gebhart/patrepeval huggingface dataset:
The consistent coalitional value for hyperplane games (2004)

We introduce a value for hyperplane games with coalition structure. This value coincides with the consistent value for trivial coalition structures, and with the Owen value for transferable utility games with coalition structure. Furthermore, we present two characterizations: the first one using a consistency property and the second one using properties of balanced contributions.
Successful treatment of recalcitrant cutaneous sarcoidosis with fumaric acid esters (2002)

On the basis of our findings FAE therapy seems to be a safe and effective regimen for patients with recalcitrant cutaneous sarcoidosis. Nevertheless further investigations are necessary to confirm our preliminary results.
Isolation and characterization of HsfA3, a new heat stress transcription factor of Lycopersicon peruvianum (2000)

Stress-induced transcription of heat shock proteins (Hsps) in eukaryotes is mediated by a conserved class of transcription factors called heat stress transcription factors (Hsfs). Here we report the isolation and functional characterization of HsfA3, a new member of the Hsf family. HsfA3 was cloned from a tomato heat stress cDNA library by yeast two-hybrid screening, using HsfA1 as a bait. HsfA3 is a single-copy gene with all the conserved sequence elements characteristic of a heat stress transcription factor. The constitutively expressed HsfA3 is mainly found in the cytoplasm under control conditions and in the nucleus under heat stress conditions. Functionally, HsfA3 behaves similarly to the already known members of tomato Hsf family. It is able to substitute yeast Hsf for viability functions and is a strong activator of Hsf-dependent reporter constructs both in tobacco protoplasts and yeast. Finally, similar to the AHA motifs in HsfA1 and HsfA2, the activator function depends on four short peptide motifs with a central tryptophan residue found in the C-terminal domain of HsfA3.
Modulation of the classical multidrug resistance (MDR) phenotype by RNA interference (RNAi) (2003)

For reversal of MDR1 gene-dependent multidrug resistance (MDR), two small interfering RNA (siRNA) constructs were designed to inhibit MDR1 expression by RNA interference. SiRNA duplexes were used to treat human pancreatic carcinoma (EPP85-181RDB) and gastric carcinoma (EPG85-257RDB) cells. In both cellular systems, siRNAs could specifically inhibit MDR1 expression up to 91% at the mRNA and protein levels. Resistance against daunorubicin was decreased to 89% (EPP85-181RDB) or 58% (EPG85-257RDB). The data indicate that this approach may be applicable to cancer patients as a specific means to reverse tumors with a P-glycoprotein-dependent MDR phenotype back to a drug-sensitive one.
Effects of Electromagnetic Field Exposure on Neuroendocrine Function (1992)

There is now increasing interest in the possibility that exposure to static or extremely low frequency (ELF: 0–300 Hz; including 50 and 60-Hz powerline frequencies) electric and magnetic fields are associated with increased risk for certain cancers (Savitz and Calle, 1987), emotional depression (Perry and Pearl, 1988; Wilson, 1988), and changes in reproductive function and development (Wertheimer and Leeper, 1986). It now appears possible that EMF-induced changes in pineal gland function may account wholly, or in part, for these effects. We present here a discussion of this hypothesis.
A uniform geometrical theory of diffraction for an edge in a perfectly conducting surface (1974)

A compact dyadic diffraction coefficient for electromagnetic waves obliquely incident on a curved edse formed by perfectly conducting curved ot plane surfaces is obtained. This diffraction coefficient remains valid in the transition regions adjacent to shadow and reflection boundaries, where the diffraction coefficients of Keller's original theory fail. Our method is based on Keller's method of the canonical problem, which in this case is the perfectly conducting wedge illuminated by plane, cylindrical, conical, and spherical waves. When the proper ray-fixed coordinate system is introduced, the dyadic diffraction coefficient for the wedge is found to be the sum of only two dyads, and it is shown that this is also true for the dyadic diffraction coefficients of higher order edges. One dyad contains the acoustic soft diffraction coefficient; the other dyad contains the acoustic hard diffraction coefficient. The expressions for the acoustic wedge diffraction coefficients contain Fresenel integrals, which ensure that the total field is continuous at shadow and reflection boundaries. The diffraction coefficients have the same form for the different types of edge illumination; only the arguments of the Fresnel integrals are different. Since diffraction is a local phenomenon, and locally the curved edge structure is wedge shaped, this result is readily extended to the curved wedge. It is interesting that even though the polarizations and the wavefront curvatures of the incident, reflected, and diffracted waves are markedly different, the total field calculated from this high-frequency solution for the curved wedge is continuous at shadow and reflection boundaries.
Epitope scanning using virtual matrix-based algorithms (2000)

Protein sequence and expression databases (transcriptomes) contain the information required to identify epitopes capable of generating protective immune responses in humans. A key event in the initiation of an immune response against disease is the presentation of antigenic peptide epitopes to T cells by human leukocyte antigen (HLA) molecules. Computational filtering tools that allow the prediction of HLA/epitope interaction can be applied to sequence databases to select for candidate epitopes, thus minimising the subsequent amount of laboratory work. Here, the basic principles of epitope prediction and a summary of the available prediction approaches are presented, with a particular emphasis on the use of algorithms based on virtual HLA-II quantitative matrices, capable of predicting promiscuous HLA-II ligands.
Branch capture reactions: displacers derived from asymmetric PCR (1991)

Branch capture reactions (BCR) contain three DNA species: (i) a recipient restriction fragment terminating in an overhang, (ii) a displacer strand containing two adjacent sequences, with one complementary to the overhang and to contiguous nucleotides within the recipient duplex and (iii) a linker which is complementary to the second displacer sequence. Branched complexes containing all three species may be captured by ligation of the linker to the recipient overhang. The use of 5-MedC in the displacer facilitates BCR. High temperature ligation with a thermostable enzyme increased specificity for ligation to the correct recipient in a complex mixture of restriction fragments. Displacer synthesis by PCR permitted separate reactions of formation of stable displacement complexes and of high-temperature ligation. Ethylene glycol-containing buffer permitted PCR with 5-MedCTP or high G + C products using thermostable polymerases. BCR may be used to modify the ends of one recipient DNA duplex in a population of duplex DNA fragments. Modification of the recipient could be used to facilitate detection, affinity chromatography or cloning. By using PCR to obtain a BCR displacer, the sequence non-homologous to the recipient duplex may be expanded to include the sequence of a selectable marker, thus facilitating chromosome walking.
Cryopreservation of Human Fat for Soft Tissue Augmentation (2005)

Viability of adipocytes frozen at -20 degrees C was very low when analyzed by staining, and no cultures could be established from any of the specimens. In contrast, viable adipocytes were recovered from samples that were controlled-rate frozen in the presence of cryoprotectants and stored in nitrogen vapor. CONCLUSION. Our results indicate that fat frozen at -20 degrees C is not viable and thus provides no advantage over inert fillers. The methods here described could readily be transferred to the clinical setting after further laboratory study.
Infection of Human Cells by Dengue Virus Is Modulated by Different Cell Types and Viral Strains (2000)

Although prior studies have investigated cellular infection by dengue virus (DV), many have used highly passaged strains. We have reassessed cellular infection by DV type 2 (DV2) using prototype and low-passage isolates representing genotypes from different geographic areas. We observed marked variation in the susceptibility to infection among cell types by different DV2 strains. HepG2 hepatoma cells were susceptible to infection by all DV2 strains assayed. Although the prototype strain generated higher titers of secreted virus than the low-passage isolates, this difference did not correspond to positive- or negative-strand viral RNA levels and thus may reflect variation in efficiency among DV2 isolates to translate viral proteins or package and/or secrete virus. In contrast, human foreskin fibroblasts were susceptible to the prototype and low-passage Thai isolates but not to five Nicaraguan strains tested, as reflected by the absence of accumulation of negative-strand viral RNA, viral antigen, and infectious virus. A similar pattern was observed with the antibody-dependent pathway of infection. U937 and THP-1 myeloid cells and peripheral blood monocytes were infected in the presence of enhancing antibodies by the prototype strain but not by low-passage Nicaraguan isolates. Again, the barrier appeared to be prior to negative-strand accumulation. Thus, depending on the cell type and viral isolate, blocks that limit the production of infectious virus in vitro may occur at distinct steps in the pathway of cellular infection.
Prevention of Pulmonary Hypertension by Angiotensin-Converting Enzyme 2 Gene Transfer (2009)

In spite of recent advancements in the treatment of pulmonary hypertension, successful control has yet to be accomplished. The abundant presence of angiotensin-converting enzyme 2 (ACE2) in the lungs and its impressive effect in the prevention of acute lung injury led us to test the hypothesis that pulmonary overexpression of this enzyme could produce beneficial outcomes against pulmonary hypertension. Monocrotaline (MCT) treatment of mice for 8 weeks resulted in significant increases in right ventricular systolic pressure, right ventricle:left ventricle plus septal weight ratio, and muscularization of pulmonary vessels. Administration of a lentiviral vector containing ACE2, 7 days before MCT treatment prevented the increases in right ventricular systolic pressure (control: 25+/-1 mm Hg; MCT: 44+/-5 mm Hg; MCT+ACE2: 26+/-1 mm Hg; n=6; P<0.05) and right ventricle:left ventricle plus septal weight ratio (control: 0.25+/-0.01; MCT: 0.31+/-0.01; MCT+ACE2: 0.26+/-0.01; n=8; P<0.05). A significant attenuation in muscularization of pulmonary vessels induced by MCT was also observed in animals overexpressing ACE2. These beneficial effects were associated with an increase in the angiotensin II type 2 receptor:angiotensin II type 1 receptor mRNA ratio. Also, pulmonary hypertension-induced increases in proinflammatory cytokines were significantly attenuated by lentiviral vector-containing ACE2 treatment. Furthermore, ACE2 gene transfer in mice after 6 weeks of MCT treatment resulted in a significant reversal of right ventricular systolic pressure. These observations demonstrate that ACE2 overexpression prevents and reverses right ventricular systolic pressure and associated pathophysiology in MCT-induced pulmonary hypertension by a mechanism involving a shift from the vasoconstrictive, proliferative, and fibrotic axes to the vasoprotective axis of the renin-angiotensin system and inhibition of proinflammatory cytokines.
Synergistic effects of IL-7 and IL-12 on human T cell activation. (1995)

We have previously demonstrated that human rIL-12 alone can augment the development of cytotoxic activity in stimulated CD8+ T cells. The present study was undertaken to examine the interactions of rIL-7 and rIL-12 on human peripheral blood T cell activation and CTL differentiation. Purified T lymphocytes were pulsed overnight with immobilized alpha-CD3 and then cultured for 3 additional days with IL-7 and/or IL-12. The combination of IL-7 and IL-12 synergistically enhanced the proliferation of either fresh CD3+ T cells or an IL-2-dependent CD4+ T cell line, Kit-225-K6. This synergy was seen on both subsets of T cells; however, CD8+ T cells were usually more responsive to IL-7 and IL-12 at lower concentrations than were CD4+ T cells. Furthermore, these cytokines additively/synergistically augmented the cytotoxic activity of CD8+ T cells. Abs to IL-2 and IL-2R alpha blocked the synergistic effect on proliferation of CD4+ T cells, but had a minimal effect on the synergistic response of the proliferative and cytotoxic activity of CD8+ T cells. Examination of the effects of IL-7 and IL-12 on the expression of IL-12 receptor on T cells revealed an increase in the subunit of IL-12R by IL-7 as determined by flow cytometric analysis. We analyzed the effects on IFN-gamma production by CD8+ T cells and found that IL-7 alone did not induce detectable levels of IFN-gamma production but together with IL-12 it synergistically enhanced the production of IFN-gamma. We also found that IFN-gamma was probably not required for enhanced CTL activity of CD8+ T cells, because Ab to human IFN-gamma did not block additive/synergistic effects of either cytokine. The synergistic stimulatory activity of IL-7 and IL-12 may be of significance in vivo and may provide an alternative mechanism of stimulating T cells for use in immunotherapy.
Recurrent turnover of senescent cells during regeneration of a complex structure (2015)

Cellular senescence has been recently linked to the promotion of age-related pathologies, including a decline in regenerative capacity. While such capacity deteriorates with age in mammals, it remains intact in species such as salamanders, which have an extensive repertoire of regeneration and can undergo multiple episodes through their lifespan. Here we show that, surprisingly, there is a significant induction of cellular senescence during salamander limb regeneration, but that rapid and effective mechanisms of senescent cell clearance operate in normal and regenerating tissues. Furthermore, the number of senescent cells does not increase upon repetitive amputation or ageing, in contrast to mammals. Finally, we identify the macrophage as a critical player in this efficient senescent cell clearance mechanism. We propose that effective immunosurveillance of senescent cells in salamanders supports their ability to undergo regeneration throughout their lifespan.
On building fast kd-Trees for Ray Tracing, and on doing that in O(N log N) (2006)

Though a large variety of efficiency structures for ray tracing exist, kd-trees today seem to slowly become the method of choice. In particular, kd-trees built with cost estimation functions such as a surface area heuristic (SAH) seem to be important for reaching high performance. Unfortunately, most algorithms for building such trees have a time complexity of O(N log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> N), or even O(N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). In this paper, we analyze the state of the art in building good kd-trees for ray tracing, and eventually propose an algorithm that builds SAH kd-trees in O(N log N), the theoretical lower bound
NMDA Channel Regulation by Channel-Associated Protein Tyrosine Kinase Src (1997)

The N-methyl-D-aspartate (NMDA) receptor mediates synaptic transmission and plasticity in the central nervous system (CNS) and is regulated by tyrosine phosphorylation. In membrane patches excised from mammalian central neurons, the endogenous tyrosine kinase Src was shown to regulate the activity of NMDA channels. The action of Src required a sequence [Src(40-58)] within the noncatalytic, unique domain of Src. In addition, Src coprecipitated with NMDA receptor proteins. Finally, endogenous Src regulated the function of NMDA receptors at synapses. Thus, NMDA receptor regulation by Src may be important in development, plasticity, and pathology in the CNS.
Janus-AT Bases:  Synthesis, Self-Assembly, and Solid State Structures (2006)

The high yielding synthesis of heterocycles with defined H-bond accepting and donating capabilities provides for the design of self-assembling structures and specific recognition of biological targets. Herein we report the syntheses and solid-state structures of three self-complementary uracil/thymine derivatives where each presents the standard ADA face inherently complementary to adenine and a synthetically appended DAD face complementary to uracil/thymine. These heterocycles, which have never before been reported or characterized, represent diaminopurine-uracil/thymine hybrids that, in two of the three cases, relate to previously reported heterocyclic hybrids of G and C. All three heterocycles crystallized to afford the first X-ray crystal structures of self-complementary heterocycles capable of ADA-DAD pairing. The potential use in DNA and RNA recognition are briefly discussed.
Decellularization for whole organ bioengineering (2013)

Organ transplantation in an orthotopic location is the current treatment for end-stage organ failure. However, the need for transplantable organs far exceeds the number of available donor organs. As a result, new options, such as tissue engineering and regenerative medicine, have been explored to achieve functional organ replacement. Although there have been many advances in the laboratory leading to the reconstruction of tissue and organ structures in vitro, these efforts have fallen short of producing organs that contain intact vascular networks capable of nutrient and gas exchange and are suitable for transplantation. Recently, advances in whole organ decellularization techniques have enabled the fabrication of scaffolds for engineering new organs. These scaffolds, consisting of naturally-derived extracellular matrix (ECM), provide biological signals and maintain tissue microarchitecture, including intact vascular systems that could integrate into the recipient's circulatory system. The decellularization techniques have led to the development of scaffolds for multiple organs, including the heart, liver, lung and kidney. While the experimental studies involving the use of decellularized organ scaffolds are encouraging, the translation of whole organ engineering into the clinic is still distant. This paper reviews recently described techniques used to decellularize whole organs such as the heart, lung, liver and kidney and describes possible methods for using these matrices for whole organ engineering.
Deletions in the alpha-globin gene complex in alpha-thalassemic mice. (1981)

Three induced, heritable mutations in the mouse cause alpha-thalassemias. The adult alpha-globin genes on each mutant chromosome are no longer expressed. Embryos heterozygous for one normal and any of the three mutant chromosomes also seem to be deficient in embryonic alpha-globin-like x-globin, suggesting that the x-globin gene is nearby and also inactivated. A normal genetic polymorphism for a specific EcoRI site in or around the mouse alpha-globin gene complex has been used here to show that each of the three mutated chromosomes has a deletion that includes the segment of a 12-kilobase EcoRI band which normally carries one of the two adult alpha-globin genes. The deletion of the comparable part of the second alpha-globin gene site is also inferred. Nonetheless, a 4.7-kilobase EcoRI segment which carries a characterized alpha-globin-like pseudogene is still present in each mutant. These mutations were recovered after triethylenemelamine or x-ray treatments.
Gliding robotic fish for mobile sampling of aquatic environments (2014)

Aquatic ecosystems and processes exhibit a high degree of spatial and temporal heterogeneity, which presents significant challenges for their monitoring. In this paper we report a novel underwater robot, called gliding robotic fish, as an emerging platform for mobile sensing in aquatic environments that can potentially provide high spatiotemporal coverage. The robot represents a hybrid of an underwater glider and a robotic fish, and is capable of exploiting gliding to achieve energy-efficient locomotion while using a fish-like active tail to achieve high maneuverability. Preliminary field-test results are presented, where the robot was used to sample the Kalamazoo River and the Wintergreen Lake in Michigan for concentrations of crude oil and harmful algae, respectively.
Bactericidal activity of deptomycin (LY146032) compared with those of ciprofloxacin, vancomycin, and ampicillin against enterococci as determined by kill-kinetic studies (1987)

This study used kill-kinetic methods to provide data on the bactericidal activity of subinhibitory (1/2 X MIC), inhibitory (1 x MIC), and suprainhibitory (4X, 6X, and 8X MIC) concentrations of deptomycin (LY146032) against strains of enterococci compared with those of ciprofloxacin, vancomycin, and ampicillin. Deptomycin was the most active agent tested, as determined by broth microdilution methods, with all strains being inhibited at concentrations less than or equal to 2 micrograms/ml. The kill-kinetic demonstrated that deptomycin had greater activity at all concentrations tested than the other cell wall-active agents; regrowth was seen, however, at lower concentrations. At higher concentrations (6X and 8X MIC), all agents tested demonstrated the same or less bactericidal activity than at 4X MIC, presumably due to the Eagle effect. Nevertheless, these results suggest that further evaluation of deptomycin as a therapeutic agent for serious enterococcal infections is warranted.
Recent Advances in Fetal Nucleic Acids in Maternal Plasma (2005)

The discovery of cell-free fetal DNA in maternal plasma in 1997 has opened up new possibilities for noninvasive prenatal diagnosis. Circulating fetal DNA molecules have been detected in maternal plasma from the first trimester onwards and can be robustly detected using a variety of molecular methods. This approach has been used for the prenatal investigation of sex-linked diseases, fetal RhD status, and prenatal exclusion of beta-thalassemia major. Recently, fetal RNA has also been found in maternal plasma. Such fetal RNA has been shown to originate from the placenta and to be remarkably stable. The use of microarray-based approaches has made it feasible to rapidly generate new circulating RNA markers. It is hoped that further developments in this field will make the routine and widespread practice of noninvasive nucleic acid-based prenatal diagnosis for common pregnancy-associated disorders feasible in the near future.
The immunogenicity of VP7, a rotavirus antigen resident in the endoplasmic reticulum, is enhanced by cell surface expression (1990)

The glycoprotein VP7, the major serotype antigen of rotaviruses, is localized to the endoplasmic reticulum (ER) of the cell, where it is retained as a membrane-associated protein before assembly into mature virus particles. Wild-type VP7 expressed by a recombinant vaccinia virus was also located internally and was poorly antigenic. Using recombinant techniques, a correctly processed, secreted form of VP7 (S.C. Stirzaker and G.W. Both, Cell 56:741-747, 1989) was modified by addition to its C terminus of the membrane anchor and cytoplasmic domains from the influenza virus hemagglutinin. The hybrid protein was directed to the surface of cells, where it was anchored in the plasma membrane. When expressed in mice and rabbits by a recombinant vaccinia virus, the surface-anchored antigen stimulated a level of rotavirus-specific antibodies that was greater than 100-fold above the level induced by wild-type VP7. T-cell responses to the novel antigen were also elevated in comparison with the wild-type, intracellular protein. Cell surface anchoring may provide a strategy to increase the immunogenicity of intracellular antigens from other parasites and viruses.