gebhart/patrepeval huggingface dataset:
Monte Carlo simulation of solvent effects on the threading of poly(ethylene oxide) (2004)

Recently, we described a coarse-grained model of poly(ethylene oxide) (PEO) and then employed that model to study the amount of spontaneous threading of cyclic molecules by linear chains in the melt (Helfer et al Macromolecules at press). We now use that coarse-grained model to determine how the amount of threading is affected by dilution of the PEO melt with good, Θ, or poor solvents. We employ two distinctly different methods for incorporating the solvent. One method employs explicit coarse-grained solvent molecules, which have the same size as a coarse-grained bead of the polymer. Solvents of different quality are produced by changes in the values of the interaction energies between solvent and polymer beads. The other method does not employ explicit solvent particles but simply modifies the attractive part of the discretized Lennard-Jones potential that describes the pair-wise long-range interaction of coarse-grained PEO while leaving unchanged the rotational isomeric state model that describes the short-range intramolecular interactions. The thermodynamic quality of this implicit solvent is inferred from its effect on the mean square radius of gyration of PEO. The intermolecular pair correlation functions show that cyclic and linear molecules aggregate together in a poor solvent, which contributes to the increase in the amount of threading, relative to the situation found at the same concentration in a good solvent. However, the magnitude of this effect of the poor solvent is insufficient to overcome the decrease in threading upon increasing dilution expected from simple application of the law of mass action. Although the qualitative effects are similar for the two different methods of treating the solvent, quantitative comparison suggests that the use of explicit solvent particles gives a stronger connection with the anticipated behaviour of real systems. The present results for equilibrium structures in a Monte Carlo simulation are not as sensitive to the details of the treatment of the solvent as were earlier results (Chang and Yethiraj 2001 J. Chem. Phys. 114 7688) for the dynamics of the collapse of a single chain in a poor solvent.
Synthesis and Evaluation of [DUPA-6-Ahx-Lys (DOTA)-6-Ahx-RM2], a Novel, Bivalent Targeting Ligand for GRPr/PSMA Biomarkers of Prostate Cancer (2018)

In this study, we have prepared a novel, dual-biomarker, targeting ligand having high affinity and specificity for PSMA/GRPr receptors that are expressed on most prostate cancers.  [DUPA-6-Ahx-Lys(DOTA)-6-Ahx-RM2] was synthesized and the new conjugate was metallated macroscopically with GaCl 3 , InCl 3 , and LuCl 3 to form [DUPA-6-Ahx-Lys(M-DOTA)-6-Ahx-RM2] (where M = Ga, In, or Lu).  These new agents, when radiolabeled with Ga-68, In-111, or Lu-177 hold theranostic potential for patients presenting with prostate cancer disease.
Mechanically strong and fire-retardant nanocomposite aerogels based on cellulose nanofibers and montmorillonite clay (2016)

Mechanically strong and fire-retardant nanocomposite aerogels based on cellulose nanofibers and montmorillonite clay
Wavelength-Dependent Absorption in Structurally Tailored Randomly Branched Vertical Arrays of InSb Nanowires (2012)

Arrays of semiconductor nanowires are of potential interest for applications including photovoltaic devices and IR detectors/imagers. While nominally uniform arrays have typically been studied, arrays containing nanowires with multiple diameters and/or random distributions of diameters could allow tailoring of the photonic properties of the arrays. In this Letter, we demonstrate the growth and optical properties of randomly branched InSb nanowire arrays. The structure mentioned can be approximated as three vertically stacked regions, with average diameters of 20, 100, and 150 nm within the respective layers. Reflectance and transmittance measurements on structures with different average nanowire lengths have been performed over the wavelength range of 300-2000 nm, and absorbance has been calculated from these measurements. The structures show low reflectance over the visible and IR regions and wavelength-dependent absorbance in the IR region. A model considering the diameter-dependent photonic coupling (at a given wavelength) and random distribution of nanowire diameters within the regions has been developed. The diameter-dependent photonic coupling results in a roll-off in the absorbance spectra at wavelengths well below the bulk cutoff of ∼7 μm, and randomness is observed to broaden the absorbance response. Varying the average diameters would allow tailoring of the wavelength dependent absorption within various layers, which could be employed in photovoltaic devices or wavelength-dependent IR imagers.
Investigation on liquid chromatographic separation of basic compounds using silica column with aqueous/organic mobile phase containing triethylamine and acetic acid (2004)

A high-performance liquid chromatography (HPLC) method using silica column eluted with aqueous solvent mobile phase containing triethylamine (TEA) and acetic acid (ACH) at trace percentages was characterized for the analysis of basic compounds. The key mechanism of this system is ion-exchange accompanying interaction of silanol groups. The increase in the ACH concentration in the mobile phase minimizes the ionization of the silanol group, leading to reduced retention time. However, the greater extent of ionization of silanol caused by the increase of TEA concentration helps to retain basic compounds in the column. Further, the protonated TEA that is positively charged also competes for the ionized silanol group with basic compounds, resulting in the modification of retention time. On the other hand, the retention becomes longer with increasing proportion of either organic or aqueous solvent in mobile phase, and partial replacement of methanol with acetonitrile.
Multidrug Resistance Protein MRP1 Reconstituted into Lipid Vesicles:  Secondary Structure and Nucleotide-Induced Tertiary Structure Changes (2000)

Multidrug resistance protein MRP1 is an ATP-dependent drug efflux pump that confers resistance in human cancer cells to various chemotherapeutic drugs. We have reconstituted purified MRP1 in lipid vesicles. The reconstituted protein conserves ATPase and drug transport activity. Structural analysis of MRP1 was investigated by infrared spectroscopy for the first time. This technique offers a unique opportunity to determine structural parameters characterizing a membrane protein in its lipid environment. Addition of different ligands (MgATP, MgATPgammaS, MgADP and P(i), and MgADP) did not significantly affect the MRP1 secondary structure, which is made of 46% alpha-helix, 26% beta-sheet, 12% beta-turns, and 17% random coil. Binding of MgATP increased the protein accessibility to the solvent, suggesting a modification in the tertiary organization of the protein. Hydrolysis of MgATP to MgADP and P(i) did not significantly change the global accessibility of the protein. Release of P(i), after hydrolysis, caused a decrease in the accessibility of MRP1 to the water phase which brings the protein back to its initial conformation. All together, the data demonstrate that MRP1 adopts different structures during its catalytic cycle.
Selective Electrochemical Oxidation of Coal in Aqueous Alkaline Electrolyte (1995)

In this study, we report on the selective electrochemical oxidation of coal at room temperature in an alkaline slurry at 1.0 V (vs. SCE) with little or no oxygen production. Electrode activities and selectivities toward coal oxidation and oxygen evolution were determined by monitoring and analyzing anodic and cathodic gas products. The activities of platinum and various nickel surfaces were compared. Results indicate that coal reacts predominantly with OH radicals during the first 300 to 400 C/g of coal at an initial rate of 0.23 A/cm2 in a slurry containing 14.3 g of coal per liter. After the 400 C/g level is achieved, the rate of coal oxidation begins to decrease, and oxygen evolution becomes appreciable. Coal oxidation continues to greater than 900 C/g coal. The 900 C/g reaction level corresponds to approximately one electron per six carbon atoms in the coal substrate and exceeds that expected for any type of surface passivation/functionalization. The rate‐controlling steps in the coal reaction sequence appear to be OH radical formation on the electrode surface during the first 400 C/g of reaction and contacting of unreacted coal particles with the electrode thereafter. Coal oxidation competes with oxygen evolution, but the latter becomes significant only after the coal substrate has been depleted.
Thermal-Aware Power Migration in Many-Core Processors (2010)

The demand for greater performance in applications involving high levels of parallelism and sequential computation, has led to an increase in design complexity, has rendered the single-core processor obsolete for such applications and resulted in more cores being put onto a single chip. While improving performance, this has lead to increased power densities and, consequently, increased die temperature. Also, the power distribution across the die surface is not uniform, resulting in hot spots. The increase in die temperature results in decreased performance and reliability and increased leakage currents and cooling costs. Spreading activity across a multi-core chip is increasingly being considered as a way to contain chip temperatures while minimally degrading performance. This paper investigates power migration, or “core hopping,” which involves dynamic allocation of workload among the cores on a many-core processor. This work numerically analyzed core hopping for different configurations of a many-core processor, and performed the migration based on both time of activity and temperature of individual cores. Based on the analysis, this work demonstrated a notable drop in junction temperature of about 8°C.
Optical and Mössbauer spectra of manganese-bearing phlogopites; Fe (super 3+) IV-Mn (super pi L) VI pair absorption as the origin of reverse pleochroism (1983)

Samples containing Mn (super 2+) VI and Fe (super 3+) VI are normal pleochroic, while samples containing Mn (super 2+) VI and Fe (super 3+) IV are reverse pleochroic. Chemical and optical differences are reflected by pronounced variations in the shape and band content of the optical absorption spectra. Intense absorption bands are assigned to Fe (super 3+) IV-Mn (super 2+) VI pair transitions. Inverse temperature dependence on sample cooling.--Modified journal abstract.
A scannable pulse-to-static conversion register array for self-timed circuits (2000)

This paper describes the design and hardware results of a scannable pulse-to-static conversion register array for self-timed circuits. The circuits include a self-timed control circuit and a 64-bit register array, both designed utilizing self-resetting CMOS (SRCMOS) circuit techniques. The self-timed feature of the control block allows it to require only one system clock input. The evaluation, reset, and write-enable controls are all generated within the control macro. The register array is a level-sensitive scan design, which is compatible and complies with SRCMOS test modes. This type of register array can facilitate the synchronous/asynchronous interfaces, pipelined operation, power management, and testing of advanced digital systems employing a mixture of static and dynamic circuits to achieve low power and high performance.
Dynamic recognition and mirage using neuro-metamaterials (2022)

Breakthroughs in the field of object recognition facilitate ubiquitous applications in the modern world, ranging from security and surveillance equipment to accessibility devices for the visually impaired. Recently-emerged optical computing provides a fundamentally new computing modality to accelerate its solution with photons; however, it still necessitates digital processing for in situ application, inextricably tied to Moore's law. Here, from an entirely optical perspective, we introduce the concept of neuro-metamaterials that can be applied to realize a dynamic object- recognition system. The neuro-metamaterials are fabricated from inhomogeneous metamaterials or transmission metasurfaces, and optimized using, such as topology optimization and deep learning. We demonstrate the concept in experiments where living rabbits play freely in front of the neuro-metamaterials, which enable to perceive in light speed the rabbits' representative postures. Furthermore, we show how this capability enables a new physical mechanism for creating dynamic optical mirages, through which a sequence of rabbit movements is converted into a holographic video of a different animal. Our work provides deep insight into how metamaterials could facilitate a myriad of in situ applications, such as illusive cloaking and speed-of-light information display, processing, and encryption, possibly ushering in an "Optical Internet of Things" era.
Measurement of inclusive production of neutral hadrons from Z decays (1994)

We present a study of the inclusive production of π0, η, Ks0 and Λ based on 929,000 hadronic Z decays recorded with the L3 detector at LEP. The measured inclusive momentum distributions have been compared with predictions from parton shower models as well as an analytical Quantum Chromodynamics calculation. Comparing to low energy e+e- data, we find that QCD describes the energy evolution of the hadron spectrum.
Cohesive motion control as a regulation problem (2016)

We study derivation of distributed control laws for the cohesive motion problem of multi-agent systems. In the literature, stability analysis of the established control laws for this objective are heavily dependent on the number of the agents and are left incomplete. We convert the original problem setup to an equivalent linear state regulation problem. We define the inter-agent relative position variables as system states and derive a linear system dynamics. State regulation of the system corresponds to solving the cohesive motion objective. Further, we design a distributed control law to regulate the system states, which eventually corresponds to an easy-to-implement, proportional control law for each agent. Finally, we derive a sufficient condition on the agent speed bounds for distance maintenance in minimally persistent formations.
On-chip Heaters for Tension Tuning of Graphene Nanodrums (2018)

For the study and application of graphene membranes, it is essential to have means to control their resonance frequency and temperature. Here, we present an on-chip heater platform for local tuning of in-plane tension in graphene mechanical resonators. By Joule heating of a metallic suspension ring we show thermomechanical resonance frequency tuning in a few-layer (FL) graphene nanodrum, which is accompanied by an increase in its quality factor, which we attribute to the increase of the in-plane tension. The in situ control of temperature, in-plane tension, resonance frequency, and quality factor of suspended two-dimensional (2D) nanodrums makes this device a unique platform for investigating the origin of dissipation in these ultrathin structures and can be of fundamental importance for studying the thermal properties of 2D materials. Moreover, by simultaneously controlling the heater and the backgate voltage, we can independently control the resonance frequency and quality factor, which is of great importance for applications in sensors and resonant mechanical filters.
Sparse Matrix Factorization (2013)

We investigate the problem of factorizing a matrix into several sparse matrices and propose an algorithm for this under randomness and sparsity assumptions. This problem can be viewed as a simplification of the deep learning problem where finding a factorization corresponds to finding edges in different layers and values of hidden units. We prove that under certain assumptions for a sparse linear deep network with $n$ nodes in each layer, our algorithm is able to recover the structure of the network and values of top layer hidden units for depths up to $\tilde O(n^{1/6})$. We further discuss the relation among sparse matrix factorization, deep learning, sparse recovery and dictionary learning.
High extraction efficiency structures (2006)

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Optoelectronic intelligence (2021)

General intelligence involves the integration of many sources of information into a coherent, adaptive model of the world. To design and construct hardware for general intelligence, we must consider principles of both neuroscience and very-large-scale integration. For large neural systems capable of general intelligence, the attributes of photonics for communication and electronics for computation are complementary and interdependent. Using light for communication enables high fan-out as well as low-latency signaling across large systems with no traffic-dependent bottlenecks. For computation, the inherent nonlinearities, high speed, and low power consumption of Josephson circuits are conducive to complex neural functions. Operation at 4 K enables the use of single-photon detectors and silicon light sources, two features that lead to efficiency and economical scalability. Here, I sketch a concept for optoelectronic hardware, beginning with synaptic circuits, continuing through wafer-scale integration, and extending to systems interconnected with fiber-optic tracts, potentially at the scale of the human brain and beyond.
Dose adequacy and assessment (2009)

Abstract Chapter 8 discusses dose adequacy and assessment, including theoretical and practical aspects of renal replacement therapy dose, and continuous vs intermittent dose delivery.
Estimating Crosstalk Between Diagonal Cores in Four-Core Fibers with Square Lattice Structure (2022)

The length dependence of inter-core crosstalk between diagonal cores (diagonal XT) in a 4-core fiber was determined experimentally and theoretically. The diagonal XT was dominated by one received from a core two hops away.
Slicing spreadsheets (1999)

Spreadsheet languages, which include commercial spreadsheets and various research systems, have proven to be flexible tools in many domain specific settings. Research shows, however, that spreadsheets often contain faults. We would like to provide at least some of the benefits of formal testing and debugging methodologies to spreadsheet developers. This paper presents an integrated testing and debugging methodology for spreadsheets. To accommodate the modeless and incremental development, testing and debugging activities that occur during spreadsheet creation, our methodology is tightly integrated into the spreadsheet environment. To accommodate the users of spreadsheet languages, we provide an interface to our methodology that does not require an understanding of testing and debugging theory, and that takes advantage of the immediate visual feedback that is characteristic of the spreadsheet paradigm.
An enhanced joint equalization algorithm for full-duplex DMT transceivers (2003)

An objective function incorporating the factors that affect the system throughput is proposed, and an enhanced joint time-domain equalization algorithm is developed for full-duplex discrete multitone (DMT) transceivers. This algorithm is able to shorten the channel and echo impulse responses using a single filter while keeping the system throughput high.
TNF-α drives remodeling of blood vessels and lymphatics in sustained airway inflammation in mice (2009)

Inflammation is associated with blood vessel and lymphatic vessel proliferation and remodeling. The microvasculature of the mouse trachea provides an ideal opportunity to study this process, as Mycoplasma pulmonis infection of mouse airways induces widespread and sustained vessel remodeling, including enlargement of capillaries into venules and lymphangiogenesis. Although the mediators responsible for these vascular changes in mice have not been identified, VEGF-A is known not to be involved. Here, we sought to determine whether TNF-alpha drives the changes in blood vessels and lymphatics in M. pulmonis-infected mice. The endothelial cells, but not pericytes, of blood vessels, but not lymphatics, were immunoreactive for TNF receptor 1 (TNF-R1) and lymphotoxin B receptors. Most TNF-R2 immunoreactivity was on leukocytes. Infection resulted in a large and sustained increase in TNF-alpha expression, as measured by real-time quantitative RT-PCR, and smaller increases in lymphotoxins and TNF receptors that preceded vessel remodeling. Substantially less vessel remodeling and lymphangiogenesis occurred when TNF-alpha signaling was inhibited by a blocking antibody or was silenced in Tnfr1-/- mice. When administered after infection was established, the TNF-alpha-specific antibody slowed but did not reverse blood vessel remodeling and lymphangiogenesis. The action of TNF-alpha on blood vessels is probably mediated through direct effects on endothelial cells, but its effects on lymphangiogenesis may require inflammatory mediators from recruited leukocytes. We conclude that TNF-alpha is a strong candidate for a mediator that drives blood vessel remodeling and lymphangiogenesis in inflammation.
Assessment of the Safety of Certolizumab Pegol for the Treatment of Crohnʼs Disease at a Single North American Center (2010)

Purpose: Although the data from clinical trials in regards to the safety of CZP for the treatment of Crohn's Disease (CD) is widely available, there is limited published data specifically evaluating the safety of CZP in clinical practice. As such, we evaluated the safety of CZP in a single site practice, including both standard dosing (400mg once monthly) as well as split dosing (200mg every 2 weeks). Methods: Study Design: This study was a retrospective chart review of CZP treated CD patients seen at the University of Washington's Inflammatory Bowel Diseases Clinic (IBD) between April 1, 2008 and August 1, 2009. Safety Evaluation: Patients seen in the University of Washington's IBD clinic are evaluated for adverse effects (AE) to current clinical treatment at each visit. For this safety evaluation, the number of AEs associated with CZP while on treatment as well as 90 days post treatment discontinuation were captured and assessed in relation to both standard dosing as well as split dosing. Results: Sixty nine patients (36 women, 33 men) were included in the standard dosing analysis; 12 patients reported adverse events (17%) and the total number of distinct events was 18. 9 (50%) of the AEs reported were infectious; 5 (28%) were considered complications secondary to CD; 3 (17%) were classified as drug reactions to CZP; and 1 (5.5%) patient was diagnosed with Hodgkins Lymphoma. Thirty one patients (14 women, 17 men) were included in the split dosing analysis; 5 patients reported adverse events (16%) and the total number of distinct events was 6. 4 (67%) of the AEs reported were infectious; 1 (17%) was considered a complication secondary to CD; and 1 (3%) was an unrelated skin disorder. A majority of patients included in this analysis and reporting infectious adverse events were on concomitant immunosuppression (78% and 100% respectively) and 6 (67%) patients reporting infections in the standard dosing group had indwelling lines. Conclusion: At a single North American site, treatment with certolizumab pegol was found to be generally safe and well tolerated. In both the standard dosing group (400 mg once monthly) and the dose modification group (200 mg ever 2 weeks) the most common adverse events reported were infections. Only 1 AE, an injection site reaction in the standard dosing group, was assessed by the treating gastroenterologist as probably related. Although the sample size in this analysis was limited, the number of adverse events reported at this single site is comparable to the frequency in previously published clinical trial data. Disclosure: Scott D. Lee, MD-Consultant: UCB Pharma; Speakers Bureau: UCB Pharma; Grant/Research Support: UCB Pharma Ghassan T. Wahbeh, MD-Consultant: UCB Pharma; Speakers Bureau: UCB Pharma.