gebhart/patrepeval huggingface dataset:
Computationally Designed Bispecific MD2/CD14 Binding Peptides Show TLR4 Agonist Activity (2018)

Toll-like receptor 4 plays an important role in the regulation of the innate and adaptive immune response. The majority of TLR4 activators currently in clinical use are derivatives of its prototypic ligand LPS. The discovery of innovative TLR4 activators has the potential of providing new therapeutic immunomodulators and adjuvants. We used computational design methods to predict and optimize a total of 53 cyclic and linear peptides targeting myeloid differentiation 2 (MD2) and cluster of differentiation 14 (CD14), both coreceptors of human TLR4. Activity of the designed peptides was first assessed using NF-κB reporter cell lines expressing either TLR4/MD2 or TLR4/CD14 receptors, then binding to CD14 and MD2 confirmed and quantified using MicroScale Thermophoresis. Finally, we incubated select peptides in human whole blood and observed their ability to induce cytokine production, either alone or in synergy with LPS. Our data demonstrate the advantage of computational design for the discovery of new TLR4 peptide activators with little structural resemblance to known ligands and indicate an efficient strategy with which to identify TLR4 targeting peptides that could be used as easy-to-produce alternatives to LPS-derived molecules in a variety of settings.
Remote control structural exciters for structural data acquisition system calibrations (2002)

The Air Force invented a new calibration technique, which allows one person to perform multiple end-to-end mechanical calibrations of structural dynamics measurement systems. An end-to-end calibration means a full calibration of instrumentation from the physical input to the transducer to the output where the analog or digital signal is normally analyzed. It is difficult to stimulate mounted and embedded transducers with known physical inputs. Normally two people calibrate-one at the transducer holds or attaches the exciter and one operates the recorder. This new technique uses remote control structural exciters to stimulate measurement transducers contained in structures, with a measurable input level, and the output signal is communicated to a data recorder. The Air Force demonstrated this patented technique by using accelerometers in the laboratory. A commercial off-the-shelf vibration paging system sends a signal from a master control unit to individual exciters that stimulate accelerometers mounted on structures. A reference accelerometer measures the input. Engineers validated the technique using eight different exciters in a completely randomized block design experiment consisting of three 2-level factors: material, structural thickness and excitation mode. The engineers measured amplitude, frequency and transfer function between the accelerometers. This paper describes the invention and looks at potential field applications to insure data integrity in structural data acquisition systems on aging commercial and military vehicles.
A Micromachined Platform for Three Dimensional Dielectrophoretic Assembly of Gold Nanoparticles for Nanodevices (2007)

This paper reports a novel technological approach for three-dimensional (3D) assembly of gold nanoparticles with an average diameter of 52 nm using dielectrophoresis (DEP). To realize the 3D assembly, the authors have designed and fabricated a versatile self-aligned micromachined platform which is applicable for assembling metallic nanoparticles and nanostructures. The assembly process is achieved at room temperature and is compatible with conventional semiconductor fabrication and large scale nanoassembly. The current-voltage curves obtained from the 3D gold nanoparticle bridges demonstrate that the assembly is functional with resistance values between -26 and 118 Ohms. This method has applications in making high density three-dimensional interconnects, vertically integrated nano sensors and for in-line testing of manufactured conductive nanoelements.
Design and fabrication of terahertz quantum cascade laser structure based on III‐nitride semiconductors (2009)

Abstract We have designed a resonant phonon‐type GaN/In 0.05 Al 0.23 Ga 0.72 N quantum cascade structure, emitting at 7.6 terahertz, in which the population inversion could be obtained by making calculations based on self‐consistent rate equation model. We also fabricated the designed quantum cascade structure using radio‐frequency molecular beam epitaxy. Clear satellite peaks patterns in high resolution X‐ray diffraction and sharp interfaces between GaN wells and InAlGaN barriers in high resolution transmission electron microscopy image were both observed, indicating that almost the same structure as that of our design had been fabricated successfully. These results indicate that III‐Nitride semiconductors would be promising materials for terahertz quantum cascade lasers. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A novel software framework for magnetic particle imaging reconstruction (2022)

Abstract Magnetic particle imaging is a novel tomographic imaging technique that enables noninvasive and highly sensitive imaging of superparamagnetic iron oxide nanoparticles distributed in living subjects. Several studies have reported on the development of reconstruction algorithms; however, a unified software framework for magnetic particle imaging reconstruction has yet to be developed. Herein, we propose a high‐performance, flexible, and easy‐to‐use magnetic particle imaging reconstruction framework using the Python programming language. The magnetic particle imaging reconstruction framework consists of the data access, preprocessing, image reconstruction, and postprocessing phases. We used the proposed framework to simulate the x‐space and system matrix‐based reconstruction methods with Cartesian and Lissajous scan trajectories. The reconstruction results of an open magnetic particle imaging dataset and a numerically simulated phantom demonstrated that the magnetic particle imaging reconstruction framework provides a reliable and accessible environment for magnetic particle imaging reconstruction, which can be extended and customized.
A Rate of Change of Torque Sensor (2007)

A sensor having an output signal indicative of the time rate of change (ROC) of torque is described. Operating on the same magnetoelastic principles as polarized band torque transducers except for the replacement of field intensity sensors with flux linking multiturn coils, ROC sensors respond exclusively to the variational components of the torque. ROC sensors provide unmatched sensitivity to small and rapid torque variations exposing detail often lost in the noise and bandwidth limitations of more complex and more costly torque transducers
Soluble corn fiber modulates calcium absorption by altering colonic microbiota (2013)

Soluble corn fiber (SCF) has been shown to increase calcium (Ca) absorption. Animal models suggest colonic bacteria can influence Ca absorption; the mechanism is not understood in humans. This study assessed the effect of SCF on fecal microbiota in relation to Ca absorption in a racially diverse group of teens. Twenty‐four boys and girls (12–15 y; 45.8% Asian, 25% Hispanic, 29.2% Multiracial) participated in two 3‐week metabolic Ca balance studies testing 0 and 12 g/d SCF on a low Ca diet (600 mg/d), characteristic of usual intakes. Microbial community composition, evaluated in fecal samples collected during each treatment, was assessed with 454 pyrosequencing of PCR amplified 16S rRNA genes. Ca absorption increased by 12% with SCF consumption compared to no SCF. This increase correlated with a decrease in other Erysipelotrichaceae ( P <0.04) and increases in Bacteroides ( P <0.03), Alistipes ( P <0.05), Butyricicoccus ( P <0.04), Oscillibacter ( P <0.008) and Dialister ( P <0.003) but not changes in Lactobacillus ( P =0.07) and Parabacteroides ( P =0.07). These bacterial genera have been identified as short chain fatty acid producers while Bacteroides is capable of fermenting fibers like SCF. The bacterial changes suggest SCF may increase Ca absorption through fermentation. This is the first study to show that increases in specific bacteria were significantly correlated with the observed increase in calcium absorption. Grant Funding Source : Tate & Lyle Health & Nutrition Sciences
Odako growth of dense arrays of single-walled carbon nanotubes attached to carbon surfaces (2009)

A novel process is demonstrated whereby dense arrays of single-walled carbon nanotubes (SWNT) are grown directly at the interface of a carbon material or carbon fiber. This growth process combines the concepts of SWNT tip growth and alumina-supported SWNT base growth to yield what we refer to as “odako” growth. In odako growth, an alumina flake detaches from the carbon surface and supports catalytic growth of dense SWNT arrays at the tip, leaving a direct interface between the carbon surface and the dense SWNT arrays. In addition to being a new and novel form of SWNT array growth, this technique provides a route toward future development of many important applications for dense aligned SWNT arrays.
Interferon-Gamma Pathway Regulates Emergence of Engraftable Hematopoietic Stem and Progenitor Cells from Human Pluripotent Stem Cells (2017)

Abstract Derivation of functional human hematopoietic stem cells (HSCs) from autologous human pluripotent stem cells (PSCs) has been an elusive goal in hematology research. Building upon recent evidence that HSCs are derived from definitive hemogenic endothelium (HE), we identified 7TFs (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1, SPI1) that were sufficient to convert human PSC-derived HE into engraftable hematopoietic stem and progenitor cells (HSPCs) with long-term and multilineage capacity (HE-7TF cells, Sugimura et al, Nature 2017). In the current study, we attempted to define signaling pathways that further enhance engraftment of HE-7TF cells. We investigated the source of our long-term engraftable cells by sorting CD34+CD43+CD45+ triple positive cells and CD34+CD43-CD45- single positive cells from HE-7TF cells. We transplanted these two cell populations into non-irradiated c-Kit deficient immune-deficient recipients, and monitored engraftment capacity after 8 weeks of transplantation. 2 out of 5 mice transplanted with triple positive cells showed multi-lineage engraftment, whereas 5 mice transplanted with single positive cells did not, suggesting that CD34+CD43+CD45+ triple positive cells are the source of long-term engraftment in our system. We then investigated what signaling pathways regulate the emergence of CD34+CD43+CD45+ triple positive cells from HE. From high-throughput screening of 2,000 receptor ligands, cytokines/morphogens, hormone, and chemical compounds, we observed that interferon-gamma (IFNγ) increased CD34+CD43+CD45+ triple positive cells 6 to 8-fold in 5 independent experiments. The effect was abrogated by the addition of IFNα. Collectively, these data demonstrate that the IFNγ pathway promotes the emergence of engraftable HSPCs from human PSC-derived HE. Disclosures No relevant conflicts of interest to declare.
Phytase activity of<i>Selenomonas ruminantium</i>: a preliminary characterization (1999)

Obligately anaerobic ruminal bacteria have been found to possess phytase activity, in particular, Selenomonas ruminantium. The phytase activity of S. ruminantium JY35 was produced late in growth and required neither phytate for induction nor phosphate limitation for derepression. The activity was completely cell‐associated with a significant fraction extractable by a magnesium chloride solution. Zymogram analysis suggested that the activity was the result of a single gene product of a monomeric nature and approximately 46 kDa in size. The phytase had a temperature optimum of 50–55 °C, but activity dropped off sharply at 60 °C. Phytase activity was optimal over the pH range of 4·0–5·5, and dependent on the nature of the buffer used. Activity was inhibited by citric acid buffer and by the addition of 5 mmol l−1 Fe2+, Fe3+, Cu2+, Zn2+ and Hg2+. The addition of 5 mmol l–1 Pb2+ to the enzyme assay appeared to enhance activity of the enzyme.
Engineering a delta protein kinase C inhibitor that selectively inhibits interaction and phosphorylation of one substrate of the multi‐substrate kinase (582.3) (2014)

Rationale: Many kinases phosphorylate multiple substrates. To assess the role of an individual phosphorylation event without using laborious mutagenesis studies, selective pharmacological tools that inhibit phosphorylation of specific one substrate are needed. We focused on delta protein kinase C (δPKC) because δPKC activation after heart attack leads to cardiac damage. We reasoned that since pyruvate dehydrogenase kinase (PDK) phosphorylation by δPKC leads to inhibition of ATP production, it might be critical in the injurious effect δPKC after heart attack. To determine if of the many substrates of δPKC, PDK is the substrate that mediates this injurious effect in the heart, we designed a selective inhibitor of δPKC binding and phosphorylation of PDK. Methods: We designed a short peptide inhibitor that mimics a unique interaction between PDK and δPKC to selectively inhibit δPKC phosphorylation of PDK. This protein‐protein interaction inhibitory peptide (PPIIP) was used in vitro, in cells and in intact heart, in models of heart attack. Results: PDK/δPKC interaction was inhibited by PPIIP in vitro and in vivo. PDK/δPKC PPIIP selectively inhibited phosphorylation of PDK without affecting phosphorylation of several other δPKC substrates. Treatment with PDK/δPKC PPIIP inhibited myocardial infarction‐induced PDK phosphorylation without inhibiting the phosphorylation of other δPKC substrates. Further, PDK/δPKC PPIIP treatment led to a 50% reduction in infarct size, in release of cardiac enzyme (a measure of cell lysis) and in JNK phosphorylation, all markers of cardiac injury. Conclusion: PDK/δPKC PPIIP is a selective inhibitor of PDK phosphorylation by δPKC. Of the several δPKC‐mediated phosphorylation events following heart attack, δPKC‐induced PDK phosphorylation is sufficient to cause cardiac injury as a selective inhibitor of this phosphorylation event alone was sufficient to provide great reduction in δPKC‐mediated cardiac injury after heart attack.
Carbon nanotube based non-volatile memory and charge sensors (2005)

Beyond 65 nm node, the ultra-narrow channel memory device serves as a possible technology for further scaling. A self-assembled carbon nanotube (CNT) channel with self aligned metal nanocrystals is proposed as an alternative to Si based ultra-narrow channel memory. The device demonstrates large memory window and single-electron sensitivity. The analysis of the transport in the CNT channel using non-equilibrium Green's function (NEGF) formalism confirms single electron sensitivity quantitatively at room temperature. The CNT channel conductance exhibits sensitivity to position of the charge along the channel. The NEGF based analysis is easily extended to the application of CNTFET as a charge sensor. The electrostatics of the CNT-nanocrystal memory was analyzed for transport between nanocrystal and CNT. Despite the nanocrystal being in close proximity of the CNT, it is strongly coupled to the gate electrode electrostatically. This effect is not observed in the planar 2D Si- based nanocrystal memory. It obviates a major trade-off in memory design of scaling the control dielectric to decrease operational voltage, while ensuring low gate leakage and should allow ultra-low voltage operations. Large tunneling current should also enhance write times. Large electric field asymmetry should enable a better write/retention ratio.
Modeling the G-protein-coupled neuropeptide Y Y1 receptor agonist and antagonist binding sites (1997)

Neuropeptide Y (NPY) receptors belong to the G-protein-coupled receptor (GPCR) superfamily and mediate several physiological responses, such as blood pressure, food intake, sedation and memory retention. To understand the interactions between the NPY Y1 receptor subtype and its ligands, computer modeling was applied to the natural peptide agonist, NPY and a small molecule antagonist, BIBP3226. An agonist and antagonist binding domain was elucidated using mutagenesis data for the Y1 receptor as well as for other GPCR families. The agonist and antagonist ligands which were investigated appear to share common residues for their interaction within the transmembrane regions of the Y1 receptor structure, including Gln120, Asn283 and His306. This is in contrast to findings with tachykinin receptors where the binding domains of the non-peptide antagonists have very little in common with the binding domains of the agonist, substance-P. In addition, a hydrogen bond between the hydroxyl group of Tyr36 of NPY and the side chain of Gln219, an interaction that is absent in the model complex between Y1 and the antagonist BIBP3226, is proposed as one of the potential interactions necessary for receptor activation.
Conversational multi-modal browser: an integrated multi-modal browser and dialog manager (2003)

This paper describes a multi-modal, free flow browser. A multi-modal browser allows the user to perform tasks via any of several modalities, such as speech and GUI or devices available sequentially or concurrently. A free-flow or mixed initiative browser allows the user to choose the navigation across an application and the order in which tasks are completed. This paper describes a system to provide flow conversational capability across modalities or devices. Multi-modal interaction is provided using a DOM based MVC multi-modal browser extended with an event-driven form-based dialog manager. We use XForms-based device independent authoring for the application. This paper details the XForms-based programming model of conversational applications, the principles and architecture of an XForms-based and event driven, task oriented, mixed initiative dialog manager and the integration of a dialog manager and a multi-modal browser using a standard-based DOM event driven interface. The dialog manager relies on a DOM based representation of the form-based framework presented by Papineni (1999) and Davies et al. (1999) to provide free-flow dialog management. It determines the user's intention by measuring the relevance of user input to different tasks. It also provides focus determination by determining the next logical turn in the conversation.
Steroid hormone‐induced male sex determination in an amniotic vertebrate (1992)

In many reptiles, sex is determined by the temperature at which the eggs are incubated (i.e., temperature-dependent sex determination, or TSD). Past studies have shown that exogenous steroid hormones can override the effects of temperature and induce female sex determination. However, past attempts to induce male sex determination have consistently failed. In the present study, sex determination was studied in a turtle with TSD. By utilizing an incubation temperature regimen that resulted in approximately a 1:1 sex ratio in the control group, sex determination was shown to be sensitive to both exogenous androgen and estrogen treatments: androgen induced the production of male hatchlings, whereas estrogen induced the production of female hatchlings. This is the first report of an amniotic vertebrate in which an exogenous steroid hormone induces male sex determination.
Confocal Raman microspectroscopy: measuring the effects of topical moisturizers on stratum corneum water gradient in vivo (2006)

The stratum corneum (SC) water concentration gradient is fundamental to skin's role as a barrier, regulating its physical and biochemical properties. Standard instruments utilizing changes in SC electrical properties to estimate SC water concentration provide simple, rapid measurements but cannot provide true interval data as a function of depth. Confocal Raman spectroscopy (CRS) of human subjects provides non-invasive, real-time, in vivo measures of molecular concentration profiles. A state-of-the-art confocal Raman microspectrometer equipped with a fiber-coupled laser source operating at a wavelength of 671 nm was used to obtain measurements in the high wavenumber region (~2400-4000 cm<sup>-1</sup>). An aircooled, high-sensitivity back-illuminated, deep-depletion CCD camera captured radiation scattered inelastically from focal planes within the skin in vivo (a high-precision, computer-controlled piezo-electric stage and objective allowing depth resolutions of <5 μm, with over-sampling). High-wavenumber data were analyzed to provide semi-quantitative measures of water concentration ([water] / [protein + water]) across the SC. This new technique was used to study changes in SC water concentration gradients in human skin in vivo, in response to treatment with topical moisturizing products. The results of a blinded, randomized 3-week study in human volunteers will be presented, in particular, the significant, unique effects of a topical moisturizer containing niacinamide on SC water concentration gradient, as measured by CRS, in vivo. The approach to compare SC water gradient effects will be discussed and the utility of this exciting new method will be compared and contrasted to existing methodology.
Hierarchical organization of silicate/surfactant system: Biomimetic inorganic materials (2000)

Mesoporous silica MCM-41 with adjustable and uniformed pore sizes in the range of 1.5 to 10.0 nm, which possesses hexagonal arrangement of uniformly sized channel mesopores, has been the focus of recent investigations. MCM-41 silica possess a wide variety of morphologies. We have found a new way of synthesizing MCM-41 with novel tubular and spherical morphology. Hollow spheres and tubular structures with various topological structures can be obtained in different ranges of water/surfactant/alcohol molar ratio. The sample synthesized with C16TMABr-silicate system with suitable water content leads to tubular morphology. Surfactants with shorter carbon chain length would inhibit the formation of tubular morphology. The sample synthesized with C14TMAB-silicate system with added short chain alcohols leads to hollow spherical morphology with internal pillars. This structure follows from a transformation from the lamellae phase. Detailed studies of mechanism for the formation of these intricate hierarchical orders of the aluminosilicates are discussed. The hierarchical structures are biomimetic and can be understood from the physics of amphiphile organization.
A wideband 700W push-pull Doherty amplifier (2015)

A push-pull Doherty Power Amplifier (DPA) is proposed that uses a wideband power combiner BALUN, which is capable to provide the optimum fundamental and 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> harmonic loading conditions over a large operating bandwidth to the active devices. A 700W DPA demonstrator using these techniques provides high average efficiency (> 40%) for a 7.5dB PAR DVB-T signal over a 37% relative RF-bandwidth.
Data communication between brain implants and computer (2003)

Recent advances in neuroscience, microelectronics, and information technology have allowed construction of miniature, but highly intelligent, devices to be implanted within the brain to perform in vitro diagnostic and therapeutic functions. However, there exists a significant problem in establishing an effective wireless data communication link between brain implants and external computer. This communication investigates this link and presents a new design using the mechanism of volume conduction of biological tissues. A theoretical model of volume conduction of the head is utilized to compute signal strength in data communication and the result is evaluated by a physical model. The two-way data communication sensitivity of the volume conduction channel is found to be symmetric, as suggested by the reciprocity theorem. A high-performance, x-shaped volume conduction antenna has been designed. Experiments are performed on animals which demonstrate the effectiveness of this volume conduction approach.