gebhart/patrepeval huggingface dataset:
A dual-mode hemispherical sparse array for 3D passive acoustic mapping and skull localization within a clinical MRI guided focused ultrasound device (2018)

Previous work has demonstrated that passive acoustic imaging may be used alongside MRI for monitoring of focused ultrasound therapy. However, past implementations have generally made use of either linear arrays originally designed for diagnostic imaging or custom narrowband arrays specific to in-house therapeutic transducer designs, neither of which is fully compatible with clinical MR-guided focused ultrasound (MRgFUS) devices. Here we have designed an array which is suitable for use within an FDA-approved MR-guided transcranial focused ultrasound device, within the bore of a 3 Tesla clinical MRI scanner. The array is constructed from 5 × 0.4 mm piezoceramic disc elements arranged in pseudorandom fashion on a low-profile laser-cut acrylic frame designed to fit between the therapeutic elements of a 230 kHz InSightec ExAblate 4000 transducer. By exploiting thickness and radial resonance modes of the piezo discs the array is capable of both B-mode imaging at 5 MHz for skull localization, as well as passive reception at the second harmonic of the therapy array for detection of cavitation and 3D passive acoustic imaging. In active mode, the array was able to perform B-mode imaging of a human skull, showing the outer skull surface with good qualitative agreement with MR imaging. Extension to 3D showed the array was able to locate the skull within ±2 mm/2° of reference points derived from MRI, which could potentially allow registration of a patient to the therapy system without the expense of real-time MRI. In passive mode, the array was able to resolve a point source in 3D within a ±10 mm region about each axis from the focus, detect cavitation (SNR ~ 12 dB) at burst lengths from 10 cycles to continuous wave, and produce 3D acoustic maps in a flow phantom. Finally, the array was used to detect and map cavitation associated with microbubble activity in the brain in nonhuman primates.
Catheter-based ventricle-coronary vein bypass (2005)

The goal of this study was to investigate the feasibility of a catheter-based ventricle-to-coronary vein bypass (VPASS) in order to achieve retrograde myocardial perfusion by a conduit (VSTENT) from the left ventricle (LV) to the anterior interventricular vein (AIV). Percutaneous coronary venous arterialization has been proposed as a potential treatment strategy for otherwise untreatable coronary artery disease. In an acute setting, the VSTENT implant was deployed percutaneously using the VPASS procedure in five swine. Coronary venous flow and pressure patterns were measured before and after VSTENT implant deployment with and without AIV and left anterior descending artery (LAD) occlusion. In a separate chronic pilot study, the VPASS procedure was completed on two animals that had a mid-LAD occlusion or LAD stenosis. At day 30 post-VPASS procedure, left ventriculography and magnetic resonance imaging (MRI) were performed to assess the patency and myocardial viability of the VSTENT implants. Pre-VSTENT implantation, the mid-AIV systolic wedge pressure was significantly lower than LV systolic pressure during AIV blockage (46 +/- 19 vs. 90 +/- 16 mm Hg; P < 0.01). The VSTENT implant deployment was performed without complication and achieved equalization of the AIV and LV systolic pressures and creation of retrograde flow in the distal AIV (maximal flow velocity: 37 +/- 7 cm/sec). At day 30 post-VPASS procedure, left ventriculography showed VSTENT implant patency. MRI perfusion images demonstrated myocardial viability even with an LAD occlusion. Coronary retrograde perfusion using the VPASS procedure is feasible and may represent a potential technique for end-stage myocardial ischemia.
Associations of Preoperative Patient Mental Health and Sociodemographic and Clinical Characteristics With Baseline Pain, Function, and Satisfaction in Patients Undergoing Rotator Cuff Repairs (2019)

Large/massive tear size, lower VR-12 MCS, and several additional patient and disease-specific factors are associated with baseline PROMs in patients undergoing rotator cuff repair. Further studies are needed to investigate whether these factors will also predict poor postoperative PROMs.
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions (2011)

The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.
Focal lesion in the splenium of the corpus callosum in epileptic patients: antiepileptic drug toxicity? (1999)

A discrete, focal, ovoid, nonhemorrhagic lesion in the splenium of the corpus callosum may be seen on brain MR images of patients with epilepsy. The lesion is considered to be reversible demyelination related to AEDs toxicity.
Numerical Simulations of Dam-break Floods with MPM (2017)

Due to the ability to model large deformations and the ease of dealing with boundary conditions in a Lagrangian framework, the material point method is getting more popularity in geotechnical engineering applications. In this paper, the material point is tentatively applied to model problems of hydrodynamics as an introduction to this field. Dam-break flows with different initial aspect ratios are simulated in both the material point method and an extensively verified shallow water equations model. In order to test the accuracy and stability of the material point method, simulations of dam-break flows are carried out and the results are in good agreement with other validated numerical methods and experimental data. From the comparisons between the simulations in both the material point method and shallow water equations model, a critical aspect ratio value for the applicability of the shallow water equations is found to be 1. The material point method shows its potential to tackle hydrodynamics related problems.
A MAGNETIC FLOW CYTOMETER WITH INTEGRATED MICROFLUIDICS (2014)

A chip scale flow cytometer realized in a standard CMOS process uses magnetic beads as labels. The material dependent complex susceptibility is used to differentiate between label classes for multi-target flow cytometry. The chip is embedded in a microfluidic cartridge and operation verified with an embryonic fibroblast assay.
Unifying the User and Kernel Environments (1997)

Vendors of commercial operating systems today invest resources in two very different environments—one for userlevel (application or server) programming and one for kernel-level (device driver or subsystem) programming. The kernel environment is typically more restrictive, with completely different interfaces and programming conventions. Based on our experience developing and deploying an operating system for an interactive TV system, we believe that it is desirable to unify the user and kernel environments. We structured our operating system to provide common programming and run-time environments for user-level code and kernel-level code. For example, modules loaded into the kernel did not have any restrictions on their use of shared libraries or stack space. We found that unifying the user and kernel environments with common interfaces and run-time requirements, common documentation, and a common debugger produced significant software-engineering benefits. In addition, we could transparently collocate trusted server code in the kernel to reduce memory usage and improve performance.
Advances in Protecting Remote Component Authentication (2012)

Abstract—Component authentication allows verifying the genuineness of various components being part of a machine or a system or connected to control equipment. Various technologies are used, ranging from holograms, hidden marks, special inks to cryptography-based component authentication. Typical cryptography-based mechanisms employ a challenge-response-based component authentication mechanism. These mechanisms have been designed originally for a local verification, i.e., for an authentication performed in direct vicinity of the product to be verified. This paper describes an attack on challenge-response component authentication when supporting a remote component authentication and describes a new security measure to prevent this attack. Keywords-device authentication, counterfeiting, tunneled authentication I.
Unstable Growth of Curvature Perturbations in Nonsingular Bouncing Cosmologies (2010)

Bouncing cosmologies require an ekpyrotic contracting phase ($w\ensuremath{\gg}1$) in order to achieve flatness, homogeneity, and isotropy. Models with a nonsingular bounce further require a bouncing phase that violates the null energy condition ($w&lt;\ensuremath{-}1$). We show that the transition from the ekpyrotic phase to the bouncing phase creates problems for cosmological perturbations. A component of the adiabatic curvature perturbations, though decaying and negligible during the ekpyrotic phase, is exponentially amplified just before $w$ approaches $\ensuremath{-}1$, enough to spoil the scale-invariant perturbation spectrum.
Identification of 18‐oxo‐9,10‐epoxystearic acid, a novel compound in the cutin of young apple fruits (1973)

Abstract 18‐Oxo‐9,10‐epoxystearic acid was identified in the cutin of young apple fruits by hydrogenolysis with LiAlH 4 , deuterolysis with LiAlD 4 , CrO 3 oxidation of deuterated product followed by reduction with LiAlH 4 and mass spectrometry of the products.
Chemomechanical surface patterning and functionalization of silicon surfaces using an atomic force microscope (2003)

Surface modification and patterning at the nanoscale is a frontier in science with significant possible applications in biomedical technology and nanoelectronics. Here we show that an atomic force microscope (AFM) can be employed to simultaneously pattern and functionalize hydrogen-terminated silicon (111) surfaces. The AFM probe was used to break Si–H and Si–Si bonds in the presence of reactive molecules, which covalently bonded to the scribed Si surface. Functionalized patches and patterned lines of molecules were produced. Linewidths down to 30 nm were made by varying the force at the tip.
The Reactivity of Epoxides with Lithium 2,2,6,6-Tetramethylpiperidide in Combination with Organolithiums or Grignard Reagents (2007)

The scope and limitations of lithium 2,2,6,6-tetramethylpiperidide (LTMP)-modified reductive alkylation of epoxides is detailed. A variety of organolithiums are added to terminal and 2,2-disubstituted epoxides in the presence of LTMP to generate alkenes in a completely regio- and highly stereoselective manner. Arylated alkenes, dienes, allylsilanes, and enynes are accessed using this procedure. The methodology is applied in the synthesis of the roller leaf moth pheromone, (3E,5Z)-dodecadienyl acetate. The corresponding reaction without LTMP has also been examined, and a study using deuterated epoxides provides insight into the mechanism. In the presence of LTMP, Grignard reagents are also shown to produce E-alkenes directly from epoxides.
Magnetic Resonance Studies of Gaseous Atomic Hydrogen at Low Temperatures (1979)

Magnetic resonance studies are reported for a low-density gas of hydrogen atoms for $4.2&lt;T&lt;77$ K. The resonance observed is between the two lowest hyperfine levels in a field of 6.5 kG, where this splitting has its minimum value (765 MHz). Information is obtained about translational diffusion through ${\mathrm{He}}^{4}$ and ${\mathrm{H}}_{2}$ buffer gases, frequency shifts and broadening due to wall collisions, and the effects of spin-exchange broadening.
Soot Modeling in Gas Turbine Combustors (1997)

A method is presented for predicting soot in gas turbine combustors. A soot formation/oxidation model due to Fairweather et al [1992] has been employed. This model has been implemented in the CONCERT code which is a fully elliptic three-dimensional (3-D) body-fitted computational fluid dynamics (CFD) code based on pressure correction techniques. The combustion model used here is based on an assumed probability density function (PDF) parameterized by the mean and variance of the mixture fraction and a β-PDF shape. In the soot modeling, two additional transport equations corresponding to the soot mass fraction and the soot number density are solved. As an initial validation, calculations were performed in a simple propane jet diffusion flame for which experimental soot concentration measurements along the centerline and along the radius at various axial downstream stations were available from the literature. Soot predictions were compared with measured data which showed reasonable agreement. Next, soot predictions were made in a 3-D model of a CF6-80LEC engine single annular combustor over a range of operating pressures and temperatures. Although the fuel in the combustor is Jet-A, the soot computations assumed propane to be the surrogate fuel. To account for this fuel change, the soot production term was increased by a factor of 10X. In addition, the oxidation term was increased by a factor of 4X to account for uncertainties in the assumed collision frequencies. The soot model was also tested against two other combustors, a CF6-80C and a CFM56-5B. Comparison of the predicted scot concentrations with measured smoke numbers showed fairly good correlation within the range of the soot model parameters studied. More work has to be performed to address several modeling issues including sensitivity to oxidation rate coefficients and scalar diffusion.
Targeting the Dark Lipid Kinase PIP4K2C with a Potent and Selective Binder and Degrader (2023)

Abstract Phosphatidylinositol 5‐phosphate 4‐kinase, type II, gamma (PIP4K2C) remains a poorly understood lipid kinase with minimal enzymatic activity but potential scaffolding roles in immune modulation and autophagy‐dependent catabolism. Achieving potent and selective agents for PIP4K2C while sparing other lipid and non‐lipid kinases has been challenging. Here, we report the discovery of the highly potent PIP4K2C binder TMX‐4102, which shows exclusive binding selectivity for PIP4K2C. Furthermore, we elaborated the PIP4K2C binder into TMX‐4153, a bivalent degrader capable of rapidly and selectively degrading endogenous PIP4K2C. Collectively, our work demonstrates that PIP4K2C is a tractable and degradable target, and that TMX‐4102 and TMX‐4153 are useful leads to further interrogate the biological roles and therapeutic potential of PIP4K2C.
Developmental Control of Apoptosis by the Immunophilin Aryl Hydrocarbon Receptor-interacting Protein (AIP) Involves Mitochondrial Import of the Survivin Protein (2011)

Survivin is a multifunctional protein with essential roles in cell division and inhibition of apoptosis, but the molecular underpinnings of its cytoprotective properties are poorly understood. Here we show that homozygous deletion of the aryl hydrocarbon receptor-interacting protein (AIP), a survivin-associated immunophilin, causes embryonic lethality in mice by embryonic day 13.5-14, increased apoptosis of Ter119(-)/CD71(-) early erythropoietic progenitors, and loss of survivin expression in its cytosolic and mitochondrial compartments in vivo. In import assays using recombinant proteins, AIP directly mediated the import of survivin to mitochondria, thus enabling its anti-apoptotic function, whereas a survivin 1-141 mutant that does not bind AIP was not imported to mitochondria and failed to inhibit apoptosis. AIP-directed mitochondrial import of survivin did not affect cell division, was independent of the organelle transmembrane potential, did not require the chaperone Heat Shock Protein 90 (Hsp90), and was inhibited by cytosolic factor(s) present in normal cells. shRNA knockdown of the mitochondrial import receptor Tom20 abolished mitochondrial import of survivin and sensitized tumor cells to apoptosis, whereas silencing of Tom70 had no effect. Therefore, an AIP-Tom20 recognition contributes to cell survival in development and cancer by mediating the mitochondrial import of survivin.
Antagonism between granulocytic maturation and deacetylase inhibitor-induced apoptosis in acute promyelocytic leukaemia cells (2014)

Our results could explain the therapeutic limitations occurring with ATRA and class I HDACi combinations. Pro-apoptotic effects caused by pan-HDAC inhibition are not blunted by ATRA-induced differentiation and may provide a clinically interesting alternative.
TLR8 and complement C5 induce cytokine release and thrombin activation in human whole blood challenged with Gram-positive bacteria (2020)

We recently showed that TLR8 is critical for the detection of Gram-positive bacteria by human monocytes. Here, we hypothesized that TLR8 and complement together regulate antibacterial responses in human blood. Anticoagulated blood was treated with selective inhibitors of TLR8 and/or complement C5, and then challenged with live Streptococcus agalactiae (Group B streptococcus, GBS), Staphylococcus aureus, or Escherichia coli. Cytokine production, plasma membrane permeability, bacterial survival, phagocytosis, and activation of coagulation was examined. GBS and S. aureus, but not E. coli, triggered TLR8-dependent production of IL-12p70, IL-1β, TNF, and IL-6 in fresh human whole blood. In purified polymorphonuclear neutrophils (PMN), GBS and S. aureus induced IL-8 release in part via TLR8, whereas PMN plasma membrane leakage and extracellular DNA levels increased independently of TLR8. TLR8 was more important than C5 for bacteria-induced production of IL-12p70, IL-1β, and TNF in blood, whereas IL-8 release was more C5 dependent. Both TLR8 and C5 induced IL-6 release and activation of prothrombin cleavage, and here their combined effects were additive. Blocking of C5 or C5aR1 attenuated phagocytosis and increased the extracellular growth of GBS in blood, whereas TLR8 inhibition neither reduced phagocytosis nor intracellular killing of GBS and S. aureus. In conclusion, TLR8 is more important than C5 for production of IL-12p70, IL-1β, and TNF upon GBS and S. aureus infection in blood, whereas C5 is central for IL-8 release and phagocytosis. Both TLR8 and C5 mediate IL-6 release and activation of coagulation during challenge with Gram-positive bacteria in blood.
Long-term stable, sub-femtosecond timing distribution via a 12-km polarization-maintaining fiber link: approaching 10^−21 link stability (2013)

Long-term stable, sub-femtosecond timing distribution over a 1.2-km polarization-maintaining (PM) fiber-optic link using balanced optical cross-correlators for link stabilization is demonstrated. Novel dispersion-compensating PM fiber was developed to construct a dispersion-slope-compensated PM link, which eliminated slow timing drifts and jumps previously induced by polarization mode dispersion in standard single-mode fiber. Numerical simulations of nonlinear pulse propagation in the fiber link confirmed potential sub-100-as timing stability for pulse energies below 70 pJ. Link operation for 16 days showed ~0.6 fs RMS timing drift and during a 3-day interval only ~0.13 fs drift, which corresponds to a stability level of 10(-21).
Percutaneous Implantation of an Entirely Intracardiac Leadless Pacemaker (2015)

The leadless cardiac pacemaker met prespecified pacing and sensing requirements in the large majority of patients. Device-related serious adverse events occurred in approximately 1 in 15 patients. (Funded by St. Jude Medical; LEADLESS II ClinicalTrials.gov number, NCT02030418.).
A Novel Positron Emission Tomography Reporter Gene/Reporter Probe for the Central Nervous System (2018)

78 Objectives: Gene therapy is limited by a lack of appropriate imaging techniques that can successfully monitor delivery/expression of the therapy. We set out to develop a novel positron emission tomography (PET) reporter gene system for monitoring gene therapy specifically within the central nervous system (CNS). In this study, we have over-expressed an isoform of pyruvate kinase (PKM2) in the CNS of mice, delivered by an associated-adeno virus (AAV9). The expression of PKM2 was imaged using [18F]DASA-23 PET. PKM2 is particularly suited as a reporter gene in the CNS as it has very low endogenous expression in the healthy brain and its corresponding reporter probe ([18F]DASA-23) has been shown to freely cross the blood brain barrier (BBB) allowing imaging in the CNS. Methods: The utility of PKM2 as a PET reporter gene was first validated in cell culture by overexpressing PKM2 in HeLa cells by transfecting with varying levels of a PKM2 containing plasmid. Following transfection, analysis by [18F]DASA-23 uptake and qPCR was performed. Moving to in vivo studies, mice were infected with AAV9 containing the PKM2 gene via stereotactic injection into one side of the brain. Dynamic small animal PET/CT imaging of [18F]DASA-23 was serially carried out over a period of 2 months to observe the increase in PKM2 expression over time. After 2 months, the mouse brains were excised for analysis of PKM2 expression, including PKM2 mRNA levels determined by qPCR, autoradiography, and immunohistochemistry (IHC) on adjacent sections of excised brains. Results: Cell culture studies showed that increasing the concentration of PKM2 containing plasmid resulted in an increase in [18F]DASA-23 uptake where plasmid concentrations of 0.625, 1.5 and 2.5 μg/mL gave 145 ± 9, 201 ± 12 and 302 ± 31 %uptake/mg protein respectively (R2=0.92, P
Design and Analysis of Copper and Aluminum Interconnects for All-Spin Logic (2014)

In this paper, a conventional spin-valve configuration combined with spin-torque-driven switching is used as an energy efficient interconnect structure for all-spin logic. Both Cu and Al interconnect materials are analyzed based on physical models for spin injection, spin transport, and magnetization dynamics. The results indicate proposed metallic interconnects dissipate less energy as compared with all-spin logic interconnects based on the nonlocal spin-valve configuration. Compared with a similar spin interconnect with an Si channel, the spin currents and injection efficiencies are predicted to be higher when a metal like Cu or Al is used due to no Schottky barrier at the interface. Because of the longer spin relaxation length (SRL) in Al as compared with Cu, the delay and energy dissipation are lower when Al is used especially at longer lengths where signal loss becomes important. While metallic spin interconnects are faster and more energy efficient in short lengths because of their smaller resistances and higher spin injection efficiencies, they are outperformed by spin interconnects with Si channels at long lengths because the SRLs in Si can be as long as many micrometers, whereas in metals they are limited to a few hundred nanometers.