gebhart/patrepeval huggingface dataset:
Lupus auto-antibodies act as positive allosteric modulators at NMDA receptors and induce spatial memory deficits (2019)

ABSTRACT Patients with Systemic lupus erythematosus (SLE) experience various peripheral and central nervous system manifestations including spatial memory impairment. A subset of auto-antibodies (DNRAbs) cross-react with the GluN2A and GluN2B subunits of the NMDA receptor (NMDAR). We find that these DNRAbs act as positive allosteric modulators on NMDARs with GluN2A-containing NMDARs, even those containing a single GluN2A subunit, exhibiting a much greater sensitivity to DNRAbs than those with exclusively GluN2B. Accordingly, GluN2A-specific antagonists provide greater protection from DNRAb-mediated neuronal cell death than GluN2B antagonists. Using transgenic mice to perturb expression of either GluN2A or GluN2B in vivo , we find that DNRAb-mediated disruption of spatial memory characterized by early neuronal cell death and subsequent microglia-dependent pathologies requires GluN2A-containing NMDARs. Our results indicate that GluN2A-specific antagonists or negative allosteric modulators are strong candidates to treat SLE patients with nervous system dysfunction.
Post-WCMP leakage detection and monitoring on 65-nm devices using an advanced e-beam inspection system (2005)

N+/P-well junction leakage was studied with an electron beam (e-beam) inspection system by detection of the gray level of the tungsten plug (W-plug) in the defect images of post tungsten chemical mechanical polish (WCMP) inspection. Leakage results of wafer acceptance tests (WAT) show a strong correlation with the e-beam inspection results. Failure analysis results reveal that the junction leakage is caused by lateral diffusion of nickel silicide underneath the spacer. The extrusion length correlates with the gray level of the tungsten plug very well.
Restoration and demosaicing for pixel mixture images in dsc video clips (2005)

This paper proposes restoration methods for "pixel mixture". Pixel mixture is a function for saving readout time for digital still cameras (DSCs), which mixes together two pixels on CCD. Pixel mixture reduces the number of pixels to be read out from CCD, and it enables video rate read out from DSCs of more than a million pixels. In this paper, an iterative method is presented in order to recover the image. Both restoration and demosaicing are performed at the same time. Our approach achieves the result of smaller mean square error than conventional interpolation methods.
Application of the floating-gate technique to the study of the n-MOSFET gate current evolution due to hot-carrier aging (1990)

The evolution of the gate current-voltage (I/sub g/-V/sub gs/) characteristics of n-MOSFETs induced by DC stresses at different gate voltage over drain voltage (V/sub ds/) ratios is studied by the floating-gate (FG) measurement technique. It is shown that the I/sub g/-V/sub gs/ curves are always lowered after aging, and that the kinetics are dependent on the aging conditions. A time power law is representative of the V/sub gs/=V/sub ds/ case. It is demonstrated that electron traps are created in the oxide by both hot-hole and hot-electron injection stresses. They are not present in the devices before aging. They can be easily charged and discharged by short electron and hole injections, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Leukemic target susceptibility to natural killer cytotoxicity: relationship with BCR-ABL expression (2002)

Chronic myeloid leukemia is a clonal myeloproliferative expansion of transformed primitive hematopoietic progenitor cells characterized by high-level expression of BCR-ABL chimeric gene, which induces growth factor independence. However, the influence of BCR-ABL expression on cell-mediated cytotoxicity is poorly understood. In the present study, we asked whether BCR-ABL expression interferes with leukemic target sensitivity to natural killer (NK) cell cytolysis. Our approach was based on the use of 2 BCR-ABL transfectants of the pluripotent hematopoietic cell line UT-7 expressing low (UT-7/E8, UT-7/G6) and high (UT-7/9) levels of BCR-ABL. As effector cells, we used CD56(bright), CD16-, CD2- NK cells differentiated in vitro from CD34 cord blood progenitors. We demonstrated that BCR-ABL transfectants UT-7/9 were lysed by NK cells with a higher efficiency than parental and low UT-7/E8.1 and UT-7/G6 transfectants. This enhanced susceptibility to lysis correlated with an increase in expression of intercellular adhesion molecule 1 (ICAM-1) by target cells. Treatment of UT-7/9 cells by STI571 (a specific inhibitor of the abl kinase) resulted in a decrease in NK susceptibility to lysis and ICAM-1 down-regulation in target cells. Furthermore, the constitutive activation of nuclear factor-kappaB (NF-kappaB) detected in BCR-ABL transfectant UT-7/9, was significantly attenuated when cells were treated by STI571. Interestingly, inhibition of NF-kappaB activation by BAY11-67082 (a specific NF-kappaB inhibitor) resulted in down-regulation of ICAM-1 expression and a subsequent decrease in NK-induced killing of UT-7/9 transfectants. Our results show that oncogenic transformation by BCR-ABL may increase susceptibility of leukemic progenitors to NK cell cytotoxicity by a mechanism involving overexpression of ICAM-1 as a consequence of NF-kappaB activation.
Structure and Association of Human Lactoferrin Peptides withEscherichia coliLipopolysaccharide (2004)

An 11-amino-acid amphipathic synthetic peptide homologous to a helical region on helix 1 of human lactoferrin HLP-2 exhibited bactericidal activity against Escherichia coli serotype O111, whereas an analogue synthesized with Pro substituted for Met, HLP-6, had greatly reduced antimicrobial activity. The bactericidal activity of HLP-2 was 10-fold greater than that of HLP-6 in both buffer and growth medium by time-kill assays. These assays also showed a pronounced lag phase that was both concentration and time dependent and that was far greater for HLP-2 than for HLP-6. Both peptides, however, were shown to be equally efficient in destabilizing the outer membrane when the hydrophobic probe 1-N-phenylnaphthylamine was used and to have the same lipopolysaccharide (LPS) binding affinity, as shown by polymyxin B displacement. Circular dichroism (CD) spectroscopy was used to study the structure and the organization of the peptides in solution and upon interaction with E. coli LPS. In the presence of LPS, HLP-2 and HLP-6 were found to bind and adopt a beta-strand conformation rather than an alpha-helix, as shown by nonimmobilized ligand interaction assay-CD spectroscopy. Furthermore, this assay was used to show that there is a time-dependent association of peptide that results in an ordered formation of peptide aggregates. The rate of interpeptide association was far greater in HLP-2 LPS than in HLP-6 LPS, which was consistent with the lag phase observed on the killing curves. These results allow us to propose a mechanism by which HLP-2 folds and self-assembles at the outer membrane surface before exerting its activity.
Merging techniques for performing data fusion on the web (2001)

Data fusion on the Web refers to the merging, into a unified single list, of the ranked document lists, which are retrieved in response to a user query by more than one Web search engine. It is performed by metasearch engines and their merging algorithms utilise the information present in the ranked lists of retrieved documents provided to them by the underlying search engines, such as the rank positions of the retrieved documents and their retrieval scores. In this paper, merging techniques are introduced that take into account not only the rank positions, but also the title and the summary accompanying the retrieved documents. Furthermore, the data fusion process is viewed as being similar to the combination of belief in uncertain reasoning and is modelled using Dempster-Shafer's theory of evidence. Our evaluation experiments indicate that the above merging techniques yield improvements in the effectiveness and that their effectiveness is comparable to that of the approach that merges the ranked lists by downloading and analysing the Web documents.
The TWEAK/Fn14 pathway as an aggravating and perpetuating factor in inflammatory diseases; focus on inflammatory bowel diseases (2012)

The TWEAK/Fn14 pathway is a ligand/receptor pair of the TNFSF that has emerged as a prominent player in normal and pathological tissue remodeling. TWEAK/Fn14 pathway activation drives many processes relevant to autoimmune and inflammatory diseases. IBDs, including CD and UC, are chronic, relapsing inflammatory diseases of the GI tract. These diseases differ in their clinical, macroscopic, and histopathological presentation; however, pathological processes that prominently contribute, more or less in each case, include breakdown of the mucosal epithelial barrier, chronic inflammation, and tissue remodeling with fibrosis. TWEAK may promote the pathogenesis of IBD by signaling through Fn14, which can be up-regulated on IECs, thereby contributing to breakdown of the mucosal barrier; the induction of IEC-derived mediators that promote chronic inflammation and shape gut immunity against commensal flora; and delayed healing and fibrosis. TWEAK may also exert its action on endothelial and stromal cell types, including smooth muscle cells and fibroblasts, to promote chronic inflammation, dysregulated tissue repair, and fibrosis. Here, we review the data supporting an emerging role of the TWEAK/Fn14 pathway in autoimmune and inflammatory diseases, with a particular focus on IBD, and discuss how it interplays with other prominent pathways, including IL-13, TNF-α, and TGF-β, to aggravate and perpetuate the pathological processes underlying IBD.
Incorporating Radiopacity into Implantable Polymeric Biomedical Devices for Clinical Radiological Monitoring (2023)

Longitudinal radiological monitoring of biomedical devices is increasingly important, driven by risk of device failure following implantation. Polymeric devices are poorly visualized with clinical imaging, hampering efforts to use diagnostic imaging to predict failure and enable intervention. Introducing nanoparticle contrast agents into polymers is a potential method for creating radiopaque materials that can be monitored via computed tomography. However, properties of composites may be altered with nanoparticle addition, jeopardizing device functionality. This, we investigated material and biomechanical response of model nanoparticle-doped biomedical devices (phantoms), created from 0-40wt% TaO <sub>x</sub> nanoparticles in polycaprolactone, poly(lactide-co-glycolide) 85:15 and 50:50, representing non-, slow and fast degrading systems, respectively. Phantoms degraded over 20 weeks in vitro, in simulated physiological environments: healthy tissue (pH 7.4), inflammation (pH 6.5), and lysosomal conditions (pH 5.5), while radiopacity, structural stability, mechanical strength and mass loss were monitored. The polymer matrix determined overall degradation kinetics, which increased with lower pH and higher TaO <sub>x</sub> content. Importantly, all radiopaque phantoms could be monitored for a full 20-weeks. Phantoms implanted in vivo and serially imaged, demonstrated similar results. An optimal range of 5-20wt% TaO <sub>x</sub> nanoparticles balanced radiopacity requirements with implant properties, facilitating next-generation biomedical devices.
Optogenetic dissection of neuronal circuits in zebrafish using viral gene transfer and the Tet system (2009)

The conditional expression of transgenes at high levels in sparse and specific populations of neurons is important for high-resolution optogenetic analyses of neuronal circuits. We explored two complementary methods, viral gene delivery and the iTet-Off system, to express transgenes in the brain of zebrafish. High-level gene expression in neurons was achieved by Sindbis and Rabies viruses. The Tet system produced strong and specific gene expression that could be modulated conveniently by doxycycline. Moreover, transgenic lines showed expression in distinct, sparse and stable populations of neurons that appeared to be subsets of the neurons targeted by the promoter driving the Tet-activator. The Tet system therefore provides the opportunity to generate libraries of diverse expression patterns similar to gene trap approaches or the thy-1 promoter in mice, but with the additional possibility to pre-select cell types of interest. In transgenic lines expressing channelrhodopsin-2, action potential firing could be precisely controlled by two-photon stimulation at low laser power, presumably because the expression levels of the Tet-controlled genes were high even in adults. In channelrhodopsin-2-expressing larvae, optical stimulation with a single blue LED evoked distinct swimming behaviors including backward swimming. These approaches provide new opportunities for the optogenetic dissection of neuronal circuit structure and function.
Opportunities to Innovate Today (2012)

We have mentioned before that you do not need to invent new technology to innovate in your organization, industry, market, or geography. Innovators do not have to be inventors.
Photobiomodulation (blue and green light) encourages osteoblastic-differentiation of human adipose-derived stem cells: role of intracellular calcium and light-gated ion channels (2016)

Human adipose-derived stem cells (hASCs) have the potential to differentiate into several different cell types including osteoblasts. Photobiomodulation (PBM) or low level laser therapy (LLLT) using red or near-infrared wavelengths has been reported to have effects on both proliferation and osteogenic differentiation of stem cells. We examined the effects of delivering four different wavelengths (420 nm, 540 nm, 660 nm, 810 nm) at the same dose (3 J/cm2) five times (every two days) on hASCs cultured in osteogenic medium over three weeks. We measured expression of the following transcription factors by RT-PCR: RUNX2, osterix, and the osteoblast protein, osteocalcin. The 420 nm and 540 nm wavelengths were more effective in stimulating osteoblast differentiation compared to 660 nm and 810 nm. Intracellular calcium was higher after 420 nm and 540 nm, and could be inhibited by capsazepine and SKF96365, which also inhibited osteogenic differentiation. We hypothesize that activation of light-gated calcium ion channels by blue and green light could explain our results.
Characterization of an Omnitrap-Orbitrap Platform Equipped with Infrared Multiphoton Dissociation, Ultraviolet Photodissociation, and Electron Capture Dissociation for the Analysis of Peptides and Proteins (2023)

We describe an instrument configuration based on the Orbitrap Exploris 480 mass spectrometer that has been coupled to an Omnitrap platform. The Omnitrap possesses three distinct ion-activation regions that can be used to perform resonant-based collision-induced dissociation, several forms of electron-associated fragmentation, and ultraviolet photodissociation. Each section can also be combined with infrared multiphoton dissociation. In this work, we demonstrate all these modes of operation in a range of peptides and proteins. The results show that this instrument configuration produces similar data to previous implementations of each activation technique and at similar efficiency levels. We demonstrate that this unique instrument configuration is extremely versatile for the investigation of polypeptides.
Etching characteristics of TiN used as hard mask in dielectric etch process (2006)

This study focuses on the etching characteristics of a TiN hard mask in terms of etch rate and faceting when using a dielectric etch process. The etching experiments have been performed on blanket wafers and patterned structures in an inductively coupled plasma using a conventional CF4∕Ar based plasma. The etch rate and faceting of TiN have been measured as a function of the plasma parameters (bias power and pressure) and also plasma chemistries (Ar dilution and CH2F2 addition). The TiN etch rate is about 30nmmin−1 using the base line process conditions (70SCCM CF4, source power of 500W, bias power of 100W, and pressure of 4mTorr). Lower etch rate is observed at lower pressure and bias power and with higher Ar dilution and CH2F2 addition. The faceting is strongly reduced at lower bias power and higher pressure whereas higher Ar dilution and CH2F2 addition have no clear effect on the facet formation. Surface analysis using x-ray photoelectrons spectroscopy reveal that the top surface of TiN is mainly fluorinated in the steady state etching regime whatever the plasma conditions. Plasma diagnostics have been also performed thanks to an optical emission spectrometer, an ion mass spectrometer, and a capacitive probe to determine the fluorine concentration and the ion flux composition and density, respectively. The whole results show that the etching of TiN is mainly controlled by the fluorine concentration and the ions energy dissipated on the surface. The etch rate and faceting evolution will be discussed and interpreted in terms of plasma surface interaction.
Structural studies on tRNA acceptor stem microhelices: exchange of the discriminator base A73 for G in human tRNALeu switches the acceptor specificity from leucine to serine possibly by decreasing the stability of the terminal G1-C72 base pair (1997)

Correct recognition of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (aaRS) is crucial to the maintenance of translational fidelity. The discriminator base A73 in human tRNALeuis critical for its specific recognition by the aaRS. Exchanging A73 for G abolishes leucine acceptance and converts it into a serine acceptor in vitro . Two RNA microhelices of 24 nt length that correspond to the tRNALeuacceptor stem and differ only in the discriminator base were synthesized: a wild-type tRNALeumicrohelix, where nt 21 corresponds to the discriminator base position 73, and an A21G mutant microhelix. To investigate whether different identities of both tRNAs are caused by conformational differences, NMR and UV melting experiments were performed on both microhelices. Two-dimentional NOESY spectra showed both microhelices to exhibit the same overall conformation at their 3'-CCA ends. Thermodynamic analysis and melting behaviour of the base-paired imino protons observed by NMR spectroscopy suggest that the A21G (A73G in tRNA) exchange results in a decrease of melting transition cooperativity and a destabilization of the terminal G1-C20 (G1-C72 in tRNA) base pair. Furthermore, the fact that this 3'-terminal imino proton is more solvent-exposed at physiological temperature might be another indication for the importance of the stability of the terminal base pair for specific tRNA recognition.
Supplementary Figure 3 from p53–Pirh2 Complex Promotes Twist1 Degradation and Inhibits EMT (2023)

&lt;p&gt;Mdm2 does not interact with Twist1. (A) Mdm2 and Twist1 were transfected in HEK293T. Western blot was used to detected the effect of Mdm2 on Twist1 protein level. (B) Mdm2 was immunoprecipitated in HEK293T cells that were transfected with Mdm2 and Twist1 plasmids. p53 was detected in the IP product by western blot. Twist1 was not detected in the IP product.&lt;/p&gt;
Design of LLC Resonant Converters Based on Operation-Mode Analysis for Level Two PHEV Battery Chargers (2014)

In this paper, the efficiency-oriented design considerations are discussed based on the operation-mode analysis of the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LLC</i> converter considering the characteristics of charging profiles. The mode boundaries and distribution are obtained from the precise time-domain model. The operation modes featuring both-side soft-switching capability are identified to design the operating trace of the charging process. Then the design constraints for achieving soft switching with the load varying from zero up to the maximum are discussed. Finally, a charging trajectory design methodology is proposed and validated through experiments on a prototype converting 390 V from the dc power source to the battery emulator in the range of 250–450 V at 6.6 kW with a peak efficiency of 97.96%.
Defect Analysis of Electric and Photonic Double Layer Substrate made by SIMOX 3D sculpting (2006)

From the viewpoint of electric device fabrication, we examined a SIMOX 3D sculpting method (Koonath, 2003) that three dimensionally integrate electric circuits and photonic circuits on an SOI substrate. We investigated buried optical waveguide structure underneath the silicon surface and defect characteristics on the surface of the substrate made by 8" size SIMOX 3D sculpting. As a result, we showed that balancing between no defects on the silicon surface and a formation of buried waveguide is achievable when the BOX by SIMOX 3D sculpting is continuous
Analysis of subspace fitting and ML techniques for parameter estimation from sensor array data (1992)

It is shown that the multidimensional signal subspace method, termed weighted subspace fitting (WSF), is asymptotically efficient. This results in a novel, compact matrix expression for the Cramer-Rao bound (CRB) on the estimation error variance. The asymptotic analysis of the maximum likelihood (ML) and WSF methods is extended to deterministic emitter signals. The asymptotic properties of the estimates for this case are shown to be identical to the Gaussian emitter signal case, i.e. independent of the actual signal waveforms. Conclusions concerning the modeling aspect of the sensor array problem are drawn.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Data from Cancer-Induced Immunosuppression: IL-18–Elicited Immunoablative NK Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;During cancer development, a number of regulatory cell subsets and immunosuppressive cytokines subvert adaptive immune responses. Although it has been shown that tumor-derived interleukin (IL)-18 participates in the PD-1–dependent tumor progression in NK cell–controlled cancers, the mechanistic cues underlying this immunosuppression remain unknown. Here, we show that IL-18 converts a subset of Kit&lt;sup&gt;−&lt;/sup&gt; (CD11b&lt;sup&gt;−&lt;/sup&gt;) into Kit&lt;sup&gt;+&lt;/sup&gt; natural killer (NK) cells, which accumulate in all lymphoid organs of tumor bearers and mediate immunoablative functions. Kit&lt;sup&gt;+&lt;/sup&gt; NK cells overexpressed B7-H1/PD-L1, a ligand for PD-1. The adoptive transfer of Kit&lt;sup&gt;+&lt;/sup&gt; NK cells promoted tumor growth in two pulmonary metastases tumor models and significantly reduced the dendritic and NK cell pools residing in lymphoid organs in a B7-H1–dependent manner. Neutralization of IL-18 by RNA interference in tumors or systemically by IL-18–binding protein dramatically reduced the accumulation of Kit&lt;sup&gt;+&lt;/sup&gt;CD11b&lt;sup&gt;−&lt;/sup&gt; NK cells in tumor bearers. Together, our findings show that IL-18 produced by tumor cells elicits Kit&lt;sup&gt;+&lt;/sup&gt;CD11b&lt;sup&gt;−&lt;/sup&gt; NK cells endowed with B7-H1–dependent immunoablative functions in mice. &lt;i&gt;Cancer Res; 72(11); 2757–67. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;