gebhart/patrepeval huggingface dataset:
Regulation of cdk2 Activity in Endothelial Cells That Are Inhibited From Growth by Cell Contact (2000)

Endothelial cells (ECs) are quiescent in normal blood vessels but undergo rapid bursts of proliferation after vascular injury and during angiogenesis. Here we show that the activity of cyclin-dependent kinase-2 (cdk2), a key regulator of the G1 and S phases of the cell cycle, is expressed at high levels in proliferating ECs but at low levels in ECs that are contact-inhibited for growth. Despite these differences in kinase activity, the protein levels of cdk2 and 1 of its activating subunits, cyclin E, are not modulated by these different growth conditions. The cdk inhibitor p27 is highly expressed in contact-inhibited but not proliferating ECs, whereas the level of cyclin A protein is preferentially expressed in proliferating ECs. p27 protein was detected in immunoprecipitable complexes with cdk2 or cyclin E in cultures that were contact-inhibited for growth. The functional significance of the p27 induction was indicated by the detection of a heat-stable cdk2 inhibitory activity that was induced by endothelial cell-cell contact and could be immunodepleted with anti-p27 antibodies. In a confluent EC monolayer, cdk2 kinase activity was activated by a scraping injury that led to cell migration and proliferation. The injury-induced activation of cdk2 coincided with the downregulation of p27 and the induction of cyclin A. These data demonstrate that p27 is induced in confluent cultures of ECs. They also indicate that both p27 induction and cyclin A downregulation contribute to the inhibition of cdk2 and cell proliferation by cell-cell contact in ECs.
[Pyrido[2,3-b]pyrazines inhibiting both erlotinib-sensitive and erlotinib-resistant cell lines, and their preparation via regioselective condensation reaction]. (2014)

The EGFR inhibitor erlotinib possesses high anti-tumor effect but despite the good clinical responses in most of the cases recrudescence occures. This can be attributed to a secondary, acquired mutation causing resistance to tyrosine kinase inhibitors. In our work we were looking for small-molecule inhibitors, which simultaneously affect on the proliferation of erlotinib-sensitive PC9 cells and PC9-ER erlotinib-resistant cells. A set of molecules were selected from Vichem Chemie Research Ltd.'s kinase inhibitor compound library (Nested Chemical Library™). According to the results of medium throughput screening (MTS) of this set of compounds, novel structures with pyrido[2,3-b]pyrazine core were designed. These compounds were proved to be effective inhibitors of resistant cells in phenotypic screening. Based on these results structure-activity relationships were set up. The pyrido[2,3-b]pyrazine core was synthesized by a condensation reaction, which resulting two asymmetric products. In the reaction two regioisomer intermediates formed, and one of the products is the intermediate of the effective compounds. This condensation reaction was optimized, the regioisomers were identified by NMR analysis and X-ray crystallography. As a result of optimization we found that lower reaction temperature and replacement of dimethylformamide solvent with trifluoroacetic acid provided the undesired isomer in less than 2 % ratio.
Other Methods for Glycoside Synthesis: Sections 5.1 and 5.2 (2008)

This chapter contains sections titled: Orthoesters and Related Derivatives Introduction Sugar 1,2-Orthoesters 1,2-O-Alkyl Orthoesters as Glycosyl Donors – Early Developments 1,2-O-Cyanoethylidene Derivatives 1,2-Thioorthoester Derivatives Internal Orthoesters Miscellaneous Orthoesters Orthoester to Glycoside Rearrangement – The Two-Stage Glycosylation Method Revisited Self-Condensation of Mannose 1,2-Orthoesters: Ready Access to (1 → 2)-Linked Mannose Oligosaccharides Rearrangement of Sugar–Sugar Orthoesters Leading to 1,2-cis-Glycosidic Linkages n-Pentenyl-1,2-Orthoesters: Glycosyl Donors with Novel Implications Divergent–Convergent Synthesis of Glycosylaminoglycan 120 from Glycosyl Donors and Acceptors Ensuing from NPOEs From NPOEs to the 1,2-β-Linked Oligomannans of Candida albicans From NPOEs to the Synthesis of a Malaria Candidate Glycosylphosphatidylinositol (GPI) From NPOEs to the Preparation of Glycolipids for Multivalent Presentation The Lipoarabinomannan Components of the Cell Wall Complex of Mycobacterium tuberculosis: NPOEs in Chemoselective, Regioselective and Three-Component Double Differential Glycosidations Relevance of NPOEs to the Regioselectivity in the Glycosylation of Primary Versus Secondary Hydroxyls Iterative Regioselective Glycosylations of Unprotected Glycosyl Donors and Acceptors NPOEs of Furanoses: Key Intermediates in the Elaboration of the Arabino Fragment of LAM Conclusions and Future Directions Typical Experimental Procedures General Procedure for the Preparation of Orthoesters General Procedure for Glycosidation with n-Pentenyl Orthoesters References Other Methods for Glycoside Synthesis: Dehydro and Anhydro Derivatives Introduction Glycals in Glycoside Synthesis Preparation of Glycals Glycals as Glycosyl Donors Anhydro Sugars as Glycosyl Donors 1,2-Anhydro Sugars 1,6-Anhydro Sugars as Glycosyl Donors Conclusion General Experimental Procedures General Method for the Preparation of 2-Deoxy-2-Iodoglycosides from Glycals Preparation of 1,2-Anhydro-tri-O-Benzyl-α-d-Glucose and General Method for Its Use as a Glycosyl Donor in the Formation of β-Glycosides General Method for the Preparation of 2-Deoxy-2-Iodoglycosylbenzenesulfonamides from Glycals and Its Use as Glycosyl Donors in the Synthesis of 2-Benzenesulfonamido-2-Deoxy-β-Glycosides References
AcurosCTS: A fast, linear Boltzmann transport equation solver for computed tomography scatter – Part I: Core algorithms and validation (2018)

Acuros CTS enables a fast and accurate calculation of scatter images by deterministically solving the LBTE thus offering a computationally attractive alternative to Monte Carlo methods. Part II describes the application of Acuros CTS to scatter correction of CBCT scans on the TrueBeam system.
Supplementary Figure 1 from Identification of microRNA-135b in Stool as a Potential Noninvasive Biomarker for Colorectal Cancer and Adenoma (2023)

&lt;p&gt;PDF file - 141KB, Flow-chart of exclusion of subjects in the study.&lt;/p&gt;
Recent Trends in the Incidence and Survival of Stage 1A Pancreatic Cancer: A Surveillance, Epidemiology, and End Results Analysis (2020)

Abstract Background Rapid access to pancreatic imaging and regular pancreatic surveillance may help identify stage I pancreatic cancer. We investigated recent trends in the stage of newly diagnosed pancreatic ductal adenocarcinoma (PDACs), age at diagnosis, and survival. Methods Trends in age-adjusted incidence of stage IA PDAC between 2004 and 2016 were determined from the National Cancer Institute’s Surveillance, Epidemiology and End Results database. All tests were two-sided. Results The incidence of stage IA PDAC cases diagnosed increased statistically significantly from 2004 to 2016 (annual percent change = 14.5, 95% confidence interval [CI] = 11.4 to 17.7; P &amp;lt; .001). During the study period, average age at diagnosis for stage IA and IB casesAQ3 declined by 3.5 years (95% CI = 1.2 to 5.9; P = .004) and 5.5 years (95% CI = 3.4 to 7.6; P &amp;lt; .001), whereas average age increased for higher-stage cases (by 0.6 to 1.4 years). Among stage IA cases, the proportion of blacks was smaller (10.2% vs 12.5%), and the proportion of other non-Caucasians was higher compared with higher-stage cases (11.9% vs 8.4%; P &amp;lt; .001). Stage IA cases were more likely to carry insurance (vs Medicaid or none) than higher-stage cases (cases aged younger than 65 years; odds ratio = 2.45, 95% CI = 1.96 to 3.06; P &amp;lt; .001). The 5-year overall survival for stage IA PDAC improved from 44.7% (95% CI = 31.4 to 63.7) in 2004 to 83.7% (95% CI = 78.6% to 89.2%) in 2012; 10-year survival improved from 36.7% (95% CI = 24.1 to 55.8) in 2004 to 49.0% (95% CI = 37.2% to 64.6%) in 2007. Conclusions In recent years, the proportion of patients diagnosed with stage IA PDAC has increased, their average age at diagnosis has decreased, and their overall survival has improved. These trends may be the result of improved early diagnosis and early detection.
Fully embedded board level optical interconnects: from point-to-point interconnection to optical bus architecture (2008)

This paper presents the latest progress toward fully embedded board level optical interconnects in the aspect of optical bus architecture design, waveguide fabrication and device integration. A bidirectional optical bus architecture is designed and can be fabricated by a one-step pattern transfer method, which can form a large cross section multimode waveguide array with 45&deg; micro-mirrors by silicon hard molding method. The waveguide propagation loss is reduced to 0.09dB/cm and the coupling efficiency of the metal-coated reflecting mirror is experimentally measured to be 85%. The active optoelectronic devices, vertical surface emitter lasers and p-i-n photodiodes, are integrated with the mirror-ended waveguide array, and successfully demonstrate a 10 Gbps signal transmission over the embeddable optical layer.
Application of Image Processing to Characterize Patterning Noise in Self-Assembled Nano-Masks for Bit-Patterned Media (2009)

In bit-patterned media (BPM), media noise is expected to be dominated by fabrication imperfections and to manifest as island size and spacing fluctuations. Previous work has shown that media noise has a significant impact on the error rates of BPM channels. Thus, having a realistic model of media noise is essential to evaluate the performance of the BPM channels. In this work, we apply image processing techniques to a scanning electron microscope image of a candidate BPM nano-mask, produced by a self-assembly technique, to estimate likely size and location fluctuations of the islands. These statistics may also be useful to characterize the samples of candidate BPM masks. We assume that these observed fluctuations are representative of patterning noise that might result from such a mask. The results indicate that these fluctuations are correlated and can be modeled by Gaussian random processes. Using estimated characteristics of islands size and location fluctuations, we model the correlated media noise and investigate the performance of BPM channels in the presence of such correlated media noise.
Supplementary Table S6 from Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer (2023)

&lt;p&gt;CRISPR-Cas9 screen enrichment analysis&lt;/p&gt;
Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis (2023)

The single-cell atlas of the peripheral immune system in IPF, reveals an outcome-predictive increase in classical monocytes and Tregs, as well as evidence for a lung-blood immune recruitment axis involving CCL7 (for classical monocytes) and CCL18/CCL22 (for Tregs).
Artificial Olfactory Brain for Mixture Identification (2008)

The odor transduction process has a large time constant and is susceptible to vari-ous types of noise. Therefore, the olfactory code at the sensor/receptor level is in general a slow and highly variable indicator of the input odor in both natural and artificial situations. Insects overcome this problem by using a neuronal device in their Antennal Lobe (AL), which transforms the identity code of olfactory recep-tors to a spatio-temporal code. This transformation improves the decision of the Mushroom Bodies (MBs), the subsequent classifier, in both speed and accuracy. Here we propose a rate model based on two intrinsic mechanisms in the insect AL, namely integration and inhibition. Then we present a MB classifier model that re-sembles the sparse and random structure of insect MB. A local Hebbian learning procedure governs the plasticity in the model. These formulations not only help to understand the signal conditioning and classification methods of insect olfactory systems, but also can be leveraged in synthetic problems. Among them, we con-sider here the discrimination of odor mixtures from pure odors. We show on a set of records from metal-oxide gas sensors that the cascade of these two new mod-els facilitates fast and accurate discrimination of even highly imbalanced mixtures from pure odors. 1
Relationship and Prognostic Value of Endogenous Interferon-??, ??2-Microglobulin, and Neopterin Serum Levels in Patients with Kaposi Sarcoma and AIDS (1991)

We investigated whether elevated serum levels of beta 2-microglobulin and neopterin were related to the abnormal in vivo production of interferon described in patients with human immunodeficiency virus (HIV) infection, and whether these factors might add to measurements of CD4+ T cells in predicting survival and tumor regression in patients with Kaposi sarcoma associated with AIDS. beta 2-Microglobulin and neopterin levels were strongly correlated (r = 0.82), and were each significantly higher in patients with detectable serum interferon-alpha activity. Inverse correlations were observed between prognosis and levels of these serum products. Prediction by CD4+ T-cell count of tumor regression after treatment with interferon-alpha and zidovudine was improved by each of two factors: (a) the presence or absence of endogenous interferon-alpha activity, and (b) a combined variable reflecting relative levels of the interferon-inducible products, beta 2-microglobulin and neopterin. The level of beta 2-microglobulin was the single best predictor of survival. When beta 2-microglobulin was not considered, the endogenous interferon-alpha variable was the best predictor of survival, and the prediction was enhanced by addition of the combined variable, or the neopterin value alone. We conclude that serologic markers, which directly or indirectly reflect activation of the endogenous interferon system, may be valuable adjuncts to CD4+ T-cell counts in assessing prognosis and selecting and evaluating treatments for patients with Kaposi sarcoma and AIDS.
Imaging over an unlimited bandwidth with a single diffractive surface (2019)

It is generally thought that correcting chromatic aberrations in imaging requires multiple surfaces. Here, we show that by allowing the phase in the image plane of a flat lens to be a free parameter, it is possible to correct chromatic aberrations over an almost unlimited bandwidth with a single diffractive surface. Specifically, we designed, fabricated and characterized a flat multi-level diffractive lens (MDL) that images at the wavelengths from 450nm to 850nm. We experimentally characterized the focusing efficiency, modulation-transfer function, wavefront aberrations, vignetting, distortion and signal-to-noise ratio performance of a camera comprised of this MDL and a conventional image sensor. Further, we designed two MDLs with operating wavelengths from 500nm to 15μm, and from 2μm to 150μm, respectively. With no apparent limitation in the operating bandwidth, such flat lenses could replace multiple refractive surfaces that are traditionally required for chromatic corrections, leading to thinner, lighter and simpler imaging systems with bandwidth limited primarily by the quantum efficiency of the sensor.
Development of Peltate Glandular Trichomes of Peppermint (2000)

Cryofixation and conventional chemical fixation methods were employed to examine the ultrastructure of developing peltate glandular trichomes of peppermint (Mentha x piperita). Our results are discussed in relation to monoterpene production and the mechanism of essential oil secretion. Peltate glands arise as epidermal protuberances (initials) that divide asymmetrically to produce a vacuolate basal cell, a stalk cell, and a cytoplasmically dense apical cell. Further divisions of the apical cell produce a peltate trichome with one basal cell, one stalk cell, and eight glandular (secretory) disc cells. Presecretory gland cells resemble meristematic cells because they contain proplastids, small vacuoles, and large nuclei. The secretory phase coincides with the separation and filling of the sub-cuticular oil storage space, the maturation of glandular disc cell leucoplasts in which monoterpene biosynthesis is known to be initiated, and the formation of extensive smooth endoplasmic reticulum at which hydroxylation steps of the monoterpene biosynthetic pathway occur. The smooth endoplasmic reticulum of the secretory cells appears to form associations with both the leucoplasts and the plasma membrane bordering the sub-cuticular oil storage cavity, often contains densely staining material, and may be involved with the transport of the monoterpene-rich secretion product. Associated changes in the ultrastructure of the secretory stage stalk cell are also described, as is the ultrastructure of the fragile post-secretory gland for which cryofixation methods are particularly well suited for the preservation of organizational integrity.
Air Damping Characteristics of Integrated Accelerometers with a Single-Side Air Gap. (1997)

In this paper, damping characteristics of piezoresistive integrated silicon accelerometers, in which a micromachined seismic mass is suspended by four narrow beams from the surrounding frame that incorporates peripheral circuitry and squeeze film damping effect is provided by a single-side air gap under the seismic mass, were analyzed and numerically calculated. The output waveforms for applied sinusoidal accelerations are different from those of accelerometers with symmetrical air-gap structure when subject to large accelerations. The calculated results are compared with measured characteristics of the fabricated devices.
Investigation of deep levels in SiC-Schottky diodes with frequency resolved admittance spectroscopy (2015)

We show that the technique of Frequency Resolved Admittance Spectroscopy (FRAS) allows the identification of deep traps with reduced measurement effort compared to Deep Level Transient Spectroscopy (DLTS). This is shown by the analysis of radiation defects introduced in n-type 4H-SiC 1700V Schottky diodes.
Kinetics and Thermodynamics of Drug Permeation Through Silicone Elastomers iv. Effect of Polymer Backbone Structure (1986)

The effect of silicone polymer backbone structure on the permeability of progesterone and testosterone through silicone membranes was investigated in the capsule-type drug delivery system at 25, 37 and 50°C, respectively. Three types of polymer were studied: (I) (Me2SiCH2)x, (II) (Me2Sl-CH4-SiMe2O)x, and (III) [Me2Si(CH2)n SiMe2O] x, where n=2, 6 and 8.Permeabilities of progesterone in these polymers were found to decrease in the following order: Polymer (III) < Polymer (I) < Polymer (II). The same order was also observed for the permeabilities of testosterone, but their values were one order of magnitude lower than those of progesterone. Incorporation of the phenylene group in the polymer backbone in Polymer (II) caused a significant decrease in the diffusion coefficient but an increase in the solubility coefficient. The net effect is a 50% decrease in the permeability with respect to (Me2 SiO)x. This effect was found to be less pronounced with alkylene group in Polymer (III).The activation energies of permeation for progesterone through these polymers were found to be in the range of 12-21 kcal/mole.
A hybrid land grid array socket connector design for achieving higher signalling data rates (2017)

This paper presents an improved hybrid land grid array socket connector design enabling high speed bus signaling data rates up to 50Gb/s. Observed limitations in an existing connector such as impedance mismatches and crosstalk are treated and improved. The improved connector structural differences from the existing connector are presented and motivated. Electromagnetic modelling for the improved and existing connectors has been carried out to validate the design concept and compare signal integrity properties.
Aleatory Construction Based on Jamming: Stability Through Self‐Confinement (2017)

The physical process of jamming could take architectural sustainability/recyclability to a whole new level. It involves achieving structural rigidity through the crowding of particles within a confined space, rather than by permanent bonding. Project Z‐Form, a collaboration between a team of physicists from the JaegerLab at the University of Chicago – including PhD students Kieran Murphy and Leah Roth and professor Heinrich Jaeger – and artist Dan Peterman , sets out to develop a pourable material that not only self‐supports but can also bear loads. Here they explain the project and the concepts behind it.
Early life rhinovirus infection exacerbates house-dust-mite induced lung disease more severely in female mice (2016)

We conclude that early life rhinovirus infection influences the development of house-dust-mite induced lung disease in female, but not male mice.
Experimental performance comparison of Duobinary and PSBT modulation formats for long-haul 40 Gb/s transmission on G652 fibre (2012)

International audience
5-Lipoxygenase: A Promising Drug Target Against Inflammatory Diseases-Biochemical and Pharmacological Regulation (2014)

5-Lipoxygenase (5-LO) is the key enzyme involved in the synthesis of pro-inflammatory leukotrienes (LTs) and has become a prime target for new drug discovery research and development efforts by the pharmaceutical and biotech industry. The pathophysiological effects of LTs can be modulated by the selective inhibition of 5-LO. In this review, we summarize the established dogma and recent progress on the biochemical and pharmacological regulation of 5-LO and its diverse cellular partners. In the last decade, significant research efforts have led to the exploitation of 5-LO pathway for developing new drugs against inflammatory diseases. Despite few setbacks, a number of promising molecules have moved into clinical development. These fundamental discoveries and proof-of-concept studies will ultimately be helpful in delineating how 5-LO pathway participates in the development of disease phenotype and what are possible key biomarkers of disease progression and regression. Elucidation of molecular mechanism-of-action of 5-LO in individual cell types will pave the way for improving efficacy parameters. Taken together, this combined knowledge about the 5-LO pathway would be helpful in planning collaborative and targeted R&D efforts, by the academic laboratories and pharmaceutical/ biotech industry, for the discovery and development of novel, efficacious and safer drugs against multiple diseases.
Fully-integrated bipolar-based LNA for W-CDMA application: Theory, design and implementation (2007)

This paper presents a fully-integrated low-noise amplifier (LNA) to W-CDMA applications. A noise/input impedance matching methodology is applied to design the input stage of the LNA cascode topology. For circuit manufacturing, we have used a BiCMOS SiGe:C 0.25mum process which is well suited to low-noise applications. Good overall measured performances, in good agreement with simulation, are obtained.