gebhart/patrepeval huggingface dataset:
Rapamycin-FKBP Inhibits Cell Cycle Regulators of Proliferation in Vascular Smooth Muscle Cells (1995)

Multiple growth factors can stimulate quiescent vascular smooth muscle cells to exit from G0 and reenter the cell cycle. The macrolide antibiotic rapamycin, bound to its cytosolic receptor FKBP, is an immunosuppressant and a potent inhibitor of cellular proliferation. In the present study, the antiproliferative effects of rapamycin on human and rat vascular smooth muscle cells were examined and compared with the effects of a related immunosuppressant, FK520. In vascular smooth muscle cells, rapamycin, at concentrations as low as 1 ng/mL, inhibited DNA synthesis and cell growth. FK520, an analogue of the immunosuppressant FK506, is structurally related to rapamycin and binds to FKBP but did not inhibit vascular smooth muscle cell growth. Molar excesses of FK520 blocked the antiproliferative effects of rapamycin, indicating that the effects of rapamycin required binding to FKBP. Rapamycin-FKBP inhibited retinoblastoma protein phosphorylation at the G1/S transition. This inhibition of retinoblastoma protein phosphorylation was associated with a decrease in p33cdk2 kinase activity. These observations suggest that rapamycin, but not FK520, inhibits vascular smooth muscle cell proliferation by reducing cell-cycle kinase activity.
Pathways of Reductive Fragmentation of Heterocyclic Nitroarylmethyl Quaternary Ammonium Prodrugs of Mechlorethamine (2002)

Kriste, A. G., Tercel, M., Anderson, R. F., Ferry, D. M. and Wilson, W. R. Pathways of Reductive Fragmentation of Heterocyclic Nitroarylmethyl Quaternary Ammonium Prodrugs of Mechlorethamine. Radiat. Res. 158, 753–762 (2002).Nitroarylmethyl quaternary (NMQ) ammonium salts have potential as prodrugs for enzymatic or radiolytic reduction to release amine effectors under hypoxia. Earlier studies demonstrated one-electron release of the cytotoxic amine mechlorethamine (HN2) from 4-nitroimidazolyl and 2-nitropyrrolyl NMQ prodrugs (but not from nitrobenzyl analogs) through intramolecular electron transfer. In this study we determined whether this is a general feature of heterocyclic NMQ prodrugs of HN2 and examined the reductive pathways in detail using pulse and steady-state radiolysis. The kinetics of radical fragmentation varied by more than four orders of magnitude, independently of the one-electron reduction potential, within the series of eight nitroheterocycles examined. In addition to the compounds identified previously, new 2-nitropyrrole and 3-nitrothiophene NMQ prodrugs were found to provide efficient HN2 release (G > 0.5 μmol/J in anoxic formate buffer). However, the nitrothiophene was sensitive to nucleophilic displacement of HN2, making it less promising. Product analysis by HPLC/mass spectrometry identified symmetrical dimers arising from benzyl-type radical intermediates but also demonstrated that these dimers are not reliable markers for the intramolecular fragmentation of the initial nitro radical anion. This study elucidated multiple competing pathways for reductive fragmentation of NMQ prodrugs and identified the preferred electron acceptors for use in the development of analogs that release more potent cytotoxins.
The Influence of the Maternal Heart Rate on the Uterine Artery Pulsatility Index in the Pregnant Ewe (1999)

We investigated the influence of the maternal heart rate on the uterine artery pulsatility index in pregnant ewes. We used an external pacemaker to alter the heart rate of 5 pregnant ewes at 16-17 weeks of pregnancy and examined the effect of changes in the maternal heart rate on the uterine artery flow velocity waveforms and the pulsatility index, as determined by Doppler velocimetry. The uterine artery pulsatility index showed a significant negative correlation with the maternal heart rate. There were no significant changes in other hemodynamic parameters. The maternal heart rate had a significant influence on the uterine artery pulsatility index.
Quantum repeaters based on atomic ensembles and linear optics (2011)

The distribution of quantum states over long distances is limited by photon loss. Straightforward amplification as in classical telecommunications is not an option in quantum communication because of the no-cloning theorem. This problem could be overcome by implementing quantum repeater protocols, which create long-distance entanglement from shorter-distance entanglement via entanglement swapping. Such protocols require the capacity to create entanglement in a heralded fashion, to store it in quantum memories, and to swap it. One attractive general strategy for realizing quantum repeaters is based on the use of atomic ensembles as quantum memories, in combination with linear optical techniques and photon counting to perform all required operations. Here the theoretical and experimental status quo of this very active field are reviewed. The potentials of different approaches are compared quantitatively, with a focus on the most immediate goal of outperforming the direct transmission of photons.
Influence of cationic lipid concentration on properties of lipid&ndash;polymer hybrid nanospheres for gene delivery (2015)

Nanoparticles have been widely used for nonviral gene delivery. Recently, cationic hybrid nanoparticles consisting of two different materials were suggested as a promising delivery vehicle. In this study, nanospheres with a poly(D,L-lactic-co-glycolic acid) (PLGA) core and cationic lipid shell were prepared, and the effect of cationic lipid concentrations on the properties of lipid polymer hybrid nanocarriers investigated. Lipid-polymer hybrid nanospheres (LPHNSs) were fabricated by the emulsion-solvent evaporation method using different concentrations of cationic lipids and characterized for size, surface charge, stability, plasmid DNA-binding capacity, cytotoxicity, and transfection efficiency. All LPHNSs had narrow size distribution with positive surface charges (ζ-potential 52-60 mV), and showed excellent plasmid DNA-binding capacity. In vitro cytotoxicity measurements with HEK293T, HeLa, HaCaT, and HepG2 cells also showed that LPHNSs exhibited less cytotoxicity than conventional transfection agents, such as Lipofectamine and polyethyleneimine-PLGA. As cationic lipid concentrations increased, the particle size of LPHNSs decreased while their ζ-potential increased. In addition, the in vitro transfection efficiency of LPHNSs increased as lipid concentration increased.
Rapid antibiotic susceptibility testing by tracking single cell growth in a microfluidic agarose channel system (2012)

Sepsis is one of the major causes of death in the US, necessitating rapid treatment with proper antibiotics. Conventional systems for antibiotic susceptibility testing (AST) take far too long (16-24 h) for the timely treatment of sepsis. This is because they rely on measuring optical density, which relates to bacterial growth, to determine the minimal inhibitory concentrations (MICs) of relevant antibiotics. Thus, there is a desperate need for more improved and rapid AST (RAST) systems. The RAST system can also reduce the growing number of clinical problems that are associated with antibiotic resistance caused by methicillin-resistant Staphylococcus aureus, vancomycin-resistant Staphylococcus aureus, and vancomycin-resistant enterococci. In this study, we demonstrate a microfluidic agarose channel (MAC) system that reduces the AST assay time for determining MICs by single bacterial time lapse imaging. The MAC system immobilizes bacteria by using agarose in a microfluidic culture chamber so that single cell growth can be tracked by microscopy. Time lapse images of single bacterial cells under different antibiotic culture conditions were analyzed by image processing to determine MICs. Three standard bacteria from the Clinical and Laboratory Standard Institute (CLSI) were tested with several kinds of antibiotics. MIC values that were well matched with those of the CLSI were obtained within only 3-4 h. We expect that the MAC system can offer rapid diagnosis of sepsis and thus, more efficient and proper medication in the clinical setting.
A NOVEL HYBRID PRINTING SYSTEM FOR THE GENERATION OF ORGANIZED BLADDER TISSUE (2009)

You have accessJournal of Urology1 Apr 2009A NOVEL HYBRID PRINTING SYSTEM FOR THE GENERATION OF ORGANIZED BLADDER TISSUE Claudius Fullhase, Roberto Soler, Anthony Atala, Karl-Erik Andersson, and James J Yoo Claudius FullhaseClaudius Fullhase , Roberto SolerRoberto Soler , Anthony AtalaAnthony Atala , Karl-Erik AnderssonKarl-Erik Andersson , and James J YooJames J Yoo View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)60805-3AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "A NOVEL HYBRID PRINTING SYSTEM FOR THE GENERATION OF ORGANIZED BLADDER TISSUE." The Journal of Urology, 181(4S), pp. 282–283 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 282-283 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information Claudius Fullhase More articles by this author Roberto Soler More articles by this author Anthony Atala More articles by this author Karl-Erik Andersson More articles by this author James J Yoo More articles by this author Expand All Advertisement PDF downloadLoading ...
Gamma Oscillations in the Hippocampus (2010)

Gamma oscillations are thought to temporally link the activity of distributed cells. We discuss mechanisms of gamma oscillations in the hippocampus and review evidence supporting a functional role for such oscillations in several key hippocampal operations, including cell grouping, dynamic routing, and memory. We propose that memory encoding and retrieval are coordinated by different frequencies of hippocampal gamma oscillations and suggest how transitions between slow and fast gamma may occur.
Synthesis of Albumin and Malic Enzyme in Wheat‐Germ Lysates and Xenopus laevis Oocytes Programmed with Chicken‐Liver Messenger RNA (1979)

Undegraded, biologically-active, polyadenylated RNA was isolated from chicken liver by a rapid, simple procedure. Liver cells were dispersed mechanically and then broken gently by controlled Dounce homogenization in the absence of detergent or ribonuclease inhibitors. After removing lysosomes and mitochondria by centrifugation, RNA was precipitated at pH 5.2. Polyadenylated mRNA was isolated directly from the detergent-solubilized precipitate by oligo(dT)-cellulose chromatography. The resulting RNA was translated into liver-specific peptides in both the wheat germ lysate and Xenopus laevis oocytes. Translatable albumin mRNA was detected in the liver cytoplasm of both fed 3-week-old chicks and unfed, day-old chicks. Translatable malic enzyme mRNA was only detected in the livers from the fed chicks.
Fitting a mixture model by expectation maximization to discover motifs in biopolymers. (1994)

The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs. The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input. It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset.
Association of phycoerythrin and phycocyanin: in vitro formation of a functional energy transferring phycobilisome complex of Porphyridium sordidum (1981)

Functional in vitro association and dissociation of a phycobiliprotein complex, isolated from phycobilisomes of the red alga Porphyridium sordidum, were studied. The complex contained large bangiophyceaen phycoerythrin and cyanophytan phycocyanin in an equimolar ration and had absorption maxima at 625, 567, and 550 nm and a shoulder at 495 nm. Emission at 655 nm (with excitation at 545 nm) from phycocyanin indicated functional coupling. The complex was stable over a wide buffer concentration range, and, notably, it was maximally stable in low phosphate, less than 0.01 M, unlike the phycobilisomes, which dissociate at this concentration. Its molecular weight was estimated to be ca. 510000, and by electron microscopy it was seen to consist of two units of similar size. The complex in 0.1 M phosphate was separated on a sucrose gradient into a homogeneous phycoerythrin band and a spectrally heterogeneous phycocyanin band. In vitro association of phycoerythrin and phycocyanin resulted in a complex with the same absorbance, emission, sedimentation and molar pigment ratio as those of the native complex. The spectrally heterogeneous phycocyanin fractions from the dissociation gradient varied in the degree of association with phycoerythrin. Phycocyanin fractions absorbing from 622 to 633 nm exhibited high associability (greater than 70%), whereas those with maxima at 617-620 nm had low associability (less than 30%). The presence of a 30000 molecular weight polypeptide accompanied high associability, where it was ca. 2-fold more prominent. It is suggested that this polypeptide is involved in complex formation and could serve either in the stabilization of the conformational state of cyanophytan phycocyanin or as a direct linker between phycobiliproteins.
Towards the Self Healing Vehicle (2007)

This paper addresses the question of how an intelligent vehicle could play a more proactive role in fault management. In particular, it describes the concept of the Self Healing Vehicle: a vehicle with the ability to autonomously predict or detect and diagnose failure conditions, confirm any given diagnosis, and perform appropriate corrective intervention(s), including the use of telematics to interact with external service providers and infrastructures. The key research questions that need to be answered in order for a self healing vehicle to be realised are explored, and a framework for how this concept might be realised is presented.
Human papillomavirus vaccines for the prevention and treatment of cervical cancer. (2004)

The identification of human papillomavirus (HPV) as a cause of cervical cancer and its precursor lesions indicates that HPV vaccines can potentially be used to prevent or treat cervical cancer and other HPV-associated malignancies. Prophylactic HPV vaccines aim to prevent infection by producing neutralizing antibodies against HPV capsid proteins L1 and L2. However, because HPV-infected basal keratinocytes and HPV-transformed cells generally do not express L1 or L2, therapeutic HPV vaccines are being developed to treat established HPV infections and HPV-associated malignancies by targeting non-structural early viral antigens of HPV, such as E6 and E7 (two viral oncogenic proteins required for the induction and maintenance of malignant cancer). Results from preclinical HPV vaccine studies have led to several HPV vaccine clinical trials. If these prophylactic and therapeutic HPV vaccines prove as successful in patients as they have in animal models, HPV vaccines may have a role in the control of HPV infection and HPV-associated disease.
The human saphenous vein in pharmacology: effect of a new micronized flavonoidic fraction (Daflon 500 mg) on norepinephrine induced contraction. (1995)

Local acidosis (pH 6.4) depresses reactivity of vascular smooth muscle and especially the response of human isolated saphenous veins to exogenous norepinephrine. Experiments were performed to study, under acidosis conditions, the interaction between Daflon 500 mg, a micronized fraction of 90% diosmin and 10% hesperidin, and norepinephrine on human rings of veins. Varicose veins were obtained by conservative varicose veins surgery and normal veins from patients undergoing coronary artery bypass graft surgery. Isometric tension was recorded from venous rings in organ chambers filled with Krebs-Henseleit solution (pH 7.4; 37 degrees C). Metabolic acidosis (from pH 7.4 to 6.4) was obtained by lowering the HCO3- concentration of the Krebs-Henseleit solution. Cumulative concentration-response curves for norepinephrine (10(-7) to 10(-5)M) were obtained at pH 6.4 in the presence or in the absence of Daflon 500 mg (10(-5)M) added 20 min previously to the organ bath. Under acidotic conditions, Daflon 500 mg induced a shift to the left of the concentration-response curves for norepinephrine. This potentiation was significant in both normal and varicose veins and was increased in proportion with the pathological status of the venous rings. These results support the therapeutic benefits of Daflon 500 mg in chronic venous insufficiency.
Online Multi-object Tracking via Structural Constraint Event Aggregation (2016)

Multi-object tracking (MOT) becomes more challenging when objects of interest have similar appearances. In that case, the motion cues are particularly useful for discriminating multiple objects. However, for online 2D MOT in scenes acquired from moving cameras, observable motion cues are complicated by global camera movements and thus not always smooth or predictable. To deal with such unexpected camera motion for online 2D MOT, a structural motion constraint between objects has been utilized thanks to its robustness to camera motion. In this paper, we propose a new data association method that effectively exploits structural motion constraints in the presence of large camera motion. In addition, to further improve the robustness of data association against mis-detections and false positives, a novel event aggregation approach is developed to integrate structural constraints in assignment costs for online MOT. Experimental results on a large number of datasets demonstrate the effectiveness of the proposed algorithm for online 2D MOT.
Mechanisms of eosinophil adherence to cultured vascular endothelial cells. Eosinophils bind to the cytokine-induced ligand vascular cell adhesion molecule-1 via the very late activation antigen-4 integrin receptor. (1991)

We have examined the mechanisms involved in the adherence of normal peripheral blood eosinophils to cultured human umbilical vein endothelial cells (HEC) under three conditions: (a) adherence in the absence of treatment of HEC or eosinophils with activating agents (basal adherence); (b) adherence induced by stimulation of eosinophils with phorbol ester (eosinophil-dependent adherence); and (c) adherence induced by pretreatment of HEC with LPS, tumor necrosis factor (TNF), or IL-1 (endothelial-dependent adherence). A mechanism was identified that was equally active in basal, eosinophil-dependent, and endothelial-dependent adherence. This mechanism was optimally active in the presence of both Ca++ and Mg++, and reduced in the presence of Ca++ only or Mg++ only. Furthermore, like the other mechanisms of eosinophil adherence, it was active at 37 degrees C but not at 4 degrees C. A second mechanism of adherence was involved in eosinophil- and in endothelial-dependent adherence. This mechanism was dependent on the CD11/CD18 adhesion complex of eosinophils (i.e., inhibited by anti-CD18 MAb) and it was active in the presence of Ca++ and Mg++ or Mg++ only, but not Ca++ only. The third mechanism of adherence was specific for endothelial-dependent adherence. It involved the endothelial ligand vascular cell adhesion molecule-1 (VCAM-1) and the eosinophil receptor very late activation antigen-4 (VLA-4, CD49d/CD29, i.e., inhibited by anti-VCAM-1 MAb or anti-VLA-4 MAb). This mechanism was active in the presence of Ca++ and Mg++ but not of Ca++ only or Mg++ only, and was not up- or downregulated when eosinophils were stimulated with phorbol ester. In contrast, the endothelial leukocyte adhesion molecule-1 (ELAM-1), that binds neutrophils and monocytes, was not involved in eosinophil adherence to LPS-, TNF-, or IL-1-stimulated HEC (i.e., not inhibited by anti-ELAM-1 MAb). We conclude that eosinophils, like monocytes and lymphocytes, bind to the cytokine-induced endothelial ligand VCAM-1 via the integrin receptor VLA-4.
The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme. (1991)

The N-end rule relates the in vivo half-life of a protein to the identity of its amino-terminal residue. Distinct versions of the N-end rule operate in all organisms examined, from mammals to bacteria. We show that UBC2(RAD6), one of at least seven ubiquitin-conjugating enzymes in the yeast Saccharomyces cerevisiae, is essential for multiubiquitination and degradation of the N-end rule substrates. We also show that UBC2 is physically associated with UBR1, the recognition component of the N-end rule pathway. These results indicate that some of the UBC2 functions, which include DNA repair, induced mutagenesis, sporulation, and regulation of retrotransposition, are mediated by protein degradation via the N-end rule pathway.
The role of trehalose synthesis for the acquisition of thermotolerance in yeast (1994)

In baker's yeast (Saccharomyces cerevisiae), accumulation of the non-reducing disaccharide, trehalose, is triggered by stimuli that activate the heat-shock response. Previously, trehalose levels have been shown to be closely correlated with thermotolerance, suggesting a protective function of this substance. Genetic evidence in support of this view is presented in an accompanying paper [De Virgilio, C., Hottiger, T., Dominguez, J., Boller, T. & Wiemken, A. (1993) Eur. J. Biochem. 219, 179-186]. In this study, we have examined the effect of trehalose on the thermal stability of proteins, a parameter thought to be a major determinant of thermotolerance. Physiological concentrations of trehalose (up to 0.5 M) were found to efficiently protect enzymes of yeast (glucose-6P-dehydrogenase, phosphoglucose-isomerase) as well as enzymes of non-yeast origin (bovine glutamic dehydrogenase, EcoRI) against heat inactivation in vitro. Trehalose also reduced the heat-induced formation of protein aggregates. The disaccharide proved to be a compatible solute, as even at very high concentrations (up to 1 M) it did not significantly interfere with the activity of test enzymes. Trehalose was at least as good or better a protein stabilizer than any of a number of other compatible solutes (including sugars, polyalcohols and amino acids), while the structurally related trehalose-6P was devoid of any protective effect. Thermoprotection of enzymes by trehalose was evident even in solutions containing high concentrations of yeast protein or substrate. The data indicate that trehalose accumulation may increase the thermotolerance of yeast by enhancing protein stability in intact cells.
Solder Joint Reliability of a Low Cost Chip Size Package - NuCSP (1997)

The accumulated elasto-plastic strain range and the time-dependent elasto-plastic-creep deformation of a wire bondable land grid array (LGA) chip size package (NuCSP) assembly's solder joint under thermal cycling condition are presented. The solder is assumed to be a temperature-dependent material. The thermal fatigue life of the solder joint is estimated based on two methods, namely, the accumulated plastic strain range and Coffin-Manson equation, and viscoplastic strain energy density and an empirical equation based on the assumption of linear fatigue crack growth.