gebhart/patrepeval huggingface dataset:
Abstract 3719: Bicyclic peptides for PET imaging of MT1-MMP expressing tumors (2017)

Abstract The Bicycle® technology is based on repertoires of short peptides displayed on the surface of bacteriophages which can be modified with homo-trifunctional organochemical scaffolds, thus creating large diverse libraries of constrained, bicyclic peptides. These large combinatorial libraries have been extensively used for iterative selections to identify high affinity binding peptides to a wide array of targets, including receptors, interleukins and proteases. Bicyclic peptides are chemically synthesized macrocyclic entities with drug-like properties that exhibit sub-nanomolar affinities and exquisite selectivity towards targets. Unlike biologics, their synthetic nature allows facile modulation of metabolic and pharmacokinetic properties, as well as site-specific conjugation to effector molecules such as fluorophores, radionuclides, and cytotoxic drugs. In the present work, novel phage display derived bicyclic peptides were identified targeting the matrix metalloproteinase 14 (also known as MT1-MMP), a tumor associated surface protein overexpressed in a variety of cancers (i.e. lung, breast). A prototype bicyclic peptide with high affinity to MT1-MMP (Kd at ~1 nM) was identified, and confocal microscopy using fluoresceinated bicyclic peptide derivatives shows target-dependent internalisation in MT1-MMP+ cells. In the in vivo mouse, selective tumor binding in an MT1-MMP+ xenograft model is demonstrated for a DOTA conjugate loaded with Ga-68 or Lu-177. Upon proteolytic optimization of the prototype bicycle peptide, a striking enhancement in tumor signal is observed in biodistribution studies. Compared to radiolabeled antibodies directed against the same target, the lead compound showed fast background clearance (&lt; 1 %ID/g for all organs apart from kidneys) resulting in high imaging contrast in µPET studies as early as 30 minutes post injection. Importantly, most of the non-tumor associated bicyclic peptide rapidly clears into the bladder. Together, tumor targeting bicyclic peptides can, through their small size and high selectivity, facilitate efficient penetration and visualization of tumors in vivo, demonstrating their potential as diagnostic imaging agents in profiling and therapeutic management of patients. Citation Format: Daniel Teufel, Helen Harrison, Spencer Campbell, Catherine Stace, Edward Walker, Robert J. Lutz, Peter Park, Matthias Eder, Ulrike Bauder-Wüst, Ursula Schierbaum, Karin Leotta, Klaus Kopka, Uwe Haberkorn. Bicyclic peptides for PET imaging of MT1-MMP expressing tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3719. doi:10.1158/1538-7445.AM2017-3719
Carbon-doped SnS2 nanostructure as a high-efficiency solar fuel catalyst under visible light (2018)

Photocatalytic formation of hydrocarbons using solar energy via artificial photosynthesis is a highly desirable renewable-energy source for replacing conventional fossil fuels. Using an L-cysteine-based hydrothermal process, here we synthesize a carbon-doped SnS<sub>2</sub> (SnS<sub>2</sub>-C) metal dichalcogenide nanostructure, which exhibits a highly active and selective photocatalytic conversion of CO<sub>2</sub> to hydrocarbons under visible-light. The interstitial carbon doping induced microstrain in the SnS<sub>2</sub> lattice, resulting in different photophysical properties as compared with undoped SnS<sub>2</sub>. This SnS<sub>2</sub>-C photocatalyst significantly enhances the CO<sub>2</sub> reduction activity under visible light, attaining a photochemical quantum efficiency of above 0.7%. The SnS<sub>2</sub>-C photocatalyst represents an important contribution towards high quantum efficiency artificial photosynthesis based on gas phase photocatalytic CO<sub>2</sub> reduction under visible light, where the in situ carbon-doped SnS<sub>2</sub> nanostructure improves the stability and the light harvesting and charge separation efficiency, and significantly enhances the photocatalytic activity.
A 1.4-nm gold cluster covalently attached to antibodies improves immunolabeling. (1992)

A large gold cluster (Au1.4nm) was covalently coupled to IgG and Fab' fragments. Its gold core is 1.4 nm in diameter and the Fab'-Au1.4nm immunoconjugate is the smallest gold immunoprobe that can be seen directly in the conventional electron microscope. It is useful in high-resolution immunolabeling, providing a resolution of 7.0 nm. The cluster's visibility can be enhanced with silver development for use in EM or light microscopy for histological purposes, or to detect less than or equal to 0.2 pg of antigen in immunoblots. By using a gold compound with covalent attachment, a number of advantages over colloidal gold probes are realized, including better resolution, stability, uniformity, sensitivity, and complete absence of aggregation; its small size should also improve penetration and more quantitative labeling of antigenic sites.
Chiral separation with dipeptide-terminated polymeric surfactants: The effect of an extra heteroatom on the polar head group (2000)

Chiral recognition of two binaphthyl derivatives and three benzodiazepines were studied by use of polymeric surfactants in electrokinetic chromatography. Four specific dipeptide terminated (multichiral) micelle polymers were synthesized for this study. These include poly (sodium-N-undecanoyl-L-alanyl-leucinate)-(poly L-SUAL), poly (sodium-N-undecanoyl-L-valyl-leucinate) (poly L-SUVL), poly (sodium-N-undecanoyl-L-seryl-leucinate) (poly L-SUSL), and poly(sodium-N-undecanoyl-L-threonyl-leucinate) (poly L-SUTL). In addition to the chiral separation study, the physicochemical properties (critical micelle concentration and specific rotation) of each polymer were investigated. The molecular weights of the various dipeptide-terminated micelle polymers were determined using analytical ultracentrifugation. These dipeptide-terminated micelle polymers were designed to study the effect of the extra heteroatom at the polar head group of the micelle polymer (i.e., poly L-SUSL compared to poly L-SUAL and poly L-SUTL compared to poly L-SUVL) on the enantiomeric separation of the binaphthyl derivatives and benzodiazepines. The synergistic effect of three chiral centers (poly L-SUTL) provided improved resolution over that of two chiral centered dipeptide-terminated micelle polymer in the case of (±)-temazepam, (±)-oxazepam, (±)-binaphthol, and (±)-binaphthol phosphate. The chiral recognition mechanisms in these cases were additionally controlled by the presence of the extra heteroatom located on the polar head group of the micelle polymers.
UCDS: Unifying connected dominating set with low message complexity, fault tolerance, and flexible dominating factor (2011)

A connected dominating set (CDS) of a graph G consists of a set of dominating nodes, where each node in G is either a member of the set or 1 hop away from a member, and a set of connecting nodes, which connect disjoint sets of dominating nodes. CDSs have traditionally been used in mobile ad-hoc networks for routing applications [1], but these networks could benefit from CDSs in other areas as well, including channel access, link adaptation, energy consumption, power control, and dynamic resource management. It has been shown in [13] and [14] that the minimum dominating set problem (MDS) and minimum connected dominating sets problem (MCDS) are NP-Complete. The following is a presentation of a simple, efficient CDS heuristic that works equally well for and runs independently of all of these CDS applications. For its ability to simultaneously support multiple applications it is called the “Unifying Connected Dominating Set” (UCDS) protocol.
Mining people's trips from large scale geo-tagged photos (2010)

Photo sharing is one of the most popular Web services. Photo sharing sites provide functions to add tags and geo-tags to photos to make photo organization easy. Considering that people take photos to record something that attracts them, geo-tagged photos are a rich data source that reflects people's memorable events associated with locations. In this paper, we focus on geo-tagged photos and propose a method to detect people's frequent trip patterns, i.e., typical sequences of visited cities and durations of stay as well as descriptive tags that characterize the trip patterns. Our method first segments photo collections into trips and categorizes them based on their trip themes, such as visiting landmarks or communing with nature. Our method mines frequent trip patterns for each trip theme category. We crawled 5.7 million geo-tagged photos and performed photo trip pattern mining. The experimental result shows that our method outperforms other baseline methods and can correctly segment photo collections into photo trips with an accuracy of 78%. For trip categorization, our method can categorize about 80% of trips using tags and titles of photos and visited cities as features. Finally, we illustrate interesting examples of trip patterns detected from our dataset and show an application with which users can search frequent trip patterns by querying a destination, visit duration, and trip theme on the trip.
A self-reference sensing technique for ultra-sensitive chemical and biological detection using whispering gallery microresonators (2011)

Ultra-sensitive and label-free chemical and biological sensing devices are of great importance to biomedical research, clinical diagnostics, environmental monitoring, and homeland security applications. Optical sensors based on ultra-highquality Whispering-Gallery-Mode (WGM) micro-resonators, in which light-matter interactions are significantly enhanced, have shown great promise in achieving compact sensors with high sensitivity and reliability. However, traditional sensing mechanisms based on monitoring the frequency shift of a single resonance faces challenges since the resonant frequency is sensitive not only to the sensing targets but also to many types of disturbances in the environment, such as temperature variation and mechanical instability of the system. The analysis of the signals is also affected by the positions of sensing targets on the resonator. Thus, it is difficult to distinguish signals coming from different sources, which introduces 'false positive' detection. We report a novel self-reference sensing mechanism based on mode splitting, a phenomenon in which a high-quality optical mode in a WGM resonator splits into two modes due to intra-cavity Rayleigh scattering. In particular, we demonstrated that the two split modes that can be induced by a single nanoparticle reside in the same resonator and serve as a reference to each other. As a result, a self-reference sensing scheme is formed. This allows us to develop a position-independent sensing scheme to accurately estimate the sizes of nanoparticles. So far we have achieved position-independent detecting and sizing of single nanoparticles down to 20 nm in radius with a single-shot measurement using an on-chip high-quality WGM microtoroid resonator.
Optimizing Hierarchical Classification with Adaptive Node Collapses (2018)

A mechanism is provided in a data processing system having a processor and a memory. The memory comprises instructions which are executed by the processor to cause the processor to implement a training system for finding an optimal surface for hierarchical classification task on an ontology. The training system receives a training data set and a hierarchical classification ontology data structure. The training system generates a neural network architecture based on the training data set and the hierarchical classification ontology data structure. The neural network architecture comprises an indicative layer, a parent tier (PT) output and a lower leaf tier (LLT) output. The training system trains the neural network architecture to classify the training data set to leaf nodes at the LLT output and parent nodes at the PT output. The indicative layer in the neural network architecture determines a surface that passes through each path from a root to a leaf node in the hierarchical ontology data structure. The training system trains a classifier model for a cognitive system using the surface and the training data set.
Applications of pumped-multiplexed Yb-doped fiber lasers (2003)

We report on applications of Yb<sup>3+</sup>-doped fiber-laser systems in the micro-processing and the markign of different materials. We have demonstrated the drilling of small holes in glass slides with a thickness of 1 mm using a fiber-laser system wtih an otuput-power of about 35 watts. Furthermore, we have used a narrowband fiber-laser system with an output-power of a few watts for the marking of thin plastic films and samples of anodized aluminum. These applications are based on the experience of more than 10 years in the design, development and preparation of rare-earth doped double-clad silica fibers at the IPHT e.V. Jena. We systematically have optimized the composition and the geometry of these specialty fibers. So we could manufacture very efficient samples which were tested in several fiber-laser setups with output-powers of up to almost 200 watts. Especialy, in the high-power region we could solve some thermal problems using new concepts for the double-clad fiber cross section. We successfully designed, prepared and tested so-called Large-Mode-Area fibers as well as fibers with two or mroe refractive indices in the pump-core. Additionally, we increased the available pump-power of the one-end-pumped fiber-laser systems using a wavelength-multiplexed diode-laser fiber-coupled system.
Moment switching in nanotube magnetic force probes (2007)

Magnetic images of high density vertically recorded media using metal-coated carbon nanotube tips exhibit a doubling of the spatial frequency under some conditions (Deng et al 2004 Appl. Phys. Lett. 85 6263). Here we demonstrate that this spatial frequency doubling is due to the switching of the moment direction of the nanotube tip. This results in a signal which is proportional to the absolute value of the signal normally observed in MFM. Our modeling indicates that a significant fraction of the tip volume is involved in the observed switching, and that it should be possible to image high bit densities with nanotube magnetic force sensors.
Active-Site Properties of Phrixotrix Railroad Worm Green and Red Bioluminescence-Eliciting Luciferases (2006)

The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green-(PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferinbinding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Mutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the redemitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.
<title>Ferroelectric and antiferroelectric liquid crystals for optical phase modulation</title> (2000)

A novel liquid crystalline material for optical phase modulation is proposed. The material consists of banana shaped dimer molecules, which form a lamellar phase, e.g. a smectic phase. A helical superstructure is induced by means of chiral fragments included in the molecular structure. Due to polyphilic segregation of hydrogenated and fluorinated molecule segments a cancellation of transversal dipole moments can be avoided and a net polarization of single layers will be obtained. The polarized layers may form ferroelectric or antiferroelectric structures. Application of an electric field in light propagation direction will deform the helix until total unwinding without reorienting the optical axes of the material, but changing the refractive index for one polarization direction. An estimation of the refractive indices of the material, its index modulation capability and the behavior under electric field is presented in this paper. The possible application of the material in phase modulators is discussed.
Electron Accelerators for Novel Cargo Inspection Methods (2017)

One of the main factors limiting the performance of conventional x-ray cargo inspection with material discrimination (MD) is the interlaced mode of system operation. Such systems use pulsed linac or betatron x-ray generators and produce alternate bremsstrahlung pulses with lower- and higher- end-point energies. Consequently, these systems provide about 50 mm lower penetration than a system operated in a non-interlaced mode, have a limited range of cargo areal densities with valid MD, and cannot perform MD of objects smaller than the pulse separation. Also, the limited pulse repetition rate of x-ray generators in interlaced mode limits the radiographic image quality at nominal commercial speeds of vehicles or trains. Several new methods of cargo inspection with MD were recently introduced to address the above-mentioned limitations: dual-energy methods based on Scintillation-Cherenkov detectors [1]; multi-energy method based on intrapulse time-varying of spectral content of x-ray [1], [2]; multi-energy method utilized ramping-up energy packet of short x-ray pulses [3], [4]; and methods based on multi-energy betatron [5], [6]. All of these methods have electron accelerators as a core element. However, the accelerator requirements and, thus, their designs, are different for each system. In this paper, we will discuss the requirements for the accelerators, provide some details about their designs, and present several novel solutions for current and future projects.
Template‐Free Pseudomorphic Synthesis of Tungsten Carbide Nanorods (2012)

A unique nanorod-structured tungsten carbide material with high specific surface area of 198 m(2) g(-1) is successfully synthesized for the first time by pseudomorphic transformation of chemically synthesized WO(3) nanorods through a high-temperature method. An electrocatalyst composed of Pt nanoparticles supported on WC nanorods demonstrates higher electrocatalytic activity for methanol electro-oxidation, better tolerance to CO poisoning, and superior performance for cathodic electrocatalytic hydrogen evolution than a Pt/C catalyst. This work provides a novel method to synthesize high-surface-area nanorod-structured WC materials by preparing oxide precursors with the desired external morphology, thus offering great potential for a broad range of applications of these materials in related reaction systems.
Medium chain triglycerides and structured lipids as unique nonglucose energy sources in hyperalimentation (1987)

This brief review will discuss recent work concerning new intravenous lipid emulsions for future use in clinical patients. Intravenous lipid emulsions currently available in the United States are derived from soybean or safflower oils and serve as sources of nonglucose, nitrogen-sparing calories and the essential fatty acid linoleic acid. Because of concerns that much of the infused long chain triglyceride is not oxidized readily and that there may be some immune system impairment, newer emulsions utilizing medium chain triglycerides have been developed.
Flux-Weakening Regime Operation of an Interior Permanent-Magnet Synchronous Motor Drive (1987)

The interior permanent magnet (IPM) synchronous motor is compatible with extended-speed-range constant-power operation by means of flux-weakening control. Flux weakening uses stator current components to counter the fixed-amplitude magnetic airgap flux generated by the rotor magnets, performing a role similar to field weakening in a separately excited dc motor. The nature of current regulator saturation caused by the finite inverter dc source voltage is described, marked by premature torque and power degradation at high speeds in the absence of flux-weakening control. This is followed by presentation of a new flux-weakening control algorithm developed as a modification of an established feedforward IPM torque control algorithm described previously in the literature. Attractive features of this new algorithm include smooth drive transitions into and out of the flux-weakening mode, fast response, as well as automatic adjustment to changes in the dc source voltage. Simulation and empirical test results from a 3-hp laboratory IPM motor drive are used to confirm the constant-power operating envelope achieved using the new flux-weakening control algorithm.
The potential use of saliva to detect recurrence of disease in women with breast carcinoma (2002)

This preliminary study appears to indicate that c-erbB-2 protein expression in saliva may be a very useful diagnostic tool for measuring patient response to chemotherapy and/or surgical treatment of their disease.
Cache refreshing for online social news feeds (2013)

Several social networking applications enable users to view the events generated by other users, typically friends in the social network, in the form of ``news feeds''. Friends and events are typically maintained per user and cached in memory to enable efficient generation of news feeds. Caching user friends and events, however, raises concerns about the freshness of news feeds as users may not observe the most recent events when cache content becomes stale. Mechanisms to keep cache content fresh are thus critical for user satisfaction while computing news feeds efficiently through caching.
A Low-Temperature Energy-Efficient Acid Gas Removal Process (1983)

The CNG process removes sulfurous compounds, trace contaminants, and carbon dioxide from medium to high pressure gas streams containing substantial amounts of carbon dioxide. Process features include 1) absorption of sulfurous compounds and trace contaminants with pure liquid carbon dioxide, 2) regeneration of pure carbon dioxide with simultaneous concentration of hydrogen sulfide and trace contaminants by triple-point crystallization, and 3) absorption of carbon dioxide with a slurry of organic liquid containing solid carbon dioxide. These process features utilize unique properties of carbon dioxide, and enable small driving forces for heat and mass transfer, small absorbent flows, and relatively small process equipment.