gebhart/patrepeval huggingface dataset:
Hepatocellular cytokeratins as substrates of transglutaminases. (1989)

To examine whether hepatocellular cytokeratins can serve as substrates of transglutaminases (TG) TG-catalyzed incorporation of [3H]putrescine into, as well as cross-linking of, cytokeratins was studied. Purified guinea pig liver TG and mouse liver TG present in 105,000 x g supernatants were used as enzymes. Isolated mouse liver cytokeratin filaments, heterotypic tetramers (A2D2), as well as cytokeratin filaments reconstituted from isolated and column-purified liver cytokeratin polypeptides A and D served as substrates. Moreover, to more closely mimic the situation within the cell, mouse liver homogenate containing cytokeratins was also used. Cross-linked proteins were identified as cytokeratins by immunoblotting after sodium dodecyl sulfate-polyacrylamide gel electrophoresis using cytokeratin antibodies. The results indicated that mouse liver cytokeratins can serve as substrates of homologous and heterologous TG. However, liver cytokeratin components A and D differed in this respect. Depending on the experimental conditions either components D or components A were better substrates of TG-mediated cross-linking as revealed by increased high molecular weight aggregates, which failed to enter the gels, concomitant with a decrease of the monomer band suggesting a more intimate relationship between homologous cytokeratin polypeptides within the filament. The results presented provide the basis for studies of TG-induced cross-linking of cytoskeletal components in hepatocytes that may occur during liver cell injury associated with increased intracellular Ca2+ concentrations.
Interaction of a Monoclonal IgE-Specific Antibody with Cell-Surface IgE−FcεRI:  Characterization of Equilibrium Binding and Secretory Response (2004)

Aggregation of FcepsilonRI, the high-affinity cell-surface receptor for IgE antibody, is required for degranulation of basophils and mast cells, but not all receptor aggregates elicit this cellular response. The stereochemical constraints on clusters of FcepsilonRI that are able to signal cellular responses, such as degranulation, have yet to be fully defined. To improve our understanding of the properties of FcepsilonRI aggregates that influence receptor signaling, we have studied the interaction of 23G3, a rat IgG(1)(kappa) IgE-specific monoclonal antibody, with IgE-FcepsilonRI complexes on rat mucosal-type mast cells (RBL-2H3 line). We find that 23G3 is a potent secretagogue. This property and the structural features of 23G3 (two symmetrically arrayed IgE-specific binding sites) make 23G3 a potentially valuable reagent for investigating the relationship between FcepsilonRI clustering and FcepsilonRI-mediated signaling events. To develop a mathematical model of 23G3-induced aggregation of FcepsilonRI, we used fluorimetry and flow cytometry to quantitatively monitor equilibrium binding of FITC-labeled 23G3 intact Ab and its Fab' fragment to cell-surface IgE. The results indicate that IgE bound to FcepsilonRI expresses two epitopes for 23G3 binding; that 23G3 binds IgE resident on the cell surface with negative cooperativity; and that 23G3 appears to induce mostly but not exclusively noncyclic dimeric aggregates of FcepsilonRI. There is no simple relationship between receptor aggregation at equilibrium and the degranulation response. Further studies are needed to establish how 23G3-induced aggregation of IgE-FcepsilonRI correlates with cellular responses.
The Digital Revolution: A New Paradigm for Microfluidics (2008)

Abstract The digital revolution has come to microfluidics. In digital microfluidics (DMF), discrete droplets are manipulated by applying electrical fields to an array of electrodes. In contrast to microchannels, in DMF each sample and reagent is individually addressable, which facilitates exquisite control over chemical reactions. Here, we review the state‐of‐the‐art in DMF, with a discussion of device formats, actuation physics, and biological and nonbiological applications. Along the way, we identify the key players in the field, and speculate on the advances and challenges that lie ahead. As with other fronts in the digital revolution, there have been and will be unexpected developments as DMF matures, but we posit that the future is bright for this promising technology.
Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel (2005)

We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the approximately 1.5-nm alpha-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3'-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5'-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3'-threaded DNA or 5' DNA differ by approximately 30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5' end, assuming an asymmetric conformation. As a result, the bases of a 5'-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore.
Binding and neutralization of vascular endothelial growth factor (VEGF) and related ligands by VEGF Trap, ranibizumab and bevacizumab (2012)

Pharmacological inhibition of VEGF-A has proven to be effective in inhibiting angiogenesis and vascular leak associated with cancers and various eye diseases. However, little information is currently available on the binding kinetics and relative biological activity of various VEGF inhibitors. Therefore, we have evaluated the binding kinetics of two anti-VEGF antibodies, ranibizumab and bevacizumab, and VEGF Trap (also known as aflibercept), a novel type of soluble decoy receptor, with substantially higher affinity than conventional soluble VEGF receptors. VEGF Trap bound to all isoforms of human VEGF-A tested with subpicomolar affinity. Ranibizumab and bevacizumab also bound human VEGF-A, but with markedly lower affinity. The association rate for VEGF Trap binding to VEGF-A was orders of magnitude faster than that measured for bevacizumab and ranibizumab. Similarly, in cell-based bioassays, VEGF Trap inhibited the activation of VEGFR1 and VEGFR2, as well as VEGF-A induced calcium mobilization and migration in human endothelial cells more potently than ranibizumab or bevacizumab. Only VEGF Trap bound human PlGF and VEGF-B, and inhibited VEGFR1 activation and HUVEC migration induced by PlGF. These data differentiate VEGF Trap from ranibizumab and bevacizumab in terms of its markedly higher affinity for VEGF-A, as well as its ability to bind VEGF-B and PlGF.
Optically mediated nerve stimulation: Identification of injury thresholds (2007)

Results confirm that optical stimulation has the potential to become a powerful non-contact clinical and research tool for brief nerve stimulation with low risk of nerve thermal damage.
Clonal evolution of a follicular lymphoma: evidence for antigen selection. (1992)

The potential role antigens play in growth stimulation or in clonal selection of follicular lymphomas is unknown. To study this issue, we sequenced the immunoglobulin heavy chain variable region genes expressed by a follicular lymphoma from multiple biopsy specimens and also cloned and sequenced the corresponding germ-line variable gene from this patient. Comparison to the germ-line gene revealed numerous nucleotide substitutions in all of the lymphoma variable gene sequences. Some of the substitutions may have occurred in the nonmalignant precursor B cell that gave rise to this lymphoma because they were shared among all of the variable genes, but many of the mutations accumulated as the malignant clone expanded. The mutations were distributed in such a way that strongly suggested the majority of tumor cells had been positively selected through their antigen receptor. This was especially evident for the mutations that developed late in the clonal evolution of this lymphoma. These findings indicate that antigen stimulation may be involved in the growth of follicular lymphoma tumors.
Subcellular Compartmentation of the Diterpene Carnosic Acid and Its Derivatives in the Leaves of Rosemary (2001)

The potent antioxidant properties of rosemary (Rosmarinus officinalis) extracts have been attributed to its major diterpene, carnosic acid. Carnosic acid has received considerable attention in food science and biomedicine, but little is known about its function in the plant in vivo. We recently found that highly oxidized diterpenes increase in rosemary plants exposed to drought and high light stress as a result of the antioxidant activity of carnosic acid (S. Munné-Bosch, K. Schwarz, L. Alegre [1999] Plant Physiol 121: 1047-1052). To elucidate the significance of the antioxidant function of carnosic acid in vivo we measured the relative amounts of carnosic acid and its metabolites in different compartments of rosemary leaves. Subcellular localization studies show that carnosic acid protects chloroplasts from oxidative stress in vivo by following a highly regulated compartmentation of oxidation products. Carnosic acid scavenges free radicals within the chloroplasts, giving rise to diterpene alcohols, mainly isorosmanol. This oxidation product is O-methylated within the chloroplasts, and the resulting form, 11,12-di-O-methylisorosmanol, is transferred to the plasma membrane. This appears to represent a mechanism of a way out for free radicals from chloroplasts. Carnosic acid also undergoes direct O-methylation within the chloroplasts, and its derived product, 12-O-methylcarnosic acid, accumulates in the plasma membrane. O-methylated diterpenes do not display antioxidant activity, but they may influence the stability of the plasma membrane. This study shows the relevance of the compartmentation of carnosic acid metabolism to the protection of rosemary plants from oxidative stress in vivo.
Extending Aromatase-Inhibitor Adjuvant Therapy to 10 Years (2020)

Treatment with an aromatase inhibitor for 5 years as up-front monotherapy or after tamoxifen therapy is the treatment of choice for hormone-receptor–positive early breast cancer in postmenopausal women. Extending treatment with an aromatase inhibitor to 10 years may further reduce the risk of breast-cancer recurrence.
Potassium channels in articular chondrocytes (2012)

Chondrocytes are the resident cells of cartilage, which synthesize and maintain the extracellular matrix. The range of known potassium channels expressed by these unique cells is continually increasing. Since chondrocytes are non-excitable, and do not need to be repolarized following action potentials, the function of potassium channels in these cells has, until recently, remained completely unknown. However, recent advances in both traditional physiology and "omic" technologies have enhanced our knowledge and understanding of the chondrocyte channelome. A large number of potassium channels have been identified and a number of putative, but credible, functions have been proposed. Members of each of the potassium channel sub-families (calcium activated, inward rectifier, voltage-gated and tandem pore) have all been identified. Mechanotransduction, cell volume regulation, apoptosis and chondrogenesis all appear to involve potassium channels. Since evidence suggests that potassium channel gene transcription is altered in osteoarthritis, future studies are needed that investigate potassium channels as potential cellular biomarkers and therapeutic targets for treatment of degenerative joint conditions.
Parasitic reset in the programming transient of PCMs (2005)

We studied the programming dynamics in phase change memory cells. It is shown that programming in stand-alone cells is strongly affected by the parasitic capacitance in the measurement setup, leading to a current overshoot after threshold switching of the amorphous chalcogenide. This results in a parasitic melting and quenching of the active material, affecting the current distribution during program and the final phase distribution in the active material. The relevance of this artefact for real-device operation is discussed with reference to the value of the parasitic capacitance.
Co-translational, Intraribosomal Cleavage of Polypeptides by the Foot-and-mouth Disease Virus 2A Peptide (2003)

During co-translational protein import into the endoplasmic reticulum ribosomes are docked onto the translocon. This prevents inappropriate exposure of nascent chains to the cytosol and, conversely, cytosolic factors from gaining access to the nascent chain. We exploited this property of co-translational translocation to examine the mechanism of polypeptide cleavage by the 2A peptide of the foot-and-mouth disease virus. We find that the scission reaction is unaffected by placing 2A into a co-translationally targeted protein. Moreover, the portion of the polypeptide C-terminal to the cleavage site remains in the cytosol unless it contains its own signal sequence. The pattern of cleavage is consistent with the proposal that the 2A-mediated cleavage reaction occurs within the ribosome itself. In addition, our data indicate that the ribosome-translocon complex detects the break in the nascent chain and prevents any downstream protein lacking a signal sequence from gaining access to the endoplasmic reticulum.
Tension increase correlated to refractive-index change in fibers containing UV-written Bragg gratings (1995)

A strong axial tension increase induced by UV laser radiation is observed in the cores of single-mode optical fibers containing Bragg gratings, independently of the initial core stress. The induced index modulation of the gratings is linearly correlated to stress changes with a slope of (0.8 +/- 0.2) x 10(-4) mm(2)/kg. The phenomenon can be explained by a structural change of the glass in the fiber core into a more compact configuration.
Data compression: Techniques and applications : hardware and software considerations (1987)

From the Publisher:
Provides professionals and students with a path to faster data transmission times and reduced transmission costs with its in-depth examination of practical and easy-to-implement data-compression techniques. Retaining all data compression fundamentals from the first two editions, the Third Edition expands to include information on the structure and operation of several popular compression algorithms new to the market, including Microcom Networking Protocol (MNP) Class 5 data compression and MNP Class 7 Enhanced Data Compression. Numerous methods to enhance the efficiency of both character-oriented and statistical compression techniques are included as is a new chapter on character compression that discusses three methods to be used to obtain the special compression indicating character.
Ureaplasma urealyticum biovar specificity and diversity are encoded in multiple-banded antigen gene (1994)

Ureaplasma urealyticum is a commensal organism of the lower genital tract of females, but in a subpopulation of individuals, it can invade the upper genital tract. It is a significant cause of chorioamnionitis and neonatal morbidity and mortality. There are 14 recognized serovars of U. urealyticum; these can be divided into two distinct clusters or biovars. Biovar 1 is composed of serovars 1, 3, 6, and 14, Biovar 2 is composed of serovars 2, 4, 5, 7, 8, 9, 10, 11, 12, and 13. We previously identified a surface antigen, the multiple-banded (MB) antigen, which contains both serovar-specific and cross-reactive epitopes. Genotypic characterization of the C-terminal region of the MB antigen of serovar 3 indicates that serovar specificity and MB antigen size variation reside in that domain. In the present study, we used PCR analysis with primers derived from the serovar 3 MB antigen gene DNA sequence to determine if the MB antigen gene was present in the remaining 13 reference serovars as well as in invasive clinical isolates. The results indicated that not only was the MB antigen gene present in all serovars but that the genes' 5' regions were markers of biovar specificity and diversity. Further analysis of this region should reveal the phylogenetic relationship among serovars of U. urealyticum and, possibly, their invasive potential.
Expression and gene sequence of outer surface protein C of Borrelia burgdorferi reisolated from chronically infected mice (1994)

OspC from Borrelia burgdorferi reisolated from mice persistently infected with cloned spirochetes was examined. In all cases, the sequence of the ospC gene was identical to that of the original inoculant. We conclude that variation of ospC is not necessary for evasion of the host immune system.
Extracorporeal elimination of TNF-α-producing CD14dullCD16+ monocytes in leukocytapheresis therapy for ulcerative colitis (2006)

The present findings revealed the real target of proinflammatory CD14(dull)CD16(+) monocytes removed during LCAP treatment of UC and that LCAP might be used as an extracorporeal anti-TNF-alpha therapy, expanding the clinical applications of this procedure to include the treatment of Crohn's disease.
Real-time quadrature projection complex conjugate resolved Fourier domain optical coherence tomography (2006)

We present a novel algorithm for full-range imaging by suppression of the complex conjugate artifact in phase-shifting Fourier domain optical coherence tomography. This technique utilizes the projection of multiple phase-shifted interferograms onto an orthogonal basis set to reconstruct the complex interferogram. Full-range imaging with >30 dB suppression of the symmetric artifact is demonstrated using a 3 x 3 fiber coupler swept source OCT system, providing a depth range of 6.6mm with -8 dB roll-off in sensitivity at the depth boundaries relative to DC. Real-time display of full-range images of the anterior segment of the human eye acquired in vivo at a line rate of 6.67 kHz are presented.
Peptide-Polymer Conjugates: From Fundamental Science to Application (2013)

Peptide/protein-polymer conjugates make up a new class of soft matter comprising natural and synthetic building blocks. They have the potential to combine the advantages of proteins and synthetic polymers (i.e., the precise chemical structure and diverse functionalities of biomolecules and the stability and processability of synthetic polymers) to generate hybrid materials with properties yet to be realized with either component alone. Here we briefly discuss recent developments in the design, fundamental understanding, and self-assembly of various peptide-polymer conjugates, as well as emerging biological and nonbiological applications that range from nanomedicine, to separation, and beyond.
Insulin-like growth factor I protects and rescues hippocampal neurons against β-amyloid- and human amylin-induced toxicity (1997)

Insulin-like growth factors (IGF-I and IGF-II) are well known trophic factors and their specific receptors are uniquely distributed throughout the brain, being especially concentrated in the hippocampal formation. IGFs possess neurotrophic activities in the hippocampus, an area severely affected in Alzheimer disease. These data, together with the evidence that beta-amyloid (Abeta)-derived peptides likely play an important role in the neurodegenerative process observed in Alzheimer disease, led us to investigate if IGFs could be neuroprotective to hippocampal neurons against toxicity induced by amyloidogenic derivatives. Exposure of rat primary hippocampal neurons to different concentrations of Abeta25-35, Abeta1-40, Abeta1-42, and human amylin produced marked toxicity, while similar concentrations of two control Abeta peptides-reverse (Abeta40-1) and scrambled sequence (Abeta25-35)-and rat amylin failed to exhibit any significant effect on neuronal survival. IGF-I (10-100 nM) significantly protected hippocampal neurons against neurotoxicity induced by Abeta derivatives and human amylin. The homolog IGF-II was also effective although less potent than IGF-I suggesting the involvement of a typical IGF-I receptor in the observed neuroprotective effect. Most interestingly, IGF-I (10-100 nM) was even able to rescue neurons pre-exposed (up to 4 days) to amyloidogenic peptides. Other neurotrophic factors are reported to lack such rescuing abilities. These results suggest that IGF-I may have unique properties as a potent neuroprotective and neurorescuing agent against amyloid-related neurotoxicity.
Thiooligosaccharide Conjugate Vaccines Evoke Antibodies Specific for Native Antigens (2005)

Wenn S SO viel besser ist: Konjugierte Impfstoffe, die S-Glycoside enthalten, induzieren kohlenhydratspezifische Antikörper, die auch mit den entsprechenden O-Glycosiden reagieren, und umgekehrt. In allen vier untersuchten Systemen ist die antigenspezifische Antwort auf S-Glycoside entweder ähnlich der auf O-Glycoside oder besser als diese. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z502179_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Inappropriate apoptosis of salivary and lacrimal gland epithelium of immunodeficient NOD-scid mice. (1999)

These results suggest a potential apoptotic process dependent on Fas:FasL interactions occurring in NOD-scid glandular secretory epithelial cells in the absence of lymphocytic infiltration.
The effect of fluid/rock ratio on feldspar dissolution and illite formation under reservoir conditions (1986)

Abstract Experiments on the conversion of feldspar to illite reveal that variation of the fluid/rock ratio (flow rate) has a significant effect on the kinetics of feldspar dissolution and illite formation. Dissolution of albite in near-neutral KCl solution at 200°C and 500 bar shows that the Si and Na release rate per unit surface area of albite is faster with higher fluid/rock ratio. These results have application to the interpretation of secondary porosity formation. The experiments also reveal a special set of conditions under which rapid illite formation can occur. In contrast to the slow process of illite formation in neutral solution, there can be mass nucleation and growth of illite platelets on albite surfaces in an initially acidic solution with low fluid/rock ratio. In similar experiments with higher fluid/rock ratio, kaolinite forms instead of illite because there is insufficient solid to titrate the large volume of solution. This study suggests that illitization of feldspar or kaolinite may be triggered by a decreased rate of acidic fluid-influx during burial diagenesis.