gebhart/patrepeval huggingface dataset:
A new metaconverse and outer region for finite-blocklength MACs (2013)

An outer rate region for the Discrete Memoryless Multiple Access Channel is given, and is shown to coincide with a recently derived inner rate region within a o(1/√n) term-except in the vicinity of the corner points of the Ahlswede-Liao pentagonal region, where the gap is O(1/√n). The derivation is based on a new metaconverse under the maximum error probability criterion and on strong large deviations for Neyman-Pearson tests.
Mutational Analysis of the Signal-Sensing Domain of ResE Histidine Kinase fromBacillus subtilis (2004)

The Bacillus subtilis ResD-ResE two-component regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extracytoplasmic loop. It also has a cytoplasmic PAS subdomain between the HAMP linker and C-terminal kinase domain. In an attempt to identify the signal-sensing subdomain of ResE, a series of deletions and amino acid substitutions were generated in the N-terminal domain. The results indicated that cytoplasmic ResE lacking the transmembrane segments and the extracytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. This activity was eliminated by the deletion of the PAS subdomain, demonstrating that the PAS subdomain participates in signal reception. The study also raised the possibility that the extracytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism in B. subtilis.
CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins (2001)

A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. We have identified a conserved eukaryotic protein, human CHMP1, which is strongly implicated in multivesicular body formation. Immunocytochemistry and biochemical fractionation localize CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, overexpression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homolog of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes. Yeast Chm1p belongs to a structurally-related, but rather divergent family of proteins, including Vps24p and Snf7p and three novel proteins, Chm2p, Chm5p and Chm6p, which are all essential for multivesicular body sorting. These observations identify the conserved CHMP/Chmp family as a set of proteins fundamental to understanding multivesicular body sorting in eukaryotic organisms.
Reversible substrate binding at copper centers in neutral copper(i) carbene complexes derived from bis(3-tert-butylimidazole-2-ylidene)methane (2009)

Deprotonation of the CH2-bridged bis-imidazolium salt [H2(BIM(tBu))]Br2 followed by reaction with CuBr afforded polymeric [(BIM(tBu))2(CuBr)2]n (3), where BIM(tBu) = bis(3-tert-butylimidazole-2-ylidene)methane. In the solid state, compound 3 is an organometallic polymer with an unusual (-L-Cu-(micro-Br)2-Cu-L-)n type of bonding. The reaction of 3 with nitrogen bases N-tert-butylimidazole or piperidine splits the polymer and afforded the corresponding mononuclear amine adducts [(BIM(tBu))2(CuBr)2(amine)] (6 and 7, respectively). Their molecular structures revealed a unique bonding pattern, which has no precedents in copper-NHC coordination chemistry. The amine binding energies in 6 or 7 of 0.7-7.7 kcal mol(-1), calculated by DFT methods, are consistent with an experimentally observed ligand exchange in solution, fast on the NMR time scale.
75-GHz f/sub T/ SiGe-base heterojunction bipolar transistors (1990)

The fabrication of silicon heterojunction bipolar transistors which have a record unity-current-gain cutoff frequency (f/sub T/) of 75 GHz for a collector-base bias of 1 V, an intrinsic base sheet resistance (R/sub bi/) of 17 k Omega / Square Operator , and an emitter width of 0.9 mu m is discussed. This performance level, which represents an increase by almost a factor of 2 in the speed of a Si bipolar transistor, was achieved in a poly-emitter bipolar process by using SiGe for the base material. The germanium was graded in the 45-nm base to create a drift field of approximately 20 kV/cm, resulting in an intrinsic transit time of only 1.9 ps.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors (2007)

PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP {4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid} as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.
LABORATORY INVESTIGATIONS IN SUPPORT OF FLUID-BED FLUORIDE VOLATILITY PROCESSES. PART II. THE PROPERTIES OF PLUTONIUM HEXAFLUORIDE (1963)

All of the properties of plutonium hexfluoride reported up to May 1983 are summarized, andd pentinent data are presented in detail. Included are the preparation of plutonium hexafluoride, physical properties, absorption spectra, chemical reactions, decomposition of plutonium hexafluoride by radiation and heat, the corrosion of materials of construction by plutonium hexafluoride, and a summary of the biological and radiological hazards from plutonium hexafluoride. An expanded vapor pressure table is appended. 122 references are included. (auth)
A New Recovery Mechanism in Superscalar Microprocessors by Recovering Critical Misprediction (2011)

Current trends in modern out-of-order processors involve implementing deeper pipelines and a large instruction window to achieve high performance, which lead to the penalty of the branch misprediction recovery being a critical factor in overall processor performance. Multi path execution is proposed to reduce this penalty by executing both paths following a branch, simultaneously. However, there are some drawbacks in this mechanism, such as design complexity caused by processing both paths after a branch and performance degradation due to hardware resource competition between two paths. In this paper, we propose a new recovery mechanism, called Recovery Critical Misprediction (RCM), to reduce the penalty of branch misprediction recovery. The mechanism uses a small trace cache to save the decoded instructions from the alternative path following a branch. Then, during the subsequent predictions, the trace cache is accessed. If there is a hit, the processor forks the second path of this branch at the renamed stage so that the design complexity in the fetch stage and decode stage is alleviated. The most contribution of this paper is that our proposed mechanism employs critical path prediction to identify the branches that will be most harmful if mispredicted. Only the critical branch can save its alternative path into the trace cache, which not only increases the usefulness of a limited size of trace cache but also avoids the performance degradation caused by the forked non-critical branch. Experimental results employing SPECint 2000 benchmark show that a processor with our proposed RCM improves IPC value by 10.05% compared with a conventional processor.
Approximate message-passing inference algorithm (2007)

In a recent result, Weitz (D. Weitz, 2006) established equivalence between the marginal distribution of a node, say <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</i> , in any binary pair-wise Markov random field (MRF), say G, with the marginal distribution of the root node in the self-avoid walk tree of the G starting at v. Analogous result for max-marginal distribution holds for the reason that addition and multiplication commute in the same way as addition and maximum. This remarkable connection suggests a message-passing algorithm for computing exact marginal and max-marginal in any binary MRF <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</i> . In this paper, we exploit this property along with appropriate graph partitioning scheme to design approximate message passing algorithms for computing max-marginal of nodes or maximum a-posteriori assignment (MAP) in a binary MRF G. Our algorithm can provide provably arbitrarily small error for a large class of graphs including planar graphs. Our algorithms are linear in number of nodes G with constant dependent on the approximation error. For precise evaluation of computation cost of algorithm, we obtain a novel tight characterization of the size of self-avoiding walk tree for any connected graph as a function of number of edges and nodes.
McGraw-Hill encyclopedia of astronomy (1983)

This edition includes 250 alphabetically arranged articles on astronomy and astrophysics-most selected from the McGraw-Hill Encyclopedia of Science and Technology, Seventh Edition, with 30 written by leading authorities especially for this volume-and more than 400 illustrations, including 14 color plates. It covers the latest data, advances, discoveries, models, theories, and scientific methods, and provides quick access to every subject of classical and modern astronomy. An indispensable tool for scientists, students, librarians, science writers, serious amateur astronomers, and all others who need reliable, accurate, detailed, and up-to-date technical information on a wide variety of astronomical topics in a readily accessible format.
Detection of epithelial messenger RNA in the plasma of breast cancer patients is associated with poor prognosis tumor characteristics. (2001)

We conclude that epithelial tumor RNA is detectable in plasma from breast cancer patients and that this finding is associated with a probable poor prognosis and circulating tumor cells.
Nanometer size diesel exhaust particles are selectively toxic to dopaminergic neurons: the role of microglia, phagocytosis, and NADPH oxidase (2004)

The contributing role of environmental factors to the development of Parkinson's disease has become increasingly evident. We report that mesencephalic neuron-glia cultures treated with diesel exhaust particles (DEP; 0.22 microM) (5-50 microg/ml) resulted in a dose-dependent decrease in dopaminergic (DA) neurons, as determined by DA-uptake assay and tyrosine-hydroxylase immunocytochemistry (ICC). The selective toxicity of DEP for DA neurons was demonstrated by the lack of DEP effect on both GABA uptake and Neu-N immunoreactive cell number. The critical role of microglia was demonstrated by the failure of neuron-enriched cultures to exhibit DEP-induced DA neurotoxicity, where DEP-induced DA neuron death was reinstated with the addition of microglia to neuron-enriched cultures. OX-42 ICC staining of DEP treated neuron-glia cultures revealed changes in microglia morphology indicative of activation. Intracellular reactive oxygen species and superoxide were produced from enriched-microglia cultures in response to DEP. Neuron-glia cultures from NADPH oxidase deficient (PHOX-/-) mice were insensitive to DEP neurotoxicity when compared with control mice (PHOX+/+). Cytochalasin D inhibited DEP-induced superoxide production in enriched-microglia cultures, implying that DEP must be phagocytized by microglia to produce superoxide. Together, these in vitro data indicate that DEP selectively damages DA neurons through the phagocytic activation of microglial NADPH oxidase and consequent oxidative insult.
Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions (2002)

Regulation of gene expression by premature termination of transcription, or transcription attenuation, is a common regulatory strategy in bacteria. Various mechanisms of regulating transcription termination have been uncovered, each can be placed in either of two broad categories of termination events. Many mechanisms involve choosing between two alternative hairpin structures in an RNA transcript, with the decision dependent on interactions between ribosome and transcript, tRNA and transcript, or protein and transcript. In other examples, modification of the transcription elongation complex is the crucial event. This article will describe and compare several of these regulatory strategies, and will cite specific examples to illustrate the different mechanisms employed.
Growth factors: the wound healing therapy of the future? (2003)

'Growth factors' is an umbrella term used to describe a variety of chemical messengers found in a wide range of tissues, which have a number of functions including the regulation of cell and tissue growth and development. Several growth factors have been proposed as ideal agents to promote wound healing. This review discusses their functions and how they can be applied in the management of chronic wounds.
Canonical Wnt/β-catenin Signaling (2004)

This animation provides an interactive presentation of the Wnt signaling pathway as it may occur in multiple cell types. This animation would be useful in teaching developmental biology, immunology, and cell signaling courses. Activation of Wnt pathways can modulate cell proliferation, cell survival, cell behavior, and cell fate. In the basal, unstimulated state in the absence of ligand, there is a constitutively active kinase, which phosphorylates target proteins, resulting in their degradation. Thus, the presence of the ligand Wnt inactivates the kinase allowing accumulation of beta-catenin, which then translocates to the nucleus and acts as a transcriptional regulator.
An improved method for in vitro perfusion of human skin (1985)

We have developed a procedure for establishing a long-living supravital skin preparation. Our model has made in vitro perfusion of human cutis, fatty tissue and lymph nodes possible. We describe the method of preparation, the technical construction and preliminary results of our experiments.
Alteration of glycosylation renders HIV sensitive to inactivation by normal human serum (1997)

Retroviruses from various mammalian species, excluding humans, are effectively inactivated in normal human serum (NHS). Recent studies have shown that NHS inactivation of retroviruses occurs through natural Ab recognition of a terminal glycosidic moiety on the viral envelope that is acquired during replication in the host cell. This carbohydrate structure (the alpha-galactosyl epitope) is expressed on the cells of most mammals, with the exception of humans and other Old World primates. In this study, NHS sensitivity of HIV was assessed following viral propagation in human cells that were manipulated to express the alpha-galactosyl epitope. HUT-78 cells were transduced with an exogenous alpha1-3-galactosyl transferase gene, which codes for the terminal glycosyl transferase responsible for generation of the alpha-galactosyl epitope. The transduced HUT-78 cells expressed high levels of the alpha-galactosyl epitope on their membrane surface, rendering them sensitive to killing in NHS. Similarly, HIV passaged through these cells acquired the alpha-galactosyl epitope in association with the envelope glycoprotein gp120 and was also effectively inactivated in NHS. Viral inactivation was abolished by the addition of a synthetic disaccharide that contains the alpha-galactosyl epitope, indicating that virolysis is mediated by anti-alpha-galactosyl natural Ab. These results demonstrate that, like other retroviruses bearing the alpha-galactosyl epitope, HIV modified to express this epitope is inactivated in NHS. Furthermore, these data suggest that expression of the alpha-galactosyl epitope on the surface of viruses may have implications in the interspecies transmission of such viruses to humans.
Nitric Oxide–Related Brain Damage in Acute Ischemic Stroke (2000)

Our clinical findings suggest an important role of NO generation in acute ischemic stroke. Increased NO-m in CSF are associated with a greater brain injury and early neurological deterioration.
Nitric Oxide Synthase Inhibitors as Antidepressants (2010)

Affective and anxiety disorders are widely distributed disorders with severe social and economic effects. Evidence is emphatic that effective treatment helps to restore function and quality of life. Due to the action of most modern antidepressant drugs, serotonergic mechanisms have traditionally been suggested to play major roles in the pathophysiology of mood and stress-related disorders. However, a few clinical and several pre-clinical studies, strongly suggest involvement of the nitric oxide (NO) signaling pathway in these disorders. Moreover, several of the conventional neurotransmitters, including serotonin, glutamate and GABA, are intimately regulated by NO, and distinct classes of antidepressants have been found to modulate the hippocampal NO level in vivo. The NO system is therefore a potential target for antidepressant and anxiolytic drug action in acute therapy as well as in prophylaxis. This paper reviews the effect of drugs modulating NO synthesis in anxiety and depression.
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution‐state structure of the nucleocapsid protein from HIV‐1 (1992)

All retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys-1His array (CCHC = C-X2-C-X4-H-X4-C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc-binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc-edge extended X-ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus-bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840-847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys-1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV-1 NC protein and have determined its three-dimensional solution-state structure. The CCHC arrays of HIV-1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV-1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid-binding results provide a basis for the rational design of new NC-targeted antiviral agents and vaccines for the control of AIDS.
Fast Intra Prediction Mode Decision Algorithm for HEVC (2013)

This paper proposes a novel fast intra-prediction algorithm that exploits the Sobel operator to replace the Hadamard transform used in the Rough Mode Decision (RMD) process of intra prediction in High Efficiency Video Coding (HEVC). First, the Sobel operator is used to calculate the vector direction of each pixel. A judgment is then made on which prediction mode the vector belongs to, and a histogram is applied in the scheme to generate the statistics of prediction modes for each prediction unit. Finally, the prediction mode candidates are placed in the candidate list for the rate-distortion optimization process. Experimental results show that our proposed algorithm for RMD significantly reduces the complexity of the encoder with an acceptable degradation of quality and BD-rate compared with HM7.0. DOI:  http://dx.doi.org/10.11591/telkomnika.v11i10.3396
Quad-phase correlation filters for pattern recognition (1989)

A quad-phase-only filter (QPOF) is introduced. It is shown that the QPOF can have improved correlation response and signal-to-noise ratio with respect to the Hartley binary phase-only filter for some objects.