gebhart/patrepeval huggingface dataset:
HIV-1 Tat promotes monocyte chemoattractant protein-1 secretion followed by transmigration of monocytes (2001)

The mechanism whereby HIV-infected cells transit from the bloodstream into tissues is not well defined. This phenomenon was addressed by studying the effects of HIV-1 Tat, a protein secreted by infected cells, on human lung microvascular endothelial cells (HMVEC-Ls). It was found that monocyte chemoattractant protein-1 (MCP-1) was released from HMVEC-Ls in a dose- and time-dependent manner after Tat treatment. MCP-1 is a potent beta-chemokine that recruits monocytes and T cells and promotes cell adhesion and transmigration across an endothelial monolayer. It was also observed that MCP-1 and the culture medium from Tat-treated HMVEC-Ls were chemotactic for CD14(+) monocytes from human peripheral blood and for THP-1, a promonocytic cell line used as a model system. To characterize the signaling pathways underlying the observed induction of MCP-1, HMVEC-Ls were treated with 2 different protein kinase inhibitors: PD98059, a MAP kinase inhibitor, and GF109203X, a protein kinase C (PKC) inhibitor. MCP-1 release was significantly reduced when PKC was inhibited, and slightly decreased when PI3 kinase was blocked; no effect on MCP-1 release was observed on MAP kinase inhibition. Similarly, transmigration of THP-1 cells was significantly impaired by the PKC inhibitor, but not by the other tested inhibitors. These data indicate that the HIV-1 Tat protein may act as a protocytokine by causing the release of MCP-1 from the endothelial monolayer, and thereby facilitating monocyte transmigration into tissues via a PKC signaling pathway.
Magnetoresistance of semiconductor-metal hybrid structures: The effects of material parameters and contact resistance (2003)

We have used the finite element method to study the extraordinary magnetoresistance (EMR) effect of semiconductor-metal hybrid structures in rectangular device geometries. These have recently been found to exhibit intriguing properties interesting for magnetic-field sensors. Current and potential distributions in the devices are calculated in an applied magnetic field. By these means, we investigate the EMR effect, in particular, as a function of material parameters and of the contact resistance ${\ensuremath{\rho}}_{c}$ between the semiconductor and the metal. In our calculations we find that ${\ensuremath{\rho}}_{c}$ should be within a specific operation regime in order to obtain a pronounced magnetoresistance effect. We show that by means of the electron mobility in the semiconductor the voltage and the current sensitivity of a hybrid device can be optimized with respect to an operation field in the 10-mT range.
Nijmegen Breakage Syndrome Cells Fail To Induce the p53-Mediated DNA Damage Response following Exposure to Ionizing Radiation (1997)

The functionality of the p53-mediated pathway, activated in response to DNA damage, has been assessed in primary fibroblast cell cultures and Epstein-Barr virus-transformed lymphoblastoid cell lines derived from Nijmegen breakage syndrome (NBS) patients. This autosomal recessive disease is characterized by microcephaly, growth and mental retardation, chromosomal instability, radiosensitivity, and high cancer incidence. The recent mapping of the NBS gene to chromosome 8q21 demonstrates that NBS is genetically distinct from ataxia telangiectasia (AT). Changes in p53 protein levels were significantly reduced and delayed in all the NBS fibroblast cell cultures and lymphoblastoid cell lines examined compared to normal cultures over a 4-h period postirradiation (5 Gy). The transcriptional activation of p21(WAF1/CIP1) mRNA was also lower in 12 NBS fibroblast cultures examined. In agreement with an abrogated p53 function, NBS cells exposed to ionizing radiation show an abnormal cell cycle arrest at G1-S and a prolonged accumulation of cells in the G2 phase. In contrast, exposure to the alkylating agent methyl methanesulfonate results in similar increases of p53 and p21(WAF1/CIP1) mRNA in both cell types. The ATM gene transcript was found to be expressed at similar levels in NBS and normal cells, whereas it was strongly reduced in the AT homozygote cells examined. These results suggest that the ATM gene product cannot substitute for that of the NBS gene in the signaling of cellular damage produced by ionizing radiation and that both are involved in the activation of p53. The suboptimal p53-mediated response could contribute to the high cancer risk and radiosensitivity seen in NBS patients.
Oxadiazoles as Ester Bioisosteric Replacements in Compounds Related to Disoxaril. Antirhinovirus Activity (1994)

A series of 1,2,4-oxadiazoles has been prepared as ester bioisosteres and tested against 15 human rhinovirus serotypes, and the MIC80, the concentration which inhibits 80% or 12 of the serotypes tested, was determined. Homologation of the alkyl group attached to the oxadiazole ring resulted in a reduction in activity with increased chain length. Introduction of hydrophilic groups in this position rendered the compounds inactive. Increasing the length of the side chain attached to the isoxazole ring resulted in an increase in activity. Replacement of the methyl with alkoxyalkyl substituents retained activity; however, introduction of a hydroxyl group on to the side chain reduced activity. Compound 8a, where both the isoxazole and oxadiazole rings were substituted with methyl groups, was one of the most active compounds in the series. A comparison was made between 8a and the two isomeric oxadiazoles 41 and 46, and an attempt was made to explain the difference in activity by examining electrostatic potential maps and by an energy profiling study. No conclusive results were obtained from these studies.
Synergistic Anti-Tumor Responses After Administration of Agonistic Antibodies to CD40 and IL-2: Coordination of Dendritic and CD8+ Cell Responses (2003)

In cancer, the coordinate engagement of professional APC and Ag-specific cell-mediated effector cells may be vital for the induction of effective antitumor responses. We speculated that the enhanced differentiation and function of dendritic cells through CD40 engagement combined with IL-2 administration to stimulate T cell expansion would act coordinately to enhance the adaptive immune response against cancer. In mice bearing orthotopic metastatic renal cell carcinoma, only the combination of an agonist Ab to CD40 and IL-2, but neither agent administered alone, induced complete regression of metastatic tumor and specific immunity to subsequent rechallenge in the majority of treated mice. The combination of anti-CD40 and IL-2 resulted in significant increases in dendritic cell and CD8(+) T cell number in advanced tumor-bearing mice compared with either agent administered singly. The antitumor effects of anti-CD40 and IL-2 were found to be dependent on CD8(+) T cells, IFN-gamma, IL-12 p40, and Fas ligand. CD40 stimulation and IL-2 may therefore be of use to promote antitumor responses in advanced metastatic cancer.
Targeted gold nanorod contrast agent for prostate cancer detection by photoacoustic imaging (2007)

A targeted gold nanoparticle has been developed as a contrast agent for photoacoustic medical imaging. We have studied cancer cell targeting by antibody conjugated gold nanorods for high contrast photoacoustic imaging. By changing the aspect ratio of the elongated “rod” shape of the gold nanoparticle, its plasmon peak absorption wavelength can be tuned to the near IR (700–900nm) for an increased penetration depth into biological tissue. Effective cell targeting and sensitive photoacoustic detection of a single layer of cells are demonstrated. Combining ultrasound with contrast agent based photoacoustic imaging is proposed as a visual tool to compound molecular and structural information for early stage prostate cancer detection.
Allergy: Immunological and Clinical Aspects. (1985)

best, appears as single paragraphs or footnotes in most ENT or neurology textbooks.Vertigo in children, acrophobia (vertigo as understood by Hitchcock's film), migrainous vertigo, motion sickness, barotrauma and vertigo in neck disorders are all reviewed in depth with plenty of references.
Kinetic Characterization of Single Strand Break Ligation in Duplex DNA by T4 DNA Ligase (2011)

T4 DNA ligase catalyzes phosphodiester bond formation between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA in three steps: 1) enzyme-adenylylate formation by reaction with ATP; 2) adenylyl transfer to a 5'-phosphorylated polynucleotide to generate adenylylated DNA; and 3) phosphodiester bond formation with release of AMP. This investigation used synthetic, nicked DNA substrates possessing either a 5'-phosphate or a 5'-adenylyl phosphate. Steady state experiments with a nicked substrate containing juxtaposed dC and 5'-phosphorylated dT deoxynucleotides (substrate 1) yielded kcat and kcat/Km values of 0.4±0.1 s(-1) and 150±50 μm(-1) s(-1), respectively. Under identical reaction conditions, turnover of an adenylylated version of this substrate (substrate 1A) yielded kcat and kcat/Km values of 0.64±0.08 s(-1) and 240±40 μm(-1) s(-1). Single turnover experiments utilizing substrate 1 gave fits for the forward rates of Step 2 (k2) and Step 3 (k3) of 5.3 and 38 s(-1), respectively, with the slowest step ∼10-fold faster than the rate of turnover seen under steady state conditions. Single turnover experiments with substrate 1A produced a Step 3 forward rate constant of 4.3 s(-1), also faster than the turnover rate of 1A. Enzyme self-adenylylation was confirmed to also occur on a fast time scale (∼6 s(-1)), indicating that the rate-limiting step for T4 DNA ligase nick sealing is not a chemical step but rather is most likely product release. Pre-steady state reactions displayed a clear burst phase, consistent with this conclusion.
Biomonitoring of Aristolactam-DNA Adducts in Human Tissues Using Ultra-Performance Liquid Chromatography/Ion-Trap Mass Spectrometry (2012)

Aristolochic acids (AAs) are a structurally related family of nephrotoxic and carcinogenic nitrophenanthrene compounds found in Aristolochia herbaceous plants, many of which have been used worldwide for medicinal purposes. AAs have been implicated in the etiology of so-called Chinese herbs nephropathy and of Balkan endemic nephropathy. Both of these disease syndromes are associated with carcinomas of the upper urinary tract (UUC). 8-Methoxy-6-nitrophenanthro-[3,4-d]-1,3-dioxolo-5-carboxylic acid (AA-I) is a principal component of Aristolochia herbs. Following metabolic activation, AA-I reacts with DNA to form aristolactam (AL-I)-DNA adducts. We have developed a sensitive analytical method, using ultraperformance liquid chromatography-electrospray ionization/multistage mass spectrometry (UPLC-ESI/MS(n)) with a linear quadrupole ion-trap mass spectrometer, to measure 7-(deoxyadenosin-N(6)-yl) aristolactam I (dA-AL-I) and 7-(deoxyguanosin-N(2)-yl) aristolactam I (dG-AL-I) adducts. Using 10 μg of DNA for measurements, the lower limits of quantitation of dA-AL-I and dG-AL-I are, respectively, 0.3 and 1.0 adducts per 10(8) DNA bases. We have used UPLC-ESI/MS(n) to quantify AL-DNA adducts in tissues of rodents exposed to AA and in the renal cortex of patients with UUC who reside in Taiwan, where the incidence of this uncommon cancer is the highest reported for any country in the world. In human tissues, dA-AL-I was detected at levels ranging from 9 to 338 adducts per 10(8) DNA bases, whereas dG-AL-I was not found. We conclude that UPLC-ESI/MS(n) is a highly sensitive, specific and robust analytical method, positioned to supplant (32)P-postlabeling techniques currently used for biomonitoring of DNA adducts in human tissues. Importantly, UPLC-ESI/MS(n) could be used to document exposure to AA, the toxicant responsible for AA nephropathy and its associated UUC.
Using IDDs for Packet Filtering (2002)

Firewalls are one of the key technologies used to control the traffic going in and out of a network. A central feature of the firewall is the &lt;em&gt;packet filter&lt;/em&gt;. In this paper, we propose a complete framework for packet classification. Through two applications we demonstrate that both performance and security can be improved.&lt;br /&gt; &lt;br /&gt;We show that a traditional ordered rule set can always be expressed as a first-order logic formula on integer variables. Moreover, we emphasize that, with such specification, the packet filtering problem is known to be constant time. We propose to represent the first-order logic formula as &lt;em&gt; Interval Decision Diagrams&lt;/em&gt;. This structure has several advantages. First, the algorithm for removing redundancy and unnecessary tests is very simple. Secondly, it allows us to handle integer variables which makes it efficient on a generic CPUs. And, finally, we introduce an extension of IDDs called &lt;em&gt;Multi-Terminal Interval Decision Diagrams&lt;/em&gt; in order to deal with any number of policies.&lt;br /&gt; &lt;br /&gt;In matter of efficiency, we evaluate the performance our framework through a prototype toolkit composed by a &lt;em&gt; compiler&lt;/em&gt; and a &lt;em&gt;packet filter&lt;/em&gt;. The results of the experiments shows that this method is efficient in terms of CPU usage and has a low storage requirements.&lt;br /&gt; &lt;br /&gt;Finally, we outline a tool, called &lt;em&gt;Network Access Verifier&lt;/em&gt;. This tool demonstrates how the IDD representation can be used for verifying access properties of a network. In total, potentially improving the security of a network.
Half-life of porcine antibodies absorbed from a colostrum supplement containing porcine immunoglobulins (2012)

Absorption of immunoglobulins (Ig) at birth from colostrum is essential for piglet survival. The objective was to evaluate the half-life of antibodies absorbed in the bloodstream of newborn piglets orally fed a colostrum supplement (CS) containing energy (fat and carbohydrates) and IgG from porcine plasma. Viable piglets (n = 23; 900 to 1,800 g BW) from 6 sows were colostrum deprived and blood sampled and within the next 2 h of life randomly allocated to either control group (n = 9) providing 30 mL of Ig-free milk replacer or a group (n = 14) receiving 30 mL of CS by oral gavage. Piglets were transported to a Biosafety Level 3 facility (Centre de Recerca en Sanitat Animal, Spain) and fed Ig-free milk replacer every 3 to 4 h for 15 d. Survival, weight, plasma IgG content by radial immunodiffusion (RID), and antibodies against porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome (PRRS), Mycoplasma hyopneumoniae (Mhy), and swine influenza virus (SIV) were determined by specific ELISA before treatment administration, at 24 h, and weekly for 56 d. Clinical symptoms were not observed for either group. Mortality index was lower (17 vs. 38%; P < 0.02) and BW higher (17.7 vs. 15.3 kg; P = 0.035) for pigs supplemented with CS than piglets in the control group. At 24 h postadministration, the CS group had a plasma IgG mean of 7.6 ± 0.06 vs. 0.14 ± 0.03 mg/mL for the control group. The IgG levels in the CS group decayed until day 21 when de novo synthesis of IgG was detected in 25% of piglets. Half-life of antibody concentration (HLAC) by RID was 6.2 d. In the CS group, efficiency of PCV2 and PPV antibody transfer was high. For PCV2, all animals remained positive by day 56 and the calculated HLAC was 17.7 d. For PPV, 72.7% of piglets were ELISA positive by day 35 and HLAC was 12.0 d. For PRRS, all piglets remained positive by day 14 and the calculated HLAC was 11.9 d. For Mhy and SIV the calculated HLAC were 8.4 and 3.0 d. In summary, half-life of antibodies derived from blood plasma in the bloodstream of newborn piglets varied from 3.0 to 17.7 d. The study also confirm that antibodies derived from porcine plasma were well absorbed and can be an useful tool for providing protection against several or specific pathogens and can be a good alternative to formulate CS for newborn piglets.
Conformational stabilization and crystallization of the SecA translocation ATPase fromBacillus subtilis (2001)

SecA is the peripheral membrane-associated subunit of the enzyme complex 'preprotein translocase' which assists the selective transport of presecretory proteins into and across bacterial membranes. The SecA protein acts as the molecular motor that drives the translocation of presecretory proteins through the membrane in a stepwise fashion concomitant with large conformational changes accompanying its own membrane insertion/retraction reaction cycle coupled to ATPase activity. The high flexibility of SecA causes a dynamic conformational heterogeneity which presents a barrier to growth of crystals of high diffraction quality. As shown by fluorescence spectroscopy, the T(m) of the endothermic transition of cytosolic SecA from Bacillus subtilis is shifted to higher temperatures in the presence of 30% glycerol, indicating stabilization of the protein in its compact membrane-retracted conformational state. High glycerol concentrations are also necessary to obtain three-dimensional crystals suitable for X-ray diffraction analysis, suggesting that stabilization of the conformational dynamics of SecA may be required for effective crystallization. The SecA crystals grow as hexagonal bipyramids in the trigonal space group P3(1)12; they possess unit-cell parameters a = 130.8, b = 130.8, c = 150.4 A at 100 K and diffract X-rays to approximately 2.70 A using a high-flux synchrotron-radiation source.
A 25-kDa NH2-terminal fragment carries all the antibacterial activities of the human neutrophil 60-kDa bactericidal/permeability-increasing protein. (1987)

We have isolated, after limited proteolysis of the bactericidal/permeability-increasing protein (BPI) of human neutrophils, a 25-kDa fragment that possesses the bactericidal and envelope-altering activities of the 60-kDa parent protein. On a molar basis, the fragment is as potent as holo-human BPI against rough Escherichia coli, is more potent than holo-BPI against more resistant smooth E. coli, and retains the specificity of BPI toward Gram-negative bacteria. NH2-terminal amino acid sequence analysis shows that the fragment is derived from the NH2 terminus of the BPI molecule. These findings suggest that all of the molecular determinants of the antibacterial properties of BPI reside within the NH2-terminal 25-kDa segment, implying a novel structural/functional organization for a cytotoxic protein.
<title>Determination of direction-independent optical path length distribution of cells using rotational-diversity transmitted-light differential-interference-contrast (DIC) images</title> (1998)

Two different phase-estimation methods that have been developed for the computation of the optical path-length (OPL) distribution of a specimen from DIC image for the determination of the OPL distribution. The second phase- estimation method is based on the conjugate-gradient optimization method and estimates the OPL distribution using rotational-diversity DIC images; i.e. multiple DIC images obtained by rotating the specimen. For this study, 24 different DIC images of a single bovine spermatozoa head acquired by rotating the cell by approximately 15 degrees between images. The images were registered and aligned using fiducial marks, and then processed with both methods. Results obtained with the filtering method were found to be dependent on the orientation of the cell with respect to the shear direction. Comparison of the integrated optical path length (IOPL) computed with the filtering method and the rotational-diversity method using two, four and eight DIC images at different rotation angels showed that the IOPL estimated with the rotational-diversity method is less dependent on the rotation angel, even when only two images separated by 90-degree cell rotation are used for the phase estimation. Our results show that the use of rotational- diversity images in the determination of the OPL distribution is very beneficial because it overcomes the directional dependence of DIC imaging.
Cholesteryl-(l-Lactic Acid)nBuilding Blocks for Self-Assembling Biomaterials (2002)

The synthesis and properties of a novel set of building blocks for the preparation of self-assembling biomaterials are described. These molecules consist of a relatively short oligo(l-lactic acid)n̄ segment (n̄ = 10−40) that is substituted with a cholesterol moiety as an end group and in some cases has a second biofunctional substituent at its other terminus. The cholesterol moiety not only serves to induce liquid crystalline properties and drive the self-assembly of these oligomers, but also is expected to have an effect on the interaction of cells with these materials. The cholesteryl−(l-lactic acid)n̄ (CLAn̄) oligomers form thermotropic liquid crystals and self-assemble into lamellar structures consisting of interdigitated bilayers. In addition, the CLAn̄ oligomers can be homogeneously blended with poly(l-lactic acid), thereby offering the possibility to improve the cell interaction properties of this common surgical biomaterial. Furthermore, the secondary alcohol terminus of the CLAn̄ oligomers allows the opportunity to introduce additional bioactive substituents such as cholesterol, indomethacin (an antiinflammatory drug), and pyrene and rhodamine B (which can act as fluorescent labels for bioimaging purposes) and various α-amino acids. These biofunctional CLAn̄ oligomers can also be homogeneously mixed with the unsubstituted CLAn̄ oligomers and thus could enable a further noncovalent functionalization of self-assembling biomaterials.
Cytotoxicity of Human p I 7 Interleukin-1 for Pancreatic Islets of Langerhans (1986)

Activated mononuclear cells appear to be important effector cells in autoimmune beta cell destruction leading to insulin-dependent (type 1) diabetes mellitus. Conditioned medium from activated mononuclear cells (from human blood) is cytotoxic to isolated rat and human islets of Langerhans. This cytotoxic activity was eliminated from crude cytokine preparations by adsorption with immobilized, purified antibody to interleukin-1 (IL-1). The islet-inhibitory activity and the IL-1 activity (determined by its comitogenic effect on thymocytes) were recovered by acid wash. Purified natural IL-1 and recombinant IL-1 derived from the predominant pI 7 form of human IL-1, consistently inhibited the insulin response. The pI 6 and pI 5 forms of natural IL-1 were ineffective. Natural and recombinant IL-1 exhibited similar dose responses in their islet-inhibitory effect and their thymocyte-stimulatory activity. Concentrations of IL-1 that inhibited islet activity were in the picomolar range. Hence, monocyte-derived pI 7 IL-1 may contribute to islet cell damage and therefore to the development of insulin-dependent diabetes mellitus.
The bone marrow in murine AIDS (1993)

In order to increase the understanding of blood cytopenias in HIV infection we have investigated the bone marrow in murine AIDS. C57BL/6 mice infected with the LP-BM5 retrovirus show a decrease in cellularity, numerous haemophagocytic histiocytes, a reduction of all erythroid precursor cells, an increase in eosinophil number and an increase in lymphocytes. Immunostaining with an anti-Pr60gag antibody shows that the majority of bone marrow cells express the viral protein. Thus, the bone marrow in MAIDS has many similarities with the bone marrow from patients with advanced AIDS and may prove useful as a model for therapy aimed at treating blood cytopenias.