gebhart/patrepeval huggingface dataset:
Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize (2010)

High-copy transposons have been effectively exploited as mutagens in a variety of organisms. However, their utility for phenotype-driven forward genetics has been hampered by the difficulty of identifying the specific insertions responsible for phenotypes of interest. We describe a new method that can substantially increase the throughput of linking a disrupted gene to a known phenotype in high-copy Mutator (Mu) transposon lines in maize. The approach uses the Illumina platform to obtain sequences flanking Mu elements in pooled, bar-coded DNA samples. Insertion sites are compared among individuals of suitable genotype to identify those that are linked to the mutation of interest. DNA is prepared for sequencing by mechanical shearing, adapter ligation, and selection of DNA fragments harboring Mu flanking sequences by hybridization to a biotinylated oligonucleotide corresponding to the Mu terminal inverted repeat. This method yields dense clusters of sequence reads that tile approximately 400 bp flanking each side of each heritable insertion. The utility of the approach is demonstrated by identifying the causal insertions in four genes whose disruption blocks chloroplast biogenesis at various steps: thylakoid protein targeting (cpSecE), chloroplast gene expression (polynucleotide phosphorylase and PTAC12), and prosthetic group attachment (HCF208/CCB2). This method adds to the tools available for phenotype-driven Mu tagging in maize, and could be adapted for use with other high-copy transposons. A by-product of the approach is the identification of numerous heritable insertions that are unrelated to the targeted phenotype, which can contribute to community insertion resources.
Macrophage infiltration correlates with tumor stage and angiogenesis in human malignant melanoma: possible involvement of TNFalpha and IL-1alpha. (2000)

We examined whether macrophage infiltration is associated with angiogenesis in cutaneous melanoma. The numbers of macrophages and microvessels increased significantly with increasing depth of tumor and with tumor angiogenesis. Macrophage infiltration thus appeared to provide a useful diagnostic marker for the progression of cutaneous melanoma. We further examined whether human melanoma cells produce angiogenic factors in response to macrophage-derived cytokines, tumor necrosis factor alpha (TNFalpha) and interleukin-1 alpha (IL-1alpha). Treatment of melanoma cells with TNFalpha and IL-1alpha in vitro enhanced the production of interleukin-8 (IL-8) and vascular endothelial growth factor (VEGF), and of basic fibroblast growth factor (bFGF) to a lesser degree, in human melanoma cells. Lipopolysaccharide (LPS)-activated human monocytes enhanced production of IL-8, VEGF, TNF alpha, as well as IL-1alpha, but not bFGF. Co-culture of human monocytes and human melanoma cells was also found to significantly enhance production of IL-8 and VEGF in the absence and presence of LPS, compared with either monocytes or melanoma cells alone. The production of IL-8 and VEGF from co-cultured melanoma cells and LPS-activated monocytes was blocked when anti-TNF-alpha antibody or anti-IL-1alpha antibody was co-administrated. This is direct evidence that production of the potent angiogenic factors IL-8 and VEGF from melanoma cells is up-regulated through TNFalpha and/or IL-1alpha secreted by activated monocytes/macrophages, influencing both tumor growth and angiogenesis in melanomas.
The use of a wate-soluble carbodiimide as a coupling reagent in the passive hemagglutination test. (1966)

A simplified method is described for coupling proteins to red cells using the water-soluble carbodiimide, 1 - ethyl - 3 - (3 - dimethylaminopropyl) carbodiimide hydrochloride. The procedure is simpler than BDB coupling and the sensitized cells are more stable than those in the BDB system. The data indicated a marked similarity in the specificity and sensitivity of ECDI-and BDB-hemagglutination.
Aspects of error resilience for block based video coders in multimedia communications (1996)

Publisher Summary This chapter discusses the aspects of error resilience for block-based video coders. To stop the accumulation of errors in a video sequence, INTRA frames are sent at a higher rate to refresh the error-affected scene. Because of their sensitivity, I-frames need to be protected against errors to meet the requirements of their transmission. The robust I-frame error-resilience algorithm used with the H.263 video coder yields better robustness than conventional codes. It has been shown that two-way decoding algorithm is an efficient error-resilience algorithm when used with reversible code words. This helps to locate the erroneous bits and the affected area to minimize the effect of error on the overall QoS. Synchronization of the video decoder can be recovered with a negligible increase in the overall bit rate.
Evaluation of papnet<sup>trade;</sup> system for rescreening of negative cervical smears (1995)

We rescreened 2,238 cervicovaginal smears conventionally prepared with Papanicolaou stain by PAPNET system. The slides screened manually as negative, were sent to PAPNET system. The image tapes were reviewed on a high-resolution monitor, and categorized as negative, unsatisfactory, and atypical. All atypical cases were rescreened manually. Abnormal cases were reviewed by a cytopathologist. Two-thousand one hundred and two (94%) cases rescreened by PAPNET were negative. Nine of 45 unsatisfactory cases by PAPNET were unsatisfactory by manual review. Ninety-one (4.0%) cases by PAPNET were atypical. On manual rescreening, 86 of 91 were negative, 20% showing benign cellular changes; five of 91 were atypical, the atypia, however, not exceeding low-grade category. The detection rate by PAPNET method was 0.2% (five of 2,238 cases). We conclude: 1) In a cytology laboratory with good quality control, PAPNET rescreening does not significantly increase the detection rate. 2) For cytology laboratories without in-house rescreening, PAPNET offers an alternative at a price. 3) The PAPNET system also offers a tool by which a laboratory can occasionally monitor its performance. 4) The cost benefit analysis of the system requires further study and scrutiny.
Importance of nitric oxide for local increases of blood flow in rat cerebellar cortex during electrical stimulation. (1994)

The endothelium-derived relaxing factor, probably nitric oxide (NO), is a potent vasodilator that regulates the vascular tone in several vascular beds, including the brain. We explored the possibility that NO might be of importance for the increase of cerebral blood flow (CBF) associated with activity of the well-defined neuronal circuits of the rat cerebellar cortex. Laser-Doppler flowmetry was used to measure increases of cerebellar blood flow evoked by trains of electrical stimulations of the dorsal surface. The evoked increases of CBF were frequency-dependent, being larger on than off the parallel fiber tracts, suggesting that conduction along parallel fibers and synaptic activation of target cells were important for the increase of CBF. This was verified experimentally since the evoked CBF increases were abolished by tetrodotoxin and reduced by 10 mM Mg2+ and selective antagonists for non-N-methyl-D-aspartate receptors. The cerebellar cortex contains high levels of NO synthase. This raised the possibility that NO was involved in the increase of CBF associated with neuronal activation. NO synthase inhibition by topical application of NG-nitro-L-arginine attenuated the evoked CBF increase by about 50%. This effect was partially reversed by pretreatment with L-arginine, the natural substrate for the enzyme, while NG-nitro-D-arginine, the inactive enantiomer, had no effect on the evoked CBF increases. Simultaneous blockade of non-N-methyl-D-aspartate receptors and NO synthase had no further suppressing effect on the blood flow increase than either substance alone, suggesting that the NO-dependent flow rise was dependent on postsynaptic mechanisms. These findings are consistent with the idea that local synthesis of NO is involved in the transduction mechanism between neuronal activity and increased CBF.
Blood compatibility of heparinized polyurethanes (1985)

Heparin - immobilized polyurethane (HI-PU) catheters implanted in canine femoral and jugular veins for one hour periods exhibited significant reduction in thrombus formation compared with untreated PU contralateral controls. PU catheters coated with a 9% heparin dispersion in PU, capable of releasing active heparin for several hours, provided even greater improvement in antithrombogenicity. Both types of heparinized surface displayed reduced platelet aggregation and fibrin formation, although platelet adhesion was somewhat higher on the HI material than on the heparin-releasing (HR) surface.
A Semantic Enhanced Service Proxy Framework for Internet of Things (2010)

This paper proposes a semantic enhanced service proxy framework for internet-of-things cloud. The framework exposes IoT cloud's smart objects as services by virtue of service orientation and virtualization. The framework uses an adapter oriented approach to address the issue of connectivity with different types of smart objects. We employ a query based service re-route mechanism to decouple service provider and service consumer. We propose micro-formats based service description template for associating smart object location with its service end-point. As a step toward enhancing smart objects service publication and discovery, we adopt a service advertisement approach within the IoT cloud perimeter that automates service publication and discovery process. Our proof-of-concept prototype implementation shows that the existing technology enablers are capable of realizing the service oriented IoT vision, which does not only plug smart objects into the internet but also link the information resided in smart objects into the fabric of the web.
Multilevel Amplitude Modulation Using A Composite-Resonator Vertical-Cavity Laser (2009)

Modulation characteristics of a composite-resonator vertical-cavity laser (CRVCL) can be engineered by modulating the carrier and photon densities in the two optically coupled cavities simultaneously. The total modulation response is a superposition of the individual modulation response from each cavity, when direct modulation is applied to both cavities. This property enables the CRVCL to produce multilevel signaling for optical communication. A demonstration of four-level amplitude modulation at 2.5 Gb/s is shown.
Microbial Cellulases and Their Industrial Applications (2011)

Microbial cellulases have shown their potential application in various industries including pulp and paper, textile, laundry, biofuel production, food and feed industry, brewing, and agriculture. Due to the complexity of enzyme system and immense industrial potential, cellulases have been a potential candidate for research by both the academic and industrial research groups. Nowadays, significant attentions have been devoted to the current knowledge of cellulase production and the challenges in cellulase research especially in the direction of improving the process economics of various industries. Scientific and technological developments and the future prospects for application of cellulases in different industries are discussed in this paper.
Decision criteria for the selectionof analytical instruments usedin clinical chemistry: III Non–monetary criteria (1980)

This article has no abstract.
Host Cell Detection of Noncoding Stuffer DNA Contained in Helper-Dependent Adenovirus Vectors Leads to Epigenetic Repression of Transgene Expression (2009)

Helper-dependent adenovirus (hdAd) vectors have shown great promise as therapeutic gene delivery vehicles in gene therapy applications. However, the level and duration of gene expression from hdAd can differ considerably depending on the nature of the noncoding stuffer DNA contained within the vector. For example, an hdAd containing 22 kb of prokaryotic DNA (hdAd-prok) expresses its transgene 60-fold less efficiently than a similar vector containing eukaryotic DNA (hdAd-euk). Here we have determined the mechanistic basis of this phenomenon. Although neither vector was subjected to CpG methylation and both genomes associated with cellular histones to similar degrees, hdAd-prok chromatin was actively deacetylated. Insertion of an insulator element between the transgene and the bacterial DNA derepressed hdAd-prok, suggesting that foreign DNA nucleates repressive chromatin structures that spread to the transgene. We found that Sp100B/Sp100HMG and Daxx play a role in repressing transgene expression from hdAd and act independently of PML bodies. Thus, we have identified nuclear factors involved in recognizing foreign DNA and have determined the mechanism by which associated genes are repressed.
The structures of the lipooligosaccharide and capsule polysaccharide of <i>Campylobacter jejuni</i> genome sequenced strain NCTC 11168 (2002)

Campylobacter jejuni infections are one of the leading causes of human gastroenteritis and are suspected of being a precursor to Guillain-Barré and Miller-Fisher syndromes. Recently, the complete genome sequence of C. jejuni NCTC 11168 was described. In this study, the molecular structure of the lipooligosaccharide and capsular polysaccharide of C. jejuni NCTC 11168 was investigated. The lipooligosaccharide was shown to exhibit carbohydrate structures analogous to the GM1a and GM2 carbohydrate epitopes of human gangliosides (shown below): The high Mr capsule polysaccharide was composed of beta-d-Ribp, beta-d-GalfNAc, alpha-d-GlcpA6(NGro), a uronic acid amidated with 2-amino-2-deoxyglycerol at C-6, and 6-O-methyl-d-glycero-alpha-l-gluco-heptopyranose as a side-branch (shown below): The structural information presented here will aid in the identification and characterization of specific enzymes that are involved in the biosynthesis of these structures and may lead to the discovery of potential therapeutic targets. In addition, the correlation of carbohydrate structure with gene complement will aid in the elucidation of the role of these surface carbohydrates in C. jejuni pathogenesis.
<sup>14</sup>N NQR spectrometer for explosive detection: A review (2016)

The explosive detection via NQR is based on presence of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> N as all explosives usually contain nitrogen. The detected nitrogen nuclei contained in explosives and other nitrogen containing materials gives different frequencies and also different explosives have their own NQR frequencies, explosives can be detected and uniquely identified by <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> N NQR frequency. A Review on research and development in the field of detection of <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> N using NQR has been presented in this paper.
Virtual Modeling of Urban Environments (1996)

Researchers at UCLA's Departments of Architecture and Urban Planning are using state-of-the-art visual simulation technology to build virtual worlds that can be used by planners, designers, and community groups to visualize and evaluate proposed changes and new developments in the urban environment. This paper focuses on the modeling methodology that has evolved for efficiently creating three-dimensional (3D) virtual urban worlds. It is illustrated with reference to actual projects that have recently been completed or are currently under development.
An Implementation Technique for Walsh Functions (1971)

A technique is presented for the generation of any finite set of Walsh functions in both serial and parallel form. It uses a straightforward constructive definition of these functions. In order to simultaneously generate the first 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> functions, [(2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2n</sup> -1)/3] storage devices and (2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n+2</sup> -5) logic gates are required.
Inline automated defect classification: a novel approach to defect management (2005)

In this work, we have developed a specific automated classification scheme based on defect size, pattern density, and optical polarity. According to our defectivity control plan, this scheme has been applied to brightfield inspections across multiple devices, as well as to our 120 nm and 90 nm technologies. The classifiers account for both size and location, while distinguishing between killer and non killer defects. The defects in array areas have higher kill ratios (KR) than those in logic or open areas. Similarly, extra-pattern defects (bright pixels) have higher KR than particles (dark pixels). After a period of baselining, we were able to set control limits for each class at each layer. Out-of-spec events can be triggered by both total and killer defect densities. As a result, we can now focus our scanning electron microscope (SEM) review primarily on those defects classified by inline automated defect classification (iADC) as killers, thus enabling better utilization of this expensive tool. As the population of SEM-reviewed defects became biased, we re-normalized to the individual iADC bin populations. iADC classification can ultimately be used to prioritize yield activity based on bin-to-defect correlation. Calculating kill ratios per iADC bin by layer provides statistically significant information, unlike total defect densities. We have shown that iADC can be used for the three main defectivity control activities: excursion monitoring, evaluation of experiments, and yield improvement through yield impact evaluation
An Improved Continuous Flow Diffusion Cloud Chamber (1976)

A slightly improved version of the continuous flow diffusion cloud chamber which has been described earlier (Hudson and Squires, 1973) has been rotated so that the plates are vertical instead of horizontal, the air flow remaining horizontal. Without other modification, its count agrees with that of the improved horizontal version to within about 1% over the supersaturation range 1.0–0.5%. The vertical mode of operation has certain advantages over even the improved horizontal chamber; in particular, it extends downward the supersaturation range over which reliable results can be obtained. Satisfactory plateaus can be obtained at least down to a supersaturation of about 0.1%. Two vertical chambers have been found to agree to about 1% in the supersaturation range 1.0–0.25%, and to about 10% down to a supersaturation of 0.1%.
Mapping of SPARC/BM-40/Osteonectin-binding Sites on Fibrillar Collagens (2008)

The 33-kDa matrix protein SPARC (BM-40, osteonectin) binds several collagen types with moderate affinity. The collagen-binding site resides in helix alphaA of the extracellular calcium-binding domain of SPARC and is partially masked by helix alphaC. Previously, we found that the removal of helix alphaC caused a 10-fold increase in the affinity of SPARC for collagen, and we identified amino acids crucial for binding by site-directed mutagenesis. In this study, we used rotary shadowing, CNBr peptides, and synthetic peptides to map binding sites of SPARC onto collagens I, II, and III. Rotary shadowing and electron microscopy of SPARC-collagen complexes identified a major binding site approximately 180 nm from the C terminus of collagen. SPARC binding was also detected with lower frequency near the matrix metalloproteinase cleavage site. These data fit well with our analysis of SPARC binding to CNBr peptides, denaturation of which abolished binding, indicating triple-helical conformation of collagen to be essential. SPARC binding was substantially decreased in two of seven alpha2(I) mutant procollagen I samples and after N-acetylation of Lys/Hyl side chains in wild-type collagen. Synthetic peptides of collagen III were used to locate the binding sites, and we found SPARC binding activity in a synthetic triple-helical peptide containing the sequence GPOGPSGPRGQOGVMGFOGPKGNDGAO (where O indicates 4-hydroxyproline), with affinity for SPARC comparable with that of procollagen III. This sequence is conserved among alpha chains of collagens I, II, III, and V. In vitro collagen fibrillogenesis was delayed in the presence of SPARC, suggesting that SPARC might modulate collagen fibril assembly in vivo.
Titanium Oxide Nanoparticles Precipitated from Low‐Temperature Aqueous Solutions: III. Thin Film Properties (2011)

In our previous reports (Part I and II), we have identified precursor “supersaturation” as a key parameter to control the precipitation behavior of titania nanoparticles in a temperature‐driven hydrolysis process from the chemical bath of soluble titanium salt. Through this protocol, a methodology was developed to grow titania films with controlled microstructures and phases. In this study, we deposited titania films containing anatase or rutile as a dominant phase along with microstructures of various film densities, which were characterized for their dielectric, optical, photoelectrochemical, and mechanical properties. Specific microstructures and the constituting phases were responsible for a wide variation of such properties of titania thin films. This study aims to provide the systematic explanation for evolution of the phases as a function of the degree of supersaturation, along with the discussion of their effects on the aforementioned engineering properties.
Role of azaamino acid residue in β‐turn formation and stability in designed peptide (2000)

The structural perturbation induced by C(alpha)-->N(alpha) exchange in azaamino acid-containing peptides was predicted by ab initio calculation of the 6-31G* and 3-21G* levels. The global energy-minimum conformations for model compounds, For-azaXaa-NH2 (Xaa=Gly, Ala, Leu) appeared to be the beta-turn motif with a dihedral angle of phi= +/- 90 degrees, psi=0 degrees. This suggests that incorporation of the azaXaa residue into the i+2 position of designed peptides could stabilize the beta-turn structure. The model azaLeu-containing peptide, Boc-Phe-azaLeu-Ala-OMe, which is predicted to adopt a beta-turn conformation was designed and synthesized in order to experimentally elucidate the role of the azaamino acid residue. Its structural preference in organic solvents was investigated using 1H NMR, molecular modelling and IR spectroscopy. The temperature coefficients of amide protons, the characteristic NOE patterns, the restrained molecular dynamics simulation and IR spectroscopy defined the dihedral angles [ (phi i+1, psi i+1) (phi i+2, psi i+2)] of the Phe-azaLeu fragment in the model peptide, Boc-Phe-azaLeu-Ala-OMe, as [(-59 degrees, 127 degrees) (107 degrees, -4 degrees)]. This solution conformation supports a betaII-turn structural preference in azaLeu-containing peptides as predicted by the quantum chemical calculation. Therefore, intercalation of the azaamino acid residue into the i+2 position in synthetic peptides is expected to provide a stable beta-turn formation, and this could be utilized in the design of new peptidomimetics adopting a beta-turn scaffold.