gebhart/patrepeval huggingface dataset:
Thec1 genes of P1 and P7 (1989)

The c1 genes of the heteroimmune phages P1 and P7 were sequenced and their products were compared. P7c1 expression was correlated with the translation in vitro of a protein whose predicted molecular weight (33,000 daltons) is indistinguishable from that of the P1c1 repressor. The c1 regions from both P1 and P7 were found to contain open reading frames capable of coding for a 283-amino acid protein whose predicted secondary structure lacks the helix-turn-helix motif commonly associated with repressor proteins. Two P1c1 amber mutations were localized to the 283-amino acid open reading frame. The P1c1 and P7c1 sequences were found to differ at only 18 positions, all but two of which alter the third position of the affected codon and do not alter the amino acid sequence of the protein. Plasmids expressing the c1 gene from either phage cause the repression of transcription from a cloned promoter situated upstream of P1c1.
Altered Calcium Homeostasis and Ultrastructure in Motoneurons of Mice Caused by Passively Transferred Anti-motoneuronal IgG (1997)

Calcium homeostasis and ultrastructure are altered in motor axon terminals (AT) of amyotrophic lateral sclerosis (ALS) patients and in mice injected with ALS IgG and exhibit increased density of synaptic vesicles and increased intracellular calcium. To develop an immune-mediated passive transfer experimental model of both systemic weakness and altered morphology, mice were inoculated intraperitoneally with anti-motoneuronal IgG. Animals initially manifested muscle stiffness and evidence of autonomic cholinergic hyperactivity. Electron microscopic cytochemistry within 12 hours (h) demonstrated significantly increased density of synaptic vesicles and calcium both in axon terminals of neuromuscular junctions and synaptic boutons on spinal motoneurons. After 24 h the mice were severely weak and premorbid. The number of synaptic vesicles was still larger than normal, but calcium was depleted from axon terminals and synaptic boutons. The motoneuron perikarya demonstrated the dilatation of the Golgi system and the rough endoplasmic reticulum with an increased amount of calcium. The NMDA receptor antagonist, MK-801, and the L-type calcium channel antagonist, Diltiazem, prevented clinical symptoms and some morphological alterations. These data demonstrate that high titer anti-motoneuronal IgG can induce severe weakness and produce similar ultrastructural features of motor axon terminals in human ALS and in mice injected with ALS IgG, and support a key role for calcium in selective vulnerability of motoneurons.
Extraordinarily Robust Polyproline Type I Peptoid Helices Generated via the Incorporation of α-Chiral Aromatic N-1-Naphthylethyl Side Chains (2011)

Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 Å. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.
Lateral epitaxy of low defect density GaN layers via organometallic vapor phase epitaxy (1997)

Organometallic vapor phase lateral epitaxy and coalescence of GaN layers originating from GaN stripes deposited within 3-μm-wide windows spaced 3 μm apart and contained in SiO2 masks on GaN/AlN/6H–SiC(0001) substrates are reported. The extent and microstructural characteristics of the lateral overgrowth were a strong function of stripe orientation. A high density of threading dislocations, originating from the interface of the underlying GaN with the AlN buffer layer, were contained in the GaN grown in the window regions. The overgrowth regions, by contrast, contained a very low density of dislocations. The coalesced layers had a rms surface roughness of 0.25 nm.
Dissecting Protein−Protein Interactions Using Directed Evolution (2011)

Protein-protein interactions are essential for life. They are responsible for most cellular functions and when they go awry often lead to disease. Proteins are inherently complex. They are flexible macromolecules whose constituent amino acid components act in combinatorial and networked ways when they engage one another in binding interactions. It is just this complexity that allows them to conduct such a broad array of biological functions. Despite decades of intense study of the molecular basis of protein-protein interactions, key gaps in our understanding remain, hindering our ability to accurately predict the specificities and affinities of their interactions. Until recently, most protein-protein investigations have been probed experimentally at the single-amino acid level, making them, by definition, incapable of capturing the combinatorial nature of, and networked communications between, the numerous residues within and outside of the protein-protein interface. This aspect of protein-protein interactions, however, is emerging as a major driving force for protein affinity and specificity. Understanding a combinatorial process necessarily requires a combinatorial experimental tool. Much like the organisms in which they reside, proteins naturally evolve over time, through a combinatorial process of mutagenesis and selection, to functionally associate. Elucidating the process by which proteins have evolved may be one of the keys to deciphering the molecular rules that govern their interactions with one another. Directed evolution is a technique performed in the laboratory that mimics natural evolution on a tractable time scale that has been utilized widely to engineer proteins with novel capabilities, including altered binding properties. In this review, we discuss directed evolution as an emerging tool for dissecting protein-protein interactions.
Analytical Methods for the Bioavailability Evaluation of Hydroxypyridinonate Actinide Decorporation Agents in Pre-Clinical Pharmacokinetic Studies (2013)

The hydroxypyridinonate ligands 5-LIO(Me-3,2-HOPO) and 3,4,3-LI(1,2-HOPO) are two lead compounds under development for actinide chelation therapy. Methods to quantify these actinide decorporation agents in plasma are necessary to study their in vivo pharmacokinetic behavior. Such bioanalytical methods were developed with rat plasma, using liquid chromatography coupled with tandem mass spectrometry, and have a detection range of 0.05 to 2.5 μg/mL and 0.1 to 5 μg/mL for 5-LIO(Me-3,2-HOPO) and 3,4,3-LI(1,2-HOPO), respectively. These methods were used to determine the in vivo plasma pharmacokinetics of the free acid and four salt forms of each ligand after a single intravenous or oral administration in rats. The different salt forms displayed similar pharmacokinetic profiles to those of the corresponding free acid, and the use of salt co-formers did not improve the oral bioavailability of the active pharmaceutical ingredients in rats. The described bioanalytical detection methods were successfully applied to the selection of solid-state forms of 5âLIO(Me-3,2-HOPO) and 3,4,3-LI(1,2-HOPO) for future preclinical development activities, and will be adapted for use with plasma from other species.
The elusive peripheral blood hemopoietic stem cell. (1993)

Long-term culture initiating cells (LTC-IC) are primitive hemopoietic progenitors that give rise to clonogenic cells when provided with a supportive feeder layer of mesenchymal cells. These LTC-IC possess many of the characteristics expected of marrow-repopulating "stem cells" including high proliferative and multilineage-differentiative capacity and resistance to 4-hydroperoxy-cyclophosphamide (4-HC) killing. In addition, stem cells are known to persist and may proliferate in murine LTC, and human marrow grown in LTC has been successfully used as hemopoietic support for myeloablative therapy. LTC-IC, as well as clonogenic precursors, circulate in normal peripheral blood, and the concentration of both progenitor types can be increased by cytotoxic chemotherapy and/or growth factors. When mobilized peripheral blood cells are used as hemopoietic support for high-dose chemo/radiotherapy, engraftment has often been more rapid than that achieved with autologous marrow. Thus, primitive hemopoietic cells circulate in human blood, which can enable hemopoietic reconstitution following aggressive therapy for malignant disease.
Characterization of H9 Subtype Influenza Viruses from the Ducks of Southern China: a Candidate for the Next Influenza Pandemic in Humans? (2003)

A current view of the emergence of pandemic influenza viruses envisages a gene flow from the aquatic avian reservoir to humans via reassortment in pigs, the hypothetical "mixing vessel." Understanding arising from recent H5N1 influenza outbreaks in Hong Kong since 1997 and the isolation of avian H9N2 virus from humans raises alternative options for the emergence of a new pandemic virus. Here we report that H9N2 influenza viruses established in terrestrial poultry in southern China are transmitted back to domestic ducks, in which the viruses generate multiple reassortants. These novel H9N2 viruses are double or even triple reassortants that have amino acid signatures in their hemagglutinin, indicating their potential to directly infect humans. Some of them contain gene segments that are closely related to those of A/Hong Kong/156/97 (H5N1/97, H5N1) or A/Quail/Hong Kong/G1/97 (G1-like, H9N2). More importantly, some of their internal genes are closely related to those of novel H5N1 viruses isolated during the outbreak in Hong Kong in 2001. This study reveals a two-way transmission of influenza virus between terrestrial and aquatic birds that facilitates the generation of novel reassortant H9N2 influenza viruses. Such reassortants may directly or indirectly play a role in the emergence of the next pandemic virus.
CRYSTALS - Kyber: A CCA-Secure Module-Lattice-Based KEM (2018)

Rapid advances in quantum computing, together with the announcement by the National Institute of Standards and Technology (NIST) to define new standards for digitalsignature, encryption, and key-establishment protocols, have created significant interest in post-quantum cryptographic schemes. This paper introduces Kyber (part of CRYSTALS - Cryptographic Suite for Algebraic Lattices - a package submitted to NIST post-quantum standardization effort in November 2017), a portfolio of post-quantum cryptographic primitives built around a key-encapsulation mechanism (KEM), based on hardness assumptions over module lattices. Our KEM is most naturally seen as a successor to the NEWHOPE KEM (Usenix 2016). In particular, the key and ciphertext sizes of our new construction are about half the size, the KEM offers CCA instead of only passive security, the security is based on a more general (and flexible) lattice problem, and our optimized implementation results in essentially the same running time as the aforementioned scheme. We first introduce a CPA-secure public-key encryption scheme, apply a variant of the Fujisaki-Okamoto transform to create a CCA-secure KEM, and eventually construct, in a black-box manner, CCA-secure encryption, key exchange, and authenticated-key-exchange schemes. The security of our primitives is based on the hardness of Module-LWE in the classical and quantum random oracle models, and our concrete parameters conservatively target more than 128 bits of postquantum security.
The aryl hydrocarbon receptor: a perspective on potential roles in the immune system (2009)

The aryl hydrocarbon receptor (AHR) is a protein best known for its role in mediating toxicity. Over 30 years of research has uncovered additional roles for the AHR in xenobiotic metabolism and normal vascular development. Activation of the AHR has long been known to cause immunotoxicity, including thymic involution. Recent data suggesting a role for the AHR in regulatory T-cell (Treg) and T-helper 17 (Th17) cell development have only added to the excitement about this biology. In this review, we will attempt to illustrate what is currently known about AHR biology in the hope that data from fields as diverse as evolutionary biology and pharmacology will help elucidate the mechanism by which AHR modifies immune responses. We also will discuss the complexities of AHR pharmacology and genetics that may influence future studies of AHR in the immune system.
Isocyanide insertion chemistry. Synthesis and structural characterization of bridging imidoyl complexes of nickel and amide formation by intramolecular coupling of acyl and imidoyl functionalities (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsocyanide insertion chemistry. Synthesis and structural characterization of bridging imidoyl complexes of nickel and amide formation by intramolecular coupling of acyl and imidoyl functionalitiesJuan Campora, Enrique Gutierrez, Angeles Monge, Manuel L. Poveda, Caridad Ruiz, and Ernesto CarmonaCite this: Organometallics 1993, 12, 10, 4025–4031Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/om00034a039https://doi.org/10.1021/om00034a039research-articleACS PublicationsRequest reuse permissionsArticle Views167Altmetric-Citations21LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A digital signal processing algorithm for detecting arcing faults on power distribution feeders (1989)

Signal processing hardware and software that can be used to improve the detection of certain power system faults using computer relays are discussed. Integrated systems and architectures for monitoring several fault-sensitive parameters have been investigated. A suggested architecture utilizing several processors is presented. Several fault-sensitive parameters for the detection of arcing faults are presented. A detection methodology based on these parameters is described, and a partial solution to the problem of directionality is discussed. The use of a knowledge-based environment to modify protection criteria is suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Physics of solar cells : from principles to new concepts (2005)

List of Symbols.Preface.1 Problems of the Energy Economy.1.1 Energy economy.1.2 Estimate of the maximum reserves of fossil energy.1.3 The greenhouse effect.2 Photons.2.1 Black-body radiation.2.2 Kirchhoff's law of radiation for non-black bodies.2.3 The solar spectrum.2.4 Concentration of the solar radiation.2.5 Maximum efficiency of solar energy conversion.3 Semiconductors.3.1 Electrons in semiconductors.3.2 Holes.3.3 Doping.3.4 Quasi-Fermi distributions.3.5 Generation of electrons and holes.3.6 Recombination of electrons and holes.3.7 Light emission by semiconductors.4 Conversion of Thermal Radiation into Chemical Energy.4.1 Maximum efficiency for the production of chemical energy.5 Conversion of Chemical Energy into Electrical Energy.5.1 Transport of electrons and holes.5.2 Separation of electrons and holes.5.3 Diffusion length of minority carriers.5.4 Dielectric relaxation.5.5 Ambipolar diffusion.5.6 Dember effect.5.7 Mathematical description.6 Basic Structure of Solar Cells.6.1 A chemical solar cell.6.2 Basic mechanisms in solar cells.6.3 Dye solar cell.6.4 The pn-junction.6.5 pn-junction with impurity recombination, two-diode model.6.6 Hetero-junctions.6.7 Semiconductor-metal contact.6.8 The role of the electric field in solar cells.7 Limitations on Energy Conversion in Solar Cells.7.1 Maximum efficiency of solar cells.7.2 Efficiency of solar cells as a function of their energy gap.7.3 The optimal silicon solar cell.7.4 Thin-film solar cells.7.5 Equivalent circuit.7.6 Temperature dependence of the open-circuit voltage.7.7 Intensity dependence of the efficiency.7.8 Efficiencies of the individual energy conversion processes.8 Concepts for Improving the Efficiency of Solar Cells.8.1 Tandem cells.8.2 Concentrator cells.8.3 Thermo-photovoltaic energy conversion.8.4 Impact ionization.8.5 Two-step excitation in three-level systems.9 Prospects for the Future.Appendix.Index.
An overview of religion on campus (1989)

Abstract Religion on campus is diversified, but it is built on a common history of patterns and characteristics that can be used to assist student services professionals.
Transient protection: efficient one-flask syntheses of protected deoxynucleosides (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTransient protection: efficient one-flask syntheses of protected deoxynucleosidesG. S. Ti, B. L. Gaffney, and R. A. JonesCite this: J. Am. Chem. Soc. 1982, 104, 5, 1316–1319Publication Date (Print):March 1, 1982Publication History Published online1 May 2002Published inissue 1 March 1982https://pubs.acs.org/doi/10.1021/ja00369a029https://doi.org/10.1021/ja00369a029research-articleACS PublicationsRequest reuse permissionsArticle Views3172Altmetric-Citations382LEARN 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
Guarantor and reputation based trust model for Social Internet of Things (2015)

The addition of social networking to Internet of Things (IoT) has led to the paradigm of Social Internet of Things (SIoT). It is where digital devices called objects mimic the social behavior of their human counterparts and build up social relationships with other objects in order to provide services to the humans. One of the obstacles in realizing this idea is trust management. The most complex question in trust building is `How can objects trust the information provided by other objects?' This paper proposes a new trust model based on Guarantor and Reputation for SIoT. The former requests an object to find a guarantor at an agreed commission rate in order to get service from another object; the latter uses reputation of a node to measure its trustworthiness. By simulating this model using an architecture based on real world scenarios, it was concluded that the trust model can be employed in different scenarios in SIoT and the use of penalties for malicious activity enables the model to detect and isolate malicious nodes.
SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis (2005)

SNPAnalyzer is a software that performs four essential statistical analyses of SNPs in a common computational environment. It is composed of three main modules: (i) data manipulation, (ii) analysis and (iii) visualization. The data manipulation module is responsible for data input and output, and handles genotype, phenotype and genetic distance data. To ensure user convenience, the data format is simple. The analysis module performs statistical calculations and consists of four subcomponents: (i) Hardy-Weinberg equilibrium, (ii) Haplotype Estimation, (iii) linkage disequilibrium (LD) and (iv) quantitative trait locus analysis. The main feature of the analysis module is multiple implementations of different algorithms and indices for haplotype estimation and for LD analysis. This enables users to compare separate results generated by different algorithms, which help to avoid biased results acquired by applying a single statistical algorithm. The performance of all implemented algorithms has been validated using experimentally proven datasets. The visualization module presents most of the analyzed results as figures, rather than as simple text, which aids in the intuitive understanding of complex data. The SNPAnalyzer has been developed using C and C++ and is available at http://www.istech.info/istech/board/login_form.jsp.