gebhart/patrepeval huggingface dataset:
Strict control of telomerase activation using Cre-mediated inversion (2006)

This binary expression system thus provides a useful genetic means to strictly regulate the expression of a given gene, or to control the expression of at least two different genes in a mutually exclusive manner.
Casting curved shadows on curved surfaces (1978)

Shadowing has historically been used to increase the intelligibility of scenes in electron microscopy and aerial survey. Various methods have been published for the determination of shadows in computer synthesized scenes. The display of shadows may make the shape and relative position of objects in such scenes more comprehensible; it is a technique lending vividness and realism to computer animation.To date, algorithms for the determination of shadows have been restricted to scenes constructed of planar polygons. A simple algorithm is described which utilizes Z-buffer visible surface computation to display shadows cast by objects modelled of smooth surface patches. The method can be applied to all environments, in fact, for which visible surfaces can be computed. The cost of determining the shadows associated with each light source is roughly twice the cost of rendering the scene without shadows, plus a fixed transformation overhead which depends on the image resolution. No extra entities are added to the scene description in the shadowing process. This comprehensive algorithm, which permits curved shadows to be cast on curved surfaces, is contrasted with a less costly method for casting the shadows of the environment on a single ground plane.In order to attain good results, the discrete nature of the visible-surface computations must be treated with care. The effects of dither, interpolation, and geometric quantization at different stages of the shadowing algorithm are examined. The special problems posed by self-shadowing surfaces are described.
Experimental Testing of Gerotor and Scroll Expanders Used in, and Energetic and Exergetic Modeling of, an Organic Rankine Cycle (2009)

This paper presents the experimental testing of relatively cost-effective expanders in an organic Rankine cycle (ORC) to produce power from low-grade energy. Gerotor and scroll expanders were the two types of expanders tested to determine their applicability in producing power from low-grade energy. The results of the experimental testing showed that both types of expanders were good candidates to be used in an ORC. The gerotor and scroll expanders tested produced 2.07 kW and 2.96 kW, and had isentropic efficiencies of 0.85 and 0.83, respectively. Also the paper presents results of an analytical model produced that predicted improved cycle efficiency with certain changes. One change was the flow rate of the working fluid in the cycle was properly matched with the inlet pocket volume and rotational speed of the expander. Also, the volumetric expansion ratio of the expander was matched to the specific volume ratio of the working fluid (R-123) across the expander. The model incorporated the efficiencies of the expanders and pump obtained during experimental testing, and combined two expanders in series to match the specific volume ratio of the working fluid. The model determined the power produced by the expanders, and subtracted the power required by the working fluid pump and the condenser fan. From that, the model calculated the net power produced to be 6271 W and the overall energy efficiency of the cycle to be 7.7%. When the ORC was simulated to be integrated with the exhaust of a stationary engine, the exergetic efficiency, exergy destroyed, and reduction in diesel fuel while still producing the same amount of power during 2500 h of operation were 22.1%, 22,169 W, and 4,012 L (1060 U.S. gal), respectively. Consequently, the model presents a very realistic design based on results from experimental testing to cost-effectively use low-grade energy.
The Amino-terminal Part of PRELP Binds to Heparin and Heparan Sulfate (2000)

PRELP (proline, arginine-rich end leucine-rich repeat protein) is an extracellular matrix leucine-rich repeat protein. The amino-terminal region of PRELP differs from that of other leucine-rich repeat proteins in containing a high number of proline and arginine residues. The clustered proline and basic residues are conserved in rat, bovine, and human PRELP. Although the function of PRELP is not yet known, the clustered arginine residues suggest a heparan sulfate/heparin-binding capacity. We show here that PRELP indeed binds heparin and heparan sulfate. Truncated PRELP without the amino-terminal region does not bind heparin. The dissociation constant for the interaction of PRELP with heparin was determined by an in solution binding assay and by surface plasmon resonance analysis to be in the range of 10-30 nm. A 6-mer heparin oligosaccharide was the smallest size showing binding to PRELP. The binding increased with increasing length up to an 18-mer and depended on the degree of sulfation of heparin as well as heparan sulfate. Sulfate groups at all positions were shown to be of importance for the binding. Fibroblasts bind PRELP, and this interaction is inhibited with heparin, suggesting a function for PRELP as a linker between the matrix and cell surface proteoglycans.
On Compatibility of Web Services (2003)

This paper is concerned with the application of Web services to distributed, cross-organizational business processes. Web services provide a platform independent concept of components and composition. Thus, they seem to be a proper technology to cover the heterogenous structures within distributed business processes: One Web service realizes a local subprocess. A distributed business process is realized by the composition of a set of Web services. Although the technological basement is given, there is a lot of open questions: Do two Web services fit together in a way, that the composition yields a deadlockfree system? – the question of compatibility. Can one Web service be exchanged by another within a composed system without running into problems? – the question of equivalence. Can we reason about the quality of one given Web service without considering the environment it will by used in? In this paper we present the notion of usability – our quality criterion of a Web service. This criterion is intuitive and can be easily proven locally. Moreover, this notion allows to answer the other questions mentioned above. The approach and the results presented in this paper are taken from a larger framework for modeling and analyzing business processes by help of Web services published in my PhD thesis [9]. 1
Pivoting the Plant Immune System from Dissection to Deployment (2013)

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls.
Functional Interactions Between the Thrombin Receptor and the T-Cell Antigen Receptor in Human T-Cell Lines (1997)

The proteolytically activated thrombin receptor (TR) is expressed by T lymphocytes, which suggests that thrombin may modulate T-cell activation at sites of hemostatic stress. We examined the relationship between TR function and T-cell activation in the Jurkat human T-cell line and in T-cell lines with defined defects in T-cell antigen receptor (TCR) function. Stimulation with thrombin or the synthetic TR peptide SFLLRN produced intracellular Ca2+ transients in Jurkat cells. As the concentration of TR agonist was increased, peak Ca2+ mobilization increased, but influx of extracellular Ca2+ decreased. TR signaling was enhanced in a TCR-negative Jurkat line and in T-cell lines deficient in the tyrosine kinase lck or the tyrosine phosphatase CD45, both of which are essential for normal TCR function. TCR cross-linking with anti-CD3 IgM desensitized TR signaling in Jurkat cells, but not in CD45-deficient cells. A proteinase-activated receptor (PAR-2)-specific agonist peptide, SLIGKV, produced small Ca2+ transients in both MEG-01 human megakaryocytic cells and Jurkat cells, but was less potent than the TR-specific agonist TFRIFD in both cell types. Like TR signaling, PAR-2 signaling was enhanced in TCR-negative or lck-deficient Jurkat clones. These findings provide evidence for functional cross-talk between proteolytically activated receptors and the TCR.
Dichotomous Musical Worlds: Interactions between the Musical Lives of Adolescents and School Music-Learning Culture (2022)

This ethnographic study investigated the interactions between the musical lives of adolescents and school music-learning culture in a suburban high school. Participants included two music teachers and seven adolescents. Framed within a symbolic interactionist perspective (Blumer, 1969), data were collected via methods consistent with qualitative inquiry, including an innovative data collection technique utilizing music elicitation interviews with adolescents. Findings emerged from the data via thematic analysis (Grbich, 2007). Findings indicate limited interactions between the musical lives of adolescents and school music-learning culture because participants portrayed and experienced a dichotomy between the musical assumptions and practices inside and outside of school. Interactions occurred when participants engaged in sharing musical capital that overcame segmentation among music learning, out-of-school experience, and elective participation in secondary school music programs. Supporting findings indicate that the school music-learning culture derived from teachers' negotiating between two major influences: 1) their own musical values, which were based on their musical backgrounds and the long-established professional tradition of formal performance emphases in school music programs; and 2) the musical values of their students. Adolescents self-defined their musical lives as largely informal musical activities commonly experienced outside of school. They expressed a wealth of personal musical knowledge and described their affinity for music across four dimensions: 1) expression and feeling, 2) relevance, 3) quality in artistry and craftsmanship, and 4) diversity. Three themes describe how adolescents? personal relationships with music influenced their beliefs and choices regarding music participation and learning: 1) musical roots: nurturing personal and social connections with music, 2) motivated learning: seeking relevance and challenge, and 3) finding a voice: striving toward musical independence. Findings indicate that music teachers may enhance interactions between adolescents? musical lives and school music-learning culture by acknowledging students? musical engagement outside of school, honoring their personal musical knowledge and interests, and making them collaborators in developing music-learning models rooted in their affinity for, and personal relationships with, music.
The field and radiation impedance of mechanical radiators on the free surface of a semi-infinite isotropic solid (1954)

Abstract Definite integral representations are obtained for the field at an arbitrary point in a semi­ infinite solid, due to stresses on the free surface which vary sinusoidally with time. From these integrals, asymptotic expressions have been obtained for the field at infinity in the solid, and polar diagrams showing the variation of field strength with direction are given. Integrals are also found for the mean displacement over the externally stressed region of the surface, and these have been evaluated numerically in a number of cases to obtain the radiation impedance of the sources represented by such stress systems.
Bilateral caudate and putamen grafts of embryonic mesencephalic tissue treated with lazaroids in Parkinson's disease (2000)

Five parkinsonian patients were transplanted bilaterally into the putamen and caudate nucleus with human embryonic mesencephalic tissue from between seven and nine donors. To increase graft survival, the lipid peroxidation inhibitor tirilazad mesylate was administered to the tissue before implantation and intravenously to the patients for 3 days thereafter. During the second postoperative year, the mean daily L-dopa dose was reduced by 54% and the UPDRS (Unified Parkinson's Disease Rating Scale) motor score in `off' phase was reduced by a mean of 40%. At 10–23 months after grafting, PET showed a mean 61% increase of 6-L-[18F]fluorodopa uptake in the putamen, and 24% increase in the caudate nucleus, compared with preoperative values. No obvious differences in the pattern of motor recovery were observed between these and other previously studied cases with putamen grafts alone. The amount of mesencephalic tissue implanted in each putamen and caudate nucleus was 42 and 50% lower, respectively, compared with previously transplanted patients from our centre. Despite this reduction in grafted tissue, the magnitudes of symptomatic relief and graft survival were very similar. These findings suggest that tirilazad mesylate may improve survival of grafted dopamine neurons in patients, which is in agreement with observations in experimental animals.
Effective Formation of Silicone-in-Fluorocarbon-in-Water Double Emulsions: Studies on Droplet Morphology and Stability (2002)

ABSTRACT Silicone-in-fluorocarbon-in-water double emulsions were prepared by controlling carefully the characteristics of the emulsions composed of silicone, perfluoropoly-ethoxymethoxy difluorohydroxyethyl ether (PFPE–OH) and fluorosurfactant. In the emulsion formulation, PFPE–OH incorporated had a great influence on the droplet morphology and the stability of double emulsions. Moreover, it was observed that among the fluorocarbons, the silicone-in-fluorocarbon-in-water double emulsions could be formed effectively in the presence of a fluorosurfactant. The double emulsions prepared in this study maintained their initial emulsion stability for a long time at high temperature, meaning great usefulness in the cosmetic industry.
A Water‐Borne Adhesive Modeled after the Sandcastle Glue of P. californica (2008)

Polyacrylate glue protein analogs of the glue secreted by Phragmatopoma californica, a marine polycheate, were synthesized with phosphate, primary amine, and catechol sidechains with molar ratios similar to the natural glue proteins. Aqueous mixtures of the mimetic polyelectrolytes condensed into liquid complex coacervates around neutral pH. Wet cortical bone specimens bonded with the coacervates, oxidatively crosslinked through catechol sidechains, had bond strengths nearly 40% of the strength of a commercial cyanoacrylate. The unique material properties of complex coacervates may be ideal for development of clinically useful adhesives and other biomaterials.
Perturbation of the antigen-binding site and staphylococcal Protein A-binding site of IgG before significant changes in global conformation during denaturation: an equilibrium study (1997)

Although conformational perturbation of the active sites of many enzymes has been reported to precede global molecular conformational changes [Tsou (1993) Science 262, 380-381], little effort has been made to compare the susceptibility of the ligand-binding site of proteins and the protein molecules as a whole to perturbation by denaturants. Immunoglobulin is chosen in this study to address this problem. It is found that the variable and constant regions (Fv and Fc) of a monoclonal antibody of an IgG subclass against adenylate kinase lose their abilities to bind antigen and staphylococcal Protein A after treatment with guanidinium chloride concentrations considerably lower than those required to change the global conformation of the antibody as a whole, as detected by fluorescence and second-derivative UV absorption spectroscopy. These results indicate that both ligand-binding sites of the antibody concerned are more fragile than the molecule as a whole and that the Fv and Fc regions of the antibody molecule unfold sequentially during denaturation.
Asymmetric Organic Catalysis with Modified Cinchona Alkaloids (2004)

Insights into the role played by modified cinchona alkaloids in the Sharpless asymmetric dihydroxylation inspired studies of modified cinchona alkaloids as chiral organic catalysts that lead to the development of highly enantioselective alcoholyses for the desymmetrization, kinetic resolution, and dynamic kinetic resolution of cyclic anhydrides, cyanation of ketones, and 1,4-addition of thiols to cylic enones. These studies demonstrate the potential of modified cinchona alkaloids as broadly useful chiral organic catalysts for asymmetric synthesis.
DMSO extraction of sulfones from selectively oxidized fuels (1999)

Dimethyl sulfoxide (DSMO) is an effective solvent extracting aromatic sulfones from petroleum distillate. Such sulfones may be prepared by selective oxidation of thiophenic compounds with peroxyacids. The combination of oxidation and extraction provides a route to sulfur removal that does not require high pressure hydrogenation and may allow small refiners with no on-site hydrogen to make fuels that meet sulfur regulations. Sulfur levels below 500 ppm have been achieved routinely in laboratory work.
Size-Controllable Region-of-Interest in Scalable Image Representation (2010)

Differentiating region-of-interest (ROI) from non-ROI in an image in terms of relative size as well as fidelity becomes an important functionality for future visual communication environment with a variety of display devices. In this paper, we propose a scalable image representation with the ROI functionality in the spatial domain, which allows us to generate a hierarchy of images with arbitrary sizes. The ROI functionality of our scalable representation is a result of a nonuniform grid transformation in the spatial domain, where only the center of ROI and an expansion parameter are to be known. Our grid transformation guarantees no loss of information within the area of ROI.
Infection frequency of dendritic cells and CD4+ T lymphocytes in spleens of human immunodeficiency virus-positive patients (1995)

Dendritic cells (DC) are specialized antigen-presenting leukocytes that are responsible for the activation of naive as well as memory T lymphocytes. If infected by human immunodeficiency virus (HIV), DC may transfer virus to CD4+ lymphocytes. However, the question of whether DC are infected in vivo is controversial. As HIV infection is more active in secondary lymphoid organs than in blood, infection of splenic DC isolated from HIV-seropositive patients was investigated. Splenic DC were first enriched and characterized by flow cytometry from HIV- donors. After direct isolation, they were negative for monocyte and T- and B-lymphocyte markers, negative for CD1a, but positive for major histocompatibility complex class II and CD4. After in vitro maturation, major histocompatibility complex class II expression increased, while CD4 expression was lost. Extensive purification from the spleens of seven HIV+ patients was performed by fluorescence-activated cell sorting. The frequency of cells harboring HIV DNA in purified populations was quantified by limiting-dilution PCR. Directly isolated DC (average, 1/3,000; range, 1/720 to 1/18,000) were in each patient 10 to 100 times less infected than CD4+ T lymphocytes (average, 1/52; range, 1/17 to 1/190). On average, 1/1,450 (1/320 to 1/6,100) unseparated mononuclear splenocytes (containing 5% CD4+ lymphocytes) harbored HIV DNA. In conclusion, in these HIV+ patient spleens, DC seem to be infected, but HIV-DNA positive CD4+ T lymphocytes accounted for the vast majority of infected mononuclear splenocytes.
Soft switching multi-phase boost converter for photovoltaic system (2008)

In this paper, we proposed soft switching multi-phase boost converter. A high efficiency power conversion device is required to obtain constant voltage from solar cells of which output voltage fluctuates very severely by irradiance and temperature. Using the proposed converter, we can control input voltage that fluctuates within operation range to constant output voltage, and it can reduce input current ripple and output voltage ripple. In addition, using ZVS (zero voltage switching) and ZCS (zero current switching), switching losses are reduced. We performed simulation and experiment for the proposed soft switching multi-phase boost converter.
Human receptors for sweet and umami taste (2002)

The three members of the T1R class of taste-specific G protein-coupled receptors have been hypothesized to function in combination as heterodimeric sweet taste receptors. Here we show that human T1R2/T1R3 recognizes diverse natural and synthetic sweeteners. In contrast, human T1R1/T1R3 responds to the umami taste stimulus l-glutamate, and this response is enhanced by 5'-ribonucleotides, a hallmark of umami taste. The ligand specificities of rat T1R2/T1R3 and T1R1/T1R3 correspond to those of their human counterparts. These findings implicate the T1Rs in umami taste and suggest that sweet and umami taste receptors share a common subunit.
Organization and nucleotide sequence of the DNA polymerase gene from the archaeon Pyrococcus furiosus (1993)

We cloned the gene encoding the thermostable DNA polymerase from the archaeon Pyrococcus furiosus. The DNA fragment of 2785 base pair (bp) containing the structural gene for DNA polymerase was sequenced. DNA polymerase (Pfu polymerase), as deduced from the DNA sequence, consisted of 775 amino acids, had a molecular weight of 90, 109, and was structurally homologous to the alpha-like DNA polymerases (family B) represented by human DNA polymerase alpha and Escherichia coli DNA polymerase II. An unrooted phylogenetic tree of the alpha-like DNA polymerases based on the amino acid sequence alignment was constructed. Pfu polymerase, with two other archaeon polymerases, constitutes a group with some animal viruses. The transcription initiation sites of the pol gene were identified by analysis of in vivo transcripts of both from P. furiosus and E. coli, and the promoters were assigned upstream of the pol coding region. A typical promoter sequence for the archaeon was found at a reasonable distance from the transcription initiation site in P. furiosus.
Endothelin receptor-A is required for the recruitment of antitumor T cells and modulates chemotherapy induction of cancer stem cells (2013)

These studies indicate a critical role for ETRA in the regulation of immune cell recruitment and in the CSC resistance to chemotherapy.