gebhart/patrepeval huggingface dataset:
Adjuvant Capecitabine, Docetaxel, Cyclophosphamide, and Epirubicin for Early Breast Cancer: Final Analysis of the Randomized FinXX Trial (2011)

Integration of capecitabine into a regimen that contains docetaxel, epirubicin, and cyclophosphamide did not improve RFS significantly compared with a similar regimen without capecitabine.
An Open Source GPU-Based Beamformer for Real-Time Ultrasound Imaging and Applications (2019)

Recent technological advances in graphics processing unit (GPU)-based computing have made it possible to visualize customized beamforming pipelines and algorithms in real-time. However, GPU programming is challenging and poses a significant barrier to its widespread adoption in the ultrasound research community. Here, we present an open source GPU beamformer with the intent of making GPU beamforming more accessible to a wider audience. The beamformer was written in C++/CUDA and is comprised of a library of core classes to perform typical ultrasound-related tasks, such as applying focusing delays. Classes are arranged into a computational graph that is fixed at compile-time, enabling high throughput at runtime. Concrete examples are provided to demonstrate how to interface the beamforming library with the MATLAB-based Verasonics platform to perform live B-mode and Doppler imaging. Also provided is an example of deploying a TensorFlow neural network in real-time via TensorRT. Compilation was performed using CMake to allow for cross-platform compatibility. Including overhead for data acquisition, the beamformer achieved live B-mode imaging with a Verasonics Vantage 256 system at 55 frames per second using a single NVIDIA Titan V GPU. The open source GPU beamformer can be used as a starting point for real-time algorithm deployment.
TOXICITY OF METAL-CONTAMINATED SEDIMENTS FROM THE UPPER CLARK FORK RIVER, MONTANA, TO AQUATIC INVERTEBRATES AND FISH IN LABORATORY EXPOSURES (1994)

Sediments of the upper Clark Fork River, from the Butte and Anaconda area to Milltown Reservoir (230 km downstream), are contaminated with As, Cd, Cu, Pb, Mn, and Zn primarily from mining activities. The toxicity of pore water from these sediments was determined using Daphnia magna (48-h exposure), rainbow trout (96-h exposure), and Microtox®. However, pore-water data from these exposures were questionable because of changes in the toxicity of pore-water samples after 5 to 7 d of storage. Whole-sediment tests were conducted with Hyalella azteca (28-d exposure), Chironomus riparius (14-d exposure), rainbow trout (Oncorhynchus mykiss) 21- to 28-d exposure and Daphnia magna (2- to 22-d exposure). Sediment samples from Milltown Reservoir and the Clark Fork River were not generally lethal to test organisms. However, both reduced growth and delayed sexual maturation of amphipods were associated with exposure to elevated concentrations of metals in sediments from the reservoir and river. Relative sensitivity (most sensitive to least sensitive) of organisms in whole-sediment toxicity tests was: Hyalella azteca > Chironomus riparius > rainbow trout > Daphnia magna. Relative sensitivity (most sensitive to least sensitive) of the three end points evaluated with Hyalella azteca was: length > sexual maturation > survival. The lack of lethal effects on organisms may be related to temporal differences in sediment, acid-volatile sulfide, or organic carbon.
A Multi-site Study of a Breast Density Deep Learning Model for\n Full-field Digital Mammography Images and Synthetic Mammography Images (2020)

Purpose: To develop a Breast Imaging Reporting and Data System (BI-RADS)\nbreast density deep learning (DL) model in a multi-site setting for synthetic\ntwo-dimensional mammography (SM) images derived from digital breast\ntomosynthesis exams using full-field digital mammography (FFDM) images and\nlimited SM data.\n Materials and Methods: A DL model was trained to predict BI-RADS breast\ndensity using FFDM images acquired from 2008 to 2017 (Site 1: 57492 patients,\n187627 exams, 750752 images) for this retrospective study. The FFDM model was\nevaluated using SM datasets from two institutions (Site 1: 3842 patients, 3866\nexams, 14472 images, acquired from 2016 to 2017; Site 2: 7557 patients, 16283\nexams, 63973 images, 2015 to 2019). Each of the three datasets were then split\ninto training, validation, and test datasets. Adaptation methods were\ninvestigated to improve performance on the SM datasets and the effect of\ndataset size on each adaptation method is considered. Statistical significance\nwas assessed using confidence intervals (CI), estimated by bootstrapping.\n Results: Without adaptation, the model demonstrated substantial agreement\nwith the original reporting radiologists for all three datasets (Site 1 FFDM:\nlinearly-weighted $\\kappa_w$ = 0.75 [95% CI: 0.74, 0.76]; Site 1 SM: $\\kappa_w$\n= 0.71 [95% CI: 0.64, 0.78]; Site 2 SM: $\\kappa_w$ = 0.72 [95% CI: 0.70,\n0.75]). With adaptation, performance improved for Site 2 (Site 1: $\\kappa_w$ =\n0.72 [95% CI: 0.66, 0.79], 0.71 vs 0.72, P = .80; Site 2: $\\kappa_w$ = 0.79\n[95% CI: 0.76, 0.81], 0.72 vs 0.79, P $&lt;$ .001) using only 500 SM images from\nthat site.\n Conclusion: A BI-RADS breast density DL model demonstrated strong performance\non FFDM and SM images from two institutions without training on SM images and\nimproved using few SM images.\n
Immortalization capacity of HPV types is inversely related to chromosomal instability (2016)

High-risk human papillomavirus (hrHPV) types induce immortalization of primary human epithelial cells. Previously we demonstrated that immortalization of human foreskin keratinocytes (HFKs) is HPV type dependent, as reflected by the presence or absence of a crisis period before reaching immortality. This study determined how the immortalization capacity of ten hrHPV types relates to DNA damage induction and overall genomic instability in HFKs.Twenty five cell cultures obtained by transduction of ten hrHPV types (i.e. HPV16/18/31/33/35/45/51/59/66/70 E6E7) in two or three HFK donors each were studied.All hrHPV-transduced HFKs showed an increased number of double strand DNA breaks compared to controls, without exhibiting significant differences between types. However, immortal descendants of HPV-transduced HFKs that underwent a prior crisis period (HPV45/51/59/66/70-transduced HFKs) showed significantly more chromosomal aberrations compared to those without crisis (HPV16/18/31/33/35-transduced HFKs). Notably, the hTERT locus at 5p was exclusively gained in cells with a history of crisis and coincided with increased expression. Chromothripsis was detected in one cell line in which multiple rearrangements within chromosome 8 resulted in a gain of MYC.Together we demonstrated that upon HPV-induced immortalization, the number of chromosomal aberrations is inversely related to the viral immortalization capacity. We propose that hrHPV types with reduced immortalization capacity in vitro, reflected by a crisis period, require more genetic host cell aberrations to facilitate immortalization than types that can immortalize without crisis. This may in part explain the observed differences in HPV-type prevalence in cervical cancers and emphasizes that changes in the host cell genome contribute to HPV-induced carcinogenesis.
Soluble Tumor Necrosis Factor Receptor Expression in Patients with Metastatic Renal Cell Carcinoma Treated with Interleukin-2-Based lmmunotherapy (1993)

Two distinct types of soluble tumor necrosis factor alpha receptors (sTNFRs), which are felt to represent proteolytic cleavage products of the extracellular domains of membrane-bound TNFRs of molecular mass, 55 and 75 kDa, are found in the serum and urine of humans. We have measured the serum concentrations of these receptors in eight patients with metastatic renal cell carcinoma during treatment with interleukin-2 (IL-2)-based immunotherapy. The mean pretreatment concentration of sTNFR-55 kDa (p < 0.05) but not sTNFR-75 kDa was significantly elevated prior to the onset of immunotherapy. In one patient the concentrations of both sTNFRs decreased dramatically following removal of the primary tumor. There were significant increases in the concentrations of both sTNFRs in patients treated with IL-2-based therapy that included in vivo primed tumor infiltrating lymphocytes (pTILs); some of these patients eventually achieved a complete response to therapy. These data demonstrate that sTNFR-55 kDa is elevated in patients with metastatic renal cell carcinoma prior to therapy and that IL-2-based therapy that included pTIL cells results in a further increase in sTNFRs.
Murine double minute 2 as a therapeutic target for radiation sensitization of lung cancer (2005)

Murine double minute 2 (MDM2) inhibits p53-mediated functions, which are essential for therapies using DNA-damaging agents. The purpose of this study was to determine whether MDM2 inhibition enhances the radiosensitivity of a lung cancer model. The effects of MDM2 inhibition on tumor vasculature were also studied. Transient transfection of H460 lung cancer cells and human umbilical vascular endothelial cells (HUVEC) with antisense oligonucleotides (ASODN) against MDM2 resulted in a reduced level of MDM2 and increased levels of p21 and p53. Clonogenic assays showed that inhibition of MDM2 greatly decreased cell survival following irradiation. Quantification of apoptotic cells by 7-aminoactinomycin D staining and of senescent cells by X-gal staining showed that both processes were significantly increased in H460 cells treated with MDM2-specific ASODN and radiation. H460 xenografts that were treated with MDM2 ASODN plus radiotherapy also showed significant growth delay (P < 0.001) and increased apoptosis by terminal deoxynucleotidyl transferase-mediated nick end labeling staining. HUVECs transfected with MDM2-specific ASODN showed impaired viability and migration with decreased tube formation. Doppler studies showed that tumor blood flow was compromised when H460 xenografts were treated with MDM2-specific ASODN and radiation. A combination of radiotherapy and inhibition of MDM2 through the antisense approach results in improved tumor control in the H460 lung cancer model. This implies that a similar strategy should be investigated among patients with locally advanced lung cancer, receiving thoracic radiotherapy.
Supplementary Methods from Characterization of the Selective Indoleamine 2,3-Dioxygenase-1 (IDO1) Catalytic Inhibitor EOS200271/PF-06840003 Supports IDO1 as a Critical Resistance Mechanism to PD-(L)1 Blockade Therapy (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Purification of the intermediate filament-associated protein, synemin, from chicken smooth muscle. Studies on its physicochemical properties, interaction with desmin, and phosphorylation. (1983)

Synemin, a 230,000-dalton protein associated with desmin- and vimentin-containing intermediate filaments (Granger, B. L., and Lazarides, E. (1980) Cell 22, 727-738), has been purified from gizzard smooth muscle and biochemically characterized. Purification was achieved by extracting the salt-insoluble pellet of muscle protein with 6 M urea and chromatography of the urea extract on columns of hydroxylapatite, DEAE-Sephacel, and phosphocellulose. The soluble form of synemin is a globular tetramer of 980,000 daltons with a S20,w of 22.4 +/- 3.2. Synemin has a pI of 5.34, in agreement with its high content in glutamic acid (20%), and is rich in serine (11%) and poor in cysteine (0.4%). Synemin is phosphorylated in smooth muscle and is one of the muscle proteins with the highest capacity to incorporate exogenously added [32P]phosphate. Of the [32P] phosphate incorporated into synemin, 95% is bound to serine and only 5% to threonine. The phosphorylation of synemin is enhanced by the cyclic AMP analog, 8-Br-cyclic AMP. Immunofluorescence studies using anti-synemin antibodies show that purified synemin binds to filaments of desmin assembled in vitro. Synemin specifically inhibits the immunoprecipitation of purified soluble desmin by anti-desmin antibodies, indicating that synemin interacts in vitro with soluble desmin.
Simulations of string vibrations with boundary conditions of third kind using the functional transformation method (2005)

The functional transformation method (FTM) is an established mathematical method for accurate simulation of multidimensional physical systems from various fields of science, including optics, heat and mass transfer, electrical engineering, and acoustics. It is a frequency-domain method based on the decomposition into eigenvectors and eigenfrequencies of the underlying physical problem. In this article, the FTM is applied to real-time simulations of vibrating strings which are ideally fixed at one end while the fixing at the other end is modeled by a frequency-dependent input impedance. Thus, boundary conditions of third kind are applied to the model at the end fixed with the input impedance. It is shown that accurate and stable simulations are achieved with nearly the same computational cost as with strings ideally fixed at both ends.
Reduced Salience and Enhanced Central Executive Connectivity Following PTSD Treatment (2019)

The results support previous models relating CPT to central executive network and enhanced cognitive control while unraveling a previously unknown neurobiological mechanism of PCT treatment, demonstrating treatment-specific reduction in salience connectivity during trauma recollection.
Universal Adversarial Attacks on Spoken Language Assessment Systems (2020)

There is an increasing demand for automated spoken language assessment (SLA) systems, partly driven by the performance improvements that have come from deep learning based approaches. One aspect of deep learning systems is that they do not require expert derived features, operating directly on the original signal such as a speech recognition (ASR) transcript. This, however, increases their potential susceptibility to adversarial attacks as a form of candidate malpractice. In this paper the sensitivity of SLA systems to a universal black-box attack on the ASR text output is explored. The aim is to obtain a single, universal phrase to maximally increase any candidate's score. Four approaches to detect such adversarial attacks are also described. All the systems, and associated detection approaches, are evaluated on a free (spontaneous) speaking section from a Business English test. It is shown that on deep learning based SLA systems the average candidate score can be increased by almost one grade level using a single six word phrase appended to the end of the response hypothesis. Although these large gains can be obtained, they can be easily detected based on detection shifts from the scores of a “traditional” Gaussian Process based grader.
ChemInform Abstract: Synthetic Approaches to the Manumycin A, B, and C Antibiotics: The First Total Synthesis of (+)‐Manumycin A. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The Biology behind Gene Expression: A Basic Tutorial (2006)

Microarrays measure the relative levels of gene expression within a set of cells isolated through an experimental procedure. Analysis of microarray data requires an understanding of how the mRNA measured with a microarray is generated within a cell, how it is processed to produce a protein that carries out the work of the cell, and how the creation of the protein relates to the changes in the cellular machinery, and thus to the phenotype observed.
A 100 Gb/s PAM4 Two-Segment Silicon Microring Resonator Modulator Using a Standard Foundry Process (2022)

A compact two-segment depletion mode silicon microring resonator modulator with PAM4 modulation data rate up to 100 Gb/s has been demonstrated. The microring resonator modulator exhibits a free spectrum range of ∼5.7 nm, a quality factor of ∼3600, a DC extinction ratio of ∼13 dB, an electro-optical phase shift efficiency Vπ·L of ∼1 V·cm, and an electro-optical bandwidth of ∼40 GHz.
Homeoprotein Intercellular Transfer, the Hidden Face of Cell-Penetrating Peptides (2010)

Cell-Penetrating Peptides (CPPs) are small peptides internalized by live cells, gaining access to their cytoplasm and intracellular organelles (i.e., mitochondria, nucleus) and are used as pharmacological tools. This is indeed a very important issue, fully justifying the efforts of several groups to better understand the mechanisms of peptide transduction and to verify if and how this strategy can be translated into therapeutic improvements. However, the discovery of peptide transduction is a consequence of that of a novel signaling mechanism based on the intercellular transfer of homeoprotein transcription factors. Indeed, the first and probably most popular CPPs (Tat and Penetratin) correspond to domains that drive TAT (HIV) and homeoprotein transcription factors into the cells. These findings have fostered several studies on transduction and allowed the design of "nonnatural" CPPs. As useful as they are, these lines of research have, in general, neglected the fact that protein transduction is a signaling mechanism, in its own right, with important physiological functions. In this chapter, I describe some of these functions and propose that this class of signaling molecules, in particular homeoproteins, may also be used as therapeutic agents.
The Effects of Pelvic Incidence in the Functional Anatomy of the Hip Joint (2020)

Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
On the Force-Closure Analysis of n-DOF Cable-Driven Open Chains Based on Reciprocal Screw Theory (2011)

It has been mathematically proven that a completely restrained n- degree-of-freedom (n-DOF) single rigid-bodied cable-driven platform requires a minimum of n + 1 cables with positive tension to fully constrain it. However, the force-closure analysis of open chains that are driven by cables is still an open question. For the case of an n -DOF cable-driven open chain, the following two important questions arise. 1) How can the force-closure analysis be carried out for a given cable routing configuration, while retaining the geometric insights of the problem? 2) Are n + 1 cables sufficient to fully constrain the entire chain? This paper addresses these issues by proposing a systematic and novel approach based on the reciprocal screw theory. The key idea is to express wrenches acting on the open chain as linear combinations of the reciprocal screws and determine the total required torques at each joint. This is followed by equating the joint torques that are provided by the cable forces with the joint torques, which are required by the external wrenches, and checking for force closure. The proposed methodology can analyze open chains with arbitrary cable routing configuration. The analysis shows that the entire n-DOF open chain requires a minimum of n + 1 cables to fully constrain it.
Fabrication of Medium Power Insulated Gate Bipolar Transistors Using 300 mm Magnetic Czochralski Silicon Wafers (2019)

The use of silicon wafer substrates with a diameter of 300 mm for the manufacturing of electronic devices strongly increases the overall productivity of a device manufacturing line. However, float‐zone (FZ) silicon, which is traditionally used for insulated gate bipolar transistors (IGBTs), is not available for wafer diameters exceeding 200 mm. Therefore, a silicon material fabricated by the magnetic Czochralski (m:Cz) method has to be used for IGBT production on 300 mm wafers. Critical issues of this material are the so‐called crystal originated particles (COPs) and the strong axial variation of the doping level along the crystal. Furthermore, the m:Cz material contains a relatively high concentration of oxygen so that the influence of carbon/oxygen complexes has to be considered. C I O I complexes can be decorated with hydrogen atoms, resulting in donor‐like complexes. In particular, the application of proton irradiation for the doping of the field‐stop zone results in a relatively high concentration of interstitial carbon, which is continuatively associated with the generation of undesired donors. It is shown that the electrical behavior of IGBTs fabricated on FZ substrates can be well reproduced using the m:Cz material if the parameters of the hydrogen implantation are adjusted appropriately.
Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq (2017)

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of <i>Oryza sativa</i> L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.
Decomposition of dicyclohexyl peroxydicarbonate and OO-tert-butyl O-cyclohexyl peroxycarbonate (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDecomposition of dicyclohexyl peroxydicarbonate and OO-tert-butyl O-cyclohexyl peroxycarbonateDale E. Van SickleCite this: J. Org. Chem. 1969, 34, 11, 3446–3451Publication Date (Print):November 1, 1969Publication History Published online1 May 2002Published inissue 1 November 1969https://pubs.acs.org/doi/10.1021/jo01263a051https://doi.org/10.1021/jo01263a051research-articleACS PublicationsRequest reuse permissionsArticle Views239Altmetric-Citations30LEARN 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