gebhart/patrepeval huggingface dataset:
Exploiting sparseness in de novo genome assembly (2012)

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.
Synthesis, characterization, and curing of hyperbranched allyl ether–maleate functional ester resins (1993)

Abstract A model two‐step synthesis of a saturated hyperbranched hydroxyl‐terminated ester has been developed to show a synthesis route. Three different series of hyperbranched esters with different terminations have been synthesized to relate some of their properties to their structures. This route has then been used to synthesize three different allyl ethermaleate functional hyperbranched ester resins in a two‐step procedure. The resins have been characterized with respect to rheology, structure, and properties, and the differences are discussed. The allyl ether‐maleate functional resins have also been studied with respect to curing performance and final film properties. © 1993 John Wiley & Sons, Inc.
High frequency operation of JTL ring oscillator with a passive transmission line (2001)

We have designed ring oscillators to test rapid single flux quantum (RSFQ) circuits with passive transmission lines at high frequencies. To reduce the width of the transmission line, design methods for increasing the characteristic impedance of the transmission line have been investigated and then we designed a 5-stage of Josephson transmission line (JTL) receiver which can transform the impedance from 1 to 4 /spl Omega/ by changing the critical current and the inductance. The receiver, driver, and micro-strip line were inserted in a ring oscillator. The ring oscillator fabricated with the Nb/AlOx/Nb junction process was successfully operated at frequencies ranging from 6 to 10 GHz for line lengths of 0.6, 3, 6, and 9 mm. The usefulness of the impedance transformation was then confirmed experimentally. A propagation delay per unit length of 8.4 ps/mm was also obtained.
The design and implementation of the Montage multimedia mail system (2002)

The Montage multimedia electronic mail system is presented along with its model for multimedia documents. Montage makes use of a simpler format than more generalized hypermedia systems. It is the authors' belief that the Montage model is more effective than general hypertext for the task of creating user-to-user messages. Furthermore, Montage is designed to be runtime extensible to novel media types by its users. Thus the system does not have to know ahead of time all the possible media users may want to send. The system is built on top of existing mail transport protocols for flexibility and portability. A discussion is presented of the design of the mailer along with experiences gained from its implementation. The user interface to the system is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis and Dual Antagonistic Activity against Thromboxane A<SUB>2</SUB> and Leukotriene D<SUB>4</SUB> of Benzenesulfonamide Derivatives (1997)

In order to find dual antagonists against both thromboxane A2 (TXA2) and leukotriene D4 (LTD4) receptors for a new antiasthmatic agent, various benzenesulfonamide derivatives were synthesized and evaluated for those pharmacological effects. TXA2 and LTD4 antagonistic activities in vitro were evaluated by the inhibitory effects on LTD4-induced and U-46619-induced contraction of guinea-pig trachea. Furthermore, TXA2 and LTD4 antagonistic activities in vivo were evaluated by the inhibitory effects on LTD4-induced and U-46619-induced bronchoconstriction of guinea-pig after oral administration of test compounds. It was found that 4-[5-[1-(4-chlorobenzenesulfonamido)-5-methylhexyl]-2-thi eny l]butyric acid and 4-[5-[1-(4-fluorobenzenesulfonamido)-5-methyl-hexyl]-2-thienyl]but yric acid possess good anti-LTD4 and anti-TXA2 activities by oral administration.
Multilateration tracking and synchronization over wide areas (2003)

We study technical issues involving a wide-area surveillance system using multilateration sensors. A satellite clock reference scheme is seen as a better solution for synchronization of widely dispersed sensors. We then describe a direct solution approach to derive target positions. Techniques are developed for resolving solution ambiguities, including different sensor combinations and tracking algorithms. It is also proposed that signal strength comparison and other techniques be used to enhance the tracking performance and accuracies with Mode A/C data. Finally, some flight test results are shown to demonstrate the feasibility of multilateration system for wide-area surveillance.
Learning in the Machine: Random Backpropagation and the Deep Learning Channel (2016)

Random backpropagation (RBP) is a variant of the backpropagation algorithm for training neural networks, where the transpose of the forward matrices are replaced by fixed random matrices in the calculation of the weight updates. It is remarkable both because of its effectiveness, in spite of using random matrices to communicate error information, and because it completely removes the taxing requirement of maintaining symmetric weights in a physical neural system. To better understand random backpropagation, we first connect it to the notions of local learning and learning channels. Through this connection, we derive several alternatives to RBP, including skipped RBP (SRPB), adaptive RBP (ARBP), sparse RBP, and their combinations (e.g. ASRBP) and analyze their computational complexity. We then study their behavior through simulations using the MNIST and CIFAR-10 bechnmark datasets. These simulations show that most of these variants work robustly, almost as well as backpropagation, and that multiplication by the derivatives of the activation functions is important. As a follow-up, we study also the low-end of the number of bits required to communicate error information over the learning channel. We then provide partial intuitive explanations for some of the remarkable properties of RBP and its variations. Finally, we prove several mathematical results, including the convergence to fixed points of linear chains of arbitrary length, the convergence to fixed points of linear autoencoders with decorrelated data, the long-term existence of solutions for linear systems with a single hidden layer and convergence in special cases, and the convergence to fixed points of non-linear chains, when the derivative of the activation functions is included.
Reference Correlation of the Viscosity of <i>n</i>-Hexane from the Triple Point to 600 K and up to 100 MPa (2013)

This paper contains new, representative reference equations for the viscosity of n-hexane. The equations are based in part upon a body of experimental data that has been critically assessed for internal consistency and for agreement with theory whenever possible. The correlations are valid from the triple point to 600 K, and at pressures up to 100 MPa. We estimate the expanded uncertainty at a 95% confidence level to be 2% for the liquid phase at temperatures from the triple point to 450 K and pressures to 100 MPa. For the liquid at 450–600 K at pressures to 100 MPa, the expanded uncertainty at the 95% confidence level is 6%, and is 0.3% for the low-density gas at pressures to 0.3 MPa.
Role of MAP Kinase Activation in Interleukin-8 Production by Human BEAS-2B Bronchial Epithelial Cells Submitted to Cyclic Stretch (2002)

Overstretching the airways during positive pressure mechanical ventilation or attacks of acute severe asthma is associated with important biologic responses. Interleukin (IL)-8-dependent neutrophil recruitment seems to play a critical role in the process of mechanical stress-induced airway inflammation. Herein, we show that human bronchial epithelial BEAS-2B cells submitted to cyclic stretch in vitro produce IL-8, at both the mRNA and protein levels. This cellular stress "turns on" activator protein (AP)-1 and cyclic AMP (cAMP)-responding elements. The mitogen-activated protein (MAP) kinases (MAPK) p44/42, SAPK/JNK, and p38 were all rapidly activated (phosphorylated) after the initiation of the cyclic strain (5-10 min). The blockade of p38 with the pharmacologic inhibitor SB203580 abrogated IL-8 production by cell stretching, and an inhibitor of the p44/42 pathway, PD98059, partially inhibited the IL-8 response. A nonspecific tyrosine kinase inhibitor, genistein, also blocked the stretch-induced IL-8 production. This suggests that MAPK, and p38 in particular, are proximal and key intracellular signaling molecules mediating cell activation in response to cyclic stretch, a mechanical strain similar to that applied to lung epithelial cells during mechanical ventilation. Pharmacologic inhibition of the p38 pathway holds promise as a new therapeutic avenue in ventilated patients.
Nanosecond Photoreduction of Cytochrome P450cam by Channel-Specific Ru-diimine Electron Tunneling Wires (2003)

We report the synthesis and characterization of Ru-diimine complexes designed to bind to cytochrome p450cam (CYP101). The sensitizer core has the structure [Ru(L(2))L'](2+), where L' is a perfluorinated biphenyl bridge (F(8)bp) connecting 4,4'-dimethylbipyridine to an enzyme substrate (adamantane, F(8)bp-Ad), a heme ligand (imidazole, F(8)bp-Im), or F (F(9)bp). The electron-transfer (ET) driving force (-deltaG degrees ) is varied by replacing the ancillary 2,2'-bipyridine ligands with 4,4',5,5'-tetramethylbipyridine (tmRu). The four complexes all bind p450cam tightly: Ru-F(8)bp-Ad (1, K(d) = 0.077 microM); Ru-F(8)bp-Im (2, K(d) = 3.7 microM); tmRu-F(9)bp (3, K(d) = 2.1 microM); and tmRu-F(8)bp-Im (4, K(d) = 0.48 microM). Binding is predominantly driven by hydrophobic interactions between the Ru-diimine wires and the substrate access channel. With Ru-F(8)bp wires, redox reactions can be triggered on the nanosecond time scale. Ru-wire 2, which ligates the heme iron, shows a small amount of transient heme photoreduction (ca. 30%), whereas the transient photoreduction yield for 4 is 76%. Forward ET with 4 occurs in roughly 40 ns (k(f) = 2.8 x 10(7) s(-)(1)), and back ET (Fe(II) --> Ru(III), k(b) approximately 1.7 x 10(8) s(-)(1)) is near the coupling-limited rate (k(max)). Direct photoreduction was not observed for 1 or 3. The large variation in ET rates among the Ru-diimine:p450 conjugates strongly supports a through-bond model of Ru-heme electronic coupling.
Fractional ablative laser skin resurfacing: A review (2011)

Ablative laser technology has been in use for many years now. The large side effect profile however has limited its use. Fractional ablative technology is a newer development which combines a lesser side effect profile along with similar efficacy. In this paper we review fractional ablative laser skin resurfacing.
A Commentary on the Teaching of Mathematics in British Primary Schools (1972)

A presentation of the case for our approach to mathematics in the primary school: what influences have promoted it, what principles underlie it and how they are implemented, what research supports it and what we hope to achieve thereby.
Benign astrocytic and oligodendrocytic tumors of the cerebral hemispheres in children (1989)

The authors review 42 consecutive cases of benign astrocytic and oligodendrocytic tumors of the cerebral hemispheres in children undergoing surgery in the pediatric service of the Hôpital des Enfants Malades between 1975 and 1987. Epilepsy was the presenting sign in 76% of the children and remained the only clinical sign at diagnosis in 62%. Partial or complex partial seizures were observed in half of the cases, but other seizure types were also frequent. Diagnosis of the tumor as the etiological agent rested upon the results of computerized tomography or magnetic resonance imaging. Postoperative mortality (5%) and morbidity (16%) rates were low. The postoperative intelligence quotient was above 80 in 71% of the patients, and 77% of the children had no major problem in school. Although only two of the 42 patients were given postoperative radiotherapy, there were no recurrences in 82% of the survivors. The actuarial probability of nonrecurrence of the tumor was 95% at 5 years. Three patients with recurrent tumor underwent further surgery and are, at the present time, recurrence-free. The incidence of epilepsy fell from 76% before surgery to 19% after removal of the tumor alone; therefore, intraoperative electrocorticography and resection of the electrically abnormal cortex at the time of the first surgical procedure do not appear necessary. It is possible that tumor removal restores a mechanism that limits the spread of seizures and, thus, the clinical manifestations of epilepsy. Benign astrocytic and oligodendrocytic tumors of the cerebral hemispheres in children should not be treated with adjuvant radiotherapy, at least initially.
Optical binary coded ternary arithmetic and logic (1986)

Two ternary, an ordinary ternary (OT) and a binary balance ternary (BT), number representations to be used for optical computing are discussed. An unsigned OT number is represented by a string of symbols (0, 1, 2), while for the BT, the three logic symbols take on the set (−1, 0, +1). The BT symbols can represent a signed number. Using a particular binary encoding method, the three ternary symbols are converted to a pair of binary symbols. The binary coded ternary (BCT) representation has two advantages. First, it allows use of the well-developed binary optical components. Second, compared with other optical multiple-valued number encoding schemes, it reduces the number of input–output channels and thus is able to conserve the optical space–bandwidth product. As an example for arithmetic operations, BCT full addition algorithms are given. As examples for multiple-valued logic computing, BCT Post, Webb, and residue logic elements are discussed. Using the two-port Sagnac interferometric switches, optical implementations of various BCT arithmetic and logic operations are described.
Adaptive optics wavefront corrector using addressable liquid-crystal retarders II (1992)

We present recent results of our investigations into the feasibility of a wavefront corrector for adaptive optics, using nematic liquid crystal material. In particular, we are aiming at a small, flexible adaptive optics module, to be located at the focal plane of existing and new-generation telescopes in order to improve imaging quality. We address some of the specific problems investigated, concerning the theoretical behavior of the LC corrector, its comparison with other state-of-the-art wavefront correctors, modal and zonal, the speed and slew rate of the actuators, and a real-time capacitive servo loop scheme controlling the actuator retardance.
Peeking Over the Cellular Walled Gardens - A Method for Closed Network Diagnosis - (2018)

A cellular network is a closed system, and each network operator has built a unique “walled garden” for their network by combining different operation policies, network configurations, and implementation optimizations. Unfortunately, some of these combinations can induce performance degradation due to misconfiguration or unnecessary procedures. To detect such degradation, a thorough understanding of even the minor details of the standards and operator-specific implementations is important. However, it is difficult to detect such problems, as the control plane is complicated by numerous procedures. This paper introduces a simple yet powerful method that diagnoses these problems by exploiting the operator-specific implementations of cellular networks. We develop a signaling collection and analysis tool that collects control plane messages from operators and finds problems through comparative analysis. The analysis process consists of three different control plane comparison procedures that can find such problems effectively. These individual procedures use a time threshold, control flow sequence, and signaling failure as the basis for comparison. To this end, we collect approximately 3.1 million control-plane messages from 13 major cellular operators worldwide. As a case study, we analyze the circuit-switched fallback technology that triggers generation crossover between third generation and long-term evolution technologies.
Sensitive electrochemical immunosensor for matrix metalloproteinase-3 based on single-wall carbon nanotubes (2010)

A novel electrochemical immunosensor for the detection of matrix metalloproteinase-3 (MMP-3), a cancer biomarker protein, based on vertically aligned single-wall carbon nanotube (SWCNT) arrays is presented. Detection was based on a sandwich immunoassay consisting of horseradish peroxidase (14-16 labels) conjugated to a secondary antibody and/or a polymer bead loaded with multi-enzyme labels. Performance was optimized by effective minimization of non-specific binding (NSB) events using Bovine serum albumin (BSA), Tween-20 and optimization of the primary antibody and secondary antibody concentrations. Results provided a detection limit of 0.4 ng mL(-1) (7.7 pM) for the 14-16 label sensor protocol and 4 pg mL(-1) (77 fM) using a multiply enzyme labeled polymeric bead amplification strategy in 10 microL of calf serum. This immunosensor based on SWCNT arrays offers great promise for a rapid, simple, cost-effective method for clinical screening of cancer biomarkers for point-of-care diagnosis.
Prospects for Advances in Energy Conversion Technologies for Geothermal Energy Development (1975)

None
Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions (2012)

Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.
Lysosomal Acid Lipase as a Preproprotein (2004)

Lysosomal acid lipase (LAL; EC 3.1.1.13) hydrolyzes intracellular triglycerides and cholesterol esters taken up by various cell-types. Previously, LAL purified from human liver tissue was described as a preproprotein with a 27 amino acid signal peptide and a 49 amino acid propeptide. Three mutants of the putative proregion of LAL were produced and expressed in Spodoptera frugiperda insect cells. Pulse-chase experiments demonstrated that LAL undergoes proteolytical processing. The deletion of the 49 amino acids led to a complete loss of the LAL activity. The two other mutants were produced at the C-terminus of the pro-region, at positions 49 and 50, by site-directed mutagenesis. Mutant K49R showed wild-type LAL activity, but mutant G50A showed significantly reduced enzyme activity compared to wild-type LAL and a greater reduction in culture medium than in detergent cell extracts. Kinetic data suggest that mutant G50A is less stable than wild-type LAL and mutant K49R. In contrast to K49, the highly conserved amino acid residue G50 seems to be in a very important position and its mutation influences both secretion and enzyme activity of LAL. A three-dimensional model of LAL shows that K49 and G50 are localized in the loop-region between two beta-sheets, highly accessible for proteolytic enzymes. These data together indicate that LAL is indeed a preproprotein, in which the pro-region is essential for its folding and stability, secretion, and enzyme activity.
Specific In Vivo Staining of Astrocytes in the Whole Brain after Intravenous Injection of Sulforhodamine Dyes (2012)

Fluorescent staining of astrocytes without damaging or interfering with normal brain functions is essential for intravital microscopy studies. Current methods involved either transgenic mice or local intracerebral injection of sulforhodamine 101. Transgenic rat models rarely exist, and in mice, a backcross with GFAP transgenic mice may be difficult. Local injections of fluorescent dyes are invasive. Here, we propose a non-invasive, specific and ubiquitous method to stain astrocytes in vivo. This method is based on iv injection of sulforhodamine dyes and is applicable on rats and mice from postnatal age to adulthood. The astrocytes staining obtained after iv injection was maintained for nearly half a day and showed no adverse reaction on astrocytic calcium signals or electroencephalographic recordings in vivo. The high contrast of the staining facilitates the image processing and allows to quantify 3D morphological parameters of the astrocytes and to characterize their network. Our method may become a reference for in vivo staining of the whole astrocytes population in animal models of neurological disorders.
Demonstration of 300 Mbit/s free space optical link with commercial visible LED (2013)

Recently, we have introduced a method to improve modulation rate of a light emitting diode (LED) by using simple 2-cascaded Schottky diodes-capacitance current-shaping circuit. In this work, we demonstrate a high-speed free space optical link with a commercial 660 nm LED and a PIN (Si) photodiode. The system achieves an error-free data transmission at the rate of 300 Mbit/s over 11 m using on-off keying non-return-to-zero modulation.
ChemInform Abstract: Direct Oxidation of Liquid Fuels in a Solid Oxide Fuel Cell. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.