gebhart/patrepeval huggingface dataset:
In Vitro Synthesis of Cross-linked Murein and Its Attachment to Sacculi by PBP1A from Escherichia coli (2006)

The penicillin-binding protein (PBP) 1A is a major murein (peptidoglycan) synthase in Escherichia coli. The murein synthesis activity of PBP1A was studied in vitro with radioactive lipid II substrate. PBP1A produced murein glycan strands by transglycosylation and formed peptide cross-links by transpeptidation. Time course experiments revealed that PBP1A, unlike PBP1B, required the presence of polymerized glycan strands carrying monomeric peptides for cross-linking activity. PBP1A was capable of attaching nascent murein synthesized from radioactive lipid II to nonlabeled murein sacculi. The attachment of the new material occurred by transpeptidation reactions in which monomeric triand tetrapeptides in the sacculi were the acceptors.
Loss of dendrite stabilization by the Abl-related gene (Arg) kinase regulates behavioral flexibility and sensitivity to cocaine (2009)

Adolescence is characterized by increased vulnerability to developing neuropsychiatric disorders and involves a period of prefrontal cortical dendritic refinement and synaptic pruning that culminates in cytoskeletal stabilization in adulthood. The Abl-related gene (Arg) acts through p190RhoGAP to inhibit the RhoA GTPase and stabilize cortical dendritic arbors beginning in adolescence. Cortical axons, dendrites, and synapses develop normally in Arg-deficient (arg(-/-)) mice, but adult dendrites destabilize and regress; thus, arg(-/-) mice present a model of adolescent-onset dendritic simplification. We show that arg(-/-) mice are impaired in a reversal task and that deficits are grossly exacerbated by low-dose cocaine administration. Although ventral prefrontal dopamine D2 receptor levels predict "perseverative" error counts in wild-type mice, no such relationship is found in arg(-/-) mice. Moreover, arg(-/-) mice are insensitive to the disruptive effects of the D2/D3 antagonist haloperidol in reversal but show normal sensitivity to its locomotor-depressant actions. Arg deficiency and orbitofrontal cortical Arg inhibition via STI-571 infusion also enhance the psychomotor stimulant actions of cocaine. These findings provide evidence that stabilization of dendritic structure beginning in adolescence is critical for the development of adaptive and flexible behavior after cocaine exposure.
The exosomes in tumor immunity (2015)

Exosomes are a kind of nanometric membrane vesicles and can be released by almost all kinds of cells, including cancer cells. As the important mediators in intercellular communications, exosomes mediate exchange of protein and genetic material derived from parental cells. Emerging evidences show that exosomes secreted by either host cells or cancer cells are involved in tumor initiation, growth, invasion and metastasis. Moreover, communications between immune cells and cancer cells via exosomes play dual roles in modulating tumor immunity. In this review, we focus on exosome-mediated immunosuppression via inhibition of antitumor responses elicited by immune cells (DCs, NK cells, CD4<sup>+</sup> and CD8<sup>+</sup> T cells, etc.) and induction of immunosuppressive or regulatory cell populations (MDSCs, Tregs and Bregs). Transfer of cytokines, microRNAs (miRNAs) and functional mRNAs by tumor-derived exosomes (TEXs) is crucial in the immune escape. Furthermore, exosomes secreted from several kinds of immune cells (DCs, CD4<sup>+</sup> and CD8<sup>+</sup> Tregs) also participate in immunosuppression. On the other hand, we summarize the current application of DC-derived and modified tumor-derived exosomes as tumor vaccines. The potential challenges about exosome-based vaccines for clinical application are also discussed.
On-the-field calibration of an array of sensors (2010)

We address the problem of the calibration of an array of sensors by investigating theoretically and experimentally the case of 2 three-axis sensors. Our focus is on magnetometers that can be used in a low-cost inertial navigation system. Usual errors (misalignments, non-orthogonality, scale factors, biases) are accounted for. The proposed calibration method requires no specific calibration hardware. Instead, we solely use the fact that, if the sensor is properly calibrated, the norm of the sensed field must remain constant irrespective of the sensors orientation. Several strategies of calibration for an array of sensors are described along with the impact of (unavoidable) field disturbances. Experiments conducted with a couple of magneto-resistive magnetometers and data fusion results illustrate the relevance of the approach.
Isopentenyl Pyrophosphate <i>cis</i>-1,4-Polyisoprenyl Transferase from Guayule (<i>Parthenium argentatum</i> Gray) (1984)

Electron micrographs of the mesophyll cells of guayule Parthenium argentatum Gray leaves show deposits of cis-polyisoprene (rubber) in the cytoplasm in the vicinity of mitochondria and chloroplasts and demonstrate that the rubber-synthesizing enzymes are present in guayule leaves. The terminal step in the synthesis of cis-polyisoprene from isopentenyl pyrophosphate (IPP) catalyzed by isopentenyl pyrophosphate cis-1,4-polyisoprenyl transferase has been demonstrated in crude leaf extracts by the enzymic incorporation of [(14)C]isopentenyl pyrophosphate into the polymer and the recovery of [(14)C]levulinic acid following ozonolysis. The rubber transferase activity in the crude extracts of guayule leaves was 5.8 nanomoles isopentenyl pyrophosphate incorporated per milligram protein per hour. This is the first description of the rubber transferase from a nonlaticiferous plant.The specific activity (in units of nanomoles IPP converted per milligram protein per hour) of the partially purified enzyme following chromatography on diethylaminoethyl-cellulose columns was 41.7 units and contained 0.29 units of IPP isomerase activity and 0.08 units of farnesyl pyrophosphate synthetase activity. The rubber transferase requires reduced glutathione and Mg(2+) for maximal activity. There was no incorporation of IPP into cis-1,4-polyisoprene in the absence of rubber particles as primer, and Langmuir isotherm plots showed that the specific activity of the enzyme was proportional to the concentration of the enzyme on the surface of the rubber particles. For a given rubber particle distribution, enzyme activity was proportional to time, IPP concentration, and rubber concentration. The addition of 0.4 millimolar dimethylallyl pyrophosphate to the rubber transferase reaction resulted in a 2-fold increase in the incorporation of IPP into rubber. A comparison was made of the relative activities of rubber transferase in different species of Parthenium, Ficus, and Euphorbia.
Reaction of diazomethane with 2-acetyl-5,5-diphenyl-2,4-pentadienoic acid and related compounds. (1976)

Reaction of 2-acetyl-5, 5-diphenyl-2, 4-pentadienoic acid (Ia) and its methyl ester (Ib) with diazomethane gave rise to 3-acetyl-3-methoxycarbonyl-4-(β-phenylstyryl)-1-pyrazoline (IIb), which by elimination of nitrogen afforded methyl 2-acetyl-6, 6-diphenyl-3, 5-hexadienoate (IIIb). Similar reaction of 3-(γ-phenylcinnamylidene)-2, 4-pentanedione (Ic) and dimethyl γ-phenylcinnamylidenemalonate (Id) with diazomethane gave the adduct corresponding to 1-pyrazoline derivatives (IIc, IId), respectively. Heating of these compounds afforded denitrogenated products. Similarly, methyl 2-acetyl-5-phenyl-2, 4-pentadienoate (Ie) and 3-cinnamylidene-2, 4-pentanedione (If) reacted with diazomethane, followed by elimination of nitrogen, to afford methyl 2-acetyl-6-phenyl-3, 5-hexadienoate (IIIe) and 3-(4-phenyl-1, 3-butadienyl)-2, 4-pentadione (IIIf), respectively. The reaction of the pyrazoline (II) to give compound (III) involves the novel ring-cleavage of the cyclopropane intermediate, such as methyl 1-acetyl-2-(β-phenylstyryl)-cyclopropane-1-carboxylate (IX, where R1=phenyl, R2=methyl, R3=methoxy).
Improvement of open-circuit voltage and photovoltaic properties of 2D-conjugated polymers by alkylthio substitution (2014)

The photovoltaic properties of 2D-conjugated copolymer PBDTTTs were further improved by side chain engineering in a 2D-conjugated polymer.
The uptake of swainsonine, a specific inhibitor of α‐D‐mannosidase, into normal human fibroblasts in culture (1983)

Swainsonine, an indolizidine alkaloid, found in plants of the genus Swainsona, has been shown to be a strong inhibitor in vitro of the alpha-D-mannosidase activity in normal human fibroblasts. Therefore, inhibition of alpha-D-mannosidase activity in extracts of harvested cells grown with swainsonine in the medium has been used to follow the association of the alkaloid with normal human fibroblasts in culture. Swainsonine that could not be removed by extensive washing became associated with the cells within 1 min, and it is concluded that the alkaloid is internalized rapidly by the cells. The amount of swainsonine taken up into the cells depended on the length of time in contact and the concentration of swainsonine in the medium, but at 37 degrees C a plateau of internalized swainsonine occurred after 2 hr with extracellular concentrations of swainsonine of 100 microM or greater. At lower concentrations of swainsonine the rate of uptake was found to be temperature-dependent, increasing greatly at 20 degrees C. The rapidity and temperature sensitivity of the uptake, together with the observation that mannose or mannose-6-phosphate did not prevent the association, suggest that swainsonine enters the cells by permeation rather than by endocytosis. When swainsonine is withdrawn from the culture medium, there is a decrease with time of cell-associated swainsonine. The kinetics of uptake and release of swainsonine and its slightly basic nature make it likely that swainsonine is concentrated initially in the lysosomes. This rapid, but reversible, concentration of swainsonine in lysosomes would be consistent with the observed effects of the toxin in vivo.
Tuning the Chiral Environment of <i>C</i><sub>2</sub>-Symmetric Diene Ligands: Development of 3,7-Disubstituted Bicyclo[3.3.1]nona-2,6-dienes (2008)

Through the structural analysis of bicyclo[3.3.1]nona-2,6-dienes, new C(2)-symmetric chiral diene ligands 1 based on 3,7-disubstituted bicyclo[3.3.1]nona-2,6-diene framework have been designed and synthesized. These chiral ligands readily bind to rhodium(I) and provide a different chiral environment from the existing chiral dienes. The rhodium complexes thus obtained act as effective catalysts for 1,4-addition of alkenyl- and arylboronic acids to various alpha,beta-unsaturated ketones, including several combinations that were previously difficult to provide high enantioselectivity.
A biomimetic and fully regiocontrolled total synthesis of (±)-colchicine (1992)

The first fully regiocontrolled total synthesis of the alkaloid colchicine 1 is described; the key step of the reaction sequence is the efficient biomimetic conversion of the σ-homo-o-benzoquinone monoacetal 11 into the α-tropolone-O-methyl ether 13.
Education for Surveyors—A Vision for the 21st Century (1994)

Abstract The history of surveying in Australia over the last two hundred years has shown the surveyor to have played many roles besides that of solely measuring features on the earths surface. These include those of engineer, planner, land manager, land valuer, environmental manager and land developer. What has given the Australian surveyor a competitive edge over other more narrowly defined professions, is the fact that surveyors have always possessed a balance of fundamental skills in measurement science and land management. It should be noted however, that surveying education has taken many different directions in the same period, often being more influenced by overseas trends and models rather than the needs of the practising Australian surveyor—even though the role of the surveyor in the broader community in Australia has not changed to a great extent over the last two hundred years. This paper discusses the historical perspective of surveying education in Australia and draws distinctions between local and international trends. It presents a vision which recognises the surveyor’s primary role is the measurement and management of spatial data in the broadest sense. The vision is based on maintaining a balance between measurement science and land management, on retaining a strong scientific foundation to the discipline but above all else remaining flexible in today’s ever changing world. The paper illustrates this vision by describing the programmes at the University of Melbourne.
Low enrichment Mo-99 target development program at ANSTO (2002)

The Australian Nuclear Science and Technology Organisation (ANSTO, formerly AAEC) has been producing fission product Mo-99 in HIFAR, from the irradiation of Low Enrichment Uranium (LEU) UO{sub 2} targets, for nearly thirty years. Over this period, the U-235 enrichment has been increased in stages, from natural to 1.8% to 2.2%. The decision to provide Australia with a replacement research reactor (RRR) for HIFAR has created an ideal opportunity to review and improve the current Mo-99 production process from target design through to chemical processing and waste management options. ANSTO has entered into a collaboration with Argonne National Laboratory (RERTR) to develop a target using uranium metal foil with U-235 enrichment of less than 20% The initial focus has been to demonstrate use of LEU foil targets in HIFAR, using existing irradiation methodology. The current effort focussed on designing a target assembly with optimised thermohydraulic characteristics to accommodate larger LEU foils to meet Mo-99 production needs. The ultimate goal is to produce an LEU target suitable for use in the Replacement Research Reactor when it is commissioned in 2005. This paper reports our activities on: - The regulatory approval processes required in order to undertake irradiation of this new target; -Supporting calculations (neutronics, computational fluid dynamics) for safety submission; - Design challenges and changes to prototype irradiation; - Trial irradiation of LEU foil target in HIFAR; - Future target and rig development program at ANSTO. (author)
Effect of ZIF-8 Crystal Size on the O2 Electro-Reduction Performance of Pyrolyzed Fe–N–C Catalysts (2015)

The effect of ZIF-8 crystal size on the morphology and performance of Fe–N–C catalysts synthesized via the pyrolysis of a ferrous salt, phenanthroline and the metal-organic framework ZIF-8 is investigated in detail. Various ZIF-8 samples with average crystal size ranging from 100 to 1600 nm were prepared. The process parameters allowing a templating effect after argon pyrolysis were investigated. It is shown that the milling speed, used to prepare catalyst precursors, and the heating mode, used for pyrolysis, are critical factors for templating nano-ZIFs into nano-sized Fe–N–C particles with open porosity. Templating could be achieved when combining a reduced milling speed with a ramped heating mode. For templated Fe–N–C materials, the performance and activity improved with decreased ZIF-8 crystal size. With the Fe–N–C catalyst templated from the smallest ZIF-8 crystals, the current densities in H2/O2 polymer electrolyte fuel cell at 0.5 V reached ca. 900 mA cm−2, compared to only ca. 450 mA cm−2 with our previous approach. This templating process opens the path to a morphological control of Fe–N–C catalysts derived from metal-organic frameworks which, when combined with the versatility of the coordination chemistry of such materials, offers a platform for the rational design of optimized Metal–N–C catalysts.
A 0.5 V 55 $\mu \text{W}$ 64 $\times $ 2 Channel Binaural Silicon Cochlea for Event-Driven Stereo-Audio Sensing (2016)

This paper presents a 64 × 2 channel stereo-audio sensing front end with parallel asynchronous event output inspired by the biological cochlea. Each binaural channel performs feature extraction by analog bandpass filtering, and the filtered signal is encoded into events via asynchronous delta modulation (ADM). The channel central frequencies J0 are geometrically scaled across the human hearing range. Two design techniques are highlighted to achieve the high system power efficiency: source-follower-based bandpass filters (BPFs) and asynchronous delta modulation (ADM) with adaptive self-oscillating comparison. The chip was fabricated in 0.18 μm 1P6M CMOS, and occupies an area of 10.5×4.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The core cochlea system operating under a 0.5 V power supply consumes 55 μW at an output rate of 100k event/s. The measured range of J0 is from 8 Hz to 20 kHz, and the BPF quality factor Q can be tuned from 1 to almost 40. The 1σ mismatch of J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> and Q between two ears is 3.3% and 15%, respectively, across all channels at Q ≈ 10. Reconstruction of speech input from the event output of the chip is performed to validate the information integrity in event-domain representation, and vowel discrimination is demonstrated as a simple application using histograms of the output events. This type of silicon cochlea front end targets integration with embedded event-driven processors for low-power smart audio sensing with classification capabilities, such as voice activity detection and speaker identification.
The privacy-aware access control system using attribute-and role-based access control in private cloud (2011)

Cloud is a relatively new concept and so it is unsurprising that the information assurance, data protection, network security and privacy concerns have yet to be fully addressed. The cloud allows users to avoid upfront hardware and software investments, gain flexibility, collaborate with others, and take advantage of the sophisticated services. However, security is a huge issue for cloud users especially access control, user profile management and accessing services offered by the private cloud environment. A privacy enhancement system on Academic-based private cloud system using Eucalyptus open source cloud infrastructure has been proposed in this paper. This system provides the cloud users to improve the privacy and security of the private personal data. Two approaches (Role-based Access Control and Attribute-based Access Control model) are combined as a new approach (ARBAC). This means that they are applied to improve the privacy which supports both mandatory and discretionary access control needs on the target private cloud system.
How disks are `padlocked' (1986)

Copy protection uses special techniques to write information on a floppy disk, that the disk drive of an ordinary personal computer can read but cannot write. When a user makes a copy of this disk, that information will thus be lost. Software embedded in the application program can check for this unique data. If it is there, the disk is legitimate; if it is not, the disk is a copy, and the program terminates. The methods described for protecting a disk against copying are: bad sectoring; the use of spiral tracks and offset tracks which depend intimately on the hardware characteristics of the system involved; extra sectors slipped into the outer tracks of some disks; fake sectors; super sectors (write-splicing); sector alignment; wide tracks; and weak bit encoding. The legal, technical, and ethical questions that arise are explored.
Monte Carlo lookup table-based inverse model for extracting optical properties from tissue-simulating phantoms using diffuse reflectance spectroscopy (2013)

We present a Monte Carlo lookup table (MCLUT)-based inverse model for extracting optical properties from tissue-simulating phantoms. This model is valid for close source-detector separation and highly absorbing tissues. The MCLUT is based entirely on Monte Carlo simulation, which was implemented using a graphics processing unit. We used tissue-simulating phantoms to determine the accuracy of the MCLUT inverse model. Our results show strong agreement between extracted and expected optical properties, with errors rate of 1.74% for extracted reduced scattering values, 0.74% for extracted absorption values, and 2.42% for extracted hemoglobin concentration values.
ATGen: automatic test data generation using constraint logic programming and symbolic execution† (2001)

Abstract The verification and validation of software through dynamic testing is an area of software engineering where progress towards automation has been slow. In particular the automatic design and generation of test data remains, by and large, a manual activity. This is despite the high promises that the symbolic execution technique engendered when it was first proposed as a method for automatic test data generation. This paper presents an automatic test data generator based on constraint logic programming and symbolic execution. After reviewing the symbolic execution technique, approaches for the resolution of the technical difficulties that have so far prevented symbolic execution from reaching its full potential in the area of automatic test data generation are presented. ATGen, an automatic test data generator, based on symbolic execution and that uses constraint logic programming, is then discussed. Copyright © 2001 John Wiley & Sons, Ltd.
Cytochrome P450-dependent metabolism of gefitinib (2005)

The in vitro metabolism of [(14)C]-gefitinib (1-3 microM) was investigated using human liver microsomes and a range of expressed human cytochrome P450 enzymes, with particular focus on the formation of O-desmethyl-gefitinib (M523595), the major metabolite observed in human plasma. High-performance liquid chromatography with ultraviolet light, radiochemical and mass spectral analysis, together with the availability of authentic standards, enabled quantification and structural identification of metabolites. On incubation with pooled human liver microsomes, [(14)C]-gefitinib underwent rapid and extensive metabolism to a number of metabolites, although M523595 was only a minor microsomal product. Formation of most metabolites was markedly decreased by ketoconazole, but M523595 production was inhibited only by quinidine. Gefitinib was metabolized extensively by expressed CYP3A4, producing a similar range of metabolites to liver microsomes, but M523595 was not formed. CYP1A2, 2C9 and 2C19 produced no measurable metabolism of gefitinib, while CYP3A5 produced a range of metabolites similar to CYP3A4, but to a much lower degree. In contrast, CYP2D6 catalysed rapid and extensive metabolism of gefitinib to M523595. While formation of M523595 was CYP2D6 mediated, the overall metabolism of gefitinib was dependent primarily on CYP3A4, and this was not obviously diminished in liver microsomes from CYP2D6 poor metabolizers.