gebhart/patrepeval huggingface dataset:
The Streptococcal Exotoxin Streptolysin O Activates Mast Cells To Produce Tumor Necrosis Factor Alpha by p38 Mitogen-Activated Protein Kinase- and Protein Kinase C-Dependent Pathways (2003)

Streptolysin O (SLO), a major virulence factor of pyogenic streptococci, binds to cholesterol in the membranes of eukaryotic cells and oligomerizes to form large transmembrane pores. While high toxin doses are rapidly cytocidal, low doses are tolerated because a limited number of lesions can be resealed. Here, we report that at sublethal doses, SLO activates primary murine bone marrow-derived mast cells to degranulate and to rapidly induce or enhance the production of several cytokine mRNAs, including tumor necrosis factor alpha (TNF-alpha). Mast cell-derived TNF-alpha plays an important protective role in murine models of acute inflammation, and the production of this cytokine was analyzed in more detail. Release of biologically active TNF-alpha peaked approximately 4 h after stimulation with SLO. Production of TNF-alpha was blunted upon depletion of protein kinase C by pretreatment of the cells with phorbol-12 myristate-13 acetate. Transient permeabilization of mast cells with SLO also led to the activation of the stress-activated protein kinases p38 mitogen-activated protein (MAP) kinase and c-jun N-terminal kinase (JNK), and inhibition of p38 MAP kinase markedly reduced production of TNF-alpha. In contrast, secretion of preformed granule constituents triggered by membrane permeabilization was not dependent on p38 MAP kinase or on protein kinase C. Thus, transcriptional activation of mast cells following transient permeabilization might contribute to host defense against infections via the beneficial effects of TNF-alpha. However, hyperstimulation of mast cells might also lead to overproduction of TNF-alpha, which would then promote the development of toxic streptococcal syndromes.
Structure of the HIV-1 RNA packaging signal (2015)

The 5' leader of the HIV-1 genome contains conserved elements that direct selective packaging of the unspliced, dimeric viral RNA into assembling particles. By using a (2)H-edited nuclear magnetic resonance (NMR) approach, we determined the structure of a 155-nucleotide region of the leader that is independently capable of directing packaging (core encapsidation signal; Ψ(CES)). The RNA adopts an unexpected tandem three-way junction structure, in which residues of the major splice donor and translation initiation sites are sequestered by long-range base pairing and guanosines essential for both packaging and high-affinity binding to the cognate Gag protein are exposed in helical junctions. The structure reveals how translation is attenuated, Gag binding promoted, and unspliced dimeric genomes selected, by the RNA conformer that directs packaging.
Enhancing and experiencing spacetime resolution with videos and stills (2009)

We present solutions for enhancing the spatial and/or temporal resolution of videos. Our algorithm targets the emerging consumer-level hybrid cameras that can simultaneously capture video and high-resolution stills. Our technique produces a high spacetime resolution video using the high-resolution stills for rendering and the low-resolution video to guide the reconstruction and the rendering process. Our framework integrates and extends two existing algorithms, namely a high-quality optical flow algorithm and a high-quality image-based-rendering algorithm. The framework enables a variety of applications that were previously unavailable to the amateur user, such as the ability to (1) automatically create videos with high spatiotemporal resolution, and (2) shift a high-resolution still to nearby points in time to better capture a missed event.
Mimicking Photosynthetic Solar Energy Transduction (2000)

Increased understanding of photosynthetic energy conversion and advances in chemical synthesis and instrumentation have made it possible to create artificial nanoscale devices and semibiological hybrids that carry out many of the functions of the natural process. Artificial light-harvesting antennas can be synthesized and linked to artificial reaction centers that convert excitation energy to chemical potential in the form of long-lived charge separation. Artificial reaction centers can form the basis for molecular-level optoelectronic devices. In addition, they may be incorporated into the lipid bilayer membranes of artificial vesicles, where they function as components of light-driven proton pumps that generate transmembrane proton motive force. The proton gradient may be used to synthesize adenosine triphosphate via an ATP synthase enzyme. The overall energy transduction process in the liposomal system mimics the solar energy conversion system of a photosynthetic bacterium. The results of this research illustrate the advantages of designing functional nanoscale devices based on biological paradigms.
Identification of specific cytolytic immune responses against autologous tumor in humans bearing malignant melanoma. (1987)

Tumor-infiltrating lymphocytes from six patients with metastatic malignant melanoma were expanded by culture in recombinant interleukin 2. Three of the preparations were highly cytotoxic against autologous fresh melanoma tumor cells, but not against autologous fresh normal cells or allogeneic fresh tumor targets. The other three were highly cytotoxic against autologous fresh melanoma tumor cells and also had a limited capacity to kill allogeneic fresh tumor targets. The tumor-associated specific killer cells could be expanded from threefold to 95,652-fold with maintenance of specific antitumor lysis. The expanded tumor-infiltrating cells were Leu-4+ T cells, and in five of six patients the majority were Leu-3+. These studies demonstrate that the melanoma-bearing patient raises an immune response against autologous tumor and presents a method for the generation of human lymphocytes with antitumor reactivity that may be useful in the adoptive immunotherapy of tumors.
Zaprinast, a well‐known cyclic guanosine monophosphate‐specific phosphodiesterase inhibitor, is an agonist for GPR35 (2006)

We found that zaprinast, a well-known cyclic guanosine monophosphate-specific phosphodiesterase inhibitor, acted as an agonist for a G protein-coupled receptor, GPR35. In our intracellular calcium mobilization assay, zaprinast activated rat GPR35 strongly (geometric mean EC(50) value of 16nM), whereas it activated human GPR35 moderately (geometric mean EC(50) value of 840nM). We also demonstrated that GPR35 acted as a Galpha(i/o)- and Galpha(16)-coupled receptor for zaprinast when heterologously expressed in human embryonic kidney 293 (HEK 293) cells. These findings will facilitate the research on GPR35 and the drug discovery of the GPR35 modulators.
Design of Gold Nanoparticle‐Based Colorimetric Biosensing Assays (2008)

Gold nanoparticle (AuNP)-based colorimetric biosensing assays have recently attracted considerable attention in diagnostic applications due to their simplicity and versatility. This Minireview summarizes recent advances in this field and attempts to provide general guidance on how to design such assays. The key to the AuNP-based colorimetric sensing platform is the control of colloidal AuNP dispersion and aggregation stages by using biological processes (or analytes) of interest. The ability to balance interparticle attractive and repulsive forces, which determine whether AuNPs are stabilized or aggregated and, consequently, the color of the solution, is central in the design of such systems. AuNP aggregation in these assays can be induced by an "interparticle-crosslinking" mechanism in which the enthalpic benefits of interparticle bonding formation overcome interparticle repulsive forces. Alternatively, AuNP aggregation can be guided by the controlled loss of colloidal stability in a "noncrosslinking-aggregation" mechanism. In this case, as a consequence of changes in surface properties, the van der Waals attractive forces overcome interparticle repulsive forces. Using representative examples we illustrate the general strategies that are commonly used to control AuNP aggregation and dispersion in AuNP-based colorimetric assays. Understanding the factors that play important roles in such systems will not only provide guidance in designing AuNP-based colorimetric assays, but also facilitate research that exploits these principles in such areas as nanoassembly, biosciences and colloid and polymer sciences.
Efficient Bipedal Robots Based on Passive-Dynamic Walkers (2005)

Passive-dynamic walkers are simple mechanical devices, composed of solid parts connected by joints, that walk stably down a slope. They have no motors or controllers, yet can have remarkably humanlike motions. This suggests that these machines are useful models of human locomotion; however, they cannot walk on level ground. Here we present three robots based on passive-dynamics, with small active power sources substituted for gravity, which can walk on level ground. These robots use less control and less energy than other powered robots, yet walk more naturally, further suggesting the importance of passive-dynamics in human locomotion.
In-vitro enhancement of mouse embryonic development by co-culture with peritoneal macrophages (1994)

The effects of peritoneal macrophages on mouse fertilization and embryonic development in vitro were examined by a co-culture method. In experiment 1, oocytes from F1 strain mice were inseminated and cultured with a monolayer of peritoneal macrophages to determine the effects of the macrophages on fertilization. In experiment 2, 1-cell embryos, fertilized in vivo from either a non-blocking or a blocking strain, were also incubated with peritoneal macrophages to determine whether these cells overcame the developmental arrest. Although the peritoneal macrophages had an adverse effect on fertilization in the F1 strain, embryonic development was significantly improved by the co-culture. This beneficial effect on embryonic development was also observed in the embryos fertilized in vivo from the strain that exhibited a 2-cell block. These results suggest that peritoneal macrophages provide an effective co-culture system for the in-vitro development of mouse embryos.
Splanchnicectomy for Pancreatic Cancer Pain (2014)

Persistent pain is a serious problem that often contributes to a poor quality of life in pancreatic cancer patients. Medical management by opioid analgesics is often accompanied by side effects and incomplete pain relief. A celiac plexus block is a simple treatment which relieves pain, but the procedure demands a certain degree of proficiency and the duration of the effects obtained can be rather limited. Transhiatal bilateral splanchnicectomy achieves a certain denervation of splanchnic nerves, but it requires a laparotomy. Unilateral thoracoscopic splanchnicectomy is a minimally invasive procedure to cause definite denervation. Bilateral thoracoscopic splanchnicectomy is recommended for unsatisfactory cases or recurrent pain occurring after the initial unilateral splanchnicectomy. It is important to select the most suitable treatment depending on patients' actual medical state and the predicted outcomes.
Histone H2B ubiquitination and beyond (2010)

Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fully defined. Ubiquitin was proposed to bind proteins to physically bridge H2Bub1 with Set1-COMPASS/Dot1. Alternatively, the bulky ubiquitin was thought to be a "wedge" that loosens the nucleosome for factor access. Contrary to the latter possibility, recent discoveries provide evidence for nucleosome stabilization by H2Bub1 via preventing the constant H2A-H2B eviction. Recent data has also uncovered a "docking-site" on H2B for Set1-COMPASS. Collectively, these findings invoke a model, where ubiquitin acts as a "glue" to bind the nucleosome together for supporting Set1-COMPASS/Dot1 functions. This review provides an overview of these novel findings. Additionally, how H2Bub1 and its deubiquitination might alter the chromatin dynamics during transcription is discussed. Possible models for nucleosome stabilization by ubiquitin are also provided.
Alterations to either c-erbB-2(neu) or c-myc proto-oncogenes in breast carcinomas correlate with poor short-term prognosis. (1987)

We have examined the genomic organisation of c-myc, N-myc, L-myc, neu and N-ras in tissue from 41 breast carcinomas, lymph node metastases from 10 of these carcinomas, one fibrosarcoma, 10 cases of benign fibrocystic breast and six fibroadenomas. We have not observed an alteration in either N-myc or N-ras in any of the samples studied. We have seen a 2-fold amplification of L=myc in DNA from one infiltrating ductal (ID) carcinoma, but otherwise we have seen no alterations to this gene. Amplification of c-myc was seen in 22% of ID breast carcinoma sample. Levels of amplification ranged from 2- to 10-fold. We have found a significant (p less than 0.02) correlation between an altered c-myc gene and a very poor short-term prognosis. Amplification of neu was seen in 19% of ID breast carcinomas, but the levels of amplification were higher than those seen for c-myc. Alterations to neu also correlated well with poor short-term prognosis (p less than 0.0002). Finally, we have observed a low level of amplification of c-myc in DNA from a benign fibrocystic breast lesion. This lesion exhibited some features characteristic of those thought to be associated with an increased risk of developing breast cancer.
Replacement therapy for congenital Factor X deficiency (1985)

We studied a young woman with severe (less than 1%) congenital factor X deficiency during a 2-year period in order to document the levels of factor X required to provide hemostasis for vaginal bleeding, epistaxis, and hemarthroses, as well as during surgery. Factor X levels of 9 to 17 percent, achieved with fresh-frozen plasma (FFP) were satisfactory for minor bleeding. Hemostasis was achieved during emergency surgery for hemoperitoneum by increasing the factor X level to 35 percent with a Factor IX concentrate, followed with infusions of FFP to maintain levels between 10 and 20 percent for 6 days postoperatively. These data suggest that factor X levels of 10 to 20 percent are sufficient for hemostasis in factor X-deficient patients even in the immediate postoperative period.
A Strategy for the Solid-Phase Synthesis of Oligosaccharides (1993)

Repeating glycosidic linkages of oligosaccharides can be synthesized by solid-phase methods. Glycals were attached to a polystyrene copolymer with a silyl ether bond and were activated to function as glycosyl donors with 3,3-dimethyldioxirane. Glycosidation was performed by reactions with a solution-based acceptor (itself a glycal). Excess acceptor and promoter were removed by rinsing after each coupling, and the desired oligosaccharides were then easily obtained from the polymer by the addition of tetra-n-butylammonium fluoride. By this method, glycosidations are stereospecific and interior deletions are avoided.
Strategic Bidding for Price-Taker Hydroelectricity Producers (2007)

This paper introduces a stochastic programming model that integrates strategic bids or offers for electricity (in quantities and prices) in a deregulated electricity market. The model is designed to maximize the profits of a producer of electricity who manages a series of power plants along a river. The model is compared with a previously reported stochastic model where the bidding process is disregarded. The superiority of the new model is empirically demonstrated on historical data.
Comparative carcinogenicity in F344 rats of the tobacco-specific nitrosamines, N'-nitrosonornicotine and 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone. (1980)

The tobacco-specific carcinogens, N'-nitrosonornicotine (NNN) and 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK), were tested for carcinogenicity in F344 rats. Each nitrosamine in trioctanoin was administered by s.c. injection to 12 male and 12 female rats over a period of 20 weeks. The total dose of each nitrosamine was 3.4 mmol. The experiment was terminated after 12 months. NNK induced nasal cavity tumors in 83% of the males and in 83% of the females, liver tumors in 83% of the males and in 100% of the females, and lung tumors in 67% of the males and in 67% of the females. NNN induced nasal cavity tumors in 92% of the males and in 75% of the females. Only one liver tumor and no lung tumors were observed in the NNN-treated rats. These results indicate that, in the F344 rat, NNK is a more powerful carcinogen than is NNN.
Interferon-Stimulated Response Element and NFκB Sites Cooperate to Regulate Double-Stranded RNA-Induced Transcription of the IP-10 Gene (1994)

To understand the mechanisms involved in dsRNA-induced gene expression, we analyzed the poly(I/C)-induced transcription of the IFN-inducible chemokine gene IP-10 using the GRE cell line in which type I IFN genes have been deleted. Accumulation of IP-10 mRNA in GRE cells was more strongly stimulated by treatment with dsRNA than by IFN-alpha or IFN-gamma and was independent of protein synthesis. This same pattern of response was produced when GRE cells were transiently transfected with a plasmid containing 243 bases of sequence from the promoter of the murine IP-10 gene linked to the chloramphenicol acetyltransferase reporter gene. Deletion- and site-specific mutagenesis of the 243 base pair fragment indicated that an ISRE located between residues -204 and -228 was a primary target site for the action of dsRNA on this promoter. This was confirmed by results showing that two copies of this ISRE tandemly arrayed in front of the thymidine kinase promoter were able to mediate reporter gene transcription in dsRNA-stimulated cells. At least one of the two NF kappa B binding sites present in the 243 base pair IP-10 promoter is also necessary for response to dsRNA; mutation of both sites eliminates promoter activity. Thus the ISRE and one NF kappa B site cooperate to produce transcriptional response to dsRNA.
A New Class of Safe Oligosaccharide Polymer Therapy To Modify the Mucus Barrier of Chronic Respiratory Disease (2016)

The host- and bacteria-derived extracellular polysaccharide coating of the lung is a considerable challenge in chronic respiratory disease and is a powerful barrier to effective drug delivery. A low molecular weight 12-15-mer alginate oligosaccharide (OligoG CF-5/20), derived from plant biopolymers, was shown to modulate the polyanionic components of this coating. Molecular modeling and Fourier transform infrared spectroscopy demonstrated binding between OligoG CF-5/20 and respiratory mucins. Ex vivo studies showed binding induced alterations in mucin surface charge and porosity of the three-dimensional mucin networks in cystic fibrosis (CF) sputum. Human studies showed that OligoG CF-5/20 is safe for inhalation in CF patients with effective lung deposition and modifies the viscoelasticity of CF-sputum. OligoG CF-5/20 is the first inhaled polymer therapy, represents a novel mechanism of action and therapeutic approach for the treatment of chronic respiratory disease, and is currently in Phase IIb clinical trials for the treatment of CF.
Interleukin-2 Induces Early Multisystem Organ Edema Mediated by Neutrophils (1991)

Interleukin-2 (IL-2), an agent known to activate neutrophils (PMN) with thromboxane (Tx)B2 release, produces pulmonary edema within 6 hours of intravenous infusion. This study tests the role of PMN in mediating the edema. Anesthetized rats received 10(6)U recombinant human IL-2 (n = 15) or vehicle (n = 14) as a constant intravenous infusion during a period of 1 hour. At this time there was leukopenia 3.63 +/- 0.43 (x10(3)/mm3) relative to vehicle-infused control rats 6.12 +/- 0.86 and a decline in PMN, 2.19 +/- 0.14 relative to control value of 3.33 +/- 0.05 (both p less than 0.05). After 6 hours edema, as measured by increase in the wet to dry weight (W/d) ratio, was present in the lungs (4.93 +/- 0.20 relative to control 4.06 +/- 0.10), heart (4.09 +/- 0.11 versus 3.76 +/- 0.08), liver (3.50 +/- 0.10 versus 3.18 +/- 0.10), and kidney (4.25 +/- 0.07 versus 4.00 +/- 0.07) (all p less than 0.05). There was increased lung permeability demonstrated by bronchoalveolar lavage fluid protein concentration of 1970 +/- 210 micrograms/mL relative to control 460 +/- 90 micrograms/mL (p less than 0.05). Interleukin-2 resulted in lung PMN sequestration of 53 +/- 7 PMN/10 high-power fields (HPF) relative to 23 +/- 2 PMN/10 HPF in controls (p less than 0.05) and increased plasma TxB2 levels to 1290 +/- 245 pg/mL relative to control 481 +/- 93 pg/mL (p less than 0.05). Pretreatment of other rats (n = 8) with selective anti-rat neutrophil antiserum 18 hours before the experiment led to a peripheral PMN count 10% of baseline and prevented edema in the lungs (W/d ratio 4.20 +/- 0.16) and heart (3.67 +/- 0.07) (both p less than 0.05) but not liver or kidney. Protein in lung lavage was reduced to 760 +/- 220 micrograms/mL (p less than 0.05). The protection afforded by leukopenia was associated with lack of PMN sequestration and prevention of the increase in plasma Tx levels (484 +/- 120 pg/mL, p less than 0.05). These data indicate that the rapid induction of lung and heart edema with a 1-hour infusion of IL-2 in the rat is mediated, in large part, by activated PMNs.
NF-IL6, a member of the C/EBP family, regulates E1A-responsive promoters in the absence of E1A (1992)

A cDNA encoding NF-IL6, an interleukin-6 (IL-6)-regulated human nuclear factor of the C/EBP family, is demonstrated to complement the transactivation function of E1A. The endogenous NF-IL6 level varies according to cell type and correlates positively with an IL-6-regulated cellular E1A-substituting activity that was described recently (J.M. Spergel and S. Chen-Kiang, Proc. Natl. Acad. Sci. USA 88:6472-6476, 1991). When expressed by transfection in cells which contain low levels of NF-IL6 and are incapable of complementing the function of E1A proteins, NF-IL6 also transactivates the E1A-responsive E2ae and E1B promoters, to the same magnitude as E1A. Activation by NF-IL6 is concentration dependent and sequence specific: mutational studies of the E2ae promoter suggest that the promoter-proximal NF-IL6 recognition site functions as a dominant negative regulatory site whereas the promoter-distal NF-IL6 recognition site is positively regulated at low NF-IL6 concentrations and negatively regulated when the NF-IL6 level is high. Consistent with these functions, NF-IL6 alone is sufficient to complement an E1A deletion mutant dl312 in viral infection, when expressed at appropriate concentrations. These results identify NF-IL6 as a sequence-specific cellular nuclear factor which regulates E1A-responsive genes in the absence of E1A.