gebhart/patrepeval huggingface dataset:
Differential binding of BvgA to two classes of virulence genes of Bordetella pertussis directs promoter selectivity by RNA polymerase (1996)

Transcription of virulence genes of Bordetella pertussis is co-ordinately regulated by the BvgA and BvgS proteins, which are members of the two-component family of bacterial signal-transduction proteins. BvgS is the transmembrane sensor and BvgA the transcriptional regulator. By gel mobility shift assays we demonstrate that phosphorylated BvgA (BvgA approximately P) forms distinct complexes with the filamentous haemagglutinin (PFHA) promoter DNA at different BvgA approximately P: DNA ratios. DNase I protection analyses show that phosphorylation of BvgA not only enhances affinity of the protein for the binding sites of the PFHA and bvgP1 promoters, but it extends significantly the bound region towards position -35 of these promoters. Conversely, a 10-fold higher amount of BvgA approximately P is required for binding to a large DNA region, from -168 to -60, of the pertussis toxin (Ptox) promoter sequence. These findings suggest that the molecular interaction of BvgA approximately P with the Ptox promoter is different from its interaction with the PFHA and bvgP1 promoters. The sigma 70 Escherichia coli RNA polymerase (RNP) does not bind to the bvg-regulated promoters. However, following the formation of a BvgA approximately P-promoter complex, the E. coli RNP specifically recognizes and binds to the bvg-regulated promoters. Thus, BvgA approximately P exerts its action at the level of promoter recognition by directing promoter selectivity by RNP.
Basic Simulation Technologies and Fundamentals (2012)

Real-time distributed computer systems combine virtual environment (VE)– based systems, real-time peer-to-peer (P2P)–based systems, quality-of-service (QoS)–aware distributed computer systems, and hybrid systems (the systems that incorporate both real-time and non-real-time behaviors). Efficient system design for such systems requires a sound framework that can facilitate effective design modeling and simulation (M&S) as well as support for flexible testing of design alternatives. Traditional approaches to system design do not use formal system specification languages or formalisms and are based on accumulated domain knowledge. Thus, system design, in many cases, is separated from system implementation, system testing, and system validation. With the rapid 36advances of distributed real-time computer systems, the complexity of such systems is increasingly challenging traditional nonformalized design approaches. Therefore, formal design methods have been widely used for system design in recent years, and such efforts have been verified by many researchers as suitable for large-scale and complex systems. Among different formal approaches, it is worth noting that model-based system design has proved to be one of the most efficient methods to address the key concerns in complex system design [1–4]. Indeed, the model-based design approach uses a formal language to describe system design models, and such design models are then simulated to predict the performance of the system in real-world scenarios. In particular, the model-based formal design using Discrete Event System Specification (DEVS) [5–7] differentiates it from most other approaches because of its use of a unique integrative framework that can address most of the issues faced in complex system design, and in particular, distributed real-time computer systems.
Eukaryotic ribosomal subunit anti-association activity of calf liver is contained in a single polypeptide chain protein of Mr = 25,500 (eukaryotic initiation factor 6). (1982)

A protein factor that prevents the reassociation of eukaryotic 40 S and 60 S ribosomal subunits when the Mg+ concentration is raised from 1 to 5 mM has been purified to apparent electrophoretic homogeneity from postribosomal supernatant of calf liver extracts. The purified ribosomal subunit anti-association factor is a relatively heat-sensitive protein consisting of a single polypeptide chain of apparent Mr = 25,500. Direct assay for ribosomal subunit anti-association activity indicates that the majority (greater than 90% of such an activity in calf liver extracts can be accounted for by the presence of this 25,500-dalton protein factor in the postribosomal supernatant. The ribosomal salt wash protein fractions are virtually devoid of any significant ribosomal subunit anti-association or 80 S ribosome dissociation activity. The purified anti-association factor maintains a pool of ribosomal subunits by binding to 60 S ribosomal subunits and preventing them from reassociating with 40 S ribosomal subunits, rather than by dissociating 80 S monosomes. The factor neither binds to, nor seems to interact directly with, 40 S subunits. The properties of this factor are thus similar to wheat germ ribosome dissociation factor (eukaryotic initiation factor 6) described by Russell and Spremulli ((1979) J. Biol. Chem. 254, 8796-8800.
Making processes from best practice frameworks actionable (2009)

Best-practice frameworks provide guidance for organizing work in business. They enable reuse of experience within a domain. However, best practice frameworks are general and usually cover broad domains. Their guidance thus is often offered at an abstract level rather than as details of actionable tasks and processes to accomplish work. This paper presents an approach to bridge the gap between the abstractions available in best practice framework and actions that have to be performed by people or systems in a repeatable manner. We identify knowledge from best practices frameworks, categorize it and represent it in the form of reusable, interpretable templates. Template interpretation guides the refinement process from general concepts of best practices frameworks into actionable concepts such as specific tasks to be performed by assigned roles. A prototype implemented to validate the approach is also described.
Context‐Specific Genomic Selection Strategies Outperform Phenotypic Selection for Soybean Quantitative Traits in the Progeny Row Stage (2019)

Evaluating different breeding selection strategies for relative utility is necessary to choose those that maximize efficiency. Soybean [ Glycine max (L.) Merr.] seed yield and fatty acid, protein, and oil contents are all commercially important traits that display complex quantitative inheritance. A soybean population consisting of 860 F 5 –derived recombinant inbred lines (RILs), genotyped with 4867 polymorphic single nucleotide polymorphism (SNPs) was used to compare phenotypic and context specific genomic selection (GS) strategies. To simulate progeny rows, each RIL was grown in a single plot in 2010 in Knoxville, TN, and phenotype was recorded. A subset of 276 RILs with similar maturity was then grown in multilocation, replicated field trials in 2013 to compare the performance of each selection method in field conditions. Notably, the preferred method for each trait was GS. Of the GS approaches evaluated, Epistacy performed best for yield, and BayesB and/or genomic best linear unbiased prediction (G‐BLUP) were preferred for each of the other traits. Yield was the only trait for which the predictions had a large change when the number of SNPs and the number of RILs were randomly reduced for the G‐BLUP model, with the best predictions occurring when RILs with different maturity that were not grown in 2013 were removed from the training set. These findings provide important information on how soybean breeders can maximize selections from the progeny row stage for yield and fatty acid, protein, and oil contents by using appropriate selection strategies.
Review Paper: Residual Stresses in Deposited Thin-Film Material Layers for Micro- and Nano-Systems Manufacturing (2022)

This review paper covers a topic of significant importance in micro- and nano-systems development and manufacturing, specifically the residual stresses in deposited thin-film material layers and methods to control or mitigate their impact on device behavior. A residual stress is defined as the presence of a state of stress in a thin-film material layer without any externally applied forces wherein the residual stress can be compressive or tensile. While many material properties of deposited thin-film layers are dependent on the specific processing conditions, the residual stress often exhibits the most variability. It is not uncommon for residual stresses in deposited thin-film layers to vary over extremely large ranges of values (100% percent or more) and even exhibit changes in the sign of the stress state. Residual stresses in deposited layers are known to be highly dependent on a number of factors including: processing conditions used during the deposition; type of material system (thin-films and substrate materials); and other processing steps performed after the thin-film layer has been deposited, particularly those involving exposure to elevated temperatures. The origins of residual stress can involve a number of complex and interrelated factors. As a consequence, there is still no generally applicable theory to predict residual stresses in thin-films. Hence, device designers usually do not have sufficient information about the residual stresses values when they perform the device design. Obviously, this is a far less than ideal situation. The impact of this is micro- and nano-systems device development takes longer, is considerably more expensive, and presents higher risk levels. The outline of this paper is as follows: a discussion of the origins of residual stresses in deposited thin-film layers is given, followed by an example demonstrating the impact on device behavior. This is followed by a review of thin-film deposition methods outlining the process parameters known to affect the resultant residual stress in the deposited layers. Then, a review of the reported methods used to measure residual stresses in thin-films are described. A review of some of the literature to illustrate the level of variations in residual stresses depending on processing conditions is then provided. Methods which can be used to control the stresses and mitigate the impact of residual stresses in micro- and nano-systems device design and fabrication are then covered, followed by some recent development of interest.
Stereochemical and electronic spin state tuning of the metal center in the nickel(II) tropocoronands (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemical and electronic spin state tuning of the metal center in the nickel(II) tropocoronandsWilliam M. Davis, Michael M. Roberts, Arie Zask, Koji Nakanishi, Tetsuo Nozoe, and Stephen J. LippardCite this: J. Am. Chem. Soc. 1985, 107, 13, 3864–3870Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://pubs.acs.org/doi/10.1021/ja00299a018https://doi.org/10.1021/ja00299a018research-articleACS PublicationsRequest reuse permissionsArticle Views182Altmetric-Citations48LEARN 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
Suppression of ambipolar behavior in metallic source/drain metal-oxide-semiconductor field-effect transistors (2009)

We present a study on suppressing the ambipolar behavior of Schottky barrier metal-oxide-semiconductor field-effect transistors (MOSFET). Inserting a silicon nitride layer of appropriate thickness between the metallic source/drain electrodes and the silicon yields a low Schottky-barrier and simultaneously tunes the properties of the contact from metal-semiconductor-like to the behavior of a doped contact. Moreover, device characteristics of pseudo-MOSFETs reveal an efficient suppression of ambipolar behavior. Comparison with an alternative way of achieving low Schottky-barrier contacts, i.e., by inserting a strong dipole layer such as LiF between the metal and the silicon, reveals that the suppression is not a result of shifting the Fermi level closer to the conduction band but is caused by a reduction of metal-induced gap states. The trade-off between suppression of the ambipolar behavior, contact length and on-state current is investigated with simulations.
Modulation of ferroptosis sensitivity by TXNRD1 in pancreatic cancer cells (2020)

A bstract The selenoprotein thioredoxin reductase 1 (TXNRD1) plays a central role in ameliorating oxidative stress. Inhibition of TXNRD1 has been explored as a means of killing cancer cells that are thought to develop an enhanced reliance on such antioxidant proteins. In the context of ferroptosis, a non-apoptotic form of oxidative cell death, TXNRD1 has been proposed to cooperate with the phospholipid hydroperoxidase enzyme glutathione peroxidase 4 (GPX4) to protect cells from the lethal accumulation of lipid peroxides. Here, we report our unexpected finding that in pancreatic cancer cells, CRISPR–Cas9-mediated loss of TXNRD1 confers protection from ferroptosis induced by small-molecule inhibition of GPX4. Insights stemming from mechanistic interrogation of this phenomenon suggest that loss of TXNRD1 results in increased levels of GPX4 protein, potentially by influencing availability of selenocysteine, a scarce amino acid required by both proteins for proper synthesis and function. Increased abundance of GPX4 protein, in turn, protects cells from the effects of small-molecule GPX4 inhibition. These findings implicate selenoprotein regulation in governing ferroptosis sensitivity. Furthermore, by delineating a relationship between GPX4 and TXNRD1 contrary to that observed in numerous other settings, our discoveries underscore the context-specific nature of ferroptosis circuitry and its modulators.
Crystal Structure of the tRNA 3′ Processing Endoribonuclease tRNase Z from Thermotoga maritima (2005)

The maturation of the tRNA 3' end is catalyzed by a tRNA 3' processing endoribonuclease named tRNase Z (RNase Z or 3'-tRNase) in eukaryotes, Archaea, and some bacteria. The tRNase Z generally cuts the 3' extra sequence from the precursor tRNA after the discriminator nucleotide. In contrast, Thermotoga maritima tRNase Z cleaves the precursor tRNA precisely after the CCA sequence. In this study, we determined the crystal structure of T. maritima tRNase Z at 2.6-A resolution. The tRNase Z has a four-layer alphabeta/betaalpha sandwich fold, which is classified as a metallo-beta-lactamase fold, and forms a dimer. The active site is located at one edge of the beta-sandwich and is composed of conserved motifs. Based on the structure, we constructed a docking model with the tRNAs that suggests how tRNase Z may recognize the substrate tRNAs.
INVESTIGATING LOCAL IMPACTS OF HEAT-PULSE SENSORS FOR MEDIA MOISTURE CONTENT (2007)

Fresh food production and advanced life support functions on a transit mission or planetary base will require automated water and nutrient delivery for crops in the systems. The Water Offset Nutrient Delivery ExpeRiment (WONDER) investigates two types of nutrient delivery systems (NDS) that use a porous tube and capillary mat wicking material: the “substrate” module includes arcillite-based particulate media and the lower mass “bare tube” alternative uses the wicking material only. Miniature heat-pulse sensors (TMAS, Orbital Technologies, Madison, WI) are being evaluated to measure the root zone (particulate or wicking material) moisture content, which is crucial for irrigation control and monitoring. The thermal-based TMAS sensor operation is operated with a sustained energy output that could cause bias in its measurements. An investigation was conducted to examine the sensors’ effect on their local environment and to determine the minimum sampling interval required to dissipate the energy of the sensor operation. TMAS sensors were embedded individually in double-layer 7.5 cm x 7.5 cm capillary mat assemblies and the sensors sewn in place. Three levels of sampling frequency (12, 4, and 1.33 samples per hour) were applied, with 2 sensors per frequency level. A thermal infrared camera was used to monitor the heat pulse of the sensors in the wicking mat, and time lapsed infrared thermography was analyzed to determine the characteristics of the thermal changes near the heat-pulse sensors. Measurements of the thermal responses and heat dissipation times were taken before and after applying the sampling frequency treatments for seven days. Results presented illustrate the effects of thermal-based sensors on their local environment.
Blackberry leaf extract: a multifunctional anti‐aging active (2007)

Matrix metalloproteinases (MMPs) play a major role in wrinkle formation. Their expression increases with aging and is further enhanced by UV irradiation. Blackberry ( Rubus fruticosus ) leaf extract has been shown to suppress MMP‐1, ‐2 and ‐9 in cell‐free assays. We have now further explored the activity of this extract. The effect on MMP‐1 expression at the protein and the mRNA level was investigated using non‐irradiated and UVA‐irradiated human dermal fibroblasts. The extract showed a dose‐dependent reduction of the MMP‐1 protein level of both irradiated and non‐irradiated cells with an almost complete inhibition at a dosage of 0.1%. MMP‐1 mRNA expression of UVA‐irradiated cells was decreased after pre‐incubation as well as after post‐incubation with the extract. Best results were obtained with combined pre‐ and post‐treatment (0.1% extract led to 59% reduction in comparison with the respective control). Moreover, we found that blackberry leaf extract inhibits IL‐1α, a cytokine known to induce MMP expression. At a dosage of 0.2% the inhibition was 40% compared with that of the stimulated control. The extract also exhibited a potent radical scavenging activity comparable to that of α‐tocopherol as was shown by the ABTS assay. Taken together, these biological activities make blackberry leaf extract a highly efficient multifunctional anti‐aging active.
Dynamic Nuclear Polarization of Deuterated Proteins (2010)

For D's a jolly good fellow: Deuteration of proteins significantly increases the signal enhancements observed in dynamic nuclear polarization (DNP) magic-angle spinning (MAS) NMR experiments. In 13C CP-MAS spectra an enhancement of 120 is observed for perdeuterated SH3 with an exchangeable proton ratio of 50 %, whereas the enhancement is only 31 for the fully protonated SH3. The direct 13C excitation of the perdeuterated sample increases the enhancement to 148.
Papain‐Catalyzed Peptide Bond Formation: Enzyme‐Specific Activation with Guanidinophenyl Esters (2011)

The substrate mimetics approach is a versatile method for small-scale enzymatic peptide-bond synthesis in aqueous systems. The protease-recognized amino acid side chain is incorporated in an ester leaving group, the substrate mimetic. This shift of the specific moiety enables the acceptance of amino acids and peptide sequences that are normally not recognized by the enzyme. The guanidinophenyl group (OGp), a known substrate mimetic for the serine proteases trypsin and chymotrypsin, has now been applied for the first time in combination with papain, a cheap and commercially available cysteine protease. To provide insight in the binding mode of various Z-X(AA)-OGp esters, computational docking studies were performed. The results strongly point at enzyme-specific activation of the OGp esters in papain through a novel mode of action, rather than their functioning as mimetics. Furthermore, the scope of a model dipeptide synthesis was investigated with respect to both the amino acid donor and the nucleophile. Molecular dynamics simulations were carried out to prioritize 22 natural and unnatural amino acid donors for synthesis. Experimental results correlate well with the predicted ranking and show that nearly all amino acids are accepted by papain.
ChemInform Abstract: N‐Acylated α‐Amino Acids as Novel Oral Delivery Agents for Proteins. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Spatio-temporal invariants of the time-reversal operator (2006)

The DORT method gives the spatial invariants of the monochromatic time-reversal operator, at a given temporal frequency. It allows the monochromatic Green functions of point scatterers to be extracted from a data set. However, in acoustics, broadband signals are usually used and thus, it is often interesting to have the invariants in the time domain, or to know the evolution of the monochromatic Green function with frequency. It is not always easy, especially in complex media, because the sequence of the DORT eigenvectors (the invariants) changes as a function of the frequency. Thus, an invariant corresponding to a given scatterer may be the first at low frequencies, but the second at higher frequencies. Therefore, it is difficult to reconstruct a spatio-temporal Green function from monochromatic invariants. We introduce here the spatio-temporal time-reversal operator as a linear operator described by a fourth-order tensor, and deduce a method to obtain its spatio-temporal invariants. The method reduces to a more straightforward matrix decomposition, and thus can be easily implemented. Properties of the invariants are described, and applications to focusing in complex media are presented.
MG222 Slight and high reduction joint actuator for lower limbs robotic brace (2007)

A small and light weight motion unit of planetary gear reduction systems (100mm in diameter and 30mm in thickness) is proposed for use as a joint-driving module at the hip, knee and ankle joints of a lower limb robotic brace. This module is laminated by three layer-elements of planetary gear system in sandwich style. Both outside layers have same components sun, planets, and ring gears of planetary gear system. The middle layer is smaller than the outer layer by one tooth in planets and ring gears, lacking the sun gear. Also this sandwich mechanism is accomplishing itself, as an articulate joint not needing any other joint structural parts. If the lower limb brace joints were equipped with this articulate module, the self-stretching and self-walking therapy would be possible in the rehabilitation trainings. Here the motion unit were designed composed and tested its activations aiming to a lower limb's robotic brace on the torque and swinging speed.