperones it to the degradation pathway. This study focused on the identification of antagonists of the PCSK9/LDLR interaction and explored their mechanism of action using a range of functional assays, as well as determined pharmacokinetic (PK) and pharmacodynamic (PD) properties of the lead compounds. Potential inhibitors of the PCSK9/LDLR interaction were identified through a virtual screen at the PCSK9 surface where the LDLR-EGF-A binds. The top hits exhibited inhibition of PCSK9/LDLR binding in the low micromolar (μM) range, a 5-fold upregulation of the LDLR at an inhibitor concentration of 1.6 μM in recombinant cell-based assays, and an increase in the fluorescently labeled DiI-LDL uptake in the nanomolar (nM) range in situ . Pharmacological studies revealed that subcutaneous injection of 4 mg/kg of one of these compounds resulted in a 32% reduction of the total cholesterol and 20% reduction in LDL-C levels in mice fed a high fat/high cholesterol diet. Moreover, administration of 40mg/kg of atorvastatin resulted in a 27% total cholesterol reduction and 20% reduction in LDL-C level. Additional studies were performed to evaluate the effect of the combination of our PCSK9 inhibitor with atorvastatin. Administration of the PCSK9 inhibitor (4 mg/ kg) in combination with atorvastatin (40 mg/kg) resulted in more than a 40% reduction in LDL-C in mice fed a high fat/high cholesterol diet. In vivo PK and PD evaluation of our lead PCSK9 inhibitor demonstrated that it was efficacious and exhibited 13% oral bioavailability. To our knowledge, no small molecule orally bioavailable antagonist against PCSK9 has been reported, only mAbs.
Sucrose phosphorylase: a powerful transglucosylation catalyst for synthesis of α-D-glucosides as industrial fine chemicals (2009)

Sucrose phosphorylase is a bacterial transglucosidase that catalyzes conversion of sucrose and phosphate into α-D-glucose-1-phosphate and D-fructose. The enzyme utilizes a glycoside hydrolase-like double displacement mechanism that involves a catalytically competent β-glucosyl enzyme intermediate. In addition to reaction with phosphate, glucosylated sucrose phosphorylase can undergo hydrolysis to yield α-D-glucose or it can decompose via glucosyl transfer to a hydroxy group in suitable acceptor molecules, giving new α-D-glucosidic products. The glucosyl acceptor specificity of sucrose phosphorylase is reviewed, focusing on applications of the enzyme in glucoside synthesis. Polyhydroxylated compounds such as sugars and sugar alcohols are often glucosylated efficiently. Aryl alcohols and different carboxylic acids also serve as acceptors for enzymatic transglucosylation. The natural osmolyte 2-O-(α-D-glucopyranosyl)-sn-glycerol (GG) was prepared by regioselective glucosylation of glycerol from sucrose using the phosphorylase from Leuconostoc mesenteroides. An industrial process for production of GG as active ingredient of cosmetic formulations has been recently developed. General advantages of sucrose phosphorylase as a transglucosylation catalyst lie in the use of sucrose as a high-energy glucosyl donor and the usually weak hydrolase activity of the enzyme towards substrate and product.
DDTW—A Method for Gas Reservoir Evaluation Using Dual Wait-Time NMR and Density Log Data (2001)

Summary Accurate estimates of porosity, fluid saturations, and in-situ gas properties are critical for the evaluation of a gas reservoir. By combining data from a dual wait-time (DTW) nuclear magnetic resonance (NMR) log and a density log, these properties can be determined more reliably than by either of the data alone. The density and NMR dual wait-time (DDTW) technique, introduced in this paper, is applicable to reservoirs where the pore-filling fluid consists of a liquid phase and a gas phase. The low proton density of the gas phase causes a reduction in the NMR signal strength resulting in underestimation of the apparent porosity. The polarization for different wait-times depends on the spin-lattice relaxation time of each fluid and may cause additional NMR porosity underestimation. The density log, on the other hand, delivers a porosity that is overestimated because of the presence of a gas phase. These data, together with known correlations for gas properties, yield a robust approach for the gas-zone porosity, ϕ, and the flushed zone gas saturation, Sg,xo. DDTW also derives gas properties including the in-situ gas density, ρg, as well as the two NMR-related properties, hydrogen index, IH,g, and spin-lattice relaxation time, T1g. Two field examples illustrate the method, and an error propagation study shows the reliability of the technique.
Minimal expression of myotonic dystrophy: a clinical and molecular analysis. (1992)

A clinical and molecular study is reported of 83 patients considered to be minimally affected with myotonic dystrophy (DM). These had been identified in three ways: 60 subjects were identified on clinical grounds and were divided into those with and those without neuromuscular involvement (groups I and II); nine subjects were at high risk of carrying the DM gene but had a normal phenotype (group III); and 14 were parents of definitely affected patients where neither parent showed clinical abnormalities (group IV). PCR analysis of the CTG repeat in the DM gene showed a range of 70 to 230 repeats for the younger at risk patients in group III, while the asymptomatic gene carriers in group IV had 53 to 60 repeats. The sensitivity of diagnosis by EMG was found to be 39%. For ophthalmic signs this was 97.5%. This suggests that assignment on the basis of minimal clinical features carries a significant error. Molecular analysis, in conjunction with established clinical investigations, should prove valuable in the identification and exclusion of minimal myotonic dystrophy.
12.4 1.4Gsearch/s 2Mb/mm<sup>2</sup> TCAM using two-phase-precharge ML sensing and power-grid preconditioning to reduce Ldi/dt power-supply noise by 50% (2017)

Ternary Content Addressable Memory (TCAM) executes a fully parallel search of its entire memory contents and uses powerful wild-card pattern matching to return search results in a single clock cycle. This capability makes TCAM attractive for implementing fast hardware look-up tables in network routers, processor caches, and many pattern recognition applications. However, the push for higher performance and increased memory density coupled with parallel TCAM array activation during search operation creates large Ldi/dt power supply noise challenges that could result in timing fails in both TCAM and its surrounding logic.
In vivo robots for tele-surgery during long-term space flight (2006)

Long-term human space exploration will require contingencies for emergency medical procedures including some capability to perform surgery. The ability to perform Minimally Invasive Surgery (MIS), or surgery performed with long tools inserted through small incisions, would be an important capability. The use of small incisions reduces surgical risk but also eliminates the surgeon’s ability to view and touch the surgical environment directly. Robotic surgery, or robotic tele-surgery, may be a way to provide emergency surgical care in extremely forward environments such as space flight. Current surgical robots are large and require extensive support personnel. Therefore, their implementation has been limited in forward environments and they would be difficult to implement in space flight.
Comparative studies of the structural proteins and glycoproteins of equine herpesviruses 2 and 5 (1994)

The structural proteins of equine herpesvirus 2 (EHV-2) and EHV-5, recently shown to be gammaherpesviruses, were identified and compared. Labelled proteins and glycoproteins were separated by SDS-PAGE and although EHV-2 and EHV-5 had similar protein profiles, bands in some positions were virus-specific. Six glycoproteins, with distinct profiles, were identified for both EHV-2 and EHV-5. Rabbit antisera to EHV-2 and EHV-5 and horse antiserum to EHV-2 were used in radioimmunoprecipitations, Western blot analysis and ELISA to investigate the immunogenicity and cross-reactivity of virus proteins. These analyses revealed that while EHV-2 and EHV-5 proteins share many common epitopes, they also possess type-specific epitopes. A 0.71 kb region of the EHV-2 glycoprotein B (gB) gene was expressed as a fusion protein in Escherichia coli. Antiserum raised in a rabbit to the EHV-2 fusion protein was used to identify a 64K EHV-2 protein as EHV-2 gB. Antiserum to EHV-2 gB was used to identify a 66K EHV-5 protein as EHV-5 gB. These proteins, which may represent subunits of gB rather than the entire molecule, appear the most immunodominant of the structural virion proteins as identified by Western blot.
Improving Phenotypic Measurements in High-Content Imaging Screens (2017)

Abstract Image-based screening is a powerful technique to reveal how chemical, genetic, and environmental perturbations affect cellular state. Its potential is restricted by the current analysis algorithms that target a small number of cellular phenotypes and rely on expert-engineered image features. Newer algorithms that learn how to represent an image are limited by the small amount of labeled data for ground-truth, a common problem for scientific projects. We demonstrate a sensitive and robust method for distinguishing cellular phenotypes that requires no additional ground-truth data or training. It achieves state-of-the-art performance classifying drugs by similar molecular mechanism, using a Deep Metric Network that has been pre-trained on consumer images and a transformation that improves sensitivity to biological variation. However, our method is not limited to classification into predefined categories. It provides a continuous measure of the similarity between cellular phenotypes that can also detect subtle differences such as from increasing dose. The rich, biologically-meaningful image representation that our method provides can help therapy development by supporting high-throughput investigations, even exploratory ones, with more sophisticated and disease-relevant models.
Polarized 3D: High-Quality Depth Sensing with Polarization Cues (2015)

Coarse depth maps can be enhanced by using the shape information from polarization cues. We propose a framework to combine surface normals from polarization (hereafter polarization normals) with an aligned depth map. Polarization normals have not been used for depth enhancement before. This is because polarization normals suffer from physics-based artifacts, such as azimuthal ambiguity, refractive distortion and fronto-parallel signal degradation. We propose a framework to overcome these key challenges, allowing the benefits of polarization to be used to enhance depth maps. Our results demonstrate improvement with respect to state-of-the-art 3D reconstruction techniques.
Impacts of microRNA-215 on cell proliferation and chemotherapy resistance in colon cancer and osteosarcoma (2009)

2542 Background: Translational control plays a key role in resistance to anti-cancer drug treatment. MicroRNAs regulate gene expression at the post-transcriptional level, mainly by interacting with 3'-UTR of their mRNA targets. Methods: miR-215 was ectopically expressed by transient transfection in both human colon cancer cell lines and osteosarcoma cell lines. The impact of miR-215 on cell proliferation, cell cycle control, chemosensitivity and down stream targets were characterized. The expression of miR-215 in colorectal cancer specimens and normal adjacent tissues was quantified by real time-qRT-PCR analysis. Results: In this study, we discovered that miR-215 down-regulates the expression of both dihydrofolate reductase (DHFR) and thymidylate synthase (TS), two of the most important chemotherapeutic targets, in human osteosarcoma U-2 OS and colon cancer HCT-116 (wt-p53) cell lines. Cells with elevated miR-215 expression are more resistant to DHFR inhibitor methotrexate (MTX) or TS inhibitor Tomudex (TDX) treatment. Ectopically over-expressing miR-215 triggers reduced cell proliferation and increased G2 arrest, at least in part, through the induction of p53 and p21. miR-215 transfected cells with reduced proliferating phenotype were resist to MTX or TDX treatment due to deceased cell cycle in S phase. The expression of endogeneous miR-215 was highly elevated in CD133 +/HI CD44 +/HI colon cancer stem cells compared to CD133 - CD44 - colon cancer cells, suggesting that tumor stem cells may be avoiding cellular and DNA damage caused by chemotherapy with a reduced proliferating phenotype mediated by certain miRNAs such as miR-215. The elevated expression of miR-215 in colon cancer stem cells with slow proliferation rate and resistance to chemotherapy further supports the role of miR-215 in cell proliferation and chemotherapy resistance. Conclusions: miR-215 may have a unique potential as a novel therapeutic target and biomarker candidate in cancer. No significant financial relationships to disclose.
Uranium Isotope Enrichment by Chemical Method (1980)

Through basic research on the separation of uranium isotopes by the isotopic equilibrium reaction of uranus and uranyl ions, we discovered that a novel redox chromatography in adsorption columns is most efficient for the enrichment of 235U. Further studies of kinetics and multicomplexes led to the formation of two very important equations that satisfactorily predict the degree of separation of uranium isotopes. Some results from extensive single-and multicolumn experiments and a model plant currently under design for recovery of 3% enriched uranium are also described.
Distributed desk checking (2006)

Abstract Desk checking is known to be an effective reading technique for early detection of sequential program errors. This paper discusses how to extend desk checking for concurrent and distributed programs. In addition to exponential possible schedules, concurrent and distributed programs have execution states that include more than one process. The new distributed desk‐checking technique supports the selection of schedules and execution states to be reviewed. The cross‐product functional coverage technique assists in the selection process. Schedule selection guidelines that facilitate early detection and coverage are introduced. It is demonstrated that code inspection can be applied effectively to large industrial applications using the selection mechanism introduced by this technique. Industrial pilots show that distributed desk checking is an effective early error‐detection review technique. Copyright © 2006 John Wiley & Sons, Ltd.
Comparison of the Kinetics of Intestinal Colonization by Associating 5 Probiotic Bacteria Assumed Either in a Microencapsulated or in a Traditional, Uncoated Form (2012)

The microencapsulation technique used in this study is a valid approach aimed to significantly improve the survival of strains during gastroduodenal transit, thus enhancing their probiotic value and allowing the use of a 5 times lower amount.
A method for detection of atrial fibrillation using RR intervals (2002)

This work describes a method for automatic detection of atrial fibrillation (AF) based on RR intervals. We define /spl Delta/RR to be the difference between successive RR intervals. The standard density histograms of RR and /spl Delta/RR intervals are determined from data in the MIT-BIH atrial fibrillation/flutter database. The present method estimates the similarity between the standard density histograms and a best density histogram by the Kolmogorov-Smirnov (KS) test. The algorithm returns significance (p) of difference between given histograms. If the p value is smaller than a value (P/sub c/), the test density histogram is significantly different from the standard density histogram. If the test density histogram is not significantly different from the standard density histogram, we say the data is AF: Using the standard density histogram of /spl Delta/RR with P/sub c/=0.01, the average sensitivity is 93.2% and the average specificity is 96.7%.
Mass preparation and technological development of an antifreeze protein (2008)

Antifreeze protein isolated from the blood serum of Arctic and Antarctic fish is an extraordinary biomolecule that binds to ice and preserves cell structure. We recently discovered that Japanese edible fish species also contain an antifreeze protein, and established a method of isolating the protein from fish muscles. We determined that the isolated antifreeze protein consists of a mixture of many isoforms that together are more active than any single isoform. Mass preparation of antifreeze protein is currently under investigation to provide material for a variety of studies and industries.
Cloning and expression of DNA encoding a ripening form a polypeptide having sulfhydryl oxidase activity (1993)

The invention relates to recombinant DNA technology for the production of an enzyme having sulfhydryl oxidase ("SOX") activity. This SOX-enzyme can be used where the oxidation of free sulfhydryl groups (thio compounds) to the corresponding disulfides is desirable. SOX enzyme may be used for treatment of bakery products or for removal of off-flavour from milk or beer.
Fast Multiset Membership Testing Using Combinatorial Bloom Filters (2009)

In this paper we consider the problem of designing a data structure that can perform fast multiset membership testing in deterministic time. Our primary goal is to develop a hardware implementation of the data structure which uses only embedded memory blocks. Prior efforts to solve this problem involve hashing into multiple bloom filters. Such approach needs a priori knowledge of the number of elements in each set in order to size the bloom filter. We use a single bloom filter based approach and use multiple sets of hash functions to code for the set (group) id. Since a single bloom filter is used, it does not need a priori knowledge of the distribution of the elements across the different sets. We show how to improve the performance of the data structure by using constant weight error correcting codes for coding the group id. Using error correcting codes improves the performance of these data structures especially when there are large number of sets. We also outline an efficient hardware based approach to generate the the large number of hash functions that we need for this data structure. The resulting data structure, COMB, is amenable to a variety of time-critical network applications.
<title>High-power polymer optical fiber amplifiers and their applications</title> (1994)

Amplification characteristics of graded-index (GI) type organic dye doped polymer optical fiber amplifiers (POFAs) are discussed. As an organic dye for optical amplification, Rhodamine 6G, Rhodamine B, and Perylene Red are doped in the core region of polymer optical fibers (POFs). These POFA can obtain optical gain in the visible region of wavelength from 570 nm to 620 nm. POFA is promising for extraordinary high power optical amplification in comparison with rare-earth ions doped silica fiber amplifier. For example, output power of 1 kW with a gain of 30 dB can be obtained by using a Rhodamine B doped POFA at a low dye concentration of 1 ppm. Additionally, a novel solid-state POFA amplifier system is demonstrated.
Deep Panchromatic Image Guided Residual Interpolation For Multispectral Image Demosaicking (2019)

Snapshot multispectral imaging based on multispectral filter arrays (MSFA) has gained popularity recently for its size and speed. To process these multispectral images, demosaicking is the most crucial and challenging step to reduce artifacts in both spatial and spectral domain. In this work, a novel ResNet based deep learning model is first proposed to reconstruct the full-resolution panchromatic image from MSFA mosaic image. Then, the reconstructed deep panchromatic image (DPI) is deployed as the guide to recover the full-resolution multispectral image using a two-pass guided residual interpolation method. Experiment results demonstrate that the proposed method outperforms the state-of-the-art conventional and deep learning demosaicking methods both qualitatively and quantitatively.
An opposite approach to steam generation using solar power: cooler for more (2018)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text H. Song, Y. Liu, M. H. Singer, D. Ji, L. Zhou, N. Zhang, X. Zeng, Z. Bei, Z. Yu, and Q. Gan, "An opposite approach to steam generation using solar power: cooler for more," in Frontiers in Optics / Laser Science, OSA Technical Digest (Optica Publishing Group, 2018), paper JTu2A.32. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article