gebhart/patrepeval huggingface dataset:
Immunochemical characterisation of styrene maleic acid lipid particles prepared from Mycobacterium tuberculosis plasma membrane (2023)

Membrane proteins of Mycobacterium tuberculosis (Mtb) can be targeted for the development of therapeutic and prophylactic interventions against tuberculosis. We have utilized the unique membrane-solubilising properties of the styrene maleic acid copolymer <styrene:maleic acid::2:1> (SMA) to prepare and characterise 'styrene maleic acid lipid particles' from the native membrane of Mtb (MtM-SMALPs). When resolved by SDS-PAGE and visualised with coomassie blue, the molecular weights of Mtb membrane (MtM) proteins solubilised by SMA were mostly in the range of 40-70 kDa. When visualised by transmission electron microscopy, MtM-SMALPs appeared as nanoparticles of discrete shapes and sizes. The discoid nanoparticles exhibited a range of diameters of ~10-90 nm, with largest portion (~61%) ranging from 20-40 nm. MtM proteins of a molecular weight-range overlapping with that of MtM-SMALPs were also amenable to chemical cross-linking, revealing protein complex formation. Characterisation using monoclonal antibodies against seven MtM-associated antigens confirmed the incorporation of the inner membrane protein PRA, membrane-associated proteins PstS1, LpqH and Ag85, and the lipoglycan LAM into MtM-SMALPs. Conversely, the peripheral membrane proteins Acr and PspA were nearly completely excluded. Furthermore, although MtM showed an abundance of Con A-binding glycoproteins, MtM-SMALPs appeared devoid of these species. Immune responses of healthcare workers harbouring 'latent TB infection' provided additional insights. While MtM-SMALPs and MtM induced comparable levels of the cytokine IFN-γ, only MtM-SMALPs could induce the production of TNF-α. Antibodies present in the donor sera showed significantly higher binding to MtM than to MtM-SMALPs. These results have implications for the development of MtM-based immunoprophylaxis against tuberculosis.
Rising obstacle in a one-layer granular bed induced by continuous vibrations: two dynamical regimes governed by vibration velocity (2020)

The rising motion of an obstacle in a vibrated granular medium is a classic problem of granular segregation, and called the Brazil nut (BN) effect. Identification of the controlling vibration parameters of the effect is a long-standing problem. The simple possibility that the BN effect can be characterized solely by vibration velocity has recently been pointed out. The issue has become controversial over the long history of research, with only a few systems providing evidence for this simple possibility. Here, we investigate the rising motion of an obstacle in a vertically positioned one-layer granular bed under continuous vibrations. We find the rising motion is composed of two distinct regimes, and the first and second regimes are both governed, in terms of vibration parameters, solely by the vibration velocity. We further demonstrate simple scaling laws that well describe the two regimes. Our results support the emergent simple possibility for the controlling parameters of the BN effect and suggest that this feature could be universal. We propose two possible mechanisms of convection and arch effect for the two distinct regimes and demonstrate that these mechanisms explain the scaling laws followed by our experimental data.
Effects of Driving Mode and Optimal Material Selection on a Residence Times Difference-Based Fluxgate Magnetometer (2005)

In this paper, analytical and experimental results on fluxgate magnetometers, intended to sense dc magnetic field, that make use of a readout technique based on the estimation of the residence times in the stable attractors are presented. The approach, exploiting the inherent nonlinear character of the bistable core dynamics, is based on the time-domain characterization of the transitions between the two saturation states of the hysteresis loop that is inherent in the ferromagnetic core dynamics. This readout technique affords the possibility of low amplitude and frequency reference (or bias) driving signals (sinusoidal or triangular), compared to conventional fluxgates, thereby reducing the device power requirements. The efficacy of this strategy is shown through an analytical approach, and via experimental results that suggest guidelines for the optimal design of the device. Considerations of the effects of a suitable choice of the magnetic core (in terms of its hysteresis behavior) have also been included. Experiments, carried out on miniaturized laboratory fluxgate prototypes with different ferromagnetic materials, reveal good performances of the proposed methodology, including suitable sensitivity and resolution, as well as low cost.
Discovery of selective 2,4-diaminopyrimidine-based photoaffinity probes for glyoxalase I (2014)

<bold>L1-Bpyne</bold> was discovered as a potent inhibitor and cell permeable probe of glyoxalase I.
ChemInform Abstract: Synthesis of myo‐Inositol 1,4,5‐Trisphosphate 3‐Phosphorothioate (V) as an Inhibitor of myo‐Inositol 1,3,4,5‐Tetrakisphosphate 3‐ Phosphatase. (1994)

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.
A mechanism of tissue emulsification by high intensity focused ultrasound (2011)

High intensity focused ultrasound (HIFU) has been shown to emulsify tissue in histotripsy created by cavitation clouds and millisecond boiling produced by shock wave heating; however, the mechanism by which millimeter-sized boiling bubbles or cavitation bubble clouds emulsify tissue into submicron-sized pieces is not well understood. Here, we experimentally test the hypothesis that acoustic atomization occurs and a miniature acoustic fountain forms (due to radiation force) at the edge of the millimeter-sized boiling bubble. Through high-speed photography, we observed the violent removal of bovine/porcine liver fragments upon focusing a 2-MHz transducer of 70 MPa peak positive and 15 MPa peak negative pressures at the tissue–air interface. Velocity of the fountain projectiles ranged from 5 to 15 m/s. When the focal amplitudes were reduced to 15 MPa peak positive and 7 MPa peak negative pressures, atomization occurred intermittently. The fountain projectiles were collected and examined histologically using H&amp;E and NADH--diaphorase stains. Results show fragments ranging from tens of microns down to submicron in size. The larger fragments contain distinct tissue aggregates with intact cells and the small particles are cell fragments with few to no intact nuclei. [Work supported by NIH DK43881, DK070618, EB007643, DK007742, and NSBRI through NASA NCC 9--58.]
Quantitative dual-energy micro-CT with a photon-counting detector for material science and non-destructive testing (2019)

The recent progress in photon-counting detector technology using high-Z semiconductor sensors provides new possibilities for spectral x-ray imaging. The benefits of the approach to extract spectral information directly from measurements in the projection domain are very advantageous for material science studies with x-rays as polychromatic artifacts like beam-hardening are handled properly. Since related methods require accurate knowledge of all energy-dependent system parameters, we utilize an adapted semi-empirical model, which relies on a simple calibration procedure. The method enables a projection-based decomposition of photon-counting raw-data into basis material projections. The objective of this paper is to investigate the method's performance applied to x-ray micro-CT with special focus on applications in material science and non-destructive testing. Projection-based dual-energy micro-CT is shown to be of good quantitative accuracy regarding material properties such as electron densities and effective atomic numbers. Furthermore, we show that the proposed approach strongly reduces beam-hardening artifacts and improves image contrast at constant measurement time.
High Performance HTS Conductors: Long Length Production and Evaluation (1998)

Abstract : The objective of the program was for ASC to address in a systematic manner the fundamental engineering issues associated with the fabrication of reliable, rugged, high power density HTS coils and systems. The goal is to provide solid technical support for the broad array of specific applications programs funded from other DoD sources. These include the HTS coil development program funded through NRL, the minesweeping program of NAVSEA/ONR, the airborne generator program presently funded by the Air Force, and programs currently under development in electric propulsion and advanced submarine technology.
Large-Scale Optical Neural-Network Accelerators based on Coherent Detection (2019)

We present a coherent optical neural-network accelerator based on homodyne detection that is scalable to large (N &gt; 1000) networks, and analyze the fundamental quantum limits to its energy efficiency.
Animar: Augmenting the Reality of Storyboards and Animations (2014)

This paper presents Animar, a mobile application to create short animations that uses augmented reality to aid the sketching. This application was conceived using design methods and its characteristics were used to create the interface and form of interaction. The user draws each frame on a specific paper with empty rectangles and a few patterns. The software extracts the frames and rectifies the perspective distortion using image processing techniques. To help the user, Animar tracks the pattern to show a virtual onion skin of a chosen frame over another one. The animation is generated by combining all the frames extracted from the paper. Animar was developed for Android and supports multiple screen sizes from cell phones to tablets and its concept won an international contest on problem solving with augmented reality.
Influence of Coating Chemical Composition and Thickness Layer on the Wear Behavior of Cutting Tools a Business Analytics Approach (2019)

The present work analyzed the effect of coating chemical composition and thickness layer over the wear behavior of cutting tools intended for the manufacture of steel molds for injection of various materials. A business analytics approach using design of experiments was implemented to optimize wear measurements taking into account the coating variables as well as the manufacturing cost involved. Confirmatory tests carried out on real manufacturing conditions showed a wear reduction of up to 5.7 times while achieving a minimum cost of coating.
Bone marrow transplantation for adolescents and young adults with sickle cell disease: Results of a prospective multicenter pilot study (2019)

We conducted a multicenter pilot investigation of the safety and feasibility of bone marrow transplantation (BMT) in adults with severe sickle cell disease (SCD) (NCT 01565616) using a reduced toxicity preparative regimen of busulfan (13.2 mg/kg), fludarabine (175 mg/m<sup>2</sup> ) and thymoglobulin (6 mg/kg) and cyclosporine or tacrolimus and methotrexate for graft-vs-host disease (GVHD) prophylaxis. Twenty-two patients (median age 22 years; range 17-36) were enrolled at eight centers. Seventeen patients received marrow from an HLA-identical sibling donor and five patients received marrow from an 8/8 HLA-allele matched unrelated donor. Before BMT, patients had stroke, acute chest syndrome, recurrent pain events, were receiving regular red blood cell transfusions, or had an elevated tricuspid regurgitant jet (TRJ) velocity, which fulfilled eligibility criteria. Four patients developed grades II-III acute GVHD (18%) and six developed chronic GVHD (27%) that was moderate in two and severe in one patient. One patient died of intracranial hemorrhage and one of GVHD. Nineteen patients had stable donor chimerism, 1-year post-transplant. One patient who developed secondary graft failure survives disease-free after a second BMT. The one-year overall survival and event-free survival (EFS) are 91% (95% CI 68%-98%) and 86% (95% CI, 63%-95%), respectively, and 3-year EFS is 82%. Statistically significant improvements in the pain interference and physical function domains of health-related quality of life were observed. The study satisfied the primary endpoint of 1-year EFS ≥70%. This regimen is being studied in a prospective clinical trial comparing HLA-matched donor BMT with standard of care in adults with severe SCD (NCT02766465).
Allelotype of pancreatic acinar cell carcinoma (2000)

Pancreatic acinar cell carcinoma (PAC) is a rare pancreatic tumor for which no information about chromosomal and gene anomalies is available. We performed genome-wide allelotyping of 9 PACs using DNA from 5 frozen and 4 paraffin-embedded samples and 76 PCR-amplified, chromosome-specific microsatellite markers. High degrees of allelic loss were found, with a mean fractional allelic loss of 0.33. Chromosomes 1p, 4q and 17p showed loss of heterozygosity in >70% of cases and chromosomes 11q, 13q, 15q and 16q, in 60% to 70% of cases. Chromosomes 3q, 6q, 8q, 18q and 21q showed loss in 50% to 60% of cases. All of the remaining chromosomes showed no or few allelic losses. The resulting allelotype of PAC is markedly different from that of either ductal or endocrine tumors of the pancreas, and the involvement of chromosomes 4q and 16q appears to be characteristic of this tumor type. High-resolution mapping of the 12 frequently altered chromosomes in 5 cases with 222 markers permitted subchromosomal localization of regions of consensus loss on 5 chromosomes, including 1p36.31, 3p25.2, 4q26-31.1, 15q15-22.1 and 16q21-q22.1. Our findings suggest that PAC tumorigenesis involves molecular pathways different from those occurring in more common pancreatic tumor types.
A Wideband Magnetic Frequency Up‐Converter Energy Harvester (2021)

The cover illustrates a wideband mechanical energy harvester that utilizes street vibrations to power a traffic light. When this wideband harvester is placed in a vibrating environment, it converts the ambient vibrations into high-voltage electrical energy. This energy can then be used to power various sensors and electronics. Further details can be found in the article, number 2001364, by Abdullah S. Almansouri, Khaled N. Salama, and co-workers.
Microfabricated structures for the i n s i t u measurement of residual stress, Young’s modulus, and ultimate strain of thin films (1987)

Two microfabricated structures for the in situ measurement of mechanical properties of thin films, a suspended membrane, and an asymmetric ‘‘released structure,’’ are reported. For a polyimide film on silicon dioxide, the membrane measurements yield a residual tensile stress of 30 MPa and a Young’s modulus of 3 GPa. The released structures measure the ratio of residual stress to Young’s modulus, and yield 0.011 at strains comparable to the suspended membranes, and 0.015 at larger strains. The ultimate strain as measured by both structures is approximately 4%.
Fluorescent phosphorus dendrimers excited by two photons: synthesis, two-photon absorption properties and biological uses (2019)

Different types of two-photon absorbing (TPA) fluorophores have been synthesized and specifically functionalized to be incorporated in the structure of phosphorus dendrimers (highly branched macromolecules). The TPA fluorophores were included in the periphery as terminal functions, in the core, or in the branches of the dendrimer structures, respectively. Also the functionalization in two compartments (core and surface, or branches and surface) was achieved. The consequences of the location of the fluorophores on the fluorescence and TPA properties have been studied. Several of these TPA fluorescent dendrimers have water-solubilizing functions as terminal groups, and fluorophores at the core or in the branches. They have been used as fluorescent tools in biology for different purposes, such as tracers for imaging blood vessels of living animals, for determining the phenotype of cells, for deciphering the mechanism of action of anticancer compounds, and for safer photodynamic therapy.
FIGURE 1 from A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer (2023)

&lt;p&gt;ZKN-157 selectively inhibits growth and protein translation in a sensitive colorectal cancer cell line. &lt;b&gt;A,&lt;/b&gt; Chemical structure of ZKN-157. &lt;b&gt;B,&lt;/b&gt; Percent response curves showing the effect of ZKN-157 treatment in COLO320DM and SW1417 cells. Curves are representative of three independent biological experiments. Error bars are SDs of two technical replicates. Table shows GI&lt;sub&gt;50&lt;/sub&gt; and LD50 values &lt;b&gt;C,&lt;/b&gt; Cartoon showing the metabolic labeling assay workflow. &lt;b&gt;D,&lt;/b&gt; Representative Western blot membranes of two independent biological experiments showing: -AHA (no AHA reagent added to lysate), CHX (positive control for translation inhibition), DMSO (negative control), and ZKN-157 treatment (40 μmol/L). Equal protein amount for all samples were used for click chemistry reaction. Samples resuspended in equal volume were loaded on gel. Intensity from densitometry of ZKN-157–treated samples was normalized to those of DMSO samples to calculate relative protein translation. Bar graph shows normalized values from two independent experiments. Error bars are SDs.&lt;/p&gt;
Increased facilitated transport of dehydroascorbic acid without changes in sodium-dependent ascorbate transport in human melanoma cells. (1997)

Many cell types transport vitamin C solely in its oxidized form, dehydroascorbic acid, through facilitative glucose transporters. These cells accumulate large intracellular concentrations of vitamin C by reducing dehydroascorbic acid to ascorbate, a form that is trapped intracellularly. Certain specialized cells can transport vitamin C in its reduced form, ascorbate, through a sodium-dependent cotransporter. We found that normal human melanocytes and human malignant melanoma cells are able to transport vitamin C using both mechanisms. Melanoma cell lines transported dehydroascorbic acid at a rate that was at least 10 times greater than the rate of transport by melanocytes, whereas both melanoma cells and melanocytes transported ascorbate with similar efficiency. Dehydroascorbic acid transport was inhibited by deoxyglucose and cytochalasin B, indicating the direct participation of facilitative glucose transporters in the transport of oxidized vitamin C. Melanoma cells accumulated intracellular vitamin C concentrations that were up to 100 times greater than the corresponding extracellular dehydroascorbic acid concentrations, whereas intracellular accumulation of vitamin C by melanocytes never exceeded the extracellular level of dehydroascorbic acid. Melanoma cells transported dehydroascorbic acid through at least two different transporters, each with a distinct K(m), a finding that agreed well with the presence of several glucose transporter isoforms in these cells. Only one kinetic component of ascorbate uptake was identified in both melanocytes and melanoma cells, and ascorbate transport was sodium dependent and inhibited by ouabain. Both cell types were able to accumulate intracellular concentrations of vitamin C that were greater than the extracellular ascorbate concentrations. The data indicate that melanoma cells and normal melanocytes transport vitamin C using two different transport systems. The transport of dehydroascorbic acid is mediated by a facilitated mechanism via glucose transporters, whereas transport of ascorbic acid involves a sodium-ascorbate cotransporter. The differential capacity of melanoma cells to transport the oxidized form of vitamin C reflects the increased expression of facilitative transporters associated with the malignant phenotype.
Minimal order loop-free routing strategy (1990)

A multiorder routing strategy is developed which is loop-free even in the presence of link/node failures. Unlike most conventional methods in which the same routing strategy is applied indiscriminately to all nodes in the network, nodes under this proposal may adopt different routing strategies according to the network structure. Formulas are developed to determine the minimal order of routing strategy for each node to eliminate looping completely. A systematic procedure for striking a compromise between the operational overhead and network adaptability is proposed. Several illustrative examples are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Elevated levels of circulating CDH5 and FABP1 in association with human drug‐induced liver injury (2016)

These results suggest that CDH5 may have value as a susceptibility marker for DILI. FABP1 was identified as a biomarker candidate with superior characteristics regarding tissue distribution and kinetics compared to ALT but likely with limited predictive value for the development of severe DILI. Further studies are needed to determine the clinical utility of the proposed markers.
A Self-Similar Sine-Cosine Fractal Architecture for Multiport Interferometers (2022)

Multiport interferometers based on integrated beamsplitter meshes have recently captured interest as a platform for many emerging technologies. In this paper, we present a novel architecture for multiport interferometers based on the Sine-Cosine fractal decomposition of a unitary matrix. Our architecture is unique in that it is self-similar, enabling the construction of modular multi-chiplet devices. Due to this modularity, our design enjoys improved resilience to hardware imperfections as compared to conventional multiport interferometers. Additionally, the structure of our circuit enables systematic truncation, which is key in reducing the hardware footprint of the chip as well as compute time in training optical neural networks, while maintaining full connectivity. Numerical simulations show that truncation of these meshes gives robust performance even under large fabrication errors. This design is a step forward in the construction of large-scale programmable photonics, removing a major hurdle in scaling up to practical machine learning and quantum computing applications.
ChemInform Abstract: Combinatorial Organic Synthesis and Phase Separation: Back to the Future (1996)

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.
Inside Back Cover: Monodisperse Dual‐Functional Upconversion Nanoparticles Enabled Near‐Infrared Organolead Halide Perovskite Solar Cells (Angew. Chem. Int. Ed. 13/2016) (2016)

The local magnetic anisotropy NaYF4:Yb/Er upconversion nanoparticles as a mesoporous electrode into organolead halide perovskite solar cells makes it possible to operate the cells in near-infrared light. In their Communication on page 4280 ff., Z. Lin et al. show that the upconversion material broadens the solar spectral range used by the solar cell to near-infrared light and minimizes the non-absorption energy loss, thus leading to an enhanced photovoltaic performance.