gebhart/patrepeval huggingface dataset:
Strategies for tissue and organ decellularization (2012)

Decellularized tissues have been successfully used in a variety of tissue engineering/regenerative medicine applications, and more recently decellularized organs have been utilized in the first stages of organ engineering. The protocols used to decellularize simple tissues versus intact organs differ greatly. Herein, the most commonly used decellularization methods for both surgical mesh materials and whole organs are described, with consideration given to how these different processes affect the extracellular matrix and the host response to the scaffold.
Development of a Merged Conjugate Addition/Oxidative Coupling Sequence. Application to the Enantioselective Total Synthesis of Metacycloprodigiosin and Prodigiosin R1 (2009)

A merged conjugate addition/oxidative coupling sequence that represents an efficient strategy for preparing structurally diverse pyrroles has been developed. Success of the method hinged upon the controlled oxidative coupling of unsymmetrical silyl bis-enol ether intermediates, formed by the 1,4-addition of a Grignard reagent with subsequent enolate trapping by a (chloro)silylenol ether. The process was applied to the first enantioselective syntheses of the biologically active pyrrolophane natural products, metacycloprodigiosin and prodigiosin R1.
Hepatocyte-stimulating factor III shares structural and functional identity with leukemia-inhibitory factor. (1989)

The coordinate increase in the hepatic production of the acute phase plasma proteins appears to be mediated by several cytokines produced by different cell types. One factor, hepatocyte-stimulating factor III (HSF-III), constitutively produced by human squamous carcinoma (COLO-16) cells, stimulates the synthesis of the same set of acute phase plasma proteins as the structurally distinct IL-6. The physicochemical properties of HSF-III coincide with those of the T cell-derived leukemia-inhibitory factor (LIF). Human rLIF, tested on hepatoma cells, indicated a liver-regulating activity identical to HSF-III. The LIF activity is specifically neutralized by HSF-III antibodies. COLO-16 cells contain an LIF mRNA which is characteristic for lectin-stimulated T cells, suggesting that HSF-III is an epidermal cell-derived form of LIF. This result provides additional evidence for the close relationship between acute phase regulation of the liver and control of proliferation and differentiation of hemopoietic cells by identical cytokines.
Interactions of Heteroaromatic Compounds with Nucleic Acids (1975)

We have examined the origins of base specificity in intercalating ligands by studying the interaction with DNA of a series of proflavine and acridine orange analogs differing in the heteroatoms present in the chromophore. Base specificity was determined by differential dialysis of the dye against DNA samples of differing G-C content. We find that G-C specificity increases as the visible absorbance band of the chromophore moves to longer wavelength, implying a relation between specificity and polarizability of the chromophore. This can be rationalized by recognizing that the G-C pair is more polar than A-T, and should therefore interact more favorably with an easily polarized ring system. We find in addition that dimethylation of the chromophore amino groups increases specificity which we discuss in terms of steric and coupled steric-electronic contributions. Our results also bear on the origin of G-C specificity in binding actinomycin to DNA. Some of the compounds studied are as G-C specific as actinomycin, yet they lack hydrogen-bonding functions as plausible determinants of specificity. This observation gives new life to the hypothesis that the specificity of actinomycin is determined primarily by preferential interaction of the chromophore with a G-C pair.
Transcriptome analysis during cell division in plants (2002)

Using synchronized tobacco Bright Yellow-2 cells and cDNA-amplified fragment length polymorphism-based genomewide expression analysis, we built a comprehensive collection of plant cell cycle-modulated genes. Approximately 1,340 periodically expressed genes were identified, including known cell cycle control genes as well as numerous unique candidate regulatory genes. A number of plant-specific genes were found to be cell cycle modulated. Other transcript tags were derived from unknown plant genes showing homology to cell cycle-regulatory genes of other organisms. Many of the genes encode novel or uncharacterized proteins, indicating that several processes underlying cell division are still largely unknown.
A G sα mutant designed to inhibit receptor signaling through G s (1999)

Hormonal signals activate trimeric G proteins by substituting GTP for GDP bound to the G protein alpha subunit (Galpha), thereby generating two potential signaling molecules, Galpha-GTP and free Gbetagamma. The usefulness of dominant negative mutations for investigating Ras and other monomeric G proteins inspired us to create a functionally analogous dominant negative Galpha mutation. Here we describe a mutant alpha subunit designed to inhibit receptor-mediated hormonal activation of Gs, the stimulatory regulator of adenylyl cyclase. To construct this mutant, we introduced into the alpha subunit (alphas) of Gs three separate mutations chosen because they impair alphas function in complementary ways: the A366S mutant reduces affinity of alphas for binding GDP, whereas the G226A and E268A mutations impair the protein's ability to bind GTP and to assume an active conformation. The triple mutant robustly inhibits (by up to 80%) Gs-dependent hormonal stimulation of adenylyl cyclase in cultured cells. Inhibition is selective in that it does not affect cellular responses to expression of a constitutively active alphas mutant (alphas-R201C) or to agonists for receptors that activate Gq or Gi. This alphas triple mutant and cognate Galpha mutants should provide specific tools for dissection of G protein-mediated signals in cultured cells and transgenic animals.
Fluorescence detection of alkylphosphonic acids using p-(9-anthroyloxy)phenacyl bromide (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescence detection of alkylphosphonic acids using p-(9-anthroyloxy)phenacyl bromideM. C. Roach, L. W. Ungar, R. N. Zare, L. M. Reimer, D. L. Pompliano, and J. W. FrostCite this: Anal. Chem. 1987, 59, 7, 1056–1059Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://doi.org/10.1021/ac00134a027RIGHTS & PERMISSIONSArticle Views269Altmetric-Citations41LEARN 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 (516 KB) Get e-Alerts Get e-Alerts
B cell responses to a peptide epitope. II: Multiple levels of selection during maturation of primary responses (1997)

This report analyses murine primary humoral recognition of a linear domain (MEP 17–31) within a 100 amino acid polypeptide. MEP‐I. An analysis of the early primary IgM response revealed that MEP 17–31 presented at least two distinct domains for pre‐immune B cell recognition represented by MEP‐1 residues 19–23 and 26–28. However, subsequent maturation into an IgG response saw an exclusive selection for the anti‐MEP 19–23 component with loss of all alternate specificities. The IgM response to MEP 19–23 was oligoclonal and composed of diverse paratope phenotypes as evidenced by varied heavy chains of immunoglobulin V–D‐J combinations and CDR3 sequences. In contrast to the oligoclonality of IgM niAb. the mature IgG response to MEP 19–23 appeared to derive predominantly from a single progenitor. It therefore appears that maturation of primary humoral responses to polypeptide antigens involves two distinct levels of selection. While there is selection for a restricted subset of the initially induced antibody fine‐specificities, progression of the response also entails a reduction in clonal heterogeneity of B cells responding to the dominant epitope.
PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element (2008)

The transcription factor PU.1 is an important regulator of hematopoiesis; precise expression levels are critical for normal hematopoietic development and suppression of leukemia. We show here that noncoding antisense RNAs are important modulators of proper dosages of PU.1. Antisense and sense RNAs are regulated by shared evolutionarily conserved cis-regulatory elements, and we can show that antisense RNAs inhibit PU.1 expression by modulating mRNA translation. We propose that such antisense RNAs will likely be important in the regulation of many genes and may be the reason for the large number of overlapping complementary transcripts with so far unknown function.
Assembly of Fibronectin into Extracellular Matrix (1991)

The results summarized above suggest that assembly of fibronectin is a fundamental biological process and that knowledge of the process of assembly may reveal new ways by which cells interact with extracellular molecules. Deposition of a fibronectin matrix seems to be regulated as tightly as synthesis of fibronectin or expression of adhesion receptors for fibronectin and is influenced profoundly by two products of blood coagulation--TGF-beta released from platelets and factor XIII activated by thrombin. Fibronectin assembly may be important in all sorts of physiological and pathophysiological processes. Cell A--for instance, a stromal cell--can influence the behavior of cell B--for instance, a lymphocyte--by assembling fibronectin made by cell C--for instance, a hepatocyte. We hope that the testable models of assembly presented in this paper will lead to new understanding of the process of assembly and suggest new modalities for treatment of diseases that result in fibrosis, damaged tissues, and neoplastic growth.
After Globalisation (2000)

Globalisation has become an almost ubiquitous term in academic debates, policy circles, and popular culture. In this paper we critically consider geography's characteristic form of engagement with the multifaceted features of globalisation discourses and realities. Globalisation provides an entry point for assertions of the conceptual and empirical importance of space, place, context, and locality. However, we argue that this form of engagement subordinates the central, and conceptually problematic, historicism of globalisation to a set of more manageable disciplinary concerns. We provide a critical discussion of the historicist dimensions of globalisation discourses, and indicate some of the ways in which critical accounts can reproduce this historicism. By raising this problem, we suggest that space and spatiality are not always or automatically the most significant entry point for conceptual critique and engagement. The case of globalisation therefore indicates some of the limits of established forms of interdisciplinary dialogue between critical human geography and related fields.
Phase I/II trial of cyclosporine as a chemotherapy-resistance modifier in acute leukemia. (1993)

High doses of CsA, which achieve blood concentrations capable of reversing P-glycoprotein-mediated anthracycline resistance in vitro, can be incorporated into induction regimens with acceptable nonhematologic toxicity. Transient hyperbilirubinemia occurs commonly with CsA administration and may alter daunorubicin pharmacokinetics. Recommended doses of CsA for phase II and III trials are a load of 6 mg/kg and CI of 16 mg/kg/d.
Digitoxin Analogues with Improved Anticytomegalovirus Activity (2014)

Cardiac glycosides are potent inhibitors of cancer cell growth and possess antiviral activities at nanomolar concentrations. In this study we evaluated the anticytomegalovirus (CMV) activity of digitoxin and several of its analogues. We show that sugar type and sugar length attached to the steroid core structure affects its anticytomegalovirus activity. Structure-activity relationship (SAR) studies identified the l-sugar containing cardiac glycosides as having improved anti-CMV activity and may lead to better understanding of how these compounds inhibit CMV replication.
EXPOSURE : Finding malicious domains using passive DNS analysis (2011)

The domain name service (DNS) plays an important role in the operation of the Internet, providing a two-way mapping between domain names and their numerical identifiers. Given its fundamental role, it is not surprising that a wide variety of malicious activities involve the domain name service in one way or another. For example, bots resolve DNS names to locate their command and control servers, and spam mails contain URLs that link to domains that resolve to scam servers. Thus, it seems beneficial to monitor the use of the DNS system for signs that indicate that a certain name is used as part of a malicious operation. In this paper, we introduce EXPOSURE, a system that employs large-scale, passive DNS analysis techniques to detect domains that are involved in malicious activity. We use 15 features that we extract from the DNS traffic that allow us to characterize different properties of DNS names and the ways that they are queried. Our experiments with a large, real-world data set consisting of 100 billion DNS requests, and a real-life deployment for two weeks in an ISP show that our approach is scalable and that we are able to automatically identify unknown malicious domains that are misused in a variety of malicious activity (such as for botnet command and control, spamming, and phishing). 1
Observation of two in-plane epitaxial states in YBa2Cu3O7−δ films on yttria-stabilized ZrO2 (1991)

We demonstrate that two distinctly different in-plane epitaxial states of c-axis oriented YBa2Cu3O7−δ (YBCO) films on (100) yttria-stabilized ZrO2 (YSZ) single-crystal substrates can be produced independently, namely, YBCO [100]//YSZ [100] or YBCO [100]//YSZ [110]. Both in-plane epitaxial relationships can be modeled by matching YBCO and YSZ oxygen sublattices at the film-substrate interface. High critical current densities (Jc), ∼5×105–1×106 A/cm2 at 77 K, are achieved when ≳90 vol % of either orientation is present. Jc can be degraded nearly four orders of magnitude in films with mixed orientation.
CARACTÉRISATION ACOUSTIQUE ET MÉCANIQUE DES AÉROGELS DE SILICE (1992)

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Rapid visual categorization is not guided by early salience-based selection (2019)

The current dominant visual processing paradigm in both human and machine research is the feedforward, layered hierarchy of neural-like processing elements. Within this paradigm, visual saliency is seen by many to have a specific role, namely that of early selection. Early selection is thought to enable very fast visual performance by limiting processing to only the most salient candidate portions of an image. This strategy has led to a plethora of saliency algorithms that have indeed improved processing time efficiency in machine algorithms, which in turn have strengthened the suggestion that human vision also employs a similar early selection strategy. However, at least one set of critical tests of this idea has never been performed with respect to the role of early selection in human vision. How would the best of the current saliency models perform on the stimuli used by experimentalists who first provided evidence for this visual processing paradigm? Would the algorithms really provide correct candidate sub-images to enable fast categorization on those same images? Do humans really need this early selection for their impressive performance? Here, we report on a new series of tests of these questions whose results suggest that it is quite unlikely that such an early selection process has any role in human rapid visual categorization.
The three‐dimensional solution structure of a constrained peptidomimetic in water and in chloroform observation of solvent induced hydrophobic cluster (1995)

A large number of protein-protein interactions involved turn or loop regions. The excised linear peptides from these regions reveal complex conformational averaging. To circumvent this motional averaging and to stabilize the beta-turn conformation, extensive effort has been devoted to the design of constrained peptidomimetics. Here, we report the three-dimensional solution structure of a 12-membered cyclic peptidomimetic. The structures were calculated from NMR studies performed in chloroform and in water at 263 and 278K, respectively. This 12-membered cyclic scaffolding is part of a program to design and to construct conformationally stable beta-turn peptidomimetics. The impact of the surrounding environment on the conformation of this constrained peptidomimetic is discussed. The general structural features of the cyclic mimetic are retained in both environments; however, the formation of a hydrophobic patch in the aqueous solvent is evident.
A new public key cryptosystem based on higher residues (1998)

This paper describm a new pub~c-key cryptosystem based on the hardnxs of computing higher residuw modulo a composite MA integer. We introduce two versions of our scheme, one deterministic and the other probabi~stic. The deterministic version is practically oriented encryption amounts to a single exponentiation w.r.t. a modulus with at least 768 bits and a 160-bit exponent. Decryption can be suitably optimized so as to become less demanding than a couple RSA decryptions. Although slower than MA, the new sdeme is still reasonably competitive and has several specific applications. The probabilistic version exhibits an homomorphic encryption scheme whose expansion rate is much better than previously proposed such systems. Furthermore, it has se mantic security, relative to the hardness of computing higher residu~s for suitable moduE.
Quantification of all fetal nucleated cells in maternal blood between the 18th and 22nd weeks of pregnancy using molecular cytogenetic techniques (2001)

Different types of nucleated fetal cells (trophoblasts, erythroblasts, lymphocytes, and granulocytes) have been recovered in maternal peripheral blood. In spite of many attempts to estimate the number of fetal cells in maternal circulation, there is still much controversy concerning this aspect. The numbers obtained vary widely, ranging from 1 nucleated cell per 104 to 1 per 109 nucleated maternal cells. The purpose of our project was to determine the absolute number of all different types of male fetal nucleated cells per unit volume of peripheral maternal blood. Peripheral blood samples were obtained from 12 normal pregnant women known to carry a male fetus between 18 and 22 weeks of pregnancy. Three milliliters (3 ml) of maternal blood has been processed without any enrichment procedures. Fluorescence in situ hybridization (FISH) and primed in situ labeling (PRINS) were performed, and fetal XY cells were identified (among maternal XX cells) and scored by fluorescent microscopy screening. The total number of male fetal nucleated cells per milliliter of maternal blood was consistent in each woman studied and varied from 2 to 6 cells per milliliter within the group of normal pregnancies. The number of fetal cells in maternal blood, at a given period, is reproducible and can therefore be assessed by cytogenetic methods. This confirms the possibility of developing a non-invasive prenatal diagnosis test for aneuploidies. Furthermore, we demonstrate that it is possible to repeatedly identify an extremely small number of fetal cells among millions of maternal cells.
Binding of Delta1, Jagged1, and Jagged2 to Notch2 Rapidly Induces Cleavage, Nuclear Translocation, and Hyperphosphorylation of Notch2 (2000)

Delta1, Jagged1, and Jagged2, commonly designated Delta/Serrate/LAG-2 (DSL) proteins, are known to be ligands for Notch1. However, it has been less understood whether they are ligands for Notch receptors other than Notch1. Meanwhile, ligand-induced cleavage and nuclear translocation of the Notch protein are considered to be fundamental for Notch signaling, yet direct observation of the behavior of the Notch molecule after ligand binding, including cleavage and nuclear translocation, has been lacking. In this report, we investigated these issues for Notch2. All of the three DSL proteins bound to endogenous Notch2 on the surface of BaF3 cells, although characteristics of Jagged2 for binding to Notch2 apparently differed from that of Delta1 and Jagged1. After binding, the three DSL proteins induced cleavage of the membrane-spanning subunit of Notch2 (Notch2(TM)), which occurred within 15 min. In a simultaneous time course, the cleaved fragment of Notch2(TM) was translocated into the nucleus. Interestingly, the cleaved Notch2 fragment was hyperphosphorylated also in a time-dependent manner. Finally, binding of DSL proteins to Notch2 also activated the transcription of reporter genes driven by the RBP-Jkappa-responsive promoter. Together, these data indicate that all of these DSL proteins function as ligands for Notch2. Moreover, the findings of rapid cleavage, nuclear translocation, and phosphorylation of Notch2 after ligand binding facilitate the understanding of the Notch signaling.
The role of concanavalin A dissociation on positive cooperativity of binding with native and fixed erythrocytes. (1979)

Positive cooperativity demonstrated by Scatchard plot analysis of concanavalin A (con A) binding was found with native or glutaraldehyde-fixed erythrocytes. This suggests that factors other than membrane changes might be involved in the apparent increase in receptor binding affinity with increasing site occupancy. The elution pattern of 125I-con A chromatographed on Bio-Gel P-150 with decreasing concentration showed a drop in average molecular weight compatible with con A dissociation to dimers, protomers, and protomer fragments. Similarly, the per cent of 125I-con A specifically binding to Sephadex G-75 fell with decreasing concentration of con A applied. The inclusion of unlabeled carrier con A suppressed the dissociation of labeled con A in Bio-Gel P-150 and increased the per cent binding to Sephadex G-75. Both labeled and unlabeled con A were multibanded in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. As previously reported, the three major bands are consistent with intact protomer (approximately 25,000 daltons) and two fragments (approximately 13,000 and 10,000 daltons) with minor bands representing undissociated species. These observations indicate that there is a concentration-dependent association of Con A subunits which contribute to the observed positive cooperativity of con A binding to erythrocytes.