gebhart/patrepeval huggingface dataset:
A vocabulary of ancient peptides at the origin of folded proteins (2015)

The seemingly limitless diversity of proteins in nature arose from only a few thousand domain prototypes, but the origin of these themselves has remained unclear. We are pursuing the hypothesis that they arose by fusion and accretion from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis. Should this be true, contemporary domains may still contain vestiges of such peptides, which could be reconstructed by a comparative approach in the same way in which ancient vocabularies have been reconstructed by the comparative study of modern languages. To test this, we compared domains representative of known folds and identified 40 fragments whose similarity is indicative of common descent, yet which occur in domains currently not thought to be homologous. These fragments are widespread in the most ancient folds and enriched for iron-sulfur- and nucleic acid-binding. We propose that they represent the observable remnants of a primordial RNA-peptide world.
Sparkler: An Audio-Driven Interactive Live Computer Performance for Symphony Orchestra (2002)

This paper describes the design, implementation, and application of an audio-driven computer-based system for live and interactive performance with an orchestra. We begin by describing the compositional and musical goals, emphasizing the electronics aspect. We then discuss the challenges of working with an orchestra and integrating the electronics in a concert hall. We describe the hardware setup and then detail the software implementation, from audio analysis and “perceptual parameter” estimation to the generative algorithm.
Topical application of acidified nitrite to the nail renders it antifungal and causes nitrosation of cysteine groups in the nail plate (2007)

Acidified nitrite cream results in the formation of S-nitrosocysteine throughout the treated nail. Acidified nitrite treatment makes a nail antifungal. S-nitrosothiols, formed by nitrosation of nail sulphur residues, are the active component. Acidified nitrite exploits the nature of the nail barrier and utilizes it as a means of delivery of NO/nitrosothiol-mediated antifungal activity. Thus the principal obstacle to therapy in the nail becomes an effective delivery mechanism.
Security Management in Personal Network (2006)

As happened in other communications systems security is an aspect which should treated seriously in pervasive computing networks. In this paper the security of a special subset of pervasive computing network, personal network, is studied
Targeting Metabolic Modulation and Mitochondrial Dysfunction in the Treatment of Heart Failure (2017)

Despite significant improvements in morbidity and mortality with current evidence-based pharmaceutical-based treatment of heart failure (HF) over the previous decades, the burden of HF remains high. An alternative approach is currently being developed, which targets myocardial energy efficiency and the dysfunction of the cardiac mitochondria. Emerging evidence suggests that the insufficient availability of ATP to the failing myocardium can be attributed to abnormalities in the myocardial utilisation of its substrates rather than an overall lack of substrate availability. Therefore, the development of potential metabolic therapeutics has commenced including trimetazidine, ranolazine and perhexiline, as well as specific mitochondrial-targeting pharmaceuticals, such as elamipretide. Large randomised controlled trials are required to confirm the role of metabolic-modulating drugs in the treatment of heart failure, but early studies have been promising in their possible efficacy for the management of heart failure in the future.
Pt–Ru Alloyed Fuel Cell Catalysts Sputtered from a Single Alloyed Target (2011)

This work illustrates the improved performance of a direct menthol fuel cell (DMFC) Pt1–xRux alloy phase catalysts deposited via magnetron sputtering onto a carbon powder matrix from an alloyed mixed-metal target. The production of dispersed metal catalysts particles of the correct size, structure, bulk, and surface composition for effective methanol oxidation required extensive control of process parameters including sputter gas type, sputter gas concentration, deposition pressure, sputter power, and sputter type (RF or DC). Through the adjustment of these multivariate sputtering parameters, it was possible to make alloyed catalyst materials with varying crystallinity and composition ranging from Pt0.32Ru0.68 to Pt0.50Ru0.50. The careful balance of these parameters resulted in a low metal loading catalyst, ∼30 wt %, with a methanol oxidation reaction onset potential of <300 mV versus RHE and peak current of >200 uA/cm2. The optimized sputtered catalysts have increased metal utilization and outperform commercially available catalysts at fuel cell operating potentials.
Position control of manipulator with passive joints using dynamic coupling (1991)

A method of controlling the position of a manipulator composed of active and passive joints is described. The active joints have actuators and position sensors. The passive joints have holding brakes instead of actuators. While the brakes are released, the passive joints are indirectly controlled by the motion of the active joints using the coupling characteristics of manipulator dynamics. While the brakes are engaged, the passive joints are fixed and the active joints are controlled. The position of the manipulator is controlled by combining these two control modes. The basic principle of the control method and the conditions that ensure the controllability of the passive joints are described. An algorithm for point-to-point control of the manipulator is presented. The feasibility of the method is demonstrated by simulations for a manipulator with two degrees of freedom.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The role of cysteine proteases in hypoxia-induced rat renal proximal tubular injury. (1995)

The role of the lysosomal proteases cathepsins B and L and the calcium-dependent cytosolic protease calpain in hypoxia-induced renal proximal tubular injury was investigated. As compared to normoxic tubules, cathepsin B and L activity, evaluated by the specific fluorescent substrate benzyloxycarbonyl-L-phenylalanyl-L-arginine-7-amido-4-methylcoumarin, was not increased in hypoxic tubules or the medium used for incubation of hypoxic tubules in spite of high lactate dehydrogenase (LDH) release into the medium during hypoxia. These data in rat proximal tubules suggest that cathepsins are not released from lysosomes and do not gain access to the medium during hypoxia. An assay for calpain activity in isolated proximal tubules using the fluorescent substrate N-succinyl-Leu-Tyr-7-amido-4-methylcoumarin was developed. The calcium ionophore ionomycin induced a dose-dependent increase in calpain activity. This increase in calpain activity occurred prior to cell membrane damage as assessed by LDH release. Tubular calpain activity increased significantly by 7.5 min of hypoxia, before there was significant LDH release, and further increased during 20 min of hypoxia. The cysteine protease inhibitor N-benzyloxycarbonyl-Val-Phe methyl ester (CBZ) markedly decreased LDH release after 20 min of hypoxia and completely prevented the increase in calpain activity during hypoxia. The increase in calpain activity during hypoxia and the inhibitor studies with CBZ therefore supported a role for calpain as a mediator of hypoxia-induced proximal tubular injury.
Application of Fibrin Glue After Hepatectomy Might Still Be Justified (2008)

Annals of Surgery: February 2008 - Volume 247 - Issue 2 - p 399-400 doi: 10.1097/SLA.0b013e3181640286
A procedure for mapping <i>Arabidopsis</i> mutations using co‐dominant ecotype‐specific PCR‐based markers (1993)

A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplified by the polymerase chain reaction (PCR). The ecotype of origin of these amplified fragments can be determined by cleavage with a restriction endonuclease. Specifically, 18 sets of PCR primers were synthesized, each of which amplifies a single mapped DNA sequence from the Columbia and Landsberg erecta ecotypes. Also identified was at least one restriction endonuclease for each of these PCR products that generates ecotype-specific digestion patterns. Using these co-dominant cleaved amplified polymorphic sequences (CAPS), an Arabidopsis gene can be unambiguously mapped to one of the 10 Arabidopsis chromosome arms in a single cross using a limited number of F2 progeny.
Computer interpretation of engineering drawings as solid models (1988)

Much of the geometrical data relating to engineering components and assemblies is stored in the form of orthographic views, either on paper or computer files. For various engineering applications, however, it is necessary to describe objects in formal geometric modelling terms. The work reported in this thesis is concerned with the development and implementation of concepts and algorithms for the automatic interpretation of orthographic views as solid models. The various rules and conventions associated with engineering drawings are reviewed and several geometric modelling representations are briefly examined. A review of existing techniques for the automatic, and semi-automatic, interpretation of engineering drawings as solid models is given. A new theoretical approach is then presented and discussed. The author shows how the implementation of such an approach for uniform thickness objects may be extended to more general objects by introducing the concept of `approximation models'. Means by which the quality of the transformations is monitored, are also described. Detailed descriptions of the interpretation algorithms and the software package that were developed for this project are given. The process is then illustrated by a number of practical examples. Finally, the thesis concludes that, using the techniques developed, a substantial percentage of drawings of engineering components could be converted into geometric models with a specific degree of accuracy. This degree is indicative of the suitability of the model for a particular application. Further work on important details is required before a commercially acceptable package is produced.
Characteristics of CMOS device isolation for the ULSI age (2002)

Scaling requirements for abrupt active-isolation transitions, isolation depth, and isolation planarity are discussed quantitatively. We review how LOCOS and STI isolation are being improved to meet these requirements. Independent of fabrication techniques, we see that a necessary consequence of achieving the desired narrow isolation and abrupt transitions is a discrete edge parasitic. We show that the edge parasitic can be distinguished from the planar channel and can be characterized separately. Edge device sensitivities are investigated with experiment and simulation to show that design and process control of the discrete edge parasitic will be a significant thrust of device engineering for future isolation technologies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Novel Antifungal Compounds Produced by Sterile Dark, an Unidentified Wheat Rhizosphere Fungus (2005)

Two novel antifungal compounds were isolated from a culture broth of Sterile Dark, an unidentified fungus isolated from the rhizosphere of wheat grown in a continuous cropping field. These compounds were elucidated to be phthalide-based compounds by spectroscopic analyses.
The Stability of Silver(I) Complexes of Some 3- and 4-Substituted Pyridines<sup>1</sup> (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Stability of Silver(I) Complexes of Some 3- and 4-Substituted Pyridines1R. Kent Murmann and Fred BasoloCite this: J. Am. Chem. Soc. 1955, 77, 13, 3484–3486Publication Date (Print):July 1, 1955Publication History Published online1 May 2002Published inissue 1 July 1955https://pubs.acs.org/doi/10.1021/ja01618a016https://doi.org/10.1021/ja01618a016research-articleACS PublicationsRequest reuse permissionsArticle Views234Altmetric-Citations55LEARN 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
Neurophysiological Variables and Fibrinolysis in Insulin-Dependent Diabetes Treated with an Aldose Reductase Inhibitor or Placebo (1986)

In a double-blind study we randomized insulin-dependent diabetics (n = 19) into a group (n = 12) given daily 250 mg Sorbinil, a potent aldose reductase inhibitor reported to ameliorate diabetic neuropathy, and another group (n = 7) given placebo for 1 year. Objective, neurophysiological variables (biothesiometry, electromyography, nyctometri) were followed throughout the study and correlated with fibrinolytic variables in blood. We found that Sorbinil did not improve any of the selected neurophysiological variables. Neither did Sorbinil induce marked changes in the fibrinolytic activities of the extrinsic, tissue-type plasminogen activator (t-PA), or in the intrinsic factor XII-dependent or factor XII-independent (urokinase-like) plasminogen activator systems. We found no effect of Sorbinil on the activity of the fast-reacting inhibitor (PA-I) of plasminogen activator. Levels of PA-I in plasma influence the amounts of t-PA precipitated in euglobulins.
The Effect of an Estrone D-Lactam Steroid Ester Derivative on Breast Cancer Cells and Its Predicted Binding Interactions With the Ligand Binding Domain of Estrogen Receptor-α (2006)

In order to further improve the toxicity profile and the anticancer effect of chlorambucil (CBL), we have synthesized a new estrone D-lactam steroidal ester of CBL (ESBL). The aim of this study was to investigate the in vitro activity of ESBL against primary breast carcinoma (BC) cells of operable tumors in comparison with CBL. Cells derived from fresh tumor sections that were obtained from 28 postmenopausal women with ductal BC were treated with CBL and ESBL. Apoptotic cells were distinguished from viable ones with flow cytometric methods. ESBL generated a significantly higher rate of cell apoptosis and cytotoxicity than CBL. ESBL cytotoxic effect demonstrated a significant positive weak to moderate dose-dependent correlation with the ER expression. ESBL produced antineoplastic activity superior to CBL on primary BC tumors in vitro. Moreover, a docking study on the binding interactions of ESBL with the ligand binding domain (LBD) of estrogen receptor-alpha (ERalpha) was investigated. ESBL was found to be positioned inside the binding cavity with its steroidal moiety, whereas the alkylating moiety protruded out of receptor's pocket.
Scalable Store-Load Forwarding via Store Queue Index Prediction (2006)

Conventional processors use a fully-associative store queue (SQ) to implement store-load forwarding. Associative search latency does not scale well to capacities and bandwidths required by wide-issue, large window processors. In this work, we improve SQ scalability by implementing store-load forwarding using speculative indexed access rather than associative search. Our design uses prediction to identify the single SQ entry from which each dynamic load is most likely to forward. When a load executes, it either obtains its value from the predicted SQ entry (if the address of the entry matches the load address) or the data cache (otherwise). A forwarding misprediction - detected by pre-commit filtered load reexecution - results in a pipeline flush. SQ index prediction is generally accurate, but for some loads it cannot reliably identify a single SQ entry. To avoid flushes on these difficult loads while keeping the single-SQ-access-per-load invariant, a second predictor delays difficult loads until all but the youngest of their "candidate" stores have committed. Our predictors are inspired by store-load dependence predictors for load scheduling (Store Sets and the Exclusive Collision Predictor) and unify load scheduling and forwarding. Experiments on the SPEC2000 and MediaBench benchmarks show that on an 8-way issue processor with a 512-entry reorder buffer, our technique performs within 3.3% of an ideal associative SQ (same latency as the data cache) and either matches or exceeds the performance of a realistic associative SQ (slower than data cache) on 31 of 47 programs.
Two-iron rubredoxin of Pseudomonas oleovorans: production, stability and characterization of the individual iron-binding domains by optical, CD and NMR spectroscopies (2001)

A minigene encoding the C-terminal domain of the 2Fe rubredoxin of Pseudomonas oleovorans was created from the parental alk G gene contained in the expression plasmid pKK223-3. The vector directed the high-level production of the C-terminal domain of this rubredoxin; a simple procedure was used to purify the recombinant domain in the 1Fe form. The 1Fe form of the C-terminal domain was readily converted into the apoprotein and cadmium forms after precipitation with trichloroacetic acid and resolubilization in the presence or absence of cadmium chloride respectively. In steady-state assays, the recombinant 1Fe C-terminal domain is redox-active and able to transfer electrons from reduced rubredoxin reductase to cytochrome c. The absorption spectrum and dichroic features of the CD spectrum for the iron- and cadmium-substituted C-terminal domain are similar to those reported for the iron- and cadmium-substituted Desulfovibrio gigas rubredoxin [Henehen, Pountney, Zerbe and Vasak (1993) Protein Sci. 2, 1756–1764]. Difference absorption spectroscopy of the cadmium-substituted C-terminal domain revealed the presence of four Gaussian-resolved maxima at 202, 225, 240 and 276nm; from J⊘rgensen's electronegativity theory, the 240nm band is attributable to a CysS-Cd(II) charge-transfer excitation. Attempts to express the N-terminal domain of the 2Fe rubredoxin directly from a minigene were unsuccessful. However, the N-terminal domain was isolated through cleavage of an engineered 2Fe rubredoxin in which a factor Xa proteolysis site had been introduced into the putative interdomain linker. The N-terminal domain is characterized by absorption spectra typical of the 1Fe rubredoxins. The domain is folded as determined by CD and NMR spectroscopies and is redox-active. However, the N-terminal domain is less stable than the isolated C-terminal domain, a finding consistent with the known properties of the full-length 2Fe and cadmium-substituted Ps. oleovorans rubredoxin.
Human CD8+ T lymphocytes can be divided into CD45RA+ and CD45RO+ cells with different requirements for activation and differentiation (1991)

The functional distinction between CD45RA+ and CD45RO+ cells within the human CD4+ T cell subset is well established. This study was undertaken to investigate whether a similar division can be made within the CD8+ T cell population. A quantitative comparison was made of the requirements for activation and differentiation of CD8+CD45RA+ and CD8+CD45RO+ cells. Stimulation of T lymphocytes with anti-CD3 mAb immobilized at high-density induced strong proliferation and CTL activity in both CD45RA+ and CD45RO+ cells. Suboptimal TCR/CD3 triggering, in contrast, induced substantially higher levels of proliferation and CTL activity in CD8+CD45RO+ cells compared with their CD45RA+ counterparts. Lymphokine secretion (i.e., Il-2 and TNF-alpha) was under any condition more readily induced in CD8+CD45RO+ cells. Markedly, proliferation of both CD8+CD45RA+ and CD8+CD45RO+ T cells initiated by anti-CD3 mAb immobilized at high densities was not inhibited by addition of anti-CD25 mAb, in contrast to proliferation induced by suboptimal anti-CD3 mAb concentrations. These findings show that a functional division between CD45RA+ and CD45RO+ T cells with distinct requirements for activation and differentiation may also be made in the CD8+ subset.
Neuromorphic computation in multi-delay coupled models (2017)

Neuromorphic computing provides a promising platform for processing high-dimensional noisy signals on dedicated hardware. Using design elements inspired by neurobiological findings and advances in machine learning methodology, delay-coupled systems have recently been developed in the field of neuromorphic computing. Delayed feedback connections enable such systems to generate a complex representation of injected input in the internal state of single <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nodes</i> , which in our context refer to hardware components with nonlinear behavior and without any memory. In contrast to classical combinatorial circuits or feed-forward networks, this state is not distributed in space but in time. Hardware implementations with low hardware component counts are therefore particularly easy to design for delay-coupled systems. In this paper, we present an argument for using delay-coupled reservoirs using multiple feedback terms with different delays. We present a theoretical analysis of the resulting system, discuss surprising effects pertaining to the precise choice of delays, and provide a guideline for the optimal design of such systems.
: <i>Sir Philip Sidney and the English Renaissance.</i> (1955)

An abstract is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Synthesis and conformational analysis of epindolidione-derived peptide models for .beta.-sheet formation (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and conformational analysis of epindolidione-derived peptide models for .beta.-sheet formationD. S. Kemp, Benjamin R. Bowen, and Christopher C. MuendelCite this: J. Org. Chem. 1990, 55, 15, 4650–4657Publication Date (Print):July 1, 1990Publication History Published online1 May 2002Published inissue 1 July 1990https://pubs.acs.org/doi/10.1021/jo00302a033https://doi.org/10.1021/jo00302a033research-articleACS PublicationsRequest reuse permissionsArticle Views734Altmetric-Citations99LEARN 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