gebhart/patrepeval huggingface dataset:
Tumor VEGF:VEGFR2 autocrine feed-forward loop triggers angiogenesis in lung cancer (2013)

The molecular mechanisms that control the balance between antiangiogenic and proangiogenic factors and initiate the angiogenic switch in tumors remain poorly defined. By combining chemical genetics with multimodal imaging, we have identified an autocrine feed-forward loop in tumor cells in which tumor-derived VEGF stimulates VEGF production via VEGFR2-dependent activation of mTOR, substantially amplifying the initial proangiogenic signal. Disruption of this feed-forward loop by chemical perturbation or knockdown of VEGFR2 in tumor cells dramatically inhibited production of VEGF in vitro and in vivo. This disruption was sufficient to prevent tumor growth in vivo. In patients with lung cancer, we found that this VEGF:VEGFR2 feed-forward loop was active, as the level of VEGF/VEGFR2 binding in tumor cells was highly correlated to tumor angiogenesis. We further demonstrated that inhibition of tumor cell VEGFR2 induces feedback activation of the IRS/MAPK signaling cascade. Most strikingly, combined pharmacological inhibition of VEGFR2 (ZD6474) and MEK (PD0325901) in tumor cells resulted in dramatic tumor shrinkage, whereas monotherapy only modestly slowed tumor growth. Thus, a tumor cell-autonomous VEGF:VEGFR2 feed-forward loop provides signal amplification required for the establishment of fully angiogenic tumors in lung cancer. Interrupting this feed-forward loop switches tumor cells from an angiogenic to a proliferative phenotype that sensitizes tumor cells to MAPK inhibition.
Synaptotagmin 7 outperforms synaptotagmin 1 to promote the formation of large, stable fusion pores via robust membrane penetration (2022)

Abstract Synaptotagmin-1 and synaptotagmin-7 are two prominent Ca 2+ sensors that regulate exocytosis in neuronal and neuroendocrine cells. Upon binding Ca 2+ , both proteins partially penetrate lipid bilayers that bear anionic phospholipids, but the specific underlying mechanisms that enable them to trigger exocytosis remain controversial. Here, we examined the biophysical properties of these two synaptotagmin isoforms and compared their interactions with phospholipid membranes. We discovered that synaptotagmin-1•membrane interactions are greatly influenced by membrane order; tight packing of phosphatidylserine inhibits binding due to impaired membrane penetration. In contrast, synaptotagmin-7 exhibits robust membrane binding and penetration activity regardless of phospholipid acyl chain structure. Thus, synaptotagmin-7 is a “super-penetrator”. We exploited these observations to specifically isolate and examine the role of membrane penetration in synaptotagmin function. Using nanodisc-black lipid membrane electrophysiology, we demonstrate that membrane penetration is a critical component that underlies how synaptotagmin proteins regulate reconstituted, exocytic fusion pores in response to Ca 2+ .
Measurement of the charge asymmetry in top quark pair production in pp collisions at $\sqrt{s}=7\ \mathrm{TeV}$ using the ATLAS detector (2012)

A measurement of the top-antitop production charge asymmetry A C is presented using data corresponding to an integrated luminosity of 1.04 fb -1 of pp collisions at s = 7 TeV collected by the ATLAS detector at the LHC. Events are selected with a single lepton (electron or muon), missing transverse momentum and at least four jets of which at least one jet is identified as coming from a b-quark. A kinematic fit is used to reconstruct the t t event topology. After background subtraction, a Bayesian unfolding procedure is performed to correct for acceptance and detector effects. The measured value of A C is A C = -0.0190.028 (stat.)0.024 (syst.), consistent with the prediction from the MC@NLO Monte Carlo generator of A C = 0.006 0.002.
Kynureninase Is a Novel Candidate Gene for Hypertension in Spontaneously Hypertensive Rats (2002)

The rostral ventrolateral medulla (RVLM) plays a critical role in the tonic and reflexive regulation of arterial blood pressure. Recent studies have demonstrated that injection of kynurenic acid (KYN) into the RVLM of spontaneously hypertensive rats (SHR) decreases arterial blood pressure. We hypothesized that a relative increase in the excitatory amino acid-mediated drive of RVLM vasomotor neurons in SHR may be due to derangement of one of the enzymes that affect the KYN level in the brain. We selected kynureninase, kynureninase hydroxylase, kynurenine aminotransferase type I, and kynurenine aminotransferase type II as candidates that may affect the KYN level in the brainstem. We conducted association studies between polymorphisms of these genes and blood pressure in an F2 population derived from SHR and Wistar-Kyoto rats (WKY). The cosegregation analysis indicated that only the kynureninase gene (KYNU) polymorphism influenced systolic blood pressure (SBP) and residuals of systolic blood pressure after adjusting for heart rate and body weight (RSBP). KYNU was found to be located on rat chromosome 3, and quantitative trait loci analysis at this locus indicated that the logarithms of the odds scores for KYNU in terms of SBP and RSBP were 2.0 and 3.3, respectively. This association with blood pressure decreased in proportion to the distance from KYNU. The expression level of KYNU mRNA in the brainstem was about 3.1 and 2.9 times higher in 10-week-old and 16-week-old SHR than in age-matched WKY, respectively. The increased expression of KYNU in SHR is thought to decrease the KYN level. KYNU seems to be one of the genes that contributes to hypertension in SHR.
A Flip-Chip-Packaged 25.3 dBm Class-D Outphasing Power Amplifier in 32 nm CMOS for WLAN Application (2011)

A 2.4 GHz outphasing power amplifier (PA) is implemented in a 32 nm CMOS process. An inverter-based class-D PA topology is utilized to obtain low output impedance and good linearity in the outphasing system. MOS switch non-idealities, such as finite on-resistance and finite rise and fall times are analyzed for their impact on outphasing linearity and efficiency. Outphasing combining is performed via a transformer configured to achieve reduced loss at power backoff. The fabricated class-D outphasing PA delivers 25.3 dBm peak CW power with 35% total system Power Added Efficiency (includes all drivers). Average OFDM power is 19.6 dBm with efficiency 21.8% when transmitting WiFi signals with no linearization required. The PA is packaged in a flip-chip BGA package. Good linearity performance (ACPR and EVM) demonstrates the applicability of inverter-based class-D amplifiers for outphasing configurations.
Impact of therapeutic drug monitoring of antiretroviral drugs in routine clinical management of patients infected with human immunodeficiency virus and related health care costs: a real-life study in a large cohort of patients (2014)

Inclusion of TDM as part of routine clinical optimization of drug dosing in HIV-infected patients is associated with higher adherence to therapy, reduced length of hospitalization stay, and reduced cost of illness.
Erratum to: Search for a new scalar resonance decaying to a pair of Z bosons in proton-proton collisions at s = 13 $$ \sqrt{s}=13 $$ TeV (2019)

In both panels of figure 11, the unit of the z axis was mistakenly written as pb when it should have been fb. The corrected versions are shown in figure 1.
Variance stabilization of targeted estimators of causal parameters in high-dimensional settings (2017)

Exploratory analysis of high-dimensional biological sequencing data has received much attention for its ability to allow the simultaneous screening of numerous biological characteristics. While there has been an increase in the dimensionality of such data sets in studies of environmental exposure and biomarkers, two important questions have received less interest than deserved: (1) how can independent estimates of associations be derived in the context of many competing causes while avoiding model misspecification, and (2) how can accurate small-sample inference be obtained when data-adaptive techniques are employed in such contexts. The central focus of this paper is on variable importance analysis in high-dimensional biological data sets with modest sample sizes, using semiparametric statistical models. We present a method that is robust in small samples, but does not rely on arbitrary parametric assumptions, in the context of studies of gene expression and environmental exposures. Such analyses are faced with not only issues of multiple testing, but also the problem of teasing out the associations of biological expression measures with exposure, among confounds such as age, race, and smoking. Specifically, we propose the use of targeted minimum loss-based estimation (TMLE), along with a generalization of the moderated t-statistic of Smyth, relying on the influence curve representation of a statistical target parameter to obtain estimates of variable importance measures (VIM) of biomarkers. The result is a data-adaptive approach that can estimate individual associations in high-dimensional data, even with relatively small sample sizes.
Acceleration of Spectral Domain Approach for Generalized Multilayered Shielded Microstrip Interconnects Using Two Fast Convergent Series (2013)

A simple and versatile approach for the acceleration of the spectral domain approach for generalized shielded microstrip interconnects is presented. This approach uses asymptotic expansion for the Bessel's function and the Green's function followed by an approximation of infinite summation using two fast convergent sine cosine series. The asymptotic expansion coefficients of the Green's functions are found by a combination of analytical and numerical approaches. The infinite summation involved in the computation of the elements of the Galerkin matrix is accelerated using two fast convergent sine cosine series. The use of a few entire-domain basis functions gives very accurate results for the propagation constants for any mode in the general case of a multilayered shielded microstrip line. In addition to this, closed-form expressions are developed to choose the number of terms and some parameters to adaptively accelerate the convergence of the second type of fast convergent series for a given accuracy. This approach can be extended to handle multiple interconnects in the same layer and in different layers and also to include the effect of finite thickness and conductivity.
Graphene: Synthesis of Layer‐Tunable Graphene: A Combined Kinetic Implantation and Thermal Ejection Approach (Adv. Funct. Mater. 24/2015) (2015)

On page 3666, Q. Yuan, Z. Di, and colleagues take advantage of the dual metal substrate of Ni-coated Cu foils to precisely control of layer number of graphene by ion implantation and the layer number of graphene strictly corresponds to the implantation fluence as expected. Besides, the formation mechanism is explored in detail by the experimental analysis and confirmed by theoretical calculations.
Joint halftoning and watermarking (2003)

A framework to jointly halftone and watermark a grayscale images is presented. The framework needs the definition of three components: a human visual system (HVS)-based error metric between the continuous-tone image and a halftone, a watermarking scheme with a corresponding watermark detection measure, and a search strategy to traverse the space of halftones. We employ the HVS-based error metric used in the direct binary search (DBS) halftoning algorithm, and we use a block-based spread spectrum watermarking scheme and the toggle and swap search strategy of DBS. The halftone is printed on a desktop printer and scanned using a flatbed scanner. The watermark is detected from the scanned image and a number of post-processed versions of the scanned image, including one restored in Adobe PhotoShop. The results show that the watermark is extremely resilient to printing, scanning, and post-processing; for a given baseline image quality, joint optimization is better than watermarking and halftoning independently. For this particular algorithm, the original continuous-tone image is required to detect the watermark.
One-megabase yeast artificial chromosome and 400-kilobase cosmid-phage contigs containing the von Hippel-Lindau tumor suppressor and Ca(2+)-transporting adenosine triphosphatase isoform 2 genes. (1994)

We have isolated and ordered yeast artificial chromosomes (YACs) and cosmids surrounding the von Hippel-Lindau (VHL) tumor suppressor and plasma membrane Ca(2+)-transporting ATPase isoform 2 (PMCA-2) genes on chromosome 3p25-26. The YAC contig consists of six YACs and covers a region of 1 megabase. A cosmid-phage contig around VHL and PMCA-2 genes (400 kilobases) was established and integrated into the YAC map. Using these clones, we generated an EcoRI map of the 400-kilobase region. PMCA-2 and VHL complementary DNA were positioned entirely within the cosmid-phage contig as well as two polymorphic markers (D3S601 and D3S1317). This physical map of the cloned region will allow a detailed analysis of both the PMCA-2 and VHL genes. Some of the genomic clones may be useful for isolation of the full-length VHL complementary DNA.
High power COD-free operation of 0.98 µm InGaAs/GaAs/InGaPlasers with non-injection regions near the facets (1994)

The authors demonstrate the catastrophic-optical-damage-free high-output-power operation of 0.98 µm InGaAs/InGaP/GaAs buried-ridge-structure lasers with non-injection regions near the facets. A maximum output power of 466 mW and fundamental operation at 100 mW were achieved.
A deterministically controlled four-segment polarization-mode dispersion emulator (2002)

In this paper, we propose a novel design of a first- and second-order polarization-mode dispersion (PMD) emulator based on four concatenated first-order PMD segments. Instead of polarization scrambling at each junction, we set these polarization rotators according to a statistical schedule, so as to produce a realistic probability density function of the first- and second-order PMD presented in long-haul transmission fiber.
In vitro profiling of UCB1350883, a novel, highly selective antagonist of Bcl-2 (2007)

B297 The establishment and maintenance of tumours is reliant in part on the ability of tumour cells to evade apoptosis. Resistance to anticancer agents can also be mediated by the failure of treated cells to undergo apoptosis. The anti-apoptotic members of the Bcl-2 protein family play a key role in suppressing apoptosis by sequestering and neutralizing pro-apoptotic members of the family. We describe UCB1350883, a small molecule antagonist of Bcl-2 function, and its biological activity. UCB1350883 binds the BH3-binding groove of Bcl-2 and is greater than 10-fold selective for Bcl-2 over Bcl-X L , Bcl-w and Mcl-1. The inhibitor shows target-based activity in a Bcl-2-dependent mechanistic cell assay and is able to disrupt endogenous Bcl-2 complexes. We present in vitro data demonstrating the activity of UCB1350883 both alone and in combination with anti-cancer agents in tumour cell growth inhibition assays. This is the first report of a potent and selective Bcl-2 inhibitor; we discuss the importance of the inhibitory profile of compounds targeted against Bcl-2 family proteins with respect to their biological activity.
Rapid and High-Throughput pan-Orthopoxvirus Detection and Identification using PCR and Mass Spectrometry (2009)

The genus Orthopoxvirus contains several species of related viruses, including the causative agent of smallpox (Variola virus). In addition to smallpox, several other members of the genus are capable of causing human infection, including monkeypox, cowpox, and other zoonotic rodent-borne poxviruses. Therefore, a single assay that can accurately identify all orthopoxviruses could provide a valuable tool for rapid broad orthopovirus identification. We have developed a pan-Orthopoxvirus assay for identification of all members of the genus based on four PCR reactions targeting Orthopoxvirus DNA and RNA helicase and polymerase genes. The amplicons are detected using electrospray ionization-mass spectrometry (PCR/ESI-MS) on the Ibis T5000 system. We demonstrate that the assay can detect and identify a diverse collection of orthopoxviruses, provide sub-species information and characterize viruses from the blood of rabbitpox infected rabbits. The assay is sensitive at the stochastic limit of PCR and detected virus in blood containing approximately six plaque-forming units per milliliter from a rabbitpox virus-infected rabbit.
Coherent Diffraction Imaging of Buried Nanostructures in a Reflection Geometry with Extreme Ultraviolet Light (2016)

We use reflection-mode ptychography CDI with HHG illumination to image copper nanostructures buried beneath 100nm of aluminum. Our technique yields absolute reflectivity images, allowing non-destructive detection of diffusion at the Al-Cu boundary, confirmed by Auger-Electron-Spectroscopy.
Extreme-Ultraviolet Pulses with Self-Torque (2019)

Light beams carrying orbital angular momentum (OAM) are well known due to their powerful capabilities for applications in many fields, such as optical communications, microscopy, quantum optics, quantum information or microparticle manipulation. In this work we introduce a new class of light beams that possess a unique property associated with a temporal variation of their OAM: the self-torque of light. Despite the recent progress in the generation of designer ultrafast light waveforms with OAM, up to now there is no evidence for the creation of pulses with time-dependent OAM in any spectral regime. We define the self-torque of light as ħξ = ħdℓ(t)/dt, where ħℓ(t) represents the inherent time-variation of a beam's OAM. This definition has an analogy with mechanical systems that self-induce a variation of their angular momentum.
Solution-state spin-equilibrium properties of the tris[2-(2-pyridyl)imidazole]iron(II) and tris[2-(2-pyridyl)benzimidazole]iron(II) cations (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolution-state spin-equilibrium properties of the tris[2-(2-pyridyl)imidazole]iron(II) and tris[2-(2-pyridyl)benzimidazole]iron(II) cationsKaren A. Reeder, Eric V. Dose, and Lon J. WilsonCite this: Inorg. Chem. 1978, 17, 4, 1071–1075Publication Date (Print):April 1, 1978Publication History Published online1 May 2002Published inissue 1 April 1978https://pubs.acs.org/doi/10.1021/ic50182a054https://doi.org/10.1021/ic50182a054research-articleACS PublicationsRequest reuse permissionsArticle Views891Altmetric-Citations92LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Draft Genome Sequencing and Comparative Analysis of Aspergillus sojae NBRC4239 (2011)

We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.
ChemInform Abstract: SYNTHESIS OF LIPOPHILIC 18‐CROWN‐6 DIACIDS FOR THE MEMBRANE TRANSPORT OF ALKALINE‐EARTH CATIONS (1984)

Abstract Das Tetrametliyl‐weinsäurediamid (I) reagiert als Thallium‐Salz mit dem aus Diethylenglykol über den Monobenzylether (IIa) erhaltenen Iodid (IIc) zu einem Bis‐ether (IIIa), der nach Deblockierung zu (IIIb) über Bromid und Halogenaustausch zum Iodid (IIId) führt.
Percutaneous Intrapericardial Interventions Using a Highly Articulated Robotic Probe (2006)

In order to overcome the limitations of currently available assistive technologies for minimally invasive surgery (MIS), we have developed a novel highly articulated robotic probe (HARP) that can exploit its snake-like structure to navigate in a confined anatomical environment while minimally interacting with the environment along its path. We believe that for procedures involving epicardial interventions on the beating heart, cardiac MIS can be effectively realized with the HARP, entering the pericardial cavity through a subxiphoid port, reaching remote intrapericardial locations on the epicardium without causing hemodynamic and electrophysiologic interference and delivering therapeutic interventions under the direct control of the surgeon
Modeling of defect propagation/growth for in-line defect inspection optimization in VLSI fabrication (2002)

Particulate contamination deposited on silicon wafers is typically the dominant reason for yield loss in VLSI manufacturing. The transformation of contaminating particles into defects and then electrical faults is a very complex process which depends on the defect location, size, material and the underlying IC topography. A rigorous 2D topography simulator METROPOLE, has been developed to allow the prediction and correlation of the critical physical parameters (material, size and location) of contamination in the manufacturing process to device defects. The results for a large number of defect samples simulated using the above approach were compared with data gathered from the AMD-Sunnyvale fabline. A good match was obtained indicating the accuracy of this method which provided a framework for developing contamination to defect propagation/growth macromodels. We have demonstrated that the understanding of defect transformation can be applied to optimizing wafer inspection sampling strategy.
Multipliers and the LeChatelier Principle (2006)

Abstract This chapter examines Samuelson's Le Chatelier principle of how the market responds to a change in parameters of demand and supply curves. It uses examples in demand theory, economic policy, and empirical research to illustrate the principle. It also stresses the flexibility of the principle to adapt to changing assumptions. Changes from the optimizing agents to equilibrium systems whose primary use is to provide a foundation for understanding multipliers are observed. The chapter evaluates the performance of the principle performed when confronted with local optimization problems as in production function settings, and in positive feedbacks systems as in gaming situations. The principle is found progressive in that it is able to capitalize on symmetric relations among substitutes and complements. In that regard, the principle has extended research into multiplier analysis, a research area that will continue into the 21st century.