gebhart/patrepeval huggingface dataset:
Genome of Bacteriophage P1 (2004)

P1 is a bacteriophage of Escherichia coli and other enteric bacteria. It lysogenizes its hosts as a circular, low-copy-number plasmid. We have determined the complete nucleotide sequences of two strains of a P1 thermoinducible mutant, P1 c1-100. The P1 genome (93,601 bp) contains at least 117 genes, of which almost two-thirds had not been sequenced previously and 49 have no homologs in other organisms. Protein-coding genes occupy 92% of the genome and are organized in 45 operons, of which four are decisive for the choice between lysis and lysogeny. Four others ensure plasmid maintenance. The majority of the remaining 37 operons are involved in lytic development. Seventeen operons are transcribed from sigma(70) promoters directly controlled by the master phage repressor C1. Late operons are transcribed from promoters recognized by the E. coli RNA polymerase holoenzyme in the presence of the Lpa protein, the product of a C1-controlled P1 gene. Three species of P1-encoded tRNAs provide differential controls of translation, and a P1-encoded DNA methyltransferase with putative bifunctionality influences transcription, replication, and DNA packaging. The genome is particularly rich in Chi recombinogenic sites. The base content and distribution in P1 DNA indicate that replication of P1 from its plasmid origin had more impact on the base compositional asymmetries of the P1 genome than replication from the lytic origin of replication.
AMOR-an autonomous mobile robot navigation system (2002)

In this paper an autonomous mobile robot navigation system, capable of performing automated office delivery tasks, is described. The implemented prototype system is capable of autonomously navigating from one room to another designated by the operator. This involves: 1) navigation in a room, where the robot dynamically detects and avoid obstacles; 2) hall navigation, where it follows the walls by a reactive scheme; and 3) door traversing, where the robot autonomously positions the door and passes safely through it. The only a priori knowledge used by the system consists of a graph representation of the navigation environment, containing door positions. A priori, no knowledge is provided about the position, physical or geometrical properties of other objects in the environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Third Recognition Element in Bacterial Promoters: DNA Binding by the α Subunit of RNA Polymerase (1993)

A DNA sequence rich in (A+T), located upstream of the -10, -35 region of the Escherichia coli ribosomal RNA promoter rrnB P1 and called the UP element, stimulates transcription by a factor of 30 in vivo, as well as in vitro in the absence of protein factors other than RNA polymerase (RNAP). When fused to other promoters, such as lacUV5, the UP element also stimulates transcription, indicating that it is a separate promoter module. Mutations in the carboxyl-terminal region of the alpha subunit of RNAP prevent stimulation of these promoters by the UP element although the mutant enzymes are effective in transcribing the "core" promoters (those lacking the UP element). Protection of UP element DNA by the mutant RNAPs is severely reduced in footprinting experiments, suggesting that the selective decrease in transcription might result from defective interactions between alpha and the UP element. Purified alpha binds specifically to the UP element, confirming that alpha acts directly in promoter recognition. Transcription of three other promoters was also reduced by the COOH-terminal alpha mutations. These results suggest that UP elements comprise a third promoter recognition region (in addition to the -10, -35 recognition hexamers, which interact with the sigma subunit) and may account for the presence of (A+T)-rich DNA upstream of many prokaryotic promoters. Since the same alpha mutations also block activation by some transcription factors, mechanisms of promoter stimulation by upstream DNA elements and positive control by certain transcription factors may be related.
Structural analysis of the actinophae ФC31 attachment site (1991)

The lysogenisation of actinophage phi C31 in S. coelicolor J 1501 occurs by site-specific recombination. The DNA segments containing the attachment sites on the host chromosome, the phage genome and the two junctions created by the insertion of the prophage were cloned and the nucleotide sequences determined. The attachment sites (att) share an extremely short common sequence of three base pairs. Adjacent to the core sequences some direct- and inverted repeats were found as potential binding sites for proteins involved in site-specific recombination.
Lattice-free prediction of three-dimensional structure of programmed DNA assemblies (2014)

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science.
Hyper-Parameter Tuning of a Decision Tree Induction Algorithm (2016)

Supervised classification is the most studied task in Machine Learning. Among the many algorithms used in such task, Decision Tree algorithms are a popular choice, since they are robust and efficient to construct. Moreover, they have the advantage of producing comprehensible models and satisfactory accuracy levels in several application domains. Like most of the Machine Leaning methods, these algorithms have some hyper-parameters whose values directly affect the performance of the induced models. Due to the high number of possibilities for these hyper-parameter values, several studies use optimization techniques to find a good set of solutions in order to produce classifiers with good predictive performance. This study investigates how sensitive decision trees are to a hyper-parameter optimization process. Four different tuning techniques were explored to adjust J48 Decision Tree algorithm hyper-parameters. In total, experiments using 102 heterogeneous datasets analyzed the tuning effect on the induced models. The experimental results show that even presenting a low average improvement over all datasets, in most of the cases the improvement is statistically significant.
Porcine reproductive and respiratory syndrome (PRRS or blue-eared pig disease) (1992)

This paper sets out to provide a summary of the salient facts about the porcine reproductive and respiratory syndrome and to identify conclusions. It draws on the proceedings of a BVA Trust symposium held on Friday November 1, 1991, which was attended by representatives of the state veterinary services of Belgium, Germany, the Netherlands and the UK together with veterinarians involved in pig research and practice.
Highly directive radiation from sources embedded inside photonic crystals (2003)

In this work, we have experimentally and theoretically studied the angular distribution of power emitted from a radiation source embedded inside a photonic crystal. Our results show that it is possible to obtain highly directive radiation sources operating at the band edge of the photonic crystal. Half power beam widths as small as 6° have been obtained. Our results also show that the angular distribution of power strongly depends on the frequency and on the size of the photonic crystal.
3-D Object Modeling by a Camera Mounted on a Mobile Robot (2005)

This paper describes 3-D shape modeling performed by a mobile robot. We propose a method in which the robot in the real environment acquires the accurate shape and constructs a 3-D model of an object using Computer Vision techniques under the condition that position and shape of the object is unknown. A 3-D model is reconstructed from image streams which are captured by a camera mounted on the robot. The experimental results show the effectiveness of our method.
Up-regulation of ATP Binding Cassette Transporter A1 Expression by Very Low Density Lipoprotein Receptor and Apolipoprotein E Receptor 2 (2011)

Activation of very low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (apoER2) results in either pro- or anti-atherogenic effects depending on the ligand. Using reelin and apoE as ligands, we studied the impact of VLDLR- and apoER2-mediated signaling on the expression of ATP binding cassette transporter A1 (ABCA1) and cholesterol efflux using RAW264.7 cells. Treatment of these mouse macrophages with reelin or human apoE3 significantly increased ABCA1 mRNA and protein levels, and apoAI-mediated cholesterol efflux. In addition, both reelin and apoE3 significantly increased phosphorylated disabled-1 (Dab1), phosphatidylinositol 3-kinase (PI3K), protein kinase Cζ (PKCζ), and specificity protein 1 (Sp1). This reelin- or apoER2-mediated up-regulation of ABCA1 expression was suppressed by 1) knockdown of Dab1, VLDLR, and apoER2 with small interfering RNAs (siRNAs), 2) inhibition of PI3K and PKC with kinase inhibitors, 3) overexpression of kinase-dead PKCζ, and 4) inhibition of Sp1 DNA binding with mithramycin A. Activation of the Dab1-PI3K signaling pathway has been implicated in VLDLR- and apoER2-mediated cellular functions, whereas the PI3K-PKCζ-Sp1 signaling cascade has been implicated in the regulation of ABCA1 expression induced by apoE/apoB-carrying lipoproteins. Taken together, these data support a model in which activation of VLDLR and apoER2 by reelin and apoE induces ABCA1 expression and cholesterol efflux via a Dab1-PI3K-PKCζ-Sp1 signaling cascade.
Characterization of Alcohol-induced Filamentous Growth inSaccharomyces cerevisiae (2000)

Diploid cells of the budding yeast Saccharomyces cerevisiae starved for nitrogen differentiate into a filamentous growth form. Poor carbon sources such as starches can also stimulate filamentation, whereas haploid cells undergo a similar invasive growth response in rich medium. Previous work has demonstrated a role for various alcohols, by-products of amino acid metabolism, in altering cellular morphology. We found that several alcohols, notably isoamyl alcohol and 1-butanol, stimulate filamentous growth in haploid cells in which this differentiation is normally repressed. Butanol also induces cell elongation and changes in budding pattern, leading to a pseudohyphal morphology, even in liquid medium. The filamentous colony morphology and cell elongation require elements of the pheromone-responsive MAPK cascade and TEC1, whereas components of the nutrient-sensing machinery, such as MEP2, GPA2, and GPR1, do not affect this phenomenon. A screen for 1-butanol-insensitive mutants identified additional proteins that regulate polarized growth (BUD8, BEM1, BEM4, and FIG1), mitochondrial function (MSM1, MRP21, and HMI1), and a transcriptional regulator (CHD1). Furthermore, we have also found that ethanol stimulates hyperfilamentation in diploid cells, again in a MAPK-dependent manner. Together, these results suggest that yeast may sense a combination of nutrient limitation and metabolic by-products to regulate differentiation.
Multiple Domains of GlcNAc-1-phosphotransferase Mediate Recognition of Lysosomal Enzymes (2016)

The Golgi enzyme UDP-GlcNAc:lysosomal enzymeN-acetylglucosamine-1-phosphotransferase (GlcNAc-1-phosphotransferase), an α2β2γ2hexamer, mediates the initial step in the addition of the mannose 6-phosphate targeting signal on newly synthesized lysosomal enzymes. This tag serves to direct the lysosomal enzymes to lysosomes. A key property of GlcNAc-1-phosphotransferase is its unique ability to distinguish the 60 or so lysosomal enzymes from the numerous non-lysosomal glycoproteins with identical Asn-linked glycans. In this study, we demonstrate that the two Notch repeat modules and the DNA methyltransferase-associated protein interaction domain of the α subunit are key components of this recognition process. Importantly, different combinations of these domains are involved in binding to individual lysosomal enzymes. This study also identifies the γ-binding site on the α subunit and demonstrates that in the majority of instances the mannose 6-phosphate receptor homology domain of the γ subunit is required for optimal phosphorylation. These findings serve to explain how GlcNAc-1-phosphotransferase recognizes a large number of proteins that lack a common structural motif.
REGULATION OF CERAMIDE PRODUCTION AND APOPTOSIS (1998)

Ceramide is a sphingosine-based lipid signaling molecule that regulates cellular differentiation, proliferation, and apoptosis. The emerging picture suggests that coupling of ceramide to specific signaling cascades is both stimulus and cell-type specific. Ceramide action is determined within the context of other stimuli and by the subcellular topology of its production. Here, we discuss the pathways of ceramide generation and the interaction of ceramide with caspases and other apoptotic signaling cascades.
BSC-1 growth inhibitor/type beta transforming growth factor is a strong inhibitor of thymocyte proliferation. (1986)

Growth inhibitor/type beta transforming growth factor purified from BSC-1 cells and human platelets is shown to strongly inhibit the proliferation of Con A-stimulated mouse thymocytes. The inhibition can be achieved with growth inhibitor/type beta transforming growth factor concentrations approximately equal to 1/10th those necessary to inhibit keratinocyte cultures. The inhibitory effect in thymocyte cultures can be reversed by the addition of interleukin 2. These findings suggest that growth inhibitor/type beta transforming growth factor is a naturally occurring immunoregulator.
The evolving field of induced pluripotency: Recent progress and future challenges (2012)

The derivation of patient-specific pluripotent cell lines through the introduction of a few transcription factors into somatic cells has opened new avenues for the study and treatment of human disorders. Induced pluripotent stem cells (iPSCs) and their derivatives offer a unique platform for disease modeling, drug discovery and toxicology, as well as an invaluable source of cells for regenerative therapies. Here, we provide an overview of the various strategies currently available for iPSC generation, highlighting recent advances and discussing some of the challenges faced in harnessing the true potential of iPSCs for biomedical research and therapeutic applications.
Biochemical, immunological, and cell genetic studies in glycogenosis type II. (1978)

Fibroblasts from patients with the adult, juvenile, and infantile form of glycogenosis type II (Pompe disease) were cultured under standardized conditions, and the activity of acid alpha-glucosidase (E.C.3.2.1.20) towards glycogen, maltose, and 4-methylumbelliferyl-alpha-D-glucopyranoside was measured. Glycogen levels in muscle biopsies and in cultured fibroblasts from patients were determined. Residual enzyme activities varying from 7%-22% were detected in fibroblasts from patients with the adult form but not from patients with the infantile form of glycogenosis II. An inverse correlation was found between the severity of the clinical manifestation and the degree of residual enzyme activity in the fibroblasts. The kinetic and electrophoretic properties of acid alpha-glucosidase in fibroblasts from the adult patients and from control individuals were similar. Immunological studies suggested that the decrease of acid alpha-glucosidase activity is caused by a mutation that affects the production or degradation of the enzyme rather than its catalytic activity. Complementation studies were carried out by fusing fibroblasts from patients with the adult, juvenile, and infantile form of glycogenosis II, but neither conventional assays on multikaryons nor enzyme assays on single binuclear heterokaryons gave any evidence for genetic heterogeneity among these forms.
Phylogenetic Classification of Human Papillomaviruses: Correlation With Clinical Manifestations (1992)

Human papillomaviruses (HPVs) are a heterogeneous group of small dsDNA viruses which cause a variety of proliferative epithelial lesions at specific anatomical sites. Although more than 65 different virus types have been cloned and characterized, no uniform classification system exists. In order to classify HPV DNA types, phylogenetic trees were constructed based on nucleotide sequence alignments using parsimony and distance matrix algorithms. The resulting phylogenetic trees provide a classification of the HPVs into specific groups encompassing the known tissue tropism and oncogenic potential of each HPV type. The implications of a phylogenetic taxonomy on the diagnostic detection of HPVs and the concept of different HPV species are discussed.
Nucleic Acids as Therapeutic Agents (2008)

Therapeutic nucleic acids (TNAs) and its precursors are applied to treat several pathologies and infections. TNA-based therapy has different rationales and mechanisms and can be classified into three main groups: 1) Therapeutic nucleotides and nucleosides; 2) Therapeutic oligonucleotides; and 3) Therapeutic polynucleotides. This review will focus in those TNAs that have reached clinical trials with anticancer and antiviral protocols, the two most common applications of TNAs. Although therapeutic nucleotides and nucleosides that interfere with nucleic acid metabolism and DNA polymerization have been successfully used as anticancer and antiviral drugs, they often produce toxic secondary effects related to dosage and continuous use. The use of oligonucleotides such as ribozyme and antisense oligodeoxynucleotides (AS-ODNs) showed promise as therapeutic moieties but faced several issues such as nuclease sensitivity, off-target effects and efficient delivery. Nevertheless, immunostimulatory oligodeoxynucleotides and AS-ODNs represent the most successful group of therapeutic oligonucleotides in the clinic. A newer group of therapeutic oligonucleotides, the aptamers, is rapidly advancing towards early detection and treatment alternatives the have reached the commercial interest. Despite the very high in vitro efficiency of small interfering RNAs (siRNAs) they present issues with intracellular target accessibility, specificity and delivery. DNA vaccines showed great promise, but they resulted in very poor responses in the clinic and further development is uncertain. Despite their many issues, the exquisite specificity and versatility of therapeutic oligonucleotides attracts a great deal of research and resources that will certainly convert them in the TNA of choice for treating cancer and viral diseases in the near future.
Scaling law in liquid drop coalescence driven by surface tension (2004)

This Letter reports experimental results on the coalescence of two liquid drops driven by surface tension. Using a high speed imaging system, we studied the early-time evolution of the liquid bridge that is formed upon the initial contact of two liquid drops in air. Experimental results confirmed the scaling law that was proposed by Eggers et al. based on a simple and yet elegant physical argument. We found that the liquid bridge radius rb follows the scaling law rb∝t1/2 in the inertial regime. Further experiments demonstrate that such scaling law is robust when using fluids of different viscosities and surface tensions. The prefactor of the scaling law, rb/t1/2, is shown to be ∝R1/4, where R is the inverse of the drop curvature at the point of contact. The dimensionless prefactor is measured to be in the range of 1.03–1.29, which is lower than 1.62, a prefactor predicted by the numerical simulation of Duchemin et al. for inviscid drop coalescence.
Microenvironmental and cellular consequences of altered blood flow in tumours (2003)

Tumour angiogenesis is triggered by various signals characteristic of the tumour microenvironment, including low oxygen tension, low extracellular pH and low glucose concentration. Tumour microvasculature is chaotic, producing perfusion heterogeneities which can be visualized by MRI and other modalities. Inefficient perfusion in tumours produces regions of transient and chronic hypoxia. Tumour hypoxia is associated with adverse clinical outcomes and reduced patient survival. Hypoxia may be a factor in activation of extracellular matrix-degrading proteases, and some studies have correlated primary tumour hypoxia with likelihood of tumour cell dissemination. Exposure to hypoxia either induces or selects for cells that are hyperglycolytic, and this in turn produces local acidosis which is also a common feature of solid tumours. Increased glucose uptake in hyperglycolyzing tumour cells is the basis of lesion-visualization in positron emission tomography using 18F-fluorodeoxyglucose. Tumour acidity can reduce the effectiveness of weak-base drugs, but can be exploited to increase the anti-tumour activity of weak-acid chemotherapeutics. Evidence linking tumour acidity with increased activity of several extracellular matrix-degrading enzyme systems is examined. High levels of lactate, another end-product of glycolysis, in primary lesions have been correlated with increased likelihood of metastasis. In the numerous studies correlating hypoxia, acidity and lactate with metastasis, the direction of the causality has not been adequately established. We hypothesize that adoption of a hyperglycolytic phenotype is a necessary feature of carcinogenesis itself, and confers a survival and proliferative advantage to tumour cells over surrounding normal cells. Empirical evidence supporting this "acid-mediated tumour invasion" model is discussed.
Crystal size and oxygen segregation for polycrystalline GaN (2002)

The grain size for polycrystalline GaN, grown in low-temperature gallium-rich conditions, is shown to be correlated to the oxygen content of the films. Films with lower oxygen content were observed to have larger crystals with an increased tendency to a single-preferred crystal orientation. Elastic recoil detection analysis with heavy ions (i.e., 200 MeV Au 197 ions) was used to determine the composition of the GaN films grown for the study, including the hydrogen, carbon, gallium, nitrogen, and oxygen content. Atomic force microscopy and x-ray diffraction were used to study the sample morphology. From these measurements, the available surface area of the films was found to be sufficient for a significant proportion of the oxygen present in the films to segregate at the grain boundaries. This interpretation is consistent with earlier theoretical studies of the formation and segregation of the VGa-(ON)3 defect complex at dislocation sites in gallium-rich GaN. For this work, however, the defect complex is believed to segregate at the grain boundary of the polycrystalline GaN.