gebhart/patrepeval huggingface dataset:
Specific determination of hepatitis B e antigen by antibodies targeting precore unique epitope facilitates clinical diagnosis and drug evaluation against hepatitis B virus infection (2020)

Hepatitis B e antigen (HBeAg) is a widely used marker both for chronic hepatitis B (CHB) clinical management and HBV-related basic research. However, due to its high amino acid sequence homology to hepatitis B core antigen (HBcAg), most of available anti-HBe antibodies are cross-reactive with HBcAg resulting in high interference against accurate measurement of the status and level of HBeAg. In the study, we generated several monoclonal antibodies (mAbs) targeting various epitopes on HBeAg and HBcAg. Among these mAbs, a novel mAb 16D9, which recognizes the SKLCLG (aa -10 to -5) motif on the N-terminal residues of HBeAg that is absent on HBcAg, exhibited excellent detection sensitivity and specificity in pairing with another 14A7 mAb targeting the HBeAg C-terminus (STLPETTVVRRRGR, aa141 to 154). Based on these two mAbs, we developed a novel chemiluminescent HBeAg immunoassay (NTR-HBeAg) which could detect HBeAg derived from various HBV genotypes. In contrast to widely used commercial assays, the NTR-HBeAg completely eliminated the cross-reactivity with secreted HBcAg from precore mutant (G1896A) virus in either cell culture or patient sera. The improved specificity of the NTR-HBeAg assay enables its applicability in cccDNA-targeting drug screening in cell culture systems and also provides an accurate tool for clinical HBeAg detection.
Development of highly active and coke-resilient Ni-based catalysts for low-temperature steam reformation of methane (2023)

In this work, we report on the development of highly active and stable catalysts for low temperature steam reformation of methane. The Ni-based catalysts supported on alumina were synthesized by the single step solution combustion synthesis (SCS) method. A combination of various surface and bulk sensitive analytical techniques such as XRD, cyclic TPDRO, XPS and HRTEM-SAED was utilized for detailed characterization of the catalysts. The catalyst 5NC synthesized by the SCS method exhibited superior activity and excellent stability for steam reformation of methane during the investigated period on stream for around 200 h. The light-off for methane conversion over the 5NC catalyst started at a reaction temperature of 350 °C whereas for the 5NP catalyst no activity below 600 °C was observed. Moreover, full methane conversion over the 5NC catalyst was achieved at 700 °C. Under similar conditions at reaction temperature of 700 °C, the methane decomposition rates over the 5NC catalyst was around 20 times higher than that of the 5NP catalyst. The exceptional high performance of the 5NC catalyst was attributed to the presence of surface defects, generation of nickel aluminates (NiAl2O4) nano-crystallites, uniform distribution and smaller metal oxide particle size.
Recognition of a 5‘-(A,T)GGG(A,T)<sub>2</sub>-3‘ Sequence in the Minor Groove of DNA by an Eight-Ring Hairpin Polyamide (1996)

The use of pyrrole−imidazole polyamides for the recognition of core 5‘-GGG-3‘ sequences in the minor groove of double stranded DNA is described. Two hairpin pyrrole−imidazole polyamides, ImImIm-γ-PyPyPy-β-Dp and ImImImPy-γ-PyPyPyPy-β-Dp (Im = N-methylimidazole-2-carboxamide, Py = N-methylpyrrole-2-carboxamide, β = β-alanine, γ = γ-aminobutyric acid, and Dp = ((dimethylamino)propyl)amide), as well as the corresponding EDTA affinity cleaving derivatives, were synthesized and their DNA binding properties analyzed. Quantitative DNase I footprint titrations demonstrate that ImImIm-γ-PyPyPy-β-Dp binds the formal match sequence 5‘-AGGGA-3‘ with an equilibrium association constant of Ka = 5 × 106 M-1 (10 mM Tris·HCl, 10 mM KCl, 10 mM MgCl2, and 5 mM CaCl2, pH 7.0 and 22 °C). ImImImPy-γ-PyPyPyPy-β-Dp binds the same site, 5‘-AGGGAA-3‘, approximately two orders of magnitude more tightly than the six ring polyamide, with an equilibrium association constant of Ka = 4 × 108 M-1. The eight-ring hairpin polyamide demonstrates greater specifity for single base pair mismatches than does the six ring hairpin. Polyamides with an EDTA·Fe(II) moiety at the carboxy terminus confirm that each hairpin binds in a single orientation. The high affinity recognition of a 5‘-GGG-3‘ core sequence by an eight ring polyamide containing three contiguous imidazole amino acids demonstrates the versatility of pyrrole−imidazole polyamides and broadens the sequence repertoire for DNA recognition.
ZmPep1, an Ortholog of Arabidopsis Elicitor Peptide 1, Regulates Maize Innate Immunity and Enhances Disease Resistance   (2011)

ZmPep1 is a bioactive peptide encoded by a previously uncharacterized maize (Zea mays) gene, ZmPROPEP1. ZmPROPEP1 was identified by sequence similarity as an ortholog of the Arabidopsis (Arabidopsis thaliana) AtPROPEP1 gene, which encodes the precursor protein of elicitor peptide 1 (AtPep1). Together with its receptors, AtPEPR1 and AtPEPR2, AtPep1 functions to activate and amplify innate immune responses in Arabidopsis and enhances resistance to both Pythium irregulare and Pseudomonas syringae. Candidate orthologs to the AtPROPEP1 gene have been identified from a variety of crop species; however, prior to this study, activities of the respective peptides encoded by these orthologs were unknown. Expression of the ZmPROPEP1 gene is induced by fungal infection and treatment with jasmonic acid or ZmPep1. ZmPep1 activates de novo synthesis of the hormones jasmonic acid and ethylene and induces the expression of genes encoding the defense proteins endochitinase A, PR-4, PRms, and SerPIN. ZmPep1 also stimulates the expression of Benzoxazineless1, a gene required for the biosynthesis of benzoxazinoid defenses, and the accumulation of 2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one glucoside in leaves. To ascertain whether ZmPep1-induced defenses affect resistance, maize plants were pretreated with the peptide prior to infection with fungal pathogens. Based on cell death and lesion severity, ZmPep1 pretreatment was found to enhance resistance to both southern leaf blight and anthracnose stalk rot caused by Cochliobolis heterostrophus and Colletotrichum graminicola, respectively. We present evidence that peptides belonging to the Pep family have a conserved function across plant species as endogenous regulators of innate immunity and may have potential for enhancing disease resistance in crops.
Rice WRKY45 Plays a Crucial Role in Benzothiadiazole-Inducible Blast Resistance (2007)

Benzothiadiazole (BTH) is a so-called plant activator and protects plants from diseases by activating the salicylic acid (SA) signaling pathway. By microarray screening, we identified BTH- and SA-inducible WRKY transcription factor (TF) genes that were upregulated within 3 h after BTH treatment. Overexpression of one of them, WRKY45, in rice (Oryza sativa) markedly enhanced resistance to rice blast fungus. RNA interference-mediated knockdown of WRKY45 compromised BTH-inducible resistance to blast disease, indicating that it is essential for BTH-induced defense responses. In a transient expression system, WRKY45 activated reporter gene transcription through W-boxes. Epistasis analysis suggested that WRKY45 acts in the SA signaling pathway independently of NH1, a rice ortholog of Arabidopsis thaliana NPR1, which distinguishes WRKY45 from known Arabidopsis WRKY TFs. Two defense-related genes, encoding a glutathione S-transferase and a cytochrome P450, were found to be regulated downstream of WRKY45 but were not regulated by NH1, consistent with the apparent independence of the WRKY45- and NH1-dependent pathways. Defense gene expression in WRKY45-overexpressed rice plants varied with growth conditions, suggesting that some environmental factor(s) acts downstream of WRKY45 transcription. We propose a role for WRKY45 in BTH-induced and SA-mediated defense signaling in rice and its potential utility in improving disease resistance of rice, an importance food resource worldwide.
Left ventricular paced activation in cardiac resynchronization therapy patients with left bundle branch block and relationship to its electrical substrate (2020)

LV-paced effect, which is core to CRT, is unpredictable based on conventionally used measures and should be considered during CRT optimization.
Novel polarized light emitting illumination systems for LCDs (2001)

A new, simple polymer-bilayer illumination system is presented which efficiently emits linearly polarized light for use, for example, in liquid crystal displays. Polarization of incoming light is accomplished through polarization-selective reflection at the interface between an optically isotropic light guide and a birefringent top-layer mounted thereon. Light of one polarization direction is coupled-out from the latter layer by means of an appropriate relief structure. Light of the other polarization direction is trapped in the isotropic waveguide and may be recycled, which ultimately permits polarization efficiencies that approach unity.
Low complexity algebraic multicast network codes (2003)

We present a low complexity algorithm for designing algebraic codes that achieve the information theoretic capacity for the multicast problem on directed acyclic networks. These codes operate over field sizes which are significantly smaller than those previously known, leading to significantly lower design and implementation complexity, and network link usage. These codes can be extended for networks with cycles and delays, and for robustness properties.
Structure-based engineering of designed armadillo repeat proteins. (2014)

The specific recognition of macromolecules is key for many applications in biochemical research, medical diagnostics and disease treatment. Currently the development of new recognition molecules depends on the immunization of lab animals or combinatorial biochemistry techniques. Since both approaches are elaborate and require the availability of sufficient amounts of stable target molecules we are developing a modular system that allows a rational design of peptide recognition modules. This system is based on the armadillo repeat scaffold, because natural armadillo repeat proteins bind their targets in extended anti-parallel conformations with very regular binding topologies. The development of designed armadillo repeat proteins (dArmRPs) consisting entirely of identical internal repeats (full-consensus design) has been described [1]. Although dArmRP with 2nd generation capping repeats were predominantly monomeric in solution, crystal structures of dArmRP with different numbers of internal repeats revealed domain-swapped N-caps [2]. Redesign of the N-cap significantly improved thermodynamic stability and abrogated swapping of N-caps. These 3rd generation dArmRP recognize full-consensus peptides with nanomolar affinities. The dissociation constants depend on the lengths of the targeted peptides and the number of internal repeats. Three crystal structures of complexes between dArmRPs with five or six internal repeats and the targeted full-consensus (KR)5 peptide (either free or fused to the N- and C-terminii of globular proteins) confirm that the binding mode fulfills the expected regular topology. Further crystal structures of complexes between dArmRPs and the mismatch (RR)5 peptide revealed that the dArmRPs recognize their target peptides in a side-chain specific manner. Several crystal structures confirm that 3rd generation dArmRPs behave as stable and monomeric molecules that allow the selective recognition of the targeted peptide with the expected topology. Therefore, the rational assembly of binding modules from a pool of dipeptide-specific armadillo repeats to recognize peptides with given sequences should indeed be possible.
Leveraging Atropisomerism to Obtain a Selective Inhibitor of RET Kinase with Secondary Activities Towards EGFR Mutants (2019)

Unstable atropisomerism is innate in many common scaffolds in drug discovery, commonly existing as freely rotating aryl-aryl bonds. Such compounds can access the majority of dihedral conformations around the bond axis, however most small-molecules bind their target within a narrow range of these available conformations. The remaining accessible conformations can interact with other proteins leading to compound promiscuity. Herein, we leverage atropisomerism to restrict the accessible low energy dihedral conformations available to a promiscuous kinase inhibitor and achieve highly selective and potent inhibitors of the oncogenic target RET kinase. We then evaluate our lead inhibitor against kinases that were predicted to bind compounds in a similar conformational window to RET, discovering a potent inhibitor of drug resistant EGFR mutants including L858R/T790M/C797S EGFR. Leveraging atropisomerism to restrict accessible conformational space should be a generally applicable strategy due to the prevalence of unstable atropisomerism in drug discovery.
Production of substitute natural gas. [synthesis from carbon monoxide and hydrogen] (1979)

Synthesis gases containing carbon monoxide, e.g., above 40% volume, and hydrogen are methanated to produce substitute natural gas, after CO/sub 2/ removal, wherein the synthesis gas is simultaneously saturated with water, further heated and divided into first and second feed gas streams. The first feed gas stream is catalytically methanated at a temperature of from 250 to 550/sup 0/C, and the reaction product mixed with said second feed gas stream. The mixture is methanated over a second catalyst at a temperature of from 250 to 550/sup 0/C and the product is divided into a second product gas stream and a recycle gas stream and the recycle gas stream is admixed with the first feed gas stream, prior to the first catalytic methanation. The second product gas stream is subjected to a carbon dioxide removal process to produce SNG.
Coherently amplified Raman polarization gate for imaging through scattering media (1994)

We demonstrate a new nonlinear optical field cross-correlation technique for two-dimensional imaging through scattering media. The technique, the coherently amplified Raman polarization gate, relies on both the polarization and coherence sensitivity of broadband stimulated Raman amplification to produce a high-contrast gate with temporal resolution of the order of the inverse bandwidth of the pump.
Three dimensional shear wave elastographic reconstruction of ablations (2014)

This paper presents an algorithm for three dimensional (3D) reconstruction of tumor ablations using ultrasound electrode vibration elastography. Shear wave velocity, which is used as a surrogate for tissue stiffness, is estimated by perturbing the ablation needle and tracking frame-to-frame displacements using radiofrequency ultrasound echo data. This process is repeated over many imaging planes that share a common axis of intersection collinear with needle. A 3D volume is reconstructed by solving an optimization problem which smoothly approximates shear wave velocities on a stack of transverse planes. The mean shear wave velocity estimates obtained in the phantom experiments are within 20% of those measured using a commercial shear wave imaging system.
Dynamic feature ordering for efficient registration (1999)

Existing sequential feature based registration algorithms involving search typically either select features randomly (e.g. the RANSAC approach (M. Fischler and R. Bolles, 1981)) or assume a predefined, intuitive ordering for the features (e.g. based on size or resolution). The paper presents a formal framework for computing an ordering for features which maximizes search efficiency. Features are ranked according to matching ambiguity measure, and an algorithm is proposed which couples the feature selection with the parameter estimation, resulting in a dynamic feature ordering. The analysis is extended to template features where the matching is non discrete and a sample refinement process is proposed. The framework is demonstrated effectively on the localization of a person in an image, using a kinematic model with template features. Different priors are used on the model parameters and the results demonstrate nontrivial variations in the optimal feature hierarchy.
Single-shot optical neural network (2023)

Analog optical and electronic hardware has emerged as a promising alternative to digital electronics to improve the efficiency of deep neural networks (DNNs). However, previous work has been limited in scalability (input vector length <i>K</i> ≈ 100 elements) or has required nonstandard DNN models and retraining, hindering widespread adoption. Here, we present an analog, CMOS-compatible DNN processor that uses free-space optics to reconfigurably distribute an input vector and optoelectronics for static, updatable weighting and the nonlinearity-with <i>K</i> ≈ 1000 and beyond. We demonstrate single-shot-per-layer classification of the MNIST, Fashion-MNIST, and QuickDraw datasets with standard fully connected DNNs, achieving respective accuracies of 95.6, 83.3, and 79.0% without preprocessing or retraining. We also experimentally determine the fundamental upper bound on throughput (∼0.9 exaMAC/s), set by the maximum optical bandwidth before substantial increase in error. Our combination of wide spectral and spatial bandwidths enables highly efficient computing for next-generation DNNs.
A novel synthetic route to L-proline (Amino acids ; 7) (1986)

Reaction of L-5-oxoproline esters L-2 with phosgene at 0° C gives L-5,51-dichloro-1-(chlorocarbonyl)proliene esters L-6 ,which readily lose hydrogen chloride to form L-5-chloro-1-(chloroarbonyl)-4,5-dehydroproline esters L-7. Catalytic hydrogenation (Pd/C, 180 bar) of L-7 yields L-1-(chlorocarbonyl)proline esters L-15 and thence, upon hydrolysis, L-proline ( L17 ). A "one-pot reaction" for the whole sequence is described, starting from easily accessible L-5-oxoproline esters and yielding L-proline in 78% overall yield and 99.7% optical purity.
Architecture for resource allocation services supporting interactive remote desktop sessions in utility grids (2004)

Emerging large scale utility computing systems like Grids promise computing and storage to be provided to end users as a utility. System management services deployed in the middleware are a key to enabling this vision. Utility Grids provide a challenge in terms of scale, dynamism, and heterogeneity of resources and workloads. In this paper, we present a model based architecture for resource allocation services for Utility Grids. The proposed service is built in the context of interactive remote desktop session workloads and takes application performance QoS models into consideration. The key design guidelines are hierarchical request structure, application performance models, remote desktop session performance models, site admission control, multi-variable resource assignment system, and runtime session admission control. We have also built a simulation toolkit that can handle mixed batch and remote desktop session requests, and have implemented our proposed resource allocation service into the toolkit. We present some results from experiments done using the toolkit. Our proposed architecture for resource allocation services addresses the needs of emerging utility computing systems and captures the key concepts and guidelines for building such services in these environments.
Bullatalicinone, a new potent bioactive acetogenin, and squamocin from <i>annona bullata</i> (Annonaceae) (1991)

Abstract Further fractionation of the EtOH extract of the bark of Annona bullata Rich. (Annonaceae) has led to the isolation of a new nonadjacent bis‐tetrahydrofuran acetogenin, bullatalicinone, and the known adjacent bis‐tetrahydrofuran acetogenin, squamocin. These two compounds showed potent and selective cytotoxicities for certain human tumor cell lines. Their structures have been elucidated by chemical and spectral methods. Bullatalicinone is the methylketo‐lactone derivative of bullatalicin which we found previously in this plant.
Cycling (2016)

This article presents an overview of a control systems perspective. An electric field when applied to yield functional tasks is called as functional electrical stimulation (FES). FES is commonly prescribed as a treatment for various neurological disorders. Given the existence of regions in the crank cycle where it is inefficient to produce torque, a motor can be included as another torque source. FES control of the muscles yields cadence tracking in torque efficient regions, while the motor yields cadence tracking when it is efficient for the limbs to produce torque. The inclusion of a motor enables switching between stable systems and eliminates the need for the development of sufficient dwell-time conditions. Hence, the development of adaptive switched controllers for motorized FES-cycling systems may have a closer horizon. The inclusion of a motor also expands the possible control objectives that can be pursued.
A modified version of DVR-based multicasting with security (2017)

Reverse Path Forwarding based multicasting used in Distance Vector Multicast Routing Protocol (DVMRP) has the major drawback of generating large number of duplicate and prune packets. Use of the concept of pseudo diameter reduces the number of duplicate packets. The reason is that pseudo diameter helps in the reduction of the scope of travel of a packet. In this work a new approach of multicasting with security has been proposed. The concept of pseudo diameter has been extended to further reduce the scope of travel of a packet. Use of this new concept known as super pseudo diameter while multicasting results in significant reduction of the number of prune packets generated; hence, it guarantees even better utilization of network bandwidth.
Imino Sugars That are Less Toxic but More Potent as Antivirals, <i>In Vitro</i>, Compared with N-n-Nonyl DNJ (2002)

Imino sugar glucosidase inhibitors have selective antiviral activity against certain enveloped, mammalian viruses. Deoxynojirimycins (DNJs) modified by N-alkylation to contain a nine carbon atom side chain (N-n-nonyl-deoxynojirimycin; N-nonyl-DNJ, NN-DNJ) were shown to be, for example, at least 20 times more potent in inhibiting hepatitis B virus (HBV) and bovine viral diarrhoea virus (BVDV) in cell based assays than the non-alkylated DNJ. These data suggested that modification of the alkyl side chain could influence antiviral activity. Previous work has focused on varying side chain length. In this report, the influence of side chain branching and cyclization upon toxicity and antiviral activity was explored. Briefly, using a virus secretion assay for HBV and a single step growth (yield reduction) assay for BVDV, 14 different DNJ-based sugars, possessing various N-alkyl substitutions, were tested for antiviral activity. Of the series, N-methoxy-nonyl-DNJ and N-butyl-cyclohexyl DNJ were determined to have the best selectivity index against BVDV and HBV, with the N-methoxy analogue being the most potent with micromolar antiviral activity. The results of this antiviral survey and the implications for the mechanism of action and ultimate therapeutic potential of the DNJ-based imino sugars is provided and discussed.
Resonant-Cavity Infrared Detector (RCID) with Very Thin Absorber (2019)

A resonant-cavity detector incorporating only 5 quantum wells within the absorbing region has a peak sensitivity at 4.0 μm with a measured external quantum efficiency at room temperature of 34 % and dark current density comparable with state-of-the-art HgCdTe detectors.