gebhart/patrepeval huggingface dataset:
Relationship between DNA Methylation and Mutational Patterns Induced by a Sequence Selective Minor Groove Methylating Agent (1999)

Me-lex, a methyl sulfonate ester appended to a neutral N-methylpyrrolecarboxamide-based dipeptide, was synthesized to preferentially generate N3-methyladenine (3-MeA) adducts which are expected to be cytotoxic rather than mutagenic DNA lesions. In the present study, the sequence specificity for DNA alkylation by Me-lex was determined in the p53 cDNA through the conversion of the adducted sites into single strand breaks and sequencing gel analysis. In order to establish the mutagenic and lethal properties of Me-lex lesions, a yeast expression vector harboring the human wild-type p53 cDNA was treated in vitro with Me-lex, and transfected into a yeast strain containing the ADE2 gene regulated by a p53-responsive promoter. The results showed that: 1) more than 99% of the lesions induced by Me-lex are 3-MeA; 2) the co-addition of distamycin quantitatively inhibited methylation at all minor groove sites; 3) Me-lex selectively methylated A's that are in, or immediately adjacent to, the lex equilibrium binding sites; 4) all but 6 of the 33 independent mutations were base pair substitutions, the majority of which (17/33; 52%) were AT-targeted; 5) AT --> TA transversions were the predominant mutations observed (13/33; 39%); 6) 13 out of 33 (39%) independent mutations involved a single lex-binding site encompassing positions A600-602 and 9 occurred at position 602 which is a real Me-lex mutation hotspot (n = 9, p < 10(-6), Poisson's normal distribution). A hypothetical model for the interpretation of mutational events at this site is proposed. The present work is the first report on mutational properties of Me-lex. Our results suggest that 3-MeA is not only a cytotoxic but also a premutagenic lesion which exerts this unexpected property in a strict sequence-dependent manner.
Activation of MAP kinases, pp90<sup>rsk</sup> and pp70‐S6 kinases in mouse mast cells by signaling through the c‐kit receptor tyrosine kinase or FcϵRI: rapamycin inhibits activation of pp70‐S6 kinase and proliferation in mouse mast cells (1993)

The high-affinity receptor for IgE, Fc epsilon RI, represents the major cell surface structure through which mast cells express immunologically specific secretory function. By contrast, the stem cell factor receptor (SCFR), which is encoded by c-kit, is essential for normal mast cell development. The signaling pathways initiated by the stimulation of mast cells through the Fc epsilon RI, which lacks intrinsic kinase activity, and the SCFR, a member of the receptor tyrosine kinase family, generally have been regarded to be distinct. We report here that mouse mast cells stimulated either with SCF or with IgE and specific antigen exhibit a remarkably similar pattern of activation of mitogen-activated protein kinases (MAPK), 90 kDa-S6 kinases (pp90rsk), and pp70-S6 kinases (pp70-S6K). These results indicate that all three families of protein kinases are associated with the cell surface receptor-dependent activation of secretion, as well as proliferation, in mast cells. We also show that the immunosuppressant rapamycin, but not FK506, can inhibit both SCF-dependent pp70-S6 kinase activation and SCF-dependent proliferation in mouse mast cells, without suppressing IgE- and antigen-dependent mediator release. These findings suggest that the activation of pp70-S6 kinase represents an important link in the stimulation of cell proliferation by SCF. Our results also indicate that the intracellular signaling pathways initiated by stimulation of mast cells through the Fc epsilon RI or the SCFR exhibit more overlap than has previously been appreciated.
Synthesis, Characterization, and Catalytic Properties of Diphenyl- and Dichlorobutyltin Functionalities Grafted to Insoluble Polystyrene Beads by a −(CH<sub>2</sub>)<i><sub>n</sub></i>− (<i>n</i> = 4, 6) Spacer (2001)

Insoluble diorganotin functionalized polymers of the type (P−H)1-t(P−(CH2)nSnBuX2)t, with n = 4, 6, X = Ph, Cl, and t being the degree of functionalization, were synthesized from Amberlite XE-305, an insoluble polystyrene (P−H) cross-linked with divinylbenzene. The synthesis conditions used gave rise to functionalization degrees varying from 25% to 30%. The tin-functionalized polystyrenes were characterized by elemental analysis, IR, and Raman as well as solid-state 117Sn and 13C NMR spectroscopy. Methodological and chemical features related to the determination of the functionalization degree have been investigated in detail. The catalytic activity of the Amberlite-grafted tin functionalities in transesterification reactions was studied.
Ion-implantation and activation behavior of Si in MBE-Grown GaAs on Si substrates for GaAs MESFET's (1987)

The suitability of MBE-grown GaAs layers on Si substrates has been studied for ion-implanted GaAs MESFET technology. The undoped as-grown GaAs layers had a carrier concentration below 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . Uniform Si ion implants into 4-µm-thick GaAs layers on Si were annealed at 900°C for 10 s, using a rapid-thermal-annealing (RTA) system. Both the activation and the doping profile were similar to those obtained in bulk semi-insulating GaAs under similar conditions. The SIMS profiles of Si and As atoms near the GaAs/Si heterointerface were identical before and after the RTA process, indicating negigible interdiffusion during the implant activation. Dual implants of a shallow n+ layer and an n-channel layer were used to fabricate GaAs MESFET's with a recess-gate technology. Selective oxygen ion implantation was used for device isolation. The maximum transconductance obtained was 135 mS/ mm compared to typical values of 150-180 mS/mm obtained in our laboratory on GaAs substrates in similar device structures.
Learning to discover objects in RGB-D images using correlation clustering (2013)

We introduce a method to discover objects from RGB-D image collections which does not require a user to specify the number of objects expected to be found. We propose a probabilistic formulation to find pairwise similarity between image segments, using a classifier trained on labelled pairs from the recently released RGB-D Object Dataset. We then use a correlation clustering solver to both find the optimal clustering of all the segments in the collection and to recover the number of clusters. Unlike traditional supervised learning methods, our training data need not be of the same class or category as the objects we expect to discover. We show that this parameter-free supervised clustering method has superior performance to traditional clustering methods.
Multiple-Choice Tests Exonerated, at Least of Some Charges (2012)

Among the criticisms of multiple-choice tests is that-by exposing the correct answer as one of the alternatives-such tests engage recognition processes rather than the productive retrieval processes known to enhance later recall. We tested whether multiple-choice tests could trigger productive retrieval processes-provided the alternatives were made plausible enough to enable test takers to retrieve both why the correct alternatives were correct and why the incorrect alternatives were incorrect. In two experiments, we found not only that properly constructed multiple-choice tests can indeed trigger productive retrieval processes, but also that they had one potentially important advantage over cued-recall tests. Both testing formats fostered retention of previously tested information, but multiple-choice tests also facilitated recall of information pertaining to incorrect alternatives, whereas cued-recall tests did not. Thus, multiple-choice tests can be constructed so that they exercise the very retrieval processes they have been accused of bypassing.
Molecular cloning and expression of a cDNA encoding a receptor for pituitary adenylate cyclase activating polypeptide (PACAP) (1993)

We have cloned and sequenced a novel cDNA (RPR7) encoding a receptor for pituitary adenylate cyclase activating polypeptide (PACAP). RPR7 was identified by PCR of rat pituitary cDNA, and full-length clones were isolated from a rat olfactory bulb cDNA library. When expressed in COS cells, RPR7 was functionally coupled to increases in intracellular cyclic adenosine monophosphate (cAMP) in response to stimulation by PACAP-38, PACAP-27, vasoactive intestinal peptide (VIP) and peptide histidine isoleucine (PHI). The order of potency of these ligands was PACAP-38-PACAP-27 > VIP > PHI, suggesting that the receptor corresponds to the pharmacologically characterised PACAP Type I receptor.
Plant resistance to parasitic nematodes (2002)

<title>Abstract</title> This book describes methods for evaluating the resistance and tolerance of plant cultivars to important parasitic nematode species, such as root-knot, cyst and reniform, and discusses the concepts and consequences of resistance. This book provides an invaluable source of information to all plant pathologists, nematologists and plant breeders.
Thermostable mannose-binding lectin from Dendrobium findleyanum with activities dependent on sulfhydryl content. (2008)

A mannose-binding lectin was purified from Dendrobium (D.) findleyanum pseudobulb using mannan-agarose column chromatography. After heating in the presence of SDS with or without 2-mercaptoethanol on SDS-PAGE with a continuous gradient of 8%-20% acrylamide, the purified lectin showed only one protein band with a molecular mass of 14.5 kDa. Without heating, two bands were seen on the gel at the positions of 14.5 kDa and 53.7 kDa, but a higher amount of the 53.7 kDa protein was observed in the presence of 2-mercaptoethanol. Protein identification of both protein bands by liquid chromatography-tandem mass spectrometry showed three peptide fragments identical to parts of a lectin precursor from D. officinale; the lectin was named D. findleyanum agglutinin (DFA). Using various concentrations of native-PAGE and Ferguson plot, only one protein band revealed a molecular mass of 56.2 kDa, indicating four 14.5 kDa polypeptide subunits in the DFA. Isoelectric focusing revealed that the DFA had three conformational forms with an isoelectric point of 5.18, 4.87 and 4.72, whereas 2-mercaptoethanol-treated DFA showed only one band with an isoelectric point of 5.18. DFA exhibited specificity towards mannose using the solid-phase method. The binding activity, anti-fungal activity and hemagglutination activity of DFA were not affected by heat, but were increased by free sulfhydryl groups.
The IgG Subclass Responses to Influenza Virus Haemagglutinin in the Mouse: Effect of Route of Inoculation (1989)

The influence of the route of infection, regime of inoculation and virus preparation on murine IgG subclass responses to the haemagglutinin of influenza A virus were examined. Virus preparations inoculated by the intraperitoneal, intravenous, intramuscular and intranasal routes were found to induce different IgG subclass profiles after a primary and secondary dose. IgG2a was found to be a major contributor to the responses elicited by all virus preparations irrespective of the route of inoculation. The magnitude of the response varied with the number of doses of virus and the route of inoculation; the intravenous and intramuscular routes produced the largest responses after two doses of virus. Evidence for the local production of antibody is presented and the influence of antigen presentation on the induction of different subclass is discussed.
Mitochondrial mechanism of microvascular endothelial cells apoptosis in hyperhomocysteinemia (2006)

An elevated level of homocysteine (Hcy) limits the growth and induces apoptosis. However, the mechanism of Hcy-induced programmed cell death in endothelial cells is largely unknown. We hypothesize that Hcy induces intracellular reactive oxygen species (ROS) production that leads to the loss of transmembrane mitochondrial potential (Deltapsi(m)) accompanied by the release of cytochrome-c from mitochondria. Cytochrome-c release contributes to caspase activation, such as caspase-9, caspase-6, and caspase-3, which results in the degradation of numerous nuclear proteins including poly (ADP-ribose) polymerase (PARP), which subsequently leads to the internucleosomal cleavage of DNA, resulting cell death. In this study, rat heart microvascular endothelial cells (MVEC) were treated with different doses of Hcy at different time intervals. Apoptosis was measured by DNA laddering and transferase-mediated dUTP nick-end labeling (TUNEL) assay. ROS production and MP were determined using fluorescent probes (2,7-dichlorofluorescein (DCFH-DA) and 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethyl-benzamidazolocarbocyanin iodide (JC-1), respectively, by confocal microscopy. Differential gene expression for apoptosis was analyzed by cDNA array. The results showed that Hcy-mediated ROS production preceded the loss of MP, the release of cytochrome-c, and the activation of caspase-9 and -3. Moreover the Hcy treatment resulted in a decrease in Bcl(2)/Bax ratio, evaluated by mRNA levels. Caspase-9 and -3 were activated, causing cleavage of PARP, a hallmark of apoptosis and internucleosomal DNA fragmentation. The cytotoxic effect of Hcy was blocked by using small interfering RNA (siRNA)-mediated suppression of caspase-9 in MVEC. Suppressing the activation of caspase-9 inhibited the activation of caspase -3 and enhanced the cell viability and MP. Our data suggested that Hcy-mediated ROS production promotes endothelial cell death in part by disturbing MP, which results in subsequent release of cytochrome-c and activation of caspase-9 and 3, leading to cell death.
Performance and statistical analysis of two-layer MPEG coding algorithms for ATM networks (1996)

Two-layer video encoding algorithms for asynchronous transfer mode (ATM) networks are examined. Three encoding schemes are considered to prioritise the data using either requantisation or spectral separation or a proposed hybrid combination of both methods. The hybrid coder assigns components of the video data stream to one of two priority layers based on the macroblock type and the algorithm structure. Statistics of cells-per-frame processes generated by the proposed hybrid encoder such as the cell rate distribution and autocorrelation function are evaluated. It is observed that the processes are nonstationary and a gamma density function is a suitable model for the cell rate distribution in both layers. Two multiplicative ARIMA models are derived to represent the nonstationary processes mathematically. The statistics measured from a sample video sequence compare favourably with those obtained by this model. Statistics gathered from these prioritisation schemes can be useful for network design and resource management. Simulations are performed using a 5-second video sequence.
Interleukin-7-Dependent Expansion and Persistence of Melanoma-Specific T Cells in Lymphodepleted Mice Lead to Tumor Regression and Editing (2005)

Active-specific immunotherapy with dendritic cells loaded with peptide derived from the melanoma antigen, gp100, failed to mediate regression of established B16F10 melanoma in normal mice. Dendritic cell vaccination induced activation and subsequent deletion of adoptively transferred naive CD8+ T-cell receptor transgenic (pmel-1) T cells specific for gp100 in normal mice. In lymphodepleted mice, dendritic cell vaccination produced greater T-cell expansion, long-term persistence of memory T cells, and tumor regression. Most tumors that persisted in the presence of functional memory T cells had either lost or exhibited reduced expression of MHC class I or gp100 proteins. In contrast to other naive T cells, pmel-1 T cells adoptively transferred to lymphodepleted mice exhibited faster proliferation and a more differentiated phenotype after exposure to peptide-pulsed dendritic cells. Proliferation and persistence of pmel-1 T cells was highly dependent on interleukin-7 (IL-7) in irradiated mice, and IL-15 when IL-7 was neutralized, two critical homeostatic cytokines produced in response to the irradiation-induced lymphodepletion.
Evaluation of Potential Fields mobility strategies for aerial network provisioning (2011)

In this research work we evaluate a Potential Fields based strategy for providing communication services from Unmanned Aerial Vehicles (UAVs) to a moving crowd of users on the ground. In order to reach this goal we equip UAVs with cellular / WiFi femto cells. In our approach we organize the UAVs in a meshed topology to be robust towards failures and - when compared to centralized architectures - highly adaptive to changes in the (communication) environment. We use virtual Potential Fields to influence the UAVs' mobility behavior and keep the orthogonal requirements of ground area coverage and ground service provisioning time in optimal balance.
Fibronectin enhances the opsonic and protective activity of monoclonal and polyclonal antibody against group B streptococci. (1984)

We have investigated the opsonic and protective effects of fibronectin (FN) against type III group B streptococci. When used by itself, the FN failed to promote actual internalization of group B organisms. The addition of FN to group B streptococci that had been preopsonized in an immunoglobulin preparation modified for intravenous use ( IgIV ) or a type-specific, murine monoclonal antibody of IgG isotype markedly enhanced interaction with human polymorphonuclear leukocytes (PMN). A similar enhanced effect was observed when the FN was combined with type-specific monoclonal antibody preparations of IgM and, surprisingly, IgA isotype. Preincubation experiments indicated that the major effect was upon the PMN rather than directly on the bacteria, but we could not demonstrate an effect of FN on cell surface receptors for the Fc fragment of Ig or C3b using rosetting techniques. In addition to enhancing the in vitro opsonic activity of Ig, the FN significantly increased the protective effect of the polyclonal and monoclonal Ig preparations in an animal model of neonatal group B streptococcal disease. Thus, FN appears to have a critical role in the host defense mechanisms against group B streptococci.
Quantification of the second-order nonlinear susceptibility of collagen I using a laser scanning microscope (2007)

Characteristic changes in the organization of fibrillar collagen can potentially serve as an early diagnostic marker in various pathological processes. Tissue types containing collagen I can be probed by pulsed high-intensity laser radiation, thereby generating second harmonic light that provides information about the composition and structure at a microscopic level. A technique was developed to determine the essential second harmonic generation (SHG) parameters in a laser scanning microscope setup. A rat-tail tendon frozen section was rotated in the xy-plane with the pulsed laser light propagating along the z-axis. By analyzing the generated second harmonic light in the forward direction with parallel and crossed polarizer relative to the polarization of the excitation laser beam, the second-order nonlinear optical susceptibilities of the collagen fiber were determined. Systematic variations in SHG response between ordered and less ordered structures were recorded and evaluated. A 500 microm-thick z-cut lithiumniobate (LiNbO(3)) was used as reference. The method was applied on frozen sections of malignant melanoma and normal skin tissue. Significant differences were found in the values of d(22), indicating that this parameter has a potential role in differentiating between normal and pathological processes.
Thermal Hydrogasification of Aromatic Compounds (1974)

The decomposition of simple aromatic molecules is examined to gain insight into possible reaction pathways involved in coal hydrogasification. Experimental data on benzene and anthracene decomposition kinetics in the literature suggest that the rate-determining step involves destabilization of the aromatic ring. Decomposition rates are substantially independent of hydrogen partial pressures from near zero to 100 atm; over this range the dominant product changes from solid carbon (coke) to methane gas. The associated experimental activation energies are proportional to benzene and anthracene delocalization energies as calculated from Dewars theory of odd-alternant hydrocarbons. Carbon-forming reactions and the synthesis of aromatic molecules during pyrolysis of paraffinic hydrocarbons are also studied.
Partition-based algorithm for power grid design using locality (2006)

This paper presents an efficient heuristic algorithm, which employs successive partitioning and grid-refinement scheme, for designing the power distribution network of a chip. In an iterative procedure, the chip area is recursively bipartitioned, and the wire pitches and the wire widths of the power grid in the partitions are repeatedly adjusted to meet the voltage drop and current-density specifications. By using the macromodels of the power grid constructed in the previous levels of partitioning, the scheme ensures that a small global power grid system is simulated in each iteration. The idea is based on the notion that due to the locality properties of the power grid, the effects of distant nodes and sources can be modeled more coarsely than the nearby elements, and include practical methods that enhance the convergence of the iterative conjugate-gradient-based solution engine that is used in each step. Finally, a postprocessing step at the end of the optimization is employed to maximize the alignment of wires in adjacent partitions. The effectiveness of the scheme is demonstrated by designing various power grids with real circuit parameters and realistic input current values. The proposed algorithm is able to design power grids comprising thousands of wires and more than a million electrical nodes in about 6 to 14 min. When compared to a multigrid-based power grid design scheme, it is found to save about 5% to 10% of wire area, and on an average is 12% faster.
A Review on Li-S Batteries as a High Efficiency Rechargeable Lithium Battery (2013)

Energy production and storage are critical research domains where the demands for improved energy devices and the requirement for greener energy resources are increasing. There is particularly intense interest in Lithium (Li)-ion batteries for all kinds of electrochemical energy storage. Li-ion batteries are currently the primary energy storage devices in the communications, transportation and renewable-energy sectors. However, scaling up the Li-ion battery technology to meet current increasing demands is still problematic and issues such as safety, costs, and electrode materials with higher performance are under intense investigation. The Li-sulfur (S) battery is a promising electrochemical system as a high-energy secondary battery, particularly for large-scale applications, due to its low cost, theoretically large specific capacity, theoretically high specific energy, and its ecofriendly footprint. The Li-S battery exhibits excellent potential and has attracted the attention of battery developers in large scale production in recent years. This review aims to highlight recent advances in the Li-S battery, providing an overview of the Li-ion battery applications in energy storage, then detailing the challenges facing Li-S battery and current applied strategies for improvement in its efficiency.