gebhart/patrepeval huggingface dataset:
Modified Bell–Plesset effect with compressibility: Application to double-shell ignition target designs (2003)

The effect of spherical convergence on the fluid stability of collapsing and expanding bubbles was originally treated by Bell [Los Alamos Scientific Laboratory Report No. LA-1321 (1951)] and Plesset [J. Appl. Phys. 25, 96 (1954)]. The additional effect of fluid compressibility was also considered by Bell but was limited to the case of nonzero density on only one side of a fluid interface. A more general extension is developed which considers distinct time-dependent uniform densities on both sides of an interface in a spherically converging geometry. A modified form of the velocity potential is used that avoids an unphysical divergence at the origin [Goncharov et al., Phys. Plasmas 7, 5118 (2000); Lin et al., Phys. Fluids 14, 2925 (2002)]. Two consequences of this approach are that an instability proposed by Plesset for an expanding bubble in the limit of large interior density is now absent and application to inertial confinement fusion studies of stability becomes feasible. The model is applied to a proposed ignition double-shell target design [Amendt et al., Phys. Plasmas 9, 2221 (2002)] for the National Ignition Facility [Paisner et al., Laser Focus World 30, 75 (1994)] for studying the stability of the inner surface of an imploding high-Z inner shell. Application of the Haan [Phys. Rev. A 39, 5812 (1989)] saturation criterion suggests that ignition is possible.
Characterization of the human mucin gene MUC5AC: a consensus cysteine-rich domain for 11p15 mucin genes? (1995)

To date five human mucin cDNAs (MUC2, 5A, 5B, 5C and 6) mapped to 11p15.3-15.5, so it appears that this chromosome region might contain several distinct gene loci for mucins. Three of these cDNAs, MUC5A, B and C, were cloned in our laboratory and previously published. A common number, 5, was recommended by the Human Gene Mapping Nomenclature Committee to designate them because of their common provenance from human tracheobronchial mucosa. In order to define whether they are products of the same gene locus or distinct loci, we describe in this paper physical mapping of these cDNAs using the strategy of analysis of CpG islands by pulse-field gel electrophoresis. The data suggest that MUC5A and MUC5C are part of the same gene (called MUC5AC) which is distinct from MUC5B. In the second part of this work, complete sequences of the inserts corresponding to previously described (JER47, JER58) and novel (JER62, JUL32, MAR2, MAR10 and MAR11) cDNAs of the so-called MUC5AC gene are presented and analysed. The data show that in this mucin gene, the tandem repeat domain is interrupted several times with a subdomain encoding a 130 amino acid cysteine-rich peptide in which the TR3A and TR3B peptides previously isolated by Rose et al. [Rose, Kaufman and Martin (1989) J. Biol. Chem., 264, 8193-8199] from airway mucins are found. A consensus peptide sequence for these subdomains involving invariant positions of most of the cysteines is proposed. The consensus nucleotide sequence of this subdomain is also found in the MUC2 gene and in the MUC5B gene, two other mucin genes mapped to 11p15. The functional significance for secreted mucins of these cysteine-rich subdomains and the modular organization of mucin peptides are discussed.
Major oligosaccharides in the glycoprotein of Friend murine leukemia virus: structure elucidation by one- and two-dimensional proton nuclear magnetic resonance and methylation analysis (1984)

The highly microheterogeneous, N-glycosidically linked oligosaccharides in the glycoproteins of Friend murine leukemia virus (as produced by Eveline cells) were liberated with endo-beta-N-acetylglucosaminidase H and by alkaline hydrolysis. They were fractionated (as desialylated oligosaccharitols) by gel filtration and by concanavalin A affinity chromatography, and the major fractions were analyzed by methylation-gas chromatography-mass spectrometry, by digestion with exoglycosidases, and, especially, by one- and two-dimensional proton nuclear magnetic resonance spectroscopy. Guidelines for qualitative and quantitative analysis of complex oligosaccharide mixtures by NMR were worked out and the results compared with those obtained by methylation analysis. It was found that these major fractions consist of bi-, tri-, and tetraantennary oligosaccharitols of the "complex" type (comprising a minority of species with N-acetyllactosamine repeating units), which are, in part, substituted by nonreducing terminal Gal alpha (1----3) and/or bisecting GlcNAc beta (1----4) residues.
Presentation of RGDS Epitopes on Self-Assembled Nanofibers of Branched Peptide Amphiphiles (2006)

Branched peptide amphiphile (PA) molecules bearing biological epitopes were designed and synthesized using orthogonal protecting group chemistry on amine groups at lysine residues. These molecules self-assemble into high-aspect-ratio cylindrical nanofibers, and their branched architecture enhances accessibility of epitopes for protein binding and also allows the presentation of more than one epitope in a single molecule. The RGDS cell adhesion epitope was used as a model bioactive signal on PA molecules for potential biomedical applications. Aggregation of the branched PA molecules into nanofibers was demonstrated by TEM and through shifts in the protonation profiles of peripheral amines. These systems also formed self-supporting gels in the presence of physiological fluids and other biologically relevant macromolecules such as synovial fluid and DNA, an important property for their potential use in medicine. Fluorescence anisotropy measurements on the PAs with tryptophan residues were performed to examine the effect of branching on packing and mobility of the peptides in the self-assembled nanofibers. The mobility of tryptophan residues was observed to be restricted upon packing of PA molecules into nanofibers. However, relative to linear analogues, branched molecules retain more mobility in the supramolecular aggregates.
The role of marine organisms in fouling control (1989)

The marine organisms, Tube worms, Bryozoa, Enteromerpha and Ulva Spp, have been tested to be used as antifouling agents. Each organism was incorporated as effective ingredient in two different marine paint formulations in presence of other complementary pigments. The coatings were applied on different substrates and the panels immersed in Alexandria western harbour. The environmental condition of the harbour water has been also mentioned. The antifouling durability of the coatings were followed through the calculation of the wet weight of fouling organisms accumulated on the coated panels and the control one. The result showed that the antifouling activity of the organisms depend on the paint formulation and the substrate.
An Energy-Efficient, Adiabatic Electrode Stimulator With Inductive Energy Recycling and Feedback Current Regulation (2011)

In this paper, we present a novel energy-efficient electrode stimulator. Our stimulator uses inductive storage and recycling of energy in a dynamic power supply. This supply drives an electrode in an adiabatic fashion such that energy consumption is minimized. It also utilizes a shunt current-sensor to monitor and regulate the current through the electrode via feedback, thus enabling flexible and safe stimulation. Since there are no explicit current sources or current limiters, wasteful energy dissipation across such elements is naturally avoided. The dynamic power supply allows efficient transfer of energy both to and from the electrode and is based on a DC-DC converter topology that we use in a bidirectional fashion in forward-buck or reverse-boost modes. In an exemplary electrode implementation intended for neural stimulation, we show how the stimulator combines the efficiency of voltage control and the safety and accuracy of current control in a single low-power integrated-circuit built in a standard .35 μm CMOS process. This stimulator achieves a 2x-3x reduction in energy consumption as compared to a conventional current-source-based stimulator operating from a fixed power supply. We perform a theoretical analysis of the energy efficiency that is in accord with experimental measurements. This theoretical analysis reveals that further improvements in energy efficiency may be achievable with better implementations in the future. Our electrode stimulator could be widely useful for neural, cardiac, retinal, cochlear, muscular and other biomedical implants where low power operation is important.
In vitro antibacterial activity of some plant essential oils (2006)

Majority of the oils showed antibacterial activity against the tested strains. However Cinnamon, clove and lime oils were found to be inhibiting both gram-positive and gram-negative bacteria. Cinnamon oil can be a good source of antibacterial agents.
Mode of action of linear amphipathic α-helical antimicrobial peptides (1998)

The increasing resistance of bacteria to conventional antibiotics resulted in a strong effort to develop antimicrobial compounds with new mechanisms of action. Antimicrobial peptides seem to be a promising solution to this problem. Many studies aimed at understanding their mode of action were described in the past few years. The most studied group includes the linear, mostly alpha-helical peptides. Although the exact mechanism by which they kill bacteria is not clearly understood, it has been shown that peptide-lipid interactions leading to membrane permeation play a role in their activity. Membrane permeation by amphipathic alpha-helical peptides can proceed via either one of the two mechanisms: (a) transmembrane pore formation via a "barrel-stave" mechanism; and (b) membrane destruction/solubilization via a "carpet-like" mechanism. The purpose of this review is to summarize recent studies aimed at understanding the mode of action of linear alpha-helical antimicrobial peptides. This review, which is focused on magainins, cecropins, and dermaseptins as representatives of the amphipathic alpha-helical antimicrobial peptides, supports the carpet-like rather the barrel-stave mechanism. That these peptides vary with regard to their length, amino acid composition, and next positive charge, but act via a common mechanism, may imply that other linear antimicrobial peptides that share the same properties also share the same mechanism.
Deep Learning-Based Virtual Try-On System Using Multi-Modal Feature Fusion and Generative Adversarial Networks (2017)

This paper presents a comprehensive deep learning-based virtual try-on system that addresses the challenge of realistic garment transfer in e-commerce applications. The system leverages multi-modal feature fusion combining cloth-agnostic person representation, pose estimation, and human parsing to enable identity-preserving virtual try-on. Key Contributions: • Multi-Modal Input Architecture: A 41-channel input representation combining cloth-agnostic RGB (3 channels), OpenPose Body25 pose heatmaps (18 channels), and LIP human parsing masks (20 channels) • Advanced Neural Architecture: U-Net generator with self-attention mechanisms (26.4M parameters) and spectral-normalized PatchGAN discriminator (2.8M parameters) for stable adversarial training • Sophisticated Loss Function: Multi-component objective combining adversarial loss (LSGAN), perceptual loss (VGG19, 5 layers), L1 reconstruction, and feature matching losses • Complete Pipeline Implementation: End-to-end system from data preprocessing through model training with systematic analysis of each component Technical Details: Dataset: VITON-HD (10,482 training samples, 2,032 test samples) Framework: PyTorch Architecture: U-Net with self-attention + Spectral-normalized PatchGAN Training: Proof-of-concept validation (10 epochs, CPU-based, 256×192 resolution) Evaluation: SSIM, PSNR, L1 distance metrics with comprehensive quantitative and qualitative analysis
Efficient simulation of inextensible cloth (2007)

Many textiles do not noticeably stretch under their own weight. Unfortunately, for better performance many cloth solvers disregard this fact. We propose a method to obtain very low strain along the warp and weft direction using Constrained Lagrangian Mechanics and a novel fast projection method. The resulting algorithm acts as a velocity filter that easily integrates into existing simulation code.
Current Development of siRNA Bioconjugates: From Research to the Clinic (2019)

Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
PDC Bit Selection Method Through the Analysis of Past Bit Performances (1990)

ABSTRACT A method to evaluate the performance of PDC and tricone bits is presented based on their cost, on a foot basis, and the rock strength properties (shear stress for PDC bits and compressive stress for tricone bits). The results showed that much data is needed for PDC performance evaluation when compared to a similar procedure for tricone bits, mainly due to the better description of the tricone bit when using the currently proposed IADC classification system.
Improving the mechanical properties of collagen‐based membranes using silk fibroin for corneal tissue engineering (2014)

Although collagen with outstanding biocompatibility has promising application in corneal tissue engineering, the mechanical properties of collagen-based scaffolds, especially suture retention strength, must be further improved to satisfy the requirements of clinical applications. This article describes a toughness reinforced collagen-based membrane using silk fibroin. The collagen-silk fibroin membranes based on collagen [silk fibroin (w/w) ratios of 100:5, 100:10, and 100:20] were prepared by using silk fibroin and cross-linking by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide. These membranes were analyzed by scanning electron microscopy and their optical property, and NaCl and tryptophan diffusivity had been tested. The water content was found to be dependent on the content of silk fibroin, and CS10 membrane (loading 10 wt % of silk fibroin) performed the optimal mechanical properties. Also the suture experiments have proved CS10 has high suture retention strength, which can be sutured in rabbit eyes integrally. Moreover, the composite membrane proved good biocompatibility for the proliferation of human corneal epithelial cells in vitro. Lamellar keratoplasty shows that CS10 membrane promoted complete epithelialization in 35 ± 5 days, and their transparency is restored quickly in the first month. Corneal rejection reaction, neovascularization, and keratoconus are not observed. The composite films show potential for use in the field of corneal tissue engineering.
Defense Mechanisms of Conifers (1991)

Cell-free extracts from Pinus ponderosa Lawson (ponderosa pine) and Pinus sylvestris L. (Scotch pine) wood exhibited high levels of monoterpene synthase (cyclase) activity, whereas bark extracts of these species contained no detectable activity, and they inhibited cyclase activity when added to extracts from wood, unless polyvinylpyrrolidone was included in the preparation. The molecular mass of the polyvinylpyrrolidone added was of little consequence; however, polyvinylpolypyrrolidone (a cross-linked insoluble form of the polymer) was ineffective in protecting enzyme activity. Based on these observations, methods were developed for the efficient extraction and assay of monoterpene cyclase activity from conifer stem (wood and bark) tissue. The level of monoterpene cyclase activity for a given conifer species was shown to correlate closely with the monoterpene content of the oleoresin and with the degree of anatomical complexity of the specialized resin-secreting structures. Cyclase activity and monoterpene content were lowest in the stems of species containing only isolated resin cells, such as western red cedar (Thuja plicata D. Don). Increasing levels of cyclase activity and oleoresin monoterpenes were observed in advancing from species with multicellular resin blisters (true firs [Abies]) to those with organized resin passages, such as western larch (Larix occidentalis Nutt.), Colorado blue spruce (Picea pungens Engelm.) and Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). The highest levels of cyclase activity and oleoresin monoterpenes were noted in Pinus species that contain the most highly developed resin duct systems. The relationship between biosynthetic capacity, as measured by cyclase activity, monoterpene content, and the degree of organization of the secretory structures for a given species, may reflect the total number of specialized resin-producing cells per unit mass of stem tissue.
Polymorphisms and Genomic Organization of Repetitive DNA from Centromeric Regions of Arabidopsis Chromosomes (1999)

A highly abundant repetitive DNA sequence family of Arabidopsis, AtCon, is composed of 178-bp tandemly repeated units and is located at the centromeres of all five chromosome pairs. Analysis of multiple copies of AtCon showed 95% conservation of nucleotides, with some alternative bases, and revealed two boxes, 30 and 24 bp long, that are 99% conserved. Sequences at the 3' end of these boxes showed similarity to yeast CDEI and human CENP-B DNA-protein binding motifs. When oligonucleotides from less conserved regions of AtCon were hybridized in situ and visualized by using primer extension, they were detected on specific chromosomes. When used for polymerase chain reaction with genomic DNA, single primers or primer pairs oriented in the same direction showed negligible amplification, indicating a head-to-tail repeat unit organization. Most primer pairs facing in opposite directions gave several strong bands corresponding to their positions within AtCon. However, consistent with the primer extension results, some primer pairs showed no amplification, indicating that there are chromosome-specific variants of AtCon. The results are significant because they elucidate the organization, mode of amplification, dispersion, and evolution of one of the major repeated sequence families of Arabidopsis. The evidence presented here suggests that AtCon, like human alpha satellites, plays a role in Arabidopsis centromere organization and function.
The NADPH‐linked acetoacetyl‐CoA reductase from Zoogloea ramigera (1988)

The NADPH-linked acetoacetyl-CoA reductase, (R)-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.36), from the bacterium Zoogloea ramigera, involved in the formation of D-3-hydroxybutyryl-CoA for poly(D-3-hydroxybutyrate) biosynthesis, has been purified from an over-producing Escherichia coli strain. The purification was achieved in two steps, yielding an electrophoretically homogeneous enzyme of high specific activity (608 U/mg). The enzyme is an alpha 4 homotetramer of four 25-kDa subunits. It has a Km of 2 microM and a kcat/Km of 1.8 X 10(8) M-1 s-1 for acetoacetyl-CoA; it is inhibited by acetoacetyl-CoA above 10 microM. K is 10(-10) M for the dehydrogenation. Kinetic studies of the back reaction revealed a sequential mechanism involving a ternary complex. The stereospecificity of the hydride-equivalent transfer was demonstrated using NMR techniques to be 4S (B side). Using the fingerprint method proposed by Wierenga et al. [(1986) J. Mol. Biol. 187, 101-107], we identified a 28-residue stretch (residues 3-31) as a possible NADPH fold. Finally the specificity of the reductase was examined using 3-oxo-acyl-CoA analogs and analogs lacking the adenosine 3',5'-bisphosphate moiety of CoA. Only the straight-chain C5 analog (3-oxo-propionyl-CoA) was found to be an alternative substrate (40%) for the reductase.
The inactivation of dihydroxy-acid dehydratase in Escherichia coli treated with hyperbaric oxygen occurs because of the destruction of its Fe-S cluster, but the enzyme remains in the cell in a form that can be reactivated. (1993)

The enzyme dihydroxy-acid dehydratase previously has been shown to be inactivated in vivo in Escherichia coli within minutes of exposure to hyperbaric O2. In this paper, we show its inactivation is due to the destruction of its catalytically active [4Fe-4S] cluster. The inactivation is not followed by an appreciable decrease in the amount of dihydroxy-acid dehydratase protein as determined by Western blots. Thus, the protein from the inactivated enzyme remains unproteolyzed in the cells. Dihydroxy-acid dehydratase activity recovers after the cells treated with hyperbaric O2 are returned to ambient oxygen. Since this recovery in activity is not accompanied by a significant increase in dihydroxy-acid dehydratase protein and is not prevented by chloramphenicol, it appears primarily to be due to reactivation of the previously inactivated enzyme. The reactivation occurs by reconstitution of the enzyme's Fe-S cluster. These results demonstrate that this enzyme can cycle between forms in which the Fe-S cluster is either present or absent. The facile ability to cycle between these two forms would be compatible with a regulatory role in addition to a catalytic role for this enzyme.
General and local hypothermia of the brain in the treatment of intractable epilepsy (1970)

✓ Twenty-five cases of intractable epilepsy were treated by combined deep general and local extravascular brain hypothermia plus single doses of pentothal (Thiopental) or diazepam. The final local temperature of the brain in 21 patients was below 24°C, the rectal temperatures being 27° to 30°C. There was one death 6 weeks after surgery, and in two patients slight neurological deficits were found at 3 and 6 months postoperatively. In 15 patients in whom at least 1 year had elapsed since surgery, the frequency and intensity of the seizures were reduced by 50% in two, reduced to a single seizure in five, eliminated in four, and unaltered in four. The fair and excellent results included 60% of the group. In three patients improvement in behavior and emotional stability were observed postoperatively; this change was independent of the reduction of the frequency of seizures. Postoperative changes in the electroencephalogram were less frequent than changes in the frequency of seizures and also were completely independent of the clinical results.