gebhart/patrepeval huggingface dataset:
Mechanistic Studies on the Base-Catalyzed Transformation of Neocarzinostatin Chromophore:  Roles of Bulged DNA (1999)

Nucleic acid bulges have been implicated in a number of biological processes and are specific cleavage targets for the enediyne antitumor antibiotic neocarzinostatin chromophore (NCS-chrom) in a base-catalyzed, radical-mediated reaction. Studies designed to elucidate the detailed mechanism of the base-catalyzed activation of NCS-chrom and to evaluate the roles of bulged DNA in its activation are described. They show that nucleobases in the DNA bulge are not required to form an effective bulge pocket but enhance the binding of the wedge-shaped activated drug molecule. Analysis of solvent deuterium isotope effects on NCS-chrom degradation and DNA cleavage efficiency experiments suggests that the spirolactone biradical 6 is a relatively stable species and that intramolecular quenching of the C2 radical of 6 to form the biologically active cyclospirolactone radical 7a occurs first (pathway a in Scheme 2), leaving the C6 radical to abstract the hydrogen atom from the DNA deoxyribose and to form the cyclospirolactone 8. Binding of the activated drug at the bulge site is required, but not sufficient, for efficient 8 formation, whereas cleavage of bulged DNA is not essential. Efficient generation of 8, but inefficient DNA damage generation, comes mainly from the likely high off-rate of 7a binding. The finding that thymidine 5'-carboxylic acid-ended oligonucleotide fragment can be formed in the reaction suggests that the process of DNA cleavage is rather slow and that sequential oxidations of the target 5'-carbon are possible. Study of the effect of solvent (methanol) concentration on NCS-chrom degradation indicates that bulged DNA acts to assist the intramolecular quenching of the radical at C2 by C8' ' of the naphthoate moiety by excluding solvent from the binding pocket, thus preventing the formation of spirolactones 9, and by blocking radical polymerization. Because in the absence or near absence of solvent methanol 8 formation does not reach even 10% that formed in the presence of bulged DNA, it is possible that the DNA bulge also induces a conformational change in the drug to promote the intramolecular reaction.
Regulation of Urokinase Receptor Proteolytic Function by the Tetraspanin CD82 (2005)

The high affinity interaction between the urokinase-type plasminogen activator (uPA) and its glycolipid-anchored cellular receptor (uPAR) promotes plasminogen activation and the efficient generation of pericellular proteolytic activity. We demonstrate here that expression of the tetraspanin CD82/KAI1 (a tumor metastasis suppressor) leads to a profound effect on uPAR function. Pericellular plasminogen activation was reduced by approximately 50-fold in the presence of CD82, although levels of components of the plasminogen activation system were unchanged. uPAR was present on the cell surface and molecularly intact, but radioligand binding analysis with uPA and anti-uPAR antibodies revealed that it was in a previously undetected cryptic form unable to bind uPA. This was not due to direct interactions between uPAR and CD82, as they neither co-localized on the cell surface nor could be co-immunoprecipitated. However, expression of CD82 led to a redistribution of uPAR to focal adhesions, where it was shown by double immunofluorescence labeling to co-localize with the integrin alpha(5)beta(1), which was also redistributed in the presence of CD82. Co-immunoprecipitation experiments showed that, in the presence of CD82, uPAR preferentially formed stable associations with alpha(5)beta(1), but not with a variety of other integrins, including alpha(3)beta(1). These data suggest that CD82 inhibits the proteolytic function of uPAR indirectly, directing uPAR and alpha(5)beta(1) to focal adhesions and promoting their association with a resultant loss of uPA binding. This represents a novel mechanism whereby tetraspanins, integrins, and uPAR, systems involved in cell adhesion and migration, cooperate to regulate pericellular proteolytic activity and may suggest a mechanism for the tumor-suppressive effects of CD82/KAI1.
The macrophage scavenger receptor CD163 functions as an innate immune sensor for bacteria (2008)

The plasma membrane glycoprotein receptor CD163 is a member of the scavenger receptor cystein-rich (SRCR) superfamily class B that is highly expressed on resident tissue macrophages in vivo. Previously, the molecule has been shown to act as a receptor for hemoglobin-haptoglobin complexes and to mediate cell-cell interactions between macrophages and developing erythroblasts in erythroblastic islands. Here, we provide evidence for a potential role for CD163 in host defense. In particular, we demonstrate that CD163 can function as a macrophage receptor for bacteria. CD163 was shown to bind both Gram-positive and -negative bacteria, and a previously identified cell-binding motif in the second scavenger domain of CD163 was sufficient to mediate this binding. Expression of CD163 in monocytic cells promoted bacteria-induced proinflammatory cytokine production. Finally, newly generated antagonistic antibodies against CD163 were able to potently inhibit cytokine production elicited by bacteria in freshly isolated human monocytes. These findings identify CD163 as a macrophage receptor for bacteria and suggest that, during bacterial infection, CD163 on resident tissue macrophages acts as an innate immune sensor and inducer of local inflammation.
Inducible Control of Virulence Gene Expression in Listeria monocytogenes : Temporal Requirement of Listeriolysin O during Intracellular Infection (2002)

We have constructed a lac repressor/operator-based system to tightly regulate expression of bacterial genes during intracellular infection by Listeria monocytogenes. An L. monocytogenes strain was constructed in which expression of listeriolysin O was placed under the inducible control of an isopropyl-beta-D-thiogalactopyranoside (IPTG)-dependent promoter. Listeriolysin O (LLO) is a pore-forming cytolysin that mediates lysis of L. monocytogenes-containing phagosomes. Using hemolytic-activity assays and Western blot analysis, we demonstrated dose-dependent IPTG induction of LLO during growth in broth culture. Moreover, intracellular growth of the inducible-LLO (iLLO) strain in the macrophage-like cell line J774 was strictly dependent upon IPTG. We have further shown that iLLO bacteria trapped within primary phagocytic vacuoles can be induced to escape into the cytosol following addition of IPTG to the cell culture medium, thus yielding the ability to control bacterial escape from the phagosome and the initiation of intracellular growth. Using the iLLO strain in plaque-forming assays, we demonstrated an additional requirement for LLO in facilitating cell-to-cell spread in L2 fibroblasts, a nonprofessional phagocytic cell line. Furthermore, the efficiency of cell-to-cell spread of iLLO bacteria in L2 cells was IPTG dose dependent. The potential use of this system for determining the temporal requirements of additional virulence determinants of intracellular pathogenesis is discussed.
Characterization of aggregates of hepatitis C virus glycoproteins (1999)

Hepatitis C virus (HCV) encodes two glycoproteins, E1 and E2, which assemble in oligomeric structures. Studies of HCV glycoprotein assembly using heterologous expression systems have shown that these glycoproteins can follow two pathways: a productive pathway leading to the formation of a non-covalent heterodimer; and a non-productive pathway leading to the formation of large disulfide-linked aggregates. The non-covalent HCV glycoprotein complex is probably the functional complex which plays an active role in the entry process in host cells. The aggregates are believed to be waste products; however, one can imagine that, in infected cells, they could provide HCV glycoproteins with additional functions. To further understand the potential role played by HCV glycoprotein aggregates in HCV infection, a MAb (H14) was produced which specifically recognizes these aggregates but not the non-covalent E1E2 heterodimer. The H14 epitope was shown to be present on both HCV glycoproteins and was sensitive to deglycosylation. An additional characterization of HCV glycoprotein aggregates, with the help of MAb H14, indicates that they share an epitope with a cellular protein called Mac-2 binding protein. The presence of such an epitope on HCV glycoprotein aggregates could potentially lead to the production of autoantibodies recognizing Mac-2 binding protein in HCV-infected patients.
Hemorrhage induces enhanced Kupffer cell cytotoxicity while decreasing peritoneal or splenic macrophage capacity. Involvement of cell-associated tumor necrosis factor and reactive nitrogen (1991)

Studies indicate that simple hemorrhage produces a profound depression of cell-mediated immunity, thereby contributing to an enhanced susceptibility to septic challenge in the host. However, it remains unknown whether or not the macrophages' cytotoxic capacity is altered after hemorrhage. To study this, C3H/HeN mice were bled to and maintained at a blood pressure of 35 mm Hg for 60 min, and adequately resuscitated. Mice were then killed at 2 or 24 h after hemorrhage to obtain peritoneal macrophage, splenic macrophage, and Kupffer cells. Cytotoxicity was assessed by determining the capacity of these macrophages to lyse [3H]TdR labeled WEHI-164 clone 13 or P815 tumor target cells (WEHI-164, sensitive to both soluble and cell-associated TNF vs P815 cells, insensitive to soluble TNF). Peritoneal and splenic macrophages from hemorrhaged animals exhibited a significantly reduced cytotoxic capacity, whereas Kupffer cells' ability to kill the target cells was enhanced. Similarly, the Kupffer cells' capacity to release TNF and IL-1, as well as express cell-associated forms of this cytokine are significantly enhanced on macrophages isolated 2 h after hemorrhage, whereas peritoneal macrophages are not. Furthermore, antibodies directed at mouse TNF but not against murine IL-1 alpha or murine IL-6 were able to oblate the enhanced target cell lysis of unfixed, as well as paraformaldehyde fixed (metabolically inactive) Kupffer cells. Studies using inhibitors (GN-monomethyl-arginine, superoxide dismutase, catalase, and ibuprofen) of other TNF-inducible mechanisms of target cell killing indicated that only the inhibition of the release of reactive nitrogen consistently depressed the cytotoxic capacity of Kupffer cells from hemorrhaged mice. Thus, the increased Kupffer cell cytotoxicity from hemorrhaged mice is most likely mediated through the expression of cell-associated TNF and the release of reactive nitrogen.
Chemokine:Receptor Structure, Interactions, and Antagonism (2007)

Chemokines are critical mediators of cell migration during routine immune surveillance, inflammation, and development. Chemokines bind to G protein-coupled receptors and cause conformational changes that trigger intracellular signaling pathways involved in cell movement and activation. Although chemokines evolved to benefit the host, inappropriate regulation or utilization of these proteins can contribute to or cause many diseases. Specific chemokine receptors provide the portals for HIV to get into cells, and others contribute to inflammatory diseases and cancer. Thus, there is significant interest in developing receptor antagonists. To this end, the structures of ligands coupled with mutagenesis studies have revealed mechanisms for antagonism based on modified proteins. Although little direct structural information is available on the receptors, binding of small molecules to mutant receptors has allowed the identification of key residues involved in the receptor-binding pockets. In this review, we discuss the current knowledge of chemokine:receptor structure and function, and its contribution to drug discovery.
Molecular pathology via IR and Raman spectral imaging (2013)

During the last 15 years, vibrational spectroscopic methods have been developed that can be viewed as molecular pathology methods that depend on sampling the entire genome, proteome and metabolome of cells and tissues, rather than probing for the presence of selected markers. First, this review introduces the background and fundamentals of the spectroscopies underlying the new methodologies, namely infrared and Raman spectroscopy. Then, results are presented in the context of spectral histopathology of tissues for detection of metastases in lymph nodes, squamous cell carcinoma, adenocarcinomas, brain tumors and brain metastases. Results from spectral cytopathology of cells are discussed for screening of oral and cervical mucosa, and circulating tumor cells. It is concluded that infrared and Raman spectroscopy can complement histopathology and reveal information that is available in classical methods only by costly and time-consuming steps such as immunohistochemistry, polymerase chain reaction or gene arrays. Due to the inherent sensitivity toward changes in the bio-molecular composition of different cell and tissue types, vibrational spectroscopy can even provide information that is in some cases superior to that of any one of the conventional techniques.
<title>Experimental System For Dual Energy Scanned Projection Radiography</title> (1981)

Developing digital radiography techniques provides greater diagnostic information while utilizing less invasive procedures and/or decreased patient dose. An experimental scanned projection radiography system has been built using a CT detector and data acquisition system to provide increased contrast resolution and flexibility in data manipulation. Modifications to the basic system allow dual energy scanning, and subtraction algorithms relying on the energy dependence of the mass attenuation coefficient have been implemented.
A DNA‐Dependent ATPase of Calf‐Thymus (1979)

A DNA-dependent ATPase has been purified from calf thymus. The enzyme hydrolyses ATP and dATP in the presence of heat-denatured DNA. It does not hydrolyse the corresponding nucleoside triphosphates of guanine, uridine and cytosine. The Km values for ATP and dATP are both 0.62 mM. The enzyme requires magnesium or manganese ions. Its sedimentation coefficient is about 4.4 S. The catalytic activity is inhibited by N-ethylmaleimide but is not sensitive to novobiocin and nalidixic acid which are potent inhibitors of bacterial DNA gyrase. In some cases, during purification, chromatographically distinct additional DNA-dependent ATPase activities were detected. Limited proteolysis or covalent modification of the enzyme in the tissues, or during the first steps of its extraction, are probably responsible for the appearance of these chromatographically distinct forms.
Cooperation between Th1 and Th2 cells in a murine model of eosinophilic airway inflammation (1999)

We have studied the actions of helper T lymphocyte-1 and -2 (Th1 and Th2) cells in an acute model of eosinophilic airway inflammation by infusing chicken ovalbumin-specific (OVA-specific) Th1 cells, Th2 cells, or both into unsensitized mice and challenging the mice with an OVA aerosol. OVA challenge after infusion of Th1 cells alone resulted in airway inflammation with lymphocytes and monocytes. Challenge after the infusion of Th2 cells alone resulted in minimal inflammation. In contrast, when Th1 and Th2 cells were transferred together, they cooperated to promote a robust eosinophil-predominant inflammatory response. Th1 cells alone were readily recruited to the airways after challenge, but in the absence of Th1 cells, Th2 cells did not accumulate in the airways. When transferred together, both Th1 and Th2 cells, as well as endogenous eosinophils, were effectively recruited. This recruitment was correlated with increased VCAM-1 expression in the medium- and large-sized vessels of the lung and could be inhibited by treating the mice with neutralizing antibodies to TNF-alpha or VCAM-1. These data indicate that Th2 cells require signals in addition to antigen for their effective recruitment to the airways. Th1 cells can provide these signals.
Distribution of sialosyl Tn and Tn antigens within normal and malignant colorectal epithelium (1995)

Expression of the core blood group structures sialosyl Tn (STn) and Tn is regarded as a colorectal cancer-specific change reflecting truncated synthesis of the oligosaccharide component of goblet cell mucin. The distribution of STn and Tn in normal and malignant epithelium has been studied in detail by a combination of mucin-, lectin-, and immunohistochemistry with and without pretreatment with potassium hydroxide (KOH), neuraminidase, and KOH-neuraminidase. When O-acetylated sialic acid (neuraminidase-resistant) is converted by saponification to non-O-acetylated sialic acid (neuraminidase-sensitive), normal colorectal goblet cells (mainly of the lower two-thirds of crypts) are immunoreactive with the monoclonal antibody TKH2 (specific for STn). This immunoreactivity is abolished by the interposition of neuraminidase, but goblet cells then become immunoreactive with Hb-Tn1 (specific for Tn). While colorectal cancer mucin expresses STn, expression of Tn is not seen in either goblet cell mucin or extracellular material showing the morphological and histochemical characteristics of secretory mucin. Tn expression in cancers is mainly limited to the Golgi zone and in a proportion of cases to cytoplasm and apical membrane (glycocalyx) of columnar cells and inspissated material within lumina. The material reacting with Hb-Tn1 may be upregulated, membrane-associated MUC1 glycoprotein rather than MUC2 or MUC4 goblet cell mucin. The presence of STn and cryptic Tn within normal colorectal goblet cells and the absence of Tn expression within colorectal cancer secretory mucin contradicts the generally accepted concept of cancer-specific incomplete glycoprotein synthesis within these neoplasms.
Cytomegalovirus homologs of cellular G protein-coupled receptor genes are transcribed (1991)

The genome of human cytomegalovirus (HCMV) contains three genes with homology to cellular G protein-coupled receptors (GCRs). Evidence is presented here that all three HCMV GCR genes are transcribed during infection, that they are transcribed as two sets of 3'-coterminal mRNAs, and that their transcription is restricted to the late phase of infection.
Digital karyotyping (2002)

Alterations in the genetic content of a cell are the underlying cause of many human diseases, including cancers. We have developed a method, called digital karyotyping, that provides quantitative analysis of DNA copy number at high resolution. This approach involves the isolation and enumeration of short sequence tags from specific genomic loci. Analysis of human cancer cells by using this method identified gross chromosomal changes as well as amplifications and deletions, including regions not previously known to be altered. Foreign DNA sequences not present in the normal human genome could also be readily identified. Digital karyotyping provides a broadly applicable means for systematic detection of DNA copy number changes on a genomic scale.
Selective suppression by prodigiosin of the mitogenic response of murine splenocytes. (1986)

In the course of screening for immunomodulating substances among microbial metabolites using a triple mitogen assay system, we detected an immunosuppressive activity which is similar to cyclosporin A. Two active components were isolated as red pigments from the fermentation broth of Streptomyces hiroshimensis and they were identified with prodigiosin 25-C and metacycloprodigiosin respectively. These compounds inhibited T lymphocyte proliferation which was induced by plant lectins, concanavalin A (Con A) and phytohemagglutinin (PHA), much more extensively than B lymphocyte proliferation which was induced by lipopolysaccharide (LPS). Prodigiosin 25-C completely inhibited induction of cytotoxic T cells in a mixed lymphocyte reaction (MLR) at 4 ng/ml.
International trends in prostatic cancer (1984)

The most recent data available demonstrate a 120-fold difference between the lowest and highest incidence rates of prostatic cancer, the disease being very common in North America, particularly among Blacks, and in Scandinavia, while it is rare in Japan and other oriental countries. The highest mortality for prostatic cancer is reported from St. Vincent and Grenadines, Martinique and Bermuda, from countries where the morbidity statistics are not available; the mortality rates reported from the United States and Canada are considerably lower. The incidence of and mortality from prostatic cancer have increased in most countries, in particular in areas with an initially low frequency of this disease. The ratio of mortality to incidence for prostatic cancer varies rather widely, being low in North America, Hawaii and Scandinavia. It is suggested that the observed variation in the mortality to incidence ratio for prostatic cancer could be due to differences in diagnostic practices between countries. This could explain, at least in part, the fact that the increasing trends of prostatic cancer incidence in North America are not accompanied by an increase in mortality from this tumour. This notion, however, does not exclude advances in treatment as possible determinants of the improved survival rate from prostatic cancer in this part of the world. The available statistics on prostatic cancer are based on the sum of clinically diagnosed carcinomas and those latent tumours found unexpectedly at prostatectomy and autopsy. The proportion of latent carcinomas among all prostatic cancer cases depends on the detection rate and varies from country to country, thus casting uncertainty on the comparability of prostatic cancer statistics from different areas. To avoid confusion in the statistics of prostatic cancer, it would be useful to consider introducing latent prostatic cancer as a separate entity in the next revision of the International Classification of Diseases (ICD).
Ionized sputter deposition using an extremely high plasma density pulsed magnetron discharge (2000)

Time resolved plasma probe measurements of a novel high power density pulsed plasma discharge are presented. Extreme peak power densities in the pulse (on the order of several kW cm−2) result in a very dense plasma with substrate ionic flux densities of up to 1 A cm−2 at source-to-substrate distances of several cm and at a pressure of 0.13 Pa (1 mTorr). The pulse duration was ∼100 μs with a pulse repetition frequency of 50 Hz. The plasma consists of metallic and inert gas ions, as determined from time resolved Langmuir probe measurements and in situ optical emission spectroscopy data. It was found that the plasma composition at the beginning of the pulse was dominated by Ar ions. As time elapsed metal ions were detected and finally dominated the ion composition. The effect of the process parameters on the temporal development of the ionic fluxes is discussed. The ionized portion of the sputtered metal flux was found to have an average velocity of 2500 m s−1 at 6 cm distance from the source, which conforms to the collisional cascade sputtering theory. The degree of ionization of the sputtered metal flux at a pressure of 0.13 Pa was found to be 40%±20% by comparing the total flux of deposited atoms with the charge measured for the metal ions in the pulse.
Solving the mystery of memory. (2014)

The word "memory" is derived from the ancient Greek myth of Mnemosyne, the mother of the Muses, who was "said to know everything, past, present, and future." Memory is essential to our existence, and one of neuroscience's primary missions is to understand how the brain processes memory and to improve treatments for Alzheimer's disease, traumatic brain injury, drug addiction, and the many other afflictions associated with disrupted memory. Our article traces scientists' progress in understanding memory over the last 15 years.