gebhart/patrepeval huggingface dataset:
Computational analysis of the synergy among multiple interacting genes (2007)

Diseases such as cancer are often related to collaborative effects involving interactions of multiple genes within complex pathways, or to combinations of multiple SNPs. To understand the structure of such mechanisms, it is helpful to analyze genes in terms of the purely cooperative, as opposed to independent, nature of their contributions towards a phenotype. Here, we present an information-theoretic analysis that provides a quantitative measure of the multivariate synergy and decomposes sets of genes into submodules each of which contains synergistically interacting genes. When the resulting computational tools are used for the analysis of gene expression or SNP data, this systems-based methodology provides insight into the biological mechanisms responsible for disease.
A polarized liquid crystal lens with electrically-switching mode and optically-written mode (2015)

A polarized liquid crystal (LC) lens composed of a LC layers as a polarization switch and a liquid crystal and polymer composites lens (LCPC lens) is demonstrated with electrically switching (ES) mode and optically rewritten (ORW) mode. The lens power of LCPC lens is related to a polarization state of light modulated by the LC layer whose orientations are manipulated either electrically or optically. As a result, the LC lens is not only electrically switchable, but also optically rewritable. Each mode, ES mode or ORW mode, exhibits two discrete lens powers (-1.39 Diopter and +0.7 Diopter). The demonstrated aperture size is 10 mm. The detail optical mechanism is also discussed. The Modulation Transfer Function (so-called MTF) of the lens is measured as well. In addition, the image performance and the dispersion of the LC lens are investigated. Such a polarized LC lens could be a special switch in optical systems due to dual operation modes.
Handling data skew in parallel joins in shared-nothing systems (2008)

Parallel processing continues to be important in large data warehouses. The processing requirements continue to expand in multiple dimensions. These include greater volumes, increasing number of concurrent users, more complex queries, and more applications which define complex logical, semantic, and physical data models. Shared nothing parallel database management systems [16] can scale up horizontally by adding more nodes. Most parallel algorithms, however, do not take into account data skew. Data skew occurs naturally in many applications. A query processing skewed data not only slows down its response time, but generates hot nodes, which become a bottleneck throttling the overall system performance. Motivated by real business problems, we propose a new join geography called PRPD (Partial Redistribution & Partial Duplication) to improve the performance and scalability of parallel joins in the presence of data skew in a shared-nothing system. Our experimental results show that PRPD significantly speeds up query elapsed time in the presence of data skew. Our experience shows that eliminating system bottlenecks caused by data skew improves the throughput of the whole system which is important in parallel data warehouses that often run high concurrency workloads.
Molecular Characterization of Plasmid from Bifidobacterium longum (2003)

The complete nucleotide sequence of a plasmid, pMG1, isolated from Bifidobacterium longum MG1 has been determined. This plasmid, composed of 3,862 base pairs with 65.1% of G+C content. harbors two major open reading frames (ORF) encoding putative proteins of 29 kDa (ORF I) and 71 kDa (ORF II). ORF I showed relatively high amino acid sequence homology with replication proteins of other plasmids from Gr Im-positive and -negative bacteria. Upstream of ORF I, four sets of tandem repeat sequences resembling the iteron structure of related plasmids were found. S1 endonuclease treatment and Southern blot analysis revealed that pMG1 accumulates single-stranded DNA (ssDNA) intermediate, which indicate i the rolling circle replication (RCR) mechanism of this plasmid. Homology search indicated that ORF II encodes plasmid mobilization protein, and the presence of highly conserved oriT sequence in the upstream of this gene supported this assumption. RT-PCR showed that only ORF I is expressed in vivo. Based on these results, pMG 1 was exploited to construct a shuttle vector, pBES2. It was successfully transformed into Bifidobacterium and maintained stably.
Robust stereo vision and calibration methodology for accurate three-dimensional digital image correlation measurements on submerged objects (2008)

The effect of optical refraction at an interface between optically dissimilar media is modelled in order to apply the principles of three-dimensional digital image correlation (DIC) to measure deformations on submerged objects accurately. Using an analytical formulation for refraction at an interface, a non-linear solution approach is developed to perform stereo calibration. The proposed method incorporates a simplified parametric representation for the orientation and position of an interface(s), accounting explicitly for the effects of refraction at all such interfaces in the path of each stereo camera. Separating the calibration process into two parts, a modified bundle adjustment process with an updated Levenburg—Marquardt (LM) non-linear optimization algorithm is employed to determine (a) intrinsic and extrinsic stereo camera parameters without interface refraction and (b) orientation and position of each planar interface. Detailed simulations demonstrate the efficiency, accuracy, and stability of the methodology when using multiple images of a grid pattern undergoing general rigid body motion, even in the presence of Gaussian noise in the sensor plane measurements, providing a robust framework for practical implementation of the methodology for submerged object measurements.
Virtual sensor for real-time estimation of the vehicle sideslip angle (2019)

Purpose The vehicle sideslip angle is an important state of vehicle lateral dynamics and its knowledge is crucial for the successful implementation of advanced driver-assistance systems. Measuring the vehicle sideslip angle on a production vehicle is challenging because of the exorbitant price of a physical sensor. This paper aims to present a novel framework for virtually sensing/estimating the vehicle sideslip angle. The desired level of accuracy for the estimator is to be within +/− 0.2 degree of the actual sideslip angle of the vehicle. This will make the precision of the proposed estimator at par with expensive commercially available sensors used for physically measuring the vehicle sideslip angle. Design/methodology/approach The proposed estimator uses an adaptive tire model in conjunction with a model-based observer. The performance of the estimator is evaluated through experimental tests on a rear-wheel drive vehicle. Findings Detailed experimental results show that the developed system can reliably estimate the vehicle sideslip angle during both steady state and transient maneuvers, within the desired accuracy levels. Originality/value This paper presents a novel framework for vehicle sideslip angle estimation. The presented framework combines an adaptive tire model, an unscented Kalman filter-based axle force observer and data from tire mounted sensors. Tire model adaptation is achieved by making extensions to the magic formula, by accounting for variations in the tire inflation pressure, load, tread-depth and temperature. Predictions with the adapted tire model were validated by running experiments on the Flat-Trac® machine. The benefits of using an adaptive tire model for sideslip angle estimation are demonstrated through experimental tests. The performance of the observer is satisfactory, in both transient and steady state maneuvers. Future work will focus on measuring tire slip angle and road friction information using tire mounted sensors and using that information to further enhance the robustness of the vehicle sideslip angle observer.
Robust adaptive numerical compensation for friction and force ripple in permanent-magnet linear motors (2002)

This paper describes a robust adaptive compensation method for friction and force ripple present in the dynamics of permanent-magnet linear motors. The method is used in ultraprecise positioning applications. The compensation algorithm consists of a PID component and an adaptive component for estimating friction and force ripple. The adaptive component is continuously refined on the basis of just prevailing input and output signals. Computer simulations and real-time experimental results verify the effectiveness of the proposed scheme for high-precision motion trajectory tracking.
Ultralow-threshold microcavity Raman laser on a microelectronic chip (2004)

Using ultrahigh-Q toroid microcavities on a chip, we demonstrate a monolithic microcavity Raman laser. Cavity photon lifetimes in excess of 100 ns combined with mode volumes typically of less than 1000 (microm)3 significantly reduce the threshold for stimulated Raman scattering. In conjunction with the high ideality of a tapered optical fiber coupling junction, stimulated Raman lasing is observed at an ultralow threshold (as low as 74 microW of fiber-launched power at 1550 nm) with high efficiency (up to 45% at the critical coupling point) in good agreement with theoretical modeling. Equally important, the wafer-scale nature of these devices should permit integration with other photonic, mechanical, or electrical functionality on a chip.
CloudBridge (2011)

Data center consolidation has emerged as an important tool to improve the hardware utilization of data centers and reduce delivery costs. Consolidation has traditionally used virtualization to consolidate multiple workloads as different virtual machines running on a shared physical server. Consolidation leads to reduction in the hardware and the facilities cost (e.g., space and energy) but does not reduce software maintenance cost, which is often proportional to the number of instances of the software. The ever-increasing proportion of software cost (labour and license) in data center operations make software consolidation an important tool in data centers. In this work, we investigate the problem of data center consolidation with the goal of minimizing the total costs in running a data center. We build on existing work on virtualization-driven hardware consolidation and software consolidation to design CloudBridge that reduces total data center cost. CloudBridge uses an algorithm for finding the optimal software consolidation level for workloads consolidated on a physical server. Further, it intelligently optimizes the tradeoff between hardware and software consolidation to identify suitable workloads that should be co-located on a shared physical server. We present both theoretical and experimental evidence that establishes the effectiveness of CloudBridge.
<title>Novel beam-steering micromirror device</title> (1998)

A novel type of light modulating micromirror device has been designed and fabricated. A unique hinge structure provides the device with the potential for modulating both the phase and amplitude of light signals, while its high thermal conductivity makes the device amenable to high power laser applications. An extremely high fill factor can be attained since the hinges lie entirely beneath the mirror surface. This hidden hinge structure is comprised of a single level and therefore involves a simple fabrication process. Micromirrors with dimensions ranging from 100 micrometers X 100 micrometers to 300 micrometers X 300 micrometers with maximum deflection angles from 2 degree(s) to 4 degree(s) were fabricated. The devices were characterized in terms of the reflecting surface optical quality, the operational modes attainable, the critical voltages (as low as 15 volts), and the response time (as short as 125 microsecond(s) ).
Abstract 862: Atypical protein kinase c inhibitors can repress epithelial to mesenchymal transition (type III) in malignant melanoma (2017)

Abstract Melanoma is a type of cancer occurs in melanocytes. Approximately 90% of melanoma occurs in skin (cutaneous melanoma) but can rarely arise from the mucosal surfaces or areas which neural cells migrate. Examples are eye, intestine and mouth [Eur. J. Cancer, 69: 39-42 (2016)]. 76,380 of new cases and 10,130 number of deaths are expected in 2016 in the USA due to melanoma [http://seer.cancer.gov/statfacts/html/melan.html (11/05/2016)]. Atypical PKCs contains two structurally and functionally distinct isozymes in human which are PKC-ι (iota) and PKC-ζ (zeta). They are believed to be involved in cell cycle progression, tumorigenesis, cell survival and cell migration. We believe that atypical PKCs play an important role in cell motility of melanoma by involving the signaling pathways which induces EMT-type III (Epithelial to Mesenchymal Transition). In normal melanocytes, PKC-ζ was found in low levels and PKC-ι was not detected. But both proteins are detected in very high levels in malignant melanoma [Melenoma Res. 12:201-209 (2002)]. In the current study, we have investigated the effects of novel atypical PKC inhibitors [4-(5-amino-4-carbamoylimidazol-1-yl)-2, 3-dihydroxycyclopentyl] methyl dihydrogen phosphate (ICA-1) which is specific to PKC-ι and 8-hydroxy-1, 3, 6-naphthalenetrisulfonic acid (Compound-50) which is specific to PKC-ζ on the cell proliferation, apoptosis and cell migration of two malignant melanoma cell lines (SK-MEL-2 and MeWo) compared to a normal melanocyte cell line (PCS-200-013). We showed that both inhibitors can decrease the levels of total and phosphorylated levels of PKC-ζ and PKC-ι. Furthermore, both inhibitors increased the levels of E-cadherin and decreased the levels of Vimentin which is a mesenchymal marker associated with EMT. Treatments with inhibitors altered the levels of CD44, a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion, migration and tumor cell homing during metastasis. These results suggest that both PKC-ι and PKC-ζ are involved in signaling pathways which upregulate EMT and which can be effectively suppress using ICA-1 and Compound-50. Furthermore we established that treatment with ICA-1/Compound-50 induced apoptosis as shown by increasing Caspase-3 levels and decreasing Bcl-2 levels. Citation Format: Wishrawana Sarathi Ratnayake, Mildred Acevedo-Duncan. Atypical protein kinase c inhibitors can repress epithelial to mesenchymal transition (type III) in malignant melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 862. doi:10.1158/1538-7445.AM2017-862
ChemInform Abstract: ANTIMYCOTIC IMIDAZOLES. PART 4. SYNTHESIS AND ANTIFUNGAL ACTIVITY OF KETOCONAZOLE, A NEW POTENT ORALLY ACTIVE BROAD‐SPECTRUM ANTIFUNGAL AGENT (1980)

Abstract Das Dichloraceto‐ phenon (I) wird über das Ketal (III) in das Bromid (IV) umgewandelt, das zum Ester (V) führt.
Nanomycins, new antibiotics produced by a strain of Streptomyces. III. A new component, nanomycin C, and biological activities of nanaomycin derivatives. (1975)

A new component, nanaomycin C, has been isolated from culture medium of Streptomyces rosa var. notoensis, which had been found to produce nanaomycins A and B. Nanaomycin C is an amide of nanaomycin A. Biological activities of nanaomycin C and several derivatives of nanaomycin A are also shown. Acetylnanaomycin A exhibits as strong activities against Gram-positive bacteria, fungi and Mycoplasma gallisepticum as nanaomycin A.
Harnessing tissue resident memory T cells to combat solid tumors (2017)

Abstract The immunosuppressive tumor microenvironment is barrier to successful cancer therapies. Newly discovered tissue resident memory CD8+ T cells (TRM) function to create a potent immunostimulatory environment to protect against local reinfection. As TRM are present in abundance in nearly every tissue and can be triggered by cognate peptide alone, without adjuvant, we tested whether we could hijack infection-specific TRM in tumors to reverse the immunosuppressive tumor microenvironment and enhance existing immunotherapies. Mice with established vesicular stomatitis virus (VSV)-specific skin TRM were challenged with the transplantable B16 melanoma cell line. We find VSV-specific CD8+ T cells within established tumors and by 12 hours of cognate peptide delivery, these cells upregulate IFNγ, CD25, and granzyme B. This led to 1) a 10-fold increase in intratumoral NK cells, 2) bystander memory CD8+ T cell recruitment to the tumor, 3) tumor NK cell and CD8+ T cell activation through granzyme B upregulation and 4) DC activation in tumor draining lymph nodes through CCR7 and CD86 upregulation. Ongoing studies using transplantable and autochthonous melanoma models are testing whether TRM immunotherapy synergizes with CAR T cell and checkpoint blockade immunotherapies for eradication of recalcitrant tumors. These results demonstrate proof of principal efficacy for exploiting infection-specific TRM as a tumor immunotherapy.
Multi-Selective One Dimensional Proton NMR Experiments for Rapid Screening and Binding Affinity Measurements (2003)

High-throughput ligand-based proton NMR screening performed in the presence of a spy molecule and a control molecule is a valuable tool for identifying drug leads. A limitation of the technique is represented by the severe overlap encountered in the screening of large chemical mixtures. An approach for overcoming this overlap problem is the use of multi-selective R(1) filtered and COSY or TOCSY experiments. Application of this methodology to compounds binding to the Sudlow site I of human serum albumin is presented. The screening is performed by simply monitoring the intensity of two signals. The precise measurement of the relative intensity of the two resonances permits determination of the binding constant of the NMR-hit. For a simple competition binding mechanism, the rapidly-derived NMR binding constants are in good agreement with the values derived from full-titration ITC and fluorescence spectroscopy measurements.
Progress in understanding structure-function relationships of human thyroid-stimulating hormone (1997)

This paper summarizes current advances in the structure-function relationships of human thyroid-stimulating hormone (TSH) in the context of studies on structurally related gonadotropins. Investigators have now identified specific domains in both protein and carbohydrate components of human TSH that play distinct roles in the synthesis, bioactivity, and metabolic clearance of human TSH. The principles revealed in such studies are essential to understand mechanisms of receptor activation and permit design of novel analogues with potential clinical applications. In particular, superagonists of human TSH and human chorionic gonadotropin have been recently developed using a rational approach combining evolutionary considerations, sequence comparisons, and homology modeling. Such analogues with major increases in receptor-binding affinity and signal transduction are unique tools for studies of both thyroidal and extrathyroidal actions of TSH. Moreover, similar strategies may be used to design analogues of other members of the cystine knot growth factor superfamily.
Microstructural studies of top and bottom magnetic tunnel junctions (2001)

High-resolution electron microscopy has been used to study the microstructural properties of top and bottom magnetic tunnel junctions. Different physical properties have been found for the two configurations, and they have been interpreted in terms of microstructural features. All physical parameters favor the bottom configuration except for the coupling field, which is higher for the bottom structure. This latter result has been explained by the more pronounced roughness at the interfaces between the electrodes and the insulator film.
Synthesis of superconducting La2−<i>x</i>Sr<i>x</i>CaCu2O6 using O2-hot-isostatic-pressing techniques (1991)

Superconducting 326 samples, La2−xSrxCaCu2Oz with x=0.2 and 0.4, which exhibited superconducting onsets at temperatures (Tonc’s) higher than 40 K were successfully synthesized using hot-isostatic-pressing (HIP) techniques. As starting materials, powders of conventional carbonates (SrCO3 and CaCO3) and oxides (La2O3 and CuO) were employed. Sintering of the samples was made at a variety of temperatures (Ts) for 72 h in flowing O2 gas (of 1 atm). The sintered samples were post-annealed at various temperatures (Ta) for 6 h in a mixture of 80% Ar gas and 20% O2 gas of the total pressure of 1000 atm by means of HIP techniques. Optimum combinations of Ts and Ta were determined for obtaining superconducting samples. Single-phase samples were obtained only for the composition La1.8Sr0.2CaCu2Oz for which the oxygen content, z, was determined to be 6.01±0.01 by coulometric titration. It was concluded that Ta was a crucially important factor for obtaining superconducting 326 phase with Tonc ≳ 40 K, that is, Ta ≳ 970 °C was required (for 6-h HIP annealing). It was demonstrated that a long HIP annealing was necessary to obtain a significant volume fraction for the superconducting 326 phase.
Electrical and vibration analysis of pre-compressed and pre-deflected laminated piezoelectric actuators (2002)

The electrical and vibration characterization of a novel piezoelectric actuator is performed. The actuator is a rectangular laminated flat plate with two opposite sides simply supported and two others free. Under an axial compression from the supports, the plate deforms into a stressed shallow shell. Electrical high frequency harmonic signals within relatively low-frequency "bursts" are applied to the piezoelectric layers. Depending on the precompression, pre-deflection, frequency and magnitude of electrical input, the tunable actuator can exhibit frequency/mode-controlled high-force over large area vibrations with intense displacement jumps. Novel SDoF model and simplified 1-D models have been developed. Theoretical results are compared with experimental observations and measurements.
A Steam‐Augmented Gas Turbine with Reheat Combustor for Surface Ships (1994)

ABSTRACT The steam‐augmented gas turbine (SAGT) concept has attracted attention because of its benign level of NO x emission, its increased fuel efficiency, and significant, cost‐effective increments of output power, particularly when moisture injection is increased to levels approaching 50% of air flow. Such high levels of moisture consumption distinguish the SAGT engine from commercial steam‐injected gas turbines where steam flow may be less than 15% of air flow. At the high 50% levels, the SAGT burner would operate near stoichiometric combustion ratios with specific powers exceeding 570 hp‐sec/lb. In a previous study, an intercooled, steam‐augmented, gas‐turbine concept was examined for its applicability in the Navy's DDG‐51 class ship environments, which achieves efficiencies approaching the Navy's intercooled regenerative (ICR) engine, and an impressive compactness that arises from the high specific power of steam and low air consumption. A newer SAGT engine concept, described herein, dispenses with the intercooler, but adds a low‐pressure reheat combustor. At the most efficient operating points, the efficiency of this new reheat SAGT engine at 43% exceeds the efficiency of the ICR engine, while exhibiting the compactness of the previous SAGT concept. Tabular and graphical simulation data comparing the baseline engine, with the ICR and other engine simulations, show that the maximum efficiency of the new SAGT engine occurs at powers required for cruising speeds. Since a DDG operates near cruise conditions for the majority of its mission time, a SAGT plant uses less fuel than the ICR plant. Moreover, since it eliminates the intercooler, developmental work on member elements, largely derivable from off‐the‐shelf components, is reduced. Even with conservative cost estimates, the SAGT plant is quite competitive on a first‐acquisition cost basis with the current gas turbine in the fleet.