gebhart/patrepeval huggingface dataset:
Abstract C23: MicroRNA-106b targets caspase-7 and is associated with recurrence in human prostate cancer (2012)

Abstract Previously, we found several microRNA (miR) of the polycistronic miR-106b-25 cluster to be elevated in prostate cancer. This cluster is a homolog to the prototypical oncomiR-1 (miR-17-92) and is thought to act as a super-oncogene when co-amplified with its host gene minichromosome complex maintenance component 7 (MCM7). In this study we validated our previous findings in an independent prostate cancer dataset and further found that miR-106b is elevated in metastatic tissues and associated with disease recurrence. Genome-wide analysis of miR-106b-25 correlated transcripts revealed enrichment of focal adhesion and ECM-receptor interaction genes. Further, we found miR-106b target enrichment in transcripts that were protective against recurrence, suggesting that miR-106b targets collectively have a functionally protective role in the recurrence of prostate cancer. In cell based assays, overexpression of miR-106b increased proliferation, adhesion-free survival, soft agar survival, and adhesion to ECM components (laminin, and collagen type I and IV). In addition, microarray analysis showed that miR-106b down-regulated transcripts were enriched for miR-106b targets sites and cell death pathways genes. When we compared genes that were related to recurrence, altered by miR-106b, and predicted to have miR-106b 3′UTR target sites we identified CASP7, a central executioner of apoptosis. Corroborating these findings we found that the expression of CASP7 was consistently reduced in primary human prostate tumors and metastatic lesions across multiple prostate cancer datasets, and is by itself a candidate predictor of disease recurrence. Western blot analysis in RWPE-1, 22Rv1, and LNCaP prostate cells showed that miR-106b was capable of reducing CASP7 protein levels. Direct targeting of the CASP7 3′UTR by miR-106b was confirmed using wild-type and mutant 3′UTR luciferase reporter assays. This research reveals a novel oncogenic role for the miR-106b-25 cluster in prostate cancer and, for the first time, indentifies CASP7 as a direct target of miR-106b. Future work is aimed at understanding the role of miR-106b-dependent regulation of CASP7 and the possible utility of targeting miR-106b as novel therapy for prostate cancer. Citation Format: Robert S. Hudson, Tiffany H. Dorsey, Ming Yi, Dominic Esposito, Robert M. Stephens, Carlo M. Croce, Stefan Ambs. MicroRNA-106b targets caspase-7 and is associated with recurrence in human prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C23.
Ex-vivo phantom for evaluation of ultrasound speckle tracking in the uterus (2017)

Uterine peristaltic movement plays an important role for the success of embryo implantation. This is especially relevant in the context of assisted reproductive technology. Unfortunately, the lack of tools for quantitative analysis limits our understanding of the uterine contractility. Recently, strain analysis by ultrasound speckle tracking has gained attention for the assessment of the uterine contractility. However, the absence of a ground truth hampers the optimization of this technology. This work proposes the first phantom based on a human ex-vivo uterus able to generate controlled tissue motion by sinusoidal (0,05 Hz), linear displacement of a syringe piston, injecting 3-mL water through a balloon catheter inserted into the uterine cavity. This way, controlled, realistic peristaltic movement was generated while maintaining original speckle characteristics. Uterine motion analysis was obtained by US speckle tracking on acquired B-mode imaging data using two block matching techniques, normalized cross-correlation (NCC) and sum of absolute differences (SAD). The proposed phantom based on a human ex-vivo uterus showed its value to assess US speckle tracking techniques providing a realistic ground truth that is fully controlled.
Recent Advances in Modeling Axisymmetric Swirl and Applications for Enhanced Heat Transfer and Flow Mixing (2011)

The concept of enhanced heat transfer and flow mixing using swirling jets has been investigated for nearly seven decades (Burgers, 1948; Watson and Clarke, 1947). Many practical applications of swirling jets include combustion, pharmaceuticals, tempering of metals, electrochemical mass transfer, metallurgy, propulsion, cooling of high-power electronics and computer chips, atomization, and the food industry, such as improved pizza ovens. Recently, swirling jet models have been applied to investigate heat transfer and flow mixing in nuclear reactors, including the usage of swirling jets in the lower plenum (LP) of generation-IV very high temperature gas-cooled reactors (VHTRs) to enhance mixing of the helium coolant and eliminate the formation of hot spots in the lower support plate, a safety concern (Johnson, 2008; Kim, Lim, and Lee, 2007; Laurien, Lavante, and Wang, 2010; Lavante and Laurien, 2007; Nematollahi and Nazifi, 2007; Rodriguez and El-Genk, 2008a, b, c, and d; Rodriguez, Domino, and El-Genk, 2010; Rodriguez and El-Genk, 2010a and b; Rodriguez and El-Genk, 2011). There are many devices and processes for generating vortex fields to enhance flow mixing and convective heat transfer. Figure 1 shows a static helicoid device that can be used to generate vortex fields based on the swirling angle, θ. Recent advances in swirling jet technology exploit common characteristics found in axisymmetric vortex flows, and these traits can be employed to design the vortex flow field according to the desired applications; among these are the degree of swirl (based on the swirl number, S) and the spatial distributions of the radial, azimuthal, and axial velocities. For a 3D helicoid, the vortex velocity in Cartesian coordinates can be approximated as:
High-Dose Convalescent Plasma for Treatment of Severe COVID-19 (2022)

We commend our colleagues in Brazil for completing a multicenter, open-label, randomized controlled trial (RCT) of coronavirus disease (COVID-19) convalescent plasma (CCP) against wildtype severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (1). This RCT had some strengths, including use of high-dose CCP (600 mL CCP for 3 days at a median neutralizing antibody titer of 1:128). The overall results were negative, but the authors caution that this finding probably reflects inclusion of patients late in disease, as evident by enrollment criteria (oxygen saturation <93%, partial pressure of oxygen/fraction of inspired oxygen <300, or need for mechanical ventilation), median transfusion at day 9 after symptom onset, 100% seropositivity, and 35% requiring hemodialysis at enrollment. The severity of disease in those patients means that disease was driven by inflammation as opposed to ongoing virus replication. To date, 2 CCP RCTs have shown benefit, 1 that provided outpatient treatment (D. Sullivan, et al., unpub. data, https://www.medrxiv.org/content /10.1101/2021.12.10.2126748v1) and 1 that provided inpatient treatment within 3 days of symptom onset (2). Hence, we caution against negative conclusions about the efficacy of CCP based on these data.
Calibration of transmission electron microscopic mass determination using objects with known mass distribution (1983)

An improved calibration procedure is described for dry mass determination methods, that are based on microdensitometry of transmission electron micrographs. Polystyrene latex spheres, that are supposed to have a homogeneous mass distribution, are used for the calibration procedure. By computer fitting of the theoretically expected mass distribution to the distribution measured in a line through the centre of a sphere, a mass calibration factor is obtained. The number of measurements required for a predetermined calibration accuracy can be decreased considerably as compared to other calibration methods. Accurate calibration and reproducible adjustment of the electron optical magnification are required.
Direct Binding of Ledipasvir to HCV NS5A: Mechanism of Resistance to an HCV Antiviral Agent (2015)

Ledipasvir, a direct acting antiviral agent (DAA) targeting the Hepatitis C Virus NS5A protein, exhibits picomolar activity in replicon cells. While its mechanism of action is unclear, mutations that confer resistance to ledipasvir in HCV replicon cells are located in NS5A, suggesting that NS5A is the direct target of ledipasvir. To date co-precipitation and cross-linking experiments in replicon or NS5A transfected cells have not conclusively shown a direct, specific interaction between NS5A and ledipasvir. Using recombinant, full length NS5A, we show that ledipasvir binds directly, with high affinity and specificity, to NS5A. Ledipasvir binding to recombinant NS5A is saturable with a dissociation constant in the low nanomolar range. A mutant form of NS5A (Y93H) that confers resistance to ledipasvir shows diminished binding to ledipasvir. The current study shows that ledipasvir inhibits NS5A through direct binding and that resistance to ledipasvir is the result of a reduction in binding affinity to NS5A mutants.
Abstract 4346: PI3K pathway mediated splicing defects in ER+ breast cancers (2019)

Activating mutations in PIK3CA, the gene encoding for the catalytic subunit (p100a), are the most common oncogenic alterations in estrogen receptor-positive (ER+). The majority of PIK3CA mutations occur within two hot spots; exons 9 and exon 20 which encode the helical (E545K) and kinase domains (H1047R), respectively. These mutations result in hyperactivation of the PI3K/AKT/mTOR pathway and provide the rationale for the development of inhibitors targeting the PI3K pathway. To this end, PI3K α-specific inhibitors are showing antitumor activity in patients with PIK3CA-mutant, ER-positive breast cancer. Evidence of alternative mRNA regulation and splicing in various cancers has been described in the literature. Although, the majority of events appear to have unknown clinical significance, there is evidence alternative splicing can lead to drug resistance. The role of the PI3K pathway on transcriptional regulation and mRNA processing is not well studied. Through transcriptome analysis and cell assays in mouse MEF and human MCF10A cells we demonstrate splicing defects accrue as a result of the PI3K pathway activation by the PIK3CA H1047R mutation. PI3Ka pathway inhibitors were able to restore wildtype exon inclusion levels in these mutants, suggesting a potential clinical benefit. We propose that PIK3CA H1047R imposes mRNA differential isoform regulation by acting through the most commonly mutated PI3K pathway in ER+ breast cancers and that such mutations are targetable with PI3K pathway inhibitors.Citation Format: Erik Ladewig, Lauren Fairchild, Maurizio Scaltriti, Christina Leslie, Eneda Toska, Jose Baselga. PI3K pathway mediated splicing defects in ER+ breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4346.
President, Congress and American Foreign Policy: Confrontation or Collaboration? (1976)

Journal Article President, Congress and American Foreign Policy: Confrontation or Collaboration? Get access William C. Olson William C. Olson Search for other works by this author on: Oxford Academic Google Scholar International Affairs, Volume 52, Issue 4, October 1976, Pages 565–581, https://doi.org/10.2307/2616773 Published: 01 October 1976
Self-Assembly of Squalene-Based Nucleolipids: Relating the Chemical Structure of the Bioconjugates to the Architecture of the Nanoparticles (2013)

Squalene-based nucleolipids, including anticancer or antiviral prodrugs, gave rise to nanoparticles displaying a diversity of structures upon nanoprecipitation in water. Synchrotron small-angle X-ray scattering and cryo-TEM imaging revealed that both the nature of the nucleoside and the position of the squalene moiety relative to the nucleobase determined the self-assembly of the corresponding bioconjugates. It was found that small chemical differences resulted in major differences in the self-organization of nucleolipids when squalene was grafted onto the nucleobase whereas only lamellar phases were observed when squalene was linked to the sugar moiety. The key role of hydrogen bonds between nucleobases in the formation of the lamellar phases was suggested, in agreement with molecular simulations. These findings provide a way to fine tune the supramolecular organization of squalene-based prodrugs, with the aim of improving their pharmacological activity.
FracDRAM: Fractional Values in Off-the-Shelf DRAM (2022)

As one of the cornerstones of computing, dynamic random-access memory (DRAM) is prevalent across digital systems. Over the years, researchers have proposed modifications to DRAM macros or explored alternative uses of existing DRAM chips to extend the functionality of this ubiquitous media. This work expands on the latter, providing new insights and demonstrating new functionalities in unmodified, commodity DRAM. FracDRAM is the first work to show how fractional values can be stored in off-the-shelf DRAM. We propose two primitive operations built with specially timed DRAM command sequences, to either store fractional values to the entire DRAM row or to masked bits in a row. Utilizing fractional values, this work enables more modules to perform the in-memory majority operation, increases the stability of the existing in-memory majority operation, and builds a state-of-the-art DRAM-based PUF with unmodified DRAM. In total, 582 DDR3 chips from seven major vendors are evaluated and characterized under different environments in this work. FracDRAM breaks through the conventional binary abstraction of DRAM logic, and brings new functions to the existing DRAM macro.
2.1 GHz wavelength conversion over a 100 nm input range with a side-injection light controlled bistable laser diode H. Tsuda (1993)

Broadband photonic transmission networks can be achieved not only with the fast response and massive parallelism of optical devices, but also by introducing wavelength division multiplexing (WDM) scheme. Wavelength converters are indispensable in each node of WDM photonic networks to increase the flexibility and the utilization factor.
Extraction rate equations for paprika and turmeric with certain organic solvents (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExtraction rate equations for paprika and turmeric with certain organic solventsThomas J. Houser, Tesfaye. Biftu, and Po-Fang. HsiehCite this: J. Agric. Food Chem. 1975, 23, 2, 353–355Publication Date (Print):March 1, 1975Publication History Published online1 May 2002Published inissue 1 March 1975https://pubs.acs.org/doi/10.1021/jf60198a051https://doi.org/10.1021/jf60198a051research-articleACS PublicationsRequest reuse permissionsArticle Views76Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Efficient and Functional Endothelial Repopulation of Whole Lung Organ Scaffolds (2017)

To date, efforts to generate engineered lung tissue capable of long-term function have been limited by incomplete barrier formation between air and blood and by thrombosis of the microvasculature upon exposure of blood to the collagens within the decellularized scaffold. Improved barrier function and resistance to thrombosis both depend upon the recapitulation of a confluent monolayer of functional endothelium throughout the pulmonary vasculature. This manuscript describes novel strategies to increase cell coverage of the vascular surface area, compared to previous reports in our lab and others, and reports robust production of multiple anticoagulant substances that will be key to long-term function in vivo once additional strides are made in improving barrier function. Rat lung microvascular endothelial cells were seeded into decellularized rat lungs by both the pulmonary artery and veins with the use of low-concentration cell suspensions, pulsatile, gravity-driven flow, and supraphysiological vascular pressures. Together, these strategies yielded 72.44 ± 10.52% endothelial cell nuclear coverage of the acellular matrix after 3-4 d of biomimetic bioreactor culture compared to that of the native rat lung. Immunofluorescence, Western blot, and PCR analysis of these lungs indicated robust expression of phenotypic markers such as CD31 and VE-Cadherin after time in culture. Endothelial-seeded lungs had CD31 gene expression of 0.074 ± 0.015 vs 0.021 ± 0.0023 for native lungs, <i>p</i> = 0.025, and VE-Cadherin gene expression of 0.93 ± 0.22 compared to that of the native lung at 0.13 ± 0.02, <i>p</i> = 0.023. Precursors to antithrombotic substances such as tissue plasminogen activator, prostacyclin synthase, and endothelial nitric oxide synthase were expressed at levels equal to or greater than those of the native lung. Engineered lungs reseeded with endothelial cells were implanted orthotopically and contained patent microvascular networks that had gas exchange function during mechanical ventilation on 100% O<sub>2</sub> greater than that of decelluarized lungs. Taken together, these data suggest that these engineered constructs could be compatible with long-term function in vivo when utilized in future studies in tandem with improved barrier function.
<title>Bit-rate control in overlapped transform coding of medical x-ray images</title> (1995)

In previous papers, we presented an overlapped transform-coding method for efficient data compression of medical x-ray image series. The proposed method is a lossy compression method. The distortion that is introduced by the compression is determined by the step size with which the transform coefficients are quantized. The number of bits produced per image depends on the amount of detail in the image. In principle, highly detailed images produce higher bit rates than less detailed images. For applications in which only a small number of images are recorded, the amount of time needed to store or transmit these images may not be an essential factor. In that case, some fluctuation in the bit rate may be tolerable. But for applications in which image series have to be stored or transmitted in real time, a constant bit rate is often preferred. In this paper, we explain how compression at a constant bit rate can be achieved. We propose a bit-rate control method that is capable of realizing a constant number of bits per image with a homogeneous distribution of the quantization errors over the coded image.
Cost of Equipment (2006)

This chapter contains sections titled: Base Station Structure IEEE 802.11 Wireless LAN Access Point Network Nodes Costs End-user Equipment Further Reading
Palladium Supported Porous Polyurea Frameworks as an Efficient Heterogeneous Catalyst for Suzuki-Miyaura Cross-coupling Reaction (2018)

다공성 고분자(porous organic polymer, POPs)는 높은 표면적을 가지는 무정형의 고분자이다. 본 연구에서는 우레아 축합반응으로 UPOP라는 다공성 고분자를 합성하였다. UPOP는 Brunauer-Emmett-Teller(BET) 분석을 통해 다공성을 확인하였고, 불균일 촉매 활용성을 보기 위하여 팔라듐을 담지하여 Pd@UPOP를 합성하였다. Pd@UPOP는 XPS 분석을 통해 Pd 담지를 확인하였고, Suzuki-Miyaura 커플링 반응을 이용하여 촉매활성을 측정하였다. Pd@UPOP의 촉매활성은 물과 ethanol이 3:1이고 K₂CO₃를 사용하였을 때 가장 높았다. 특히 이 조건에서 Pd@UPOP를 촉매로 사용하여 공기 중에서 반응시켰을 때 Pd 함량은 0.1 mol%였음에도 불구하고 99% 이상의 수율을 보였다. 또한 5번 재사용하였을 때도 90%의 수율을 유지하였다.
Selective neck dissection and deintensified postoperative radiation and chemotherapy for oropharyngeal cancer: A subset analysis of the university of pennsylvania transoral robotic surgery trial (2010)

SND after TORS resection of primary OPSCC enables the use of selective and deintensified adjuvant therapy to reduce regional recurrence rates.
Real-time 3D cone beam reconstruction (2005)

The paper presents a comparison of filtered back-projection and iterative approaches (modified SIRT and OSEM) where backprojection is performed on FPGA hardware and forward projection is realized by a graphics card. The FPGA-architecture allows scaling parallel processing of the backprojection with a constant memory bandwidth and it performs its task about a factor of 6 faster than conventional graphics card architectures (using a Xilinx Virtex II 6000 compared to a floating-point implementation on a graphics hardware). For the forward projection a graphics card (with NVIDIA GeForce FX 5900) is used. The system reconstructs a volume of 256/sup 3/ voxels and 60 projections (5122) within 6 seconds for each backprojection step and 12.5 s for the forward projection. As assumed filtered backprojection is the fastest method but shows most artifacts. SIRT and OSEM generate results with suppressed artifacts and require between 4 (SIRT) and 3 (OSEM) minutes for reconstruction. The limited precision of on the FPGA does not lead to any degradation in the reconstructed image quality.
Reducing Bias in AI-based Analysis of Visual Artworks (2022)

Empirical research in science and the humanities is vulnerable to bias which, by definition, implies incorrect or misleading findings. Artificial intelligence-based analysis of visual artworks is vulnerable to bias in ways specific to the domain. Works of art belong to a distinct cultural category that often prioritizes such characteristics as hand-craftsmanship, uniqueness, originality, and imaginative content; works of art are also responsive to diverse social and cultural contexts. Ascertaining which features of an artwork can be rightly ascribed to an objective &#x201C;truth,&#x201D; without which the concept of bias is not even relevant, is itself challenging. Incorporating expert knowledge into machine learning applications can help reduce bias in final estimates. We review several sources of bias that can occur across different stages of AI-based analysis, protocols and best practices for reducing bias, and approaches to measuring these biases. This systematic investigation of various types of bias can help researchers better understand bias, become aware of practical solutions, and ultimately cultivate the prudent adoption of AI-based approaches to artwork analysis.
Computer-generated holograms of images reconstructed on curved surfaces (1999)

When one illuminates a computer-generated hologram by a plane wave, the obtained two-dimensional image is usually displayed on a planar plane. Other possibilities for reconstructing images on arbitrary curved surfaces are discussed herein. As an example, the reconstruction of an image on a virtual spherical surface is demonstrated.