gebhart/patrepeval huggingface dataset:
Development and Therapeutic Implications of Selective Histone Deacetylase 6 Inhibitors (2013)

This Perspective provides an in depth look at the numerous disease states in which histone deacetylase 6 (HDAC6) has been implicated. The physiological pathways, protein-protein interactions, and non-histone substrates relating to different pathological conditions are discussed with regard to HDAC6. Furthermore, the compounds and methods used to modulate HDAC6 activity are profiled. The latter half of this Perspective analyzes reported HDAC6 selective inhibitors in terms of structure, potency, and selectivity over the other HDAC isoforms with the intent of providing a comprehensive overview of the molecular tools available. Potential obstacles and future directions of HDAC6 research are also presented.
Long working distance optical coherence tomography for pediatric imaging(Conference Presentation) (2016)

Conventional optical coherence tomography (OCT) systems have working distances of about 25 mm, and require cooperative subjects to immobilize and fixate on a target. Handheld OCT probes have also been demonstrated for successful imaging of pre-term infants and neonates up to ~1 year old. However, no technology yet exists for OCT in young children due to their lack of attention and inherent fear of large objects close to their face. In this work, we demonstrate a prototype retinal swept-source OCT system with a long working distance (from the last optical element to the subject’s eye) to facilitate pediatric imaging. To reduce the footprint and weight of the system compared to the conventional 4f scheme, a novel 2f scanning configuration was implemented to achieve a working distance of 348mm with a +/- 8° scanning angle prior to cornea. Employing two custom-designed lenses, the system design resolution was nearly diffraction limited throughout a -8D to +5D refractive corrections. A fixation target displayed on a LCD monitor and an iris camera were used to facilitate alignment and imaging. Our prototype was tested in consented adult subjects and has the potential to facilitate imaging of young children. With this apparatus, young children could potentially sit comfortably in caretaker’s lap while viewing entertainment on the fixation screen designed to direct their gaze into the imaging apparatus.
PROTECTION AGAINST SCRUB TYPHUS BY A PLASMID VACCINE ENCODING THE 56-KD OUTER MEMBRANE PROTEIN ANTIGEN GENE (2005)

The 56-kD outer membrane protein of Orientia tsutsugamushi has previously been shown to be the immunodominant antigen in scrub typhus infections. Its gene was cloned into the DNA vaccine vector pVR1012 as a vaccine candidate (pKarp56). The in vitro expression of this 56-kD antigen by pKarp56 was confirmed in tissue culture by an indirect fluorescence assay and Western blot analysis. The initial antibody responses of mice immunized with varied doses of the pKarp56 were barely detected, but increases were observed after each of three subsequent booster immunizations. Although no protection was observed with a single immunization of pKarp56, after four immunizations, 60% of the mice survived a 1,000 x 50% lethal dose (LD(50)) challenge. These results specifically confirm the importance of the 56-kD protein antigen in protective immunity against O. tsutsugamushi and demonstrate the feasibility of DNA vaccines for the prevention of scrub typhus.
Defining Strong Privacy for RFID (2007)

In this work, we consider privacy in radio frequency identification (RFID) systems. Our contribution is twofold: (1) we propose a simple, formal definition of strong privacy useful for basic analysis of RFID systems, as well as a different (weaker) definition applicable to multi-verifier systems; and (2) we apply our definition to reveal vulnerabilities in proposed privacy-enhancing RFID protocols. This paper is a highly abbreviated version of Juels, A et al, (2005)
Lipid metabolite levels of prostaglandin D<sub>2</sub> and eicosapentaenoic acid recovered from bronchoalveolar lavage fluid correlate with lung function of chronic obstructive pulmonary disease patients and controls (2009)

One-step global profiling of analyte (mRNA, protein, metabolite) biomarkers may soon replace conventional blood and histological/biopsy diagnostics technologies. It is important to establish whether the numerous blood and other body fluid-derived potential novel diagnostics will be sufficiently efficacious and precise to replace, for example, imaging and functional diagnostic tests. Currently, imaging technologies and spirometry are indispensable for the diagnosis and management of chronic obstructive pulmonary disease (COPD). To validate the concept of using body fluid biomarkers in COPD and to address the question of whether biomarker levels correlate with lung function, we measured the level of a number of biologically relevant lipids and metabolites in the bronchoalveolar lavage (BAL) fluid of COPD and control subjects and examined whether these correlate with numeric parameters of lung function. Both the diagnosis and management of COPD rely on costly and labor intensive lung function tests. Thus, there is an imminent need to replace the current diagnostic approaches with simpler clinical assays. As a first step, we demonstrate proof of principle; the correlation of lipid biomarkers as measured by LC-MS with lung function. In the apparently BAL-accessible fluid compartment, the total recovered lipid metabolite amount, particularly prostaglandin D(2) and eicosapentaenoic acid show a remarkable linear correlation with lung function (R(2)>0.7). The study outcome is encouraging for the continuation of the work toward the measurement of lipid metabolite levels in more easily obtainable biological fluids such as sputum, exhaled air condensate, urine and plasma.
Camera intrinsic blur kernel estimation: A reliable framework (2015)

This paper presents a reliable non-blind method to measure intrinsic lens blur. We first introduce an accurate camera-scene alignment framework that avoids erroneous homography estimation and camera tone curve estimation. This alignment is used to generate a sharp correspondence of a target pattern captured by the camera. Second, we introduce a Point Spread Function (PSF) estimation approach where information about the frequency spectrum of the target image is taken into account. As a result of these steps and the ability to use multiple target images in this framework, we achieve a PSF estimation method robust against noise and suitable for mobile devices. Experimental results show that the proposed method results in PSFs with more than 10 dB higher accuracy in noisy conditions compared with the PSFs generated using state-of-the-art techniques.
Ultrasound Matrix Imaging-Part I: The focused reflection matrix, the F-factor and the role of multiple scattering (2021)

This is the first article in a series of two dealing with a matrix approach for aberration quantification and correction in ultrasound imaging. Advanced synthetic beamforming relies on a double focusing operation at transmission and reception on each point of the medium. Ultrasound matrix imaging (UMI) consists in decoupling the location of these transmitted and received focal spots. The response between those virtual transducers form the so-called focused reflection matrix that actually contains much more information than a confocal ultrasound image. In this paper, a time-frequency analysis of this matrix is performed, which highlights the single and multiple scattering contributions as well as the impact of aberrations in the monochromatic and broadband regimes. Interestingly, this analysis enables the measurement of the incoherent input-output point spread function at any pixel of this image. A fitting process enables the quantification of the single scattering, multiple scattering and noise components in the image. From the single scattering contribution, a focusing criterion is defined, and its evolution used to quantify the amount of aberration throughout the ultrasound image. In contrast to the state-of-the-art coherence factor, this new indicator is robust to multiple scattering and electronic noise, thereby providing a contrasted map of the focusing quality at a much better transverse resolution. After a validation of the proof-of-concept based on time-domain simulations, UMI is applied to the in-vivo study of a human calf. Beyond this specific example, UMI opens a new route for speed-of-sound and scattering quantification in ultrasound imaging.
Technique for measuring absolute intensity of weak magnetic fields by a SQUID pick-up coil system (1992)

A method to measure the absolute intensity of a weak magnetic field is described. This method uses patterned superconducting strip lines as a spatial modulator of the field and detects the magnetic field distribution over them as a function of applied magnetic fields. The field distribution change measured by an rf SQUID system is proportional to the component of the absolute intensity of the magnetic field at the specimen that is parallel with the pick-up coil axis. The magnetic field intensity can be determined absolutely from about 1 μG by this method. A spatial resolution of the field as good as a few millimeters is obtained. Some practical limitations of this method and possible ways for improving are also discussed.
Single-Trench-Assisted Fibers for Access Networks (2010)

All-solid single-trench-assisted step-index profiles allow to improve properties of standard single-mode fibers. Macro- and micro-bending performances can significantly be increased for direct benefits in optical networks.
Application of Automated Image-guided Patch Clamp for the Study of Neurons in Brain Slices (2017)

Whole-cell patch clamp is the gold-standard method to measure the electrical properties of single cells. However, the in vitro patch clamp remains a challenging and low-throughput technique due to its complexity and high reliance on user operation and control. This manuscript demonstrates an image-guided automatic patch clamp system for in vitro whole-cell patch clamp experiments in acute brain slices. Our system implements a computer vision-based algorithm to detect fluorescently labeled cells and to target them for fully automatic patching using a micromanipulator and internal pipette pressure control. The entire process is highly automated, with minimal requirements for human intervention. Real-time experimental information, including electrical resistance and internal pipette pressure, are documented electronically for future analysis and for optimization to different cell types. Although our system is described in the context of acute brain slice recordings, it can also be applied to the automated image-guided patch clamp of dissociated neurons, organotypic slice cultures, and other non-neuronal cell types.
Modifying the pollen coat protein composition in <i>Brassica</i> (2002)

The interactions between pollen and stigma are essential for plant reproduction and are made possible by compounds, such as proteins and lipids, located on their surfaces. The pollen coat is formed in part by compounds synthesized in, and released from, the tapetum, which become transferred to the pollen coat late in pollen development. In the Brassicaceae the predominant proteins of the mature pollen coat are the tapetal oleosin-like proteins, which are highly expressed in, and ultimately transferred from, the tapetum. Here we report the modification of the protein composition of the pollen coat by the addition of an active enzyme which was synthesized in the tapetum. The marker enzyme beta-glucuronidase (GUS) was successfully targeted to the pollen coat in transgenic Brassica carinata plants expressing GUS translationally fused to a B. napus tapetal oleosin-like protein (BnOlnB;4). To our knowledge this is the first demonstration of the targeting of an enzyme to the pollen coat.
Regulation and Mechanism of Action of the Small Heat Shock Protein from the Hyperthermophilic Archaeon <i>Pyrococcus furiosus</i> (2001)

The small heat shock protein (sHSP) from the hyperthermophile Pyrococcus furiosus was specifically induced at the level of transcription by heat shock at 105 degrees C. The gene encoding this protein was cloned and overexpressed in Escherichia coli. The recombinant sHSP prevented the majority of E. coli proteins from aggregating in vitro for up to 40 min at 105 degrees C. The sHSP also prevented bovine glutamate dehydrogenase from aggregating at 56 degrees C. Survivability of E. coli overexpressing the sHSP was enhanced approximately sixfold during exposure to 50 degrees C for 2 h compared with the control culture, which did not express the sHSP. Apparently, the sHSP confers a survival advantage on mesophilic bacteria by preventing protein aggregation at supraoptimal temperatures.
Atomically Thin Ohmic Edge Contacts Between Two-Dimensional Materials (2016)

With the decrease of the dimensions of electronic devices, the role played by electrical contacts is ever increasing, eventually coming to dominate the overall device volume and total resistance. This is especially problematic for monolayers of semiconducting transition-metal dichalcogenides (TMDs), which are promising candidates for atomically thin electronics. Ideal electrical contacts to them would require the use of similarly thin electrode materials while maintaining low contact resistances. Here we report a scalable method to fabricate ohmic graphene edge contacts to two representative monolayer TMDs, MoS2 and WS2. The graphene and TMD layer are laterally connected with wafer-scale homogeneity, no observable overlap or gap, and a low average contact resistance of 30 kΩ·μm. The resulting graphene edge contacts show linear current-voltage (I-V) characteristics at room temperature, with ohmic behavior maintained down to liquid helium temperatures.
High-fidelity state transfer between leaky quantum memories (2021)

Employing the scattering-Lindblad-Hamiltonian formalism description of quantum network theory, we model the general problem of quantum state transfer between two disparate quantum memory blocks in an open quantum system. We derive an analytical expression for the fidelity of quantum state transfer between the memory blocks under the action of a specific phase space trajectory for each of the relevant classical control fields. We find a set of trajectories that maximize the state transfer fidelity between asymmetric systems. We show that, for the example where the mechanical modes of two optomechanical oscillators act as the quantum memory blocks, their optical modes and a waveguide channel connecting them can be used to achieve a quantum state transfer fidelity of 96% with realistic parameters using our optimal control solution. The effects of the intrinsic losses and the asymmetries in the physical memory parameters are discussed quantitatively.
A gas scintillator detector for 2D dose profile monitoring in pencil beam scanning and pulsed beam proton radiotherapy treatments (2017)

In order to address dosimetry demands during proton therapy treatments utilizing pencil beam scanning and/or pulsed beam accelerators, we have developed a xenon-filled gas scintillation detector (GSD) that can monitor delivered dose and 2D beam centroid position pulse-by-pulse in real time, with high response linearity up to high instantaneous dose rates. We present design considerations for the GSD and results of beam tests carried out at operating proton therapy clinics. In addition to demonstrating spatial resolution with σ of a few hundred microns in each transverse dimension and relative dose precision better than 1% over large treatment areas, the test beam results also reveal the dependence of the GSD dose normalization on dose rate, beam energy, and gas impurities. The results demonstrate the promise of the GSD technology to provide an important addition to dosimetry approaches for next-generation ion beam therapy.
Progress and challenges in the direct monolithic integration of III&#x2013;V devices and Si CMOS on silicon substrates (2009)

We present results on the direct monolithic integration of III-V devices and Si CMOS on a silicon substrate. Through optimization of device fabrication and material growth processes III-V devices with electrical performance comparable to devices grown on native III-V substrates were grown directly in windows adjacent to CMOS transistors on silicon template wafers or SOLES (Silicon on Lattices Engineered Substrates). While the results presented here are for InP HBTs, our direct heterogeneously integration approach is equally applicable to other III-V electronic (FETs, HEMTs) and opto-electronic (photodiodes, VSCLS) devices and opens the door to a new class of highly integrated, high performance, mixed signal circuits.
Successful Islet Transplantation from Nonheartbeating Donor Pancreata Using Modified Ricordi Islet Isolation Method (2006)

This demonstrates that our current protocol makes it feasible to use NHBDs for islet transplant into type 1 diabetic patients efficiently.
High voltage, high current, high di/dt solid state switch (2001)

The authors' objective was to demonstrate the feasibility of developing a compact, high voltage, high power solid-state switch based upon newly developed thyristors. The switch uses multiple 10 kV modules connected in series to achieve the desired voltage rating. These switches are intended to replace thyratrons and other high current, high voltage switches in existing (made possible by the small size of the solid-state modules) and new systems. The 10 kV switch module consists of a series array of 3 thyristors with built-in trigger circuitry. The trigger circuit uses the energy being switched to drive the thyristor gates, simplifying isolation and triggering. The elimination of the need for a separate gate drive power supply results in a straightforward process of scaling to higher voltages. This paper describes results of testing switch modules at currents up to 8 kA and di/dts of >30 kA/μs, under normal and load fault conditions. Repetition rate operation and initial results of multiple module tests are also presented. (4 pages)
Automating statistics management for query optimizers (2002)

Statistics play a key role in influencing the quality of plans chosen by a database query optimizer. We identify the statistics that are essential for an optimizer. We introduce novel techniques that help significantly reduce the set of statistics that need to be created without sacrificing the quality of query plans generated. We discuss how these techniques can be leveraged to automate statistics management in databases. We have implemented and experimentally evaluated our approach on Microsoft SQL Server 7.0.
Large Scale Placement For Multilateral Wells Using Network Optimization (2021)

Abstract Multilateral wells are an evolution of horizontal wells in which several wellbore branches radiate from the main borehole. In the last two decades, multilateral wells have been increasingly utilized in producing hydrocarbon reservoirs. The main advantage of using such technology against conventional and single-bore wells comes from the additional access to reservoir rock by maximizing the reservoir contact with fewer resources. Today, multilateral wells are rapidly becoming more complex in both designs and architecture (i.e., extended reach wells, maximum reservoir contact, and extreme reservoir contact wells). Certain multilateral design templates prevail in the industry, such as fork and fishbone types, which tend to be populated throughout the reservoir of interest with no significant changes to the original architecture and, therefore, may not fully realize the reservoir's potential. Placement of optimal multilateral wells is a multivariable problem, which is a function of determining the best well locations and trajectories in a hydrocarbon reservoir with the ultimate objectives of maximizing productivity and recovery. The placement of the multilateral wells can be subject to many constraints such as the number of wells required, maximum length limits, and overall economics. This paper introduces a novel technology for placement of multilateral wells in hydrocarbon reservoirs utilizing a transshipment network optimization approach. This method generates scenarios of multiple wells with different designs honoring the most favorable completion points in a reservoir. In addition, the algorithm was developed to find the most favorable locations and trajectories for the multilateral wells in both local and global terms. A partitioning algorithm is uniquely utilized to reduce the computational cost of the process. The proposed method will not only create different multilateral designs; it will justify the trajectories of every borehole section generated. The innovative method is capable of constructing hundreds of multilateral wells with design variations in large-scale reservoirs. As the complexity of the reservoirs (e.g., active forces that influence fluid mobility) and heterogeneity dictate variability in performance at different area of the reservoir, multilateral wells should be constructed to capture the most productive zones. The new method also allows different levels of branching for the laterals (i.e., laterals can emanate from the motherbore, from other laterals or from subsequent branches). These features set the stage for a new generation of multilateral wells to achieve the most effective reservoir contact.
Memristive switching of single-component metallic nanowires (2010)

Memristors have recently generated significant interest due to their potential use in nanoscale logic and memory devices. Of the four passive circuit elements, the memristor (a two-terminal hysteretic switch) has so far proved hard to fabricate out of a single material. Here we employ electromigration to create a reversible passive electrical switch, a memristive device, from a single-component metallic nanowire. To achieve resistive switching in a single-component structure we introduce a new class of memristors, devices in which the state variable of resistance is the system's physical geometry. By exploiting electromigration to reversibly alter the geometry, we repeatedly switch the resistance of single-component metallic nanowires between low and high states over many cycles. The reversible electromigration causes the nanowire to be cyclically narrowed to approximately 10 nm in width, resulting in a change in resistance by a factor of two. As a result, this work represents a potential route to the creation of nanoscale circuits from a single metallic element.
Description and reconstruction from image trajectories of rotational motion (2002)

A novel technique is presented for reconstructing the 3-D structure, and motion, of a scene undergoing relative rotational motion with respect to the camera. Given image correspondences of point features tracked over many frames, first, a grouping algorithm developed which exploits spatio-temporal constraints of the common motion to achieve a reliable description of discrete point correspondences as curved trajectories (general conics in the case of rotational motion) in the image plane. In contrast, trajectories fitted to points independent of each other lead to arbitrary image descriptions and very inaccurate 3-D parameters. Second, a novel closed-form solution, under perspective projection, for the 3-D motion and location of points from the computed image trajectories is presented. Both stages are applied to real image sequences with good results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>