gebhart/patrepeval huggingface dataset:
Generation and Comparative Kinetic Analysis of New Glycosynthase Mutants from <i>Streptococcus pyogenes</i> Endoglycosidases for Antibody Glycoengineering (2018)

Chemoenzymatic glycan remodeling by endoglycosidase-catalyzed deglycosylation and reglycosylation is emerging as an attractive approach for producing homogeneous glycoforms of antibodies, and the success of this approach depends on the discovery of efficient endoglycosidases and their glycosynthase mutants. We report in this paper a systematic site-directed mutagenesis of an endoglycosidase from Streptococcus pyogenes (Endo-S) at the critical Asp-233 (D233) site and evaluation of the hydrolysis and transglycosylation activities of the resulting mutants. We found that in addition to the previously identified D233A and D233Q mutants of Endo-S, most of the Asp-233 mutants discovered here were also glycosynthases that demonstrated glycosylation activity using glycan oxazoline as the donor substrate with diminished hydrolytic activity. The glycosynthase activity of the resultant mutants varied significantly depending on the nature of the amino acid substituents. Among them, the D233M mutant was identified as the most efficient glycosynthase variant with the highest transglycosylation/hydrolysis ratio, which is similar to the recently reported D184M mutant of Endo-S2, another S. pyogenes endoglycosidase. Kinetic studies of the D233M and D233A mutants of Endo-S, as well as glycosynthase mutants D184M and D184A of Endo-S2, indicated that the enhanced catalytic efficacy of the Asp-to-Met mutants of both enzymes was mainly due to an increased turnover number (increased k<sub>cat</sub>) for the glycan oxazoline substrate and the significantly enhanced substrate affinity (as judged by the reduced K<sub>M</sub> value) for the antibody acceptor.
Event-Driven Low-Power Gesture Recognition Using Differential Capacitance (2016)

Individuals with mobility impairments represent a large portion of the population. These impairments are often the sequels of strokes, spinal cord injury, or diseases, such as amyotrophic lateral sclerosis and Guillain-Barré syndrome. Many of these diagnoses manifest in upper-extremity mobility impairment, which may prohibit or make difficult actuating devices within the home. While solutions exist for smart-home automation and control, a few are approachable by those with mobility impairments. To address this issue, we designed Inviz, a touchless low-power assistive gesture recognition system that utilizes an array of textile capacitive sensors to control a smart-home automation system. We present two novel research contributions; the use of flexible textile-based capacitive arrays as differential proximity sensors, and a low-power event-driven hierarchical signal processing algorithm for capacitor sensor arrays. A fully functional prototype system is implemented and evaluated in the context of an end-to-end home automation system using intuitive swipe and hover gestures that are comfortable and approachable for users with mobility impairments. The evaluation demonstrates that the system achieves high accuracy (>90%) while maintaining low latency (<;1 s) and low energy consumption (2475 μW). In addition, we evaluate the system on a subject with upper extremity mobility impairment to verify its usage as an accessibility device.
Robust scareware image detection (2013)

In this paper, we propose an image-based detection method to identify web-based scareware attacks that is robust to evasion techniques. We evaluate the method on a large-scale data set that resulted in an equal error rate of 0.018%. Conceptually, false positives may occur when a visual element, such as a red shield, is embedded in a benign page. We suggest including additional orthogonal features or employing graders to mitigate this risk. A novel visualization technique is presented demonstrating the acquired classifier knowledge on a classified screenshot.
Detection of methylcytosine by DNA photoligation via hydrophobic interaction of the alkyl group (2009)

We report the nonenzymatic detection of 5-methylcytosine by using template-directed photoligation through 5-vinyl-2′-deoxyuridine derivatives with high selectivity. In this paper, we propose a new detection method by using hydrophobic interaction. The photoligation yield of the 5-methylcytosine case was approximately 5.6-fold higher than that in the case of cytosine.
The Application of a Behavioral Categorization Technique in the Development of User Models (1998)

This paper examines a method for the development of new user interfaces for computer systems. The CDM method (Categorizing, Describing, and Modeling method) enhances the requirements gathering phase of user interface design by capitalizing on the concept that the user population has a variety of distinguishable strategies that affect performance. In the CDM method, the user population is first categorized into a reasonable number of groups. The behaviors for each group are described and then this described behavior is qualitatively and quantitatively modeled. These models are used during the system design and operational process to optimize performance for all users. This paper focuses on the first part of the CDM method, namely categorizing users into behaviorally similar groups. Users are categorized based on cognitive measures and sales performance measures. The grouping methodology is then validated based on behavioral data. The CDM method was developed to more accurately determine system requirements for the development of a telecommunications system.
IR Focal plane array imaging devices (1975)

Use of CCD and CID technology at or near the focal plane for multiplexing and signal processing will make practical IR focal planes with thousands of detectors. Two approaches to series-parallel scan appear interesting: a sandwich like structure which uses direct injection from the IR detectors into a CCD TDI register and the use of an IR CID for premultiplexing in a series-parallel scan mode.
Bootstrapping Conversational Agents with Weak Supervision (2019)

Many conversational agents in the market today follow a standard bot development framework which requires training intent classifiers to recognize user input. The need to create a proper set of training examples is often the bottleneck in the development process. In many occasions agent developers have access to historical chat logs that can provide a good quantity as well as coverage of training examples. However, the cost of labeling them with tens to hundreds of intents often prohibits taking full advantage of these chat logs. In this paper, we present a framework called search, label, and propagate (SLP) for bootstrapping intents from existing chat logs using weak supervision. The framework reduces hours to days of labeling effort down to minutes of work by using a search engine to find examples, then relies on a data programming approach to automatically expand the labels. We report on a user study that shows positive user feedback for this new approach to build conversational agents, and demonstrates the effectiveness of using data programming for autolabeling. While the system is developed for training conversational agents, the framework has broader application in significantly reducing labeling effort for training text classifiers.
Just Add Water:  A New Fluorous Capping Reagent for Facile Purification of Peptides Synthesized on the Solid Phase (2004)

A novel fluorous capping reagent is introduced to facilitate purification during solid-phase peptide synthesis (SPPS). Reagent 1 is a trivalent iodonium salt that reacts vigorously with free amines to deliver a long-chain fluoroalkyl group. It has been used to tag all unreacted amines following the peptide coupling step in SPPS. The resulting fluoroalkylated amine is no longer able to couple in further peptide coupling steps and is also stable to standard peptide synthesis conditions. Deletion products are removed using flash fluorous chromatography to yield the pure, full-length peptide.
Optimum Thickness of Magnetic Layer for Short-Wavelength Magnetic Recording (1997)

Metal-evaporated (ME) tape contains no resin therefore, it has a high magnetic flux density that is superior to that of a conventional metal-powder (MP) tape. Thus, the ME tape has potential for use in high-density magnetic recording and in other new types of media. We prepared tapes whose magnetic layer thickness varied between 540 Å and 3190 Å. The tapes were produced continuously using Co oblique evaporation onto a base film. The fixed coercive force was maintained at about 1400 Oe. Using these tapes, we determined the optimum magnetic layer thickness needed to obtain a high video performance at short recording wavelengths. We also determined that the magnetic tape must have a certain minimum thickness for recording within a given system, and that the optimum thickness increases at a rate of 6% compared to the increase in the recording wavelengths. The difference from the theoretical ratio of 25% is thought to be due to the actual head gap length (0.22 µ m).
Static test sequence compaction based on segment reordering and accelerated vector restoration (2002)

Vector restoration based static compaction techniques report significant compaction. In this paper we propose a new technique for static compaction which gives comparable or better compaction and runs 10 to 50 times faster than the fastest method. The new technique solves the problem of compaction by dividing it into small subproblems (referred to as segments). The solutions to these segments (or subproblems) are then dynamically merged providing excellent speed up without compromising on compaction efficiency. Further speed up is achieved by compacting the individual segments using an accelerated vector-restoration based compaction technique. If a fault requires a sequence of length n to be detected, in our approach the number of vectors that need to be simulated for restoring the sequence is O(n logan), while the prevailing approaches require simulation on O(n/sup 2/) vectors. Experimental results demonstrate substantial speedups compared to the prevailing vector restoration based techniques, while giving comparable or better compaction. When compared to the fastest method, our method was 5 to 30 times faster on ISCAS circuits and 10 to 50 times faster on real-life production circuits. For example, on one of the production circuits, our method gave 27 percent compaction in 188 seconds, while an improved version of the fastest method gave 25 percent compaction in 10200 seconds. In addition, our method could successfully process large industrial designs which could not be completed by earlier techniques in 2 CPU days.
Multiple Instance Learning for Computer Aided Diagnosis (2007)

Many computer aided diagnosis (CAD) problems can be best modelled as a multiple-instance learning (MIL) problem with unbalanced data: i.e., the training data typically consists of a few positive bags, and a very large number of negative instances. Existing MIL algorithms are much too computationally expensive for these datasets. We describe CH, a framework for learning a Convex Hull representation of multiple instances that is significantly faster than existing MIL algorithms. Our CH framework applies to any standard hyperplane-based learning algorithm, and for some algorithms, is guaranteed to find the global optimal solution. Experimental studies on two different CAD applications further demonstrate that the proposed algorithm significantly improves diagnostic accuracy when compared to both MIL and traditional classifiers. Although not designed for standard MIL problems (which have both positive and negative bags and relatively balanced datasets), comparisons against other MIL methods on benchmark problems also indicate that the proposed method is competitive with the state-of-the-art.
<i>O</i>‐space imaging: Highly efficient parallel imaging using second‐order nonlinear fields as encoding gradients with no phase encoding (2010)

Recent improvements in parallel imaging have been driven by the use of greater numbers of independent surface coils placed so as to minimize aliasing along the phase-encode direction(s). However, gains from increasing the number of coils diminish as coil coupling problems begin to dominate and the ratio of acceleration gain to expense for multiple receiver chains becomes prohibitive. In this work, we redesign the spatial-encoding strategy in order to gain efficiency, achieving a gradient encoding scheme that is complementary to the spatial encoding provided by the receiver coils. This approach leads to "O-space" imaging, wherein the gradient shapes are tailored to an existing surface coil array, making more efficient use of the spatial information contained in the coil profiles. In its simplest form, for each acquired echo the Z2 spherical harmonic is used to project the object onto sets of concentric rings, while the X and Y gradients are used to offset this projection within the imaging plane. The theory is presented, an algorithm is introduced for image reconstruction, and simulations reveal that O-space encoding achieves high encoding efficiency compared to sensitivity encoding (SENSE) radial k-space trajectories, and parallel imaging technique with localized gradients (PatLoc), suggesting that O-space imaging holds great potential for accelerated scanning.
Identification of the First Human Gyrovirus, a Virus Related to Chicken Anemia Virus (2011)

We have identified in a skin swab sample from a healthy donor a new virus that we have named human gyrovirus (HGyV) because of its similarity to the chicken anemia virus (CAV), the only previously known member of the Gyrovirus genus. In particular, this virus encodes a homolog of the CAV apoptin, a protein that selectively induces apoptosis in cancer cells. By PCR screening, HGyV was found in 5 of 115 other nonlesional skin specimens but in 0 of 92 bronchoalveolar lavages or nasopharyngeal aspirates and in 0 of 92 fecal samples.
Anwendung von modellbasierter prädiktiver Regelung und Methoden der hybriden Systeme zur optimalen Produktionsplanung (Using Model Predictive Control and Hybrid Systems for Optimal Scheduling of Industrial Processes) (2003)

Abstract Optimal (re)scheduling of production in industrial processes increases economic efficiency through timely and optimal use of limited resources. In this article an approach to scheduling based on the use of hybrid systems and model predictive control is presented. Modelling flexibility, acceptable computational times, and optimal disturbance rejection are the key advantages of the approach. The main ideas are illustrated with two industrial applications.
Biochemical and Molecular Genetic Aspects of Floral Scents (2000)

The chemical composition of floral scents has been extensively investigated for hundreds of years because of the commercial value of floral volatiles in perfumery. More recently, several ecological studies have examined the roles of floral scent in the biology of the plant. However, in contrast to
Jet Noise Reduction via Fluidic Injection (2013)

In this study, a method for reducing the jet noise of a high-speed jet is presented. An array of microjets was immersed within the centerline of an underexpanded Mach 1.6 jet in an effort to reduce the overall sound pressure level and alter its spectral composition. Based on the mass flux through the microjets and the location of the microjets along the centerline of the jet, reductions of up to 5.81 dB with respect to the downstream direction and 7.99 dB with respect to the perpendicular direction can be achieved. An interesting phenomenon is discovered whereby the maximum noise reduction in the downstream direction is found with injection activated, whereas the maximum noise reduction in the perpendicular direction is found with injection deactivated. Placement of the injection tube within the flow is shown to eradicate distinct tones while flow visualizations depicted a strong augmentation in the jet plume via a modification of the shear layer and the internal shock cell structure.
Characteristics of an Arc-Seeded Microwave Plasma Torch (2004)

The design and operation of a portable microwave plasma torch is presented. An arc plasma torch running at 60 Hz and generated by a torch module is installed on the bottom wall in the narrow section of a tapered S-band rectangular cavity, and is used to seed the microwave discharge at the location where the microwave electric field is at a maximum. This tapered cavity is designed to support the TE/sub 103/ mode. With seeding, only low Q cavity and moderate microwave power (time average power of 700 W) are needed. The microwave-enhanced discharge increases the size, cycle energy, and duty cycle of the torch plasma considerably. This torch can be run without introducing gas flow to stabilize the arc and microwave discharges. Adding gas flow can increase not only the size of the torch plasma, but also its cycle energy which reaches a plateau of about 12 J/per cycle for a gas flow rate exceeding 0.393 l/s. The electron density and excitation temperature, and the composition of torch species are determined by emission spectroscopy. It is shown that, at the bottom of the torch close to the cavity wall, electrons distribute quite uniformly across the core of the torch with density and excitation temperature determined to be about 7/spl times/10/sup 13/ cm/sup -3/ and 8000 K, respectively. It is also found that this torch produces an abundance of reactive atomic oxygen.
Corneal refractive correction by laser thermal keratoplasty (1990)

We report corneal curvature modifications for rabbit corneas which we achieved by controlled heating of the cornea with a continuous Co:MgF2 laser in the 2 micron region. Our experiments were designed to flatten the cornea, which is required for myopic correction. Large changes of 6-8 diopters in corneal curvature have been stable for the one year duration of the experiments. This is a new method for correcting corneal curvature which retains normal corneal function while not requiring invasive techniques such as cutting or ablation.
Preparation and Formation Mechanism of Silver Particles with Spherical Open Structures (2011)

A new type of highly dispersible silver particles has been developed consisting of two- and three-dimensional building blocks that form spherical shapes with open structures. The first morphology consists of uniform particles that are composed of anisotropic building blocks mainly in the form of a network of platelets forming a spherical, open-structured particle. These platelets are 100–2000 nm in length, with a crystallite size in the range 20–100 nm. The second morphology consists of isotropic components that are 100–500 nm in length, with a crystallite size in the range of 20–100 nm. In both cases, the silver powder was comprised of well-defined monosized particles and was highly dispersible. These powders were prepared by rapidly mixing a silver solution with an ascorbic acid/sodium citrate solution at low pH. A mechanism is proposed for the formation of these novel structures.
Formaldehyde Gas Sensor Based on Hybrid Film: Graphene/Enzyme (2019)

Through a simple fabrication process, we fabricate tiny and cheap formaldehyde gas sensor. To do that, we used the hybrid film that consists of Chemical Vapor Deposition (CVD) graphene and formaldehyde dehydrogenase (FALDH). Since graphene sensitively shows an electrical response with the concentration of hydrogen cation in the solution, the novel graphene-based gas sensors can quickly respond with formaldehyde gas. The sensor shows the response with a low concentration of formaldehyde gas up to ppb level. It also has a great selectivity for the formaldehyde gas because it is based on the enzyme reaction. The mechanism of the reaction can be clearly explained by chemical equations.
Sensing with hollow-core photonic bandgap fibers (2010)

This paper examines the unique properties of hollow-core photonic bandgap fibers and discusses potential sensing applications of such fibers. Guidance of light in air instead of silica reduces the effect of material on light propagation and is advantageous to applications such as fiber gyroscopes. An air-silica microstructure has novel mechanical and thermal properties and can be beneficial to applications such as acoustic pressure sensors. Holey cladding provides extra flexibility for geometry modification through post thermal treatment or selective filling of the air holes and can be exploited for developing novel devices such as in-line polarizers/polarimeters, modal interferometer, wavelength filters and sensors. The confinement of gas and liquid phase materials and optical guided modes simultaneously within the hollow core allows strong light/sample interaction over an extended length and may be useful for the development of highly sensitive gas and liquid sensors.
Light scattering and optical aberrations as objective parameters to predict visual deterioration in eyes with cataracts (2004)

Loss of contrast sensitivity was predominantly due to BLS and HOA in eyes with NC and FLS and HOA in eyes with CC. Higher-order aberrations, FLS, and BLS, variables that are obtained objectively, can be used to predict quantitatively the visual deterioration in cataractous eyes.
<title>Retrieval of color patterns based on perceptual dimensions of texture and human similiarity rules</title> (1999)

While it is recognized that images are described through color, texture and shapes of objects in the scene, the general image understanding is still very difficult. Thus, to perform an image retrieval in a human-like manner one has to choose a specific domain, understand how users achieve similarity within that domain and then build a system that duplicates human performance. Since color and texture are fundamental aspects of human perception we propose a set of techniques for retrieval of color patterns. To determine how humans judge similarity of color patterns we performed a subjective study. Based on the result of the study five most relevant visual categories for the perception of pattern similarity were identified. We also determined the hierarchy of rules governing the use of these categories. Based on these results we designed a system which accepts one or more texture images as input, and depending on the query, produces a set of choices that follow human behavior in pattern matching. Processing steps in our model follow those of the human visual system, resulting in perceptually based features and distance measures. As expected, search results closely correlate wit human choices.