gebhart/patrepeval huggingface dataset:
BlockmiR AONs as Site-Specific Therapeutic MBNL Modulation in Myotonic Dystrophy 2D and 3D Muscle Cells and HSALR Mice (2023)

The symptoms of Myotonic Dystrophy Type 1 (DM1) are multi-systemic and life-threatening. The neuromuscular disorder is rooted in a non-coding CTG microsatellite expansion in the DM1 protein kinase (<i>DMPK</i>) gene that, upon transcription, physically sequesters the Muscleblind-like (MBNL) family of splicing regulator proteins. The high-affinity binding occurring between the proteins and the repetitions disallow MBNL proteins from performing their post-transcriptional splicing regulation leading to downstream molecular effects directly related to disease symptoms such as myotonia and muscle weakness. In this study, we build on previously demonstrated evidence showing that the silencing of miRNA-23b and miRNA-218 can increase MBNL1 protein in DM1 cells and mice. Here, we use blockmiR antisense technology in DM1 muscle cells, 3D mouse-derived muscle tissue, and in vivo mice to block the binding sites of these microRNAs in order to increase <i>MBNL</i> translation into protein without binding to microRNAs. The blockmiRs show therapeutic effects with the rescue of mis-splicing, MBNL subcellular localization, and highly specific transcriptomic expression. The blockmiRs are well tolerated in 3D mouse skeletal tissue inducing no immune response. In vivo, a candidate blockmiR also increases Mbnl1/2 protein and rescues grip strength, splicing, and histological phenotypes.
Discovery of Positive Allosteric Modulators for the Metabotropic Glutamate Receptor Subtype 5 from a Series of <i>N</i>-(1,3-Diphenyl-1<i>H</i>- pyrazol-5-yl)benzamides That Potentiate Receptor Function in Vivo (2004)

This report describes the discovery of the first centrally active allosteric modulators of the metabotropic glutamate receptor subtype 5 (mGluR5). Appropriately substituted N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamides (e.g., 8) have been identified as a novel class of potent positive allosteric modulators of mGluR5 that potentiate the response to glutamate. An iterative analogue library synthesis approach provided potentiators with excellent potency and selectivity for mGluR5 (vs mGluRs 1-4, 7, 8). Compound 8q demonstrated in vivo proof of concept in an animal behavior model where known antipsychotics are active, supporting the development of new antipsychotics based on the NMDA hypofunction model for schizophrenia.
An SR Flip-Flop based Physical Unclonable Functions for Hardware\n Security (2019)

Physical Unclonable Functions (PUFs) have emerged as a promising solution to\nidentify and authenticate Integrated Circuits (ICs). In this paper, we propose\na novel NAND-based Set-Reset (SR) Flip-flop (FF) PUF design for security\nenclosures of the area- and power-constrained Internet-of-Things (IoT) edge\nnode. Such SR-FF based PUF is constructed during a unique race condition that\nis (normally) avoided due to inconsistency. We have shown, when both inputs (S\nand R) are logic high ('1') and followed by logic zero ('0'), the outputs Q and\nQbar can settle down to either 0 or 1 or vice-versa depending on statistical\ndelay variations in cross-coupled paths. We incorporate the process variations\nduring SPICE-level simulations to leverage the capability of SR-FF in\ngenerating the unique identifier of an IC. Experimental results for 90nm, 45nm,\nand 32nm process nodes show the robustness of SR-FF PUF responses in terms of\nuniqueness, randomness, uniformity, and bit(s) biases. Furthermore, we perform\nphysical synthesis to evaluate the applicability of SR FF PUF on five designs\nfrom OpenCores in three design corners. The estimated overhead for power,\ntiming, and area in three design corners are negligible.\n
Multi-Channel Signal Processing Techniques in the Reproduction of Sound (1992)

<p>A general approach is presented to the design of inverse filters used in multichannel sound reproduction systems. The formulation of the problem is cast within a traditional least-squares framework. Algorithms are presented which enable the rapid adaptation of inverse filters in response to measurements made in the reproduced sound field. Experimental results and computer simulations are used to illustrate the potential for using an inverse filter matrix to manipulate the position of stereophonic images. The possibilities suggested could be used in conjunction with existing stereophonic recordings in order to improve stereophonic imaging in situations where the relative locations of loudspeakers and listeners are constrained to be nonideal.</p>
Nanocrystalline Li x Mn2 − y  O 4 Cathodes for Solid‐State Thin‐Film Rechargeable Lithium Batteries (1999)

Thin-film cathodes of lithium manganese oxide, 0.3-3 μm thick, were deposited by rf magnetron sputtering a LiMn2O4 ceramic target onto unheated substrates. The resulting films were dense, approximately 4.2 g/cm3, with a approximately 50 angstroms nanocrystalline spinel structure. The film composition was typically LixMn2-yO4 with y to approximately 0.3 and 1.2 < x < 2.2. When cycled in a thin-film rechargeable lithium battery, specific cathode capacities of 145±23 and approximately 270 mAh/g were realized for discharge from 4.5 V to either 2.5 or 1.5 V, respectively. The discharge and charge current densities were limited by the resistivity of lithium transport into and through the cathode. After thousands of cycles at 25 °C, there was a small increase in cell resistance. After several hundred cycles at 100 °C, the discharge curves developed a stable knee at approximately 4 V characteristic of crystalline LiMn2O4 cathodes. The polarization of the discharge/charge cycles were interpreted in terms of free energy of mixing curves.
Abstract 3489: A novel monoclonal antibody to native HER2 epitope detects HER2-positive CTCs, HER2 in blood, and HER2 in tissue: realistic approach for monitoring breast carcinoma. (2013)

Abstract Background: Amplification of the HER2 gene and/or overexpression of its protein product have been reported in 25% to 30% of breast carcinomas and have been associated with poorer outcomes. However, there are still highly controversial aspects of HER2 testing. In the present study, we generated a novel monoclonal antibody against human native epitope of HER2 and investigated its clinical potential in managing breast carcinoma. Methods and findings: We generated a novel monoclonal antibody (mAb), AB-HER2 using hybridoma technology and native folding of the protein as an immunogen. This mAb is of IgG1 (kappa) type. It specifically recognized both native and denatured human HER2 protein and displayed high affinity as assessed by Circulating Tumor Cells (CTCs), ELISA, immunohistochemistry assay, western blot and flow cytometry applications. We have developed a CTCs assay to detect specific HER2-positive tumor cells circulating in blood, while we did not observe any background staining in blood cells. Using AB-HER2 mAb in ELISA, we showed soluble HER2 level is significantly increased in breast cancer patients’ plasma which directly correlated with HER2 expression pattern in breast cancer tissues. Tissue expression of HER2 was determined by using immunohistochemical techniques. Most of normal tissues showed negative staining, while different levels of membrane staining were observed in cancer sections. To evaluate the immunoreactivity of HER2 associated with tumor histological types, the staining intensity in membranes were scored according to the guidelines of ASCO/CAP. We also have compared AB-HER2 mAB with commercial HER2 antibodies in all immunoassays. Conclusion: The novel AB-HER2 mAb showed improved accuracy in all immunoassays and clinical outcome. Circulating HER2-positive tumor cells, HER2 protein levels in plasma and in breast tissues significantly increased in patients with breast carcinoma compared to normal healthy controls. Our data suggest the potential clinical use of AB-HER2 mAB as a powerful immunoreagent in measuring real-time HER2 levels in managing breast cancer. Citation Format: Özge Alper, Achille Akoa, Özgül M. Alper, Cui P. Chen. A novel monoclonal antibody to native HER2 epitope detects HER2-positive CTCs, HER2 in blood, and HER2 in tissue: realistic approach for monitoring breast carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3489. doi:10.1158/1538-7445.AM2013-3489
Adaptive control for uncertain dynamical systems with nonlinear reference systems (2020)

A reference model of an adaptive control law defines how a closed-loop dynamical system under consideration has to asymptotically (or approximately) behave in the presence of system uncertainties. While it is of common practice to use reference models with linear dynamics, this can lead to limitations on the achievable closed-loop dynamical system performance – especially for applications involving highly capable dynamical systems such as highly manoeuvrable aircraft, missiles, and space launch vehicles. Because, linear reference models for these applications can only approximate the desired closed-loop behaviour of these nonlinear dynamical systems in narrow regions of the state-space. Motivated from this standpoint, this paper's contribution is to present a new adaptive control architecture for uncertain dynamical systems based on nonlinear reference models. Specifically, we analytically show that the system error between the uncertain dynamical system and the nonlinear reference model asymptotically vanishes in steady-state and its performance is guaranteed during the transient-time. We further discuss the practicality of our approach and provide numerical examples to demonstrate its efficacy.
Photomediated Synthesis of Silver Triangular Bipyramids and Prisms: The Effect of pH and BSPP (2010)

The photomediated synthesis of silver right triangular bipyramids and prisms has been studied, and we have determined that pH and [BSPP]/[Ag(+)] ratio (bis(p-sulfonatophenyl)phenylphosphine, BSPP) finely control the reaction rate and, consequently, the crystal growth pathway and morphology of final products. A fast reaction rate, realized at a high pH such as 10 or 11 and a [BSPP]/[Ag(+)] ratio close to 1.0, is necessary to synthesize (100)-faceted right triangular bipyramids in high yield by preferential deposition on (111) facets of planar-twinned seeds. A slower reaction rate, which occurs at lower pH or higher [BSPP]/[Ag(+)] ratios, results in preferential deposition on (100) facets of planar-twinned seeds and the formation of nanoparticles possessing a larger surface area defined by (111) facets, such as truncated triangular bipyramids or prisms. BSPP further influences the reaction rate by ensuring a relatively constant concentration of aqueous Ag(+). In the absence of BSPP, the aqueous [Ag(+)] steadily decreases as it is consumed and results in a continuously decreasing reaction rate, which changes the preferred facet for silver deposition. At the beginning of the reaction, growth on (111) facets almost exclusively occurs and results in the formation of right triangular bipyramids, which only have (100) facets. When the reaction rate is decreased due to the consumption of Ag(+) through the course of the reaction, the facet deposition preference changes from (111) to (100) and results in the formation of truncated bitetrahedra, with (111) facets, as the predominant product.
Double Pulse Transthoracic Defibrillation in the Calf Using Percent Fibrillation Cycle Length as Spacing Determinate (1999)

Recent studies have found that when multiple pulses of energy are used for defibrillation with implantable electrodes, the spacing between these pulses is better determined as a percentage of the fibrillation cycle length (CL), rather than as a fixed function of time. Here, this concept is further tested in the transthoracic defibrillation of calves, which are approximately the size of heavy humans. Eleven 90-110 kg calves (101 +/- 6 kg) were used in evaluating the effectiveness in achieving transthoracic ventricular defibrillation of ten double pulse waveforms (two 50 A 4-ms rectangular monopulses) having leading edge-to-edge spacings of 4 ms (a 50 A 8-ms rectangular monopulse) and 50, 60, 70, 80, 90, 100, 110, 120, 130 percent fibrillation CL, respectively. In each of these waveforms, the total time when 50 A current was flowing (on time) was 8 ms. Our results show an unequivocal adverse interaction between the pulses, when the spacing is around 60%-70% fibrillation CL; but that the two pulses combined to defibrillate as effectively as a single 8-ms pulse when the spacing is around 110%-130% fibrillation CL. Electrocardiographic analysis suggests that the adverse interaction is due to a refibrillation phenomenon. This study confirms that double pulses can interact and have a negative effect on defibrillation efficacy. Our data suggests that the mechanism of this interaction involves the second pulse reinitiating fibrillation when the pulse separation is in a critical range of values. Our results are also compatible with the hypothesis that the spacing of multiple pulses is better determined as a percentage of the fibrillation CL than as absolute time, although more study is necessary to fully test this hypothesis.
Single Output Tunable DFB Semiconductor Laser Array with Equivalent Phase Shift (2015)

We report single output tunable DFB semiconductor laser arrays in series and grating-matrix configuration designed by reconstruction equivalent chirp (REC) technique. By using interference lithography and photolithography for the grating fabrication, tunable laser arrays with good performance are experimentally realized with low cost.
Applications of 1.06-μm IR Laser Desorption on a Fourier Transform Mass Spectrometer (1998)

Various sugars, peptides, and lipids were analyzed on a Fourier transform mass spectrometer using laser desorption and ionization with and without the assistance of matrixes. A compact Nd:YAG laser with an output at 1.06 microns corresponding to fundamental frequency was employed. Gram-negative and Gram-positive bacteria were also subjected to laser desorption mass spectrometry. Characteristics ions of conjugated lipid, formed by attachment of alkali metal cations, endogenous to the cells, were observed. Particle/liquid matrixes (e.g., cobalt in glycerol) proved to be useful with the 1.06-micron laser. The particles absorb efficiently laser radiation in a broad wavelength range. The liquid provides the same advantages as in fast atom bombardment: increased signal-to-noise ratios and enhanced sample lifetimes. The effect of laser power on total ion current was shown to differ for samples with and without the particle/liquid matrix. The Fourier transform analyzer provides MS/MS capability for both positive and negative ions from complex mixtures. Ions desorbed externally are introduced into the cell via a quadrupole ion guide with a lower mass cutoff. Such a setup allows matrix ions to be excluded and thus provides excellent signal-to-noise ratios for lower mass range fragment ions formed inside the cell.
A Convenient Synthesis of 4-Homoisotwistane (1974)

Abstract Tricyclo[5.3.1.03,8] undecane (II), which would be conveniently refered to by the trivial name 4-homoisotwistane in accordance with Majerski's nomenclature,1 was first prepared by Krantz2 during the stereoselectivity study on intramolecular Diels-Alder reactions of 5-alkenylcyclohexa-1,3-dienes, and recently discovered independently by Schleyer,3 Majerski1 and us4 to be involved as a reasonably stable intermediate in acid-catalyzed isomerization of various tricycloundecane precursors to equilibrium mixtures of 1 and 2-methyladamantanes.
<title>Thinning and polishing of diamond films by diffusional reaction with metals</title> (1992)

Substantial thinning/polishing of diamond films (by as much as approximately 100 micrometers ) through simple diffusional reaction at 900 degree(s)C with Mn or Fe is reported. The observed thinning effect is attributed to the diffusional transfer of carbon atoms from diamond to manganese or iron in contact, as these metals exhibit large solid solubility for carbon at the reaction temperature. Mn appears to react with diamond much faster than Fe. Patterning of diamond films by selective area deposition of Mn films followed by reaction heat treatment and chemical etching is also described. These thinning techniques using metal powders, foils, or deposited films may conveniently be used for removal of undesirable parts of the films such as rough growth facets on the top surface or the fine grained bottom layer with inferior physical properties. These techniques also allow simultaneous thinning of a large number of diamond films.
Digital Holography-A New Paradigm in Imaging, Microscopy and Metrology (2006)

Digital Holography (DH) has brought a new impetus to the field of holography. The fields of imaging, microscopy and metrology have all benefited from these developments. In this paper some of these developments will be described with some applications in the fields of color imaging, amplitude and phase microscopy and dynamic metrology. It is envisaged that this field will rapidly advance in the next couple of years and become an expected imaging and measurement modality especially in the field of micro, nano and bio sciences.
A unified method for handling discrete and continuous uncertainty in Bayesian Stackelberg games (2012)

Given their existing and potential real-world security applications, Bayesian Stackelberg games have received significant research interest [3, 12, 8]. In these games, the defender acts as a leader, and the many different follower types model the uncertainty over discrete attacker types. Unfortunately since solving such games is an NP-hard problem, scale-up has remained a difficult challenge.This paper scales up Bayesian Stackelberg games, providing a novel unified approach to handling uncertainty not only over discrete follower types but also other key continuously distributed real world uncertainty, due to the leader's execution error, the follower's observation error, and continuous payoff uncertainty. To that end, this paper provides contributions in two parts. First, we present a new algorithm for Bayesian Stackelberg games, called HUNTER, to scale up the number of types. HUNTER combines the following five key features: i) efficient pruning via a best-first search of the leader's strategy space; ii) a novel linear program for computing tight upper bounds for this search; iii) using Bender's decomposition for solving the upper bound linear program efficiently; iv) efficient inheritance of Bender's cuts from parent to child; v) an efficient heuristic branching rule. Our experiments show that HUNTER provides orders of magnitude speedups over the best existing methods to handle discrete follower types. In the second part, we show HUNTER's efficiency for Bayesian Stackelberg games can be exploited to also handle the continuous uncertainty using sample average approximation. We experimentally show that our HUNTER-based approach also outperforms latest robust solution methods under continuously distributed uncertainty.
Sub-mJ nano-second vortex pulse generation from a stressed Yb-doped double-clad fiber amplifier (2011)

In this paper, we extend our previous work to generate high-energy nano-second vortex pulses from a Yb-doped double-clad fiber amplifier in combination with a diode-pumped Q-switched Nd:YVO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> laser. The maximum output energy of 0.83 mJ with a peak power of >;59 kW and a pulse repetition frequency of 10 kHz was measured at a pump power of 25.7 W, corresponding to an average power of 8.3 W.
Kernel-level intrusion detection method using simplification and grouping (2005)

This paper proposes the kernel-level intrusion detection method (KIDM) using simplification and grouping of intrusion detection rules. These rules group into group-rule and common-rule generated by simplification. The intrusion detection is separated into common detection and extended detection step. The packet is checked by common detection using the common-rule. If this step detects nothing, the packet is forwarded to its destination. If not, it is passed into the extended detection using the group-rule. Through grouping of similar detection rules, the search space and searching time can be greatly minimized. Using the simplified rule in intrusion detection, the packet inspection time can be largely reduced. With the help of these two steps, fast and effective intrusion detection is possible in network nodes such as router and switch
α-Conotoxin PIA Is Selective for α6 Subunit-Containing Nicotinic Acetylcholine Receptors (2003)

Until now, there have been no antagonists to discriminate between heteromeric nicotinic acetylcholine receptors (nAChRs) containing the very closely related α6 and α3 subunits. nAChRs containing α3, α4, or α6 subunits in combination with β2, occasionally β4, and sometimes β3 or α5 subunits, are thought to play important roles in cognitive function, pain perception, and the reinforcing properties of nicotine. We cloned a novel gene from the predatory marine snail Conus purpurascens . The predicted peptide, α-conotoxin PIA, potently blocks the chimeric α6/α3β2β3 subunit combination as expressed in oocytes but neither the muscle nor the major neuronal nAChR α4β2. Additionally, this toxin is the first described ligand to discriminate between nAChRs containing α6 and α3 subunits. Exploiting the unusual intron conservation of conotoxin genes may represent a more general approach for defining conotoxin ligand scaffolds to discriminate among closely related receptor populations.
Integrated Multiproduct Biorefinery for Furfural Production with Acetic Acid and Lignin Recovery: Design, Scale-Up Evaluation, and Technoeconomic Analysis (2020)

Furfural is a versatile platform and multipurpose chemical that can be produced with no carbon efficiency loss from pentose sugars present in prehydrolysate streams. Existing processes for the production of furfural are typically energy-intensive with limitations to recover value-added molecules and byproducts such as lignin and acetic acid. In this work, we demonstrate a novel integrated biorefinery process for furfural production with significant sustainability improvements to current production pathways. Higher conversion efficiency for C5 sugars into furfural is achieved with a novel reactor for producing and recovering furfural in the vapor phase that has been validated at the laboratory scale. Low molecular weight and sulfur-free lignin is also recovered while minimizing energy consumption by employing membrane filtration. Synergy was observed when lignin recovery is performed prior to furfural production. On the basis of experimental results, the scalability of the process for valorizing 3200 metric tonne/day of prehydrolysate solutions that is typically combusted in kraft dissolving pulp mills was evaluated. For a furfural production capacity of 36 tonne/day, a process configuration that stands out among four proposed alternatives was identified and designed. Significant heat energy savings (99.5%) for driving the process was achieved through a heat exchanger network design for internal heat recovery, which resulted in an energy intensity of 0.47 GJ/tonne, corresponding to 1% of the energy intensity for conventional processes. The technoeconomic assessment confirmed that even the least performing process is profitable, robust, and capital-efficient as indicated by metrics such as the internal rate of return (IRR) ranging from 30% to 46%, resistance to market uncertainty (RTMU) between 0.9 and 4.3 $/$, as well as return on capital employed (ROCE) between 49% and 91%.