gebhart/patrepeval huggingface dataset:
Automatic verification of finite-state concurrent systems using temporal logic specifications (1986)

We give an efficient procedure for verifying that a finite-state concurrent system meets a specification expressed in a (propositional, branching-time) temporal logic. Our algorithm has complexity linear in both the size of the specification and the size of the global state graph for the concurrent system. We also show how this approach can be adapted to handle fairness. We argue that our technique can provide a practical alternative to manual proof construction or use of a mechanical theorem prover for verifying many finite-state concurrent systems. Experimental results show that state machines with several hundred states can be checked in a matter of seconds.
Epithelial–Mesenchymal Transition and Stem Cell Markers in Patients with HER2-Positive Metastatic Breast Cancer (2012)

Currently, there is extensive information about circulating tumor cells (CTC) and their prognostic value; however, little is known about other characteristics of these cells. In this prospective study, we assessed the gene transcripts of epithelial-to-mesenchymal transition-inducing transcription factors (EMT-TF) and cancer stem cell (CSC) features in patients with HER2(+) metastatic breast cancer (MBC). Epithelial cells were enriched from peripheral blood mononuclear cells (PBMC) using antibody-coated anti-CD326 antibody (CD326(+)) magnetic beads, and the residual CD326(-) PBMCs were further depleted of leukocytes using anti-CD45 antibody-coated magnetic beads (CD326(-)CD45(-)). RNA was extracted from all cell fractions, reverse transcribed to cDNA, and subjected to quantitative reverse transcription PCR to detect EMT-TFs (TWIST1, SNAIL1, ZEB1, and TG2) as a measure of CTCs undergoing EMT (EMT-CTCs). In addition, PBMCs were analyzed using multiparameter flow cytometry for ALDH activity and CSCs that express CD24, CD44, and CD133. Twenty-eight patients were included in this study. At least one EMT-TF mRNA was elevated in the CTCs of 88.2% of patients and in the CD326(-)CD45(-) cell fraction of 60.7% of patients. The CD326(-)CD45(-) fraction of patients with elevated SNAIL1 and ZEB1 transcripts also had a higher percentage of ALDH(+)/CD133(+) cells in their blood than did patients with normal SNAIL1 and ZEB1 expression (P = 0.038). Our data indicate that patients with HER2(+) MBCs have EMT-CTCs. Moreover, an enrichment of CSCs was found in CD326(-)CD45(-) cells. Additional studies are needed to determine whether EMT-CTCs and CSCs have prognostic value in patients with HER2(+) MBCs treated with trastuzumab-based therapy.
Quantitative analysis of AIDS-related virus-carrying cells by plaque-forming assay using an HTLV-I-positive MT-4 cell line. (1985)

Quantitation of acquired immune deficiency syndrome (AIDS)-related virus-bearing cells was analyzed by a newly developed plaque-forming assay. A chemically adherent HTLV-I-positive MT-4 cell monolayer was used as the cytolytic responder cells to the AIDS-virus infection. When AIDS-virus-infected cells (Molt-4/HTLV-III, H9/HTLV-III, and CEM/LAV) were seeded with MT-4 cells, plaques were observed corresponding to the number of HTLV-III-positive cells plated. Plaque formation was inhibited by the addition of anti-HTLV-III-positive serum (neutralizing antibody) to the agarose medium. These data suggest that this plaque-forming assay technique should be useful for the quantitative analysis of AIDS-virus-bearing cells.
Digital Transmission of Two Television Sound Channels in Horizontal Blanking (1975)

The conventional way of transmitting television sound information on subcarriers leads to a number of difficulties in satellite communications systems using frequency modulation, because of the limited power available. In particular, when high-quality sound is required, modulation products can only be avoided by going to large bandwidths and high power compared with the actual picture transmission — and this is expensive. A method has been found for transmitting two high-quality (15-kHz bandwidth and better than 60-dB SNR) sound signals with no mutual interference between sound and video signals. No additional RF bandwidth and little additional power is required. The technique involves using a part of the line-blanking interval after shortening the synchronizing pulse. The sound signals are sampled and companded to a given number of bits in a non-return-to-zero code. At the receiving end the pulses are stored, decoded and read out with the original sampling frequency. After passing through a low-pass filter, the signals are available in the original position. Tests have been promising, and a practical application seems possible soon.
Performance considerations in designing network interfaces (1993)

Design issues that affect the performance of network input/output (I/O) are examined by analyzing the design and performance of a workstation's network interface to the 100-Mb/s FDDI token ring. Several design alternatives for partitioning functions between the network interface and the host software are evaluated. A simple model is proposed for looking at the performance of network I/O, and an effective analysis approach for predicting user-perceived throughput is demonstrated. The analysis reveals that, particularly for network interfaces that reside on an I/O bus, providing a DMA engine for data movement provides significant improvements in throughput. However, the designs for the receive and transmit sides are not necessarily symmetrical, and it is shown that host architecture considerations influence the design of each direction differently. The analysis is used to show the potential benefits of having all protocol functions on the network interface and also to point out the potential processing power needed on that network interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abnormal Ca 2+ Release, but Normal Ryanodine Receptors, in Canine and Human Heart Failure (2002)

Sarcoplasmic reticulum (SR) Ca2+ transport proteins, especially ryanodine receptors (RyR) and their accessory protein FKBP12.6, have been implicated as major players in the pathogenesis of heart failure (HF), but their role remain controversial. We used the tachycardia-induced canine model of HF and human failing hearts to investigate the density and major functional properties of RyRs, SERCA2a, and phospholamban (PLB), the main proteins regulating SR Ca2+ transport. Intracellular Ca2+ is likely to play a role in the contractile dysfunction of HF because the amplitude and kinetics of the [Ca2+]i transient were reduced in HF. Ca2+ uptake assays showed 44+/-8% reduction of Vmax in canine HF, and Western blots demonstrated that this reduction was due to decreased SERCA2a and PLB levels. Human HF showed a 30+/-5% reduction in SERCA2a, but PLB was unchanged. RyRs from canine and human HF displayed no major structural or functional differences compared with control. The P(o) of RyRs was the same for control and HF over the range of pCa 7 to 4. Subconductance states, which predominate in FKBP12.6-stripped RyRs, were equally frequent in control and HF channels. An antibody that recognizes phosphorylated RyRs yields equal intensity for control and HF channels. Further, phosphorylation of RyRs by PKA did not appear to change the RyR/FKBP12.6 association, suggesting minor beta-adrenergic stimulation of Ca2+ release through this mechanism. These results support a role for SR in the pathogenesis of HF, with abnormal Ca2+ uptake, more than Ca2+ release, contributing to the depressed and slow Ca2+ transient characteristic of HF.
Endophytic Herbaspirillum seropedicae expresses nif genes in gramineous plants (2003)

The interactions between maize, sorghum, wheat and rice plants and Herbaspirillum seropedicae were examined microscopically following inoculation with the H. seropedicae LR15 strain, a Nif+ (Pnif::gusA) mutant obtained by the insertion of a gusA-kanamycin cassette into the nifH gene of the H. seropedicae wild-type strain. The expression of the Pnif::gusA fusion was followed during the association of the diazotroph with the gramineous species. Histochemical analysis of seedlings of maize, sorghum, wheat and rice grown in vermiculite showed that strain LR15 colonized root surfaces and inner tissues. In early steps of the endophytic association, H. seropedicae colonized root exudation sites, such as axils of secondary roots and intercellular spaces of the root cortex; it then occupied the vascular tissue and there expressed nif genes. The expression of nif genes occurred in roots, stems and leaves as detected by the GUS reporter system. The expression of nif genes was also observed in bacterial colonies located in the external mucilaginous root material, 8 days after inoculation. Moreover, the colonization of plant tissue by H. seropedicae did not depend on the nitrogen-fixing ability, since similar numbers of cells were isolated from roots or shoots of the plants inoculated with Nif+ or Nif− strains.
Compositae dermatitis: a survey (1992)

Compositae dermatitis in an allergic contact dermatitis, frequently chronic, triggered by plants of the Compositae family. The condition, which is seen, in particular, in middle-aged and elderly persons, typically starts in the summer months with an acute eczema either corresponding to areas exposed to light and air, or corresponding to areas of plant contact; it disappears spontaneously during the fall of the year. Repeated exposure over a number of years may cause severe intractable dermatitis affecting the patient throughout the year. The responsible allergens are sesquiterpene lactones, and investigations to date indicate that the frequency of the allergy is similar to that seen with some of the contact allergens of the standard patch test series. The diagnosis, however, is difficult, partly due to the fact that the clinical picture may be mistaken for a photodermatosis, and partly owing to the difficulty in obtaining commercially available allergens for patch testing. The diagnosis is therefore based on testing with plant extracts, which can cause pronounced local reactions and possibly active sensitization. A survey is given of the possible modes of sensitization, sex and age distribution, the relationship to photosensitivity and atopy, as well as the possible treatment. It is concluded, on the basis of the chronic nature of the disease, and the diagnostic and treatment problems, that continued intensive research into the condition is urgently needed.
Ternary Complex Formation between MADS-box Transcription Factors and the Histone Fold Protein NF-YB (2002)

MADS-box proteins are transcription factors present in different eukaryotic kingdoms. In contrast to plants, for mammalian and yeast MADS-box proteins ternary complex formation with unrelated transcription factors was reported. We show here the first identification of such ternary interaction in plants. A rice seed-specific NF-YB was identified as partner of OsMADS18 by two-hybrid screening. NF-YB contains a histone fold motif, HFM,(1) and is part of the trimeric CCAAT-binding NF-Y complex. OsMADS18, alone or in combination with a natural partner, interacts with OsNF-YB1 through the MADS and I regions. The mouse NF-YB also associates with OsMADS18 in vivo and in vitro as a NF-YB-NF-YC dimer. Other rice MADS-box proteins do not interact in these assays, indicating specificity for the interaction. OsNF-YB1 is capable of heterodimerizing with NF-YC, but not trimerizing with NF-YA, thus precluding CCAAT binding. Mutation of the variant Asp at position 99 of the HFM alpha2-helix into a conserved serine recovers the capacity to interact with NF-YA, but not with DNA. This is the first indication that members of the NF-YB family work through mechanisms independent of the CCAAT box.
Formal modeling and verification of microprocessors (1995)

This paper presents a methodology for microprocessor verification that significantly reduces the learning curve for performing verification. The methodology is formalized in the HOL theorem-proving system. The paper includes a description of a large case study performed to evaluate the methodology. The novel aspects of this research include the use of abstract theories to formalize hardware models. Because our model is described using abstract theories, it provides a framework for both the specification and the verification. This framework reduces the number of ad hoc modeling decisions that must be made to complete the verification. Another unique aspect of our research is the use of hierarchical abstractions to reduce the number of difficult lemmas in completing the verification. Our formalism frees the user from directly reasoning about the difficult aspects of modeling the hierarchy, namely the temporal and data abstractions. We believe that our formalism, coupled with case studies and tools, allows microprocessor verification to be done by engineers with relatively little experience in microprocessor specification or logic. We are currently testing that hypothesis by using the methodology to teach graduate students formal microprocessor modeling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations in Ribosomal Protein L16 Conferring Reduced Susceptibility to Evernimicin (SCH27899): Implications for Mechanism of Action (2000)

A clinical isolate of Streptococcus pneumoniae (SP#5) that showed decreased susceptibility to evernimicin (MIC, 1.5 microgram/ml) was investigated. A 4,255-bp EcoRI fragment cloned from SP#5 was identified by its ability to transform evernimicin-susceptible S. pneumoniae R6 (MIC, 0.03 microgram/ml) such that the evernimicin MIC was 1.5 microgram/ml. Nucleotide sequence analysis of this fragment revealed that it contained portions of the S10-spc ribosomal protein operons. The nucleotide sequences of resistant and susceptible isolates were compared, and a point mutation (thymine to guanine) that causes an Ile52-Ser substitution in ribosomal protein L16 was identified. The role of this mutation in decreasing susceptibility to evernimicin was confirmed by direct transformation of the altered L16 gene. The presence of the L16 mutation in the resistant strain suggests that evernimicin is an inhibitor of protein synthesis. This was confirmed by inhibition studies using radiolabeled substrates, which showed that the addition of evernimicin at sub-MIC levels resulted in a rapid decrease in the incorporation of radiolabeled isoleucine in a susceptible isolate (SP#3) but was much less effective against SP#5. The incorporation of isoleucine showed a linear response to the dose level of evernimicin. The incorporation of other classes of labeled substrates was unaffected or much delayed, indicating that these were secondary effects.
A Spread-Deficient Cytomegalovirus for Assessment of First-Target Cells in Vaccination (2010)

Human cytomegalovirus (HCMV) is a human pathogen that causes severe disease primarily in the immunocompromised or immunologically immature individual. To date, no vaccine is available. We describe use of a spread-deficient murine CMV (MCMV) as a novel approach for betaherpesvirus vaccination. To generate a spread-deficient MCMV, the conserved, essential gene M94 was deleted. Immunization with MCMV-DeltaM94 is apathogenic and protective against wild-type challenge even in highly susceptible IFNalphabetaR(-/-) mice. MCMV-DeltaM94 was able to induce a robust CD4(+) and CD8(+) T-cell response as well as a neutralizing antibody response comparable to that induced by wild-type infection. Endothelial cells were identified as activators of CD8(+) T cells in vivo. Thus, the vaccination with a spread-deficient betaherpesvirus is a safe and protective strategy and allows the linkage between cell tropism and immunogenicity. Furthermore, genomes of MCMV-DeltaM94 were present in lungs 12 months after infection, revealing first-target cells as sites of genome maintenance.
Heteronuclear Solution-State NMR Studies of the Chromophore in Cyanobacterial Phytochrome Cph1 (2005)

Precise structural information regarding the chromophore binding pocket is essential for an understanding of photochromicity and photoconversion in phytochrome photoreceptors. To this end, we are studying the 59 kDa N-terminal module of the cyanobacterial phytochrome Cph1 from Synechocystis sp. PCC 6803 in both thermally stable forms (Pr and Pfr) using solution-state NMR spectroscopy. The protein is deuterated, while the chromophore, phycocyanobilin (PCB), is isotopically labeled with (15)N or (13)C and (15)N. We have established a simple approach for preparing labeled PCB based on BG11 medium supplemented with an appropriate buffer and NaH(13)CO(3) and Na(15)NO(3) as sole carbon and nitrogen sources, respectively. We show that structural details of the chromophore binding pocket in both Pr and Pfr forms can be obtained using multidimensional heteronuclear solution-state NMR spectroscopy. Using one-dimensional (15)N NMR spectra, we show unequivocally that the chromophore is protonated in both Pr and Pfr states.
Conformations. IV. The Conformational Preference of the Phenyl Group in Cyclohexane (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformations. IV. The Conformational Preference of the Phenyl Group in CyclohexaneEdgar W. Garbisch and Dennis B. PattersonCite this: J. Am. Chem. Soc. 1963, 85, 20, 3228–3231Publication Date (Print):October 1, 1963Publication History Published online1 May 2002Published inissue 1 October 1963https://pubs.acs.org/doi/10.1021/ja00903a038https://doi.org/10.1021/ja00903a038research-articleACS PublicationsRequest reuse permissionsArticle Views307Altmetric-Citations63LEARN 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
Providing Secure Environments for Untrusted Network Applications (1997)

Abstract: Bugs in network application programs can be exploited to compromise the system on which the application is running. When running these applications in an unsafe environment such as the Internet, the security concerns raised are a significant barrier to electronic commerce. In addition, these application programs (such as Web servers, mailservers, etc.) are usually too big and complex to be bug-free; trying to build security directly into these applications has proven to be very difficult. This paper demonstrates that a compartmented-mode workstation is a suitable platform to provide a secure environment that can contain most existing network applications. We describe how to wrap these applications in order to reduce the potential for a security breach without the need to rewrite the application completely. By minimizing the effort of transferring unsafe application services so that they are reasonably secure, we are able to accelerate the process of electronic commerce.
Cytoplasmic CUL9/PARC Ubiquitin Ligase Is a Tumor Suppressor and Promotes p53-Dependent Apoptosis (2011)

A wide range of cell stresses, including DNA damage, signal to p53 through posttranslational modification of p53. The cytoplasmic functions of p53 are emerging as an important constituent of role of p53 in tumor suppression. Here, we report that deletion of the Cul9 (formerly Parc) gene, which encodes an E3 ubiquitin ligase that binds to p53 and localizes in the cytoplasm, resulted in spontaneous tumor development, accelerated Eμ-Myc-induced lymphomagenesis, and rendered mice susceptible to carcinogenesis. Cul9-p53 double-mutant mice exhibited indistinguishable tumor phenotypes as p53 single-mutant mice, indicating that the function of Cul9 in tumor suppression is largely mediated by p53. Deletion of Cul9 had no significant effect on cell-cycle progression, but attenuated DNA damage-induced apoptosis. Ectopic expression of wild-type CUL9, but not a point mutant CUL9 deficient in p53 binding, promotes apoptosis. These results show CUL9 as a potential p53-activating E3 ligase in the cytoplasm.
Dense wavelength multiplexing of 1550 nm QKD with strong classical channels in reconfigurable networking environments (2009)

To move beyond dedicated links and networks, quantum communications signals must be integrated into networks carrying classical optical channels at power levels many orders of magnitude higher than the quantum signals themselves. We demonstrate the transmission of a 1550 nm quantum channel with up to two simultaneous 200 GHz spaced classical telecom channels, using reconfigurable optical add drop multiplexer (ROADM) technology for multiplexing and routing quantum and classical signals. The quantum channel is used to perform quantum key distribution (QKD) in the presence of noise generated as a by-product of the co-propagation of classical channels. We demonstrate that the dominant noise mechanism can arise from either four-wave mixing or spontaneous Raman scattering, depending on the optical path characteristics as well as the classical channel parameters. We quantify these impairments and discuss mitigation strategies.
Radical mechanism for the decomposition of diethyl[2,3,7,8,12,13,17,18-octaethylporphyrinato(2-)]ruthenium. Determination of the metal-carbon bond dissociation energy (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRadical mechanism for the decomposition of diethyl[2,3,7,8,12,13,17,18-octaethylporphyrinato(2-)]ruthenium. Determination of the metal-carbon bond dissociation energyJames P. Collman, Lisa. McElwee-White, Penelope J. Brothers, and E. RoseCite this: J. Am. Chem. Soc. 1986, 108, 6, 1332–1333Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://doi.org/10.1021/ja00266a053RIGHTS & PERMISSIONSArticle Views172Altmetric-Citations29LEARN 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 InReddit PDF (298 KB) Get e-Alerts Get e-Alerts