gebhart/patrepeval huggingface dataset:
Electron Transfer through Proteins (2005)

This chapter contains sections titled: Electronic Energy Landscapes Theory of Electron Tunneling Tunneling Pathways Coupling-limited ET Rates and Tests of the Pathway Model Multiple Tunneling Pathway Models Interprotein Electron Transfer: Docking and Tunneling Some New Directions in Electron Transfer Theory and Experiment Concluding Remarks
Opportunities and challenges for spintronics in the microelectronic industry (2019)

Spin-based electronics has evolved into a major field of research that broadly encompasses different classes of materials, magnetic systems, and devices. This review describes recent advances in spintronics that have the potential to impact key areas of information technology and microelectronics. We identify four main axes of research: nonvolatile memories, magnetic sensors, microwave devices, and beyond-CMOS logic. We discuss state-of-the-art developments in these areas as well as opportunities and challenges that will have to be met, both at the device and system level, in order to integrate novel spintronic functionalities and materials in mainstream microelectronic platforms.
Analysis of Scattered Signal to Estimate Reservoir Fracture Parameters (2007)

We detect fracture corridors and determine their orientation and average spacing based on an analysis of seismic coda in the frequency-wave number (f-k) domain. Fracture corridors have dimensions similar to seismic wavelengths which causes scattering. The distribution of energy in shot records in the f-k domain depends upon its orientation to the fracture strike. In the direction normal to fractures, energy reflected and transmitted at the reservoir level mostly propagates as scattered waves with slower apparent velocities than waves propagating along the fracture channels. The associated f-k spectral differences allow the identification of the preferred fracture orientation and spacing. We apply our technique to a fractured reservoir in the Lynx field, in the Canadian foothills. The estimated preferential fracture orientation is about N40°E, which agrees with regional stress measurements. The average fracture spacing is 75 m on the West side of the survey, while the fractures are more sparse on the East side. We also applied the Scattering Index methodology (Willis et al., 2006) to the same data, post-stack and pre-stack. This technique has higher resolution to map fracture distribution, intensity and orientation, and therefore complements the spectral method in providing an integrated description of reservoir fractures.
Activation of Snap-Top Capped Mesoporous Silica Nanocontainers Using Two Near-Infrared Photons (2013)

Photoactivation of "snap-top" stoppers over the pore openings of mesoporous silica nanoparticles releases intact cargo molecules from the pores. The on-command release can be stimulated by either one UV photon or two coherent near-IR photons. Two-photon activation is particularly desirable for use in biological systems because it enables good tissue penetration and precise spatial control. Stoppers were assembled by first binding photolabile coumarin-based molecules to the nanoparticle surface. Then, after the particles were loaded with cargo, bulky β-cyclodextrin (CD) molecules were noncovalently associated with the substituted coumarin molecule, blocking the pores and preventing the cargo from escaping. One-photon excitation at 376 nm or two-photon excitation at 800 nm cleaves the bond holding the coumarin to the nanopore, releasing both the CD cap and the cargo. The dynamics of both the cleavage of the cap and the cargo release was monitored using fluorescence spectroscopy. This system traps intact cargo molecules without the necessity of chemical modification, releases them with tissue-penetrating near-IR light, and has possible applications in photostimulated drug delivery.
Cardiac resynchronization therapy response in cardiac sarcoidosis (2022)

Our findings suggest variable response to CRT in patients with CS with no overall improvement in ventricular function within 6 months and a substantial proportion of patients progressing to advanced heart failure therapies.
A 28nm FD-SOI standard cell 0.6–1.2V open-loop frequency multiplier for low power SoC clocking (2016)

This paper presents a new design for SoC clocking based on open-loop frequency multiplication. The architecture, fully implemented in 28nm FD-SOI standard cells, achieves frequency tracking within one input reference period making it a promising candidate for Dynamic Voltage and Frequency Scaling (DVFS) schemes. A calibration scheme is implemented for wide voltage range (0.6-1.2V) operation and to offset P&R and variability induced mismatch. Measurements at 0.6V (0.8/0.4V FBB) show a Fmax of 93MHz with a power of 2.91mW/MHz and a jitter of 2.7 % UI.
1 kV resist technology for microcolumn-based electron-beam lithography (2000)

The objective of this article is to evaluate low-voltage electron-beam (e-beam) resists suitable for direct write on wafer and mask fabrication in the sub-100 nm regime. Low kV exposure provides the advantages of high sensitivity, reduced charging, and a lack of proximity and heating effects. However, a major concern is whether a low-voltage e-beam is capable of patterning sub-100 nm features in resist with a thickness substantially greater than the penetration range of the electrons. At 1–2 kV, the penetration range is between 30 and 100 nm, while typical resist thickness is &amp;gt;200 nm. In an effort to overcome this limitation, thin film layer techniques are evaluated for low kV e-beam exposure. Preliminary 1 kV results on two thin imaging schemes, the bilayer CARL process and top surface imaging with NTS-4 resist, are reported here. Important results achieved are high sensitivity (1–2 μC/cm2), high contrast (γ&amp;gt;10), high resolution (70 nm in ∼300 nm thick resist), good critical dimension (CD) linearity (range=7 nm, mean=8 nm), large exposure latitude (ΔCD/Δdose=0.5 nm/% change in dose), and absence of proximity effects.
Comparison of 71 bipolar disorder pharmacotherapies for kidney disorder risk: The potential hazards of polypharmacy (2019)

The findings support literature concerns about lithium nephrotoxicity and highlight the potential risks of MAOIs, MSAs, antipsychotics and psychotropic polypharmacy.
ChemInform Abstract: Stereoselective Syntheses of Trisubstituted Olefins via Platinum Catalysis: α‐Silylenones with Geometrical Complementarity. (2011)

Abstract Two complementary methods are developed to prepare α‐(Z)‐ and α‐(E)‐silylenones via alkyne activation of α‐hydroxypropargylsilanes and hydrosilylation of the ynones, respectively.
H2O2-Based Fuel Cells for Space Power Systems (2005)

A new type of fuel cell (FC) using novel fuel and oxidizer is investigated in this research. H2O2 is used in this unique FC directly at the cathode. Two types of reactant, namely a gasphase hydrogen and an aqueous NaBH4 solution, were utilized as fuel at the anode. The direct utilization of H2O2 and NaBH4 at the electrodes, as seen in experiments, results in >30% higher voltage output compared to the ordinary H2/O2 FC. Further, the unique combination of NaBH4 and H2O2, both of which are in an aqueous form, has numerous advantages from an operational point of view. This design is inherently compact compared to other cells that use gas phase reactants. Consequently the peroxide-based FC is uniquely suited for space power applications where air is not available and a high energy density fuel is essential.
Formal verification of delayed consistency protocols (2002)

In a cache-coherent shared-memory multiprocessor system, data consistency among cached copies can be delayed until synchronization points under relaxed memory consistency models. Some protocols, called 'delayed consistency protocols', take advantage of this flexibility to reduce cache miss rates and memory traffic. However, they are very complex, and validating their correctness, even at the behavioral level, is a challenge. We have successfully applied a new verification tool to verify the delayed consistency protocol at the behavioral level. The method is called SSM (Symbolic State Model). The contribution of this paper, besides verifying the protocol, is to demonstrate how to deal with relaxed memory models and latency tolerance hardware in the context of SSM.
Identification of a Stanniocalcin Paralog, Stanniocalcin-2, in Fish and the Paracrine Actions of Stanniocalcin-2 in the Mammalian Ovary (2004)

Stanniocalcin is a glycoprotein hormone important in the maintenance of calcium and phosphate homeostasis in fish. Two related mammalian stanniocalcin genes, STC1 and STC2, were found to be expressed in various tissues as paracrine regulators. We have demonstrated the existence of a second stanniocalcin gene in fish, designated fish STC2, with only 30% identity to fish STC1. However, phylogenetic analysis and comparison of the genomic structure of STC genes in vertebrates indicated that STC1 and STC2 genes were probably derived from a common ancestor gene. Based on the prominent expression of mammalian STC1 in the ovary, we tested STC2 expression in rat ovary and the regulation of STC2 expression by gonadotropins. Treatment of immature rats with pregnant mare serum gonadotropin increased STC2 transcripts, whereas subsequent treatment with human chorionic gonadotropin suppressed STC2 expression. Real-time PCR analyses also demonstrated that STC2 is expressed mainly in thecal layers. In situ hybridization studies also revealed that STC2 is expressed in thecal cell layers of antral and preovulatory follicles after gonadotropin stimulation. To elucidate the physiological functions of STC2, recombinant human and fish STC2 proteins were generated and found to be N-glycosylated homodimers. In cultured granulosa cells, treatment with human or fish STC2 suppressed FSH-induced progesterone, but not estradiol or cAMP, production. The STC2 suppression of progesterone production was associated with the inhibition of FSH-induced CYP11A and 3beta-hydroxysteroid dehydrogenase expression. Thus, STC2 is a functional homodimeric glycoprotein, and thecal cell-derived STC2 could play a paracrine role during follicular development.
Different antimetabolic effects of related lectins towards nymphal stages of Nilaparvata lugens (1995)

Abstract Insect feeding trials were carried out to determine the effects of a range of mannose‐specific lectins on third instar nymphs of the rice brown planthopper (BPH), Nilaparvata lugens. Stål. Dose response curves show that Galanthus nivalis agglutinin (GNA) has the strongest toxic effect of the lectins tested, and is effective at concentrations considerably lower than those previously reported. Narcissus pseudonarcissus agglutinin (NPA) and Allium sativum agglutinin (ASA) exhibit a significant antimetabolic effect towards the insect but were less effective (on a molar basis) than GNA. LC 50 values for GNA, NPA and ASA are approximately 4 μM, 11 μM and &gt;40 μM respectively. These mannose‐specific lectins are serologically identical, but differ in the number of subunits per protein molecule; ASA is a dimer, NPA is a trimer and GNA is a tetramer. The results obtained support the hypothesis, that the effectiveness of the mannose‐binding lectins as antimetabolites is determined by the number of subunits per molecule. Two N‐acetylglucosamine binding lectins, the dimeric Oryza sativa agglutinin (OSA) and the monomeric Urtica dioica agglutinin (UDA), were also tested but at a concentration of 0.1% w/v exhibited no significant antimetabolic effect towards BPH, although the related lectin wheatgerm agglutinin (WGA) has previously been demonstrated to be toxic towards the insect.
SMPLpix: Neural Avatars from 3D Human Models (2021)

Recent advances in deep generative models have led to an unprecedented level of realism for synthetically generated images of humans. However, one of the remaining fundamental limitations of these models is the ability to flexibly control the generative process, e.g. change the camera and human pose while retaining the subject identity. At the same time, deformable human body models like SMPL [34] and its successors provide full control over pose and shape, but rely on classic computer graphics pipelines for rendering. Such rendering pipelines require explicit mesh rasterization that (a) does not have the potential to fix artifacts or lack of realism in the original 3D geometry and (b) until recently, were not fully incorporated into deep learning frameworks. In this work, we propose to bridge the gap between classic geometry-based rendering and the latest generative networks operating in pixel space. We train a network that directly converts a sparse set of 3D mesh vertices into photorealistic images, alleviating the need for traditional rasterization mechanism. We train our model on a large corpus of human 3D models and corresponding real photos, and show the advantage over conventional differentiable renderers both in terms of the level of photorealism and rendering efficiency.
Multi-resolution dynamic meshes with arbitrary deformations (2002)

Multi-resolution techniques and models have been shown to be effective for the display and transmission of large static geometric object. Dynamic environments with internally deforming models and scientific simulations using dynamic meshes pose greater challenges in terms of time and space, and need the development of similar solutions. We introduce the T-DAG, an adaptive multi-resolution representation for dynamic meshes with arbitrary deformations including attribute, position, connectivity and topology changes. T-DAG stands for time-dependent directed acyclic graph which defines the structure supporting this representation. We also provide an incremental algorithm (in time) for constructing the T-DAG representation of a given input mesh. This enables the traversal and use of the multi-resolution dynamic model for partial playback while still constructing new time-steps.
Genome-wide identification of pseudogenes capable of disease-causing gene conversion (2006)

Pseudogenes are remnants of gene duplication (nonprocessed pseudogenes) and retrotransposition (processed pseudogenes) events. This study describes methods for identifying gene conversion candidates from predicted pseudogenes. Pseudogenes may accumulate and harbor sequence variations over time that become disease-causing mutations when transferred to genes by gene conversion. A total of 14,476 pseudogenes were identified, including 3,426 nonprocessed pseudogenes. In addition, 1,945 nonprocessed pseudogenes that are localized near their progenitor gene were evaluated for their possible role in gene conversion and disease. All 11 known, human cases of gene conversion (with deleterious effects) involving pseudogenes were successfully identified by these methods. Among the pseudogenes identified is a retinitis pigmentosa 9 (RP9) pseudogene that carries a c.509A>G mutation which produces a p.Asp170Gly substitution that is associated with the RP9 form of autosomal dominant retinitis pigmentosa (adRP). The c.509A>G mutation in RP9 is a previously unrecognized example of gene conversion between the progenitor gene and its pseudogene. Notably, two processed pseudogenes also contain mutations associated with diseases. An inosine monophosphate dehydrogenase 1 (IMPDH1) pseudogene carries a c.676G>A mutation that produces a p.Asp226Asn substitution that causes the retinitis pigmentosa 10 (RP10) form of adRP; and a phosphoglycerate kinase 1 (PGK1) pseudogene (PGK1P1) carries a c.837T>C mutation that produces a p.Ile252Thr substitution that is associated with a phosphoglycerate kinase deficiency. Ranking of nonprocessed pseudogenes as candidates for gene conversion was also performed based on the sequence characteristics of published cases of pseudogene-mediated gene conversion. All results and tools produced by this study are available for download at: http://genome.uiowa.edu/pseudogenes.
SRIRAM: A scalable resilient autonomic mesh (2003)

Mirroring and replication are common techniques for ensuring fault-tolerance and resiliency of client-server applications. Because such mirroring and replication procedures are not usually automated, they tend to be cumbersome. In this paper, we present an architecture in which the identification of sites for replicated servers, and the generation of replicas, are both automated. The design is based on a self-configuring mesh of computers and a communication mechanism between nodes that operates on a rooted spanning tree. A query-search component uses Java™language-based query capsules traveling along the branches of the spanning tree, and a caching scheme whereby the query and previous search results are cached at each node for improved efficiency. Furthermore, a security and anonymity component relies on one or more authentication servers and an anonymous communication scheme using link local addresses and indirect communication between the nodes via the spanning tree. The architecture also includes components for resource advertising and for application replication.
o-Phenylene Octamers as Surface Modifiers for Homeotropic Columnar Ordering of Discotic Liquid Crystals (2013)

Large-area homeotropic columnar ordering of π-conjugated discotic liquid crystals (LCs) is crucial for certain device applications but generally hard to achieve. Here we report polymeric o-phenylene octamer poly-1 and its monomer 1 as the first surface modifiers for homeotropic columnar order of a variety of discotic LCs up to a macroscopic length scale. Their octameric o-phenylene parts are known to fold helically into a cylinder that is reminiscent of a π-stacked column of discotic LCs. Through-view X-ray diffraction patterns of 1 suggested that this molecule adheres to the glass substrate and directs its cylindrical axis perpendicular to the glass surface. This "face-on" orientation likely nucleates the homeotropic columnar order of discotic LC materials.
Dynamic Properties of Back-emf Based Sensorless Drives (2006)

This paper investigates the speed sensitivity of back-emf based sensorless techniques for PM machines. The eigenvalues of the back-emf based estimation are speed dependent leading to performance degradation including reduced command tracking and disturbance rejection. At low speeds, it is shown that instability occur. The paper analyzes an operating point model of the permanent magnet synchronous machine for both sensor- and sensorless-based torque and position/velocity control. The sensorless techniques investigated include state filter-based and zero phase-lag observer-based approaches. In order to maintain disturbance rejection, the sensorless drives must operate at speeds significantly higher than the stability limit
Closed-Form Minkowski Sum Approximations for Efficient Optimization-Based Collision Avoidance (2022)

Motion planning methods for autonomous systems based on nonlinear programming offer great flexibility in incorporating various dynamics, objectives, and constraints. One limitation of such tools is the difficulty of efficiently representing obstacle avoidance conditions for non-trivial shapes. For example, it is possible to define collision avoidance constraints suitable for nonlinear programming solvers in the canonical setting of a circular robot navigating around M convex polytopes over N time steps. However, it requires introducing (2+L)MN additional constraints and LMN additional variables, with L being the number of halfplanes per polytope, leading to larger nonlinear programs with slower and less reliable solving time. In this paper, we overcome this issue by building closed-form representations of the collision avoidance conditions by outer-approximating the Minkowski sum conditions for collision. Our solution requires only MN constraints (and no additional variables), leading to a smaller nonlinear program. On motion planning problems for an autonomous car and quadcopter in cluttered environments, we achieve speedups of 4.8x and 8.7x respectively with significantly less variance in solve times and negligible impact on performance arising from the use of outer approximations.
Characterization of electroforming-free titanium dioxide memristors (2013)

Metal-insulator-metal (MIM) structures based on titanium dioxide have demonstrated reversible and non-volatile resistance-switching behavior and have been identified with the concept of the memristor. Microphysical studies suggest that the development of sub-oxide phases in the material drives the resistance changes. The creation of these phases, however, has a number of negative effects such as requiring an elevated voltage, increasing the device-to-device variability, damaging the electrodes due to oxygen evolution, and ultimately limiting the device lifetime. In this work we show that the deliberate inclusion of a sub-oxide layer in the MIM structure maintains the favorable switching properties of the device, while eliminating many of the negative effects. Electrical and microphysical characterization of the resulting structures was performed, utilizing X-ray and electron spectroscopy and microscopy. In contrast to structures which are not engineered with a sub-oxide layer, we observed dramatically reduced microphysical changes after electrical operation.
Integrated qualitative analysis of polymer sample by pyrolysis–gas chromatography combined with high‐resolution mass spectrometry: Using accurate mass measurement results from both electron ionization and soft ionization (2020)

This new integrated qualitative analysis method gives analytical results independent of library search results. It can be applied to a variety of SI methods including chemical ionization, photoionization, field ionization, and low-energy EI.
Pathophysiology of Ventricular Tachyarrhythmias Amenable to Electric Control (1984)

Technical advances now permit permanent implantation of devices such as antitachycardia pacemakers, cardioverters and cardioverter-defibrillators for control of ventricular tachyarrhythmias. Despite the fact that these devices have been implanted only in patients resistant to conventional medical and surgical management, their effectiveness has been very encouraging. While improved designs are anticipated, preliminary studies have clearly indicated that one of the major challenges for successful clinical use will be appropriate interfacing of the device with the pathophysiology of the patient. Failure to recognize this fact will likely lead to unsuccessful clinical application. Moreover, these new instruments appear to be complementary to, rather than a replacement for, existing medical and surgical approaches to the patient with life-threatening ventricular tachyarrhythmias.