gebhart/patrepeval huggingface dataset:
Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium (2007)

In 2003, severe acute respiratory syndrome coronavirus (SARS-CoV) emerged and caused over 8,000 human cases of infection and more than 700 deaths worldwide. Zoonotic SARS-CoV likely evolved to infect humans by a series of transmission events between humans and animals for sale in China. Using synthetic biology, we engineered the spike protein (S) from a civet strain, SZ16, into our epidemic strain infectious clone, creating the chimeric virus icSZ16-S, which was infectious but yielded progeny viruses incapable of propagating in vitro. After introducing a K479N mutation within the S receptor binding domain (RBD) of SZ16, the recombinant virus (icSZ16-S K479N) replicated in Vero cells but was severely debilitated in growth. The in vitro evolution of icSZ16-S K479N on human airway epithelial (HAE) cells produced two viruses (icSZ16-S K479N D8 and D22) with enhanced growth on HAE cells and on delayed brain tumor cells expressing the SARS-CoV receptor, human angiotensin I converting enzyme 2 (hACE2). The icSZ16-S K479N D8 and D22 virus RBDs contained mutations in ACE2 contact residues, Y442F and L472F, that remodeled S interactions with hACE2. Further, these viruses were neutralized by a human monoclonal antibody (MAb), S230.15, but the parent icSZ16-S K479N strain was eight times more resistant than the mutants. These data suggest that the human adaptation of zoonotic SARS-CoV strains may select for some variants that are highly susceptible to select MAbs that bind to RBDs. The epidemic, icSZ16-S K479N, and icSZ16-S K479N D22 viruses replicate similarly in the BALB/c mouse lung, highlighting the potential use of these zoonotic spike SARS-CoVs to assess vaccine or serotherapy efficacy in vivo.
A Low-Power 24-GHz Radar Transceiver for Automotive Hands-Free Trunk Opener Applications in a 0.13 µm SiGe BiCMOS Technology (2022)

This paper presents a 24-GHz radar system based on a low-power, low-noise, multichannel monolithic microwave integrated circuit (MMIC) for automotive hands-free trunk opener applications. The MMIC features two transmit (TX) and two receive (RX) channels. Each TX section features a fundamental frequency voltage controlled oscillator (VCO) with an 8-bit Digital-to-Analog converter (DAC) based tuning voltage source. A combination of a prescaler and frequency counter is used for on-chip monitoring of the transmission frequency. The TX delivers a maximum output power of +10 dBm. Two stages of variable gain amplifiers (VGA) configurable with a 5-bit DAC provide a dynamic range greater than 20 dB. Each RX section consists of a low noise amplifier (LNA) multiplexed to a single homodyne quadrature downconverter stage with a single-sideband noise figure (NFssb) lower than 8 dB and an adjustable conversion gain (CG) of upto 26 dB. The downconverted IF signals are further amplified by integrated programmable dc-coupled analog baseband (ABB) amplifiers with upto 50 dB of gain, and digitized by integrated 8-bit Analog-to-Digital (ADC) converters. The receivers integrate a dc-offset compensation circuit with upto ±200 mV. Designed in a 0.13 µm SiGe:C BiCMOS technology with fT/f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> of 250/380GHz, the chip consumes a maximum current of 150 mA from 1.8 V, and less than 75 µA in the standby mode.
Differentiation of finite element solutions to non-linear problems (2000)

Two extended numerical differentiation methods based on Green's second identity are presented. These may be used for postprocessing approximate solutions in general material distributions, including inhomogeneous and discontinuous material characteristics. The first method uses a general formulation with Green's functions and extended Poisson kernels for standard domains, while the second applies Green's functions to certain restricted, analytically known configurations. The singularities encountered in the necessary integral kernels for second derivatives are evaluated using finite part integration techniques. Both methods are illustrated by numerical experiments, and results are shown for differentiation of quasi-harmonic functions in inhomogeneous domains. Copyright © 2000 John Wiley & Sons, Ltd.
Volume rendering segmented data using 3D textures: a practical approach for intra-operative visualization (2006)

Volume rendering has high utility in visualization of segmented datasets. However, volume rendering of the segmented labels along with the original data causes undesirable intermixing/bleeding artifacts arising from interpolation at the sharp boundaries. This issue is further amplified in 3D textures based volume rendering due to the inaccessibility of the interpolation stage. We present an approach which helps minimize intermixing artifacts while maintaining the high performance of 3D texture based volume rendering - both of which are critical for intra-operative visualization. Our approach uses a 2D transfer function based classification scheme where label distinction is achieved through an encoding that generates unique gradient values for labels. This helps ensure that labelled voxels always map to distinct regions in the 2D transfer function, irrespective of interpolation. In contrast to previously reported algorithms, our algorithm does not require multiple passes for rendering and supports greater than 4 masks. It also allows for real-time modification of the colors/opacities of the segmented structures along with the original data. Additionally, these capabilities are available with minimal texture memory requirements amongst comparable algorithms. Results are presented on clinical and phantom data.
Passive millimeter-wave focal plane array (2006)

We built and tested a low-cost 8-by-8 millimeter-wave focal plane array using antenna-coupled micro-bolometers. The array consists of slot antennas coupled to nickel bolometers and was fabricated using optical lithography on high-resistivity silicon wafers. The measured noise equivalent temperature difference (NETD) of an individual element was 450 K. Simulation results corresponded with observed device performance. An improved design was then implemented using a square spiral antenna. We discuss the fabrication of this type of array element, including some modeling results, and present the methods and results of our measurements.
Numerical and Experimental Analysis of Single Crystal Diamond Schottky Barrier Diodes (2005)

We present our findings on the numerical and experimental analysis of diamond Schottky Barrier diodes (SBDs) comprising of intrinsic single crystal (SC) chemical vapour deposited (CVD) diamond layers grown on highly boron doped substrates also grown by CVD. Good correlation with experimental results has been achieved through numerical modelling that has incorporated previously reported data on transport physics and carrier activation. With our numerical model, we are able to match to within 12 to 15% of the measured forward characteristics of fabricated diamond SBDs up to 2 V in excess of the turn on voltage, for two different Schottky metals.
Optically Controlled Signal Amplification for DNA Computation (2015)

The hybridization chain reaction (HCR) and fuel-catalyst cycles have been applied to address the problem of signal amplification in DNA-based computation circuits. While they function efficiently, these signal amplifiers cannot be switched ON or OFF quickly and noninvasively. To overcome these limitations, a light-activated initiator strand for the HCR, which enabled fast optical OFF → ON switching, was developed. Similarly, when a light-activated version of the catalyst strand or the inhibitor strand of a fuel-catalyst cycle was applied, the cycle could be optically switched from OFF → ON or ON → OFF, respectively. To move the capabilities of these devices beyond solution-based operations, the components were embedded in agarose gels. Irradiation with customizable light patterns and at different time points demonstrated both spatial and temporal control. The addition of a translator gate enabled a spatially activated signal to travel along a predefined path, akin to a chemical wire. Overall, the addition of small light-cleavable photocaging groups to DNA signal amplification circuits enabled conditional control as well as fast photocontrol of signal amplification.
Re: Carvedilol Efficiently Protects Kidneys without Affecting the Antitumor Efficacy of Cisplatin in Mice (2014)

No AccessJournal of UrologyInvestigative Urology1 Aug 2014Re: Carvedilol Efficiently Protects Kidneys without Affecting the Antitumor Efficacy of Cisplatin in Mice Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2014.05.032AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Carvedilol Efficiently Protects Kidneys without Affecting the Antitumor Efficacy of Cisplatin in Mice." The Journal of Urology, 192(2), p. 614 © 2014 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 192Issue 2August 2014Page: 614Supplementary Materials Advertisement Copyright & Permissions© 2014 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
Fluoroquinolone antibacterial eye drops: effects on normal human corneal epithelium, stroma, and endothelium (2010)

Our study results suggest that as with LVFX, MFLX used in a normal clinical setting is unlikely to cause any obvious adverse effects on human normal cornea.
The capacity region of a class of 3-receiver broadcast channels with degraded message sets (2008)

Körner and Marton established the capacity region for the 2-receiver broadcast channel with degraded message sets. Recent results and conjectures suggest that a straightforward extension of the Körner-Marton region to more than 2 receivers is optimal. This paper shows that this is not the case. We establish the capacity region for a class of 3-receiver broadcast channels with 2 degraded message sets and show that it can be strictly larger than the straightforward extension of the Körner-Marton region. The key new idea is indirect decoding, whereby a receiver who cannot directly decode a cloud center, finds it indirectly by decoding satellite codewords. This idea is then used to establish new inner bounds on the capacity region of the general 3-receiver broadcast channel with 2 and 3 degraded message sets. These bounds are tight for some nontrivial cases.
Analysis of multiple access interference in synchronous downlink CDMA systems with random signature sequences in AWGN and fading environments (2007)

In this work, exact analysis of the multiple access interference (MAI) for synchronous downlink CDMA systems is carried out for BPSK signals with random signature sequences in both additive white Gaussian (AWGN) noise and different fading environments, namely Nakagami and Rician. Two different scenarios are considered: one with equal transmitted powers while the other considers the case of unequal transmitted power. For both cases, the exact probability density function (pdf) of MAI plus noise is derived. Finally, a number of simulation results are presented to verify our theoretical derivations.
PRDM1/BLIMP1: a tumor suppressor gene in B and T cell lymphomas (2014)

The gene encoding the human BLIMP1, prdm1, is located on chromosome 6q21, a locus frequently deleted in lymphoid tumors. BLIMP1 is able to silence its target genes in a context-dependent manner through different mechanisms. BLIMP1 is expressed in both B and T cells, in which it plays important functions. In B cells, BLIMP1 acts as the master regulator of plasma cell differentiation, repressed by BCL6 and repressing both BCL6 and PAX5. In T cells, BLIMP1 is a critical factor for most terminal effector cell differentiation in both CD4+ and CD8+ T cells. BLIMP1 is frequently inactivated in a variety of lymphomas, including diffuse large B cell lymphomas, Natural Killer cell lymphoma and anaplastic large T cell lymphoma. In this review, we will summarize the role of BLIMP1 in normal cells, focusing on lymphoid cells, and on its function as tumor suppressor gene in lymphomas.
Excimer laser-induced chemical vapor deposition of titanium silicide (1985)

A pulsed ArF excimer laser has been used to deposit thin conductive films of titanium silicide on silicon and silicon oxide substrates. The films are deposited from a gas mixture of titanium tetrachloride and silane by initiating photochemical reactions near the heated substrate. The resistivity, composition, crystal structure, and morphology of the films vary as a function of gas composition and substrate temperature. Films deposited at 400 °C, with SiH4/TiCl4 mole ratios of ∼2, have resistivities of 300 μΩ cm, which drop to 20–30 μΩ cm on annealing at 650–700 °C. At higher deposition temperatures (450–550 °C) the films have resistivities of ∼110 μΩ cm and show similar annealing behavior. The as-deposited films are a mixture of amorphous and a metastable Ti-Si crystalline phase. On annealing they convert to polycrystalline TiSi2. Films deposited at 400–450 °C are smooth and show conformal step coverage. The film roughness increases at higher deposition temperatures.
Spectral Purity Transfer for High Performance Strontium Lattice Clocks (2018)

We investigate the spectral purity transfer of highly stable lasers from 194 THz to 429 THz using optical frequency combs. In a first measurement, the purity transfer through two identical ultra-low-noise frequency combs is assessed. In a second measurement, two independently stabilized lasers at the two frequency regions are compared using simultaneously a frequency comb in transfer-oscillator mode and an optically phase locked ultra-low-noise frequency comb. The measurement reveals the relative cavity drift and the agreement of the two transfer methods.
Convolutional Networks for Image Processing by Coupled Oscillator Arrays (2014)

A coupled oscillator array is shown to approximate convolutions with Gabor filters for image processing tasks. Pixelated image fragments and filter functions are converted to voltages, differenced, and input into a corresponding array of weakly coupled Voltage Controlled Oscillators (VCOs). This is referred to as Frequency Shift Keying (FSK). Upon synchronization of the array, the common node amplitude provides a metric for the degree of match between the image fragment and the filter function. The optimal oscillator parameters for synchronization are determined and favor a moderate value of the Q-factor.
When intuition fails in assessing conditional risks: the example of the frog riddle (2017)

Recently, the educational initiative TED-Ed has published a popular brain teaser coined the 'frog riddle', which illustrates non-intuitive implications of conditional probabilities. In its intended form, the frog riddle is a reformulation of the classic boy-girl paradox. However, the authors alter the narrative of the riddle in a form, that subtly changes the way information is conveyed. The presented solution, unfortunately, does not take this point into full account, and as a consequence, lacks consistency in the sense that different parts of the problem are treated on unequal footing. We here review, how the mechanism of receiving information matters, and why this is exactly the reason that such kind of problems challenge intuitive thinking. Subsequently, we present a generalized solution, that accounts for the above difficulties, and preserves full logical consistency. Eventually, the relation to the boy-girl paradox is discussed.
Paleoclimatic variability inferred from the spectral analysis of Greenland and Antarctic ice‐core data (1997)

Paleoclimate variations occur at various time scales, between a few centuries for the Heinrich events and several hundreds of millenia for the glacial to interglacial variations. The recent ice cores from Greenland (Greenland Ice Core Project and Greenland Ice Sheet Project 2) and Antarctica (Vostok) span at least one glacial oscillation and provide many opportunities to investigate climate variations with a very fine resolution. The joint study of cores from both hemispheres allows us to distinguish between the sources of variability and helps to propose mechanisms of variations for the different time scales involved. The climate proxies we analyze are inferred from δ 18 O and δD for temperature and chemical species (such as calcium) for the joint behavior of the major ions in the atmosphere, which yield an estimate of the polar circulation index. Those data provide time series of climatic variables from which we extract the information on the dynamics of the underlying system. We used several independent spectral analysis techniques, to reduce the possibility of spurious results. Those methods encompass the multitaper spectral analysis, singular‐spectrum analysis, maximum entropy method, principal component analysis, minimum bias spectral estimates, and digital filter reconstructions. Our results show some differences between the two hemispheres in the slow variability associated with the astronomical forcing. Common features found in the three ice‐core records occur on shorter periods, between 1 and 7 kyr. The Holocene also shows recurrent common patterns between Greenland and Antarctica. We propose and discuss mechanisms to explain such behavior.
Midterm Results of Porous Tantalum Femoral Cones in Revision Total Knee Arthroplasty (2016)

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Botulinum toxin: from menace to medicine (2007)

The neurotoxins produced by the bacterium Clostridium botulinum that cause botulism are the most potent acute toxins known. There is no known cure for the flaccid muscular paralysis of botulism and for many people the disease evokes an emotive and fearful view of the toxins. Although rare, botulism is usually encountered as a food-borne disease that results from eating food contaminated with pre-formed toxin. Wound botulism and infant botulism are two other forms of the disease, although unlike food-borne botulism, these intoxications result from direct infection with the bacterium. The incidence of wound botulism has increased in recent years in drug users who inject heroin; infant botulism is now the most common form of the disease reported in the USA. Whilst these various forms of acquired botulism are frightening enough prospects, the toxins are now seen in the even more sinister context of use in weapons of biological warfare or bio-terrorism.
Development of High-Temperature, High-Power, High-Efficiency, High-Voltage Converters Using Silicon Carbide (SiC) Delivery Order 0003: SiC High Voltage Converters, N-Type Ohmic Contract Development for SiC Power Devices (2006)

The durability and reliability of metal-semiconductor contacts are two of the main factors limiting the operational high-temperature limits of SiC electronic devices. To date, nickel (Ni) has been the most widely used metal for ohmic contacts to n-type SiC. The way to make smooth Ni-silicide ? SiC interfaces and silicide top surfaces is important for producing uniformly low contact resistances to achieve device operation at high-current levels without hot spot formation and contact degradation. For as-deposited single Ni thin layers, agglomeration of Ni-silicide after annealing can happen depending on the conditions of deposition and thermal annealing processes. This is mainly due to the residual stress on the Ni films after deposition on SiC with a significantly lower coefficient of thermal expansion. Typically, an additional stress reduction layer, such as titanium, is deposition on top of the Ni thin contact film to prevent silicide agglomeration. The objective of this Delivery Order Task was to study and develop a process to produce robust, smooth ohmic contact, with low contact resistivity, to n-type SiC for high power, high temperature, and harsh radiation environments.
Authors’ Reply to “Comments on ‘Design of Highly Efficient Broadband Class-E Power Amplifier Using Synthesized Low-Pass Matching Networks”’ (2016)

The authors appreciate the comments made by Cheng <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">et al.</i> <xref ref-type="bibr" rid="ref1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1]</xref> that point out an error in <xref ref-type="bibr" rid="ref2" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[2, eq. (11)]</xref> . In <xref ref-type="bibr" rid="ref2" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[2]</xref> , this equation was formed to transform the shunt lumped capacitors into distributed representation with suspended open-ended transmission-lines. As discussed in <xref ref-type="bibr" rid="ref1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[1]</xref> , the expression of <xref ref-type="bibr" rid="ref2" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">[2, eq. (11)]</xref> should be corrected to
Targeting Bromodomains in Myeloma (2012)

Abstract Abstract SCI-6 In cancer, epigenetic proteins are among the most promising and intently pursued targets in drug discovery. This relates to the growing appreciation that cancer growth pathways are centrally influenced by proteins that modify chromatin. Already, inhibitors of DNA methyltransferases and histone deacetylases have demonstrated substantial clinical efficacy, leading to regulatory approval for use in hematologic malignancies. These events have triggered intense competition to develop inhibitors of the chromatin-modifying enzymes known as epigenetic “writers” and “erasers.” Perhaps owing to perceptions regarding the feasibility of targeting protein-protein interactions, small-molecule inhibitors of chromatin-binding modules or epigenetic “readers” have received considerably less attention. Recently, we reported the first potent small-molecule inhibitor of human bromodomains, JQ1, which exhibits selectivity for the BET family of bromodomain-containing transcriptional coactivators. Of broad relevance to cancer, we demonstrated that c-Myc expression is critically dependent on BRD4 function and localization to discrete upstream regulatory regions. Exposure of cancer cells to JQ1 prompts immediate downregulation of c-Myc expression, leading to suppression of a transcriptional program associated with proliferation, survival, and metabolic adaptation. In translational models of MYC-dependent hematologic malignancies, in particular multiple myeloma, the efficacy of JQ1 treatment establishes a mechanistic rationale for the leveraged clinical development of drug-like JQ1 derivatives. Toward this objective, we have completed chemical optimization of novel, drug-like inhibitors of BET bromodomains as reagents capable of supporting human clinical investigation. This research has established the feasibility of inhibiting epigenetic reader proteins with efficient, cell-permeable small molecules. In addition, we have developed a high-throughput platform for modeling mechanism-based, drug-drug combinations to achieve synergy in translational model systems of multiple myeloma. In support of an open-innovation model of chemical biology, we have created a chemical probe allowing the broad study of chromatin biology, which has already been provided to more than 350 academic, governmental, and industrial laboratories worldwide. Together, we have rapidly identified mechanism-based opportunities for clinical translation in cancer. Disclosures: Bradner: SHAPE Pharmaceuticals: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Acetylon Pharmaceuticals: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Tensha Therapeutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees.