gebhart/patrepeval huggingface dataset:
A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival (2019)

The specific genes and molecules that drive physiological angiogenesis differ from those involved in pathological angiogenesis, suggesting distinct mechanisms for these seemingly related processes. Unveiling genes and pathways preferentially associated with pathologic angiogenesis is key to understanding its mechanisms, thereby facilitating development of novel approaches to managing angiogenesis-dependent diseases. To better understand these different processes, we elucidated the transcriptome of the mouse retina in the well-accepted oxygen-induced retinopathy (OIR) model of pathological angiogenesis. We identified 153 genes changed between normal and OIR retinas, which represent a molecular signature relevant to other angiogenesis-dependent processes such as cancer. These genes robustly predict the survival of breast cancer patients, which was validated in an independent 1,000-patient test cohort (40% difference in 15-year survival; p = 2.56 x 10-21). These results suggest that the OIR model reveals key genes involved in pathological angiogenesis, and these may find important applications in stratifying tumors for treatment intensification or for angiogenesis-targeted therapies.
Phase sensitive inversion recovery with simultaneous dark fat rendering by virtual chemical inversion (2012)

Background On delayed-enhancement (DE-CMR), both fat and infarcted myocardium appear bright making them difficult to differentiate. Standard chemical shift fat-suppression (FatSatCS) consists of a fat-frequency selective saturation followed by readout. This approach is suboptimal in clinical DE-CMR sequences which typically have long readout times (100-200ms) and as a result, fat magnetization has significantly recovered (T1 = 290ms, 3T) when the center of k-space is acquired for linear reordering. Centric reordering can overcome this limitation, but at the cost of blurring artifacts. The phase sensitive inversion recovery (PSIR) variant of DE-CMR avoids the need to precisely set inversion time through the acquisition of a reference data set interleaved between image acquisitions. We hypothesized that modifying the reference acquisition via a Dixon-type approach could provide PSIR images that simultaneously show dark fat without added acquisition time. The result is a virtual chemically selective inversion (FatSatVCSI), without increased SAR and at no cost to signal-to-noise from pulse imperfections.
Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency (2015)

Pending further validation, a digital microfluidics platform could be an accurate point-of-care screening tool for rapid newborn G6PD screening.
SPIKE: Scalable Peer Intermediaries for Key Establishment in Sensor Networks (2015)

In a sensor network, common-key cryptography is used to establish secure communications between nodes. Since it is required to share the common key between nodes in advance to the communication, a key establishment scheme should be considered. Chan and Perring proposed a novel key establishment scheme PIKE (Peer Intermediaries for Key Establishment in Sensor Networks) in which each common key used in each communication between nodes is derived from a pre-shared key, and all common keys are different from each other. In addition, each node is required to have small number of pre-shared keys. However, the number of pre-shared key grows as the number of nodes in the network grows, and more importantly, PIKE has a problem that when the network is established, it is hard to add new nodes into the network, since storing new pre-shared keys in existing nodes is required. This paper proposes a new key establishment scheme SPIKE (Scalable Peer Intermediaries for Key Establishment in Sensor Networks), in which all nodes in the network are required to have a constant number of pre-shared keys. The proposed scheme allows the network to add new nodes after the network has been established.
Synthesis and Characterization of Zn2SiO4:Mn2+ Nanophosphors Prepared from Different Zn Source in Liquid Precursor by Flame Spray Pyrolysis (2009)

Zn2SiO4:Mn2+ nanophosphors were synthesized by flame spray pyrolysis (FSP) from different liquid precursors. Luminescence and crystalline properties were investigated as different Zn-source materials in aqueous precursor. Mn-doped zinc silicate (Zn2SiO4:Mn2+) crystalline structures were annealed low temperature of 1000° for 1hr. The emission peak was found at 525 nm for green emitting phosphor. The influence of different experimental conditions such as liquid precursor from different Zn-source and annealing temperature on both crystallinity and the luminescence properties of Zn2SiO4:Mn2+ nanophosphors were investigated.
Facile access to α-acyloxyamides via epoxide rearrangement/three-component domino reaction catalyzed by indium(III) chloride (2016)

A simple and efficient Passerini reaction of epoxides involving highly regioselective rearrangement of epoxide to aldehyde/three-component Passerini reaction catalyzed by indium(III) chloride is described. In the present protocol, epoxides served as wonderful substrates to furnish a library of α-acyloxyamides under mild reaction conditions in shorter reaction times and in good yields.
Conditionally Increased Acoustic Pressures in Nonfetal Diagnostic Ultrasound Examinations Without Contrast Agents: A Preliminary Assessment (2015)

The mechanical index (MI) has been used by the US Food and Drug Administration (FDA) since 1992 for regulatory decisions regarding the acoustic output of diagnostic ultrasound equipment. Its formula is based on predictions of acoustic cavitation under specific conditions. Since its implementation over 2 decades ago, new imaging modes have been developed that employ unique beam sequences exploiting higher-order acoustic phenomena, and, concurrently, studies of the bioeffects of ultrasound under a range of imaging scenarios have been conducted. In 2012, the American Institute of Ultrasound in Medicine Technical Standards Committee convened a working group of its Output Standards Subcommittee to examine and report on the potential risks and benefits of the use of conditionally increased acoustic pressures (CIP) under specific diagnostic imaging scenarios. The term "conditionally" is included to indicate that CIP would be considered on a per-patient basis for the duration required to obtain the necessary diagnostic information. This document is a result of that effort. In summary, a fundamental assumption in the MI calculation is the presence of a preexisting gas body. For tissues not known to contain preexisting gas bodies, based on theoretical predications and experimentally reported cavitation thresholds, we find this assumption to be invalid. We thus conclude that exceeding the recommended maximum MI level given in the FDA guidance could be warranted without concern for increased risk of cavitation in these tissues. However, there is limited literature assessing the potential clinical benefit of exceeding the MI guidelines in these tissues. The report proposes a 3-tiered approach for CIP that follows the model for employing elevated output in magnetic resonance imaging and concludes with summary recommendations to facilitate Institutional Review Board (IRB)-monitored clinical studies investigating CIP in specific tissues.
Enhanced Process Development for Interferometric Modulators (1998)

Abstract : The most significant accomplishment is the successful fabrication of devices from the test device mask set with brightness and contrast which are improved over the 5 x 7 devices. These IMods are exhibiting the expected color response, switching clearly from green to black. Actuation voltages remain in the area of 10 to 15 volts, with response times on the order of 75 microseconds. Color uniformity is also quite good, though this has only been assessed via naked eye observation. There appear to be some charging effects which are having an impact on device pull-in and released voltages.
Phase change memory for synaptic plasticity application in neuromorphic systems (2011)

In this paper, we show that Phase Change Memory (PCM) can be used to emulate specific functions of a biological synapse similar to Long Term Potentiation (LTP) and Long Term Depression (LTD) plasticity effects. The dependence of synaptic weight on programming pulse width and pulse amplitude is shown experimentally for the PCM devices. Different combinations of consecutive LTD and LTP events have been experimentally demonstrated and analyzed for the PCM synapse.
Safety, recommended dose, efficacy and immune correlates for nintedanib in combination with pembrolizumab in patients with advanced cancers (2022)

ClinicalTrials.gov, NCT02856425 . Registered August 4, 2016 - Prospectively registered.
The Joint Impact of Fading Severity, Irregular Constellation, and Non-Gaussian Noise on Signal Space Diversity-Based Relaying Networks (2019)

This work focuses on the interplay between rotation angle, transmit power, fading severity, and noise impairment severity in signal space diversity-based three time-slot decode-and-forward two-way relaying networks. Specifically, we develop a joint design for rotation angle selection and transmit power allocation, while taking into account the performance impact of fading severities on the channels and noise impairment severities on the receivers. To model different severities of fading and noise impairment, Nakagami distribution and additive non-Gaussian noise are used respectively. The objective in doing so is to promote the reliable reception of end-sources, while satisfying individual and total power budgets as well as average error probability. To this end, we start by deriving average error probabilities of end-sources for non-uniform constellations, which capture all possible signal constellations produced by using various rotation angles. Next, we formulate the joint design problem in an optimization form. Unfortunately, the resulting formulation is a non-convex optimization. To find the solution, we resort to numerical optimization. The numerical results not only validate the derived error probability expressions, but also demonstrate the efficacy of the proposed framework and provide useful insights on the interaction between rotation angle, transmit power, fading severities of the channels, and noise impairment severities at the end-sources.
A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation (2013)

Quorum sensing is a chemical communication process that bacteria use to regulate collective behaviors. Disabling quorum-sensing circuits with small molecules has been proposed as a potential strategy to prevent bacterial pathogenicity. The human pathogen Pseudomonas aeruginosa uses quorum sensing to control virulence and biofilm formation. Here, we analyze synthetic molecules for inhibition of the two P. aeruginosa quorum-sensing receptors, LasR and RhlR. Our most effective compound, meta-bromo-thiolactone (mBTL), inhibits both the production of the virulence factor pyocyanin and biofilm formation. mBTL also protects Caenorhabditis elegans and human lung epithelial cells from killing by P. aeruginosa. Both LasR and RhlR are partially inhibited by mBTL in vivo and in vitro; however, RhlR, not LasR, is the relevant in vivo target. More potent antagonists do not exhibit superior function in impeding virulence. Because LasR and RhlR reciprocally control crucial virulence factors, appropriately tuning rather than completely inhibiting their activities appears to hold the key to blocking pathogenesis in vivo.
Lack of COL6/collagen VI causes megakaryocyte dysfunction by impairing autophagy and inducing apoptosis (2022)

Endoplasmic reticulum stress is an emerging significant player in the molecular pathology of connective tissue disorders. In response to endoplasmic reticulum stress, cells can upregulate macroautophagy/autophagy, a fundamental cellular homeostatic process used by cells to degrade and recycle proteins or remove damaged organelles. In these scenarios, autophagy activation can support cell survival. Here we demonstrated by <i>in vitro</i> and <i>in vivo</i> approaches that megakaryocytes derived from <i>col6a1</i><sup>-⁄-</sup> (collagen, type VI, alpha 1) null mice display increased intracellular retention of COL6 polypeptides, endoplasmic reticulum stress and apoptosis. The unfolded protein response is activated in <i>col6a1</i><sup>-⁄-</sup> megakaryocytes, as evidenced by the upregulation of molecular chaperones, by the increased splicing of <i>Xbp1</i> mRNA and by the higher level of the pro-apoptotic regulator DDIT3/CHOP. Despite the endoplasmic reticulum stress, basal autophagy is impaired in <i>col6a1</i><sup>-⁄-</sup> megakaryocytes, which show lower BECN1 levels and reduced autophagosome maturation. Starvation and rapamycin treatment rescue the autophagic flux in <i>col6a1</i><sup>-⁄-</sup> megakaryocytes, leading to a decrease in intracellular COL6 polypeptide retention, endoplasmic reticulum stress and apoptosis. Furthermore, megakaryocytes cultured from peripheral blood hematopoietic progenitors of patients affected by Bethlem myopathy and Ullrich congenital muscular dystrophy, two COL6-related disorders, displayed increased apoptosis, endoplasmic reticulum stress and impaired autophagy. These data demonstrate that genetic disorders of collagens, endoplasmic reticulum stress and autophagy regulation in megakaryocytes may be interrelated.<b>Abbreviations:</b> 7-AAD: 7-amino-actinomycin D; ATF: activating transcriptional factor; BAX: BCL2 associated X protein; BCL2: B cell leukemia/lymphoma 2; BCL2L1/Bcl-xL: BCL2-like 1; BM: bone marrow; COL6: collagen, type VI; <i>col6a1<sup>-⁄-</sup></i>: mice that are null for <i>Col6a1</i>; DDIT3/CHOP/GADD153: DNA-damage inducible transcript 3; EGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; reticulophagy: endoplasmic reticulum-selective autophagy; HSPA5/Bip: heat shock protein 5; HSP90B1/GRP94: heat shock protein 90, beta (Grp94), member 1; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; Mk: megakaryocytes; MTOR: mechanistic target of rapamycin kinase; NIMV: noninvasive mechanical ventilation; PI3K: phosphoinositide 3-kinase; PPP1R15A/GADD34: protein phosphatase 1, regulatory subunit 15A; RT-qPCR: reverse transcription-quantitative real-time PCR; ROS: reactive oxygen species; SERPINH1/HSP47: serine (or cysteine) peptidase inhibitor, clade H, member 1; sh-RNA: short hairpin RNA; SOCE: store operated calcium entry; UCMD: Ullrich congenital muscular dystrophy; UPR: unfolded protein response; WIPI2: WD repeat domain, phosphoinositide-interacting 2; WT: wild type; XBP1: X-box binding protein 1.
Supplementary Figure 1 from A Novel Bispecific, Trivalent Antibody Construct for Targeting Pancreatic Carcinoma (2023)

Supplementary Figure 1 from A Novel Bispecific, Trivalent Antibody Construct for Targeting Pancreatic Carcinoma
Abstract P3-06-34: Plasma (p) VEGF-A and VEGFR-2 biomarker (BM) results from the BEATRICE phase III trial of bevacizumab (BEV) in triple-negative early breast cancer (BC) (2012)

Abstract Background: Several candidate BMs have been explored in randomized trials of BEV across tumor types with the aim of identifying patients (pts) deriving the most substantial benefit from BEV therapy. In phase III trials, baseline pVEGF-A and pVEGFR-2 showed potential predictive value in metastatic BC (AVADO, AVEREL), pancreatic cancer (AViTA), and gastric cancer (AVAGAST; VEGF-A only). The randomized phase III BEATRICE trial, evaluating the addition of BEV to adjuvant chemotherapy in pts with triple-negative early BC, includes a comprehensive program to identify potential BMs predicting efficacy and toxicity of BEV therapy. We report results for baseline pVEGF-A and pVEGFR-2. Methods: After selection of chemotherapy (anthracycline and/or taxane), pts with T1a-T3 operable BC were randomized 1:1 to receive ≥4 cycles of chemotherapy either alone or with 1 year of BEV 5 mg/kg/wk equivalent. The primary endpoint is invasive disease-free survival (IDFS). pEDTA samples were collected from consenting pts at baseline (before treatment, after surgery), during study treatment, and at relapse. Pts were dichotomized using the median baseline concentration of each marker as the cut-off between high and low cohorts; further exploratory analyses were also performed by quartile. Results: Between Dec 2007 and Mar 2010, 2591 pts were enrolled. Of these, 1273 (49%) consented to the BM study and 1178 (45%) were included in the BM-evaluable population (BEP). Overall, the BEP was representative of the ITT population except for lower proportions of Asian pts (12% vs 24%). IDFS was similar in the BEP and ITT populations. Baseline characteristics were balanced between arms in the BEP. Baseline pVEGF-A showed neither prognostic nor predictive value using the median as the cut-off, although with a third quartile (Q3) cut-off there was a more pronounced but non-significant differentiation between treatments (HR 0.92 [low] vs 0.64 [high]). High baseline pVEGFR-2 showed potential predictive value for BEV efficacy (HR 1.24 [low] vs 0.61 [high]; p=0.029). Conclusions: Unlike trials in metastatic BC (AVADO, AVEREL), in the adjuvant setting, baseline pVEGF-A concentration did not show predictive value for BEV efficacy with a median cut-off. However, analyses using the Q3 cut-off suggest a trend toward predictive value. High baseline pVEGFR-2 was associated with greater BEV treatment effect, consistent with previous results in AVADO and AVEREL. The impact of differing biology in the adjuvant setting, lower median VEGF-A concentration than in the metastatic setting (77.0 vs 125.0–129.1 pg/mL), and the possible influence of surgery immediately before treatment require further investigation. Additional exploratory analyses are ongoing to provide better understanding of the BEATRICE dataset and the complex biology of angiogenesis, including additional markers, changes over time, and combination signatures. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-34.
Highly selective and sensitive gas sensors for exhaled breath analysis using CuBr thin film (2016)

We have examined a p-type semi-conductor CuBr thin film used for sensor devices that indicates the order of sensitivity to ammonia in parts per billion (ppb). The CuBr thin film also indicates excellent selectivity to ammonia among reductive gases, which additionally suggests its capacity for fast quantification of the order of seconds. Moreover, CuBr thin film can be adapted to a high-sensitivity aldehyde sensor by a surface modification. Since the fabrication process of CuBr thin film is compatible with an ordinal CMOS process, there is a potential for development into highly integrated and low power consumption sensor devices. These properties make CuBr thin film a promising candidate as a gas sensing material for human-breath analysis.
RIGID CYSTOSCOPE PLATFORM FOR NOTES & SUB-CENTIMETER LESS IN A PORCINE MODEL (2009)

You have accessJournal of Urology1 Apr 2009RIGID CYSTOSCOPE PLATFORM FOR NOTES & SUB-CENTIMETER LESS IN A PORCINE MODEL Mark D Sawyer, Edward E Cherullo, Vivian E von Gruenigen, and Lee E Ponsky Mark D SawyerMark D Sawyer More articles by this author , Edward E CherulloEdward E Cherullo More articles by this author , Vivian E von GruenigenVivian E von Gruenigen More articles by this author , and Lee E PonskyLee E Ponsky More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)61221-0AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "RIGID CYSTOSCOPE PLATFORM FOR NOTES & SUB-CENTIMETER LESS IN A PORCINE MODEL." The Journal of Urology, 181(4S), pp. 429–430 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 429-430 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetricsAuthor Information Mark D Sawyer More articles by this author Edward E Cherullo More articles by this author Vivian E von Gruenigen More articles by this author Lee E Ponsky More articles by this author Expand All Advertisement PDF DownloadLoading ...
Dark-field imaging on a clinical CT system: realization of Talbot-Lau interferometry in a gantry (2022)

Computed tomography (CT) is a foundation of modern clinical diagnostics but it presently only retrieves information from X-rays attenuation. However, it is known that micro structural texture or porosity – which is well below the spatial resolution of CT – can be revealed by grating-based dark-field imaging. Diagnostic value of this sub-resolution tissue information has been demonstrated in pre-clinical studies on small-animal disease models and recently also in a first clinical radiography system.<sup>1</sup> These studies show that dark-field imaging is particularly useful for early detection and staging of lung diseases. While dark-field CT is regularly realized in laboratory environment, the transfer to human scale and bringing it to clinical application poses several technical challenges. Switching from a step-and-shoot acquisition to a mode where the gantry and acquisition operate continuously as well as reducing scan times to below seconds and ensuring stability against vibrations are key concerns when it comes to the translation of the established laboratory dark-field technology to full-body medical CT. In,<sup>2</sup> we recently demonstrated the first dark-field CT implementation, which collectively solves these roadblocks and therefore is a milestone in the development of clinical CT imaging. The prototype we present allows to reconstruct the attenuation and dark-field channels of a human thorax phantom from a one second long acquisition and covers a 45 cm diameter field of view. In this work, we present how the first dark-field CT prototype works and focus particularly on the technical design, optimized design of the gratings for CT application and the first characterization of the interferometer in the rotating gantry. We discuss which steps where particularly important for the realization and where we see potential for further improvements. These results provide key insights for future dark-field CT implementations.
An antibody-catalyzed bimolecular Diels-Alder reaction (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn antibody-catalyzed bimolecular Diels-Alder reactionAndrew C. Braisted and Peter G. SchultzCite this: J. Am. Chem. Soc. 1990, 112, 20, 7430–7431Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00176a073https://doi.org/10.1021/ja00176a073research-articleACS PublicationsRequest reuse permissionsArticle Views906Altmetric-Citations184LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts