gebhart/patrepeval huggingface dataset:
Interactions between polyamine analogs with antiproliferative effects and tRNA: a 15N NMR analysis. (1994)

N-Bisalkylpolyamine analogs have been shown to exert antiproliferative effects in many tumor models, with the bisethyl derivatives exerting the greatest activities. 15N NMR spectroscopy was used to explore the interactions between these analogs and tRNA. When tRNA was added to solutions of 15N-enriched homospermine (4-4-4), bisethylhomospermine (BE-4-4-4), bismethylhomospermine (BM-4-4-4), bisethylspermine (BE-3-4-3) and 1,19-bis(ethylamino)-5,10,15-triazanonadecane (BE-4-4-4-4), the spin-lattice relaxation times T1 of the nitrogens were strongly reduced. From the temperature dependence of these T1's we calculated the rotational activation energies (Ea) of the correlation times of the amino groups in the presence and absence of tRNA. These data indicate that: i) the N-bisethyl derivatives bind strongly to tRNA through their-NH2(+)-groups (most likely, through hydrogen bonding); ii) the binding is weakest in the N-bismethyl derivative and iii) homospermine binds very weakly and mainly through its -NH3(+)-group (most likely, through electrostatic binding). The binding of the polyamine analogs to tRNA was also estimated by the increase of the half-line widths (D1/2) of the -NH2(+)-groups, derived from the effects that tRNA has on the spin-spin relaxation time T2. The decrease of the V1/2 values of the -NH2(+)-groups in the (15N-polyamine)-tRNA complexes when the analogs were chased away by an excess of spermine confirmed the stronger binding of the bisethyl- with respect to the bismethyl derivatives, as well as the weak binding of homospermine to tRNA. A correlation was also found between the binding strengths of the analyzed polyamine analogs and their antiproliferative activities.
Suppression of the Josephson current through a narrow, mesoscopic, semiconductor channel by a single impurity (1992)

We study the Josephson current through a ballistic, normal, one-dimensional quantum channel in contact with two superconducting electrodes. A single point impurity having reflection coefficient R is placed in the normal conductor. The impurity couples the Andreev energy levels of forward and reverse moving electrons inside the junction, opening energy gaps in the quasiparticle level spectrum versus superconducting phase difference \ensuremath{\varphi}. These ``Andreev'' energy gaps suppress the Josephson current in much the same way as disorder suppresses the magnetic flux driven currents in a normal mesoscopic ring. Finite-temperature ``energy averages'' the contribution of Andreev levels above the Fermi energy with those below \ensuremath{\mu}, further suppressing the Josephson current. The portion of the Josephson current carried by scattering states outside the superconducting gap is similarly suppressed by disorder and finite temperature.
Design and testing of a white-light, steady-state diffuse reflectance spectrometer for determination of optical properties of highly scattering systems (1997)

We present a steady-state radially resolved diffuse reflectance spectrometer capable of measuring the absorption and transport scattering spectra of tissue-simulating phantoms over an adjustable 170-nm wavelength interval in the visible and near infrared. Measurements in a variety of phantoms are demonstrated over the relevant range of tissue optical properties, and the accuracy of the instrument is found to be approximately 10% in both scattering and absorption. Monte Carlo simulations designed to test the accuracy of the instrument are presented that support the experimental findings.
Resistance to Taxol in lung cancer cells associated with increased microtubule dynamics (2001)

Microtubule dynamics are crucial for mitotic spindle assembly and chromosome movement. Suppression of dynamics by Taxol appears responsible for the drug's potent ability to inhibit mitosis and cell proliferation. Although Taxol is an important chemotherapeutic agent, development of resistance limits its efficacy. To examine the role of microtubule dynamics in Taxol resistance, we measured the dynamic instability of individual rhodamine-labeled microtubules in Taxol-sensitive and -resistant living human cancer cells. Taxol-resistant A549-T12 and -T24 cell lines were selected from a human lung carcinoma cell line, A549. They are, respectively, 9- and 17-fold resistant to Taxol and require low concentrations of Taxol for proliferation. We found that microtubule dynamic instability was significantly increased in the Taxol-resistant cells. For example, with A549-T12 cells in the absence of added Taxol, microtubule dynamicity increased 57% as compared with A549 cells. The length and rate of shortening excursions increased 75 and 59%, respectively. These parameters were further increased in A549-T24 cells, with overall dynamicity increasing by 167% compared with parental cells. Thus, the decreased Taxol-sensitivity of these cells can be explained by their increased microtubule dynamics. When grown without Taxol, A549-T12 cells were blocked at the metaphase/anaphase transition and displayed abnormal mitotic spindles with uncongressed chromosomes. In the presence of 2-12 nM Taxol, the cells grew normally, suggesting that mitotic block resulted from excessive microtubule dynamics. These results indicate that microtubule dynamics play an important role in Taxol resistance, and that both excessively rapid dynamics and suppressed dynamics impair mitotic spindle function and inhibit proliferation.
Properties of VPE-grown GaN doped with Al and some iron-group metals (1979)

The influence of doping with Al and some iron-group metals on optical and electrical properties of GaN epitaxially grown from the vapor phase is reported. These impurities are the main inadvertent contaminants in GaN growth, and details on the transport of these elements to the deposition area during growth are discussed. Detailed studies are performed by the SIMS technique on impurity concentration in layers grown under different conditions of contamination. Variations in doping over the area of the grown wafers, as well as with depth into the layer, are investigated, and shown to be significant for Al and N2. These investigations are complemented by SEM cathodoluminescence topographs. Photoluminescence data strongly indicate the existence of a shallow bound exciton (binding energy 12 meV) to isoelectronic Al on Ga sites in GaN. No radiative states are observed from the iron-group contaminants. These (notably Fe and Cr) cause deep states efficient in electrical compensation of the material, which is easily made highly resistive with Fe or Cr.
Constructing the Lyapunov Function through Solving Positive Dimensional Polynomial System (2013)

We propose an approach for constructing Lyapunov function in quadratic form of a differential system. First, positive polynomial system is obtained via the local property of the Lyapunov function as well as its derivative. Then, the positive polynomial system is converted into an equation system by adding some variables. Finally, numerical technique is applied to solve the equation system. Some experiments show the efficiency of our new algorithm.
Dag consistent parallel simulation (1997)

We present a novel approach to parallel discrete event simulation based on the Cilk model of multithreaded computation. Cilk's runtime system not only manages the low-level aspects of program execution, but also provides the user with an algorithmic model of performance which can be used to predict the execution time of a parallel simulation. Moreover, a Cilk application can ``scale down'' to run on a single processor with nearly the same performance as that of serial code.A conservative parallel discrete event simulation algorithm has been developed in which communication between logical processes is achieved using Cilk's virtual memory model, dag consistent shared memory. The simulation executes in cycles, where each cycle involves a divide and conquer computation. Although local lookahead information can be exploited, the algorithm is robust in that it also calculates a global simulation time for each cycle. It can therefore be used for applications where zero lookahead may occur.
Efficient Differentiation of Hepatocytes from Human Embryonic Stem Cells Exhibiting Markers Recapitulating Liver Development In Vivo (2008)

The potential to differentiate human embryonic stem cells (hESCs) in vitro to provide an unlimited source of human hepatocytes for use in biomedical research, drug discovery, and the treatment of liver diseases holds great promise. Here we describe a three-stage process for the efficient and reproducible differentiation of hESCs to hepatocytes by priming hESCs towards definitive endoderm with activin A and sodium butyrate prior to further differentiation to hepatocytes with dimethyl sulfoxide, followed by maturation with hepatocyte growth factor and oncostatin M. We have demonstrated that differentiation of hESCs in this process recapitulates liver development in vivo: following initial differentiation, hESCs transiently express characteristic markers of the primitive streak mesendoderm before turning to the markers of the definitive endoderm; with further differentiation, expression of hepatocyte progenitor cell markers and mature hepatocyte markers emerged sequentially. Furthermore, we have provided evidence that the hESC-derived hepatocytes are able to carry out a range of hepatocyte functions: storage of glycogen, and generation and secretion of plasma proteins. More importantly, the hESC-derived hepatocytes express several members of cytochrome P450 isozymes, and these P450 isozymes are capable of converting the substrates to metabolites and respond to the chemical stimulation. Our results have provided evidence that hESCs can be differentiated efficiently in vitro to functional hepatocytes, which may be useful as an in vitro system for toxicity screening in drug discovery.
ATM local area networks (1994)

LAN emulation offers a best-effort, connectionless, packet transfer service at the MAC sublayer, implemented on top of a connection-oriented ATM network LAN emulation using switched virtual connections requires address resolution to locate the destination end station followed by connection establishment to the resulting ATM address. Address resolution may be implemented by a broadcast technique or by an address server. The broadcast method is the simplest for small networks but a combination of both is probably better. The use of the MAC address to identify an end station, with dynamic binding to its current physical location in the ATM network, allows the ATM LAN segment to be viewed as a virtual LAN. The virtual LAN model permits end stations to move and change physical location while maintaining connection to the same ATM LAN segment. This greatly simplifies the management of large data networks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
General Strategy for Biodetection in High Ionic Strength Solutions Using Transistor-Based Nanoelectronic Sensors (2015)

Transistor-based nanoelectronic sensors are capable of label-free real-time chemical and biological detection with high sensitivity and spatial resolution, although the short Debye screening length in high ionic strength solutions has made difficult applications relevant to physiological conditions. Here, we describe a new and general strategy to overcome this challenge for field-effect transistor (FET) sensors that involves incorporating a porous and biomolecule permeable polymer layer on the FET sensor. This polymer layer increases the effective screening length in the region immediately adjacent to the device surface and thereby enables detection of biomolecules in high ionic strength solutions in real-time. Studies of silicon nanowire field-effect transistors with additional polyethylene glycol (PEG) modification show that prostate specific antigen (PSA) can be readily detected in solutions with phosphate buffer (PB) concentrations as high as 150 mM, while similar devices without PEG modification only exhibit detectable signals for concentrations ≤10 mM. Concentration-dependent measurements exhibited real-time detection of PSA with a sensitivity of at least 10 nM in 100 mM PB with linear response up to the highest (1000 nM) PSA concentrations tested. The current work represents an important step toward general application of transistor-based nanoelectronic detectors for biochemical sensing in physiological environments and is expected to open up exciting opportunities for in vitro and in vivo biological sensing relevant to basic biology research through medicine.
The Protective Immune Response against Infectious Bronchitis Virus Induced by Multi-Epitope Based Peptide Vaccines (2009)

Peptide vaccine was found to be an effective and powerful approach to a variety of pathogens. To explore multi-epitope based peptide vaccines against infectious bronchitis virus (IBV), the immunogenic peptides were fused to the 3' terminal of glutathione S transferase gene (GST) and expressed in Escherichia coli. ELISA and Western blot analysis showed that the purified fusion proteins had excellent immune activity with chicken anti-IBV serum. During the vaccination course, the candidate peptide vaccines induced strong humoral and cellular response, and provided up to 80.0% immune protection, while all non-immunized chickens in the negative control group manifested obvious typical symptoms and died after virus challenge. Our finding provides a new way to develop multi-epitope based peptide vaccine against IBV.
Quantifying the Kinetic Stability of Hyperstable Proteins via Time-Dependent SDS Trapping (2011)

Globular proteins are usually in equilibrium with unfolded conformations, whereas kinetically stable proteins (KSPs) are conformationally trapped by their high unfolding transition state energy. Kinetic stability (KS) could allow proteins to maintain their activity under harsh conditions, increase a protein's half-life, or protect against misfolding-aggregation. Here we show the development of a simple method for quantifying a protein's KS that involves incubating a protein in SDS at high temperature as a function of time, running the unheated samples on SDS-PAGE, and quantifying the bands to determine the time-dependent loss of a protein's SDS resistance. Six diverse proteins, including two monomer, two dimers, and two tetramers, were studied by this method, and the kinetics of the loss of SDS resistance correlated linearly with their unfolding rate determined by circular dichroism. These results imply that the mechanism by which SDS denatures proteins involves conformational trapping, with a trapping rate that is determined and limited by the rate of protein unfolding. We applied the SDS trapping of proteins (S-TraP) method to superoxide dismutase (SOD) and transthyretin (TTR), which are highly KSPs with native unfolding rates that are difficult to measure by conventional spectroscopic methods. A combination of S-TraP experiments between 75 and 90 °C combined with Eyring plot analysis yielded an unfolding half-life of 70 ± 37 and 18 ± 6 days at 37 °C for SOD and TTR, respectively. The S-TraP method shown here is extremely accessible, sample-efficient, cost-effective, compatible with impure or complex samples, and will be useful for exploring the biological and pathological roles of kinetic stability.
In vitro characterization of four novel classes of growth hormone-releasing peptide. (1995)

Reexamination of the hexapeptide GH-releasing peptide (GHRP-6) structure/function has lead to the development of four novel classes of compound that stimulate GH release. Each class is represented as follows: a pentapeptide, G-7039; a tetrapeptide, G-7134; a pseudotripeptide, G-7502; and a rigid cyclic heptapeptide, G-7203. The EC50 values for these compounds, determined by GH dose-response curves using primary cultures of rat pituitary cells, were 0.18, 0.34, 10.6, and 0.43 nM, respectively. To demonstrate that these compounds were acting at the putative GHRP receptor, challenges were made using combinations that included GHRP-6 and GH-releasing hormone (GHRH). All four new classes further increased GH release in combination with GHRH, but not with GHRP-6. Homologous desensitization occurred after 45 min of exposure to the new compounds while the cells remained sensitive to GHRH. Somatostatin inhibited all of these compounds. Additionally, G-7039 elevated free calcium, as occurs with GHRP-6. All four classes elicited a robust GH release, a small increase in PRL, and no change in LH, FSH, ACTH, or TSH. We conclude that these novel compounds are potent and direct stimulators of pituitary GH release, with in vitro attributes that suggest mediation via a specific GHRP-like mechanism.
Intelligent crawling on the World Wide Web with arbitrary predicates (2001)

Article Share on Intelligent crawling on the World Wide Web with arbitrary predicates Authors: Charu C. Aggarwal IBM T. J. Watson Resch. Ctr., Yorktown Heights, NY IBM T. J. Watson Resch. Ctr., Yorktown Heights, NYView Profile , Fatima Al-Garawi IBM T. J. Watson Resch. Ctr., Yorktown Heights, NY IBM T. J. Watson Resch. Ctr., Yorktown Heights, NYView Profile , Philip S. Yu IBM T. J. Watson Resch. Ctr., Yorktown Heights, NY IBM T. J. Watson Resch. Ctr., Yorktown Heights, NYView Profile Authors Info & Claims WWW '01: Proceedings of the 10th international conference on World Wide WebMay 2001Pages 96–105https://doi.org/10.1145/371920.371955Published:01 April 2001Publication History 159citation1,452DownloadsMetricsTotal Citations159Total Downloads1,452Last 12 Months24Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Primary structure of the Streptomyces enzyme endo-beta-N-acetylglucosaminidase H. (1984)

We report the DNA and primary amino acid sequences of the Streptomyces plicatus enzyme endo-beta-N-acetylglucosaminidase H. Peptide sequence information was derived from enzyme isolated from Streptomyces culture medium using a combination of mass spectrometric methods and conventional techniques, including Edman degradation and carboxypeptidase Y digestion. The DNA sequence was determined by analysis of the Endo-beta-N-acetylglucosaminidase H gene cloned into the Escherichia coli plasmid pBR322 (Robbins, P. W., Wirth , D. F., and Hering , C. (1981) J. Biol. Chem. 256, 10640-10644). The enzyme from Streptomyces medium is 271 (or 269) amino acids in length and has a ragged NH2-terminal sequence beginning primarily with Ala-Pro-Val or Ala-Pro-Ala-Pro-Val. DNA resection experiments as well as the DNA sequence itself suggest that a proenzyme or, more probably, " prepro " enzyme may be the primary product of translation. The long 42 (or 44) residue leader sequence of the preproenzyme shows striking similarities to leader sequences found on proteins secreted by Bacillus species. The leader sequence is partially removed by E. coli and, as reported previously, endo-beta-N-acetylglucosaminidase H made in E. coli appears in both the periplasmic space and in the cell.
Primary Role of Functional Ischemia, Quantitative Evidence for the Two-Hit Mechanism, and Phosphodiesterase-5 Inhibitor Therapy in Mouse Muscular Dystrophy (2007)

Evidence was provided supporting the essential role of functional ischemia in contraction-induced myofiber damage in mdx mice. Furthermore, the first quantitative evidence for the "two-hit" mechanism in this disease was documented. Significantly, the vasoactive drug tadalafil, a phosphodiesterase 5 inhibitor, administered to mdx mice ameliorated muscle damage.
Spectrum of tumor angiogenesis in the bone marrow of children with acute lymphoblastic leukemia. (1997)

It has been shown that solid tumors progress in concert with an induction of tumor angiogenesis. It is not known, however, whether a similar phenomenon occurs in leukemia. Angiogenesis was characterized immunohistochemically by factor VIII staining of bone marrow biopsies and quantified by assessment of microvessel density using previously described techniques. We evaluated bone marrow biopsies from 40 children with newly diagnosed, untreated acute lymphoblastic leukemia. In 22 of the patients, we also evaluated angiogenesis after the completion of remission induction chemotherapy. Control specimens were obtained from children undergoing staging evaluations at the time of diagnosis of solid tumors and lymphomas. Microvessels were counted throughout the entire core specimen in consecutive x 200 fields, and a median count per field (cpf) was calculated. In addition, the number of microvessels in the single x 200 field with the highest microvessel density was designated as the "hot spot." Biopsies from children with leukemia and from controls showed median microvessel densities of 42 and 6 counts per field, respectively (P < or = 0.0001). Microvessel density of the hot spots of leukemia specimens and controls were also significantly different, 51 and 8, respectively (P < or = 0.0001). A computer-aided three-dimensional reconstruction model of bone marrow vascularity showed a complex, arborizing branching of microvessels in leukemic specimens compared with single, straight microvessels without branching in controls. Urinary basic fibroblast growth factor, a potent angiogenic factor, was measured in 22 of the children with newly diagnosed leukemia and in 39 normal, age-matched controls. Urinary basic fibroblast growth factor levels were increased in all 22 patients before treatment, were variable during induction chemotherapy, and demonstrated statistically insignificant decreases at the time of complete remission. These findings suggest that leukemia cells induce angiogenesis in the bone marrow and that leukemia might be angiogenesis dependent and raise the possibility for a role of antiangiogenic drugs in the treatment of leukemia.
Nuclear grading of breast carcinoma by image analysis. Classification by multivariate and neural network analysis. (1991)

The use of nuclear grade as a prognostic indicator for breast carcinoma has been limited by interobserver variability. Advances in image analysis and automated cell classification offer one approach to this problem. The authors used the CAS-100 (Cell Analysis System. Elmhurst, IL) system to measure and analyze nuclear morphometric and texture features of cytologic preparations from 35 breast carcinomas (well, moderate, and poorly differentiated) as well as benign lesions. Morphometric and Markovian texture feature data from breast cancer nuclei of various grades comprised a training set, which was then used to establish classification criteria by multivariate (Bayesian) analysis and to train a neural network system. Both systems were tested for the ability to classify the nuclear grade of individual nuclei. There was good agreement between computer classification and the grade assigned by human observer to individual nuclei using either Bayesian or neural network analysis. Thirty-one unknown cases, which were assigned an overall grade by an observer, were then analyzed by computer, and an overall grade assigned based on the grade of nucleus most frequently present. Using this method, both classification systems were able to assign a "correct" grade to low-grade lesions (approximately 70% correct) more often than to high-grade tumors (approximately 20%). Difficulty in computer assignment of high-grade tumors was explained by nuclear heterogeneity in these tumors (i.e., although the percentage of high-grade nuclei was increased compared with that of low-grade tumors, high-grade nuclei frequently did not predominate). The authors present this study to demonstrate the feasibility of using image analysis as an objective means of nuclear grading. Further studies will be needed to establish criteria for assigning overall nuclear grade based on computer analysis of imaging data.