gebhart/patrepeval huggingface dataset:
Genetic Analysis of Receptor-Gαq Coupling Selectivity (1997)

Many different G protein-linked receptors are preferentially coupled to G proteins of the Gq/11 family. To elucidate the molecular basis underlying this selectivity, different Gq/11-coupled receptors (m3 muscarinic, V1a vasopressin, and gastrin-releasing peptide receptor) were coexpressed (in COS-7 cells) with mutant alphas subunits in which residues present at the C terminus of alphas were replaced with the corresponding alphaq/11 residues. Remarkably, whereas none of the receptors was able to interact with wild type alphas to a significant extent, all three receptors gained the ability to productively couple to a mutant alphas subunit containing a single Glu --> Asn point mutation at position -3. Moreover, the m3 muscarinic and the V1a vasopressin receptors but not the GRP receptor also gained the ability to interact with a mutant alphas subunit containing a single Gln --> Glu point mutation at position -5, indicating that the alphaq/11 residues present in these mutant G protein constructs play key roles in determining the selectivity of receptor recognition. To identify the site(s) on Gq/11-coupled receptors that can functionally interact with the C terminus of alphaq/11 subunits, we next analyzed the ability of a series of hybrid m2/m3 muscarinic receptors to interact with a mutant alphas subunit (sq5) in which the last five amino acids of alphas were replaced with the corresponding alphaq/11 sequence. Similar to the wild type m2 and m3 muscarinic receptors, none of the investigated hybrid receptors was able to efficiently interact with wild type alphas. Interestingly, however, three mutant m2 receptors in which different segments of the second and third intracellular loops were replaced with the corresponding m3 receptor sequences were identified, which, in contrast to the Gi/o-coupled wild type m2 receptor, gained the ability to efficiently activate the sq5 subunit. This observation suggests that multiple intracellular receptor domains form a binding pocket for the C terminus of G protein alphaq/11 subunits.
PAM4 silicon photonic microring resonator-based transceiver circuits (2017)

Increased data rates have motivated the investigation of advanced modulation schemes, such as four-level pulseamplitude modulation (PAM4), in optical interconnect systems in order to enable longer transmission distances and operation with reduced circuit bandwidth relative to non-return-to-zero (NRZ) modulation. Employing this modulation scheme in interconnect architectures based on high-Q silicon photonic microring resonator devices, which occupy small area and allow for inherent wavelength-division multiplexing (WDM), offers a promising solution to address the dramatic increase in datacenter and high-performance computing system I/O bandwidth demands. Two ring modulator device structures are proposed for PAM4 modulation, including a single phase shifter segment device driven with a multi-level PAM4 transmitter and a two-segment device driven by two simple NRZ (MSB/LSB) transmitters. Transmitter circuits which utilize segmented pulsed-cascode high swing output stages are presented for both device structures. Output stage segmentation is utilized in the single-segment device design for PAM4 voltage level control, while in the two-segment design it is used for both independent MSB/LSB voltage levels and impedance control for output eye skew compensation. The 65nm CMOS transmitters supply a 4.4V<sub>ppd</sub> output swing for 40Gb/s operation when driving depletion-mode microring modulators implemented in a 130nm SOI process, with the single- and two-segment designs achieving 3.04 and 4.38mW/Gb/s, respectively. A PAM4 optical receiver front-end is also described which employs a large input-stage feedback resistor transimpedance amplifier (TIA) cascaded with an adaptively-tuned continuous-time linear equalizer (CTLE) for improved sensitivity. Receiver linearity, critical in PAM4 systems, is achieved with a peak-detector-based automatic gain control (AGC) loop.
Separator/Electrode Assembly Based on Thermally Stable Polymer for Safe Lithium‐Ion Batteries (2013)

A separator/electrode assembly (SEA) is prepared using a simple coating and dry phase inversion. The SEA offers a lithium ion battery with high thermal stability and excellent cycling and power capability, which makes it attractive for the high-energy, high-power Li-ion batteries that are being developed for electric vehicle applications. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Answering questions with authority (2008)

This paper presents a novel approach to textual question answering (QA) which identifies answers to natural language questions by leveraging large collections of question-answer pairs extracted from web sources or generated automatically from text.
A Wearable Microneedle‐Based Extended Gate Transistor for Real‐Time Detection of Sodium in Interstitial Fluids (Adv. Mater. 10/2022) (2022)

Biosensors In article number 2108607, Miaomiao Yuan, Hossam Haick, and co-workers report an innovative, stretchable, skin-conformal, fast-response, microneedle, extended-gate field-effect transistor biosensor for real-time detection of sodium in interstitial fluids for minimally invasive health monitoring. High sensitivity, low limit of detection, excellent biocompatibility, and on-body mechanical stability are demonstrated. This platform can be integrated with a wireless-data transmitter and the Internet-of-Things cloud for real-time monitoring and long-term analysis.
Real-time closed-world tracking (2002)

A real-time tracking algorithm that uses contextual information is described. The method is capable of simultaneously tracking multiple, non-rigid objects when erratic movement and object collisions are common. A closed-world assumption is used to adaptively select and weight image features used for correspondence. Results of algorithm testing and the limitations of the method are discussed. The algorithm has been used to track children in an interactive, narrative playspace.
Identification of a Novel Thioredoxin-1 Pseudogene on Human Chromosome 10 (2000)

Thioredoxin (Trx) is a small, ubiquitous protein of 12 kDa that acts as general dithiol-disulfide oxidoreductase via its conserved redox active site Trp-Cys-Gly-Pro-Cys which is located in a protrusion of the protein (Holmgren 1985). Mammalian cells contain two forms of thioredoxin: Trx1, a cytosolic enzyme able to translocate to the nucleus under certain stimuli and be secreted from the cells thus displaying cytokine-like properties and Trx2, a mitochondrial enzyme (Tagaya et al. 1989; Spyrou et al 1997). While many functions have been described for Trx1 for example antioxidant enzyme, modulator of transcription factors, electron donor for enzymes like ribonucleotide reductase and PAPS reductase, etc. (see introduction Spyrou et al. 1997), only an antioxidant function has been assigned to Trx2. Trx2 acts as a reductant of a mitochondrial thioredoxin-dependent peroxidase which protects cells against hydrogen peroxide treatment (Araki et al. 1999). Human Trx1 gene maps at chromosome 9q31 and several bands hybridize with a Trx1 probe in Southern blots suggesting the existence of Trx1 derived sequences in the human genome (Heppell-Parton et al. 1995; Kaghad et al. 1994). As only one active Trx1 gene has been described, the other hybridizing bands might correspond to different inactive pseudogenes (Kaghad et al. 1994), but only one Trx1 pseudogene has been described so far (GenBank accession number: AF146023 (Tonissen and Wells 1991)). We report here the sequence of a second Trx1 retrotranscribed pseudogene and propose the nomenclature wTrx1-1 and wTrx1-2.
Precision Polymerization and Polymers I. Molecular Design and Functions of Dendrimer Porphyrins. (1997)

Convergent法を利用して, ポルフィリンをコアとする空間形態が規制された一連のデンドリマーポルフィリン錯体を分子設計した. 大きなデンドリマー組織に内包された鉄ポルフィリン錯体はヘモグロビンやミオグロビンのように, 酸素分子を可逆的に吸脱着し, 水が存在しても, 酸素捕捉錯体は極めて長寿命であった. また, 一酸化炭素中においてもカルボニル化を受けにくく, 50時間という長い半減期を示した. チトクロムcモデルとして分子設計したアニオン性表面を有する水溶性デンドリマー亜鉛ポルフィリン錯体は, 水中においてメチルビオロゲンのようなカチオン性電子受容体を表面に捕捉し, 空間的に分離した電子供与体-受容体系超分子錯体を形成した. これを光励起すると, 2.6×109s-1の速度定数でデンドリマー組織を通した長距離光誘起電子移動が起こった.
Does vaccination with 4CMenB convey protection against meningococcal serogroup B strains not predicted to be covered by MATS? A study of the UK clonal complex cc269 (2019)

The Meningococcal Antigen Typing System (MATS) has been developed as an hSBA surrogate to evaluate potential coverage afforded by the 4-component meningococcal serogroup B vaccine (4CMenB: <i>Bexsero</i>, GSK). We investigated whether the lower value of MATS coverage among invasive Meningococcus serogroup B clonal complex 269 strains from the United Kingdom (53% in 2014-2015 versus 73% in 2007-2008) reflected the lower bactericidal activity of the vaccine against these isolates. A total of 34 MATS-negative strains (31 were cc269 or closely related) were tested against pooled sera from 32 or 72 4CMenB-vaccinated infants in a serum bactericidal antibody assay in presence of human complement (hSBA). All infants had received four 4CMenB doses in the first 2 y of life. Baseline sera comprised 180 pooled samples from healthy-unvaccinated 2-month-old infants. Twenty of the 34 (59%) MATS-negative strains were killed in hSBA with titers ≥4 by pooled sera from vaccinated infants. There were 13/34 strains with hSBA titers ≥4 and at least a 4-fold rise in titer with respect to pooled baseline sera, and 10/34 with hSBA titers ≥8 and at least a 4-fold rise in titer with respect to baseline. These data confirm MATS as a conservative estimate for predicting strain coverage by 4CMenB.
A Back-Illuminated High-Sensitivity Small-Pixel Color CMOS Image Sensor with Flexible Layout of Metal Wiring (2006)

A 1.3M pixel color image sensor with a back-illuminated configuration and 3.45μm square pixels is fabricated in 0.25μm 1P3M CMOS. Its sensitivity at a wavelength of 550nm is 34% better than that of a conventional device, and it falls by only 15% when the light is incident at an angle of 20 degrees. Flexibility in metal wiring layout improves device characteristics such as saturation output
Experimental demonstration of LDPC coded free-space, space-division-multiplexed systems using Orbital Angular Momentum modes (2014)

The performance of LDPC coded four-mode multiplexed Orbital Angular Momentum (OAM) data link using QPSK signal with net data rate of 320Gbit/s is experimentally investigated. The experiment results show that crosstalk effect can be efficiently mitigated and the LDPC codes with soft decoding can provide >7 dB coding depending on OAM crosstalk.
Far-Field Super-resolution Detection of Plasmonic Near-Fields (2016)

We demonstrate a far-field single molecule super-resolution method that maps plasmonic near-fields. The method is largely invariant to fluorescence quenching (arising from probe proximity to a metal), has reduced point-spread-function distortion compared to fluorescent dyes (arising from strong coupling to nanoscopic metallic features), and has a large dynamic range (of 2 orders of magnitude) allowing mapping of plasmonic field-enhancements regions. The method takes advantage of the sensitivity of quantum dot (QD) stochastic blinking to plasmonic near-fields. The modulation of the blinking characteristics thus provides an indirect measure of the local field strength. Since QD blinking can be monitored in the far-field, the method can measure localized plasmonic near-fields at high throughput using a simple far-field optical setup. Using this method, propagation lengths and penetration depths were mapped-out for silver nanowires of different diameters and for different dielectric environments, with a spatial accuracy of ∼15 nm. We initially use sparse sampling to ensure single molecule localization for accurate characterization of the plasmonic near-field with plans to increase density of emitters in further studies. The measured propagation lengths and penetration depths values agree well with Maxwell finite-difference time-domain calculations and with published literature values. This method offers advantages such as low cost, high throughput, and superresolved mapping of localized plasmonic fields at high sensitivity and fidelity.
High-Speed 2&#x00D7;2 switch for multi-wavelength message routing in on-chip silicon photonic networks (2008)

A 2 times 2 multi-wavelength silicon switch, enabling low-power on-chip message routing with ultra-compact footprints, is designed, fabricated, and tested with switching ratios, transition times, and power penalties reported.
Activation of extracellular signal-regulated kinase (ERK) by mitogenic stimuli is repressed in v-Src-transformed cells. (1997)

Stimulation of mitogenic signaling pathways results in transient activation of the extracellular signal-regulated kinase (ERK) subfamily of mitogen-activated protein kinases (MAPK) in normal cells. We demonstrate here that activation of ERKs in response to serum or phorbol ester stimulation was markedly repressed in three different rodent fibroblast cell lines stably transformed by v-Src. Activation of the MAPK/ERK kinase (MEK) was also repressed in v-Src-transformed cells, indicating that the repression occurs upstream of ERK. Consistent with repression occurring predominantly at the level of MEK, the phosphatase inhibitor orthovanadate could restore ERK activation to a limited extent in some but not all v-Src-transformed cell lines. A similar repression of ERK activation was observed in v-Ras- and v-Raf-transformed cells. In addition, ERK activity was not constitutively elevated in exponentially growing cells transformed by v-Src, v-Ras, or v-Raf as compared with normal cells. These results establish that the ERK activation pathway is repressed in rodent fibroblasts stably transformed by viral oncoproteins that chronically stimulate receptor tyrosine kinase signaling pathways. Furthermore, our findings suggest that elevated ERK activity above basal levels is not required for maintaining cell transformation by these oncoproteins. Taken together, these results indicate that ERK signaling pathways are subject to negative feedback regulation upstream of ERK as a consequence of oncogenic transformation.
Abstract 276: Role of AP1 elements and TCL1 protein in regulation of the gene encoding PTPROt (protein tyrosine phosphatase receptor-type O) in chronic lymphocytic leukemia (2011)

Abstract The gene for protein tyrosine phosphatase receptor-type O encodes two functional isoforms in a tissue-specific manner. The full-length form is expressed in epithelial cells, particularly in the brain and kidney, whereas the truncated form (PTPROt) is primarily expressed in hematopoietic cells. We have previously demonstrated that PTPROt is a bona fide tumor suppressor (J Biol Chem. 2009 Jan 2;284(1):455-64) and is down-regulated in primary CLL samples (Clin Cancer Res. 2007 Jun 1;13(11):3174-81). Further, studies from two laboratories including ours have shown that Syk and Lyn, two key protein tyrosine kinases involved in B-cell receptor signaling, are substrates of PTPROt, igniting interest in understanding deregulation of this tyrosine phosphatase in CLL. While the PTPRO promoter is methylated, the mechanism of its silencing in the pathogenesis of CLL is unexplored. Here, we utilized the Tcl1 transgenic (Tg) mouse model of CLL and a cell line with TPA-inducible expression of PTPROt to elucidate the mechanism of PTPROt silencing. This study demonstrates that PTPROt is transcriptionally silenced in CD19+ spleen B cells from Tcl1 transgenic (Tg) mouse when compared to wild type mice. As observed with primary human CLL, the methylation of PTPRO CGI (CpG island) is significantly higher in Tcl1 Tg CLL B-lymphocytes than in normal B lymphocytes. Significant suppression of PTPROt is also observed at very early time-point (∼7 wks) in CD19+ spleen B-cells from Tcl1 Tg mice compared to normal spleen B-lymphocytes from age-matched WT mice in the absence of detectable methylation at CGI. This data suggests that transcriptional silencing occurs prior to methylation. To understand further the potential transcriptional mechanism of PTPROt suppression in CLL, the role of AP1 in the expression of this gene was explored. We first demonstrate that AP-1 activation by TPA in U937 cells induces PTPROt expression with concurrent recruitment of c-fos and c-jun to its promoter. PTPROt promoter is also responsive to over- and under-expression of AP-1 confirming the role of AP-1 in PTPROt expression. Next, we demonstrate that Tcl1 can repress PTPROt promoter by altering c-fos expression and c-jun activation state. These findings further substantiate the importance of TCL1 in the pathogenesis of CLL. [Supported, in part, by grants CA101956 and CA086978]. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 276. doi:10.1158/1538-7445.AM2011-276
Photorefractive Effect in Liquid-Crystalline Polymers Containing Hydrogen-Bonding Moiety (2005)

The effect of the introduction of microdomains in polymer films on the photorefractive effect was investigated. The photorefractivity of side-chain liquid-crystalline polymers that possess a hydrogen-bonding moiety was examined using a four-wave mixing experiment. The photorefractivity was compared to that of a polymer which has no hydrogen-bonding moiety. A significant difference was found in the photorefractivity between hydrogen-bonding polymers and non-hydrogen-bonding polymers. This difference was likely due to the presence of microdomain structures in the polymers with the hydrogen-bonding moieties.
Efficient representation and interactive streaming of high-resolution panoramic views (2003)

A new system for interactive streaming of high-resolution 360/spl deg/ panoramic views over the Internet is presented. The scene is represented very efficiently using MPEG-4 BIFS and displayed at the client using the HHI 3-D MPEG-4 player. The user can navigate interactively through the scene. The navigation decisions are evaluated to trigger the streaming of the data needed to build the visible screen view and to ensure a fluent visualization of the scene. The system layout is designed to support other, more complex photo realistic 3-D environments later on and, thus, will enable the provision of a variety of new, interactive services over the Internet.
Molecules with Linear π‐Conjugated Pathways between All Substituents: Omniconjugation (2004)

Abstract In this paper, omniconjugation is introduced as a topological phenomenon in π‐conjugated systems. Omniconjugated molecules are defined by the fact that they provide direct and fully π‐conjugated pathways between all substituents attached to them. Surprisingly, until now such topologies have never been explicitly recognized or investigated from this point of view. A topological design scheme is presented as a tool, which enables for the systematic construction of this novel class of π‐electron molecular structures. Molecular building blocks with three or more connection points to the external moieties are proposed, which for the first time allows for the interconnection of many functional entities in a fully conjugated manner. In being truly conjugated, these pathways are expected to provide high transmission probabilities for holes and/or electrons. Omniconjugated structures may play an important role in the design of complex electronic circuitry based on organic molecules. On a larger scale, they may also give rise to special material properties. Although omniconjugation is based on a valence‐bond description of the system, it is shown that our concept is in good agreement with results obtained from a molecular‐orbital description of the electron probability distribution in the frontier orbitals.
Predicting sensitivity to azacytidine in non-small cell cancer lines by absence of activating mutations. (2012)

e18147 Background: A completed clinical trial has demonstrated activity of a combination of epigenetic therapies: entinostat, a histone deacetylase inhibitor, and azacytidine (AZA), a hypomethylating agent. A plasma-based biomarker assaying methylation status of key gene promoters from circulating DNA was developed. In order to test the relationship of activating mutations to sensitivity to epigenetic therapy, we treated non-small cell lung cancer (NSCLC) lines with AZA and assessed tumor growth in xenografts. Tumor from patients on trial was analyzed for mutational status. Methods: Nine NSCLC lines were treated in vitro for 72 hours with 500 nM AZA and injected to form flank tumors in NOG mice. Four lines contain no activating mutations. Of the five mutant lines, three were KRAS and two were EGFR mutations. Lines with no activating mutations are termed “mutation-negative” for known oncogenic drivers. Growth of mock versus treated tumors was compared over time to determine treatment phenotypes. Lines were grouped into four categories: augmented growth compared to mock, no treatment effect, mild inhibition of tumor growth, and marked inhibition. Seventeen tumors from the clinical trial were analyzed by SNaPshot multiplex PCR. Results: Among mutation negative lines three showed marked tumor growth inhibition and one showed mild inhibition. Among cell lines with activating mutations, one showed mild inhibition, three showed no effect, and one showed augmented tumor growth. Among 17 tumor samples from patients on study, four driver mutations were identified: 3 KRAS and one PTEN mutation. All four patients experienced progressive disease on study. Among thirteen patients with mutation negative tumors, three had stable disease and one had a complete response. Conclusions: The association between driver mutation negative status and treatment outcome in NSCLC cell lines in patients receiving AZA and entinostat merits further exploration. Future trials of epigenetic therapy in NSCLC may benefit from a biomarker enrichment strategy and the data presented here represents a potential way forward.