gebhart/patrepeval huggingface dataset:
Two Basic Regions of NCp7 Are Sufficient for Conformational Conversion of HIV-1 Dimerization Initiation Site from Kissing-loop Dimer to Extended-duplex Dimer (2001)

Nucleocapsid (NC) protein possesses nucleotide-annealing activities, which are used in various processes in retroviral life cycle. As conserved characters, the NC proteins have one or two zinc fingers of CX(2)CX(4)HX(4)C motif surrounded by basic amino acid sequences. Requirement of the zinc fingers for the annealing activities of NC protein remains controversial. In this study, we focused the requirement in the process of maturation of dimeric viral RNA. Discrimination between immature and mature dimers of synthetic RNA corresponding to the dimerization initiation site of human immunodeficiency virus type 1 (HIV-1) genomic RNA was performed based on their Mg(2+)-dependent stability in gel electrophoreses and on their distinct signal pattern from NMR analysis of imino protons. Chaperoning activity of the HIV-1 NC protein, NCp7, and its fragments for maturation of dimeric RNA was investigated using these experimental systems. We found that the two basic regions flanking the N-terminal zinc finger of NCp7, which are connected by two glycine residues instead of the zinc finger, were sufficient, although about 10 times the amounts of peptide were needed in comparison with intact NCp7. Further, it was found that the amount of basic residues rather than the amino acid sequence itself is important for the activity. The zinc fingers may involve the binding affinity and/or such a possible specific binding of NCp7 to dimerization initiation site dimer that leads to the maturation reaction.
FPGA-Assisted Real-Time RF Wireless Data Analytics System: Design, Implementation, and Statistical Analyses (2019)

A wide range of new ultra reliable low latency communication (URLLC) applications in next generation (NG) wireless systems demand real-time radio frequency (RF) data analytics of channel utilization (CU) that can help in making proactive resource allocation decisions. However, such real-time RF data analytics require processing of tens of millions of in-phase and quadrature (IQ) samples per second and sending huge quantities of samples to a resource allocating entity is not practical. We present design and implementation of an RF data analytics system which utilizes field-programmable gate arrays (FPGAs) at the network edge to process real-time streaming IQ samples from RF transceiver. FPGAs process millions of samples per second and output low-overhead descriptive statistics of wireless CU, such as mean CU values, maximum CU values, and entire histograms to obtain probability distribution of CU values, to a resource controller server where a quantile estimation based technique is used to detect congestion in CU in real-time. The FPGA-based modules are implemented on Xilinx's Zynq-7000 devices mounted with RF transceivers. We evaluate the performance of the implemented analytics system using extensive measurements, testing, and statistical analyses that are performed in both laboratory and over-the-air environments.
Chirality transfer across length-scales in nematic liquid crystals: fundamentals and applications (2010)

When a chiral dopant is dissolved in an achiral liquid crystal medium, the whole sample organizes into a helical structure with a characteristic length-scale of the order of microns. The relation between chirality at these quite different length-scales can be rationalized by a relatively simple model, which retains the relevant factors coming into play: the molecular shape of the chiral dopant, which controls the chirality of short range intermolecular interactions, and the elastic properties of the nematic environment, which control the restoring torques opposing distortion of the director. In this tutorial review the relation between molecular and phase chirality will be reviewed and several applications of the chiral doping of nematic LCs will be discussed. These range from the exploitation of the amplified molecular chirality for stereochemical purposes (e.g., the determination of the absolute configuration or the enantiomeric excess), to newer applications in physico-chemical fields. The latter take advantage of the periodicity of the chiral field, with length-scales ranging from hundreds to thousands of nanometres, which characterise the cholesteric phase.
Analysis of CD4 <sup>+</sup> T-Cell Responses to Human Papillomavirus (HPV) Type 11 L1 in Healthy Adults Reveals a High Degree of Responsiveness and Cross-Reactivity with Other HPV Types (2002)

Human papillomavirus type 11 (HPV-11) infection causes genital warts and recurrent respiratory papillomatosis. While there is compelling evidence that CD4(+) T cells play an important role in immune surveillance of HPV-associated diseases, little is known about human CD4(+) T-cell recognition of HPV-11. We have investigated the CD4(+) T-cell responses of 25 unrelated healthy donors to HPV-11 L1 virus-like particles (VLP). CD4(+) T-cell lines from 21 of 25 donors were established. Cell sorting experiments carried out on cells from six donors demonstrated that the response was located in the CD45RA(low) CD45RO(high) memory T-cell population. To determine the peptide specificity of these responses, epitope selection was analyzed by using 95 15-mer peptides spanning the entire HPV-11 L1 protein. No single region of L1 was immunodominant; responders recognized between 1 and 10 peptides, located throughout the protein, and peptide responses fell into clear HLA class II restricted patterns. Panels of L1 peptides specific for skin and genital HPV were used to show that the L1 CD4(+) T-cell responses were cross-reactive. The degree of cross-reactivity was inversely related to the degree of L1 sequence diversity between these viruses. Finally, responses to HPV-11 L1 peptides were elicited from ex vivo CD45RO(+) peripheral blood mononuclear cells, demonstrating that recognition of HPV-11 was a specific memory response and not due to in vitro selection during tissue culture. This is the first study of CD4(+) T-cell responses to HPV-11 in healthy subjects and demonstrates marked cross-reactivity with other skin and genital HPV types. This cross-reactivity may be of significance for vaccine strategies against HPV-associated clinical diseases.
Purification and subunit composition of acetohydroxyacid synthase I from Escherichia coli K-12 (1984)

Acetohydroxyacid synthase I from Escherichia coli K-12 has been purified to near homogeneity. Analysis of the purified enzyme by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed the presence of two polypeptides, one with a molecular weight of 60,000 and one with a molecular weight of 9,500. These two polypeptides were present in constant proportion to each other and to enzyme activity. The molar ratio of the two polypeptides (Mr 9,500:60,000), estimated from stained polyacrylamide gels, was 1. Antisera raised against the 60,000 Mr polypeptide precipitated both the 60,000 and the 9,500 Mr polypeptides from extracts of cells labeled with [35S]methionine. The addition of sodium dodecyl sulfate before immunoprecipitation eliminated the smaller polypeptide, and only the larger one was recovered. The hydrodynamic properties of the native enzyme confirmed a previous report that the largest enzymatically active species has a molecular weight of about 200,000; this species contains both the 60,000- and 9,500-molecular-weight polypeptides.
Iconic animation of construction simulation (1999)

This paper presents a continuous research effort the animation function in the development of the Activity-Based Construction (ABC) modeling and simulation system. ABC animation uses the constructed ABC simulation model as the animation background; and precreated images of simulation entities move around along individual execution paths on the ABC model. A library of icons consisting of common construction entities has been created in the ABC system. To perform animation function in ABC only involves one simple additional task for the user to select an appropriate icon for a simulation entity.
A retrospective view of ATM (2002)

ATM was the focus of active research and significant investment in the early to mid 1990's. This paper discusses several visions for ATM prevalent at the time, and analyzes how ATM evolved during this period. The paper also considers the implications of this history for current connection-oriented technologies, such as optical transport networks and MPLS.
Anomalous fluorinations of 3-aryl-2-hydroxypropanoic esters by diethylaminosulfur trifluoride (DAST) (1996)

Treatment of 3-aryl-2-hydroxypropanoic esters 8 with diethylaminosulfur trifluoride (DAST) gives considerable amounts of rearranged 2-aryl-3-fluoropropanoic esters 12 together with the expected products 11. The extent of rearrangement is dependent on solvent and on the substitution pattern of the aryl ring; the mechanism of rearrangement probably involves anchimeric assistance by the aryl group in the SN1 component of the reaction pathway. Recation of the isomeric 3-hydroxy-2-phenylpropanoic ester 13 shows much less rearrangement under similar conditions, and an elimination product 21 is also obtained.
Dynamic handoff decision in heterogeneous wireless systems: Q-learning approach (2012)

The satisfaction of a mobile user in a heterogeneous wireless environment relies heavily on the appropriate choice of network. With the presence of various wireless technologies and advances in smart mobile devices, the mobile terminal in next generation wireless communications will likely make intelligent handoff decisions to optimize the user Quality of Experience (QoE). This paper investigates network selection and handoff decision with the goal of maximizing user QoE. An algorithm based on Q-learning is obtained that chooses the best network based not only on the current network state but also the potential future network and device states. As opposed to other dynamic programming-based algorithms, this method does not require the knowledge of the statistics of the wireless environment, but learns an optimum policy by utilizing the mobile device's past experience. It is shown that the QoE results of the proposed Dynamic Handoff Decision (DHD) algorithm come very close to the performance of an optimum oracle algorithm, while on average fewer number of network handoffs are required.
Genetics of Resistance to Race TTKSK of <i>Puccinia graminis</i> f. sp. <i>tritici</i> in <i>Triticum monococcum</i> (2011)

Race TTKSK (or Ug99) of Puccinia graminis f. sp. tritici possesses virulence to several stem rust resistance genes commonly present in wheat cultivars grown worldwide. New variants detected in the race TTKSK lineage further broadened the virulence spectrum. The identification of sources of genetic resistance to race TTKSK and its relatives is necessary to enable the development and deployment of resistant varieties. Accessions of Triticum monococcum, an A-genome diploid wild and cultivated wheat, have previously been characterized as resistant to stem rust. Three resistance genes were identified and introgressed into hexaploid wheat: Sr21, Sr22, and Sr35. The objective of this study was to determine the genetic control and allelic relationships of resistance to race TTKSK in T. monococcum accessions identified through evaluations at the seedling stage. Generation F(2) progeny of 8 crosses between resistant and susceptible accessions and 13 crosses between resistant accessions of T. monococcum were evaluated with race TTKSK and often with North American races, including races QFCSC, TTTTF, and MCCFC. For a selected population segregating for three genes conferring resistance to race TTKSK, F(2:3) progeny were evaluated with races TTKSK, QFCSC, and TTTTF. In that population, we detected two genes conferring resistance to race TTKSK that are different from Sr21, Sr22, and Sr35. One of the new genes was effective to all races tested. The identification of these genes will facilitate the development of varieties with new resistance to race TTKSK.
A Life Cycle Cost Analysis Framework for Geologic Storage of Hydrogen (2009)

Large scale geostorage options for fuels including natural gas and petroleum offer substantial buffer capacity to meet or hedge against supply disruptions. This same notion may be applied to large scale hydrogen storage to meet industrial or transportation sector needs. This study develops an assessment tool to calculate the potential ‘gate-to-gate’ life cycle costs for large scale hydrogen geostorage options in salt caverns, and continues to develop modules for depleted oil/gas reservoirs and aquifers. The U.S. Department of Energy has an interest in these types of storage to assess the geological, geomechanical and economic viability for this type of hydrogen storage. Understanding, and looking to quantify, the value of large-scale storage in a larger hydrogen supply and demand infrastructure may prove extremely beneficial for larger infrastructure modeling efforts when looking to identify the most efficient means to fuel a hydrogen demand (e.g., industrial or transportation-centric demand). Drawing from the knowledge gained in the underground large scale storage options for natural gas and petroleum in the U.S., the potential to store relatively large volumes of CO2 in geological formations, the hydrogen storage assessment modeling will continue to build on these strengths while maintaining modeling transparency such that other modeling efforts may draw from this project.
The therapeutic potential of the mesenchymal stem cell secretome in ischaemic stroke (2018)

Mesenchymal stem cells (MSCs) hold great potential as a regenerative therapy for stroke, leading to increased repair and functional recovery in animal models of cerebral ischaemia. While it was initially hypothesised that cell replacement was an important mechanism of action of MSCs, focus has shifted to their paracrine actions or the so called "bystander" effect. MSCs secrete a wide array of growth factors, chemokines, cytokines and extracellular vesicles, commonly referred to as the MSC secretome. There is evidence suggesting the MSC secretome can promote repair through a number of mechanisms including preventing cell apoptosis, modulating the inflammatory response and promoting endogenous repair mechanisms such as angiogenesis and neurogenesis. In this review, we will discuss the in vitro approaches currently being employed to drive the MSC secretome towards a more anti-inflammatory and regenerative phenotype. We will then examine the role of the secretome in promoting repair and improving recovery in preclinical models of cerebral ischaemia.
Rapid purification of antibodies to single band purity using recycling isoelectric focusing (1982)

Abstract Recycling isoelectric focusing (RIEF) was used to isolate monoclonal antibodies from an electrophoretically heterogeneous rabbit antibody population. Milligram quantities of antibodies were processed to single band purity in 4 h. The ease of operation, extremely short run times, and high resolution of the RIEF apparatus give this system great flexibility. The demonstrated capacity of the RIEF system to process large quantities of protein suggests that the system is applicable to the largescale purification of antibodies.
Detection and Differentiation of Neutral Organic Compounds by <sup>19</sup>F NMR with a Tungsten Calix[4]arene Imido Complex (2013)

Fluorinated tungsten calix[4]arene imido complexes were synthesized and used as receptors to detect and differentiate neutral organic compounds. It was found that the binding of specific neutral organic molecules to the tungsten centers induces an upfield shift of the fluorine atom appended on the arylimido group, the extent of which is highly dependent on electronic and steric properties. We demonstrate that the specific bonding and size-selectivity of calix[4]arene tungsten-imido complex combined with (19)F NMR spectroscopy is a powerful new method for the analysis of complex mixtures.
Backbone-modified oligopeptidic bioregulators. The synthesis and configuration of thioamide, amidoxime, cyanoamidine, and amidrazone analogs of the chemotactic peptide N-formyl-methionyl-leucyl-phenylalanine (f-Met-Leu-Phe-OR) (1985)

Reaction conditions for the synthesis of thioamide, amidoxime, and N-substituted amidine analogs of the peptide bond are described. Several new amidine analogs of the chemotactic peptide f-Met-Leu-Phe-OR were synthesized using the thioamides as precursors. The assignment of the E/Z configuration was accomplished by nuclear magnetic resonance. The biological activity of these analogs is briefly described.
Coexistence of Wireless Power Transfer via Microwaves and Wireless Communication for Battery-less ZigBee Sensors (2014)

A Wireless Power Transfer (WPT), especially the WPT via microwaves, can drive a wireless communication system like a wireless sensor without battery. However, both n the WPT and in the wireless communication, we use radio waves and we have to consider suppression of interference and coexistence of both wireless systems We propose pulse-WPT for ZigBee sensors in order to suppress the interference to the wireless sensors. We show results of development of a suitable rectenna, rectifying antenna, and experimental results of coexistence of the WPT and the wireless sensors.
Reawakening educational policy and practice in rural Australia (2007)

There is nothing static about rural! Rural environments, economies and sociologies continue to change and grow, and leave educators with new, dynamic and exciting challenges. It is argued that these changes and allied decisions about rural education are often made by people who are not immersed in the concerns, nor have they a sense of nuances of living in rural communities.This paper focuses on ways of reversing our thinking ' of seeing the provision of educational opportunities grounded in a rural perspective. It draws upon the literature and current research to suggest that we need a rural lens. Through this rural lens new, different and innovative strategies, policies and ways of thinking about rural schooling, staffing practice and curriculum policy emerge. It offers practical means by which we might return to rural education issues with a rural rather than an outsiders agenda and enhance rural education in the process.
Automatic Phase-Detection and Identification by Full Use of a Single Three-Component Broadband Seismogram (2000)

Automatic-time picking continues to be a significant issue in seismo- gram analysis. Any individual method is based on separation of signal and noise in a particular domain and cannot ensure consistent onset time picking under all source, receiver, path, and noise conditions. However, a combination of three methods based on differing aspects of seismograms can be used to provide automated and consistent phase detection and interpretation using a single three-component record. For arrival detection, a combination of energy analysis, differences in instantaneous frequency, and an auto-regressive representation of the seismic record are used to develop an algorithm for robust phase extraction, suitable for use in real time. The character of the phases is extracted using polarization analysis using complex traces to separate S- and P-wave phases. The combination of four different methods offers a very effective technique for automatic arrival detection and association from a single three-component broadband seismogram and from thence an approximate event lo- cation procedure.
Dimethylarginines, Homocysteine Metabolism, and Cerebrospinal Fluid Markers for Alzheimer's Disease (2012)

Dimethylarginine and homocysteine metabolism are closely linked and alterations of both were observed in plasma and cerebrospinal fluid (CSF) of patients with Alzheimer's disease (AD). CSF parameters of homocysteine metabolism have recently been found to be associated with the CSF level of the AD biomarker phosphorylated tau (ptau) in AD patients. To investigate possible relationships between homocysteine and dimethylarginine metabolism and the AD CSF biomarkers ptau181 and amyloid-β 1-42 (Aβ42), we assessed parameters of homocysteine metabolism (CSF homocysteine, S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), 5-methyltetrahydrofolate (5-MTHF)) and dimethylarginine metabolism (plasma and CSF asymmetric dimethylarginine (ADMA), symmetric dimethylarginine, L-arginine) as well as CSF Aβ42 and ptau181 in 98 controls and 51 AD patients. Multivariate linear regression analyses were performed to assess associations between the considered parameters. SAH concentrations show significant associations to CSF ADMA levels, and CSF ADMA and L-arginine to ptau181, but not to Aβ42 concentrations in AD patients. When including concentrations of homocysteine, 5-MTHF, SAM, and SAH into the analysis, CSF ADMA concentrations independently predicted ptau181 levels in AD patients but homocysteine-related metabolites were associated with ptau181 only when ADMA was removed from the analysis model. These results suggest that CSF ADMA may interact with CNS homocysteine metabolism and may contribute to neurodegeneration and accumulation of phosphorylated tau in AD. Functional and interventional studies are needed to further proof this hypothesis.
Relationship between neuronal migration and cell-substratum adhesion: laminin and merosin promote olfactory neuronal migration but are anti-adhesive. (1991)

Regulation by the extracellular matrix (ECM) of migration, motility, and adhesion of olfactory neurons and their precursors was studied in vitro. Neuronal cells of the embryonic olfactory epithelium (OE), which undergo extensive migration in the central nervous system during normal development, were shown to be highly migratory in culture as well. Migration of OE neuronal cells was strongly dependent on substratum-bound ECM molecules, being specifically stimulated and guided by laminin (or the laminin-related molecule merosin) in preference to fibronectin, type I collagen, or type IV collagen. Motility of OE neuronal cells, examined by time-lapse video microscopy, was high on laminin-containing substrata, but negligible on fibronectin substrata. Quantitative assays of adhesion of OE neuronal cells to substrata treated with different ECM molecules demonstrated no correlation, either positive or negative, between the migratory preferences of cells and the strength of cell-substratum adhesion. Moreover, measurements of cell adhesion to substrata containing combinations of ECM proteins revealed that laminin and merosin are anti-adhesive for OE neuronal cells, i.e., cause these cells to adhere poorly to substrata that would otherwise be strongly adhesive. The evidence suggests that the anti-adhesive effect of laminin is not the result of interactions between laminin and other ECM molecules, but rather an effect of laminin on cells, which alters the way in which cells adhere. Consistent with this view, laminin was found to interfere strongly with the formation of focal contacts by OE neuronal cells.
Slippery liquid-infused substrates: a versatile preparation, unique anti-wetting and drag-reduction effect on water (2016)

Newly developed slippery liquid-infused porous surfaces (SLIPSs) are highly promising for a broad range of applications.