gebhart/patrepeval huggingface dataset:
Joint Source-Channel Coding at the Application Layer (2009)

The multicasting of an independent and identically distributed Gaussian source over a binary erasure broadcast channel is considered. This model applies to a one-to-many transmission scenario in which some mechanism at the physical layer delivers information packets with losses represented by erasures, and users are subject to different erasure probabilities. The reconstruction signal-to-noise ratio (SNR) region achieved by concatenating a multiresolution source code with a broadcast channel code is characterized and four convex optimization problems corresponding to different performance criteria are solved. Each problem defines a particular operating point on the dominant face of the SNR region. Layered joint source-channel codes are constructed based on the concatenation of embedded scalar quantizers with binary raptor encoders. The proposed schemes are shown to operate very close to the theoretical optimum.
Novel and Selective α<sub>v</sub>β<sub>3</sub> Receptor Peptide Antagonist:  Design, Synthesis, and Biological Behavior (2006)

Among RGD-dependent integrins, the alpha(v)beta3 receptor has recently received increasing attention as a therapeutic target because of its critical role in tumor-induced angiogenesis and metastasis formation. Here, we describe a new peptide antagonist of alpha(v)beta3 receptor, designed on the basis of the crystal structure of integrin alpha(v)beta3 in complex with c(RGDf[NMe]V) and the NMR structure of echistatin. Cell adhesion assays have demonstrated that the peptide is a potent and selective antagonist of the alpha(v)beta3 receptor.
Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7) (2012)

The pluripotency factor Lin28 recruits a 3' terminal uridylyl transferase (TUTase) to selectively block let-7 microRNA biogenesis in undifferentiated cells. Zcchc11 (TUTase4/TUT4) was previously identified as an enzyme responsible for Lin28-mediated pre-let-7 uridylation and control of let-7 expression. Here we investigate the protein and RNA determinants for this interaction. Biochemical dissection and reconstitution assays reveal the TUTase domains necessary and sufficient for Lin28-enhanced pre-let-7 uridylation. A single C2H2-type zinc finger domain of Zcchc11 was found to be responsible for the functional interaction with Lin28. We identify Zcchc6 (TUTase7) as an alternative TUTase that functions with Lin28 in vitro, and accordingly, we find Zcchc11 and Zcchc6 redundantly control let-7 biogenesis in embryonic stem cells. Our study indicates that Lin28 uses two different TUTases to control let-7 expression and has important implications for stem cell biology as well as cancer.
Ultra‐broadband photodetectors based on epitaxial graphene quantum dots (2018)

Abstract Graphene is an ideal material for hot‐electron bolometers due to its low heat capacity and weak electron‐phonon coupling. Nanostructuring graphene with quantum‐dot constrictions yields detectors of electromagnetic radiation with extraordinarily high intrinsic responsivity, higher than 1×10 9 V W −1 at 3 K. The sensing mechanism is bolometric in nature: the quantum confinement gap causes a strong dependence of the electrical resistance on the electron temperature. Here, we show that this quantum confinement gap does not impose a limitation on the photon energy for light detection and these quantum‐dot bolometers work in a very broad spectral range, from terahertz through telecom to ultraviolet radiation, with responsivity independent of wavelength. We also measure the power dependence of the response. Although the responsivity decreases with increasing power, it stays higher than 1×10 8 V W −1 in a wide range of absorbed power, from 1 pW to 0.4 nW.
Main Immunogenic Region Structure Promotes Binding of Conformation-Dependent Myasthenia Gravis Autoantibodies, Nicotinic Acetylcholine Receptor Conformation Maturation, and Agonist Sensitivity (2009)

The main immunogenic region (MIR) is a conformation-dependent region at the extracellular apex of alpha1 subunits of muscle nicotinic acetylcholine receptor (AChR) that is the target of half or more of the autoantibodies to muscle AChRs in human myasthenia gravis and rat experimental autoimmune myasthenia gravis. By making chimeras of human alpha1 subunits with alpha7 subunits, both MIR epitopes recognized by rat mAbs and by the patient-derived human mAb 637 to the MIR were determined to consist of two discontiguous sequences, which are adjacent only in the native conformation. The MIR, including loop alpha1 67-76 in combination with the N-terminal alpha helix alpha1 1-14, conferred high-affinity binding for most rat mAbs to the MIR. However, an additional sequence corresponding to alpha1 15-32 was required for high-affinity binding of human mAb 637. A water soluble chimera of Aplysia acetylcholine binding protein with the same alpha1 MIR sequences substituted was recognized by a majority of human, feline, and canine myasthenia gravis sera. The presence of the alpha1 MIR sequences in alpha1/alpha7 chimeras greatly promoted AChR expression and significantly altered the sensitivity to activation. This reveals a structural and functional, as well as antigenic, significance of the MIR.
Injection-Locked Wideband FM Demodulation at IF (2016)

A low-power FM demodulator operating across a 2-10-GHz IF bandwidth for its application in wideband heterodyne receivers is presented. A four-stage ring oscillator locks to one-fourth of the input FM, thereby reducing the energy required for wideband demodulation. The measurements show that the oscillator is capable of locking to at least a modulating frequency of 400 MHz, and further testing is limited by the FM source. Linear demodulation of the quadrature-phased outputs is realized using a low-power folded CMOS mixer, even as the fractional bandwidth of the input FM approaches unity. The inductorless 65-nm CMOS prototype occupies 0.17 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and dissipates 3.2 mW from 1.2 V at the quiescent point. The measured SNR sensitivity is 8 dB and the demodulator bit-error rate is 0.1% at 10 Mb/s for a 45-mVpp input signal at IF.
Optimal Cuts of Langasite, La 3 Ga 5 SiO 14 for SAW Devices (2001)

The results of a theoretical and experimen- tal investigation of the SAW propagation characteristics in an optimal region of langasite dened by the Euler an- gles from 15 to +10 , from 120 to 165 , and from 20 to 45 are presented. Based on temperature coef- cients of the elastic constants derived from experimental data, some optimal orientations of langasite characterized by high electromechanical coupling factor (k2), zero power flow angle (PFA) and low or zero temperature coecient of frequency (TCF) were found. The SAW velocity in the region of interest is highly anisotropic; this results in a sig- nicant amount of diraction, which must be taken into account in the search for orientations useful for SAW de- vices. An orientation having simultaneously zero PFA, zero TCF, negligible diraction, and relatively high piezoelectric coupling has been found and veried experimentally. The experimental results are in excellent agreement with the calculated SAW characteristics. The frequency response of a SAW device fabricated on the optimal cut of langasite is presented and demonstrates that high performance SAW lters can be realized on this optimal cut of langasite.
Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes (2013)

Steroidal glycoalkaloids (SGAs) such as α-solanine found in solanaceous food plants--as, for example, potato--are antinutritional factors for humans. Comparative coexpression analysis between tomato and potato coupled with chemical profiling revealed an array of 10 genes that partake in SGA biosynthesis. We discovered that six of them exist as a cluster on chromosome 7, whereas an additional two are adjacent in a duplicated genomic region on chromosome 12. Following systematic functional analysis, we suggest a revised SGA biosynthetic pathway starting from cholesterol up to the tetrasaccharide moiety linked to the tomato SGA aglycone. Silencing GLYCOALKALOID METABOLISM 4 prevented accumulation of SGAs in potato tubers and tomato fruit. This may provide a means for removal of unsafe, antinutritional substances present in these widely used food crops.
Suppression of the contrast of ribs in chest radiographs by means of massive training artificial neural network (2004)

We developed a method for suppression of the contrast of ribs in chest radiographs by means of a massive training artificial neural network (MTANN). The MTANN is a trainable highly nonlinear filter that can be trained by using input chest radiographs and the corresponding teacher images. We used either the soft-tissue image or the bone image obtained by use of a dual-energy subtraction technique as the teacher image for suppression of ribs in chest radiographs. When the soft-tissue images were used as the teacher images, the MTANN directly produced a "soft-tissue-image-like" image where the contrast of ribs was suppressed. When the bone images were used as the teacher images, the MTANN was able to produce a "bone-image-like" image, and then was subtracted from the corresponding chest radiograph to produce a bone-subtracted image where ribs are suppressed. Thus, the two kinds of rib-suppressed images, i.e., the soft-tissue-image-like image and the bone-subtracted image, could be produced by use of the MTANNs trained with two different teacher images. We applied each of the two trained MTANNs to non-training chest radiographs to investigate the difference between the processed images. The results showed that the contrast of ribs in chest radiographs almost disappeared, and was reduced to less than 10% in both processed images. The contrast of ribs was reduced slightly better in the soft-tissue-image-like images than in the bone-subtracted images, whereas soft-tissue opacities such as lung vessels and nodules were maintained better in the bone-subtracted images. Therefore, the use of the bone images as the teacher images for training the MTANN has produced better rib-suppressed images where soft-tissue opacities were substantially maintained. A method for rib suppression using the MTANN would be useful for radiologists as well as CAD schemes in detection of lung diseases such as nodules in chest radiographs.
Lipoprotein Nanoplatelets: Brightly Fluorescent, Zwitterionic Probes with Rapid Cellular Entry (2015)

Semiconductor nanoplatelets (NPLs) are planar nanocrystals that have recently attracted considerable attention due to their quantum-well-like physics, atomically precise thickness, and unique photophysical properties such as narrow-band fluorescence emission. These attributes are of potential interest for applications in biomolecular and cellular imaging, but it has been challenging to colloidally stabilize these nanocrystals in biological media due to their large dimensions and tendency to aggregate. Here we introduce a new colloidal material that is a hybrid between a NPL and an organic nanodisc composed of phospholipids and lipoproteins. The phospholipids adsorb to flat surfaces on the NPL, and lipoproteins bind to sharp edges to enable monodisperse NPL encapsulation with long-term stability in biological buffers and high-salt solutions. The lipoprotein NPLs (L-NPLs) are highly fluorescent, with brightness comparable to that of wavelength-matched quantum dots at both the ensemble and single-molecule levels. They also exhibit a unique feature of rapid internalization into living cells, after which they retain their fluorescence. These unique properties suggest that L-NPLs are particularly well suited for applications in live-cell single-molecule imaging and multiplexed cellular labeling.
WALNUT: Waging Doubt on the Integrity of MEMS Accelerometers with Acoustic Injection Attacks (2017)

Cyber-physical systems depend on sensors to make automated decisions. Resonant acoustic injection attacks are already known to cause malfunctions by disabling MEMS-based gyroscopes. However, an open question remains on how to move beyond denial of service attacks to achieve full adversarial control of sensor outputs. Our work investigates how analog acoustic injection attacks can damage the digital integrity of a popular type of sensor: the capacitive MEMS accelerometer. Spoofing such sensors with intentional acoustic interference enables an out-of-spec pathway for attackers to deliver chosen digital values to microprocessors and embedded systems that blindly trust the unvalidated integrity of sensor outputs. Our contributions include (1) modeling the physics of malicious acoustic interference on MEMS accelerometers, (2) discovering the circuit-level security flaws that cause the vulnerabilities by measuring acoustic injection attacks on MEMS accelerometers as well as systems that employ on these sensors, and (3) two software-only defenses that mitigate many of the risks to the integrity of MEMS accelerometer outputs. We characterize two classes of acoustic injection attacks with increasing levels of adversarial control: output biasing and output control. We test these attacks against 20 models of capacitive MEMS accelerometers from 5 different manufacturers. Our experiments find that 75% are vulnerable to output biasing, and 65% are vulnerable to output control. To illustrate end-to-end implications, we show how to inject fake steps into a Fitbit with a $5 speaker. In our self-stimulating attack, we play a malicious music file from a smartphone's speaker to control the on-board MEMS accelerometer trusted by a local app to pilot a toy RC car. In addition to offering hardware design suggestions to eliminate the root causes of insecure amplification and filtering, we introduce two low-cost software defenses that mitigate output biasing attacks: randomized sampling and 180 degree out-of-phase sampling. These software-only approaches mitigate attacks by exploiting the periodic and predictable nature of the malicious acoustic interference signal. Our results call into question the wisdom of allowing microprocessors and embedded systems to blindly trust that hardware abstractions alone will ensure the integrity of sensor outputs.
Chromogenic Oxazines for Cyanide Detection (2005)

[reaction: see text] We have designed two heterocyclic compounds for the colorimetric detection of cyanide. The skeleton of both molecules fuses a benzooxazine ring to an indoline fragment and can be assembled efficiently in three synthetic steps starting from commercial precursors. The two compounds differ in the nature of the substituent on the carbon atom at the junction of the fused heterocycles, which can be either a methyl or a phenyl group. In the presence of cyanide, both molecules are converted quantitatively into cyanoamines with the concomitant appearance of an intense band in the visible region of the absorption spectrum. The developing absorption is a result of the opening of the benzooxazine ring with the formation of a 4-nitrophenylazophenolate chromophore. Nuclear magnetic resonance spectroscopy and X-ray crystallographic analyses demonstrate that the covalent attachment of a cyanide anion to the indoline fragment is responsible for these transformations. The chromogenic process is particularly fast for the methyl-substituted oxazine and can be exploited to detect micromolar concentrations of cyanide in water. Furthermore, the colorimetric response of this compound to cyanide does not suffer the interference of the halide anions, which instead are known to complicate the detection of cyanide in conventional sensing protocols. Thus, our mechanism and compounds for the colorimetric identification of cyanide can lead to the development of practical strategies for the convenient determination of this toxic anion in aqueous environments.
Novel Suicide Ligands of Tubulin Arrest Cancer Cells in S-Phase (1999)

It is presently accepted that the mechanism of action for all anti-tumor tubulin ligands involves the perturbation of microtubule dynamics during the G2/M phase of cell division and subsequent entry into apoptosis [1]. In this report, we challenge the established dogma by describing a unique mechanism of action caused by a novel series of tubulin ligands, halogenated derivatives of acetamido benzoyl ethyl ester. We have developed a suicide ligand for tubulin, which covalently attaches to the target and shows potent cancericidal activity in tissue culture assays and in animal tumor models. These compounds target early S-phase at the G1/S transition rather than the G2/M phase and mitotic arrest. Bcl-2 phosphorylation, a marker of mitotic microtubule inhibition by other tubulin ligands was dramatically altered, phosphorylation was rapid and biphasic rather than a slow linear event. The halogenated ethyl ester series of derivatives thus constitute a unique set of tubulin ligands which induce a novel mechanism of apoptosis.
Stronger Fire-Resistant Epoxies (1988)

New curing agent improves mechanical properties and works at lower temperature. Use of aminophenoxycyclotriphosphazene curing agents yields stronger, more heat- and fire-resistant epoxy resins. Used with solvent if necessary for coating fabrics or casting films.
Modeling the Ternary Complex TCR-Vβ/CollagenII(261–273)/HLA-DR4 Associated with Rheumatoid Arthritis (2010)

This work presents a three-dimensional model for the ternary complex TCR-Vbeta/collagenII(261-273)/HLA-DR4 associated with rheumatoid arthritis that can provide insights into the molecular mechanisms of self reactivity.
Data from Selective Inhibition of EZH2 by EPZ-6438 Leads to Potent Antitumor Activity in <i>EZH2</i>-Mutant Non-Hodgkin Lymphoma (2023)

<div>Abstract<p>Mutations within the catalytic domain of the histone methyltransferase EZH2 have been identified in subsets of patients with non-Hodgkin lymphoma (NHL). These genetic alterations are hypothesized to confer an oncogenic dependency on EZH2 enzymatic activity in these cancers. We have previously reported the discovery of EPZ005678 and EPZ-6438, potent and selective <i>S</i>-adenosyl-methionine-competitive small molecule inhibitors of EZH2. Although both compounds are similar with respect to their mechanism of action and selectivity, EPZ-6438 possesses superior potency and drug-like properties, including good oral bioavailability in animals. Here, we characterize the activity of EPZ-6438 in preclinical models of NHL. EPZ-6438 selectively inhibits intracellular lysine 27 of histone H3 (H3K27) methylation in a concentration- and time-dependent manner in both <i>EZH2</i> wild-type and mutant lymphoma cells. Inhibition of H3K27 trimethylation (H3K27Me3) leads to selective cell killing of human lymphoma cell lines bearing EZH2 catalytic domain point mutations. Treatment of <i>EZH2</i>-mutant NHL xenograft-bearing mice with EPZ-6438 causes dose-dependent tumor growth inhibition, including complete and sustained tumor regressions with correlative diminution of H3K27Me3 levels in tumors and selected normal tissues. Mice dosed orally with EPZ-6438 for 28 days remained tumor free for up to 63 days after stopping compound treatment in two <i>EZH2</i>-mutant xenograft models. These data confirm the dependency of <i>EZH2</i>-mutant NHL on EZH2 activity and portend the utility of EPZ-6438 as a potential treatment for these genetically defined cancers. <i>Mol Cancer Ther; 13(4); 842–54. ©2014 AACR</i>.</p></div>
A closed-form location estimator for use with room environment microphone arrays (1997)

The linear intersection (LI) estimator, which is a closed-form method for the localization of source positions given sensor array time-delay estimate information, is presented. The LI estimator is shown to be robust and accurate, to closely model the search-based ML estimator, and to outperform a benchmark algorithm. The computational complexity of the LI estimator is suitable for use in real-time microphone-array applications where search-based location algorithms may be infeasible.
Constraint motion filtering for video stabilization (2005)

Video stabilization objective is to remove unwanted motion fluctuations from video data. Typically, this is achieved by applying a certain amount of corrective motion displacement onto each video frame, such that to cancel the effect of high frequency fluctuations (jitter) caused by unwanted camera motions. The corrective motion, whose magnitude is often limited by the system, is calculated from the observed raw motion by a procedure called motion filtering. In this paper we propose a novel motion filtering approach that takes into consideration the existence of a practical system constraint with respect to the amount of corrective motion that can be applied on each video frame. The proposed filtering procedure extends the Kalman filtering method by incorporating the system constraint in an optimal manner. The experimental results reveal that the proposed approach improves the stabilization performance in the presence of a system constraint, performing significantly better than a trivial incorporation of the system constraint into the stabilization algorithm.
Sorting methods for estimating the number of emitters and their parameters (2002)

The current literature contains many algorithms for determination of the number of emitters and their parameters when the emitter signals are all present over the observation period of the receiver. In the problem considered, emissions are of short duration, and interference between emissions at the receiver is a rare event. The receiver estimates the angle, frequency, amplitude, and time of arrival for each emission assuming that no other emissions are present. These estimates are then collected for some time interval and passed to a sorting method that estimates the number of emitters and the parameters associated with each. Two methods are presented. These methods are ad-hoc, although the 3D method resembles the Parzen with a normal kernel for estimating a probability density function and the maximum a posteriori method for estimating the parameters. The 2D method is a modification to the 3D that trades off performance for speed of execution. Both methods were evaluated using over 100 data sets. The data varies from sparse, containing 50 or less hits over the collection interval, to dense, with over 1000 hits. In sparse environments both methods produce about the same emitter reports. In dense environments, the 2D method sometimes misses emitters that the 3D method detects.
31.5L: <i>Late‐News Paper:</i> Development of a Combined Liquid Crystal and Fine Pitch Light Source Display (LFD) (2005)

Abstract We propose a novel display system that we call an LFD (combined liquid crystal and fine pitch light source display). In an LFD, an auxiliary light source patterned with a fine pitch is attached to a reflective liquid crystal display (LCD), and a light shield is formed on the observer's side of the light source. A vertical alignment LCD (VA‐LCD) is attached as the reflective LCD, and an organic light‐emitting diode (OLED) is attached as the fine pitch light source. An LFD can produce bright, high‐contrast images under any ambient light. We built a test sample and confirmed its display characteristics.