gebhart/patrepeval huggingface dataset:
Inhibition of Cardiotoxic, Nephrotoxic and Neurotoxic Effects of Doxorubicin by ICRF-159 (1983)

Cardiotoxicity of doxorubicin, 2 mg/kg i.p. twice weekly in rats, was assessed by serial electrocardiography and electron microscopy. The toxic effects were markedly inhibited by ICRF-159, 50 mg/kg p.o. given 1 h before doxorubicin. The development of nephropathy characterized by proteinuria, hyperlipidemia and glomerular and tubular changes was significantly retarded, and the degenerative changes of peripheral nerves were markedly reduced. On the other hand, ICRF-159 enhanced the depressant effects of doxorubicin on bone marrow function. Doxorubicin reduced body weight gain, caused ascites, decrease in heart and thymus weight, and increase in liver and kidney weight. These changes were also inhibited or attenuated by ICRF-159 pretreatment.
Intensified antitumor immunity by a cancer vaccine that produces granulocyte-macrophage colony-stimulating factor plus interleukin 4. (1996)

Vaccination with irradiated tumor cells genetically modified to secrete granulocyte-macrophage colony-stimulating factor (GM-CSF tumor vaccine) induces a potent systemic antitumor immunity. To develop a protocol for cancer therapy to further augment the host immune response, we examined the effects of the GM-CSF tumor vaccines simultaneously producing additional cytokines. We prepared cancer vaccines expressing double cytokines by sequential recombinant retrovirus-mediated genetic transductions. We then used a murine intracerebral tumor model in which the GM-CSF tumor vaccine was less effective in immunopotentiation and evaluated tumor vaccines producing various cytokines in conjunction with GM-CSF. The cytokine combination of GM-CSF and interleukin 4 induced more potent antitumor immunity than GM-CSF alone. An in vivo depletion test showed that CD4+, CD8+, and asialoGM1+ cells were required for the optimum function of the GM-CSF plus interleukin 4 tumor vaccine. Histological examinations revealed infiltration of inflammatory cells at the site of tumor cell challenge as well as at the site of vaccination, indicating the induction of a systemic antitumor immune response which reached the central nervous system. Our findings suggest the feasibility of applying the intensified vaccination strategy to treat human cancers including malignant brain tumors.
New insights into extracellular matrix assembly and reorganization from dynamic imaging of extracellular matrix proteins in living osteoblasts (2006)

The extracellular matrix (ECM) has been traditionally viewed as a static scaffold that supports cells and tissues. However, recent dynamic imaging studies suggest that ECM components are highly elastic and undergo continual movement and deformation. Latent transforming growth factor beta (TGFbeta) binding protein-1 (LTBP1) is an ECM glycoprotein that binds latent TGFbeta and regulates its availability and activity. LTBP1 initially co-distributes with fibronectin in the extracellular matrix of osteoblasts, and depends on fibronectin for its assembly. To gain further insights into the mechanisms of assembly of LTBP1 and its spatial and temporal interactions with fibronectin, we have performed dual fluorescence time-lapse imaging of these two proteins in living osteoblasts using fluorescent probes. Time-lapse movies showed surprisingly large fibril displacements associated with cellular movement as well as occasional breaking of LTBP1 or fibronectin-containing fibrils. Individual fibrils stretched to as much as 3.5 times or contracted to as much as one fourth of their original length. Motile cells appeared to actively mediate extracellular matrix assembly by adding 'globules' or 'packets' of matrix material onto existing fibrils. They also actively reorganized the extracellular matrix by shunting matrix material from one location to another and exchanging fibrillar material between fibrils. This cell-mediated matrix reorganization was primarily associated with the assembly and remodeling of the initial (early) matrix, whereas mature, established ECM was more stable. Displacement vector mapping showed that different matrix fibrillar networks within the same cultures can show different dynamic motion in response to cell movement and showed that the motion of fibrils was correlated with cell motion. These data suggest novel cell-mediated mechanisms for assembly and reorganization of the extracellular matrix and highlight a role for cell motility in the assembly process.
Automatable lipid bilayer formation and ion channel measurement using sessile droplets (2010)

Artificial lipid bilayer membranes have been used to reconstitute ion channels for scientific and technological applications. Membrane formation has traditionally involved slow, labor intensive processes best suited to small scale laboratory experimentation. We have recently demonstrated a high throughput method of membrane formation using automated liquid-handling robotics. We describe here the integration of membrane formation and measurement with two methods compatible with automation and high throughput liquid-handling robotics. Both of these methods create artificial lipid bilayers by joining lipid monolayers self-assembled at the interface of aqueous and organic phases using sessile aqueous droplets in contact with a measurement electrode; one using a pin tool, commonly employed in high throughput fluid handling assays, and the other using a positive displacement pipette. Membranes formed with both methods were high quality and supported measurement of ion channels at the single molecule level. Full automation of bilayer production and measurement with the positive displacement pipette was demonstrated by integrating it with a motion control platform.
Preventing Page Faults from Telling Your Secrets (2016)

New hardware primitives such as Intel SGX secure a user-level process in presence of an untrusted or compromised OS. Such "enclaved execution" systems are vulnerable to several side-channels, one of which is the page fault channel. In this paper, we show that the page fault side-channel has sufficient channel capacity to extract bits of encryption keys from commodity implementations of cryptographic routines in OpenSSL and Libgcrypt -- leaking 27% on average and up to 100% of the secret bits in many case-studies. To mitigate this, we propose a software-only defense that masks page fault patterns by determinising the program's memory access behavior. We show that such a technique can be built into a compiler, and implement it for a subset of C which is sufficient to handle the cryptographic routines we study. This defense when implemented generically can have significant overhead of up to 4000X, but with help of developer-assisted compiler optimizations, the overhead reduces to at most 29.22% in our case studies. Finally, we discuss scope for hardware-assisted defenses, and show one solution that can reduce overheads to 6.77% with support from hardware changes.
Pathways of Mucin O-Glycosylation in Normal and Malignant Rat Colonic Epithelial Cells Reveal a Mechanism for Cancer-Associated Sialyl-Tn Antigen Expression (2001)

The Sialyl-Tn antigen (Sialyl alpha-Ser/Thr) is expressed as a cancer-associated antigen on the surface of cancer cells. Its presence is associated with a poor prognosis in patients with colorectal and other cancers. We previously reported that Sialyl-Tn expression in LSC human colon cancer cells could be explained by a specific lack of the activity of core 1 beta3-Gal-transferase (Brockhausen et al., Glycoconjugate J. 15, 595-603, 1998) and an inability to synthesize the common O-glycan core structures. To support this mechanism, or find other mechanisms to explain Sialyl-Tn antigen expression, we investigated the O-glycosylation pathways in clonal rat colon cancer cell lines that were selected for positive or negative expression of Sialyl-Tn antigen, and compared these pathways to those in normal rat colonic mucosa. Normal rat colonic mucosa had very active glycosyltransferases synthesizing O-glycan core structures 1 to 4. Several sialyl-, sulfo- and fucosyltransferases were also active. An M type core 2 beta6-GlcNAc-transferase was found to be present in rat colon mucosa and all of the rat colon cancer cells. O-glycosylation pathways in rat colon cancer cells were significantly different from normal rat colonic mucosa; for example, rat colon cancer cells lost the ability to synthesize O-glycan core 3. All rat colon cancer cell lines, regardless of the Sialyl-Tn phenotype, expressed glycosyltransferases assembling complex O-glycans of core 1 and core 2 structures (unlike human LSC colon cancer cells which lack core 1 beta3-Gal-transferase activity). It was the activity of CMP-sialic acid:GalNAc-mucin alpha6-sialyltransferase that coincided with Sialyl-Tn expression. Sialyl-Tn negative cells had a several fold higher activity of core 2 beta6-GlcNAc-transferase which synthesizes complex O-glycans that may mask adjacent Sialyl-Tn epitopes. The results suggest a new mechanism controlling Sialyl-Tn expression in cancer cells.
High cell density cultivation of Bifidobacterium longum using a calcium carbonate-alginate beads system (2002)

A CaCO 3 -alginate beads system was developed for high cell density cultivation of Bifidobacterium longum and the cost-effective media were also screened. In batch process with CaCO 3 beads, two strains of B. longum showed both the highest viable cells and optical density in TPY medium, resulting in maximum optical density and viable cell counts of 12.40, 2.22×10 10 cfu/ml for B. longum ATCC 15707 and 13.71, 3.93×10 10 cfu/ml for B. longum HLC 3742. Released size distribution, according to CaCO 3 -alginate bead size preparation, was smaller than others. These results were also examined by observing their morphology. The skim milk-based medium was most adequate to cultivate B. longum as the cheapest medium, and 10% skim milk supplemented with 2% glucose and 1% yeast extract was a suitable medium, supporting the growth to 5.57×10 10 cfu/ ml for ATCC 15707 and 6.82×10 9 cfu/ml for HLC 3742. During the long-term storage at 4°C and -20°C, B. longum cultivated with CaCO 3 beads had the highest stability. Consequently, CaCO 3 -alginate beads buffer was found to be useful not only to cultivate B. longum but also to preserve cultures.
The role of dietary phytosterols in colon carcinogenesis (1992)

Epidemiological and experimental studies have shown that increased intake of plant foods and decreased meat consumption are correlated with a decreased risk for colon cancer. Many components of plant foods are suggested to mitigate colon carcinogenesis, including vitamins, minerals, and dietary fiber. Phytosterols are a common component of plant foods consumed in relatively large quantities by vegetarians, who are at lower risk for colon cancer development than individuals on a Western diet low in phytosterols. In addition, phytosterols have been shown experimentally to inhibit colon cancer development. Dietary cholesterol, although structurally similar to the phytosterols, is correlated etiologically to the incidence of colon cancer, with changes in serum cholesterol levels and fecal bile acid profiles suggested to increase susceptibility to colon tumorigenesis. The objective of this paper is to discuss the effect of dietary phytosterols on cholesterol and bile acid metabolism and how these effects may lead to a decreased risk for colon cancer development.
Identification of a Factor Xa-interactive Site within Residues 337–372 of the Factor VIII Heavy Chain (2004)

We recently demonstrated that the residues 337-372, comprising the acidic C-terminal region in A1 subunit, interact with factor Xa during the proteolytic inactivation of factor VIIIa (Nogami, K., Wakabayashi, H., and Fay, P. J. (2003) J. Biol. Chem. 278, 16502-16509). We now show this sequence is important for factor Xa-catalyzed activation of factor VIII. Peptide 337-372 markedly inhibited cofactor activation, consistent with a delay in the rate of cleavage at the A1-A2 junction. Studies using the isolated factor VIII heavy chain indicated that the peptide completely blocked cleavage at the A1-A2 junction (IC50 = 11 microm) and partially blocked cleavage at the A2-B junction (IC50 = 100 microm). Covalent cross-linking was observed between the 337-372 peptide and factor Xa following reaction with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide, and the peptide quenched the fluorescence of dansyl-Glu-Gly-Arg active site-modified factor Xa, suggesting that residues 337-372 directly interact with factor Xa. Studies using a monoclonal antibody recognizing residues 351-365 as well as the peptide to this sequence further restricted the interactive region. Mutant factor VIII molecules in which clustered acidic residues in the 337-372 segment were converted to alanine were evaluated for activation by factor Xa. Of the mutants tested, only factor Xa-catalyzed activation of the D361A/D362A/D363A mutant was inhibited with peak activity of approximately 50% and an activation rate constant of approximately 30% of the wild type values. These results indicate that the 337-372 acidic region separating A1 and A2 domains and, in particular, a cluster of acidic residues at position 361-363 contribute to a unique factor Xa-interactive site within the factor VIII heavy chain that promotes factor Xa docking during cofactor activation.
Toll‐like receptor 4 agonists adsorbed to aluminium hydroxide adjuvant attenuate ovalbumin‐specific allergic airway disease: role of MyD88 adaptor molecule and interleukin‐12/interferon‐γ axis (2008)

Toll-like receptor 4 agonists co-adsorbed with allergen onto alum down-modulate allergic lung disease and prevent the development of polarized T cell-mediated airway inflammation.
A Simple Process for Lateral Single Crystal Silicon Nanowires (2002)

In a single-mask standard photolithography based process and a single etch step, lateral silicon nanowires are fabricated according to arbitrary layout and over a range of diameters and lengths. Nanowires with diameters from ∼20 nm and with lengths ranging from 2 μm to 100 μm were fabricated in direct contact with two silicon probing pads for measurement. These nanowires are electrically isolated in the silicon-on-insulator wafer device layer, and suspended over the substrate, thereby increasing thermal and electrical isolation. Because they are formed from single crystal silicon, minimal defects are expected. The addition of a polysilicon deposition and patterning further enhances the process by allowing coaxial silicon nanostructures.
Preparation of 5‐substituted benzylbarburituric acids and investigation of the effect of the benzyl and substituted benzyl groups on the acidity of barbituric acid (1986)

Abstract The acidity of 5‐benzylbarbituric acid and a series of 5‐substituted benzylbarbituric acids has been determined in 50% ethanol/water and they were found to be more acidic than barbituric acid. The p K a s of these derivatives obey Hammett's equation indicating that their acidity is affected by substituents in the same manner as the benzoic acid ionization constants. A synthesis of these acids is described.
Compression‐induced nonplanar crack extension with application to splitting, exfoliation, and rockburst (1982)

Uniaxial compression of plates of brittle materials containing pre‐existing planar cracks oriented at certain angles with respect to the direction of overall compression has revealed that the relative frictional sliding of the faces of the pre‐existing cracks may produce, at their tips, tension cracks which deviate at sharp angles from the sliding plane. These tension cracks then continue to grow in a stable manner with increasing axial compression, curving toward an orientation parallel to the direction of axial compression. Within the framework of linear fracture mechanics, the out‐of‐plane extension of a pre‐existing straight crack, induced by overall far‐field compression, is analyzed, and various parameters which characterize the growth process are quantified. It is shown analytically that, for a wide range of pre‐existing crack orientations, the out‐of‐plane crack extension initiates at an angle close to 70° from the direction of the pre‐existing crack; the exact value of this angle, of course, depends on the friction factor and the orientation of the pre‐existing crack. It is found that the growth process is stable initially, but the rate of increase of the length of the extended portion with respect to the increasing axial compression dramatically increases after a certain extension length is attained, and in fact, this length becomes unbounded if a small lateral tension also exists. Various limiting cases are examined and the corresponding analytical estimates are compared with the numerical results, arriving at good correlations. A series of qualitative experiments is performed on thin plates of Columbia Resin CR 39, arriving at excellent agreement with the analytical results. In light of the analysis, the phenomena of axial splitting, exfoliation (or sheet fracture), and rockburst are examined, and it is suggested that they may all be the results of the out‐of‐plane (tensile) extension of pre‐existing cracks, induced by large overall far‐field compressions. This assertion is then supported by a series of experiments which show that the relative frictional sliding of the faces of one or even an array of pre‐existing cracks does not result in coplanar (sliding mode) crack growth, but rather leads to the formation of tension cracks which grow in the direction of maximum compression. Moreover, a pre‐existing crack close to a free boundary grows in a similar manner under compression parallel to the boundary, and shows no tendency to move toward the free surface. Possible lateral buckling which may result, and which may cause further unstable crack extension, is illustrated experimentally, and discussed in an effort to shed light on the phenomena of rockburst and surface spalling.
Herpes simplex virus type 2 glycoprotein gF and type 1 glycoprotein gC have related antigenic determinants (1983)

The 104-S monoclonal antibody immunoprecipitated from herpes simplex virus type 2 (HSV-2)-infected cell extracts the 75,000-molecular-weight glycoprotein gF and its 65,000-molecular-weight precursor (pgF). The precursor pgF was sensitive to endoglycosidase H digestion, indicating the presence of high mannose-type oligosaccharides, whereas the stable gF product was sensitive to neuraminidase digestion, indicating the presence of sialic acid residues. The 104-S antibody also weakly precipitated the 130,000-molecular-weight herpes simplex virus type 1 (HSV-1) glycoprotein gC from both infected cell extracts and purified preparations obtained through the use of monoclonal antibody-containing immunoadsorbent columns. Immunofluorescence tests demonstrated that the 104-S antibody reacted with antigen present in cells infected with HSV-2 strain 333 and HSV-1 strain 14012 but not with antigen present in cells infected with HSV-1 strain MP, a strain deficient in HSV-1 gC production. These findings indicate that HSV-1 gC and HSV-2 gF have antigenic determinants that are related.
Structural Safety Analysis According to the Shape of Door Impact Bar (2012)

In this study, the safest model can be selected by the simulation result of structural safety analysis according to the shape of impact bar affected at side door of automobile. The open sectional model of semicircle type has the lowest deformation and stress among 4 kinds of models. As the weight of this model has 30% in comparison with other models, it becomes most economical and stable. As the open sectional model of cap type the highest deformation and stress among 4 kinds of models, it becomes weakest. The closed models with circular and rectangular types has the stress far lower than cap type. The maximum deformation is shown at the center part of impact bar but the maximum stress occurs at the joint part between impact bar and frame.
Automatic array alignment as a step in hierarchical program transformation (2002)

Presents an original approach to automatic array alignment, the step in the hierarchical transformation system aimed at the efficient execution of shared memory programs on distributed memory machines. The array alignment algorithm deals with a broad set of intra-dimension and inter-dimension alignment preferences, including offsets, strides, permutations, embeddings, and their combinations. The authors discuss the algorithm and the tests performed on the Connection Machine CM-2.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of strigolactones exuded by Asteraceae plants (2011)

Strigolactones (SLs), originally characterized as germination stimulants for root parasitic weeds, are now recognized as hyphal branching factors for symbiotic arbuscular mycorrhizal fungi and as a novel class of plant hormones inhibiting shoot branching. In the present study, SLs in root exudates of 13 Asteraceae plants including crops, a weed, and ornamental plants were characterized. High performance liquid chromatography/tandem mass spectrometry (LC–MS/MS) analyses revealed that all the Asteraceae plants examined exuded known SLs and, except for sunflower (Helianthus annuus), high germination stimulant activities at retention times corresponding to these SLs were confirmed. The two major SLs exuded by these Asteraceae plants were orobanchyl acetate and orobanchol. 5-Deoxystrigol and 7-hydroxyorobanchyl acetate were detected in root exudates from several Asteraceae species examined in this study.
Ovulation suppression of premenstrual symptoms using oral contraceptives. (2005)

Managing premenstrual symptoms at the most fundamental level necessitates careful consideration of female reproductive biology. Inhibiting ovulation using hormonal agents is a reasonable approach for reducing premenstrual symptoms, but the benefits of agents such as gonadotropin-releasing hormone agonists and the synthetic androgen danazol are largely offset by their adverse effects and costs. Combination oral contraceptives provide an alternative that is widely accepted by women experiencing premenstrual symptoms and by their physicians; and newer formulations with lower levels of estrogen and progestin, administered using a monthly regimen with a shortened pill-free interval, appear promising for alleviating patient distress from severe premenstrual symptoms.
Phase Change Electrodes for Reducing Joule Heating During Irreversible Electroporation (2012)

Irreversible electroporation (IRE) is a non-thermal tissue ablation modality that is gaining momentum as a viable treatment option for tumors and other non-cancerous pathologies [1]. The protocol consists of delivering a series of short (∼ 100 μs) and intense (∼ 1000 V/cm) pulsed electric fields through electrodes inserted directly into or around a targeted tissue. The pulses induce a rapid buildup of charge across the plasma membrane of cells comprising the tissue that results in the creation of permanent membrane defects, ultimately leading to cell death. Because the extent of cell death relies predominately on the extent of charge buildup and not thermal processes, extracellular matrix components are spared, including major nerve and blood vessel architecture. Additionally, the ablation volume is predictable based on the electric field distribution and visible in real-time via MRI, CT, and ultrasound.