gebhart/patrepeval huggingface dataset:
Monoallelic expression and methylation of imprinted genes in human and mouse embryonic germ cell lineages (2002)

Imprinting is an epigenetic modification leading to monoallelic expression of some genes, and disrupted imprinting is believed to be a barrier to human stem cell transplantation, based on studies that suggest that epigenetic marks are unstable in mouse embryonic germ (EG) and embryonic stem (ES) cells. However, stem cell imprinting has not previously been examined directly in humans. We found that three imprinted genes, TSSC5, H19, and SNRPN, show monoallelic expression in in vitro differentiated human EG-derived cells, and a fourth gene, IGF2, shows partially relaxed imprinting at a ratio from 4:1 to 5:1, comparable to that found in normal somatic cells. In addition, we found normal methylation of an imprinting control region (ICR) that regulates H19 and IGF2 imprinting, suggesting that imprinting may not be a significant epigenetic barrier to human EG cell transplantation. Finally, we were able to construct an in vitro mouse model of genomic imprinting, by generating EG cells from 8.5-day embryos of an interspecific cross, in which undifferentiated cells show biallelic expression and acquire preferential parental allele expression after differentiation. This model should allow experimental manipulation of epigenetic modifications of cultured EG cells that may not be possible in human stem cell studies.
Surface-enhanced copper bonding wire for LSI (2009)

There is growing interest in Cu wire bonding for LSI interconnection due to cost savings and better electrical and mechanical properties. Cu bonding wires, in general, are severely limited in their use compared to Au wires; such as wire oxidation, lower bondability, forming gas of N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> +5%H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , and lower reliability. It is difficult for conventional bare Cu wires to achieve the target of LSI application. A surface-enhanced Cu wire (EX1) has been developed. It is a Pd-coated Cu wire and has many advantages compared to bare Cu wires. Stitch strength was much better under fresh conditions and maintained without any deterioration after being stored in air for a prolonged period of time. EX1 had a lifetime of over 90 days in air, although it was 7 days for the bare Cu wire. Spherical balls were formed with pure N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (hydrogen-free), whereas the bare Cu produced off-center balls. Cost-effective and secure gas, pure N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> was only available for EX1. The reliability for Cu wire bonding under conditions of high humidity was investigated in pressure cooker test (PCT). The lifetime for EX1 and the bare Cu was over 800 h and 250 h, respectively. Humidity reliability was significantly greater for EX1. Continuous cracking was formed at the bond interface for the bare Cu wire, although there was no cracking for EX1. Corrosion-induced deterioration would be the root cause of failure for bare Cu wires in PCT. EX1 improves the bond reliability by controlling diffusion at the bond interface. The excellent performance of Pd-coated Cu wire, EX1 is comparable with Au wires and suitable for LSI packaging.
Ebulitins: A new family of type 1 ribosome‐inactivating proteins (rRNA <i>N</i>‐glycosidases) from leaves of <i>Sambucus ebulus</i> L. that coexist with the type 2 ribosome‐inactivating protein ebulin 1 (1995)

A new family of single chain (type 1) ribosome-inactivating proteins (RIPs), that we have named ebulitins, have been found in mature leaves of Sambucus ebulus L., a caprifoliaceae plant also known to contain a non-toxic two chain (type 2) RIP named ebulin I in its leaves. Ebulitins are basic proteins of M(r) 32,000, 29,000 and 29,000 for ebulitins alpha, beta and gamma, respectively. The simultaneous presence of different basic type 1 and acidic type 2 RIPs in the same plant and in the same tissue is described here for the first time and opens a new door in research into RIPs.
Plasminogen activator inhibitor-1 is locked in active conformation and polymerizes upon binding ligands neutralizing its activity (2006)

Plasminogen activator inhibitor-1 (PAI-1), a member of the serpin super-family, forms a covalent complex with its target proteinases, such as tissue and urokinase plasminogen activators. Thus, PAI-1 controls the physiological and pathological proteolysis. An abnormal expression of PAI-1 has been observed in different diseases, which can be treated by returning the proteolysis back to normal physiological levels. It has been reported that some PAI-1 inhibitors neutralize its activity by accelerating the conversion of PAI-1 into a latent form. We have found small organic chemicals that also neutralize PAI-1 activity, but by a different mechanism. Using the NBD fluorescent probe [N,N'-dimethyl-N-(acetyl)-N'-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)] incorporated into the reactive center loop (RCL) of PAI-1, we measured the kinetics of conversion from an active to a latent form. Unexpectedly, we found that some inhibitors of PAI-1 arrest this serpin in its active form instead of increasing the speed of conversion. Using docking calculations, we located two possible binding sites for these chemicals. The sites are in proximity of the P1/P1' amino acids of the RCL of PAI-1. Binding in this area can inactivate PAI-1 and additionally create a steric obstacle on the RCL making insertion of this loop between the A3 and A5 strands more difficult; hence abolishing a necessary step in the conversion of this protein into the latent form. Additionally, PAI-1 inhibitors link the RCL of one PAI-1 molecule with the strand 3C and strand 4C or helix A and strand 1B regions of the other PAI-1 molecule aiding polymerization or stabilizing the junction of the two. The polymerization of PAI-1 reduces PAI-1 activity by encapsulating the critical RCL fragment inside the formed PAI-1/PAI-1 polymers.
GB Virus C Replicates in Primary T and B Lymphocytes (2006)

GB virus C (GBV-C) infection is common in humans and may persist for decades, although most infected persons clear the virus and subsequently develop antibodies to the envelope glycoprotein. GBV-C replicates in peripheral blood mononuclear cells (PBMCs) and CD4+ T lymphocytes in vitro, and depletion of CD4+ T lymphocytes has been proposed as the reason for clearance of GBV-C among persons positive for human immunodeficiency virus. We identified GBV-C RNA in purified CD4+ and CD8+ T lymphocytes and CD19+ B lymphocytes removed ex vivo from infected donors and found that GBV-C replicated in vitro in these PBMC subsets, suggesting that GBV-C is a panlymphotropic virus
Low complexity Neighboring Block based Disparity Vector Derivation in 3D-HEVC (2014)

3D-HEVC incorporates advanced inter-view prediction techniques based on more accurately derived disparity vector to better exploit the correlation between objects in different views. The efficient disparity vector derivation method, namely, Neighboring Block based Disparity Vector Derivation (NBDV) provides disparity without accessing any depth information. The NBDV has been developed as a part of the 3D-HEVC in Joint Collaborative Team on 3D Video Coding (JCT-3V) for several meeting cycles, and adopted as a common coding tool used for all the inter-view prediction techniques for high efficient coding of texture views. This paper presents a low complexity NBDV, which is the state-of-the-art disparity vector derivation method in 3D-HEVC.
New bi-prediction techniques for B pictures coding [video coding] (2004)

In the conventional video codec, B pictures usually employ five prediction modes, including bi-prediction, direct prediction, forward prediction, backward prediction and intra modes. Among them, the direct and bi-prediction modes, whose prediction values are achieved from both forward and backward reference pictures, are more efficient in exploiting the temporal correlation between the reference pictures and the current B picture. In addition, the direct mode does not require any bits for coding the motion vectors. Therefore, the blocks coded with direct or bi-predictive mode are usually much more than the other modes. To further take advantage of the bi-prediction, We propose a new bi-predictive coding technique, which can achieve a good tradeoff between the bit-rate saving for motion vector coding and the prediction accuracy. Moreover, we also propose spatial motion vector prediction and motion vector scaling techniques to improve the accuracy of the derived direct mode motion vectors. All these techniques have been adopted in the AVS video coding standard.
The role of group index engineering in series-connected photonic crystal microcavities for high density sensor microarrays (2014)

We experimentally demonstrate an efficient and robust method for series connection of photonic crystal microcavities that are coupled to photonic crystal waveguides in the slow light transmission regime. We demonstrate that group index taper engineering provides excellent optical impedance matching between the input and output strip waveguides and the photonic crystal waveguide, a nearly flat transmission over the entire guided mode spectrum and clear multi-resonance peaks corresponding to individual microcavities that are connected in series. Series connected photonic crystal microcavities are further multiplexed in parallel using cascaded multimode interference power splitters to generate a high density silicon nanophotonic microarray comprising 64 photonic crystal microcavity sensors, all of which are interrogated simultaneously at the same instant of time.
PRACTICAL SYNTHESIS AND POLYMERIZATION OF TRIFLUOROVINYLSILANES. A POSSIBLE PRECURSOR OF POLY(DIFLUOROACETYLENE) (1984)

Abstract An improved procedure for the preparation of trifluorovinylsilanes was established which involved addition of butyllithium to a mixture of chlorosilanes and commercially readily available chlorotrifluoroethylene at −78 to −130 °C, and the resulting monomer was polymerized with a catalyst such as CsF or (R2N)3S+ F2SiMe3− to give black metallic polymer which showed conductivity of 10−9 to 10−10 Ω−1cm−1.
Inclination estimation and balance of robot using Vestibular Dynamic Inclinometer (2010)

Traditionally, the sensor design for Inertial Sensing of Human movement/posture is done using an accelerometer-gyroscope combination while detection of static or dynamic activities is done using uniaxial accelerometers. A single axis accelerometer-gyroscope combination uses sensor fusion along with a Kalman Filter to estimate the inclination. The inclination is obtained by integrating angular velocity and acceleration combinations. Due to imperfect sensors, this leads to magnification of errors and drift over time. The sensor discussed in the paper, called the Vestibular Dynamic Inclinometer (VDI), uses two dual-axis accelerometers and one single axis gyroscope per axis to estimate the inclination. The concept of `equilibrium axis', the axis along which the robot is at equilibrium, is discussed. The inclination angle obtained from the VDI is relative to the equilibrium axis and thus is more desirable as a control input rather than the inclination angle relative to the absolute gravity vector (as obtained from the accelerometer-gyroscope combination). The inclination angle obtained is independent of acceleration experienced by the robot and is not obtained by integration of angular velocity or acceleration unlike traditional designs. The control strategies proposed in the paper are torque control and acceleration control. Torque control requires generation of torque at the point of contact (analogous to the hip and ankle generating balancing torque in humans) and acceleration/postural control requires the acceleration of point of contact (analogous to running in humans) to maintain the body at equilibrium. The paper also proposes Lyapunov based non-linear adaptive controllers for an inverted pendulum(which approximates a human body) for both the control strategies. The controllers guarantee asymptotic stability. Simulations are performed assuming noise in the sensors.
High-Throughput Cell and Tissue Analysis with Enhanced Molecular Coverage by Laser Ablation Electrospray Ionization Mass Spectrometry Using Ion Mobility Separation (2014)

Ambient ionization methods, such as laser ablation electrospray ionization (LAESI), facilitate the direct analysis of unperturbed cells and tissues in their native states. However, the lack of a separation step in these ionization techniques results in limited molecular coverage due to interferences, ion suppression effects, and the lack of ability to differentiate between structural isomers and isobaric species. In this contribution, LAESI mass spectrometry (MS) coupled with ion mobility separation (IMS) is utilized for the direct analysis of protein mixtures, megakaryoblast cell pellets, mouse brain sections, and Arabidopsis thaliana leaves. We demonstrate that the collision cross sections of ions generated by LAESI are similar to the ones obtained by ESI. In various applications, LAESI-IMS-MS allows for the high-throughput separation and mass spectrometric detection of biomolecules on the millisecond time scale with enhanced molecular coverage. For example, direct analysis of mouse brain tissue without IMS had yielded ∼300 ionic species, whereas with IMS over 1 100 different ions were detected. Differentiating between ions of similar mass-to-charge ratios with dissimilar drift times in complex biological samples removes some systematic distortions in isotope distribution patterns and improves the fidelity of molecular identification. Coupling IMS with LAESI-MS also expands the dynamic range by increasing the signal-to-noise ratio due to the separation of isobaric or other interfering ionic species. We have also shown that identification of potential biomarkers by LAESI can be enhanced by using the drift times of individual ions as an additional parameter in supervised orthogonal projections to latent structures discriminant analysis. Comparative analysis of drift time versus mass-to-charge ratio plots was performed for similar tissue samples to pinpoint significant metabolic differences.
Nonuniform Manual Scanning for Rapid Microwave Nondestructive Evaluation Imaging (2012)

Wideband synthetic aperture radar (SAR) technique is a robust imaging tool for microwave and millimeter-wave imaging such as nondestructive evaluation applications. In this paper, we present an alternative method to conventional raster scanning involving manually selected and nonuniformly distributed measurement positions, enabling the production of complete SAR images-potentially using only a fraction of the conventionally required measured data. The user is kept informed throughout the scanning process by a stream of real-time SAR images. Finally, data reconstruction algorithms are used offline to produce high-quality images with considerably lower background noise and image artifacts as compared to the real-time images. We also introduce a novel reconstruction method that uses the components of the SAR algorithm to advantageously exploit the inherent spatial information contained in the data, resulting in a superior data reconstruction and final SAR image. This paper presents the measurement methodology along with the images obtained from three different specimens of increasing geometrical complexity.
Structured microlens arrays for beam shaping (2003)

Structured microlens arrays are used for beam shaping, diffusion, and homogenization, providing the ability to perform complex beam shaping tasks, both intensity control and spatial energy distribution, with high efficiency (mostly limited by surface losses) and without the presence of artifacts such as zero order. Applications include excimer laser beam shaping, display screens, light-control films, and illumination.
Waveform design optimization using bandwidth and energy considerations (2008)

The problem of joint transmitter and receiver design for optimum output performance in the context of detection in the presence of clutter and noise is addressed here by maximizing the receiver output signal power to average interference plus noise ratio ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SINR</i> ) at the specific decision instant. The receiver optimization leads to output <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SINR</i> in terms of the transmit waveform, and transmitter optimization is further carried out subject to energy and bandwidth constraints. The new design proposed here leads to threshold constraints on transmit energy and the overall performance as a function of bandwidth is illustrated here for various target, clutter and noise scenes.
tRNA-mediated transcription antitermination <i>in vitro</i> : Codon–anticodon pairing independent of the ribosome (2002)

Uncharged tRNA acts as the effector for transcription antitermination of genes in the T box family in Bacillus subtilis and other Gram-positive bacteria. Genetic studies suggested that expression of these genes is induced by stabilization of an antiterminator element in the leader RNA of each target gene by the cognate uncharged tRNA. The specificity of the tRNA response is dependent on a single codon in the leader, which was postulated to pair with the anticodon of the corresponding tRNA. It was not known whether the leader RNA–tRNA interaction requires additional factors. We show here that tRNA-dependent antitermination occurs in vitro in a purified transcription system, in the absence of ribosomes or accessory factors, demonstrating that the RNA–RNA interaction is sufficient to control gene expression by antitermination. The tRNA response exhibits similar specificity in vivo and in vitro , and the antitermination reaction in vitro is independent of NusA and functions with either B. subtilis or Escherichia coli RNA polymerase.
Temperature-induced optical phase shifts in fibers (1981)

The static thermal sensitivity of the optical phase in bare and jacketed fibers has been studied both analytically and experimentally. Taking into account the exact fiber composition and geometry, the strains have been determined from the thermally induced stresses using the appropriate boundary conditions, and the resulting phase shift has been calculated. The results of this analysis are found to be in agreement with experimental results obtained from measurements employing a Mach-Zehnder fiber interferometer.
A novel approach for the improvement of open circuit voltage and fill factor of InGaAsSb/GaSb thermophotovoltaic cells (1998)

Heterojunction n-Al0.25Ga0.75As0.02Sb0.98/p-In0.16Ga0.84As0.04Sb0.96 thermophotovoltaic (TPV) cells were grown by molecular-beam epitaxy on n-GaSb-substrates. In the spectral range from 1 μm to 2.1 μm these cells, as well as homojunction n-p-In0.16Ga0.84As0.04Sb0.96 cells, have demonstrated internal quantum efficiencies exceeding 80%, despite about a 200 meV barrier in the conduction band at the heterointerface. Estimation shows that the thermal emission of the electrons photogenerated in p-region over this barrier can provide high efficiency for hetero-cells if the electron recombination time in p-In0.16Ga0.84As0.04Sb0.96 is longer than 10 ns. Keeping the same internal efficiency as homojunction cells, hetero-cells provide a unique opportunity to decrease the dark forward current and thereby increase open circuit voltage (Voc) and fill factor at a given illumination level. It is shown that the decrease of the forward current in hetero-cells is due to the lower recombination rate in n-type wider-bandgap space-charge region and to the suppression of the hole component of the forward current. The improvement in Voc reaches 100% at illumination level equivalent to 1 mA/cm2 and it decreases to 5% at the highest illumination levels (2–3 A/cm2), where the electron current component dominates in both the homo- and heterojunction cells. Values of Voc as high as 310 meV have been obtained for a hetero-cell at illumination levels of 3 A/cm2. Under this condition, the expected fill factor value is about 72% for a hetero-cell with improved series resistance. The heterojunction concept provides excellent prospects for further reduction of the dark forward current in TPV cells.
Spin-Orbit Logic with Magnetoelectric Nodes: A Scalable Charge Mediated Nonvolatile Spintronic Logic (2015)

As nanoelectronics approaches the nanometer scale, a massive effort is underway to identify the next scalable logic technology beyond Complementary Metal Oxide Semiconductor (CMOS) computing. Such computing technology needs to improve switching energy & delay at reduced dimensions, allow improved interconnects and provide a complete logic/memory family. However, a viable beyond-CMOS logic technology has remained elusive. Here, we propose a scalable spintronic logic device which operates via spin-orbit transduction combined with magneto-electric switching. The proposed Magneto-Electric Spin Orbit (MESO) logic enables a new paradigm to continue scaling of logic performance to near thermodynamic limits for GHz logic (100 kT switching energy at 100 ps delay). The proposed MESO devices scale strongly and favorably with critical dimensions of the device, showing a cubic dependence of switching energy on size, (E_m proportional to W^3), and square dependence on voltage (E_m proportional to V^2). The excellent scaling is obtained thanks to the properties of the spin orbit effects (e.g. Inverse Spin Hall Effect (ISHE) and Inverse Rashba-Edelstein Effect (IREE)) and the dependence of capacitance on size. The operating voltages for these devices are predicted to be < 100 mV allowing a significant jump ahead of historic trends of scaling voltage with size and corresponding reduction of energy. Interconnect resistance is a critical obstacle for scaling beyond 10 nm dimensions. We project a less detrimental impact of interconnect resistance and show that MESO logic is amenable for highly resistive interconnects (100 uOhm.cm-1 mOhm.cm) which opens a possibility to use nano-metallic (width < bulk electron mean free path) or doped semiconducting wires (width<5 nm). A scalable, CMOS compatible, non-volatile logic family proposed here may enable the next multi-generational scaling of computing devices.