gebhart/patrepeval huggingface dataset:
The BlueDRAGON - a system for measuring the kinematics and dynamics of minimally invasive surgical tools in-vivo (2003)

Minimally invasive surgery involves a multidimensional series of tasks requiring a synthesis between visual information and the kinematics and dynamics of the surgical tools. Analysis of these sources of information is a key step in mastering MIS, but may also be used to define objective criteria for characterizing surgical performance. The BlueDRAGON is a new system for acquiring the kinematics and dynamics of two endoscopic tools synchronized with the visual view of the surgical scene. It includes two four-bar passive mechanisms equipped with position and force torque sensors for measuring the positions and orientations of the two endoscopic tools along with the forces and torques (F/T) applied by the surgeon's hands. The methodology of decomposing the surgical task is based on a fully connected, 28 finite-states Markov model where each states corresponded to a fundamental tool/tissue interaction based on the tool kinematics and associated with unique F/T signatures. The experimental protocol includes seven MIS tasks performed on an animal model by 30 surgeons at different levels of their residency training including expert surgeons. From the preliminary analysis of these data, the major differences between residents at different skill levels are discussed. Systems like surgical robots or virtual reality simulators that inherently measure the kinematics and dynamics of the surgical tool may benefit from inclusion of the proposed methodology for the analysis of efficacy and objective evaluation of surgical skills during training.
Bioluminescent Orthotopic Mouse Models of Human Localized Non-Small Cell Lung Cancer: Feasibility and Identification of Circulating Tumour Cells (2011)

Transpleural orthotopic injection of A549-luc cells in nude mouse lung induces localized tumour, followed by lymphatic extension and specific mortality, and allowed the first time identification of CTCs in a NSCLC mice model.
Transformation of Ginsenosides to compound K(IH-901) by Lactic Acid Bacteria of Human Intestine (2003)

【When ginsenosides Rbl, Rb2, and Rc were anaerobically incubated with commercial and human intestinal lactic acid bacteria, most commercial lactic acid bacteria did not metabolize these ginsenosides to compound K. However, lactic acid bacteria, B. minimum KK-1, Bifidobacterium cholerium KK-2, and B. cuniculi K-513, isolated from human intestinal microflora transformed these ginsensosides to compound K. When the bacterial mixtures of commercial lactic acid bacteria were incubated with these ginsenosides, these compounds were not transfformed to compound K. However, when Bzfidobacterium KK-1 and KX-2 were miked, these ginsenosides were synergistically transformed to compound K. When water extract of ginseng was incubated with these mixed bifidobacteria, compound K was potently produced. Therefore, it is suggested that, if ginseng with these mixed bifidobacteria is fermented, compound K-enforced ginseng materials could be produced that show cytotoxicity against tumor cell lines.】
Administration of unmodified progesterone by nasal spray in fertile women (1995)

A 11.20-mg dose of progesterone was administered by nasal spray to five healthy fertile women in the follicular phase of the menstrual cycle. Serial blood samples were collected and Cmax (the maximum progesterone concentration reached), Tmax (the time at which Cmax was reached) and the area under the curve (AUC), with the time limits of 0 and 720 min, were calculated. Serum progesterone levels were assayed by means of a non-extraction [125I]radioimmunoassay. The mean Cmax was 4.50 +/- 2.31 ng/ml at a Tmax of 30 min; levels returned to baseline after 720 min. The mean AUC value was 1180.50 +/- 613.90 ng.h/ml. The progesterone administered by nasal spray in fertile women was effective in reaching physiological progesterone levels. Even if a nasal first-pass metabolic effect is taken into account, this route allows progesterone to avoid liver first-pass metabolism and its metabolic consequences.
End-Labeling Oligonucleotides with Chemical Tags After Synthesis (2012)

Many experimental strategies for determining nucleic acid function require labeling the nucleic acid with radioisotopes or a chemical tag. Labels enable nucleic acid detection, yield information about its state, and can serve as a handle by which the nucleic acid and associated factors can be purified from a mixture. Radioactive phosphate is commonly added to the 5' or 3' end of an oligonucleotide post synthesis using enzyme-catalyzed reactions. In contrast, chemical tags are usually added during synthesis or using reactive groups that are incorporated during synthesis. Here, we present protocols for post-synthetic conjugation of chemical tags to unmodified RNA or DNA oligonucleotides. The approach can be used to attach fluorescent dyes and biotin groups to oligonucleotides and to immobilize oligonucleotides to a solid support. Oligonucleotides tagged with fluorescent dyes are readily detected in both gel- and plate reader-based assays, while biotin- or resin-conjugated oligonucleotides are useful tools for affinity purification. Fluorescent end-labeling provides several advantages over radioactive labeling, reducing radioactivity-associated hazards and yielding a labeled molecule that does not decay while providing the sensitivity required for many procedures.
Lipidoid-Coated Iron Oxide Nanoparticles for Efficient DNA and siRNA delivery (2013)

The safe, targeted and effective delivery of gene therapeutics remains a significant barrier to their broad clinical application. Here we develop a magnetic nucleic acid delivery system composed of iron oxide nanoparticles and cationic lipid-like materials termed lipidoids. Coated nanoparticles are capable of delivering DNA and siRNA to cells in culture. The mean hydrodynamic size of these nanoparticles was systematically varied and optimized for delivery. While nanoparticles of different sizes showed similar siRNA delivery efficiency, nanoparticles of 50-100 nm displayed optimal DNA delivery activity. The application of an external magnetic field significantly enhanced the efficiency of nucleic acid delivery, with performance exceeding that of the commercially available lipid-based reagent, Lipofectamine 2000. The iron oxide nanoparticle delivery platform developed here offers the potential for magnetically guided targeting, as well as an opportunity to combine gene therapy with MRI imaging and magnetic hyperthermia.
Introduction to Genetic Engineering (1991)

Large and small molecules proteins protein synthesis more about DNA introduction to genetic engineering cutting and measuring DNA cloning vehicles DNA's and genomic libraries selection of the right fragment characterization of the passenger applications of gene cloning the computer in molecular biology ethical considerations.
Alkyltrichlorosilane-based self-assembled monolayer films for stiction reduction in silicon micromachines (1998)

We have investigated the potential of self-assembled monolayer (SAM) coatings for the purpose of adhesion reduction in microelectromechanical systems (MEMS). Two types of SAM coatings, derived from the precursor molecules octadecyltrichlorosilane [CH/sub 3/(CH/sub 2/)/sub 17/SiCl/sub 3/, OTS] and 1H,1H,2H,2H-perfluorodecyltrichlorosilane [CF/sub 3/(CF/sub 2/)/sub 7/(CH/sub 2/)/sub 2/SiCl/sub 3/, FDTS], were applied to polycrystalline silicon microstructures in a liquid-based process. Due to the hydrophobicity of these coatings, the water capillary forces responsible for the phenomenon known as release-related stiction are eliminated, and SAM-coated cantilever beams 2 /spl mu/m thick, 2 /spl mu/m above the substrate, and up to 2 mm in length emerge dry and free standing when removed from the final water rinse. The effects of SAM coating on adhesion encountered during device operation, termed in-use stiction, were characterized using arrays of cantilever beams of varying lengths. Structures made with a polycrystalline silicon of 3-nm rms roughness gave apparent works of adhesion of 30 and 8 /spl mu/J/m/sup 2/ for the OTS and FDTS SAM coatings, respectively, in comparison to 56 mJ/m/sup 2/ for standard oxide-coated structures. These results demonstrate that OTS coating reduces adhesion by more than three orders of magnitude over the conventional process and that the fluorinated SAM can lessen it further by four times. With regard to thermal stability, both SAM coatings can withstand heat treatment for 5 min at 450/spl deg/C in an N/sub 2/ ambient. In air, the OTS film begins to degrade at 150/spl deg/C while the fluorinated coating remains intact up to 400/spl deg/C. Therefore, both types of SAM coatings are compatible with several MEMS packaging techniques, with the FDTS monolayers exhibiting superior stiction and thermal stability properties to those derived from OTS. Furthermore, the FDTS formation does not require any chlorinated solvents such as carbon tetrachloride, which has been banned from industrial use, making the latter coating an industrially viable antistiction treatment.
Induction of differentiation in myeloid leukemia cell lines and acute promyelocytic leukemia cells by liposomal all-trans-retinoic acid. (1993)

All-trans-retinoic acid (ATRA) induces complete remissions in the majority of patients with acute promyelocytic leukemia. Despite continuous p.o. ATRA administration, many patients relapse after a short remission duration. In these patients, ATRA plasma concentrations were found to be very low, which was related to induction of retinoic acid-binding protein and increased drug catabolism by cytochrome P-450-mediated reactions. An i.v. ATRA formulation, which can be achieved by encapsulating ATRA into liposomes, may have the potential to overcome these unwanted effects. We investigated the ability of liposomal ATRA (L-ATRA) to induce differentiation of human myeloid leukemia cell lines (HL-60, KG-1, and THP-1). Cellular differentiation, as assessed by morphological criteria and by the expression of a mature myeloid cell surface antigen (CD11b on HL-60 and KG-1 cells), was induced by culture in the presence of L-ATRA. The ability of L-ATRA-treated HL-60 cells to reduce nitroblue tetrazolium demonstrated that they were functionally differentiated cells. Cell cycle analysis revealed significant growth inhibition of the cells after L-ATRA treatment. Following culture with L-ATRA, cells from five patients with acute promyelocytic leukemia were found to be morphologically and immunophenotypically mature myeloid cells. L-ATRA was as effective as free ATRA in inducing differentiation of the cell lines and of the cells from patients with acute promyelocytic leukemia. We conclude that L-ATRA effectively induces differentiation and may be a useful parenteral ATRA formulation for overcoming the pharmacological mechanisms that lead to "retinoid resistance."
A human alpha-arrestin protein with a potential role in cargo protein trafficking within the endocytic system (2013)

β-Arrestins are essential adaptors for G protein-coupled receptor (GPCR) trafficking. Evolutionary ancestors of the β-arrestins – dubbed α-arrestins – are present in yeast/fungi and, similar to β-arrestins, recognise cargo proteins and mediate their intracellular trafficking. Mammalian α-arrestins include five largely uncharacterised arrestin domain-containing (ARRDC1-5) proteins that display a predicted arrestin structure; the current study focuses on human ARRDC2.\nConfocal microscopy of exogenous, fluorescent protein-tagged ARRDC2 in U2OS cells in combination with compartment-specific markers indicated that ARRDC2 is dynamically distributed throughout the plasma membrane and endocytic system, predominantly to late endosomes/lysosomes. Anti-ARRDC2 immunostaining in several primary cell lines broadly supported this conclusion. ARRDC2 contains two proline-rich (PPxY) motifs that in other α-arrestins have been reported to mediate interactions with WW domain-containing NEDD4 family E3 ubiquitin ligases. Coimmunoprecipitation indicated that ARRDC2 is able to interact with several NEDD4 E3s via its PPxY motifs, and confocal microscopy suggested that this interaction may influence the subcellular targeting of the ligases. Ubiquitination of ARRDC2 was detected by coimmunoprecipitation, although this modification was independent of ARRDC2 interaction with NEDD4 E3s. ARRDC2 colocalised with agonist-stimulated, internalised GPCRs (β2-adrenergic receptor (β2AR) and δ-opioid receptor (δOR)) and colocalisation analysis indicated that this involved compartmental redistribution of ARRDC2 to receptor-containing early/recycling endosomes, suggesting a specific effect. Interaction of ARRDC2 with δOR was detected using coimmunoprecipitation, and confocal analysis suggested that ARRDC2 may influence δOR and β2AR intracellular trafficking. ARRDC2 was also found to oligomerise with itself and the β-arrestins. Confocal microscopy showed that ARRDC2 overexpression can induce the redistribution of β-arrestin1 to ARRDC2-positive vesicles, and a punctate bimolecular fluorescence complementation (BiFC) signal was detected between ARRDC2 and β-arrestin2. From this, it is speculated that α-/β-arrestins may function cooperatively or competitively to mediate discrete GPCR sorting events in the endocytic pathway.
Signalling, inflammation and arthritis: NF- B and its relevance to arthritis and inflammation (2008)

In the synovial cells of patients with RA, activation of the nuclear factor-kappaB (NF-kappaB) pathway results in the transactivation of a multitude of responsive genes that contribute to the inflammatory phenotype, including TNF-alpha from macrophages, matrix metalloproteinases from synovial fibroblasts and chemokines that recruit immune cells to the inflamed pannus. This is largely a consequence of activation of the 'canonical' NF-kappaB pathway that involves heterodimers of p50/p65. Whilst much information on the role of NF-kappaB in inflammation has been gleaned from genetic deficiency of the respective genes in mice, important differences exist in the signalling networks between human and murine immune cells and immortalized cell lines. Despite these differences at the molecular level, the importance of NF-kappaB in inflammation is undisputed and inhibition of the pathway is widely believed to have great potential as a therapeutic target in RA. Commercial effort has gone into developing inhibitors of NF-kappaB activation. However, inhibition of the NF-kappaB activation can result in an exacerbation of inflammation if TNF-alpha production by macrophages is not controlled. It will be important that such inhibitors are carefully monitored before their long-term use in chronic inflammatory conditions such as RA.
Guidelines for Improving the Lower Detection Limit of Ion‐Selective Electrodes: A Systematic Approach (2007)

Abstract Zero‐current membrane fluxes are the principal source of bias that has prohibited researchers from obtaining true, thermodynamic selectivity coefficients for membrane‐based ion‐selective electrodes (ISEs). They are also responsible for the mediocre detection limits historically seen with these types of potentiometric sensors. By choosing an experimental protocol that suppresses these fluxes, it becomes possible to obtain unbiased thermodynamic selectivity coefficients that are needed to produce ISEs with greatly improved detection limits. In this work, a Cs + ‐selective electrode based on calix[6]arene‐hexaacetic acid hexaethyl ester (Cs I) is used to systematically demonstrate how unbiased selectivity coefficients can be obtained, and how they can be used to optimize inner filling solutions for low detection limit measurements. A comparison of biased selectivity methods (e.g., classical separate solution method (SSM), fixed interference method (FIM), matched potential method (MPM)) with the unbiased modified separate solution method (MSSM) found that selectivity coefficients were underestimated in several cases by more than 4 orders of magnitude (log K Cs,Mg pot,MSSM =−8.7; log K Cs,Mg pot,SSM =−4.5). The importance of key experimental parameters, including diffusion coefficients and diffusion layer thicknesses in the aqueous and organic phases, on the minimization of ion fluxes and the improvement of lower detection limits is also described. A dramatic reduction of membrane fluxes by the covalent attachment of a Ca 2+ ‐selective ionophore to a methyl methacrylate‐decyl methacrylate (MMA‐DMA) copolymer matrix is also demonstrated. The ionophore‐immobilized ISE exhibited no super‐Nernstian response and yielded a detection limit of 40 ppt (log a Ca =−9.0) with an inner filling solution of 1×10 −3 M KCl. Finally, a set of guidelines for experimental protocols leading to obtaining unbiased selectivity coefficients and producing ISEs for trace level analyses is given.
Size-Selective Synthesis and Stabilization of Gold Organosol in CnTAC:  Enhanced Molecular Fluorescence from Gold-Bound Fluorophores (2005)

Gold nanoparticles of variable sizes have been synthesized in toluene employing two-phase (water-toluene) extraction of AuCl4- followed by its reduction with sodium borohydride in the presence of a series of cationic surfactants of a homologous series having the general formula C(n)TAC. The solubility features of the gold particles in the organic solvent have been accounted qualitatively by calculating the van der Waals interaction potential between the particles. The effect of thermal energy and medium dielectric constant on the stability of metal particles has been studied by measuring the surface plasmon resonance. The stabilization of surfactant-mediated gold particles as hydrosol or organosol has been elucidated by considering the double-layer interaction as a function of the dielectric constant of the solvent medium. The influence of the counterion of the phase transfer reagent and stabilizing ligand on the photochemical stability of the gold colloids has been investigated. The fluorescence probe 1-methylaminopyrene (MAP) was considered for the surface functionalization of the gold particles, and it has been found that there is an enhancement of molecular fluorescence from the gold-probe assembly.
5-Aminoimidazole-4-carboxamide-1-β-D-ribofuranoside Inhibits Cancer Cell Proliferation in Vitro and in Vivo via AMP-activated Protein Kinase (2005)

5-Aminoimidazole-4-carboxamide-1-beta-4-ribofuranoside (AICAR) is widely used as an AMP-kinase activator, which regulates energy homeostasis and response to metabolic stress. Here, we investigated the effect of AICAR, an AMPK activator, on proliferation of various cancer cells and observed that proliferation of all the examined cell lines was significantly inhibited by AICAR treatment due to arrest in S-phase accompanied with increased expression of p21, p27, and p53 proteins and inhibition of PI3K-Akt pathway. Inhibition in in vitro growth of cancer cells was mirrored in vivo with increased expression of p21, p27, and p53 and attenuation of Akt phosphorylation. Anti-proliferative effect of AICAR is mediated through activated AMP-activated protein kinase (AMPK) as iodotubericidin and dominant-negative AMPK expression vector reversed the AICAR-mediated growth arrest. Moreover, constitutive active AMPK arrested the cells in S-phase by inducing the expression of p21, p27, and p53 proteins and inhibiting Akt phosphorylation, suggesting the involvement of AMPK. AICAR inhibited proliferation in both LKB and LKB knock-out mouse embryo fibroblasts to similar extent and arrested cells at S-phase when transfected with dominant negative expression vector of LKB. Altogether, these results indicate that AICAR can be utilized as a therapeutic drug to inhibit cancer, and AMPK can be a potential target for treatment of various cancers independent of the functional tumor suppressor gene, LKB.
Human Peripheral Blood‐Derived Dendritic Cells do not Produce Interleukin 1α, Interleukin 1β, or Interleukin 6 (1990)

Little is known about the non-antigen-specific signals delivered to T cells by dendritic cells (DC). Because several monocyte-derived factors like interleukins 1 alpha, 1 beta, and 6 (IL-1 alpha, IL-1 beta, and IL-6) enhance the T-cell proliferative responses, we studied the production of the above-mentioned cytokines by DC separated from human peripheral blood. The intracellular expression of the proteins (IL-1 alpha and IL-6) was studied at a single-cell level using an immunolabelling technique. The supernatants and cell lysates were studied with ELISA (IL-1 alpha and IL-1 beta). Northern blotting analysis was used to quantitate the mRNA levels. Several approaches were taken to stimulate the production of IL-1 alpha, IL-1 beta, and IL-6 by DC. These included the incubation of the DC in the presence of either LPS, rIL-1, or monoclonal anti-HLA-DR antibody, or the stimulation of cells with resting allogeneic T cells. None of the stimuli was able to induce the production of IL-1 alpha, IL-1 beta, or IL-6 by DC, whereas LPS-stimulated monocytes were strong producers of these mentioned cytokines and expressed the respective mRNA. Thus we concluded that IL-1 alpha, IL-1 beta, and IL-6 are primarily monocyte-derived factors and that these factors are not needed or produced during the activation of resting T cells by DC.
A new carboxylation reaction. The vitamin K-dependent incorporation of H-14-CO3- into prothrombin. (1975)

The bovine plasma zymogen prothrombin contains a number of gamma-carboxyglutamic acid residues which are not found in an abnormal prothrombin produced when cattle are given the vitamin K antagonist dicoumarol. These modified glutamic acid residues appear to be formed post-translationally by a reaction which requires vitamin K. It has been shown that postmitochondrial supernates from vitamin K-deficient rats incorporate added H-14-CO3- minus into microsomal proteins upon the addition of vitamin K. This incorporation is dependent upon the presence of the prothrombin precursor in the microsomal preparations, and upon factors which are present in the postmicrosomal supernatant. Most of the radioactive protein which can be obtained from the microsomal pellet by extraction with 0.25% Triton X-100 has been identified as prothrombin and it can be shown that all of the radioactivity is in the amino-terminal activation fragment of prothrombin. This portion of the protein has previously been shown to contain the gamma-carboxyglutamic acid residues. Hydrolysis of the purified radioactive prothrombin resulted in a loss of 50% of the radioactivity and subsequent chromatography of the amino acid hydrolyzate demonstrated that the remaining radioactivity was entirely in glutamic acid. These results are consistent with the hypothesis that all of the H-14-CO3- minus was incorporated into the carboxyl groups of gamma-carboxyglutamic acid residues.
In vivo transcription of the 5'-terminal extracistronic region of vesicular stomatitis virus RNA (1981)

In vivo transcription and polyadenylation at the junction of the L cistron and the 5'-terminal extracistronic region of vesicular stomatitis virus RNA was investigated. Annealing of 5'32P-labeled RNA representing the 5'-terminal noncoding 77 nucleotides of vesicular stomatitis virus genomic RNA to L gene mRNA resulted in specific duplex formation. Two specific RNase T1- and RNase A resistant duplexes, 66 and 77 nucleotides long, bound to oligodeoxythymidylic acid cellulose. The specific sizes of the duplexes and their selection by oligodeoxythymidylic acid cellulose chromatography demonstrated that they were covalently linked to the polyadenylic acid tail of L gene mRNA. These data strongly suggest that the viral polymerase polyadenylates L gene mRNA in vivo by using the stretch of seven uridine residues at the end of the L cistron and that the polymerase can resume transcribing the 5'-terminal extracistronic region, resulting in a covalent linkage of the transcript to the polyadenylic acid tail of L gene mRNA.