gebhart/patrepeval huggingface dataset:
Emergence of a surface immunoglobulin recycling process during B lymphocyte differentiation. (1984)

Surface immunoglobulin (Ig)-mediated endocytosis has been investigated in rat B lymphocytes and plasma cells, using horseradish peroxidase (HRP)-labeled sheep anti-rat Ig Fab' fragment of antibody and HRP as monomeric ligands, respectively. Quantitative estimates of HRP activity associated either with plasma membrane or with endomembrane compartments were made in several experimental conditions. Binding of HRP-conjugate on B lymphocytes was followed by its endocytosis in combination with surface Ig, as shown by the progressive disappearance of plasma membrane-associated HRP activity. Between 1 and 6 h at 37 degrees C in presence of conjugate the total amount of cell-associated activity was constant. These results indicate that during this time no reappearance of surface Ig occurred by neosynthesis, by the expression of an intracellular pool or by the recycling in a free form of the previously internalized molecules. On the contrary, at saturating doses, internalization of HRP by anti-HRP plasma cells increased linearly with time at 37 degrees C in presence of antigen, when, during the same time, the plasma membrane HRP-binding capacity remained constant. Cycloheximide did not affect continuous HRP uptake. The existence of a large intracellular pool of receptors has been ruled out by experiments of removal of binding sites with pronase. In addition, monensin caused a progressive decrease in the number of surface receptors on plasma cells but not on B lymphocytes. Our data then indicate that, unlike B lymphocytes, plasma cells were able to recycle their surface Ig.
Model of Chemotherapy-Induced Myelosuppression With Parameter Consistency Across Drugs (2002)

This model predicted myelosuppression after administration of one of several different chemotherapeutic drugs. In addition, with fixed system-related parameters to proposed values, and only drug-related parameters estimated, myelosuppression can be predicted. We propose that this model can be a useful tool in the development of anticancer drugs and therapies.
Lymphocyte chemoattractant factor induces CD4-dependent intracytoplasmic signaling in lymphocytes (1991)

At present, a naturally occurring soluble ligand for CD4 has not been well described. There is much evidence to indicate that MHC class II molecules can bind to CD4; however, binding of intact class II molecules under physiologic conditions has been difficult to demonstrate. We investigated whether a previously reported human lymphokine, lymphocyte chemoattractant factor (LCF), which was described for its effects on human CD4+ lymphocytes and monocytes, could associate directly with CD4 and induce the generation of second messengers. In the present study, we demonstrate that CD4 affinity-purified natural and recombinant LCF induced a rise in intracellular calcium and increased inositol trisphosphate generation in normal human CD4+ lymphocytes and murine T cell hybridomas infected to express human CD4. Cell lines lacking human CD4 or expressing human CD4 molecules that lack the intracytoplasmic domain did not demonstrate a change in either calcium or inositol trisphosphate. The effect of LCF was blocked by coincubation with either anti-CD4 antibody or Fab fragments from anti-CD4 antibody. These studies demonstrate direct interaction of a lymphokine with CD4 and generation of second messengers as a result of the interaction.
Essential role of Mannose-binding lectin-associated serine protease-1 in activation of the complement factor D (2009)

The complement system is an essential component of innate immunity, participating in the pathogenesis of inflammatory diseases and in host defense. In the lectin complement pathway, mannose-binding lectin (MBL) and ficolins act as recognition molecules, and MBL-associated serine protease (MASP) is a key enzyme; MASP-2 is responsible for the lectin pathway activation. The function of other serine proteases (MASP-1 and MASP-3) is still obscure. In this study, we generated a MASP-1- and MASP-3-deficient mouse model (Masp1/3-/-) and found that no activation of the alternative pathway was observed in Masp1/3-/- serum. Mass spectrometric analysis revealed that circulating complement factor D (Df) in Masp1/3-/- mice is a zymogen (pro-Df) with the activation peptide QPRGR at its N terminus. These results suggested that Masp1/3-/- mice failed to convert pro-Df to its active form, whereas it was generally accepted that the activation peptide of pro-Df is removed during its secretion and factor D constitutively exists in an active form in the circulation. Furthermore, recombinant MASP-1 converted pro-Df to the active form in vitro, although the activation mechanism of pro-Df by MASP-1 is still unclear. Thus, it is clear that MASP-1 is an essential protease of both the lectin and alternative complement pathways.
Towards a Phylogeny of the Genus Vibrio Based on 16S rRNA Sequences (1992)

The inter- and intrageneric relationships of the genus Vibrio were investigated by performing a comparative analysis of the 16S rRNAs of 10 species, including four pathogenic representatives. The results of immunological and 5S rRNA studies were confirmed in that the genus is a neighboring taxon of the family Enterobacteriaceae. With regard to the intrageneric structure, Vibrio alginolyticus, Vibrio campbellii, Vibrio natriegens, Vibrio harveyi, Vibrio proteolyticus, Vibrio parahaemolyticus, and Vibrio vulnificus form the core of the genus, while Vibrio (Listonella) anguillarum, Vibrio diazotrophicus, and Vibrio hollisae are placed on the outskirts of the genus. Variable regions around positions 80, 180, and 450 could be used as target sites for genus- and species-specific oligonucleotide probes and polymerase chain reaction primers to be used in molecular identification.
Active Site of α-Chymotrypsin Activation by Association-Desolvation (1970)

High reactivity toward alpha-chymotrypsin is observed for derivatives of beta-arylpropionic acids of varied structure-L-alpha-acylamido compounds, D-cyclized compounds, and, now, L-glycolamide esters. Compensating enthalpy and entropy effects are observed which appear to be caused by changes in water of solvation. High reactivity with varied structure, and physical evidence, appear to rule out induced fit and distortion as important for this enzyme. The high reactivity results from precise fit of the hydrolyzing group at the critical serine-imidazole junction, resulting from binding of the aryl group and restriction of rotation. Part of the energy of binding is used to desolvate the reactant groups of substrate and enzyme, decreasing activation energies by several kilocalories and raising reactivity by 10(3) or more. Solvation by water stabilizes many compounds, allowing them to be present in solution in biological systems. Their reactions may occur as their reactivity is increased when they are desolvated and brought from solution into association with reactive groups in enzymes, membranes, and structured particles.
Adenosine Mimetics as Inhibitors of NAD+-Dependent Histone Deacetylases, from Kinase to Sirtuin Inhibition (2006)

NAD+-dependent histone deacetylases, sirtuins, cleave acetyl groups from lysines of histones and other proteins to regulate their activity. Identification of potent selective inhibitors would help to elucidate sirtuin biology and could lead to useful therapeutic agents. NAD+ has an adenosine moiety that is also present in the kinase cofactor ATP. Kinase inhibitors based upon adenosine mimesis may thus also target NAD+-dependent enzymes. We present a systematic approach using adenosine mimics from one cofactor class (kinase inhibitors) as a viable method to generate new lead structures in another cofactor class (sirtuin inhibitors). Our findings have broad implications for medicinal chemistry and specifically for sirtuin inhibitor design. Our results also raise a question as to whether selectivity profiling for kinase inhibitors should be limited to ATP-dependent targets.
Wireless telesurveillance system for detecting dementia (2011)

Objective We hypothesized path tortuosity (an index of casual locomotor variability) measured by a movement telesurveillance system would be suitable for assisted living facility residents clinically diagnosed with dementia. Background We examined the relationship of dementia to path tortuosity and to movement speed and path length variability, both of which increase in dementia. Methods Daytime movements of 25 elders (19 female; 14 with dementia; average age 80.6) were monitored for 30 days using radio transponders measuring location with a maximum accuracy of 20 cm. After 30 days, the Mini Mental State Exam (MMSE) and Revised Algase Wandering Scale-Community Version (RAWS-CV) were administered. Results Fractal Dimension (Fractal D), a measure of path tortuosity, correctly classified all but 2 residents with dementia; sensitivity 0.857, specificity 0.818 while the MMSE had 6 misclassifications, a sensitivity of 0.857 and a specificity of 0.727. Individual logistic regressions of dementia diagnosis on predictors MMSE and Fractal D were significant, but a logistic regression using both predictors found Fractal D marginally predictive of dementia (p=0.055) while the MMSE was not (p=0.168). Although significantly correlated with Fractal D, rate of travel and mean path distance were not predictive of dementia. Fractal D correlated negatively with overall MMSE (r= -0.44, n=25, p < 0.05) but the relationship was mediated by MMSE Geographical Orientation items. Fractal D was unrelated to the RAWS-CV. Conclusions Telesurveillance-measured path tortuosity is greater in persons diagnosed with dementia. Persons with dementia have relatively more impaired spatial memory which is required for successful navigation. Application Automatic monitoring of direction, length and speed of unconstrained movements.
Revealing uncertainty for information visualization (2008)

Uncertainty in data occurs in domains ranging from natural science to medicine to computer science. By developing ways to include uncertainty in our information visualizations we can provide more accurate visual depictions of critical datasets. One hindrance to visualizing uncertainty is that we must first understand what uncertainty is and how it is expressed by users. We reviewed existing work from several domains on uncertainty and conducted qualitative interviews with 18 people from diverse domains who self-identified as working with uncertainty. We created a classification of uncertainty representing commonalities in uncertainty across domains and that will be useful for developing appropriate visualizations of uncertainty.
Salt effects on histone subunit interactions as studied by fluorescence spectroscopy (1989)

The salt concentration dependence of the aggregation properties of calf thymus and chicken erythrocyte histones has been investigated by using fluorescence spectroscopy. The isolated H2A/H2B and H3/H4 subunit preparations were labeled with 5-(dimethylamino)naphthalene-1- sulfonyl (dansyl). This long-lived fluorescence probe allows for the observation of rotations due to tumbling of the particle and thus is a probe for changes in the size of macromolecular assemblies. The fluorescence polarization and lifetime were measured as a function of salt concentration for these isolated preparations. Next, each labeled preparation was reconstituted with its unlabeled complement, and the salt concentration dependence of histone core octamer interactions was investigated in the same manner. Salt-induced core particle formation was observed by monitoring the dansyl-labeled dimers for both the calf thymus and chicken erythrocyte preparations. Evidence for subunit dissociation of the isolated H2A-H2B preparations was also found, as well as aggregation of the isolated H3/H4 subunits to at least dimers of tetramers. The calf thymus H3/H4 preparation was in aggregated form under all conditions studied, whereas the chicken erythrocyte H3/H4 only formed aggregates at high protein or salt concentrations. We have found evidence that the dimer can displace the tetramer from the higher order aggregate in order to form core particles. Such competition between the subunit interfaces in the histone system suggests that they may play a regulatory role in histone-DNA interactions.
Natural Hook-and-loop Fasteners: Anatomy, Mechanical Properties, And Attachment Force Of The Jointed Hooks Of The Galium Aparine Fruit (2002)

Diaspores of many flowering plants are adapted to dispersal by mechanical interlocking to animal fur and feathers. In this study, the attachment force of the fruit hooks of Galium aparine plants is measured using a force tester. It ranges from 9.37 to 44.89 mN (x=23.23, SD=8.13, n=50) and depends on the hook size. Using light and scanning electron microscopy, it is found that the hook consists of two parts, a joint-like base and a hooked cone. The latter originates from the outer layer of the pericarp and may be considered as a modified hollow unicellular trichome. Staining of resin-embedded semithin sections with safranin and fast green shows that the hook wall contains cellulose and lignin. To calculate the Young's modulus, a mathematical model describing the effect of the complex hook geometry was applied. The hooks with and without the base are characterised by different values of the elastic moduli: 2.02 GPa and 23.20 GPa, respectively. Experimental data show that jointed hooks are better adapted to resist forces in different directions compared with non-jointed hooks. This effect is not present in many other plant hooks and is also unknown in industrial hook-and-loop fasteners.
P2X7 receptor signaling contributes to tissue factor–dependent thrombosis in mice (2011)

Thrombosis is initiated by tissue factor (TF), a coagulation cofactor/receptor expressed in the vessel wall, on myeloid cells, and on microparticles (MPs) with variable procoagulant activity. However, the molecular pathways that generate prothrombotic TF in vivo are poorly defined. The oxidoreductase protein disulfide isomerase (PDI) is thought to be involved in the activation of TF. Here, we found that in mouse myeloid cells, ATP-triggered signaling through purinergic receptor P2X, ligand-gated ion channel, 7 (P2X7 receptor; encoded by P2rx7) induced activation (decryption) of TF procoagulant activity and promoted release of TF+ MPs from macrophages and SMCs. The generation of prothrombotic MPs required P2X7 receptor-dependent production of ROS leading to increased availability of solvent-accessible extracellular thiols. An antibody to PDI with antithrombotic activity in vivo attenuated the release of procoagulant MPs. In addition, P2rx7-/- mice were protected from TF-dependent FeCl3-induced carotid artery thrombosis. BM chimeras revealed that P2X7 receptor prothrombotic function was present in both hematopoietic and vessel wall compartments. In contrast, an alternative anti-PDI antibody showed activities consistent with cellular activation typically induced by P2X7 receptor signaling. This anti-PDI antibody restored TF-dependent thrombosis in P2rx7-/- mice. These data suggest that PDI regulates a critical P2X7 receptor-dependent signaling pathway that generates prothrombotic TF, defining a link between inflammation and thrombosis with potential implications for antithrombotic therapy.
Current approaches to therapy for indolent non-Hodgkin's lymphoma. (1998)

Progress in the treatment of indolent non-Hodgkin's lymphoma has been slow and the disease remains incurable despite the relatively long median survival of patients. Decades of clinical trials resulted in standard chemotherapy regimens that produced relatively identical results. Two recent events, however, offer great optimism for future therapeutic progress. First, our understanding of the biology and immunology of lymphoid malignancies has increased remarkably. Second, there are a large number of new and unique chemotherapeutic and biological agents entering into clinical trials.
COOH-Terminal Src Kinase–Mediated c-Jun Phosphorylation Promotes c-Jun Degradation and Inhibits Cell Transformation (2006)

The oncoprotein c-Jun is a component of the activator protein-1 transcription factor complex, which is involved in cellular proliferation, transformation, and death. The stabilization of c-Jun is critically important for its function. The phosphorylation of c-Jun by c-Jun NH(2)-terminal kinase 1 and extracellular signal-regulated protein kinases reduces c-Jun ubiquitination resulting in increased stabilization of c-Jun. In this report, we showed that COOH-terminal Src kinase (CSK) binds with and phosphorylates c-Jun at Y26 and Y170. Phosphorylation of c-Jun by CSK, in opposition to c-Jun NH(2)-terminal kinase 1 and extracellular signal-regulated protein kinases, promoted c-Jun degradation and reduced stability. By promoting c-Jun degradation, CSK helps to maintain a low steady-state level of c-Jun, thereby inhibiting activator protein-1 activity and cell transformation caused by c-Jun. These results indicated that this function of CSK controls cell proliferation under normal growth conditions and may have implications for CSK loss of function in carcinogenesis.
Enhancement of diffraction-based biosensing using porous structures and electromagnetic surface states (2010)

Diffraction-based biosensors are often based on the adsorption of a target material on a grating made of thin layers, where the adsorption is detected by a modification of the diffracted signal. In this communication we discuss two strategies for enhancing this detection process. The first is based on the use of grating structures made of porous elements, where sensing is based on target molecules penetrating into the elements and modifying their effective index of refraction. The second is a resonant process where the effectiveness of the grating is enhanced by the coupling to surface electromagnetic states, in particular Bloch surface waves that exist at the interface between a homogeneous medium and a photonic crystal.
New Compounds. Some Diamino Peptides (1942)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Compounds. Some Diamino PeptidesRichard Baltzly, Walter Ide, and Johannes BuckCite this: J. Am. Chem. Soc. 1942, 64, 9, 2231Publication Date (Print):September 1, 1942Publication History Published online13 November 2002Published inissue 1 September 1942https://pubs.acs.org/doi/10.1021/ja01261a600https://doi.org/10.1021/ja01261a600research-articleACS PublicationsRequest reuse permissionsArticle Views89Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Functional and Probiotic Attributes of an Indigenous Isolate of Lactobacillus plantarum (2009)

The indigenous Lactobacillus plantarum Lp9 exhibited high resistance against low pH and bile and possessed antibacterial, antioxidative and cholesterol lowering properties with a potential for exploitation in the development of indigenous functional food or nutraceuticals.
Structure and developmental regulation of a wheat gene encoding the major chlorophyll a/b-binding polypeptide. (1985)

A genomic clone for a major chlorophyll a/b-binding polypeptide of the light-harvesting complex has been sequenced from wheat. This gene, whAB1.6, encodes a 70-nucleotide 5'-nontranslated spacer, a 34-amino-acid NH2-terminal extension, i.e., the transit peptide, and a mature coding protein of 232 amino acid residues. The exact molecular weight of the precursor polypeptide is 28,560. The transit peptide is basic and is rich in serines. No intervening sequences are found in this gene. The transcription start site of the whAB1.6 gene occurs at AAAC as determined by S1 nuclease analysis. Putative regulatory sequences occur upstream of the gene at -25 (TTTAAATA) and at -72 (CCAACCA). Northern blots show a single RNA species estimated to be 1,100 nucleotides. Heterogeneity of the RNA population is demonstrated in S1 nuclease analyses with a 5'-end-labeled fragment that extends 191 nucleotides into the mature protein coding sequence. At least seven different transcripts can be recognized. The highest levels of RNA transcribed from the whAB1.6 gene are found in the basal segments of the wheat leaf, whereas other chlorophyll a/b-binding transcripts in the cell show a different pattern of abundance. As a control, we show that roots do not contain chlorophyll a/b-binding RNA. The most abundant RNA species shows an interrupted homology with the whAB1.6 gene at the start of the mature protein coding sequence; another species shows homology beginning at the start of the transit peptide and does not include the nontranslated region. Chlorophyll a/b-binding polypeptides accumulate toward the tip of the leaf as shown by Western blot analysis of total thylakoid proteins.
Structure and distribution of modules in extracellular proteins (1996)

It has become standard practice to compare new amino-acid and nucleotide sequences with existing ones in the rapidly growing sequence databases. This has led to the recurring identification of certain sequence patterns, usually corresponding to less than 300 amino-acids in length. Many of these identifiable sequence regions have been shown to fold up to form a ‘domain’ structure; they are often called protein ‘modules’ (see definitions below). Proteins that contain such modules are widely distributed in biology, but they are particularly common in extracellular proteins.
212Bismuth Linked to an Antipancreatic Carcinoma Antibody: Model for Alpha-Particle-Emitter Radioimmunotherapy (1988)

For comparison of cytotoxicity from alpha-particle irradiation with that from conventional x-irradiation, 212Bi, an alpha-emitting radionuclide, was attached to a monoclonal antibody that recognizes a cell surface antigen on human pancreatic carcinoma cells. For a given level of survival, the 212Bi-antibody complex was found to be approximately 20 times more efficient in cell killing than x-irradiation and 5 times more cytotoxic when compared with the cytotoxicity of an antigen-negative cell line or an isotype-matched control antibody. High linear energy transfer radioimmunotherapy using alpha emitters linked to monoclonal antibodies may be useful in vivo and in vitro for selectively killing target cell populations, especially those resistant to other forms of treatment.
P‐29: Modeling of Amorphous Oxide Semiconductor Thin Film Transistors and Subgap Density of States (2008)

Abstract We report a model of the carrier transport and the subgap density of states in a representative amorphous oxide semiconductor, amorphous InGaZnO 4 (a‐IGZO), for device simulation of a‐IGZO TFTs. Compared to hydrogenated amorphous silicon, a‐IGZO exhibits much lower densities of tail states and deep gap states, leading to the small subthreshold swings and high mobilities.