gebhart/patrepeval huggingface dataset:
Tumor-Marker Detection by Isotachophoresis in Porous Membranes (1992)

Isotachophoresis (ITP) is a very powerful electrophoretic method for separation of native macromolecules as well as substances of low molecular weight (Haglund, 1970; Chrambach, 1980). ITP combines very effective concentration of the substances with their sharp separation according to electrophoretic mobility of each component. Since ITP is hardly compatible with electroosmosis, it is usually carried out in free medium, as in capillary electrophoresis, or in gels lacking electroosmotic properties. We have modified ITP using highly “electroosmotic” cellulose acetate (CAM) as a supporting medium (Abelev and Karamova, 1982, 1984). This modification (ITP-CAM) has two major advantages over “standard” ITP:
Quantification of glomerular number and size distribution in normal rat kidneys using magnetic resonance imaging (2011)

MRI provides a new method for measuring these important microanatomical markers of disease risk and leads the way to in vivo analysis of these parameters, including longitudinal studies of animal models of CKD.
Abstract 411: PI3 Kinase gamma control of Arginase-1 expression promotes tumor immunosuppression (2012)

Abstract Tumor inflammation promotes angiogenesis, immunosuppression, and tumor growth. Tumor associated myeloid cells, which include incompletely differentiated myeloid derived suppressor cells, macrophages and granulocytes, establish an immunosuppressive microenvironment in tumors through the expression of Arginase-1, which depletes the tumor microenvironment of arginine, thereby promoting T cell death and NK cell inhibition. Suppression of Arginase-1 expression and function could alter the course of cancer therapy by stimulating anti-tumor immunity to work in concert with anti-tumor vaccine or chemotherapeutic agents targeting tumor cell proliferation and survival. We found that myeloid cells express Arginase-1 in response to IL-6 stimulation in a Jak2/Stat3 and PI3Kinase gamma/mTORc1 dependent manner by promoting the activation of the transcriptional enhancer C/EBPbeta. Pharmacological or genetic blockade of Jak2, Stat3, PI3Kgamma, mTOR or C/EBPbeta suppressed expression of Arginase-1. Suppression of PI3Kgamma or Arginase-1 expression blocked myeloid cell induced death of T cells in vitro. PI3Kgamma inhibition blocked Arginase-1 expression in vivo, thereby increasing the number of CD8+ T cells in tumors, stimulating T cell-mediated cytotoxicity of tumor cells in vivo and suppressing growth and metastasis of implanted and spontaneous tumors. These studies reveal that suppression of Arginase-1 expression with PI3Kgamma or Jak2/Stat3 inhibitors can serve as an effective therapeutic strategy in oncology. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 411. doi:1538-7445.AM2012-411
Simulations of the Morphology of Cylinder-Forming Asymmetric Diblock Copolymer Thin Films on Nanopatterned Substrates (2003)

We report a first study on the use of chemically nanopatterned substrates to induce long-range ordering (in the plane of the film) of perpendicular cylinders confined between the substrate and an upper homogeneous surface. Two conditions are essential for obtaining the long-range ordering: a lower hexagonally patterned substrate, commensurate with perpendicular cylinders having the same dimensions and packing as in the bulk, and an upper neutral or weakly preferential surface for the longer blocks. By examining the spatial fluctuations of perpendicular cylinders, we propose that combining nanopatterned substrates with electric fields perpendicular to the film could reach the ultimate goal of producing long-range ordered perpendicular cylinders as templates for nanolithography.
Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens (2016)

The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are the leading cause of nosocomial infections throughout the world. Most of them are multidrug resistant isolates, which is one of the greatest challenges in clinical practice. Multidrug resistance is amongst the top three threats to global public health and is usually caused by excessive drug usage or prescription, inappropriate use of antimicrobials, and substandard pharmaceuticals. Understanding the resistance mechanisms of these bacteria is crucial for the development of novel antimicrobial agents or other alternative tools to combat these public health challenges. Greater mechanistic understanding would also aid in the prediction of underlying or even unknown mechanisms of resistance, which could be applied to other emerging multidrug resistant pathogens. In this review, we summarize the known antimicrobial resistance mechanisms of ESKAPE pathogens.
Ordering the Cytochrome c–initiated Caspase Cascade: Hierarchical Activation of Caspases-2, -3, -6, -7, -8, and -10 in a Caspase-9–dependent Manner (1999)

Exit of cytochrome c from mitochondria into the cytosol has been implicated as an important step in apoptosis. In the cytosol, cytochrome c binds to the CED-4 homologue, Apaf-1, thereby triggering Apaf-1-mediated activation of caspase-9. Caspase-9 is thought to propagate the death signal by triggering other caspase activation events, the details of which remain obscure. Here, we report that six additional caspases (caspases-2, -3, -6, -7, -8, and -10) are processed in cell-free extracts in response to cytochrome c, and that three others (caspases-1, -4, and -5) failed to be activated under the same conditions. In vitro association assays confirmed that caspase-9 selectively bound to Apaf-1, whereas caspases-1, -2, -3, -6, -7, -8, and -10 did not. Depletion of caspase-9 from cell extracts abrogated cytochrome c-inducible activation of caspases-2, -3, -6, -7, -8, and -10, suggesting that caspase-9 is required for all of these downstream caspase activation events. Immunodepletion of caspases-3, -6, and -7 from cell extracts enabled us to order the sequence of caspase activation events downstream of caspase-9 and reveal the presence of a branched caspase cascade. Caspase-3 is required for the activation of four other caspases (-2, -6, -8, and -10) in this pathway and also participates in a feedback amplification loop involving caspase-9.
A vibrotactile music system based on sensory substitution. (2011)

The idea of the project reported here was to design a system that builds on touch to enable people with severe hearing impairments to “listen” to music through a process called sensory substitution. The goal was to transform the auditory parameter space into one that is adequate for haptic perception. The approach reported here builds on (i) the design of a haptic display, a tabletop device with 8–24 actuators that can be driven individually, (ii) machine learning algorithms, and (iii) a psychophysical study to determine which music cues can be perceived through touch. The latter was necessary because vibrotactile perception is not yet well understood in the context of music perception. The double-blind study analyzes how vibrotactile stimuli contribute to the perception, cognition, and distinction of sounds in human participants who have been trained versus those who have not. In order to ensure that normal-hearing participants could not hear sounds radiated from the haptic display, sound isolating headphones were used to playback pink noise during the experiment.
Voltage‐gated sodium channels and pain pathways (2004)

Acute, inflammatory, and neuropathic pain can all be attenuated or abolished by local treatment with sodium channel blockers such as lidocaine. The peripheral input that drives pain perception thus depends on the presence of functional voltage-gated sodium channels. Remarkably, two voltage-gated sodium channel genes (Nav1.8 and Nav1.9) are expressed selectively in damage-sensing peripheral neurons, while a third channel (Nav1.7) is found predominantly in sensory and sympathetic neurons. An embryonic channel (Nav1.3) is also upregulated in damaged peripheral nerves and associated with increased electrical excitability in neuropathic pain states. A combination of antisense and knock-out studies support a specialized role for these sodium channels in pain pathways, and pharmacological studies with conotoxins suggest that isotype-specific antagonists should be feasible. Taken together, these data suggest that isotype-specific sodium channel blockers could be useful analgesics.
HPLC를 이용한 축산물중 잔류페니실린 및 클로람페니콜의 동시분석법 연구 (2000)

This study was carried out to simultaneous determination of penicillin G and chloramphenicol in livestock products by HPLC. The results abstained were as follows 1. Penicillin G and chloramphenicol were analyzed by HPLC on symmetry C18 column with acetonitrile-0.1 M phosphate buffer containing 0.0157 M thiosulfate (25: 75) as mobile phase at UV 325nm and 280nm, respectively. 2. Samples were applied to a Sep-pak Cig cartridge, from which eluted penicillin derivatized with 2 M 1,2,4-triazole containing 0.001 M mercuric chloride. 3. The average recovery rates of penicillin G and chloramphenicol were 81.8% and 80.3%, respectively, and the detection limits were 5 ppb (5tg/kg: 7.91U/kg) for penicillin G and chloramphenicol in porcine and bovine muscle.
Study of Cockpit's Perspective on Human-Human Interactions to Guide Collaborative Decision Making Design in Air Traffic Management (2008)

This field research studies human-human interactions (HHI), seen from cockpit's perspective in context of collaborative decision making (CDM) during flight operation situations. It is based on the assumption that cooperation among all participating operators achieves positive effect on CDM operation. The aim of the research is to identify, how factors driving cooperative behaviour are established in flight operation situations during day-today HHI at action level. Obtained results are used to guide future CDM design with simulation software development and system behaviour simulation. In this paper, a cockpit survey is introduced which examines two highly dynamic flight operation situations. Both situations are usually time constrained, change quickly and require synchronous human-human cooperation between pilots and multiple other operators. The first one, turn-round operation, involves HHI with information sharing via face-to-face or technological means and HHI with task/decision making distribution between pilots and other operators. The second one, the flight operation itself, involves HHI with information sharing only via technological means and HHI with task/decision making distribution between pilots and other operators.
The ontogeny of germinal centre forming capacity of neonatal rat spleen. (1987)

In non-specifically immunized rats, bred under conventional conditions, the first 'spontaneous' germinal centres were observed by 21 days after birth. Deliberate antigenic stimulation led to an earlier appearance of germinal centres in neonatal spleen: immunization with sheep red blood cells as early as 7 days after birth resulted in germinal centre formation in the spleen as observed 7 days later. By that time the first primary follicles could also be observed, in both immunized and non-immunized rats. Although 3-day-old rats upon antigenic stimulation failed to generate germinal centres in their spleen, transfer experiments of 3-day-old spleen cells to lethally X-irradiated syngeneic adult recipients indicated that 3-day-old spleens at least contained all the essential lymphoid elements (B and T cells) needed for germinal centre formation. These results strongly suggest that the failure to induce germinal centres in 3-day-old rats is most probably due to an immaturity of their splenic microenvironment. Immunohistochemical staining of frozen sections of neonatal rat spleen using mAb ED 5 and MRC OX-2 showed that follicular dendritic cells (FDC) were found as soon as primary follicles were found (i.e. by 14 days after birth). The appearance of FDC in neonatal spleens was not influenced by deliberate antigenic stimulation nor by the administration of adult spleen cells. We postulate that, during the development of FDC, a splenic microenvironment is created that allows primary follicle formation and the generation of germinal centres.
The Ferrocenylethynyl Unit: a Stable Hormone Tag (2001)

We prepared the organometallic complex 17α-(ferrocenylethynyl)estradiol (=[(3,17β-dihydroxyestra-1,3,5(10)-trien-17α-yl)ethynyl]ferrocene; FcEE; 1) by a novel synthetic method. This metallocene possesses sufficient stability in aqueous media to permit the study of its biological properties. Thus, we were able to show that, despite the addition of a bulky substituent at the 17α position of the steroid, the metallocene is still well- recognized by an antibody specific to estradiol (CR=40%) and by both subtypes (ERα, ERβ) of the estrogen receptor (at 0°, RBA=28 and 37%, resp.). A DCI-MS study of the stability of the carbocation [FcEE−OH]+ showed moderate stabilization of the carbocation, in agreement with the pK value of −0.72 found for the metallocene by means of Deno's method. The presence of the ferrocene allows the electrochemical detection of FcEE (1) by HPLC-ED, with a detection limit of ca. 1 nM, suitable for quantitative pharmacological analysis.
Fatty acid composition of seed oils from sixAdansonia species with particular reference to cyclopropane and cyclopropene acids (1982)

The oil content of sixAdansonia species (Bombacaceae family) of Madagascar (Adansonia grandidieri, A. za, A. digitata, A. fony, A. madagascariensis andA. suarenzensis) and Africa (A. digitata) ranges from 8 to 46%. All the oils give a positive response to the Halphen test. Malvalic, sterculic and dihydrosterculic acids were detected using gas liquid chromatography-mass spectrometry (GLC-MS). Epoxy or hydroxy fatty acids were not found in these oils. Fatty acid composition was determined by GLC using glass capillary columns coated with BDS and Carbowax 20 M. Results obtained for cyclopropenic fatty acids (CPEFA) were compared to those given by glass capillary GLC after derivatization with silver nitrate in methanol, by hydrogen bromide titration and by proton magnetic resonance (PMR). Good agreement was observed for the results given by the various methods. Malvalic acid content ranges from 3 to 28%, sterculic acid from 1 to 8% and dihydrosterculic acid from 1.5 to 5.1%. Odd-numbered fatty acids (Pentadecanoic and hepatadecanoic) were also observed in minute amounts (0.1-1.1%). Among the normal fatty acids, we observed mainly palmitic (21-46%), oleic (15-40%) and linoleic (12-32%). The relationship between fatty acid composition andAdansonia species is discussed.
The herpesviral Fc receptor fcr-1 down-regulates the NKG2D ligands MULT-1 and H60 (2006)

Members of the alpha- and beta-subfamily of herpesviridae encode glycoproteins that specifically bind to the Fc part of immunoglobulin (Ig)G. Plasma membrane resident herpesviral Fc receptors seem to prevent virus-specific IgG from activating antibody-dependent effector functions. We show that the mouse cytomegalovirus (MCMV) molecule fcr-1 promotes a rapid down-regulation of NKG2D ligands murine UL16-binding protein like transcript (MULT)-1 and H60 from the cell surface. Deletion of the m138/fcr-1 gene from the MCMV genome attenuates viral replication to natural killer (NK) cell response in an NKG2D-dependent manner in vivo. A distinct N-terminal module within the fcr-1 ectodomain in conjunction with the fcr-1 transmembrane domain was required to dispose MULT-1 to degradation in lysosomes. In contrast, down-modulation of H60 required the complete fcr-1 ectodomain, implying independent modes of fcr-1 interaction with the NKG2D ligands. The results establish a novel viral strategy for down-modulating NK cell responses and highlight the impressive diversity of Fc receptor functions.
Ebola and Marburg Viruses: Pathogenesis and Development of Countermeasures (2005)

Ebola and Marburg viruses, family Filoviridae, are among the best known examples of emerging and re-emerging pathogens. Although outbreaks have been sporadic and geographically restricted to areas of Central Africa, the hemorrhagic fevers caused by these viruses are remarkably severe and are associated with high case fatality rates often exceeding 80 percent. In addition to humans, these viruses have decimated populations of wild apes in Central Africa. Currently, there are no vaccines or effective therapies available for human use. Progress in understanding the geneses of the pathophysiological changes that make filoviral infections of humans so destructive has been slow, primarily because these viruses require special containment for safe research. However, an increasing understanding of the molecular mechanisms of filoviral pathogenesis, facilitated by the development of new tools to elucidate critical regulatory elements in the viral life cycle, is providing new targets that can be exploited for therapeutic interventions. In addition, substantial progress has been made in developing recombinant vaccines against these viruses.
Tannic Acid Mediated Suppression of PNIPAAm Microgels Thermoresponsive Behavior (2011)

Tannic acid (TA) complexation with poly(N-isopropylacrylamide) (PNIPAAm) microgels changed their morphology and temperature responsiveness, depending on TA concentration and pH (below the TA pKa). Complexes prepared with a low TA content had higher low critical solution temperature than pure PNIPAAm microgels as a consequence of the hydrophilic character of TA; however, above a concentration threshold, TA physically cross-links the polymeric network, altering their morphology and suppressing the thermodynamically driven PNIPAAm coil-to-globule transition. DRIFT spectral analysis indicated that within PNIPAAm−TA complexes hydrogen bonds were established between PNIPAAm amide and TA phenolic (C═O···H-O and N−H···O−H) and ester (N−H···O−C) groups. At pH 4, H-bonding was more diverse and extensive than at pH 7; hence the complexes thermoresponsive behavior was altered at lower TA contents for the acidic pH. Above the TA pKa, H-bonding is destabilized and the complexes recovered their spherical morphology and the ability to respond to temperature stimulus, thus demonstrating a reversible process with pH.
Differential transcription of baculovirus late and very late promoters: fractionation of nuclear extracts by phosphocellulose chromatography (1995)

An in vitro transcription system based on cytidine-free cassette was developed for the late 39k gene and the very late polyhedrin gene of Autographa californica nuclear polyhedrosis virus (AcNPV). Optimization of transcription conditions revealed that a preincubation step was not required for transcription of late and very late promoters, although preincubation was essential for efficient transcription from an early promoter. The 39k and polyhedrin constructs were actively transcribed by nuclear extracts prepared from AcNPV-infected Spodoptera frugiperda cells at 12 or 36 h postinfection but not by nuclear extracts prepared from uninfected or infected cells harvested during the early phase of infection. Transcription from the very late polyhedrin promoter was fivefold higher than that from the 39k late promoter with the nuclear extract prepared at 36 h postinfection. The 36-h extract was fractionated by phosphocellulose chromatography. Transcription activity eluted in two fractions, at 0.3 and 0.5 M KCl. Both the 39k and polyhedrin constructs were transcribed by these fractions; however, the patterns of late and very late transcription were distinctly different. With the 0.3 M fraction, incorporation into the 39k transcript was approximately 10-fold higher than incorporation into the polyhedrin transcript. Alternatively, with the 0.5 M fraction, transcription of the polyhedrin construct was twofold higher than transcription of the 39k construct. These results indicate that this in vitro system will be useful for purification and identification of factors that discriminate between late and very late promoters.
Molecular mechanisms that control endothelial cell contacts (2000)

Endothelial cell contacts control the permeability of the blood vessel wall. This allows the endothelium to form a barrier for solutes, macromolecules, and leukocytes between the vessel lumen and the interstitial space. Loss of this barrier function in pathophysiological situations can lead to extracellular oedema. The ability of leukocytes to enter tissue at sites of inflammation is dependent on molecular mechanisms that allow leukocytes to adhere to the endothelium and to migrate through the endothelial cell layer and the underlying basal lamina. It is a commonly accepted working hypothesis that inter-endothelial cell contacts are actively opened and closed during this process. Angiogenesis is another important process that requires well-controlled regulation of inter-endothelial cell contacts. The formation of new blood vessels by sprouting from pre-existing vessels depends on the loosening of established endothelial cell contacts and the migration of endothelial cells that form the outgrowing sprouts. This review focuses on the molecular composition of endothelial cell surface proteins and proteins of the cytoskeletal undercoat of the plasma membrane at sites of inter-endothelial cell contacts and discusses the current knowledge about the potential role of such molecules in the regulation of endothelial cell contacts.
Use of wild‐type p53 to achieve complete treatment sensitization of tumor cells expressing endogenous mutant p53 (1995)

It is known that transfer of the wild-type p53 gene into p53-negative cells from transgenic mice increases their sensitivity to drug and radiation-induced apoptosis. However, unlike many human tumors, these transgenic cells do not express mutant p53, and it is not known from these earlier studies whether wild-type p53 dominates the effects of mutant p53 with respect to drug and radiation sensitivity. We addressed this question in glioblastoma, a disease characterized by an unusually high level of intrinsic resistance to therapy and poor prognosis: mean survival time from diagnosis is only about 1 yr. We introduced the gene for wild-type p53 into human T98G glioblastoma cells, which express endogenous mutant p53 but not wild-type p53. Stable transfectants that co-expressed mutant and wild-type p53 had enhanced sensitivity to cisplatin and gamma radiation, compared with parental cells, control vector-transduced cells, and transduced cells that had lost expression of wild-type p53. Transient wild-type p53 expression after high-efficiency gene transfer by a p53 adenovirus also sensitized the cells to cisplatin and correlated with the induction of apoptosis. The sensitization effect was also observed in p53 adenovirus-infected H23 small cell lung carcinoma cells, which express endogenous mutant p53. Therefore, wild-type p53 gene transfer has dominant effects over mutant p53 in sensitizing tumor cells to therapy, which supports the potential of p53 gene therapy to enhance the efficacy of traditional therapy.