gebhart/patrepeval huggingface dataset:
Association of lipids with integral membrane surface proteins of Mycoplasma hyorhinis (1988)

Triton X-114 (TX-114)-phase fractionation was used to identify and characterize integral membrane surface proteins of the wall-less procaryote Mycoplasma hyorhinis GDL. Phase fractionation of mycoplasmas followed by analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed selective partitioning of approximately 30 [35S]methionine-labeled intrinsic membrane proteins into the TX-114 phase. Similar analysis of [3H]palmitate-labeled cells showed that approximately 20 proteins of this organism were associated with lipid, all of which also efficiently partitioned as integral membrane components into the detergent phase. Immunoblotting and immunoprecipitation of TX-114-phase proteins from 125I-surface-labeled cells with four monoclonal antibodies to distinct surface epitopes of M. hyorhinis identified surface proteins p120, p70, p42, and p23 as intrinsic membrane components. Immunoprecipitation of [3H]palmitate-labeled TX-114-phase proteins further established that surface proteins p120, p70, and p23 (a molecule that mediates complement-dependent mycoplasmacidal monoclonal antibody activity) were among the lipid-associated proteins of this organism. Two of these proteins, p120 and p123, were acidic (pI less than or equal to 4.5), as shown by two-dimensional isoelectric focusing. This study established that M. hyorhinis contains an abundance of integral membrane proteins tightly associated with lipids and that many of these proteins are exposed at the external surface of the single limiting plasma membrane. Monoclonal antibodies are reported that will allow detailed analysis of the structure and processing of lipid-associated mycoplasma proteins.
Effects of fluid‐induced shear on articular chondrocyte morphology and metabolism in vitro (1995)

This study tested the effects of fluid-induced shear on high density monolayer cultures of adult articular chondrocytes. Fluid-induced shear (1.6 Pa) was applied by cone viscometer to normal human and bovine articular chondrocytes for periods of 24, 48, and 72 hours. At 48 and 72 hours, fluid-induced shear caused individual chondrocytes to elongate and align tangential to the direction of cone rotation. Fluid-induced shear stimulated glycosaminoglycan synthesis by 2-fold (p < 0.05) and increased the length of newly synthesized chains in human and bovine chondrocytes. In human chondrocytes, the hydrodynamic size of newly synthesized proteoglycans also was increased. After 48 hours of fluid-induced shear, the release of prostaglandin E2 from the chondrocytes was increased 10 to 20-fold. In human chondrocytes, mRNA signal levels for tissue inhibitor of metalloproteinase increased 9-fold in response to shear compared with the controls. In contrast, mRNA signal levels for the neutral metalloproteinases, collagenase, stromelysin, and 72 kD gelatinase, did not show such major changes. This study demonstrated that articular chondrocyte metabolism responds directly to physical stimulation in vitro and suggests that mechanical loading may directly influence cartilage homeostasis in vivo.
Construction and analysis of monomobile DNA junctions (1988)

Immobile DNA junctions are complexes of oligomeric DNA strands that interact to yield branched structures in which the branch point cannot migrate. This is achieved by minimizing the sequence symmetry in the flanking arms, so that base pairs lock at the branch site. Here, we report the design, synthesis, and analysis of two semimobile junctions, structures in which a controlled extent of branch point migratory freedom is deliberately introduced. We have constructed two minimally symmetric four-arm semimobile junctions from synthetic deoxy 17-mers. These junctions, termed "monomobile", contain a single pair of base pairs (A-T or C-G) which can migrate at the site of branching, while the rest of the junction is immobile. We have demonstrated by gel electrophoresis techniques that these junctions form and that they have the predicted 1:1:1:1 stoichiometry. We have compared these junctions with the immobile junction on which they are based, by means of hydroxyl radical protection experiments. From these data, both migratory conformers can be seen to coexist in solution. The semimobile junction with the C-G base pair has the same crossover and stacking pattern observed for the immobile junction, while the junction with the A-T base pair has the opposite pattern. We conclude that crossover and stacking patterns are a direct consequence of the base pairs which flank the junction. In addition, the data indicate that the crossover pattern biases for these junctions are much greater than are the migratory biases.
The transcriptome of cervical ripening in human pregnancy before the onset of labor at term: Identification of novel molecular functions involved in this process (2009)

(1) This is the first description of the changes in the human cervical transcriptome with ripening before the onset of labor. (2) Biological processes, pathways and molecular functions were identified with the use of this unbiased approach. (3) In contrast to cervical dilation after term labor, inflammation-related genes did not emerge as differentially regulated with cervical ripening. (4) Myocardin was identified as a novel gene upregulated in human cervical ripening.
Expansion of the alpha 2-adrenergic receptor family: cloning and characterization of a human alpha 2-adrenergic receptor subtype, the gene for which is located on chromosome 2. (1990)

Pharmacologic, biochemical, and genetic analyses have demonstrated the existence of multiple alpha 2-adrenergic receptor (alpha 2AR) subtypes. We have cloned a human alpha 2AR by using the polymerase chain reaction with oligonucleotide primers homologous to conserved regions of the previously cloned alpha 2ARs, the genes for which are located on human chromosomes 4 (C4) and 10 (C10). The deduced amino acid sequence encodes a protein of 450 amino acids whose putative topology is similar to that of the family of guanine nucleotide-binding protein-coupled receptors, but whose structure most closely resembles that of the alpha 2ARs. Competition curve analysis of the binding properties of the receptor expressed in COS-7 cells with a variety of adrenergic ligands demonstrates a unique alpha 2AR pharmacology. Hybridization with somatic cell hybrids shows that the gene for this receptor is located on chromosome 2. Northern blot analysis of various rat tissues shows expression in liver and kidney. The unique pharmacology and tissue localization of this receptor suggest that this is an alpha 2AR subtype not previously identified by classical pharmacological or ligand binding approaches.
Investigation of small printed antennas suitable for mobile communication handsets (2002)

A thorough investigation of resistively loaded patches is provided. Comparisons with shorted patches are given such that the advantages and disadvantages of this new form of printed antenna can be established. Terminating a cavity backed shorted patch with a resistive load is also examined in an attempt to improve its impedance behavior. Again, the tradeoffs of using this technology are presented.
Development of a novel microfluidic immunoassay for the detection of Helicobacter pylori infection (2004)

The miniaturization of laboratory processes offers substantial advantages over traditional techniques in terms of cost, speed, and potential for multistage automation. To date, only a few studies have reported successful microfluidics-based immunoassays, most of which rely on fluorescence detection technologies. The goal of this study was to develop a poly(dimethylsiloxane) microfluidics-based immunoassay methodology and a versatile colorimetric quantification scheme for the detection of visual colour changes resulting from immune reactions in microchannels. The novel immunoassay technique was applied towards the detection of Helicobacter pylori infection using 20 human serum samples of known infection status, and results compared with conventional nitrocellulose membrane-based dot-ELISA. The microchannel immunoassay reliably detected H. pylori antigens in quantities on the order of 10 ng, which provides a sensitivity of detection comparable to conventional dot-blot assays. Sensitivity was 100%, specificity was 90%, positive predictive value 91%, and negative predictive value 100%, with an overall accuracy of 95%. The software developed generated results that were consistent with visual observations and by automatically taking into account background intensity changes, the software minimized subjectivity. Volumes of solutions used were 100-fold less compared with conventional immunoassays. Miniaturization of the ELISA using this technique provides a means for the accurate diagnosis of microbial infection while minimizing waste production.
Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of c - myc and its regulated genes (2002)

The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which c-myc and genes regulated by c-myc showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and de novo DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to de novo DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and de novo DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.
Blood-brain barrier transport of neuropeptides: analysis with a metabolically stable dermorphin analogue (1994)

To avoid the confounding effect of metabolic degradation, the stable mu-opioid peptide agonist [D-Arg2,Lys4]-dermorphin analogue (DALDA) was used to quantitate blood-brain barrier (BBB) permeability by intravenous injection and internal carotid artery perfusion techniques. With intravenous injection, the BBB permeability-surface area products for [3H]DALDA (0.84 +/- 0.13 microliters.min-1.g-1) and [14C]sucrose (0.39 +/- 0.05 microliters.min-1.g-1) correlated with the lipid solubility of the two molecules: the 1-octanol-Ringer partition coefficient for DALDA was approximately 2 log orders greater than that for sucrose. The brain delivery of [3H]DALDA at 30 min after intravenous administration was 0.019 +/- 0.002% of the injected dose per gram, and analgesia was induced with a 5-mg/kg dose administered systemically. In contrast to the result after intravenous injection, the BBB permeability-surface area product for DALDA estimated with the internal carotid artery perfusion technique was manyfold greater. This was due to nonspecific absorption of the peptide into the cerebral microvasculature, which precluded use of the capillary depletion technique to study transcytosis through the BBB after internal carotid artery perfusion. The present studies show that the brain delivery of a metabolically stable peptide, such as DALDA, is comparable to that for sucrose, correlates with lipid solubility, and is mediated by a nonsaturable mechanism, probably free diffusion.
Minimal error drift in frequency scalability for motion-compensated DCT coding (1994)

The authors mathematically analyze the drift of low-resolution images obtained from a smaller IDCT of a subset of the DCT coefficients of the full-resolution images in motion-compensated hybrid predictive/DCT coding such as MPEG-2, which allows for frequency scalability. Using this mathematical structure, they derive a low-resolution decoder that has the theoretically minimum possible drift, and propose techniques for implementation that produce substantial improvement in real sequences. The minimum drift can also be used as a milestone, to be compared with other techniques of drift reduction (of worse performance but lower complexity). For the case where leakage is used to reduce the drift, the authors determine a minimum-energy non-uniform DCT-domain leakage matrix which is no more complex than uniform leakage, but gives a substantial improvement. Finally, they note that DCT-based pyramidal coding is essentially the same as the drift case, and thus they use the same mathematical structure to derive the theoretically-best upward predictor in pyramidal coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Acute inflammatory responses to mechanical lesions in the CNS: differences between brain and spinal cord (1999)

Lesion-induced inflammatory responses in both brain and spinal cord have recently become a topic of active investigation. Using C57BL/6J mice, we compared the tissue reaction in these two central nervous system (CNS) compartments with mechanical lesions of similar size involving both grey and white matter. This evaluation included the quantitative assessment of neutrophils, lymphocytes and activated macrophages/microglia, as well as astrocyte activation, upregulation of vascular cell adhesion molecules (ICAM-1, VCAM-1, PECAM) and the extent of blood-brain barrier (BBB) breakdown. Time points analysed post-lesioning included 1, 2, 4 and 7 days (as well as 10 and 14 days for the BBB). We found clear evidence that the acute inflammatory response to traumatic injury is significantly greater in the spinal cord than in the cerebral cortex. The numbers of both neutrophils and macrophages recruited to the lesion site were significantly higher in the spinal cord than in the brain, and the recruitment of these cells into the surrounding parenchyma was also more widespread in the cord. The area of BBB breakdown was substantially larger in the spinal cord and vascular damage persisted for a longer period. In the brain, as in spinal cord, the area to which neutrophils were recruited correlated well with the area of BBB breakdown. It will be of interest to determine the extent to which the infiltration of inflammatory cells contributes, either directly or indirectly, to the vascular permeability and secondary tissue damage or, conversely, to local tissue repair in the brain and the spinal cord.
Productive Nanosystems: A Technology Roadmap (2007)

Report of the 2007 Productive Nanosystems workshop sponsored by Waitt Family Foundation, Batelle, the Foresight Institute, Sun Microsystems, and Zyvex Labs: The Roadmap project provided a unique, cross-disciplinary process for exploring current capabilities and near-term opportunities in atomically precise technologies (APT), and explored pathways leading toward advanced atomically precise manufacturing (APM).
FGF2 Specifies hESC-Derived Definitive Endoderm into Foregut/Midgut Cell Lineages in a Concentration-Dependent Manner (2009)

Fibroblast growth factor (FGF) signaling controls axis formation during endoderm development. Studies in lower vertebrates have demonstrated that FGF2 primarily patterns the ventral foregut endoderm into liver and lung, whereas FGF4 exhibits broad anterior-posterior and left-right patterning activities. Furthermore, an inductive role of FGF2 during dorsal pancreas formation has been shown. However, whether FGF2 plays a similar role during human endoderm development remains unknown. Here, we show that FGF2 specifies hESC-derived definitive endoderm (DE) into different foregut lineages in a dosage-dependent manner. Specifically, increasing concentrations of FGF2 inhibits hepatocyte differentiation, whereas intermediate concentration of FGF2 promotes differentiation toward a pancreatic cell fate. At high FGF2 levels specification of midgut endoderm into small intestinal progenitors is increased at the expense of PDX1(+) pancreatic progenitors. High FGF2 concentrations also promote differentiation toward an anterior foregut pulmonary cell fate. Finally, by dissecting the FGF receptor intracellular pathway that regulates pancreas specification, we demonstrate for the first time to the best of our knowledge that induction of PDX1(+) pancreatic progenitors relies on FGF2-mediated activation of the MAPK signaling pathway. Altogether, these observations suggest a broader gut endodermal patterning activity of FGF2 that corresponds to what has previously been advocated for FGF4, implying a functional switch from FGF4 to FGF2 during evolution. Thus, our results provide new knowledge of how cell fate specification of human DE is controlled-facts that will be of great value for future regenerative cell therapies.
Liberation Theology: An Introduction to Its History and Themes (1986)

In the first part of this overview of Latin American liberation theology I trace the development of, and opposition to, the movement between 1968 and 1984. In the second part I examine six of liberation theology's leading characteristics: solidarity with the poor, conscientization (consciousness raising), the emphasis on orthopraxy, the recognition of structural violence, liberation and the Bible, and base communities. The article concludes with a brief overview of this special issue of Counseling and Values.
Redesigning an FKBP–ligand interface to generate chemical dimerizers with novel specificity (1998)

FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituent in place of a carbonyl group exhibited sub-nanomolar affinity and 1,000-fold selectivity for a mutant FKBP with a compensating truncation of a phenylalanine residue. Structural and functional analysis of the new pocket showed that recognition is surprisingly relaxed, with the modified ligand only partially filling the engineered cavity. We incorporated the specificity pocket into a fusion protein containing FKBP and the intracellular domain of the Fas receptor. Cells expressing this modified chimeric protein potently underwent apoptosis in response to AP1903, a homodimer of the modified ligand, both in culture and when implanted into mice. Remodeled dimerizers such as AP1903 are ideal reagents for controlling the activities of cells that have been modified by gene therapy procedures, without interference from endogenous FKBP.
Comparison of etching processes of silicon and germanium in SF6–O2 radio-frequency plasma (1995)

Reactive ion etching of Si and Ge in SF6–O2 is investigated. Etch rate shows that Si etching is selective with respect to Ge in SF6–O2 (O2&amp;lt;50%); the reverse is observed in SF6–O2 (O2≳50%). In agreement with the compared evolution of the F and O concentration in the plasma and of the etch product formation rate obtained respectively, by optical emission spectroscopy and mass spectrometry, the x-ray photon spectroscopy surface analysis reveals that the growth of a SiOxFy layer quenches the Si etching whereas the formation of GeOxFy does not inhibit Ge etching. Using a simple model, an experimental surface reactivity is defined and expressed in function of the experimental data. Results suggest a different behavior for sulfur and oxygen on both materials.
Molecular Mechanisms of Bitter and Sweet Taste Transduction (2002)

The sense of taste plays a critical role in the life and nutritional status of humans and other organisms. Human taste perception may be categorized according to four well known and widely accepted descriptors, sweet, bitter, salty, and sour (corresponding to particular taste qualities or modalities), and two more controversial qualities: fat and amino acid taste. The ability to identify sweet-tasting foodstuffs is particularly important as it provides us and other vertebrates with a means to seek out needed carbohydrates with high nutritive value. The perception of bitter, on the other hand, is essential for its protective value, enabling humans to avoid potentially deadly plant alkaloids and other environmental toxins. The focus of this review is on recent advances in our understanding of the transduction elements and signaling mechanisms underlying bitter and sweet taste transduction (see Fig.
Antifibrotic activities of pirfenidone in animal models (2011)

Pirfenidone is an orally active small molecule that has recently been evaluated in large clinical trials for the treatment of idiopathic pulmonary fibrosis, a fatal disease in which the uncontrolled deposition of extracellular matrix leads to progressive loss of lung function. This review describes the activity of pirfenidone in several well-characterised animal models of fibrosis in the lung, liver, heart and kidney. In these studies, treatment-related reductions in fibrosis are associated with modulation of cytokines and growth factors, with the most commonly reported effect being reduction of transforming growth factor-β. The consistent antifibrotic activity of pirfenidone in a broad array of animal models provides a strong preclinical rationale for the clinical characterisation of pirfenidone in pulmonary fibrosis and, potentially, other conditions with a significant fibrotic component.
Expression of the basement membrane heparan sulfate proteoglycan (perlecan) in human synovium and in cultured human synovial cells. (1995)

The presence of perlecan in human synovium and the modulation of the biosynthesis of its core protein by TGF-beta and FGF suggest that, in addition to its structural role, this unique heparan sulfate proteoglycan may be involved in normal synovial membrane function and in the pathogenesis of arthritis.
Colorectal premalignancy is associated with consensus molecular subtypes 1 and 2 (2018)

Based on our observations made in premalignancy, we propose a model of pathway activation associated with CMS classification in colorectal carcinogenesis. Specifically, while adenomatous polyps are largely CMS2, most hyperplastic and serrated polyps are CMS1 and may transition into other CMS groups during evolution into carcinomas. Our findings shed light on the transcriptional landscape of premalignant colonic polyps and may help guide the development of future biomarkers or preventive treatments for CRC.
Anti‐interferon‐γ antibody protects mice against the generalized Shwartzman reaction (1987)

A generalized Shwartzman reaction was found to occur in non-SPF-NMRI mice given a local injection of S. marcescens lipopolysaccharide (LPS) in the footpad, followed, with an interval of 24 h, by an i.v. injection. The reaction occurred several hours after the second injection. It was characterized by disseminated subcutaneous bleedings at the mouth, anus, conjuctiva, nose tip and tail end. Most mice died within 24-48 h. The size of the LPS dose given in the footpad (5 micrograms) was found to be critical in that the reaction failed to occur with higher as well as lower doses. The reaction was found to be completely absent in mice that had received one or more systemic injections of monoclonal antibodies with neutralizing potential for murine interferon-gamma (IFN-gamma). Mice treated with control preparations, including a monoclonal antibody with binding but no neutralizing activity for murine IFN-gamma, remained sensitive to induction of the reaction. These observations assign a crucial role to endogenous IFN-gamma in the elicitation of the generalized Shwartzman reaction and open perspectives for the prevention or therapy of clinical conditions related to the Shwartzman reaction by the use of antibodies to IFN-gamma.