gebhart/patrepeval huggingface dataset:
Efficient gene targeting in the moss <i>Physcomitrella patens</i> (1997)

The moss Physcomitrella patens is used as a genetic model system to study plant development, taking advantage of the fact that the haploid gametophyte dominates in its life cycle. Transformation experiments designed to target three single-copy genomic loci were performed to determine the efficiency of gene targeting in this plant. Mean transformation rates were 10-fold higher with the targeting vectors and molecular evidence for the integration of exogenous DNA into each targeted locus by homologous recombination is provided. The efficiency of gene targeting determined in these experiments is above 90%, which is in the range of that observed in yeast and several orders of magnitude higher than previous reports of gene targeting in plants. Thus, gene knock-out and allele replacement approaches are directly accessible to study plant development in the moss Physcomitrella patens. Moreover, efficient gene targeting has so far only been observed in lower eukaryotes such as protozoa, yeasts and filamentous fungi, and, as shown here the first example from the plant kingdom is a haplobiontic moss. This suggests a possible correlation between efficient gene targeting and haplophase in eukaryotes.
The role of vascular endothelial growth factors and their receptors in malignant melanomas. (2008)

Vascular endothelial growth factors (VEGFs) have a leading role among variety of angiogenic factors. Together with their receptors, they play an important role in endothelial cell proliferation and/or elongation, migration and vascular morphogenesis. In order to determine their possible role in malignant melanoma progression, VEGF (representing VEGFA), VEGF-C and VEGFR-1, -2, -3 immunohistochemical expression on formalin-fixed, paraffin-embedded tissue sections were evaluated. A total of 196 tissue samples consisting of 130 malignant melanomas (MM) with various vertical depth of invasion, 15 metastatic melanomas, and 66 nevi including dysplastic nevi and melanocytic nevi were analysed. Production of both VEGFs were common in benign melanocytic tumors while MM exhibited significant upregulation of VEGF (p<0.0027) and VEGF-C (p<0.0001). The proteins were also detected within stromal cells surrounding tumors, particularly in fibrocytes/ fibroblasts, macrophages and endothelial cells. They also exhibited significant increase in malignant lesions (p<0.0001). VEGFRs were localized in tumor, as well in stromal cells. Although expression of VEGF receptors was significantly higher in MM versus nevi (p<0.002 for VEGFR-1, p<0.004 for VEGFR-2 and p<0.0001 for VEGFR-3), a considerable percentage of MM were negative. There were no correlations between sentinel node positivity and all investigated proteins. When clinical outcome was evaluated, progression of the disease positively correlated with VEGF (p<0,007) and VEGF-C (p<0,008) expression VEGF (p<0.001) and VEGF-C (p<0.0001) positively correlated with nestin expression in the capillary endothelium, which was used for angiogenesis detection. Our work demonstrated that upregulation of VEGFs is associated with progression of malignant melanomas. The protein expression in the tumor microenvironment highlights their importance in malignant stromal phenotype which may serve as a potential target for the anticancer therapy.
Exploring optimization parameters to increase ssDNA recombineering in<i>Lactococcus lactis</i>and<i>Lactobacillus reuteri</i> (2012)

Single-stranded DNA (ssDNA) recombineering is a technology which is used to make subtle changes in the chromosome of several bacterial genera. Cells which express a single-stranded DNA binding protein (RecT or Bet) are transformed with an oligonucleotide which is incorporated via an annealing and replication-dependent mechanism. By in silico analysis we identified ssDNA binding protein homologs in the genus Lactobacillus and Lactococcus lactis. To assess whether we could further improve the recombineering efficiency in Lactobacillus reuteri ATCC PTA 6475 we expressed several RecT homologs in this strain. RecT derived from Enterococcus faecalis CRMEN 19 yielded comparable efficiencies compared with a native RecT protein, but none of the other proteins further increased the recombineering efficiency. We successfully improved recombineering efficiency 10-fold in L. lactis by increasing oligonucleotide concentration combined with the use of oligonucleotides containing phosphorothioate-linkages (PTOs). Surprisingly, neither increased oligonucleotide concentration nor PTO linkages enhanced recombineering in L. reuteri 6475. To emphasize the utility of this technology in improving probiotic features we modified six bases in a transcriptional regulatory element region of the pdu-operon of L. reuteri 6475, yielding a 3-fold increase in the production of the antimicrobial compound reuterin. Directed genetic modification of lactic acid bacteria through ssDNA recombineering will simplify strain improvement in a way that, when mutating a single base, is genetically indistinguishable from strains obtained through directed evolution.
Thru-less calibration algorithm and measurement system for on-wafer large-signal characterisation of microwave devices (2010)

A reflection-based thru-less de-embedding technique for voltage and current waveforms and absolute power flow measurements suitable for on-wafer large-signal characterisation of microwave transistors is proposed. Based on the novel calibration technique developed, which does not require any special ‘golden standard’ for waveform calibration purposes, a comprehensive and relatively inexpensive power flow, impedance and waveform measurement system, using the microwave transition analyser as a two-channel receiver, is developed. The proposed calibration algorithm is fast, simple and accurate for power de-embedding and waveform measurements. This kind of on-wafer power de-embedding and waveform measurement is helpful in the design of switching-mode power amplifiers. The developed system was tested for both 50 Ω and non-50 Ω terminated passive and active devices, and the obtained results show very good agreement with those obtained with commercial instruments.
<b>Cardiac output and blood pressure during active and passive standing</b> (1996)

The present study compared the haemodynamic pattern of active and passive standing. We used non-invasive techniques with beat-to-beat evaluation of blood pressure, heart rate and stroke volume. Seven healthy subjects, aged 24-41 (mean 30) years were examined. Finger blood pressure was continuously recorded by volume clamp technique (Finapres), and simultaneous beat-to-beat beat stroke volume was obtained, using an ultrasound Doppler technique, from the product of the valvular area and the aortic flow velocity time integral in the ascending aorta from the suprasternal notch. Measurements were performed at rest, during active standing and following passive tilt (60 degrees). Active standing caused a transient but greater reduction of blood pressure and a higher increase of heart rate than passive tilt during the first 30s (delta mean blood pressure: -39 +/- 10 vs. -16 +/- 7 mmHg, delta heart rate: 35 +/- 8 vs. 12 +/- 7 beats m-1 (active standing vs. passive tilt; P < 0.01). There was a significantly larger increase in cardiac output during active standing (37 +/- 24 vs. 0 +/- 15%, P < 0.01) and a more marked decrease in total peripheral resistance (-58 +/- 11 vs. -16 +/- 17%, P < 0.01). A precipitous rise in intra-abdominal pressure (43 +/- 22 mmHg) could be observed upon rising only in active standing. This was interpreted as an indication of translocation of blood to the thorax. There was no significant difference in haemodynamic changes during the later stage of standing (1-7 min) between both manoeuvres. These results suggest that active standing causes a marked blood pressure reduction in the initial phase which seems to reflect systemic vasodilatation caused by activation of cardiopulmonary baroreflexes, probably due to a rapid shift of blood from the splanchnic vessels in addition to the shift from muscular vessels associated with abdominal and calf muscle contraction. Moreover, the ultrasound Doppler technique was found to be a more adequate method for rapid beat-to-beat evaluation of cardiac output during orthostatic manoeuvres.
On the Equivalence between Kernel Quadrature Rules and Random Feature\n Expansions (2015)

We show that kernel-based quadrature rules for computing integrals can be\nseen as a special case of random feature expansions for positive definite\nkernels, for a particular decomposition that always exists for such kernels. We\nprovide a theoretical analysis of the number of required samples for a given\napproximation error, leading to both upper and lower bounds that are based\nsolely on the eigenvalues of the associated integral operator and match up to\nlogarithmic terms. In particular, we show that the upper bound may be obtained\nfrom independent and identically distributed samples from a specific\nnon-uniform distribution, while the lower bound if valid for any set of points.\nApplying our results to kernel-based quadrature, while our results are fairly\ngeneral, we recover known upper and lower bounds for the special cases of\nSobolev spaces. Moreover, our results extend to the more general problem of\nfull function approximations (beyond simply computing an integral), with\nresults in L2- and L$\\infty$-norm that match known results for special cases.\nApplying our results to random features, we show an improvement of the number\nof random features needed to preserve the generalization guarantees for\nlearning with Lipschitz-continuous losses.\n
Periodic chains of gold nanoparticles and the role of oxygen during the growth of silicon nanowires (2006)

The introduction of oxygen during silicon monoxide–vapor liquid solid growth of silicon nanowires causes a shift in silicon suboxide stoichiometry resulting in an increased formation of silicon dioxide at the nanowire surface. This leads to instabilities of the usual cylindrical nanowire core-shell structure, where the liquid gold/silicon alloy droplet at the nanowire tip is incorporated inside a silicon dioxide nanowire to form a periodic array of nanoparticles. The structure and the composition of the resulting nanostructure are investigated using transmission electron microscopy. The influence of the oxygen is investigated experimentally and supports the authors’ model of the formation mechanism.
A random DEM technique with minimal element transition rate for high-speed DACs (2014)

This paper presents a random dynamic element matching (DEM) technique for current-steering digital-to-analog converters (DACs). It randomizes the element selection process, and keeps the number of transitions to minimum. As a result, it does not introduce extra dynamic errors caused by inter-symbol interference (ISI). This technique also alleviates the impact of linear gradient errors due to the fabrication process. A behavioral Matlab model for 12-bit segmented current-steering DAC is developed. Simulation results proves that the proposed algorithm improves the DAC linearity effectively.
Ectopic RNase E sites promote bypass of 5′‐end‐dependent mRNA decay in <i>Escherichia coli</i> (2002)

In Escherichia coli, 5'-terminal stem-loops form major impediments to mRNA decay, yet conditions that determine their effectiveness or the use of alternative decay pathway(s) are unclear. A synthetic 5'-terminal hairpin stabilizes the rpsT mRNA sixfold. This stabilization is dependent on efficient translational initiation and ribosome transit through at least two-thirds of the coding sequence past a major RNase E cleavage site in the rpsT mRNA. Insertion of a 12-15 residue 'ectopic' RNase E cleavage site from either the rne leader or 9S pre-rRNA into the 5'-non-coding region of the rpsT mRNA significantly reduces the stabilizing effect of the terminal stem-loop, dependent on RNase E. A similar insertion into the rpsT coding sequence is partially destabilizing. These findings demonstrate that RNase E can bypass an interaction with the 5'-terminus, and exploit an alternative 'internal entry' pathway. We propose a model for degradation of the rpsT mRNA, which explains the hierarchy of protection afforded by different 5'-termini, the use of internal entry for bypass of barriers to decay, 'ectopic sites' and the role of translating ribosomes.
[Compare NRT value of straight electrode and contour electrode in Nucleus 24 cochlear implant system]. (2012)

The contour electrode requires less power consumption than straight electrode in Nucleus 24 cochlear implant system.
Synthesis and characterization of single‐wall‐carbon‐nanotube‐doped emeraldine salt and base polyaniline nanocomposites (2005)

Abstract Nanocomposites of polyaniline (PANI) and single‐wall carbon nanotubes (SWNTs) were prepared and characterized via resonance Raman and electronic absorption spectroscopy (ultraviolet–visible/near‐infrared). The chemical synthesis of PANI was performed in the presence of SWNTs in concentrations ranging from 10 to 50 wt % (SWNT/PANI). The obtained materials were hydrophilic, homogeneous composite compounds. The chemical interaction between PANI (in the conducting emeraldine salt form and in the insulating emeraldine base form) and metallic and semiconducting nanotubes was investigated. The emeraldine salt form of the polymer was significantly stabilized in the composite in comparison with plain PANI. A selective electronic interaction process between PANI and metallic SWNTs was found. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 815–822, 2005
High density recording on SmCo/Cr thin film media (1992)

SmCo/Cr thin films with coercivity up to 3000 Oe were prepared by RF-diode sputtering. Hard disks were fabricated using glass substrates and the recording properties, carrier-to-integrated-noise ratio, media noise, and overwritability were evaluated using conventional thin-film inductive heads. The influence of the thickness of the Cr underlayer, SmCo magnetic layer, and Cr overlayer on media noise was studied. The intergranular exchange and magnetostatic interaction effects present in SmCo/Cr media were measured from their remanence magnetization curves and correlated with media noise values obtained from recording measurements. The media noise in SmCo/Cr disks varied little with increasing linear density, and no supralinear increase in noise as explained by a transition noise model was observed. A thin Cr underlayer (<100 nm) gave the lowest noise SmCo media. An isolated pulse-to-integrated-noise ratio of 44 dB and an overwritability of better than 45 dB were obtained for SmCo/Cr hard disks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Self‐assembling phospholipid tubules (1994)

Lipid‐based tubules serve as models for the development of advanced materials based upon molecular self‐assembly. The processes by which tubules are formed and how they are coated with metals (nickel in the Figure) or used as templates in order to increase the strength of the final material are described. Their electrical and magnetic properties are discussed. magnified image
Design of Novel Three-Dimensional Coordination Polymers Based on Triangular Trinuclear Copper 1,2,4-Triazolate Units (2006)

By controlling the molar ratios of copper dichloride dihydrate and 1,2,4-triazole (trz), we generated a series of novel three-dimensional coordination polymers constructed from μ3-oxo or μ3-Cl triangular copper units, exhibiting six-connected porous self-penetrating net, graphite layer, and inorganic−organic hybrid network structures, respectively.
Analysis of conformal antennas for avionics applications (2007)

Conformal antennas might have an important impact on communication and navigation applications on aircraft, ships and other vehicles. This thesis work presents a general study on conformal antennas and their potential application on aircraft structures. Several electromagnetic simulations are performed in order to provide a comparative analysis of arbitrary conformal antennas with their planar counterparts and determine the advantages and disadvantages of each case. The worthiness of integrating these antennas on aircraft fuselages is investigated by simulating the antennas on an aircraft footprint. In addition, a new type of conformal antenna is introduced. Some attractive characteristics of this antenna are its nearly omnidirectional radiation patterns and its small physical size compared to other microstrip antennas of the same frequency range. A prototype of this new structure is designed for the Galileo frequency band E1 (1.559 - 1.591 GHz) and circular polarization in one hemisphere.
Animal welfare: concepts and measurement2 (1991)

The term "welfare" refers to the state of an individual in relation to its environment, and this can be measured. Both failure to cope with the environment and difficulty in coping are indicators of poor welfare. Suffering and poor welfare often occur together, but welfare can be poor without suffering and welfare should not be defined solely in terms of subjective experiences. The situations that result in poor welfare are reviewed in this study with special reference to those in which an individual lacks control over interactions with its environment. The indicators of poor welfare include the following: reduced life expectancy, impaired growth, impaired reproduction, body damage, disease, immunosuppression, adrenal activity, behavior anomalies, and self-narcotization. The uses of measures of responsiveness, stereotypies, and animal preferences in welfare assessment are discussed. The need to make direct measurement of poor welfare as well as to use sophisticated studies of animal preferences is emphasized.
Micro-optical instrumentation for process spectroscopy (2004)

Traditional laboratory ultraviolet/visible/near-infrared spectroscopy instruments are tabletop-sized pieces of equipment that exhibit very high performance, but are generally too large and costly to be widely distributed for process control applications or used as spectroscopic sensors. Utilizing a unique, and proven, micro-optical technology platform origi-nally developed, qualified and deployed in the telecommunications industry, we have developed a new class of spectro-scopic micro-instrumentation that has laboratory quality resolution and spectral range, with superior speed and robust-ness. The fundamentally lower cost and small form factor of the technology will enable widespread use in process moni-toring and control. This disruption in the ground rules of spectroscopic analysis in these processes is enabled by the re-placement of large optics and detector arrays with a high-finesse, high-speed micro electro mechanical system (MEMS) tunable filter and a single detector, that enable the manufacture of a high performance and extremely rugged spectrome-ter in the footprint of a credit card. Specific process monitoring and control applications discussed in the paper include pharmaceutical, gas sensing and chemical processing applications.
Concentrating aqueous dispersions ofStaphylococcus Epidermidis bacteria by swelling of thermosensitive poly[(N-isopropylacrylamide)-co-(acrylic acid)] hydrogels (2000)

A novel method for concentrating of bacteria dispersions without loss of bacterial viability has been developed. Bioseparation was facilitated by the swelling of a thermoresponsive hydrogel in a dilute bacterial dispersion. Hydrogels were prepared by free radical copolymerization in aqueous solution of N-isopropylacrylamide (NIPA) and acrylic acid (AA) with N,N ′-methylene bisacrylamide (BIS) as crosslinker. Hydrogels of a single comonomer composition and three concentrations of BIS were employed. The potential of the corresponding xerogels as bioseparation devices was assessed by swelling to equilibrium at 5°C in aqueous dispersions of the bacterium Staphylococcus Epidermidis. The resultant increase in concentration of dispersion, the concentrated dispersion being commonly termed the `raffinate', was measured by the spread plate technique. An efficiency of separation η was obtained from this increase, coupled with that calculated from the measured degree of swelling. It has been shown that high values of η can be achieved. It has also been shown that separation efficiency is dependent on the procedure employed in the sampling of the concentrated dispersion. Without agitation of the swollen hydrogel/raffinate prior to sampling no concentration increase was measured, i. e. η was 0%. However, η increased to values of 50–80% on agitation (via a vortex mixer) of the hydrogel/raffinate prior to raffinate sampling. The need for agitation and the reduction in the value of η from its theoretical maximum (100%) may indicate the adsorption of the bacteria onto the surface of the hydrogel. The effect of the bacterial dispersion on the swelling properties of the hydrogels was also investigated. It was found that the swelling ratio (= mass of hydrogel/mass of xerogel) and lower critical swelling temperature of the hydrogels in the bacterial dispersion and pure water were identical.
The E3 Ubiquitin Ligase Ro52 Negatively Regulates IFN-β Production Post-Pathogen Recognition by Polyubiquitin-Mediated Degradation of IRF3 (2008)

Induction of type I IFNs is a fundamental cellular response to both viral and bacterial infection. The role of the transcription factor IRF3 is well established in driving this process. However, equally as important are cellular mechanisms for turning off type I IFN production to limit this response. In this respect, IRF3 has previously been shown to be targeted for ubiquitin-mediated degradation postviral detection to turn off the IFN-beta response. In this study, we provide evidence that the E3 ligase Ro52 (TRIM21) targets IRF3 for degradation post-pathogen recognition receptor activation. We demonstrate that Ro52 interacts with IRF3 via its C-terminal SPRY domain, resulting in the polyubiquitination and proteasomal degradation of the transcription factor. Ro52-mediated IRF3 degradation significantly inhibits IFN-beta promoter activity, an effect that is reversed in the presence of the proteasomal inhibitor MG132. Specific targeting of Ro52 using short hairpin RNA rescues IRF3 degradation following polyI:C-stimulation of HEK293T cells, with a subsequent increase in IFN-beta production. Additionally, shRNA targeting of murine Ro52 enhances the production of the IRF3-dependent chemokine RANTES following Sendai virus infection of murine fibroblasts. Collectively, this demonstrates a novel role for Ro52 in turning off and thus limiting IRF3-dependent type I IFN production by targeting the transcription factor for polyubiquitination and subsequent proteasomal degradation.
Thermal analysis and validation of MCMs (2002)

A thermal analysis methodology has been developed for modules with multiple heat sources to expedite the thermal design cycle, the majority of which takes place prior to the delivery of functional silicon. This methodology utilizes linear superposition to comprehend interactions between various heat sources within an MCM. Therefore, it is applicable to designs where material properties can be assumed constant with respect to the temperature range of interest. In design applications, this methodology can be used with good results for forced convection boundary conditions, as well as (within acceptable design limitations) natural convection boundary conditions. A case study is presented herein to demonstrate the analysis techniques and to validate the method using experimental data. Although design specific data has not been incorporated here, this methodology proved its usefulness in the next generation DRAM thermal design.