gebhart/patrepeval huggingface dataset:
Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation (2015)

A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated.
L[subscript 2]-gain optimization for robust bipedal walking on unknown terrain (2013)

In this paper we seek to quantify and explicitly optimize the robustness of a control system for a robot walking on terrain with uncertain geometry. Geometric perturbations to the terrain enter the equations of motion through a relocation of the hybrid event “guards” which trigger an impact event; these perturbations can have a large effect on the stability of the robot and do not fit into the traditional robust control analysis and design methodologies without additional machinery. We attempt to provide that machinery here. In particular, we quantify the robustness of the system to terrain perturbations by defining an L[subscript 2] gain from terrain perturbations to deviations from the nominal limit cycle. We show that the solution to a periodic dissipation inequality provides a sufficient upper bound on this gain for a linear approximation of the dynamics around the limit cycle, and we formulate a semidefinite programming problem to compute the L[subscript 2] gain for the system with a fixed linear controller. We then use either binary search or an iterative optimization method to construct a linear robust controller and to minimize the L[subscript 2] gain. The simulation results on canonical robots suggest that the L[subscript 2] gain is closely correlated to the actual number of steps traversed on the rough terrain, and our controller can improve the robot's robustness to terrain disturbances.
Novel approach for ultrafast aberration correction and real-time speed-of-sound mapping (2021)

We propose here a real time approach for aberration correction and Speed Of Sound quantification in the context of ultrafast ultrasound imaging. Theoretical works demonstrate the physical meaning of Singular Value Decomposition of the Ultrafast Compound Matrix. In heterogeneous media, we show that the first spatial and angular singular vectors retrieve respectively the non-aberrated image, and the aberration law. In vitro and in vivo experiments probe the efficiency of our method for angular coherence optimization through severe aberrations. Besides correcting the image, it provides knowledge of phase and amplitude aberration, allowing also a local Speed Of Sound estimation.
Metalloporphyrin Two-Dimensional Polymers via Metal-Catalyst-Free C–C Bond Formation for Efficient Catalytic Hydrogen Evolution (2018)

A sensible design plays a pivotal role in developing new two-dimensional polymers. Recent years have witnessed many such potential ways utilizing boraxine, imine, phenazine, and C–C linkages, etc., in this direction. However, a metal catalyst-free direct C–C bond remains unexplored in two-dimensional polymer synthesis. Herein, we report an octahydroxy decorated metalloporphyrin based C–C bond linked two-dimensional polymer, synthesized via a metal-catalyst-free route. As a simple strategy, refluxing monomer porphyrin and squaric acid resulted in the formation of freestanding polymer films with crystalline layered morphology. The effect of the central metal ion in tuning H2 evolution is investigated with the finding that a bimetallic (Co and Ni) porphyrin polymer significantly enhanced the performance leading to 670 μmol of H2 generation. The overpotential (105 mV), Tafel slope (74.1 mV/decade), and Faradaic efficiency (97%) testify to efficiency nearly equivalent to that of Pt/C. The overall performance and stability of polymer displays the excellence of a new catalyst design.
Amplification of Plasma at Different Initial Temperatures inside a Microhole by a Short Laser Pulse and the Effect on the Hole Sidewall (2016)

Microholes with diameters varying with the hole depth have promising applications in important applications, but their manufacturing is difficult when the diameter of the hole is very small and/or varies complicatedly with the depth. In the authors’ previous work (Dabir-Moghaddam et al., 2016), physics-based modeling study has been carried out on the interaction of a short laser pulse with a plasma plume that pre-exists in a microhole and the resulted effect on the sidewall of the hole. The model calculations have implied that a novel dual-pulse laser ablation and plasma amplification (LAPA) technique is potentially feasible for drilling microholes with diameters that are different at different hole depths. In this paper, further model calculations have been performed to study the effect of different initial plasma temperatures. Under the studied conditions, it has been found that laser amplification of a plasma plume with a higher initial temperature can lead to a larger heat flux to the hole sidewall surface and a larger surface vaporization depth in the sidewall, which indicates that more significant material removal will be expected. On the other hand, a lower initial plasma temperature can lead to more non-uniform vaporization depths at different sidewall locations, indicating that a spatially more selective material removal will be expected.
IL-6-independent association of elevated serum neopterin levels with prevalent frailty in community-dwelling older adults (2011)

elevated neopterin levels had IL-6-independent association with prevalent frailty, suggesting potential monocyte/macrophage-mediated immune activation in the frail elderly.
Temperature-Programmed Electrospray–Differential Mobility Analysis for Characterization of Ligated Nanoparticles in Complex Media (2013)

An electrospray-differential mobility analyzer (ES-DMA) was operated with an aerosol flow-mode, temperature-programmed approach to enhance its ability to characterize the particle size distributions (PSDs) of nanoscale particles (NPs) in the presence of adsorbed and free ligands. Titanium dioxide NPs (TiO2-NPs) stabilized by citric acid (CA) or bovine serum albumin (BSA) were utilized as representative systems. Transmission electron microscopy (TEM) and inductively coupled plasma mass spectrometry were used to provide visual information and elemental-based PSDs, respectively. Results show that the interference resulting from electrospray-dried nonvolatile salt residual nanoscale particles (S-NPs) could be effectively reduced using the thermal treatment process: PSDs were accurately measured at temperatures above 200 °C for CA-stabilized TiO2-NPs and above 400 °C for BSA-stabilized TiO2-NPs. Moreover, TEM confirmed the volumetric shrinkage of S-NPs due to thermal treatment and also showed that the primary structure of TiO2-NPs was relatively stable over the temperature range studied (i.e., below 700 °C). Conversely, the shape factor for TiO2-NPs decreased after treatment above 500 °C, possibly due to a change in the secondary (aggregate) structure. S-NPs from BSA-stabilized TiO2-NPs exhibited higher global activation energies toward induced volumetric shrinkage than those of CA-stabilized TiO2-NPs, suggesting that activation energy is dependent on ligand size. This prototype study demonstrates the efficacy of using ES-DMA coupled with thermal treatment for characterizing the physical state of NPs, even in a complex medium (e.g., containing plasma proteins) and in the presence of particle agglomerates induced by interaction with binding ligands.
Fast response in‐plane switching liquid crystal display mode optimized for high‐resolution virtual‐reality head‐mounted display (2020)

Abstract We propose to apply short‐range lurch control in‐plane switching (SLC‐IPS) as a fast response liquid crystal display (LCD) mode to virtual reality applications, where fast response times and high resolutions are essential. In this study, we discuss the SLC‐IPS electrode structure optimized for high‐resolution virtual reality applications. To maintain transmittance at high resolutions, we developed a one‐sided branch electrode structure with convex parts. The issue of slow response times can be resolved using the convex part of the electrode structure by analyzing the imaginary boundaries characterizing the SLC‐IPS. Thus, a response time of less than 2.2 ms can be obtained over all tones using a 1001‐ppi high‐resolution SLC‐IPS LCD.
Connectivity and Topology Invariance in Self-Assembled and Halogen-Bonded Anionic (6,3)-Networks (2017)

We report here that the halogen bond driven self-assembly of 1,3,5-trifluorotriiodobenzene with tetraethylammonium and -phosphonium bromides affords 1:1 co-crystals, wherein the mutual induced fit of the triiodobenzene derivative and the bromide anions (halogen bond donor and acceptors, respectively) elicits the potential of these two tectons to function as tritopic modules (6,3). Supramolecular anionic networks are present in the two co-crystals wherein the donor and the acceptor alternate at the vertexes of the hexagonal frames and cations are accommodated in the potential empty space encircled by the frames. The change of one component in a self-assembled multi-component co-crystal often results in a change in its supramolecular connectivity and topology. Our systems have the same supramolecular features of corresponding iodide analogues as the metric aspects seem to prevail over other aspects in controlling the self-assembly process.
Gene signature of circulating platelet‐bound neutrophils is associated with poor prognosis in cancer patients (2022)

Beyond their critical role in hemostasis, platelets physically interact with neutrophils to form neutrophil-platelet aggregates (NPAs), enhancing neutrophil effector functions during inflammation. NPAs may also promote disease worsening in various inflammatory diseases. However, characterization of NPAs in cancer remains totally unexplored. Using ImageStreamX (ISX) imaging flow cytometer, we were not only allowed able to detect CD15<sup>+</sup> CD14<sup>-</sup> CD36<sup>+</sup> ITGA2B<sup>+</sup> NPAs in both healthy donors' (HDs) and cancer patients' bloods, but we also showed that NPAs result from the binding of platelets preferentially to low-density neutrophils (LDNs) as opposed to normal-density neutrophils (NDNs). By reanalyzing two independent public scRNAseq data of whole blood leukocytes from cancer patients and HDs, we could identify a subset of neutrophils with high platelet gene expression that may correspond to NPAs. Moreover, we showed that cancer patients' derived NPAs possessed a distinct molecular signature compared to the other neutrophil subsets, independently of platelet genes. Gene ontology (GO) term enrichment analysis of this NPAs-associated neutrophil transcriptomic signature revealed a significant enrichment of neutrophil degranulation, chemotaxis and trans-endothelial migration GO terms. Lastly, using The Cancer Genome Atlas (TCGA), we could show by multivariate Cox analysis that the NPAs-associated neutrophil transcriptomic signature was associated with a worse patient prognosis in several cancer types. These results suggest that neutrophils from NPAs are systemically primed by platelets empowering them with cancer progression capacities once at tumor site. NPAs may therefore hold clinical utility as novel noninvasive blood prognostic biomarker in cancer patients with solid tumors.
Device Performance of Emerging Photovoltaic Materials (Version 3) (2022)

Abstract Following the 2nd release of the “Emerging PV reports,” the best achievements in the performance of emerging photovoltaic devices in diverse emerging photovoltaic research subjects are summarized, as reported in peer‐reviewed articles in academic journals since August 2021. Updated graphs, tables, and analyses are provided with several performance parameters, e.g., power conversion efficiency, open‐circuit voltage, short‐circuit current density, fill factor, light utilization efficiency, and stability test energy yield. These parameters are presented as a function of the photovoltaic bandgap energy and the average visible transmittance for each technology and application, and are put into perspective using, e.g., the detailed balance efficiency limit. The 3rd installment of the “Emerging PV reports” extends the scope toward triple junction solar cells.
Precision of flapless implant placement using real-time surgical navigation: a case series. (2009)

Optical computerized navigation is vulnerable to technological and technical errors. Yet, the present case series suggests that less than 1 mm of mean linear deviation and less than 4 degrees of angular deviation might be attainable.
PON transceiver technologies for ≥50  Gbits/s per λ: Alamouti coding and heterodyne detection [Invited] (2019)

There has been an ongoing quest for transceiver technologies to be employed in next-generation passive optical networks (PONs) beyond 25G due to the growing number of subscribers and connected devices per subscriber and the ever-increasing bandwidth demand per device/application. Given the cost and loss/power budget requirements, the candidates seem to be digital signal processing (DSP)-aided intensity-modulation/direct detection (IM-DD) and low-complexity coherent transceivers. Here, we experimentally demonstrate a 100G coherent-lite PON using a novel transceiver DSP chain that utilizes a frequency-diverse dual-polarization RF pilot tone pair. The proposed scheme enables the implementation of Alamouti coding for single-carrier signaling, which is used in conjunction with heterodyne detection, achieving a significant complexity reduction in a coherent optical network unit (ONU) receiver. It consists of a single balanced photodiode followed by an analog-to-digital converter, offering comparable optical complexity to its DD counterpart, at the expense of DSP complexity in the ONU. The performance of a transceiver architecture facilitated by the proposed DSP was assessed in both back-to-back operation and up to 80 km standard single-mode fiber transmission using an <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mo>∼</mml:mo> <mml:mn>1</mml:mn> <mml:mspace width="thinmathspace"/> <mml:mspace width="thinmathspace"/> <mml:mtext>MHz</mml:mtext> </mml:math> linewidth distributed feedback laser as an ONU laser. At the hard-decision forward error correction (7% overhead) threshold, assumed to be <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mn>4</mml:mn> <mml:mo>×</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:msup> <mml:mn>10</mml:mn> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>−</mml:mo> <mml:mn>3</mml:mn> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> , a receiver sensitivity of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mo>−</mml:mo> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>29.6</mml:mn> </mml:mrow> <mml:mspace width="thinmathspace"/> <mml:mspace width="thinmathspace"/> <mml:mtext>dBm</mml:mtext> </mml:math> and a loss budget of 36.6 dB at a launch power of 7 dBm are achieved.
Competition of Secondary versus Tertiary Carbenium Routes for the Type B Isomerization of Alkenes over Acid Zeolites Quantified by Ab Initio Molecular Dynamics Simulations (2019)

The skeletal isomerization of alkenes catalyzed by zeolites involves secondary and tertiary carbenium ions for which respective reactivity cannot be easily assessed by standard theoretical approaches. Thanks to ab initio molecular dynamics, starting from 4-methyl-hex-1-ene (a monobranched C7 alkene), we identify and compare two mechanistic routes for skeletal isomerization: (i) a type B isomerization transforming a secondary carbenium into a tertiary carbenium (conventional route), and (ii) a two-step route involving an intramolecular 1,3 hydride-shift producing a tertiary carbenium, followed by a type B isomerization between two tertiary carbenium ions. We find that, in the case of the secondary cation, the relevant species from a kinetic point of view is the corresponding π-complex. The transition states found for type B isomerization reactions are edge-protonated cyclopropanes (edge-PCP) that exhibit similar stabilities and structures. The transition state for the 1,3-hydride shift is an edge-type PCP with one elongated C–C bond that is more stable than the one found for type B isomerization. From this analysis, we deduce relevant kinetic constants and quantify the respective contribution of both pathways to the global reaction rate. Although the secondary carbenium ions are poorly stable species, we show that they can hold a significant part of the reaction flux. Finally, we discuss, in detail, our kinetic and mechanistic insights with previous kinetic modeling data reported in the literature.
Energetics and Mechanism of Organolanthanide-Mediated Aminoalkene Hydroamination/Cyclization. A Density Functional Theory Analysis (2004)

This contribution focuses on organolanthanide-mediated hydroamination processes and analyzes the hydroamination/cyclization of a prototypical aminoalkene, NH2(CH2)3CHCH2, catalyzed by Cp2LaCH(TMS)2, using density functional theory. The reaction is found to occur in two steps, namely, cyclization to form La−C and C−N bonds, and subsequent La−C protonolysis. Calculations have been carried out for (i) insertion of the olefinic moiety into the La−N bond via a four-center transition state and (ii) protonolysis by a second substrate molecule. The cyclized amine then dissociates, thus restoring the active catalyst. DFT energy profiles have been determined for the turnover-limiting insertion of the 1-amidopent-4-ene CC double bond into the La−NH− bond. DFT calculations of geometries and the stabilities of reactants, intermediates, and products have been analyzed. The picture that emerges involves concerted, rate-limiting, slightly endothermic insertion of the alkene fragment into the La−N(amido) bond via a highly organized, seven-membered chairlike cyclic transition state (ΔH⧧calcd = 11.3 kcal/mol, ΔS⧧calcd = −14.6 cal/mol K). The resulting cyclopentylmethyl complex then undergoes exothermic protonolysis to yield an amine-amido complex, the resting state of the catalyst. Thermodynamic and kinetic estimates are in excellent agreement with experimental data.
Influence of Structure and Organic‐Inorganic Phase Interactions on Coating Mechanical Properties in the Ternary Goethite:Poly(HEMA):Silica System (2012)

Abstract The trapping of nanoparticles inside a hybrid matrix is of great importance for the design of flexible devices with good mechanical properties and for the manipulation of nanoparticles whilst avoiding the use of nanopowders. In this work, transparent coloured coatings on glass were prepared by incorporating Goethite nanorods in a silica:PHEMA [poly(hydroxyethyl methacrylate)] hybrid matrix. Results show that incorporation of Goethite with a volume content higher than 27 % leads to the formation of a porous structure through a phase separation mechanism which induces a dramatic collapse of the mechanical properties. When the Goethite volume content is below 16 %, the mechanical properties of the coating are governed by the interactions between organic and inorganic domains. Goethite interacts preferentially with the silica network through the formation of hydrogen bonds and no direct interactions with PHEMA were observed. In the absence of strong covalent bonds between the silica:PHEMA hybrid and the nanoparticles, Goethite nanorods do not provide any mechanical strengthening. As a result, interpenetration between silica and PHEMA networks enables fine tuning of the final mechanical properties with the coating silica content.
Stiffness-Matched Extracellular Matrices Comprising Collagen or Fibrin Differentially Affect Cell-Mediated Remodeling and Peri-Cellular Stiffness (2022)

Abstract Cells are known to continuously remodel their local extracellular matrix (ECM) and in a reciprocal way, they can also respond to mechanical and biochemical properties of their fibrous environment. In this study, we measured how stiffness around dermal fibroblasts (DFs) and human fibrosarcoma HT1080 cells differs with concentration of rat tail type 1 collagen (T1C) and type of ECM. Peri-cellular stiffness was probed in four directions using multi-axes optical tweezers active microrheology (AMR). First, we found that neither cell type significantly altered local stiffness landscape at different concentrations of T1C. Next, rat tail T1C, bovine skin T1C and fibrin cell-free hydrogels were polymerized at concentrations formulated to match median stiffness value. Each of these hydrogels exhibited distinct fiber architecture. Stiffness landscape and fibronectin secretion, but not nuclear/cytoplasmic YAP ratio differed with ECM type. Further, cell response to Y27632 or BB94 treatments, inhibiting cell contractility and activity of matrix metalloproteinases, respectively, was also dependent on ECM type. Given differential effect of tested ECMs on peri-cellular stiffness landscape, treatment effect and cell properties, this study underscores the need for peri-cellular and not bulk stiffness measurements in studies on cellular mechanotransduction.
Shared direct memory access on the Explorer 2-LX (1990)

Advances in Expert System technology and Artificial Intelligence have provided a framework for applying automated Intelligence to the solution of problems which were generally perceived as intractable using more classical approaches. As a result, hybrid architectures and parallel processing capability have become more common in computing environments. The Texas Instruments Explorer II-LX is an example of a machine which combines a symbolic processing environment, and a computationally oriented environment in a single chassis for integrated problem solutions. This user's manual is an attempt to make these capabilities more accessible to a wider range of engineers and programmers with problems well suited to solution in such an environment.
Observation and Control of Shock Waves in Individual Nanoplasmas (2014)

Using an apparatus that images the momentum distribution of individual, isolated 100-nm-scale plasmas, we make the first experimental observation of shock waves in nanoplasmas. We demonstrate that the introduction of a heating pulse prior to the main laser pulse increases the intensity of the shock wave, producing a strong burst of quasimonoenergetic ions with an energy spread of less than 15%. Numerical hydrodynamic calculations confirm the appearance of accelerating shock waves and provide a mechanism for the generation and control of these shock waves. This observation of distinct shock waves in dense plasmas enables the control, study, and exploitation of nanoscale shock phenomena with tabletop-scale lasers.