gebhart/patrepeval huggingface dataset:
Trajectory design for formations of robots by kinetic energy shaping (2003)

We develop a method for generating smooth trajectories for a set of mobile robots. Given two end configurations, by tuning one parameter, the user can choose an interpolating trajectory from a continuum of curves varying from that corresponding to maintaining a rigid formation to motion of the robots toward each other The idea behind our method is to change the original constant kinetic energy metric in the configuration space and can be summarized into three steps. First, the energy of the motion as a rigid structure is decoupled from the energy of motion along directions that violate the rigid constraints. Next, the metric is "shaped" by assigning different weights to each term. Finally, geodesic flow is constructed for the modified metric. The optimal motions generated on the manifolds of rigid body displacements in 3D space or in plane, and the uniform rectilinear motion of each robot corresponding to a totally uncorrelated approach are particular cases of our general treatment.
Soluble and processable regioregular poly(3-hexylthiophene) for thin film field-effect transistor applications with high mobility (1996)

The electrical characteristics of field-effect transistors using solution cast regioregular poly(3-hexylthiophene) are discussed. We demonstrate that both high field-effect mobilities (ca. 0.045 cm2/V s in the accumulation mode and 0.01 cm2/V s in the depletion mode), and relatively high on/off current ratios (greater than 103) can be achieved. We find that the film quality and field-effect mobility are strongly dependent on the choice of solvents. In addition, treating a film with ammonia or heating to 100 °C under N2 can increase the on/off ratio without decreasing the mobility.
Evaluation of the effects of four media on human intestinal microbiota culture in vitro (2019)

The human intestinal microbiota has an important role in the maintenance of human health and disease pathogenesis. The aim of this research was to investigate the impact of four media on human intestinal microbiota metabolite and composition changes, we performed in vitro batch culture using intestinal microbiota samples from three fecal microbiota transplantation (FMT) donors. After 48 h culture, gut microbiota medium (GMM) had the highest production of acetic acid (73.00 ± 7.56 mM) and propionic acid (16.79 ± 1.59 mM), bacterial growth media (BGM) had the highest production of butyric acid (13.39 ± 0.56 mM). In addition, brain heart infusion (BHI) promoted (p < 0.05) the growth of Bacteroidetes, especially Bacteroides after 48 h, GMM resulted in a significant increase (p < 0.05) in Actinobacteria and increased the beneficial genus Bifidobacterium, fastidious anaerobe broth (FAB) increased Firmicutes population, and BGM promoted the growth of Escherichia-Shigella and Akkermansia. The results suggest that four media had different effects on the human intestinal microbiota metabolism and composition in vitro. These results may facilitate the culture of bacteria from the human intestinal microbiota.
Speckle photography fringe analysis: assessment of current algorithms (1989)

The accuracy and reliability of four fringe analysis algorithms have been assessed, using Young's fringe patterns calculated from computer generated speckle patterns. The 1-D integration, 1-D autocorrelation, 2-D Fourier transform, and 2-D Walsh transform methods all estimated the two in-plane displacement components with negligible systematic error; the random errors were found to vary in proportion to sigma(2)/VR (speckle diameter = sigma, fringe visibility = V, and radius of laser probe beam = R), with the lowest errors given by the 2-D Fourier transform method.
Prognostic significance of p105 (c-erbB-2 HER2/neu) serum levels in patients with ovarian cancer. (1997)

Our results suggest that ovarian cancer patients with elevated p105 serum levels may have a poor clinical outcome.
Allogeneic Mesenchymal Stem Cells for Treatment of Experimental Autoimmune Encephalomyelitis (2009)

The use of allogeneic "universal donor" mesenchymal stromal cells (MSCs) may be a substantial clinical convenience for treatment of autoimmune ailments such as multiple sclerosis. We therefore tested whether allogeneic MSCs can be exploited for treatment of experimental autoimmune encephalomyelitis (EAE) in mice with otherwise intact immune system. Administration of allogeneic Balb/c-derived MSCs to C57Bl/6 mice with pre-established EAE led to a significant decrease in disease score over time comparable to that achieved with syngeneic MSCs, and was correlated with a significant blunting of immune cell infiltration to the spinal cord and reduced circulating levels of interferon-gamma (IFN-gamma) and interleukin-17. Pretreatment of allogeneic MSCs with IFN-gamma increased the expression levels of CCL2 as well as major histocompatibility complex I (MHCI) and MHCII, but also led to complete loss of suppressive activity in vivo that correlated with immune rejection. In conclusion, allogeneic MSCs can suppress the manifestations of EAE, yet retain the potential for alloimmunization.
Enzyme Catalysed Synthesis in Ambient Temperature Ionic Liquids (2001)

The activity of three different lipases, a glycosidase and a protease in ionic liquids has been studied. Ambient temperature ionic liquids are a new class of solvents that are nonvolatile and nonflammable and thus an interesting alternative to classical organic solvents. Monitoring the synthesis of a simple ester, all lipases were found to exhibit both excellent activity and stability in the non-polar ionic liquid 1-butyl-3-methylimidazohum hexaflurophosphate ([bmin][PF6], 1). Furthermore, β-galactosidase from E. coli and the Subtilisin protease SavinaseTM were both found to exhibit a hydrolytic activity in a 50% aqueous solution of the water-miscible ionic liquid 1-butyl-3-methyhmidazoUum tetra-fluoroborate ([bmin][BF4], 2) comparable to the activity observed in 50% aqueous solutions of ethanol and acetonitrile.
Standardization of Two Immunoassays for Human Glandular Kallikrein 2 (2003)

Calibration with a common calibrator substantially increased agreement between the assays. The ek-rhK2 variant provided the best performance of all tested rhK2 variants and should undergo mass spectrometry and amino acid analysis for exact mass determination and value assignment to evaluate its potential as a reference material for immunoassays for hK2.
Structure and Function of Human Growth Hormone: Implications for the Hematopoietins (1993)

CONTENTS PERSPECTIVE AND OVERVIEW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 LIGANDS FOR HEMATOPOIETIC RECEPTORS ARE FOUR-HELIX BUNDLES 331 THE EXTRACELLULAR DOMAINS OF THE HEMATOPOIETIC RECEPTORS 334 ONE hGH BINDS TWO RECEPTORS 337 Mutational Analysis 337 Crystallographic Analysis 341 FUNCTIONAL AND STRUCTURAL EPITOPES ON hGH OVERLAP 342 IMPLICATIONS FOR OTHER HEMATOPOIETINS 344 Hematopoietic Hormones 344 Extracellular Receptor Domains 345 MECHANISM(S) FOR ACTIVATION OF THE GROWTH-HORMONE RECEPTOR 346 FUTURE APPLICATIONS ... .... 348
Cofermentation of Cellobiose and Galactose by an Engineered Saccharomyces cerevisiae Strain (2011)

We demonstrate improved ethanol yield and productivity through cofermentation of cellobiose and galactose by an engineered Saccharomyces cerevisiae strain expressing genes coding for cellodextrin transporter (cdt-1) and intracellular β-glucosidase (gh1-1) from Neurospora crassa. Simultaneous fermentation of cellobiose and galactose can be applied to producing biofuels from hydrolysates of marine plant biomass.
Altered TCR Signaling from Geometrically Repatterned Immunological Synapses (2005)

The immunological synapse is a specialized cell-cell junction that is defined by large-scale spatial patterns of receptors and signaling molecules yet remains largely enigmatic in terms of formation and function. We used supported bilayer membranes and nanometer-scale structures fabricated onto the underlying substrate to impose geometric constraints on immunological synapse formation. Analysis of the resulting alternatively patterned synapses revealed a causal relation between the radial position of T cell receptors (TCRs) and signaling activity, with prolonged signaling from TCR microclusters that had been mechanically trapped in the peripheral regions of the synapse. These results are consistent with a model of the synapse in which spatial translocation of TCRs represents a direct mechanism of signal regulation.
Towards a Theory of Generalizing System Call Representation for In-Execution Malware Detection (2010)

The major contribution of this paper is two-folds: (1) we present our novel variable-length system call representation scheme compared to existing fixed- length sequence schemes, and (2) using this representation, we present our in-execution malware detector that can not only identify zero-day malware without any a priori knowledge but can also detect a malicious process while it is executing. Our representation scheme - a more generalized version of n-gram - can be visualized in a k-dimensional hyperspace in which processes move depending upon their sequence of system calls. The process marks its impact in space by generating hyper-grams that are later used to evaluate an unknown process according to their profile. The proposed technique is evaluated on a real world dataset extracted from a Linux System. The results of our analysis show that our in-execution malware detector with hyper- gram representation achieves low processing overheads and improved detection accuracies as compared to conventional n-grams.
Combination treatment with arsenic trioxide and irradiation enhances cell-killing effects in human fibrosarcoma cells in vitro and in vivo through induction of both autophagy and apoptosis (2010)

The traditional treatments for fibrosarcoma have limited efficacy. Therefore, new therapeutic strategies and/or new adjuvant drugs still need to be explored. Accumulating evidence indicates that programmed cell death (PCD) is closely related to anticancer therapy. Many studies have shown that tumor cells treated with anticancer drugs experience the induction of type I PCD, apoptosis, and type II PCD, autophagy. In the present study, we investigated the anticancer effects of ionizing radiation (IR) combined with arsenic trioxide (ATO) in human fibrosarcoma cells in vitro and in xenograft tumors in SCID mice in vivo. We found that IR increased the population of HT1080 cells in the G2/M phase in a time-dependent manner within 9 h. IR treatment combined with ATO at this time point induced a significantly prolonged G2/M arrest and consequently enhanced cell death. Furthermore, damage of mitochondria membrane potential could be involved in the underlying mechanisms. The enhanced cytotoxic effect of combined treatment occurred due to the increased induction of more autophagy and apoptosis through the inhibition of Akt and the activation of ERK1/2 signaling pathways in HT1080 cells. The combined treatment of HT1080 cells pretreated with Z-VAD or 3-MA resulted in a significant reduction in AO-positive cells, apoptotic cells and cytotoxicity. In in vivo studies, the combination of IR and ATO significantly reduced the tumor volume in SCID mice that had received a subcutaneous injection of HT1080 cells. The data suggest that a combination of IR and ATO could be a new potential therapeutic strategy for the treatment of fibrosarcoma.
Do protein motifs read the histone code? (2005)

The existence of different patterns of chemical modifications (acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation) of the histone tails led, some years ago, to the histone code hypothesis. According to this hypothesis, these modifications would provide binding sites for proteins that can change the chromatin state to either active or repressed. Interestingly, some protein domains present in histone-modifying enzymes are known to interact with these covalent marks in the histone tails. This was first shown for the bromodomain, which was found to interact selectively with acetylated lysines at the histone tails. More recently, it has been described that the chromodomain can be targeted to methylation marks in histone N-terminal domains. Finally, the interaction between the SANT domain and histones is also well documented. Overall, experimental evidence suggests that these domains could be involved in the recruitment of histone-modifying enzymes to discrete chromosomal locations, and/or in the regulation their enzymatic activity. Within this context, we review the distribution of bromodomains, chromodomains and SANT domains among chromatin-modifying enzymes and discuss how they can contribute to the translation of the histone code.
Stress-related diseases -- a potential role for nitric oxide. (2002)

Profound connections between stress and various disease processes exist. Thereby, common pathophysiological pathways in stress-related diseases have been described, and they involve stress hormone (cortisol, NE) and, in particular, NO activity. Thus, NO has detrimental capacities. However, NO not only exerts deleterious but also strongly ameliorating effects. The balance between both properties is crucial. Yet, nitric oxide involvement in stress-related diseases represents a common pathway, with various pathophysiological analogies, that may be accessible for strategies using stress management and relaxation response techniques.
DNA base-pair substitutions detected in double-stranded DNA with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (1995)

We demonstrate the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for identifying the presence or absence of single base-pair substitutions in a short section of the cystic fibrosis gene. The analysis was performed in two ways: (i) the molecular weight of known lengths of single-stranded DNA from a section of this gene was determined by mass spectrometry, and (ii) short complementary strands from the identical section of the gene were denatured and the difference in molecular weight of the strands was determined. Oligonucleotides corresponding to the wild type sequence were synthesized. The G551D or the R553X mutations were created by introducing single-base substitutions in this oligonucleotide. We recreated double-stranded DNA by annealing each of these three oligonucleotides to complementary oligonucleotides. The MALDI mass spectrometric technique, operating at a mass resolution approaching 1000, correctly identified five of these six oligonucleotides. The most reliable identification was obtained by measuring the difference in molecular weight of the denatured strands. The difference in molecular weight of the complementary strands comprising the wild type, the G551D and the R553X is 52.2 Da, 83.2 Da and 21.2 Da, respectively. The MALDI analysis shows promise as a rapid way to detect the presence of base-pair substitutions without the need for sequencing.
The impact of mitral regurgitation on patients undergoing catheter ablation of atrial fibrillation (2011)

Mitral regurgitation was associated with increased AF recurrence after AF ablation, but its impact was mediated by LA size. Left atrium size was the only independent predictor of AF recurrence. The high percentage of MR that was likely secondary to AF may have impacted our findings and deserves further study.
A Hot Spot of Binding Energy in a Hormone-Receptor Interface (1995)

The x-ray crystal structure of the complex between human growth hormone (hGH) and the extracellular domian of its first bound receptor (hGHbp) shows that about 30 side chains from each protein make contact. Individual replacement of contact residues in the hGHbp with alanine showed that a central hydrophobic region, dominated by two tryptophan residues, accounts for more than three-quarters of the binding free energy. This "functional epitope" is surrounded by less important contact residues that are generally hydrophilic and partially hydrated, so that the interface resembles a cross section through a globular protein. The functionally important residues on the hGHbp directly contact those on hGH. Thus, only a small and complementary set of contact residues maintains binding affinity, a property that may be general to protein-protein interfaces.
Growth Hormone Preferentially Induces the Rapid, Transient Expression of SOCS-3, a Novel Inhibitor of Cytokine Receptor Signaling (1998)

Four members (SOCS-1, SOCS-2, SOCS-3, and CIS) of a family of cytokine-inducible, negative regulators of cytokine receptor signaling have recently been identified. To address whether any of these genes are induced in response to growth hormone (GH), serum-starved 3T3-F442A fibroblasts were incubated with GH for various time points, and the expression of the SOCS gene family was analyzed by Northern blotting. GH stimulated the rapid, transient induction of SOCS-3 mRNA, peaking 30 min after the initiation of GH exposure and declining to basal levels by 2 h. Expression of the other SOCS genes (SOCS-1, SOCS-2, CIS) was also up-regulated by GH, although to a lesser extent than SOCS-3 and with differing kinetics. SOCS-3 expression was also strongly induced in 3T3-F442A cells treated with leukemia-inhibitory factor (LIF), with weaker induction of SOCS-1 and CIS being observed. The preferential induction of SOCS-3 mRNA was also observed in hepatic RNA isolated from the livers of mice that had received a single supraphysiological dose of GH intraperitoneally. Co-transfection studies revealed that constitutive expression of SOCS-1 and SOCS-3, but not SOCS-2 or CIS, blocked GH-induced transactivation of the GH-responsive serine protease inhibitor 2.1 gene promoter.
Role of macrophages and colony-stimulating factor-1 in murine antiglomerular basement membrane glomerulonephritis. (1995)

Macrophages have been shown to mediate glomerular injury in antiglomerular basement membrane (anti-GBM) glomerulonephritis in rats and rabbits. To evaluate the role of macrophages and the macrophage-related cytokines, colony stimulating factor-1 (CSF-1), monocyte chemoattractant protein-1 (MCP-1) and RANTES, accelerated anti-GBM nephritis was studied in op/op mutant mice, which lack CSF-1 and are severely macrophage deficient, and in heterozygous op/+ control mice. Observations were made 24 h and 3 days after the injection of rabbit anti-mouse GBM antibody in mice preimmunized with rabbit immunoglobulin G. Proteinuria rose progressively in both groups but did not differ between them (urine protein/creatinine ratio at 3 days: 1.01 +/- 0.38 in op/op versus 1.45 +/- 0.43 in op/+; P, not significant). In both op/op and op/+ mice, anti-GBM nephritis was associated with renal expression of mRNA for RANTES and MCP-1 and barely detectable levels of mRNA for CSF-1. In contrast, these cytokines were not expressed in sham-injected mice. Morphologic lesions appeared earlier in op/op mice but were comparable by Day 3. Glomerular injury consisted of capillary thrombosis and endothelial cell damage associated with mild to moderate leukocyte infiltration. Despite enhanced expression of mRNA for RANTES and MCP-1, glomerular macrophage infiltration was not increased in op/+ mice. It was concluded that, in mice, in contrast to rats and rabbits, accelerated anti-GBM nephritis may develop in the absence of both CSF-1 and macrophage infiltration.
Phytotherapy Research, Vol. 11 (6), pp. 454-456 (1997). Diuretic and antidiuretic activity of the leaf extracts ofVernonia cinerea. (Less) (Fam. Compositae) (1998)

A typesetting error occurred in the caption to Table 2 on page 455. The caption to Table 2 should read: ‘Table 2. Dose response study of antidiuretic effects of Vernonia cinerea methanol leaf extract (VCMLE) in rats’ rather than: ‘Table 2. Dose response study of diuretic effects of Vernonia cinerea chloroform leaf extract (VCMLE) in rats’ Also, in Tables 2 and 3, the heading in column 6 should read: ‘Antidiuretic activity of extract (F/N)’ rather than: ‘Antidiuretic activity of extract (N/F)’.
In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. (1985)

DNA topoisomerase II has been immunochemically identified on protein blots as a major polypeptide component of the Drosophila nuclear matrix-pore complex-lamina fraction. Indirect immunofluorescence analyses of larval cryosections have confirmed the nuclear localization of topoisomerase II in situ. Although apparently excluded from the nucleolus, the topoisomerase protein is otherwise distributed throughout the interior of interphase nuclei. Similar immunocytochemical studies performed with permeabilized whole giant cells from third-instar larval salivary glands have shown topoisomerase II to be largely restricted to the polytene chromosomes. Upon nuclear disassembly during mitosis, the topoisomerase polypeptide appears to redistribute diffusely throughout the cell. Faint immunofluorescent staining of mitotic chromosomes is also observed.
Neuropathic Pain in Rats with a Partial Sciatic Nerve Ligation Is Alleviated by Intravenous Injection of Monoclonal Antibody to High Mobility Group Box-1 (2013)

High mobility group box-1 (HMGB1) is associated with the pathogenesis of inflammatory diseases. A previous study reported that intravenous injection of anti-HMGB1 monoclonal antibody significantly attenuated brain edema in a rat model of stroke, possibly by attenuating glial activation. Peripheral nerve injury leads to increased activity of glia in the spinal cord dorsal horn. Thus, it is possible that the anti-HMGB1 antibody could also be efficacious in attenuating peripheral nerve injury-induced pain. Following partial sciatic nerve ligation (PSNL), rats were treated with either anti-HMGB1 or control IgG. Intravenous treatment with anti-HMGB1 monoclonal antibody (2 mg/kg) significantly ameliorated PSNL-induced hind paw tactile hypersensitivity at 7, 14 and 21 days, but not 3 days, after ligation, whereas control IgG had no effect on tactile hypersensitivity. The expression of HMGB1 protein in the spinal dorsal horn was significantly increased 7, 14 and 21 days after PSNL; the efficacy of the anti-HMGB1 antibody is likely related to the presence of HMGB1 protein. Also, the injury-induced translocation of HMGB1 from the nucleus to the cytosol occurred mainly in dorsal horn neurons and not in astrocytes and microglia, indicating a neuronal source of HMGB1. Markers of astrocyte (glial fibrillary acidic protein (GFAP)), microglia (ionized calcium binding adaptor molecule 1 (Iba1)) and spinal neuron (cFos) activity were greatly increased in the ipsilateral dorsal horn side compared to the sham-operated side 21 days after PSNL. Anti-HMGB1 monoclonal antibody treatment significantly decreased the injury-induced expression of cFos and Iba1, but not GFAP. The results demonstrate that nerve injury evokes the synthesis and release of HMGB1 from spinal neurons, facilitating the activity of both microglia and neurons, which in turn leads to symptoms of neuropathic pain. Thus, the targeting of HMGB1 could be a useful therapeutic strategy in the treatment of chronic pain.
Cauliflower Mosaic Virus 35S Promoter-Controlled DNA Copies of Cowpea Mosaic Virus RNAs are Infectious on Plants (1993)

Clones have been constructed that contain full-length cDNA copies of cowpea mosaic virus RNA1 and RNA2, downstream of the cauliflower mosaic virus 35S promoter. The clones, when linearized downstream of the viral sequences, give rise to cowpea mosaic virus-like symptoms when inoculated onto cowpea plants. Viral RNA and virions can be detected in the inoculated plants, demonstrating that the clones are directly infectious.