gebhart/patrepeval huggingface dataset:
Super-Exponential Blind Adaptive Beamforming (2004)

The objective of the beamforming with the exploitation of a sensor array is to enhance the signals of the sources from desired directions, suppress the noises and the interfering signals from other directions, and/or simultaneously provide the localization of the associated sources. In this paper, we present a higher order cumulant-based beamforming algorithm, namely, the super-exponential blind adaptive beamforming algorithm, which is extended from the super-exponential algorithm (SEA) and the inverse filter criteria (IFC). While both SEA and IFC assume noise-free conditions, this requirement is no longer needed, and all the noise components are taken into account in the proposed algorithm. Two special conditions are derived under which the proposed blind beamforming algorithm achieves the performance of the corresponding optimal nonblind beamformer in the sense of minimum mean square error (MMSE). Simulation results show that the proposed algorithm is effective and robust to diverse initial weight vectors; its performance with the use of the fourth-order cumulants is close to that of the nonblind optimal MMSE beamformer.
Rat liver heme oxygenase. High level expression of a truncated soluble form and nature of the meso-hydroxylating species. (1993)

A rat heme oxygenase (HO-1) gene without the sequence coding for the last 23 amino acids has been constructed and expressed behind the pho A promoter in Escherichia coli. The enzyme is expressed at high levels as a soluble catalytically active protein that causes the bacterial cells to accumulate biliverdin. The purified truncated heme-heme oxygenase complex is spectroscopically indistinguishable from the complex with the native enzyme and converts heme to biliverdin when reconstituted with rat liver cytochrome P450 reductase. Reaction of the recombinant heme-heme oxygenase complex with H2O2 produces a species with the spectroscopic properties of verdoheme. Unidentified products are obtained when this intermediate is directly extracted from the protein, but biliverdin is obtained if the verdoheme-protein complex is exposed to cytochrome P450 reductase and NADPH before the extraction step. In contrast, reaction of the heme-heme oxygenase complex with meta-chloroperbenzoic acid (mCPBA), tert-butylhydroperoxide, or cumene hydroperoxide yields a ferryl (FeIV = O) complex. Reaction of the heme-heme oxygenase complex with mCPBA also produces an EPR-detectable protein radical. In accord with formation of a ferryl intermediate, recombinant heme oxygenase catalyzes the mCPBA- and alkylhydroperoxide-dependent peroxidation of 2-methoxyphenol (guaiacol). Guaiacol oxidation is not observed during turnover of the enzyme by cytochrome P450 reductase/NADPH or H2O2. Conversely, biliverdin is not formed with tert-butylhydroperoxide or mCPBA. H2O2 thus supports the first step of the normal catalytic oxidation of heme by heme oxygenase, but alkyl and acyl hydroperoxides do not. These results suggest that the alpha-meso-hydroxylation required for biliverdin formation is mediated by the distal of the two oxygens in the iron-dioxygen intermediate (Fe-O-O) engendered by reaction with either cytochrome P450 reductase/NADPH or H2O2.
Targeting TGF beta signaling for cancer therapy (2005)

Transforming growth factor (TGF) betas are multifunctional polypeptides that regulate several cellular functions, including cell growth and differentiation, extra cellular matrix production, motility and immunosuppression. The growth-inhibiting properties of TGFbeta have gained much attention into its role as a tumor suppressor. There is, however, now increasing evidence that TGFbeta switches roles, from tumor suppressor to tumor promoter, as the tumor progresses. Given the integral role of TGFbeta in the tumor progression, it follows that TGFbeta signaling offers an attractive target for cancer therapy. Several strategies including the use of antisense oligonucleotides for TGFbeta, TGFbeta antibodies, dominant negative TGFbeta receptor II, and small drug-molecules to inhibit TGFbeta receptor I kinase have shown great promise in the preclinical studies. These new findings, coupled with progressing clinical trials indicate that inhibition of TGFbeta signaling may, indeed, be a viable option to cancer therapy. This review summarizes the TGFbeta signaling, the dual role of TGFbeta--as a tumor suppressor and tumor promoter, and various strategies targeted against TGFbeta signaling for cancer therapy. The next few years promise to better our understanding of approaching cancer therapy with an eye to the inhibition of TGFbeta signaling.
Nnal‐like proteins are active metallocarboxypeptidases of a new and diverse M14 subfamily (2007)

Nna1 has some sequence similarity to metallocarboxypeptidases, but the biochemical characterization of Nna1 has not previously been reported. In this work we performed a detailed genomic scan and found >100 Nna1 homologues in bacteria, Protista, and Animalia, including several paralogs in most eukaryotic species. Phylogenetic analysis of the Nna1-like sequences demonstrates a major divergence between Nna1-like peptidases and the previously known metallocarboxypeptidases subfamilies: M14A, M14B, and M14C. Conformational modeling of representative Nna1-like proteins from a variety of species indicates an unusually open active site, a property that might facilitate its action on a wide variety of peptide and protein substrates. To test this, we expressed a recombinant form of one of the Nna1-like peptidases from Caenorhabditis elegans and demonstrated that this protein is a fully functional metallocarboxypeptidase that cleaves a range of C-terminal amino acids from synthetic peptides. The enzymatic activity is activated by ATP/ADP and salt-inactivated, and is preferentially inhibited by Z-Glu-Tyr dipeptide, which is without precedent in metallocarboxypeptidases and resembles tubulin carboxypeptidase functioning; this hypothesis is strongly reinforced by the results depicted in Kalinina et al. published as accompanying paper in this journal. Our findings demonstrate that the M14 family of metallocarboxypeptidases is more complex and diverse than expected, and that Nna1-like peptidases are functional variants of such enzymes, representing a novel subfamily (we propose the name M14D) that contributes substantially to such diversity.
Solution structure of the complex between poxvirus-encoded CC chemokine inhibitor vCCI and human MIP-1β (2006)

Chemokines (chemotactic cytokines) comprise a large family of proteins that recruit and activate leukocytes, giving chemokines a major role in both immune response and inflammation-related diseases. The poxvirus-encoded viral CC chemokine inhibitor (vCCI) binds to many CC chemokines with high affinity, acting as a potent inhibitor of chemokine action. We have used heteronuclear multidimensional NMR to determine the structure of an orthopoxvirus vCCI in complex with a human CC chemokine, MIP-1beta (macrophage inflammatory protein 1beta). vCCI binds to the chemokine with 1:1 stoichiometry, forming a complex of 311 aa. vCCI uses residues from its beta-sheet II to interact with a surface of MIP-1beta that includes residues adjacent to its N terminus, as well as residues in the 20's region and the 40's loop. This structure reveals the strategy used by vCCI to tightly bind numerous chemokines while retaining selectivity for the CC chemokine subfamily.
Monocular Video-Based Trailer Coupler Detection Using Multiplexer Convolutional Neural Network (2017)

This paper presents an automated monocular-camera-based computer vision system for autonomous self-backing-up a vehicle towards a trailer, by continuously estimating the 3D trailer coupler position and feeding it to the vehicle control system, until the alignment of the tow hitch with the trailers coupler. This system is made possible through our proposed distance-driven Multiplexer-CNN method, which selects the most suitable CNN using the estimated coupler-to-vehicle distance. The input of the multiplexer is a group made of a CNN detector, trackers, and 3D localizer. In the CNN detector, we propose a novel algorithm to provide a presence confidence score with each detection. The score reflects the existence of the target object in a region, as well as how accurate is the 2D target detection. We demonstrate the accuracy and efficiency of the system on a large trailer database. Our system achieves an estimation error of 1.4 cm when the ball reaches the coupler, while running at 18.9 FPS on a regular PC.
Application Of Polyelectrolyte Multilayers For Photolithographic Patterning Of Diverse Mammalian Cell Types In Serum Free Medium (2008)

Integration of living cells with novel microdevices requires the development of innovative technologies for manipulating cells. Chemical surface patterning has been proven as an effective method to control the attachment and growth of diverse cell populations. Patterning polyelectrolyte multilayers through the combination of layer-by-layer self-assembly technique and photolithography offers a simple, versatile and silicon compatible approach that overcomes chemical surface patterning limitations, such as short-term stability and low protein adsorption resistance. In this study, direct photolithographic patterning of PAA/PAAm and PAA/PAH polyelectrolyte multilayers was developed to pattern mammalian neuronal, skeletal and cardiac muscle cells. For all studied cell types, PAA/PAAm multilayers behaved as a negative surface, completely preventing cell attachment. In contrast, PAA/PAH multilayers have shown a cell-selective behavior, promoting the attachment and growth of neuronal cells (embryonic rat hippocampal and NG108-15 cells) to a greater extent, while providing a little attachment for neonatal rat cardiac and skeletal muscle cells (C2C12 cell line). PAA/PAAm multilayer cellular patterns have also shown a remarkable protein adsorption resistance. Protein adsorption protocols commonly used for surface treatment in cell culture did not compromise the cell attachment inhibiting feature of the PAA/PAAm multilayer patterns. The combination of polyelectrolyte multilayer patterns with different adsorbed proteins could expand the applicability of this technology to cell types that require specific proteins either on the surface or in the medium for attachment or differentiation, and could not be patterned using the traditional methods.
Ultra-low-voltage floating-gate transconductance amplifiers (2001)

Ultra-low-voltage (ULV) floating-gate differential amplifiers are presented. In this paper, we present several different approaches to CMOS ULV amplifier design. Sinh-shaped and tanh-shaped transconductance amplifiers are described. Measured results are provided.
Block of TRPC5 channels by 2‐aminoethoxydiphenyl borate: a differential, extracellular and voltage‐dependent effect (2005)

1 2-aminoethoxydiphenyl borate (2-APB) has been widely used to examine the roles of inositol 1,4,5-trisphosphate receptors (IP3Rs) and store-operated Ca2+ entry and is an emerging modulator of cationic channels encoded by transient receptor potential (TRP) genes. 2 Using Ca2+-indicator dye and patch-clamp recording we first examined the blocking effect of 2-APB on human TRPC5 channels expressed in HEK-293 cells. 3 The concentration-response curve has an IC50 of 20 microM and slope close to 1.0, suggesting one 2-APB molecule binds per channel. The blocking effect is not shared by other Ca2+ channel blockers including methoxyverapamil, nifedipine, N-propargylnitrendipine, or berberine. 4 In whole-cell and excised membrane patch recordings, 2-APB acts from the extracellular but not intracellular face of the membrane. 5 Block of TRPC5 by 2-APB is less at positive voltages, suggesting that it enters the electric field or acts by modulating channel gating. 6 2-APB also blocks TRPC6 and TRPM3 expressed in HEK-293 cells, but not TRPM2. 7 Block of TRP channels by 2-APB may be relevant to cell proliferation because 2-APB has a greater inhibitory effect on proliferation in cells overexpressing TRPC5. 8 Our data indicate a specific and functionally important binding site on TRPC5 that enables block by 2-APB. The site is only available via an extracellular route and the block shows mild voltage-dependence.
Formation and propagation of meter-scale laser filaments in water (2013)

We report the demonstration, characterization, and modeling of meter-scale underwater optical filaments using a nanosecond pulsed laser. We observed single filament formation for P/PCRIT = 1–5, where PCRIT ∼ 1 MW in water. We employed a variable distance water tube to characterize laser pulse evolution and filament formation. Filaments with uniform radius 50 ± 10 μm persisted for 55 cm (&amp;gt;35 Rayleigh lengths). Significant forward Stimulated Raman Scattering (up to 60%) was observed and characterized. Simulation results for propagation distances and radii were in agreement with experiment, and predict a structured plasma with peak density of 1.5 × 1018 cm−3.
Missense mutations of the BRAF gene in human lung adenocarcinoma. (2002)

Mutations of the BRAF protein serine/threonine kinase gene have recently been identified in a variety of human cancers, most notably melanomas. We sought to determine the frequency of BRAF mutations in human lung cancer pathogenesis. Analysis of BRAF sequence from 127 primary human lung adenocarcinomas revealed mutations in two tumor specimens, one in exon 11 (G465V), and a second in exon 15 (L596R). These specimens belong to the same adenocarcinoma subgroup as defined by clustering of gene expression data. BRAF may provide a target for anticancer chemotherapy in a subset of lung adenocarcinoma patients.
Maternal medicine: Morphometric placental villous and vascular abnormalities in early‐ and late‐onset pre‐eclampsia with and without fetal growth restriction (2006)

Isolated early-onset PET was associated with abnormal placental morphology, but placentas from late-onset PET were morphologically similar to placentas from gestational-age-matched controls, confirming the existence of two subsets of this condition and supporting the hypothesis that late-onset PET is a maternal disorder and not a placental disease.
Traumatic Brain Injury and Vestibular Pathology as a Comorbidity After Blast Exposure (2009)

Blasts or explosions are the most common mechanisms of injury in modern warfare. Traumatic brain injury (TBI) is a frequent consequence of exposure to such attacks. Although the management of orthopedic, integumentary, neurocognitive, and neurobehavioral sequelae in survivors of blasts has been described in the literature, less attention has been paid to the physical therapist examination and care of people with dizziness and blast-induced TBI (BITBI). Dizziness is a common clinical finding in people with BITBI; however, many US military service members who have been exposed to blasts and who are returning from Iraq and Afghanistan also complain of vertigo, gaze instability, motion intolerance, and other symptoms consistent with peripheral vestibular pathology. To date, few studies have addressed such "vestibular" complaints in service members injured by blasts. Given the demonstrated efficacy of treating the signs and symptoms associated with vestibular pathology, vestibular rehabilitation may have important implications for the successful care of service members who have been injured by blasts and who are complaining of vertigo or other symptoms consistent with vestibular pathology. In addition, there is a great need to build consensus on the clinical best practices for the assessment and management of BITBI and blast-related dizziness. The purpose of this review is to summarize the findings of clinicians and scientists conducting research on the effects of blasts with the aims of defining the scope of the problem, describing and characterizing the effects of blasts, reviewing relevant patients' characteristics and sensorimotor deficits associated with BITBI, and suggesting clinical best practices for the rehabilitation of BITBI and blast-related dizziness.
Registration of Biplane Angiography and Intravascular Ultrasound for 3D Vessel Reconstruction (2004)

The proposed methodology can be used to improve the current state-of-the-art IVB treatment planning by enabling computerized dosage computations on a highly accurate 3D model.
Stabilization of two-stranded ribohomopolymer helices and destabilization of a three-stranded helix by ethidium bromide (1974)

Thermal-denaturation profiles of helical polynucleotides have been measured in the presence of increasing concentrations of ethidium bromide. The poly(A).poly(U) helix is strongly stabilized by binding of ethidium, to much the same extent as is DNA, but the stabilizing effect on poly(I).poly(C) is much smaller. In the poly(A).2poly(U) system the drug selectively destabilizes and eventually destroys the triple helix, leaving only the double-helix-to-coil transition.
Spatiality in videoconferencing (2006)

In this paper, we explore ways to combine the video of a remote person with a shared tabletop display to best emulate face-to-face collaboration. Using a simple photo application we compare a variety of social and performance measures of collaboration of a standard non-spatial 2D interface with two approaches for adding spatial cues to videoconferencing: one based on simulated immersive 3D, the other based on video streams in a physically fixed arrangement around an interactive table. A face-to-face condition is included as a 'gold-standard' control. As expected, social presence and task measures were superior in the face-to-face condition, but there were also important differences between the 2D and spatial interfaces. In particular, the spatial interfaces positively influenced social presence and copresence measures in comparison to 2D, but the task measures favored the two-dimensional interface.
Protein Kinase Cι Promotes Nicotine-induced Migration and Invasion of Cancer Cells via Phosphorylation of μ- and m-Calpains (2005)

Nicotine is a major component in cigarette smoke that activates the growth-promoting pathways to facilitate the development of lung cancer. However, it is not clear whether nicotine affects cell motility to facilitate tumor metastasis. Here we discovered that nicotine potently induces phosphorylation of both mu- and m-calpains via activation of protein kinase Ciota (PKCiota), which is associated with accelerated migration and invasion of human lung cancer cells. Purified PKCiota directly phosphorylates mu- and m-calpains in vitro. Overexpression of PKCiota results in increased phosphorylation of both mu- and m-calpains in vivo. Nicotine also induces activation of c-Src, which is a known PKCiota upstream kinase. Treatment of cells with the alpha(7) nicotinic acetylcholine receptor inhibitor alpha-bungarotoxin can block nicotine-induced calpain phosphorylation with suppression of calpain activity, wound healing, cell migration, and invasion, indicating that nicotine-induced calpain phosphorylation occurs, at least in part, through a signaling pathway involving the upstream alpha(7) nicotinic acetylcholine receptor. Intriguingly, depletion of PKCiota by RNA interference suppresses nicotine-induced calpain phosphorylation, calpain activity, cell migration, and invasion, indicating that PKCiota is a necessary component in nicotine-mediated cell motility signaling. Importantly, nicotine potently induces secretion of mu- and m-calpains from lung cancer cells into culture medium, which may have potential to cleave substrates in the extracellular matrix. These findings reveal a novel role for PKCiota as a nicotine-activated, physiological calpain kinase that directly phosphorylates and activates calpains, leading to enhanced migration and invasion of human lung cancer cells.
Inhibition of human telomerase in immortal human cells leads to progressive telomere shortening and cell death (1999)

The correlation between telomerase activity and human tumors has led to the hypothesis that tumor growth requires reactivation of telomerase and that telomerase inhibitors represent a class of chemotherapeutic agents. Herein, we examine the effects of inhibition of telomerase inside human cells. Peptide nucleic acid and 2'-O-MeRNA oligomers inhibit telomerase, leading to progressive telomere shortening and causing immortal human breast epithelial cells to undergo apoptosis with increasing frequency until no cells remain. Telomere shortening is reversible: if inhibitor addition is terminated, telomeres regain their initial lengths. Our results validate telomerase as a target for the discovery of anticancer drugs and supply general insights into the properties that successful agents will require regardless of chemical type. Chemically similar oligonucleotides are in clinical trials and have well characterized pharmacokinetics, making the inhibitors we describe practical lead compounds for testing for an antitelomerase chemotherapeutic strategy.
Anti‐EGFR antibody‐drug conjugate for triple‐negative breast cancer therapy (2020)

Triple-negative breast cancers (TNBCs) are highly aggressive, metastatic and recurrent. Cytotoxic chemotherapies with limited clinical benefits and severe side effects are the standard therapeutic strategies, but, to date, there is no efficacious targeted therapy. Literature and our data showed that epidermal growth factor receptor (EGFR) is overexpressed on TNBC cell surface and is a promising oncological target. The objective of this study was to develop an antibody-drug conjugate (ADC) to target EGFR<sup>+</sup> TNBC and deliver high-potency drug. First, we constructed an ADC by conjugating anti-EGFR monoclonal antibody with mertansine which inhibits microtubule assembly via linker Sulfo-SMCC. Second, we confirmed the TNBC-targeting specificity of anti-EGFR ADC by evaluating its surface binding and internalization in MDA-MB-468 cells and targeting to TNBC xenograft in subcutaneous mouse mode. The live-cell and live-animal imaging with confocal laser scanning microscopy and In Vivo Imaging System (IVIS) confirmed the TNBC-targeting. Finally, both in vitro toxicity assay and in vivo anti-cancer efficacy study in TNBC xenograft models showed that the constructed ADC significantly inhibited TNBC growth, and the pharmacokinetics study indicated its high circulation stability. This study indicated that the anti-EGFR ADC has a great potential to against TNBC.
Antisense suppression of tau in cultured rat oligodendrocytes inhibits process formation (2008)

The microtubule-associated protein tau is integral to neuronal process development and has a role in the pathogenesis of several neurodegenerative conditions. We examined possible roles for tau in cultured oligodendrocyte process formation by using antisense oligonucleotide treatment. Inhibition of tau synthesis with single oligonucleotides resulted in decreased tau protein levels and significantly shorter cellular processes. Simultaneous use of two nonoverlapping oligonucleotides caused a major reduction in tau levels and severely inhibited process outgrowth. The timing of oligonucleotide addition to oligodendrocyte cultures was important, with addition of antisense at the time of plating into culture having the most significant effect on morphology through reduction of tau expression.