gebhart/patrepeval huggingface dataset:
Berberine Inhibits Oxygen Consumption Rate Independent of Alteration in Cardiolipin Levels in H9c2 Cells (2017)

Small clinical studies have shown that oral treatment with the plant alkaloid berberine (BBR) reduces blood glucose levels similar to that of metformin and have promoted its use as a novel anti-diabetic therapy. However, in vitro studies have shown that high concentrations of BBR potently inhibit cell proliferation through inhibition of mitochondrial function. Cardiolipin (Ptd<sub>2</sub>Gro) is a key phospholipid required for regulating mitochondrial bioenergetic function. We examined if BBR inhibited oxygen consumption rate in H9c2 cardiac myocytes through alteration in Ptd<sub>2</sub>Gro metabolism. Treatment of H9c2 cells with BBR resulted in a rapid (within minutes) concentration-dependent decrease in the oxygen consumption rate (OCR) as determined using a Seahorse XF24 analyzer. Concentrations of BBR as low as 1 µM were effective in inhibiting OCR. In addition, all concentrations of BBR inhibited the fatty acid-mediated increase in OCR that was observed in untreated cells. Treatment of H9c2 cells with up to 25 µM BBR for 24 h markedly reduced [<sup>3</sup>H]thymidine incorporation into cells but did not alter the pool size of Ptd<sub>2</sub>Gro. In contrast, 12.5 µM BBR increased [1-<sup>14</sup>C]palmitate incorporation into Ptd<sub>2</sub>Gro and 12.5 µM and 25 µM BBR reduced [1-<sup>14</sup>C]oleate incorporation into Ptd<sub>2</sub>Gro. Protein kinase C delta (PKCδ) activation through its increased membrane association is known to alter Ptd<sub>2</sub>Gro distribution within mitochondria. BBR treatment resulted in a decrease in membrane-associated PKCδ and attenuated the palmitate-mediated increase in PKCδ membrane-association. Thus, BBR treatment of H9c2 cardiac myocytes inhibits cellular OCR independent of alteration in Ptd<sub>2</sub>Gro levels.
Self-Focusing in Damage Experiments Revisited (1986)

Last year we reported that the power of importance in self-focusing experiments is the second critical power, P2, defined by P2=3.77 P1 rather than the often quoted P1=c λ2/(32π2n2). Here n2 is the nonlinear refractive index, c the speed of light and λ the wavelength (both in vacuum). The factor of 3.77 is a numerical factor coming from computer calculations as discussed by Marburger [1]. We also presented a method by which we could obtain n2 at irradiances very near to damage. In addition, we showed the experimental conditions under which self-focusing is unimportant in damage experiments. We have now extended these results so that in damage experiments where self-focusing is important we can estimate the reduced spot size within the bulk at damage and, thus, obtain the damaging electric field magnitude. This we do by observing the far field time integrated spatial irradiance distribution. We present data for SiO2, NaCl, BK-7, and CS2.
Nucleation of focal conic domains in smectic A liquid crystals (1994)

The first-order structural transitions caused by an external magnetic field or by a surface anchoring are considered for a smectic A liquid crystal in the restricted geometry of a flat cell. The transition occurs by nucleation of focal conic domains. The free energy of the system is calculated as a function of the order parameter ρ= domain radius/cell thickness for finite value of the splay (K) and a saddle-splay ($\bar{K}$) elastic constants and the anchoring coefficient. For small ρ the behavior of the system is defined by the balance of the stabilising elastic term and destabilising field (or anchoring) term. Homogeneous nucleation from ideal uniform state is hindered by high energetic barrier unless $\bar{K}$ is positive and comparable (or larger) than K. A few possible scenarios of heterogeneous nucleation have been considered, among them the nucleation at local layer undulations and the nucleation at field-induced dislocations. The most effective and general scenario is the nucleation at distortions (dislocations) caused by bulk or surface irregularities. The expansion of the domain (ρ≫1) is governed by the balance between the field and surface anchoring and does not depend directly on the elastic constants. The saturation field that provides the domain expansion can be smaller than the threshold field for other known mechanisms of the SmA instabilities.
Peripheral Neuropathy Induced by Microtubule-Targeted Chemotherapies: Insights into Acute Injury and Long-term Recovery (2017)

Chemotherapy-induced peripheral neuropathy (CIPN) is a major cause of disability in cancer survivors. CIPN investigations in preclinical model systems have focused on either behaviors or acute changes in nerve conduction velocity (NCV) and amplitude, but greater understanding of the underlying nature of axonal injury and its long-term processes is needed as cancer patients live longer. In this study, we used multiple independent endpoints to systematically characterize CIPN recovery in mice exposed to the antitubulin cancer drugs eribulin, ixabepilone, paclitaxel, or vinorelbine at MTDs. All of the drugs ablated intraepidermal nerve fibers and produced axonopathy, with a secondary disruption in myelin structure within 2 weeks of drug administration. In addition, all of the drugs reduced sensory NCV and amplitude, with greater deficits after paclitaxel and lesser deficits after ixabepilone. These effects correlated with degeneration in dorsal root ganglia (DRG) and sciatic nerve and abundance of Schwann cells. Although most injuries were fully reversible after 3-6 months after administration of eribulin, vinorelbine, and ixabepilone, we observed delayed recovery after paclitaxel that produced a more severe, pervasive, and prolonged neurotoxicity. Compared with other agents, paclitaxel also displayed a unique prolonged exposure in sciatic nerve and DRG. The most sensitive indicator of toxicity was axonopathy and secondary myelin changes accompanied by a reduction in intraepidermal nerve fiber density. Taken together, our findings suggest that intraepidermal nerve fiber density and changes in NCV and amplitude might provide measures of axonal injury to guide clinical practice.<b>Significance:</b> This detailed preclinical study of the long-term effects of widely used antitubulin cancer drugs on the peripheral nervous system may help guide clinical evaluations to improve personalized care in limiting neurotoxicity in cancer survivors. <i>Cancer Res; 78(3); 817-29. ©2017 AACR</i>.
Surface normal coupling to multiple-slot and cover-slotted silicon nanocrystalline waveguides and ring resonators (2014)

Grating couplers are ideal for coupling into the tightly confined propagation modes of semiconductor waveguides. In addition, nonlinear optics has benefited from the sub-diffraction limit confinement of horizontal slot waveguides. By combining these two advancements, slot-based nonlinear optics with mode areas less than 0.02 &mu;m<sup>2</sup> can become as routine as twisting fiber connectors together. Surface normal fiber alignment to a chip is also highly desirable from time, cost, and manufacturing considerations. To meet these considerable design challenges, a custom genetic algorithm is created which, starting from purely random designs, creates a unique four stage grating coupler for two novel horizontal slot waveguide platforms. For horizontal multiple-slot waveguides filled with silicon nanocrystal, a theoretical fiber-towaveguide coupling efficiency of 68% is obtained. For thin silicon waveguides clad with optically active silicon nanocrystal, known as cover-slot waveguides, a theoretical fiber-to-waveguide coupling efficiency of 47% is obtained, and 1 dB and 3 dB theoretical bandwidths of 70 nm and 150 nm are obtained, respectively. Both waveguide platforms are fabricated from scratch, and their respective on-chip grating couplers are experimentally measured from a standard single mode fiber array that is mounted surface normally. The horizontal multiple-slot grating coupler achieved an experimental 60% coupling efficiency, and the horizontal cover-slot grating coupler achieved an experimental 38.7% coupling efficiency, with an extrapolated 1 dB bandwidth of 66 nm. This report demonstrates the promise of genetic algorithm-based design by reducing to practice the first large bandwidth vertical grating coupler to a novel silicon nanocrystal horizontal cover-slot waveguide.
3D silicon electrodes with built-in glass capillaries for dielectrophoretic single-cell positioning and anaylisis (2015)

We present microfluidic designs for dielectrophoretic positioning of single cells and their subsequent analysis based on 3D silicon electrodes featuring built-in capillaries. The designs are presented through numerical simulations as well as experimental validations showing effectiveness of dielectrophoretic forces in trapping single cells. Single-cell experiments are also demonstrated including viability assays and ionophore-mediated intracellular calcium flux assays. Seal resistance measurements between the capillaries and cells trapped, which are essential for patch-clamp assays, are reported.
Thickness determination of poly-Si/poly-oxide/poly-Si/SiO 2 /Si structure by ellipsometer (1993)

An ellipsometry measurement method is proposed to measure the poly-Si/poly-oxide/poly-Si/SiO2/Si structure. The thickness of each layer in this structure can be easily obtained by a conventional ellipsometry measurement. The measured result is consistent with that of cross-sectional TEM.
Neutron Scattering and Computational Studies of the Structure and Dynamics of NaMgH3 (2009)

NaMgH3 has been prepared by the solid state reaction of NaH and MgH2 under high temperature and high hydrogen pressure conditions via the Molten State Process (MSP) developed at Savannah River National Laboratory. The neutron vibrational spectrum of sodium magnesium hydride, NaMgH3, has been collected at 10 K on the Filter Difference Spectrometer (FDS) at the Los Alamos Neutron Scattering Center. Computational optimization of the structure of NaMgH3 indicates a rhombohedral structure 3.7 kJ/mol above the published orthorhombic structure. This suggests possible structural disorder or coexistence of the rhombohedral phase with an orthorhombic structure. Comparison of the calculated vibrational spectra for the rhombohedral and orthorhombic structures with the experimental vibrational spectrum collected on the Filter Difference Spectrometer at Los Alamos National Laboratory supports the presence of two phases or of structural disorder in the material.
ArabidopsisRECEPTOR-LIKE PROTEIN30 and Receptor-Like Kinase SUPPRESSOR OF BIR1-1/EVERSHED Mediate Innate Immunity to Necrotrophic Fungi (2013)

Effective plant defense strategies rely in part on the perception of non-self determinants, so-called microbe-associated molecular patterns (MAMPs), by transmembrane pattern recognition receptors leading to MAMP-triggered immunity. Plant resistance against necrotrophic pathogens with a broad host range is complex and yet not well understood. Particularly, it is unclear if resistance to necrotrophs involves pattern recognition receptors. Here, we partially purified a novel proteinaceous elicitor called sclerotinia culture filtrate elicitor1 (SCFE1) from the necrotrophic fungal pathogen Sclerotinia sclerotiorum that induces typical MAMP-triggered immune responses in Arabidopsis thaliana. Analysis of natural genetic variation revealed five Arabidopsis accessions (Mt-0, Lov-1, Lov-5, Br-0, and Sq-1) that are fully insensitive to the SCFE1-containing fraction. We used a forward genetics approach and mapped the locus determining SCFE1 sensitivity to receptor-like protein30 (RLP30). We also show that SCFE1-triggered immune responses engage a signaling pathway dependent on the regulatory receptor-like kinases brassinosteroid insensitive1-associated receptor kinase1 (BAK1) and Suppressor of BIR1-1/evershed (SOBIR1/EVR). Mutants of RLP30, BAK1, and SOBIR1 are more susceptible to S. sclerotiorum and the related fungus Botrytis cinerea. The presence of an elicitor in S. sclerotiorum evoking MAMP-triggered immune responses and sensed by RLP30/SOBIR1/BAK1 demonstrates the relevance of MAMP-triggered immunity in resistance to necrotrophic fungi.
Withaferin-A kills cancer cells with and without telomerase: chemical, computational and experimental evidences (2017)

Maintenance of telomere length is the most consistent attribute of cancer cells. Tightly connected to their capacity to overcome replicative mortality, it is achieved either by activation of telomerase or an Alternative mechanism of Lengthening of Telomeres (ALT). Disruption of either of these mechanisms has been shown to induce DNA damage signalling leading to senescence or apoptosis. Telomerase inhibitors are considered as potential anticancer drugs but are ineffective for ALT cancers (~15% of all cancers). Withaferin-A (Wi-A), a major constituent of the medicinal plant, Withania somnifera (Ashwagandha), has been shown to exert anti-tumour activity. However, its effect on either telomerase or ALT mechanisms has not been investigated. Here, by using isogenic cancer cells with/without telomerase, we found that Wi-A caused stronger cytotoxicity to ALT cells. It was associated with inhibition of ALT-associated promyelocytic leukemia nuclear bodies, an established marker of ALT. Comparative analyses of telomerase positive and ALT cells revealed that Wi-A caused stronger telomere dysfunction and upregulation of DNA damage response in ALT cells. Molecular computational and experimental analyses revealed that Wi-A led to Myc-Mad mediated transcriptional suppression of NBS-1, an MRN complex protein that is an essential component of the ALT mechanism. The results suggest that Wi-A could be a new candidate drug for ALT cancers.
Chimeric protein for selective cell attachment onto cellulosic substrates (2007)

We have developed a fusion protein (CBD-LG) incorporating a cellulose-binding domain and an antibody binding domain, protein LG, to provide an adaptor molecule for cell separation with regenerated cellulose hollow fiber arrays. A single hollow fiber cell adhesion assay utilizing a CD34+ cell line, KG1a, was used to investigate whether ligand affinity interactions were strong enough for cell attachment and separation. CBD-LG efficiently captured CD34+ cells labeled with the mouse IgG2a monoclonal antibody MHCD3400. However, it was not possible to bind CD34+ cells labeled with an IgG1 antibody (HPCA-2). The low affinity of HPCA-2 for LG was overcome by secondary antibodies: KG1a cells that were dual labeled with HPCA-2 followed by rat anti-mouse IgG1 adhered inside hollow fibers coated with CBD-LG. Alternatively, immobilized rabbit polyclonal anti-mouse IgG1 captured cells labeled with HPCA-2. The development of an adaptor molecule to display recombinant domains at the surface of hollow fibers will be an effective tool to investigate cellular ligand-receptor interactions, a necessary step in the development of hollow fiber bioreactors for manufacture of human cellular products.
The John Insall Award: No Benefit of Minimally Invasive TKA on Gait and Strength Outcomes: A Randomized Controlled Trial (2012)

Level I, therapeutic study. See Instructions to Authors for a complete description of levels of evidence.
Analysis of omics data with genome-scale models of metabolism (2012)

Over the past decade a massive amount of research has been dedicated to generating omics data to gain insight into a variety of biological phenomena, including cancer, obesity, biofuel production, and infection. Although most of these omics data are available publicly, there is a growing concern that much of these data sit in databases without being used or fully analyzed. Statistical inference methods have been widely applied to gain insight into which genes may influence the activities of others in a given omics data set, however, they do not provide information on the underlying mechanisms or whether the interactions are direct or distal. Biochemically, genetically, and genomically consistent knowledge bases are increasingly being used to extract deeper biological knowledge and understanding from these data sets than possible by inferential methods. This improvement is largely due to knowledge bases providing a validated biological context for interpreting the data.
Automatic Bass Line Transcription from Streaming Polyphonic Audio (2007)

This paper proposes a method for the automatic transcription of the bass line in polyphonic music. The method uses a multiple-FO estimator as a front-end and this is followed by acoustic and musicological models. The acoustic modeling consists of separate models for bass notes and rests. The musicological model estimates the key and determines probabilities for the transitions between notes using a conventional bigram or a variable-order Markov model. The transcription is obtained with Viterbi decoding through the note and rest models. In addition, a causal algorithm is presented which allows transcription of streaming audio. The method was evaluated using 87 minutes of music from the RWC Popular Music Database. Recall and precision rates of 64% and 60%, respectively, were achieved for discrete note events.
The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C (2021)

Lysosome dysfunction is a shared feature of rare lysosomal storage diseases and common age-related neurodegenerative diseases. Microglia, the brain-resident macrophages, are particularly vulnerable to lysosome dysfunction because of the phagocytic stress of clearing dying neurons, myelin, and debris. CD22 is a negative regulator of microglial homeostasis in the aging mouse brain, and soluble CD22 (sCD22) is increased in the cerebrospinal fluid of patients with Niemann-Pick type C disease (NPC). However, the role of CD22 in the human brain remains unknown. In contrast to previous findings in mice, here, we show that CD22 is expressed by oligodendrocytes in the human brain and binds to sialic acid–dependent ligands on microglia. Using unbiased genetic and proteomic screens, we identify insulin-like growth factor 2 receptor (IGF2R) as the binding partner of sCD22 on human myeloid cells. Targeted truncation of IGF2R revealed that sCD22 docks near critical mannose 6-phosphate–binding domains, where it disrupts lysosomal protein trafficking. Interfering with the sCD22-IGF2R interaction using CD22 blocking antibodies ameliorated lysosome dysfunction in human <i>NPC1</i> mutant induced pluripotent stem cell–derived microglia-like cells without harming oligodendrocytes in vitro. These findings reinforce the differences between mouse and human microglia and provide a candidate microglia-directed immunotherapeutic to treat NPC.
A reevaluation of the branching ratio for the reaction of amidogen with nitric oxide (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleA reevaluation of the branching ratio for the reaction of amidogen with nitric oxideJoel A. Silver and Charles E. KolbCite this: J. Phys. Chem. 1987, 91, 13, 3713–3714Publication Date (Print):June 1, 1987Publication History Published online1 May 2002Published inissue 1 June 1987https://pubs.acs.org/doi/10.1021/j100297a051https://doi.org/10.1021/j100297a051research-articleACS PublicationsRequest reuse permissionsArticle Views37Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
High-phase-resolution 77-GHz-band radar module for near-field millimeter-wave imaging (2010)

Near-field millimeter-wave (MMW) imaging is a unique approach for inspecting cracks in covered concrete surfaces to assess the deterioration of concrete structures. We have developed a 77-GHz-band radar module with in-phase and quadrature detection which is superior to measuring both of the amplitude and phase of MMW in a near-field range. A monostatic radar system is hybrid integrated into the module with a constant-width antipodal tapered slot antenna with an antenna gain of 14.5 dBi which is connected to a microstrip-line coupler with an isolation of higher than 26 dB using a leakage cancellation technique. In distance measurements in free space, the phase resolution is less than 8 degrees corresponding to the distance resolution of smaller than 0.01 mm, which is high enough to distinguish MMW signals scattered by the cracks from multiple reflection of the concrete surfaces and inside aggregates.
A High-Speed Millimeter-Wave QPSK Transmitter in 28nm CMOS FD-SOI for Polymer Microwave Fibers Applications (2019)

Benefiting from considerable progress in the design of low-power, low cost and high-speed millimeter-wave circuits, Polymer Microwave Fibers (PMF) are gaining interest in the context of serial links. In this work, an innovative dual-band Quadrature Phase Shift Keying (QPSK) architecture, which is based on integrated wideband and low loss differential hybrid couplers, is proposed to increase data rate capability while still preserving low power and moderate range potentials. A circuit demonstrator in 28 nm CMOS FD-SOI is presented to validate the concepts. It achieves fifth harmonic locking on a wide continuous locking range and realizes 9 Gb/s data rate in the E-band.
Index and Adjacent Level Kinematics After Cervical Disc Replacement and Anterior Fusion (2010)

TDR with the porous coated motion implant is able to restore and maintain lordotic alignment and disc height and maintain angular motion while allowing for similar translation to that seen before surgery. In contrast, after ACDF, the superior adjacent level developed increased angular motion compared with preoperative range of motion. This study provides in vivo data regarding the functioning of TDR and ACDF and their impact on adjacent-level kinematics.