gebhart/patrepeval huggingface dataset:
Transposon mutagenesis of type III group B Streptococcus: correlation of capsule expression with virulence. (1987)

The capsular polysaccharide of type III group B Streptococcus (GBS) is thought to be a major factor in the virulence of this organism. Transposon mutagenesis was used to obtain isogenic strains of a GBS serotype III clinical isolate (COH 31r/s) with site-specific mutations in the gene(s) responsible for capsule production. The self-conjugative transposon Tn916 was transferred to strain COH 31r/s during incubation with Streptococcus faecalis strain CG110 on membrane filters. Eleven transconjugant clones did not bind type III GBS antiserum by immunoblot. Immunofluorescence, competitive ELISA, and electron microscopy confirmed the absence of detectable GBS type III capsular polysaccharide in one of the transconjugants, COH 31-15. Southern hybridization analysis with a Tn916 probe confirmed the presence of the transposon sequence within each mutant. A 3.0-kilobase EcoRI fragment that flanked the Tn916 sequence was subcloned from mutant COH 31-15. This fragment shared homology with DNA from the other GBS serotypes, suggesting a common sequence for capsulation shared by organisms of different capsular types. Loss of capsule expression resulted in loss of virulence in a neonatal rat model. We conclude that a gene common to all capsular types of GBS is required for surface expression of the type III capsule and that inactivation of this gene by Tn916 results in the loss of virulence.
Cloning Vectors Based on Cryptic Plasmids Isolated from Lactic Acid Bacteria:Their Characteristics and Potential Applications in Biotechnology (2004)

Lactic acid bacteria (LAB) are Gram positive bacteria, widely distributed in nature, and industrially important as they are used in a variety of industrial food fermentations. The use of genetic engineering techniques is an effective means of enhancing the industrial applicability of LAB. However, when using genetic engineering technology, safety becomes an essential factor for the application of improved LAB to the food industry. Cloning and expression systems should be derived preferably from LAB cryptic plasmids that generally encode genes for which functions can be proposed, but no phenotypes can be observed. However, some plasmid-encoded functions have been discovered in cryptic plasmids originating from Lactobacillus, Streptococcus thermophilus, and Pediococcus spp. and can be used as selective marker systems in vector construction. This article presents information concerning LAB cryptic plasmids, and their structures, functions, and applications. A total of 134 cryptic plasmids collated are discussed.
Ultra-sensitive protein detection using single molecule arrays (SiMoA): the potential for detecting single molecules of botulinum toxin (2012)

Single molecule arrays (SiMoA) make it possible to detect subfemtomolar concentrations of proteins in complex samples. We describe the basis of SiMoA and its potential application in the detection of proteins, such as botulinum neurotoxin (BoNT), from pathogenic bacteria. We also provide a concept for an integrated handheld SiMoA device for the detection of very low concentrations of BoNT in the field.
Rules governing the crystal packing of mono- and dialcohols (2001)

A new program, Mercury, has been used to survey 144 monoalcohol (C(m)H(n)OH) and 101 dialcohol [C(m)H(n)(OH)(2)] crystal structures. Results show that their hydrogen-bonding patterns are strongly correlated with steric effects. Primary monoalcohols have a strong preference to form infinite ...OH...OH... chains. Secondary monoalcohols form chains and rings of hydrogen bonds with about equal facility. Tertiary monoalcohols very often form isolated OH...O hydrogen bonds or structures containing no OH...O hydrogen bonds at all. In the latter case, however, the structures almost invariably contain CH...O and/or OH...pi interactions. Substitution on the beta-carbon(s) of monoalcohols has a profound effect on packing patterns, with increased substitution disfavouring chains and rings. Dialcohols show a much stronger preference for chains of hydrogen bonds, compared with monoalcohols. This is particularly so when at least one of the hydroxyl groups is primary, in which case chains are overwhelmingly preferred. Once again, substitution on the beta-C atoms is influential, heavy substitution tending to lead to packing arrangements that involve isolated or intramolecular OH...O hydrogen bonds. Dialcohols almost never crystallize without at least some OH...O hydrogen-bond formation. In both monoalcohols and dialcohols, chains show a stronger preference to be helical (usually threefold helices) as steric hindrance increases. Hydrogen-bonded rings usually contain four OH...O hydrogen bonds. It is possible that empirical observations such as these may aid crystal-structure prediction.
GCD10, a translational repressor of GCN4, is the RNA-binding subunit of eukaryotic translation initiation factor-3. (1995)

GCN4 mRNA is translated by a reinitiation mechanism involving four short upstream open reading frames (uORFs) in its leader sequence. Decreasing the activity of eukaryotic initiation factor-2 (eIF-2) by phosphorylation inhibits general translation in yeast but stimulates GCN4 expression by allowing ribosomes to scan past the uORFs and reinitiate at GCN4 instead. GCD10 was first identified genetically as a translational repressor of GCN4. We show here that GCD10 is an essential protein of 54.6 kD that is required in vivo for the initiation of total protein synthesis. GCD10 binds RNA in vitro and we present strong biochemical evidence that it is identical to the RNA-binding subunit of yeast initiation factor-3 (eIF-3). eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. We suggest that gcd10 mutations decrease the ability of eIF-3 to stimulate binding of eIF-2/GTP/Met-tRNA(iMet) ternary complexes to small ribosomal subunits in vivo. This would explain why mutations in eIF-3 mimic eIF-2 alpha phosphorylation in allowing ribosomes to bypass the uORFs and reinitiate at GCN4. Our results indicate that GCN4 expression provides a sensitive in vivo assay for the function of eIF-3 in initiation complex formation.
Nanoscale CMOS for mm-Wave Applications (2007)

Aggressive technology scaling of CMOS has culminated in a low-cost high volume commercial process technology with F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> > 150 GHz and F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> > 200 GHz. This paper discusses the key trends in CMOS scaling that have led to this level of performance and attempts to predict the performance down to 45 nm. The design of active and passive components in CMOS for power gain and low noise are discussed in detail and unique features of CMOS technology are highlighted. Experimental results derived from a 60 GHz amplifier in 90 nm CMOS and a complete 60 GHz front-end receiver in 130 nm CMOS are reported.
Controlling the Future of Matter (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTControlling the Future of MatterBern Kohler, Jeffrey L. Krause, Ferenc Raksi, Kent R. Wilson, Vladislav V. Yakovlev, Robert M. Whitnell, and YiJing YanCite this: Acc. Chem. Res. 1995, 28, 3, 133–140Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/ar00051a006https://doi.org/10.1021/ar00051a006research-articleACS PublicationsRequest reuse permissionsArticle Views741Altmetric-Citations141LEARN 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
'Defying the Clock' – a Profile of Australians who ignore Retirement Planning (2002)

The Australian population is ageing. In the last 20 years, the number of people aged 65 years and over has increased by 65 percent and those over 85 years have increased by 156 percent. At the same time as the age structure of the population has changed, successive Australian Governments have signified that they are worried by an increasing dependency rate and have put in place a comprehensive retirement incomes policy. However, anecdotally there is a significant sector of the population which has not attempted to come to grips with the problem of their postretirement incomes and has neither planned nor started pre-retirement wealth accumulation. This research builds a profile of this sector and finds that the typical non-planner is likely to be a single, low-income, relatively lowly educated casual female employee. This finding has important implications for government retirement-incomes and education policies.
Mirror Puppeteering (2015)

Mirror Puppeteering is a system for easily creating gestures ("animations") for robotic toys, custom robots, and virtual characters. Lay users can record animations by simply moving a robot's limbs in front of a webcam. Makers and hobbyists can use the system to easily set up their custom-built robots for animation. Gamers and amateur animators can real-time control or save animations for virtual characters. Our system works by tracking circular markers on the robot's surface and translating these into motor commands, using a calibration map between marker locations in camera space and motor angles. New robots can be quickly set up for Mirror Puppeteering without knowledge of the robot's 3D structure, as we demonstrate on several robots. In a user study, participants found our method more enjoyable, usable, easy to learn, and successful than traditional animation methods.
Human Matrix Attachment Regions Insulate Transgene Expression from Chromosomal Position Effects in Drosophila melanogaster (1998)

Germ line transformation of white- Drosophila embryos with P-element vectors containing white expression cassettes results in flies with different eye color phenotypes due to position effects at the sites of transgene insertion. These position effects can be cured by specific DNA elements, such as the Drosophila scs and scs' elements, that have insulator activity in vivo. We have used this system to determine whether human matrix attachment regions (MARs) can function as insulator elements in vivo. Two different human MARs, from the apolipoprotein B and alpha1-antitrypsin loci, insulated white transgene expression from position effects in Drosophila melanogaster. Both elements reduced variability in transgene expression without enhancing levels of white gene expression. In contrast, expression of white transgenes containing human DNA segments without matrix-binding activity was highly variable in Drosophila transformants. These data indicate that human MARs can function as insulator elements in vivo.
Synthesis and Characterization of the Arylomycin Lipoglycopeptide Antibiotics and the Crystallographic Analysis of Their Complex with Signal Peptidase (2011)

Glycosylation of natural products, including antibiotics, often plays an important role in determining their physical properties and their biological activity, and thus their potential as drug candidates. The arylomycin class of antibiotics inhibits bacterial type I signal peptidase and is comprised of three related series of natural products with a lipopeptide tail attached to a core macrocycle. Previously, we reported the total synthesis of several A series derivatives, which have unmodified core macrocycles, as well as B series derivatives, which have a nitrated macrocycle. We now report the synthesis and biological evaluation of lipoglycopeptide arylomycin variants whose macrocycles are glycosylated with a deoxy-α-mannose substituent, and also in some cases hydroxylated. The synthesis of the derivatives bearing each possible deoxy-α-mannose enantiomer allowed us to assign the absolute stereochemistry of the sugar in the natural product and also to show that while glycosylation does not alter antibacterial activity, it does appear to improve solubility. Crystallographic structural studies of a lipoglycopeptide arylomycin bound to its signal peptidase target reveal the molecular interactions that underlie inhibition and also that the mannose is directed away from the binding site into solvent which suggests that other modifications may be made at the same position to further increase solubility and thus reduce protein binding and possibly optimize the pharmacokinetics of the scaffold.
Some fundamental properties of speckle* (1976)

A speckle pattern formed in polarized monochromatic light may be regarded as resulting from a classical random walk in the complex plane. The resulting irradiance fluctuations obey negative exponential statistics, with ratio of standard deviation to mean (i.e., contrast) of unity. Reduction of this contrast, or smoothing of the speckle, requires diversity in polarization, space, frequency, or time. Addition of M uncorrelated speckle patterns on an intensity basis can reduce the contrast by 1/√M. However, addition of speckle patterns on a complex amplitude basis provides no reduction of contrast. The distribution of scale sizes in a speckle pattern (i.e., the Wiener spectrum) is investigated from a physical point of view.
A single amino acid deletion at the amino terminus of influenza virus hemagglutinin causes malfolding and blocks exocytosis of the molecule in mammalian cells. (1992)

I am investigating the role of protein folding in the transport of influenza virus hemagglutinin (HA), a membrane-bound protein, along the exocytotic pathway. From a previous work (Gething, M.-J., McCammon, K., and Sambrook, J. (1986) Cell 46, 939-950), it has been shown that a subset of alterations of the COOH-terminal sequences of the HA molecule inhibit folding and impede its transport to the cell surface. Current studies establish that the integrity of the NH2-terminal sequences of the HA is essential for assembly and transport of the molecule. Mutants lacking just 1 or 2 amino acids immediately COOH-terminal to the signal cleavage site are translocated and core glycosylated, but also incorrectly folded. The mutant molecules are not terminally glycosylated and are thus confined inside the cells. A hypothesis will be presented to explain why sequences at opposite ends of the HA molecule are essential for the assembly of native structures and why correct folding is necessary for transport along the exocytotic pathway of mammalian cells.
Some heuristics for generating tree-like FBDD types (1996)

Reduced ordered binary decision diagrams (OBDD's) are nowadays the state-of-the-art representation scheme for Boolean functions in Boolean manipulation. Recent results have shown that it is possible to use the more general concept of free binary decision diagrams (FBDD's) without giving up most of the useful computational properties of OBDD's, but possibly reducing the space requirements considerably. The amount of space reduction depends essentially on the shape of so-called FBDD-types the Boolean manipulation in terms of FBDD's is based on. Here, we propose some heuristics for deriving tree-like FBDD-types from given circuit descriptions. The experimental results we obtained clearly demonstrate that the FBDD-approach is not only of theoretical interest, but also of practical usefulness even in the ease of using merely such simple-structured tree-based FBDD-types as produced by the investigated heuristics.
A frequency-domain algorithm to upscale ambisonic sound scenes (2012)

In this paper, a novel algorithm for upscaling ambisonic sound scenes in the frequency domain is presented. This algorithm makes use of compressed sensing techniques to calculate a set of upscaling filters. These filters are then used to increase the spherical harmonic order of a set of ambisonic sound signals to higher orders. Upscaled ambisonic sound scenes have a greater spatial resolution, which allows more loudspeakers to be used during the playback, resulting in a larger sweet spot and improved sound quality. A formal listening test was conducted to evaluate the perceptual quality of sound fields reproduced using this technique. Results show that the proposed algorithm significantly improves the perceptual fidelity of the sound field reproduction, in comparison to classical ambisonic methods.
Gene expression and cytopathic effect of vaccinia virus inactivated by psoralen and long-wave UV light (1996)

Induction of the cytopathic effect (CPE) in cells infected with poxvirus seems ubiquitous in that it has been associated with all different strains and preparations of poxviruses, regardless of the replicating status of these viruses. The study of the mechanisms by which CPE is induced by nonreplicating poxviruses is hampered by the lack of any noncytopathic mutant strains and preparations. In this paper, we report on the patterns of gene expression and induction of CPE by vaccinia viruses treated by limited cross-linking with psoralen and long-wave UV light (PLWUV). We show that treatment of cell-free virus with PLWUV could inactivate viral replication without abolishing the ability of the virus to infect cells. Viral transcription as indicated by reporter genes was generally enhanced and prolonged under early viral promoters and abolished under late promoters. Furthermore, increasing the levels of cross-linking with PLWUV resulted in a decrease and abolishment of viral expression of a large reporter gene and a concomitant loss of the induction of CPE. Cells infected with such a virus were able to express the reporter genes and proliferate. The generation of nonreplicating and noncytopathic recombinant vaccinia viruses may help in studies of the mechanisms of CPE induction by poxvirus and may facilitate the use of poxviral vectors in broader areas of research and clinical applications.
Identification of a core member of the SWI/SNF complex, BAF155/SMARCC1, as a human tumor suppressor gene (2011)

Recent studies have established that two core members of the SWI/SNF chromatin remodeling complex, BRG1 and SNF5/INI1, possess tumor-suppressor activity in human and mouse cancers. While the third core member, BAF155, has been implicated by several studies as having a potential role in tumor development, direct evidence for its tumor suppressor activity has remained lacking. Therefore, we screened for BAF155 deficiency in a large number of human tumor cell lines. We identified 2 cell lines, the SNUC2B colon carcinoma and the SKOV3 ovarian carcinoma, displaying a complete loss of protein expression while maintaining normal levels of mRNA expression. The SKOV3 cell line possesses a heterozygous 4bp deletion that results in an 855AA truncated protein, while the cause of the loss of BAF155 expression in the SNUC2B cell line appears due to a post-transcriptional error. However, the lack of detectable BAF155 expression did not affect sensitivity to RB-mediated cell cycle arrest. Re-expression of full length but not a truncated form of BAF155 in the two cancer cell lines leads to reduced colony forming ability characterized by replicative senescence but not apoptosis. Collectively, these data suggest that loss of BAF155 expression represents another mechanism for inactivation of SWI/SNF complex activity in the development in human cancer. Our results further indicate that the c-terminus proline-glutamine rich domain plays a critical role in the tumor suppressor activity of this protein.
Molecular biology of RNA (1987)

The book's contents are: RNA as an Enzyme; RNA: Structure, Function, and Isolation; RNA Splicing; RNA Viruses; RNA in DNA Replication; and RNA in Regulation and Repression.
A few autoreactive cells in an autoimmune infiltrate control a vast population of nonspecific cells: a tale of smart bombs and the infantry. (1996)

Inflammatory infiltrates in tissue-specific autoimmune disease comprise a collection of T cells with specificity for an antigen in the target organ. These specific cells recruit a population of nonspecific T cells and macrophages. The rare tissue-specific T cells in the infiltrate have the capacity to regulate both the influx and the efflux of cells from the tissue. Administration of an altered peptide ligand for the specific T cell which triggers autoimmunity can lead to the regression of the entire inflammatory ensemble in a few hours. Interleukin 4 is a critical cytokine involved in the regression of the inflammatory infiltrate.
Adam12 in Human Liver Cancers: Tgf–β–Regulated Expression in Stellate Cells Is Associated With Matrix Remodeling (2003)

"A disintegrin and metalloproteinases" (ADAMs) form a family of cell-surface glycoproteins with potential protease and cell-adhesion activities. We have investigated ADAM expression in human liver cancers and their regulation by several cytokines involved in liver injury. Using degenerative RT-PCR, cDNA encoding sequences for ADAM9 and ADAM12 were identified in human activated hepatic stellate cells (HSCs). Northern blot analyses showed that HSCs, but not hepatocytes, expressed transcripts for ADAM9 messenger RNA (mRNA) and both the long and short forms of ADAM12. This expression was associated with the transition from quiescent to activated state of rat HSCs and markedly increased in human livers with cirrhosis. ADAM12 but not ADAM9 expression was up-regulated by transforming growth factor beta (TGF-beta) in human activated HSCs. The PI3K inhibitor LY294002 and the mitogen-activated protein kinase kinase (MEK) inhibitor UO126 prevented ADAM12 induction by TGF-beta, suggesting the involvement of PI3K and MEK activities. In vivo, the steady-state of both ADAM9 and ADAM12 mRNA levels was nearly undetectable in both normal livers and benign tumors and increased in hepatocellular carcinomas (up to 3- and 6-fold, respectively) and liver metastases from colonic carcinomas (up to 40- and 60-fold, respectively). The up-regulation of both ADAM9 and ADAM12 was correlated with an increase in matrix metalloproteinase 2 expression and activity. In conclusion, in liver cancers ADAM9 and ADAM12 expression is associated with tumor aggressiveness and progression.