gebhart/patrepeval huggingface dataset:
Conformational changes accompanying proteolytic cleavage of human complement protein C3b by the regulatory enzyme factor I and its cofactor H. Spectroscopic and enzymological studies. (1983)

The conformational basis for the loss of C3b functional site expression following its conversion to iC3b by the regulatory proteins factor H and factor I has been examined by a number of spectroscopic techniques including the fluorescence of the extrinsic probe 8-anilino-1-naphthalenesulfonate, circular dichroism, and UV absorption difference spectroscopy. These techniques all detected significant conformational alterations accompanying the proteolytic cleavage event. To a substantial extent, the observed spectral changes tended to reverse those seen in the original conversion of native C3 to its functionally active C3b form. Similar changes were also seen when the thioester-cleaved, but peptide chain-intact, form of C3 was acted upon by the regulatory proteins. The most dramatic effect was seen in the 8-anilino-1-naphthalenesulfonate fluorescence system where the fluorescence enhancement observed upon conversion of C3 to C3b, which presumably reflects an increase in surface hydrophobicity, is lost upon further cleavage of the molecule to iC3b. This marked signal change forms the basis of a simple spectrofluorometric assay with which to study the enzymatic properties of factor I for its true substrate: the complex formed between C3b and factor H. Using this assay, factor I was found to display very tight binding of its substance, the Km at 25 degrees C being on the order of 0.025-0.1 microM, but it was also found to show a low rate of cleavage, the turnover number being less than 10 min-1 at this temperature.
A superoxide dismutase from the archaeon <i>Sulfolobus solfataricus</i> is an extracellular enzyme and prevents the deactivation by superoxide of cell‐bound proteins (2000)

An oxygen-induced iron superoxide dismutase was found in the culture fluid of the thermoacidophilic crenarchaeon Sulfolobus solfataricus during growth on glucose-rich media. This protein was also identified as being associated with the cell-surface, with the amount of the released and cell-bound protein fractions depending on the growth phase of the cells. The steady decrease in cell-associated superoxide dismutase during continued growth correlated with the increase of free superoxide dismutase in the medium. Both enzyme fractions were purified to homogeneity and found to be active with different catalytic efficiency, with the released superoxide dismutase showing a fourfold lower specific activity. Characterization in comparison with the cytosolic superoxide dismutase revealed identical N-terminal sequences, electrophoretic mobility, isoelectric point, and molecular mass for all three differently located enzymes. In order to clarify the physiological role of the cell-associated superoxide dismutase, the prevention of cell-bound protein deactivation by oxyradicals was also investigated. Glucose dehydrogenase, which was chosen as a model enzyme, was demonstrated to be located on the cell surface and to be inactivated by potassium superoxide by in vivo assays. The direct protective effect of superoxide dismutase on glucose dehydrogenase was demonstrated by in vitro assays on the free released enzyme. Similarly, the prevention of deactivation by potassium superoxide was also demonstrated for the integral membrane protein succinate dehydrogenase by intact cell assay. Superoxide dismutase added to cells was shown to moderately reduce the critical damaging peroxidation and hence play a major role in maintaining the integrity of the outer cell envelope components.
Purification of Single-Walled Carbon Nanotubes Using a Supercritical Fluid Extraction Method (2007)

Metal catalyst used in the production of single-walled carbon nanotubes (SWNTs) can be effectively removed from the as-grown nanotubes by an in situ chelation/supercritical fluid carbon dioxide extraction method. A pretreatment procedure using bulk electrolysis with ethylenediaminetetraacetic acid significantly improves the efficiency of supercritical fluid extraction probably by removing the amorphous carbon associated with the metal from the SWNTs. More than 98% of the iron impurity can be removed from the as-grown SWNTs using this two-step purification method without obvious damage to the nanotube structures according to our spectroscopic data.
Is pulsed ultrasound mutagenic? (1983)

The possibility that microsecond pulses of 3 MHz ultrasound may interact at the cellular level, with genetic consequences, was investigated using two different endpoints. The Ames mammalian microsome test was employed to assess mutagenicity and viability in Salmonella typhimurium bacteria, while the sister chromatid exchange frequency provided an indicator of ultrasound induced effects at the chromosome level in Chinese hamster ovary cells.
Probing Hydrogen Bonding and Proton Mobility in Dicyanoimidazole Monomers and Polymers (2004)

Hydrogen bonding and proton mobility are important features in many polymers. In this work, hydrogen bonding is studied in both monomers and polymers of dicyanoimidazoles using infrared and solid-state NMR spectroscopy and polymer viscosity studies. Hydrogen bonding accounts for an unusual complexity in the nitrogen−hydrogen stretching region of the infrared spectra. The influence of hydrogen bonding on properties was observed in several dicyanoimidazole polymers through polymer viscosity studies and estimation of Mark−Houwink parameters. The Mark−Houwink a value decreases, representing a less stiff chain, in poly(1-methyl-2-vinyl-4,5-dicyanoimidazole) compared to poly(2-vinyl-4,5-dicyanoimidazole) because hydrogen bonding is eliminated. By dissolving poly(2-vinyl-4,5-dicyanoimidazole) in NH3(aq), a polymer electrolyte results. Although hydrogen bonding is eliminated, electronic repulsions contribute to an increase in a or chain stiffness. Proton mobility in dicyanoimidazole polymers was studied with an innovative solid-state NMR technique using double-quantum (DQ) filtering and fast magic angle spinning (MAS = 30 kHz). Using this approach, several types of hydrogen bonds were identified and proton mobility in poly(2-vinyl-4,5-dicyanoimidazole) was detected.
CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing (2019)

Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector . A server running CNspector loaded with the figures from this paper can be accessed at https://shiny.wehi.edu.au/jmarkham/CNspector/index.html .
Vulcanizate Structure, Relaxation, and Tensile Strength of Polyisoprenes (1963)

Abstract The tensile strength of lightly-filled sulfur vulcanizates of 1,4- cis polyisoprene is lower the more the specimen has undergone deformation after removal of a definite stress. With equal tensile strength, this deformation multiplied by the modulus is proportional to the square of the filler concentration. Along with this deformation the volume of the elongated specimen increases through the formation of internal stress cracks. Rupture originates even at lower stresses in the neighborhood of the filler particles. It is affected by the size of the filler particles as well as by the chemical nature of the filler and by the structure of the network. Encouraged by these results we checked the network structure. We examined the stresses at high elongations, the photoelaetic homogeneity and the turbidities and viscosities of solutions of the degraded vulcanizates, and found small local variations in crosslink density and differences in the number of elastically-ineffective chain ends. The number of these chain ends and the local variations of crosslink density may increase greatly during vulcanization, and substantially reduce the tensile strength.
Special Fibres For Application Environments (1990)

Susceptibility analysis of optical fibres in application environment reveals that the performance depends directly on component specialization 1,2,3. The major task for environment oriented component specialization is to remove the harmful results of ex-cessive environmental sensitivity on the whole system. We are interested here in the design of special fibres of very high reliability for narrow band/wideband communication channels ans sensory/telemetric systems with depressed (or enhanced) sensitivity to specific environmental reactions or measurands. A considerable interest exists in modifying the properties of standard optical fibres by incorporating additional desensitizing/sensitizing layers or dopants to reduce (or enhance) a given effect.
Microtronic Flow Transducer (1989)

Novel microelectronic airflow and gas-flow transducer developed. Has no moving parts and constructed by use of variation on ordinary technology for processing of planar silicon microelectronics, where hundreds or thousands of identical devices concurrently produced on single chip as easily as can one. Gas-flow transducer based upon integrated Wheatstone bridge in silicon chip. Legs doped with gold and isolated thermally by etching away surrounding material (except corners). Because of small size, sensitivity, and good directional capability of new transducer, numerous potential applications in measurement of vortexes, flows in inlets to pipes, and other complicated flows.
Targeting the PD-1/PD-L1 Immune Evasion Axis With DNA Aptamers as a Novel Therapeutic Strategy for the Treatment of Disseminated Cancers (2015)

Blocking the immunoinhibitory PD-1:PD-L1 pathway using monoclonal antibodies has led to dramatic clinical responses by reversing tumor immune evasion and provoking robust and durable antitumor responses. Anti-PD-1 antibodies have now been approved for the treatment of melanoma, and are being clinically tested in a number of other tumor types as both a monotherapy and as part of combination regimens. Here, we report the development of DNA aptamers as synthetic, nonimmunogenic antibody mimics, which bind specifically to the murine extracellular domain of PD-1 and block the PD-1:PD-L1 interaction. One such aptamer, MP7, functionally inhibits the PD-L1-mediated suppression of IL-2 secretion in primary T-cells. A PEGylated form of MP7 retains the ability to block the PD-1:PD-L1 interaction, and significantly suppresses the growth of PD-L1+ colon carcinoma cells in vivo with a potency equivalent to an antagonistic anti-PD-1 antibody. Importantly, the anti-PD-1 DNA aptamer treatment was not associated with off-target TLR-9-related immune responses. Due to the inherent advantages of aptamers including their lack of immunogenicity, low cost, long shelf life, and ease of synthesis, PD-1 antagonistic aptamers may represent an attractive alternative over antibody-based anti PD-1 therapeutics.
Reactor design considerations in mineral sequestration of carbon dioxide (2001)

One of the promising approaches to lowering the anthropogenic carbon dioxide levels in the atmosphere is mineral sequestration. In this approach, the carbon dioxide reacts with alkaline earth containing silicate minerals forming magnesium and/or calcium carbonates. Mineral carbonation is a multiphase reaction process involving gas, liquid and solid phases. The effective design and scale-up of the slurry reactor for mineral carbonation will require careful delineation of the rate determining step and how it changes with the scale of the reactor. The shrinking core model was used to describe the mineral carbonation reaction. Analysis of laboratory data indicates that the transformations of olivine and serpentine are controlled by chemical reaction and diffusion through an ash layer respectively. Rate parameters for olivine and serpentine carbonation are estimated from the laboratory data.
Learned Step Size Quantization (2019)

Deep networks run with low precision operations at inference time offer power and space advantages over high precision alternatives, but need to overcome the challenge of maintaining high accuracy as precision decreases. Here, we present a method for training such networks, Learned Step Size Quantization, that achieves the highest accuracy to date on the ImageNet dataset when using models, from a variety of architectures, with weights and activations quantized to 2-, 3- or 4-bits of precision, and that can train 3-bit models that reach full precision baseline accuracy. Our approach builds upon existing methods for learning weights in quantized networks by improving how the quantizer itself is configured. Specifically, we introduce a novel means to estimate and scale the task loss gradient at each weight and activation layer's quantizer step size, such that it can be learned in conjunction with other network parameters. This approach works using different levels of precision as needed for a given system and requires only a simple modification of existing training code.
Delivery of Oligonucleotides and Analogues: The Oligonucleotide Conjugate‐Based Approach (2010)

Carrier conjugates: Oligonucleotide-based therapeutic strategies are moving closer to use in patients, but bench work is still needed. Although oligonucleotides are validated and powerful tools in basic research, their delivery is still the major issue impeding their use as therapeutics. Carrier–oligonucleotide conjugates currently in development are reviewed here.
What Is So Special about Aerosol-OT? 1. Aqueous Systems (2000)

To identify why Aerosol-OT (sodium bis(2-ethylhexyl) sulfosuccinate) is such a versatile surfactant, adsorption and aggregation in aqueous solutions have been investigated with 11 different AOT-related compounds. The first set, denoted di-CnSS with n = 4, 5, 6, 7, and 8, contain linear chains. In addition six different branched chain systems have been studied, including Aerosol-OT itself. These surfactants span extremes of branching, from 3,5,5-trimethyl-1-hexyl, through 2-ethyl-1-hexyl (AOT), to 1-ethyl-2-methyl-1-pentyl (see Figure 1), and therefore it is possible to delineate structure−performance relationships. For one model compound, di-C6SS, adsorption studies were made with two complementary techniques, drop volume tensiometry (DVT) and neutron reflection (NR). The tensiometrically derived area per molecule at the critical micelle concentration Acmc was 60 ± 3 Å2, which is in excellent agreement with that obtained directly by neutrons, 59 ± 2 Å2. The procedures for obtaining a sufficiently high surface chemical purity and the application of the Gibbs equation, to achieve agreement between DVT and NR, are discussed. Partial structure factor experiments with di-C6SS gave quantitative information on the interfacial structure in terms of surfactant and solvent distributions, and the results are compared with those obtained previously for AOT (Prog. Colloid Polym. Sci. 1995, 98, 243 and J. Phys. Chem. B 1997, 101, 1615). For the di-CnSS systems classic effects of chain carbon number on surface tension behavior, critical micelle concentrations (cmc's), and Acmc were observed. With the branched chain compounds a significant increase in Acmc was found, between 10 and 20 Å2, over those for equivalent carbon number straight chain systems. Furthermore, slight variations in Acmc were detected, reflecting changes in packing owing to differing extents of chain branching. The efficiency of packing was correlated with chain structure by introducing an empirical branching factor. In dilute aqueous systems regular Aerosol-OT behaves in a readily understandable fashion, fitting into the general pattern of behavior for all these sulfosuccinates: no special effects due to the 2-ethyl-1-hexyl chains were noted.
Pharmacokinetics and pharmacodynamics of combination chemotherapy with paclitaxel and epirubicin in breast cancer patients (2002)

Paclitaxel/Cremophor EL affects the disposition of epirubicinol and epirubicin. Furthermore, the slope factor of the Emax relationship between neutropenia and tC0.1 of paclitaxel suggests that the drugs might also interact at the pharmacodynamic level.
Characterization and High‐Temperature Mechanical Behavior of an Oxide/Oxide Composite (2003)

An oxide/oxide ceramic fiber‐matrix composite (CMC) has been extensively characterized for high‐temperature aerospace structural applications. This CMC is called GEN‐IV™, and it has a porous and cracked aluminosilicate matrix reinforced by 3M Nextel 610™ alumina fibers woven in a balanced eight harness weave (8HSW). This CMC has been specifically designed without an interphase between the fiber and matrix, and it relies on the porous matrix for flaw tolerance. Stress‐strain response is nearly linear to failure and without a well‐defined proportional limit in tension and compression. In‐plane shear and interlaminar strength increases with increasing temperature. The 1000°C fatigue limit in air at 105 cycles is 160 MPa, and the residual tensile strength of run‐out specimens is not affected by the fatigue loading. The creep‐rupture resistance above 1000°C is relatively poor, but it can be improved with a more‐creep‐resistant fiber.
Structural damage detection and localization using <scp>NETSHM</scp> (2006)

Structural health monitoring (SHM) is an important application area for wireless sensor networks. SHM techniques attempt to autonomously detect and localize damage in large civil structures. Structural engineers often implement and test SHM algorithms in a higher level language such as C/Matlab. In this paper, we describe the design and evaluation of NETSHM, a sensor network system that allows structural engineers to program SHM applications in Matlab or C at a high level of abstraction. In particular, structural engineers do not have to understand the intricacies of wireless networking, or the details of sensor data acquisition. We have implemented a damage detection technique and a damage localization technique on a complete NETSHM prototype. Our experiments on small and medium-scale structures show that NETSHM is able to detect and localized damage perfectly with very few false-positives and no false negatives, and that it is robust even in realistic wireless environments.
CELL WALL CONFORMATION IN DRY SEEDS IN RELATION TO THE PRESERVATION OF STRUCTURAL INTEGRITY DURING DESICCATION (1982)

Internal tissues of mature air‐dry seeds, prepared anhydrously for observation with the scanning electron microscope, exhibit cell wall structure which is different from that observed in aqueously fixed (hydrated) seed tissues. In a wide range of dry seeds observed (six members of the Cucurbitaceae, two species of Yucca, Hibiscus esculentus, Phaseolus vulgaris , and Helianthus annuus ) cell walls exhibit a unique collapsed structure. The manner of cell wall collapse is characteristic for a given species and ranges from a highly regular folding pattern in the Cucurbitaceae to random wrinkling of the walls in Hibiscus. Evidence suggests that the regular patterns of wall folding may result from a mechanism located in the cell wall. Wall collapse in dry seeds is explained as a means of coordinating wall and protoplasmic shrinkage during desiccation and is thought to be essential for preserving the structural integrity of the tissue by conserving intercellular communication and plasmalemma‐cell wall association. Implications of these observations may relate to retention of viability in seeds.
Humidity Measurements using Commercial Microwave Links (2011)

Atmospheric humidity strongly affects the economy of nature and has a cardinal part in a variety of environmental processes (e.g. Allan et al., 1999). As the most influential of greenhouse gases, it absorbs long-wave terrestrial radiation. Through the water vapour evaporation and recondensation cycle, it plays a central part in the Earth's energy redistribution mechanism by transferring heat energy from the surface to the atmosphere. Meteorological decision-support for weather forecasting is based on atmospheric model results, the accuracy of which is determined by the quality of its initial conditions or forcing data. Humidity, in particular, is a critical variable in the initialization of these models. The Mesoscale Alpine Programme (MAP) which set out to improve prediction of the regional weather, and specifically rainfall and flooding, concluded that accurate moisture fields for initialization were of great importance in achieving improved results (Ducrocq et al., 2002). Humidity measurements are predominantly obtained by either surface stations, radiosondes or satellite systems. The typical surface station instruments commonly provide only very local, point, observations, and therefore suffer from low spatial resolution. Moisture though, is a field with an unusually high variability in the mesoscale as demonstrated, for instance, by structure functions (Lilly & Gal-Chen, 1983). Compounding this problem is the limited accessibility to position humidity gauges in heterogeneous terrain, or areas with complex topography. Satellites allow for a large area to be covered, but are frequently not accurate enough in measuring surface level moisture while this near-surface moisture is, in most cases, the important variable for convection. Radiosondes, which are typically launched only 2-4 times a day, also provide very limited information. Additionally, these monitoring methods are costly for implementation, deployment and maintenance. Because of surface perturbation a point measurement close to the surface (for example 2m from the ground as in a standard meteorological surface station) is not satisfactory for model initialization. What is ideally required for meteorological modeling purposes is an area average measurement of near-surface moisture over a box with the scale of the model's grid and at an altitude of a few tens of meters. Current measuring tools cannot effectively provide this type of data. The method we present in this chapter provides a unique way of obtaining precisely this type of measurement. We introduce a technique, originally published by David et al. (2009), to measure atmospheric humidity using data collected by wireless communication networks.