gebhart/patrepeval huggingface dataset:
CD27-CD27 ligand/CD70 interactions enhance alloantigen-induced proliferation and cytolytic activity in CD8+ T lymphocytes. (1995)

To study the role of CD27-CD27 ligand (CD27L)/CD70 interactions in the generation of murine allospecific T cell responses, SF9 cells or cell membranes expressing recombinant human CD70 were added to in vitro MLC containing C57BL/6 (H-2b) responder cells and class I and II MHC disparate H-2b/d stimulator cells. Alloantigen-specific CTL generation, CD8+ T cell proliferation, and levels of N-alpha-benzyloxycarbonyl-L-lysine thiobenzyl esterase activity were enhanced in the presence of human CD27L/CD70 expressed on SF9 cell membranes. Enhancement of CD8+ T cell responses occurred in the absence of any discernible effects on CD4+ T cell proliferation or IL-2 responses. Additional studies demonstrated that CD27L/CD70-expressing membranes enhanced proliferative responses to class I MHC differences but had no effect on proliferative responses to class II MHC disparities. Enhancement of allospecific CTL generation was also observed when CD27L/CD70-expressing membranes were added only during the last 24 to 48 h of 5-day MLC. Thus, the present studies suggest that CD27-CD27L/CD70 interactions can selectively enhance differentiation of Ag-specific CD8+ T cell effector mechanisms under conditions in which Th cell responses are not altered.
pH on–off switching of antibody-hapten binding by site-specific chemical modification of tyrosine (1994)

Tetranitromethane (TNM) chemically mutates the binding sites of antibodies so that the nitrated antibodies exhibit pH-dependent binding near physiological pH. Three monoclonal antibodies were selectively modified, each under different conditions, with the resultant loss of binding activity at pH > 8 which is recovered at pH < 6. Recovery and loss of binding are ascribed to the protonation and deprotonation, respectively, of the hydroxyl group of the resulting 3-nitrotyrosine side chain (pKa approximately 7) at the binding site of these antibodies. pH on-off dependency of binding activity, common to all TNM-modified antibodies studied by us so far, may find use in a variety of applications in which controlled modulation under mild conditions is required.
Characterizing the Mechanism of Action of Double-Stranded RNA Activity against Western Corn Rootworm (Diabrotica virgifera virgifera LeConte) (2012)

RNA interference (RNAi) has previously been shown to be effective in western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) larvae via oral delivery of synthetic double-stranded RNA (dsRNA) in an artificial diet bioassay, as well as by ingestion of transgenic corn plant tissues engineered to express dsRNA. Although the RNAi machinery components appear to be conserved in Coleopteran insects, the key steps in this process have not been reported for WCR. Here we characterized the sequence of events that result in mortality after ingestion of a dsRNA designed against WCR larvae. We selected the Snf7 ortholog (DvSnf7) as the target mRNA, which encodes an essential protein involved in intracellular trafficking. Our results showed that dsRNAs greater than or equal to approximately 60 base-pairs (bp) are required for biological activity in artificial diet bioassays. Additionally, 240 bp dsRNAs containing a single 21 bp match to the target sequence were also efficacious, whereas 21 bp short interfering (si) RNAs matching the target sequence were not. This result was further investigated in WCR midgut tissues: uptake of 240 bp dsRNA was evident in WCR midgut cells while a 21 bp siRNA was not, supporting the size-activity relationship established in diet bioassays. DvSnf7 suppression was observed in a time-dependent manner with suppression at the mRNA level preceding suppression at the protein level when a 240 bp dsRNA was fed to WCR larvae. DvSnf7 suppression was shown to spread to tissues beyond the midgut within 24 h after dsRNA ingestion. These events (dsRNA uptake, target mRNA and protein suppression, systemic spreading, growth inhibition and eventual mortality) comprise the overall mechanism of action by which DvSnf7 dsRNA affects WCR via oral delivery and provides insights as to how targeted dsRNAs in general are active against insects.
Cloning of a cDNA encoding diacylglycerol acyltransferase from Arabidopsis thaliana and its functional expression (1999)

Triacylglycerols are the most important storage lipids in most plants and animals. Acyl-CoA:diacylglycerol acyltransferase (EC 2.3.1.20) catalyzes the final step of the pathway of triacylglycerol synthesis and is the only step which is unique to this process. Diacylglycerol acyltransferase is required for the synthesis of storage oil in a wide range of oil-bearing seeds and fruits and in floral structures such as petals, anthers and pollen. We describe the first cloning and functional expression of a cDNA encoding diacylglycerol acyltransferase from a plant. The cDNA, cloned from Arabidopsis thaliana, encodes a 520 amino acid protein with a predicted molecular mass of 59.0 kDa which shares 38% amino acid sequence identity with diacylglycerol acyltransferase from mouse. When expressed in insect cell cultures, the protein catalyzes the synthesis of [14C]triacylglycerol from [14C]diacylglycerol and acyl-CoA. Primer extension analysis revealed that the transcription begins 225 bases before the translation start site, yielding an unusually long 5' untranslated region. The gene is expressed in a wide range of tissues but most strongly in developing embryos and petals of flowers.
Involvement of vascular endothelial growth factor in exercise induced bronchoconstriction in asthmatic patients (2002)

Excessive production of VEGF in asthmatic airways may contribute to the pathogenesis of EIB via increased airway vascular permeability.
Pancreatic Cancer: What About Screening and Detection? (2013)

Pancreatic cancer is the fourth leading cause of cancer-related death in both sexes in the United States. In 2013, it is expected to account for 7% of all female cancer deaths and 6% of all male cancer deaths in the USA. Late presentation of the disease and poor prognosis even after complete operative resection, justify the necessity for early detection of pancreatic cancer as well as identifying high-risk individuals (screening). Herein, the authors summarize the data presented at the 2013 American Society of Clinical Oncology (ASCO) Annual Meeting regarding screening and early detection of pancreatic cancer (Abstracts #4045 and #4052).
Tunable dielectrophoresis for sheathless 3D focusing (2015)

We report on a novel tunable insulator-based dielectrophoresis (TiDEP) for three-dimensional, sheathless, single-stream cell and bacteria focusing. For the first time, objects as small as sub-micron sized bacteria are continuously focused in the center of a channel without sheath flows. TiDEP is realized by sandwiching a 3D microfluidic channel with high aspect ratio sidewalls between two conductive, featureless indium tin oxide (ITO) glass substrates. The tunable electric field pattern is realized by deforming the channel's sidewalls to change its cross-sectional geometry. Compared to prior DEP works, this new TiDEP can provide a long DEP interaction distance to focus small objects into a single stream in the center of a channel in high-speed flows.
Cross-linking of alpha 2-plasmin inhibitor to fibrin catalyzed by activated fibrin-stabilizing factor. (1982)

During blood coagulation alpha 2-plasmin inhibitor (alpha 2PI) is cross-linked with fibrin by an activated fibrin-stabilizing factor (FSFa) plasma transglutaminase, activated coagulation factor XIII). When alpha 2PI was treated with FSFa in the absence of acceptor amino groups, the inhibitor lost more than 90% of its capacity to be cross-linked to fibrin because of hydrolysis of the gamma-carboxamides of FSFa-susceptible glutamine residues. Chemical modifications of the inhibitor's lysine epsilon-amino groups did not affect the cross-linking capacity of the inhibitor with fibrin, whereas the same chemical modifications in fibrinogen resulted in a remarkable loss of cross-linking capacity. These observations suggest that alpha 2PI plays a role as an acyl donor with its FSFa-susceptible glutamine residues in the cross-linking reaction with fibrin, and fibrin serves as an acyl acceptor with its lysine residues. The number of FSFa-susceptible glutamine residues/molecule of the inhibitor was estimated by measuring the maximum incorporation of [3H]histamine into the inhibitor and by analyzing the distribution of radioactivity in a tryptic digest of [14C]histamine-incorporated alpha 2PI.l It was found that each inhibitor molecule has one glutamine residue that is most susceptible to FSFa. When the radioactive histamine-incorporated inhibitor was reacted with excess amounts of plasmin, a small fragment carrying all the released radioactivity was rapidly released from the NH2-terminal part of the inhibitor moiety of the complex. The NH2-terminal amino acid sequence of the inhibitor was analyzed before and after treatment with FSFa or before and after incorporation of radioactive histamine. The glutamine residue at the second position from the NH2-terminal end was converted to a glutamic acid residue when the inhibitor was treated with FSFa. When the radioactive histamine-incorporated inhibitor ws analyzed, the radioactivity was found predominantly at the second position from the NH2-terminal end. These results indicate that the glutamine residue susceptible to FSFa in alpha 2PI is located next to the NH2-terminal residue.
The Optogenetic Catechism (2009)

An emerging set of methods enables an experimental dialogue with biological systems composed of many interacting cell types--in particular, with neural circuits in the brain. These methods are sometimes called "optogenetic" because they use light-responsive proteins ("opto-") encoded in DNA ("-genetic"). Optogenetic devices can be introduced into tissues or whole organisms by genetic manipulation and be expressed in anatomically or functionally defined groups of cells. Two kinds of devices perform complementary functions: Light-driven actuators control electrochemical signals, while light-emitting sensors report them. Actuators pose questions by delivering targeted perturbations; sensors (and other measurements) signal answers. These catechisms are beginning to yield previously unattainable insight into the organization of neural circuits, the regulation of their collective dynamics, and the causal relationships between cellular activity patterns and behavior.
<title>Perception of binary texture and the generation of stochastic halftone screens</title> (1995)

Stochastic halftone screens can be used in ordered dither halftoning algorithms to generate binary image textures that have shaped power spectra. This paper will examine some techniques for modeling perception of binary texture. Alternative methods for constructing grayscale dot profiles will be discussed, with the aim of improving the visual optimality of the entire grayscale dot profile.
The role of nutrition in promoting growth in pre-term infants with bronchopulmonary dysplasia: a prospective non-randomised interventional cohort study (2014)

On the basis of the above findings, it seems that improved nutritional management promotes post-natal ponderal growth in pre-term infants with BPD.
T Cell Growth Factor: Parameters of Production and a Quantitative Microassay for Activity (1978)

Several soluble factors have recently been associated with the proliferation and differentiation of thymus-derived lymphocytes. One of these factors present in medium conditioned by T cell mitogen-stimulated lymphocytes has the ability to promote the long-term culture of normal and antigen-specific cytotoxic T cells. We report a method to test for this proliferative stimulus in the form of a sensitive microassay based upon the tritiated-thymidine incorporation of continuous murine tumor-specific cytotoxic T cell lines (CTLL). The microassay requires microliter quantitites of sample fluid and is amenable to quantitative analysis. This highly reproducible, quantitative assay for T cell growth factor (TCGF) has allowed investigation as to the kinetics of TCGF generation and has revealed that T lymphocytes are required for its production. Further investigation has supported the notion that this nonspecies-specific factor is actively removed from tissue culture medium by the proliferation of either T cell mitogen-activated lymphocytes or CTLL.
Enzymatic Activation of Second-Generation Dendritic Prodrugs:  Conjugation of Self-Immolative Dendrimers with Poly(ethylene glycol) via Click Chemistry (2006)

Single-triggered disassemble dendrimers were recently developed and introduced as a potential platform for a multi-prodrug. These unique structural dendrimers can release all of their tail units through a self-immolative chain fragmentation initiated by a single cleavage at the dendrimer's core. There are several examples for the bioactivation of first-generation self-immolative dendritic prodrugs. However, enzymatic activation failed for second-generation self-immolative dendrimers. The hydrophobic large molecular structure of the dendritic prodrugs results in aggregation under aqueous conditions and prevented the enzyme from reaching the triggering substrate. Here we show a simple solution for the enzymatic activation of second-generation self-immolative dendrimers. Poly(ethylene glycol) (PEG) was conjugated to the dendritic platform via click chemistry. The poly(ethylene glycol) tails significantly decreased the hydrophobic properties of the dendrimers and thereby prevented aggregate formation. We designed and synthesized a dendritic prodrug with four molecules of the anticancer agent camptothecin and a trigger that can be activated by penicillin-G-amidase. The PEG5000-conjugated, self-immolative dendritic prodrug was effectively activated by penicillin-G-amidase under physiological conditions and free camptothecin was released to the reaction media. Cell-growth inhibition assays demonstrated increased toxicity of the dendritic prodrug upon incubation with the enzyme.
Polymorphic C-terminal β-Sheet Interactions Determine the Formation of Fibril or Amyloid β-derived Diffusible Ligand-like Globulomer for the Alzheimer Aβ42 Dodecamer (2010)

The relationship between amyloid deposition and cellular toxicity is still controversial. In addition to fibril-forming oligomers, other soluble Aβ forms (amyloid β-derived diffusible ligands (ADDLs)) were also suggested to form and to present different morphologies and mechanisms of toxicity. One ADDL type, the "globulomer," apparently forms independently of the fibril aggregation pathway. Even though many studies argue that such soluble Aβ oligomers are off fibril formation pathways, they may nonetheless share some structural similarity with protofibrils. NMR data of globulomer intermediates, "preglobulomers," suggested parallel in-register C-terminal β-sheets, with different N-terminal conformations. Based on experimental data, we computationally investigate four classes of Aβ dodecamers: fibril, fibril oligomer, prefibril/preglobulomer cluster, and globulomer models. Our simulations of the solvent protection of double-layered fibril and globulomer models reproduce experimental observations. Using a single layer Aβ fibril oligomer β-sheet model, we found that the C-terminal β-sheet in the fibril oligomer is mostly curved, preventing it from quickly forming a fibril and leading to its breaking into shorter pieces. The simulations also indicate that β-sheets packed orthogonally could be the most stable species for Aβ dodecamers. The major difference between fibril-forming oligomers and ADDL-like oligomers (globulomers) could be the exposure of Met-35 patches. Although the Met-35 patches are necessarily exposed in fibril-forming oligomers to allow their maturation into fibrils, the Met-35 patches in the globulomer are covered by other residues in the orthogonally packed Aβ peptides. Our results call attention to the possible existence of certain "critical intermediates" that can lead to both seeds and other soluble ADDL-like oligomers.
Fabrication of hybrid superconductor–semiconductor nanostructures by integrated ultraviolet-atomic force microscope lithography (1997)

Hybrid superconductor–semiconductor (S–Sm) nanostructures were fabricated by integrating standard ultraviolet photolithography and direct patterning of photoresist with an atomic force microscope (AFM). This novel technology was used to fabricate Nb–InAs–Nb weak links comparable in length to the coherence length. These structures exhibit high critical currents up to 10 μA/μm in planar geometry at 0.3 K. The fabrication protocol is based on the modification of photolithographically defined patterns by AFM static ploughing of the photoresist. Wet chemical etching is subsequently used for the definition of nanoscale S–Sm–S bridges. Additionally Lift-off procedures allowed the fabrication of submicron superconducting bridges. Successful fabrication of the nanostructures was verified by electrical characterization and by AFM and scanning electron microscope structural characterization.
A novel reassortant canine H3N1 influenza virus between pandemic H1N1 and canine H3N2 influenza viruses in Korea (2011)

During recent canine influenza surveillance in South Korea, a novel H3N1 canine influenza virus (CIV) that is a putative reassortant between pandemic H1N1 2009 and H3N2 CIVs was isolated. Genetic analysis of eight genes of the influenza virus revealed that the novel H3N1 isolate presented high similarities (99.1-99.9 %) to pandemic influenza H1N1, except for in the haemagglutinin (HA) gene. The HA gene nucleotide sequence of the novel CIV H3N1 was similar (99.6 %) to that of CIV H3N2 isolated in Korea and China. Dogs infected with the novel H3N1 CIV did not show any notable symptoms, in contrast to dogs infected with H3N2 CIV. Despite no visible clinical signs of disease, nasal shedding of virus was detected and the infected dogs presented mild histopathological changes.
Rapid 3D radiofrequency field mapping using catalyzed double‐angle method (2009)

A new method is presented for rapid and accurate large volumetric radiofrequency (RF) field (B(1) (+)) mapping. This method is a modification of the double-angle method (DAM), which accelerates imaging speed and applies 3D acquisition to improve B(1) (+) measurement accuracy. It reduces repetition time and scan time by introducing a catalyzation RF pulse chain at the end of each DAM repetition cycle. The catalyzation pulse chain ensures that, after each TR period, the longitudinal magnetizations reach the same state for both measurements at two flip angles for the DAM so that the long TR requirement (TR >or= 5 T(1)) for complete relaxation of longitudinal magnetization of DAM becomes unnecessary. A multi-echo imaging sequence is additionally incorporated to further improve the efficiency of data acquisition. Simulations demonstrate an excellent flip angle measurement accuracy for catalyzed DAM even with TR << T(1). Phantom and in vivo volunteer studies are presented to demonstrate the catalyzation effect upon B(1)(+) mapping and the application of 3D catalyzed DAM for rapid and accurate large volume RF field mapping.
Mechanisms of cancer chemoprevention in hepatic carcinogenesis: modulation of focal lesion growth in mice (1999)

Studies in our laboratory have concentrated on further understanding the mechanism by which chemicals induce cancer and the means to prevent or retard this process. Recent investigations have revolved around the role of oxidative stress and oxidative damage in the induction of cancer by nongenotoxic carcinogens. Hepatocarcinogenic compounds including selective chlorinated hydrocarbons appeared to induce oxidative stress in the liver. This oxidative stress and oxidative damage in turn may be responsible for the tumor-promoting activity of these compounds. Reduction of oxidative damage by antioxidants, or dietary-restriction, results in an ablation of the induction of selective cell growth by these agents. The oxidative stress induced by nongenotoxic agents may influence cell proliferation and/or apoptosis in the preneoplastic cells. Our studies with nongenotoxic hepatic carcinogens showed a dose-dependent increase in oxidative stress and an increase in hepatic focal lesion growth. Antioxidant dietary supplementation or caloric restriction prevented the lesion growth. This appeared to be through an increase in apoptosis in the hepatic lesions.
Network Motifs: Simple Building Blocks of Complex Networks (2002)

Complex networks are studied across many fields of science. To uncover their structural design principles, we defined "network motifs," patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.
Migraine: new treatment options from molecular biology (2005)

Migraine is a common, disabling, multifactorial, episodic neurovascular disorder of largely unknown etiology. The disease is typically characterized by recurrent attacks of headaches and associated autonomic and neurologic symptoms. Current acute and prophylactic treatment options are far from optimal and in many cases, empirically chosen. Clearly, improved treatment is desperately needed. New drug targets may emerge from molecular research as the unravelling of the molecular basis of migraine should improve our understanding of the disease, notably why patients experience attacks so frequently. The first two migraine genes discovered in families with hemiplegic migraine encode ion transporters, emphasising that dysfunction of ion transport may be an important factor in migraine. Therefore, ion transporters can be considered as novel targets for the development of future antimigraine drugs. Molecular biologic research will increasingly become important in understanding the pathophysiology of migraine and in identifying potential molecular targets for novel treatments.