gebhart/patrepeval huggingface dataset:
The impact of CRISPR repeat sequence on structures of a Cas6 protein–RNA complex (2012)

The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of a noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.
The Structure of Copolymers. II<sup>1</sup> (1944)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Structure of Copolymers. II1Frederick T. WallCite this: J. Am. Chem. Soc. 1944, 66, 12, 2050–2057Publication Date (Print):December 1, 1944Publication History Published online1 May 2002Published inissue 1 December 1944https://pubs.acs.org/doi/10.1021/ja01240a014https://doi.org/10.1021/ja01240a014research-articleACS PublicationsRequest reuse permissionsArticle Views459Altmetric-Citations236LEARN 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
Interaction of Pathogenic <i>Neisseria</i> with Host Defenses What Happens <i>in Vivo</i>?a (1994)

N. gonorrhoeae initiates infection by adhering to and invading columnar epithelial cells. Over time these activities often induce inflammation, with the influx of neutrophils and serum into the urethral lumen, cervical os, conjunctiva, and the like. At least some of these infected niches contain CMP-NANA (cytidine monophospho-N-acetyl neuraminic acid, also called CMP-sialic), contain sialylated gonococci, and are relatively or strictly anaerobic due to neutrophil and gonococcal metabolism and to the site of disease, that is, the peritoneal cavity. Gonococci thus encounter environmental conditions, reagents, and substrates in the human body that are not normally present in vitro. Knapp and Clark were the first to successfully grow gonococci anaerobically in an easily reproducible system, allowing researchers to begin to investigate in vitro the effects of anaerobiosis on gonococcal virulence traits. As a result of a series of elegant and in depth studies, Smith and Parsons and their colleagues showed that growth in CMP-NANA confers on the gonococcus a high degree of phenotypic (readily reversible) serum resistance and that CMP-NANA is available in vivo at sites of gonococcal infection and disease; gonococci become covalently coated with sialic acid and they become serum resistant (reviewed in refs. 8-10). Given that gonococci growing in the absence of oxygen or in the presence of CMP-NANA probably more closely resemble gonococci growing inside the human host, we studied several possible virulence traits of gonococci cultivated under these conditions. We first observed that anaerobic growth (in the absence of CMP-NANA) increases gonococcal resistance to killing by low (but not high) concentrations of normal human serum. We also asked whether anaerobic growth affected gonococcal association with host cells. Contrary to the effects on serum killing, anaerobic growth (in the absence of CMP-NANA) does not appear to affect the ability of gonococci (expressing certain adhesive outer membrane proteins called Opa proteins) to bind to and enter human epithelial cell lines or to bind to or resist killing by human neutrophils. The results from studies investigating the modulatory role of CMP-NANA were more striking. Growth in CMP-NANA dramatically inhibits the adherence of Opa+ gonococci to human neutrophils. It does not, however, appear to significantly decrease their sensitivity to phagocytic killing or to in vitro killing by lysosomal contents (aqueous extracts of human neutrophil granules).(ABSTRACT TRUNCATED AT 400 WORDS)
Simultaneous <i>in situ</i> electrochemical, surface plasmon optical, and atomic force microscopy measurements: Investigation of conjugated polymer electropolymerization (2006)

We report the simultaneous in situ electrochemical, optical, and surface morphological studies of conjugated polymer ultrathin film formation using a novel combined electrochemical instrumentation–surface plasmon resonance spectroscopy–atomic force microscopy. The initial stages of the electropolymerization of poly(3,4-ethylenedioxythiophene) films on flat gold electrode/substrates were observed in all three experiments simultaneously. In addition to the electrochemical information obtained, the surface plasmon optical technique showed the deposition of the film, and provided electrochromic behavior of the deposited film. Simultaneously, atomic force microscopy gave surface morphological properties and domain growth of the film. The complementarity of the information obtained from the combined techniques is useful for the investigation of polymer growth mechanism between cyclic voltammetry and potentiostatic deposition methods.
The Potentiation of IFN-γ and Induction of Cytotoxic Proteins by Pegylated IL-10 in Human CD8 T Cells (2015)

Interleukin-10 (IL-10) exerts both immunosuppressive and immunostimulatory effects. While the immunosuppressive effects are widely known, it has only been recently reported that pegylated recombinant human IL-10 (PEG-rHuIL-10) elicits potent interferon-γ (IFN-γ) and CD8 T-cell-dependent antitumor effects in murine tumor models. In this study, we show that PEG-rHuIL-10 exerts immune inhibitory effects on human peripheral blood mononuclear cell (PBMC) bulk cultures and stimulatory effects in CD8 T cells within the same culture. Also, in isolated CD8 T cells, PEG-rHuIL-10 potentiates prototypic Tc1 cytokine IFN-γ expression and induces perforin and granzyme B secretion. IFN-γ and granzyme B secretion is dependent on T-cell receptor ligation and is therefore not indiscriminately released by PEG-rHuIL-10 treatment. STAT3, NF-κB, AP1, and MEK inhibition blocks IFN-γ potentiation, while perforin induction is impeded by AP1 inhibition, and granzyme B induction is blocked by both AP1 and MEK inhibition. These results extend previous pegylated IL-10 preclinical findings to human CD8 T cells and implicate a strong degree of translation for pegylated IL-10 use in cancer therapy.
Analysis of brain activation by visual and auditory stimulation after visual and auditory simultaneous stimulation using F-MRI (2005)

It is said that the auditory spatial perception is strongly affected by visual cues, and when auditory and visual stimulation are given form different positions simultaneously, the source position of sound is mislead to the direction of visual stimulation. The purpose of this study is analyzing the brain response on f-MRI by simultaneous stimulation of auditory and visually sensors. f-MRI of some subjects were measured by using simultaneous stimulation, and the results of these experiments were analyzed and assessed. From these experiments, following characteristics became clear. 1) Simultaneous stimulation activate each cortex stronger than the results of single stimulation. 2) After giving auditory and visual stimulus as preliminary stimulation to subject, one type of stimulus was given to the subject. From this stimulation, both cortex were activated. This activation was weaker than the time of actually giving simultaneous stimulus. From investigation of these results, it seems that the relationship between auditory and visual cortex become clear.
PyMT5: multi-mode translation of natural language and Python code with transformers (2020)

Simultaneously modeling source code and natural language has many exciting applications in automated software development and understanding. Pursuant to achieving such technology, we introduce PYMT5, the PYTHON method text-to-text transfer transformer, which is trained to translate between all pairs of PYTHON method feature combinations: a single model that can both predict whole methods from natural language documentation strings (docstrings) and summarize code into docstrings of any common style. We present an analysis and modeling effort of a large-scale parallel corpus of 26 million PYTHON methods and 7.7 million method-docstring pairs, demonstrating that for docstring and method generation, PYMT5 outperforms similarlysized auto-regressive language models (GPT2) which were English pre-trained or randomly initialized. On the CODE-SEARCHNET test set, our best model predicts 92.1% syntactically correct method bodies, achieved a BLEU score of 8.59 for method generation and 16.3 for docstring
Temperature and Temperature Profile Measurements in the Combustor Flowpath Using Structured Emission Thermography (2003)

Structured Emission Thermometry (SET) is a new optical technique for deriving temperature and species concentrations in high-temperature regions of a combustor flow-path from measurements of water and soot emission spectra in the 1 micron region. A prototype instrument has been built for gas- and liquid-fuel combustors with temperatures ranging from 1400–2500K (2100–4000F). This instrument can be used for test stand instrumentation and routine monitoring in fixed installations. With further evolution, the technique may be suitable for an aircraft engine control system. The emissions are measured along narrow lines of sight using small, simple passive fiber probes placed at a short standoff distance from the hot gas flow-path. With proper placement of multiple probes, data may be collected over overlapping lines of sight and inverted to produce a low-resolution spatial map of the temperature and emitter density in the flow-path. In this work, we describe a series of combustor measurements, including cross-validation measurements in a well-controlled laboratory flame and measurements in combustor test stands. Both line-of-sight measurements and reconstructed temperature profiles are presented and discussed.
The Spectral Mother (2001)

The most vivid of Wordsworth’s recollections of his mother from the Cockermouth days, before she died when he was seven, are included in his ‘Autobiographical Memoranda’, dictated at Rydal Mount in 1847:
Analysis of Doppler-effect on satellite constellations with wavelength division multiplexing architectures (2009)

With the development of optical space communications, a global space-based optical backbone network is currently proposed by using broadband laser inter-satellite links (ISLs) which enable routing traffic through the space. Satellite optical networking techniques based on wavelength division multiplexing (WDM) ISLs can transit significantly high data rates signals. In this letter, a new function of wavelength excursion due to Doppler-effect is developed for the ISLs, considering the conception of pointing ahead mechanism. The characteristic of wavelength excursion induced by Doppler-effect is examined in one of low earth orbit (LEO) satellite constellation networks named the next-generation LEO system (NeLS) with WDM ISLs assumed, and the influence on its communications caused by wavelength excursion is analyzed.
Pericardial and Ventricular Pressure (1960)

In anesthetized open-chest and closed-chest dogs subjected to plethora and hemorrhage, pressures were measured simultaneously in the right atrium, right and left ventricles, and the pleural and pericardial spaces. It was found that an increase in ventricular end-diastolic pressure above approximately 1 mm. Hg was associated with a rise in pericardial pressure of nearly the same amount. Thus, the practice of defining "effective" ventricular end-diastolic pressure as the difference between the ventricular and intrapleural pressure gives erroneous values when ventricular end-diastolic pressure is greater than a few mm. Hg. The true ventricular transmural pressure is the difference between ventricular end-diastolic and pericardial end-diastolic pressure and has a value of no more than 2 or 3 mm. Hg under all except the most abnormal circumstances. When ventricular end-diastolic pressure is greater than a few mm. Hg, the pericardial pressure at the end of systole is likewise elevated, but to a lesser degree. Thus, when ventricular end-diastolic pressure is elevated, the measured ventricular end-systolic pressure is greater than the pressure developed by ventricular muscular contraction because end-systolic pressure is the algebraic sum of the pressure developed by ventricular muscular contraction and the pressure in the pericardial space. This error in ventricular systolic pressure may be relatively large for the right and small for the left ventricle. Pericardial pressure decreases during ventricular systole, lowers the pressure on the outside of the atria, and thus, tends to draw blood into the right atrium during ventricular systole.
Superfast-Trainable Multi-Class Probabilistic Classifier by Least-Squares Posterior Fitting (2010)

Kernel logistic regression (KLR) is a powerful and flexible classification algorithm, which possesses an ability to provide the confidence of class prediction. However, its training—typically carried out by (quasi-)Newton methods—is rather time-consuming. In this paper, we propose an alternative probabilistic classification algorithm called Least-Squares Probabilistic Classifier (LSPC). KLR models the class-posterior probability by the log-linear combination of kernel functions and its parameters are learned by (regularized) maximum likelihood. In contrast, LSPC employs the linear combination of kernel functions and its parameters are learned by regularized least-squares fitting of the true class-posterior probability. Thanks to this linear regularized least-squares formulation, the solution of LSPC can be computed analytically just by solving a regularized system of linear equations in a class-wise manner. Thus LSPC is computationally very efficient and numerically stable. Through experiments, we show that the computation time of LSPC is faster than that of KLR by two orders of magnitude, with comparable classification accuracy.
Influencing Hematopoietic Differentiation of Mouse Embryonic Stem Cells using Soluble Heparin and Heparan Sulfate Saccharides (2010)

Heparan sulfate proteoglycans (HSPG) encompass some of the most abundant macromolecules on the surface of almost every cell type. Heparan sulfate (HS) chains provide a key interaction surface for the binding of numerous proteins such as growth factors and morphogens, helping to define the ability of a cell to respond selectively to environmental cues. The specificity of HS-protein interactions are governed predominantly by the order and positioning of sulfate groups, with distinct cell types expressing unique sets of HS epitopes. Embryos deficient in HS-synthesis (Ext1(-/-)) exhibit pre-gastrulation lethality and lack recognizable organized mesoderm and extraembryonic tissues. Here we demonstrate that embryonic stem cells (ESCs) derived from Ext1(-/-) embryos are unable to differentiate into hematopoietic lineages, instead retaining ESC marker expression throughout embryoid body (EB) culture. However hematopoietic differentiation can be restored by the addition of soluble heparin. Consistent with specific size and composition requirements for HS:growth factor signaling, chains measuring at least 12 saccharides were required for partial rescue of hematopoiesis with longer chains (18 saccharides or more) required for complete rescue. Critically N- and 6-O-sulfate groups were essential for rescue. Heparin addition restored the activity of multiple signaling pathways including bone morphogenic protein (BMP) with activation of phospho-SMADs re-established by the addition of heparin. Heparin addition to wild-type cultures also altered the outcome of differentiation, promoting hematopoiesis at low concentrations, yet inhibiting blood formation at high concentrations. Thus altering the levels of HS and HS sulfation within differentiating ESC cultures provides an attractive and accessible mechanism for influencing cell fate.
Jellyfish mesogloea collagen. Characterization of molecules as alpha 1 alpha 2 alpha 3 heterotrimers. (1985)

The mesogloea collagen of a primitive animal, the jellyfish Stomolophus nomurai, belonging to the class Scyphozoa in the Coelenterata, was studied with respect to its chain structure. Most of the mesogloea collagen was solubilized by limited digestion with pepsin and isolated by selective precipitation at 0.9 m NaCl in 0.5 M acetic acid. Upon denaturation, the pepsin-solubilized collagen produced three distinct alpha chains, alpha 1, alpha 2, and alpha 3, in comparable amounts which were separable by CM-cellulose chromatography. The nonidentity of these alpha chains was confirmed by amino acid and carbohydrate analyses and peptide mapping. Furthermore, the introduction of intramolecular cross-links into native molecules by formaldehyde yielded a large proportion of gamma 123 chain with chain structure alpha 1 alpha 2 alpha 3, as judged by chromatographic behavior and peptide maps. We concluded that mesogloea collagen is comprised of alpha 1 alpha 2 alpha 3 heterotrimers and is chemically like vertebrate Type V collagen. On the other hand, sea anemone mesogloea collagen from the class Anthozoa was previously reported to comprise (alpha)3 homotrimers (Katzman, R. L., and Kang, A. H. (1972) J. Biol. Chem. 247, 5486-5489). On the basis of these findings, we assume that alpha 1 alpha 2 alpha 3 heterotrimers arose in evolution with the divergence of Scyphozoa and Anthozoa.
MPI-IO/L: efficient remote I/O for MPI-IO via logistical networking (2006)

Scientific applications often need to access remotely located files, but many remote I/O systems lack standard APIs that allow efficient and direct access from application codes. This work presents MPI-IO/L, a remote I/O facility for MPI-IO using logistical networking. This combination not only provides high-performance and direct remote I/O using the standard parallel I/O interface but also offers convenient management and sharing of remote files. We show the performance trade-offs with various remote I/O approaches implemented in the system, which can help scientists identify preferable I/O options for their own applications. We also discuss how logistical networking could be improved to work better with parallel I/O systems such as ROMIO.
Auto-cleavable Ribozyme Sequence Attached to Brome Mosaic Virus cDNAs Enhances Accumulation of Viral RNAs Transcribed In Vivo from the cDNAs. (1997)

[in Japanese]
THE MODAL LOGIC AND FUZZY COGNITIVE MAPS IN TELEPRESENCE (1996)

Telepresence is constituted of a robotic system controlled by a human operator at a remote control station. In these systems the human operator is immerse in a virtual reality and the robot is controlled at distance by human operator. Often the human operator has that repeat tasks through robot. In this article we propose that the telepresence can use semi-autonomous (semi-reactive) robots, that execute the tasks that the operator repeats often, However, to create a relationship between the human operator and the semi-autonomous (semi-reactive) robot, it is necessary to develop a logic that combines the knowledge of the reactive robot and the knowledge of the human operator. On the other hand, in the last years we have seen the possibility to structure virtual worlds with Fuzzy Cognitive Maps. These maps can model virtual worlds with numerous actors. Moreover these FCMs can combine different virtual worlds. In this article we introduce a multi-agent modal logic of knowledge and belief that can be used in design of telep resence with semi-reactive robots. In this logic we describe possible worlds (“states of nature”) by fuzzy cognitive maps.
Hybrid-Mode-Assisted Long-Distance Excitation of Short-Range Surface Plasmons in a Nanotip-Enhanced Step-Index Fiber (2016)

We propose and experimentally demonstrate a monolithic nanowire-enhanced fiber-based nanoprobe for the broadband delivery of light (550-730 nm) to a deep subwavelength scale using short-range surface plasmons. The geometry is formed by a step index fiber with an integrated gold nanowire in its core and a protruding gold nanotip with sub-10 nm apex radius. We present a novel coupling scheme to excite short-range surface plasmons, whereby the radially polarized hybrid mode propagating inside the nanowire section excites the plasmonic mode close to the fiber endface, which is in turn superfocused down to nanoscale dimensions at the tip apex. We show that in this all-integrated fiber-plasmonic coupling scheme the wire length can be orders of magnitude longer than the attenuation length of short-range plasmon polaritons, yielding a broadband plasmon excitation and reducing demands in fabrication. We observe that the scattered light in the far-field from the nanotip is axially polarized and preferentially excited by a radially polarized input, unambiguously revealing that it originates from a short-range plasmon propagating on the nanotip, in agreement with simulations. This novel excitation scheme will have important applications in near-field microscopy and nanophotonics and potentially offers significantly improved resolution compared to current delivery near-field probes.