gebhart/patrepeval huggingface dataset:
Variations in Amino Acid Composition of Antisense Peptide-Phosphorodiamidate Morpholino Oligomer Affect Potency against <i>Escherichia coli</i> In Vitro and In Vivo (2008)

The potency of antisense peptide-phosphorodiamidate morpholino oligomers (PPMOs) was improved by varying the peptide composition. An antisense phosphorodiamidate morpholino oligomer (PMO) complementary to the mRNA of the essential gene acpP (which encodes the acyl carrier protein required for lipid biosynthesis) in Escherichia coli was conjugated to the 5' ends of various cationic membrane-penetrating peptides. Each peptide had one of three repeating sequence motifs: C-N-N (motif 1), C-N (motif 2), or C-N-C (motif 3), where C is a cationic residue and N is a nonpolar residue. Variations in the cationic residues included arginine, lysine, and ornithine (O). Variations in the nonpolar residues included phenylalanine, valine, beta-alanine (B), and 6-aminohexanoic acid (X). The MICs of the PPMOs varied from 0.625 to >80 microM (about 3 to 480 microg/ml). Three of the most potent were the (RX)(6)B-, (RXR)(4)XB-, and (RFR)(4)XB-AcpP PMOs, which were further tested in mice infected with E. coli. The (RXR)(4)XB-AcpP PMO was the most potent of the three conjugates tested in mice. The administration of 30 microg (1.5 mg/kg of body weight) (RXR)(4)XB-AcpP PMO at 15 min postinfection reduced CFU/ml in blood by 10(2) to 10(3) within 2 to 12 h compared to the numbers in water-treated controls. All mice treated with 30 microg/dose of (RXR)(4)XB-AcpP PMO survived infection, whereas all water-treated mice died 12 h postinfection. The reduction in CFU/ml in blood was proportional to the dose of PPMO from 30 to 300 microg/ml. In summary, the C-N-C motif was more effective than the other two motifs, arginine was more effective than lysine or ornithine, phenylalanine was more effective than 6-aminohexanoic acid in vitro but not necessarily in vivo, and (RXR)(4)XB-AcpP PMO reduced bacterial infection and promoted survival at clinically relevant doses.
High-contrast waveguides in sputtered pure TeO,_2 glass thin films (2008)

We present a technological approach to the realization of channeled optical waveguides, starting from reactively sputtered tellurite glass thin films, grown on silica-coated 4" Si wafers. In particular, optical lithographic process and etching recipes have been developed to overcome the solubility of TeO(2) films in aqueous solutions, and to process them into high-index contrast structures with minimized post-etch roughness. Optical tests on preliminary rib waveguide geometries feature 6.3 dB/cm propagation loss for fundamental TE mode at lambda = 1.5 microm.
The immunity arising from continuous low-level infection with <i>Eimeria maxima</i> and <i>Eimeria acervulina</i> (1976)

Chicks were given daily inoculations of 1 or 5 oocysts of Eimeria maxima or 5 or 20 oocysts of E. acervulina. The inoculations ceased after 20 days with E. maxima or 25 days with E. acervulina when oocyst production had stopped. The responses to subsequent heavy challenges showed that with both species the immunity arising from the serial inoculations was stronger and/or more enduring than that produced by single inoculations of comparable numbers of oocysts.
TinyTPM: A lightweight module aimed to IP protection and trusted embedded platforms (2011)

Currently, embedded system implementations are increasingly exploiting reconfigurable devices such as Field Programmable Gate Arrays (FPGAs). Due to the volatile nature of SRAM-based FPGAs it is necessary to secure such systems against intellectual property (IP) theft and overproduction. Additionally, the trustworthy operation of these systems has to be guarded in order to protect the processed data. We propose in this paper a novel cryptographic module called TinyTPM, which enforces trustworthy operation and IP protection for embedded systems. Our approach covers the following two key principles: (i) trustworthy attestation of the embedded system state, (ii) IP protection by providing authenticated and encrypted update procedures for FPGAs. The TinyTPM consumes only a few resources and is therefore well-suited to design secure, efficient, and low cost FPGA-based embedded systems. This architecture has been implemented as a proof-of-concept on top of a Xilinx Virtex-5 FPGA platform and demonstrates both, security and efficiency.
Least Squares Quantization in PCM (1982)

Abstract-It has long been realized that in pulse-code modulation (PCM), with a given ensemble of signals to handle, the quantum values should be spaced more closely in the voltage regions where the signal amplitude is more likely to fall. It has been shown by Panter and Dite that, in the limit as the number of quanta becomes infinite, the asymptotic fractional density of quanta per unit voltage should vary as the one-third power of the probability density per unit voltage of signal amplitudes. In this paper the corresponding result for any finite number of quanta is derived; that is, necessary conditions are found that the quanta and associated quantization intervals of an optimum finite quantization scheme must satisfy. The optimization criterion used is that the average quantization noise power be a minimum. It is shown that the result obtained here goes over into the Panter and Dite result as the number of quanta become large. The optimum quantization schemes for 26 quanta, b = 1,2, t,7, are given numerically for Gaussian and for Laplacian distribution of signal amplitudes. T I.
Reduced complexity modeling and reproduction of colored textures (2000)

An unsupervised color texture synthesis-by analysis method is described. The texture is reproduced to appear perceptually similar to a given prototype by copying its statistical properties up to the second order. The synthesized texture is obtained at the output of a single-input three-output nonlinear system driven by a realization of a white Gaussian random field. Significant complexity reduction is gained by exploiting the rank deficiency of the cross power spectral density matrix of the color texture samples.
Synthesis and Anti‐HIV Properties of New Carbamate Prodrugs of AZT (2012)

A series of new 5'-O-carbamate prodrugs of AZT have been prepared. The stability in biological media, anti-HIV properties and pharmacokinetic parameters in dogs were evaluated. The compounds display moderate anti-HIV activity in cell culture. After oral administration of carbamate IV in dogs, both intact prodrug IV and released AZT were discovered in dog blood. Pharmacokinetic parameters of the compound IV were estimated. Half-life (T(1/2)) of AZT released after oral administration of IV in dogs was close to that after administration of AZT itself, and time to the maximum concentration (T(max)) of AZT released from IV was two and three times longer compared with that of AZT and H-phosphonate AZT, respectively. Acute toxicity was more than five times less if compared with AZT. As a result, we consider this series of carbamate derivatives of AZT as perspective for development of anti-HIV agents.
Probe–sample interactions in reflection near-field scanning optical microscopy (1995)

Reflection near-field scanning optical microscopy with an asymmetric detector orientation is demonstrated. The effects of the probe-sample interactions are studied for different polarizations, detector orientations, and sample reflectivity. It is shown that the orientation of the detector can introduce shadowing in the images, which is opposite from the naive interpretation and which is dependent on the optical properties of the sample. Near-field optical images of metallic test patterns in reflection are shown that exhibit a lateral resolution of 40 nm.
An experimental determination of absolute half-cell emf’s and single ion free energies of solvation (1977)

The concept of absolute half-cell emf is discussed and defined as VMS-φM for the reaction M→M+(solution)+e−(M), where VMS is the electrostatic potential difference between metal electrode and solution and φM the work function of metal in contact with solution. It is shown that this quantity is equal to VRS-φR, where VRS is the electrostatic potential difference between a reference electrode in air above the solution and the solution, and φR the work function in air of this reference. The quantity VRS′, the potential difference between reference electrode and the solution surface, was found experimentally by the vibrating condenser method for a number of half-cells, and φR was determined photoelectrically. It is shown from the variation of VRS′ with electrolyte concentration that the potential difference betwen the bulk of pure H2O and its air interface is ∼0.05 V, the surface being negative relative to bulk, and that this potential is increasingly screened out as electrolyte concentration increases. From these results for several different half-cells the absolute value of the standard half-cell emf for H2→2H+ is found to be −4.73±0.05 V. This result permits the calculation of single ion free energies of solvation. It is shown that the simple Born model as used by Latimer, Pitzer, and Slansky works remarkably well for simple cations, including polyvalent ones, and for spherical anions, but breaks down for complex anions like OH−, NO−3, etc. Ions in which chemical bonding effects to the solvent play an important role show anomalously high solvation energies. The solvation energy of H+ is −10.98 eV in H2O and varies very little from this value in several different solvents, suggesting that free H+ may predominate in these solvents. This could result from the fact that the small effective radius of free H+ leads to a greater solvation energy than the combination of bond formation and solvation of the resultant much larger ion (H solvent)+. Similar arguments can be used to explain why for instance Fe3+ is not reduced by H2O despite the fact that the third ionization potential of Fe is 30 and that of water 12.6 eV. Other possible applications of the method used in these experiments are discussed.
An architecture for compact associative memories with deca-ns nearest-match capability up to large distances (2002)

Associative-memory architecture for Hamming-distance search, compact implementation, and short nearest-matches times up to large distances are proposed. The main ideas are fast analog word comparison and self-adaptive winner-line-up amplification. An implementation in a 0.6 /spl mu/m 2-poly 3-metal CMOS technology with 32 rows and 128 columns verifies the key concepts. Search time is <38 ns.
Expression of ABH and X (Lex) antigens on platelets and lymphocytes (1988)

We used a panel of reagents, polyclonal and monoclonal antibodies, and lectins to define the expression of the ABH- and Lewis-related specificities on platelets and lymphocytes. We also determined the expression of the alpha 2- and alpha 3-L-fucosyltransferases necessary for their biosynthesis. The antigens that could be detected by immunofluorescence and Western blot analysis were based on type 2 monofucosylated structures. Antibodies directed toward types 1, 3, and 4 ABH-, X- and Lewis-related antigenic determinants were always negative because the small amounts of ABH and Lewis antigens adsorbed from the serum could not be detected by these techniques. The presence of the type 2 ABH antigens on intrinsic glycoproteins was controlled by the H gene. This correlates with the presence of alpha 2-L-fucosyltransferase and the absence of alpha 3-L-fucosyltransferase on platelets. In contrast, ABH antigens were not detected by immunofluorescence on normal peripheral lymphocytes. These cells thus have only the small amounts of antigens adsorbed from the serum, these being under control of the secretor and Lewis genes. This correlates with the absence of alpha 2-L-fucosyltransferase on lymphocytes. When lymphocytes were transformed in vitro by the Epstein-Barr virus (EBV), however, they strongly expressed the X and sialylated X antigens, which are specific markers of normal granulocytes and monocytes, respectively. Treatment of EBV-transformed lymphoblastoid cell lines with 12-O-tetradecanoylphorbol-13-O-acetate significantly decreased the expression of X and sialylated X antigens along with that of surface immunoglobulins, whereas it induced a significant expression of the H antigen under control of the H gene.
The Cauchy Problem for the Heat Equation (1967)

Part I is devoted to the consideration of a Cauchy-like problem for the heat equation. Let $u(x,t)$ satisfy the heat equation in $D = \{ (x,t):0 < x < s(t),0 < t \leqq T\} $ and let $u(x,0) = \varphi (x),u(s(t),t) = f(t)$, and $u_x (s(t),t) = g(t)$. An a priori estimate of $| u |$ in terms of the data f, g, $\varphi $ and $\max _D | {u_x } |$ is derived and applied to an error analysis of a numerical procedure for obtaining an approximate solution of the problem. The results of Part I are applied in Part II to an inverse Stef an problem, which consists of determining a heat influx necessary to give a desired free boundary. An a posteriori estimate of the error in the position of the free boundary is determined without the assumption of the existence of a solution of the stated problem, and an a priori bound is derived in the case a solution exists. In Part III the technique of Part I is modified to treat the standard Cauchy problem in which $u(x,0)$ is not specified.
Determination of the Human Cardiomyocyte mRNA and miRNA Differentiation Network by Fine-Scale Profiling (2011)

To gain insight into the molecular regulation of human heart development, a detailed comparison of the mRNA and miRNA transcriptomes across differentiating human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and biopsies from fetal, adult, and hypertensive human hearts was performed. Gene ontology analysis of the mRNA expression levels of the hiPSCs differentiating into cardiomyocytes revealed 3 distinct groups of genes: pluripotent specific, transitional cardiac specification, and mature cardiomyocyte specific. Hierarchical clustering of the mRNA data revealed that the transcriptome of hiPSC cardiomyocytes largely stabilizes 20 days after initiation of differentiation. Nevertheless, analysis of cells continuously cultured for 120 days indicated that the cardiomyocytes continued to mature toward a more adult-like gene expression pattern. Analysis of cardiomyocyte-specific miRNAs (miR-1, miR-133a/b, and miR-208a/b) revealed an miRNA pattern indicative of stem cell to cardiomyocyte specification. A biostatistitical approach integrated the miRNA and mRNA expression profiles revealing a cardiomyocyte differentiation miRNA network and identified putative mRNAs targeted by multiple miRNAs. Together, these data reveal the miRNA network in human heart development and support the notion that overlapping miRNA networks re-enforce transcriptional control during developmental specification.
SENSORY PROPERTIES OF EXTRUDED CORN MEAL RELATED TO THE SPATIAL DISTRIBUTION OF PROCESS CONDITIONS (1994)

ABSTRACT The quality determining factors of extruded products are affected by the temperature, shear and pressure generated by any input to the extruder during the short residence time (< 120s). Although the relationship of process history to measurable product qualities has been established, sensory qualities have not been well correlated to these process responses. Sensory attributes of extruded corn meal products were investigated and correlated to measured physical properties in this study. Corn meal was extruded in a twin screw extruder (Baker Perkins MPF 50/25; LD ratio 15:1) with step increases in screw speed from 200‐400 rpm, and moisture from 16‐22%. Principal component analysis (PCA) of main factors from sensory color, crispness, and adhesiveness was correlated to process torque, pressure and temperature. Spatial distribution of process response and product attributes showed crispness to be dependent on extrusion temperature. Porosity and adhesiveness were not correlated to any measured process response. PCA analysis identified significant differences in the effects of moisture and screw speed input to the extruder on product properties.
On-Demand Web Search Using Browser-Based Volunteer Computing (2012)

Current solutions to the problem of finding valuable information on the Web suffer from several limitations, including inconvenient query languages, arbitrary sorting or results and out-of-date information. In this paper a different solution to this problem is described. It is based on the idea of distributed processing of web pages in real-time. To provide sufficient performance, the approach of volunteer computing is utilized. It is based on using web browsers of users visiting particular web pages. The browsers perform necessary computation in background, executing programs written in JavaScript. In this paper the architecture of the on-demand web crawling system is presented and details concerning implementation are provided.
VMbuddies: Coordinating Live Migration of Multi-Tier Applications in Cloud Environments (2014)

Enabled by virtualization technologies, various multi-tier applications (such as web applications) are hosted by virtual machines (VMs) in cloud data centers. Live migration of multi-tier applications across geographically distributed data centers is important for load management, power saving, routine server maintenance and quality-of-service. Different from a single-VM migration, VMs in a multi-tier application are closely correlated, which results in a correlated VM migrations problem. Current live migration algorithms for single-VM cause significant application performance degradation because intermediate data exchange between different VMs suffers relatively low bandwidth and high latency across distributed data centers. In this paper, we design and implement a coordination system called VMbuddies for correlated VM migrations in the cloud. Particularly, we propose an adaptive network bandwidth allocation algorithm to minimize the migration cost in terms of migration completion time, network traffic and migration downtime. Experiments using a public benchmark show that VMbuddies significantly reduces the performance degradation and migration cost of multi-tier applications.
Improving yields through effective diagnostics: A MCM-D/C example (2002)

Partitioning of defects in process, tools, contamination and handling has been used effectively at the IBM Thin Films Packaging manufacturing facility for many years to track and improve yields. To design for manufacturability (DFM) means to take into consideration all the elements that affect yields, such as tooling, clean room environment process selection, ground rules, repairability and test. On multilevel structures, final test alone does not allow for effective diagnostics, since most yield losses occur from sub-level defects. Early feedback to establish root cause can be obtained via in-line test inspection and measurement. Also, it is at these sub-levels where surface repairs for opens and shorts can be done easily. This paper discusses how to improve yields through effective diagnostics. Specific examples illustrate how scattered plots, failure analysis, job traceability and correlations have been used on the IBM MCM-D/C manufacturing line for real time defect diagnosis.
The development of a configuration control tool (2002)

The development of a flexible configuration control tool for a dynamic software system is discussed. The configuration management tool provides the ability to automatically install or remove software patches from any software baseline. Its innovative concept is that configuration changes are temporary as long as desired. Installation and removal of patches requires only shutting down the application code, setting the desired configuration through a user-friendly interface, and then restarting the application. If a patch survives the rigors of operations for a few weeks, it is safe to permanently incorporate it into the baseline. If a patch fails while in the temporary state, it can easily be removed. The results of using this tool are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Influence of n<sup>+</sup>-layer-gate gap on short-channel effects of GaAs self-aligned MESFET's (SAINT) (1983)

Short-channel effects of GaAs n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -gate self-aligned MESFET's are investigated for different n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer-gate gaps. The gate lengths range from 0.1 to 1.5 µm. The fabrication features are self-aligned implantation for n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer technology (SAINT) and an electron-beam direct writing. The n+-layer-gate gap is controlled by the undercut process in the bottom resist of a multilayer resist acting as n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ion implantation mask. It is shown that the short-channel effects such as an increase in subthreshold current and a negative shift of threshold voltage can be substantially alleviated by enlarging the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -layer-gate gap from 0.15 to 0.3 µm.
Improvement of Azimuth Accuracy by Use of Iterative Total Field Calibration Technique and Compensation for System Environment Effects (1989)

ABSTRACT The accuracy of directional well survey measurements transmitted by downhole tools can be improved by a number of techniques, a major factor being the ability to identify and correct constituent errors in calibrating the individual sensors used to calculate the directional parameters of a wellbore. The Total Field Calibration method is an iterative technique which enables both the analysis and correction of these constituent errors, and which is applicable to any three-axis orientation module that measures one of the earth's natural field vectors. These may include the gravitational, magnetic or rotational fields. Based on the known total field intensity at the location of calibration, the technique converges upon the set of values for bias, scale factor, and misalignment corrections which will minimize the residual error in the calculated total field. This calibration program has the advantages of insensitivity to operator positioning error, accuracy limited only by that of the data acquisition equipment, and applicability to multiple types of devices. It also gives an indication of residual errors such as nonlinearity and hysteresis, in addition to the typical bias, scale factor, and angular misalignment. By applying the technique at various temperatures to derive polynomial corrections which are then applied to the digitized outputs, a thermally modeled system can be realized. This results in a sensor module which has been calibrated as a complete system to remove errors caused either internally or in combination with environmental effects. Use of the Total Field Calibration method on an MWD tool with triaxial accelerometers and magnetometers results in improved performance, as illustrated by data obtained both in surface tests and in actual downhole operation.