gebhart/patrepeval huggingface dataset:
An improved variable length coding scheme using structured LDPC codes (2010)

This paper proposes an improved coding scheme for various transmission lengths by combining shortening and puncturing with the conventional lifting method. Considering both of cycle conditions and ACE spectrum, we design the base-matrix in the framework of PEG construction. Only one base-matrix is required to support a wide rage of coding lengths for our proposed scheme, where the lifting factors are set in non-uniformly distributed values. The transmission configurations with arbitrary lengths within the coding range can be achieved by shortening and puncturing. Moreover, our proposed scheme provides better error performance than the traditional structured LDPC codes lifted by many different factors, when the shortening and puncturing patters are optimally selected by numerical methods.
Selective inhibition of binding of Bacillus thuringiensis Cry1Ab toxin to cadherin-like and aminopeptidase proteins in brush-border membranes and dissociated epithelial cells from Bombyx mori (2007)

Binding analyses with denatured epithelial membrane proteins from Bt (Bacillus thuringiensis) demonstrated at least two kinds of proteins, APNs (aminopeptidases N) and cadherin-like proteins, as possible receptors for the Cry1A class of Bt toxins. Two alternative models have been proposed, both based on initial toxin binding to a cadherin-like protein, but one involving APN and the other not. We have used two Bombyx mori strains (J65 and Kin), which are highly susceptible to Cry1Ab, to study the role of these two types of receptors on Cry1Ab toxin binding and cytotoxicity by means of the inhibitory effect of antibodies. BBMVs (brush-border membrane vesicles) of strain J65 incubated with labelled 125I-Cry1Ab revealed a marked reduction in reversible and irreversible binding when anti-BtR175 (a cadherin-like protein) was used for BBMV pre-treatment. By contrast, the anti-APN1 antibody specifically affected the irreversible binding, while the reversible binding component was not affected. This is the first time that binding of Cry1Ab to APN1 and to a cadherin-like protein from BBMVs in solution has been shown. Dissociated epithelial cells from the Kin strain were used to test the inhibitory effect of the antibodies on the cytotoxicity of Cry1Ab. Pre-incubation of the cells with the anti-BtR175 antibody conferred protection against Cry1Ab, but not the anti-APN1 antibody. Therefore our results seem to support the two models of the mode of action of Cry1Ab in Lepidoptera, depending on whether BBMVs or intact dissociated cells are used, suggesting that both pathways may co-operate for the toxicity of Cry1A toxins in vivo.
The Intestinal Barrier in Irritable Bowel Syndrome: Subtype-Specific Effects of the Systemic Compartment in an In Vitro Model (2015)

Basolateral exposure of spheroids to plasma of IBS-D patients resulted in a significantly increased FD4 permeation, which was partially abolished by selective inhibition of tryptase and LPS. These findings point to a role of systemic tryptase and LPS in the epithelial barrier alterations observed in patients with IBS-D.
Electroreduction of Oxygen in a Series of Room Temperature Ionic Liquids Composed of Group 15-Centered Cations and Anions (2004)

The electrochemical reduction of oxygen is reported in four room temperature ionic liquids (RTILs) based on quaternary alkyl -onium cations and heavily fluorinated anions in which the central atom is either nitrogen or phosphorus. Data were collected using cyclic voltammetry and potential step chronoamperometry at gold, platinum, and glassy carbon disk electrodes of micrometer dimension under water-free conditions at a controlled temperature. Analysis via fitting to appropriate theoretical equations was then carried out to obtain kinetic and thermodynamic information pertaining to the electrochemical processes observed. In the quaternary ammonium electrolytes, reduction of oxygen was found to occur reversibly to give stable superoxide, in an analogous manner to that seen in conventional aprotic solvents such as dimethyl sufoxide and acetonitrile. The most significant difference is in the relative rate of diffusion; the diffusion coefficients of oxygen in the RTILs are an order of magnitude lower than in common organic solvents, and for superoxide these values are reduced by a further factor of 10. In the quaternary phosphonium ionic liquids, however, more complex voltammetry is observed, akin to that expected for the reduction of oxygen in acidified organic media. This is shown to be consistent with the occurrence of a proton abstraction reaction between the electrogenerated superoxide and quaternary alkyl phosphonium cations following the initial electron transfer.
Nonequilibrium Equality for Free Energy Differences (1997)

An expression is derived for the equilibrium free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the other. Two well-known identities emerge as limiting cases of this result.
Overcrowded molecules. II. 4,5-Bis(2-pyridyl)phenanthrene-3,6-diols (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOvercrowded molecules. II. 4,5-Bis(2-pyridyl)phenanthrene-3,6-diolsDonald L. Fields and Thomas H. ReganCite this: J. Org. Chem. 1971, 36, 20, 2991–2995Publication Date (Print):October 1, 1971Publication History Published online1 May 2002Published inissue 1 October 1971https://pubs.acs.org/doi/10.1021/jo00819a018https://doi.org/10.1021/jo00819a018research-articleACS PublicationsRequest reuse permissionsArticle Views89Altmetric-Citations14LEARN 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
Most lymphoid organ dendritic cell types are phenotypically and functionally immature (2003)

Dendritic cells (DCs) have been thought to follow a life history, typified by Langerhans cells (LCs), with 2 major developmental stages: an immature stage that captures antigens in the periphery and a mature stage that presents those antigens in the lymphoid organs. However, a systematic assessment of the maturity of lymphoid organ DCs has been lacking. We have analyzed the maturity of the DC types found in the steady state in the spleen, lymph nodes (LNs), and thymus. The DCs that migrate into the iliac, mesenteric, mediastinal, or subcutaneous LNs from peripheral tissues were mature and therefore could not process and present newly encountered antigens. However, all the other DC types were phenotypically and functionally immature: they expressed low levels of surface major histocompatibility complex class II (MHC II) and CD86, accumulated MHC II in their endosomes, and could present newly encountered antigens. These immature DCs could be induced to mature by culture in vitro or by inoculation of inflammatory stimuli in vivo. Therefore, the lymphoid organs contain a large cohort of immature DCs, most likely for the maintenance of peripheral tolerance, which can respond to infections reaching those organs and mature in situ.
The timed infusion paradigm for melatonin delivery: What has it taught us about the melatonin signal, its reception, and the photoperiodic control of seasonal responses? (1993)

This review summarizes the evidence showing that the duration of the nocturnal secretory profile of pineal melatonin (MEL) is critical for eliciting seasonally appropriate reproductive physiological and behavioral responses in mammals. We review experiments using the timed infusion paradigm (TIP) to deliver MEL either systemically or centrally to pinealectomized hamsters and sheep. In this paradigm, MEL is infused, usually once daily, for a specific number of hours and at a predetermined time of day. This experimental strategy tests most directly those features of the MEL signal that are necessary to trigger photoperiodic responses. The data suggest that the duration of the MEL stimulation is the critical feature of the MEL signal for both inhibitory and stimulatory effects of the hormone on the photoperiodic control of reproductive development in juvenile Siberian hamsters, and for the photoperiodic control of reproductive and metabolic responses in adult Siberian and Syrian hamsters and sheep. The use of the TIP reveals the importance of the frequency of the signal presentation of MEL and suggests the importance of a period of low-to-absent circulating concentrations of the hormone. The TIP also reveals that the characteristics of the MEL signal that regulate male sexual behavior are similar to those that are critical for reproductive and metabolic responses in Syrian hamsters. We summarize the locations of possible functional MEL target sites identified by combining the TIP with traditional brain lesion techniques. Evidence from such studies suggests that the integrity of the suprachiasmatic nucleus (SCN) region in Siberian hamsters and the anterior hypothalamus in Syrian hamsters is necessary for the response to short-day MEL signals. The TIP has been used to deliver MEL to putative target sites for the hormone in the brain of juvenile and adult Siberian hamsters. The results of these preliminary experiments suggest that the regions of specific MEL binding in this species, especially the SCN, are effective sites where MEL may stimulate short-day-type responses. In contrast, results from intracranial application of MEL in sheep suggest the medial basal hypothalamus as a critical site of action. Finally, we also discuss potential applications of the TIP for identification of brain MEL target sites, understanding of other photoperiodic phenomena and responses, and resolution of the cellular/molecular basis underlying the reception and interpretation of MEL signals.(ABSTRACT TRUNCATED AT 400 WORDS)
Detection and Confirmation of Staphylococcal Enterotoxin B in Apple Juice and Milk Using Piezoelectric-Excited Millimeter-Sized Cantilever Sensors at 2.5 fg/mL (2007)

A sensitive and reliable method for the detection of a model toxin, staphylococcal enterotoxin B (SEB) in buffer, apple juice, and milk is shown using piezoelectric-excited, millimeter-sized cantilever (PEMC) sensors. Limit of detection in spiked milk and apple juice samples is 10 and 100 fg, respectively. PEMC sensors (2 mm(2)) are prepared by immobilizing a polyclonal antibody specific to SEB, which was exposed to 1 mL of 1% milk and apple juice containing 10 fg-10 ng. Sensor response to 100 fg, 1 pg, and 10 pg of SEB in apple juice resulted in resonance frequency decreases of 113 +/- 18 (n = 4), 308 +/- 24 (n = 4), and 521 +/- 20 (n = 2) Hz, respectively. In milk, 10 fg, 100 fg, 1 pg, and 10 pg of SEB resulted in resonance frequency decreases of 126 +/- 18 (n = 2), 143 +/- 35 (n = 4), 310 +/- 32 (n = 5), and 557 +/- 25 (n = 2) Hz, respectively. Positive detection of SEB in the sample solution was observed within the first 20 min. The responses of the sensor to positive (SEB present, but no antibody on sensor), negative (SEB absent, antibody on sensor), and buffer (SEB absent, antibody on sensor) controls were -17 +/- 10 (n = 3), -9 +/- 5 (n = 3), and -6 +/- 12 (n = 18) Hz, respectively. Positive verification of SEB detection was confirmed by two methods: (1) low-pH buffer release caused increase in resonance frequency, and (2) second antibody binding to SEB attached to sensor that caused further resonance frequency decrease. The significance of these results is that PEMC sensors can reliably detect SEB at 10-100 fg (effective concentration of 2.5 and 25 fg/mL) in complex fluids without sample preparation or the use of labeled reagents.
Autocrine Regulation of Myocyte Cx43 Expression by VEGF (2002)

Cardiac myocytes can rapidly adjust their expression of gap junction channel proteins in response to changes in load. Previously, we showed that after only 1 hour of linear pulsatile stretch (110% of resting cell length; 3 Hz), expression of connexin43 (Cx43) by cultured neonatal rat ventricular myocytes is increased by approximately 2-fold and impulse propagation is significantly more rapid. In the present study, we tested the hypothesis that vascular endothelial growth factor (VEGF), acting downstream of transforming growth factor-beta (TGF-beta), mediates stretch-induced upregulation of Cx43 expression by cardiac myocytes. Incubation of nonstretched cells with exogenous VEGF (100 ng/mL) or TGF-beta (10 ng/mL) for 1 hour increased Cx43 expression by approximately 1.8-fold, comparable to that observed in cells subjected to pulsatile stretch for 1 hour. Stretch-induced upregulation of Cx43 expression was blocked by either anti-VEGF antibody or anti-TGF-beta antibody. Stretch-induced enhancement of conduction was also blocked by anti-VEGF antibody. ELISA assay showed that VEGF was secreted into the culture medium during stretch. Furthermore, stretch-conditioned medium stimulated Cx43 expression in nonstretched cells. This effect was also blocked by anti-VEGF antibody. Upregulation of Cx43 expression stimulated by exogenous TGF-beta was blocked by anti-VEGF antibody, but VEGF-stimulation of Cx43 expression was not blocked by anti-TGF-beta antibody. Thus, stretch-induced upregulation of Cx43 expression is mediated, at least in part, by VEGF, which acts downstream of TGF-beta. Because the cultures contained only approximately 5% nonmyocytic cells, these results indicate that myocyte-derived VEGF, secreted in response to stretch, acts in an autocrine fashion to enhance intercellular coupling.
Point-contact silicon solar cells (1984)

A new type of silicon photovoltaic cell designed for high-concentration applications is presented. The device is called the point-contact-cell and shows potential for achieving energy conversion efficiencies in the neighborhood of 28 percent at the design operating point of 500× geometric concentration and 60°C cell temperature. This cell has alternating n and p regions that form a polkadot array on the bottom surface. A two-layermetallization on the bottom provides contact. Initial experimental results have yielded a cell with 20-percent efficiency at a concentration of 88.
Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies (2004)

Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.
Many pulmonary pathogenic bacteria bind specifically to the carbohydrate sequence GalNAc beta 1-4Gal found in some glycolipids. (1988)

Pneumonia is one of the most common causes of death from infectious disease in the United States. To examine the possible role of carbohydrates as adhesion receptors for infection, several pulmonary pathogenic bacteria were studied for binding to glycosphingolipids. Radiolabeled bacteria were layered on thin-layer chromatograms of separated glycosphingolipids, and bound bacteria were detected by autoradiography. The classic triad of infectious bacteria found in cystic fibrosis, Pseudomonas aeruginosa, Haemophilus influenzae, and Staphylococcus aureus, along with other bacteria commonly implicated in typical pneumonia, such as Streptococcus pneumoniae, Klebsiella pneumoniae, and certain Escherichia coli, bind specifically to fucosylasialo-GM1 (Fuc alpha 1-2Gal beta 1-3GalNAc beta 1-4Gal beta 1-4Cer), asialo-GM1 (Gal beta 1-3GalNAc beta 1-4Gal beta-1-4Galc beta 1-1Cer), and asialo-GM2 (GalNAc beta 1-4Gal beta 1-4Glc beta 1-1Cer). Bacteria maintained in nutrient medium bind better than the same cells suspended in buffer. They do not bind to galactosylceramide, glucosylceramide, lactosylceramide, trihexosylceramide, globoside, paragloboside, Forssman glycosphingolipid, or several other glycosphingolipids tested, including the gangliosides GM1, GM2, GM3, GD1a, GD1b, GT1b, and Cad. The finding that these pathogens do not bind to lactosylceramide suggests that beta 1-4-linked GalNAc, which is positioned internally in fucosylasialo-GM1 and asialo-GM1 and terminally in asialo-GM2, is required for binding. beta-N-Acetylgalactosamine itself, however, is not sufficient for binding, as the bacteria did not bind to globoside, which contains the terminal sequence GalNAc beta 1-3Gal. These data suggest that these bacteria require at least terminal or internal GalNAc beta 1-4Gal sequences unsubstituted with sialyl residues for binding. Other bacteria, including Mycoplasma pneumoniae, Streptococcus pyogenes, Salmonella species, and some E. coli, do not bind to the GalNAc beta 1-4Gal sequence. The biological relevance of these data is suggested by our finding that substantial amounts of asialo-GM1 occur in human lung tissue.
Controlling the dynamic range of a Josephson parametric amplifier (2014)

One of the central challenges in the development of parametric amplifiers is the control of the dynamic range relative to its gain and bandwidth, which typically limits quantum limited amplification to signals which contain only a few photons per inverse bandwidth. Here, we discuss the control of the dynamic range of Josephson parametric amplifiers by using Josephson junction arrays. We discuss gain, bandwidth, noise, and dynamic range properties of both a transmission line and a lumped element based parametric amplifier. Based on these investigations we derive useful design criteria, which may find broad application in the development of practical parametric amplifiers.
Recent Developments in Texaphyrin Chemistry and Drug Discovery (2013)

Texaphyrins are pentaaza expanded porphyrins with the ability to form stable complexes with a variety of metal cations, particularly those of the lanthanide series. In biological milieus, texaphyrins act as redox mediators and mediate the production of reactive oxygen species (ROS). In this review, newer studies involving texaphyrin complexes targeting several different applications in anticancer therapy are described. In particular, the preparation of bismuth and lead texaphyrin complexes as potential α-core emitters for radiotherapy is detailed, as are gadolinium texaphyrin functionalized magnetic nanoparticles with features that make them of interest as dual-mode magnetic resonance imaging contrast agents and as constructs with anticancer activity mediated through ROS-induced sensitization and concurrent hyperthermia. Also discussed are gadolinium texaphyrin complexes as possible carrier systems for the targeted delivery of platinum payloads.
The copper chelator trientine has an antiangiogenic effect against hepatocellular carcinoma, possibly through inhibition of interleukin‐8 production (2002)

Recent studies have revealed that copper is an important cofactor for several angiogenic agents. We examined the antiangiogenic effect against hepatocellular carcinoma (HCC) of the copper chelator trientine, especially focusing on the relationship between copper and interleukin-8 (IL-8), a potent angiogenic factor produced by hepatoma cells. HuH-7 hepatoma cells were transplanted into nude mice and the growth of xenograft tumors was compared to and without administration of trientine. Using the resected tumor, microvessel density, apoptotic potential and proliferative activity were analyzed histologically and IL-8 mRNA was semiquantified by RT-PCR. In addition, HuH-7 cells were cultured in control medium, medium supplemented with copper, medium supplemented with trientine and medium supplemented with both copper and trientine. Human IL-8 levels were measured in the supernatants by ELISA. Using the extracts from cultured cells, IL-8 mRNA was semiquantified by RT-PCR. Trientine suppressed the growth of xenograft tumors significantly. Histologically, apoptotic potential was increased significantly and microvessel density, decreased. The production of IL-8 from the tumor was suppressed by trientine. In vitro, IL-8 production by HuH-7 cells in copper-containing medium was significantly greater than that in copper-free medium, and this effect was weakened when trientine was added. However, no significant change was apparent when trientine was added to the medium alone. In conclusion, the chelating effect of trientine prevented copper from functioning as a cofactor in angiogenesis, which resulted in reduced IL-8 production from HuH-7 cells.
Patent review: therapeutic applications for antisense oligonucleotides 1999-2000. (2000)

Over 200 patents disclosing antisense sequences have been published in the last year. 30 Of these, in which a therapeutic application is claimed, have been reviewed in this article. We have classified these under the headings of antibacterial, antiviral, inflammation, cardiovascular, apoptosis and anticancer. Although not exhaustive or covering all diseases, major areas of antisense research have been addressed.