gebhart/patrepeval huggingface dataset:
Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and Shadowing[W] (2003)

In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3-kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae species, several other motifs, but not the LFY and WUS binding sites identified previously, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for the activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection but also demonstrate that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.
PRAD1/lCyclin D1 proto‐oncogene: Genomic organization, 5′ dna sequence, and sequence of a tumor‐specific rearrangement breakpoint (1993)

PRAD1 (previously D11S287) is a putative proto-oncogene at 11q13, activated by overexpression through gene rearrangement or gene amplification in several types of human tumors including parathyroid adenomas, centrocytic lymphomas and other B-cell tumors with t(11;14), and breast cancers. PRAD1 (also CCND1) encodes cyclin D1, which may regulate the G1-S phase transition in the cell cycle. Here, we report the cloning and characterization of the chromosomal PRAD1/cyclin D1 gene and the sequence of its promoter region. The gene spans about 15 kb and has 5 exons; its promoter region has Sp1 binding sites and no obvious TATA box, characteristics of housekeeping genes and growth-regulating genes. Furthermore, an E2F binding motif present close to the major transcription start site may be involved in cell cycle-dependent expression of this gene. We also report the sequence of DNAs spanning joining regions of a reciprocal parathyroid hormone/PRAD1 gene rearrangement in a parathyroid adenoma. Comparison with normal sequences suggests that the rearrangement was not a simple break-and-ligate event, but rather involved multiple steps, including two microdeletions and a microinversion. Very short sequences conserved near the breakpoints and symmetrical elements in the eventually inverted DNA segment might have played a role in this illegitimate complex recombination, which may have similarities with a constitutional translocation in Duchenne muscular dystrophy.
Caress of the Gaze: A Gaze Actuated 3D Printed Body Architecture (2016)

This paper describes the design process behind Caress of the Gaze, a project that represents a new approach to the design of a gaze-actuated, 3D printed body architectureÂas a form of proto-architectural studyÂproviding a framework for an interactive dynamic design. The design process engages with three main issues. Firstly, it aims to look at form or geometry as a means of controlling material behavior by exploring the tectonic properties of multi-material 3D printing technologies. Secondly, it addresses novel actuation systems by using Shape Memory Alloy (SMA) in order to achieve life-like behavior. Thirdly, it explores the possibility of engaging with interactive systems by investigating how our clothing could interact with other people as a primary interface, using vision-based eye-gaze tracking technologies. In so doing, this paper describes a radically alternative approach not only to the production of garments but also to the ways we interact with the world around us. Therefore, the paper addresses the emerging field of shape-changing 3D printed structures and interactive systems that bridge the worlds of robotics, architecture, technology, and design.
Satellite cells, connective tissue fibroblasts and their interactions are crucial for muscle regeneration (2011)

Muscle regeneration requires the coordinated interaction of multiple cell types. Satellite cells have been implicated as the primary stem cell responsible for regenerating muscle, yet the necessity of these cells for regeneration has not been tested. Connective tissue fibroblasts also are likely to play a role in regeneration, as connective tissue fibrosis is a hallmark of regenerating muscle. However, the lack of molecular markers for these fibroblasts has precluded an investigation of their role. Using Tcf4, a newly identified fibroblast marker, and Pax7, a satellite cell marker, we found that after injury satellite cells and fibroblasts rapidly proliferate in close proximity to one another. To test the role of satellite cells and fibroblasts in muscle regeneration in vivo, we created Pax7(CreERT2) and Tcf4(CreERT2) mice and crossed these to R26R(DTA) mice to genetically ablate satellite cells and fibroblasts. Ablation of satellite cells resulted in a complete loss of regenerated muscle, as well as misregulation of fibroblasts and a dramatic increase in connective tissue. Ablation of fibroblasts altered the dynamics of satellite cells, leading to premature satellite cell differentiation, depletion of the early pool of satellite cells, and smaller regenerated myofibers. Thus, we provide direct, genetic evidence that satellite cells are required for muscle regeneration and also identify resident fibroblasts as a novel and vital component of the niche regulating satellite cell expansion during regeneration. Furthermore, we demonstrate that reciprocal interactions between fibroblasts and satellite cells contribute significantly to efficient, effective muscle regeneration.
Arc-length-based axial deformation and length preserved animation (2002)

In real life, some objects may deform along axial curves and the lengths of their skeletons usually remain constant during the axial deformation, such as a swimming fish, a swaying tree, etc. This paper presents a practical approach of arc-length-based axial deformation and axial-length-preserved animation. The space spanned by the arc-length parameter and the rotation-minimizing frame on the axis is taken as the embedding space. During animation, the keyframe axial curves are consistently approximated by polylines after sufficient subdivisions and both the edge lengths and the directional vertex angles of the keyframe polylines (or unit edge vectors) are then interpolated to generate the intermediate polylines which are regarded as the discrete expressions of the intermediate axes. Experiments show that our method is very useful, intuitive and easy to control.
Wafer-scale processing, assembly, and testing of tunneling infrared detectors (2002)

The individual assembly of early tunneling sensors required time and skill which were incompatible with high volume production and which produced a very large variation in key device operating parameters. This paper describes the first successful fully wafer-scale production of tunneling sensors. The sensors produced in this process feature noise and sensitivity characteristics consistent with the best tunneling sensors developed so far and are appropriate for use as state-of-the-art uncooled infrared detectors.
Soft Drink Consumption and Risk of Developing Cardiometabolic Risk Factors and the Metabolic Syndrome in Middle-Aged Adults in the Community (2007)

In middle-aged adults, soft drink consumption is associated with a higher prevalence and incidence of multiple metabolic risk factors.
Polyclonally triggered B cells in the peripheral blood and bone marrow of normal individuals and in patients with systemic lupus erythematosus and primary sjögren's syndrome (1981)

Numbers of B cells spontaneously secreting Ig (IgG, IgA, and IgM) were determined by a plaque-forming cell (PFC) assay simultaneously in the peripheral blood and bone marrow of normal individuals, patients with systemic lupus erythematosus (SLE), and patients with primary Sjögren's syndrome. Normal individuals had 382 (+/- 89) PFC per 10(6) mononuclear cells in peripheral blood. Patients with either active or inactive Sjögren's syndrome had normal numbers of spontaneous Ig-secreting cells in peripheral blood (P greater than 0.2). Conversely, patients with inactive as well as active SLE had markedly increased spontaneous PFC (P less than 0.05 and P less than 0.001, respectively). Patients with active SLE had significantly greater PFC than patients with inactive SLE; 3,984 (+/- 960) versus 1,605 (+/- 527) PFC per 10(6) mononuclear cells (P less than 0.05). The lack of increased numbers of activated B cells in the blood of patients with Sjögren's syndrome was not explained by a preferential sequestration of activated B cells in the bone marrow. However, of particular interest was the finding that the bone marrow served not only as a major source of virgin B cells but as a lymphoid organ of either in situ activation of B cells or sequestration for activated B cells. Normal individuals had approximately a 20-fold relative increase of activated B cells per 10(6) mononuclear cells in the bone marrow compared to peripheral blood, while patients with inactive and active SLE both had a 35-fold relative increase in activated B cells in bone marrow compared to peripheral blood. The potential relevance of circulating activated B cells and their sequestration in lymphoid organs is discussed concerning the discrepancy in this regard between Sjögren's syndrome and SLE, and our understanding of the significance of polyclonal B cell activation in the pathogenesis of these diseases.
Analogs of the hormonal form of vitamin D and their possible use in leukemia. (1988)

We have concluded a large analog study that suggests that specific analogs of 1,25-(OH)2D3 can be prepared that have markedly enhanced activity in promoting differentiation of HL-60 promyelocytes to benign monocytes. We have observed that lengthening the side chain of 1,25-(OH)2D3 increases activity in HL-60 by 1 order of magnitude when the side chain is increased in length by 1 carbon. At the same time, the biological activity of these compounds in serum calcium elevation is either unchanged or diminished. Thus, lengthening the side chain may well provide a preferentially active form of vitamin D on the promyelocytes. Shortening the side chain has resulted a 10-fold loss of activity in HL-60 for each carbon removed. Furthermore, elimination of the 26- and 27-carbons decreases biological activity by 100-fold. If, however, the hydroxyl is left off the side chain and small hydrocarbon side chains of ethyl or isopropyl are substituted, very high activity in HL-60 is achieved without activity in mobilizing calcium in vivo. We, therefore, have compounds in hand which illustrate at least in vitro specific activity in HL-60.
Passive and synaptic properties of hippocampal neurons grown in microcultures and in mass cultures (1995)

1. We used whole cell recordings to compare passive membrane properties and synaptic properties of postnatal rat hippocampal neurons grown for 7-15 days in either conventional mass cultures or on physically restricted microisland cultures. Despite matching microisland and mass culture cell across several variables, there were significant differences between neurons in the two groups regarding passive membrane characteristics and synaptic properties. 2. Microisland neurons displayed significantly faster charging of the membrane capacitance than mass culture counterparts matched with microisland neurons for age, somal diameter, and transmitter phenotype. When we used a two-compartment equivalent circuit model to quantify this result, microisland neurons displayed approximately half the distal capacitance of mass culture neurons. These data suggest that microisland neurons elaborate less extensive neuritic arborizations than mass culture neurons. 3. Evoked synaptic responses were enhanced on microislands compared with mass cultures. Excitatory and inhibitory autaptic currents were more frequent and displayed larger amplitudes on single-neuron microislands than in matched mass culture neurons. 4. In recordings from pairs of neurons in the two environments, we observed a significantly higher probability of obtaining a monosynaptic response on two-neuron microislands than in matched mass culture pairs (85% vs. 42%). Evoked excitatory postsynaptic currents were also significantly larger in the microisland environment, with evoked excitatory synaptic currents from two-neuron microislands exhibiting a mean amplitude 20-fold larger than mass culture monosynaptic responses. 5. The differences in evoked synaptic responses were not reflected in differences in the amplitude or frequency of spontaneous miniature excitatory postsynaptic currents (mEPSCs). Analysis of mEPSC rise times, decay times, and peak amplitudes within individual cells suggests that electrotonic filtering is not an important contributor to the variability of peak amplitudes and decay times of synaptic currents in cells of either culture environment. However, composite data across neurons in both cultures reveal a significant correlation between mEPSC rise and decay times. 6. Out results suggest that the microisland preparation may be a useful tool for exploring factors that influence synapse formation and development. Additionally, the preparation is a particularly convenient model for the study of single-neuron-mediated synaptic events.
Multilingual generation and summarization of job adverts (1997)

A multilingual Internet-based employment advertisement system is described. Job ads are submitted as e-mail texts, analysed by an example-based pattern matcher and stored in language-independent schemas in an object-oriented database. Users can search the database in their own language and get customized summaries of the job ads. The query engine uses symbolic case-based reasoning techniques, while the generation module integrates canned text, templates, and grammar rules to produce texts and hypertexts in a simple way.
Effects of evodiamine and rutaecarpine on the secretion of corticosterone by Zona fasciculata‐reticularis cells in male rats (2009)

Evodiamine (EVO) and rutaecarpine (RUT) are two bioactive alkaloid isolated from Chinese herb named Wu-Chu-Yu. Previous studies have shown that EVO and RUT possess thermoregulation, vascular regulation, anti-allergic, anti-nociceptive and anti-inflammatory activities. The mechanisms of EVO and RUT effect on steroidogenesis are not clear. The goal of this study was to characterize the mechanism by which EVO and RUT affect corticosterone production in rat zona fasciculata-reticularis (ZFR) cells. ZFR cells were isolated from adrenal glands of male rats and incubated with adrenalcorticotropin (ACTH, 10(-9) M), forskolin (an adenylyl cyclase activator, 10(-5) M), 8-bromo-adenosine 3':5'-cyclic monophosphate (8-Br-cAMP, a permeable cAMP analog, 10(-4) M), or steroidogenic precursors including 25-hydroxycholesterol, pregnenolone, progesterone, and deoxycorticosterone, 10(-5) M each, in the presence or absence of EVO and RUT respectively (0-10(-3) M) at 37 degrees C for 1 h. The concentrations of corticosterone, pregnenolone and progesterone in the media were measured by radioimmunoassay. After administration of ZFR cells with EVO or RUT (10(-4) M) for 60 and 120 min, Western blot analysis was employed to explore the influence of EVO and RUT on the expression of cytochrome P450 side chain cleavage enzyme (P450scc) and steroidogenic acute regulatory protein (StAR). EVO and RUT reduced both basal and ACTH-, forskolin-, as well as 8-Br-cAMP-stimulated corticosterone production in rat ZFR cells. The enhanced corticosterone production caused by the administration of four steroidogenic precursors was decreased following EVO or RUT challenge. These results suggest that EVO and RUT inhibit corticosterone production in rat ZFR cells via a mechanism involving: (1) a decreased activity of cAMP-related pathways; (2) a decreased activity of the steroidogenic enzymes, that is, 3beta-hydroxysteroid dehydrogenase (3beta-HSD) and 11beta-hydroxylase (P450c11), during steroidogenesis; and (3) an inhibition of StAR protein expression.
Epidermal growth factor (EGF) induces oligomerization of soluble, extracellular, ligand-binding domain of EGF receptor. A low resolution projection structure of the ligand-binding domain (1991)

Ligand-induced oligomerization is a universal phenomenon among growth factor receptors. Although the mechanism involved is yet to be defined, much evidence indicates that receptor oligomerization plays a crucial role in receptor activation and signal transduction. Here we show that epidermal growth factor (EGF) is able to stimulate the oligomerization of a recombinant, soluble, extracellular ligand-binding domain of EGF receptor. Covalent cross-linking experiments, analysis by sodium dodecyl sulfate-gel electrophoresis, size exclusion chromatography, and electron microscopy demonstrate that receptor dimers, trimers and larger multimers are formed in response to EGF. This establishes that receptor oligomerization is an intrinsic property of the extracellular ligand-binding domain of EGF receptor. Ligand-induced conformational change in the extracellular domain will stimulate receptor-receptor interactions. This may bring about the allosteric change involved in signal transduction from the extracellular domain across the plasma membrane, resulting in the activation of the cytoplasmic kinase domain. Electron microscopic images of individual extracellular ligand-binding domains appear as clusters of four similarly-sized stain-excluding areas arranged around a central, relatively less stain-excluded area. This suggests that the extracellular ligand-binding domain is structurally composed of four separate domains.
Self-Organized Discotic Liquid Crystals for High-Efficiency Organic Photovoltaics (2001)

Self-organization of liquid crystalline and crystalline-conjugated materials has been used to create, directly from solution, thin films with structures optimized for use in photodiodes. The discotic liquid crystal hexa-peri-hexabenzocoronene was used in combination with a perylene dye to produce thin films with vertically segregated perylene and hexabenzocoronene, with large interfacial surface area. When incorporated into diode structures, these films show photovoltaic response with external quantum efficiencies of more than 34 percent near 490 nanometers. These efficiencies result from efficient photoinduced charge transfer between the hexabenzocoronene and perylene, as well as from effective transport of charges through vertically segregated perylene and hexabenzocoronene pi systems. This development demonstrates that complex structures can be engineered from novel materials by means of simple solution-processing steps and may enable inexpensive, high-performance, thin-film photovoltaic technology.
<title>Optical inspection techniques for security instrumentation</title> (1996)

This paper reviews four optical inspection systems, in which development TNO Institute of Applied Physics was involved: (1) intaglio scanning and recognition, (2) banknote quality inspection, (3) visualization and reading of a finger pattern, and (4) 3DAS authentication. (1) Intaglio is reserved for high security printing. It renders a tactile relief that can be recognized by a laser scanning technique. This technique is applied by various national banks to detect counterfeit banknotes returning from circulation. A new system is proposed that will detect intaglio on arbitrary wrinkled banknotes. (2) A banknote fitness inspection system (BFIS) that inspects banknotes in specularly reflected light is described. As modern banknotes are provided increasingly with reflective security foils, a new system is proposed that inspects banknotes in specular and diffuse reflection, as well as in transmission. (3) An alternative visualization method for visualization of finger patterns is described, employing a reflective elastomer. A CD scanning system reads the finger patterns. (4) A nonwoven structure has two advantageous properties for card authentication: a random structure which renders each few square millimeters of the pattern uniqueness (identification) and a 3D structure which makes it virtually impossible to be counterfeited (authentication). Both properties are inspected by an extremely simple lenseless reader.
Nanocomposite microstructures with tunable mechanical and chemical properties (2010)

We report a two-step chemical vapor deposition (CVD) method for fabrication of hierarchical polymer-coated carbon nanotube (CNT) microstructures having tunable mechanical properties and accessible chemical functionality. Diverse geometries of vertically aligned CNTs were grown from lithographically patterned catalyst films, and the CNT microstructures were chemically functionalized via poly[4-trifluoroacetyl-p-xylylene-co-p-xylylene] made by chemical vapor deposition polymerization. The polymer coating conformally coated the individual CNTs and CNT bundles within the CNT "forest". The chemical structure of the polymer films was verified by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR). Simple control of the mechanical properties of the nanocomposite structures can be achieved by adjusting the deposition times during CVD polymerization. Increasing the polymer film thickness from 10 nm to 27 nm resulted in a change of the Young's modulus from 65 to 80 MPa. These values are substantially higher than the 36 MPa measured for the as-grown CNTs without polymer coating. The effect of the polymer coating in reinforcing the connectivity among CNTs within the structures has been understood using an analytical model. Finally, chemical functionality of the CNT composite structures after CVD polymerization was verified by a 4-fold fluorescence enhancement after binding of a dye to the coated CNT microstructures. This technique can be adapted to a wide variety of reactive coatings and facilitates attachment of chemical groups and functional nanostructures on the surfaces of the CNTs; therefore, this material could serve as a tunable platform for coupling mechanical and chemical responses in materials for environmental and biological sensing.
A 47-kDa human nuclear protein recognized by antikinetochore autoimmune sera is homologous with the protein encoded by RCC1, a gene implicated in onset of chromosome condensation. (1990)

Several autoimmune sera from patients with Raynaud phenomenon decorated mammalian kinetochores and bound to a 47-kDa protein on immunoblots of nuclear lysates. Antibody affinity-purified from immunoblots of the 47-kDa band recognized kinetochores, but due to crossreaction with an 18-kDa protein, localization remains elusive. We used one of these sera to purify the antigen from HeLa cells synchronized in mitosis as a noncovalent complex with a 25-kDa protein. The antigen was released from DNA by intercalation with 25 mM chloroquine. Ion-exchange chromatography yielded the pure complex with an apparent molecular size of 68 kDa, which was separated into its components by gel filtration in 6 M guanidinium chloride. Upon two-dimensional gel electrophoresis the 47-kDa protein gave two main spots of pI 6.6 and 6.7, respectively. Posttranslational modification is indicated by additional antigenic spots, by lack of a free alpha-amino group, and by chromatographic behavior of peptides on reversed-phase chromatography. The amino acid sequence for 205 residues of the 47-kDa protein has been established. This sequence is highly homologous with the translated reading frame of RCC1, a gene reportedly involved in regulating onset of mammalian chromosome condensation.