gebhart/patrepeval huggingface dataset:
Microfabricated capped channels for biomolecular motor-based transport (2005)

Kinesins are molecular motors that transport intracellular cargo along microtubules and provide a model system for force generation that can be exploited for biomotor powered nano- and micro-machines. To use this biological system for microscale transport, the most common approach is to reverse the biological geometry and move microtubules along surfaces functionalized with kinesin motors. The microtubules then become potential transport vehicles for sensors and lab-on-a-chip applications. A key requirement for extracting useful work from this system is confinement and control of microtubule movements over kinesin-coated surfaces. The open channel approaches used to date are limited because microtubules that lose contact with the kinesin motors rapidly diffuse away. As a step toward making stand-alone devices incorporating kinesin motors and microtubules, we have developed methods to fabricate capped channels that provide three-dimensional microtubule confinement. We first tested the activity of kinesin motors on a range of surfaces and found that motors were functional on a number of hydrophilic surfaces and nonfunctional on hydrophobic surfaces. In this work, SU-8 photoresist is used to fabricate open channels and a layer of bisbenzocyclobutene (BCB) or dry-film photoresist is used to encapsulate the channels. To allow sample introduction, we fabricate a hierarchical series of microfluidic channels. In this approach, macroscale (/spl sim/250-/spl mu/m) channels in glass or silicon substrates are used to hold fine-gauge stainless steel tubing and allow connection to various fluid sources and intermediate scale (/spl sim/50-/spl mu/m) channels fabricated in thick (/spl sim/50-/spl mu/m) dry-film photoresist are used to connect the macroscale channels to microscale (1-15-/spl mu/m) SU-8 photoresist channels. This paper is the first demonstration of kinesin-based microtubule transport in enclosed microfluidic channels and provides an important step toward packaging these biomolecular motors into functional devices.
Synthesis of (−)-Methyl Atisenoate and (−)-Isoatisine (2014)

Key words C–H functionalization - ent-atisane diterpenes - diterpenoid alkaloids
Phylogenomic Based Comparative Studies on Indian and American CommensalIsolates. (2018)

Staphylococcus epidermidis is a prominent commensal member of human skin microbiome and an emerging nosocomial pathogen, making it a good model organism to provide genomic insights, correlating its transition between commensalism and pathogenicity. While there are numerous studies to understand differences in commensal and pathogenic isolates, systematic efforts to understand variation and evolutionary pattern in multiple strains isolated from healthy individuals are lacking. In the present study, using whole genome sequencing and analysis, we report presence of diverse lineages of S. epidermidis isolates in healthy individuals from two geographically diverse locations of India and North America. Further, there is distinct pattern in the distribution of candidate gene(s) for pathogenicity and commensalism. The pattern is not only reflected in lineages but is also based on geographic origin of the isolates. This is evident by the fact that North American isolates under this study are more genomically dynamic and harbor pathogenicity markers in higher frequency. On the other hand, isolates of Indian origin are less genomically dynamic, harbor less pathogenicity marker genes and possess two unique antimicrobial peptide gene clusters. This study provides a basis to understand the nature of selection pressure in a key human skin commensal bacterium with implications in its management as an opportunistic pathogen.
Decreased Sensitivity of Tristetraprolin-deficient Cells to p38 Inhibitors Suggests the Involvement of Tristetraprolin in the p38 Signaling Pathway (2001)

Treatment of macrophages with pyridinyl imidazole inhibitors of p38 protein kinases can inhibit lipopolysaccharide-stimulated tumor necrosis factor alpha secretion. However, bone marrow-derived macrophages from tristetraprolin (TTP)-deficient mice were less sensitive than normal macrophages to this effect of p38 inhibitors, despite evidence for normal p38 activation in response to lipopolysaccharide. TTP is known to cause decreased stability of tumor necrosis factor alpha and granulocyte-macrophage colony-stimulating factor mRNAs after binding to an AU-rich element in their 3'-untranslated regions. A recombinant TTP fusion protein could be phosphorylated by a recombinant p38 kinase in cell-free assays and was phosphorylated to the same extent by immunoprecipitated p38 derived from normal and TTP-deficient cells stimulated with lipopolysaccharide; in both cases, the enzyme activity was inhibited by the p38 inhibitors. TTP phosphorylation also was increased in intact macrophages after lipopolysaccharide stimulation, an effect that was blocked by the p38 inhibitors. Finally, TTP in mammalian cell extracts bound less well to an AU-rich element RNA probe than did the same amount of TTP following dephosphorylation. These results suggest that TTP may be a component of the signaling cascade, initiated by inflammatory stimuli and mediated in part by activation of p38, that ultimately leads to enhanced secretion of tumor necrosis factor alpha.
Synthesis, properties, and applications of silicon nanocrystals (2013)

Silicon nanocrystals have been widely investigated for several years because of their many interesting properties and their potential use in several applications. This field has grown enormously after the observation of quantum confinement in porous silicon and remains an area of great interest for different reasons. Most importantly, silicon is already widely used in the semiconductor industry, is nontoxic at least in its bulk form, is the second most earth-abundant element in the crust, and is relatively cheap to process. A large number of groups have investigated silicon in the form of nanocrystals, and the authors intend to provide a comprehensive review of their contribution to the field. The author has decided to address first the synthesis and properties of silicon nanocrystals. Several different techniques, such as nucleation in substoichiometric thin films or gas-phase nucleation and growth in silane-containing nonthermal plasmas, have been proposed for the controlled synthesis of silicon nanoparticles. The author outlines the strengths and weaknesses of each approach and identify the research groups that have advanced each particular synthesis technique. The understanding of the properties of silicon nanocrystals has evolved as new synthetic approaches were developed, and for that reason the material properties are discussed together with its production approach. The use of silicon nanocrystals for the development of novel electronic devices, light emitting devices, photovoltaic cells, and for biorelated applications will be discussed. Waste heat recovery and energy storage applications are also discussed.
Pb loss in Pb(Zr,Ti)O3 ceramics observed by <i>in situ</i> ionic conductivity measurements (2011)

Analysis of the impedance spectra of Nb-doped Pb(Zr,Ti)O3 (PZT) embedded capacitors revealed that the ionic conductivity increased monotonically during annealing at 700 °C. Furthermore, the rate of increase was lowered by a reduction in the ambient pO2. The results could be explained by a model in which oxygen vacancies are generated as a consequence of Pb evaporation from the PZT. At 700 °C, this process is most likely limited by surface kinetics rather than Pb bulk diffusion. It was shown that the Pb loss could be completely recovered by annealing in a high activity Pb source with a commensurate reduction in oxygen vacancy concentration. The electronic conductivity was predominantly p-type and was relatively unaffected by the Pb loss throughout the course of the experiment.
The Habitable Exoplanet Observatory (HabEx) Mission Concept Study Interim Report (2018)

For the first time in human history, technologies have matured sufficiently to enable a mission capable of discovering and characterizing habitable planets like Earth orbiting sunlike stars other than the Sun. At the same time, such a platform would enable unique science not possible from ground-based facilities. This science is broad and exciting, ranging from new investigations of our own solar system to a full range of astrophysics disciplines. The Habitable Exoplanet Observatory, or HabEx, is one of four studies currently being undertaken by NASA in preparation for the 2020 Astrophysics Decadal Survey. HabEx has been designed to be the Great Observatory of the 2030s, with community involvement through a competed and funded Guest Observer (GO) program. This interim report describes the HabEx baseline concept, which is a space-based 4-meter diameter telescope mission concept with ultraviolet (UV), optical, and near-infrared (near-IR) imaging and spectroscopy capabilities. More information on HabEx can be found at https://www.jpl.nasa.gov/habex
Density‐Controlled Metal Nanocluster with Modulated Surface for pH‐Universal and Robust Water Splitting (2023)

Abstract Reducing the particle sizes of transition metals (TMs) and avoiding their aggregation are crucial for increasing the TMs atom utilization and enhancing their industrial potential. However, it is still challenging to achieve uniform distributed and density‐controlled TMs nanoclusters (NCs) under high temperatures due to the strong interatomic metallic bonds and high surface energy of NCs. Herein, a series of TMs NCs with controllable density and nitrogen‐modulated surface are prepared with the assistance of a selected covalent organic polymer (COP), which can provide continuous anchoring sites and size‐limited skeletons. The prepared Ir NCs show superior hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) activities than commercial Pt/C and Ir/C in both acid and alkaline media. In particular, the as‐prepared Ir NCs exhibit remarkable full water splitting performance, reaching a current density of 10 mA cm −2 at ultralow overpotentials of 1.42 and 1.43 V in alkaline and acidic electrolyte, respectively. The excellent electrocatalytic activities are attributed to the increased surface atom utilization and the improved intrinsic activity of Ir NCs. More importantly, the Ir NCs catalyst shows superior long‐term stability due to the strong interaction between Ir NCs and the N‐doped carbon layer.
Successful management of fibrosing mediastinitis with severe vascular compromise: Report of two cases and literature review (2019)

Fibrosing mediastinitis is a rare disorder characterized by the invasive proliferation of fibrous tissue within the mediastinum. This fibrosis can result in compression of intrathoracic structures including the pulmonary vasculature leading to clinical symptoms and complications like pulmonary hypertension. Here, we present two cases of young patients with fibrosing mediastinitis complicated by pulmonary artery stenosis requiring medical and endovascular management with excellent results.
DOP54 Identification and development of a 1st in class naturally-derived protein that drives mucosal healing and is orally delivered by an engineered cellular therapy targeting the gastro-intestinal tract (2022)

Abstract Background In Inflammatory Bowel Disease (IBD), intestinal barrier dysfunction and epithelial cell injury are believed to be associated with activation of the immune system to drive disease-associated inflammation, which together constitute key features of active disease. Existing drugs used to treat IBD induce endoscopic remission and improvements in mucosal healing in only a minor proportion of patients, driving a critical need for therapies which lead directly to mucosal healing. Furthermore, predicting patients who may benefit from therapeutics that address specific mechanisms of mucosal healing may augment response rates. Methods We screened proteins, identified from a meta-analysis of healthy human microbiome, in cellular assays and animal models related to mucosal injury, with the goal of identifying novel therapeutics that have the potential to directly induce mucosal healing. The proteins identified were further optimized by protein engineering to increase their stability as well as gastro-intestinal (GI) targeting via oral administration. For this, therapeutic proteins were expressed using a probiotic, Lactococcus lactis (L.lactis), engineered to display the recombinant proteins on the cell surface, and evaluated for activity in DSS- and DNBS-induced models of colitis in mice. Mechanism of action studies using computational and laboratory based methods to analyze gene expression and direct molecular interactions with human proteins, enabled the identification of pathways modulated by the candidate molecules. These pathways were further evaluated for their ability to identify biomarkers in specific patients most suitable for treatment in a precision medicine approach. Results We have identified a novel, healthy microbiome-derived protein that demonstrated robust activity in human epithelial injury assays in vitro. The protein reduced intestinal injury related pathology in mice when orally administered to target directly the GI tract. SG-5-00455, the product based on an L.lactis strain expressing the candidate therapeutic protein, reduced pathology scores, inflammation and barrier function related LPS-binding protein levels to levels comparable to those obtained glucagon-like peptide 2 (GLP-2), as well as improving dysregulated tissue repair and fibrosis-associated gene expression and proteins levels. SG-5-0455 treatment did not result in systemic exposure, driving its therapeutic activity in a GI-localized manner by targeting pathways related to tissue injury and fibrinolysis. Conclusion SG-5-00455, through its novel mechanism of action and oral delivery to directly target tissue repair pathways in the GI-tract, offers the potential to address a large critical need in IBD.
An ACCC-containing protein-binding sequence in the neighbourhood of the decanucleotide recognition site of the immunoglobulin gene promoter (1988)

The decanucleotide (dc) box TNATTTGCAT is an important functional element in the K light chain gene promoter and was shown to bind nuclear proteins. We now describe the binding of nuclear factor III to dc containing oligonucleotides and define a second protein binding site in the neighbourhood of dc which turned out to be recognized by a partially purified NFIII preparation but not by highly purified NFIII (abbreviations ref. 1). This site comprises an ACCC-containing sequence element. It was further characterized by the hydroxyl radical footprinting method which is applicable to 40 bp long oligonucleotides. The significance of the ACCC-containing sequence and of the previously described 15mer sequence pd is discussed.
Kinetic Control of Electron Transfer at Doped Zinc Oxide/Redox-active Molecule Interface for Photocurrent Rectification (2014)

Abstract Reactivity of redox-active molecules for heterogeneous electron-transfer processes at the surface of doped zinc oxide substrates depended on their energy levels. The redox-active molecules with negative redox potentials displayed a reversible electrochemical response but those with positive redox potentials were characterized by slow electrode kinetics, which was attributed to more than three times larger heterogeneous electron-transfer rate constant for the former redox-active molecules. A photovoltaic cell using methyl viologen as an acceptor molecule, TEMPOL as a donor molecule, and the doped ZnO as the transparent conducting substrate gave high photovoltage, which was ascribed to the reactivity of the redox-active molecules at the doped ZnO surface.
Measurement of J/ψ polarization in pp collisions at $\sqrt{s}=7\ \mathrm{TeV}$ (2013)

An angular analysis of the decay <i>J</i>/<i>ψ</i>→<i>μ</i><sup>+</sup><i>μ</i><sup>-</sup> is performed to measure the polarization of prompt <i>J</i>/<i>ψ</i> mesons produced in <i>pp</i> collisions at [Formula: see text]. The dataset corresponds to an integrated luminosity of 0.37 fb<sup>-1</sup> collected with the LHCb detector. The measurement is presented as a function of transverse momentum, <i>p</i><sub>T</sub>, and rapidity, <i>y</i>, of the <i>J</i>/<i>ψ</i> meson, in the kinematic region 2<<i>p</i><sub>T</sub><15 GeV/<i>c</i> and 2.0<<i>y</i><4.5.
Impact of Lubricating Oil Condition on Exhaust Particulate Matter Emissions from Light Duty Vehicles (2010)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Limited technical studies to speciate particulate matter (PM) emissions from gasoline fueled vehicles have indicated that the lubricating oil may play an important role. It is unclear, however, how this contribution changes with the condition of the lubricant over time. In this study, we hypothesize that the mileage accumulated on the lubricant will affect PM emissions, with a goal of identifying the point of lubricant mileage at which PM emissions are minimized or at least stabilized relative to fresh lubricant.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This program tested two low-mileage Tier 2 gasoline vehicles at multiple lubricant mileage intervals ranging from zero to 5000 miles. The LA92 cycle was used for emissions testing. Non-oxygenated certification fuel and splash blended 10% and 20% ethanol blends were used as test fuels. Results collected indicate that both the magnitude and variability of PM mass emissions decrease in the first 2000 miles of lubricant break-in, with potential increases as lubricant ages and decreases its performance activity. Fuel dilution of the lubricant with ethanol does not appear to deteriorate lubricant quality beyond expectations based on mileage alone.&lt;/div&gt;&lt;/div&gt;
Micro wind turbine system integration guidelines PMSG and inverter front end choices (2012)

This paper is aimed at the modeling and simulation of wind power system, with particular emphasis on small wind turbines employing surface permanent magnet synchronous generators (SPMSGs). Generator and inverter front-end interaction is analytically and numerically modeled, in order to evaluate the generator's efficiency depending on its electric parameters, both during normal and power limited operation. Passive and active rectifier front-end are taken into account to assess the influence of power electronics front-end over system performances. The final target of this work is to determine design guidelines for small wind turbine system optimization. The analysis is carried out through simulations which take into account the interactions of the SPMSG's electrical parameters and through the evaluation of the generator's efficiency at different operating conditions and inverter front-end architectures. The data obtained was further validated with experimental characterization of two different system architectures.
Coordination Abilities of a Fragment Containing D<sup>1</sup> and H<sup>12</sup> Residues of Neuropeptide γ and Products of Metal-Catalyzed Oxidation (2010)

Stoichiometry, stability constants, and solution structures of copper(II) complexes of the (1-2,10-21)NPgamma (D(1)-A(2)-K(10)-R-H(12)-K-T-D-S-F-V-G-L-M(21)-NH(2)) and Ac-(1-2,10-21)NPgamma (Ac-D(1)-A(2)-K(10)-R-H(12)-K-T-D-S-F-V-G-L-M(21)-NH(2)) fragments of neuropeptide gamma were determined in aqueous solution in the pH range 2.5-10.5. The potentiometric and spectroscopic data (UV-vis, CD, EPR) show that an N-terminal Asp residue stabilizes significantly the copper(II) complexes with 1N {NH(2), beta-COO(-)} and 2N {NH(2), beta-COO(-), N(Im)} coordination modes of the (1-2,10-21)NPgamma as the result of coordination through the beta-carboxylate group. In a wide pH range of 4-9, the imidazole nitrogen of His(12) is coordinated to form a macrochelate. The (1-2,10-21)NPgamma peptide consists of 14 amino acid residues and contains an N-terminal amine group and the histidine residue, and as it is suggested, this fragment is able to bind two equivalents of copper(II) ions. The postmortem studies support the involvement of oxidative stress and the production of reactive oxygen species in neurodegenerative diseases. The susceptibility of proteins to oxidative damage is highly dependent on the specific properties of individual proteins, such as unique sequence motifs, surface accessibility, protein folding, and subcelluar localization. Metal-catalyzed oxidation of proteins is mainly a site-specific process in which one or a few amino acids at metal-binding sites on the protein are preferentially oxidized. To elucidate the products of the copper(II)-catalyzed oxidation of the (1-2,10-21)NPgamma and Ac-(1-2,10-21)NPgamma fragments of neuropeptide gamma, the liquid chromatography-mass spectrometry method and the use of Cu(II)/hydrogen peroxide as a model oxidizing system were employed. For both peptides, the oxidation of the methionine residue to methionine sulfoxide for the solutions containing peptide-hydrogen peroxide was observed. The oxidations of the histidine to 2-oxo-histidine and the methionine sulfoxide to sulfone were detected for the Cu(II)-Ac-(1-2,10-21)NPgamma-hydrogen peroxide 1:1:4 molar ratio system. Fragmentations of both peptides near the His residue were observed, supporting the participation of this (His) residue in the coordination of the copper(II) ions.
A molecular detection approach for a cotton aphid-parasitoid complex in northern China (2019)

Aphid-parasitoid interactions have been widely used as a model system in research studies on the structure and functions of arthropod food web. Research on aphid-parasitoid food webs is hindered by their micromorphological characteristics and the high amount of labor associated with their development. Species-specific primers for cotton aphids and their parasitoids were designed and integrated into two multiplex PCRs and six singleplex PCRs, and all PCRs were optimized to achieve high specificity and sensitivity (100-10,000 DNA copies). One cotton aphid (Aphis gossypii) as well as three primary parasitoid and seven hyperparasitoid species or genera were detected using this molecular approach. This group comprises all the primary parasitoids and 97.2-99.6% of the hyperparasitoids reported in cotton fields in northern China. A tritrophic aphid-primary parasitoid-hyperparasitoid food web was then established. The described method constitutes an efficient tool for quantitatively describing the aphid-primary parasitoid-hyperparasitoid food webs and assessing the efficiency of the biological control of parasitoids in cotton fields in northern China.
Study of $J/\psi$ photo-production in lead-lead peripheral collisions at $\sqrt{s_{\rm NN}}$ = 5 TeV (2021)

The photo-production of $J/\\psi$ mesons at low transverse momentum is studied in peripheral lead-lead collisions collected by the LHCb experiment at a centre-of-mass energy per nucleon pair of 5 TeV, corresponding to an integrated luminosity of 210 $\\rm{\\mu b}^{-1}$. The $J/\\psi$ candidates are reconstructed through the prompt decay into two muons of opposite charge in the rapidity region of $2.0&lt;y&lt;4.5$. The results significantly improve previous measurements and are compared to the latest theoretical prediction.
5 Lanthanide Complexes Used for Optical Imaging (2021)

Lanthanide complexes have been widely used in bioassay for over forty years, but their usefulness in optical imaging is only now beginning to be appreciated fully. In this chapter, we explore the fundamental spectroscopic properties of lanthanide ions that make them ideal as components in probes for optical imaging: their large pseudo Stokes’ shift and long luminescence lifetimes facilitate the elimination of background signals, while the nature of the energy transfer pathways involved in sensitizing lanthanide emission makes all of them amenable to perturbation by their surroundings. We explore the use of lanthanide tags and labels in cellular imaging,