gebhart/patrepeval huggingface dataset:
σ <sup>B</sup> Activity in a <i>Staphylococcus aureus hemB</i> Mutant (2005)

Inactivation of hemB in Staphylococcus aureus strain Newman resulted in a small-colony phenotype and was accompanied by an altered expression pattern of global regulators and control of virulence factor production. Transcription profiles followed over 15 h by Northern blot analyses revealed that transcripts of the global regulators arl, rot, sae, sarR, sarS, srr, svrA, and sigB disappeared after the exponential phase and that both agr transcripts were completely absent in the hemB mutant. Apart from a general concentration of transcriptional activity to the exponential phase, premature gene expression was observed for rot, hla, and spa. Nevertheless, reported sigmaB-dependent transcripts, such as sarC and clfA, were produced throughout the 15-h growth period monitored. The absence of these transcripts in a hemB sigB double mutant demonstrated their dependence on sigmaB and indicated an unexpected, permanent sigmaB activity in the hemB mutant. Variations in the extents of the directly sigmaB-controlled asp23, rsbVW-sigB, and sarC transcripts argue for additional factors modulating sigmaB activity. This study provides the first extended synopsis of the transcriptional patterns of different regulators over the entire growth cycle in the widely used Newman strain.
ESD protection consideration in nanoscale CMOS technology (2011)

The thinner gate oxide in nanoscale CMOS technologies seriously degraded the electrostatic discharge (ESD) robustness of IC products. As the feature sizes in nanoscale CMOS technologies are further scaling down, the on-chip ESD protection designs are more challenging. The ESD protection considerations, including ESD design window, area efficiency, leakage current, and high-voltage tolerance, were presented in this abstract. Some possible solutions against these issues in nanoscale CMOS technologies were also included in this paper.
Review of Third Generation Light Sources (2010)

In 1994, ESRF in Grenoble opened the era of third-generation light sources, and the first batch of third-generation machines immediately followed with ALS, Elettra, TLS, PLS, and Spring-8 in hard and soft X-ray regimes. For high brightness, these machines adopted a low-emittance storage-ring lattice and many straight sections for advanced undulators. With ever-growing user demands from materials science to life science research, many more facilities followed in this decade. The machine operations dramatically improved for more effective user services, along with technological advances in advanced diagnostics and controls, survey and alignments, top-up injections, super-conducting cavities, and in-vacuum undulators. There are now about 70 light sources in the world, and important scientific discoveries are driven from these facilities, including research resulting in a few Nobel Prizes. In this paper, we review the advancement of these third-generation machines.
Effect of Multiple-Transistor Charge Collection on Single-Event Transient Pulse Widths (2011)

Heavy-ion data from a 130-nm bulk CMOS process shows a counterproductive result in using a common single-event charge collection mitigation technique. Guard bands, which are well contacts that surround individual transistors, can reduce single-event pulsewidths for normal strikes, but increase them for angled strikes. Calibrated 3-D TCAD mixed-mode modeling has identified a multiple-transistor charge collection mechanism that explains the experimental data, namely that angled strikes result in charge collection in the normally ON device that increases the restoring current on the struck device.
Surface acoustic wave resonators on a ZnO-on-Si layered medium (1983)

The adaptation of surface acoustic wave resonator technology to a ZnO-on-Si layered medium is presented. Several distributed reflector schemes are considered, including shorted and isolated metallic strips, as well as grooves etched in the ZnO layer. In the case of etched groove reflectors, a first-order velocity perturbation arises due to the dispersive nature of the layered medium. Unique resonator design considerations result from the reflector array velocity and reflectivity characteristics. Transverse mode resonances are characterized and their effect on resonator response eliminated by a novel transducer design. A technique for temperature compensating the devices by use of a thermal SiO2 layer is discussed.
Modelling transcriptional regulation using Gaussian processes (2007)

Modelling the dynamics of transcriptional processes in the cell requires the knowledge of a number of key biological quantities.While some of them are relatively easy to measure, such as mRNA decay rates and mRNA abundance levels, it is still very hard to measure the active concentration levels of the transcription factor proteins that drive the process and the sensitivity of target genes to these concentrations.In this paper we show how these quantities for a given transcription factor can be inferred from gene expression levels of a set of known target genes.We treat the protein concentration as a latent function with a Gaussian process prior, and include the sensitivities, mRNA decay rates and baseline expression levels as hyperparameters.We apply this procedure to a human leukemia dataset, focusing on the tumour repressor p53 and obtaining results in good accordance with recent biological studies.
A multi-stage neural network classifier for ECG events (2005)

In this paper, a multi-stage network including two multilayer perceptron (MLP) and one self organizing map (SOM) networks is presented. The input of the network is a combination of independent features and the compressed ECG data. The proposed network as a form of data fusion, performs better than using the raw data or individual features. We classified six common ECG waveforms using ten ECG records of the MIT/BIH arrhythmia database. An average recognition rate of 0.883 was achieved within a short training and testing time.
Radiation hardening of polytetrafluoroethylene against chemical etching (1988)

Abstract Exposure of polytetrafluoroethylene (PTFE) to MgKα x‐rays (1253.6 eV) for times as short as 10 min is observed to lead to permanent radiation hardening toward chemical etching. X‐ray‐dosed surfaces are visibly less etched, and the loss of F is over a factor of 2 smaller. For PTFE itself, the x‐ray photoelectron spectrum shows only slight changes for x‐ray exposures up to several hours, but thermal desorption spectroscopy yields a direct correlation between the desorption of low‐molecular‐weight fluorocarbons and x‐ray exposures down to the order of minutes. Irradiation of PTFE is know to lead to molecular weight degradation and branching and/or crosslinking through free radical reactions. The degradation reactions are the source of the low‐molecular‐weight fluorocarbons which desorb at elevated temperatures. Branching and/or crosslinking, which produce a more rigid, thermally stable structure, are proposed as the mechanism for resistance to chemical etching. Similar resistance to chemical etching, in the absence of x‐rays, is observed for the fluorinated ethylene‐propylene copolymer which contains intrinsic fluorinated methyl group side chains.
Attention meter (2006)

This paper shows how a software toolkit can allow graphic designers to make camera-based interactive environments in a short period of time without experience in user interface design or machine vision. The Attention Meter, a vision-based input toolkit, gives users an analysis of faces found in a given image stream, including facial expression, body motion, and attentive activities. This data is fed to a text file that can be easily understood by humans and programs alike. A four day workshop demonstrated that some Flash-savvy architecture students could construct interactive spaces (e.g. TaiKer-KTV and ScreamMarket) based on body and head motions.
Filling the gap in LNAantisense oligo gapmers: the effects of unlocked nucleic acid (UNA) and 4′- <i>C</i> -hydroxymethyl-DNA modifications on RNase H recruitment and efficacy of an LNA gapmer (2009)

Stability against nucleases, affinity for the targeted mRNA and the ability to recruit RNase H are prerequisites for antisense oligonucleotide (AON) applications where gene expression knockdown is required. Typically chimeric gapmer AON designs are used with a central continuous stretch of RNase H recruiting nucleotides (e.g. phosphorothioate DNA), flanked by affinity and stability-enhancing modified nucleotides. However, many types of nucleotide modifications in the central DNA gap can disturb RNase H function. Here we present studies into two different types of nucleotide modifications, a flexible acyclic RNA analog named unlocked nucleic acid (UNA) and 4'-C-hydroxymethyl-DNA in the gap of an LNA (locked nucleic acid) flanked gapmer. We compared the efficacy of mRNA degradation by the gap modified LNA antisense gapmers in cell-free assays and cultured cells. This study shows that both UNA and 4'-C-hydroxymethyl-DNA gap insertions are compatible with RNase H activity when used sparingly. However, multiple 4'-C-hydroxymethyl-DNA modifications are better tolerated by RNase H than multiple UNA modifications in the gap. Furthermore, this report shows that LNA gapmer AONs with multiple 4'-C-hydroxymethyl-DNA moieties in the gap can mediate target knockdown in vivo.
Re - Creating the Botanics: Towards a Sense of Place in Virtual Environments (2003)

The EC funded project BENOGO seeks to re-create real places using photo-realisticimmersive virtual reality technology and in so doing investigates the nature ofpresence and sense of place in such environments. We discuss the first stages in ourwork investigating how far a sense of place can be created in a virtual environmentand benchmarked against the real world. This paper reports early studies whichinvestigated sense of place in a real-world location – a glasshouse in a botanicalgarden – and the first in a series of planned experiments with its virtual equivalent.The results provide preliminary indications of which elements of sense of placemanage to penetrate the considerable constraints of the current virtual environmentand how the virtual experience might be redesigned in future. We also discusstechniques for investigating sense of place in this context and briefly describe the nextsteps in the work.
Calcium sulphate dihydrate: an useful excipient for tablets containing labile actives. (2004)

Tablets containing an angiotensin-converting enzyme inhibitor and either calcium sulphate dihydrate or lactose monohydrate as main excipients (fillers) exhibited similar technical properties and stability.
Photochemistry of adsorbed molecules. XV. Localized atomic scattering in the photolysis of HI/LiF(001) and HI/NaF(001) (1996)

We have compared the ‘‘elastic’’ H atom angular-scattering, Pel(θ′), of HI(ad) photolyzed at 248 nm for LiF and NaF substrates, both experimentally and theoretically. The observed Pel(θ′) for elastic scattering were similar for LiF and NaF, with a peak in the range 43°–48°. The Pel(θ′) for H from HI/NaF was broader than that for H from HI/LiF. Energy distributions, P(ET′), for H recoiling from HI/LiF and HI/NaF are also reported. A semiempirical potential-energy surface (pes) is given for HI adsorbed on NaF, based on an earlier one for LiF [J. Chem. Phys. 94, 978 (1991)]. Ab initio ‘‘density function theory’’ (DFT) calculations were performed to verify the suitability of this pes; the DFT points were in satisfactory agreement with the semiempirical pes. For HI/LiF the DFT calculation gave a heat of adsorption of about 9 kcal/mol, the semiempirical model gave 5 kcal/mol, and experiment gave 7 kcal/mol. We have computed H atom scattering by the classical trajectory method for two different models one involving dense and the other perforated arrangements of the HI adsorbate molecules. Comparison with the experimental results showed that the second model gave a better description of both Pel(θ′) and P(ET′) for HI/LiF and HI/NaF. The calculations showed that the angular and energy distributions of the scattered H were sensitive to the size of the vacancies between adjacent adsorbate molecules. The study also indicates the importance of unit-cell size in relation to the size of the adsorbate molecule in determining adsorbate geometry and hence the energy and angular distributions of the scattered photofragments.
Progress and Challenges Towards Terahertz CMOS Integrated Circuits (2010)

Key components of systems operating at high millimeter wave and sub-millimeter wave/terahertz frequencies, a 140-GHz fundamental mode voltage controlled oscillator (VCO) in 90-nm CMOS, a 410-GHz push-push VCO with an on-chip patch antenna in 45-nm CMOS, and a 125-GHz Schottky diode frequency doubler, a 50-GHz phase-locked loop with a frequency doubled output at 100 GHz, a 180-GHz Schottky diode detector and a 700-GHz plasma wave detector in 130-nm CMOS are demonstrated. Based on these, and the performance trends of nMOS transistors and Schottky diodes fabricated in CMOS, paths to terahertz CMOS circuits and systems including key challenges that must be addressed are suggested. The terahertz CMOS is a new opportunity for the silicon integrated circuits community.
ADAMTS-4 activity in synovial fluid as a biomarker of inflammation and effusion (2015)

The main finding of this study is that ADAMTS-4 levels in synovial fluid are most strongly correlated with inflammation and severity of effusion in the knee. Further study is required to determine if it could provide a useful tool to aid clinical diagnoses, indicate treatment, to monitor progression of joint degeneration or OA or alternatively the success of treatment.
Enhancement of detection and quantification of rotavirus in stool using a modified real‐time RT‐PCR assay (2008)

A sensitive and specific real-time RT-PCR assay to detect rotavirus in stool samples was optimized and validated using a wide range of rotavirus genotypes. The target of the original TaqMan(R) assay is an 87 bp fragment of the highly conserved non-structural protein 3 (NSP3) gene. Here we modified the original assay by introducing degeneracy into the forward primer to account for sequence variation between rotavirus genotypes, added four nucleotides at the 3' end of the reverse primer to reduce its stability, and modified the probe label. Amplification and detection conditions were optimized using purified dsRNA from two cultivated strains. The limit of detection of the modified assay was calculated to be approximately 44 genome copies per reaction. To validate the reactivity of the assay, 103 archived RNAs that had been extracted from stools and genotyped during routine U.S. surveillance were tested. Samples were selected to represent both rare and common genotypes that have been detected in U.S. children. Nine genotypes known to be circulating in the United States were detected by the real-time assay demonstrating broad reactivity. In addition, other enteric viruses were not detected demonstrating that the assay is specific for rotavirus and does not cross-react with other viruses potentially present in stool samples. This real-time assay is an important addition to the arsenal of molecular tools available to quickly identify rotavirus in stool samples during routine surveillance.
Fungal Zoospore-Mediated Delivery of a Foreign Gene to Wheat Roots (1994)

The primitive fungus Olpidium brassicae is an obligate plant parasite that acts as a natural virus vector transmitting tobacco necrosis virus and certain other viruses to roots of many monocotyledonous and dicotyledonous plants. Plasmid pAM981, carrying the chloramphenicol acetyltransferase (CAT) gene, was packaged by dissociated capsid protein of tobacco necrosis virus. The resulting nucleoprotein complexes were acquired by O. brassicae zoospores and transmitted to wheat roots. Transient expression of CAT in wheat roots was detected, indicating that transformation can be achieved if plants can be regenerated from root tissue
Establishment of a Cell-Based Assay for Screening of Compounds Inhibiting Very Early Events in the Cytomegalovirus Replication Cycle and Characterization of a Compound Identified Using the Assay (2008)

To simplify the detection of infectious human cytomegalovirus (HCMV), we generated a cell line that produced luciferase in a dose-dependent manner upon HCMV infection. Using this cell line, we identified anti-HCMV compounds from a diverse library of 9,600 compounds. One of them, 1-(3,5-dichloro-4-pyridyl)piperidine-4-carboxamide (DPPC), was effective against HCMV (Towne strain) infection of human lung fibroblast cells at a 50% effective concentration of 2.5 microM. DPPC also inhibited the growth of clinical HCMV isolates and guinea pig and mouse cytomegaloviruses. Experiments using various time frames for treatment of the cells with DPPC demonstrated that DPPC was effective during the first 24 h after HCMV infection. DPPC treatment decreased not only viral DNA replication but also IE1 and IE2 expression at mRNA and protein levels in the HCMV-infected cells. However, DPPC did not inhibit the attachment of HCMV particles to the cell surface. DPPC is a unique compound that targets the very early phase of cytomegalovirus infection, probably by disrupting a pathway that is important after viral entry but before immediate-early gene expression.
Vaccine-Associated Paralytic Poliomyelitis: A Review of the Epidemiology and Estimation of the Global Burden (2014)

Because many high-income countries have replaced OPV with inactivated poliovirus vaccine, the VAPP burden is concentrated in lower-income countries. The planned universal introduction of inactivated poliovirus vaccine is likely to substantially decrease the global VAPP burden by 80%-90%.
Quantitative genome-scale analysis of protein localization in an asymmetric bacterium (2009)

Despite the importance of subcellular localization for cellular activities, the lack of high-throughput, high-resolution imaging and quantitation methodologies has limited genomic localization analysis to a small number of archival studies focused on C-terminal fluorescent protein fusions. Here, we develop a high-throughput pipeline for generating, imaging, and quantitating fluorescent protein fusions that we use for the quantitative genomic assessment of the distributions of both N- and C-terminal fluorescent protein fusions. We identify nearly 300 localized Caulobacter crescentus proteins, up to 10-fold more than were previously characterized. The localized proteins tend to be involved in spatially or temporally dynamic processes and proteins that function together and often localize together as well. The distributions of the localized proteins were quantitated by using our recently described projected system of internal coordinates from interpolated contours (PSICIC) image analysis toolkit, leading to the identification of cellular regions that are over- or under-enriched in localized proteins and of potential differences in the mechanisms that target proteins to different subcellular destinations. The Caulobacter localizome data thus represent a resource for studying both global properties of protein localization and specific protein functions, whereas the localization analysis pipeline is a methodological resource that can be readily applied to other systems.
Construction of a low speed flux focusing magnetic gear (2013)

The experimental results are presented for a low speed flux focusing magnetic gear utilizing ferrite magnets. The performance of this ferrite magnetic gear is compared with a hybrid magnet magnetic gear with NdFeB magnets on the inner rotor and ferrite magnets on the outer rotor. The peak torque and efficiency is measured.
An N-glycosylation Analysis of Human Alpha-2-Macroglobulin Using an Integrated Approach (2012)

Assignment of glycosylation sites and site microheterogeneity is of both biological and clinical significance. Herein, the detailed N-glycosylation pattern of human serum alpha-2-macroglobulin was studied using an integrative approach, including permethylation of N-glycans, collision induced dissociation (CID) and electron transfer dissociation (ETD) of chymotryptic N-glycopeptides, and partial deglycosylation of chymotryptic N-glycopeptides with endo-β-N-acetylglucosaminidase F3 (Endo F3). Three N-glycosylation sites were found to be occupied by four biantennary complex type N-glycans using N-glycan analysis and the ETD/CID method. Endo F3 assisted mass spectrometric analysis yielded five N-glycosylation sites with and without core fucosylation. In total, six out of eight potential N-glycosylation sites were identified using this approach. This integrative approach was performed using only 10 μL of human serum for both N-glycosylation site assignment and site microheterogeneity determination.
Optical encryption based on computational ghost imaging (2010)

Ghost imaging is an optical technique in which the information of an object is encoded in the correlation of the intensity fluctuations of light. The computational version of this fascinating phenomenon emulates, offline, the optical propagation through the reference arm, enabling 3D visualization of a complex object whose transmitted light is measured by a bucket detector. In this Letter, we show how computational ghost imaging can be used to encrypt and transmit object information to a remote party. Important features, such as key compressibility and vulnerability to eavesdropping, are experimentally analyzed.
Flooding frequencies for urban drainage design (1966)

The effects on expected rainfall intensity, run off, pipe sizes and cost, of using different flooding frequencies for road drainage design are illustrated for a typical situation, Sydney.
Global Elimination Algorithm and Architecture Design for Fast Block Matching Motion Estimation (2004)

This paper presents a new block matching motion estimation algorithm and its VLSI architecture design. The proposed global elimination algorithm (GEA) was derived from successive elimination algorithm (SEA), which can skip unnecessary sum of absolute difference (SAD) calculation by comparing minimum SAD with subsampled SAD (SSAD). Our basic idea is to separate the decision of early termination and SAD calculation for each candidate block to make data flow more regular and suitable for hardware. In short, we first compare the rough characteristics of all candidate blocks with the current block (SSAD). In turn, we select several best roughly matched candidate blocks to re-compare them with the current block by using detailed characteristics (SAD). Other features of GEA include fixed processing cycles, no initial guess, and high video quality (almost the same as full search). Unlike other fast algorithms, the mapping of GEA to hardware is very simple. We proposed an architecture that is composed of a systolic part to efficiently compute SSAD, an adder tree to support both SSAD and SAD calculations, and a comparator tree to avoid expensive sorting circuits. Simulation results show that our design is much more area efficient than many full-search architectures while maintaining high video quality and processing capability.