gebhart/patrepeval huggingface dataset:
A New Tyrosyl Radical on Phe208 as Ligand to the Diiron Center in Escherichia coli Ribonucleotide Reductase, Mutant R2-Y122H (2005)

The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.
INTESTINAL FLORA IN NEW-BORN INFANTS (1935)

Following our first article on the bacterial flora of first passage specimens of meconium from fifty new-born infants<sup>1</sup>we studied the daily microbial changes in the feces of ten normal breast-fed infants up to the tenth day, when they left the hospital. <h3>HISTORICAL REVIEW</h3> The early invasion of the intestinal tracts of new-born infants by bacteria, either ascending or descending, often within ten hours after birth and before feeding, first observed microscopically by Breslau<sup>2</sup>in 1866, was confirmed by Billroth<sup>3</sup>in 1874 and by Nothnagel<sup>4</sup>in 1881. Using iodine as a stain, Nothnagel assumed to identify Saccharomyces ellipsoideus, Bacillus subtilis and the so-called clostridium of Prazmowski, which he regarded as identical with Bacillus amylobacter of Trecul and van Tieghem and the "vibrion septique" of Pasteur; but we feel that even now, with greatly improved methods of staining, identification of any of these is impossible. Nothnagel was
Special Issue Imaging Processing-Algorithm and System. The Marathon Image Processing System with the Universal DSP. (1991)

The development of the Marathon image processing system which measures step frequency and automatically controls the camera by processing the image through the Marathon program is discussed.
Microfluidic flow meter and viscometer utilizing flow-induced vibration on an optic fiber cantilever (2011)

This paper presents a microfluidic flow sensor for the detections of velocity and viscosity, especially for ultra-low viscosity applications. An etched optic fiber with the diameter of 9 mm is embedded in a microfluidic chip to couple laser light into the microfluidic channel. An flow induced vibration causes periodic flapping motion of the optic fiber cantilever. Through the frequency analysis, the fluidic properties including the flow rate and the viscosity can be detected and identified. Results show that this developed sensor is capable of sensing liquid samples with the flow rates from 2.5 ml/min to 15.0 ml/min and the viscosities from 0.306 cP to 1.2 cP. In addition, air samples(0.0148 cP) with various flow rates can also be detected using the developed sensor. The developed flow sensor provides a simple and straight forward method for sensing flow characteristics in a microfluidic channel.
Model-Based Personalization within an Adaptable Human-Machine Interface Environment that is Capable of Learning from User Interactions (2010)

The paper describes a multimodal interface architecture that is capable of automatic adaptation to the user by learning from the user's interaction patterns. The introduced architecture consists of a general way to specify multimodal HMI systems based on models with modes, transitions and guards as well as a mechanism to apply adaptations during the runtime process. Adaptations are defined as modifications of models which are specified during the specification process and used during the runtime process to control the program flow. To provide the developer with a flexible but secure way to define personalization uses cases in form of adaption rules we introduce modification boundaries that are defined as an additional model based on the same formalism as the models used for the program flow. The framework will be discussed by means of an example: Analyzing the interaction of the user after a recognition of a yet unknown speech command to infer and apply adequate modifications of the model to connect the unknown speech command with a typical user interaction.
Cyproterone Acetate for Treatment of Hot Flashes after Orchiectomy (1985)

No AccessJournal of Urology1 Jul 1985Cyproterone Acetate for Treatment of Hot Flashes after Orchiectomy Timothy D. Moon Timothy D. MoonTimothy D. Moon View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)47043-1AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Cyproterone Acetate for Treatment of Hot Flashes after Orchiectomy." The Journal of Urology, 134(1), pp. 155–156 © 1985 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited byKarling P, Hammar M and Varenhorst E (2018) Prevalence and Duration of Hot Flushes After Surgical or Medical Castration in Men with Prostatic CarcinomaJournal of Urology, VOL. 152, NO. 4, (1170-1173), Online publication date: 1-Oct-1994.Loprinzi C, Goldberg R, O'Fallon J, Quella S, Miser A, Mynderse L, Brown L, Tschetter L, Wilwerding M, Dose A and Oesterling J (2018) Transdermal Clonidine for Ameliorating Post-Orchiectomy Hot FlashesJournal of Urology, VOL. 151, NO. 3, (634-636), Online publication date: 1-Mar-1994. Volume 134Issue 1July 1985Page: 155-156 Advertisement Copyright & Permissions© 1985 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Timothy D. Moon More articles by this author Expand All Advertisement PDF downloadLoading ...
Treatment of autoimmune myasthenia gravis (2003)

Autoimmune myasthenia gravis (MG) is associated with antibodies directed against the nicotinic acetylcholine receptor (AChR) in 85% of patients. Other postsynaptic neuromuscular junction antigens are implicated, e.g., muscle-specific receptor tyrosine kinase (MuSK), in a number of the remaining 15% of patients, so-called seronegative MG. The autoimmune attack generally leads to decreased concentrations of the AChR and damage to the structure of the endplate itself. This information has guided the empiric treatment of patients with MG and has suggested new treatment strategies. Whereas the outcome of patients with MG has improved because of more effective symptomatic treatment, including advances in critical care medicine and the use of cholinesterase inhibitors, the greatest advances have come from therapies that directly reduce the autoimmune attack or modify its effects on the AChR and the surrounding endplate. Immune-directed treatment of patients with MG, which is guided by this information and by data from the management of other autoimmune disease, is aimed at inducing an immunologic remission and then maintaining that remission. Remission induction is usually accomplished through the use of high-dose corticosteroids, frequently in conjunction with IV immunoglobulin or plasmapheresis. Maintenance of the remission is usually accomplished by slow tapering of the corticosteroids along with the use of "steroid-sparing" agents, which include azathioprine, thymectomy, and possibly mycophenolate. Therapy usually begins with cholinesterase inhibitors. If necessary, immune-directed treatment is added, beginning with either thymectomy or high-dose corticosteroids. The short-term therapies, i.e., IV immunoglobulin or plasmapheresis, may be effective in the early stages of treatment or later during an exacerbation. Steroid-sparing medications are usually added to facilitate the tapering phase.
Smoother Mo films for molded FEAs by addition of N 2 to Ar sputter gas (2011)

Molybdenum field emitter arrays (FEAs) fabricated by molding and a self-aligned gate process [1] have been successfully used to fabricate stacked-double-gate FEAs [2, 3], and to demonstrate high-acceleration field compatibility [4], and near infrared laser-induced field-emission [5]. For higher brightness cathodes, we are currently developing nanoscale (300nm emitters, 750 nm pitch) molded molybdenum FEAs. As emitter dimensions approach the grain size for sputtered molybdenum films, roughness in the metal grain structure, for example due to self-shadowing when coating topographic features, becomes increasingly significant for the FEA structures. Fig. 1 illustrates topographic roughening for a) coating of concave, pyramidal Si molds to make the emitters, and b) gate metallization coated over one convex emitter on a demolded FEA. During mold coating the roughness creates axial pores in the emitter tips which the subsequent evaporated and electroplated metal layers cannot fill. For gate apertures with diameter < 0.5 µm, the molybdenum grain structure distorts the aperture shape.
Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. (2001)

The Unified Medical Language System (UMLS) is a large repository of some 800,000 concepts for the biomedical domain, organized by several millions of inter-concept relationships, either inherited from the source vocabularies, or specifically generated. This paper focuses on hierarchical relationships in the UMLS Metathesaurus, and especially, on circular hierarchical relationships. Using the metaphor of a disease, we first analyze the causal mechanisms for circular hierarchical relationships. Then, we discuss methods to identify and remove these relationships. Finally, we briefly discuss the consequences of these relationships for applications based on the UMLS, and we propose some prevention measures.
Synthesis of nonsymmetrically 3,4‐disubstituted 1,2,5‐thiadiazole dioxides (1998)

Abstract A synthetic pathway for obtaining arylamino, alkylamino 3,4‐disubstituted 1,2,5‐thiadiazole dioxide derivatives has been developed. This methodology could be applied to obtain potential biologically active molecules.
Generation of 2A-Linked Multicistronic Cassettes by Recombinant PCR (2012)

The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. Expression of more than two genes using conventional approaches has several limitations, most notably imbalanced protein expression and large size. The use of 2A peptide sequences alleviates these concerns. They are small (18-22 amino acids) and have divergent amino-terminal sequences, which minimizes the chance for homologous recombination and allows for multiple, different 2A peptide sequences to be used within a single vector. Importantly, separation of genes placed between 2A peptide sequences is nearly 100%, which allows for stoichiometric and concordant expression of the genes, regardless of the order of placement within the vector. This protocol describes the use of recombinant polymerase chain reaction (PCR) to connect multiple 2A-linked protein sequences. The final construct is subcloned into an expression vector.
Flame retardancy and dielectric properties of dicyclopentadiene‐based benzoxazine cured with a phosphorus‐containing phenolic resin (2008)

Abstract A dicyclopentadiene‐based benzoxazine (DCPDBZ) was prepared and separately copolymerized with melamine–phenol formaldehyde novolac or phosphorus‐containing phenolic resin (phosphorus‐containing diphenol) at various molar ratios. Their curing behaviors were characterized by differential scanning calorimetry. The electrical properties of the cured resins were studied with a dielectric analyzer. The glass‐transition temperatures were measured by dynamic mechanical analysis. The thermal stability and flame retardancy were determined by thermogravimetric analysis and a UL‐94 vertical test. These data were compared with those of bisphenol A benzoxazine and 4,4′‐biphenol benzoxazine systems. The effects of the diphenol structure and cured composition on the dielectric properties, moisture resistance, glass‐transition temperature, thermal stability, and flame retardancy are discussed. The DCPDBZ copolymerized with phosphorus‐containing novolac exhibited better dielectric properties, moisture resistance, and flame retardancy than those of the melamine‐modified system. The flame retardancy of the cured benzoxazine/phosphorus‐containing phenolic resins increased with increasing phosphorus content. The results indicate that the bisphenol A and 4,4′‐biphenol systems with a phosphorus content of about 0.6% and the dicyclopentadiene system with a phosphorus content of about 0.8% could achieve a flame‐retardancy rating of UL‐94 V‐0. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Reaction of phthalic anhydrides with methyl isocyanoacetate: A useful synthesis of 1,2-dihydro-1-oxoisoquinolines. (1979)

Nitro-1, 2-dihydro-1-oxoisoquinoline-3-carboxylate compounds (5a, b and 9a, b) were synthesized by the reaction of methyl isocyanoacetate with nitrophthalic anhydrides in the presence of 1, 8-diazabicyclo [5. 4. 0] undec-7-ene (DBU), followed by esterification with diazomethane and hydrolysis with HCl. In these reactions, the methylidenephthalide compound (10) was also obtained by hydrolysis of the oxazole-4-carboxylate compound (8b) due to the presence of the bulky ortho nitro group. Moreover, 1, 2-dihydro-4-hydroxy-1-oxoisoquinoline-3-carboxylic acid (16) was prepared via the oxazole dicarboxylic acid compound (15) in good yield.
TL1A Promotes Lung Tissue Fibrosis and Airway Remodeling (2020)

Lung fibrosis and tissue remodeling are features of chronic diseases such as severe asthma, idiopathic pulmonary fibrosis, and systemic sclerosis. However, fibrosis-targeted therapies are currently limited. We demonstrate in mouse models of allergen- and bleomycin-driven airway inflammation that neutralization of the TNF family cytokine TL1A through Ab blocking or genetic deletion of its receptor DR3 restricted increases in peribronchial smooth muscle mass and accumulation of lung collagen, primary features of remodeling. TL1A was found as a soluble molecule in the airways and expressed on the surface of alveolar macrophages, dendritic cells, innate lymphoid type 2 cells, and subpopulations of lung structural cells. DR3 was found on CD4 T cells, innate lymphoid type 2 cells, macrophages, fibroblasts, and some epithelial cells. Suggesting in part a direct activity on lung structural cells, administration of recombinant TL1A into the naive mouse airways drove remodeling in the absence of other inflammatory stimuli, innate lymphoid cells, and adaptive immunity. Correspondingly, human lung fibroblasts and bronchial epithelial cells were found to express DR3 and responded to TL1A by proliferating and/or producing fibrotic molecules such as collagen and periostin. Reagents that disrupt the interaction of TL1A with DR3 then have the potential to prevent deregulated tissue cell activity in lung diseases that involve fibrosis and remodeling.
“Minimalist” Cyclopropene-Containing Photo-Cross-Linkers Suitable for Live-Cell Imaging and Affinity-Based Protein Labeling (2014)

Target identification of bioactive compounds within the native cellular environment is important in biomedical research and drug discovery, but it has traditionally been carried out in vitro. Information about how such molecules interact with their endogenous targets (on and off) is currently highly limited. An ideal strategy would be one that recapitulates protein-small molecule interactions in situ (e.g., in living cells) and at the same time enables enrichment of these complexes for subsequent proteome-wide target identification. Similarly, small molecule-based imaging approaches are becoming increasingly available for in situ monitoring of a variety of proteins including enzymes. Chemical proteomic strategies for simultaneous bioimaging and target identification of noncovalent bioactive compounds in live mammalian cells, however, are currently not available. This is due to a lack of photoaffinity labels that are minimally modified from their parental compounds, yet chemically tractable using copper-free bioorthogonal chemistry. We have herein developed novel minimalist linkers containing both an alkyl diazirine and a cyclopropene. We have shown chemical probes (e.g., BD-2) made from such linkers could be used for simultaneous in situ imaging and covalent labeling of endogenous BRD-4 (an important epigenetic protein) via a rapid, copper-free, tetrazine-cyclopropene ligation reaction (k2 > 5 M(-1) s(-1)). The key features of our cyclopropenes, with their unique C-1 linkage to BRD-4-targeting moiety, are their tunable reactivity and solubility, relative stability, and synthetic accessibility. BD-2, which is a linker-modified analogue of (+)-JQ1 (a recently discovered nanomolar protein-protein-interaction inhibitor of BRD-4), was subsequently used in a cell-based proteome profiling experiment for large-scale identification of potential off-targets of (+)-JQ1. Several newly identified targets were subsequently confirmed by preliminary validation experiments.
Invited review: Enteric methane in dairy cattle production: Quantifying the opportunities and impact of reducing emissions (2014)

Many opportunities exist to reduce enteric methane (CH4) and other greenhouse gas (GHG) emissions per unit of product from ruminant livestock. Research over the past century in genetics, animal health, microbiology, nutrition, and physiology has led to improvements in dairy production where intensively managed farms have GHG emissions as low as 1 kg of CO2 equivalents (CO2e)/kg of energy-corrected milk (ECM), compared with >7 kg of CO2e/kg of ECM in extensive systems. The objectives of this review are to evaluate options that have been demonstrated to mitigate enteric CH4 emissions per unit of ECM (CH4/ECM) from dairy cattle on a quantitative basis and in a sustained manner and to integrate approaches in genetics, feeding and nutrition, physiology, and health to emphasize why herd productivity, not individual animal productivity, is important to environmental sustainability. A nutrition model based on carbohydrate digestion was used to evaluate the effect of feeding and nutrition strategies on CH4/ECM, and a meta-analysis was conducted to quantify the effects of lipid supplementation on CH4/ECM. A second model combining herd structure dynamics and production level was used to estimate the effect of genetic and management strategies that increase milk yield and reduce culling on CH4/ECM. Some of these approaches discussed require further research, but many could be implemented now. Past efforts in CH4 mitigation have largely focused on identifying and evaluating CH4 mitigation approaches based on nutrition, feeding, and modifications of rumen function. Nutrition and feeding approaches may be able to reduce CH4/ECM by 2.5 to 15%, whereas rumen modifiers have had very little success in terms of sustained CH4 reductions without compromising milk production. More significant reductions of 15 to 30% CH4/ECM can be achieved by combinations of genetic and management approaches, including improvements in heat abatement, disease and fertility management, performance-enhancing technologies, and facility design to increase feed efficiency and life-time productivity of individual animals and herds. Many of the approaches discussed are only partially additive, and all approaches to reducing enteric CH4 emissions should consider the economic impacts on farm profitability and the relationships between enteric CH4 and other GHG.
Interconnect materials challenges for sub 20 nm technology nodes: Ultra low-k dielectrics (2012)

This presentation is an overview of ultra low dielectric constant (low-k) materials that have been developed for sub 20 nm technology nodes. These dielectrics include highly porous organosilicate glasses (OSG: both PECVD and spin-on) and new classes of materials like metal organic frameworks (MOF) and covalent organic frameworks (COF). In addition to the extended overview of the materials properties, new technological approaches helping to reduce plasma induced degradation (damage) and allowing the pore sealing are also discussed. For the plasma damage reduction, pore stuffing technologies are considered as promising. For the sealing of ultra low-k materials that have pore size larger than 3-5 nm, special PMO (periodic mesoporous oxide) have been developed and discussed.
Optical Devices in Ophthalmology and Optometry (2014)

Optical devices in ophthalmology and optometry , Optical devices in ophthalmology and optometry , کتابخانه مرکزی دانشگاه علوم پزشکی ایران
Isolation and characterization of centroacinar/terminal ductal progenitor cells in adult mouse pancreas (2009)

The question of whether dedicated progenitor cells exist in adult vertebrate pancreas remains controversial. Centroacinar cells and terminal duct (CA/TD) cells lie at the junction between peripheral acinar cells and the adjacent ductal epithelium, and are frequently included among cell types proposed as candidate pancreatic progenitors. However these cells have not previously been isolated in a manner that allows formal assessment of their progenitor capacities. We have found that a subset of adult CA/TD cells are characterized by high levels of ALDH1 enzymatic activity, related to high-level expression of both Aldh1a1 and Aldh1a7. This allows their isolation by FACS using a fluorogenic ALDH1 substrate. FACS-isolated CA/TD cells are relatively depleted of transcripts associated with differentiated pancreatic cell types. In contrast, they are markedly enriched for transcripts encoding Sca1, Sdf1, c-Met, Nestin, and Sox9, markers previously associated with progenitor populations in embryonic pancreas and other tissues. FACS-sorted CA/TD cells are uniquely able to form self-renewing "pancreatospheres" in suspension culture, even when plated at clonal density. These spheres display a capacity for spontaneous endocrine and exocrine differentiation, as well as glucose-responsive insulin secretion. In addition, when injected into cultured embryonic dorsal pancreatic buds, these adult cells display a unique capacity to contribute to both the embryonic endocrine and exocrine lineages. Finally, these cells demonstrate dramatic expansion in the setting of chronic epithelial injury. These findings suggest that CA/TD cells are indeed capable of progenitor function and may contribute to the maintenance of tissue homeostasis in adult mouse pancreas.