gebhart/patrepeval huggingface dataset:
Streptococcus plasmid pAM alpha 1 is a composite of two separable replicons, one of which is closely related to Bacillus plasmid pBC16 (1983)

A tetracycline resistance plasmid of Streptococcus faecalis, pAM alpha 1, is shown to contain two independent sets of replication functions, separated from each other on either side by short (300- to 400-base-pair) sequences of homology. The homologous sequences are oriented as direct repeats and therefore permit the dissociation of pAM alpha 1 into its component replicons, referred to here as pAM alpha 1 delta 1 and pAM alpha 1 delta 2, as the reciprocal products of a simple intramolecular recombination. pAM alpha 1 delta 1 is a 4.6-kilobase plasmid which carries the tet gene, and pAM alpha 1 delta 2 is a 5.1-kilobase plasmid which carries no known selectable marker. pAM alpha 1 delta 1 is shown to replicate efficiently in Bacillus subtilis and to confer tetracycline resistance on Bacillus hosts. We demonstrate by restriction mapping analysis that pAM alpha 1 delta 1 is virtually identical to a 4.6-kilobase tetracycline resistance plasmid of Bacillus cereus, pBC16, which is known to show extensive homology to plasmid isolates from Staphylococcus species (such as pUB110), as well as from other Bacillus species. The pAM alpha 1 delta 1-pBC16-pUB110 replicon thus exists naturally in at least three different gram-positive genera, indicating that these plasmids have a high degree of interspecific functional adaptability and supporting the view that plasmid DNA is commonly exchanged among many species of gram-positive bacteria in their natural environments.
Universal serial bus enhances virtual instrument-based distributed power monitoring (2001)

The universal serial bus (USB) links a distributed multicircuit power monitoring system to its virtual instrument (VI) host computer. The distributed interconnection provides enhanced system performance at reduced cost, since the USB host controller is a standard function of up-to-date personal computers (PCs) and low-cost high-performance USB hardware is readily available. The 12 Mb/s, recently updated to 480 Mb/s, transfer rate of the USB improves data transmission capability and boosts the real-time performance of the whole VI monitoring system when compared with conventional serial communications. In addition, the USB dynamic attachment and removal feature allows each meter to be connected or disconnected from its VI host computer without any system interruption. However, the complete VI solutions are not currently supported by any USB hosts and devices. This paper presents an innovative USB VI strategy to implement integrated power monitoring applications and shows its superior performance.
Sol-Gel Synthesis of Barium Titanate Powders Using Barium Acetate and Titanium(IV) Isopropoxide (1988)

A sol-gel process for low-temperature preparation of BaTiO{sub 3} powders is described. Chemical polymerization between barium acetate and titanium(IV) isopropoxide leads to the formation of barium titanate gels. After suitable drying and calcination treatments, the barium titanate gels were converted to BaTiO{sub 3} powders. The barium titanate gels and powders were characterized by TGA, DTA, and XRD. The results of these analyses indicate that it is possible to obtain stoichiometric (Ba/Ti = 0.99), homogeneous, high-purity BaTiO{sub 3} powders using relatively inexpensive barium acetate as a starting material.
<i>In situ</i> formation of silver nanoparticles in photocrosslinking polymers (2011)

Nanocomposites of cross-linked methacrylate polymers with silver nanoparticles have been synthesized by coupling photoinitiated free radical polymerization of dimethacrylates with in situ silver ion reduction. A polymerizable methacrylate bearing a secondary amino functional group was used to increase the solubility of the silver salt in the hydrophobic resin system. Fourier transform infrared spectroscopy (FTIR) revealed that the silver ion reduction had no significant effect on the degree of vinyl conversion of the methacrylate. X-ray photoelectron spectroscopy (XPS) measurements showed an increased silver concentration at the composite surface compared to the expected concentration based on the total amount of silver salt added. Furthermore, the surface silver concentration leveled off when the silver salt mass fractions were 0.08% or greater. Composites with low concentrations of silver salt (< 0.08% by mass) exhibited comparable mechanical properties to those containing no silver. Transmission electron microscopy (TEM) confirmed that the silver nanoparticles formed within the polymer matrix were nanocrystalline in nature and primarily ≈ 3 nm in diameter, with some large particle aggregates. Composites containing silver nanoparticles were shown to reduce bacterial colonization with as little as 0.03% (by mass) silver salt, while additional amounts of silver salt did not further decrease their surface colonization. With a substantial effect on bacterial growth and minimal effects on mechanical properties, the in situ formation of silver nanoparticles within methacrylate materials is a promising technique for synthesizing antibacterial nanocomposites for biomedical applications.
Chronic Low‐Dose UVA Irradiation Induces Local Suppression of Contact Hypersensitivity, Langerhans Cell Depletion and Suppressor Cell Activation in C3H/HeJ Mice (1996)

It has previously been demonstrated that chronic low-dose solar-simulated UV radiation could induce both local and systemic immunosuppression as well as tolerance to a topically applied hapten. In this study, we have used a chronic low-dose UV-irradiation protocol to investigate the effects of UVA on the skin immune system of C3H/ HeJ mice. Irradiation with UVA + B significantly suppressed the local and systemic primary contact hypersensitivity (CHS) response to the hapten 2,4,6-trinitrochlorobenzene. Furthermore UVA + B reduced Langerhans cell (LC) and dendritic epidermal T cell (DETC) densities in chronically UV-irradiated mice. Ultraviolet A irradiation induced local, but not systemic, immunosuppression and reduced LC (32%) but not DETC from the epidermis compared to the shaved control animals. Treatment of mice with both UVA + B and UVA radiation also induced an impaired secondary CHS response, and this tolerance was transferable with spleen cells. These results suggest that depletion of LC, but not DETC, may be involved in UVA-induced local immunosuppression in our model, and that tolerance was induced in the presence of normal numbers of DETC. Hence exposure of C3H/HeJ mice 5 days per week for 4 weeks with UVA can induce local immunosuppression and tolerance.
Enhancing the Success of Human Islet Isolation Through Optimization and Characterization of Pancreas Dissociation Enzyme (2007)

A major obstacle to successful human islet isolation has been the variability of the enzymatic digestion phase. The aim of this study was to define optimal enzyme activity ranges normalized by the pancreas weight and to identify valid parameters for the optimal selection of successful lots of collagenase enzyme blends. Our results from 251 islet isolations showed that optimization of thermolysin dosage based on Caseinase unit/g pancreas contributed considerably to islet isolation outcome but that collagenase dosage measured by the manufacturer (Wünsch unit/g pancreas) was not a major determinant of islet isolation outcome. We also found that lot-to-lot inconsistency of enzyme performance was not explained by the activity values provided by the manufacturer, but rather by an in-house assay of class I collagenase (CI) and class II collagenase (CII); using a lot with a lower CII/CI resulted in a higher success rate. The odds of successful isolation was 8.67 times higher when a vial with CII/CI ratio <0.204 was used than when a vial with CII/CI >or=0.204 was used, suggesting that CII/CI ratio may be a strong predictor to distinguish potential lot success. This study provides a framework for improved enzymatic digestion in human islet isolation.
Software maintenance: An approach to impact analysis of objects change (1995)

Abstract The maintenance of a software system requires a tool for impact analysis and the propagation of change. This paper presents a knowledge‐based model for both. This model is generic because it is not based on any language or design method. Therefore, it can be applied on the basis of ‘problem’ to be solved. It also captures four life‐cycle phases: requirement, specification, design and programming . We also provide a domain‐specific view that allows the dependency analysis of fine‐grain objects. Two kinds of dependencies are identified: inter‐phase dependencies , these are dependency relations between the objects of the one phase and another; and intra‐phase dependencies , these are dependency relations between the objects of the same phase. In order to validate this model, we also present a prototype based on two life‐cycle phases: design and programming .
Moving phase transitions in laser-irradiated biological tissue (1979)

A theory of laser-induced phase transitions in an absorptive medium with internal scattering is developed in order to improve our understanding of the multiplicity of phenomena occurring in the application of lasers in medicine. The redistributive internal scattering phenomenon, which has successfully explained several anomalies in tissue heating without phase transitions, is studied in detail. Several interesting results including general profile independent formulas for the back- and forwardscattered power and an explanation of the popcorn effect or laser-induced decrepitation commonly observed in high-intensity irradiation are obtained, the application of the latter to the theory of laser drilling being touched on in a footnote. The behavior of moving phase transitions in one dimension (plane incoming wave) is studied. The heat equation is solved for the pure absorption model in terms of the unknown depth of the phase front; this solution is used to derive a numerical procedure to find the time dependence of the phase-front depth as well as an analytic expression of its initial time dependence.
Reduced power dissipation through truncated multiplication (1999)

Reducing the power dissipation of parallel multipliers is important in the design of digital signal processing systems. In many of these systems, the products of parallel multipliers are rounded to avoid growth in word size. The power dissipation and area of rounded parallel multipliers can be significantly reduced by a technique known as truncated multiplication. With this technique, the least significant columns of the multiplication matrix are not used. Instead, the carries generated by these columns are estimated. This estimate is added with the most significant columns to produce the rounded product. This paper presents the design and implementation of parallel truncated multipliers. Simulations indicate that truncated parallel multipliers dissipate between 29 and 40 percent less power than standard parallel multipliers for operand sizes of 16 and 32 bits.
Homologous recombination between coinjected DNA sequences peaks in early to mid-S phase. (1987)

We have examined the effect of cell cycle position on homologous recombination between plasmid molecules coinjected into synchronized rat fibroblasts. Recombination activity was found to be low in G1 and to rise 10- to 15-fold, peaking in early to mid-S phase.
In-Depth Analysis of the Antibody Response of Individuals Exposed to Primary Dengue Virus Infection (2011)

Humans who experience a primary dengue virus (DENV) infection develop antibodies that preferentially neutralize the homologous serotype responsible for infection. Affected individuals also generate cross-reactive antibodies against heterologous DENV serotypes, which are non-neutralizing. Dengue cross-reactive, non-neutralizing antibodies can enhance infection of Fc receptor bearing cells and, potentially, exacerbate disease. The actual binding sites of human antibody on the DENV particle are not well defined. We characterized the specificity and neutralization potency of polyclonal serum antibodies and memory B-cell derived monoclonal antibodies (hMAbs) from 2 individuals exposed to primary DENV infections. Most DENV-specific hMAbs were serotype cross-reactive and weakly neutralizing. Moreover, many hMAbs bound to the viral pre-membrane protein and other sites on the virus that were not preserved when the viral envelope protein was produced as a soluble, recombinant antigen (rE protein). Nonetheless, by modifying the screening procedure to detect rare antibodies that bound to rE, we were able to isolate and map human antibodies that strongly neutralized the homologous serotype of DENV. Our MAbs results indicate that, in these two individuals exposed to primary DENV infections, a small fraction of the total antibody response was responsible for virus neutralization.
A CMOS adaptive antenna-impedance-tuning IC operating in the 850MHz-to-2GHz band (2009)

An adaptive antenna-tuning units (AATU) utilizing analog mismatch detection and mixed-signal matching-state search circuits operating in a frequency band from 850 MHz to 2 GHz is presented. The fully integrated AATU IC is fabricated in a 0.18 mum 6-layer metal CMOS process.
Proteomics of Synechocystis sp. Strain PCC 6803 (2002)

Cyanobacteria are unique prokaryotes since they in addition to outer and plasma membranes contain the photosynthetic membranes (thylakoids). The plasma membranes of Synechocystis 6803, which can be completely purified by density centrifugation and polymer two-phase partitioning, have been found to be more complex than previously anticipated, i.e. they appear to be essential for assembly of the two photosystems. A proteomic approach for the characterization of cyanobacterial plasma membranes using two-dimensional gel electrophoresis and mass spectrometry analysis revealed a total of 57 different membrane proteins of which 17 are integral membrane spanning proteins. Among the 40 peripheral proteins 20 are located on the periplasmic side of the membrane, while 20 are on the cytoplasmic side. Among the proteins identified are subunits of the two photosystems as well as Vipp1, which has been suggested to be involved in vesicular transport between plasma and thylakoid membranes and is thus relevant to the possibility that plasma membranes are the initial site for photosystem biogenesis. Four subunits of the Pilus complex responsible for cell motility were also identified as well as several subunits of the TolC and TonB transport systems. Several periplasmic and ATP-binding proteins of ATP-binding cassette transporters were also identified as were two subunits of the F(0) membrane part of the ATP synthase.
<scp>d</scp>-Amino Acids Modulate the Cellular Response of Enzymatic-Instructed Supramolecular Nanofibers of Small Peptides (2014)

Peptides made of D-amino acids, as the enantiomer of corresponding L-peptides, are able to resist proteolysis. It is, however, unclear or much less explored whether or how D-amino acids affect the cellular response of supramolecular nanofibers formed by enzyme-triggered self-assembly of D-peptides. In this work, we choose a cell compatible molecule, Nap-L-Phe-L-Phe-L-(p)Tyr (LLL-1P), and systematically replace the L-amino acids in this tripeptidic precursor or its hydrogelator by the corresponding D-amino acid(s). The replacement of even one D-amino acid in this tripeptidic precursor increases its proteolytic resistance. The results of static light scattering and TEM images show the formation of nanostructures upon the addition of alkaline phosphatase, even at concentrations below the minimum gelation concentration (mgc). All these isomers are able to form ordered nanostructures and exhibit different morphologies. According to the cell viability assay on these stereochemical isomers, cells exhibit drastically different responses to the enantiomeric precursors, but almost same responses to the enantiomeric hydrogelators. Furthermore, the different cellular responses of LLL-1P and DDD-1P largely originate from the ecto-phosphatases catalyzed self-assembly of DDD-1 on the surface of cells. Therefore, this report not only illustrates a new way for tailoring the properties of supramolecular assemblies, but also provides new insights to answering the fundamental question of how mammalian cells respond to enzymatic formation of nanoscale supramolecular assemblies (e.g., nanofibers) of D-peptides.
Analysis of power supply networks in VLSI circuits (1991)

Although the trend toward finer geometries and larger chips has produced faster systems, it has also created larger voltage drops and higher current densities in chip power supply networks. Excessive voltage drops in the power supply lines cause incorrect circuit operation, and high current densities lead to circuit failure via electromigration. Analyzing this power supply noise by hand for large circuits is difficult and error prone; automatic checking tools are needed to make the analysis easier. This thesis describes Ariel, a CAD tool that helps VLSI designers analyze power supply noise. The system consists of three main components, a resistance extractor, a current estimator, and a linear solver, that are used together to determine the voltage drops and current density along the supply lines. The resistance extractor includes two parts: a fast extractor that calculates resistances quickly using simple heuristics, and a slower, more accurate finite element extractor. Despite its simplicity, the fast extractor obtained nearly the same results as the finite element one and is two orders of magnitude faster. The system also contains two current estimators, one for CMOS
Geometry-guided progressive lossless 3D mesh coding with octree (OT) decomposition (2005)

A new progressive lossless 3D triangular mesh encoder is proposed in this work, which can encode any 3D triangular mesh with an arbitrary topological structure. Given a mesh, the quantized 3D vertices are first partitioned into an octree (OT) structure, which is then traversed from the root and gradually to the leaves. During the traversal, each 3D cell in the tree front is subdivided into eight childcells. For each cell subdivision, both local geometry and connectivity changes are encoded, where the connectivity coding is guided by the geometry coding. Furthermore, prioritized cell subdivision is performed in the tree front to provide better rate-distortion (RD) performance. Experiments show that the proposed mesh coder outperforms the kd-tree algorithm in both geometry and connectivity coding efficiency. For the geometry coding part, the range of improvement is typically around 10%~20%, but may go up to 50%~60% for meshes with highly regular geometry data and/or tight clustering of vertices.
Nanophotonic interferometer realizing all-optical exclusive or gate on a silicon chip (2009)

We present an all optical approach allowing the realization of microscale logic exclusive or (XOR) gate based on special interferometer configuration. The operation device includes two close optical waveguides realized on a silicon chip. A thin metallic layer of a few nanometers that separates the two waveguides causes a relative phase shift of between them. The structure performs interference of the two input beams while demonstrating XOR logic gate operation at the amplitude of the resulted output. The logic operation is realized after small propagation distance of <1.8 µm.
A novel mechanism by which probucol lowers low density lipoprotein levels demonstrated in the LDL receptor-deficient rabbit. (1984)

Treatment of low density lipoprotein (LDL) receptor-deficient rabbits (WHHL rabbits) with probucol (1% w/w in a chow diet) lowered their LDL-cholesterol levels by 36%, consonant with the reported effectiveness of the drug in patients deficient in the LDL receptor. Initial studies of LDL fractional catabolic rate (FCR) using 125I-labeled LDL prepared from the serum of untreated WHHL rabbits showed no difference between probucol-treated WHHL rabbits and untreated WHHL rabbits. When, however, 125I-labeled LDL was prepared from donor WHHL rabbits under treatment with probucol and injected back into them, the FCR was found to be increased by about 50% above that measured simultaneously using 131I-labeled LDL prepared from untreated WHHL donors. The labeled LDL from probucol-treated donors was also metabolized more rapidly than that from untreated donors when injected into untreated WHHL rabbits or into untreated wild-type New Zealand White rabbits. Finally, it was shown that rabbit skin fibroblasts in culture degraded labeled LDL prepared from probucol-treated WHHL rabbits more rapidly than that prepared from untreated WHHL donors. This was true both for normal rabbit fibroblasts and also for WHHL skin fibroblasts, although the absolute degradation rates in the latter were, of course, much lower for both forms of LDL. The data indicate that a major mechanism by which probucol lowers LDL levels relates not to changes in the cellular mechanisms for LDL uptake or to changes in LDL production but rather to intrinsic changes in the structure and metabolism of the plasma LDL of the probucol-treated animal.(ABSTRACT TRUNCATED AT 250 WORDS)
Integrated PDMS/CMOS Microsystem for Autonomous Incubation and Imaging in Cell Culture Studies (2006)

We discuss the design, fabrication and testing of a hybrid microsystem for stand-alone cell culture, incubation and imaging. The micro-incubator is engineered through the integration of two CMOS dies. The first for the heater and temperature sensor, and a second die for imaging. A multilayer PDMS (polydimethylsiloxane) structures is used to create not only the fluidic structures but to encapsulate the CMOS dies. The microfluidic features include fluidic channels, a 4mm diameter, 30μL, culture well and a 25 micron thick PDMS membrane that covers the top of the culture well, acting as barrier to contaminants while allowing the cells to exchange gases with the ambient environment. The micro-incubator interface includes with a flexible polyimide ribbon cable and four fluidic ports. The complete structure has a size of (2.5×2.5×0.6cm3). We have employed the device to successfully culture BHK-21 cells autonomously over a sixty hour period in ambient environment.
A 400-to-900 MHz receiver with dual-domain harmonic rejection exploiting adaptive interference cancellation (2009)

Wideband direct-conversion harmonic-rejection (HR) receivers for software- defined radio aim to remove or relax the pre-mixer RF filters, which are inflexible, bulky and costly. HR schemes are often used, but amplitude and phase mismatches limit HR to between 30 and 40 dB. A quick calculation shows that much more rejection is wanted: in order to bring harmonic responses down to the noise floor (e.g. -100 dBm in 10 MHz for 4 dB NF), and cope with interferers between -40 and 0 dBm, an HR of 60 to 100 dB is needed. Also in terrestrial TV receivers and in applications like DVB-H with co-existence requirements with GSM/WLAN transmitters in a small telephone, high HR is needed. In this work, an architecture aiming for >80 dB HR is shown. It consists of an analog front-end followed by adaptive interference cancellation (AIC) in the digital domain. AIC is known for its ability to adapt to and mitigate unknown system non-idealities, e.g. gain and phase imbalances. Due to its adaptivity it can achieve large improvements, provided the interference estimate is accurate. To the authors' knowledge, they are the first to explore AIC for HR and previously presented simulation results. Here a new and different architecture and measured results with the RF part implemented in 65 nm CMOS and the AIC in software are presented.