gebhart/patrepeval huggingface dataset:
Cellular Trafficking of Quantum Dot-Ligand Bioconjugates and Their Induction of Changes in Normal Routing of Unconjugated Ligands (2008)

Can quantum dots (Qdots) act as relevant intracellular probes to investigate routing of ligands in live cells? The intracellular trafficking of Qdots that were coupled to the plant toxin ricin, Shiga toxin, or the ligand transferrin (Tf) was studied by confocal fluorescence microscopy. The Tf:Qdots were internalized by clathrin-dependent endocytosis as fast as Tf, but their recycling was blocked. Unlike Shiga toxin, the Shiga:Qdot bioconjugate was not routed to the Golgi apparatus. The internalized ricin:Qdot bioconjugates localized to the same endosomes as ricin itself but could not be visualized in the Golgi apparatus. Importantly, we find that the endosomal accumulation of ricin:Qdots affects endosome-to-Golgi transport of both ricin and Shiga toxin: Transport of ricin was reduced whereas transport of Shiga toxin was increased. In conclusion, the data reveal that, although coupling of Qdots to a ligand does not necessarily change the endocytic pathway normally used by the ligands studied, it appears that the ligand-coupled Qdot nanoparticles can be arrested within endosomes and somehow perturb the normal endosomal sorting in cells. Thus, the results demonstrate that Qdots may have severe consequences on cell physiology.
Bibliography on diarrhoeal diseases. (1994)

Acquired Immunodeficiency Syndrome 067 Caeliac Disease 018, 047 Aeromonas 044, 049 Campylobacter 086 Aeromonas hydrophila 048 Campylobacter coli 052, 064 Aeromonas sobria 006, 048 Campylobacter Infections 001, 086 Alanine 069, 073 Campylobacter jejuni 001, 052, 064 Albendazole 088 Carcinoma 070 Amino Acids 073 Cephalosporins 016 Aminobutyric Acids 044 Cereals 045, 059 Aminoglycosides 020 Child Growth 054, 088 Amoebiasis 056 Cholera 090, 100 Anthelmintics 061, 088 Cholera Toxin 025 Anthropometry 093 Cloning, Molecular 100 Antibiotics 060 Clostridium difficile 016, 079, 094 Antibodies 027 Clostridium perfringens 036 Antibodies, Bacterial 012, 014, 039, 044, Colitis, Haemorrhagic 041, 091 083, 085 Colitis, Pseudomembranous 016 Antibodies, Monoclonal 004, 012, 018, 048 Colitis, Ulcerative 092 Antibodies, Protozoan 010, 076 Colony Count, Microbial 002 Antibody Formation 001 Colostrum 024 Antibody Specificity 018 Communicable Diseases 055 Antidiarrhoeals 025 Coronaviridae 073 Antigens, Bacterial 012,030,083 Cross Infection 017, 074, 090 Antigens, Colonization Factor 039 Cryptosporidiosis 024 Ascaris lumbricoides 088 Cryptosporidium 024 Bacteria 029, 094 Culture Media 006, 029 Bacteria, Enteropathogenic 019 Cytotoxins 008, 091 Bacterial Adhesions 022, 026, 039, 083 Dehydration 045, 059 Bacterial Growth 063 Diagnosis, Laboratory 004, 008, 029, 036, Bacterial Infections 060 037, 041, 046, 047, 049, 055, 057, 075, Bacterial Outer Membrane Proteins 064, 083 078, 082 Bacterial Proteins 063 Diarrhoea 004, 019, 025, 028, 032, 033, Bacterial Toxins 006 050, 052, 058, 070, 072, 087 Bacterial Vaccines 030 Diarrhoea, Acute 028, 034, 059, 069, 078, Biopsy 047 096 Blotting, Western 037 Diarrhoea, Chronic 009, 047, 067, 068, Breast Feeding 019, 097 077, 094, 095
Functional and Multifunctional Nanoparticles for Bioimaging and Biosensing (2009)

Herein, we describe the synthesis of functional and multifunctional nanoparticles (NPs), derived from our recent work, for bioimaging and biosensing applications. The functionalized NPs involve quantum dots (QDs), magnetic particles (MPs) and noble metal NPs for the aforementioned applications. A diverse silica coating approaches (reverse microemulsion and thin silanization) are delineated for the design of water-soluble NPs. We also review the synthesis of silica-coated bifunctional NPs consisting of MPs and QDs for live cell imaging of human liver cancer cells (HepG2) and mouse fibroblast cells (NIH-3T3). Using silica coated NPs, various NPs that are functionalized with antibody, oligonucleotide, biotin and dextran are efficiently used for protein detection.
Integrated System for Rapid PCR-Based DNA Analysis in Microfluidic Devices (2000)

An integrated system for rapid PCR-based analysis on a microchip has been demonstrated. The system couples a compact thermal cycling assembly based on dual Peltier thermoelectric elements with a microchip gel electrophoresis platform. This configuration allows fast (approximately 1 min/ cycle) and efficient DNA amplification on-chip followed by electrophoretic sizing and detection on the same chip. An on-chip DNA concentration technique has been incorporated into the system to further reduce analysis time by decreasing the number of thermal cycles required. The concentration injection scheme enables detection of PCR products after performing as few as 10 thermal cycles, with a total analysis time of less than 20 min. The starting template copy number was less than 15 per injection volume.
The GRB2/Sem‐5 adaptor protein (1994)

GRB2/Sem-5 is a 25-kDa adaptor protein which contains a central Src homology type 2 (SH2) domain flanked by two Src homology type 3 (SH3) domains. GRB2/Sem-5 was first identified due to the essential role of the sem-5 gene product in the vulval induction pathway in Caenorhabditis elegans. The SH2 domain of GRB2/Sem-5 binds to a number of tyrosine phosphorylated proteins, most notably the epidermal growth factor receptor, the insulin receptor substrate IRS-1 and another putative adaptor protein, Shc. The SH3 domains bind to Sos, a guanine nucleotide exchange factor for Ras proteins. GRB2/Sem-5 brings together Sos and tyrosine phosphoproteins into a complex and thereby may regulate the nucleotide exchange rate of Ras and hence its activation state.
The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis (2008)

The vertebrate gut harbors a vast community of bacterial mutualists, the composition of which is modulated by the host immune system. Many gastrointestinal (GI) diseases are expected to be associated with disruptions of host-bacterial interactions, but relatively few comprehensive studies have been reported. We have used the rhesus macaque model to investigate forces shaping GI bacterial communities. We used DNA bar coding and pyrosequencing to characterize 141,000 sequences of 16S rRNA genes obtained from 100 uncultured GI bacterial samples, allowing quantitative analysis of community composition in health and disease. Microbial communities of macaques were distinct from those of mice and humans in both abundance and types of taxa present. The macaque communities differed among samples from intestinal mucosa, colonic contents, and stool, paralleling studies of humans. Communities also differed among animals, over time within individual animals, and between males and females. To investigate changes associated with disease, samples of colonic contents taken at necropsy were compared between healthy animals and animals with colitis and undergoing antibiotic therapy. Communities from diseased and healthy animals also differed significantly in composition. This work provides comprehensive data and improved methods for studying the role of commensal microbiota in macaque models of GI diseases and provides a model for the large-scale screening of the human gut microbiome.
Speed of Change in Pancreatic Mass and in Intestinal Bacteriology of Parenterally Fed Rats (1980)

1. Indices of pancreatic mass and bacterial counts for jejunal and ileal mucosa were studied in rats after 3, 6, 10 and 15 days of total parenteral nutrition and compared with the results from orally fed and sham intravenously fed control rats. 2. Pancreatic wet weight corrected for body weight decreased significantly by 31--42% after 3, 6, 10 and 15 days of total parenteral nutrition. The most striking decrease occurred within 3 days. Other indices of pancreatic mass (protein and DNA) showed a similar pattern suggesting pancreatic hypoplasia. There was more DNA per g of pancreas, indicating that unless there were changes in tissue water cellular hypotrophy must have accompanied the hypoplasia. 3. Pancreatic RNA also decreased significantly after 3--10 days of total parenteral nutrition, suggesting reduced protein synthesis. 4. Bacterial counts (log number) whether expressed as number/unit length of intestine or number/g wet weight of mucosa were decreased for anaerobic bacteria in the jejunum after 3--15 days of total parenteral nutrition. In the ileum both aerobic and anaerobic bacteria increased after 6 days of parenteral nutrition and then decreased significantly. 5. The changes in bacterial flora are unlikely to account for the adaptive hypoplasia seen in the intestine of intravenously fed rats.
3D inversion of time‐lapse CSEM data based on dynamic reservoir simulations of the Harding field, North Sea (2011)

Recent studies have inferred the feasibility of time‐lapse controlled‐source electromagnetic (CSEM) methods for the monitoring of offshore oil and gas fields. The time‐lapse CSEM inverse problem is highly constrained though inherently 3D since the geometry of the reservoir is established prior to production from high‐resolution seismic surveys, rock and fluid properties are measured from well logs, and multiple history‐matched production scenarios are contained in dynamic reservoir models. Using Archie's Law, rock and fluid properties from dynamic reservoir simulations of the Harding field in the North Sea were converted to resistivity, from preproduction in 1996 to decommissioning in 2016. CSEM data were simulated for each state. We demonstrate how 3D inversion can be used for monitoring the oil‐water contact from preproduction to the end of oil production in 2011, and for monitoring of the gas‐water contact from 2011 to 2016 during gas production. In particular, we show that focusing regularization is able to recover sharp resistivity contrasts across the oil‐water and gas‐water boundaries, whereas smooth regularization fails to recover an adequate resistivity contrast.
Genetic analysis of the linkage between chromosome 11q and atopy (1992)

Previous work has suggested that there is a genetic predisposition for the development of both asthma and atopy. A recent study has also shown that there is a striking link between chromosome 11q and the IgE response underlying asthma and rhinitis. To further assess the linkage between chromosome 11q and atopy, we have studied nine families of two and, in many instances, three generations with the index case having asthma and/or atopy. Using two restriction fragment length polymorphism probes associated with the regions 11q12-q13.2, namely PYGM and INT2, we have been unable to confirm a significant link between this region of chromosome 11q and atopy as defined by a positive skin-prick test and/or a raised specific IgE and/or a raised total IgE.
Molecular Characterization of CYP73A9 andCYP82A1 P450 Genes Involved in Plant Defense in Pea (2000)

Cytochrome P450 monooxygenases (P450s) mediate a wide range of oxidative reactions involved in the biosynthesis of phenylpropanoids, terpenes, and alkaloids. Two pea (Pisum sativum) P450 cDNAs (CYP73A9v1, encoding trans-cinnamic acid hydroxylase [t-CAH] in the core phenylpropanoid pathway, and CYP82A1v1, possibly encoding an activity in a late branch of the phenylpropanoid pathway) have previously been described. Of three CYP73A9 genes now isolated, the CYP73A9v1 gene is full-length with two introns at positions conserved in other t-CAH genes, and the CYP73A9v2 and CYP73A9v3 gene fragments are 5'-truncated and lack introns. The full-length CYP82A1v2 gene contains a single intron at an alternate position. Nucleotide searches of the CYP73A9v1 and CYP82A1v2 promoters have indicated that the regulatory sequences for these early and late phenylpropanoid transcripts are substantially different. The P-, L-, and H-boxes identified in white light-, ultraviolet light-, and elicitor-induced footprints in early phenylpropanoid promoters (phenylalanine ammonia lyase [PAL], 4-coumarate coenzyme A:ligase [4-CL], and chalcone synthase [CHS]) are conserved in the t-CAH promoter and are absent from the CYP82A1v2 promoter. Both promoters contain TCA motifs identified in stress-responsive promoters, box IV elements identified in elicitor-responsive PAL and CHS promoters, and spatially conserved wound-response elements potentially coordinating regulation of these wound-responsive promoters.
Recognition of phosphate monoester dianion by an alkoxide-bridged dinuclear zinc(ii) complex (2004)

Recognition of phosphate monoester dianion by an alkoxide-bridged dinuclear zinc(II) complex (Zn2L3+) has been studied (L = alkoxide species of 1,3-bis[bis(pyridin-2-ylmethyl)amino]propan-2-ol). Potentiometric pH titration study disclosed a 1 : 1 phenyl phosphate complexation with Zn2L3+ in aqueous solution. The dissociation constant (= [Zn2L3+][PhOPO3(2-)]/[Zn2L3+-PhOPO3(2-)]) is an extremely small value of 2.5 x 10(-8) mol dm(-3) at 25 degrees C with I = 0.10 (NaNO3). The X-ray crystal analysis of the dizinc(II) complex with p-nitrophenyl phosphate showed that the phosphate dianion binds as a bridging ligand to the two zinc(II) ions.
Nor-ursodeoxycholic acid reverses hepatocyte-specific nemo-dependent steatohepatitis (2010)

Overall, our work demonstrates the contribution of bile acids metabolism to the progression of NASH in the absence of hepatocyte-NF-kB through mechanisms involving DR5-apoptosis, inflammation and fibrosis. Our work suggests a potential therapeutic effect of NorUDCA in attenuating the progression of NASH.
Sensitization to Hyperthermia below 43° C Induced in Chinese Hamster Ovary Cells by Step-Down Heating2 (1980)

Step-down heating (SDH) of Chinese hamster ovary cells consisted of an acute heat treatment at an elevated temperature followed immediately by chronic exposure to a lower hyperthermic temperature [step-down temperature (SDT)]. The survival curve at the SDT showed a reduced D0 (dose required to reduce the cell population to 37% on exponential part of the curve) relative to that of control cells only for SDT of 43 degrees C or less. The ratio r of D0's, D0 (control)/D0 (SDH), varied inversely with the SDT (e.g., r = 13 for SDT = 40 degrees C, whereas r = 1.3 for SDT = 43 degrees C). The degree of sensitization, as measured by r, was independent of the conditioning temperature (CT) and the conditioning time, provided that the CT was above 43 degrees C and the conditioning treatment reduced cell survival to 60% or less. The ratio r could be defined mathematically as a function of the activation energies for heat-induced cell killing above and below 43 degrees C, the SDT, and the CT. Biphasic heat survival curves, which appeared with heating at constant temperature below 43 degrees C, also appeared under SDH conditions, which suggested that thermotolerance, as represented by the resistant phase of the biphasic survival curve, was not affected by SDH. Fractionation experiments to measure the loss of interaction of heat damage remaining from the conditioning treatment with the low-temperature heat damage showed that 63% of the 45 degrees C sublethal damage was removed by 67 minutes at a constant exponential rate.
High‐grade Atrioventricular Block Triggered by Spontaneous and Stimulation‐induced Epileptic Activity in the Left Temporal Lobe (2004)

Cardiac bradyarrhythmias may play a pivotal role in the pathophysiology of sudden unexpected death in epilepsy (SUDEP). We describe a patient with left temporal lobe epilepsy in whom high-grade atrioventricular conduction blocks were triggered by both spontaneous and stimulation-induced epileptic activity in the left temporal lobe. Electrophysiological data obtained by surface and intracranial electrodes point to a cerebral cardioarrhythmogenesis in the left amygdala and anterior hippocampus.
Assessment of Processed Porcine Extracellular Matrix as a Protective Barrier in a Rabbit Nerve Wrap Model (2010)

Nerve wrapping can improve outcomes by protecting nerves in a scarred tissue bed. Autologous tissue wraps have shown good results, but there are limitations associated with harvesting and availability. Extracellular matrix (ECM) derived from porcine small intestinal submucosa offers an attractive off-the-shelf option. This study evaluated this material as a nerve wrap. The sciatic nerves of 18 New Zealand rabbits were exposed and then wrapped, while the contralateral side served as sham control. Presence and quality of adhesions, motor conduction velocity (MCV), and histology were evaluated at 1, 2, and 6 months ( N = 6 animals per time point). The quality, extent, tenacity, and overall impression of adhesions were not different from control at any time point ( P = 0.18 to 0.99). MCV was also not statistically different from control (1 month, P = 0.35; 2 months, P = 0.20; 6 months, P = 0.83). Histology demonstrated that wrapped nerves were healthy in terms of myelination, density, and vascularity compared with controls. Vascularization and incorporation of the ECM material could be visualized at explants. All assessments supported the feasibility and safety of this material as a nerve wrap. Its ability to function as a protective barrier has strong implications for clinical use in trauma and/or recurrent compression neuropathies.
Interatrial septum pacing avoids the adverse effect of interatrial delay in biventricular pacing: an echo-Doppler evaluation (2002)

IAD produces different left and right atrioventricular sequences in BVP. IASP combined with BVP, by resynchronizing both atria and ventricles, is able to avoid this adverse effect.
Differential gene expression profile of MAGE family in taiwanese patients with colorectal cancer (2010)

This is the first comprehensive report to clarify the differential expression profile of whole MAGE family in CRCs, and it might provide some crucial information about the carcinogenesis and progression in Taiwanese patients with CRC.
Transport of albumin into the intestinal lumen of the rat (1997)

The intestine is considered a major site for the breakdown and clearance of serum proteins. The mechanism of transport of macromolecules from the serosa into the lumen is unclear. The present study was designed to characterize the serosal to mucosal movement of albumin. Transport of bovine serum albumin (BSA) was assessed in short-circuited Ussing chambers, using stripped rat jejunum devoid of Peyer's patches. To define the kinetics of serosal to mucosal albumin transport the serosal surface was exposed to BSA at varying concentrations (0.5-5 mg.mL-1). Fluids from the mucosal compartment were sampled over time and assayed for immunologically intact BSA by ELISA. All subsequent experiments utilized a concentration of cold BSA (2 mg.mL-1) that produced maximal levels of intact BSA transport. To assess total BSA transport (intact BSA plus degraded BSA), 10 microCi (1 Ci = 37 GBq) 125I-labelled BSA was added to the serosal surface in addition to 2 mg.mL-1 cold BSA. To further characterize BSA transport tissues were treated with sodium fluoride (NaF) (metabolic inhibitor) or colchicine (an inhibitor of microtubule polymerization) or with the nerve blocker tetrodotoxin (TTX). All experiments using inhibitors were performed in paired tissues obtained from the same animal. Transport of intact BSA into the intestinal lumen was a saturable process, with a Vmax of 251 +/- 13 ng.cm-2.h-1 and a Km of 0.72 +/- 0.1 mg.mL-1, and represented 7% of the total BSA flux into the intestinal lumen. In the presence of NaF (2 x 10(-3) M), transport of both intact and total BSA was significantly inhibited (intact: control 374 +/- 80 vs. NaF 46 +/- 11, 88% inhibition; total: control 3288 +/- 296 vs. NaF 2550 +/- 235 ng.cm-2.h-1, 22% inhibition; p < 0.05). In addition, colchicine significantly inhibited intact BSA transport (control 339 +/- 15 vs. colchicine 206 +/- 13 ng.cm-2.h-1, 39% inhibition; p < 0.05). TTX had no effect on intact BSA flux. The findings suggest that transport of intact BSA from the serosa into the intestinal lumen is a saturable, energy-dependent process, which involves microtubules but is not under neural regulation.
A cloned pathogenicity island from enteropathogenic Escherichia coli confers the attaching and effacing phenotype on E. coli K‐12 (1997)

Attaching and effacing (AE) bacteria are a diverse group of gastrointestinal pathogens, comprising members of four genera, that cause the intestinal epithelial microvilli to be replaced with raised clusters of filamentous actin that conform to the surface of attached bacteria. We have cloned a 35.4 kb 'pathogenicity island' from the prototype AE bacterium, enteropathogenic Escherichia coli, containing all previously described AE genes. Transfer of this pathogenicity island to avirulent E. coli converts the recipients into strains that secrete virulence proteins, induce host signal-transduction pathways, and cause AE lesions on cultured epithelial cells. These results demonstrate that this pathogenicity island contains all pathogen-specific genes necessary for inducing AE lesions, and that the defining feature of this class of pathogens can be acquired by an avirulent bacterium in a single genetic step.
Advanced Technology Testbeds for Distributed, Survivable Command, Control and Communications (C<sup>3</sup>) (1982)

Two testbeds have been established to transfer emerging technology from the research community to the military thereby providing a basis for developing new military concepts for force effectiveness and survivability. Although still emerging, these technologies are now being presented to the user to make it possible to investigate (today) command, control and communications (C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) concepts that might otherwise not be considered for another decade. The technologies being transferred include: automated tactical reporting systems, advanced packet-switched communication, automated man-machine interfaces, communication network and internetwork environments, automated display and analysis of data, and techniques for automatically disseminating information into redundant/distributed data bases. Expectations are that the testbeds will ultimately lead to the definition of military distributed C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> architectures that will permit a commander to execute his mission in the "battlefield of the future" more effectively.
Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing (2003)

The expression of short hairpin RNAs in several organisms silences gene expression by targeted mRNA degradation. This RNA interference (RNAi) pathway can also affect the genome, as DNA methylation arises at loci homologous to the target RNA in plants. We demonstrate in fission yeast that expression of a synthetic hairpin RNA is sufficient to silence the homologous locus in trans and causes the assembly of a patch of silent Swi6 chromatin with cohesin. This requires components of the RNAi machinery and Clr4 histone methyltransferase for small interfering RNA generation. A similar process represses several meiotic genes through nearby retrotransposon long terminal repeats (LTRs). These analyses directly implicate interspersed LTRs in regulating gene expression during cellular differentiation.
Thermally Stable, Efficient Polymer Solar Cells with Nanoscale Control of the Interpenetrating Network Morphology (2005)

Abstract By applying the specific fabrication conditions summarized in the Experimental section and post‐production annealing at 150 °C, polymer solar cells with power‐conversion efficiency approaching 5 % are demonstrated. These devices exhibit remarkable thermal stability. We attribute the improved performance to changes in the bulk heterojunction material induced by thermal annealing. The improved nanoscale morphology, the increased crystallinity of the semiconducting polymer, and the improved contact to the electron‐collecting electrode facilitate charge generation, charge transport to, and charge collection at the electrodes, thereby enhancing the device efficiency by lowering the series resistance of the polymer solar cells.