gebhart/patrepeval huggingface dataset:
Oligonucleotide‐Based Mimetics of Hepatocyte Growth Factor (2015)

Abstract Oligonucleotide‐based hepatocyte growth factor (HGF) mimetics are described. A DNA aptamer to Met, a cognate receptor for HGF, was shown to induce Met activation when used in dimer form. The most potent aptamer dimer, ss‐0, which was composed solely of 100‐mer single‐stranded DNA, exhibited nanomolar potency. Aptamer ss‐0 reproduced HGF‐induced cellular behaviors, including migration and proliferation. The present work sheds light on oligonucleotides as a novel chemical entity for the design of growth factor mimetics.
Lite-Sparse Hierarchical Partial Power Processing for Second-Use Battery Energy Storage Systems (2021)

The explosive growth of electric vehicles (EVs) is leading to a surge in retired EV batteries, which are typically recycled despite having nearly 80% available capacity. Repurposing automotive batteries for second-use battery energy storage systems (2-BESS) has both economical and environmental benefits. The challenge with second-use batteries is the heterogeneity in their state of health. This paper introduces a new strategy to optimize 2-BESS performance despite the heterogeneity of individual batteries while reducing the cost of power conversion. In this paper, the statistical distribution of the power heterogeneity in the supply of batteries is used to optimize the choice of power converters and design the power flow within the battery energy storage system (BESS) to optimize power capability. By leveraging a new lite-sparse hierarchical partial power processing (LS-HiPPP) approach, we study how a hierarchy in partial power processing (PPP) partitions power converters to significantly reduce converter ratings, process less power to achieve high system efficiency with lower cost (lower efficiency) converters, and take advantage of economies of scale by requiring only a minimal number of sets of identical converters. Our results demonstrate that LS-HiPPP architectures offer the best tradeoff between battery utilization and converter cost and have higher system efficiency than conventional partial power processing (C-PPP) in all cases.
Application of In Situ X-ray Absorption Spectroscopy to Study Dilute Chromium Ions in a Molten Chloride Salt (2019)

The local structure of dilute CrCl&lt;sub&gt;3&lt;/sub&gt; in a molten MgCl&lt;sub&gt;2&lt;/sub&gt;:KCl salt was investigated by &lt;i&gt;in situ&lt;/i&gt; x-ray absorption spectroscopy (XAS) at temperatures from room temperature to 800&lt;sup&gt;o&lt;/sup&gt;C. This constitutes the first experiment where dilute Cr speciation is explored in a molten chloride salt, ostensibly due to the compounding challenges arising from a low Cr concentration in a matrix of heavy absorbers at extreme temperatures. CrCl&lt;sub&gt;3&lt;/sub&gt; was confirmed to be the stable species between 200 and 500&lt;sup&gt;o&lt;/sup&gt;C, while mobility of metal ions at higher temperature (&gt;700&lt;sup&gt;o&lt;/sup&gt;C) prevented confirmation of the local structure.
Structure, Electrochemistry, and Magnetism of the Iron(III)‐Substituted Keggin Dimer, [Fe6(OH)3(A‐α‐GeW9O34 (OH)3)2]11‐. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Exploiting built-in delay lines for applying launch-on-capture at-speed testing on self-timed circuits (2018)

The application of scan-based at-speed delay testing on asynchronous circuits is not trivial. Their unorthodox design leaves them generally incompatible with traditional synchronous design and test tools, as well as standard automatic test equipment. The correct generation of at-speed test clocks and the use of conventional automatic test patterns generation (ATPG) tools are some of the problems that face the application of at-speed testing on asynchronous circuits. This paper presents a method of applying scan-based at-speed testing on single-rail bundleddata handshake-free (self-timed) asynchronous circuits by taking advantage of built-in delay lines. The proposed test method uses launch-on-capture scan-based testing with endpoint masking and generates the test patterns using conventional ATPG tools. The proposed test is applied on circuits in a self-timed microprocessor fabricated in 28nm FD-SOI CMOS technology. This method is validated by the reported test coverage and simulation results, along with post-silicon test results on a Teradyne FLEX tester.
Liquid Metal-Organic Frameworks: Formation Mechanism, Structure and Properties (2017)

Metal--organic frameworks are a novel family of chemically diverse materials,
with applications in a wide field covering engineering, physics, chemistry,
biology and medicine. Research so far has focused almost entirely on
crystalline structures, yet a clear trend has emerged shifting the emphasis
onto disordered states of MOFs, including defective by design crystals, as
well as amorphous phases such as glasses and gels. Here we introduce a MOF
liquid, a strongly associated liquid obtained by melting a zeolitic imidazolate
framework (ZIF), with retention of chemical configuration, coordinative bonding
modes, and porosity of the parent crystalline framework. We combine in-situ
variable temperature X-ray, ex-situ neutron pair distribution function
experiments, and first principles molecular dynamics simulations to study the
melting phenomenon and the nature of the liquid obtained, focusing on
structural characterization at the molecular scale, dynamics of the species,
and thermodynamics of the solid--liquid transition.
Computational Investigations of Trichoderma Reesei Cel7A Suggest New Routes for Enzyme Activity Improvements (2012)

The Trichoderma reesei Family 7 cellulase (Cel7A) is a key industrial enzyme in the production of biofuels from lignocellulosic biomass. It is a multi-modular enzyme with a Family 1 carbohydrate-binding module, a flexible O-glycosylated linker, and a large catalytic domain. We have used simulation to elucidate new functions for the 3 sub-domains, which suggests new routes to increase the activity of this central enzyme. These findings include new roles for glycosylation, which we have shown can be used to tune the binding affinity. We have also examined the structures of the catalytically-active complex of Cel7A and its non-processive counterpart, Cel7B, engaged on cellulose, which suggests allosteric mechanisms involved in chain binding when these cellulases are complexed on cellulose. Our computational results also suggest that product inhibition varies significantly between Cel7A and Cel7B, and we offer a molecular-level explanation for this observation. Finally, we discuss simulations of the absolute and relative binding free energy of cellulose ligands and various mutations along the CD tunnel, which will affect processivity and the ability of Cel7A (and related enzymes) to digest cellulose. These results highlight new considerations in protein engineering for processive and non-processive cellulases for production of lignocellulosic biofuels.
Versatile Battery Chargers for New Age Batteries (2011)

This paper proposes two designs for a versatile charger capable of charging a range of batteries ranging from the conventional Li ion and Ni-Cd batteries to the more recent thin film batteries. The charger is equipped with a low power micro controller which enables the user to specify the kind of battery to be charged as well as calibrate the current and the voltage levels. The charger is capable of working in both, the Constant Current (CC) as well as the Constant Voltage (CV) mode. The constant current mode has the options of trickle charge and fast charge, the values of which can be calibrated beforehand. The charger implements a simple and efficient algorithm using the micro controller to decide the charging methodology and also detect end-points to avoid overcharging. One of the designs offers a very high accuracy of 0.02%/V in the charging current across input voltage values ranging from 2V to 5.5V, while the other has a power consumption of less than 1mW (for charging at 3V and current values of the order of a few microamperes), which opens up the possibility of powering the device using energy harvesting sources.
Requirements and Characteristics of Electronic Warfare Receivers (2004)

In this chapter, the information contained in a radar pulse will be presented first. Then some of the difficulties encountered in receiver research will be stated. A very simple discussion on analog and digital receivers will then be presented and, finally, the characteristics of EW receivers will be discussed. If several definitions of one term are available, only the ones that have a direct impact on EW receivers will be discussed. All the characteristics presented here are measurable quantities and the measurements will be presented in Chapter 14. Finally, the research trend in EW receivers will be discussed. Readers with EW background can skip this chapter.
Modeling meso- and microstructure in materials patterned with acoustic focusing (2021)

We conduct numerical simulations of acoustic focusing in dense suspensions to map the design space of acoustically patterned materials and understand the relationships between input parameters, structural features, and functional properties. We develop closed-form expressions for acoustic forces on particles, enabling rapid simulation of thousands of particles, and find excellent agreement with experimentally focused patterns over a range of conditions. We map the geometrical and microstructural features of focused particle patterns and their dependence on processing parameters. We find that mesostructural geometrical features (focused line height, width, and profile shape) can be controlled reliably over a broad range by modulating input parameters, and that while microstructural features are less readily modulated via input parameters, they are well-suited for various transport properties in functional materials. Notably, packing density nears the random close packing limit at 0.64, and particle contact density shows anisotropy favoring particle contacts along the focused lines. These results guide process design for controlling the properties of patterned materials, and outline the property ranges accessible via acoustic focusing. Additionally, we discuss the dependence of material functionalities, particularly electrical, thermal, and ionic transport properties, on the meso- and micro-structural features of patterned composite materials in the context of acoustic focusing.
A two stage structure for high order multi-bit Σ-Δ ADC with multiplier-less digital correction logic (2002)

This paper presents the design methodology of /spl Sigma/-/spl Delta/ ADC that uses a high order single bit first stage, and a multi bit first order second stage and introduces a novel multiplier-less high order digital correction block. The selection of the number of bits and order is done by design graphs that are obtained through numerous simulations under practical tolerances in implementation parameters. By using an example of a 3rd order first stage with a 5-bit second stage, we show that the over-sampling ratio can be reduced to (=<32) while achieving a high bit resolution (>16 bits) for 2% mismatch implementation tolerances between analog and digital parts. Our approach results in an overall increase in the maximum baseband frequency, while the additional digital correction logic is minimal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enhancing Energy Efficiency via Device‐to‐Device Proximity Services (2017)

This chapter presents three device-to-device (D2D) proximity services-based energy efficient communications schemes, namely, energy efficient cooperative wireless multicasting, green relay assisted D2D communications and green content brokerage. In green relay assisted D2D communications, the chapter introduces green relay nodes to increase the link data rate of D2D communications by leveraging cooperative communications. It proposes a novel green relay assisted D2D communications architecture, in which relay nodes powered by green energy are deployed to increase the data rates of D2D communications. In designing green relay assisted D2D communications, the chapter considers a wireless network consisting of 2N UEs and M green relay nodes, with the UEs forming N SD pairs. By leveraging D2D communications, he/she designs a novel mobile traffic offloading scheme, content brokerage. In designing the green content brokerage scheme, the he/she considers a cellular network consisting of one MBS, N UEs and one GCB.
A 5-Year Follow-up of Patients Treated for Full-Thickness Rotator Cuff Tears: A Prospective Cohort Study (2021)

Patients with RCTs tended to improve regardless of whether they received operative or nonoperative treatment, but patients who underwent operative treatment improved faster. There appear to be several predictors of improved and worsened outcomes for patients with RCTs undergoing operative or nonoperative treatment.
Analysis of Blacklist Update Frequency for Countering Malware Attacks on Websites (2013)

We proposes a method for determining the frequency for monitoring the activities of a malware download site used for malware attacks on websites. In recent years, there has been an increase in attacks exploiting vulnerabilities in web applications for infecting websites with malware and maliciously using those websites as attack platforms. One scheme for countering such attacks is to blacklist malware download sites and filter out access to them from user websites. However, a malware download site is often constructed through the use of an ordinary website that has been maliciously manipulated by an attacker. Once the malware has been deleted from the malware download site, this scheme must be able to unblacklist that site to prevent normal user websites from being falsely detected as malware download sites. However, if a malware download site is frequently monitored for the presence of malware, the attacker may sense this monitoring and relocate that malware on a different site. This means that an attack will not be detected until the newly generated malware download site is discovered. In response to these problems, we clarify the change in attack-detection accuracy caused by attacker behavior. This is done by modeling attacker behavior, specifying a state-transition model with respect to the blacklisting of a malware download site, and analyzing these models with synthetically generated attack patterns and measured attack patterns in an operation network. From this analysis, we derive the optimal monitoring frequency that maximizes the true detection rate while minimizing the false detection rate.
Supplementary Figure 2 from Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models (2023)

&lt;p&gt;Variant Allele Frequencies for the CDXF1 model.&lt;/p&gt;
Characterization of a novel phosphatidylinositol 3-phosphate-binding protein containing two FYVE fingers in tandem that is targeted to the Golgi (2001)

We have identified a novel protein of predicted molecular mass 40 kDa that contains two FYVE domains in tandem and has therefore been named TAFF1 (TAndem FYVE Fingers-1). The protein is expressed predominantly in heart and binds to PtdIns3P specifically, even though the FYVE domains in TAFF1 lacks the first Arg of the consensus sequence R(K/R)HHCR, critical for the PtdIns3P binding of other FYVE domains identified so far. The first Arg is replaced by a Thr and Ser in the N-terminal and C-terminal FYVE domains of TAFF1 respectively. Mutational analysis indicates that both FYVE domains are required for high affinity binding to PtdIns3P. Cell localization studies using a green fluorescent protein fusion show that TAFF1 is localized to the Golgi, and that the Golgi targeting sequence is located within the N-terminal 187 residues and not in either FYVE domain.
A test for dependence between two point processes on the real line (2014)

Many scientific questions rely on determining whether two sequences of event times are associated. This article introduces a likelihood ratio test which can be parameterised in several ways to detect different forms of dependence. A common finite-sample distribution is derived, and shown to be asymptotically related to a weighted Kolmogorov-Smirnov test. Analysis leading to these results also motivates a more general tool for diagnosing dependence. The methodology is demonstrated on data generated on an email network, showing evidence of information flow using only timing information. Implementation code is available in the R package `mppa'.
3-D fabrication of microfluidic channels in fused silica using focused femtosecond laser beams (2005)

We demonstrate polarization dependence of the etch rate in femtosecond laser fabrication of 3-D microfluidic channels. We also show the existence of an energy threshold at which etching becomes highly selective.
From motor control to team play in simulated humanoid football (2022)

Learning to combine control at the level of joint torques with longer-term goal-directed behavior is a long-standing challenge for physically embodied artificial agents. Intelligent behavior in the physical world unfolds across multiple spatial and temporal scales: Although movements are ultimately executed at the level of instantaneous muscle tensions or joint torques, they must be selected to serve goals that are defined on much longer time scales and that often involve complex interactions with the environment and other agents. Recent research has demonstrated the potential of learning-based approaches applied to the respective problems of complex movement, long-term planning, and multiagent coordination. However, their integration traditionally required the design and optimization of independent subsystems and remains challenging. In this work, we tackled the integration of motor control and long-horizon decision-making in the context of simulated humanoid football, which requires agile motor control and multiagent coordination. We optimized teams of agents to play simulated football via reinforcement learning, constraining the solution space to that of plausible movements learned using human motion capture data. They were trained to maximize several environment rewards and to imitate pretrained football-specific skills if doing so led to improved performance. The result is a team of coordinated humanoid football players that exhibit complex behavior at different scales, quantified by a range of analysis and statistics, including those used in real-world sport analytics. Our work constitutes a complete demonstration of learned integrated decision-making at multiple scales in a multiagent setting.
<title>Multivariate optical computation for predictive spectroscopy</title> (1998)

A novel optical approach to predicting chemical and physical properties based on principal component analysis (PCA) is proposed and evaluated using a data set from earlier work. In our approach, a regression vector produced by PCA is designed into the structure of a set of paired optical filters. Light passing through the paired filters produces an analog detector signal directly proportional to the chemical/physical property for which the regression vector was designed. This simple optical computational method for predictive spectroscopy is evaluated in several ways, using the example data for numeric simulation. First, we evaluate the sensitivity of the method to various types of spectroscopy errors commonly encountered, and find the method to have the same susceptibilities toward error as standard methods. Second, we use propagation of errors to determine the effects of detector noise on the predictive power of the method, finding the optical computation approach to have a large multiplex advantage over conventional methods. Third, we use two different design approaches to the construction of the paired filter set for the example measurement to evaluate manufacturability, finding that adequate methods exist to design appropriate optical devices. Fourth, we numerically simulate the predictive errors introduced by design errors in the paired filters, finding that predictive errors are not increased over conventional methods. Fifth, we consider how the performance of the method is affected by light intensities that are not linearly related to chemical composition, and find that the method is only marginally affected. In summary, we conclude that many types of predictive measurements based upon use of regression vectors and linear mathematics can be performed more rapidly, more effectively, and at considerably lower cost by the proposed optical computation method than by traditional dispersive or interferometric instrumentation. Although our simulations have used Raman experimental data, the method is equally applicable to NIR, UV-Vis, IR, fluorescence and other spectroscopies.
Self-aware computing in the Angstrom processor (2012)

Addressing the challenges of extreme scale computing requires holistic design of new programming models and systems that support those models. This paper discusses the Angstrom processor, which is designed to support a new Self-aware Computing (SEEC) model. In SEEC, applications explicitly state goals, while other systems components provide actions that the SEEC runtime system can use to meet those goals. Angstrom supports this model by exposing sensors and adaptations that traditionally would be managed independently by hardware. This exposure allows SEEC to coordinate hardware actions with actions specified by other parts of the system, and allows the SEEC runtime system to meet application goals while reducing costs (e.g., power consumption).
Cervical Sagittal Range of Motion as a Predictor of Symptom Severity in Cervical Spondylotic Myelopathy (2017)

3.
A two-segment optical DAC 40 Gb/s PAM4 silicon microring resonator modulator transmitter in 65nm CMOS (2017)

A two-segment silicon photonic microring modulator implements an optical DAC for PAM4 modulation. Independent level and edge-rate control is achieved using segmented MSB/LSB pulsed-cascode drivers. The 65nm CMOS transmitter achieves 40Gb/s operation at 4.38mW/Gb/s while driving each microring modulator segment with 4.4V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ppd</sub> swing.
Expression of a Fungal Hydrophobin in theSaccharomyces cerevisiaeCell Wall: Effect on Cell Surface Properties and Immobilization (2002)

The aim of this work was to modify the cell surface properties of Saccharomyces cerevisiae by expression of the HFBI hydrophobin of the filamentous fungus Trichoderma reesei on the yeast cell surface. The second aim was to study the immobilization capacity of the modified cells. Fusion to the Flo1p flocculin was used to target the HFBI moiety to the cell wall. Determination of cell surface characteristics with contact angle and zeta potential measurements indicated that HFBI-producing cells are more apolar and slightly less negatively charged than the parent cells. Adsorption of the yeast cells to different commercial supports was studied. A twofold increase in the binding affinity of the hydrophobin-producing yeast to hydrophobic silicone-based materials was observed, while no improvement in the interaction with hydrophilic carriers could be seen compared to that of the parent cells. Hydrophobic interactions between the yeast cells and the support are suggested to play a major role in attachment. Also, a slight increase in the initial adsorption rate of the hydrophobin yeast was observed. Furthermore, due to the engineered cell surface, hydrophobin-producing yeast cells were efficiently separated in an aqueous two-phase system by using a nonionic polyoxyethylene detergent, C(12-18)EO(5).