gebhart/patrepeval huggingface dataset:
Membrane-binding domains and cytopathogenesis of the matrix protein of vesicular stomatitis virus (1994)

The membrane-binding affinity of the matrix (M) protein of vesicular stomatitis virus (VSV) was examined by comparing the cellular distribution of wild-type (wt) virus M protein with that of temperature-sensitive (ts) and deletion mutants probed by indirect fluorescent-antibody staining and fractionation of infected or plasmid-transfected CV1 cells. The M-gene mutant tsO23 caused cytopathic rounding of cells infected at permissive temperature but not of cells at the nonpermissive temperature; wt VSV also causes rounding, which prohibits study of M protein distribution by fluorescent-antibody staining. Little or no M protein can be detected in the plasma membrane of cells infected with tsO23 at the nonpermissive temperature, whereas approximately 20% of the M protein colocalized with the membrane fraction of cells infected with tsO23 at the permissive temperature. Cells transfected with a plasmid expressing intact 229-amino-acid wt M protein (M1-229) exhibited cytopathic cell rounding and actin filament dissolution, whereas cells retained normal polygonal morphology and actin filaments when transfected with plasmids expressing M proteins truncated to the first 74 N-terminal amino acids (M1-74) or deleted of the first 50 amino acids (M51-229) or amino acids 1 to 50 and 75 to 106 (M51-74/107-229). Truncated proteins M1-74 and M51-229 were readily detectable in the plasma membrane and cytosol of transfected cells as determined by both fluorescent-antibody staining and cell fractionation, as was the plasmid-expressed intact wt M protein. However, the expressed doubly deleted protein M51-74/107-229 could not be detected in plasma membrane by fluorescent-antibody staining or by cell fractionation, suggesting the presence of two membrane-binding sites spanning the region of amino acids 1 to 50 and amino acids 75 to 106 of the VSV M protein. These in vivo data were confirmed by an in vitro binding assay in which intact M protein and its deletion mutants were reconstituted in high- or low-ionic-strength buffers with synthetic membranes in the form of sonicated unilammelar vesicles. The results of these experiments appear to confirm the presence of two membrane-binding sites on the VSV M protein, one binding peripherally by electrostatic forces at the highly charged NH2 terminus and the other stably binding membrane integration of hydrophobic amino acids and located by a hydropathy plot between amino acids 88 and 119.
A Multicenter Retrospective Study of the Clinical Results of the LINK®SB CharitéA Intervertebral Prosthesis. The Initial European Experience (1994)

This study represents the largest multicenter case series of any functional artificial disc implantation. Carefully controlled, prospective studies that compare disc implantation and fusion are warranted.
Integrated circuits based on nanoscale vacuum phototubes (2008)

We present and experimentally verify a concept for electronic devices based on nanoscale vacuum phototubes. Such devices are expected to be both reliable and amenable to large-scale integration. We further suggest several generalizations of the concept and discuss possible applications and advantages.
Large blue shift of light emitting porous silicon by boiling water treatment (1993)

A boiling water treatment of light emitting porous silicon can give rise to a large blue shift of its photoluminescence spectrum and meanwhile strengthen the skeleton of porous Si by filling up many pores with aqueous oxide. A stable blue-green light emission at the peak wavelength down to 500 nm is achieved. FTIR measurements show that the formation of Si dihydride on the sidewall surfaces of the Si rods is not responsible to the visible luminescence for the very thin Si wires.
Specificity Determinants in Neurotrophin-3 and Design of Nerve Growth Factor-Based trkC Agonists by Changing Central β-Strand Bundle Residues to Their Neurotrophin-3 Analogs (1997)

Neurotrophic factors mediate their signal by binding to specific cell surface receptors of the trk family. The binding sites of neurotrophin-3 (NT-3) and nerve growth factor (NGF) to their preferred receptors trkC and trkA, respectively, were previously determined by mutational analyses. These and other studies showed that trkA can discriminate between NGF and NT-3 primarily by recognition of their N-terminal residues. The mechanism of trkC discrimination, however, remained unclear especially since the most important residue in NT-3 involved in binding to trkC, R103, is conserved in all neurotrophins. In this study residues that are part of the central beta-strand bundle of NT-3 and are not conserved among the neurotrophins were grafted onto NGF and tested for recruitment of trkC affinity. Exchange of NGF residues at positions 18, 20, 23, 29, 84, and 86 by their NT-3 counterparts resulted in NGF variants that bound to trkC, while maintaining their affinity to trkA, and were able to induce autophosphorylation and differentiation of PC12 cells expressing trkC. These variants show that the amino acid at position 23 (glycine in NGF, threonine in NT-3) is critical for trkC recognition while other residues fine tune the specificity of NT-3 for trkC. The results demonstrate the importance of nonconserved residues of the central beta-strand bundle region for the interaction of NT-3 with trkC and emphasize the different mechanism of specificity determination that is employed in the NT-3/trkC and NGF/trkA ligand/receptor pairs.
Mapping Cognition to the Brain Through Neural Interactions (1999)

Brain imaging methods, such as positron emission tomography (PET) and functional magnetic resonance imaging (fMRI), provide a unique opportunity to study the neurobiology of human memory. As these methods can measure most of the brain, it is possible to examine the operations of large-scale neural systems and their relation to cognition. Two neuroimaging studies, one concerning working memory and the other episodic memory retrieval, serve as examples of application of two analytic methods that are optimised for the quantification of neural systems, structural equation modelling, and partial least squares. Structural equation modelling was used to explore shifting prefrontal and limbic interactions from the right to the left hemisphere in a delayed match-to-sample task for faces. A feature of the functional network for short delays was strong right hemisphere interactions between hippocampus, inferior prefrontal, and anterior cingulate cortices. At longer delays, these same three areas were strongly linked, but in the left hemisphere, which was interpreted as reflecting change in task strategy from perceptual to elaborate encoding with increasing delay. The primary manipulation in the memory retrieval study was different levels of retrieval success. The partial least squares method was used to determine whether the image-wide pattern of covariances of Brodmann areas 10 and 45/47 in right prefrontal cortex (RPFC) and the left hippocampus (LGH) could be mapped on to retrieval levels. Area 10 and LGH showed an opposite pattern of functional connectivity with a large expanse of bilateral limbic cortices that was equivalent for all levels of retrieval as well as the baseline task. However, only during high retrieval was area 45/47 included in this pattern. The results suggest that activity in portions of the RPFC can reflect either memory retrieval mode or retrieval success depending on other brain regions to which it is functionally linked, and imply that regional activity must be evaluated within the neural context in which it occurs. The general hypothesis that learning and memory are emergent properties of large-scale neural network interactions is discussed, emphasising that a region can play a different role across many functions and that role is governed by its interactions with anatomically related regions.
1-Antitrypsin deficiency * 3: Clinical manifestations and natural history (2004)

A review of the clinical manifestations of alpha(1)-antitrypsin (AAT) deficiency, including lung disease and liver disease, and risk factors affecting the rate of decline in lung function in AAT deficient patients.
Effect of Alkyl Chain Length and Degree of Substitution on the Complexation of Sulfoalkyl Ether β-Cyclodextrins with Steroids (1997)

This study was designed to test how the sulfoalkyl ether (SAE) modification of beta-cyclodextrin (beta-CD) affects the binding capacity of testosterone and progesterone, thereby enhancing their solubility. The SAE-beta-CD derivatives contain either sulfopropyl ether (SPE) or sulfobutyl ether (SBE) groups on the 2-, 3-, and 6-hydroxyl positions of the dextrose moieties. SAE-beta-CDs are a mixture of positional and regional isomers containing from one to as many as 12 SAE groups per CD. The effect of chain length and the degree of substitution on complexation behavior was investigated by the phase-solubility method. The results were compared with those obtained with beta-CD, where possible, and with hydroxypropyl-beta-CD (HP-beta-CD). To determine the effect of degree of substitution (DS) on the binding, mixtures of SAE-beta-CDs with multiple substitution levels and varying average degrees of substitution were studied as well as mixtures of SAE-beta-CDs that contained the same degree of substitution. Mixtures that contained SAE-beta-CDs of the same degree of substitution were isolated from the multiple substitution level mixtures by ion-exchange chromatography and purified for investigation. Unlike the parent beta-CD, linear increases in the apparent solubilities of testosterone and progesterone were observed, and the binding potentials were comparable to those of beta-CD or better. The results demonstrate that the binding potentials of the SAE-beta-CD derivatives were dependent on the guest molecule, the degree of substitution, and the alkyl ether chain length. Our previous study showed the inhibition of complexation by direct sulfonation of the beta-CD. However, in the present work, interferences with the charged sulfonate groups were avoided by repositioning them away from the cavity. Increasing the degree of substitution assisted in complex formation; however, its effects were limited. Reduction of the alkyl chain length, as in the case of SPE-beta-CD compared with SBE-beta-CD, decreased the complexation potential. This decrease in complexation potential was further suppressed with an increase in the number of substituents placed on the CD torus. Generally, the binding potential of SAE-beta-CD derivatives increased with increasing alkyl chain length. However, placement of more than an optimum number of SAE groups on the CD torus resulted in inhibition of complexation.
Treatments to induce the nucleation and growth of apatite-like layers on polymeric surfaces and foams (1997)

In this work, a bioactive glass is used as a percusor of calcium-phosphate (Ca-P) film deposition onto several polymer-based materials. Both bioinert (high molecular weight polyethylene, HMWPE), and biodegradable (corn starch-based blends, SEVA-C) polymers, unreinforced or reinforced with hydroxylapatite (HA), were coated by the very simple proposed route. Also polyurethane (PU) foams, with an open-cell structure, were mineralized by the proposed method. In fact, it was possible to induce the growth of the Ca-P films not only at the surface, but also in the bulk of the PU foam. These cellular materials are intended for cancellous bone replacement applications. The morphology of the formed films was strongly dependent on the used substrate, its polar character, and on the presence of HA in its composition, as observed by SEM. Nevertheless, a well defined needly like structure was observed in all samples at high magnifications. The Ca:P ratios of the films were between 1.5 and 1.7, i.e. in the range of tricalcium phosphate-hydroxylapatite. Raman spectroscopy and thin-film x-ray diffraction (XRD) evidenced the formation of mostly amorphous calcium-phosphate films. After scraping the coating from the polymer surface and heat-treating the resulting powder at 1000 degrees C for 1 h, HA and beta-tricalcium phosphate (TCP) typical peaks were found on XRD patterns.
A practical architecture for reliable quantum computers (2002)

Quantum computation has advanced to the point where system-level solutions can help close the gap between emerging quantum technologies and real-world computing requirements. Empirical studies of practical quantum architectures are just beginning to appear in the literature. Elementary architectural concepts are still lacking: How do we provide quantum storage, data paths, classical control circuits, parallelism, and system integration? And, crucially, how can we design architectures to reduce error-correction overhead? The authors describe a proposed architecture that uses code teleportation, quantum memory refresh units, dynamic compilation of quantum programs, and scalable error correction to achieve system-level efficiencies. They assert that their work indicates the underlying technology's reliability is crucial; practical architectures will require quantum technologies with error rates between 10/sup -6/ and 10/sup -9/.
Antiandrogen Flutamide Protects Male Mice From Androgen-Dependent Toxicity in Three Models of Spinal Bulbar Muscular Atrophy (2014)

Spinal and bulbar muscular atrophy (SBMA) is a late-onset, progressive neurodegenerative disease linked to a polyglutamine (polyQ) expansion in the androgen receptor (AR). Men affected by SBMA show marked muscle weakness and atrophy, typically emerging midlife. Given the androgen-dependent nature of this disease, one might expect AR antagonists to have therapeutic value for treating SBMA. However, current work from animal models suggests otherwise, raising questions about whether polyQ-expanded AR exerts androgen-dependent toxicity through mechanisms distinct from normal AR function. In this study, we asked whether the nonsteroidal AR antagonist flutamide, delivered via a time-release pellet, could reverse or prevent androgen-dependent AR toxicity in three different mouse models of SBMA: the AR97Q transgenic (Tg) model, a knock-in (KI) model, and a myogenic Tg model. We find that flutamide protects mice from androgen-dependent AR toxicity in all three SBMA models, preventing or reversing motor dysfunction in the Tg models and significantly extending the life span in KI males. Given that flutamide effectively protects against androgen-dependent disease in three different mouse models of SBMA, our data are proof of principle that AR antagonists have therapeutic potential for treating SBMA in humans and support the notion that toxicity caused by polyQ-expanded AR uses at least some of the same mechanisms as normal AR before diverging to produce disease and muscle atrophy.
The 3′-Untranslated Region of Hepatitis C Virus RNA Enhances Translation from an Internal Ribosomal Entry Site (1998)

Translation of most eukaryotic mRNAs and many viral RNAs is enhanced by their poly(A) tails. Hepatitis C virus (HCV) contains a positive-stranded RNA genome which does not have a poly(A) tail but has a stretch of 98 nucleotides (X region) at the 3'-untranslated region (UTR), which assumes a highly conserved stem-loop structure. This X region binds a polypyrimidine tract-binding protein (PTB), which also binds to the internal ribosome entry site (IRES) in HCV 5'-UTR. These RNA-protein interactions may regulate its translation. We generated a set of HCV RNAs differing only in their 3'-UTRs and compared their translation efficiencies. HCV RNA containing the X region was translated three- to fivefold more than the corresponding RNAs without this region. Mutations that abolished PTB binding in the X region reduced, but did not completely abolish, enhancement in translation. The X region also enhanced translation from another unrelated IRES (from encephalomyocarditis virus RNA), but did not affect the 5'-end-dependent translation of globin mRNA in either monocistronic or bicistronic RNAs. It did not appear to affect RNA stability. The free X region added in trans, however, did not enhance translation, indicating that the translational enhancement by the X region occurs only in cis. These results demonstrate that the highly conserved 3' end of HCV RNA provides a novel mechanism for enhancement of HCV translation and may offer a target for antiviral agents.
Self-Enhanced Catalytic Activities of Functionalized Graphene Sheets in the Combustion of Nitromethane: Molecular Dynamic Simulations by Molecular Reactive Force Field (2014)

Functionalized graphene sheet (FGS) is a promising additive that enhances fuel/propellant combustion, and the determination of its mechanism has attracted much interest. In the present study, a series of molecular dynamic simulations based on a reactive force field (ReaxFF) are performed to explore the catalytic activity (CA) of FGS in the thermal decay of nitromethane (NM, CH3NO2). FGSs and pristine graphene sheets (GSs) are oxidized in hot NM liquid to increase their functionalities and subsequently show self-enhanced CAs during the decay. The CAs result from the interatomic exchanges between the functional groups on the sheets and the NM liquid, i.e., mainly between H and O atoms. CA is dependent on the density of NM, functionalities of sheets, and temperature. The GSs and FGSs that originally exhibit different functionalities tend to possess similar functionalities and consequently similar CAs as temperature increases. Other carbon materials and their oxides can accelerate combustion of other fuels/propellants similar to NM, provided that they can be dispersed and their key reaction steps in combustion are similar to NM.
Myeloperoxidase-catalyzed incorporation of amines into proteins: role of hypochlorous acid and dichloramines (1982)

Myeloperoxidase-catalyzed oxidation of chloride (Cl-) to hypochlorous acid (HOCl) resulted in formation of mono- and dichloramine derivatives (RNHCl and RNCl2) of primary amines. The RNCl2 derivatives could undergo a reaction that resulted in incorporation of the R moiety into proteins. The probable mechanism was attack of RNCl2 or an intermediate formed in the decomposition of RNCl2 on histidine, tyrosine, and cystine residues and on lysine residues at high pH. Incorporation of radioactivity from labeled amines into stable, high molecular weight derivatives of proteins was measured by acid or acetone precipitation and by gel chromatography and electrophoresis. Whereas formation of RNCl2 was favored at low pH, the subsequent incorporation reaction was favored at high pH. Up to several hours were required for the maximum amount of incorporation, which was less than 10% of the label in RNCl2. For the amines tested, incorporation was in the order histamine greater than 1,2-diaminoethane greater than putrescine greater than taurine greater than lysine greater than glucosamine greater than leucine greater than methylamine. Initiation of the reaction required HOCl, and oxidized forms of bromide, iodide, or thiocyanate did not substitute. Inhibitors of incorporation fell into three classes. First, ammonia or amines competed with the labeled amine for reaction with HOCl, so that larger amounts of HOCl were required. Second, readily oxidized substances such as sulfhydryl or diketo compounds or thioethers (methionine) reduced RNCl2. Third, certain compounds competed with protein as the acceptor for the incorporation reaction. The amount required to block incorporation into protein depended on protein concentration. Among these inhibitors were imidazole compounds (histidine), phenols (tyrosine), and disulfides (glutathione disulfide, GSSG). Low yields of derivatives of histidine, tyrosine, and GSSG were detected by thin-layer chromatography. Acid-precipitable derivatives were obtained by reacting RNCl2 with polyhistidine or polytyrosine, and to a lesser extent with polylysine at high pH, but not with other poly(amino acids). Precipitable derivatives were also obtained by incubating MPO-containing extracts from leukocyte granules with hydrogen peroxide, Cl-, and labeled amines. The extracts were found to have a high content of substances with primary amino groups, which competed for incorporation. The results account for oxidative incorporation of amines into proteins in leukocytes and provide evidence that HOCl and nitrogen-chlorine (N-Cl) derivatives are formed in these cells. The characteristics of the incorporation reaction suggest that it would not contribute significantly to the antimicrobial activity of myeloperoxidase (MPO). Nevertheless, the reaction may provide a sensitive method for studying MPO action in vivo.
Invasive onychocytic carcinoma (2015)

Neoplasms originating from nail matrix keratinocytes are very rare. Onychomatricoma and onychocytic matricoma are benign tumors arising from nail matrix keratinocytes. Only one case of onychocytic carcinoma, the malignant counterpart of onychocytic matricoma, has been reported in the literature. Herein, we describe a case of invasive onychocytic carcinoma. Two biopsy specimens of the tumor, obtained at early and invasive stages, were examined histopathologically. The first biopsy specimen showed a retiform proliferation of eosinophilic and basophilic cells in the nail matrix. The second biopsy specimen showed a retiform basophilic cell proliferation with focal keratinization. Similar to normal nail matrix keratinocytes, the proliferating basophilic cells failed to express cytokeratin (CK)1, CK6 and CK10. Focal expression of hair-specific keratins, including K31, K85 and K86, was observed. On the basis of these findings, the tumor was identified as an invasive malignant tumor originating from nail matrix keratinocytes.
Induction and suppression of interferon‐inducible protein (IP)‐10 in reperfused myocardial infarcts may regulate angiogenesis (2001)

ABSTRACT Regulation of angiogenesis is dependent on the net biological balance between expression of angiogenic and angiostatic molecules in the injured tissue. Using a canine model of myocardial ischemia/reperfusion, we demonstrated that expression of the angiostatic chemokine interferon‐ inducible protein (IP‐10) peaked at 1–3 h of reperfusion and virtually disappeared by 24 h of reperfusion. IP‐10 mRNA and protein were localized in the venular endothelium during early reperfusion of ischemic myocardial segments and were not detected after 24 h. Endothelial cell proliferation was first noted after 24 h of reperfusion, and αv β3 expressing neovessels were seen after 72–120 h of reperfusion, suggesting that neovascularization began only when IP‐10 expression was markedly reduced. Isolated canine venular endothelial cells expressed high levels of IP‐10 and IL‐8 mRNA upon stimulation with tumor necrosis factor (TNF) ‐α and endotoxin. Transforming growth factor (TGF) ‐β, but not interleukin (IL) ‐10, decreased TNF‐α‐mediated IP‐10 expression in canine endothelial cells. In contrast, TNF‐α‐mediated IL‐8 induction was not affected by incubation with IL‐10 or TGF‐β. Induction of angiostatic factors, such as IP‐10, in the first hours following injury may be important in inhibiting premature neovessel formation, until the appropriate supportive matrix is present. IP‐10 down‐regulation by active TGF‐β may mediate the onset of neovascularization by allowing unopposed VEGF‐ and IL‐8‐mediated angiogenic activity.