gebhart/patrepeval huggingface dataset:
Assembly of Large, High G+C Bacterial DNA Fragments in Yeast (2012)

The ability to assemble large pieces of prokaryotic DNA by yeast recombination has great application in synthetic biology, but cloning large pieces of high G+C prokaryotic DNA in yeast can be challenging. Additional considerations in cloning large pieces of high G+C DNA in yeast may be related to toxic genes, to the size of the DNA, or to the absence of yeast origins of replication within the sequence. As an example of our ability to clone high G+C DNA in yeast, we chose to work with Synechococcus elongatus PCC 7942, which has an average G+C content of 55%. We determined that no regions of the chromosome are toxic to yeast and that S. elongatus DNA fragments over ~200 kb are not stably maintained. DNA constructs with a total size under 200 kb could be readily assembled, even with 62 kb of overlapping sequence between pieces. Addition of yeast origins of replication throughout allowed us to increase the total size of DNA that could be assembled to at least 454 kb. Thus, cloning strategies utilizing yeast recombination with large, high G+C prokaryotic sequences should include yeast origins of replication as a part of the design process.
A time-multiplexed FPGA (2002)

This paper describes the architecture of a time-multiplexed FPGA. Eight configurations of the FPGA are stored in on-chip memory. This inactive on-chip memory is distributed around the chip, and accessible so that the entire configuration of the FPGA can be changed in a single cycle of the memory. The entire configuration of the FPGA can be loaded from this on-chip memory in 30 ns. Inactive memory is accessible as block RAM for applications. The FPGA is based on the Xilinx XC4000E FPGA, and includes extensions for dealing with state saving and forwarding and for increased routing demand due to time-multiplexing the hardware.
Structure of the Bacteriophage φKZ Lytic Transglycosylase gp144 (2007)

Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage phi KZ has been determined to 2.5-A resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. phi KZ gp144 is a 260-residue alpha-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G D-Ala-D-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu 115 in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the phi KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine)(4) has been determined to 2.6-A resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.
Fast Microwave-Assisted Preparation of Aryl and Vinyl Nitriles and the Corresponding Tetrazoles from Organo-halides (2000)

Aryl and vinyl nitriles have been prepared in very high yields from the corresponding bromides using palladium-catalyzed reactions with microwave irradiation employed as the energy source. Furthermore, flash heating was used successfully for the conversion of these nitriles into aryl and vinyl tetrazoles by cycloaddition reactions. One-pot transformation of aryl halides directly to the aryl tetrazoles could be accomplished both in solution and on solid support. All reactions were completed in minutes rather than in hours or days as previously reported with the standard thermal heating technique. A very potent HIV-1 protease inhibitor (K(i) = 0. 56 nM), comprising two tetrazole heterocycles as carboxyl group bioisosteres, was prepared in one pot by microwave-promoted cyanation of a bromo precursor and a subsequent cycloaddition reaction. The temperature-time profiles at 13, 20, and 60 W magnetron input power in DMF are presented.
Tomato Heat Stress Transcription Factor HsfB1 Represents a Novel Type of General Transcription Coactivator with a Histone-Like Motif Interacting with the Plant CREB Binding Protein Ortholog HAC1[W] (2004)

In contrast with the class A heat stress transcription factors (HSFs) of plants, a considerable number of HSFs assigned to classes B and C have no evident function as transcription activators on their own. However, in the following article, we provide evidence that tomato (Lycopersicon peruvianum) HsfB1 represents a novel type of coactivator cooperating with class A HSFs (e.g., with tomato HsfA1). Provided the appropriate promoter architecture, the two HSFs assemble into an enhanceosome-like complex, resulting in strong synergistic activation of reporter gene expression. Moreover, HsfB1 also cooperates in a similar manner with other activators, for example, with the ASF1/2 enhancer binding proteins of the 35S promoter of Cauliflower mosaic virus or with yet unidentified activators controlling housekeeping gene expression. By these effects, HsfB1 may help to maintain and/or restore expression of certain viral or housekeeping genes during ongoing heat stress. The coactivator function of HsfB1 depends on a histone-like motif in its C-terminal domain with an indispensable Lys residue in the center (GRGKMMK). This motif is required for recruitment of the plant CREB binding protein (CBP) ortholog HAC1. HsfA1, HsfB1, and HAC1/CBP form ternary complexes in vitro and in vivo with markedly enhanced efficiency in promoter recognition and transcription activation in plant and mammalian (COS7) cells. Using small interfering RNA-mediated knock down of HAC1 expression in Arabidopsis thaliana mesophyll protoplasts, the crucial role for the coactivator function of HsfB1 was confirmed.
Protein synthesis in antigen processing. (1988)

Recent studies indicate that Ag pass through a chloroquine-sensitive intracellular pathway in accessory cells before they are recognized by class II-restricted T cells. Our results indicate that this is also true for insulin. Unexpectedly, we find that protein synthesis is required for optimal accessory cell-dependent processing of insulin and other proteins by adherent macrophages. Treatment of APC with inhibitors of protein synthesis, before and during exposure to Ag, inhibits their subsequent ability to activate murine T cell hybridomas. Experiments are described which suggest that this effect is localized to intracellular processing of Ag rather than uptake or presentation, per se. Inhibition is reversible, and is not observed in special situations where intracellular processing of Ag is not required. A distinct lag period is required for inhibition of processing after inhibition of macrophage protein synthesis. One possible interpretation is that protein synthesis is necessary for maintenance of a labile protein crucial for intracellular processing of Ag. Alternatively, the susceptibility of processing to inhibitors of protein synthesis may reflect an obligate intracellular association of Ag and newly synthesized class II histocompatibility molecules.
Buffer tree synthesis with consideration of temporal locality, sink polarity requirements, solution cost and blockages (2002)

We give an overview of a buffer tree synthesis package which pays particular attention to the following issues: routing and buffer blockages, minimization of interconnect and buffer costs, exploitation of temporal locality among the sinks and addressing sink polarity requirements. Experimental results demonstrate the effectiveness of the tool in comparison with previously proposed techniques.
Identification of mutations in the genes for the pollen allergens of eastern red cedar (Juniperus virginiana) (2001)

These findings suggest that mutations in the genes or post-translational modifications of two potentially allergenic proteins might help to explain why the pollen of eastern red cedar is reported to be less allergenic than those of other members of Cupressaceae and Taxodiaceae families.
Thymidine kinase, thymidylate synthase, and dihydropyrimidine dehydrogenase profiles of cell lines of the National Cancer Institute's Anticancer Drug Screen. (2001)

The lack of correlation may in part be attributable to the influence of downstream factors such as p53, the observation that the more sensitive cell lines with faster doubling times also had higher TS levels, and the standard procedure of the screen that uses a relatively short (48-h) drug exposure.
Definition of the Human Androgen Receptor Gene Structure Permits the Identification of Mutations that Cause Androgen Resistance: Premature Termination of the Receptor Protein at Amino Acid Residue 588 Causes Complete Androgen Resistance (1990)

We have isolated and characterized the gene encoding the human androgen receptor. The coding sequence is divided into eight coding exons and spans a minimum of 54 kilobases. The positions of the exon boundaries are highly conserved when compared to the location of the exon boundaries of the chicken progesterone and human estrogen receptor genes. Definition of the intron/exon boundaries has permitted the synthesis of specific oligonucleotides for use in the amplification of segments of the androgen receptor gene from samples of total genomic DNA. This technique allows the analysis of all segments of the androgen receptor gene except a small region of exon 1 that encodes the glycine homopolymeric segment. Using these methods we have analyzed samples of DNA prepared from a patient with complete androgen resistance and have detected a single nucleotide substitution at nucleotide 1924 in exon 3 of the androgen receptor gene that results in the conversion of a lysine codon into a premature termination codon at amino acid position 588. The introduction of a termination codon into the sequence of the normal androgen receptor cDNA at this position leads to a decrease in the amount of mRNA encoding the human androgen receptor and the synthesis of a truncated receptor protein that is unable to bind ligand and is unable to activate the long terminal repeat of the mouse mammary tumor virus in cotransfection assays.
Urodynamic assessment of patients with stress incontinence: how effective are urethral pressure profilometry and abdominal leak point pressures at case selection and predicting outcome? (2004)

It is not apparent that either abdominal leak point pressure measurement or urethral pressure profilometry can accurately predict which patients will achieve the best outcome of surgical treatment for stress urinary incontinence. Other parameters assessed during urodynamic evaluation might provide prognostic information regarding the risk of voiding dysfunction postoperatively and the possibility of persistent urge-related leakage following surgery, though not directly predict cure. A multi-institutional randomized study comparing the outcome between patients in whom treatment was determined with the urodynamic information known, compared with patients in whom this information was unknown would further enhance our understanding of the usefulness of urodynamics in the preoperative evaluation of women with stress urinary incontinence.
Age-Related Macular Degeneration and the Other Double Helix The Cogan Lecture (2011)

The study and therapy of age-related macular degeneration (AMD), a leading cause of blindness worldwide, have taken great strides over the past decade. During the same time, a central role for RNA in many human diseases has been discovered. We have identified anti-angiogenic functions for synthetic double stranded RNAs (dsRNAs) in neovascular AMD and cytotoxic functions for endogenous dsRNAs in atrophic AMD. These findings provide new insights into the pathogenesis and therapy of both forms of AMD.
Isomerisation of allyl phenyl ethers and allylphenols with transition metal catalysts (1973)

Isomerisation of allyl phenyl ethers with PdCl2(PhCN)2 in boiling benzene gives quantitatively phenyl prop-1-enyl ethers with the cis-isomer predominating. Varying the substituents in all three positions of the allyl group shows that the reaction is sensitive to steric effects and the results are discussed in terms of an intermediate π-allyl(hydrido)palladium complex and also a sigmatropic [1,3] hydrogen shift within a π-olefinpalladium complex. The effect of other transition metals on the isomerisation is summarised. The isomerisation of allylphenols to trans-(prop-1-enyl)phenols is discussed in terms of these mechanisms and conformations of the side chains.
Single-Phase Synthesis of Functionalized Gold Nanoparticles (2004)

A single-phase synthesis of thiolate monolayer-protected gold clusters (MPCs) is described. This method avoids the problem of persistent ionic contamination from residual phase-transfer catalyst while retaining the versatility associated with the commonly used two-phase Brust synthesis. MPCs having alkyl, diphenylacetylene, ether, amide, or ester functionalities were prepared by this single-phase synthesis and characterized via 1H NMR, FT-IR, and UV−vis absorption spectroscopy, TGA, STM, and TEM. Comparisons of products synthesized by this method and by existing methods are made for a subset of MPCs. Results are considered in the context of using MPC thin films as chemically sensitive interface layers in chemiresistor vapor sensors.
Gene Expression Profiling of Differentiated Thyroid Neoplasms (2004)

Our study show the following: (1) differences in gene expression between tumor and nontumor bearing normal thyroid tissue can be identified, (2) a set of genes differentiate follicular neoplasm from follicular variant of papillary carcinoma, (3) follicular adenoma and carcinoma share many of the differentiated genes, and (4) gene expression differences identify conventional papillary carcinoma from the follicular variant.
Mechanisms of Oxidant Stress-Induced Acute Tissue Injury (1995)

During the last 25 years, a large body of experimental evidence has accumulated from pharmacological intervention studies that suggests an important role for reactive oxygen species in numerous pathophysiological processes. While a variety of chemical mechanisms of reactive oxygen-induced damage to lipids, proteins, and DNA is fairly well understood, the molecular pathology of oxidant stress-induced tissue injury in vivo remains unclear in most cases. Recent advances indicate that the direct destructive potential of reactive oxygen in vivo is limited by the extensive detoxification capacity of most cells and may be restricted to a small fraction of cells exposed to a locally high oxidant stress. However, reactive oxygen species can participate in recruitment of inflammatory cells by upregulation of adhesion molecules and generation of chemotactic factors, and are necessary for protease-mediated cell injury in vivo. Reactive oxygen species can also scavenge other biologically active molecules (e.g., nitric oxide), thereby modulating indirectly their effector cells. In addition to the discussed effects relevant for acute injury, other oxidant stress-induced mechanisms (e.g., DNA modifications) may be relevant in chronic disease states. A solid mechanistic understanding of the role of reactive oxygen species in the overall pathophysiology is critical for providing a rationale for antioxidant therapy and the targeted development of new antioxidant drugs.
Promotion and inhibition of flower formation in a dayneutral plant in grafts with a short-day plant and a long-day plant (1977)

Flower formation in the dayneutral tobacco (Nicotiana tabacum L.) cultivar "Trapezond" was accelerated by graft union with the short-day tobacco "Maryland Mammoth" when the grafts were kept on short days and by graft union with the long-day plant N. silvestris L. when they were kept on long days. When Maryland Mammoth/Trapezond grafts were kept on long days, flower formation in Trapezond was not, or only slightly, delayed compared to Trapezond/Trapezond controls; but when N. silvestris/Trapezond grafts were kept on short days, flower formation in Trapezond was inhibited and its growth changed to dwarf-like habit. The former results indicate transmission of flower-promoting material(s) ("florigen") from photoperiodic plants maintained under flower-promoting daylength conditions to a dayneutral graft partner; the latter indicate the presence in the long-day plant N. silvestris under short-day conditions of potent flower-inhibiting and growth-regulating material(s) that can also be transmitted to a day-neutral partner. Analogous flower-inhibitory materials seem not to be present, or to be present to a much lesser extent, in the short-day plant Maryland Mammoth under long-day conditions.
RUMINANT NUTRITION SYMPOSIUM: Ruminant Production and Metabolic Responses to Heat Stress1,2 (2011)

Heat stress compromises efficient animal production by marginalizing nutrition, management, and genetic selection efforts to maximize performance endpoints. Modifying farm infrastructure has yielded modest success in mitigating heat stress-related losses, yet poor production during the summer remains arguably the costliest issue facing livestock producers. Reduced output (e.g., milk yield and muscle growth) during heat stress was traditionally thought to result from decreased nutrient intake (i.e., a classic biological response shared by all animals during environmental-induced hyperthermia). Our recent observations have begun to challenge this belief and indicate heat-stressed animals employ novel homeorhetic strategies to direct metabolic and fuel selection priorities independently of nutrient intake or energy balance. Alterations in systemic physiology support a shift in carbohydrate metabolism, evident by increased basal and stimulated circulating insulin concentrations. Perhaps most intriguing given the energetic shortfall of the heat-stressed animal is the apparent lack of basal adipose tissue mobilization coupled with a reduced responsiveness to lipolytic stimuli. Thus, the heat stress response markedly alters postabsorptive carbohydrate, lipid, and protein metabolism independently of reduced feed intake through coordinated changes in fuel supply and utilization by multiple tissues. Interestingly, the systemic, cellular, and molecular changes appear conserved amongst different species and physiological states. Ultimately, these changes result in the reprioritization of fuel selection during heat stress, which appears to be primarily responsible for reduced ruminant animal productivity during the warm summer months.
BCL-2 Is a Downstream Target of ATF5 That Mediates the Prosurvival Function of ATF5 in a Cell Type-dependent Manner (2011)

ATF5 loss of function has been shown previously to cause apoptotic cell death in glioblastoma and breast cancer cells but not in non-transformed astrocytes and human breast epithelial cells. The mechanism for the cell type-dependent survival function of ATF5 is unknown. We report here that the anti-apoptotic factor BCL-2 is a downstream target of ATF5 that mediates the prosurvival function of ATF5 in C6 glioma cells and MCF-7 breast cancer cells. ATF5 binds to an ATF5-specific regulatory element that is downstream of and adjacent to the negative regulatory element in the BCL-2 P2 promoter, stimulating BCL-2 expression. Highlighting the critical role of BCL-2 in ATF5-dependent cancer cell survival, expression of BCL-2 blocks death of C6 and MCF-7 cells induced by dominant-negative ATF5, and depletion of BCL-2 impairs ATF5-promoted cell survival. Moreover, we found that BCL-2 expression is not regulated by ATF5 in non-transformed rat astrocytes, mouse embryonic fibroblasts, and human breast epithelial cells, where expression of BCL-2 but not ATF5 is required for cell survival. These findings identify BCL-2 as an essential mediator for the cancer-specific cell survival function of ATF5 in glioblastoma and breast cancer cells and provide direct evidence that the cell type-specific function of ATF5 derives from differential regulation of downstream targets by ATF5 in different types of cells.
Computer vision-based gesture recognition for an augmented reality interface (2004)

Wearable computing and Augmented Reality applications call for less obtrusive and more intuitive human computer interfaces than keyboards and mice. One way to realise such interfaces is using gestures, e.g., for pointing in order to replace the mouse. The less obtrusive way of gesture recognition is to use computer vision based methods. This paper presents a computer vision-based gesture interface that is part of an Augmented Reality system. It can recognise a 3D pointing gesture, a click gesture, and five static gestures. A lookup-table based colour segmentation and a fast gesture recognition method are presented that enable for 25Hz performance on a standard PC.
Tocilizumab, a humanized anti-interleukin-6 receptor antibody, ameliorated clinical symptoms and MRI findings of a patient with ankylosing spondylitis (2011)

Journal Article Tocilizumab, a humanized anti-interleukin-6 receptor antibody, ameliorated clinical symptoms and MRI findings of a patient with ankylosing spondylitis Get access Yoshihito Shima, Yoshihito Shima Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsuya Tomita, Tetsuya Tomita Department of Orthopaedics, Osaka University Graduate School of Medicine, Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Taeko Ishii, Taeko Ishii Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan Search for other works by this author on: Oxford Academic Google Scholar Atsuyoshi Morishima, Atsuyoshi Morishima Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan Search for other works by this author on: Oxford Academic Google Scholar Yuichi Maeda, Yuichi Maeda Department of Rheumatology, National Hospital Organization, Osaka Minami Medical Center, Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Atsushi Ogata, Atsushi Ogata Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan Search for other works by this author on: Oxford Academic Google Scholar Tadamitsu Kishimoto, Tadamitsu Kishimoto Laboratory of Immune Regulation, Osaka University Graduate School of Frontier Biosciences, Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Toshio Tanaka Toshio Tanaka Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan Correspondence to: Toshio Tanaka, Department of Respiratory Medicine, Allergy and Rheumatic Diseases, Osaka University Graduate School of Medicine, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan e-mail: ttanak@imed3.med.osaka-u.ac.jp Search for other works by this author on: Oxford Academic Google Scholar Modern Rheumatology, Volume 21, Issue 4, 1 August 2011, Pages 436–439, https://doi.org/10.3109/s10165-011-0416-9 Published: 01 August 2011 Article history Received: 17 December 2010 Accepted: 13 January 2011 Published: 01 August 2011