gebhart/patrepeval huggingface dataset:
Advances in automatic, manual and microwave-assisted solid-phase peptide synthesis. (2008)

Solid-phase strategies speed up the production of both short- and long-sequence peptides compared with solution methodologies. Therefore, solid-phase peptide synthesis (SPPS), proposed by Merrifield in the early 1960s, contributed to the 'Peptide Revolution' in the fields of diagnostics, and drug and vaccine development. Since then, peptide chemistry research has aimed to optimize these synthetic procedures, focusing on areas such as amide bond formation (the coupling step), solid supports and automation. Particular attention was devoted to the environmental impact of SPPS: the requirement for large amounts of organic solvents meant high costs for industrial peptide manufacturing that needed to be reduced. SPPS, alone or in hybrid technologies, has become strategic for the production of peptides as active pharmaceutical ingredients on a commercial scale.
New GM1 Ganglioside Derivatives for Selective Single and Double Labelling of the Natural Glycosphingolipid Skeleton (2009)

Abstract Selective single and double labelling of the natural ganglioside GM1 enables one to introduce various markers into different parts of the glycosphingolipid molecule without changing the natural skeleton. To that end, N ‐Fmoc‐2‐amino‐, N ‐Fmoc‐18‐amino‐ and S ‐(ethoxythiocarbonyl)‐18‐mercaptostearic acids have been prepared and coupled with the primary amino group in the sphingosine part of lyso‐GM1 and deAc‐deAcyl‐GM1 gangliosides. The products of these coupling reactions – building blocks 16a , 16b , 16c , 26 and 27 – may be used for the synthesis of GM1 derivatives with one or two fluorescent dye moieties or other labels of various polarities. Examples of various labelling strategies, using hydrophilic and lipophilic photostable fluorescent dyes, have been made available. The GM1 derivatives 17a , 22a and 23c labelled with the fluorescent dye ATTO 647N or the doubly labelled derivative 25b can be used as probes in fluorescence correlation spectroscopy (in conventional microscopy or stimulated emission depletion nanoscopy) to study the diffusion of lipid analogues in model or live cell membranes.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Burnt Clay Bricks as an Alternative Filter Media for Pebble Matrix Filters (PMF) (2016)

"ENGINEER", established in 1973 by The Institution of Engineers, is a Journal for dissemination of Engineering knowledge, published quarterly.If you are interested in contributing an Original Technical Paper based on research by the author(s) (intended for Section I) or an Original Article of Professional or Technical interest related to Engineering. (Section II) to this journal please go through the publication checklist which can be downloaded from here.Cover DescriptionCover images show a few views of 5000 DWT Misje Vita built by Colombo Dockyard PLC.
Horizontal molecular orientation in solution-processed organic light-emitting diodes (2015)

Horizontal orientation of the emission transition dipole moments achieved in glassy vapor-deposited organic thin films leads to an enhancement of the light out-coupling efficiency in organic light-emitting diodes (OLEDs). Here, our combined study of variable angle spectroscopic ellipsometry and angle dependent photoluminescence demonstrates that such a horizontal orientation can be achieved in glassy spin-coated organic films based on a composite blend of a heptafluorene derivative as a dopant and a 4,4′-bis(N-carbazolyl)-1,1′-biphenyl as a host. Solution-processed fluorescent OLEDs with horizontally oriented heptafluorene emitters were then fabricated and emitted deep blue electroluminescence with an external quantum efficiency as high as 5.3%.
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning (2016)

Medicinal chemistry patents contain rich information about chemical compounds. Although much effort has been devoted to extracting chemical entities from scientific literature, limited numbers of patent mining systems are publically available, probably due to the lack of large manually annotated corpora. To accelerate the development of information extraction systems for medicinal chemistry patents, the 2015 BioCreative V challenge organized a track on Chemical and Drug Named Entity Recognition from patent text (CHEMDNER patents). This track included three individual subtasks: (i) Chemical Entity Mention Recognition in Patents (CEMP), (ii) Chemical Passage Detection (CPD) and (iii) Gene and Protein Related Object task (GPRO). We participated in the two subtasks of CEMP and CPD using machine learning-based systems. Our machine learning-based systems employed the algorithms of conditional random fields (CRF) and structured support vector machines (SSVMs), respectively. To improve the performance of the NER systems, two strategies were proposed for feature engineering: (i) domain knowledge features of dictionaries, chemical structural patterns and semantic type information present in the context of the candidate chemical and (ii) unsupervised feature learning algorithms to generate word representation features by Brown clustering and a novel binarized Word embedding to enhance the generalizability of the system. Further, the system output for the CPD task was yielded based on the patent titles and abstracts with chemicals recognized in the CEMP task.The effects of the proposed feature strategies on both the machine learning-based systems were investigated. Our best system achieved the second best performance among 21 participating teams in CEMP with a precision of 87.18%, a recall of 90.78% and aF-measure of 88.94% and was the top performing system among nine participating teams in CPD with a sensitivity of 98.60%, a specificity of 87.21%, an accuracy of 94.75%, a Matthew's correlation coefficient (MCC) of 88.24%, a precision at full recall (P_full_R) of 66.57% and an area under the precision-recall curve (AUC_PR) of 0.9347. The SSVM-based CEMP systems outperformed the CRF-based CEMP systems when using the same features. Features generated from both the domain knowledge and unsupervised learning algorithms significantly improved the chemical NER task on patents.Database URL:http:// database. oxfordjournals. org/ content/ 2016/ baw049.
Multi-drug and Metabolite Quantification in Postmortem Blood by Liquid Chromatography–High-Resolution Mass Spectrometry: Comparison with Nominal Mass Technology (2014)

High-resolution mass spectrometry (HRMS) is being applied in postmortem drug screening as an alternative to nominal mass spectrometry, and additional evaluation in quantitative casework is needed. We report quantitative analysis of benzoylecgonine, citalopram, cocaethylene, cocaine, codeine, dextromethorphan, dihydrocodeine, diphenhydramine, 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone and oxymorphone in postmortem blood by ultra-performance liquid chromatography (UPLC)-MS(E)/time-of-flight (TOF). The method employs analyte-matched deuterated internal standardization and MS(E) acquisition of precursor and product ions at low (6 eV) and ramped (10-40 eV) collision energies, respectively. Quantification was performed using precursor ion data obtained with a mass extraction window of ± 5 ppm. Fragment and residual precursor ion acquisitions at ramped collision energies were evaluated as additional analyte identifiers. Extraction recovery of >60% and matrix effect of <20% were determined for all analytes and internal standards. Defined limits of detection (10 ng/mL) and quantification (25 ng/mL) were validated along with a linearity analytical range of 25-3,000 ng/mL (R(2) > 0.99) for all analytes. Parallel UPLC-MS(E)/TOF and UPLC-MS/MS analysis showed comparable precision and bias along with concordance of 253 positive (y = 1.002x + 1.523; R(2) = 0.993) and 2,269 negative analyte findings in 159 postmortem cases. Analytical performance and correlation studies demonstrate accurate quantification by UPLC-MS(E)/TOF and extended application of HRMS in postmortem casework.
Mannose corrects altered N-glycosylation in carbohydrate-deficient glycoprotein syndrome fibroblasts. (1996)

Type I carbohydrate-deficient glycoprotein syndrome (CDGS) patients fail to add entire N-linked oligosaccharide chains to some serum glycoproteins. Here we show that four CDGS fibroblast cell lines have two related glycosylation abnormalities. First, they incorporate 3-10-fold less [3H] mannose into proteins, and, second, the size of the lipid-linked oligosaccharide precursor (LLO) is much smaller than in controls. Addition of exogenous mannose, but not glucose, to these CDGS cells corrects both the lowered [3H] mannose incorporation and the size of LLO. These corrections are not permanent, and the defects immediately reappear when mannose is removed. To explore further the basis of mannose correction, we analyzed the amount of 3H-labeled LLO intermediates. Except for dolichol-P-mannose, other precursors, including mannose, mannose-6-phosphate, mannose-1-phosphate, and GDP-mannose, all showed a 3-10-fold decrease in CDGS cells. Thus, there are no obvious lesions in the intracellular conversion of mannose into LLO, and, once inside the cell, [3H]mannose appeared to be metabolized normally. Initial velocities of [3H]mannose uptake were two- to threefold less in CDGS cells compared with controls, and this slower transport may partially explain the reduced [3H]mannose incorporation in CDGS cells. Since we previously showed that the enzymes converting glucose to mannose-6-phosphate appear to be normal, our results suggest that cells may acquire or generate mannose in other ways. Although we have not identified the primary defect in CDGS, these studies show that intracellular mannose is limited and that some patients might benefit from including mannose in their regular diets.
Large area radiation source for water and wastewater treatment (2011)

There is a strong desire for processes that improve the safety of water supplies and that minimize disinfection byproducts. Stellarray is developing mercury-free next-generation x-ray and UV-C radiation sources in flat-panel and pipe form factors for water and wastewater treatment applications. These new radiation sources are designed to sterilize sludge and effluent, and to enable new treatment approaches to emerging environmental concerns such as the accumulation of estrogenic compounds in water. Our UV-C source, based on cathodoluminescent technology, differs significantly from traditional disinfection approaches using mercury arc lamps or UV LEDs. Our sources accelerate electrons across a vacuum gap, converting their energy into UV-C when striking a phosphor, or x-rays when striking a metallic anode target. Stellarray's large area radiation sources for wastewater treatment allow matching of the radiation source area to the sterilization target area for maximum coverage and improved efficiency.
How to Enhance Gas Removal from Porous Electrodes? (2016)

This article presents a structure-based modeling approach to optimize gas evolution at an electrolyte-flooded porous electrode. By providing hydrophobic islands as preferential nucleation sites on the surface of the electrode, it is possible to nucleate and grow bubbles outside of the pore space, facilitating their release into the electrolyte. Bubbles that grow at preferential nucleation sites act as a sink for dissolved gas produced in electrode reactions, effectively suctioning it from the electrolyte-filled pores. According to the model, high oversaturation is necessary to nucleate bubbles inside of the pores. The high oversaturation allows establishing large concentration gradients in the pores that drive a diffusion flux towards the preferential nucleation sites. This diffusion flux keeps the pores bubble-free, avoiding deactivation of the electrochemically active surface area of the electrode as well as mechanical stress that would otherwise lead to catalyst degradation. The transport regime of the dissolved gas, viz. diffusion control vs. transfer control at the liquid-gas interface, determines the bubble growth law.
Vascular endothelial growth factor in patients with high-altitude pulmonary edema (2003)

To examine the role of VEGF in the pathogenesis of high-altitude pulmonary edema (HAPE), we measured the concentrations of VEGF in venous serum and bronchoalveolar lavage fluid in patients with HAPE and in healthy volunteers. The VEGF in venous serum of the patients was normal at admission and significantly increased at recovery. Similarly, the VEGF in bronchoalveolar lavage fluid of the patients was increased at recovery compared with admission, but values at both admission and recovery were significantly lower than those of the controls. The present finding suggests that VEGF probably is destroyed in the lung of HAPE, and it appears less likely to have a critical part in the pathogenesis of HAPE but has rather an important role in the repair process for the impaired cell layer.
Tunneling nanotubes mediate rescue of prematurely senescent endothelial cells by endothelial progenitors: exchange of lysosomal pool (2011)

Although therapeutic effect of adoptive transfer of endothelial progenitor cells (EPC) has been well-substantiated, the actual engraftment is relatively low compared to a robust functional improvement of vasculopathy. Cellular mechanisms governing this action remain elusive. A recently discovered cell-cell communication via tunneling nanotube (TNT) formation is capable of transferring mitochondria and lysosomes between the cells - "organellar diakinesis". Based on the previous demonstration of lysosomal dysfunction in endothelial cells exposed to AGE-modified collagen I, we inquired whether TNT mechanism may be involved in EPC-mediated repair of stressed endothelial cells. Here we demonstrate that EPC selectively and multiplicatively establish TNT communication with stressed endothelia. The guidance cues for the selectivity are provided by exofacially exposed phosphatidylserine moieties. Lysosomal transfer is associated with the preservation of lysosomal pH gradient, functionally reconstituting lysosomal pool of stressed cells and improving endothelial cell viability, reducing premature senescence and apoptosis. In vivo, adoptive transfer of EPC to streptozotocin-diabetic mice results in a TNT-dependent reduction of senescent endothelial cells and correction of endothelium-dependent vasorelaxation. Collectively, these data establish a selective multiplicative effect of TNT between EPC and stressed endothelia, reconstitution of the lysosomal pool, and improved viability and function of stressed endothelia.
Multiple ubiquitination of calmodulin results in one polyubiquitin chain linked to calmodulin (1990)

In the presence of Ca2+ and ATP/Mg2+ mammalian calmodulin can be covalently coupled to ubiquitin by ubiquityl calmodulin synthetase (uCaM-synthetase). Three ubiquitin derivatives 125I-CT-ubiquitin (prepared by the chloramine-T method), 125I-BH-ubiquitin (prepared by the Bolton-Hunter method) and methylated forms of ubiquitin were tested with native calmodulin. Alternatively native ubiquitin was tested with the Bolton-Hunter derivative of calmodulin (125I-BH-calmodulin). Up to three molecules of ubiquitin can be incorporated into one molecule of calmodulin. Since both native forms of ubiquitin and calmodulin are good substrates of uCaM-synthetase, ubiquitination is not a result of an altered conformation (i.e. denaturation) of either protein. With 125I-BH-calmodulin it is demonstrated that calmodulin is also present in the higher molecular weight ubiquitin conjugates. If methylated ubiquitin is employed as substrate for uCaM-synthetase only one conjugate corresponding to the mono-ubiquitination product of calmodulin is formed. This demonstrates that only a single lysine residue in calmodulin is conjugated to ubiquitin. All other higher molecular weight ubiquitin-calmodulin conjugates must therefore be composed of one molecule of calmodulin to which an oligo- or poly-ubiquitin chain is linked. Since it can be shown that the mono-ubiquitination product of calmodulin still contains ca. 1 mol trimethyllysine/mol calmodulin, the poly-ubiquitin chain is not linked to lysine 115 of calmodulin. In addition a demethylation of trimethyllysine 115 by enzymes in reticulocyte lysate or the DEAE-enriched enzyme fraction with subsequent ubiquitination at this site of calmodulin can also be excluded.
Materials for Low‐Temperature Fuel Cells (2014)

KEY MATERIALS FOR LOW-TEMPERATURE FUEL CELLS: AN INTRODUCTION ALKALINE ANION EXCHANGE MEMBRANE FUEL CELLS Fuel Cells PEM Fuel Cell Principles Alkaline Fuel Cells Summary CATALYST SUPPORT MATERIALS FOR PROTON EXCHANGE MEMBRANE FUEL CELLS Introduction Current Status of Support Materials and Role of Carbon as Support in Fuel Cells Novel Carbon Materials as Electrocatalyst Support for Fuel Cells Conductive Metal Oxide as Support Materials Metal Carbides and Metal Nitrides as Catalyst Supports Conducting Polymer as Support Materials for Fuel Cells Conducting Polymer-Grafted Carbon Materials 3M Nanostructured Thin Film as Support Materials for Fuel Cells Summary and Outlook ANODE CATALYSTS FOR LOW-TEMPERATURE DIRECT ALCOHOL FUEL CELLS Introduction Anode Catalysts for Direct Methanol Fuel Cells: Improved Performance of Binary and Ternary Catalysts Anode Catalysts for Direct Ethanol Fuel Cells: Break C-C Bond to Achieve Complete 12-Electron-Transfer Oxidation Anode Catalysts for Direct Polyol Fuel Cells (Ethylene Glycol, Glycerol): Cogenerate Electricity and Valuable Chemicals Based on Anion Exchange Membrane Platform Synthetic Methods of Metal Electrocatalysts Carbon Nanomaterials as Anode Catalyst Support Future Challenges and Opportunities MEMBRANES FOR DIRECT METHANOL FUEL CELLS Introduction Basic Principles of Direct Methanol Fuel Cell Operation Membranes for Direct Methanol Fuel Cells Membrane Properties Summary Conclusions HYDROXIDE EXCHANGE MEMBRANES AND IONOMERS Introduction Requirements Fabrications and Categories Structure and Properties of Cationic Functional Group Structure and Properties of Polymer Main Chain Structure and Properties of Chemical Cross-Linking Prospective MATERIALS FOR MICROBIAL FUEL CELLS Introduction MFC Configuration Anode Materials Cathode Separators Outlook BIOELECTROCHEMICAL SYSTEMS Bioelectrochemical Systems and Bioelectrocatalysis On the Nature of Microbial Bioelectrocatalysis Microbial Electron Transfer Mechanisms From Physiology to Technology: Microbial Bioelectrochemical Systems Applicatin Potential of BES Technology Characterization of BESs and Microbial Bioelectrocatalysts Conclusions MATERIALS FOR MICROFLUIDIC FUEL CELLS Introduction Fundamentals Membraneless LFFC Designs and the Materials in Use Fuel, Oxidant, and Electrolytes Conclusions PROGRESS IN ELECTROCATALYSTS FOR DIRECT ALCOHOL FUEL CELLS Introduction Developing an Effective Method to Prepare Electrocatalysts Electrocatalysts for ORR Electrocatalysts for MOR Electrocatalysts for Ethanol Electrooxidation Conclusions Index
A quasi(unidirectional) Tellegen gyrator (2006)

We show that magnetoelectric (ME) laminate composites have characteristics of a previously conjectured, but unfound, fifth network circuit element—the Tellegen gyrator. Our findings establish that ME laminate composites (i) are nonreciprocal electrical elements, (ii) have significant nondissipative I-V conversion near a resonance frequency, and (iii) act like a unidirectional gyrator, i.e., an ideal Tellegen gyrator connected with a capacitor on one side and an inductor on the other.
Partial and complete detachment of neutrophils and eosinophils from schistosomula: evidence for the establishment of continuity between a fused and normal parasite membrane. (1980)

Neutrophils and eosinophils adhering to the surface of schistosomula of Schistosoma mansoni have been partially or completely detached with hypertonic sucrose or by pipetting. The sucrose-treated neutrophils are attached only in areas where there are pentalaminar fusions between the neutrophil and tegumental membranes, suggesting that these fusions attach the cells to the parasites. Pipetting breaks many of the attached cells. In thin section, the tegumental membrane underlying these cells is seen to be pentalaminar. By freeze-fracture techniques, modified attachment areas are found. The edge zone often appears as a single strand of intramembrane particles (IMPs) on the P2 face and as a groove on the E2 face. The edge zone may also have large discontinuities, in which case it no longer separates membrane faces of unequal IMP density from one another. In addition, the IMPs on the IMP-rich areas become aggregated and surrounded by craters in the membrane. These experiments suggest that the fusions may be the mechanism by which the parasite acquires some host membrane components on its surface. On the other hand, eosinophil plasma membranes are seen adhering to a layer of electron-dense material on the parasite after the cells have been disrupted by pipetting. This suggests that eosinophils adhere to the parasite surface through their discharged granule material and not by membrane fusions.
Probabilistic Future Prediction for Video Scene Understanding (2020)

We present a novel deep learning architecture for probabilistic future prediction from video. We predict the future semantics, geometry and motion of complex real-world urban scenes and use this representation to control an autonomous vehicle. This work is the first to jointly predict ego-motion, static scene, and the motion of dynamic agents in a probabilistic manner, which allows sampling consistent, highly probable futures from a compact latent space. Our model learns a representation from RGB video with a spatio-temporal convolutional module. The learned representation can be explicitly decoded to future semantic segmentation, depth, and optical flow, in addition to being an input to a learnt driving policy. To model the stochasticity of the future, we introduce a conditional variational approach which minimises the divergence between the present distribution (what could happen given what we have seen) and the future distribution (what we observe actually happens). During inference, diverse futures are generated by sampling from the present distribution.
MicroRNA29a regulates the expression of the nuclear oncogene Ski (2011)

MicroRNAs (miRNAs) are small, noncoding RNA molecules that regulate growth and differentiation. miRNAs are frequently located at cancer-specific fragile sites in the human genome, such as chromosome 7q. The nuclear oncogene SKI is up-regulated in acute myeloid leukemia (AML) with -7/del7q. Here we asked whether loss of miRNAs on chromosome 7q may explain this up-regulation. miR-29a expression was found to be down-regulated in AML with -7/del7q. Forced expression of miR-29a down-regulated Ski and its target gene, Nr-CAM, whereas miR-29a inhibition induced Ski expression. Luciferase assays validated a functional binding site for miR-29a in the 3' untranslated region of SKI. Finally, in samples of AML patients, we observed an inverse correlation of Ski and miR-29a expression, respectively. In conclusion, up-regulation of Ski in AML with -7/del7q is caused by loss of miR-29a. miR-29a may therefore function as an important tumor suppressor in AML by restraining expression of the SKI oncogene.
Hydrologic Response of a forested Mountain Watershed to Thinning: a Case Study (1985)

The paper deals with the effect of thinning (20%) on peak flow and fort-nightly runoff in a forested mountainous watershed near Dehra Dun, U.P. India. It has been found that the peak rate of flow increased by 8.6% in the first year (significant at 5% level) but the effect was insignificant in the second year after thinning. There was no significant effect on the total volume of fort-nightly runoff either in the first year or in the second year after thinning.