gebhart/patrepeval huggingface dataset:
Motion compensation aided motion adaptive de-interlacing for real-time video processing applications (2008)

This paper presents a low-complexity motion compensation (MC) aided motion adaptive (MA) de-interlacing method, aiming at effectively leveraging the fact human eyes are not sensitive to high spatial frequency with rapid motion. The basic idea is to enhance MA de-interlacing by applying MC de-interlacing to process slow-moving objects. Compared with conventional MC de-interlacing, the motion estimation only needs to search in a much smaller area and can adaptively switch between the same parity and opposite parity fields according to the motion vector. Simulation demonstrates that the proposed method only incurs less than 5% of computational complexity of general MC de-interlacing, and meanwhile can improve the PSNR by up to 10 dB compared with conventional MA methods. Its silicon cost and energy consumption are further evaluated by an ASIC design at 0.13 mum technology node.
ECG‐correlated image reconstruction from subsecond multi‐slice spiral CT scans of the heart (2000)

Subsecond spiral computed tomography (CT) offers great potential for improving heart imaging. The new multi-row detector technology adds significantly to this potential. We therefore developed and validated dedicated cardiac reconstruction algorithms for imaging the heart with subsecond multi-slice spiral CT utilizing electrocardiogram (ECG) information. The single-slice cardiac z-interpolation algorithms 180 degrees CI and 180 degrees CD [Med. Phys. 25, 2417-2431 (1998)] were generalized to allow imaging of the heart for M-slice scanners. Two classes of algorithms were investigated: 180 degrees MCD (multi-slice cardio delta), a partial scan reconstruction of 180 degrees + delta data with a < phi (fan angle) resulting in effective scan times of 250 ms (central ray) when a 0.5 s rotation mode is available, and 180 degrees MCI (multi-slice cardio interpolation), a piecewise weighted interpolation between successive spiral data segments belonging to the same heart phase, potentially providing a relative temporal resolution of 12.5% of the heart cycle when a four-slice scanner is used and the table increment is chosen to be greater than or equal to the collimated slice thickness. Data segments are selected by correlation with the simultaneously recorded ECG signal. Theoretical studies, computer simulations, as well as patient measurements were carried out for a multi-slice scanner providing M = 4 slices to evaluate these new approaches and determine the optimal scan protocol. Both algorithms, 180 degrees MCD and 180 degrees MCI, provide significant improvements in image quality, including extremely arythmic cases. Artifacts in the reconstructed images as well as in 3D displays such as multiplanar reformations were largely reduced as compared to the standard z-interpolation algorithm 180 degrees MLI (multi-slice linear interpolation). Image quality appears adequate for precise calcium scoring and CT angiography of the coronary arteries with conventional subsecond multislice spiral CT. It turned out that for heart rates fH > or = 70 min(-1) the partial scan approach 180 degrees MCD yields unsatisfactory results as compared to 180 degrees MCI. Our theoretical considerations show that a freely selectable scanner rotation time chosen as a function of the patient's heart rate, would further improve the relative temporal resolution and thus further reduce motion artifacts. In our case an additional 0.6 s mode besides the available 0.5 s mode would be very helpful. Moreover, if technically feasible, lower rotation times such as 0.3 s or even less would result in improved image quality. The use of multi-slice techniques for cardiac CT together with the new z-interpolation methods improves the quality of heart imaging significantly. The high temporal resolution of 180 degrees MCI is adequate for spatial and temporal tracking of anatomic structures of the heart (4D reconstruction).
Surface acoustic wave unidirectional transducers for quantum applications (2017)

The conversion efficiency of electric microwave signals into surface acoustic waves in different types of superconducting transducers is studied with the aim of quantum applications. We compare delay lines containing either conventional symmetric transducers (IDTs) or unidirectional transducers (UDTs) at 2.3 GHz and 10 mK. The UDT delay lines improve the insertion loss with 4.7 dB and a directivity of 22 dB is found for each UDT, indicating that 99.4% of the acoustic power goes in the desired direction. The power lost in the undesired direction accounts for more than 90% of the total loss in IDT delay lines, but only ∼3% of the total loss in the floating electrode unidirectional transducer delay lines.
Rbx1, a Component of the VHL Tumor Suppressor Complex and SCF Ubiquitin Ligase (1999)

The von Hippel–Lindau (VHL) tumor suppressor gene is mutated in most human kidney cancers. The VHL protein is part of a complex that includes Elongin B, Elongin C, and Cullin-2, proteins associated with transcriptional elongation and ubiquitination. Here it is shown that the endogenous VHL complex in rat liver also includes Rbx1, an evolutionarily conserved protein that contains a RING-H2 fingerlike motif and that interacts with Cullins. The yeast homolog of Rbx1 is a subunit and potent activator of the Cdc53-containing SCF Cdc4 ubiquitin ligase required for ubiquitination of the cyclin-dependent kinase inhibitor Sic1 and for the G 1 to S cell cycle transition. These findings provide a further link between VHL and the cellular ubiquitination machinery.
<title>Water-soluble resist for environmentally friendly lithography</title> (1996)

This paper describes an 'environmentally friendly,' water castable, water developable photoresist system. The chemically amplified negative-tone resist system consists of three water-soluble components: a polymer, poly(methyl acrylamidoglycolate methyl ether), [poly(MAGME)]; a photoacid generator, dimethyl dihydroxyphenylsulfonium triflate and a crosslinker, butanediol. Poly(MAGME) was synthesized by solution free radical polymerization. In the three-component resist system, the acid generated by photolysis of the photoacid generator catalyzes the crosslinking of poly(MAGME) in the exposed regions during post-exposure baking, thus rendering the exposed regions insoluble in water. Negative tone relief images are obtained by developing with pure water. The resist is able to resolve 1 micrometer line/space features (1:1 aspect ratio) with an exposure dose of 100 mJ/cm<SUP>2</SUP> at 248 nm. The resist can be used to generate etched copper relief images on printed circuit boards using aqueous sodium persulfate as the etchant. The crosslinking mechanism has been investigated by model compound studies using <SUP>13</SUP>C NMR. These studies have revealed that the acid catalyzed reaction of the poly(MAGME) with butanediol proceeds via both transesterification and transacetalization (transaminalization) reactions at low temperatures, and also via transamidation at high temperatures.
Mechanisms of daptomycin resistance in Staphylococcus aureus: role of the cell membrane and cell wall (2012)

The bactericidal, cell membrane-targeting lipopeptide antibiotic daptomycin (DAP) is an important agent in treating invasive Staphylococcus aureus infections. However, there have been numerous recent reports of development of daptomycin resistance (DAP-R) during therapy with this agent. The mechanisms of DAP-R in S. aureus appear to be quite diverse. DAP-R strains often exhibit progressive accumulation of single nucleotide polymorphisms in the multipeptide resistance factor gene (mprF) and the yycFG components of the yycFGHI operon. Both loci are involved in key cell membrane (CM) events, with mprF being responsible for the synthesis and outer CM translocation of the positively charged phospholipid, lysyl-phosphotidylglycerol (L-PG), while the yyc operon is involved in the generalized response to stressors such as antimicrobials. In addition, other perturbations of the CM have been identified in DAP-R strains, including extremes in CM order, resistance to CM depolarization and permeabilization, and reduced surface binding of DAP. Moreover, modifications of the cell wall (CW) appear to also contribute to DAP-R, including enhanced expression of the dlt operon (involved in d-alanylation of CW teichoic acids) and progressive CW thickening.
Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex (2005)

Soft tissues are preserved within hindlimb elements of Tyrannosaurus rex (Museum of the Rockies specimen 1125). Removal of the mineral phase reveals transparent, flexible, hollow blood vessels containing small round microstructures that can be expressed from the vessels into solution. Some regions of the demineralized bone matrix are highly fibrous, and the matrix possesses elasticity and resilience. Three populations of microstructures have cell-like morphology. Thus, some dinosaurian soft tissues may retain some of their original flexibility, elasticity, and resilience.
The preparation and properties of tris(triphenylphosphine)halogenorhodium(I) and some reactions thereof including catalytic homogeneous hydrogenation of olefins and acetylenes and their derivatives (1966)

Tris(triphenylphosphine)chlororhodium(I), RhCl(PPh3)3, has been prepared by the interaction of an excess of triphenylphosphine with rhodium(III) chloride hydrate in ethanol; the corresponding bromide and iodide are also described. The dissociation of the complex in various solvents has been investigated, and its reactions with hydrogen, ethylene, and carbon monoxide and aldehydes studied. Dihydrido- and ethylene complexes have been isolated and studied by nuclear magnetic resonance (n.m.r.) spectroscopy. Approximate values for the formation constants of ethylene and propylene complexes have been obtained; the latter is lower by a factor of over 103. By electron spin resonance spectroscopy, the complex RhCl(PPh3)3 has been shown to contain trace amounts of a paramagnetic species, probably a rhodium(II) complex.In homogeneous solution the tris(triphenylphosphine) complexes are exceedingly active catalysts for the rapid and homogeneous hydrogenation, at ca. 1 atmosphere of hydrogen pressure and room temperature, of unsaturated compounds containing isolated olefinic and acetylenic linkages.The rates of hydrogenation of hept-1-ene, cyclohexene and hex-1-yne have been studied quantitatively and the dependence on factors such as substrate and catalyst concentration, temperature, and pressure determined. The data can be accommodated by a rate expression of the form: Rate =Kp[S][A]//1 +K1p+K2[S] where [S] and [A] are the olefin and catalyst concentrations, respectively, and p is the concentration of hydrogen in solution.From the data for cyclohexene the activation energy for the rate determining step is Ea= 22·9 kcal. mole–1(ΔH‡= 22·3 kcal. mole–1) and the value of ΔS‡= 12·9 e.u.It is shown that the rate of hydrogen–deuterium exchange under selected conditions is quite slow compared with the rates of hydrogenation of olefins and, furthermore, that when H2–D2 mixtures are used in the reactions, alkanes and dideuteroalkanes are the major products. Reductions of maleic and fumaric acids with deuterium shows that cis-addition occurs preferentially. Similarly, in the reduction of hex-2-yne to n-hexane, cis-hex-2-ene is found to be the major olefin intermediate.A mechanism for the hydrogenation is proposed in which the metal complex serves as a template to which a hydrogen molecule and an olefin molecule are briefly co-ordinated before transfer of one to the other takes place. The low kinetic isotope effect (rate H2/rate D2= 0·9) suggests that synchronous breaking of Rh–H bonds and making of C–H bonds takes place in the transition state involving two simultaneous three-centre interactions.
The V3 Loop Is Accessible on the Surface of Most Human Immunodeficiency Virus Type 1 Primary Isolates and Serves as a Neutralization Epitope (2004)

Antibodies (Abs) against the V3 loop of the human immunodeficiency virus type 1 gp120 envelope glycoprotein were initially considered to mediate only type-specific neutralization of T-cell-line-adapted viruses. However, recent data show that cross-neutralizing V3 Abs also exist, and primary isolates can be efficiently neutralized with anti-V3 monoclonal Abs (MAbs). The neutralizing activities of anti-V3 polyclonal Abs and MAbs may, however, be limited due to antigenic variations of the V3 region, a lack of V3 exposure on the surface of intact virions, or Ab specificity. For clarification of this issue, a panel of 32 human anti-V3 MAbs were screened for neutralization of an SF162-pseudotyped virus in a luciferase assay. MAbs selected with a V3 fusion protein whose V3 region mimics the conformation of the native virus were significantly more potent than MAbs selected with V3 peptides. Seven MAbs were further tested for neutralizing activity against 13 clade B viruses in a single-round peripheral blood mononuclear cell assay. While there was a spectrum of virus sensitivities to the anti-V3 MAbs observed, 12 of the 13 viruses were neutralized by one or more of the anti-V3 MAbs. MAb binding to intact virions correlated significantly with binding to solubilized gp120s and with the potency of neutralization. These results demonstrate that the V3 loop is accessible on the native virus envelope, that the strength of binding of anti-V3 Abs correlates with the potency of neutralization, that V3 epitopes may be shared rather than type specific, and that Abs against the V3 loop, particularly those targeting conformational epitopes, can mediate the neutralization of primary isolates.
A system for concomitant overexpression of four periplasmic folding catalysts to improve secretory protein production in Escherichia coli (2006)

Although Escherichia coli is in wide use for preparative protein expression, problems with the folding of the recombinant gene product and protein aggregation are frequently encountered. Apart from cytoplasmic expression, this is also true for secretion into the bacterial periplasm, the method of choice for the production of proteins that carry structural disulfide bonds. Here we report the construction of the helper plasmid pTUM4, which effects overexpression of four established periplasmic chaperones and folding catalysts: the thiol-disulfide oxidoreductases DsbA and DsbC that catalyze the formation and isomerization of disulfide bridges and the peptidyl-prolyl cis/trans-isomerases with chaperone activity, FkpA and SurA. pTUM4 carries a p15a origin of replication and a chloramphenicol resistance gene and, thus, it is compatible with many conventional expression vectors that use the ColEI origin and an ampicillin resistance. Its positive effects on the yield of soluble recombinant protein and the homogeneity of disulfide pattern are illustrated here using the human plasma retinol-binding protein as well as the extracellular carbohydrate recognition domain of the dendritic cell membrane receptor DC-SIGN. Hence, pTUM4 represents a novel helper vector which complements existing cytosolic chaperone coexpression plasmids and should be useful for the functional secretion of various recombinant proteins with hampered folding efficiency.
A botulinum toxin–derived targeted secretion inhibitor downregulates the GH/IGF1 axis (2012)

Botulinum neurotoxins (BoNTs) are zinc endopeptidases that block release of the neurotransmitter acetylcholine in neuromuscular synapses through cleavage of soluble N-ethylmaleimide-sensitive fusion (NSF) attachment protein receptor (SNARE) proteins, which promote fusion of synaptic vesicles to the plasma membrane. We designed and tested a BoNT-derived targeted secretion inhibitor (TSI) targeting pituitary somatotroph cells to suppress growth hormone (GH) secretion and treat acromegaly. This recombinant protein, called SXN101742, contains a modified GH-releasing hormone (GHRH) domain and the endopeptidase domain of botulinum toxin serotype D (GHRH-LHN/D, where HN/D indicates endopeptidase and translocation domain type D). In vitro, SXN101742 targeted the GHRH receptor and depleted a SNARE protein involved in GH exocytosis, vesicle-associated membrane protein 2 (VAMP2). In vivo, administering SXN101742 to growing rats produced a dose-dependent inhibition of GH synthesis, storage, and secretion. Consequently, hepatic IGF1 production and resultant circulating IGF1 levels were reduced. Accordingly, body weight, body length, organ weight, and bone mass acquisition were all decreased, reflecting the biological impact of SXN101742 on the GH/IGF1 axis. An inactivating 2-amino acid substitution within the zinc coordination site of the endopeptidase domain completely abolished SXN101742 inhibitory actions on GH and IGF1. Thus, genetically reengineered BoNTs can be targeted to nonneural cells to selectively inhibit hormone secretion, representing a new approach to treating hormonal excess.
A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva (2013)

A microfluidic chip integrating DNA extraction, amplification, and detection for the identification of bacteria in saliva is described. The chip design integrated a monolithic aluminum oxide membrane (AOM) for DNA extraction with seven parallel reaction wells for real-time polymerase chain reaction (rtPCR) amplification of the extracted DNA. Samples were first heated to lyse target organisms and then added to the chip and filtered through the nanoporous AOM to extract the DNA. PCR reagents were added to each of the wells and the chip was thermocycled. Identification of Streptococcus mutans in a saliva sample is demonstrated along with the detection of 300 fg (100-125 copies) of both methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) genomic DNA (gDNA) spiked into a saliva sample. Multiple target species and strains of bacteria can be simultaneously identified in the same sample by varying the primers and probes used in each of the seven reaction wells. In initial tests, as little as 30 fg (8-12 copies) of MSSA gDNA in buffer has been successfully amplified and detected with this device.
Functional characterization of Ost3p. Loss of the 34-kD subunit of the Saccharomyces cerevisiae oligosaccharyltransferase results in biased underglycosylation of acceptor substrates. (1995)

Within the lumen of the rough endoplasmic reticulum, oligosaccharyltransferase catalyzes the en bloc transfer of a high mannose oligosaccharide moiety from the lipid-linked oligosaccharide donor to asparagine acceptor sites in nascent polypeptides. The Saccharomyces cerevisiae oligosaccharyltransferase was purified as a heteroligomeric complex consisting of six subunits (alpha-zeta) having apparent molecular masses of 64 kD (Ost1p), 45 kD (Wbp1p), 34 kD, 30 kD (Swp1p), 16 kD, and 9 kD. Here we report a structural and functional characterization of Ost3p which corresponds to the 34-kD gamma-subunit of the oligosaccharyltransferase. Unlike Ost1p, Wbp1p, and Swp1p, expression of Ost3p is not essential for viability of yeast. Instead, ost3 null mutant yeast grow at wild-type rates on solid or in liquid media irrespective of culture temperature. Nonetheless, detergent extracts prepared from ost3 null mutant membranes are twofold less active than extracts prepared from wild-type membranes in an in vitro oligosaccharyltransferase assay. Furthermore, loss of Ost3p is accompanied by significant underglycosylation of soluble and membrane-bound glycoproteins in vivo. Compared to the previously characterized ost1-1 mutant in the oligosaccharyltransferase, and the alg5 mutant in the oligosaccharide assembly pathway, ost3 null mutant yeast appear to be selectively impaired in the glycosylation of several membrane glycoproteins. The latter observation suggests that Ost3p may enhance oligosaccharide transfer in vivo to a subset of acceptor substrates.
The role of oncostatin M in animal and human connective tissue collagen turnover and its localization within the rheumatoid joint (1998)

Objective To study the interaction of interleukin-1α (IL-1α) and oncostatin M (OSM) in promoting cartilage collagen destruction. Methods Bovine, porcine, and human cartilage and human chondrocytes were studied in culture. The levels of collagenase (matrix metalloproteinase 1 [MMP-1]) and tissue inhibitor of metalloproteinases 1 (TIMP-1) were measured by bioassay and enzyme-linked immunosorbent assay (ELISA). The levels of OSM in rheumatoid synovial fluid were measured by ELISA. Results When combined with OSM, IL-1α IL-1β, and tumor necrosis factor α released proteoglycan and collagen from cartilage. OSM was the only member of the IL-6 family to have this effect. Human tendon also responded to IL-1α and OSM. OSM increased the production of MMP-1 and TIMP-1 but when combined with IL-1α, synergistically promoted MMP-1 production in human chondrocytes and synovial fibroblasts. High levels of OSM were found in human rheumatoid synovial fluids, and confocal microscopy showed that OSM was produced by macrophages in rheumatoid synovial tissue. Conclusion These results highlight an important new mechanism by which there is irreversible loss of collagen from cartilage.
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998 (1998)

SWISS-PROT (http://www.expasy.ch/) is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: an increase in the number and scope of model organisms; cross-references to two additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT.
Charge Movement Associated with the Opening and Closing of the Activation Gates of the Na Channels (1974)

The sodium current (I(Na)) that develops after step depolarization of a voltage clamped squid axon is preceded by a transient outward current that is closely associated with the opening of the activation gates of the Na pores. This "gating current" is best seen when permeant ions (Na and K) are replaced by relatively impermeant ones, and when the linear portion of capacitative current is eliminated by adding current from positive steps to that from exactly equal negative ones. During opening of the Na pores gating current is outward, and as the pores close there is an inward tail of current that decays with approximately the same time-course as I(Na) recorded in Na-containing medium. Both outward and inward gating current are unaffected by tetrodotoxin (TTX). Gating current is capacitative in origin, the result of relatively slow reorientation of charged or dipolar molecules in a suddenly altered membrane field. Close association with the Na activation process is clear from the time-course of gating current, and from the fact that three procedures that reversibly block I(Na) also block gating current: internal perfusion with Zn(2+), prolonged depolarization of the membrane, and inactivation of I(Na) with a short positive prepulse.