gebhart/patrepeval huggingface dataset:
A reaction landscape identifies the intermediates critical for self‐assembly of virus capsids and other polyhedral structures (2005)

The capsids of spherical viruses may contain from tens to hundreds of copies of the capsid protein(s). Despite their complexity, these particles assemble rapidly and with high fidelity. Subunit and capsid represent unique end states. However, the number of intermediate states in these reactions can be enormous-a situation analogous to the protein folding problem. Approaches to accurately model capsid assembly are still in their infancy. In this paper, we describe a sail-shaped reaction landscape, defined by the number of subunits in each species, the predicted prevalence of each species, and species stability. Prevalence can be calculated from the probability of synthesis of a given intermediate and correlates well with the appearance of intermediates in kinetics simulations. In these landscapes, we find that only those intermediates along the leading edge make a significant contribution to assembly. Although the total number of intermediates grows exponentially with capsid size, the number of leading-edge intermediates grows at a much slower rate. This result suggests that only a minute fraction of intermediates needs to be considered when describing capsid assembly.
National Survey of Materials Engineering Program (1994)

In December 1989, an ASCE task committee conducted an opinion survey of civil engineering programs in the United States accredited by the Accreditation Board for Engineering and Technology to assess the present status of civil engineering materials courses and to report the results to both ASCE and the responding departments. The committee sought department views of the importance of materials courses and the desired course content in a typical civil engineering program. The respondents were asked to rate the relative importance of topics in design and rehabilitation. The results suggested that traditional civil engineering materials are typically taught in a three‐lecture, one‐laboratory sequence. The questionnaire revealed information on the equipment and other facilities to be marginal at best. Availability and quality of classroom instructional material are rated “good” by the respondents. In the area of incorporating real‐world problems into the materials course(s), the respondents report that the courses generally are not broad enough to accomplish this objective. The task committee's recommendations for improving the materials engineering sequence are included.
Improving QoS in satellite networks using cross-layer mechanisms (2009)

Quality of service (QoS) support can be enforced across several protocol layers by enhancing specific mechanisms such as resource management, power control, scheduling, queuing models and transport protocols. However, even if designed independently, one single layer adaptation impacts other layers, for example, coding rate adaptation at the physical layer impacts the available rate for transport protocols and can induce buffer overflow and congestion. We argue throughout the present study that collaborative mechanisms are efficient and allow an adaptation to network changes at all layers more than single layer standard mechanisms. The main idea is to use available information from layers that are not adjacent in order to optimize the overall performance of a system. The network is seen as a collaborative layer system, where decisions are taken to increase the QoS offered to end-users. We search to bring to light specific layer mechanisms and illustrate how QoS can be improved on the forward and return link in bent-pipe geostationary satellite systems. (5 pages)
Colloidal Nanocrystal Frameworks (2015)

Colloidal nanocrystal frameworks (CNFs) are a modular class of mesostructured porous materials, which are assembled from pre-formed nanocrystal building units using suitably designed block copolymer architecture-directing agents. The functional attributes of these frameworks are determined both by the physiochemical characteristics of the nanocrystal components as well as their ordered arrangements in space. It is noteworthy that their assembly schemes are readily amenable to more than one type of framework component, yielding a multivariate landscape to navigate mesoscale phenomena arising from the coupled interactions of different nanocrystals within the framework. Early reports indicate surprisingly efficient propagation of both matter and energy within and along the surfaces of these frameworks, although there remains much to be learned about the origins of their structural, electronic, and dynamic properties, and how they feed back across multiple length and time scales.
Application of a maximum likelihood algorithm to ultrasound modulated optical tomography (2011)

In pulsed ultrasound modulated optical tomography (USMOT), as an ultrasound (U/S) pulse propagates, it performs as a
scanning probe within the sample, and modulates the scattered light spatially distributed along the axis of propagation.
By detecting and processing the modulated signal, the information along the U/S axis of the sample (1D image) is
studied. The signal is modelled as a convolution of the U/S pulse and the ultrasonic and optical properties of the medium
along the U/S focus. Based upon this model, a Maximum Likelihood (ML) method for image reconstruction is
established. The ML data inversion technique for a pulsed USMOT signal is, for the first time to our knowledge,
investigated both theoretically and practically. The ML method inverts the pulsed USMOT signal to retrieve the spatially
varying properties of the sample along the U/S scanning column, and then the optical absorption property can be
acquired. The results show that the ML method can serve as a useful fitting tool for a pulsed USMOT signal even in the
presence of noise. The work illustrates the application of this iterative algorithm on simulated and experimental data.
Experimental results using 5cm thick animal tissue phantoms (scattering coefficient μs is 6.5cm-1) demonstrate that the
resolution is better than 100μm using a 10MHz transducer.
Electronic Nature of Nonlinear Optical Properties of a Symmetrical Two-Photon Absorbing Fluorene Derivative: Experimental Study and Theoretical Modeling (2018)

A comprehensive experimental and theoretical study of linear photophysical properties, such as excited-state relaxation, two-photon absorption, and stimulated emission spectra of the symmetrical fluorene derivative 2,2′-((1E,1′E)-(9,9-diethyl-9H-fluorene-2,7-diyl)bis(ethene-2,1-diyl))bis(1-methyl-1H-pyrrole) (1), is presented. The steady-state absorption, fluorescence, excitation, and excitation anisotropy spectra of 1 in organic solvents of different polarities are investigated experimentally and modeled. The fluorescence solvatochromism of 1 suggests the occurrence of symmetry breaking in the first excited state. The nature of fast relaxation processes in the excited state of 1, with the characteristic times of several picoseconds, is investigated by transient absorption femtosecond pump–probe spectroscopy. The spectral properties of 1 are satisfactorily described by an essential-state model that, accounting for electron–vibration coupling and for polar solvation, addresses spectroscopic features not only in terms of band position and intensities but also in terms of band shapes. Specifically, we present the first calculation of frequency-resolved two-photon-excited fluorescence anisotropy spectra. Our results demonstrate that electron–vibration coupling and polar solvation quite naturally explain the puzzling experimental observation of large deviations of the anisotropies from the values expected on the basis of the relative orientation of the molecular transition dipole moments.
HETEROTYPIC ADIPOGENIC PHENOTYPE WHEN EMPLOYING CHONDROGENIC TREATMENT OF HUMAN MESENCHYMAL STEM CELLS (2006)

Bone marrow- derived human mesenchymal stem cells (hMSCs) have the ability to differentiate into multiple lineages. This plasticity allows them to be ideal in tissue engineering. The recent conventional method for chondrogenesis of human stem cells of pellet culture does not maintain an applicable nature within tissue engineering due to the limit of cells that can be cultured within a pellet and the difficulty of manipulation when the pellets are formed. The objective of this investigation was to attain chondrogenesis using hMSCs in high density monolayer culture using established methods. Donated hMSCs (AllCells, LLC) were isolated and expanded using basal media. Upon 90% confluence, the cultures were plated at a density of 24,000 cells/cm2 in 6-well plates. Three groups were used: 1) undifferentiated controls with basal media, 2) serum-free media with 10 ng/ml TGF-β3, and 3) serum-free media with cyclic, biweekly exposure to 10 ng/ml TGF-β3 and 10 ng/ml BMP-6. Groups were analyzed for extracellular matrix deposition both histologically and quantitatively. The TGF-β3 alone group had significantly higher s-GAG content from the other groups and the control group was siginificantly higher than the cyclic treatment. Lipid deposits were observed in the TGF-β3/BMP-6 cyclic group as evident with the positive oil red-o stain and the significantly higher glycerol content over the other groups.
Dosimetric properties of Mn 2+ -doped Ca 2 BO 3 Cl (2022)

Abstract We synthesized Ca 2 BO 3 Cl with various amounts of MnCl 2 to fabricate phosphors for radiation dosimetry. After the synthesis, we evaluated their scintillation, thermally-stimulated luminescence (TSL), and optically-stimulated luminescence (OSL) characteristics. A scintillation peak derived from the 4 T 1 → 6 A 1 transition of Mn 2+ appeared at approximately 600 nm in the MnCl 2 -doped Ca 2 BO 3 Cl. Further, their decay time constants were approximately 0.13 ms that should be ascribed to the 4 T 1 → 6 A 1 transition. Moreover, the MnCl 2 -doped Ca 2 BO 3 Cl exhibited TSL glow peaks at approximately 85 °C, 170 °C, and 280 °C. The linear response of the 0.1% MnCl 2 -doped Ca 2 BO 3 Cl was confirmed in the X-ray dose range of 10–3000 mGy. In addition, a weak OSL peak derived from the 4 T 1 → 6 A 1 transition was detected at around 600 nm from the 0.1% and 0.5% MnCl 2 -doped Ca 2 BO 3 Cl.
Vaccine effectiveness against SARS-CoV-2 transmission and infections among household and other close contacts of confirmed cases, the Netherlands, February to May 2021 (2021)

Several studies report high effectiveness of COVID-19 vaccines against SARS-CoV-2 infection and severe disease, however an important knowledge gap is the vaccine effectiveness against transmission (VET). We present estimates of the VET to household and other close contacts in the Netherlands, from February to May 2021, using contact monitoring data. The secondary attack rate among household contacts was lower for fully vaccinated than unvaccinated index cases (11% vs 31%), with an adjusted VET of 71% (95% confidence interval: 63-77).
Redistribution of Bruton's tyrosine kinase by activation of phosphatidylinositol 3-kinase and Rho-family GTPases (2000)

Bruton's tyrosine kinase (Btk) is a member of the Tec family of protein tyrosine kinases (PTK) characterized by an N-terminal pleckstrin homology domain (PH) thought to directly interact with phosphoinositides. We report here that wild-type (wt) and also a gain-of-function mutant of Btk are redistributed following a wide range of receptor-mediated stimuli through phosphatidylinositol 3-kinase (PI 3-K) activation. Employing chimeric Btk with green fluorescent protein in transient transfections resulted in Btk translocation to the cytoplasmic membrane of live cells through various forms of upstream PI 3-K activation. The redistribution was blocked by pharmacological and biological inhibitors of PI 3-K. A gain-of-function mutant of Btk was found to be a potent inducer of lamellipodia and/or membrane ruffle formation. In the presence of constitutively active forms of Rac1 and Cdc42, Btk is co-localized with actin in these regions. Formation of the membrane structures was blocked by the dominant negative form of N17-Rac1. Therefore, Btk forms a link between a vast number of cell surface receptors activating PI 3-K and certain members of the Rho-family of small GTPases. In the chicken B cell line, DT40, cells lacking Btk differed from wt cells in the actin pattern and showed decreased capacity to form aggregates, further suggesting that cytoskeletal regulation mediated by Btk may be of physiological relevance.
Counteracting the Metabolic Effects of Glucose Load in Peritoneal Dialysis Patients; an Exercise-Based Approach (2019)

Glucose-based peritoneal dialysis (PD) solutions are the predominantly used dialysate in PD patients. Glucose absorption has been shown to be associated with several unfavorable metabolic complications. Several studies have shown positive effects of exercise in end-stage renal disease patients. This paper provides an overview of glucose-associated metabolic complications, and proposed exercise regimens to counteract the caloric load associated with glucose absorption.
Evaluation of Additive Manufacturing for Stainless Steel Components (2016)

This collaboration between Oak Ridge National Laboratory and General Electric Company aimed to evaluate the mechanical properties, microstructure, and porosity of the additively manufactured 316L stainless steel by ORNL’s Renishaw AM250 machine for nuclear application. The program also evaluated the stress corrosion cracking and corrosion fatigue crack growth rate of the same material in high temperature water environments. Results show the properties of this material to be similar to the properties of 316L stainless steel fabricated additively with equipment from other manufacturers with slightly higher porosity. The stress corrosion crack growth rate is similar to that for wrought 316L stainless steel for an oxygenated high temperature water environment and slightly higher for a hydrogenated high temperature water environment. Optimized heat treatment of this material is expected to improve performance in high temperature water environments.
Degrees of Freedom of Holographic MIMO Channels (2020)

We consider spatially-constrained apertures of rectangular symmetry and aim to retrieve the limit to the average number of channel spatial degrees of freedom (DoF), obtained elsewhere through different analyses and tools. Unlike prior works, we use a novel Fourier plane-wave series expansion of the channel, recently introduced in [1], where a statistical model for the small-scale fading in the far-field is developed on the basis of a continuous-space and physics-based orthonormal expansion over the Cartesian spatial Fourier basis. This expansion yields a set of statistically independent random coefficients whose cardinality directly gives the limit to the average number of DoF. The treatment is limited to an isotropic scattering environment but can be extended to the non-isotropic case through the linear-system theoretic interpretation of plane-wave propagation.
<title>Free-space optical interconnection of 3D optoelectronic VLSI chip stacks</title> (2001)

Large-scale computer and data-communication systems have reached a bottleneck in performance in recent years due to the limitations of electronic interconnections for data transfer. One potential solution is based on the use of optoelectronic device arrays for free space optical interconnects. In this paper, we present the design and implementation of a 16x16 3D distributed optoelectronic crossbar switch. The core of this system is three optoelectronic VLSI chip-stack modules, plus an optical interconnection layer. Each optoelectronic chip-stack contains 16 VLSI chips and one 16x16 VCSEL/MSM array. Each VLSI chip includes 64 electronic I/Os, 16 optical I/Os, and four 16x16 crossbar switch. The optical interconnect layer uses a hybrid approach including micro-optics, macro-optics, and diffraction gratings. This layer has been optimized for large optomechanical tolerance. Each chip-stack module is 14x14x9 mm3 and the packaged system is 108x68x110 mm3. The target performance is 16 Gb/s throughput per logic channel and 128 Gb/s bisection bandwidth. At the present time, the VLSI chips have been fabricated, functionally tested, and packaged into 3D chip-stack modules, and the optoelectronics layer has been flip-chip bonded to the 3D chip-stack. In this talk we will present the results of our component and system testing.
Challenges in Genetic Testing for Clinical Trials of Inherited and Orphan Retinal Diseases (2005)

The Proceedings of the First International Symposium on Translational Clinical Research for Inherited and Orphan Retinal Diseases: Sponsored by the National Neurovision Research Institute Inc.: Clinical Trials: Genetic Typing in Clinical Trials
LoRa Physical Layer Evaluation for Point-to-Point Links and Coverage\n Measurements in Diverse Environments (2019)

This paper focuses on Point-to-Point LoRa connections. We report on coverage\nmeasurements performed in three distinct environments, i.e., coastal, forest\nand urban. Our field experiments demonstrate coverage up to 1 km with antennas\nat only 1.5 m height in an urban scenario. In free Line-of-Sight (LoS) this\ncoverage is extended to 4 km. Based on these results, we are developing a path\nloss model in future work. The developed hardware and software including\nmeasurements are open-source.\n
The hybrid approach for large scale network access and querying (2012)

Geospatially querying and analyzing large high-resolution spatial networks is critical to most of defense and security applications to support military intelligence. However, the majority of existing solutions either store the entire network in memory, which is not scalable, or adopt a disk-based network representation (i.e., SNDB), where routing and spatial queries may incur high I/O overhead and hence are inefficient. In this paper, we present a flexible architecture for large spatial network storage using quadtree. In particular, this hybrid approach preserves network connectivity and proximity within each partition for local search while enabling heuristics to minimize the I/O overhead for queries of large scale. We further develop efficient algorithms to process spatial queries based on this hybrid storage schema.
Three-Dimensional Monolayers:  Nanometer-Sized Electrodes of Alkanethiolate-Stabilized Gold Cluster Molecules (1997)

Rotated disk electrode voltammetry is described for CH2Cl2 solutions of cluster molecules with nanometer-sized gold cores and stabilizing ligand shells consisting of mixed monolayers of octanethiolate and ω-ferrocenyloctanethiolate ligands in molar ratios ranging from 2:1 to 24:1. Voltammograms for the cluster molecules exhibit a ferrocene oxidation wave with a limiting current that is under hydrodynamic mass transport control. The current−potential curves preceding (“prewave”) and following (“postwave”) the ferrocene wave, which are ideally flat, are decidedly sloped. The Δi/ΔE slopes are proportional to the square root of electrode rotation rate, i.e., are also under hydrodynamic control. The Δi/ΔE slopes are due to the charging of the electrical double layers of the cluster molecules, showing them to act as diffusing, molecule-sized “nanoelectrodes”. A theoretical analysis is presented of the transport control of the double layer charging. Possible reasons that the values of the cluster molecule capacitance (per unit surface area of cluster molecule, which entails use of models for the shape of the Au core of the cluster) are somewhat larger than the literature expectation for octanethiolate monolayers on flat gold surfaces are discussed. The tiny capacitances of the cluster molecules means that changing their charges by small potential increments can require an average of less than a single electron per cluster molecule.
Hexadienyloxycarbonyl (Hdoc) - A Mild Acid Labile Protecting Group for Amines (2003)

Hexadienyloxycarbonyl is an amine protecting group which can be cleaved with 1% TFA in CH2Cl2. It is stable to Pd(0) and basic conditions and is proposed as a useful alternative to the trityl and Bpoc protecting groups.
Linear colloidal crystal arrays by electrohydrodynamic printing (2008)

We use electrohydrodynamic jets of colloidal suspensions to produce arrays of colloidal crystalline stripes on surfaces. A critical factor in maintaining a stable jet is the distance of separation between the nozzle and the surface. Colloidal crystalline stripes are produced as two wetting lines of the deployed suspension merge during drying. To ensure that the two wetting lines merge, the “deployed-line-width” to “particle size” ratio is kept below a critical value so that the capillary forces overcome the frictional forces between the particles and the substrate.
Towards Bundle Adjustment for Satellite Imaging via Quantum Machine Learning (2022)

Given is a set of images, where all images show views of the same area at different points in time and from different viewpoints. The task is the alignment of all images such that relevant information, e.g., poses, changes, and terrain, can be extracted from the fused image. In this work, we focus on quantum methods for keypoint extraction and feature matching, due to the demanding computational complexity of these sub-tasks. To this end, k-medoids clustering, kernel density clustering, nearest neighbor search, and kernel methods are investigated and it is explained how these methods can be re-formulated for quantum annealers and gate-based quantum computers. Experimental results obtained on digital quantum emulation hardware, quantum annealers, and quantum gate computers show that classical systems still deliver superior results. However, the proposed methods are ready for the current and upcoming generations of quantum computing devices which have the potential to outperform classical systems in the near future.
Model of two-picometer deuteron clusters for LENR supported by laser emission of nuclear reactions products (2013)

Results about nuclear reactions of deuterons in 2 pm distance was specified in support of the experiments for LENR based on an evaluation of results of Prelas et al. were a Coulomb screening by a factor 13 was derived. These results were especially fitting the later results of ultrahigh density clusters fulfilling conditions of Bose-Einstein condensation where the conditions of surface states with swimming electron layers appeared to be of advantage. These results are now supported by recent measurement of emission of nuclear reaction products from the states of clusters within the voids in crystals (Schottky defects). An evaluation of these developments is presented for comparison about ongoing experimental results of LENR with the measurements of large amounts of neutrons from &#13;\nnuclear reactions in the LENR sources. These results are supported by the detailed quantum mechanical &#13;\nevaluation of the Coulomb screening computations which arrived at the same values as the &#13;\nphenomenological evaluations of the measurements of Prelas et al. t