gebhart/patrepeval huggingface dataset:
New Techniques of Optical Microscopy and Microspectroscopy (1991)

The last few years have seen an upsurge of interest in the study of cells by optical microscopy. The development of techniques such as confocal microscopy and the availability of extremely sensitive digital imaging devices are revolutionising the field. A number of groups have developed new ways of making spectroscopic measurements at the microscopic level, accompanied by the introduction of appropriate sensor molecules for cellular assays. This volume brings together these various advances in order to provide the reader with an up to date account of what can now be achieved with modern optical microscopic methods
Expression and interactions of the two closely related homeobox genes Phox2a and Phox2b during neurogenesis (1997)

Recent evidence suggests that specific families of homeodomain transcription factors control the generation and survival of distinct neuronal types. We had previously characterized the homeobox gene Phox2a, which is expressed in differentiating neurons of the central and peripheral autonomic nervous system as well as in motor nuclei of the hindbrain. Targeted deletion of the Phox2a gene affects part of the structures in which it is expressed: the locus coeruleus, visceral sensory and parasympathetic ganglia and, as we show here, the nuclei of the IIIrd and IVth cranial nerves. We now report on the characterization of Phox2b, a close relative of Phox2a, with an identical homeodomain. Phox2a and Phox2b are co-expressed at most sites, therefore suggesting a broader role for Phox2 genes in the specification of the autonomic nervous system and cranial motor nuclei than revealed by the Phox2a knock-out mice. A detailed analysis of the relative timing of Phox2a and Phox2b expression at various sites suggests positive cross-regulations, which are substantiated by the loss of Phox2b expression in cranial ganglia of Phox2a-deficient mice. In the major part of the rhombencephalon, Phox2b expression precedes that of Phox2a and starts in the proliferative neuroepithelium, in a pattern strikingly restricted on the dorsoventral axis and at rhombomeric borders. This suggests that Phox2b links early patterning events to the differentiation of defined neuronal populations in the hindbrain.
Pertussis Toxin S1 Mutant with Reduced Enzyme Activity and a Conserved Protective Epitope (1988)

Pertussis toxin (PTX) is a major virulence factor in whooping cough and can elicit protective antibodies. Amino acid residues 8 to 15 of PTX subunit S1 are important for the adenosine diphosphate-ribosyltransferase activity associated with the pathobiological effects of PTX. Furthermore, this region contains at least a portion of an epitope that elicits both toxin-neutralizing and protective antibody responses in mice. The gene encoding the S1 subunit was subjected to site-specific mutagenesis in this critical region. A mutant containing a single amino acid substitution (Arg9----Lys) had reduced enzymatic activity (approximately 0.02% of control) while retaining the protective epitope. This analog S1 molecule may provide the basis for a genetically detoxified PTX with potential for use as a component of an acellular vaccine against whooping cough.
Advances in the field of nanooncology (2010)

Nanooncology, the application of nanobiotechnology to the management of cancer, is currently the most important chapter of nanomedicine. Nanobiotechnology has refined and extended the limits of molecular diagnosis of cancer, for example, through the use of gold nanoparticles and quantum dots. Nanobiotechnology has also improved the discovery of cancer biomarkers, one such example being the sensitive detection of multiple protein biomarkers by nanobiosensors. Magnetic nanoparticles can capture circulating tumor cells in the bloodstream followed by rapid photoacoustic detection. Nanoparticles enable targeted drug delivery in cancer that increases efficacy and decreases adverse effects through reducing the dosage of anticancer drugs administered. Nanoparticulate anticancer drugs can cross some of the biological barriers and achieve therapeutic concentrations in tumor and spare the surrounding normal tissues from toxic effects. Nanoparticle constructs facilitate the delivery of various forms of energy for noninvasive thermal destruction of surgically inaccessible malignant tumors. Nanoparticle-based optical imaging of tumors as well as contrast agents to enhance detection of tumors by magnetic resonance imaging can be combined with delivery of therapeutic agents for cancer. Monoclonal antibody nanoparticle complexes are under investigation for diagnosis as well as targeted delivery of cancer therapy. Nanoparticle-based chemotherapeutic agents are already on the market, and several are in clinical trials. Personalization of cancer therapies is based on a better understanding of the disease at the molecular level, which is facilitated by nanobiotechnology. Nanobiotechnology will facilitate the combination of diagnostics with therapeutics, which is an important feature of a personalized medicine approach to cancer.
Identification, Quantification, and Sensory Characterization of Steviol Glycosides from Differently ProcessedStevia rebaudianaCommercial Extracts (2014)

Stevia rebaudiana is known for its sweet-tasting ent-kaurene diterpenoid glycosides. Several manufacturing strategies are currently employed to obtain Stevia sweeteners with the lowest possible off-flavors. The chemical composition of four commercial S. rebaudiana extracts, obtained by different technologies, was characterized using UHPLC-ESI-MS(n). The composition of one of the ethanol-crystallized extracts (EC2) was entirely rebaudioside A, whereas the enzymatically modified (EM) extract contained the lowest concentration of this compound (2.7 mg/100 mg). The membrane-purified (MP) extract had the highest content of minor natural steviol glycosides (23.7 mg/100 mg total extract) versus an average of 2.4 mg/100 mg total extract for the EC samples. Thirteen trained panelists evaluated sweetness, bitterness, licorice, and metallic attributes of all four extracts. The highest licorice intensity (p ≤ 0.05) was found for MP. Both samples EC1 and EC2, despite their different chemical compositions, showed no significant differences in sensory perception.
Cloning, purification, and characterization of .beta.-cystathionase from E. coli (1982)

The Clarke-Carbon clone bank of hybrid plasmid Escherichia coli DNA has been screened for plasmids able to complement an E. coli strain deficient for the production of beta-cystathionase. Clone 4-14 had the ability to complement a deletion mutation at this locus and expressed higher levels of beta-cystathionase than the wild-type strain. The transfer of the plasmid carried by this clone to a strain that constitutively expresses all the enzymes of the methionine biosynthetic pathway results in 100-fold overproduction of beta-cystathionase as compared to wild-type levels. With use of this strain, an efficient three-step purification scheme is described that gives 90% pure enzyme in 54% yield with a specific activity of 215 IU/mg. This enzyme is characterized as to molecular weight (280 000), number of subunits (six), pyridoxal phosphate binding (5.7 mol of pyridoxal phosphate bound/mol of protein, Km of 0.005 mM), amino acid composition, substrate specificity, and kinetic properties.
Vitronectin gene expression in the adult human retina. (1999)

The results constitute the first evidence for Vn gene expression by adult neurons in the mammalian central nervous system. The identification of the photoreceptors as a cellular source of Vn suggests that these cells have the potential to make a biosynthetic contribution to the Vn that is found in drusen.
Structure-Activity Relationships of the Kvβ1 Inactivation Domain and Its Putative Receptor Probed Using Peptide Analogs of Voltage-gated Potassium Channel α- and β-Subunits (1998)

Certain beta-subunits exert profound effects on the kinetics of voltage-gated (Kv) potassium channel inactivation through an interaction between the amino-terminal "inactivation domain" of the beta-subunit and a "receptor" located at or near the cytoplasmic mouth of the channel pore. Here we used a bacterial random peptide library to examine the structural requirements for this interaction. To identify peptides that bind Kv1.1 we screened the library against a synthetic peptide corresponding to the predicted S4-S5 cytoplasmic loop of the Kv1.1 alpha-subunit (residues 313-328). Among the highest affinity interactors were peptides with significant homology to the amino terminus of Kvbeta1. We performed a second screen using a peptide from the amino terminus of Kvbeta1 (residues 2-31) as "bait" and identified peptide sequences with significant homology to the S4-S5 loop of Kv1.1. A series of synthetic peptides containing mutations of the wild-type Kvbeta1 and Kv1.1 sequences were examined for their ability to inhibit Kvbeta1/Kv1.1 binding. Amino acids Arg20 and Leu21 in Kvbeta1 and residues Arg324 and Leu328 in Kv1.1 were found to be important for the interaction. Taken together, these data provide support for the contention that the S4-S5 loop of the Kv1.1 alpha subunit is the likely acceptor for the Kvbeta1 inactivation domain and provide information about residues that may underlie the protein-protein interactions responsible for beta-subunit mediated Kv channel inactivation.
Effective vaginal DNA delivery with high transfection efficiency is a good system for induction of higher local vaginal immune responses (2009)

These results suggested that direct vaginal DNA vaccines under high transfection conditions induced higher local vaginal antibody than that by intranasal or intradermal administration, and peptide carriers effectively elevated mucosal immune responses. Therefore, this vaginal DNA vaccination method may be expected to be useful in the prevention and treatment methods for vaginal infectious diseases such as HIV infection.
The applications of anti-CD20 antibodies to treat various B cells disorders (2018)

B-lymphocyte antigen CD20 (called CD20) is known as an activated-glycosylated phosphoprotein which is expressed on the surface of all B-cells. CD20 is involved in the regulation of trans-membrane Ca<sup>2+</sup> conductance and also play critical roles in cell-cycle progression during human B cell proliferation and activation. The appearance of monoclonal antibody (mAb) technology provided an effective field for targeted therapy in treatment of a variety of diseases such as cancer, and autoimmune diseases. Anti-CD20 is one of important antibodies which could be employed in treatment of several diseases. Increasing evidences revealed that efficacy of different anti-CD20 antibodies is implicated by their function. Hence, evaluation of anti-CD20 antibodies function could provide and introduce new anti-CD20 based therapies. In the present study, we summarized several applications of anti-CD20 antibodies in various immune related disorders including B-CLL (B-cell chronic lymphocytic leukemia), rheumatoid arthritis (RA), multiple sclerosis (MS) and melanoma.
(4-Aminomethyl)phenylguanidine derivatives as nonpeptidic highly selective inhibitors of human urokinase (2000)

Increased expression of the serine protease urokinase-type plasminogen activator (uPA) in tumor tissues is highly correlated with tumor cell migration, invasion, proliferation, progression, and metastasis. Thus inhibition of uPA activity represents a promising target for antimetastatic therapy. So far, only the x-ray crystal structure of uPA inactivated by H-Glu-Gly-Arg-chloromethylketone has been reported, thus limited data are available for a rational structure-based design of uPA inhibitors. Taking into account the trypsin-like arginine specificity of uPA, (4-aminomethyl)phenylguanidine was selected as a potential P1 residue and iterative derivatization of its amino group with various hydrophobic residues, and structure-activity relationship-based optimization of the spacer in terms of hydrogen bond acceptor/donor properties led to N-(1-adamantyl)-N'-(4-guanidinobenzyl)urea as a highly selective nonpeptidic uPA inhibitor. The x-ray crystal structure of the uPA B-chain complexed with this inhibitor revealed a surprising binding mode consisting of the expected insertion of the phenylguanidine moiety into the S1 pocket, but with the adamantyl residue protruding toward the hydrophobic S1' enzyme subsite, thus exposing the ureido group to hydrogen-bonding interactions. Although in this enzyme-bound state the inhibitor is crossing the active site, interactions with the catalytic residues Ser-195 and His-57 are not observed, but their side chains are spatially displaced for steric reasons. Compared with other trypsin-like serine proteases, the S2 and S3/S4 pockets of uPA are reduced in size because of the 99-insertion loop. Therefore, the peculiar binding mode of the new type of uPA inhibitors offers the possibility of exploiting optimized interactions at the S1'/S2' subsites to further enhance selectivity and potency. Because crystals of the uPA/benzamidine complex allow inhibitor exchange by soaking procedures, the structure-based design of new generations of uPA inhibitors can rely on the assistance of x-ray analysis.
Microstructure and Mechanics of the Chorioamnion Membrane with an Emphasis on Fracture Properties (2007)

The normal mechanical functioning of an intact chorioamnion (CA) membrane is essential to successful human reproduction. The amnion and the chorion, separately and together as the bilayer chorioamnion, serve barrier and container functions throughout gestation, and these two important roles are required from conception to birth. The event associated with the "breaking of waters" is a landmark event in labor and delivery. Mechanical rupture of the CA membrane is part of the natural sequence of term delivery, but has serious implications when rupture occurs prior to term; preterm premature rupture of the CA membrane (PPROM) is associated with one-third of premature births. The current manuscript reviews PPROM from a clinical, anatomical, and mechanical perspective with a special focus on the clinically relevant fracture properties of these membranes. Emphasis is given to the link between membrane structure and properties at macroscopic and microscopic length scales. Because it has been demonstrated that the mechanical properties of prematurely failed membranes are not different from membranes of the same gestational age that have remained intact, membrane failure is a local process that must be explored in terms of local changes in structure and properties of isolated portions of the membrane. Future diagnostic techniques aimed at detection of changes in membrane structure (including thickness) and altered mechanical stiffness or strength may allow for prefailure diagnosis of membrane weak spots, thus opening the door for potential intervention and treatment techniques for preterm membrane rupture.
Characterization of the Cathode Spot (1987)

A general description of arc cathode spots is given with respect to structure, size, and temporal behavior. The density of the metal vapor plasma outside the spot is presented as a function of the coordinates, calculated on the basis of ion currents flowing to screens and probes. Extrapolation to the region within the spot indicates plasma densities in excess of 1025 m-3. Recent studies of spot current density suggest values of about 1012 A/m2. In this connection, the problem of the electrical conductivity of the spot plasma is discussed. Finally, experiments on spot lifetime and models of crater formation are reviewed.
GP120: Biologic Aspects of Structural Features (2001)

HIV-1 particles are decorated with a network of densely arranged envelope spikes on their surface. Each spike is formed of a trimer of heterodimers of the gp120 surface and the gp41 transmembrane glycoproteins. These molecules mediate HIV-1 entry into target cells, initiating the HIV-1 replication cycle. They are a target for entry-blocking drugs and for neutralizing Abs that could contribute to vaccine protection. The crystal structure of the core of gp120 has been recently solved. It reveals the structure of the conserved HIV-1 receptor binding sites and some of the mechanisms evolved by HIV-1 to escape Ab responses. The gp120 consists of three faces. One is largely inaccessible on the native trimer, and two faces are exposed but apparently have low immunogenicity, particularly on primary viruses. We have modeled HIV-1 neutralization by a CD4 binding site monoclonal Ab, and we propose that neutralization takes place by inhibition of the interaction between gp120 and the target cell membrane receptors as a result of steric hindrance. Knowledge of gp120 structure and function should assist in the design of new drugs as well as of an effective vaccine. In the latter case, circumventing the low immunogenicity of the HIV-1 envelope spike is a major challenge.
Demonstration of (Ca2+‐Mg2+‐ATPase activity of the neural cell adhesion molecule (1993)

In this study a possible association between (Ca(2+)-Mg2+)-ATPase activity and the neural cell adhesion molecule, NCAM, was investigated. The effects of various detergents on ATPase activity were evaluated, and it was found that solubilization of rat brain microsomes with 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, CHAPS, released a major fraction of the (Ca(2+)-Mg2+)-ATPase activity together with NCAM. Using different types of solid phase immunoadsorption it was shown that NCAM antibodies selectively isolated ATPase activity. Furthermore, agarose gel immunoelectrophoresis of solubilized brain microsomes followed by ATPase assay directly in the gel revealed ATPase activity associated with the NCAM immunoprecipitate. The NCAM-associated enzyme activity had a broad nucleoside triphosphate specificity and no strict selectivity for divalent cations, indicating that the enzyme probably is an ecto-ATPase. This raises a series of intriguing questions in relation to NCAM adhesive functions.
Potential Antipsoriatic Agents:  Lapacho Compounds as Potent Inhibitors of HaCaT Cell Growth (1999)

A number of lapacho compounds, representing the most common constituents of the inner bark of Tabebuia impetiginosa, together with some synthetic analogues, were evaluated in vitro against the growth of the human keratinocyte cell line HaCaT. With an IC(50) value of 0.7 microM, beta-lapachone (4) displayed activity comparable to that of the antipsoriatic drug anthralin. 2-Acetyl-8-hydroxynaphtho[2,3-b]furan-4,9-dione (7), which was prepared in a four-step synthesis from 2,8-dihydroxy-1, 4-naphthoquinone, was the most potent inhibitor among the known lapacho-derived compounds and inhibited cell growth with an IC(50) value of 0.35 microM. Furthermore, other active constituents of lapacho inhibited keratinocyte growth, with IC(50) values in the range of 0.5-3.0 microM. However, as already observed with anthralin, treatment of HaCaT cells with these potent lapacho compounds also caused remarkable damage to the plasma membrane. This was documented by leakage of lactate dehydrogenase into the culture medium, which significantly exceeded that of the vehicle control. Because of their potent activity against the growth of human keratinocytes, some lapacho-derived compounds appear to be promising as effective antipsoriatic agents.
Intraocular injection of tamoxifen‐loaded nanoparticles: a new treatment of experimental autoimmune uveoretinitis (2004)

In this study, we tested the efficiency of an intravitreal injection of tamoxifen, a non-steroidal estrogen receptor modulator, in retinal soluble antigen (S-Ag)-induced experimental autoimmune uveoretinitis (EAU). To increase the bioavailability of tamoxifen, we incorporated tamoxifen into polyethylene glycol (PEG)-coated nanoparticles (NP-PEG-TAM). The localization of the nanoparticles within the eye was investigated using fluorescent-labeled PEG-coated nanoparticles after injection into the vitreous cavity of rats with EAU. Some nanoparticles were distributed extracellularly throughout the ocular tissues, others were concentrated in resident ocular cells and in infiltrating macrophages. Whereas the injection of free tamoxifen did not alter the course of EAU, injection of NP-PEG-TAM performed 1-2 days before the expected onset of the disease in controls resulted in significant inhibition of EAU. NP-PEG-TAM injection significantly reduced EAU compared to injection of NP-PEG-TAM with 17beta-estradiol (E2), suggesting that tamoxifen is acting as a partial antagonist to E2. Diminished infiltration by MHC class II(+) inflammatory cells and low expression of TNF-alpha, IL-1beta, and RANTES mRNA were noted in eyes of NP-PEG-TAM-treated rats. Intravitreal injection of NP-PEG-TAM decreased S-Ag lymphocyte proliferation, IFN-gamma production by inguinal lymph node cells, and specific delayed-type hypersensitivity indicative of a reduced Th1-type response. It increased the anti-S-Ag IgG1 isotype indicating an antibody class switch to Th2 response. These data suggest that NP-PEG-TAM inhibition of EAU could result from a form of immune deviation. Tamoxifen-loaded nanoparticles may represent a new option for the treatment of experimental uveitis.
Human myocyte-specific enhancer factor 2 comprises a group of tissue-restricted MADS box transcription factors. (1992)

The MEF2 site is an essential element of muscle enhancers and promoters that is bound by a nuclear activity found, so far, only in muscle and required for tissue-specific transcription. We have cloned a group of transcription factors from human muscle that are responsible for this activity: They are present in muscle-specific DNA-binding complexes, have a target sequence specificity identical to that of the endogenous activity, and are MEF2 site-dependent transcriptional activators. These MEF2 proteins comprise several alternatively spliced isoforms from one gene and a related factor encoded by a second gene. All share a conserved amino-terminal DNA-binding domain that includes the MADS homology. MEF2 transcripts are ubiquitous but accumulate preferentially in skeletal muscle, heart, and brain. Specific alternatively spliced isoforms are restricted to these tissues, correlating exactly with the presence of endogenous MEF2 activity. Furthermore, MEF2 protein is detected only in skeletal and cardiac muscle nuclei and not in myoblast and nonmuscle cells. Thus, post-transcriptional regulation is important in the generation of tissue-specific MEF2 activity. Cardiac and smooth, as well as skeletal, muscles contain functionally saturating levels of MEF2 trans-activating factors that are absent in nonmuscle cells. Moreover, MEF2 is induced in nonmuscle cells by MyoD; however, MEF2 alone is insufficient to produce the full muscle phenotype. Implications for the molecular mechanisms of myogenesis are considered.
Probabilistic classification and clustering in relational data (2001)

Supervised and unsupervised learning methods have traditionally focused on data consisting of independent instances of a single type. However, many real-world domains are best described by relational models in which instances of multiple types are related to each other in complex ways. For example, in a scientific paper domain, papers are related to each other via citation, and are also related to their authors. In this case, the label of one entity (e.g., the topic of the paper) is often correlated with the labels of related entities. We propose a general class of models for classification and clustering in relational domains that capture probabilistic dependencies between related instances. We show how to learn such models efficiently from data. We present empirical results on two real world data sets. Our experiments in a transductive classification setting indicate that accuracy can be significantly improved by modeling relational dependencies. Our algorithm automatically induces a very natural behavior, where our knowledge about one instance helps us classify related ones, which in turn help us classify others. In an unsupervised setting, our models produced coherent clusters with a very natural interpretation, even for instance types that do not have any attributes. 1