gebhart/patrepeval huggingface dataset:
Radical Alkenylation of α-Halo Carbonyl Compounds with Alkenylindiums (2004)

Alkenylation reaction of alpha-halo carbonyl compounds with alkenylindiums proceeded via a radical process in the presence of triethylborane. Unactivated alkene moieties as well as a styryl group could be introduced by this method. The geometry of the carbon-carbon double bonds of the alkenylindiums was retained. Preparation of an alkenylindium via a hydroindation of 1-alkyne followed by radical alkenylation established an efficient one-pot strategy. [reaction: see text]
Dephosphorylation of the Core Septin, AspB, in a Protein Phosphatase 2A-Dependent Manner Impacts Its Localization and Function in the Fungal Pathogen Aspergillus fumigatus (2016)

Septins are a conserved family of GTPases that form hetero-oligomeric complexes and perform diverse functions in higher eukaryotes, excluding plants. Our previous studies in the human fungal pathogen Aspergillus fumigatus revealed that the core septin, AspB, a CDC3 ortholog, is required for septation, conidiation, and conidial cell wall organization. Although AspB is important for these cellular functions, nothing is known about the role of kinases or phosphatases in the posttranslational regulation and localization of septins in A. fumigatus. In this study, we assessed the function of the Gin4 and Cla4 kinases and the PP2A regulatory subunit ParA, in the regulation of AspB using genetic and phosphoproteomic approaches. Gene deletion analyses revealed that Cla4 and ParA are indispensable for hyphal extension, and Gin4, Cla4, and ParA are each required for conidiation and normal septation. While deletion of gin4 resulted in larger interseptal distances and hypervirulence, a phenotype mimicking aspB deletion, deletion of cla4 and parA caused hyperseptation without impacting virulence, indicating divergent roles in regulating septation. Phosphoproteomic analyses revealed that AspB is phosphorylated at five residues in the GTPase domain (S134, S137, S247, T297, and T301) and two residues at its C-terminus (S416 and S461) in the wild-type, Δgin4 and Δcla4 strains. However, concomitant with the differential localization pattern of AspB and hyperseptation in the ΔparA strain, AspB remained phosphorylated at two additional residues, T68 in the N-terminal polybasic region and S447 in the coiled-coil domain. Generation of nonphosphorylatable and phosphomimetic strains surrounding each differentially phosphorylated residue revealed that only AspB (mt) -T68E showed increased interseptal distances, suggesting that dephosphorylation of T68 is important for proper septation. This study highlights the importance of septin phosphorylation/dephosphorylation in the regulation of A. fumigatus hyphal septation.
Stereospecific Lithium Aluminum Hydride Reduction of 2,3-Dimethylquinoxaline and Related Triazanaphthalenes<sup>1</sup> (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific Lithium Aluminum Hydride Reduction of 2,3-Dimethylquinoxaline and Related Triazanaphthalenes1Roy C. DeSelms and Harry S. MosherCite this: J. Am. Chem. Soc. 1960, 82, 14, 3762–3765Publication Date (Print):July 1, 1960Publication History Published online1 May 2002Published inissue 1 July 1960https://pubs.acs.org/doi/10.1021/ja01499a072https://doi.org/10.1021/ja01499a072research-articleACS PublicationsRequest reuse permissionsArticle Views175Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bringing bioelectricity to light: all-optical electrophysiology using microbial rhodopsins (2014)

My work has focused on the development and application of fluorescent voltage-sensitive proteins based on microbial rhodopsins. These probes led to the discovery of electrical activity in the bacterium Escherichia coli, the first robust optical recordings of action potentials (APs) in mammalian neurons using a genetically encoded voltage reporter, and the development of a genetically targetable all-optical electrophysiology system.\nI first introduce an engineered fluorescent voltage sensor based on green-absorbing proteorhodopsin. Expression of the proteorhodopsin optical proton sensor (PROPS) in E. coli revealed electrical spiking at up to 1 hertz. Spiking was sensitive to chemical and physical perturbations and coincided with rapid efflux of a small-molecule fluorophore, suggesting that bacterial efflux machinery may be electrically regulated.\nI then present another microbial rhodopsin, Archaerhodopsin 3 (Arch), whose endogenous fluorescence exhibited a twofold increase in brightness between -150 mV and +150 mV and a sub-millisecond response time. In rat hippocampal neurons, Arch detected single electrically triggered APs with an optical signal-to-noise ratio > 10. A mutant, Arch(D95N), lacked endogenous proton pumping and had 50% greater sensitivity than the wild type but had a slower response (41 ms). Nonetheless, Arch(D95N) also resolved individual APs.\nFinally, I introduce evolved archaerhodopsin-based voltage indicators and a spectrally orthogonal channelrhodopsin actuator, which together enabled all-optical electrophysiology. A directed evolution screen yielded two mutants, QuasAr1 and QuasAr2, that showed improved brightness and voltage sensitivity relative to previous archaerhodopsin-based sensors, and microsecond response times. An engineered channelrhodopsin actuator, CheRiff, showed high light sensitivity and rapid kinetics. A coexpression vector, Optopatch, enabled cross-talk-free genetically targeted all-optical electrophysiology. In cultured neurons, the Optopatch system probed membrane voltage across temporal and spatial scales, from the sub-cellular and sub-millisecond dynamics of AP propagation, to the simultaneous measurement of firing patterns of many neurons in a circuit. In brain slices, Optopatch induced and reported APs and subthreshold events with high signal-to-noise ratios. In human stem cell-derived neurons, Optopatch measurements revealed homeostatic tuning of intrinsic excitability, a subtle form of plasticity that had yet to be observed in human neurons.\nThe suite of tools and techniques presented here enable high-throughput, genetically targeted, and spatially resolved electrophysiology without the use of conventional electrodes.
Percutaneous Fixation of a Fifth Metatarsal Base Fracture (2021)

Owing to a vascular watershed, zone II and III fifth metatarsal base fractures commonly progress to nonunion without operative intervention. This article and the accompanying video demonstrate the use of intramedullary screw fixation for a fifth metatarsal base fracture and review treatment decisions involved with management of these injuries.
Characterization of the Post Dry‐Etch Cleaning of Silicon for Ti‐Self‐Aligned Silicide Technology (1999)

The Si surface after reactive ion etching (RIE) and different cleaning procedures was characterized by angle resolved X‐ray photoelectron spectroscopy, high‐resolution transmission microscopy, and atomic force microscopy. It was shown that polymers, silicon carbides (Si‒C bonds), and chemisorbed fluorine (Si‒F), cover the silicon surface after RIE in a mixture. The last two residues penetrate the surface layer of a silicon substrate. polymers are removed by oxygen plasma but Si‒C and Si‒F bonds related residues cannot be removed by "oxygen plasma/diluted HF" treatment. These compounds can be removed only by additional etching of the silicon surface layer. According to our experimental conditions a silicon consumption of 2.8 nm was enough to eliminate these compounds. By comparing different cleaning recipes and conditions it was found that ‐plasma/HF/APM (ammonia‐hydrogen peroxide mixture) provides the best cleaning characteristics. APM removes fluorine and carbon contamination by precise, controlled etching of silicon with high etch selectivity toward an spacer. The silicon surface after the cleaning is quite smooth. It was demonstrated that the post spacer‐etch cleaning of ‐plasma/HF/APM is a robust process for Ti‐salicide technology with respect to the reduction of the leakage current between poly‐Si and source/drain. © 1999 The Electrochemical Society. All rights reserved.
Characterization of five esterases from Listeria monocytogenes and use of their electrophoretic polymorphism for strain typing (1995)

Esterases from Listeria monocytogenes strains isolated from cheeses were analyzed by starch gel electrophoresis. Five esterases, numbered from EST 1 to EST 5 in order of decreasing anodal migration, were identified. The EST 1, EST 3, EST 4, and EST 5 set was most active toward alpha-naphthyl propionate, while EST 2 was most active toward alpha-naphthyl acetate. Results from inhibitor studies suggest that all of these esterases were EC class 3.1.1.1 carboxylesterases, except that EST 1 and EST 3 also showed some sensitivity to parahydroxymercuribenzoate. Polymorphism of these five esterases was observed in the population. Twelve esterase patterns were defined and used to subdivide serotypes.
Fourier Analysis (1996)

The frequency domain plays a central role in our discussion and analysis throughout this book. It is thus appropriate to begin with a treatment of Fourier theory. There are four basic Fourier transforms. These are:
Carbothermic Reduction in the Combustion Bed Packed with Composite Pellets of Iron Oxide and Coal. (2000)

Process feasibility has been experimentally studied on a new reduction concept using the composite pellets of iron ore and coal powders in their combustion bed. A key to realize this concept will be a method to prevent reoxidation of metallic iron formed during the process. To examine the optimum measure, reductionexperiment using a single composite tablet was first conducted. Coating the tablet with a CaO bearing material, i.e., Ca(OH)2 or CaCO3 powder, gives a certain suppression effect on the reoxidation at high temperature. On the basis of this result, reduction experiment in the combustion bed packed with the composite pellets were carried out under various conditions. An proper condition could not be found to perfectly prevent the reoxidation of metallic iron. However, the reoxidation was significantly suppressed by the admixing of CaO bearing material to the mixture or the coating it around the composite pellets. The maximum reduction and metallization degrees obtained were 72 and 64%, respectively. It suggests that the proposed process has a potential to produce partially-reduced iron burdens to a subsequent reduction/melting process such as the blast furnace.
Improvement of hot carrier reliability with deuterium anneals for manufacturing multilevel metal/dielectric MOS systems (1998)

This paper discusses new experimental findings critical for process integration of deuterium post-metal anneals to improve channel hot carrier reliability in manufacturing multilevel metal CMOS integrated circuits. Detailed account of the deuterium process optimization experiments varying temperature, time, and ambient is given. Specifically, the first demonstration of the large hydrogen/deuterium isotope effect for multilevel metal/dielectric MOS systems is reported. Previous accounts of the isotope effect had been limited to CMOS structures with one-level of dielectric/metal and to about a 10 fold improvement in reliability. Deuterium, instead of hydrogen is introduced via an optimized post-metal anneal process to achieve a 50-100 fold improvement in transistor channel hot carrier lifetime. The benefits of the deuterium anneal are still observed even if the post-metal anneal is followed by the final SiN cap wafer passivation process. It is concluded that the deuterium post-metal anneal process is suitable for manufacturing high performance CMOS products and fully compatible with traditional integrated circuit processes.
The Growth and Cytopathogenicity of Vesicular Stomatitis Virus in Tissue Culture (1955)

Summary Vesicular stomatitis virus (VSV) produces a cytopathogenic effect in roller-tube cultures of bovine tongue epithelium and guinea-pig kidney. Infectivity is first detected at about 15 hours by the formation of microscopic plaques of killed epithelial cells. Later the plaques increase in size and give the epithelial sheets a moth-eaten appearance. A titration-passage technique was devised to carry New Jersey type VSV in serial passage to a final dilution of 10-62. In this method each effective passage is made with a dilution of the preceding fluid which contains a minimal number of infectious units. The tissue culture virus retained its ability to infect chick embryos and to produce typical vesicular stomatitis in guinea pigs and cattle. The cytopathogenic activity of New Jersey type culture virus was neutralized by New Jersey immune but not by normal or Indiana immune guinea pig serum. Guinea pig cell clusters prepared by trypsinization were found to produce extensive coverage of the tube with cellular outgrowth. This technique was used for virus assay in which titers were read by color changes in the pH indicator as well as by cytologic change. Conventional serial passage of New Jersey type VSV in such cultures produced material with a tissue culture ID50 value of 106.2 per ml. Indiana type VSV extracted from infected bovine tongues gave tissue culture ID50 values of this same magnitude.
Alternative chemistries for the synthesis of thrombospondin‐1 type 1 repeats (2010)

Synthetic protein engineering has benefited from the development of diverse methods for the synthesis of functionalized peptide fragments and approaches for their subsequent assembly into full length polypeptides. Here we describe a series of synthetic approaches for the total chemical synthesis of the second type 1 repeat of thrombospondin-1 (TSR2) that vary in both the location of the ligation site and alpha-amine protecting group strategy (Boc/Fmoc) used for the synthesis of the associated peptide fragments. These syntheses illustrate that challenging peptide sequences can result from the protecting group strategy as well as from sequence-dependent factors. Importantly, we find that such challenges can be overcome by altering the chemistry used for solid phase peptide synthesis, the choice of ligation site, and the resin used as a solid support. From these studies, we have developed a robust synthetic route to the TSR2 polypeptide consisting of native chemical ligation between an N-terminal fragment synthesized by Boc-SPPS and a C-terminal fragment synthesized by Fmoc-SPPS. Finally, the folded TSR2 domain is obtained following an optimized oxidative folding protocol using an excess of oxidized glutathione. This optimized synthesis will enable the use of unnatural amino acids to probe the unusual structure and anti-angiogenic activity of this protein domain.
The significance of intracytoplasmic proteins in Reed-Sternberg cells (1978)

Lymphoid tissue of 42 patients with Hodgkin's disease was studied with immunohistological techniques on the light microscopic and ultrastructural level. The presence of IgG in some Reed-Sternberg (R-S) cells was confirmed, and in addition serial sections and a double staining technique revealed that these cells also contained both kappa and lambda light chains. Furthermore two serum proteins, human serum albumin and alpha-1-antitrypsin, were demonstrated in the same positive R-S cells. The ultrastructural localization of the immunoglobulin and of human serum albumin was not related to any protein synthesizing organelle or to structures related to endocytosis. It is suggested that the presence of immunoglobulin in R-S cells is the result of a disturbance of the cell wall integrity with subsequent nonspecific diffusion of immunoglobulin and other serum proteins into the cell. The presence of IgG therefore can not be taken as an argument for a B-cell origin of R-S cells. Possible mechanisms for the cell wall damage are discussed.
Experimental Analysis of a Cantilever Beam With a Shunted Piezoelectric Periodic Array (2010)

The use of both shunted piezoelectric elements and periodic arrays have been investigated independently as well as used in conjunction to modify the vibration of a system. Piezoelectric patches bonded to a cantilever beam which are shunted with an active circuit, specifically a negative capacitance shunt, can control broadband flexural vibrations of a structure. Also, periodic arrays integrated into a structure allow for modification of propagating waves through the mechanical “stop-bands”. The performance of a combined shunted periodic piezoelectric patch array will be analyzed here by investigating the velocity amplitude of the beam away from the array and in the array section, and the number of control elements in the array.
Polygalacturonate Lyase of a Bacillus Species Associated with Increase in Permeability of Sitka Spruce (Picea sitchensis) (1972)

SUMMARY: The extracellular polygalacturonate lyase of a Bacillus species isolated from water-stored Sitka spruce (Picea sitchensis) was purified by ammonium sulphate fractionation and CM-cellulose chromatography. Its specific activity increased 59-fold and amylase, protease and xylanase activities were removed. Degradation of the substrate was accompanied by a large decrease in viscosity, suggesting random attack. While calcium and strontium ions activated the enzyme, most divalent cations caused inhibition. Addition of EDTA resulted in complete inactivation. Enzyme activity was higher with acid soluble pectic acid than with sodium polypectate. The purified enzyme was stable over a wide pH range and had considerable resistance to thermal inactivation. This stability explains the enzyme's prolonged activity in water-stored spruce sapwood.
Towards the development of a bioartificial pancreas: a 13C NMR study on the effects of alginate/poly-L-lysine/alginate entrapment on glucose metabolism by beta TC3 mouse insulinoma cells. (1997)

We have utilized 13C NMR spectroscopy to investigate glucose metabolism in the mouse insulinoma Beta TC3 cell line. Cells were cultured and examined both as monolayers and entrapped in alginate/poly-L-lysine/alginate beads. Entrapped cultures were tested at 3 and 30 days post-entrapment. The purpose of this study was to assess whether the entrapped environment affects glucose metabolism and insulin secretion. Both monolayer and entrapped cultures were fed with 10 mM [1-(13)C]-glucose for 4 hrs. prior to extraction with perchloric acid. Our data revealed that beta TC3 cells possess a reduced tricarboxylic acid (TCA) activity in the entrapment cultures, and that they metabolized pyruvate primarily via pyruvate dehydrogenase regardless of the mode or age of the culture.
The Gurkhas. By W. Brook Northey and C. J. Morris. 8 1/2 in. x 5 1/2 in. pp. xxxvii, 282. John Lane. 18s. (1929)

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Enhancement of Dendritic Cell Therapy for Malignancy by Co-Activation of CD1d Restricted NKT Cells, NK Cells, and Antigen CTL. (2006)

Abstract Human Vα24+ Natural Killer T (NKT) cells are cytotoxic against a range of malignancies, including human lymphoma and myeloid leukaemia in vitro and in murine models in vivo. Human NKT cells are activated by α-galactosylceramide (KRN7000) when presented by the MHC Class I-like molecule, CD1d, expressed by antigen presenting cells, particularly dendritic cells (DCs). Successful activation of human NKT cell antitumor activity in a clinical setting, particularly if this also activates natural killer (NK) cells and enhances tumor-specific cytotoxic T lymphocyte (CTL) activity, has the potential to be more potent and effective than current strategies focusing entirely on activation of peptide antigen specific CTL. In order to evaluate this we initiated a clinical study aiming to determine whether all three cell types could be activated with a single therapy. Melanoma was evaluated because of the known responsiveness to DC based immune therapy and the availability of well-defined peptide tumor antigens amenable to evaluation in a large number of subjects. Subjects with stage IV metastatic melanoma who were HLA-A*0201 were randomized to receive multiple intradermal or intravenous treatments with autologous mature monocyte derived DC pulsed with KRN7000, 4 peptide antigens (Mart-1, gp100, tyrosinase and Mage 3) or both. Peripheral blood NKT cells, NK cells and CD8+ CTL specific for the four melanoma antigens were monitored before, during, and after the series of treatments using 5 color flow cytometry. Antigen specific CTL were monitored using tetramers obtained from Beckman Coulter. Our results were that DC pulsed with KRN7000 + peptide were able to activate NKT cells and NK cells as well as increase the number of tumour antigen specific CTL. Activation of NKT and NK cells was most marked after intravenous treatment. However increased tumor antigen specific CTL were observed after treatment by both routes. Minor disease responses and stabilization were noted in subjects with non-bulky disease. We conclude that activation of NKT, NK and antigen specific CTL is possible with a single modality of immune therapy and that this is associated with disease responses.
Plant derived antioxidants and antifibrotic drugs: past, present and future (2014)

Devaraj Ezhilarasan, Etienne Sokal, Sivanesan Karthikeyan, Mustapha Najimi* Institut de Recherche Experimentale et Clinique, Laboratory of Pediatric Hepatology and Cell Therapy, Universite Catholique de Louvain, Brussels, Belgium Department of Pharmacology and Environmental Toxicology, Food and Hepatotoxicology Laboratory, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, India Journal of Coastal Life Medicine 2014; 2(9): 738-745
Multicategory image classification by the optical implementation of the Kittler-Young transform (1990)

The Kittler-Young (KY) transform is a feature-extraction linear algorithm. The information of the class means and the class variances are optimally utilized in the KY transform, such that high space-bandwidth product pattern recognition can be performed. Another important feature of the KY transform is the capability to perform multiple-category pattern recognition. A three-category image classification is performed on an optical-matrix multiplication system by using the KY transform. The first three basis KY basis images, which are the column vectors of the KY transform matrix, are written onto the first liquid-crystal television (LCTV), while a target image is displayed on the second LCTV. After the optical inner-product and addition operations, the first three KY features of the target image are present at the output plane. These KY features are detected by a charge-coupled device camera and are fed to a pseudoinverse classifier.