gebhart/patrepeval huggingface dataset:
Engineering human interleukin-6 to obtain variants with strongly enhanced bioactivity. (1996)

Interleukin-6 (IL-6) triggers the formation of a high affinity receptor complex with the ligand binding subunit IL-6Ralpha and the signal transducing chain gp130. Since the intracytoplasmic region of the IL-6Ralpha does not contribute to signaling, soluble forms of the extracytoplasmic domain (sIL-6Ralpha), potentiate IL-6 bioactivity and induce a cytokine-responsive status in cells expressing gp130 only. This observation, together with the detection of high levels of circulating soluble human IL-6Ralpha (shIL-6Ralpha) in sera, suggests that the hIL-6-shIL-6Ralpha complex is an alternative form of the cytokine. Here we describe the generation of human IL-6 (hIL-6) variants with strongly enhanced shIL-6Ralpha binding activity and bioactivity. Homology modeling and site-directed mutagenesis of hIL-6 suggested that the binding interface for hIL-6Ralpha is constituted by the C-terminal portion of the D-helix and residues contained in the AB loop. Four libraries of hIL-6 mutants were generated by each time fully randomizing four different amino acids in the predicted AB loop. These libraries were displayed monovalently on filamentous phage surface and sorted separately for binding to immobilized shIL-6Ralpha. Mutants were selected which, when expressed as soluble proteins, showed a 10- to 40-fold improvement in shIL-6Ralpha binding; a further increase (up to 70-fold) was achieved by combining variants isolated from different libraries. Interestingly, high affinity hIL-6 variants show strongly enhanced bioactivity on cells expressing gp13O in the presence of shIL-6Ralpha at concentrations similar to those normally found in human sera.
Supporting time-constrained SQL queries in oracle (2007)

The growing nature of databases, and the flexibility inherent in the SQL query language that allows arbitrarily complex formulations, can result in queries that take inordinate amount of time to complete. To mitigate this problem, strategies that are optimized to return the ‘first-few rows ’ or ‘top-k rows ’ (in case of sorted results) are usually employed. However, both these strategies can lead to unpredictable query processing times. Thus, in this paper we propose supporting time-constrained SQL queries. Specifically, a user issues a SQL query as before but additionally provides nature of constraint (soft or hard), an upper bound for query processing time, and acceptable nature of results (partial or approximate). The DBMS takes the criteria (constraint type, time limit, quality of result) into account in generating the query execution plan, which is expected (guaranteed) to complete in the allocated time for soft (hard) time constraint. If partial results are acceptable then the technique of reducing result set cardinality (i.e. returning first few or top-k rows) is used, whereas if approximate results are acceptable then sampling is used, to compute query results within the specified time limit. For the latter case, we argue that trading off quality of results for predictable response time is quite useful. However, for this case, we provide additional aggregate functions to estimate the aggregate values and to compute the associated confidence interval. This paper presents the notion of time-constrained SQL queries, discusses the challenges in supporting such a construct, describes a framework for supporting such queries, and outlines its implementation in Oracle Database by exploiting Oracle’s cost-based optimizer and extensibility capabilities. 1.
Filtering Out Deep Brain Stimulation Artifacts Using a Nonlinear Oscillatory Model (2009)

This letter is devoted to the suppression of spurious signals (artifacts) in records of neural activity during deep brain stimulation. An approach based on nonlinear adaptive model with self-oscillations is proposed. We developed an algorithm of adaptive filtering based on this approach. The proposed algorithm was tested using recordings collected from patients during the stimulation. This was then compared to existing methods and showed the best performance.
Vesicular Stomatitis Virus as a Vector To Deliver Virus-Like Particles of Human Norovirus: a New Vaccine Candidate against an Important Noncultivable Virus (2011)

Human norovirus (HuNoV) is a major causative agent of food-borne gastroenteritis worldwide. Currently, there are no vaccines or effective therapeutic interventions for this virus. Development of an attenuated vaccine for HuNoV has been hampered by the inability to grow the virus in cell culture. Thus, a vector-based vaccine may be ideal. In this study, we constructed a recombinant vesicular stomatitis virus (rVSV-VP1) expressing VP1, the major capsid protein of HuNoV. Expression of the capsid protein by VSV resulted in the formation of HuNoV virus-like particles (VLPs) that are morphologically and antigenically similar to native virions. Recombinant rVSV-VP1 was attenuated in cultured mammalian cells as well as in mice. Mice inoculated with a single dose of rVSV-VP1 through intranasal and oral routes stimulated a significantly stronger humoral and cellular immune response than baculovirus-expressed VLP vaccination. Moreover, we demonstrated that mice inoculated with rVSV-VP1 triggered a comparable level of fecal and vaginal IgA antibody. Taken together, the VSV recombinant system not only provides a new approach to generate HuNoV VLPs in vitro but also a new avenue for the development of vectored vaccines against norovirus and other noncultivable viruses.
Small Molecule Isotope Resolved Formula Enumerator: a Tool for Assigning Isotopologues and Metabolites in Fourier Transform Mass Spectra (2019)

Improvements in Fourier Transform Mass Spectrometry (FT-MS) enable increasingly more complex experiments in the field of metabolomics. What is directly detected in FT-MS spectra are spectral features (peaks) that correspond to sets of adducted and charged forms of specific molecules in the sample. The robust assignment of these features is an essential step for MS-based metabolomics experiments, but the sheer complexity of what is detected and a variety of analytically-introduced variance, errors, and artifacts has hindered the systematic analysis of complex patterns of observed peaks with respect to isotope content. We have devel-oped a method called SMIRFE that detect small biomolecules and determines their elemental molecular formula (EMF) using de-tected sets of isotopologue peaks sharing the same EMF. SMIRFE does not use a database of known metabolite formulas, instead a nearly comprehensive search space of all isotopologues within a mass range is constructed and used for assignment. This search space can be tailored for different isotope labeling patterns expected in different stable isotope tracing experiments. Using consumer-level computing equipment, a large search space of 2000 daltons was constructed and assignment performance was evaluated and validated using verified assignments on a pair of peak lists derived from spectra containing unlabeled and 15N-labeled versions of amino acids derivatized using ethylchloroformate. SMIRFE identified 18 of 18 predicted derivatized EMFs and each assignment was evaluated statistically and assigned an e-value representing the probability to occur by chance.
Approximated sum-product decoding for LDPC codes (2012)

This paper proposes an approximated sum-product decoding algorithm for LDPC codes. The proposed decoding algorithm may be efficiently implemented through integer additions, comparisons, and bit-shift operations without multiplications and memories. Moreover, it doesn't require any channel information such as signal to noise ratio and operate with just the received values from channel.
Stirling-Cycle Refrigerator Containing Piezoelectric Pumps (1995)

Advanced Stirling-cycle cryogenic apparatus suitable for cooling sensitive infrared detectors to very low temperatures. Working fluid in refrigerator helium. Working fluid compressed and circulated by three piezoelectrically actuated diaphragm pumps offering advantages of greater reliability, relative simplicity, and lower cost.
Force Adaptation in Human Walking With Symmetrically Applied Downward Forces on the Pelvis (2013)

The application of external constraints and/or applied forces during movement can lead to reactive as well as adaptive changes in human motion. Previous research has shown adaptation in walking kinematics when external forces were applied to a leg. This work aims to study adaptation in human walking when externally applied forces were present on the pelvis during the swing and stance phases of both legs. A novel tethered pelvic assist device (TPAD) was used to passively apply symmetric downward forces on the human pelvis while walking. During the experiment, eight healthy subjects walked on a treadmill at a constant speed while their kinematics and foot pressure data were recorded.
Duo-mold imprinting of three-dimensional polymeric structures (2004)

We present a new method of imprinting three dimensional (3D) polymeric micro- and nanostructures using a duo-mold process. In this method, two patterned Si molds are surface treated to have different surface energies. A polymer solution is spin-coated onto one of the molds, forming a planarized thin film on the mold. The two molds are pressed together at an appropriate temperature and pressure and then released. The patterned thin film adhering to one of the molds is then pressed onto a substrate at an appropriate temperature and pressure to form supported 3D structures. Alternatively, the patterned thin film on the mold may be released to form freestanding 3D structures. A key success factor in this process is the silane-based surface treatments to enable the patterning of the thin polymer film and final release from the mold to form 3D structures. We demonstrate various polymethyl methacrylate 3D structures with combinations of grating, circular-, and square-patterned molds. The duo-mold process is a potentially low-cost and high-throughput method to fabricate 3D polymeric micro- and nanostructures.
Assembly comprising a Water Turbine and a Generator, the Rotor of which is Direct-Connected to each one of the Blades the Turbine : PCT-application for Swedish patent SE 0400667-2 (2005)

In this thesis permanent magnet direct drive generator for power conversion from water currents is studied. Water currents as a power source involves a number of constrains as well as possibilities, especially when direct drive and permanent magnets are considered. The high power fluxes and low current velocities of a water current, in combination with its natural variations, will affect the way the generator is operated and, flowingly, the appearance of the generator. The work in this thesis can, thus, be categorized into two general topics, generator technology and optimization. Under the first topic, fundamental generator technology is used to increase the efficiency of a water current generator. Under the latter topic, water current generators are optimized to a specific environment. The conclusion drawn from this work is that it is possible to design very low speed direct drive generators with good electromagnetic properties and wide efficiency peak.
Segmentation of lung region based on using parallel implementation of joint MGRF: Validation on 3D realistic lung phantoms (2013)

The segmentation of the lung tissues in chest Computed Tomography (CT) images is an important step for developing any Computer-Aided Diagnostic (CAD) system for lung cancer and other pulmonary diseases. In this paper, we introduce a new framework to generate 3D realistic synthetic phantoms to validate our developed Joint Markov-Gibbs based lung segmentation approach from CT data. Our framework is based on using a 3D generalized Gauss-Markov Random Field (GGMRF) model of voxel intensities with pairwise interaction to model the 3D appearance of the lung tissues. Then, the appearance of the generated 3D phantoms is simulated based on iterative minimization of an energy function that is based on using the learned 3D-GGMRF image model. These 3D realistic phantoms can be used to evaluate the performance of any lung segmentation approach. In this paper, we used the 3D realistic phantoms to evaluate the performance of our developed lung segmentation approach based on using the Dice Similarity Coefficient (DSC) metric and the Receiver Operating Characteristics (ROC). The DSC demonstrated that our approach achieves a mean DSC value of 0.994 ± 0.0034. Moreover, the ROC analysis for our method showed the best performance (area 0.99), while intensity showed the worst performance (area 0.92).
Sampled fiber grating based-dispersion slope compensator (1999)

We propose a novel design for a compact dispersion slope compensator based on sampled fiber Bragg gratings. By chirping the sample function in a sampled grating, we show that the dispersion slope can be controlled to match that of current transmission fibers. Interleaving several sampled gratings provides an effective technique to reduce UV-induced refractive index requirements to readily achievable levels.
Multi-Criterion Partial Clustering Algorithm for Wireless Sensor Networks (2022)

Cluster architectures are an effective approach for organizing sensor networks to balance the load and prolong network life. To cluster wireless sensor networks, this paper proposes an energy-efficient distributed algorithm. This algorithm uses two techniques (partial clustering and multi-criterion cluster formation) for efficient use of the sensor nodes’ energy. When a header expends a certain amount of power, it only notifies the nodes in its cluster that new clustering is required in the next round. Therefore, in contrast to previous studies that performed complete clustering, clustering in the present work is performed partially, which considerably reduces the clustering overhead. In addition, a multi-criterion score is calculated for each node. In this algorithm, a node with the highest remaining energy and score is a more suitable candidate to be selected as the head of the cluster. In addition, a regular node becomes the member of the cluster with the highest score in its vicinity. The experiments reveal the superiority of the proposed algorithm over other simulated algorithms in terms of energy savings and network lifetime.
Holey MoS<sub>2</sub> Nanosheets with Photocatalytic Metal Rich Edges by Ambient Electrospray Deposition for Solar Water Disinfection (2018)

A new method for creating nanopores in single-layer molybdenum disulfide (MoS<sub>2</sub>) nanosheets (NSs) by the electrospray deposition of silver ions on a water suspension of the former is introduced. Electrospray-deposited silver ions react with the MoS<sub>2</sub> NSs at the liquid-air interface, resulting in Ag<sub>2</sub>S nanoparticles which enter the solution, leaving the NSs with holes of 3-5 nm diameter. Specific reaction with the S of MoS<sub>2</sub> NSs leads to Mo-rich edges. Such Mo-rich defects are highly efficient for the generation of active oxygen species such as H<sub>2</sub>O<sub>2</sub> under visible light which causes efficient disinfection of water. 10<sup>5</sup> times higher efficiency in disinfection for the holey MoS<sub>2</sub> NSs in comparison to normal MoS<sub>2</sub> NSs is shown. Experiments are performed with multiple bacterial strains and a virus strain, demonstrating the utility of the method for practical applications. A conceptual prototype is also presented.
Succinate production from sucrose by metabolic engineered <i>escherichia coli</i> strains under aerobic conditions (2011)

Two metabolically engineered E. coli strains HL2765k and HL27659k, while capable of producing succinate from glucose with high yields, are not able to grow and produce succinate on sucrose. Consequently, the pUR400 plasmid containing scrK, Y, A, B, and R genes was introduced into HL2765k and HL27659k, respectively. Shake flask culture studies showed that the resulting strains can utilize sucrose; the strain HL2765k pUR400 and HL27659k pUR400 can produce succinate aerobically with a molar yield of 0.78 ± 0.02 mol/mol and 1.35 ± 0.13 mol/mol, respectively. On introduction of the plasmid pHL413, which encodes the heterologous pyruvate carboxylase (PYC) from Lactococcus lactis, the molar succinate yield increased to 1.60 ± 0.01 mol of succinate per mole of sucrose by the HL2765k pUR400 pHL413 strain and to 1.84 ± 0.10 by the HL27659k pUR400 pHL413 strain. In aerobic batch bioreactor studies, the succinate production rate was faster, and succinate production reached 101.83 mM with a yield of 1.90 when dissolved oxygen (DO) was controlled at 40 ± 7%. In addition, the results showed that DO had an important effect on succinate production by influencing PYC activity. This work demonstrates the possibility of producing succinate aerobically using sucrose as the carbon source.
Skippy (2008)

The storage manager of a general-purpose database system can retain consistent disk page level snapshots and run application programs "back-in-time" against long-lived past states, virtualized to look like the current state. This opens the possibility that functions, such as on-line trend analysis and audit, formerly available in specialized temporal databases, can become available to general applications in general-purpose databases.
A Highly Sensitive Displacing Device Using Piezoelectric Bimorph with Double-Support Structure (1983)

In order to improve displacing devices, new methods for supporting a bimorph element with a double-support structure were investigated. Consideration of bending properties revealed that, when the bimorph element was bent, the cross-sections at both of the bimorph element's ends rotated. A double-support bimorph element with U-shaped metal plates at each end was designed, the result being used. It was found that the displacement for the double-support bimorph with U-shaped metal plates was approximately 4 times larger than the displacement for a conventional double-support bimorph.
Tunable Chirp Managed Laser (2008)

We demonstrate a compact tunable chirp managed laser (CML) comprising a radio-frequency switch, a directly modulated distributed feedback laser array, a microelectromechanical systems mirror, and an optical filter and obtain error-free transmission performance over 30 nm at 10.7 Gb/s up to 200 km without electrical dispersion compensation (EDC) or optical dispersion compensation. Transmission distance is stretched to 300 km over the same wavelength range by adding a standard EDC to the receiver.
Improved microgrid arrangement for integrated imaging polarimeters (2014)

For almost 20 years, microgrid polarimetric imaging systems have been built using a 2×2 repeating pattern of polarization analyzers. In this Letter, we show that superior spatial resolution is achieved over this 2×2 case when the analyzers are arranged in a 2×4 repeating pattern. This unconventional result, in which a more distributed sampling pattern results in finer spatial resolution, is also achieved without affecting the conditioning of the polarimetric data-reduction matrix. Proof is provided theoretically and through Stokes image reconstruction of synthesized data.
New Cobalt Catalysts for Hydroformylations in Two‐Phase Systems (1996)

Not water, but polyethyleneglycol serves as the solvent for the cobalt complex 1 (R  CH2CH2(OCH2CH2)nOH, n = 9), an efficient catalyst for the hydroformylation of 1-hexene. Because complex 1 is not soluble in unpolar solvents, this highly chemoselective reaction can be conducted in the two-phase system polyethyleneglycol/hexene.
A Novel Stopping Method for Induction Motors Operating From Variable Frequency Drives (2004)

Many applications involving induction motors that are controlled using variable frequency drives require the ability to stop quickly. These applications include emergency stops, quick stopping of fans, centrifuges, presses, etc. The technique that is widely accepted in the industry for achieving quick stopping makes use of brake resistors in series with a power semiconductor switch. The switch-resistor combination (brake-unit) is applied across the dc bus. The fastest decelerating time achievable depends on the size of the resistors and the switch employed. In this paper, the authors propose a novel method of achieving quick stopping times without the use of any brake-unit. The stopping times achievable depend on the inverter rating, motor parameters, and the inertia of the load. The proposed method uses the concept of achieving large slip condition between the rotating motor and the commanded drive output frequency. Control of current through the motor during the process of stopping is achieved by modifying the V/f pattern. Experimental test results with and without this method on a large inertia motor-load combination show that the proposed stopping method is able to reduce the stopping time significantly compared to normal decelerated stop without the need for a braking unit.
Synthesis of tetrahydro-2-furyl derivatives of 5-substituted uracils. (1979)

Addition of 5-fluorouracil (1) to the double bond of 2, 3-dihydrofuran (3) without using any catalyst progressed smoothly at an elevated temperature and afforded an equilibrium mixture of 1-(tetrahydro-2-furyl)-5-fluorouracil (5) and 1, 3-bis (tetrahydro-2-furyl)-5-fluorouracil (7). By choosing favourable reaction conditions, each of these compounds was obtained in high yield. Thermal decomposition of 7 gave an equimolar mixture of 3 and 5. At a higher temperature, 5 underwent thermal reaction to yield 1 and 3. Study of the present addition reaction was extended to other 5-substituted uracils (8, R=-H, -CH3, -Cl, -Br, -COOCH3, -CONH2, -CN) which furnished the corresponding 1-(tetrahydro-2-furyl)-and 1, 3-bis (tetrahydro-2-furyl)-derivatives (9-15, 18-23) with high yields. A very small amount of 3-(tetrahydro-2-furyl)-5-substituted uracils (6, 16, 17) by-produced in the reactions was isolated and the structures unequivocally identified.
Preprocessing of SAR interferometric data using anisotropic diffusion filter (2007)

The most commonly used smoothing algorithms for complex data processing are blurring functions (i.e., Hanning, Taylor weighting, Gaussian, etc.). Unfortunately, the filters so designed blur the edges in a Synthetic Aperture Radar (SAR) scene, reduce the accuracy of features, and blur the fringe lines in an interferogram. For the Digital Surface Map (DSM) extraction, the blurring of these fringe lines causes inaccuracies in the height of the unwrapped terrain surface. Our goal here is to perform spatially non-uniform smoothing to overcome the above mentioned disadvantages. This is achieved by using a Complex Anisotropic Non-Linear Diffuser (CANDI) filter that is a spatially varying. In particular, an appropriate choice of the convection function in the CANDI filter is able to accomplish the non-uniform smoothing. This boundary sharpening intra-region smoothing filter acts on interferometric SAR (IFSAR) data with noise to produce an interferogram with significantly reduced noise contents and desirable local smoothing. Results of CANDI filtering will be discussed and compared with those obtained by using the standard filters on simulated data.