gebhart/patrepeval huggingface dataset:
Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes (2014)

Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. Such activatable probes with near-infrared (NIR) emission would be ideal for in vivo imaging but have proven difficult to engineer. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. We used the probes for mammalian cell surface imaging and, in conjunction with a new class of cyclooctyne D-amino acids, for visualization of bacterial peptidoglycan without the need to wash away unreacted probe.
Time–frequency analysis of lamb waves caused by partial discharges and free particles in GIS (2003)

Abstract We investigated the propagation properties of Lamb waves in a GIS tank, using time–frequency analysis to diagnose the insulation performance of GIS. We measured the acoustic signals excited by metallic particles colliding with the tank sheath, and those emitted by partial discharge in the GIS. The wavelet transform was used to decompose the wave data into its time–frequency components. As a result, it was confirmed that Lamb waves with the dispersive property of the velocity are excited and propagate in a spiral path along the tank wall due to the cylindrical structure of the tank. Taking these results into consideration, we propose a new technique for identification of defect locations in GIS based on time–frequency analysis of acoustic signals with the wavelet transform. © 2003 Wiley Periodicals, Inc. Electr Eng Jpn, 145(3): 25–32, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/eej.10163
A lightweight virtual machine monitor for Blue Gene/P (2012)

In this paper, we present a lightweight, micro-kernel-based virtual machine monitor (VMM) for the Blue Gene/P supercomputer. Our VMM comprises a small µ-kernel with virtualization capabilities and, atop, a user-level VMM component that manages virtual Blue Gene/P cores, memory, and interconnects; we also support running native applications directly atop the µ-kernel. Our design goal is to enable compatibility to standard operating systems such as Linux on BG/P via virtualization, but to also keep the amount of kernel functionality small enough to facilitate shortening the path to applications and lowering operating system noise. Our prototype implementation successfully virtualizes a Blue Gene/P version of Linux with support for Ethernet-based communication mapped onto Blue Gene/P’s collective and torus network devices. Our first experiences and experiments show that our VMM still shows a substantial performance hit, and that support for native application environments is a key requirement towards fully exploiting the capabilities of a supercomputer. Altogether, our approach poses an interesting operating system alternative for supercomputers, providing the convenience of a fully featured commodity software stack, while also promising to deliver the scalability and low latency of an HPC operating system.
Advantages of the Half-Circle Suture Needle for Reconstructing Small Cutaneous Surgical Wounds (2014)

1Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, 2Department of Dermatology, University of California at Irvine, Irvine, California, 3School of Medicine, University of California at Irvine, Irvine, California, 4Private Practice, Newport Beach, California, 5College of Human Ecology, Cornell University, Ithaca, New York, 6School of Medicine, University of California, Irvine, California,
The Key Role of Genomics in Modern Vaccine and Drug Design for Emerging Infectious Diseases (2009)

It can be argued that the arrival of the "genomics era" has significantly shifted the paradigm of vaccine and therapeutics development from microbiological to sequence-based approaches. Genome sequences provide a previously unattainable route to investigate the mechanisms that underpin pathogenesis. Genomics, transcriptomics, metabolomics, structural genomics, proteomics, and immunomics are being exploited to perfect the identification of targets, to design new vaccines and drugs, and to predict their effects in patients. Furthermore, human genomics and related studies are providing insights into aspects of host biology that are important in infectious disease. This ever-growing body of genomic data and new genome-based approaches will play a critical role in the future to enable timely development of vaccines and therapeutics to control emerging infectious diseases.
Saccharide modified silica particles by enzymatic grafting (1997)

Abstract The surface of silica particles has been chemically modified with oligo‐ or poly‐(α,1←4)‐ D ‐glucopyranose (amylose) chains of various length by covalently attaching maltoheptaose derivatives to the solid support and enzymatic polymerization of glucose‐1‐phosphate with potato phosphorylase (E.C. 2.4.1.1) as catalyst. The characterization of the products by solid‐state NMR spectroscopy showed an interesting dependence of the linewidth with the grafting density of the glucan chains. The modified silica particles showed chiral discrimination in liquid chromatography.
Weaver's triangle (2009)

Weaver’s Triangle: a photographic exhibition at Mid Pennine Arts gallery documenting an ancient heritage site prior to major regeneration work
Chronic Myocardial Infarction is a Substrate for Bradycardia‐Induced Spontaneous Tachyarrhythmias and Sudden Death in Conscious Animals (2006)

The combination of MI and bradycardia secondary to AV node ablation in sheep produces a higher incidence of VT than bradycardia alone, suggesting that this preparation can serve as a model for the study of VT and sudden cardiac death.
Intrinsic differences in ultrasonic backscatter properties between the left and right ventricles of fetal hearts (2009)

It is thought that the cardiac chambers differ in their morphological and contractile properties from an early embryonic stage of development. We hypothesized that a noninvasive ultrasonic backscatter investigation might illustrate fundamental differences in myocardial properties of the two ventricles during heart development. The goals of this investigation were: 1) to measure the apparent level of backscatter from the left and right ventricular walls of excised, mid-gestational fetal pig hearts; 2) to measure the magnitude of the cyclic variation over the heart cycle of ultrasonic backscatter from the left and right ventricular free walls of mid-gestational fetal human hearts in utero; and 3) to determine if the observed cyclic variation of backscatter results are consistent with predictions relating overall backscatter levels and the magnitudes of cyclic variation. Broadband (30 to 60 MHz) integrated backscatter measurements were obtained from the left and right ventricular myocardium from 16 excised, formalin-fixed, mid-gestational fetal pig heart specimens using a 50-MHz single-element transducer measurement system. Separately, measurements of the magnitude of cyclic variation of backscatter from the left and right ventricular walls of the hearts of 16 structurally normal mid-gestational human fetuses were obtained from analyses of echocardiographic images obtained using a specially-configured commercial imaging system. For each of the 16 fetal pig hearts, the level of apparent integrated backscatter from the right ventricular myocardium was larger than that from the left ventricular myocardium, exhibiting mean values of -35.9 ? 2.0 dB and -40.1 ? 1.9 dB (mean ? SD; p < 0.001), respectively. For the human fetuses, the magnitude of cyclic variation of backscatter was found to be greater for the left ventricular free wall than for the right ventricular free wall (4.5 ? 1.1 dB vs. 2.3 ? 0.9 dB, respectively; mean ? SD; p < 0.0001). Measurements of the level of apparent backscatter (fetal pigs) and cyclic variation of backscatter (human fetuses) demonstrate significant differences between the left and right ventricular myocardium. The measured results are consistent with previously described models relating overall backscatter levels and the magnitudes of cyclic variation that predict the magnitude of cyclic variation should decrease as the level of backscatter from the myocardium increases. Results of this study suggest cyclic variation measurements may offer a useful approach for characterizing intrinsic differences in myocardial properties of the two ventricles in assessing fetal heart development.
Supplementary Table S3 from ERK Inhibitor LY3214996 Targets ERK Pathway–Driven Cancers: A Therapeutic Approach Toward Precision Medicine (2023)

&lt;p&gt;Summary of antitumor activity of LY3214996 and other MAPK pathway inhibitors in cancer models with dominant MAPK pathway alterations&lt;/p&gt;
Characterization of genetic variation in Icelandic cattle (2014)

Identification of genetic variation in cattle breeds using next-generation sequencing technology has focused on the modern production cattle breeds. We focused on one of the oldest indigenous breeds, the Icelandic cattle breed.<br/>Sequencing of two individuals enabled identification of more than 8 million SNPs and more than one million short indels. Annotation of the genetic variants identified a substantial number of functional SNPs and variants. The number of genetic variants identified in the Icelandic cattle breed is on the same level as previously seen in other studies on Holstein cattle
Chirped fibre gratings produced by tilting the fibre (1995)

A new and simple method for writing chirped fibre gratings is presented. It involves the use of a phase mask combined with a spherical lens and requires a controlled tilt between the fibre and the phase mask surface. A chirped grating has been written in a hydrogen-loaded standard telecommunication fibre. A peak reflectivity of 96% and a bandwidth of 6.0 nm have been achieved. This technique allows the production of a large range of chirp magnitudes.
Figure S6 from JAK1/STAT3 Activation through a Proinflammatory Cytokine Pathway Leads to Resistance to Molecularly Targeted Therapy in Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Figure S6. Prevention of rhOSM-induced EMT-related changes by inhibition of OSMR/LIFR or STAT3. H23 cells were transfected with an siRNA specific for OSMR/LIFR, STAT3, JUN, or scrambled negative control for 72 hours. Cells were treated with rhOSM (1 ng/mL) for 1 week and cell lysates were analyzed for the indicated proteins by Western blotting.&lt;/p&gt;
Charge characterization in metal-gate/high-κ layers: Effect of post-deposition annealing and gate electrode (2007)

The effect of varying interfacial SiO2 and high-κ thickness on charge density within the gate stack are examined. It is demonstrated that there is a significant effect of the gate electrode on the charge density levels within the stack, with one order of magnitude lower charge in the case of Ni3Si2 electrodes, than in the case of tantalum-rich metal electrodes. The effect of post-deposition annealing on high-κ HfSixOy(Nz) stacks is less significant that that of the electrode. The reasons behind these findings are discussed.
Optimized Write Strategy for 4× Speed BD-RE (2005)

We studied an optimized write strategy for a 4× speed phase-change Blu-ray disc system for further practical implementation. This was performed by simulation using three-dimensional alternating directional implicit thermal analysis and crystallization modeling. We evaluated and confirmed this approach by implementing it in 2× recording with commercially available 23 GB discs.
Adaptive security and privacy for mHealth sensing (2011)

As healthcare in many countries faces an aging population and rising costs, mobile Health (mHealth) sensing technologies promise a new opportunity. However, the privacy concerns associated with mHealth sensing are a limiting factor for their widespread adoption. The use of wireless body area networks pose a particular challenge. Although there exist protocols that provide a secure and private communication channel between two devices, the large transmission overhead associated with these protocols limit their application to low-power mHealth sensing devices. We propose an adaptive security model that enables use of privacy-preserving protocols in lowpower mHealth sensing by reducing the network overhead in the transmissions, while maintaining the security and privacy properties provided by the protocols. 1
Bacterial Energetics at High pH: What Happens to the H + Cycle When the Extracellular H + Concentration Decreases? (2007)

A decrease in the extracellular H+ concentration creates difficulties for membrane-linked energetics in bacteria employing H+ as the coupling ion. At high extracellular pH (pHo), H+ ions pumped from the cell by, say, the respiratory chain, are immediately neutralized by the alkaline extracellular medium. Under such conditions, the only driving force that might compel outer H+ ions to return to cytosol and perform their function is the electric potential difference across the cytoplasmic membrane (delta psi). However, when delta pH in the opposite direction is equal to, e.g., 2 pH units (intracellular pH = 7.5 at pHo = 9.5), delta psi would be so high that the risk of membrane electric breakdown would increase. This is why some bacteria deal with high pH by, for example, replacing H+ by Na+ as the coupling ion rather than by increasing delta psi. It has been shown in several species of bacteria that the alkalinization of the growth medium induces primary Na+ pumps (e.g. Na(+)-motive respiratory chain enzymes and Na+ ATPase). Electrogenic Na+ efflux via these pumps produces an electrochemical Na+ potential difference (delta mu Na+) composed of delta psi and delta pNa+. delta mu Na+ can be used to perform various types of membrane-linked work. The delta psi constituent of delta mu Na+ may maintain electrophoretic influx of H+ such that the alkalinization of cytoplasm is prevented. The latter function may be supported by a mechanism based on the uphill influx of Cl- instead of Na+. This seems to be the case for alkaliphilic and halophilic Natronobacter pharaonis. There is an indication that not only Na+ but also Ca2+ may substitute for H+ in Gleobacter violaceus growing at high pH.
Dielectric properties of ‘‘diamondlike’’ carbon prepared by rf plasma deposition (1985)

Metal-carbon-metal structures were fabricated using either gold or aluminum evaporated electrodes and rf plasma (methane) deposited ‘‘diamondlike’’ carbon films. ac-conductance and capacitance versus voltage and frequency (10 Hz to 13 MHz) data were taken to determine the dielectric properties of these films. Conductance versus frequency data fit a generalized power law, consistent with both dc and hopping conduction components. The capacitance versus frequency data are well matched to the conductance versus frequency data, as predicted by a Kramers-Kronig analysis. The dielectric loss tangent is nearly constant at 0.5 to 1.0% over the frequency range from 1 to 100 kHz. The dc resistivity is above 1013 Ω cm, and the dc breakdown strength is above 8×106 V/cm in properly prepared samples.
Predictive control of DC-link voltage in an active-front-end rectifier (2011)

Model predictive control (MPC) has been successfully applied to several power converters topologies, mainly because of the finite set of inputs which are given by the available switching states of these devices. However, MPC could not directly control the DC-link voltage in active-front-end(AFE) rectifiers, because they feature a non minimum phase behavior that produces an initial inverse dynamic and mislead the optimization stage selecting a wrong switching state. To avoid this effect, the DC-link voltage is usually controlled using a linear PI controller and an inner current or power control loop. However, the linear controller is difficult to design and presents a restricted dynamic behavior. In this paper, a DC-link voltage MPC is proposed. The proposed controller calculates the required active power reference based on the output power and the energy stored in the DC-link capacitor. Simulation results shows a good dynamic response and a zero steady state error.
Robust Rearrangement Planning Using Nonprehensile Interaction (2016)

As we work to move robots out of factories and into human environments, we must empower robots to interact freely in unstructured, cluttered spaces. Humans do this easily, using diverse, whole-arm, nonprehensile actions such as pushing or pulling in everyday tasks. These interaction strategies make difficult tasks easier and impossible tasks possible. In this thesis, we aim to enable robots with similar capabilities. In particular, we formulate methods for planning robust open-loop trajectories that solve the rearrangement planning problem using nonprehensile interactions. In these problems, a robot must plan in a cluttered environment, reasoning about moving multiple objects in order to achieve a goal. The problem is difficult because we must plan in continuous, high-dimensional state and action spaces. Additionally, during planning we must respect the physical constraints induced by the nonprehensile interaction between the robot and the objects in the scene. Our key insight is that by embedding physics models directly into our planners we can naturally produce solutions that use nonprehensile interactions such as pushing. This also allows us to easily generate plans that exhibit full arm manipulation and simultaneous object interaction without the need for programmer defined high-level primitives that specifically encode this interaction. We show that by generating these diverse actions, we are able to find solutions for motion planning problems in highly cluttered, unstructured environments. In the first part of this thesis we formulate the rearrangement planning problem as a classical motion planning problem. We show that we can embed physics simulators into randomized planners. We propose methods for reducing the search space and speeding planning time in order to make the planners useful in real-world scenarios. The second part of the thesis tackles the imperfect and imprecise worlds that reflect the true reality for robots working in human environments. We pose the rearrangement planning under uncertainty problem as an instance of conformant probabilistic planning and offer methods for solving the problem. We demonstrate the effectiveness of our algorithms on two platforms: the home care robot HERB and the NASA rover K-Rex. We demonstrate expanded autonomous capability on HERB, allowing him to work better in high clutter, completing previously infeasible tasks and speeding feasible task execution. In addition, we show these planners increase autonomy for the NASA rover K-Rex by allowing the rover to actively interact with the environment.
Protein-drug binding free energy computation incorporating protein flexibility and its significance in predicting mutation-induced drug resistance in oncogenic kinases (2020)

Accurate prediction of binding affinities of drug candidates to their targets remains challenging because of protein flexibility. In case of CDK2 and ERK2 kinases, conformational flexibility of the glycine-rich loop in the drug-binding site was identified using MD simulations. The binding free energy (delta-G) of twenty-four ATP-competitive inhibitors toward these kinases was
Autonomous Manufacturing Using Machine Learning: A Computational Case Study With a Limited Manufacturing Budget (2020)

Abstract This paper studies the concept of manufacturing systems that autonomously learn how to build parts to a user-specified performance. To perform such a function, these manufacturing systems need to be adaptable to continually change their process or design parameters based on new data, have inline performance sensing to generate data, and have a cognition element to learn the correct process or design parameters to achieve the specified performance. Here, we study the cognition element, investigating a panel of supervised and reinforcement learning machine learning algorithms on a computational emulation of a manufacturing process, focusing on machine learning algorithms that perform well under a limited manufacturing, thus data generation, budget. The case manufacturing study is for the manufacture of an acoustic metamaterial and performance is defined by a metric of conformity with a desired acoustic transmission spectra. We find that offline supervised learning algorithms, which dominate the machine learning community, require an infeasible number of manufacturing observations to suitably optimize the manufacturing process. Online algorithms, which continually modify the parameter search space to focus in on favorable parameter sets, show the potential to optimize a manufacturing process under a considerably smaller manufacturing budget.
Area and Power Efficient Synthesis of DPA-Resistant Cryptographic S-Boxes (2007)

This paper presents a novel design methodology for the hardware implementation of non-linear bijective functions, commonly used in most symmetric-key cryptographic algorithms and known as substitution boxes (S-boxes). The proposed technique thwarts a particularly relevant class of side-channel attacks against cryptographic hardware, that of differential power analysis attacks (DPA). In the proposed approach, the cost of the countermeasure is kept low in terms of silicon process overheads (standard CMOS gates used), area requirement, power consumption and latency, when compared to existing countermeasures. Its effectiveness is proven by showing resistance to simulated DPA attacks using power curves derived with SPICE simulation
Register leakage masking using Gray code (2012)

Since their introduction in 1996, the effectiveness of side channel attacks has been highly improved and many countermeasures have been invalidated. A very common countermeasure consists in randomizing sensitive variables of algorithms by masking techniques. In this paper, we propose a new way to apply this strategy to secure hardware implementations of block ciphers. The main advantage of the proposed solution is that the masked variables and the masking material can be manipulated simultaneously without leaking sensitive information in the Hamming distance model. Moreover, we show that the leaking information stays very limited when the deterministic part of the real leakage slightly deviates from the Hamming distance. Finally, we apply our method to protect an AES hardware implementation and we show that the performances are suitable for practical implementations.
Cloning and Transcriptional Analysis of the Gene Encoding 5-Aminolevulinic Acid Synthase of the White-Rot FungusPhanerochaete sordidaYK-624 (2011)

In this study, we cloned the gene encoding 5-aminolevulinic acid synthase (ALAS) from the hyper-lignin-degrading fungus Phanerochaete sordida YK-624. The deduced amino acid sequence showed highest identity (93.0%) to ALAS of P. chrysosporium. Expression of the gene encoding ALAS, which we named aas, corresponded temporally with the expression and activity of manganese peroxidase.