gebhart/patrepeval huggingface dataset:
Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically driven Monte Carlo and molecular dynamics methods (1998)

Conformational analysis of the neurohypophyseal hormones oxytocin (OT) and arginine-vasopressin (AVP) has been carried out using two different computational approaches and three force fields, namely by the Electrostatically Driven Monte Carlo (EDMC) method, with the Empirical Conformational Energy Program for Peptides (ECEPP/3) force field or with the ECEPP/3 force field plus a hydration-shell model, and by simulated-annealing molecular dynamics with the Consistent Valence Force Field (CVFF). The low-energy conformations obtained for both hormones were classified using the minimal-tree clustering algorithm and characterized according to the locations of beta-turns in the cyclic moieties. Calculations with the CVFF force field located conformations with a beta-turn at residues 3 and 4 as the lowest energy ones both for OT and for AVP. In the ECEPP/3 force field the lowest energy conformation of OT contained a beta-turn at residues 2 and 3, conformations with this location of the turn being higher in energy for AVP. The latter difference can be attributed to the difference in the size of the side chain in position 3 of the sequences: the bulkier phenylalanine residue of AVP in combination with the bulky Tyr2 residue hinders the formation of a turn at residues 2 and 3. Conformations of OT and AVP with a turn at residues 3,4 were in the best agreement with the x-ray structures of deaminooxytocin and pressinoic acid (the cyclic moiety of vasopressin), respectively, and with the nmr-derived distance constraints. Generally, the low-energy conformations obtained with the hydration-shell model were in a better agreement with the experimental data than the conformations calculated in vacuo. It was found, however, that the obtained low-energy conformations do not satisfy all of the nmr-derived distance constraints and the nuclear Overhauser effect pattern observed in nmr studies can be fully explained only by assuming a dynamic equilibrium between conformations with beta-turns at residues 2,3, 3,4, and 4,5. The low-energy structures of OT with a beta-turn at residues 2,3 have the disulfide ring conformations close to the model proposed recently for a potent bicyclic antagonist of OT [M. D. Shenderovich et al. (1994) Polish Journal of Chemistry, Vol. 25, pp. 921-927], although the native hormone differs from the bicyclic analogue by the conformation of the C-terminal tripeptide. This finding confirms the hypothesis of different receptor-bound conformations of agonists and antagonists of OT.
Modeling the prosody of hidden events for improved word recognition (1999)

We investigate a new approach for using speech prosody as a knowledge source for speech recognition. The idea is to penalize word hypotheses that are inconsistent with prosodic features such as duration and pitch. To model the interaction between words and prosody we modify the language model to represent hidden events such as sentence boundaries and various forms of disfluency, and combine with it decision trees that predict such events from prosodic features. N-best rescoring experiments on the Switchboard corpus show a small but consistent reduction of word error as a result of this modeling. We conclude with a preliminary analysis of the types of errors that are corrected by the prosodically informed model.
Arthroscopic Revision of Failed Open Anterior Stabilization of the Shoulder (SS‐06) (2007)

The purpose of this study is to report the results of arthroscopic Bankart repair following failed open stabilization. We reviewed 22 patients with recurrent anterior instability after open surgical stabilization. There were 17 men and five women with an average age of 31 years (range, 15-65). The previous interventions consisted of 16 osseous transfers, three open Bankart repairs and three capsular shifts. The causes of failure were additional trauma in 12 patients and bone-block complications in 13. All patients had distension of the antero-inferior capsule. Labral re-attachment and capsulo-ligamentous re-tensioning with suture anchors was performed in all cases with an additional rotator interval closure in four patients and an inferior capsular plication in 12 patients. The bone block screws were removed in eight patients. Nineteen patients were evaluated at an average follow-up of 43 months (range, 24-72). One patient had recurrent subluxations, and two had persistent apprehension. Eight patients (42%) were still painful. Anterior elevation was unchanged and loss of external rotation was 6°. Nine patients returned to sport at the same level, and all patients returned to their previous occupation. Eighty-nine percent were satisfied or very satisfied. The mean subjective shoulder value (SSV), Walch-Duplay, Rowe and UCLA scores were 83% ± 23%, 85 ± 21, 81 ± 23 and 30 ± 7 points, respectively. Arthroscopic revision of open anterior shoulder stabilization gives satisfactory results. The shoulders are both stable and functional. However, our enthusiasm is tempered by some cases of persistent pain.
Semigrand canonical Monte Carlo simulation with Gibbs-Duhem integration technique for alloy phase diagrams (2003)

Formulation is given for the Gibbs-Duhem integration (GDI) method in the semigrand canonical (SGC) ensemble, in which the total number of particles N is fixed with the specified chemical potential differences between species Δμ i (≡μ i -Δμ 1 ;i =2,3,...). Demonstration of the SGC Monte Carlo simulation with the GDI technique is given for a pseudo-binary semiconductor alloy, In x Ga 1-x N.
The large ribosomal subunit from Deinococcus radiodurans complexed with Methymycin (2009)

Summary The crystal structure of the complex of the large ribosomal subunit of the pathogen model Deinococcus radiodurans with the macrolide antibiotic methymycin, bearing a 12 membered macrolactone ring macrolide that contains a single amino sugar, shows that methymycin binds to the peptidyl transferase center (PTC) rather than to the high affinity macrolide binding pocket at the upper end of the ribosomal exit tunnel. This unexpected binding mode results in fairly efficient blockage of the 3’end of the A-site tRNA location, thus indicating the superiority of spatial-functional considerations over the formation of the typical high affinity macrolide interactions that due to the small size of methymycin could have led to incomplete blockage of the exit tunnel. Its binding involves rearrangements of several PTC nucleotides, some of which were shown previously to be flexible. Comparisons between the binding modes of methymycin and other antibiotics are presented and discussed.
Author response: Intelligent classification of platelet aggregates by agonist type (2020)

An intelligent method is developed to morphologically classify platelet aggregates by agonist type, which potentially opens a window on novel clinical diagnostics and therapeutics of thrombotic disorders.
The Use of Plastic Films and Sprayable Reflective Particle Films to Increase Light Penetration in Apple Canopies and Improve Apple Color and Weight (2007)

The objective of the present study was to examine the effect of a reflective, aluminized plastic film (APF), a reflective, particle-based film applied to the tree (PFT), a reflective, particle film applied to the west side of the tree (PFW), or a particle-based reflective film applied to the grass between tree rows (RPF) on ‘Empire’ apple [ Malus domestica (Borkh.)] color and fruit weight in a multiyear study. The APF treatment consistently increased red color and was the only treatment to increase fruit red color from the lower portion of the west side of the tree. The PFT, PFW, and RPF treatments inconsistently improved apple red color. The APF treatment reflected ≈6 times the amount of photosynthetically active radiation ( PAR ) as the RPF and reflected different red/far-red light ratios (R/FR). In all years, average fruit weight was increased by the RPF, PFT, and PFW treatments compared with the untreated control and APF treatment. The mechanism responsible for the increased fruit weight may be the altered light quality, not quantity, reflected from the RPF treatments. The reflected light has enhanced far-red radiation, which may have beneficial effects on both fruit color and fruit weight. The effect of enhanced far-red radiation on increased fruit weight may be a phytochrome-mediated process affecting dry matter partitioning.
Organic Field Effect Transistor Semiconductor Blends for Advanced Electronic Devices Including UV Phototransistors and Single Walled Carbon Nanotube Enhanced Devices (2015)

Two major projects involving the use of solution processed blended semiconductors for organic field effect transistors (OFET) were explored. The first incorporated unsorted single walled carbon nanotubes (SWCNTs) into a diketopyrrolopyrrole-quarterthiophene (DPP-QT) semiconductor to enhance the mobility of the OFET. 2 wt % SWCNT was found to be the optimal blend ratio, nearly doubling the device mobility (0.6 to 0.98 cm^2/V·s). Beyond this ratio, the metallic content of the SWCNT’s dropped the on/off ratio below acceptable levels. When source drain metals who’s work function poorly matched that of the DPP-QT semiconductors highest occupied molecular orbital (HOMO) were used, the SWCNT could dramatically reduce the charge injection ratio with best results achieved for Al, dropping the contact resistance from 10^5 to 45 MΩ. The second project explored the addition of small molecule additives into a UV-sensitive semiconductor 2,7-dipentyl[1]benzothieno[3,2-b][1] benzothiophene (C5-BTBT) mixed with a polymethyl methacrylate (PMMA) polymer binder. We generated a C5-BTBT based phototransistor sensitive to UV-A light. The HOMO and lowest unoccupied molecular orbital (LUMO) of C5-BTBT and the various additives were measured and discovered to play a critical role in how the device operates. We discovered if an additive has a LUMO lower in energy than C5-BTBT, it can act as a charge trap for a photogenerated electron. Electron deficient additives were found to retain a trapped electron for an extended period of time, allowing the device to remain in a high current state for an extended period of time (&gt;1 hour). This provides an opportunity for the device to be used as an optical memory system or photoswitch. The best system could detect UV-A with a Pill &gt; 10^5 and a photoresponsivity of 40 A/W at a Pinc of 0.0427 mW/cm^2.
A compact Blumlein PFN with optimized performance index (2002)

A compact Blumlein pulse forming network (PFN) was designed using lumped elements for the generation of a 50-kV flat-top voltage pulse of /spl ap/1 /spl mu/s duration. The 'performance index' of the network (which is a measure of its pulse response during transient switching) was optimized by minimizing the overshoot and the ringing in the output pulse, using a damping resistor technique. The network was analyzed and computer-simulated to achieve the best pulse shape by choosing appropriate damping resistors required to obtain the minimum performance index within the design criteria for the given system. The Blumlein PFN fabricated accordingly is capable of generating a nearly flat-top voltage pulse as predicted by simulation, and suitable for research and industrial applications where a flat-top high voltage pulse without ringing is required. It has been used successfully to characterize the preflashover behavior of dielectric materials under high electric fields.
Algorithm Unrolling: Interpretable, Efficient Deep Learning for Signal and Image Processing (2021)

Deep neural networks provide unprecedented performance gains in many real-world problems in signal and image processing. Despite these gains, the future development and practical deployment of deep networks are hindered by their black-box nature, i.e., a lack of interpretability and the need for very large training sets. An emerging technique called algorithm unrolling, or unfolding, offers promise in eliminating these issues by providing a concrete and systematic connection between iterative algorithms that are widely used in signal processing and deep neural networks. Unrolling methods were first proposed to develop fast neural network approximations for sparse coding. More recently, this direction has attracted enormous attention, and it is rapidly growing in both theoretic investigations and practical applications. The increasing popularity of unrolled deep networks is due, in part, to their potential in developing efficient, high-performance (yet interpretable) network architectures from reasonably sized training sets.
Development of a LiMnFePO4 / Li4Ti5O12 2Ah Pouch Cell: An Example of the Effective Integration of New Materials (2022)

One of the most promising approaches for limiting climate change is the use of alternative and greener sources of energy (wind, solar, etc.). The electricity generated from these sources fluctuates, however, and a storage solution is needed. The advent of energy storage for wind farms, solar plants, etc., requires a new generation of batteries. It is therefore imperative that a battery with high energy density, a longer life cycle and improved safety be developed. In this paper, we describe our efforts to develop a safe and long-life cycle LiMnFePO 4 (LMFP)/Li 4 Ti 5 O 12 (LTO) 2Ah pouch cell. One of the major challenges faced in this pursuit was gas evolution during cycling. Various side reactions with active materials resulted in the generation of gas during cycling. To circumvent this, we implemented several mitigation strategies. To combat electrolyte degradation (1.0 M LiPF 6 in carbonate solvents) due to Mn 2+ dissolution in LMFP, we integrated a new class of polymer as a binder in the cathode preparation, which effectively decreased the degradation during cycling. This polymer also has high voltage stability. 1 At the battery’s negative electrode, we developed a new carbon coating method on LTO that minimizes electrolyte degradation and optimizes high C-rate preformances, especially fast charging performances. 2 Although these new materials reduce gas evolution, they do not eliminate it. Therefore, we developed the first polymer capable of trapping the carbon dioxide, major component of gases generated during cycling and, in turn, preventing pouch cell inflation. This polymer was integrated in a pouch cell in the form of an insoluble trapping sheet. 3 Although relatively simple, this technology made the pouch cells safer. This unique approach is versatile and can be implemented in pouch cells with any type of chemistry when gas scavenging is required. The 2Ah pouch cells did not experience any inflation during extensive cycling and aging. Cells cycled more then 750 cycles at 45 o C with a rate of 1C – 1C before reaching 80% retention capacity. Reference (1) Daigle, J.-C.; Asakawa, Y.; Zaghib, K. Polymer additives and their use in electrode materials and electrochemical cells. WO2020061710A1, 2020. (2) Daigle, J.-C.; Asakawa, Y.; Beaupre, M.; Gariepy, V.; Vieillette, R.; Laul, D.; Trudeau, M.; Zaghib, K. Boosting Ultra-Fast Charge Battery Performance: Filling Porous nanoLi4Ti5O12 Particles with 3D Network of N-doped Carbons. Sci. Rep. 2019, 9 (1), 1-9, DOI: 10.1038/s41598-019-53195-1. (3) Daigle, J.-C.; Asakawa, Y.; Perea, A.; Dontigny, M.; Zaghib, K. Novel polymer coating for chemically absorbing CO2 for safe Li-ion battery. Sci. Rep. 2020, 10 (1), 10305, DOI: 10.1038/s41598-020-67123-1.
Intracranial Penetration During Temporal Soft Tissue Filler Injection—Is It Possible? (2017)

Based on the results of this investigation, it can be concluded that there is a risk for intracranial penetration performing the deep temple injection technique with direct pressure on the bone.
Influence of internal solitons on sound propagation in shallow water with a summer strong thermocline (1993)

Analysis of extensive data has shown that the internal waves in the coastal zone exhibit the properties of solitons. Using experimental data and numerical simulation results, this paper shows what happens to sound propagation if internal solitons are present in shallow water with a strong summer thermocline. The experiments were conducted in the Yellow Sea off the China coast during the summer, where strong thermoclines with more than 10 °C temperature difference are often present. In order to provide a clear physical picture on the true problem, a carefully chosen simple ocean model is used to show the resonant interaction of sound waves with internal solitons, including signal frequency, soliton wavelength, and packet length resonances. Then, the numerical model is extended to include the classic characteristic properties of more realistic ocean soliton packets. Under the resonance condition acoustic mode coupling transfers a significant amount of energy from lower modes into higher-order modes that have much larger attenuation rates. This becomes a new attenuation mechanism for shallow water with a strong thermocline. The ‘‘resonancelike’’ behavior predicted by the PE analysis is consistent with mode coupling theory. [Work supported by ONR and IAAS.]
A high speed multifocal multiphoton fluorescence lifetime imaging microscope for live-cell FRET imaging (2015)

We demonstrate diffraction limited multiphoton imaging in a massively parallel, fully addressable time-resolved multi-beam multiphoton microscope capable of producing fluorescence lifetime images with sub-50ps temporal resolution. This imaging platform offers a significant improvement in acquisition speed over single-beam laser scanning FLIM by a factor of 64 without compromising in either the temporal or spatial resolutions of the system. We demonstrate FLIM acquisition at 500 ms with live cells expressing green fluorescent protein. The applicability of the technique to imaging protein-protein interactions in live cells is exemplified by observation of time-dependent FRET between the epidermal growth factor receptor (EGFR) and the adapter protein Grb2 following stimulation with the receptor ligand. Furthermore, ligand-dependent association of HER2-HER3 receptor tyrosine kinases was observed on a similar timescale and involved the internalisation and accumulation or receptor heterodimers within endosomes. These data demonstrate the broad applicability of this novel FLIM technique to the spatio-temporal dynamics of protein-protein interaction.
Comparative Cleavage Sites within the Reactive-Site Loop of Native and Oxidized α1-Proteinase Inhibitor by Selected Bacterial Proteinases (1999)

Human alpha1-proteinase inhibitor (alpha1-PI) is responsible for the tight control of neutrophil elastase activity which, if down regulated, may cause local excessive tissue degradation. Many bacterial proteinases can inactivate alpha1-PI by hydrolytic cleavage within its reactive site, resulting in the down regulation of elastase, and this mechanism is likely to contribute to the connective tissue damage often associated with bacterial infections. Another pathway of the inactivation of alpha1-PI is reversible and involves oxidation of a critical active-site methionine residue that may influence inhibitor susceptibility to proteolytic inactivation. Hence, the aim of this work was to determine whether this oxidation event might affectthe rate and pattern of the cleavage of the alpha1-PI reactive-site loop by selected bacterial proteinases, including thermolysin, aureolysin, serralysin, pseudolysin, Staphylococcus aureus serine proteinase, streptopain, and periodontain. A shift of cleavage specificity was observed after alpha1-PI oxidation, with a preference for the Glu354-Ala355 bond by most of the proteinases tested. Only aureolysin and serralysin cleave the oxidized form of alpha1-PI faster than the native inhibitor, suggesting that bacteria which secrete these metalloproteinases may specifically take advantage of the host defense oxidative mechanism to accelerate elimination of alpha1-PI and, consequently, tissue degradation by neutrophil elastase.
Effective Drive Current for Pass-Gate Transistors (2016)

A two-point expression of effective drive current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> _PG) for pass-gate (PG) transistors is proposed for the first time. We demonstrate that the proposed expression of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> _PG estimates the PG latency with a reasonable accuracy (relative error <;15%) under different technology nodes from 90 to 20 nm and a wide range of biasing conditions including gate overdrive voltage up to 0.4 V and nonzero body bias between -0.3 and 0.3 V. The effective drive current expression is simple to use, independent of process technologies, and maintains accuracy when transistors are scaled down to deep submicron regime with severe nonidealities such as drain-induced barrier lowering. I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> _PG provides a simple yet efficient approach for technology evaluation and projection for PG heavy applications such as field-programmable gate array routing. We also show that the previously proposed static CMOS effective drive current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff_inv</sub> ) is not a valid figure of merit when applied to PG transistors, because PG transistors operate in a different regime from the transistors in CMOS inverters. The scaling trend of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> _PG is discussed, which illustrates the I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> _PG does not improve from device scaling as much as CMOS saturation current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dsat</sub> ) and effective drive current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff_inv</sub> ) do.
Tackling Performance Variability Due to RAS Mechanisms with PID-Controlled DVFS (2014)

As technology nodes approach deca-nanometer dimensions, many phenomena threaten the binary correctness of processor operation. Computer architects typically enhance their designs with reliability, availability and serviceability (RAS) schemes to correct such errors, in many cases at the cost of extra clock cycles, which, in turn, leads to processor performance variability. The goal of the current paper is to absorb this variability using Dynamic Voltage and Frequency Scaling (DVFS). A closed-loop implementation is proposed, which configures the clock frequency based on observed metrics that encapsulate performance variability due to RAS mechanisms. That way, performance dependability and predictability is achieved. We simulate the transient and steady state behavior of our approach, reporting responsiveness within less than 1 ms. We also assess our idea using the power model of real processor and report a maximum energy overhead of roughly 10 percent for dependable performance in the presence of RAS temporal overheads.