gebhart/patrepeval huggingface dataset:
Sortase C-Mediated Anchoring of BasI to the Cell Wall Envelope of Bacillus anthracis (2007)

Vegetative forms of Bacillus anthracis replicate in tissues of an infected host and precipitate lethal anthrax disease. Upon host death, bacilli form dormant spores that contaminate the environment, thereby gaining entry into new hosts where spores germinate and once again replicate as vegetative forms. We show here that sortase C, an enzyme that is required for the formation of infectious spores, anchors BasI polypeptide to the envelope of predivisional sporulating bacilli. BasI anchoring to the cell wall requires the active site cysteine of sortase C and an LPNTA motif sorting signal at the C-terminal end of the BasI precursor. The LPNTA motif of BasI is cleaved between the threonine (T) and the alanine (A) residue; the C-terminal carboxyl group of threonine is subsequently amide linked to the side chain amino group of diaminopimelic acid within the wall peptides of B. anthracis peptidoglycan.
Malarial Hemozoin Activates the NLRP3 Inflammasome through Lyn and Syk Kinases (2009)

The intraerythrocytic parasite Plasmodium -- the causative agent of malaria -- produces an inorganic crystal called hemozoin (Hz) during the heme detoxification process, which is released into the circulation during erythrocyte lysis. Hz is rapidly ingested by phagocytes and induces the production of several pro-inflammatory mediators such as interleukin-1beta (IL-1beta). However, the mechanism regulating Hz recognition and IL-1beta maturation has not been identified. Here, we show that Hz induces IL-1beta production. Using knockout mice, we showed that Hz-induced IL-1beta and inflammation are dependent on NOD-like receptor containing pyrin domain 3 (NLRP3), ASC and caspase-1, but not NLRC4 (NLR containing CARD domain). Furthermore, the absence of NLRP3 or IL-1beta augmented survival to malaria caused by P. chabaudi adami DS. Although much has been discovered regarding the NLRP3 inflammasome induction, the mechanism whereby this intracellular multimolecular complex is activated remains unclear. We further demonstrate, using pharmacological and genetic intervention, that the tyrosine kinases Syk and Lyn play a critical role in activation of this inflammasome. These findings not only identify one way by which the immune system is alerted to malarial infection but also are one of the first to suggest a role for tyrosine kinase signaling pathways in regulation of the NLRP3 inflammasome.
Theory of bistability in nonlinear distributed feedback structures (1979)

We show that optical bistability can occur in a distributed feedback structure with an intensity-dependent refractive index. Analytical expressions for the transmissivity are obtained and a comparison with Fabry-Perot-type devices is presented.
2,19-Dihydroxy-3-oxo-(2α,4α,19α)-24-nor-olean-12-en-28-oic acid monohydrate (2007)

The title triterpenoid compound, C29H44O5·H2O, was isolated from Terminalia triptera. The mol­ecule contains five fused six-membered rings, with three rings in chair, one in an envelope and one in half-chair conformations. The D and E rings are cis-fused, while the other ring junctions are trans-fused. An intra­molecular O—H⋯O hydrogen bond generates an S(5) ring motif. In the crystal structure, the mol­ecules are linked into a three-dimensional network by O—H⋯O hydrogen bonds and a weak C—H⋯O inter­molecular inter­action. The crystal structure is stabilized by intra- and inter­molecular O—H⋯O hydrogen bonds and weak C—H⋯O inter­actions.
Interleukin 12 and Interleukin 4 Control T Cell Adhesion to Endothelial Selectins through Opposite Effects on α1,3-fucosyltransferase VII Gene Expression (1998)

The alpha1,3-fucosyltransferase, FucT-VII, is crucial for the formation of ligands for all three selectins, and its expression regulates the synthesis of these ligands. Short-term polarized T helper (Th)1, but not Th2 or naive CD4(+) T cells, can home to sites of inflammation, but the molecular basis for this difference has remained unclear. Here we show that naive CD4(+) T cells do not express FucT-VII and fail to bind vascular selectins. We also show that when CD4(+) T cells are activated in the presence of the Th1 polarizing cytokine interleukin (IL)-12, levels of FucT-VII mRNA and binding to E- and P-selectin are significantly augmented. In contrast, activation of CD4(+) T cells in the presence of IL-4, a Th2 polarizing cytokine, inhibited FucT-VII expression and binding to vascular selectins. T cell activation upregulated expression of the Core2 transferase, C2GnT, equivalently regardless of the presence or absence of polarizing cytokines. These data indicate that the selective ability of Th1 cells, as opposed to Th2 cells or naive CD4(+) T cells, to recognize vascular selectins and home to sites of inflammation is controlled principally by the expression of a single gene, FucT-VII.
Turbulence Free Ghost Imaging: Experiments and Results (2011)

We present and analyze experiments at ARL that achieve remote turbulence-free ghost imaging that is virtually free from the adverse effects of turbulence distortion. Obscurant penetrating GI experiments are also presented. Recently remote imaging and stand-off detection have been accomplished using ghost imaging (GI) 1 .T hese experiments suggested that ghost imaging might be free from the effects of turbulence distortions 1, 2 .I n this study we report the first experiments that achieve turbulence-free ghost imaging that is virtually free from the adverse effects of turbulence. Single sensor, obscured, Bessel, and compressive GI experiments are also presented. Figure 1. Ghost images of “ARL”: Left: No Turbulence. Right: With Turbulence. Turbulence is induced by instability mechanisms such as mechanical forcing and buoyancy and produce timespace variations in light propagation and photon counts, i.e. optical turbulence. Common optical turbulence power law scaling are based on idealized assumptions of isotropy, homogeneity, and stationarity of the turbulence as formulated by Tatarskii, Kolmogorov, Wolf, Fried, Twiss, and colleagues. In practice and by Navier-Stokes solutions 3 , turbulence in the atmosphere is never stationary and is generally inhomogeneous and anisotropic. Figure 2. Left: Laboratory layout of Turbulence Free ghost imaging experiments. Middle: Real-time imaging of GI experiment turbulence. Right: Classical distorted instantaneous image through turbulence. In our experiments we performed ghost imaging through turbulence caused by heating of the air inducing turbulent motion in the target and reference beam paths. Real-time imaging of the turbulence allows us to investigate more detailed physics in the analysis of turbulence-free ghost imaging and its applications.
Speech recognition using factorial hidden Markov models for separation in the feature space (2006)

This paper proposes an algorithm for the recognition and separation of speech signals in non-stationary noise, such as another speaker. We present a method to combine hidden Markov models (HMMs) trained for the speech and noise into a factorial HMM to model the mixture signal. Robustness is obtained by separating the speech and noise signals in a feature domain, which discards unnecessary information. We use mel-cepstral coefficients (MFCCs) as features, and estimate the distribution of mixture MFCCs from the distributions of the target speech and noise. A decoding algorithm is proposed for finding the state transition paths and estimating gains for the speech and noise from a mixture signal. Simulations were carried out using speech material where two speakers were mixed at various levels, and even for high noise level (9 dB above the speech level), the method produced relatively good (60% word recognition accuracy) results. Audio demonstrations are available at www.cs.tut.fi/˜tuomasv. IndexTerms: speech recognition, speech separation, factorial hidden Markov model.
A new model of autoimmune disease. Experimental autoimmune uveoretinitis induced in mice with two different retinal antigens. (1988)

Experimental autoimmune uveoretinitis (EAU) is an organ-specific, T lymphocyte-mediated autoimmune disease, which serves as a model for several human ocular inflammations of an apparently autoimmune nature. EAU pathology in some rodents and in monkeys can readily be induced by immunization with several different retinal proteins; however, advancing research into the cellular mechanisms of this disease has raised the need for an EAU model in an immunologically and genetically well defined species. We report here the induction of EAU in the mouse, which has hitherto been considered a species refractory to EAU, with two retinal Ag, the retinal soluble Ag and the interphotoreceptor retinoid-binding protein. Although all the mouse strains tested exhibited lymphocyte responses and antibody titers to both retinal Ag, EAU was inducible in only some of the strains, and the uveitogenic responses to retinal soluble Ag and interphotoreceptor retinoid-binding protein appeared to be mutually exclusive. The EAU model in mice was found to differ in several respects from the EAU model in other rodent species. Induction of the disease was achieved with a relatively high dose of Ag and an intensified immunization protocol, and the onset of disease was later, the duration was longer, and the course was less acute. Anterior segment involvement was slight or nonexistent, and damage to the retina and uvea was of a focal rather than of a diffuse nature. Murine EAU appeared to approximate some types of human uveitis more closely than the EAU models described in other rodent species with respect to its pathologic manifestations as well as its more chronic course. The relatively longer duration of the active stage of disease in murine EAU should facilitate therapeutic intervention in established disease, which was not feasible in the more acute models of EAU. The extensive knowledge of the immunologic parameters of the mouse and the availability of genetically defined strains should be of great value in the study of cellular mechanisms and immunogenetics of ocular autoimmune disease.
Fast Spectrogram Inversion Using Multi-Head Convolutional Neural Networks (2018)

We propose the multi-head convolutional neural network (MCNN) for waveform synthesis from spectrograms. Nonlinear interpolation in MCNN is employed with transposed convolution layers in parallel heads. MCNN enables significantly better utilization of modern multi-core processors than commonly used iterative algorithms like Griffin-Lim, and yields very fast (more than 300 × real time) runtime. For training of MCNN, we use a large-scale speech recognition dataset and losses defined on waveforms that are related to perceptual audio quality. We demonstrate that MCNN constitutes a very promising approach for high-quality speech synthesis, without any iterative algorithms or autoregression in computations.
APE: Analyses of Phylogenetics and Evolution in R language (2004)

The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
Retrovirus maturation—an extraordinary structural transformation (2016)

Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.
Salicylate Accumulation Inhibits Growth at Chilling Temperature in Arabidopsis (2004)

The growth of Arabidopsis plants in chilling conditions could be related to their levels of salicylic acid (SA). Plants with the SA hydroxylase NahG transgene grew at similar rates to Col-0 wild types at 23 degrees C, and growth of both genotypes was slowed by transfer to 5 degrees C. However, at 5 degrees C, NahG plants displayed relative growth rates about one-third greater than Col-0, so that by 2 months NahG plants were typically 2.7-fold larger. This resulted primarily from greater cell expansion in NahG rosette leaves. Specific leaf areas and leaf area ratios remained similar in both genotypes. Net assimilation rates were similar in both genotypes at 23 degrees C, but higher in NahG at 5 degrees C. Chlorophyll fluorescence measurements revealed no PSII photodamage in chilled leaves of either genotype. Col-0 shoots at 5 degrees C accumulated SA, particularly in glucosylated form. SA in NahG shoots showed similar tendencies at 5 degrees C, but at greatly depleted levels. Catechol was not detected as a metabolite of the NahG transgene product. We also examined growth and SA levels in SA signaling and metabolism mutants at 5 degrees C. The partially SA-insensitive npr1 mutant displayed growth intermediate between NahG and Col-0, while the SA-deficient eds5 mutant behaved like NahG. In contrast, the cpr1 mutant at 5 degrees C accumulated very high levels of SA and its growth was much more inhibited than wild type. At both temperatures, cpr1 was the only SA-responsive genotype in which oxidative damage (measured as thiobarbituric acid-reactive substances) was significantly different from wild type.
All-fiber filter for efficient dispersion compensation (1991)

A dispersive filter is proposed that is based on the coupling, with a chirped periodic perturbation, of two copropagating waveguide modes that have different group velocities. Numerical calculations show that a nearly constant dispersion can be obtained over the filter bandwidth. Pulse recompression by a factor of 10 or more is possible. The filter could be made with photoinduced refractive-index gratings in optical filters.
Why not treat human cancer with interleukin-1 blockade? (2010)

The clinical successes of targeting angiogenesis provide a basis for trials of interleukin-1 (IL-1) blockade and particularly anti-IL-1beta as an add-on therapy in human metastatic disease. In animal studies for over 20 years, IL-1 has been demonstrated to increase adherence of tumor cells to the endothelium in vitro, and administration of IL-1 to mice increases the number of metastatic colonies and tumor growth. Importantly, reducing endogenous IL-1 activity, particularly IL-1beta, with the naturally occurring IL-1 receptor antagonist (IL-1Ra) reduces both metastasis as well as tumor burden. Inhibition of IL-1 activity prevents in vivo blood vessel formation induced by products released from hypoxic macrophages or vascular endothelial cell growth factor itself. Mice deficient in IL-1beta do not form blood vessels in matrigels embedded with vascular endothelial cell growth factor or containing products of macrophages. Recombinant IL-1Ra (anakinra) has been administered to over 1,000 patients with septic shock resulting in a consistent reduction in all-cause 28-day mortality. Approved for treatment of rheumatoid arthritis, anakinra has a remarkable safety record. Anakinra resulted in decreased blood vessels in the pannus of affected joints in patients with rheumatoid arthritis. Neutralizing monoclonal antibodies to IL-1beta and a soluble receptor to IL-1 are approved for treating chronic inflammatory diseases. Given the availability of three therapeutic agents for limiting IL-1 activity, the safety of blocking IL-1, and the clear benefit of blocking IL-1 activity in animal models of metastasis and angiogenesis, clinical trials of IL-1 blockade should be initiated, particularly as an add-on therapy of patients receiving antiangiogenesis-based therapies.
Reference Input/Output Medium Metric RGB Color Encodings (RIMM/ROMM RGB) (2000)

A new color encoding specification known as Reference Output Medium Metric RGB (ROMM RGB) is defined. This color encoding is intended to be used for storing, interchanging and manipulating images that exist in a rendered image state without imposing the gamut limitations normally associated with device-specific color spaces. ROMM RGB was designed to provide a large enough color gamut to encompass most common output devices, while simultaneously satisfying a number of other important criteria. It is defined in a way that is tightly linked to the ICC profile connection space (PCS) and is suitable for use as an Adobe Photoshop™ working color space. A companion color encoding specification, known as Reference Input Medium Metric RGB (RIMM RGB), is also defined. This encoding can be used to represent images in an unrendered scene image state.
Super-Aromatic Properties of Furan. II. The Friedel—Crafts Reaction (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSuper-Aromatic Properties of Furan. II. The Friedel—Crafts ReactionHenry Gilman and N. O. CallowayCite this: J. Am. Chem. Soc. 1933, 55, 10, 4197–4205Publication Date (Print):October 1, 1933Publication History Published online1 May 2002Published inissue 1 October 1933https://pubs.acs.org/doi/10.1021/ja01337a053https://doi.org/10.1021/ja01337a053research-articleACS PublicationsRequest reuse permissionsArticle Views770Altmetric-Citations40LEARN 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
Transcriptional Regulation of the Muscle Creatine Kinase Gene and Regulated Expression in Transfected Mouse Myoblasts (1986)

The muscle-specific form of creatine kinase (MCK) is induced in differentiating myoblast cultures, and a dramatic increase in mRNA levels precedes and parallels the increase in MCK protein. To study this induction, the complete MCK gene was cloned and characterized. The transcription unit was shown to span 11 kilobases and to contain seven introns. The splice junctions were identified and shown to conform to the appropriate consensus sequences. Close homology with branchpoint consensuses was found upstream of the 3' splice sites in six of seven cases. Transcriptional regulation of the gene in differentiating myoblast cultures was demonstrated by nuclear run-on experiments; increases in transcription accounted for a major part of the increased mRNA levels. Regulated expression of a transfected MCK gene containing the entire transcription unit with 3.3 kilobases of 5'-flanking sequence was also demonstrated during differentiation of the MM14 mouse myoblast cell line. The MCK 5'-flanking region was sufficient to confer transcriptional regulation to a heterologous structural gene, since chloramphenicol acetyl transferase activity was induced during differentiation of cultures transfected with an MCK-chloramphenicol acetyl transferase fusion construct. Examination of the DNA sequence immediately upstream of the transcription start site revealed a 17-nucleotide element which occurred three times. Comparisons with other muscle-specific genes which are also transcriptionally regulated during myogenesis revealed upstream homologies in the alpha-actin and myosin heavy chain genes, but not in the myosin light-chain genes, with the regions containing these repeats. We suggest that coordinate control of a subset of muscle genes may occur via recognition of these common sequences.
Kinetic analysis of cytokine‐mediated receptor assembly using engineered FC heterodimers (2013)

A method for analyzing ligand-receptor binding kinetics is described, which is based on an engineered FC domain (FChk) that forms a covalent heterodimer. To validate the system, the type I IFN receptors (IFNAR1 and IFNAR2) were expressed as IFNAR1-FChk, IFNAR2-FCkh, and IFNAR1/IFNAR2-FChk fusion proteins. Surface plasmon resonance (SPR) analysis of binary IFNα2a/IFNAR interactions confirmed prior affinity measurements, while the affinity of the IFNα2a/IFNAR1/IFNAR2-FChk interaction reproduced the affinity of IFNα2a binding to living cells. In cellular assays, IFNAR1/IFNAR2-FChk potently neutralized IFNα2a bioactivity with an inhibitory concentration equivalent to the KD measured by SPR. These studies suggest that FChk provides a simple reagent to evaluate the binding kinetics of multiple ligand-receptor signaling systems that control cell growth, development, and immunity.
Animal models of rheumatoid arthritis (2009)

Animal models have been used extensively in studies of rheumatoid arthritis pathogenesis. Despite the inherent limitations of all animal models, several rodent models have significantly progressed our understanding of the fundamental mechanisms underpinning rheumatoid arthritis and contributed to several current major advances in treatment. These models include the induced arthritis models such as collagen-induced arthritis, collagen-antibody-induced arthritis, zymosan-induced arthritis, and the methylated BSA model, and the genetically manipulated or spontaneous arthritis models such as the TNF-alpha-transgenic mouse, K/BxN mouse, and the Skg mouse. Here, we describe these animal models and discuss their advantages and limitations.
Towards Text Communication Services (1983)

Standards are important for the widespread and economical introduction of many text and image-based communication services. The role of standards in the policies and developments of the French Post Telecommunication and Telediffusion Administration for a variety of telematic services is discussed.
RETRIEVABLE CLOSED CELL INTRACRANIAL STENT FOR FOREIGN BODY AND CLOT REMOVAL (2008)

These in vitro and in vivo studies suggest the potential use of retrievable stents for the removal of foreign bodies or clot from the intracranial circulation.
Improving identifier informativeness using part of speech information (2011)

Recent software development tools have exploited the mining of natural language information found within software and its supporting documentation. To make the most of this information, researchers have drawn upon the work of the natural language processing community for tools and techniques. One such tool provides part-of-speech information, which finds application in improving the searching of software repositories and extracting domain information found in identifiers.
Hillocks, Pits, and Etch Rate in Germanium Crystals (1957)

Symmetric faceted etch hillocks have been observed on certain germanium surface orientations exposed to an H2O2–HF (Superoxol) etchant. Considerations of surface curvature and etch rate lead to the conclusion that the faces bounding the hillocks must be at saddle points on an etch rate vs orientation surface. A measurement of etch rate throughout the stereographic triangle has supported this conclusion. The formation of dislocation pits and hillocks is discussed in terms of the variation of surface etch rate with orientation.