gebhart/patrepeval huggingface dataset:
Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells (2011)

Long interspersed element-1 (L1) retrotransposons compose ∼20% of the mammalian genome, and ongoing L1 retrotransposition events can impact genetic diversity by various mechanisms. Previous studies have demonstrated that endogenous L1 retrotransposition can occur in the germ line and during early embryonic development. In addition, recent data indicate that engineered human L1s can undergo somatic retrotransposition in human neural progenitor cells and that an increase in human-specific L1 DNA content can be detected in the brains of normal controls, as well as in Rett syndrome patients. Here, we demonstrate an increase in the retrotransposition efficiency of engineered human L1s in cells that lack or contain severely reduced levels of ataxia telangiectasia mutated, a serine/threonine kinase involved in DNA damage signaling and neurodegenerative disease. We demonstrate that the increase in L1 retrotransposition in ataxia telangiectasia mutated-deficient cells most likely occurs by conventional target-site primed reverse transcription and generate either longer, or perhaps more, L1 retrotransposition events per cell. Finally, we provide evidence suggesting an increase in human-specific L1 DNA copy number in postmortem brain tissue derived from ataxia telangiectasia patients compared with healthy controls. Together, these data suggest that cellular proteins involved in the DNA damage response may modulate L1 retrotransposition.
Design of variable magnetization pattern machines for dynamic changes in the back-EMF waveform (2017)

Variable magnetization pattern machines (VMPMs) capable of dynamic changes in the magnetization pattern and magnitude are discussed in this paper. These machines can behave like brushless DC machines if they have a uniform magnetization pattern. If the magnetization pattern on the permanent magnet is shaped to be sinusoidal through a controlled demagnetizing process, they could behave like brushless AC machines. This paper presents the fundamental principles and the design methods of VMPMs. The design methods including parametric analysis and the overall results are evaluated using finite element analysis (FEA).
Lifetime Maximization for Joint Estimation in Wireless Sensor Networks (2006)

We consider the lifetime maximization problem for joint estimation in wireless sensor network. In the joint estimation problem, each sensor observes a noise-corrupted version of a physical quantity, then amplifies and forwards the observation to the destination (fusion center) through a wireless channel. The fusion center combines the data and constructs a joint estimate. The sensors may communicate with the destination through either orthogonal or shared channels. We develop algorithms that jointly determine the transmit power of sensors as a function of sensor measurement noises, wireless channel coefficients, and the available battery power at sensors. The objective of the algorithm is to maximize the lifetime of the network, while a certain quality of estimation at the fusion center is maintained throughout the lifetime of the network. It is observed that the present algorithm behaves differently compared to minimum-transmit-power strategies, and performs better in terms of the longevity of the network.
Effect of time diversity in hybrid ARQ considering space and path diversity for VSF-OFCDM downlink broadband wireless access (2005)

The paper investigates the effect of time diversity derived from hybrid automatic repeat request (ARQ) with packet combining considering space and path diversity schemes on variable spreading factor orthogonal frequency and code division multiplexing (VSF-OFCDM) packet wireless access in a downlink broadband multipath fading channel based on laboratory and field experiments. The results show that, for a fixed modulation and channel coding scheme (MCS), time diversity derived from hybrid ARQ is effective in reducing the required received signal-to-interference-plus-noise power ratio (SINR) according to an increase in the number of transmissions, M, up to 10, even when the diversity effects are obtained through two-branch antenna diversity reception and path diversity by a number of multipaths greater than 12 observed in a real fading channel. Meanwhile, in combined use with the adaptive modulation and channel coding (AMC) scheme associated with space and path diversity, we clarify that the gain derived through time diversity is almost saturated at M=4 in chase combining and M=2 in incremental redundancy, since the improvement in the residual packet error rate (PER) obtained through time diversity becomes small owing to the low PER in the initial packet transmission arising from appropriately selecting the optimum MCS in AMC.
Foveated Thermal Computational Imaging in the Wild Using All-Silicon Meta-Optics (2022)

Foveated imaging provides a better tradeoff between situational awareness (field of view) and resolution and is critical in long-wavelength infrared regimes because of the size, weight, power, and cost of thermal sensors. We demonstrate computational foveated imaging by exploiting the ability of a meta-optical frontend to discriminate between different polarization states and a computational backend to reconstruct the captured image/video. The frontend is a three-element optic: the first element which we call the "foveal" element is a metalens that focuses s-polarized light at a distance of $f_1$ without affecting the p-polarized light; the second element which we call the "perifoveal" element is another metalens that focuses p-polarized light at a distance of $f_2$ without affecting the s-polarized light. The third element is a freely rotating polarizer that dynamically changes the mixing ratios between the two polarization states. Both the foveal element (focal length = 150mm; diameter = 75mm), and the perifoveal element (focal length = 25mm; diameter = 25mm) were fabricated as polarization-sensitive, all-silicon, meta surfaces resulting in a large-aperture, 1:6 foveal expansion, thermal imaging capability. A computational backend then utilizes a deep image prior to separate the resultant multiplexed image or video into a foveated image consisting of a high-resolution center and a lower-resolution large field of view context. We build a first-of-its-kind prototype system and demonstrate 12 frames per second real-time, thermal, foveated image, and video capture in the wild.
Optical Fiber Sensor-Fused Additive Manufacturing and Its Applications in Residual Stress Measurements in Titanium Parts (2016)

This paper reports optical fiber embedding in titanium parts using additive manufacturing process. Residual stress incurred during laser processing on the sensor-embedded parts was measured using Rayleigh scattering distributed sensing scheme with 5-mm spatial resolutions.
Transcatheter Therapies for Tricuspid Valve Failure (2015)

Journal of Structural Heart Disease is the official journal of the PICS Foundation, the organization that runs the largest structural/congenital course of its kind “PICS/AICS” [Pediatric and Adult Interventional Cardiac Symposium,” which will be devoted to all structural and congenital heart diseases.
Discovery of Novel Class of Histone Deacetylase Inhibitors as Anticancer Agents (2021)

Abstract Selective inhibition of histone deacetylases (HDACs) is a paramount strategy in the field of anticancer lead drug development. However, the lack of selectivity among these isozymes and the adverse side effects that arise from the inhibition of certain HDACs limits their clinical applications. Phenotypic screening of an in-house pilot library of about 70 small molecules against various HDAC isozymes led to the discovery of five compounds which displayed varying degrees of HDAC isozyme selectivity. The anticancer activities of these molecules were validated using various biological assays including transcriptomic studies. Compounds 15 , 14 , and 19 possessed selective inhibitory activity against HDAC5, while 28 displayed selective inhibition of HDAC1 and HDAC2. Compound 22 was found to be a selective inhibitor for HDAC3 and HDAC9. In the MCF7 breast cancer cell line the new compounds showed potent anti-proliferative activity, increased acetylation of histones and induced cells apoptosis. The new compounds’ apoptotic effects were validated through the upregulation of caspases3 and 7 and downregulation of C-MYC, BCL2, BCL3 and NFĸB genes. Furthermore, the new compounds arrested cell cycle at different phases, which was confirmed through downregulation of the CDK1, 2, 4, 6, E2F1 and RB1 proteins. Together our findings provide the foundation for the development of new chemical probes as potential lead drug candidates for the treatment of cancer.
Molecular Diagnosis of a BRAF Papillary Thyroid Carcinoma with Multiple Chromosome Abnormalities and Rare Adrenal and Hypothalamic Metastases (2006)

Unusual metastases may be associated with multiple molecular and cytogenetic abnormalities. Thus, molecular and cell-biological studies can allow otherwise difficult thyroid tumor diagnosis and may be used for targeted, individualized selection of potential treatments.
Optimization of Automotive Wheel Lugnut Tightening (2007)

&lt;div class="htmlview paragraph"&gt;An experimental procedure is presented in order to study the simultaneous tightening of automotive wheel lugnuts and to enhance the clamp load uniformity and repeatability. Two different tightening strategies are investigated, namely, the torque-only and the torque-angle control methods. The effect of the tightening speed, initial threshold torque level, and the torque steps is investigated. The study is conducted on two different wheel materials, namely, steel and aluminum. Lugnut tightening is accomplished by using a five-spindle DC fastening system in either a torque-only or torque-angle control mode. The achieved clamp load in each lugnut is monitored by using inserted force washers (load cells). The torque tension data is analyzed and discussed for both steel and aluminum wheels, in order to select the optimum tightening process that achieves the desired uniform clamp load in the wheel lugnuts assembly.&lt;/div&gt;
Driving low-power wearable systems with an adaptively-controlled foot-strike scavenging platform (2013)

We explore the use of Dielectric Elastomer (DE) micro-generators as a means to scavenge energy from foot-strikes and power wearable systems. While they exhibit large energy densities, DEs must be closely controlled to maximize the energy they transduce. Towards this end, we propose a DE micro-generator array configuration that enhances transduction efficiency, and the use of foot pressure sensors to realize accurate control of the individual DEs. Statistical techniques are applied to customize performance for a user's gait and enable energy-optimized adaptive online control of the system. Simulations based on experimentally collected foot pressure datasets, empirical characterization of DE mechanical behavior and a detailed model of DE electrical behavior show that the proposed system can achieve between 45 and 66mJ per stride.
Apolipoprotein B mediates the capacity of low density lipoprotein to suppress neutrophil stimulation by particulates. (1986)

Low density lipoprotein (LDL) inhibits phagocytosis of certain negatively charged particulates and also inhibits subsequent cellular secretory and oxidative responses to these particulates. In the present work, we have defined the structural features of LDL involved in this activity. Starch-heptane extraction depleted greater than 95% of neutral lipids but had little effect on the capacity of LDL to inhibit monosodium urate crystal- or polystyrene latex bead-induced neutrophil chemiluminescence (CL). Liposomes containing gamma-palmitoyl-beta-oleoylphosphatidylcholine (PC) with unesterified cholesterol (PC:cholesterol = 2:1), PC and sphingomyelin (PC:sphingomyelin = 2.3:1), or PC alone lacked the capacity to inhibit urate-induced CL. However, incorporation of apoB-100 into liposomes via cholate dialysis rendered them nearly as inhibitory for urate-induced neutrophil CL as LDL on a protein weight basis. Moreover, delipidated apoB-100, containing less than 3% residual phospholipid, inhibited neutrophil responses to urate crystals or latex beads (degranulation and superoxide anion release) in a stimulus-specific manner. Modifications of the lysine residues of apoB (e.g. acetylation) reduced both the capacity of LDL to inhibit urate crystal-induced CL and to bind to urate crystals. The effects of apoB lysine residue modification were reversible, proportional to the extent of modification, and were not attributable to alteration of the net charge of apoB. Thus, the apoB-100 of LDL both mediates and shares the capacity of native LDL to inhibit certain neutrophil responses to particulates.
Oxygen Microscopy by Two‐Photon‐Excited Phosphorescence (2008)

High-resolution images of oxygen distributions in microheterogeneous samples are obtained by two-photon laser scanning microscopy (2P LSM), using a newly developed dendritic nanoprobe with internally enhanced two-photon absorption (2PA) cross-section. In this probe, energy is harvested by a 2PA antenna, which passes excitation onto a phosphorescent metalloporphyrin via intramolecular energy transfer. The 2P LSM allows sectioning of oxygen gradients with near diffraction-limited resolution, and lifetime-based acquisition eliminates dependence on the local probe concentration. The technique is validated on objects with a priori known oxygen distributions and applied to imaging of pO(2) in cells.
Dual-Layer Light Source with Textured Lighting Gel (2022)

We propose a new light source representation to intuitively model complicated lighting effects with simple user interactions. Our representation uses two layers; an emissive layer which is a traditional diffuse area light source with a constant emission, and a lighting gel layer which introduces variations to the emission. The lighting gel layer is mapped with a texture for colored shadows without modeling a 3D scene. The two layers are transformed independently to cast the texture with different effects. To cast lighting on a planar canvas in 2D design, the proposed light source can be created and edited in the 2D canvas directly, without switching to 3D world space.
CMOS Technology for Wireless Applications (2017)

Design in complementary metal oxide semiconductor (CMOS) is considerably more challenging than with bipolar transistors. Semiconductor technologies are usually referred to by the lithography node, designated by its minimum feature length, for example, 90 nm CMOS. Bipolar transistors, particularly silicon germanium heterostructure bipolar transistors (HBT) implemented in bipolar/CMOS (BiCMOS) technologies, have dominated the market in chip designs for wireless applications. The chapter introduces a model methodology for capturing process variation in scaled CMOS technologies. It considers potential cost reductions when migrating applications from BiCMOS to CMOS. The single most compelling argument for using CMOS to implement wireless applications is integration density. It is likely that competitive pressure will dictate that wireless applications, which can be implemented with acceptable performance in CMOS, will be implemented in CMOS. Relative process simplicity and high manufacturing capacity contribute to lower die cost of CMOS when compared to BiCMOS or compound semiconductor technologies.
Data from Inhibition of Bromodomain Proteins for the Treatment of Human Diffuse Large B-cell Lymphoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Approximately 50% of patients with diffuse large B-cell lymphoma (DLBCL) enter long-term remission after standard chemotherapy. Patients with DLBCL who do not respond to chemotherapy have few treatment options. There remains a critical need to identify effective and targeted therapeutics for DLBCL.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Recent studies have highlighted the incidence of increased c-MYC protein in DLBCL and the correlation between high levels of c-MYC protein and poor survival prognosis of patients with DLBCL, suggesting that c-MYC is a compelling target for DLBCL therapy. The small molecule JQ1 suppresses &lt;i&gt;c-MYC&lt;/i&gt; expression through inhibition of the bromodomain and extra-terminal (BET) family of bromodomain proteins. We investigated whether JQ1 can inhibit proliferation of DLBCL cells in culture and xenograft models &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We show that JQ1 at nanomolar concentrations efficiently inhibited proliferation of human DLBCL cells in a dose-dependent manner regardless of their molecular subtypes, suggesting a broad effect of JQ1 in DLBCL. The initial G&lt;sub&gt;1&lt;/sub&gt; arrest induced by JQ1 treatment in DLBCL cells was followed by either apoptosis or senescence. The expression of &lt;i&gt;c-MYC&lt;/i&gt; was suppressed as a result of JQ1 treatment from the natural, chromosomally translocated, or amplified loci. Furthermore, JQ1 treatment significantly suppressed growth of DLBCL cells engrafted in mice and improved survival of engrafted mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; Our results demonstrate that inhibition of the BET family of bromodomain proteins by JQ1 has potential clinical use in the treatment of DLBCL. &lt;i&gt;Clin Cancer Res; 21(1); 113–22. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Mottok and Gascoyne, p. 4&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Correspondence (1994)

Jules Stein Eye Institute University of California at Los Angeles (Lewis) Stanford Medical Center Stanford, California (Blumenkranz) Cornell University New York, New York (Chang)
Qualifying 5G SA for L4 Automated Vehicles in a Multi-PLMN Experimental Testbed (2021)

National roaming, multi-SIM and edge computing constitute key 5G technologies for the cooperative perception and remote driving of L4 (automated) vehicles. To that end, this article reports our progress to trial these technologies at the multi-PLMN experimental 5G SA testbed of Aalto University, Finland. Overall, the objective is to qualify 5G as a core connectivity for connected, cooperative and automated mobility.
A Novel Micro-CT Based Anatomically Accurate Finite Element Model for Simulation-Aided Assessment of Mitral Valve Repairs (2013)

Many surgeons have come to view mitral valve (MV) repair as the treatment of choice in patients with mitral regurgitation (MR) [1]. According to recent long-term studies, the recurrence of significant MR after repair may be much higher than previously believed, particularly in patients with (ischemic mitral regurgitation) IMR [2]. We hypothesize that the restoration of homeostatic normal MV leaflet tissue stress in IMR repair techniques ultimately leads to improved repair durability. Therefore, the objective of this study is to develop a novel micro-anatomically accurate 3D finite element (FE) model that incorporates detailed collagen fiber architecture, accurate constitutive models, and micro-anatomically realistic valvular geometry to investigate the functional mitral valve and to aid in the assessment of the mitral valve repairs, especially the linking between the interstitial cellular deformations at the cellular level, the mechanobiological behaviors at the tissue level and the organ level mechanical responses as normal and repaired mitral valves maintaining their homeostatic state.
Special Issue on Nonlinear-Optic Waveguide Materials and Devices. Potential of Nonlinear Optical Waveguides. (1993)

Owing to the high density photon confinement nature of optical waveguide, it is expected that the nonlinear-optical waveguide devices gain improved performance over the bulk counterparts. The potential and the problem of useful nonlinear devices are discussed with special focus on (1) nonlinear-optical materials, (2) all optical switching devices, and (3) nonlinear optical signal conversion systems. It is concluded that these devices will open a profound way of ultrafast optical signal processing, if a good combination of material, device and system technologies is established.
Paper-Based Potentiometric Ion Sensing (2014)

This paper describes the design and fabrication of ion-sensing electrochemical paper-based analytical devices (EPADs) in which a miniaturized paper reference electrode is integrated with a small ion-selective paper electrode (ISPE) for potentiometric measurements. Ion-sensing EPADs use printed wax barriers to define electrochemical sample and reference zones. Single-layer EPADs for sensing of chloride ions include wax-defined sample and reference zones that each incorporate a Ag/AgCl electrode. In EPADs developed for other electrolytes (potassium, sodium, and calcium ions), a PVC-based ion-selective membrane is added to separate the sample zone from a paper indicator electrode. After the addition of a small volume (less than 10 μL) of sample and reference solutions to different zones, ion-sensing EPADs exhibit a linear response, over 3 orders of magnitude, in ranges of electrolyte concentrations that are relevant to a variety of applications, with a slope close to the theoretical value (59.2/z mV). Ion-selective EPADs provide a portable, inexpensive, and disposable way of measuring concentrations of electrolyte ions in aqueous solutions.
The use of laser annealing to reduce parasitic series resistances in MOS devices (2002)

As the size of metal-oxide-semiconductor (MOS) devices continues to be scaled aggressively, new technologies must be developed in order to meet future device requirements. One area that faces serious challenges involves reducing the parasitic series resistances between the channel and the contact. In this work, we demonstrate that laser annealing is a potential alternative annealing technique to form ultra-shallow, low resistivity junctions. This method benefits from the ability to create abrupt, uniform dopant profiles with active concentrations that can exceed the equilibrium solubility limits. We also address some of the issues preventing its adaptation into the semiconductor-processing scheme, including the annealing of patterned structures, dopant deactivation and junction depth control.
Determination of Threshold Failure Levels of Semiconductor Diodes and Transistors Due to Pulse Voltages (1968)

Theoretical predictions of circuit failure in an Electromagnetic Pulse (EMP) environment require a knowledge of failure levels for each component of the circuit due to surge voltages or currents. For most circuits, the semiconductor devices are the weakest elements with respect to such failure. This paper presents the results of an extensive experimental program to determine pulse power failure levels of semiconductor junctions. Approximately 80 different types of silicon diodes and transistors were studied with variations in junction areas from 10-4to 10-1 cm2 and with widely varying junction geometries. Power levels of up to two kilowatts, with time durations of 0.1 to 20 microseconds, were applied to semiconductor junctions in both forward and reverse polarity modes. A semi-empirical formula, based on experimental data and on a simple thermal failure model is given. From the formula one can make order-of-magnitude estimates of the failure level as a function of pulse length for many silicon diodes or transistors whose junction area is known.