gebhart/patrepeval huggingface dataset:
Relationship between internucleotide linkage geometry and the stability of RNA (1999)

The inherent chemical instability of RNA under physiological conditions is primarily due to the spontaneous cleavage of phosphodiester linkages via intramolecular transesterification reactions. Although the protonation state of the nucleophilic 2'-hydroxyl group is a critical determinant of the rate of RNA cleavage, the precise geometry of the chemical groups that comprise each internucleotide linkage also has a significant impact on cleavage activity. Specifically, transesterification is expected to be proportional to the relative in-line character of the linkage. We have examined the rates of spontaneous cleavage of various RNAs for which the secondary and tertiary structures have previously been modeled using either NMR or X-ray crystallographic data. Rate constants determined for the spontaneous cleavage of different RNA linkages vary by almost 10,000-fold, most likely reflecting the contribution that secondary and tertiary structures make towards the overall chemical stability of RNA. Moreover, a correlation is observed between RNA cleavage rate and the relative in-line fitness of each internucleotide linkage. One linkage located within an ATP-binding RNA aptamer is predicted to adopt most closely the ideal conformation for in-line attack. This linkage has a rate constant for transesterification that is approximately 12-fold greater than is observed for an unconstrained linkage and was found to be the most labile among a total of 136 different sites examined. The implications of this relationship for the chemical stability of RNA and for the mechanisms of nucleases and ribozymes are discussed.
Variation in a major surface protein of Lyme disease spirochetes (1984)

Two monoclonal antibodies (H6831 and H5TS) differed in their indirect immunofluorescence reactivity when tested against 14 strains of Lyme disease spirochetes. Strains were bound by both antibodies, by H6831 or H5TS alone, or by neither. Western blot and immunoprecipitation studies revealed that the determinants of both antibodies were associated with abundant proteins with apparent subunit molecular weights of ca. 34,000 (34K-range proteins). The following results indicated that the 34K-range proteins were exposed on the surface of the spirochetes. (i) Antibody H6831 agglutinated the spirochetes; (ii) immune electron microscopy showed that the H6831 determinant was associated with the outer membrane; (iii) radiolabeled H6831 bound to live organisms; and (iv) proteases effectively removed the 34K-range proteins from intact cells. With their demonstrated variability and exposure on the surface, the 34K-range proteins may contribute to the serotype specificity of Lyme disease spirochetes.
The role of galE in the biosynthesis and function of gonococcal lipopolysaccharide (1993)

Lipopolysaccharide is an essential component of the outer membrane of Gram-negative bacteria and an important virulence factor of many pathogens, such as Neisseria gonorrhoeae. We have cloned the gonococcal galE gene which was found to be located in the gonococcal homologue of the meningococcal capsule gene complex region D. Sequence alignment indicated extensive homology with the Escherichia coli and Salmonella GalE proteins. Mutants with insertions in the galE gene were used as a tool to characterize the structure and function of gonococcal lipopolysaccharide. They displayed deep rough phenotypes, and chemical analysis confirmed the loss of galactose from the mutant lipopolysaccharide. Functional analysis indicated that the terminal oligosaccharides contain galactose and that these are lost in galE mutants. The importance of these oligosaccharides in gonococcal biology is clear from the fact that they contain the epitopes that are the targets for killing by normal human serum, and the acceptor site for sialic acid, which acts to protect the gonococcus from this killing. Furthermore, infection experiments in vitro indicate that the galE mutants exhibit unaltered intergonococcal adhesion as well as adhesion to, and invasion of, epithelial cells.
国际原子能机构与不扩散核武器条约——核查挑战 挑战性核问题指明前进方向 (2005)

5年以前,全球性《不扩散核武器条约》成员国针对不扩散和裁军以及核技术的和平利用商定了若干前瞻性基本原则。这一点作为全球不扩散体制和在这方面多边合作的一项重要成就受到广泛欢迎。这一冷战时期诞生的《不扩散核武器条约》体制似乎得到加强,并且更好地适应迎接21世纪的挑战。
Promoter-targeted selection and isolation of neural progenitor cells from the adult human ventricular zone (2000)

Adult humans, like their nonhuman mammalian counterparts, harbor persistent neural progenitor cells in the forebrain ventricular lining. In the absence of adequate surface markers, however, these cells have proven difficult to isolate for study. We have previously identified and selected neural progenitor cells from both the fetal and adult rodent ventricular zone (VZ), by sorting forebrain cells transfected with plasmid DNA encoding the gene for green fluorescent protein driven by the early neuronal promoter for Talpha1 tubulin (P/Talpha1:hGFP). We have now extended this approach by purifying both P/Talpha1:hGFP tubulin-defined neuronal progenitors, as well as potentially less committed E/nestin:hGFP-defined neural progenitor cells, from the adult human VZ. The ventricular wall of the temporal horn of the lateral ventricle was dissected from temporal lobes obtained from four adult patients undergoing therapeutic lobectomy. These samples were dissociated, and the cultured cells transduced with either P/Talpha1:hGFP or E/nestin:EGFP plasmid DNA. A week later, the cells were redissociated, selected via fluorescence-activated cell sorting (FACS) on the basis of neural promoter-driven GFP expression, and replated. The majority of these cells expressed the early neuronal protein betaIII-tubulin upon FACS; within the week thereafter, most matured as morphologically evident neurons that coexpressed betaIII-tubulin and microtubule-associated protein (MAP)-2. Many of these neurons had incorporated bromodeoxyuridine in vitro in the days before FACS, indicating their mitogenesis in vitro. Thus, the use of fluorescent transgenes under the control of early neural promoters permits the enrichment of neuronal progenitor cells from the adult human ventricular zone. The specific acquisition, in both purity and number, of residual neural progenitor cells from the adult human brain may now permit hitherto unfeasible studies of both their biology and practical application.
Regulated proteolysis of Trop2 drives epithelial hyperplasia and stem cell self-renewal via β-catenin signaling (2012)

The cell surface protein Trop2 is expressed on immature stem/progenitor-like cells and is overexpressed in many epithelial cancers. However the biological function of Trop2 in tissue maintenance and tumorigenesis remains unclear. In this study, we demonstrate that Trop2 is a regulator of self-renewal, proliferation, and transformation. Trop2 controls these processes through a mechanism of regulated intramembrane proteolysis that leads to cleavage of Trop2, creating two products: the extracellular domain and the intracellular domain. The intracellular domain of Trop2 is released from the membrane and accumulates in the nucleus. Heightened expression of the Trop2 intracellular domain promotes stem/progenitor self-renewal through signaling via β-catenin and is sufficient to initiate precursor lesions to prostate cancer in vivo. Importantly, we demonstrate that loss of β-catenin or Trop2 loss-of-function cleavage mutants abrogates Trop2-driven self-renewal and hyperplasia in the prostate. These findings suggest that heightened expression of Trop2 is selected for in epithelial cancers to enhance the stem-like properties of self-renewal and proliferation. Defining the mechanism of Trop2 function in self-renewal and transformation is essential to identify new therapeutic strategies to block Trop2 activation in cancer.
Imaging strongly scattering media using a multiple frequency distorted Born iterative method (1998)

The distorted Born iterative (DBI) method is a powerful approach for solving the inverse scattering problem for ultrasound tomographic imaging. This method alternates between solving the inverse scattering problem for the scattering function and the forward scattering problem for the total field and the inhomogeneous Green's function. The algorithm is initialized using the basic Born inverse solution. One fundamental problem is the algorithm diverges for strongly scattering media. This is caused by the limitation of the Born assumption in estimating the initial step of the algorithm. We present a multiple frequency DBI approach to alleviate this problem, thus extending the applicability of the DBI method to the level of dealing with biological tissue. In this multiple frequency approach, a low frequency DBI-based solution, is used to initialize the algorithm at higher frequencies. The low frequency allows convergence of the algorithm to a contrast level that is close to the true level, however, with a poor spatial resolution. The high frequency improves the spatial resolution while preserving convergence because the difference between the true contrast and the initial contrast is relatively small. We present numerical simulations that demonstrate the ability of this method to reconstruct strongly scattering regions.
Long‐term treatment with lansoprazole for patients with Zollinger–Ellison syndrome (1996)

Lansoprazole effectively inhibits acid and pepsin secretion in Zollinger-Ellison syndrome patients without any demonstrated side-effects. Despite strict acid control, post-gastrectomy Zollinger-Ellison syndrome patients were more liable to ulcer relapse, while oesophagitis was not a marker for therapeutic difficulty.
Mitochondrial Aβ: a potential focal point for neuronal metabolic dysfunction in Alzheimer's disease (2005)

Although amyloid-beta peptide (Abeta) is the neurotoxic species implicated in the pathogenesis of Alzheimer's disease (AD), mechanisms through which intracellular Abeta impairs cellular properties, resulting in neuronal dysfunction, remain to be clarified. Here we demonstrate that intracellular Abeta is present in mitochondria from brains of transgenic mice with targeted neuronal overexpression of mutant human amyloid precursor protein and AD patients. Abeta progressively accumulates in mitochondria and is associated with diminished enzymatic activity of respiratory chain complexes (III and IV) and a reduction in the rate of oxygen consumption. Importantly, mitochondria-associated Abeta, principally Abeta42, was detected as early as 4 months, before extensive extracellular Abeta deposits. Our studies delineate a new means through which Abeta potentially impairs neuronal energetics, contributing to cellular dysfunction in AD.
A method for incorporating macromolecules into adherent cells. (1984)

We describe a simple method for loading exogenous macromolecules into the cytoplasm of mammalian cells adherent to tissue culture dishes. Culture medium was replaced with a thin layer of fluorescently labeled macromolecules, the cells were harvested from the substrate by scraping with a rubber policeman, transferred immediately to ice cold media, washed, and then replated for culture. We refer to the method as "scrape-loading." Viability of cells was 50-60% immediately after scrape-loading and was 90% for those cells remaining after 24 h of culture. About 40% of adherent, well-spread fibroblasts contained fluorescent molecules 18 h after scrape-loading of labeled dextrans, ovalbumin, or immunoglobulin-G. On average, 10(7) dextran molecules (70,000-mol wt) were incorporated into each fibroblast by scrape-loading in 10 mg/ml dextran. The extent of loading depended on the concentration and molecular weight of the dextrans used. A fluorescent analog of actin could also be loaded into fibroblasts where it labeled stress fibers. HeLa cells, a macrophage-like cell line, 1774A.1, and human neutrophils were all successfully loaded with dextran by scraping. The method of scrape-loading should be applicable to a broad range of adherent cell types, and useful for loading of diverse kinds of macromolecules.
p16 Stimulates CDC42-Dependent Migration of Hepatocellular Carcinoma Cells (2013)

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide. Tumor dissemination to the extra-hepatic region of the portal vein, lymph nodes, lungs or bones contributes to the high mortality seen in HCC; yet, the molecular mechanisms responsible for HCC metastasis remain unclear. Prior studies have suggested a potential link between accumulated cytoplasm-localized p16 and tumor progression. Here we report that p16 enhances metastasis-associated phenotypes in HCC cells - ectopic p16 expression increased cell migration in vitro, and lung colonization after intravenous injection, whereas knockdown of endogenous p16 reduced cell migration. Interestingly, analysis of p16 mutants indicated that the Cdk4 interaction domain is required for stimulation of HCC cell migration; however, knockdown of Cdk4 and Cdk6 showed that these proteins are dispensable for this phenomenon. Intriguingly, we found that in p16-positive HCC samples, p16 protein is predominantly localized in the cytoplasm. In addition, we identified a potential role for nuclear-cytoplasmic shuttling in p16-stimulated migration, consistent with the predominantly cytoplasmic localization of p16 in IHC-positive HCC samples. Finally, we determined that p16-stimulated cell migration requires the Cdc42 GTPase. Our results demonstrate for the first time a pro-migratory role for p16, and suggest a potential mechanism for the observed association between cytoplasmic p16 and tumor progression in diverse tumor types.
Selective inhibition of rRNA transcription downregulates E2F-1: a new p53-independent mechanism linking cell growth to cell proliferation (2011)

The tumour suppressor p53 negatively controls cell cycle progression in response to perturbed ribosome biogenesis in mammalian cells, thus coordinating growth with proliferation. Unlike mammalian cells, p53 is not involved in the growth control of proliferation in yeasts and flies. We investigated whether a p53-independent mechanism of response to inadequate ribosome biogenesis rate is also present in mammalian cells. We studied the effect of specific inhibition of rRNA synthesis on cell cycle progression in human cancer cell lines using the small-interfering RNA procedure to silence the POLR1A gene, which encodes the catalytic subunit of RNA polymerase I. We found that interference of POLR1A inhibited the synthesis of rRNA and hindered cell cycle progression in cells with inactivated p53, as a consequence of downregulation of the transcription factor E2F-1. Downregulation of E2F-1 was due to release of the ribosomal protein L11, which inactivated the E2F-1-stabilising function of the E3 ubiquitin protein ligase MDM2. These results demonstrated the existence of a p53-independent mechanism that links cell growth to cell proliferation in mammalian cells, and suggested that selective targeting of the RNA polymerase I transcription machinery might be advisable to hinder proliferation of p53-deficient cancer cells.
Applications of Blockchains in the Internet of Things: A Comprehensive Survey (2018)

The blockchain technology has revolutionized the digital currency space with the pioneering cryptocurrency platform named Bitcoin. From an abstract perspective, a blockchain is a distributed ledger capable of maintaining an immutable log of transactions happening in a network. In recent years, this technology has attracted significant scientific interest in research areas beyond the financial sector, one of them being the Internet of Things (IoT). In this context, the blockchain is seen as the missing link toward building a truly decentralized, trustless, and secure environment for the IoT and, in this survey, we aim to shape a coherent and comprehensive picture of the current state-of-the-art efforts in this direction. We start with fundamental working principles of blockchains and how blockchain-based systems achieve the characteristics of decentralization, security, and auditability. From there, we build our narrative on the challenges posed by the current centralized IoT models, followed by recent advances made both in industry and research to solve these challenges and effectively use blockchains to provide a decentralized, secure medium for the IoT.
Efficient Particle Production by Minimal Gag Constructs Which Retain the Carboxy-Terminal Domain of Human Immunodeficiency Virus Type 1 Capsid-p2 and a Late Assembly Domain (2000)

The human immunodeficiency virus type 1 (HIV-1) Gag precursor Pr55(gag) by itself is capable of assembling into retrovirus-like particles (VLP). In the present study, we attempted to identify the minimal Gag sequences required for the formation of VLP. Our results show that about 80% of Pr55(gag) can be either deleted or replaced by heterologous sequences without significantly compromising VLP production. The smallest chimeric molecule still able to efficiently form VLP was only about 16 kDa. This minimal Gag construct contained the leucine zipper domain of the yeast transcription factor GCN4 to substitute for the assembly function of nucleocapsid (NC), followed by a P-P-P-P-Y motif to provide late budding (L) domain function, and retained only the myristylation signal and the C-terminal capsid-p2 domain of Pr55(gag). We also show that the L domain function of HIV-1 p6(gag) is not dependent on the presence of an active viral protease and that the NC domain of Pr55(gag) is dispensable for the incorporation of Vpr into VLP.
Redirecting the specificity of ubiquitination by modifying ubiquitin-conjugating enzymes. (1995)

Depletion of specific cellular proteins is a powerful tool in biological research and has many medical and agricultural benefits. In contrast to genetic methods currently available to attenuate protein levels, we describe an alternative approach that redirects the ubiquitin-dependent proteolytic pathway to facilitate specific proteolytic removal. Degradation via the ubiquitin pathway requires the prior attachment of multiple ubiquitins to the target protein. This attachment is accomplished, in part, by a family of enzymes designated E2s (or ubiquitin-conjugating enzymes), some of which use domains near their C termini for target recognition. Here, we demonstrate that E2 target recognition can be redefined by engineering E2s to contain appropriate protein-binding peptides fused to their C termini. In five dissimilar examples, chimeric E2s were created that recognized and ubiquitinated their respective binding partners with high specificity. We also show that ubiquitination of one protein targeted by this method led to its ATP-dependent degradation in vitro. Thus, by exploiting interacting domains derived from natural and synthetic ligands, it may be possible to design E2s capable of directing the selective removal of many intracellular proteins.
p16 alterations and deletion mapping of 9p21-p22 in malignant mesothelioma. (1994)

To determine whether p16 is altered in human malignant mesothelioma (MM), molecular analysis of multiple 9p loci was performed on 40 cell lines and 23 primary tumors from 42 MM patients. We identified homozygous deletions of p16 in 34 (85%) cell lines and a point mutation in 1 line. Down-regulation of p16 was observed in 4 of the remaining cell lines, 1 of which displayed a DNA rearrangement of p16. Homozygous deletions of p16 were identified in 5 of 23 (22%) primary tumors; no mutations or rearrangements were found in these specimens. Four cell lines displayed a single homozygous deletion proximal to or distal to p16; 4 others had 2 nonoverlapping deletions, one involving p16 and the other involving a region proximal to this locus. These data indicate that alterations of p16 are a common occurrence in MM cell lines and, to a lesser extent, in primary tumors. Furthermore, deletions of 9p21-p22 outside of the p16 locus may reflect the involvement of other putative tumor suppressor genes that could also contribute to the pathogenesis of some MMs.
Digital Readout of Target Binding with Attomole Detection Limits via Enzyme Amplification in Femtoliter Arrays (2006)

In this communication, single molecules of beta-galactosidase were captured on a 1 mm femtoliter array using biotin-streptavidin binding. The femtoliter arrays, containing 24 000 individual reaction chambers, permit digital concentration readout as the percentage of reaction vessels that successfully capture a target molecule is correlated to the bulk target concentration. This capture and readout approach should prove useful for DNA and antibody assays that utilize an enzyme label to catalyze the generation of a fluorescent signal.
Influence of antidepressant drugs on learning and memory paradigms in mice. (1996)

Effect of antidepressant drugs (amitriptyline, imipramine and fluoxetine) on cognitive functions, impaired by the muscarinic antagonist scopolamine were investigated in mice. The changes in learning and memory tasks were studied using transfer latency on elevated plus maze and employing number of descents in passive avoidance paradigms. Amitriptyline and imipramine showed significant memory impairment. They also potentiated scopolamine-induced memory deficit in a significant way. Amitriptyline and imipramine impair cognitive function possibly due to their anticholinergic properties. Fluoxetine, a newer antidepressant, however showed no effect on learning and memory. It significantly reversed the scopolamine-induced memory impairment in both the tests. Fluoxetine with no anticholinergic property may prove to be a better drug in endogenous depression in elderly patients.
Formulation Development of Phase 1–2 Biopharmaceuticals: An Efficient and Timely Approach (2010)

This chapter contains sections titled: Introduction Formulation Options and Lessons Learned Preformulation of Unusual Proteins Assessment of Formulation Performance Summary References
Use of Antimicrobial Agents in Animal Feeds: Implications for Human Health (1987)

The inclusion of subtherapeutic doses of antimicrobial agents in animal feed is credited for having contributed to lower costs of meat, milk, and eggs. The practice often is associated with the acquisition of resistant enteric flora by the involved animals, a phenomenon that in turn may contribute to the human reservoir of coliforms and salmonellae resistant to antimicrobial agents. Farm workers may transiently acquire resistant intestinal flora and on rare occasions develop salmonellosis. Although irrefutable evidence of the growth-promoting properties of antibiotics in animal feed was provided 30-40 years ago, additional studies--with a focus on mechanisms of the effect--are presently needed. It may be possible to identify factors effective in promoting growth without deleterious effects on the intestinal flora. A national program of surveillance of antimicrobial administration (in both subtherapeutic and therapeutic doses) to food-producing animals should be established. Molecular epidemiologic research efforts must be undertaken to determine whether genetic information of animal origin contributes significantly to the human environmental pool of antimicrobial resistance. In the meantime, it does not appear that the banning of drugs as feed additives, with concomitant unrestricted use of these agents for the treatment of both animals and people, would favorably influence the problems of antimicrobial resistance and salmonellosis in human populations.