gebhart/patrepeval huggingface dataset:
Synthetic logic circuits using RNA aptamer against T7 RNA polymerase (2014)

Abstract Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro . Using in vitro transcription assays, we first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks. As a step to quickly assess the feasibility of aptamer functions in vivo , a cell-free expression system was used as a breadboard to emulate the in vivo conditions of E. coli . We tested the aptamer and its three sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. In vivo expression of aptamer and its variants demonstrated control over GFP expression driven by T7 RNA polymerase with different response curves, indicating its ability to serve as building blocks for both logic circuits and transcriptional cascades. This work elucidates the potential of RNA-based regulators for cell programming with improved controllability leveraging the fast production and degradation time scales of RNA molecules.
The Neural Processing of Second Language Comprehension Modulated bythe Degree of Proficiency: A Listening Connected Speech fMRI Study (2012)

While the neural network encompassing the processing of the mother tongue (L1) is well defined and has revealed the existence of a bilateral ventral pathway and a left dorsal pathway in which 3 loops have been defined, the question of the processing of a second language (L2) is still a matter of debate. Among variables accounting for the discrepancies in results, the degree of L2 proficiency appears to be one of the main factors. The present study aimed at assessing both pathways in L2, making it possible to determine the degree of mastery of the different speech components (prosody, phonology, semantics and syntax) that are intrinsically embedded within connected speech and that vary according to the degree of proficiency using high degrees of prosodic information. Two groups of high and moderate proficiency in L2 performed an fMRI comprehension task in L1 and L2. The modifications in brain activity observed within the dorsal and the ventral pathways according to L2 proficiency suggest that different processes of L2 are supported by differences in the integrated activity within distributed networks that included the left STSp, the left Spt and the left pars triangularis.
Electromechanical Modeling of the Low-Frequency Zigzag Micro-Energy Harvester (2011)

An analytical electromechanical model is proposed to predict the deflection, voltage, and the power output of a proposed low-frequency micro-harvesting structure. The high natural frequencies of the existing designs of micro-scale vibrational energy harvesters are serious drawbacks. A zigzag design is proposed to overcome this limitation. First, the natural frequencies and the mode shapes of the zigzag structure are calculated. The piezoelectric direct and reverse effect equations, together with the electrical equations, are used to relate the voltage output of the structure to the base vibrations magnitude and frequency. The closed-form solution of the continuous electromechanical vibrations gives the power output as a function of base acceleration spectrum. The usefulness of the design is proved by the significant increase of the power output from the same base accelerations, providing a method of designing a micro-scale harvester with low natural frequency. The optimal mechanical and electrical conditions for power generation are investigated through the case studies.
A layered networking protocol designed to minimize complexity (1988)

The design of a networking protocol for the use in connecting heterogeneous computer systems is presented. The design describes a protocol based on a layered philosophy and provides for a minimum cost connections between the computer system in the network. For each layer of the network the design choices used in the network protocol are presented and a simple file transfer mechanism and message passing facility are presented with their interfaces to the network.
Optimizing the benefit of multiple sclerosis therapy: the importance of treatment adherence (2010)

Poor treatment adherence is problematic in many therapy areas, including multiple sclerosis (MS). Several immunomodulatory drugs are available for the treatment of MS, all of which require frequent parenteral administration. Current first-line therapies are two formulations of interferon (IFN) beta-1a, one of IFN beta-1b, and one of glatiramer acetate. Discontinuation of treatment is common, particularly in the first few months after initiation. Although the true effect of poor adherence to MS therapy is not known, it is likely to lead to a fall in treatment efficacy. Many factors influence a patient's adherence to treatment, including the patient's MS subtype and disability level, cognitive impairment resulting from MS, perceived lack of efficacy of the prescribed medication, and adverse events associated with MS therapy. This article summarizes the barriers to adherence to MS therapies, and discusses patient management strategies that can be employed to encourage adherence. Future advances in the field of MS treatment will be explored, including the development of orally administered drugs, which may enhance adherence.
A Data Stream Processing Optimisation Framework for Edge Computing Applications (2018)

Data Stream Processing (DSP) is a widely used programming paradigm to process an unbounded event stream. Often, DSP frameworks are deployed on the cloud with a scalable resource model. One of the key requirements of DSP is to produce results with low latency. With the emergence of IoT, many event sources have been located outside the cloud which can result in higher end-to-end latency due to communication overhead. However, due to the abundance of resources at the IoT layer, Edge computing has emerged as a viable computational paradigm. In this paper, we devise an optimisation framework, consisting of a constraint satisfaction formulation and a system model, that aims to minimise end-to-end latency through appropriate placement of DSP operators either on cloud nodes or edge devices, i.e. deployed in an edge-cloud integrated environment. We test our optimisation framework using OMNeT++, with realistic topologies and power consumption data, and show that it is capable of achieving approx 1.65 times reduction of latency compared to edge-only and cloud-only placements, which in turn also reduces the energy consumption per event by up to approx 4% at the edge layer. To the best of our knowledge our optimisation framework is the first of its kind to integrate power, bandwidth and CPU constraints with latency minimisation.
Social Media in Schools (2013)

In the sphere of education, social media has posed enormous challenges and unleashed its potential as a venue to communicate with stakeholders. This case is a fictionalized version of several real cases related to the school leaders’ struggle with utilizing social media to accomplish changes in schools. This case describes two high school administrators’ exploration in school’s use of social media. All people and schools’ names are pseudonyms. The narratives in this case are presented to deepen the understanding of the role of schools’ social media in creating social capital, and to raise the acute awareness of legal issues of schools’ social media.
Suppressors of Cancer Cell Proliferation from Fig (<i>Ficus </i><i>c</i><i>arica</i>) Resin:  Isolation and Structure Elucidation (2001)

A mixture of 6-O-acyl-beta-D-glucosyl-beta-sitosterols, the acyl moeity being primarily palmitoyl and linoleyl with minor amounts of stearyl and oleyl, has been isolated as a potent cytotoxic agent from fig (Ficuscarica) latex and soybeans. Identity was established by spectroscopic methods (NMR, MS) and confirmed by chemical synthesis. Both the natural and the synthetic compounds showed in vitro inhibitory effects on proliferation of various cancer cell lines.
The Structure of Cucumber Mosaic Virus and Comparison to Cowpea Chlorotic Mottle Virus (2000)

The structure of cucumber mosaic virus (CMV; strain Fny) has been determined to a 3.2-A resolution using X-ray crystallography. Despite the fact that CMV has only 19% capsid protein sequence identity (34% similarity) to cowpea chlorotic mottle virus (CCMV), the core structures of these two members of the Bromoviridae family are highly homologous. As suggested by a previous low-resolution structural study, the 305-A diameter (maximum) of CMV is approximately 12 A larger than that of CCMV. In CCMV, the structures of the A, B, and C subunits are nearly identical except in their N termini. In contrast, the structures of two loops in subunit A of CMV differ from those in B and C. These loops are 6 and 7 residues longer than the analogous regions in CCMV. Unlike that of CCMV, the capsid of CMV does not undergo swelling at pH 7.0 and is stable at pH 9.0. This may be partly due to the fact that the N termini of the B and C subunits form a unique bundle of six amphipathic helices oriented down into the virion core at the threefold axes. In addition, while CCMV has a cluster of aspartic acid residues at the quasi-threefold axis that are proposed to bind metal in a pH-dependent manner, this cluster is replaced by complementing acids and bases in CMV. Finally, this structure clearly demonstrates that the residues important for aphid transmission lie at the outermost portion of the betaH-betaI loop and yields details of the portions of the virus that are hypothesized to mediate binding to aphid mouthparts.
SOIL PH AND ITS ROLE IN CYANOBACTERIAL ABUNDANCE AND DIVERSITY IN RICE FIELD SOILS (2007)

The influence of soil pH was evaluated on the abundance and generic diversity of cyanobacteria in soil samples collected from diverse rice soil ecologies of India. Qualitative and quantitative studies of the 52 soil samples collected from nine agroecologies was carried out using enrichment, MPN (Most Probable Number) techniques and diversity indices were measured. A total of 166 forms, including 130 heterocystous and 36 non-heterocystous isolates were isolated and the highest percentage of abundance of heterocystous forms was observed at pH of 8.1. Highest Shannon's diversity index was recorded at a pH of 6.9, followed by pH of 7.4, while indices of richness and evenness (J and E) were highest in soil samples of pH of 9.3. This study highlighted the successful colonization of cyanobacteria in rice field soils of diverse pH and the need for enrichment of the native flora as a means of exploiting the full potential of cyanobacterial biofertilizers in agriculture
Effects of Metabolic Modifiers Such as Carnitines, Coenzyme Q10, and PUFAs against Different Forms of Neurotoxic Insults: Metabolic Inhibitors, MPTP, and Methamphetamine (2005)

A number of strategies using the nutritional approach are emerging for the protection of the brain from damage caused by metabolic toxins, age, or disease. Neural dysfunction and metabolic imbalances underlie many diseases, and the inclusion of metabolic modifiers may provide an alternative and early intervention approach that may prevent further damage. Various models have been developed to study the impact of metabolism on brain function. These have also proven useful in expanding our understanding of neurodegeneration processes. For example, the metabolic compromise induced by inhibitors such as 3-nitropropionic acid (3-NPA), rotenone, and 1-methyl-4-phenylpyridinium (MPP+) can cause neurodegeneration in animal models and these models are thought to simulate the processes that may lead to diseases such as Huntington's and Parkinson's diseases. These inhibitors of metabolism are thought to selectively kill neurons by inhibiting various mitochondrial enzymes. However, the eventual cell death is attributed to oxidative stress damage of selectively vulnerable cells, especially highly differentiated neurons. Various studies indicate that the neurotoxicity resulting from these types of metabolic compromise is related to mitochondrial dysfunction and may be ameliorated by metabolic modifiers such as L-carnitine (L-C), creatine, and coenzyme Q10, as well as by antioxidants such as lipoic acid, vitamin E, and resveratrol. Mitochondrial function and cellular metabolism are also affected by the dietary intake of essential polyunsaturated fatty acids (PUFAs), which may regulate membrane composition and influence cellular processes, especially the inflammatory pathways. Cellular metabolic function may also be ameliorated by caloric restriction diets. L-C is a naturally occurring quaternary ammonium compound that is a vital cofactor for the mitochondrial entry and oxidation of fatty acids. Any factors affecting L-C levels may also affect ATP levels. This endogenous compound, L-C, together with its acetyl ester, acetyl-L-carnitine (ALC), also participates in the control of the mitochondrial acyl-CoA/CoA ratio, peroxisomal oxidation of fatty acids, and production of ketone bodies. A deficiency of carnitine is known to have major deleterious effects on the CNS. We have examined L-C and its acetylated derivative, ALC, as potential neuroprotective compounds using various known metabolic inhibitors, as well as against drugs of abuse such as methamphetamine.
REBASE--restriction enzymes and DNA methyltransferases (2004)

REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in restriction-modification. It contains both published and unpublished work with information about recognition and cleavage sites, isoschizomers, commercial availability, crystal and sequence data. Experimentally characterized homing endonucleases are also included. Additionally, REBASE contains complete and up-to-date information about the methylation sensitivity of restriction endonucleases. An extensive analysis is included of the restriction-modification systems that are predicted to be present in the sequenced bacterial and archaeal genomes from GenBank. The contents of REBASE are available by browsing from the web (http://rebase.neb. com/rebase/rebase.html) and through selected compilations by ftp (ftp.neb.com) and as monthly updates that can be requested via email.
Strong, Asymmetric Flux Pinning by Miscut-Growth-Initiated Columnar Defects in Epitaxial<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>YBa</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>Cu</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mi>O</mml:mi></mml:mrow><mml:mrow><mml:mn>7</mml:mn><mml:mo>−</mml:mo><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>Films (1995)

Strong flux pinning and a pronounced asymmetric angular dependence of ${J}_{c}(H,\ensuremath{\theta})$ have been discovered in ${{\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}\mathrm{O}}_{7\ensuremath{-}x}$ films grown on miscut, mosaic LaAl${\mathrm{O}}_{3}$ substrate surfaces. A new pinning peak, which at low fields is nearly as strong as the ``intrinsic pinning,'' is observed for magnetic field orientations between the $c$ axis and the Cu${\mathrm{O}}_{2}$ plane. Cross-section transmission electron microscopy reveals columnar growth defects (2--3 nm diameter) aligned near the $c$ axis, in concentrations $\ensuremath{\sim}{10}^{10}{\mathrm{cm}}^{\ensuremath{-}2}$. The results demonstrate that deliberately modified substrate surfaces may introduce technologically useful flux pinning in ${{\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}\mathrm{O}}_{7\ensuremath{-}x}$ films.
Mobile Communications Design Fundamentals (1993)

From the Publisher:
The most recent addition to William C. Y. Lee's acclaimed series on mobile and cellular communications, Mobile Communications Design Fundamentals, Second Edition offers designers, researchers, and students an up-to-date, invaluable guide to the theoretical framework of mobile radio communications and how such systems are designed. With an abundance of new material, this Second Edition covers leading-edge Personal Communications Service (PCS), microcell, and CDMA systems, providing all the theoretical and design knowledge and know-how needed to design with both present and future technology. Useful as a professional handbook or as a senior/graduate level text, the book provides complete coverage of the differences between fixed and wireless radio systems, up to and including the new FCC-promoted PCS systems; an authoritative description of the mobile radio environment that gives engineers the necessary technical background to confidently select the appropriate radio technology; definitive, clearly presented design parameters for both the base and mobile units; troubleshooting approaches that help you anticipate the problems associated with each system and solve them when they arise; comprehensive guidelines for how to develop the system design and frequency plan and how to tackle all capacity issues, and new information on CDMA, a hot broadband radio technology...boosting microcell technology capacity with system planning...built in prediction...analyzing digital communication systems...and covering noncellular mobile radio systems, including those for data communication. With more than half of the material in this new edition based on the author's own widely recognized research work, Mobile Communications Design Fundamentals is a book no one interested in the new wave in mobile communications can afford to miss.
The Rhesus Site (2014)

The Rhesus Site is a resource for information of the 'Rhesus' blood group. It is intended for specialists and non-specialists. The website details research in the field relevant for transfusion medicine, immunohematology, and molecular research. Link areas guide to important publications and to methodological resources for Rhesus. Many data originally presented at The Rhesus Site have been formally published later. The 'RhesusBase' section represents the largest database for RHD alleles; the 'RhesusSurveillance' section details the results of the largest prospective observational study on anti-D immunization events in D-positive patients. Visitors to the website are encouraged to explore the intricacies of the most complex blood group gene locus.
Ultrathin Free‐Standing Ternary‐Alloy Nanosheets (2016)

A synthesis strategy for the preparation of ultrathin free-standing ternary-alloy nanosheets is reported. Ultrathin Pd-Pt-Ag nanosheets with a thickness of approximately 3 nm were successfully prepared by co-reduction of the metal precursors in an appropriate molar ratio in the presence of CO. Both the presence of CO and the interplay between the constituent metals provide fine control over the anisotropic two-dimensional growth of the ternary-alloy nanostructure. The prepared Pd-Pt-Ag nanosheets were superior catalysts of ethanol electrooxidation owing to their specific structural and compositional characteristics. This approach will pave the way for the design of multicomponent 2D nanomaterials with unprecedented functions.
Phenolic Compounds and Antioxidant Capacity of Georgia-Grown Blueberries and Blackberries (2002)

Blueberries and blackberries grown at various locations in Georgia were collected and analyzed for flavonoids, total anthocyanins, total polyphenols, and Trolox-equivalent antioxidant capacity (TEAC). Each sample was analyzed for phenolic acids (gallic acid, p-hydroxybenzoic acid, caffeic acid, ferulic acid, and ellagic acid) and flavonoids (catechin, epicatechin, myricetin, quercetin, and kaempferol). A high-performance liquid chromatographic (HPLC) method with photodiode array detection was used for analysis. Compounds were analyzed as aglycons after acid hydrolysis with 1.2 M HCl. Identification of each compound was based on retention time and UV spectra by comparison with pure commercial standards. Phenolic acids ranged from 0.19 to 258.90 mg/100 g fresh weight (FW), and flavonoids ranged from 2.50 to 387.48 mg/100 g FW. Total polyphenols ranged from 261.95 to 929.62 mg/100 g FW, and total anthocyanins ranged from 12.70 to 197.34 mg/100 g FW. TEAC values varied from 8.11 to a maximum of 38.29 microM/g FW. A linear relationship was observed between TEAC values and total polyphenols or total anthocyanins. The data indicate that blueberries and blackberries are rich sources of antioxidants.
Review on tension in the natural and reconstructed anterior cruciate ligament (1994)

This article reviews the methodology and results of published studies concerned with tension in the natural and reconstructed anterior cruciate ligament (ACL). This also includes studies of fiber length changes with knee motion and the relationships between graft tunnel placements and isometricity. Little work has been done in vivo: in humans, length changes of the anterior ACL fibers have been measured at operation, while animal longitudinal studies have been few and have given conflicting results. Work in vitro has used many methods to study ACL tension directly or indirectly, via length changes in fibers, but many authors have reported variable results, caused partly by inter-specimen differences and lack of control of forces or kinematics. It seems likely that different grafts require different peroperative tensions to restore normal stability when measured immediately after application at one knee position. But graft placement and the angle at which tensioning is performed also matter. Over-tensioning constrains knees under load cycling. Similarly, it is difficult to measure and therefore also to decide how tension should be distributed between an ACL graft and and augmentation to the graft. It was concluded that the published studies provide many guidelines for the effects of different graft placements or tensioning protocols but, overall, there is little firm evidence on which to recommend any particular ACL reconstruction protocol.
Unanticipated Antigens: Translation Initiation at CUG with Leucine (2004)

Major histocompatibility class I molecules display tens of thousands of peptides on the cell surface for immune surveillance by T cells. The peptide repertoire represents virtually all cellular translation products, and can thus reveal a foreign presence inside the cell. These peptides are derived from not only conventional but also cryptic translational reading frames, including some without conventional AUG codons. To define the mechanism that generates these cryptic peptides, we used T cells as probes to analyze the peptides generated in transfected cells. We found that when CUG acts as an alternate initiation codon, it can be decoded as leucine rather than the expected methionine residue. The leucine start does not depend on an internal ribosome entry site-like mRNA structure, and its efficiency is enhanced by the Kozak nucleotide context. Furthermore, ribosomes scan 5' to 3' specifically for the CUG initiation codon in a eukaryotic translation initiation factor 2-independent manner. Because eukaryotic translation initiation factor 2 is frequently targeted to inhibit protein synthesis, this novel translation mechanism allows stressed cells to display antigenic peptides. This initiation mechanism could also be used at non-AUG initiation codons often found in viral transcripts as well as in a growing list of cellular genes.