gebhart/patrepeval huggingface dataset:
Center-surround divergence of feature statistics for salient object detection (2011)

In this paper, we introduce a new method to detect salient objects in images. The approach is based on the standard structure of cognitive visual attention models, but realizes the computation of saliency in each feature dimension in an information-theoretic way. The method allows a consistent computation of all feature channels and a well-founded fusion of these channels to a saliency map. Our framework enables the computation of arbitrarily scaled features and local center-surround pairs in an efficient manner. We show that our approach outperforms eight state-of-the-art saliency detectors in terms of precision and recall.
Topoisomerase levels determine chemotherapy response in vitro and in vivo (2008)

Topoisomerase poisons are chemotherapeutic agents that are used extensively for treating human malignancies. These drugs can be highly effective, yet tumors are frequently refractory to treatment or become resistant upon tumor relapse. Using a pool-based RNAi screening approach and a well characterized mouse model of lymphoma, we explored the genetic basis for heterogeneous responses to topoisomerase poisons in vitro and in vivo. These experiments identified Top2A expression levels as major determinants of response to the topoisomerase 2 poison doxorubicin and showed that suppression of Top2A produces resistance to doxorubicin in vitro and in vivo. Analogously, using a targeted RNAi approach, we demonstrated that suppression of Top1 produces resistance to the topoisomerase 1 poison camptothecin yet hypersensitizes cancer cells to doxorubicin. Importantly, lymphomas relapsing after treatment display spontaneous changes in topoisomerase levels as predicted by in vitro gene knockdown studies. These results highlight the utility of pooled shRNA screens for identifying genetic determinants of chemotherapy response and suggest strategies for improving the effectiveness of topoisomerase poisons in the clinic.
Involvement of the brain type of ryanodine receptor in T‐cell proliferation (1994)

Cloning and sequence analysis of cDNA showed that the brain type of ryanodine receptor (RYR) is expressed in human Jurkat T-lymphocyte cells. Fura-2 measurements revealed that the RYR in T-cells functions as a ryanodine-sensitive, caffeine-insensitive Ca2+ release channel. Furthermore, ryanodine stimulated proliferation and altered the growth pattern of cultured human T-cells when added together with FK506.
Magnetic Ceramics: I, General Methods of Magnetic Ferrite Preparation (1955)

Various methods of preparing the technically important ferrospinels are discussed; particular attention is given to the reactivity and homogeneity of the final mixture. The reactivity and intimacy of mixing of the initial components may be improved by the use of chemical methods of comminution and mixing, viz., thermal decomposition of the mixed chemicals, chemical precipitation of the components, or ignition of the components in a fine state of division. The use of controlled partial pressures of oxygen (CO 2 ‐CO mixtures) for the preparation of magnetite and manganese ferrite is discussed. The feasibility of the application of these methods on a commercial scale is outlined.
The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals (2004)

The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH(2)) has been determined to 2.35 A resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.
Stock price pattern matching system-dynamic programming neural networks approach (2003)

The dynamic programming neural network (DNN). DNN is based on the integration of the neural and dynamic programming matching method (DP-matching). In order to find patterns similar to a specified pattern in the database, two problems must be solved. One is a nonlinear time elasticity for the patterns. This nonlinearity is normalized by DP-matching. The second is a bias which was generated by differences in names and time span. This bias is eliminated by a stock price normalization method and a neural network. A stock price pattern matching system using the DNN approach was developed on an NEC EWS4800 workstation. This system has a graphical user interface on an X-Window system. A subjective evaluation was conducted. The stock price patterns which were classified by DNN were evaluated by three chartists (human experts). High correlation was found between the similarity by DNN and the evaluation by chartists. The proposed DNN system is able to match patterns, which chartists judge as similar patterns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PCV3-associated disease in the United States swine herd (2019)

Porcine circovirus-associated disease encompasses multiple disease syndromes including porcine circovirus 2 systemic diseases, reproductive failure, and porcine dermatitis and nephropathy syndrome. Until recently, porcine circovirus 2 was the only species associated with the porcine circovirus-associated disease. In this report, diagnostic investigations of thirty-six field cases submitted from multiple production systems, numerous sites and varied geographic locations demonstrated porcine circovirus 3 within lesions by in situ hybridization including fetuses with myocarditis, weak-born neonatal piglets with encephalitis and myocarditis, from cases of porcine dermatitis and nephropathy syndrome, and in weaned pigs with systemic periarteritis. Porcine circovirus 3 was detected by PCR in numerous fetuses and perinatal piglets at high viral loads (trillions of genome copies per mL of tissue homogenate). Samples from all cases in this study were assayed and found negative for porcine circovirus 2 by PCR. Metagenomic sequencing was performed on a subset of reproductive cases, consisting of sixteen fetuses/fetal sample pools. PCV3 was identified in all pools and the only virus identified in fourteen pools. Based on these data, porcine circovirus 3 is considered a putative cause of reproductive failure, encephalitis and myocarditis in perinatal piglets, porcine dermatitis and nephropathy syndrome, and periarteritis in swine in the United States.
Application of Solid Ash Based Catalysts in Heterogeneous Catalysis (2008)

Solid wastes, fly ash, and bottom ash are generated from coal and biomass combustion. Fly ash is mainly composed of various metal oxides and possesses higher thermal stability. Utilization of fly ash for other industrial applications provides a cost-effective and environmentally friendly way of recycling this solid waste, significantly reducing its environmental effects. On the one hand, due to the higher stability of its major component, aluminosilicates, fly ash could be employed as catalyst support by impregnation of other active components for various reactions. On the other hand, other chemical compounds in fly ash such as Fe2O3 could also provide an active component making fly ash a catalyst for some reactions. In this paper, physicochemical properties of fly ash and its applications for heterogeneous catalysis as a catalyst support or catalyst in a variety of catalytic reactions were reviewed. Fly-ash-supported catalysts have shown good catalytic activities for H2 production, deSO(x), deNO(x), hydrocarbon oxidation,and hydrocracking, which are comparable to commercially used catalysts. As a catalyst itself, fly ash can also be effective for gas-phase oxidation of volatile organic compounds, aqueous-phase oxidation of organics, solid plastic pyrolysis, and solvent-free organic synthesis.
Neisseria meningitidisserogroup B: laboratory correlates of protection (2002)

Meningococcal disease in the Western countries is frequently caused by Neisseria meningitidis serogroup B. Major efforts have been made to develop a safe and efficacious vaccine against this serogroup which is suitable for use in infants and young children. To assess the quality of the immune response after vaccination with candidate vaccines, laboratory correlates of protection are needed. For serogroups A and C, serum bactericidal activity (SBA) is a well established predictor for protection, but for serogroup B other mechanisms besides SBA may also be involved in conferring protection from disease. Several laboratory methods for identification and evaluation of the immunogenicity of possible vaccine antigens are described in this review.
DNA Polyfluorophores for Real‐Time Multicolor Tracking of Dynamic Biological Systems (2012)

Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.
Ecto-Nucleotidases and Nucleoside Transporters Mediate Activation of Adenosine Receptors on Hippocampal Mossy Fibers by P2X7Receptor Agonist 2′-3′-O-(4-Benzoylbenzoyl)-ATP (2004)

The ionotropic and cytolytic P2X7 receptor is typically found on immune cells, where it is involved in the release of cytokines. Recently, P2X7 receptors were reported to be localized to presynaptic nerve terminals and to modulate transmitter release. In the present study, we reassessed this unexpected role of P2X7 receptors at hippocampal mossy fiber-CA3 synapses. In agreement with previous findings, the widely used P2X7 agonist 2'-3'-O-(4-benzoylbenzoyl)-adenosine-5'-triphosphate (BzATP) clearly depressed field potentials (fEPSPs); however, no evidence for an involvement of P2X7 receptors could be obtained. First, depression of fEPSPs by BzATP was unchanged in P2X7-/- mice. Second, experiments using P2X7-/- mice, immunohistochemistry, and electron microscopy showed that the antigen detected by frequently used P2X7 antibodies is not compatible with a plasmalemmal P2X7 receptor. Third, BzATP did not alter Ca2+ levels in synaptic terminals. In contrast, the depression of fEPSPs by BzATP was fully blocked by adenosine (A1) receptor antagonists. Furthermore, the application of BzATP also activated postsynaptic A1 receptor-coupled K+ channels. This effect of BzATP was mimicked by ATP and adenosine and was completely prevented by enzymes specifically degrading adenosine. Activation of A1-coupled K+ channels by BzATP was dependent on ecto-nucleotidases, extracellular enzymes that convert ATP to adenosine. Moreover, the opening of A1-coupled K+ channels by BzATP was dependent on nucleoside transporters. Taken together, our results indicate that BzATP is extracellularly catabolized to Bz-adenosine and subsequently hetero-exchanged for intracellular adenosine and then depresses mossy fiber fEPSPs through presynaptic A1 receptors rather than through P2X7 receptors. Thus, the present study casts doubts on the neuronal localization of P2X7 receptors in rodent hippocampus.
The Role of the Ventral Medial Prefrontal Cortex in Social Decision Making (2009)

Convergent evidence has revealed that the ventromedial prefrontal cortex (VMPFC) is important for social decision making; however, its exact function is still under debate. Studying behavioral performance of patients with VMPFC lesions is one important way of learning about the role of VMPFC in
The Synthesis of N-Aryl-5(S)-aminomethyl-2-oxazolidinone Antibacterials and Derivatives in One Step from Aryl Carbamates (2003)

Since 1993, a significant process research and development effort directed towards the large-scale synthesis of oxazolidinone antibacterial agents has been ongoing in both Early Chemical Process Research and Development, and Chemical Process Research and Development at Pharmacia. This work has led to the successful development of the current commercial process to produce Zyvox (linezolid), recently approved by the FDA as an antibacterial. While this synthesis is appropriate for the preparation of linezolid in particular, a more convergent and versatile synthesis was developed for the rapid preparation of numerous other oxazolidinone analogues. Toward this end, economical methods for the large-scale preparation of N-[(2S)-2-(acetyloxy)-3-chloropropyl]acetamide 3 and tert-butyl [(2S)-3-chloro-2-hydroxypropyl]carbamate 27 from commercially available (S)-epichlorohydrin via the common intermediate (2S)-1-amino-3-chloro-2-propanol hydrochloride 2a were developed. Also, general methods for coupling these reagents with N-aryl carbamates to give N-aryl-5(S)-aminomethyl-2-oxazolidinone derivatives in one step were developed. These reagents and procedures have proven widely applicable in the preparation of a diverse array of oxazolidinone analogues such as 23 and 28 in both process and medicinal chemistry research.
Unnatural Amino Acid Incorporation into Virus-Like Particles (2008)

Virus-like particles composed of hepatitis B virus (HBV) or bacteriophage Qbeta capsid proteins have been labeled with azide- or alkyne-containing unnatural amino acids by expression in a methionine auxotrophic strain of E. coli. The substitution does not affect the ability of the particles to self-assemble into icosahedral structures indistinguishable from native forms. The azide and alkyne groups were addressed by Cu(I)-catalyzed [3 + 2] cycloaddition: HBV particles were decomposed by the formation of more than 120 triazole linkages per capsid in a location-dependent manner, whereas Qbeta suffered no such instability. The marriage of these well-known techniques of sense-codon reassignment and bioorthogonal chemical coupling provides the capability to construct polyvalent particles displaying a wide variety of functional groups with near-perfect control of spacing.
Prolongation of Scrapie Incubation Period by an Injection of Dextran Sulphate 500 within the Month Before or After Infection (1986)

A single intraperitoneal injection of 250 micrograms dextran sulphate 500 (DS500) reduced the susceptibility of mice to scrapie given by the same route. A lower dose (25 micrograms) was less effective but still produced significant incubation period lengthening, while a high dose (2.5 mg) further increased the degree of prolongation. This reduced susceptibility occurred with DS500 administered up to at least 4 weeks prior to intraperitoneal scrapie inoculation and up to at least 2 weeks after scrapie inoculation. A reduced average effect, but more variable between mice, was obtained with DS500 given 1 month or 2 months after scrapie. The effective scrapie titre was reduced by 90% when DS500 was injected either 72 h before or 7 h after ME7 scrapie. Using a relatively lower but normally still fatal dose of the 22A strain of scrapie approximately 50% of the treated mice survived. The effective 90% loss of titre was consistent with either of these strains of scrapie in 11 different inbred strains of mice (BALB/c, BSC, BRVR, C3H, C57BL, IM, LM, MM, RIII, VL and VM). No significant increase in the prolongation effect was obtained using multiple DS500 doses in two different time combinations. DS500 causes long-term interference in both the early processing and the replication of scrapie agent, unlike those immunomodulators which increase susceptibility.
Mediator generation and signaling events in alveolar epithelial cells attacked byS. aureusα-toxin (2002)

Staphylococcus aureus alpha-toxin is a pore-forming bacterial exotoxin that has been implicated as a significant virulence factor in human staphylococcal diseases. In primary cultures of rat pneumocyte type II cells and the human A549 alveolar epithelial cell line, purified alpha-toxin provoked rapid-onset phosphatidylinositol (PtdIns) hydrolysis as well as liberation of nitric oxide and the prostanoids PGE(2), PGI(2), and thromboxane A(2). In addition, sustained upregulation of proinflammatory interleukin (IL)-8 mRNA expression and protein secretion occurred. "Priming" with low-dose IL-1beta markedly enhanced the IL-8 response to alpha-toxin, which was then accompanied by IL-6 appearance. The cytokine response was blocked by the intracellular Ca(2+)-chelating reagent 1,2-bis(2-aminophenoxy)-ethane-N,N,N',N'-tetraacetic acid, the protein kinase C inhibitor bis-indolyl maleimide I, as well as two independent inhibitors of nuclear factor-kappaB activation, pyrrolidine dithiocarbamate and caffeic acid phenethyl ester. We conclude that alveolar epithelial cells are highly reactive target cells of staphylococcal alpha-toxin. alpha-Toxin pore-associated transmembrane Ca(2+) flux and PtdIns hydrolysis-related signaling with downstream activation of protein kinase C and nuclear translocation of nuclear factor-kappaB are suggested to represent important underlying mechanisms. Such reactivity of the alveolar epithelial cells may be relevant for pathogenic sequelae in staphylococcal lung disease.
How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA (2010)

CCA-adding enzymes [ATP(CTP):tRNA nucleotidyltransferases] add CCA onto the 3' end of transfer RNA (tRNA) precursors without using a nucleic acid template. Although the mechanism by which cytosine (C) is selected at position 75 of tRNA has been established, the mechanism by which adenine (A) is selected at position 76 remains elusive. Here, we report five cocrystal structures of the enzyme complexed with both a tRNA mimic and nucleoside triphosphates under catalytically active conditions. These structures suggest that adenosine 5'-monophosphate is incorporated onto the A76 position of the tRNA via a carboxylate-assisted, one-metal-ion mechanism with aspartate 110 functioning as a general base. The discrimination against incorporation of cytidine 5'-triphosphate (CTP) at position 76 arises from improper placement of the α phosphate of the incoming CTP, which results from the interaction of C with arginine 224 and prevents the nucleophilic attack by the 3' hydroxyl group of cytidine75.
B- and T-lymphocyte responses to an immunodominant epitope of human immunodeficiency virus (1988)

Using synthetic peptides, we characterized the B-lymphocyte (antibody) and T-lymphocyte (proliferation) responses to an immunodominant epitope of human immunodeficiency virus type 1 (HIV-1) located near the amino-terminal end of the transmembrane glycoprotein (env amino acids 598 to 609). Both immunoglobulin M (IgM) and IgG antibodies against this epitope appeared early after primary infection with HIV-1. In an animal model, the IgG response to a synthetic peptide derived from this sequence was T-helper-cell dependent, whereas the IgM response was T-cell independent. In addition, antibody generated by immunization with this peptide had HIV-1-neutralizing activity. Greater than 99% (201 of 203) of patients infected with HIV-1 generated antibody to this peptide in vivo; however, only 24% (7 of 29) had T cells that proliferated in response to this peptide in vitro. These observations suggest that different HIV-1 gp41 epitopes elicit B-cell and T-cell immune responses.
Effects on the mitosis of normal and tumor cells induced by light treatment of different wavelengths (1999)

Dependent upon the irradiation parameter, light of a defined wavelength does affect the mitotic rate of both normal as well as tumor cells. It could be hypothesized that the action spectra of the cellular response indicate the participation of endogenous porphyrins and cytochromes as primary photoreceptors. Taking into account all light induced processes, the term biomodulation should preferably be used.
Transactivation of Sphingosine-1–Phosphate Receptors by FcεRI Triggering Is Required for Normal Mast Cell Degranulation and Chemotaxis (2004)

Mast cells secrete various substances that initiate and perpetuate allergic responses. Cross-linking of the high-affinity receptor for IgE (FcepsilonRI) in RBL-2H3 and bone marrow-derived mast cells activates sphingosine kinase (SphK), which leads to generation and secretion of the potent sphingolipid mediator, sphingosine-1-phosphate (S1P). In turn, S1P activates its receptors S1P1 and S1P2 that are present in mast cells. Moreover, inhibition of SphK blocks FcepsilonRI-mediated internalization of these receptors and markedly reduces degranulation and chemotaxis. Although transactivation of S1P1 and Gi signaling are important for cytoskeletal rearrangements and migration of mast cells toward antigen, they are dispensable for FcepsilonRI-triggered degranulation. However, S1P2, whose expression is up-regulated by FcepsilonRI cross-linking, was required for degranulation and inhibited migration toward antigen. Together, our results suggest that activation of SphKs and consequently S1PRs by FcepsilonRI triggering plays a crucial role in mast cell functions and might be involved in the movement of mast cells to sites of inflammation.
The Distribution of the Matricellular Protein Thrombospondin 2 in Tissues of Embryonic and Adult Mice (1998)

Mice that lack the matricellular protein thrombospondin 2 (TSP2) develop a pleiotropic phenotype characterized by morphological changes in connective tissues, an increase in vascular density, and a propensity for bleeding. Furthermore, dermal cells derived from TSP2-null mice display adhesion defects, a finding that implicates TSP2 in cell-matrix interactions. To gain a better understanding of the participation of TSP2 in the development and maturation of the mouse, we examined its distribution in embryonic and adult tissues. Special attention was paid to the presence of TSP2 in collagen fibers, because collagen fibrils in the TSP2-null mouse appear to be irregular in size and contour by electron microscopy. Immunohistochemical analysis of Day 15 and Day 18 embryos revealed TSP2 in areas of chondrogenesis, osteogenesis, and vasculogenesis, and in dermal and other connective tissue-forming cells. Distinctly different patterns of deposition of TSP2 were observed in areas of developing cartilage and bone at Days 15 and 18 of embryonic development. A survey of adult tissues revealed TSP2 in dermal fibroblasts, articular chondrocytes, Purkinje cells in the cerebellum, Leidig cells in the testis, and in the adrenal cortex. Dermal fibroblasts were also shown to synthesize TSP2 in vitro. The distribution of TSP2 during development is in keeping with its participation in the formation of a variety of connective tissues. In adult tissues, TSP2 is located in the pericellular environment, where it can potentially influence the cell-matrix interactions associated with cell movement and tissue repair.
Multimedia Network File Servers: Multi-Channel Delay Sensitive (1993)

Delay sensitive media such as audio and video are becoming integrated in the standard user interface. In this paper we consider simultaneous multiple access, such as would be performed by a multimedia network fileserver. To simplify the discussion, we consider only audio retrieval. The extension to storage and other delay sensitive datatypes is straightforward. This paper builds on the necessity of avoiding starvation of the consumer, and the assumption that certain sets of reads lead to a net increase in the number of samples buffered, to establish a theoretical framework for studying simultaneous multipleaccess. Our approach allows the possibility of splitting data into sorting sets for the purpose of reducing disk latencies, and gives an optimal algorithm for the reduction. It explicitly handles both contiguousandnon-contiguous file layouts. Using the theoretical framework, designers can evaluate the approach which is best suited to their situation.