gebhart/patrepeval huggingface dataset:
14-3-3 Proteins Interact with Specific MEK Kinases (1998)

MEK (mitogen-activated protein kinase/extracellular signal-regulated kinase kinase) kinases (MEKKs) regulate c-Jun N-terminal kinase and extracellular response kinase pathways. The 14-3-3zeta and 14-3-3epsilon isoforms were isolated in a two-hybrid screen for proteins interacting with the N-terminal regulatory domain of MEKK3. 14-3-3 proteins bound both the N-terminal regulatory and C-terminal kinase domains of MEKK3. The binding affinity of 14-3-3 for the MEKK3 N terminus was 90 nM, demonstrating a high affinity interaction. 14-3-3 proteins also interacted with MEKK1 and MEKK2, but not MEKK4. Endogenous 14-3-3 protein and MEKK1 and MEKK2 were similarly distributed in the cell, consistent with their in vitro interactions. MEKK1 and 14-3-3 proteins colocalized using two-color digital confocal immunofluorescence. Binding of 14-3-3 proteins mapped to the N-terminal 393 residues of 196-kDa MEKK1. Unlike MEKK2 and MEKK3, the C-terminal kinase domain of MEKK1 demonstrated little or no ability to interact with 14-3-3 proteins. MEKK1, but not MEKK2, -3 or -4, is a caspase-3 substrate that when cleaved releases the kinase domain from the N-terminal regulatory domain. Functionally, caspase-3 cleavage of MEKK1 releases the kinase domain from the N-terminal 14-3-3-binding region, demonstrating that caspases can selectively alter protein kinase interactions with regulatory proteins. With regard to MEKK1, -2 and -3, 14-3-3 proteins do not appear to directly influence activity, but rather function as "scaffolds" for protein-protein interactions.
Synthesis of sugar alcohols by hydrolytic hydrogenation of cellulose over supported metal catalysts (2010)

Cellulose is converted into sorbitol and related sugar compounds over water-tolerant and durable carbon-supported Pt catalysts under aqueous hydrogenation conditions. Pre-treatment of cellulose with ball-milling effectively reduces the crystallinity and particle size of cellulose, which results in high conversion of cellulose to sorbitol and mannitol. The selectivity of sorbitol increases by using Cl-free metal precursors in the catalyst preparation as residual Cl on the catalysts promotes the side-reactions. The transformation of cellulose to sorbitol consists of the hydrolysis of cellulose to glucoseviawater-soluble oligosaccharides and the successive hydrogenation of glucose to sorbitol. The hydrolysis of cellulose is the rate-determining step, and the Pt catalysts promote both the hydrolysis and the hydrogenation steps.
Towards a practical and effective method for Web services test case generation (2009)

This paper proposes a method for Web services test case generation, which is centered on a practical test data generation framework that has higher probability to penetrate the service implementation logic. This presented framework leverages both the information contained in the WSDL/XSD files and the information provided by testers as well as enables testers to customize the fields to be tested, field constraints and data generation rules. The proposed method can generate test cases that are effective in detecting defects and efficient in reducing test time. This paper also presents preliminary empirical evidence to illustrate the value of the method.
Position noise in scanning superconducting quantum interference device microscopy (2004)

Experimentally obtained magnetic field images contain not only magnetic field noise, but also uncertainty in the position at which the data points are recorded. Such position noise degrades the images where the magnetic field gradients are strongest. Our high-Tc scanning superconducting quantum interference device (SQUID) microscope was found to be limited by a position noise of about 0.145 μm. For a straight wire carrying 500 μA with a rms magnetic noise of 0.185 nT, and source–sample separation 150 μm, we find that the rms position noise must be less than 62 nm for it to have less impact on the image quality than intrinsic magnetic SQUID noise.
A Renaissance of Interest in Aminoglycoside Antibiotics (2001)

Aminoglycoside antibiotics remain to the present date as important chemotherapeutic agents, which have been in clinical use for over 50 years. These antibiotics are multifunctional and have been challenging targets for synthetic chemists. Recent developments in understanding of the mechanism of action and of resistance to these agents have stimulated additional interest in these antibiotics. The present report discussed these efforts in the field for the past few years.
Recent progress and current opinions in Brillouin microscopy for life science applications (2020)

Many important biological functions and processes are reflected in cell and tissue mechanical properties such as elasticity and viscosity. However, current techniques used for measuring these properties have major limitations, such as that they can often not measure inside intact cells and/or require physical contact-which cells can react to and change. Brillouin light scattering offers the ability to measure mechanical properties in a non-contact and label-free manner inside of objects with high spatial resolution using light, and hence has emerged as an attractive method during the past decade. This new approach, coined "Brillouin microscopy," which integrates highly interdisciplinary concepts from physics, engineering, and mechanobiology, has led to a vibrant new community that has organized itself via a European funded (COST Action) network. Here we share our current assessment and opinion of the field, as emerged from a recent dedicated workshop. In particular, we discuss the prospects towards improved and more bio-compatible instrumentation, novel strategies to infer more accurate and quantitative mechanical measurements, as well as our current view on the biomechanical interpretation of the Brillouin spectra.
Visualizing vein patterns from color skin images based on image mapping for forensics analysis (2013)

Traditionally, it was difficult to use vein patterns in evidence images for forensic identification, because they were nearly invisible in color images. We proposed a computational method based on skin optics to uncover vein patterns from color images. However, its performance is dependent on the accuracy of the skin optical model. In this paper, we propose an algorithm based on image mapping to visualize vein patterns. It extracts information from a pair of synchronized color and near infrared (NIR) images, and uses a neural network (NN) to map RGB values to NIR intensities. In addition, an NN weight adjustment scheme is proposed to improve the robustness of the algorithm. The proposed algorithm was examined on a database with 300 pairs of color and NIR images collected from the forearms of 150 subjects. The automatic matching results from the proposed algorithm were better than those from our previous method, and comparable to the results from matching NIR images with NIR images.
Insights into the Anti‐inflammatory Action of the Soluble Epoxide Hydrolase Inhibitor through Systems Biology based in silico Modeling Approach. (2008)

The arachidonic acid (AA) cascade is involved in inflammation, pain, and multiple pathological states. Products of AA metabolism include the inflammatory leukotrienes and prostaglandins as well as the anti‐inflammatory epoxyeicosatrienoic acids (EETs). We used a dynamic in silico platform comprising of AA, tumor necrosis factor alpha and toll‐like receptor signaling blocks. The goal of this study was to validate the in silico platform with experimental data and use it to probe into the mode of action of the anti‐inflammatory affects of the soluble epoxide hydrolase inhibitor (sEHI). Previous in vivo results demonstrated that use of sEHI attenuated the effects of LPS induced inflammation without affecting prostacyclin to thromboxane ratio and concurrent use of a cyclooxygenase (COX) inhibitor demonstrated synergistic effects. In silico analysis of sEHI demonstrated identical results. Both in vivo and in silico analyses indicate that increase in EETs may mediate the inhibition on the COX enzymes. The in silico results also gave insight that the EETs mediate reduction in expression of COX2 and inflammatory cytokines through inhibition at the level of nuclear factor kappa B transcription. Thus, this study shows that in silico analysis of AA metabolism is consistent with in vivo results and that predictive analysis is particularly useful and highly practical for streamlining hypothesis generation and testing.
On-wafer integration of nitrides and Si devices: Bringing the power of polarization to Si (2009)

The seamless integration of AlGaN/GaN transistors and Si CMOS electronics on the same chip will revolutionize digital and mixed signal electronics. In this talk we describe our group's effort on demonstrating this integration. Si-GaN-Si virtual substrates have been recently fabricated through substrate removal and wafer bonding processes. The very high thermal stability of nitrides allows for the fabrication of Si CMOS electronics on these substrates without degrading the performance of the embedded nitride layer. In addition, GaN transistors on Si (001) have been fabricated on these substrates for the first time. Some of the many new circuits and devices that this integration allows include high power analog-to-digital converters, high speed differential amplifiers, normally-off power transistors, and highly-compact power regulator circuits.
A Subspace Approach to Spectral Quantification for MR Spectroscopic Imaging (2017)

The proposed approach transforms how the MRSI spectral quantification problem is solved and enables efficient and effective use of spatiospectral priors to improve parameter estimation. The resulting algorithm is expected to be useful for a wide range of quantitative metabolic imaging studies using MRSI.
Renovation of the injured heart with myocardial tissue engineering (2006)

Tissue engineering aims to create, repair and/or replace tissues and organs by using cells, scaffolds, biologically active molecules and physiologic signals. It is an interdisciplinary field that integrates aspects of engineering, chemistry, biology and medicine. One of the most challenging goals in the field of cardiovascular tissue engineering is the creation of a heart muscle patch. This review describes the principles, achievements and challenges of achieving this ambitious goal of creating contractile heart muscle. In addition, the new strategy of in situ and injectable tissue engineering for myocardial repair and regeneration is presented.
Energy angular momentum closed-loop guidance (2014)

A novel guidance algorithm for launch vehicle ascent to the desired mission orbit is proposed. The algorithm uses total specific energy and orbital angular momentum as new state vector parameters. These parameters are ideally suited for the ascent guidance task, since the guidance algorithm steers the launch vehicle along a pre-flight optimal trajectory in energy angular momentum space. The guidance algorithm targets apogee, perigee, inclination and right ascension of ascending node. Computational complexities are avoided by eliminating time in the guidance computation and replacing it with angular momentum magnitude. As a result, vehicle acceleration, mass, thrust, length of motor burns, and staging times are also eliminated from the pitch plane guidance calculations. The algorithm does not involve launch vehicle or target state propagation, which results in minimal computational effort. Proof of concept of the new algorithm is presented using several numerical examples that illustrate performance results.
MONOCLONAL ANTIIDIOTYPIC ANTIBODIES NEUTRALIZE CYTOTOXIC EFFECTS OF ANTI-??GAL ANTIBODIES (1996)

The aims of this study were to produce and characterize mouse monoclonal antiidiotypic antibodies (AIAs) that specifically bind human antipig (anti-alphaGal) antibodies and to select those AIAs that neutralize the cytotoxicity of human or baboon serum to pig (PK15) cells. Mice were immunized with human anti-pig antibodies, and hybridomas were produced using conventional techniques. From a total of 480 clones, 11 produced AIAs that bound with high affinity to human anti-alpha Gal IgG and F(ab')2 fragments, and individually reduced serum cytotoxicity to pig cells by 40 - 90%. Seven of the AIAs also bound to human peripheral B lymphocytes (that express the same idiotypes as the antibodies produce). Several combinations of two or three AIAs provided 100% protection of PK15 cells. Selected AIAs injected intravenously into baboons reduced the cytotoxicity of subsequently drawn sera by 50--80% for >48 hr. The cytotoxicity studies also indicated that there are at least two dominant idiotypes expressed in the human anti-alphaGal population. We conclude that AIAs against anti-alphaGal antibodies could be successfully used in 1) preoperative characterization of a recipient's anti-alphaGal profile, (2) prevention of hyperacute rejection of a pig organ, and (3) specific immunosuppression through elimination of anti-alphaGal-producing B lymphocytes.
Variation in <i>Xanthomonas campestris</i> NRRL B-1459: Characterization of Xanthan Products of Differing Pyruvic Acid Content (1977)

Normal xanthan-producing strains of the bacterium Xanthomonas campestris NRRL B-1459 are characterized by their efficient conversion (~60%) of substrates such as D-glucose into extracellular polysaccharide that gives culture fluids of high viscosity (6,000 to 8,000 cpoise) and pyruvic acid contents of about 4.5%. Various substrains have been found in certain stock cultures that produce xanthan differing in yield, viscosity and other solution properties, and in pyruvic acid content. Analysis of xanthan products from these substrains and from commercial sources shows that the pyruvate content can vary at least from 2.5% to 4.8%, while the sugar composition (D-glucose, D-mannose, and D-glucuronic acid) remains constant. The precipitation, rehydration, and rheological behavior of all xanthan samples having high (4.0% to 4.8%) pyruvate were similar but significantly different from those samples having low (2.5% to 3.0%) pyruvate which display different properties. At xanthan concentrations of 0.1% to 0.5%, high pyruvate samples are more viscous (sometimes 2 to 3X more), particularly in the presence of salt, than low pyruvate samples. Brief heating (95° C, 3 min) of low-pyruvate solutions caused their solution properties to become more like high-pyruvate when observed in the presence of salt. Other rheological properties of both pyruvate types are examined.
An Efficient Piezoelectric Energy Harvesting Interface Circuit Using a Bias-Flip Rectifier and Shared Inductor (2010)

Harvesting ambient vibration energy through piezoelectric means is a popular energy harvesting technique which can potentially supply 10-100's of ¿W of available power. One of the main limitations of existing piezoelectric harvesters is in their interface circuitry. In this paper, a bias-flip rectifier circuit that can improve the power extraction capability from piezoelectric harvesters over conventional full-bridge rectifiers and voltage doublers by greater than 4X is implemented in a 0.35 ¿m CMOS process. An efficient control circuit to regulate the output voltage of the rectifier and recharge a storage capacitor is presented. The inductor used within the bias-flip rectifier is shared efficiently with a multitude of switching DC-DC converters within the system reducing the overall component count.
Laser Surface Melting of Stainless Steel Anodes for Reduced Hydrogen Outgassing (Postprint) (2016)

Abstract : Anodes of 304 stainless steel have been processed by a continuous wave Yb fiber laser with a wavelength of 1.064 m and subjected to 50 keV electron bombardment in order to determine the extent to which hydrogen outgassing is reduced by the laser surface melting treatment. The results show a reduction in outgassing, by approximately a factor of four compared to that from untreated stainless steel. This is attributed to a reduction in the number of grain boundaries which serve as trapping sites for hydrogen in stainless steel. Such laser treated anodes do not require post-processing to preserve the benefits of the treatment and are excellent candidates for use in high power source devices.
Characterization of a membrane binding loop leads to engineering botulinum neurotoxin B with improved therapeutic efficacy (2020)

Botulinum neurotoxins (BoNTs) are a family of bacterial toxins with seven major serotypes (BoNT/A-G). The ability of these toxins to target and bind to motor nerve terminals is a key factor determining their potency and efficacy. Among these toxins, BoNT/B is one of the two types approved for medical and cosmetic uses. Besides binding to well-established receptors, an extended loop in the C-terminal receptor-binding domain (HC) of BoNT/B (HC/B) has been proposed to also contribute to toxin binding to neurons by interacting with lipid membranes (termed lipid-binding loop [LBL]). Analogous loops exist in the HCs of BoNT/C, D, G, and a chimeric toxin DC. However, it has been challenging to detect and characterize binding of LBLs to lipid membranes. Here, using the nanodisc system and biolayer interferometry assays, we find that HC/DC, C, and G, but not HC/B and HC/D, are capable of binding to receptor-free lipids directly, with HC/DC having the highest level of binding. Mutagenesis studies demonstrate the critical role of consecutive aromatic residues at the tip of the LBL for binding of HC/DC to lipid membranes. Taking advantage of this insight, we then create a "gain-of-function" mutant HC/B by replacing two nonaromatic residues at the tip of its LBL with tryptophan. Cocrystallization studies confirm that these two tryptophan residues do not alter the structure of HC/B or the interactions with its receptors. Such a mutated HC/B gains the ability to bind receptor-free lipid membranes and shows enhanced binding to cultured neurons. Finally, full-length BoNT/B containing two tryptophan mutations in its LBL, together with two additional mutations (E1191M/S1199Y) that increase binding to human receptors, is produced and evaluated in mice in vivo using Digit Abduction Score assays. This mutant toxin shows enhanced efficacy in paralyzing local muscles at the injection site and lower systemic diffusion, thus extending both safety range and duration of paralysis compared with the control BoNT/B. These findings establish a mechanistic understanding of LBL-lipid interactions and create a modified BoNT/B with improved therapeutic efficacy.
Radical Reaction of Sodium Hypophosphite with Terminal Alkynes: Synthesis of 1,1‐Bis‐H‐phosphinates. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Dark-field optical coherence microscopy (2010)

Many solutions have been proposed to produce phase quantitative images of biological cell samples. Among these, Spectral Domain Phase Microscopy combines the fast imaging speed and high sensitivity of Optical Coherence Microscopy (OCM) in the Fourier domain with the high phase stability of common-path interferometry. We report on a new illumination scheme for OCM that enhances the sensitivity for backscattered light and detects the weak sample signal, otherwise buried by the signal from specular reflection. With the use of a Bessel-like beam, a dark-field configuration was realized. Sensitivity measurements for three different illumination configurations were performed to compare our method to standard OCM and extended focus OCM. Using a well-defined scattering and reflecting object, we demonstrated an attenuation of -40 dB of the DC-component and a relative gain of 30 dB for scattered light, compared to standard OCM. In a second step, we applied this technique, referred to as dark-field Optical Coherence Microscopy (dfOCM), to living cells. Chinese hamster ovarian cells were applied in a drop of medium on a coverslide. The cells of ~15 μm in diameter and even internal cell structures were visualized in the acquired tomograms.
Characterization and ex vivo Expansion of Human Placenta-Derived Natural Killer Cells for Cancer Immunotherapy (2013)

Recent clinical studies suggest that adoptive transfer of donor-derived natural killer (NK) cells may improve clinical outcome in hematological malignancies and some solid tumors by direct anti-tumor effects as well as by reduction of graft versus host disease (GVHD). NK cells have also been shown to enhance transplant engraftment during allogeneic hematopoietic stem cell transplantation (HSCT) for hematological malignancies. The limited ex vivo expansion potential of NK cells from peripheral blood (PB) or umbilical cord blood (UCB) has however restricted their therapeutic potential. Here we define methods to efficiently generate NK cells from donor-matched, full-term human placenta perfusate (termed Human Placenta-Derived Stem Cell, HPDSC) and UCB. Following isolation from cryopreserved donor-matched HPDSC and UCB units, CD56+CD3- placenta-derived NK cells, termed pNK cells, were expanded in culture for up to 3 weeks to yield an average of 1.2 billion cells per donor that were >80% CD56+CD3-, comparable to doses previously utilized in clinical applications. Ex vivo-expanded pNK cells exhibited a marked increase in anti-tumor cytolytic activity coinciding with the significantly increased expression of NKG2D, NKp46, and NKp44 (p < 0.001, p < 0.001, and p < 0.05, respectively). Strong cytolytic activity was observed against a wide range of tumor cell lines in vitro. pNK cells display a distinct microRNA (miRNA) expression profile, immunophenotype, and greater anti-tumor capacity in vitro compared to PB NK cells used in recent clinical trials. With further development, pNK may represent a novel and effective cellular immunotherapy for patients with high clinical needs and few other therapeutic options.
Dual transmission model of the fetal heart tone (2004)

Detection of the fetal heart tone by auscultation is sometimes easy, other times very difficult. In the model proposed here, the level of difficulty depends upon the position of the fetus within the maternal abdomen. If the fetus lies in the classical left/right occiput anterior position (head down, back against the maternal abdominal wall), detection by a sensor or stethoscope on the maternal abdominal surface is easy. In this mode, named here the ‘‘direct contact’’ mode, the heartbeat pushes the fetus against the detecting sensor. The motion generates pressure by impact and does not involve acoustic propagation at all. If the fetus lies in a persistent occiput posterior position (spine-to-spine, fetus facing forward), detection is difficult. In this, the ‘‘fluid propagation’’ mode, sound generated by the fetal heart and propagating across the amniotic fluid produces extremely weak signals at the maternal surface, typically 30 dB lower than those of the direct contact mode. This reduction in tone level can be compensated by judicious selection of detection frequency band and by exploiting the difference between the background noise levels of the two modes. Experimental clinical results, demonstrating the tones associated with the two respective modes, will be presented.
Multicore fiber-based 5-mode multiplexer/demultiplexer (2017)

A five-mode multiplexer/demultiplexer based on a partially elongated five-core fiber is presented. Multiplexing operation is experimentally verified. Mode selectivity higher than 95% at 1550 nm, for both the LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> and the LP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">21</sub> mode, is achieved.