gebhart/patrepeval huggingface dataset:
Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate (2011)

Conversion of lignocellulose to biofuels is partly inefficient due to the deleterious impact of cellulose crystallinity on enzymatic saccharification. We demonstrate how the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils. We provide a molecular-scale explanation of these phenomena through molecular dynamics (MD) simulations and enzymatic assays. Ammonia transformed the naturally occurring crystalline allomorph I(β) to III(I), which led to a decrease in the number of cellulose intrasheet hydrogen bonds and an increase in the number of intersheet hydrogen bonds. This rearrangement of the hydrogen bond network within cellulose III(I), which increased the number of solvent-exposed glucan chain hydrogen bonds with water by ~50%, was accompanied by enhanced saccharification rates by up to 5-fold (closest to amorphous cellulose) and 60-70% lower maximum surface-bound cellulase capacity. The enhancement in apparent cellulase activity was attributed to the "amorphous-like" nature of the cellulose III(I) fibril surface that facilitated easier glucan chain extraction. Unrestricted substrate accessibility to active-site clefts of certain endocellulase families further accelerated deconstruction of cellulose III(I). Structural and dynamical features of cellulose III(I), revealed by MD simulations, gave additional insights into the role of cellulose crystal structure on fibril surface hydration that influences interfacial enzyme binding. Subtle alterations within the cellulose hydrogen bond network provide an attractive way to enhance its deconstruction and offer unique insight into the nature of cellulose recalcitrance. This approach can lead to unconventional pathways for development of novel pretreatments and engineered cellulases for cost-effective biofuels production.
β-Keto Esters Derived from 2-(Trimethylsilyl)ethanol: An Orthogonal Protective Group for β-Keto Esters (2008)

β-Keto esters derived from 2-(trimethylsilyl)ethanol undergo cleavage and decarboxylation when treated with 0.75 equivalents of tetrabutylammonium fluoride trihydrate in tetrahydrofuran at 50 ˚C, while β-keto esters derived from methanol, tert-butyl alcohol, allyl alcohol, or benzyl alcohol stay intact. Conversely, methyl­-, tert-butyl-, allyl-, or benzyl β-keto esters can be cleaved and decarboxylated without the 2-(trimethylsilyl)ethyl β-keto esters being affected. Similarly, mixed bis(β-keto esters) derived from 2-(trimethylsilyl)ethanol and methanol, tert-butyl alcohol, allyl alcohol, or benzyl alcohol can be defunctionalized chemoselectively under the same reaction conditions.
Sequence analysis of the lysin gene region of the prolate lactococcal bacteriophage c2 (1993)

Approximately 80% of the genome of the prolate-headed lactococcal bacteriophage c2 was cloned into shuttle vectors pSA3 and pFX3 in Escherichia coli and transferred to Lactococcus lactis. A 1.67-kilobase EcoRV fragment containing the gene for the phage lysin was identified and the position and orientation of the phage lysin gene in the physical map of the phage were determined. The phage lysin was expressed in E. coli and its sequence was determined and compared with the sequences of other bacteriophage lytic genes. The sequence was similar, but not identical, to that of the related lactococcal phage m13, having a number of silent substitutions and an apparent deletion that altered the carboxy terminus of the protein. Possible alternative translation initiation codons for the lysin gene and two possible alternative mechanisms for access of the lysin enzyme to the cell wall are discussed. An open reading frame upstream of the putative lysin gene was found to be 177 base pairs longer than that reported for phage m13. A codon usage table for the lysin genes of several phages as well as for reported gene sequences from L. lactis and lactococcal bacteriophages is presented.
New Emphasis on Fuel Volatility-Effects on Vehicle Warmup with Quick-Release Chokes (1972)

&lt;div class="htmlview paragraph"&gt;Quick-release chokes may become an essential feature of advanced exhaust emission control systems to minimize emissions during warmup. However, quick-release chokes greatly impair warmup driveability when gasolines of conventional volatility are used. Consequently, modifications of gasoline volatility were investigated as one approach to restoring warmup driveability with quick-release chokes.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Warmup driveability of two test cars equipped with quick-release chokes was measured on a chassis dynamometer at 40 and 68 F using fuels with widely different volatility characteristics. Warmup driveability was essentially restored by increasing fuel volatility in the 40-90% ASTM distillation range. Front-end volatility up to the 40% point had very little effect.&lt;/div&gt;
Orderly hematopoietic development of induced pluripotent stem cells via Flk‐1+ hemoangiogenic progenitors (2009)

Induced pluripotent stem (iPS) cells, reprogrammed somatic cells with embryonic stem (ES) cell-like characteristics, are generated by the introduction of combinations of specific transcription factors. Little is known about the differentiation of iPS cells in vitro. Here we demonstrate that murine iPS cells produce various hematopoietic cell lineages when incubated on a layer of OP9 stromal cells. During this differentiation, iPS cells went through an intermediate stage consisting of progenitor cells that were positive for the early mesodermal marker Flk-1 and for the sequential expression of other genes that are associated with hematopoietic and endothelial development. Flk-1(+) cells differentiated into primitive and definitive hematopoietic cells, as well as into endothelial cells. Furthermore, Flk-1(+) populations contained common bilineage progenitors that could generate both hematopoietic and endothelial lineages from single cells. Our results demonstrate that iPS cell-derived cells, like ES cells, can follow a similar hematopoietic route to that seen in normal embryogenesis. This finding highlights the potential use of iPS cells in clinical areas such as regenerative medicine, disease investigation, and drug screening.
Functional domains in the heavy-chain region of factor XI: a high molecular weight kininogen-binding site and a substrate-binding site for factor IX (1989)

To probe the molecular interactions of factor XI we have prepared two monoclonal antibodies (MoAbs; 5F7 and 3C1), each of which binds the heavy chain of reduced and alkylated factor XIa. Competitive solid phase radioimmunoassay (RIA) binding studies revealed that 5F7 and 3C1 are directed against different epitopes within factor XI. One antibody (5F7) blocked the surface-mediated proteolytic activation of factor XI and its binding to HMW kininogen, but had no effect on factor-XIa-catalyzed factor IX activation. The other antibody (3C1) is a competitive inhibitor of factor-IX activation by factor XIa, but blocked factor-XI binding to HMW kininogen only at 1,000-fold higher concentration than 5F7. Moreover, HMW kininogen had no effect on the kinetics of factor-XIa-catalyzed factor-IX activation. Furthermore, factor XI CNBr peptide fragments that bind to the 5F7 and 3C1 antibodies were isolated. The peptides that bound to the 5F7 antibody blocked the binding of HMW kininogen to factor XI but did not inhibit factor-XIa-catalyzed factor-IX activation. However, the peptides isolated by the 3C1 antibody inhibited factor-XIa-catalyzed factor-IX activation and had no effect on factor-XI binding to HMW kininogen. Our results indicate that distinct functional domains within the heavy chain region of factor XI are important for the binding of factor XI to HMW kininogen and for activation of factor IX by factor XIa.
Heat shock protein 27 prevents cellular polyglutamine toxicity and suppresses the increase of reactive oxygen species caused by huntingtin (2002)

Neuronal loss and intraneuronal protein aggregates are characteristics of Huntington's disease (HD), which is one of 10 known neurodegenerative disorders caused by an expanded polyglutamine [poly(Q)] tract in the disease protein. N-terminal fragments of mutant huntingtin produce intracellular aggregates and cause toxicity. Several studies have shown that chaperones suppress poly(Q) aggregation and toxicity/cell death, but the mechanisms by which they prevent poly(Q)-mediated cell death remain unclear. In the present study, we identified heat shock protein 27 (HSP27) as a suppressor of poly(Q) mediated cell death, using a cellular model of HD. In contrast to HSP40/70 chaperones, we showed that HSP27 suppressed poly(Q) death without suppressing poly(Q) aggregation. We tested the hypotheses that HSP27 may reduce poly(Q)-mediated cell death either by binding cytochrome c and inhibiting the mitochondrial death pathway or by protecting against reactive oxygen species (ROS). While poly(Q)-induced cell death was reduced by inhibiting cytochrome c (cyt c) release from mitochondria, protection by HSP27 was regulated by its phosphorylation status and was independent of its ability to bind to cyt c. However, we observed that mutant huntingtin caused increased levels of ROS in neuronal and non-neuronal cells. ROS contributed to cell death because both N-acetyl-L-cysteine and glutathione in its reduced form suppressed poly(Q)-mediated cell death. HSP27 decreased ROS in cells expressing mutant huntingtin, suggesting that this chaperone protects cells against oxidative stress. We propose that a poly(Q) mutation can induce ROS that directly contribute to cell death and that HSP27 is an antagonist of this process.
Multicomponent RNA plant virus infection derived from cloned viral cDNA (1984)

In vitro transcripts from mixtures of appropriate brome mosaic virus (BMV) cDNA clones are infectious when inoculated onto barley plants. Infectivity depends on in vitro transcription and on the presence of transcripts from clones of all three BMV genetic components. Infectivity is destroyed by RNase after transcription, but it is insensitive to RNase before or to DNase after transcription. Virion RNAs from plants infected with cDNA transcripts hybridize to BMV-specific probes and coelectrophorese with virion RNAs propagated from conventional inoculum. Direct RNA sequencing shows that a deletion in the noncoding region of one infectious BMV clone is preserved in viral RNA from plants systemically infected with transcript mixtures representing that clone.
The Design and Application of a Pediatric Centrifugal Pump (1997)

This centrifugal pump (CP) includes two parts: the blood pump and the driving apparatus. They are connected by six twin magnetic disc plates and driven by a magnetic DC motor (120W). The blood pump had six leaves deadlocked between two plastic discs. Six leaves were set at 30 degrees angles, separately. In the lower chamber of the CP, there was an inlay magnetic disc, which is connected with the disc leaves by an axis. This axis was sealed by silicon rubber and a ceramic ring. The priming volume of the blood chamber was 34 ml. In vitro testing showed that the free hemoglobin caused by the CP was much less than that caused by a roller pump after 180 min. The effect of this CP on blood cell damage was also studied in an animal model. Six goats were placed on cardiopulmonary bypass for 180 min. Perfusion flow rates were maintained between 1.5 and 2.5 L/min. The plasma free hemoglobin was lower in the CP group (6.04 mg/dL) than in the roller pump group (32.25 mg/dL), p < 0.01. The CP has been used in ten pediatric patients undergoing cardiopulmonary bypass surgery. The patients' ages were from three to five years, and body weights were from 15 to 20 kg. Perfusion flow rates were maintained between 1.8 and 2.5 L/min, and bypass times were from 30 to 50 min. The rotation speeds were from 2000 to 2500 rpm. All the patients recovered smoothly, and no hemoglobinuria occurred.
Ion channel redistribution and function during development of the myelinated axon (1998)

The development of myelinated axons represents one of the most complex interactions among different cell types in the nervous system. Striking changes occur in both morphology and function in the early postnatal period. Myelination effectively isolates electrically most of the axolemma and dramatically alters the pathways for current flow that are required for rapid, reliable, and efficient conduction. Correspondingly, ion channels must be directed to and stabilized at their required sites. In the case of Na+ channels, this requires a 25-fold increase in density within nodes of Ranvier, and, in mammalian fibers, a virtually complete spatial separation from voltage-dependent K+ channels. Nodes must also be properly spaced to ensure a high conduction velocity and energy efficiency without compromising the safety factor for reliable propagation. In this review, we consider the events responsible for axon development, emphasizing the involvement of ion channels. We discuss the current state of research in this area, including some controversies regarding mechanisms of neuron-glial communication.
A-RAM Memory Cell: Concept and Operation (2010)

Capacitorless single-transistor (1T) DRAM cells are envisioned for replacing the conventional DRAMs where the storage capacitor can hardly be further miniaturized. We propose a totally different 1T-DRAM cell, named A-RAM, which is compatible with SOI CMOS deep scaling. Its novelty comes from the partitioning of the transistor body into two distinct ultrathin regions separated by a thin dielectric. The holes are physically confined in the upper semibody and govern the electron current flowing into the lower semibody. The systematic simulations show that the A-RAM is attractive for low-power and embedded memory applications since it exhibits enhanced state definition, retention, scalability, and simple waveforms for word and bit lines.
Data Analytics for Smart Parking Applications (2016)

We consider real-life smart parking systems where parking lot occupancy data are collected from field sensor devices and sent to backend servers for further processing and usage for applications. Our objective is to make these data useful to end users, such as parking managers, and, ultimately, to citizens. To this end, we concoct and validate an automated classification algorithm having two objectives: (1) outlier detection: to detect sensors with anomalous behavioral patterns, i.e., outliers; and (2) clustering: to group the parking sensors exhibiting similar patterns into distinct clusters. We first analyze the statistics of real parking data, obtaining suitable simulation models for parking traces. We then consider a simple classification algorithm based on the empirical complementary distribution function of occupancy times and show its limitations. Hence, we design a more sophisticated algorithm exploiting unsupervised learning techniques (self-organizing maps). These are tuned following a supervised approach using our trace generator and are compared against other clustering schemes, namely expectation maximization, k-means clustering and DBSCAN, considering six months of data from a real sensor deployment. Our approach is found to be superior in terms of classification accuracy, while also being capable of identifying all of the outliers in the dataset.
Junction Resistivity of Carrier-Selective Polysilicon on Oxide Junctions and Its Impact on Solar Cell Performance (2016)

We investigate the junction resistivity of high-quality carrier-selective polysilicon on oxide (POLO) junctions with the transfer length method. We demonstrate n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> POLO junctions with a saturation current density J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C,poly</sub> of 6.2 fA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a junction resistivity ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> of 0.6 mΩcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , counterdoped n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> POLO junctions with 2.7 fA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 1.3 mΩcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> POLO junctions with 6.7 fA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 0.2 mΩcm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Such low junction resistivities and saturation current densities correspond to excellent selectivities S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sub> of up to 16.2. The efficiency potential for back-junction back-contact solar cells with these POLO junctions was determined to be larger than 25 % by numerical device simulations. We demonstrate experimentally a back-junction back-contact solar cell with p-type and n-type POLO junctions with an independently confirmed efficiency of 24.25 %.
Prednisolone Treatment in Asthma Is Associated with Modulation of Bronchoalveolar Lavage Cell Interleukin-4, Interleukin-5, and Interferon-γ Cytokine Gene Expression (1993)

Although corticosteroids are effective in improving asthma symptoms and bronchial responsiveness, their mechanism of action is unknown. We examined whether changes in bronchial responsiveness with corticosteroid therapy of asthma are accompanied by a reduction in cytokine gene expression and eosinophil infiltration in the airways. Bronchoalveolar lavage (BAL) was performed in 18 patients with moderate asthma before and after 2 wk of treatment with prednisolone, 0.6 mg/kg/day, or matched placebo in a randomized double-blind parallel group study. Cells were counted in BAL cytocentrifuge preparations, and the numbers of cells expressing cytokine mRNA were assessed by in situ hybridization using 35S-labeled RNA probes. When the actively treated and placebo groups were compared, there was a decrease in airway methacholine responsiveness (p < 0.01) after prednisolone. This was accompanied by a decrease in bronchoalveolar lavage eosinophils (p < 0.05), a reduction in the numbers of BAL cells per 1,000 expressing mRNA for interleukin-4 (IL-4, p < 0.01) and interleukin-5 (IL-5, p < 0.005), and an increase in numbers of cells expressing mRNA for interferon-gamma (p < 0.005). These results are compatible with the hypothesis that the beneficial effects of corticosteroids in asthma may result from modulation of cytokine production, with consequent inhibition of local bronchial eosinophilia.
Chemical Synthesis of Natural Product Peptides:  Coupling Methods for the Incorporation of Noncoded Amino Acids into Peptides (1997)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical Synthesis of Natural Product Peptides: Coupling Methods for the Incorporation of Noncoded Amino Acids into PeptidesJohn M. Humphrey and A. Richard ChamberlinView Author Information Department of Chemistry, University of California, Irvine, California 92717Cite this: Chem. Rev. 1997, 97, 6, 2243–2266Publication Date (Web):October 1, 1997Publication History Received13 January 1997Revised24 June 1997Published online1 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/cr950005shttps://doi.org/10.1021/cr950005sresearch-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views12225Altmetric-Citations1014LEARN 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 SUBJECTS:Alkyls,Cyclization,Monomers,Organic compounds,Peptides and proteins Get e-Alerts
Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form (1998)

The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6(3)22 to a resolution of 2.2 A. This protease is bound with a 14-mer peptide representing the central region of the NS4A protein. There are two molecules of the NS3(1-180)-NS4A(21'-34') complex per asymmetric unit. Each displays a familiar chymotrypsin-like fold that includes two beta-barrel domains and four short alpha-helices. The catalytic triad (Ser-139, His-57, and Asp-81) is located in the crevice between the beta-barrel domains. The NS4A peptide forms an almost completely enclosed peptide surface association with the protease. In contrast to the reported H strain complex of NS3 protease-NS4A peptide in a trigonal crystal form (Kim JL et al., 1996, Cell 87:343-355), the N-terminus of the NS3 protease is well-ordered in both molecules in the asymmetric unit of our hexagonal crystal form. The folding of the N-terminal region of the NS3 protease is due to the formation of a three-helix bundle as a result of crystal packing. When compared with the unbound structure (Love RA et al., 1996, Cell 87:331-342), the binding of the NS4A peptide leads to the ordering of the N-terminal 28 residues of the NS3 protease into a beta-strand and an alpha-helix and also causes local rearrangements important for a catalytically favorable conformation at the active site. Our analysis provides experimental support for the proposal that binding of an NS4A-mimicking peptide, which increases catalytic rates, is necessary but not sufficient for formation of a well-ordered, compact and, hence, highly active protease molecule.