gebhart/patrepeval huggingface dataset:
Efficient Transcriptional Silencing in Saccharomyces cerevisiae Requires a Heterochromatin Histone Acetylation Pattern (1996)

Heterochromatin in metazoans induces transcriptional silencing, as exemplified by position effect variegation in Drosophila melanogaster and X-chromosome inactivation in mammals. Heterochromatic DNA is packaged in nucleosomes that are distinct in their acetylation pattern from those present in euchromatin, although the role these differences play in the structure of heterochromatin or in the effects of heterochromatin on transcriptional activity is unclear. Here we report that, as observed in the facultative heterochromatin of the inactive X chromosome in female mammalian cells, histones H3 and H4 in chromatin spanning the transcriptionally silenced mating-type cassettes of the yeast Saccharomyces cerevisiae are hypoacetylated relative to histones H3 and H4 of transcriptionally active regions of the genome. By immunoprecipitation of chromatin fragments with antibodies specific for H4 acetylated at particular lysine residues, we found that only three of the four lysine residues in the amino-terminal domain of histone H4 spanning the silent cassettes are hypoacetylated. Lysine 12 shows significant acetylation levels. This is identical to the pattern of histone H4 acetylation observed in centric heterochromatin of D. melanogaster. These two observations provide additional evidence that the silent cassettes are encompassed in the yeast equivalent of metazoan heterochromatin. Further, mutational analysis of the amino-terminal domain of histone H4 in S. cerevisiae demonstrated that this observed pattern of histone H4 acetylation is required for transcriptional silencing. This result, in conjunction with prior mutational analyses of yeast histones H3 and H4, indicates that the particular pattern of nucleosome acetylation found in heterochromatin is required for its effects on transcription and is not simply a side effect of heterochromatin formation.
Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W] (2004)

The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
A Fully Magnetically Levitated Circulatory Pump for Advanced Heart Failure (2016)

Among patients with advanced heart failure, implantation of a fully magnetically levitated centrifugal-flow pump was associated with better outcomes at 6 months than was implantation of an axial-flow pump, primarily because of the lower rate of reoperation for pump malfunction. (Funded by St. Jude Medical; MOMENTUM 3 ClinicalTrials.gov number, NCT02224755 .).
Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. (2001)

Restriction-modification (RM) systems comprise two opposing enzymatic activities: a restriction endonuclease, that targets specific DNA sequences and performs endonucleolytic cleavage, and a modification methyltransferase that renders these sequences resistant to cleavage. Studies on molecular genetics and biochemistry of RM systems have been carried out over the past four decades, laying foundations for modern molecular biology and providing important models for mechanisms of highly specific protein-DNA interactions. Although the number of known, relevant sequences 3D structures of RM proteins is growing steadily, we do not fully understand their functional diversities from an evolutionary perspective and we are not yet able to engineer new sequence specificities based on rational approaches. Recent findings on the evolution of RM systems and on their structures and mechanisms of action have led to a picture in which conserved modules with defined function are shared between different RM proteins and other enzymes involved in nucleic acid biochemistry. On the other hand, it has been realized that some of the modules have been replaced in the evolution by unrelated domains exerting similar function. The aim of this review is to give a survey on the recent progress in the field of structural phylogeny of RM enzymes with special emphasis on studies of sequence-structure-function relationships and emerging potential applications in biotechnology.
Stereocontrolled synthesis of phosphorothioate DNA by an oxazaphospholidine approach (2003)

Stereocontrolled synthesis of oligodeoxyribonucleoside phosphorothioates using nucleoside 3'-O-oxazaphospholidine derivatives as monomer units is described. N-(Cyanomethyl)pyrrolidinium triflate (CMPT) was found to be effective as an activator for the highly diastereoselective internucleotidec bond formation. The present method was applied to the solid-phase synthesis of stereoregulated oligodeoxyribonucleoside phosphorothioates.
Colistin: The Revival of Polymyxins for the Management of Multidrug-Resistant Gram-Negative Bacterial Infections (2005)

The emergence of multidrug-resistant gram-negative bacteria and the lack of new antibiotics to combat them have led to the revival of polymyxins, an old class of cationic, cyclic polypeptide antibiotics. Polymyxin B and polymyxin E (colistin) are the 2 polymyxins used in clinical practice. Most of the reintroduction of polymyxins during the last few years is related to colistin. The polymyxins are active against selected gram-negative bacteria, including Acinetobacter species, Pseudomonas aeruginosa, Klebsiella species, and Enterobacter species. These drugs have been used extensively worldwide for decades for local use. However, parenteral use of these drugs was abandoned approximately 20 years ago in most countries, except for treatment of patients with cystic fibrosis, because of reports of common and serious nephrotoxicity and neurotoxicity. Recent studies of patients who received intravenous polymyxins for the treatment of serious P. aeruginosa and Acinetobacter baumannii infections of various types, including pneumonia, bacteremia, and urinary tract infections, have led to the conclusion that these antibiotics have acceptable effectiveness and considerably less toxicity than was reported in old studies.
Pathogenic Role of Oxidative Stress in Vascular Angiotensin-Converting Enzyme Activation in Long-Term Blockade of Nitric Oxide Synthesis in Rats (1999)

Inhibition of nitric oxide (NO) synthesis with N(omega)-nitro-L-arginine methyl ester (L-NAME) activates vascular angiotensin-converting enzyme (ACE) and causes oxidative stress. We investigated the role of oxidative stress in the pathogenesis of ACE activation in rats. Studies involved aortas of rats receiving no treatment, L-NAME, L-NAME plus L-arginine, or L-NAME plus an antioxidant drug (N-acetylcysteine, allopurinol, or ebselen) for 7 days. L-NAME significantly increased oxidative stress (O(2)(-)) and ACE activity. The increased O(2)(-) production was normalized by removal of endothelium. Immunohistochemistry showed the increased ACE activity in the endothelial layer. Treatment with antioxidant drugs did not affect the L-NAME-induced increase in systolic arterial pressure but did prevent increases in vascular O(2)(-) production and ACE activity. These results implicate oxidative stress in the pathogenesis of vascular ACE activation in rats with long-term inhibition of NO synthesis. The observed effects of antioxidant drugs on ACE activation do not appear to involve the hypertension induced by L-NAME.
Glyphosate resistance in perennial Sorghum halepense (Johnsongrass), endowed by reduced glyphosate translocation and leaf uptake (2011)

The results of the present investigation indicate that reduced glyphosate translocation to meristems is the primary mechanism endowing glyphosate resistance in S. halepense from cropping fields in Argentina. To a lesser extent, reduced glyphosate leaf uptake has also been shown to be involved in glyphosate-resistant S. halepense.
Visual snippets (2009)

People regularly interact with different representations of Web pages. A person looking for new information may initially find a Web page represented as a short snippet rendered by a search engine. When he wants to return to the same page the next day, the page may instead be represented by a link in his browser history. Previous research has explored how to best represent Web pages in support of specific task types, but, as we find in this paper, consistency in representation across tasks is also important. We explore how different representations are used in a variety of contexts and present a compact representation that supports both the identification of new, relevant Web pages and the re-finding of previously viewed pages.
Genes Involved in the Uptake and Catabolism of Gluconate by Escherichia coli (1975)

The isolation and properties of a mutant of Escherichia coli K12 that is totally unable to take up and utilize gluconate are described. Genetical analysis shows this phenotype to be associated with two lesions. One phenotype, designated GntM-, is the result of a mutation in a gene co-transducible with malA; the other, designated GNTS-, is the result of a mutation in a gene (GntS) co-transducible with fdp. The GntS--phenotype differs little from that of wild-type cells, but GntM- GntS+ organisms grow on gluconate only after a prolonged lag and form a gluconate uptake system that is strongly repressed by pyruvate. Moreover, such GntM- mutants readily give rise to further mutants that form a gluconate uptake system, gluconate kinase and 6-phosphogluconate dehydratase consititutively; in partial diploids, this constitutivity is recessive to the inducible character. It is postulated that the GntM- phenotype is due to malfunction of a negative control gene gntR, and that gntS+ specifies the activity of a gluconate uptake system.
Simulations of neuromuscular control in lamprey swimming (1999)

The neuronal generation of vertebrate locomotion has been extensively studied in the lamprey. Models at different levels of abstraction are being used to describe this system, from abstract nonlinear oscillators to interconnected model neurons comprising multiple compartments and a Hodgkin-Huxley representation of the most relevant ion channels. To study the role of sensory feedback by simulation, it eventually also becomes necessary to incorporate the mechanical movements in the models. By using simplifying models of muscle activation, body mechanics, counteracting water forces, and sensory feedback through stretch receptors and vestibular organs, we have been able to close the feedback loop to enable studies of the interaction between the neuronal and the mechanical systems. The neuromechanical simulations reveal that the currently known network is sufficient for generating a whole repertoire of swimming patterns. Swimming at different speeds and with different wavelengths, together with the performance of lateral turns can all be achieved by simply varying the brainstem input. The neuronal mechanisms behind pitch and roll manoeuvres are less clear. We have put forward a 'crossed-oscillators' hypothesis where partly separate dorsal and ventral circuits are postulated. Neuromechanical simulations of this system show that it is also capable of generating realistic pitch turns and rolls, and that vestibular signals can stabilize the posture during swimming.
Universal TA Cloning (2000)

TA cloning is one of the simplest and most efficient methods for the cloning of PCR products. The procedure exploits the terminal transferase activity of certain thermophilic DNA polymerases, including Thermus aquaticus (Taq) polymerase. Taq polymerase has non-template dependent activity which preferentially adds a single adenosine to the 3'-ends of a double stranded DNA molecule, and thus most of the molecules PCR amplified by Taq polymerase possess single 3'-A overhangs. The use of a linearized "T-vector" which has single 3'-T overhangs on both ends allows direct, high-efficiency cloning of PCR products, facilitated by complementarity between the PCR product 3'-A overhangs and vector 3'-T overhangs. The TA cloning method can be easily modified so that the same T-vector can be used to clone any double-stranded DNA fragment, including PCR products amplified by any DNA polymerase, as well as all blunt- and sticky-ended DNA species. This technique is especially useful when compatible restriction sites are not available for the subcloning of DNA fragments from one vector to another. Directional cloning is made possible by appropriate hemi-phosphorylation of both the T-vectors and the inserts. With a single T-vector at hand, any DNA fragment can be cloned without compromising the cloning efficiency. The universal TA cloning method is thus both convenient and labor-saving.
Review article Flatulence — Causes, relation to diet and remedies (1988)

In addition to causing embarrassment and unease, flatulence is linked to a variety of symptoms, some of which may be distressing. This review describes the origins of intestinal gas, its composition and methods which have been developed for its analysis. Emphasis is placed upon the effects of legumes in the diet in producing excessive intestinal gas and, particularly, on the role of raffinose-type oligosaccharides, containing alpha-galactosidic groupings. Suggestions for overcoming the problem are presented, including drug treatment, enzyme treatment, food processing and plant breeding. It is emphasised that removal of all raffinose-oligosaccharides from beans does not remove the problem of flatulence in animals and man; the compounds responsible--though assumed to be polysaccharides (or polysaccharide-derived oligomers formed by processing or cooking)--have yet to be characterised.
Epidemiology of periodontal disease: a review and clinical perspectives. (2001)

The purpose of this paper is to assimilate epidemiological evidence for the prevalence of periodontal disease in human populations, and for comprehensive understanding of the disease for health care providers. Periodontal disease is a pathological condition affecting the supporting structures of teeth. It is characterised by a bacterial challenge that can instigate a destructive host response leading to periodontal attachment loss, bone loss and ultimately, possible tooth loss. The specifics of the disease process are obscured by our incomplete understanding of the role of various risk factors. Periodontal epidemiology literature lacks consistency in methodology of research, which includes various definitions for periodontal disease and health; different approaches to measuring periodontal indices of pocket depth, and attachment loss; inconsistent study designs and lack of adjustments to known risk factors. These inconsistencies do not allow for effective comparison of epidemiological studies, which is essential to find strong associations of risk factors with periodontal disease, which in turn is necessary for the interpretation of risk and causality. This paper will address several areas within the topic of periodontal disease epidemiology, including definitions of periodontal disease instituted by researchers, approaches to epidemiological studies in periodontitis, and risk factors in periodontal disease. Consideration is given to aspects of design and analyses relevant to evaluation of reports in the literature. For the clinical practitioner this review provides a theoretical framework to approach patients with comprehensive knowledge of not only the disease presentation, but also the environmental factors that govern past history, present condition and future response to treatments and interventions.
The SpaTeC composite event language for spatio-temporal reasoning in mobile systems (2009)

In mobile systems, the requirements on composite event detection are fundamentally different from those in distributed systems. Composite event detection must be driven not just by the time of occurrence of an event, but also by its location of occurrence; composite event detection, as applied in traditional distributed event-based systems, needs to be reassessed. In this paper, we motivate the need to support spatio-temporal relations between composite events in mobile systems and introduce SpaTeC, a composite event language that enables simultaneous matching of event occurrences over space and time. Composite event operators provide for coarse spatio-temporal reasoning. Spatial and temporal restrictions constrain composite event detection in space and time and provide a basis for event filtering and spatio-temporal routing. Time and location stamps use a guaranteed bounds model for location estimation and time synchronization. The semantics of SpaTeC event operators is defined within this framework.
Elevated glucose impairs endothelium-dependent relaxation by activating protein kinase C. (1991)

A possible relationship between protein kinase C activation and impaired receptor-mediated endothelium-dependent relaxation in diabetes mellitus was examined in isolated aorta from normal rabbit exposed to elevated glucose. Aorta treated for 10 min with 4-phorbol 12-myristate 13-acetate (PMA), a protein kinase C activator, showed decreased relaxations to the endothelium-dependent vasodilator, acetylcholine, similar to normal aorta exposed to elevated glucose (22 and 44 mM) for 6 h. Relaxations to the receptor-independent endothelium-dependent vasodilator, A23187, and those caused by the direct smooth muscle vasodilator, sodium nitroprusside, were unaffected by treatment with PMA or exposure to elevated glucose. Indomethacin increased relaxations to acetylcholine of aorta treated with PMA indicating a role for vasoconstrictor prostanoids. PMA caused a significant increase in basal and acetylcholine-stimulated release of vasoconstrictor prostanoids including thromboxane A2 from aortic segments with, but not without endothelium. Protein kinase C inhibitors, H-7 or sphingosine, restored the abnormal acetylcholine-induced relaxations as well as suppressed the abnormal release of prostanoids in aorta exposed to elevated glucose. These findings suggest that the dysfunction of receptor-mediated endothelium-dependent relaxation associated with exposure to elevated glucose is due to increased production of vasoconstrictor prostanoids by the endothelium as a consequence of protein kinase C activation.
Gene Amplification in Mammalian Cells: A Comprehensive Guide (1992)

Serves as a comprehensive review to the substantial impact of gene amplification in molecular biology, genetic engineering and medical science. The book covers the mechanism of gene amplification, organization and structure of amplified genes.
Els paisatges de la postmodernitat (2005)

Cronica del 'II Seminari Internacional sobre Paisatge', celebrat a Olot, els dies 21,22 i 23 d'octubre de 2004, dedicat al tema 'Els Paisatges de la postmodernitat' i dirigit pel catedratic de geografia humana de la Universitat de Girona Joan Nogue. L'objectiu ha estat posar en comu des d'una optica interdisciplinaria, no nomes academica sino tambe oberta a d'altres esferes del coneixement com la literatura, la pintura o el cinema, la diversitat de perspectives per interpretar els paisatges contemporanis, que hom aglutina sota el concepte de postmodernitat
ROLE OF "AGENIZED" FLOUR IN THE PRODUCTION OF RUNNING FITS (1947)

Recently, Mellanby (1946)<sup>1</sup>has shown that when white flour is bleached with nitrogen trichloride, known as the "agene" process, a toxic product is produced which will induce running fits when the flour is included in rations fed to dogs. Earlier, Arnold and Elvehjem (1939)<sup>2</sup>prepared a heat-processed dog food of wheat flour and meat scraps which consistently caused running fits when fed to dogs. Wagner and Elvehjem (1944)<sup>3</sup>were able to produce running fits in dogs when commercial wheat gluten was included in the ration. By increasing the amount of gluten fits could be induced in proportionally shorter lengths of time. This work confirmed an observation made by Parry,<sup>4</sup>while working here, that this canine disease was caused by some toxic product in the wheat protein. The condition called running fits, or "canine hysteria" as used by the English workers, causes dogs to become hypersensitive to
Quasi-orthogonal sequences for code-division multiple-access systems (2000)

The notion of quasi-orthogonal sequence (QOS) as a means of increasing the number of channels in synchronous code-division multiple-access (CDMA) systems that employ Walsh sequences for spreading information signals and separating channels is introduced. It is shown that a QOS sequence may be regarded as a class of Bent (almost Bent) functions possessing, in addition, a certain window property. Such sequences while increasing the system capacity, minimize interference to the existing set of Walsh sequences. The window property gives the system the ability to handle variable data rates. A general procedure of constructing QOSs from well-known families of binary sequences with good correlation, including the Kasami and Gold (1967) sequence families, as well as from the binary Kerdock code is provided. Examples of QOSs are presented for small lengths. Some examples of quaternary QOSs drawn from Family A are also included.
Protein profiles associated with survival in lung adenocarcinoma (2003)

Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here we identify proteins associated with patient survival in lung adenocarcinoma. A total of 682 individual protein spots were quantified in 90 lung adenocarcinomas by using quantitative two-dimensional polyacrylamide gel electrophoresis analysis. A leave-one-out cross-validation procedure using the top 20 survival-associated proteins identified by Cox modeling indicated that protein profiles as a whole can predict survival in stage I tumor patients (P = 0.01). Thirty-three of 46 survival-associated proteins were identified by using mass spectrometry. Expression of 12 candidate proteins was confirmed as tumor-derived with immunohistochemical analysis and tissue microarrays. Oligonucleotide microarray results from both the same tumors and from an independent study showed mRNAs associated with survival for 11 of 27 encoded genes. Combined analysis of protein and mRNA data revealed 11 components of the glycolysis pathway as associated with poor survival. Among these candidates, phosphoglycerate kinase 1 was associated with survival in the protein study, in both mRNA studies and in an independent validation set of 117 adenocarcinomas and squamous lung tumors using tissue microarrays. Elevated levels of phosphoglycerate kinase 1 in the serum were also significantly correlated with poor outcome in a validation set of 107 patients with lung adenocarcinomas using ELISA analysis. These studies identify new prognostic biomarkers and indicate that protein expression profiles can predict the outcome of patients with early-stage lung cancer.