gebhart/patrepeval huggingface dataset:
In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases (2013)

Drug metabolizing enzymes play a key role in the metabolism, elimination and detoxification of xenobiotics, drugs and endogenous molecules. While their principal role is to detoxify organisms by modifying compounds, such as pollutants or drugs, for a rapid excretion, in some cases they render their substrates more toxic thereby inducing severe side effects and adverse drug reactions, or their inhibition can lead to drug-drug interactions. We focus on sulfotransferases (SULTs), a family of phase II metabolizing enzymes, acting on a large number of drugs and hormones and showing important structural flexibility. Here we report a novel in silico structure-based approach to probe ligand binding to SULTs. We explored the flexibility of SULTs by molecular dynamics (MD) simulations in order to identify the most suitable multiple receptor conformations for ligand binding prediction. Then, we employed structure-based docking-scoring approach to predict ligand binding and finally we combined the predicted interaction energies by using a QSAR methodology. The results showed that our protocol successfully prioritizes potent binders for the studied here SULT1 isoforms, and give new insights on specific molecular mechanisms for diverse ligands' binding related to their binding sites plasticity. Our best QSAR models, introducing predicted protein-ligand interaction energy by using docking, showed accuracy of 67.28%, 78.00% and 75.46%, for the isoforms SULT1A1, SULT1A3 and SULT1E1, respectively. To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility, along with a QSAR approach, to identify small molecules that can interact with II phase dug metabolizing enzymes.
Resonant based microwave biosensor for biological cells discrimination (2010)

This publication deals with a resonant RF-based biosensor for in-liquid operation. Stop-band filter modeling and characterizations are investigated in order to discriminate dead and alive suspensions of human cultured cells. This proof of concept demonstrator features noticeable contrasts on both resonant frequency (7%) and amplitude (2.1 dB). Theses results consequently demonstrate that RF detection can provide a non invasive sensing technique, which is compatible with a lab-on-a-chip approach to discriminate the pathological state of cells.
Damage-Free Planarization of 4H-SiC (0001) by Catalyst-Referred Etching (2007)

We report the damage-free planarization of 4H-SiC (0001) wafers using a new planarization technique we named CAtalyst-Referred Etching (CARE). The CARE setup equipped with a polishing pad made of a catalyst is almost the same as a lapping setup. Since the catalyst generates reactive species that activate only when they are next to the catalyst surface, SiC can be chemically removed in contact with the catalyst surface with a pressure noticeably lower than that in a conventional polishing process. The processed surfaces were observed by optical interferometry and AFM. These observations presented a marked reduction in surface roughness. A step-terrace structure was observed with a step height of approximately 3み, corresponding to one-bilayer thickness of Si and C, in the AFM images. To estimate the crystallographic properties of the CARE-processed surface, the surfaces were observed by cross-sectional TEM. The TEM images showed that a more crystallographically well-ordered surface was realized in comparison with the conventional CMP-processed surface.
VISUALIZATION OF THE BLOOD FLOW INSIDE THE SINGLE PIVOT BEARING SUPPORTED CENTRIFUGAL BLOOD PUMP USING THE COMPUTATIONAL FLUID DYNAMICS ANALYSIS (2002)

In this study, the blood flow field inside the single pivot bearing supported centrifugal blood pump was calculated using the computational fluid dynamics (CFD) method to understand the flow pattern, which has influence on antithrombogenecity and hemolysis inside the pump. The pump model with mesh grids was generated according to the structure of the real pump. Then the flow field inside the pump was computed, and the flow pattern was visualized. For the validation of the simulation, both the pressure rise and the flow discharge estimated from the simulation were compared with those of the experiments. The graph of the pressure rise following the discharge flow showed that both curvatures of the pressure had a good agreement, but the simulated pressure shifted about 30–40mmHg from the experimental pressure at each flow. It is considered that this gap was caused by the simplification of the model from the real pump such as the impeller vibration. From the flow pattern, the stagnation of the flow in the region behind the impeller and the separation of the stream at the bending region of the inlet tube were found. Since these region, where the flow is not smooth, causes thrombus formation and hemolysis, the re-design of the pump structure should be considered. The effect of the different shapes of the inlet tube on the flow field inside the pump will be investigated in the future in order to optimize the flow in the inlet.
Infrared Spectroscopy in Conservation Science (2000)

Part 1 History of infrared spectroscopy: additional reading. Part 2 Infrared absorption theory: electromagnetic radiation absorption theory infrared spectra infrared regions summary additional reading. Part 3 Sample collection and preparation: sampling methodology sampling implementation sample collection and preparation procedures summary additional reading. Part 4 Infrared analysis methods: infrared transmission measurements infrared reflection measurements infrared microspectroscopy summary additional reading. Part 5 Spectral interpretation: infrared spectra qualitative analysis identification of materials used in art and art conservation quantitative analysis mathematical manipulations of spectra summary additional reading. Part 6 Case studies: identification and characterization of materials deterioration studies the case studies case study 1 - ultramarine pigments case study 2 - creosote lac resin case study 3 - Chumash Indian paints case study 4 - varnish on a desk case study 5 - reflection versus transmission case study 6 -painting cross sections case study 7 - vikane case study 8 -parylene case study 9 - cellulose nitrate sculptures 10 - Dead Sea scrolls summary appendices.
Importance of AMPA Receptors for Hippocampal Synaptic Plasticity But Not for Spatial Learning (1999)

Gene-targeted mice lacking the L-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) receptor subunit GluR-A exhibited normal development, life expectancy, and fine structure of neuronal dendrites and synapses. In hippocampal CA1 pyramidal neurons, GluR-A-/- mice showed a reduction in functional AMPA receptors, with the remaining receptors preferentially targeted to synapses. Thus, the CA1 soma-patch currents were strongly reduced, but glutamatergic synaptic currents were unaltered; and evoked dendritic and spinous Ca2+ transients, Ca2+-dependent gene activation, and hippocampal field potentials were as in the wild type. In adult GluR-A-/- mice, associative long-term potentiation (LTP) was absent in CA3 to CA1 synapses, but spatial learning in the water maze was not impaired. The results suggest that CA1 hippocampal LTP is controlled by the number or subunit composition of AMPA receptors and show a dichotomy between LTP in CA1 and acquisition of spatial memory.
Isolation and Cultivation in vitro of the Actinomycete Causing Root Nodulation in <i>Comptonia</i> (1978)

The soil actinomycete causing formation of nitrogen-fixing symbiotic nodules on roots of the woody angiosperm Comptonia peregrina (L.) Coult. (Myricaceae) has been isolated from surface-sterilized root nodules after incubation and enzyme maceration. The filamentous bacterium grows slowly in pure culture on a yeast extract medium, producing sporogenous bodies which form large numbers of ovoid spores. Reinfection of sand-grown or aeroponically grown seedlings of Comptonia was achieved repeatedly with inocula prepared from suspensions of the Comptonia isolate. The same actinomycete has been reisolated from these seedling nodules. The induced nodules are highly active in the acetylene-reduction assay, and plants grow vigorously without an exogenous supply of fixed nitrogen.
<i>In vitro</i>evaluation and pharmacokinetics in dogs of guar gum and Eudragit FS30D-coated colon-targeted pellets of indomethacin (2007)

A pH- and enzyme-dependent colon-targeted multi-unit delivery system of indomethacin was developed by coating guar gum and Eudragit FS30D sequentially onto drug-loaded pellets in a fluidized bed coater. In vitro studies showed that smaller coating weight gain of guar gum resulted in reduced release lag time t10 (10% release time), but favored degradation by enzymes (galactomannanase). A cumulative weight gain (CWG) of 44% provided sufficient enzymatic sensitivity and protection of the core. Under gradient pH conditions (pH = 1.2, 6.8, 7.4 and 6.5 for 2, 2, 1 and 15 h, respectively), indomethacin was released from Eudragit FS30D-coated pellets quickly after changing pH to 7.4. For guar gum/Eudragit FS30D double-coated pellets, only about 5% of the drug was released after another 1 h, showing retarding effect by guar gum coating. After changing pH to 6.5 and addition of galactomannanase, enzyme-dependent drug release was observed. Pharmacokinetic study in beagle dogs showed that fastest absorption with the smallest Tmax and Tlag was observed for uncoated pellets. The Tmax and Tlag of Eudragit FS30D-coated pellets were postponed to about 2.5 and 1 h, respectively. After a further guar gum coating, Tlag was further postponed to about 2.8 h, about 2 h of additional lag time on the basis of Eudragit FS30D coating. It is indicated that the guar gum/Eudragit FS30D-coated system has potential to be used to deliver drugs to the colon.
Flow cytometry in clinical pathology (2011)

Flow cytometry has had an impact upon all areas of clinical pathology and now, in the 21st century, it is truly coming of age. This study reviews the application of flow cytometry within clinical pathology with an emphasis upon haematology and immunology. The basic principles of flow cytometry are discussed, including the principles and considerations of the flow-cell and hydrodynamic focusing, detector layout and function, use of fluorochromes and multicolour flow cytometry (spectral overlap and colour compensation), alongside the strategies available for sample preparation, data acquisition and analysis, reporting of results, internal quality control, external quality assessment and flow sorting. The practice of flow cytometry is discussed, including the principles and pitfalls associated with leukocyte immunophenotyping for leukaemia and lymphoma diagnosis, immune deficiency, predicting and monitoring response to monoclonal antibody therapy, rare event detection and screening for genetic disease. Each section is illustrated with a case study. Future directions are also discussed.
Traffic Sign Detection System for Locating Road Intersections and Roundabouts: The Chilean Case (2017)

This paper presents a traffic sign detection method for signs close to road intersections and roundabouts, such as stop and yield (give way) signs. The proposed method relies on statistical templates built using color information for both segmentation and classification. The segmentation method uses the RGB-normalized (ErEgEb) color space for ROIs (Regions of Interest) generation based on a chromaticity filter, where templates at 10 scales are applied to the entire image. Templates consider the mean and standard deviation of normalized color of the traffic signs to build thresholding intervals where the expected color should lie for a given sign. The classification stage employs the information of the statistical templates over YCbCr and ErEgEb color spaces, for which the background has been previously removed by using a probability function that models the probability that the pixel corresponds to a sign given its chromaticity values. This work includes an analysis of the detection rate as a function of the distance between the vehicle and the sign. Such information is useful to validate the robustness of the approach and is often not included in the existing literature. The detection rates, as a function of distance, are compared to those of the well-known Viola-Jones method. The results show that for distances less than 48 m, the proposed method achieves a detection rate of 87.5 % and 95.4 % for yield and stop signs, respectively. For distances less than 30 m, the detection rate is 100 % for both signs. The Viola-Jones approach has detection rates below 20 % for distances between 30 and 48 m, and barely improves in the 20-30 m range with detection rates of up to 60 % . Thus, the proposed method provides a robust alternative for intersection detection that relies on statistical color-based templates instead of shape information. The experiments employed videos of traffic signs taken in several streets of Santiago, Chile, using a research platform implemented at the Robotics and Automation Laboratory of PUC to develop driver assistance systems.
Advanced real-time scheduling using the IEEE 802.5 token ring (2003)

An approach for scheduling the IEEE 802.5 token ring for hard real-time applications is presented that not only guarantees deadlines for synchronous class messages, but also greatly reduces asynchronous class response times. Highly responsive guaranteed service is introduced for alert class asynchronous messages. Conventional use of the IEEE 802.5 token ring provides synchronous communication services using time-domain multiplexing (TDM) while relegating asynchronous class message services to background status. An algorithmic-based scheduling approach is presented that supports a priori schedulability determination for arbitrary synchronous message sets without the costly time-line development, testing, and tuning associated with TDM techniques. This capability allows the IEEE 802.5 to support dynamic, adaptive and reconfigurable run-time environments where the inflexibility of TDM would be prohibitive. Advanced real-time scheduling applied to the IEEE 802.5 token ring greatly enhances the responsiveness of asynchronous class messages while still maintaining guaranteed service for the synchronous class.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Designing to Reduce Construction Costs (1976)

This paper describes interrelationships between engineering design, construction, and operation costs for a facility, and shows how the level of influence over those costs decreases precipitously as the project evolves. The level of influence is by far the greatest during engineering and design, while actual expenditures at that stage are relatively small. The level of influence concept can be helpful in forming contractual arrangements that minimize the suboptimization of costs for one party at the expense of overall project costs and benefits. Contractual arrangements should be drawn so as to assure that current construction and operations knowledge will be injected in the design process. Construction Management and design-construct, if appropriately tailored to the needs of a particular situation, can be helpful for this purpose. A second important conclusion is that efforts to suboptimize design costs by requiring competitive bidding for professional services are likely to produce much higher project costs in the long run.
Crosslinking of reactive α‐olefins and maleic anhydride copolymers as oil sorbers (2007)

Abstract Octene (OC) and tetradecene (TD) monomers were copolymerized with maleic anhydride (MA) with a low conversion (<10% conversion) to determine their reactivity ratios. The monomers were copolymerized with different molar percentages of MA and OC or TD (90/10, 70/30, 50/50, and 10/90) with benzoyl peroxide as an initiator to produce MA/α‐olefin copolymers of different compositions. Fourier transform infrared was used to determine the copolymer compositions. The monomer reactivity ratios of the MA/OC and MA/TD copolymers were determined with the Fineman–Ross and Kelen–Tudos methods. Crosslinked MA/TD and MA/OC (50 : 50 mol/mol) copolymers were prepared by the condensation of the prepared linear copolymers with different glycols. The crosslinked copolymers were evaluated for oil absorbency applications. The effects of the glycol type, composition, crosslinker weight percentage, and type of oil on the swelling properties of the crosslinked polymers were studied with oil absorption tests. The swelling parameters, such as the maximum oil absorbency, characteristic oil absorbency, characteristic swelling time, and swelling rate constant, were evaluated for the synthesized sorbers. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 871–881, 2007
The Military-Industrial Complex (1970)

On his free weekends he took from its patent holster the black sidearm, clicked off the safety half-way across the back lot, and sat ?we could see him, his legs
Ordering broken unit tests for focused debugging (2004)

Current unit test frameworks present broken unit tests in an arbitrary order, but developers want to focus on the most specific ones first. We have therefore inferred a partial order of unit tests corresponding to a coverage hierarchy of their sets of covered method signatures: When several unit tests in this coverage hierarchy break, we can guide the developer to the test calling the smallest number of methods. Our experiments with four case studies indicate that this partial order is semantically meaningful, since faults that cause a unit test to break generally cause less specific unit tests to break as well.
Extracellular iron acquisition by mycobacteria: role of the exochelins and evidence against the participation of mycobactin (1975)

Mycobacterium bovis var. BCG was grown under iron-deficient conditions in the presence and absence of 1% Tween 80. Mycobactin, the iron iron ionophore of mycobacteria, was found solely within the bacteria grown in the absence of Tween, but low concentrations (0.75 mug/ml) of it appeared in the medium in the presence of the surfactant. Both types of medium contain agents, named exochelins, which could solubilize iron. 55Fe added to spent culture media was recovered only chelated to these compounds. Two exochelins were detected, isolated, and purified. Neither were precursors or breakdown products of mycobactin. In the desferri-form, exochelin MB-2, the major component, reversed the inhibitory effect of serum on the growth of BCG, and in their ferri-forms exochelins MB-1, MB-2, and MS (from Mycobacterium smegmatis) stimulated the growth of their producing organism in the presence of serum. Exochelin MB-2 could physically remove iron from ferritin, and BCG used ferritin as a source of iron during growth even when ferritin was separated from the bacteria by a dialysis membrane. As solutions of the exochelins were freely dialyzable, whereas solutions of mycobactin, even in Tween, were not, only exochelin could have been active in this experiment. The exochelins are proposed as the functional extracellular iron-binding agents of BCG and other mycobacteria, the role of mycobactin being confined to that of a cell wall iron transporter.
Botulinum Toxin Injections for Simple Partial Motor Seizures Associated with Pain (2012)

Intractable epilepsy with painful partial motor seizures is a relatively rare and difficult disorder to treat. We evaluated the usefulness of botulinum toxin to reduce ictal pain. Two patients received two or four botulinum toxin (BTX) injections at one-to-two-month intervals. Patient 1 had painful seizures of the right arm and hand. Patient 2 had painful seizures involving the left foot and leg. Injections were discontinued after improved seizure control following resective surgery. Both patients received significant pain relief from the injections with analgesia lasting at least two months. Seizure severity was reduced, but seizure frequency and duration were unaffected. For these patients, BTX was effective in temporarily relieving pain associated with muscle contraction in simple partial motor seizures. Our findings do not support the hypothesis that modulation of motor end-organ feedback affects focal seizure generation. BTX is a safe and reversible treatment that should be considered as part of adjunctive therapy after failure to achieve control of painful partial motor seizures.
Sub-10 nm Nanofabrication <i>via</i> Nanoimprint Directed Self-Assembly of Block Copolymers (2011)

Directed self-assembly (DSA) of block copolymers (BCPs), either by selective wetting of surface chemical prepatterns or by graphoepitaxial alignment with surface topography, has ushered in a new era for high-resolution nanopatterning. These pioneering approaches, while effective, require expensive and time-consuming lithographic patterning of each substrate to direct the assembly. To overcome this shortcoming, nanoimprint molds--attainable via low-cost optical lithography--were investigated for their potential to be reusable and efficiently template the assembly of block copolymers (BCPs) while under complete confinement. Nanoimprint directed self-assembly conveniently avoids repetitive and expensive chemical or topographical prepatterning of substrates. To demonstrate this technique for high-resolution nanofabrication, we aligned sub-10 nm resolution nanopatterns using a cylinder-forming, organic-inorganic hybrid block copolymer, polystyrene-block-polydimethylsiloxane (PS-b-PDMS). Nanopatterns derived from oxidized PDMS microdomains were successfully transferred into the underlying substrate using plasma etching. In the development phase of this procedure, we investigated the role of mold treatments and pattern geometries as DSA of BCPs are driven by interfacial chemistry and physics. In the optimized route, silicon molds treated with PDMS surface brushes promoted rapid BCP alignment and reliable mold release while appropriate mold geometries provided a single layer of cylinders and negligible residual layers as required for pattern transfer. Molds thus produced were reusable to the same efficacy between nanoimprints. We also demonstrated that shear flow during the nanoimprint process enhanced the alignment of the BCP near open edges, which may be engineered in future schemes to control the BCP microdomain alignment kinetics during DSA.