gebhart/patrepeval huggingface dataset:
Polymorphisms in genes in the SREBP1 signalling pathway and SCD are associated with milk fatty acid composition in Holstein cattle (2011)

Genes in the sterol regulatory element-binding protein-1 (SREBP1) pathway play a central role in regulation of milk fat synthesis, especially the de-novo synthesis of saturated fatty acids. SCD, a SREBP-responsive gene, is the key enzyme in the synthesis of monounsaturated fatty acids in the mammary gland. In the present study, we discovered SNP in candidate genes associated with this signalling pathway and SCD to identify genetic markers that can be used for genetic and metabolically directed selection in cattle. We resequenced six candidate genes in the SREBP1 pathway (SREBP1, SCAP, INSIG1, INSIG2, MBTPS1, MBTPS2) and two genes for SCD (SCD1 and SCD5) and discovered 47 Tag SNP that were used in a marker-trait association study. Milk and blood samples were collected from Holstein cows in their 1st or 2nd parity at 100-150 days of lactation. Individual fatty acids from C4 to C20, saturated fatty acid (SFA) content, monounsaturated fatty acid content, polyunsaturated fatty acid content and desaturase indexes were measured and used to perform the asociation analysis. Polymorphisms in the SCD5 and INSIG2 genes were the most representative markers associated with SFA/unsaturated fatty acid (UFA) ratio in milk. The analysis of desaturation activity determined that markers in the SCD1 and SCD5 genes showed the most significant effects. DGAT1 K232A marker was included in the study to examine the effect of this marker on the variation of milk fatty acids in our Holstein population. The percentage of variance explained by DGAT1 in the analysis was only 6% of SFA/UFA ratio. Milk fat depression was observed in one of the dairy herds and in this particular dairy one SNP in the SREBP1 gene (rs41912290) accounted for 40% of the phenotypic variance. Our results provide detailed SNP information for key genes in the SREBP1 signalling pathway and SCD that can be used to change milk fat composition by marker-assisted breeding to meet consumer demands regarding human health, as well as furthering understanding of technological aspects of cows' milk.
Double-Layer Liquid Crystal Lens (2004)

A liquid crystal (LC) lens of two LC layers is proposed to increase the lens focusing power. The lens structure is developed from the lens of one LC layer with an insulating glass substrate between the electrode and the LC layer reported before. The LC lens preserves the high optical quality and its focal length is electrically tunable. The focusing power of the lens becomes much larger than two times that of the LC lens with one LC layer. The properties of the LC lens are measured and the mechanisms of the power enhancement are discussed.
Detection of anti-Borrelia burgdorferi antibody responses with the borreliacidal antibody test, indirect fluorescent-antibody assay performed by flow cytometry, and western immunoblotting (1996)

Borreliacidal antibodies participate in the resolution of Lyme disease by clearing Borrelia burgdorferi sensu lato from the host. Detection of borreliacidal antibodies is also valuable for determination of the specific serodiagnosis of Lyme disease. We show in this work that antibody detected by the borreliacidal antibody test did not correlate with antibody detected by the indirect fluorescent-antibody assay or Western immunoblotting. Detection of borreliacidal antibody decreased with elimination of the spirochete from the host in the presence or absence of therapy. By contrast, the antibody responses detected by the indirect fluorescent-antibody assay or Western immunoblotting remained elevated or continued to expand, respectively. This suggests that the borreliacidal antibody test is a prognostic indicator for clearance of the spirochete. Additional investigations with humans are needed to confirm the prognostic potential of the borreliacidal antibody test.
A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide (1993)

An oligodeoxynucleotide that readily flips to the Z-DNA conformation in 10mM MgCl2 was produced by using Klenow enzyme to incorporate 5-bromodeoxycytosine and deoxyguanosine into a (dC-dG)22 template. During synthesis the oligomer can be labeled with 32P to high specific activity. The labeled oligodeoxynucleotide can be used in bandshift experiment to detect proteins that bind Z-DNA. This allows the binding specificity of such proteins to be determined with high reliability using unlabeled linear and supercoiled DNA competitors. In addition, because the radioactive oligodeoxynucleotide contains bromine atoms, DNA-protein complexes can be readily crosslinked using UV light. This allows an estimate to be made of the molecular weight of the proteins that bind to the radioactive probe. Both techniques are demonstrated using a goat polyclonal anti-Z-DNA antiserum.
Electrically tunable laser based on heliconical cholesteric(Conference Presentation) (2016)

STUDENT CONTRIBUTION: Cholesteric liquid crystals (CLC) self-assemble into a periodic supramolecular helical structure with properties of a one-dimensional photonic crystal. The CLCs doped with a fluorescent dye and optical pump enable a distributed feedback cavity and lasing [1]. Although lasing was observed in range of wavelength from near UV to near IR, a practical method of tuning of emission wavelength from a dye-doped CLC without structural destruction of a helix is not demonstrated yet. In this work, we demonstrate an electrically tunable dye-doped CLC laser based on the so-called oblique helicoidal, or heliconical, CLC state [2,3]. In this state, the molecules twist around the helicoidal axis, making an angle smaller than 90 degrees with the axis. Molecular tilt makes the heliconical structure different from the regular CLC (in which the molecules are perpendicular to the axis) and enable electric tunability [2,3]. An electric field applied parallel to the heliconical axis changes the pitch but does not realign the axis. When the field increases, the pitch decreases. As a result, the selective reflection band and a lasing wavelength move towards shorter wavelength. Using heliconical CLC and two laser dyes DCM and LD688, we demonstrate effective tuning of the laser emission wavelength from 574 nm to 722 nm. With appropriate laser dyes, the spectrum can be extended from near UV to near IR. Efficient electric tuning in the broad spectral range and small size of the heliconical cholesteric lasers makes them potentially useful for optical and biomedical applications. [1] P. Palffy-Muhoay, W.Y. Cao, M. Moreira, B. Taheri, A. Munoz, Photonics and lasing in liquid crystal [2] J. Xiang, S.V. Shiyanovskii, C.T. Imrie, O.D. Lavrentovich, Electrooptic Response of Chiral Nematic Liquid Crystals with Oblique Helicoidal Director, Phys Rev Lett, 112 (2014) 217801. [3] J. Xiang, Y.N. Li, Q. Li, D.A. Paterson, J.M.D. Storey, C.T. Imrie, O.D. Lavrentovich, Electrically Tunable Selective Reflection of Light from Ultraviolet to Visible and Infrared by Heliconical Cholesterics, Adv Mater, 27 (2015) 3014-3018.
Design of patient-specific focused ultrasound arrays for non-invasive brain therapy with increased trans-skull transmission and steering range (2017)

The use of a phased array of ultrasound transducer elements to sonicate through the skull has opened the way for new treatments and the delivery of therapeutics beyond the blood-brain barrier. The limited steering range of current clinical devices, particularly at higher frequencies, limits the regions of the brain that are considered treatable by ultrasound. A new array design is introduced that allows for high levels of beam steering and increased transmission throughout the brain. These improvements are achieved using concave transducers normal to the outer-skull surface in a patient-specific configuration to target within the skull, so that the far-field of each beam is within the brain. It is shown that by using pulsed ultrasound waves timed to arrive in-phase at the desired target, sufficient levels of acoustic energy are delivered for blood-brain barrier opening throughout the brain.
An undersampled high‐directivity microstrip patch array with a reduced number of radiating elements inspired on the Sierpinski fractal (2003)

Abstract A high‐directivity microstrip array using multilevel elements based on fractal geometry is theoretically compared with an array using circular patches. Within the same electrical area, the same directivity can be obtained. However, the number of elements for the fractal‐based array is 2.84 times less, thus reducing the complexity of the feeding network and the overall array. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 37: 100–103, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10836
A two moment RC delay metric for performance optimization (2000)

For performance optimization tasks such as floorplanning, placement, buffer insertion, wire sizing, and global routing, the Elmore RC delay metric More accurate delay computation methods are typically either CPU intensive or difficult to implement. To bridge this gap between accuracy and simplicity, we propose the D2M RC delay metric, which is virtually as simple and fast as the Elmore metric but is significantly more accurate. The new metric is theoretically bounded above by the Elmore delay, yet it rarely is more than a few percent below the actual delay. Consequently, the metric behaves like the Elmore metric in that it generally overestimates delay, but with consistently less error. Further, the metric is extremely accurate at the far end of RC lines.
Ultrasonic System Measures Elastic Properties Of Composites (1993)

Measurements with leaky Lamb waves yield data on properties and defects of panels. System nondestructively measures elastic properties of, and defects in, panel of laminated fiber/matrix material. Ultrasonic transducers operating in pitch/catch mode excite and detect leaky Lamb waves in specimen. Elastic properties of specimen and defects within it characterized from dispersion curves of Lamb waves.
Scheduling and Control of Startup Process for Single-Arm Cluster Tools With Residency Time Constraints (2016)

Due to the trends of larger wafer diameters and smaller lot sizes, cluster tools need to switch from processing one lot of wafers to another frequently. This leads to more transient periods in wafer fabrication, which includes startup and close-down processes. Their efficient scheduling and control problems become more and more important. They become very difficult to solve especially when wafer residency time constraints must be considered. Most previous studies focused on the steady periodic schedule for cluster tools. Little research was on the transient processes of cluster tools despite their increasing importance. In order to optimize a startup transient process, this work develops a Petri net model to describe its behavior for a single-arm cluster tool. Then, based on the model, for the case that the workloads among the steps can be properly balanced, this work proposes a scheduling algorithm to find an optimal and feasible schedule for the startup process. For the other cases schedulable at the steady state, a linear programming model is developed to find an optimal and feasible schedule for the startup process. Finally, illustrative examples are given to show the applications of the proposed method.
NetEgg: A Scenario-Based Programming Toolkit for SDN Policies (2018)

Recent emergence of software-defined networks offers an opportunity to design domain-specific programming abstractions aimed at network operators. In this paper, we propose scenario-based programming, a framework that allows network operators to program network policies by describing example behaviors in representative scenarios. Given these scenarios, our synthesis algorithm automatically infers the controller state that needs to be maintained along with the rules to process network events and update state. We have developed the NetEgg scenario-based programming tool, which can execute the generated policy implementation on top of a centralized controller, but also automatically infers flow-table rules that can be pushed to switches to improve throughput. We evaluate the performance of NetEgg based on the computational requirements of our synthesis algorithm as well as the overhead introduced by the generated policy implementation, and we study the usability of NetEgg based on a user study. Our results show that our synthesis algorithm can generate policy implementations in less than a second for all policies we studied, and the automatically generated policy implementations have performance comparable to their hand-crafted implementations. Our user study shows that the proposed scenario-based programming approach can reduce the programming time by 50% and the error rate by 32% compared with an alternative programming approach.
Flexible needle steering for percutaneous therapies (2006)

Objective: A robotic system is presented for flexible needle steering and control in soft tissue. Materials and Methods: Flexible needle insertion into a deformable tissue is modeled as a linear beam supported by virtual springs, where the stiffness coefficients of the springs can vary along the needle. Using this simplified model, the forward and inverse kinematics of the needle are solved analytically, thus enabling both path planning and path correction in real time. Given target and obstacle locations, the computer calculates the needle tip trajectory that will avoid the obstacle and hit the target. Using the inverse kinematics algorithm, the corresponding needle base maneuver needed to follow this trajectory is calculated.Results: It is demonstrated that the needle tip path is not unique and can be optimized to minimize lateral pressure of the needle body on the tissue. Needle steering, i.e., the needle base movements that steer the needle tip, is not intuitive. Therefore, the needle insertion procedure is best performed by a robot. The model was verified experimentally on muscle and liver tissues by robotically assisted insertion of a flexible spinal needle. During insertion, the position and shape of the needle were recorded by X-ray.Conclusions: This study demonstrates the ability to curve a flexible needle by its base motion in order to achieve a planned tip trajectory.
Noise-tolerant quantum speedups in quantum annealing without fine tuning (2020)

Abstract Quantum annealing is a powerful alternative model of quantum computing, which can succeed in the presence of environmental noise even without error correction. However, despite great effort, no conclusive demonstration of a quantum speedup (relative to state of the art classical algorithms) has been shown for these systems, and rigorous theoretical proofs of a quantum advantage (such as the adiabatic formulation of Grover’s search problem) generally rely on exponential precision in at least some aspects of the system, an unphysical resource guaranteed to be scrambled by experimental uncertainties and random noise. In this work, we propose a new variant of quantum annealing, called RFQA, which can maintain a scalable quantum speedup in the face of noise and modest control precision. Specifically, we consider a modification of flux qubit-based quantum annealing which includes low-frequency oscillations in the directions of the transverse field terms as the system evolves. We show that this method produces a quantum speedup for finding ground states in the Grover problem and quantum random energy model, and thus should be widely applicable to other hard optimization problems which can be formulated as quantum spin glasses. Further, we explore three realistic noise channels and show that the speedup from RFQA is resilient to 1/ f -like local potential fluctuations and local heating from interaction with a sufficiently low temperature bath. Another noise channel, bath-assisted quantum cooling transitions, actually accelerates the algorithm and may outweigh the negative effects of the others. We also detail how RFQA may be implemented experimentally with current technology.
54.5: Holographic Screens for 3 Dimensional Image Projection (2000)

Abstract A full color transmission type holographic screen having a size of 40cm × 60cm are developed recently at Korea Institute of Science and Technology. This screen can be operated in reflection mode by adding a mirror at its back. This operation extends viewing angle of the screen to be more than 30degree. This wide viewing angle permits the screen to be operated in viewer tracking regime. By mosaicking the screens, a 120cm × 80cm screen is made. The mosaicked screen shows a good image performance.
The deubiquitylase USP10 regulates integrin β1 and β5 and fibrotic wound healing (2017)

Scarring and fibrotic disease result from the persistence of myofibroblasts characterized by high surface expression of αv integrins and subsequent activation of the transforming growth factor β (TGFβ) proteins; however, the mechanism controlling their surface abundance is unknown. Genetic screening revealed that human primary stromal corneal myofibroblasts overexpress a subset of deubiquitylating enzymes (DUBs), which remove ubiquitin from proteins, preventing degradation. Silencing of the DUB USP10 induces a buildup of ubiquitin on integrins β1 and β5 in cell lysates, whereas recombinant USP10 removes ubiquitin from these integrin subunits. Correspondingly, the loss and gain of USP10 decreases and increases, respectively, αv/β1/β5 protein levels, without altering gene expression. Consequently, endogenous TGFβ is activated and the fibrotic markers alpha-smooth muscle actin (α-SMA) and cellular fibronectin (FN-EDA) are induced. Blocking either TGFβ signaling or cell-surface αv integrins after USP10 overexpression prevents or reduces fibrotic marker expression. Finally, silencing of USP10 in an <i>ex vivo</i> cornea organ culture model prevents the induction of fibrotic markers and promotes regenerative healing. This novel mechanism puts DUB expression at the head of a cascade regulating integrin abundance and suggests USP10 as a novel antifibrotic target.
Receptor Agonism and Antagonism of Dietary Bitter Compounds (2011)

Food contains complex blends of structurally diverse bitter compounds that trigger bitterness through activation of one or more of the ∼25 human TAS2 bitter taste receptors. It remains unsolved, however, whether the perceived bitterness of binary bitter-compound mixtures can be considered an additive function of all bitter-inducing chemicals in the mouth, suggesting that little mutual interaction takes place among bitter substances or if mixture suppression and synergism occurs. Here we report on two natural sesquiterpene lactones from edible plants, which stimulate distinct sets of hTAS2Rs in transfected cells. Both chemicals also robustly inhibit different but overlapping subsets of agonist-activated hTAS2Rs. These findings demonstrate that mixtures of bitter compounds, because they normally occur in human foodstuff, likely elicit bitter perception in a complex and not in a merely additive manner. An unexpected implication of this discovery is that, during evolution, the naturally occurring bitter taste receptor antagonists have shaped some of the pharmacological properties of the receptors, such as overlapping recognition profiles and breadth of tuning.
A 2-Transistor Sub-1V Low Power Temperature Compensated CMOS Voltage Reference (2014)

This paper presents the design of a CMOS sub-1V voltage reference using a 2-transistor Self-Cascode MOSFET structure able to get low power consumption, temperature compensation, and small area. An efficient design procedure applied to this simple topology relying on NMOS transistors with different threshold voltages allows attaining large immunity against bias current and supply voltage variations. Besides that, the two transistors can operate in weak, moderate, or strong inversion making the design flexible in terms of area and power consumption. Implemented in a 0.18μm standard CMOS technology, the circuit provides a 400mV voltage reference with a variation of ±0.18% from -20°C to 75°C (or less than 15ppm/°C), operates from 3.6V down to 800mV while biased with a 5nA resistor-less PTAT current source that varies ±30% over PVT, and consumes less than 20nA. The complete circuit including the current source and the 2-transistor Self-Cascode MOSFET occupies an area of 0.01mm2.
Induction of CspA, an <i>E. coli</i> major cold‐shock protein, upon nutritional upshift at 37 °C (2001)

Background The synthesis of CspA, the major cold‐shock protein of Escherichia coli , is dramatically induced upon cold shock. It was recently reported that there is massive presence of CspA under nonstress conditions, and it is thus claimed that CspA as the cold‐shock protein is a misnomer . Results Here, we re‐examined and confirmed that CspA is induced upon culture dilution at 37 °C. However, its induction level is one‐sixth of the cold‐shock‐induced level, clearly indicating that the major stress that induces CspA is cold shock. It was further found that CspA induction can be achieved not only by culture dilution but also by the simple addition of nutrients, and that it was almost completely abolished in the presence of rifampicin or nalidixic acid. Nutritional upshift causes the induction of only CspA but not other cold‐shock‐inducible CspA homologues. The amount of cspA mRNA rapidly and transiently increased by culture dilution, but its stability was not significantly changed . Conclusions These results suggest that CspA is a nutritional‐upshift stress protein as well as a cold‐shock stress protein, and that CspA induction following nutritional upshift may be due to transcriptional activation .
Selective Growth and Integration of Silver Nanoparticles on Silver Nanowires at Room Conditions for Transparent Nano-Network Electrode (2014)

Recently, metal nanowires have received great research interests due to their potential as next-generation flexible transparent electrodes. While great efforts have been devoted to develop enabling nanowire electrodes, reduced contact resistance of the metal nanowires and improved electrical stability under continuous bias operation are key issues for practical applications. Here, we propose and demonstrate an approach through a low-cost, robust, room temperature and room atmosphere process to fabricate a conductive silver nano-network comprising silver nanowires and silver nanoparticles. To be more specific, silver nanoparticles are selectively grown and chemically integrated in situ at the junction where silver nanowires meet. The site-selective growth of silver nanoparticles is achieved by a plasmon-induced chemical reaction using a simple light source at very low optical power density. Compared to silver nanowire electrodes without chemical treatment, we observe tremendous conductivity improvement in our silver nano-networks, while the loss in optical transmission is negligible. Furthermore, the silver nano-networks exhibit superior electrical stability under continuous bias operation compared to silver nanowire electrodes formed by thermal annealing. Interestingly, our silver nano-network is readily peeled off in water, which can be easily transferred to other substrates and devices for versatile applications. We demonstrate the feasibly transferrable silver conductive nano-network as the top electrode in organic solar cells. Consequently, the transparent and conductive silver nano-networks formed by our approach would be an excellent candidate for various applications in optoelectronics and electronics.