gebhart/patrepeval huggingface dataset:
Bringing Source-Level Debugging Frameworks to Hardware Generators (2022)

High-level hardware generators have significantly increased the productivity of design engineers. They use software engineering constructs to reduce the repetition required to express complex designs and enable more composability. However, these benefits are undermined by a lack of debugging infrastructure, requiring hardware designers to debug generated, usually incomprehensible, RTL code. This paper describes a framework that connects modern software source-level debugging frameworks to RTL created from hardware generators. Our working prototype offers an Integrated Development Environment (IDE) experience for generators such as RocketChip (Chisel), allowing designers to set breakpoints in complex source code, relate RTL simulation state back to source-level variables, and do forward and backward debugging, with almost no simulation overhead (less than 5%).
Control of segmental asymmetry in Drosophila embryos (1993)

During Drosophila development, an important aspect of body patterning is the division of the embryo into repeating morphological units referred to as parasegments. The parasegmental domains are first defined at the blastoderm stage by alternating stripes of transcripts encoded by the pair-rule genes fushi tarazu (ftz) and even-skipped (eve) and later by stripes encoded by the segment polarity genes engrailed (en) and wingless. Here, we show that the runt gene (run) is required to generate asymmetries within these parasegmental domains. Using a heat-shock-inducible run transgene, we found that ectopic run expression leads to rapid repression of eve stripes and a somewhat delayed expansion of ftz stripes. Unexpectedly, we also found that ectopic run was a rapid and potent repressor of odd-numbered en stripes. Two remarkably different segmental phenotypes were generated as a consequence of these effects. In solving the mechanisms underlying these phenotypes, we discovered that the positioning of en stripes is largely determined by the actions of negative regulators. Our data indicate that run is required to limit the domains of en expression in the odd-numbered parasegments, while the odd-skipped gene is required to limit the domains of en expression in the even-numbered parasegments. Activation of en at the anterior margins of both sets of parasegments requires the repression of run and odd by the product of the eve gene. The spatial restriction of gene expression via negative and double negative pathways such as these is likely to be a common theme during development.
Off-Line Detection of Static Eccentricity in Salient-Pole Synchronous Machines (2018)

Since synchronous generators are the main electric power producing devices, it is crucial to guarantee their safe and reliable operation. However, faults may appear and inflict great losses. So, condition monitoring of such machines is critical to avoid unscheduled stops and unplanned maintenance. This paper works towards that direction. The authors are proposing a new off-line method to reliably detect the static eccentricity fault in synchronous salient pole electrical machines. The method is based on the monitoring of all three phase currents of the machine during locked rotor at three different rotor positions. A pseudo zero-sequence current is then calculated, the frequency spectrum of which can reveal reliable indicators to detect this fault. The proposed method has been tested experimentally with success, while the results indicate that it is possible to estimate the fault level severity.
Information Harvesting for Far-Field RF Power Transfer through Index Modulation (2022)

By the sixth-generation (6G) era, Internet-of-Things (IoT) evolves into an enormous scale of technologies and use-cases. As the IoT systems are comprised of a huge amount of low-power network elements, sensors, and smart devices, connected with each other, it is important to have a sufficient level of energy resources for carrying out assigned communication tasks and receiving software/firmware updates from the network management. Aside from splitting data and power into different domains as in simultaneous data communication and RF power transfer, a novel protocol, information harvesting (IH), has been recently introduced, which lies on transmitting information on top of the existing wireless power transfer mechanism. In this paper, we investigate the implementation of IH in terms of secrecy capacity and energy harvesting capability. The numerical results show that the IH may turn out to be a pivotal methodology that converts existing wireless power transfer mechanisms into data transmission tools by deploying an indexing in transmitter entities.
GENE EXPRESSION OF VEGF AND ITS RECEPTORS Flk-1/KDR AND Flt-1 IN CULTURED AND TRANSPLANTED RAT ISLETS1 (2001)

The delayed expression of VEGF receptors in the diabetic recipients could reflect impaired angiogenesis caused by the diabetic milieu; this delay could contribute to the less outcomes of grafts transplanted into a hyperglycemic environment.
A Temperature Formulation of the Space-Averaged Reactor Kinetics Equations (1971)

Techniques are described for the solution of the space-averaged kinetics equations directly in terms of temperature. A good agreement with single and repetitive pulse experimental data from a TRIGA reactor is demonstrated. The results of the method agree not only with the symmetric portion of the pulse but also with the pulse tail. The required feedback and neutron parameters are determined by conventional techniques; however, the heat-transfer decay constant is normalized to experimental data through measurement of the time-dependent reactivity via a double-pulse method.
A comparison study of different excitation wavelengths to determine the relative content of key biomolecules in breast cancer and breast normal tissue (2015)

Fluorescence profiles from breast cancer and breast normal tissue samples with excitation wavelengths at 280 nm and 340 nm were obtained using the conventional LS-50 Perkin-Elmer spectrometer. Fluorescence ratios from these tissue samples, demonstrated by emission peaks at 340 nm, 440 nm and 460 nm and likely representing tryptophan and NADH, show increased relative content of tryptophan in malignant samples. Double ratio (DR) techniques were used to measure the severity of disease. The single excitation double ratio (Single-DR) method utilizes the emission intensity peaks from the spectrum acquired using a single excitation of 280 nm; while the dual excitation double ratio (dual-DR) method utilizes the emission intensity peaks from the spectra acquired using an excitation of 280 nm and 340 nm. Single-DR and dual-DR from 13 patients with breast carcinoma were compared in terms of their efficiency to distinguish high from low/intermediate tumors. Similar results were found with both methods. Results suggest that dual excitation wavelengths may be as effective as single excitation wavelength in calculating the relative content of biomolecules in breast cancer tissue, as well as for the assessment of the malignant potential of these tumors.
Normal Magnetic Resonance Imaging with Abnormal Discography (1988)

In degenerative lumbar spine disease, recent studies have supported the clinical usefulness of discography, especially when used with computed tomography (CT) scanning. The role and capabilities of magnetic resonance imaging (MRI) scanning are currently evolving and being defined. This study reviews a series of patients with prolonged disabling symptoms who had normal MRI scans and abnormal discography. Discograms and discogram-CT scans may at times allow detection of clinically correlative and significant pathology (usually annular disruptions) not suggested by MRI scanning. This fact should be considered in patients with normal MRI scanning and continuing unexplained symptomatology.
Exploring characteristics of neural network architecture computation for enabling SAR ATR (2021)

Neural network approaches have periodically been explored in the pursuit of high performing SAR ATR solutions. With deep neural networks (DNNs) now offering many state-of-the-art solutions to computer vision tasks, neural networks are once again being revisited for ATR processing. Here, we characterize and explore a suite of neural network architectural topologies. In doing so, we assess how different architectural approaches impact performance and consider the associated computational costs. This includes characterizing network depth, width, scale, connectivity patterns, as well as convolution layer optimizations. We have explored a suite of architectural topologies applied to both the canonical MSTAR dataset, as well as the more operationally realistic Synthetic and Measured Paired and Labeled Experiment (SAMPLE) dataset. The latter pairs high fidelity computational models of targets with actual measured SAR data. Effectively, this dataset offers the ability to train a DNN on simulated data and test the network performance on measured data. Not only does our in-depth architecture topology analysis offer insight into how different architectural approaches impact performance, but we also have trained DNNs attaining state-of-the-art performance on both datasets. Furthermore, beyond just accuracy, we also assess how efficiently an accelerator architecture executes these neural networks. Specifically, Using an analytical assessment tool, we forecast energy and latency for an edge TPU like architecture. Taken together, this tradespace exploration offers insight into the interplay of accuracy, energy, and latency for executing these networks.
Guided SH-SAW characterization of elasticity variations of mesoporous TiO (2010)

Anomalous responses of acoustic humidity sensors coated with mesoporous titania have been observed at high humidity levels, due to capillary contraction that alters the film mechanical behavior. As the methods commonly used to assess the elasticity of thin films are difficult to apply during sorption, a dedicated method for the characterization of the variations of the elastic shear modulus of thin films under humidity exposure has been developed. The method combines a guided shear-horizontal surface acoustic wave (guided SH-SAW or Love wave) platform with environmental ellipsometric porosimetry (EEP). In the presented approach, EEP measures the thickness of the film and its adsorbed humidity volume fraction under vapor exposure, while the guided SH-SAW platform provides the phase velocity shifts induced by water sorption. These parameters then feed an accurate model of Love wave propagation in the multilayered platform for the derivation of the shear modulus of the sensitive film. The method was applied to 100±10 nm thick mesoporous titania films, with 25±1% porosity, under relative humidity exposure in the 3%-95% range. It successfully determined decreases of 39% and 67% of the shear modulus during adsorption and desorption, respectively, from a 3.1 GPa initial value.
A broadband soft horn antenna with inhomogeneous metasurface coatings (2012)

This paper presents the design of a conical horn antenna with inhomogeneous metasurface coatings on the interior wall, which is shown to provide symmetrical radiation patterns with low sidelobe and cross-polarization levels over a broad bandwidth. By engineering the metasurfaces with regard to their surface impedances, we demonstrate a metahorn with improved return loss and enhanced radiation characteristics compared to those with uniform liners.
Application of Data Science to Quantify the Effect of Propofol Infusion on Postoperative Nausea and Vomiting. (2022)

The effectiveness of propofol infusion on postoperative nausea and vomiting (PONV) is poorly understood in relation to various patient and procedure characteristics. This retrospective cohort study aimed to quantify the effectiveness of propofol infusion when administered either via total intravenous administration (TIVA) or combined intravenous anesthesia (CIVA) with inhalational agents on PONV. The relationship between propofol infusion and PONV was characterized controlling for patient demographics, procedure characteristics, PONV risk factors, and antiemetic drugs in adult patients (age ≥18 years) undergoing general anesthesia. Learned coefficients from multivariate regression models were reported as "lift" which represents the percentage change in the base likelihood of observing PONV if a variable is present versus absent. In a total of 41,490 patients, models showed that propofol infusion has a naive effect on PONV with a lift of -41% (<i>P</i> < .001) when using TIVA and -17% (<i>P</i> < .001) when using CIVA. Adding interaction terms to the model resulted in the loss of statistical significance in these relationships (lift of -30%, <i>P</i> = .23, when using TIVA, and -42%, <i>P</i> = .36, when using CIVA). It was further found that CIVA/TIVA are ineffective in short cases (CIVA * short surgery duration: lift = 49%, <i>P</i> < .001 and TIVA * short surgery duration: lift = 56%, <i>P</i> < .001).
Calibrating metal contents in caged Gammarus fossarum towards ecological disturbance: identifying threshold concentrations above which macroinvertebrate populations collapse (2015)

Contamination levels of aquatic ecosystems and ecological effects must be assessed, as stated by the WFD. However, linking both issues remains difficult, yet necessary to implement restoration. Recently an active biomonitoring approach has been developed using caged Gammarus fossarum to assess trends of bioavailable contamination levels in freshwater systems. This new tool overcomes most drawbacks associated to other currently used methods, allowing an accurate comparison of contamination levels between stations, seasons or years.\nOur study aimed at calibrating this active biomonitoring tool in order to interpret bioavailable contamination levels in term of risk for ecological disturbance. For this, a national scale investigation has been performed to obtain the bioavailable contamination levels and ecological indices (diversity and abundance) for 117 sites representative of French watercourses.\nConcentrations of 11 metals quantified in G. fossarum have been analysed against ecological indicators. No link was revealed between bioavailable contamination levels and global ecological indicators used for WFD implementation; in contrast, clear relationships were established with sensitive macroinvertebrate abundances. This allowed determining thresholds for five elements above which populations are endangered. These ecological impairment thresholds are discussed accordingly to the bioavailable background accumulated contamination values previously determined in G. fossarum at the French national scale.
Abstract 5360: Targeting H3K27 Methylation by 3-Deazaneplanocin A (DZNep) in lung and esophageal cancers. (2013)

Abstract Polycomb repressor complex-2 (PRC-2) is aberrantly expressed in a variety of human malignancies including lung and esophageal cancers. PRC-2 contains three main core proteins, enhancer of zeste 2 (EZH2), suppressor of zeste 12 (SUZ12), and embryonic ectoderm development (EED). In the present study, we sought to examine the effects of PRC-2 expression in lung and esophageal cancers, and to determine if PRC-2 is a potential therapeutic target in these malignancies. qRT-PCR analysis demonstrated significant over-expression of EZH2, SUZ12, and EED in cultured lung and esophageal cancer cells as well as primary tumors relative to normal or immortalized aerodigestive tract epithelial cells, or normal lung or esophageal tissues. Over-expression of individual PRC-2 components appeared to coincide with tumor histology; for example EZH2 was particularly over-expressed in small cell lung cancers, whereas EED appeared to be over-expressed primarily in esophageal cancers. DZNep mediated dose-dependent depletion of EZH2, EED and SUZ12, with corresponding decreases in global H3K27Me3 levels in cultured lung and esophageal cancer cells. Depletion of PRC-2 expression/activity coincided with growth arrest in these cancer cells. The growth inhibitory effects of DZNep in lung cancer cells were recapitulated byshRNA-mediated knock-down of EZH2 in these cells. DZNep induced expression of Dkk-1, a putative tumor suppressor that we have previously reported to be repressed by polycomb-mediated mechanisms in lung cancer cells and cultured normal respiratory epithelia following exposure to cigarette smoke condensate (CSC). Chromatin immunoprecipitation (ChIP) experiments demonstrated that DZNep-mediated activation of Dkk-1 coincided with decreased levels of H3K27Me3 within the Dkk-1 promoter. qRT-PCR and immunoblot experiments revealed that exposure of lung cancer cells to DZNep before or concurrent with CSC abrogated tobacco-mediated repression of Dkk-1 in vitro. Subsequent experiments demonstrated that daily intra-peritoneal (IP) injections of CSC significantly decreased Dkk-1 gene expression in subcutaneous A549 and Calu-6 xenografts, and enhanced growth of these tumors in nude mice. IP administration of DZNep (2.5 mg/kg BID q4 days every 7 days) significantly abrogated the enhancement effect of cigarette smoke on growth of lung cancer xenografts; this phenomenon coincided with decreased EZH2 and increased Dkk-1 expression in these xenografts. Collectively, these findings support development of DZNep for inhibiting PRC-2 expression in thoracic malignancies. Citation Format: Mahadev Rao, Young Hong, Scott Atay, Trevor Upham, Julie Hong, Nicole Datrice, Mary Zhang, Enrique Zudaire, Victor Marquez, David Schrump. Targeting H3K27 Methylation by 3-Deazaneplanocin A (DZNep) in lung and esophageal cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5360. doi:10.1158/1538-7445.AM2013-5360
Image-based assessment of fractional flow reserve (2015)

Pressure-derived fractional flow reserve (FFR) is an index of the haemodynamic significance of a coronary lesion. Numerous studies have provided robust evidence that FFR-guided percutaneous coronary intervention is associated with better clinical outcomes and reduces the need for repeat revascularisation. Although FFR is regarded as the gold standard for assessing lesion severity, it has limited clinical applications, mainly because it is a relatively expensive and time-consuming procedure. To overcome these limitations, several computational-based methodologies have been developed which enable estimation of the FFR in three-dimensional models derived from anatomic imaging data. Multislice computed tomographic coronary angiography and quantitative coronary angiography have been proposed for coronary reconstruction and computational evaluation of the FFR. In this review article, we describe the currently available methodologies for the computational estimation of FFR, present evidence derived from their clinical evaluations, stress their limitations, and discuss their potential value in clinical practice.
Supplementary Table 1 from <i>In Vivo</i> Detection of HSP90 Identifies Breast Cancers with Aggressive Behavior (2023)

&lt;p&gt;Metastatic Capacities of 4T1 and Subclones&lt;/p&gt;
MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors (2019)

Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. In this study, we screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers. We discovered <i>MDM2</i> and <i>MDM4</i>, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual), we show that MRT cells were more sensitive than other p53 wild-type cancer cell lines to inhibition of MDM2 alone as well as dual inhibition of MDM2/4. These compounds caused significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of <i>TP53</i>. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRTs, sensitized cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth <i>in vivo</i>, with a 5-day idasanutlin pulse causing marked regression of all xenografts, including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene <i>TP53</i> and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer. SIGNIFICANCE: This study identifies two targets, MDM2 and MDM4, as vulnerabilities in a deadly pediatric cancer and provides preclinical evidence that compounds inhibiting these proteins have therapeutic potential.
Proteoglycan-4 regulates fibroblast to myofibroblast transition and expression of fibrotic genes in the synovium (2020)

PRG4 is an endogenous antifibrotic modulator in the joint and its effect on myofibroblast formation is partially mediated by CD44, but CD44 is not required to demonstrate an antifibrotic effect in vivo.
Characterization of mouse ALCAM (CD166): the CD6‐binding domain is conserved in different homologs and mediates cross‐species binding (1997)

Activated leukocyte cell adhesion molecule (ALCAM; CD166) is a member of the immunoglobulin gene superfamily (IgSF) which is expressed by activated leukocytes and thymic epithelial cells and is a ligand for the lymphocyte antigen CD6. Herein, we report on the isolation and characterization of cDNA clones encoding mouse ALCAM (mALCAM). Comparison of the predicted amino acid sequence of mALCAM and human ALCAM (hALCAM) showed an overall identity of 93%. Binding studies with truncated forms of the extracellular region of mALCAM showed that the CD6 binding site is located in the N-terminal Ig-like domain and that mALCAM is capable of binding both human and mouse CD6. Mutagenesis studies on hALCAM suggested that residues critical for CD6 binding map to the predicted A'GFCC'C" beta-sheet of ALCAM's N-terminal binding domain. Residue differences in the N-terminal domains of mALCAM and hALCAM were analyzed with the aid of a molecular model of ALCAM. All residues critical for CD6 binding are conserved in both mALCAM and hALCAM, whereas residue differences map to the predicted BED face which is opposite the CD6 binding site on hALCAM. These findings provide a molecular rationale for the observed cross-species CD6/ALCAM interaction and the apparent inability to generate monoclonal antibodies (mAb) against the CD6 binding site. RNA blot analysis showed that mRNA transcripts encoding mALCAM are expressed in the brain, lung, liver, and the kidney, as well as by activated leukocytes and a number of cell lines. A rat mAb specific for mALCAM was produced and by two-color immunofluorescence studies was shown to bind to both activated CD4+ and CD8+ T cells.
Vitamin D as an Early Predictor of Multiple Sclerosis Activity and Progression (2014)

Among patients with MS mainly treated with interferon beta-1b, low 25(OH)D levels early in the disease course are a strong risk factor for long-term MS activity and progression.
Controlled-ambient photolithography of polysilane resists at 193 nm (1989)

Various polysilanes have been examined as self-developed photoresists at 193 nm and the benefits of imaging these materials in controlled, reactive ambients have been determined. Plasticization of the irradiated polymer due to reaction with oxygen is avoided when dry, oxygen-free ambients are employed. In addition, the redeposition of silicon from the ablated polysilane, which is prevalent in a one-pulse imaging mode, is greatly reduced when NF3 or CF2Cl2 are used as exposure ambients. Laser desorption mass spectrometry indicates that thermally activated decomposition of the polysilanes at fluences &amp;gt;100 mJ/cm2 causes more extensive fragmentation of the desorbed molecules. This results in the formation of higher volatility products upon halogenation.