gebhart/patrepeval huggingface dataset:
Utility of QDot® bioconjugates in the detection of ERG gene re‐arrangements in prostate cancer (2009)

Prostate cancer (PCA) is one of the most prevalent malignancies affecting men worldwide. Recent discovery of ERG gene re‐arrangements in PCA and their strong association with disease progression has therapeutic and diagnostic implications. Gene fusions identified thus far are characterized by 5' genomic regulatory elements ( TMPRSS2), fused to the ETS family of transcription factors (TF), that can lead to over‐expression of oncogenic TF. In this report, we have developed an automated assay that includes novel FISH probes in conjunction with Qdot‐antibody conjugates, to detect the various ERG re‐arrangements. We have shown sensitive and specific detection of gene rearrangements in xenografts, H1660, LnCAP, and VCAP. These data confirmed previous reports of homozygous intronic deletion, no deletion, and varied deletions of 5'ERG region of Chr 21 in the respective xenografts. Imaging with FISH filters we observed robust signal at 20x magnification. This study outlines the development of novel gene probes and fluorescent bioconjugates that enable simultaneous detection of the 5' and 3' ERG translocations in PCA.
Wavelength-selective semiconductor in-line fibrephotodetectors (2000)

A photodetector which extracts and detects light at a specific wavelength travelling through a fibre is presented. The detector is a semiconductor waveguide evanescently coupled to a singlemode fibre. The full width at half-maximum of the photocurrent response is 1.6 nm, and the external quantum efficiency is 75%.
Development of a predictive corrosion model using locality-specific corrosion indices (2017)

The U.S. Department of Defense has characterized the current approach to corrosion maintenance, which is based on simply finding and fixing damage before it becomes a concern, as inadequate to maintain missioncritical equipment and facilities to support stationing decisions. There is a need to go beyond corrosion prediction and management approaches to consider the impact of climate change on stationing decisions. To address this concern, there is a need to develop defensible, accurate approaches to project how certain installation metrics involving materials degradation are likely to change in the near future. The first step in creating a tool to meet this need is to determine how selected quantitative data, or chosen installation "metrics," will change over some specified period. This work developed and tested a corrosivity model capable of predicting corrosivity at specific sites.
Viewpoint information-theoretic measures for 3D shape similarity (2013)

We present an information-theoretic framework to compute the shape similarity between 3D polygonal models. From an information channel between a sphere of viewpoints and the polygonal mesh of a model, an information sphere is obtained and used as a shape descriptor of the model. Given two models, the minimum distance between their information spheres, the distance between their information histograms, and the difference of their mutual information are introduced as methods to calculate the similarity matrix between 3D models. The performance of these techniques is tested using the Princeton Shape Benchmark database.
IEEE 802.21 and Proxy Mobile IPv6: A network controlled mobility solution (2011)

Abstract: IP Mobility has been deeply investigated in the past years and standard-ization bodies (e.g., IETF, 3GPP and IEEE) have specified a wide suite of protocols enabling seamless mobility across heterogeneous wireless access technologies. How-ever, such mobility helping technologies are not yet widely spread as compared to other emerging technologies like WiFi hotspots. This paper aims at filling this gap between research and real deployments by specifying and implementing a scheme for mobility support in wireless heterogeneous environments. In our solution, mo-bility management is achieved via the Proxy Mobile IPv6 protocol while optimized handover control is provided by the integration of the IEEE 802.21 framework with Proxy Mobile IPv6. The paper also includes the performance evaluation of the pro-posed platform, shows results obtained through live experiments on the field.
AMD GPUs as an Alternative to NVIDIA for Supporting Real-Time Workloads (2020)

Graphics processing units (GPUs) manufactured by NVIDIA continue to dominate many fields of research, including real-time GPU-management. NVIDIA’s status as a key enabling technology for deep learning and image processing makes this unsurprising, especially when combined with the company’s push into embedded, safety-critical domains like autonomous driving. NVIDIA’s primary competitor, AMD, has received comparatively little attention, due in part to few embedded offerings and a lack of support from popular deep-learning toolkits. Recently, however, AMD’s ROCm (Radeon Open Compute) software platform was made available to address at least the second of these two issues, but is ROCm worth the attention of safety-critical software developers? In order to answer this question, this paper explores the features and pitfalls of AMD GPUs, focusing on contrasting details with NVIDIA’s GPU hardware and software. We argue that an open software stack such as ROCm may be able to provide much-needed flexibility and reproducibility in the context of real-time GPU research, where new algorithmic or analysis techniques should typically remain agnostic to the underlying GPU architecture. In support of this claim, we summarize how closed-source platforms have obstructed prior research using NVIDIA GPUs, and then demonstrate that AMD may be a viable alternative by modifying components of the ROCm software stack to implement spatial partitioning. Finally, we present a case study using the PyTorch deep-learning framework that demonstrates the impact such modifications can have on complex real-world software.
ChemInform Abstract: SYNTH. VON RADICININ‐ANALOGA 2. MITT. RED. VON 4H,5H‐PYRANO(4,3‐B)PYRAN‐4,5‐DION‐DERIVATEN (1971)

Abstract Bei der Hydrierung des Pyrano‐pyran‐dions (Ib) mit Raney‐Nickel werden die hydrierten Pyrano‐pyran‐dione (IIb), (IIIb) und (IVb) erhalten.
High Speed Imaging of 1 MHz Driven Microbubbles in Contact with a Rigid Wall (2009)

Since the introduction of megasonic cleaning in semiconductor industry a debate has been going on about which physical mechanism is responsible for the removal of particles. Because of the high frequency range it was believed that acoustic cavitation could not occur and cleaning was attributed to phenomena like Eckart and Schlichting streaming or pressure build-up on particles [1,2]. Recently it was shown however, that the removal of nanoparticles is closely related to the presence of acoustic cavitation in megasonic cleaning systems [3]. The dependence of particle removal efficiency on the concentration of dissolved gas and the presence of sonoluminescence are clear (but indirect) indications that the underlying mechanism is related to bubble dynamics. As the requirements for cleaning in semiconductor processing are ever more stringent, it becomes necessary to obtain a thorough understanding of the physical behavior of acoustically driven microbubbles in contact with a solid wall. In particular, the forces exerted thereby which might clean or damage a substrate are of interest. Here, a step in this direction is taken by visualization of both the removal of nanoparticles and the sub-microsecond timescale dynamics of the cavitation bubbles responsible thereof.
Optical Biomarkers Associated with the Invasive Potential of Tumor Cells in Engineered Tissue Models (2010)

Intrinsic two-photon excited fluorescence (TPEF) images of epithelial tumor cells embedded in collagen matrices reveal distinct morphologies and organization from the subcellular to the tissue level associated with motility and invasive potential of cells.
Defining the “Three-Dimensional Sagittal Plane” in Thoracic Adolescent Idiopathic Scoliosis (2015)

Routine 2-D measurements of thoracic kyphosis erroneously underestimate the preoperative loss of kyphosis in AIS because of errors associated with axial plane rotation, an inherent component of thoracic scoliosis.
Intrinsic Fluorescence and Diffuse Reflectance Spectroscopy Identify Superficial Foam Cells in Coronary Plaques Prone to Erosion (2006)

Our combined IFS and DRS technique accurately detects SFCs in thick fibrous cap atheromas and PIT lesions. Because SFCs are associated with histological markers of plaque erosion, our spectroscopic technique could prove useful in identifying vulnerable plaques.
An Angle-Independent Cross-Sectional Doppler Method for Flow Estimation in the Common Carotid Artery (2020)

The Doppler ultrasound is the most common technique for noninvasive quantification of blood flow, which, in turn, is of major clinical importance for the assessment of the cardiovascular condition. In this article, a method is proposed in which the vessel is imaged in the short axis, which has the advantage of capturing the whole flow profile while measuring the vessel area simultaneously. This view is easier to obtain than the longitudinal image that is currently used in flow velocity estimation, reducing operator dependence. However, the Doppler angle in cross-sectional images is unknown since the vessel wall can no longer be used to estimate the flow direction. The proposed method to estimate the Doppler angle in these images is based on the elliptical intersection between a cylindrical vessel and the ultrasound plane. The parameters of this ellipse (major axis, minor axis, and rotation) are used to estimate the Doppler angle by solving a least-squares problem. Theoretical feasibility was shown in a geometrical model, after which the Doppler angle was estimated in simulated ultrasound images generated in Field II, yielding a mean error within 4°. In vitro, across 15 short-axis measurements with a wide variety of Doppler angles, errors in the flow estimates were below 10%, and in vivo, the average velocities in systole obtained from longitudinal ( v=69.1 cm/s) and cross-sectional ( v=66.5 cm/s) acquisitions were in agreement. Further research is required to validate these results on a larger population.
Bringing automated, remote‐sensed, machine learning methods to monitoring crop landscapes at scale (2019)

Abstract This article provides an overview of how recent advances in machine learning and the availability of data from earth observing satellites can dramatically improve our ability to automatically map croplands over long periods and over large regions. It discusses three applications in the domain of crop monitoring where machine learning (ML) approaches are beginning to show great promise. For each application, it highlights machine learning challenges, proposed approaches, and recent results. The article concludes with discussion of major challenges that need to be addressed before ML approaches will reach their full potential for this problem of great societal relevance.
Methods for Adenowirus-Mediated Gene Transfer to Airway Epithelium (2003)

Recombinant adenoviral vectors have proven to be extremely efficient tools for transferring genes into multiple organ systems including the lung (1-5), liver (6-10), muscle (11,12), joint (13), vasculature (14,15), and central nervous system (16-18). The lung presents unique advantages as a target organ for the evaluation of these vectors as tools for in vivo gene therapy owing to the accessibility of target cells by direct instillation or inhalation of recombinant virus in the airway. Multiple therapeutic applications of gene therapy to the lung include both inherited disorders such as cystic fibrosis (CF) and α-antitrypsin deficiency, as well as acquired disorders such as bronchitis, asthma, emphysema, and respiratory malignancies. The most widely studied application to date has involved the analysis of recombinant adenoviruses for gene therapy of CF lung disease (1-5). To this end, multiple phase I clinical trails are now underway evaluating the safety of recombinant adenoviral vectors for gene therapy of cystic fibrosis lung disease (19). This clinical application of these vectors in CF lung disease presents the largest comprehensive effort of in vivo gene therapy to date. Such a substantial effort has offered the advantage of multiple preclinical studies evaluating delivery of adenoviral vectors to the lung in numerous animal models such as the cotton rat (4,5,20), human bronchial xenografts (1), mouse (21), and nonhuman primates (2,3,22,23).
Direct write 3-dimensional nanopatterning using probes (2010)

A high-resolution probe based patterning method is presented using organic resists that respond to the presence of a hot tip by local material desorption. Thereby arbitrarily shaped patterns can be written in the organic films in the form of a topographic relief. The patterning process is highly reproducible and repeatable enabling the creation complex relief structures with arbitrary texture also in the vertical dimension. The patterns can be readily transferred into silicon using standard RIE technology. The new technique offers a cost-effective and competitive alternative to high-resolution electron-beam lithography in terms of both resolution and speed.
Cooperative alterations of Rb pathway regulators in mouse primary T cell lymphomas (1999)

Alterations in the Rb pathway have been described in many different tumors. In order to study this cell cycle regulatory mechanism in murine T cell lymphomas, we have analyzed the RNA and protein expression of the cyclin D1, cdk4 and retinoblastoma genes in primary tumor samples. We have detected overexpression of the cyclin D1 gene and deficient expression of the retinoblastoma gene in 42 and 28% of these tumors, respectively. The immunohistochemical analysis showed that these RT-PCR results are correlated with a significant increase in the number of positive cells for cyclin D1 and a moderate decrease in the expression of Rb protein, respectively. The analysis of cyclin D1, Rb, p15(INK4b) and p16(INK4a) showed that 75% of lymphomas had alterations in these genes and indicates that the Rb pathway is frequently altered in mouse primary T cell lymphomas. Moreover, 31% of lymphomas presented simultaneous alterations in at least two of these genes, suggesting the importance of concurrent alteration of different Rb pathway regulators. In addition, we have characterized these samples for mutational status of the N-ras and K-ras genes. We have only detected mutations in codon 12 of K-ras in six of 49 lymphomas (12%). Interestingly, five of these lymphomas also showed alterations in at least one of the Rb pathway regulators analyzed here. Taken together, these data suggest that deregulation of the Rb pathway regulators and/or oncogenic activation of K-ras may represent a common important clue in progression of murine T cell lymphomas.
Improving providers' survival estimates and selection of prognosis‐ and guidelines‐appropriate treatment for patients with symptomatic bone metastases: Development of the Bone Metastases Ensemble Trees for Survival Decision Support Platform (2022)

We describe the successful development of a provider-facing decision support platform to aid in the provision of palliative RT in better alignment with patient and disease features. Impact of the BMETS-DSP on decision outcomes will be further assessed in a randomised, controlled study.
Proceedings of the 2008 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2008)

It is with great pleasure that I welcome you to SIGMETRICS 2008. Performance modeling and measurement are critical in the design and development of information technologies, ranging from computer systems to computer networks and the World Wide Web. Over the past decades we have seen an increasing influence of the modeling and measurement work in various disciplines in computer science. As a result, our community has been growing with broader application backgrounds and technical interests.

This year's conference program is particularly exciting, with a number of new features. For the first time, the main conference has grown to a program of three full days with 36 papers. Also for the first time, we have a demo competition and a student thesis panel. In addition, there are three keynotes given by illustrious scholars from academia, Francois Baccelli (member of the French Academy of Sciences); from a funding agency, Jeannette Wing (Assistant Director of the Computer and Information Science and Engineering Directorate of the National Science Foundation); and from industry, Harrick Vin (Vice President of Research and Development at Tata Consultancy Services). Also new this year is a panel on Performance Analysis in the Real World, where all the panelists come from industrial production environments and will provide an industrial perspective of performance modeling and analysis.

The conference program is further augmented with stimulating tutorials and workshops. This year, there are nine excellent tutorials on topics ranging from analysis and control techniques to performance engineering methodology and network economics. The MAthematical performance Modeling and Analysis (MAMA) workshop continues its success with its 10th edition in 2008. The Workshop on Hot Topics in METRICS (HotMetrics) will be inaugurated immediately after the main conference, in parallel with the third International Workshop on Feedback Control Implementation and Design in Computing Systems and Networks (FeBID). These tutorials and workshops complement the main conference and significantly enhance SIGMETRICS 2008.
Retroviruses expressing different levels of the normal epidermal growth factor receptor: Biological properties and new bioassay (1989)

Two retroviral DNAs that encode the normal human epidermal growth factor (EGF) receptor hEGFR have been generated by inserting a hEGFR cDNA into two different retroviral vectors. One DNA (pCO11-EGFR-neo) also contained a linked selectable marker gene (neoR). The other (pCO12-EGFR) only expresses hEGFR. When introduced into NIH3T3 cells, the two DNAs and the viruses derived from them induced a fully transformed phenotype, including focal transformation and growth in agar or low serum, but transformation depended entirely upon EGF being present in the growth medium. Compared with pCO11-EGFR-neo, pCO12-EGFR induced EGF-dependent transformation 2-5 times more efficiently and expressed higher numbers of receptors (4 x 10(5) vs. 1 x 10(5) EGF receptors per cell). The results indicate that transforming potential is directly related to the number of EGF receptors. In defined, serum-free medium that contained only very low concentrations of insulin (0.6 microgram/ml) and transferrin (0.6 micrograms/ml), hEGFR-virus infected cells were able to grow with EGF as the only growth factor. Moreover, daily incubation of the cells with EGF for only 30 min was sufficient to induce growth. NR6 cells, which lack endogenous EGF receptors, were transformed as efficiently as NIH3T3 cells by the hEGFR virus. The dose-dependent growth response to EGF of infected NR6 cells grown in serum-free medium can be used as a highly sensitive bioassay for the quantitative assessment of EGF and transforming growth factor type alpha (TGF alpha). This bioassay is at least as sensitive as previously reported radioimmunoassays and can measure a much wider concentration range (10 pg-100 ng/ml). Uninfected NR6 cells or NR6 cells infected by helper virus alone can be used as controls for the EGF specificity of growth stimulation.
Array comparative genomic hybridization with cyanin cis -platinum-labeled DNAs (2004)

Fluorescent cis-platinum compounds that react with the N7 atom of guanine are useful for labeling nucleic acids influorescence hybridization applications. Here we report that cyanin (CyN) cis-platinum labeling of DNA samples for array comparative genomic hybridizations (arrayCGH) can be achieved reproducibly and reliably. We demonstrate that degrees of labeling of approximately 1% of all nucleotides in test and reference DNA samples with CyN3- and CyN5-cis-platinum produces arrayCGH signal-to-background ratios ranging from 30 to 40. The arrayCGH results achieved during analyses of mouse and human tumor samples were comparable to those achieved using enzymatic labeling. Thus, we conclude that Cy-cis-platinum labeling is an alternative to enzymatic labeling for arrayCGH.
The chemistry of magnesium chloride supported catalysts for polypropylene (1991)

Abstract The reactions between the components of high activity catalysts for polypropylene, aluminum alkyls, magnesium chloride, titanium halides and Lewis bases, are discussed with particular reference made on their influence on the activity and stereospecificity of the catalytic system.
A Practical Data-Reuse Adaptive Algorithm For Acoustic Echo Cancellation (2012)

Publication in the conference proceedings of EUSIPCO, Bucharest, Romania, 2012
Prostasin regulates PD-L1 expression in human lung cancer cells (2021)

The serine protease prostasin is a negative regulator of lipopolysaccharide-induced inflammation and has a role in the regulation of cellular immunity. Prostasin expression in cancer cells inhibits migration and metastasis, and reduces epithelial-mesenchymal transition. Programmed death-ligand 1 (PD-L1) is a negative regulator of the immune response and its expression in cancer cells interferes with immune surveillance. The aim of the present study was to investigate if prostasin regulates PD-L1 expression. We established sublines overexpressing various forms of prostasin as well as a subline deficient for the prostasin gene from the Calu-3 human lung cancer cells. We report here that PD-L1 expression induced by interferon-γ (IFNγ) is further enhanced in cells overexpressing the wildtype membrane-anchored prostasin. The PD-L1 protein was localized on the cell surface and released into the culture medium in extracellular vesicles (EVs) with the protease-active prostasin. The epidermal growth factor-epidermal growth factor receptor (EGF-EGFR), protein kinase C (PKC), and mitogen-activated protein kinase (MAPK) participated in the prostasin-mediated up-regulation of PD-L1 expression. A Gene Set Enrichment Analysis (GSEA) of patient lung tumors in The Cancer Genome Atlas (TCGA) database revealed that prostasin and PD-L1 regulate common signaling pathways during tumorigenesis and tumor progression.
Myocardial Revascularization During Postinfarction Shock (1973)

If measures are taken swiftly enough to halt the advance of necrosis in the infarcted myocardium by reducing its work and improving its oxygen supply, even patients in cardiogenic shock can be saved. A staged approach is described; it calls for a trial of circulatory assistance via balloon counterpulsation followed, if necessary, by aortocoronary bypass grafting in patients whose myocardial loss is not prohibitive.
Mapping of Transition Metal Redox Energies in Phosphates with NASICON Structure by Lithium Intercalation (1997)

The position of several transition metal redox energies with respect to the Fermi energy of lithium in phosphates with sodium super ionic conductor (NASICON) framework were determined electrochemically upon lithium intercalation. The materials studied were , and all having NASICON framework. The positions of the redox couples were found centered at the following energies: at 3.8 eV, at 2.8 eV, at 2.5 eV, at 2.2 eV, at 1.8 eV, and at 1.7 eV below the Fermi energy of lithium. Several of these redox couples were found to overlap each other. Some of these materials look promising as positive electrode materials for ‐ion batteries.