gebhart/patrepeval huggingface dataset:
Comparative Analysis and Serovar-Specific Identification of Multiple-Banded Antigen Genes of <i>Ureaplasma urealyticum</i> Biovar 1 (1999)

Ureaplasma urealyticum is a causative agent of nongonococcal urethritis and is implicated in the pathogenesis of several other diseases. The species is divided into 14 serovars and two biovars, of which biovar 1 is most commonly isolated from clinical specimens. Reported associations between individual serovars and diseases have been difficult to confirm because of practical difficulties with serotyping. The multiple-banded antigen (MBA) is the predominant U. urealyticum antigen recognized during infections in humans and probably has a significant role in virulence. The 5' end of the MBA gene is relatively conserved but contains biovar, and possibly serovar, specificity. The 5' ends of the MBA genes of standard strains of U. urealyticum biovar 1, consisting of serovars 1, 3, 6, and 14, were amplified, cloned into pUC19, and sequenced to identify serovar-specific differences. The 5' end of the MBA gene sequence of serovar 3 was identical with the previously published sequence and differed by only three bases from that of serovar 14. Significant differences between the MBA gene sequences allowed biovar 1 to be divided into two subgroups, containing serovars 3/14 and serovars 1 and 6, respectively, using primers UMS-125-UMA269 and UMS-125-UMA269'. Serovars 1 and 6 were distinguished by restriction enzyme analysis of the amplicon and/or by PCR specific for serovar 6. These methods were used to identify and type U. urealyticum in 185 (46.3%) of 400 genital specimens from women. Biovar 1 was detected in 89.2% and biovar 2 in 18.3% of positive specimens. Of 165 specimens containing U. urealyticum biovar 1, 22.2% contained more than one serovar and 46.7, 46.1, and 25.5% contained serovars 1, 3/14, and 6, respectively. U. urealyticum was found in a significantly higher proportion of pregnant women than in sex workers and other women attending a sexually transmissible diseases clinic (P < 0.01). The methods described are relatively rapid, practicable, and specific for serotyping isolates and for direct detection and identification of individual serovars in clinical specimens containing U. urealyticum biovar 1.
Development of an Intergenotypic Hepatitis C Virus (HCV) Cell Culture Method To Assess Antiviral Susceptibilities and Resistance Development of HCV NS3 Protease Genes from HCV Genotypes 1 to 6 (2010)

Protease inhibitors (PIs) of hepatitis C virus (HCV) provide an additional or alternative therapy for chronic infection. However, assessment of their efficacy and ability to inhibit replication of different genotypes is hampered by the lack of a convenient animal model or a method for in vitro culture of HCV other than the type 1/2-based replicons and the infectious genotype 2a clone JFH1. To address this problem, we constructed a panel of replication-competent chimeric Jc1 (pFK JFH1/J6/C-846) clones containing protease and NS4A coding sequences from all six major genotypes, enabling the determination of replication and the susceptibility to PIs. Chimeras showed substantial variability in replication kinetics, attributable in part to naturally occurring polymorphisms and differing requirements for adaptive mutations in NS3 and NS4A. Through calculation of 50% inhibitory concentrations (IC(50)s) of BILN 2061, measuring reduction in the number of focus-forming units/ml (FFU/ml) and replication inhibition, consistent genotype-associated differences in antiviral susceptibilities were observed. IC(50)s for genotype 1b, 4a, and 6a-derived chimeras (1 to 3 nM) were approximately 100-fold lower than those for genotypes 2a, 3a, and 5a (range, 80 to 720 nM), implying major differences in response to therapy. In vitro passage in increasing concentrations of BILN 2061 rapidly induced resistance-associated mutations at position 168 in chimeras of all 6 genotypes and at position 156 in genotypes 1b and 4a, each with substantial variability in the identity of substituted amino acids. The system will allow future comprehensive phenotypic characterization of naturally occurring and treatment-induced mutations for PIs in trial or entering clinical use.
StarCraft Micromanagement With Reinforcement Learning and Curriculum Transfer Learning (2018)

Real-time strategy games have been an important field of game artificial intelligence in recent years. This paper presents a reinforcement learning and curriculum transfer learning method to control multiple units in StarCraft micro management. We define an efficient state representation, which breaks down the complexity caused by the large state space in the game environment. Then, a parameter sharing multi-agent gradient descent Sarsa(λ) algorithm is proposed to train the units. The learning policy is shared among our units to encourage cooperative behaviors. We use a neural network as a function approximator to estimate the action-value function, and propose a reward function to help units balance their move and attack. In addition, a transfer learning method is used to extend our model to more difficult scenarios, which accelerates the training process and improves the learning performance. In small-scale scenarios, our units successfully learn to combat and defeat the built-in AI with 100% win rates. In large-scale scenarios, the curriculum transfer learning method is used to progressively train a group of units, and it shows superior performance over some baseline methods in target scenarios. With reinforcement learning and curriculum transfer learning, our units are able to learn appropriate strategies in StarCraft micro management scenarios.
A multifunctional polyketide–peptide synthetase essential for albicidin biosynthesis in Xanthomonas albilineans The GenBank accession number for the sequence determined in this work is AF239749. (2001)

Albicidins, a family of potent antibiotics and phytotoxins produced by the sugarcane leaf scald pathogen Xanthomonas albilineans, inhibit DNA replication in bacteria and plastids. A gene located by Tn5-tagging was confirmed by complementation to participate in albicidin biosynthesis. The gene (xabB) encodes a large protein (predicted M:(r) 525695), with a modular architecture indicative of a multifunctional polyketide synthase (PKS) linked to a non-ribosomal peptide synthetase (NRPS). At 4801 amino acids in length, XabB is the largest reported PKS-NRPS. Twelve catalytic domains in this multifunctional enzyme are arranged in the order N terminus-acyl-CoA ligase (AL)-acyl carrier protein (ACP)-beta-ketoacyl synthase (KS)-beta-ketoacyl reductase (KR)-ACP-ACP-KS-peptidyl carrier protein (PCP)-condensation (C)-adenylation-PCP-C. The modular architecture of XabB indicates likely steps in albicidin biosynthesis and approaches to enhance antibiotic yield. The novel pattern of domains, in comparison with known PKS-NRPS enzymes for antibiotic production, also contributes to the knowledge base for rational design of enzymes producing novel antibiotics.
Rap1 Regulates the Formation of E-Cadherin-Based Cell-Cell Contacts (2004)

In epithelial tissues, cells are linked to their neighbors through specialized cell-cell adhesion proteins. E-cadherin is one of the most important membrane proteins for the establishment of intimate cell-cell contacts, but the molecular mechanism by which it is recruited to contact sites is largely unknown. We report here that the cytoplasmic domain of E-cadherin interacts with C3G, a guanine nucleotide exchange factor for Rap1. In epithelial cell cultures, ligation of the extracellular domain of E-cadherin enhances Rap1 activity, which in turn is necessary for the proper targeting of E-cadherin molecules to maturing cell-cell contacts. Furthermore, our data suggest that Cdc42 functions downstream of Rap1 in this process. We conclude that Rap1 plays a vital role in the establishment of E-cadherin-based cell-cell adhesion.
Lp compression, traveling salesmen, and stable walks (2011)

We show that if H is a group of polynomial growth whose growth rate is at least quadratic, then the Lp compression of the wreath product Z≀H equals max{1p,12}. We also show that the Lp compression of Z≀Z equals max{p2p−1,23} and that the Lp compression of (Z≀Z)0 (the zero section of Z≀Z, equipped with the metric induced from Z≀Z) equals max{p+12p,34}. The fact that the Hilbert compression exponent of Z≀Z equals 2/3 while the Hilbert compression exponent of (Z≀Z)0 equals 3/4 is used to show that there exists a Lipschitz function f:(Z≀Z)0→L2 which cannot be extended to a Lipschitz function defined on all of Z≀Z.
SU-FF-I-18: Optimization of FDK Reconstruction Parameters to Minimize Aliasing and Reduce Metal Artifacts (2007)

Purpose: To maximize SNR, suppress metal artifacts and minimize backprojection times for FDK-based cone-beam CT (CBCT) reconstructions by optimizing binning, filtering and backprojection parameters, and to investigate the performance of new multi-core CPU's. Methods and Materials: CBCT reconstruction times can be reduced by filtering and downsampling high resolution flat panel projection data to match the reconstruction matrix pitch, and by using nearest neighbor interpolation (NN) for backprojection. However, metal artifacts and noise aliasing may result. To investigate the tradeoffs involved, a frequency-domain noise power spectrum (NPS) model was developed. Phantom and clinical CBCT data were acquired using the On-Board Imager and reconstructed with a range of pre-processing and backprojection parameters while keeping image MTF constant. Image noise, including the amount of noise aliasing, and metal artifacts were evaluated. Reconstruction times were measured on Xeon workstations comprising either two single-core, dual-core, or quad-core CPU's. Results: Two types of metal artifacts emerged. A moiré pattern is produced if insufficient projection data densities in the transaxial direction are maintained, while radial streaks are produced by insufficiently dense axial data. For best image quality aliased noise should be less than 5% of the total image noise, and projection data should be 1.5–2.0× denser than the reconstructed image matrix pitch for backprojection with bilinear interpolation. NN interpolation is not preferred. Although backprojection times increased by ∼50% with these higher projection data densities, overall reconstruction times for relatively large image matrices (512×512×188, 675 projections), were <50 seconds using the quad-core workstation which is sufficiently fast for IGRT applications. Conclusions: Optimal use of high data densities coupled with bilinear interpolation for backprojection can suppress some metal artifacts and minimize noise aliasing. New multi-core CPU architectures provide sufficient speed to make such reconstructions clinically practical. Conflict of Interest: Employees of Varian Medical Systems.
Laser Crystallization of Organic–Inorganic Hybrid Perovskite Solar Cells (2016)

Organic-inorganic hybrid perovskites attract enormous research interest for next generation solar energy harvest. Synergistic crystalline structures comprising organic and inorganic components enable solution processing of perovskite films. A reliable crystallization method for perovskites, compatible with fast continuous process over large-area flexible substrates, is crucial for high performance solar cell production. Here, we present laser crystallization of hybrid perovskite solar cells using near-infrared (NIR) laser (λ = 1064 nm). Crystalline morphology of CH3NH3PbI3 (MAPbI3) perovskite films are widely controllable with laser irradiation condition while maintaining film uniformity. Photothermal heating effectively assisted by interfacial photoconversion layers is critical for phase transformation without beam damage of multilayered device structures. Notably, laser crystallization attains higher device performances than conventional thermal annealing. Fast laser crystallization with manufacture level scan rate (1 m min(-1)) demonstrates inverted-type perovskite solar cells with 11.3 and 8.0% efficiencies on typical glass and flexible polymer substrates, respectively, without rigorous device optimization.
Guided cost learning: deep inverse optimal control via policy optimization (2016)

Reinforcement learning can acquire complex behaviors from high-level specifications. However, defining a cost function that can be optimized effectively and encodes the correct task is challenging in practice. We explore how inverse optimal control (IOC) can be used to learn behaviors from demonstrations, with applications to torque control of high-dimensional robotic systems. Our method addresses two key challenges in inverse optimal control: first, the need for informative features and effective regularization to impose structure on the cost, and second, the difficulty of learning the cost function under unknown dynamics for high-dimensional continuous systems. To address the former challenge, we present an algorithm capable of learning arbitrary nonlinear cost functions, such as neural networks, without meticulous feature engineering. To address the latter challenge, we formulate an efficient sample-based approximation for MaxEnt IOC. We evaluate our method on a series of simulated tasks and real-world robotic manipulation problems, demonstrating substantial improvement over prior methods both in terms of task complexity and sample efficiency.
High-Resolution Imaging of Single Fluorescent Molecules with the Optical Near-Field of a Metal Tip (2004)

We show that a concentration of light at a metal tip allows near-field optical imaging of single fluorescent dye molecules at very high resolution, despite strong quenching effects. Details as small as 10 nm were observed in the fluorescence patterns of single Cy-3 dyes bound to the termini of DNA. Data evaluation by model fitting determines the positions of the dyes to an accuracy even better than 1 nm and also yields their 3D orientation. The metal tip simultaneously provides high-resolution topographic imaging complementing the optical signal for a detailed surface examination.
Consortium Blockchain-Based SIFT: Outsourcing Encrypted Feature Extraction in the D2D Network (2018)

Privacy-preserving outsourcing algorithms for feature extraction not only reduce users' storage and computation overhead but also preserve the image privacy. However, the existing schemes still suffer from deficiencies induced by security, applications, efficiency and storage. To solve the problems, we implement a consortium chain-based outsourcing feature extraction scheme over encrypted images by using the smart contract, distributed autonomous corporation (DAC), sharding technique, and device to device (D2D) communication, which is secure, widely applied, highly efficient, and has less storage overhead. First, the effectiveness, security, and performance of our scheme are analyzed. Then, the efficiency and storage overhead of our scheme are presented by conducting experimental results.
Long-Short Transformer: Efficient Transformers for Language and Vision (2021)

Transformers have achieved success in both language and vision domains. However, it is prohibitively expensive to scale them to long sequences such as long documents or high-resolution images, because self-attention mechanism has quadratic time and memory complexities with respect to the input sequence length. In this paper, we propose Long-Short Transformer (Transformer-LS), an efficient self-attention mechanism for modeling long sequences with linear complexity for both language and vision tasks. It aggregates a novel long-range attention with dynamic projection to model distant correlations and a short-term attention to capture fine-grained local correlations. We propose a dual normalization strategy to account for the scale mismatch between the two attention mechanisms. Transformer-LS can be applied to both autoregressive and bidirectional models without additional complexity. Our method outperforms the state-of-the-art models on multiple tasks in language and vision domains, including the Long Range Arena benchmark, autoregressive language modeling, and ImageNet classification. For instance, Transformer-LS achieves 0.97 test BPC on enwik8 using half the number of parameters than previous method, while being faster and is able to handle 3x as long sequences compared to its full-attention version on the same hardware. On ImageNet, it can obtain the state-of-the-art results (e.g., a moderate size of 55.8M model solely trained on 224x224 ImageNet-1K can obtain Top-1 accuracy 84.1%), while being more scalable on high-resolution images. The source code and models are released at https://github.com/NVIDIA/transformer-ls.
New Ring-Opening Polymerization of Phosphorus-Containing Cyclic Monomers (2002)

A living cationic ring-opening polymerization of a six-membered cyclic phosphonite initiated with a new catalyst system of a halobenzene with NiBr 2 is disclosed. Furthermore, we report a cationic ring-opening polymerization of a three-membered cyclic phosphine, giving rise directly to the polyphosphine derivative.
Transcriptional Down-Regulation of Human Gonadotropin-Releasing Hormone (GnRH) Receptor Gene by GnRH: Role of Protein Kinase C and Activating Protein 1* (2000)

Clinical applications of GnRH agonists (GnRHa) are based primarily on the decrease in gonadotropin release after down-regulation of the GnRH receptor (GnRHR) by continuous GnRHa administration. However, the molecular mechanisms underlying the transcriptional regulation of the human GnRHR gene after prolonged GnRH treatment remain poorly understood. In the present study GnRHa-mediated regulation of human GnRHR gene transcription was studied by transiently transfecting the mouse gonadotrope-derived (alphaT3-1) cells with a 2297-bp human GnRHR promoter-luciferase construct (p2300-LucF). A dose- and time-dependent decrease in human GnRHR promoter activity was observed after GnRHa treatment. An average 71% decrease in promoter activity was observed after 24-h treatment with 0.1 microM GnRHa, which was blocked by cotreatment of the GnRH antagonist, antide. This effect was mimicked by phorbol 12-myristate 13-acetate (TPA) administration. In addition, the GnRHa- and TPA-mediated decrease in the human GnRHR promoter activity was reversed by a specific protein kinase C (PKC) inhibitor, GF109203X, or depletion of PKC by TPA pretreatment. These findings indicate that the activation of the PKC pathway is important in regulating the human GnRHR gene expression. By progressive 5'-deletion studies, we have identified a 248-bp DNA fragment (-1018 to -771, relative to the translation start site) at the 5'-flanking region of the human GnRHR gene that is responsible for the GnRHa-mediated down-regulation of human GnRHR promoter activity. Analysis of this sequence reveals the existence of two putative activating protein-1 (AP-1) sites with 87% homology to the consensus sequence (5'-TGA(G/C)T(C/A)A-3'), located at -1000 to -994 (5'-TTAGACA-3', in complementary orientation) and -943 to 937 (5'-TGAATAA-3'). Using competitive gel mobility shift assays, AP-1 binding was observed within this 248-bp region. Site-directed mutation of the putative AP-1-binding site located at -1000 to -994 abolished the GnRHa-induced inhibition. Further competitive GMSA and supershift experiments confirmed the identity of AP-1 binding in this region. By the use of Western blot analysis, a significant increase in c-Jun (100%; P < 0.05) and c-Fos (50%; P < 0.05) protein levels was observed after GnRHa treatment in alphaT3-1 cells. In addition, our data suggested that a change in AP-1 composition, particularly c-Fos, was important in mediating GnRHa-induced inhibition of human GnRHR gene expression. We conclude that activation of the PKC pathway by GnRH is important in controlling human GnRHR gene expression. In addition, the putative AP-1-binding site located at -1000 to -994 of the human GnRHR5'-flanking region has been functionally identified to be involved in mediating this down-regulatory effect.
Effect of Tip Clearance on Fan Noise and Aerodynamic Performance (2005)

The aerodynamic performance results indicate that the fan adiabatic efficiency was highest with nominal tip clearance (about 91.8% at design speed) and decreased as fan tip clearance increased. Differences in fan efficiency between tip clearance configurations was small below 77.5% fan design speed, about 0.5% maximum, and got larger as fan speed increased, to around 1% maximum at 100% fan design speed. The decreases in efficiency are due to a lower blade loading and higher temperature rise over the outer 20% of the blade span; the mechanism is the tip leakage flow from pressure to suction surface of the fan blade, which increases as the fan tip gap increases. Farfield acoustic results show that changes in the noise level are primarily aft-radiating and are on the order of 1 to 5 dB in fan broadband noise level as measured for the rotor-alone configuration (which had no stators). There were very small changes in noise level with tip clearance for the 54-vane Baseline Outlet Guide Vane configuration. Small changes in noise were also seen for the other two Outlet Guide Vane configurations tested - the 26-vane radial Low Count Outlet Guide Vanes and the 26-vane aft swept Low Noise Outlet Guide Vanes. The rotor alone acoustic results suggest that tip clearance changes induce broadband noise changes at the fan tip, but that the noise differences are masked by the rotor wake/stator interaction noise generated with the Outlet Guide Vanes installed. The magnitude of the rotor/stator interaction tones showed small increases with increasing fan tip gap at fan speeds below transonic, indicating slightly stronger interactions with the larger tip vortex wakes that formed with larger tip gaps. The broadband levels, for the most part, only showed the effect of Outlet Guide Vane geometry on the magnitude of the noise as the tip gap changed. The Laser Doppler Velocimetry flow field results show that the flow downstream of the tip of the blades changes very little with changes in the tip clearance when operating at the approach condition. At both the cut-back and take-off speeds, significant changes in the tip flow occur with changes in the tip clearance. Since these changes in the tip flow are not *
Photopolymerized Injectable RGD‐Modified Fumarated Poly(ethylene glycol) Diglycidyl Ether Hydrogels for Cell Growth (2008)

In this study, photopolymerized hydrogels of fumarated poly(ethylene glycol) diglycidyl-co- poly(ethylene glycol) diacrylate have been synthesized and modified with cell adhesion peptide, Arg-Gly-Asp (RGD). The structural and mechanical properties of the hydrogels are found to be poly(ethylene glycol) diacrylate (PEGDA) dependent. The percentage of gelation is increased from 72 to 89 wt.-% when the amount of the crosslinker co-monomer (PEGDA) in the hydrogel formulation is increased from 20 to 40 wt.-%. In the present case, the equilibrium mass swelling is decreased from 216 to 93%. The viscosities of the uncured formulations have also been measured and likewise, the results were influenced by the increasing amount of PEGDA that reduced the value from 83 to 36 cP. The compressive modulus of the prepared hydrogels was improved with the addition of the PEGDA. Cell growth experiments have been performed by comparing the properties of the hydrogels with and without RGD units. The results show that RGD units enhance the adhesion of cells to the surface of the hydrogels. SEM-EDS studies reveal that nitrogen and calcium are produced on the osteoblast-seeded surface of the scaffold within the culture time period. [Figure: see text].