gebhart/patrepeval huggingface dataset:
Magnetic resonance imaging in individuals with cardiovascular implantable electronic devices (2008)

Magnetic resonance (MR) imaging has unparalleled soft-tissue imaging capabilities. The presence of devices such as pacemakers and implantable cardioverter-defibrillators (ICDs), however, was historically considered a contraindication to MR imaging. We summarize the potential hazards of the device-MR environment interaction, and present updated information regarding in vitro and in vivo experiments suggesting that certain pacemaker and ICD systems may indeed be MR-safe. Recent reports on several hundred patients with implantable pacemakers and ICDs who underwent MR scan safely indicate that, under certain conditions, individuals with these implanted systems may benefit from MR imaging. We believe that, on a case-by-case basis, the diagnostic benefit from MR imaging outweighs the presumed risks for some pacemaker and ICD patients. Thus for some patients, the risks presented by MR imaging under specific, characterized scanning and monitoring conditions may be acceptable given the diagnostic benefit of this powerful imaging modality. This may have major clinical implications on current imaging practice. A strategy for the performance of MR imaging in these individuals is proposed.
Extracting Interpretable Physical Parameters from Spatiotemporal Systems using Unsupervised Learning (2019)

Experimental data is often affected by uncontrolled variables that make analysis and interpretation difficult. For spatiotemporal systems, this problem is further exacerbated by their intricate dynamics. Modern machine learning methods are particularly well-suited for analyzing and modeling complex datasets, but to be effective in science, the result needs to be interpretable. We demonstrate an unsupervised learning technique for extracting interpretable physical parameters from noisy spatiotemporal data and for building a transferable model of the system. In particular, we implement a physics-informed architecture based on variational autoencoders that is designed for analyzing systems governed by partial differential equations (PDEs). The architecture is trained end-to-end and extracts latent parameters that parameterize the dynamics of a learned predictive model for the system. To test our method, we train our model on simulated data from a variety of PDEs with varying dynamical parameters that act as uncontrolled variables. Numerical experiments show that our method can accurately identify relevant parameters and extract them from raw and even noisy spatiotemporal data (tested with roughly 10% added noise). These extracted parameters correlate well (linearly with $R^2 &gt; 0.95$) with the ground truth physical parameters used to generate the datasets. We then apply this method to nonlinear fiber propagation data, generated by an ab-initio simulation, to demonstrate its capabilities on a more realistic dataset. Our method for discovering interpretable latent parameters in spatiotemporal systems will allow us to better analyze and understand real-world phenomena and datasets, which often have unknown and uncontrolled variables that alter the system dynamics and cause varying behaviors that are difficult to disentangle.
An improved procedure for isolation of high-quality RNA from nematode-infected Arabidopsis roots through laser capture microdissection (2016)

The use of optimal sucrose concentrations as cryoprotection plays a key role in RNA stability and morphology of sections. Treatment with higher sucrose concentrations minimizes the risk of RNA degradation, whereas longer incubation times help maintaining the morphology of tissue sections. Our method allows isolating high-quality RNA from nematode feeding sites that is suitable for downstream applications such as microarray experiments.
Abstract 1182: New bioluminescent strategies to measure kinetics of immune cell-mediated cytotoxicity (2019)

Abstract The number of immunotherapeutic strategies for treating cancer have expanded in recent years, increasing the need for assays that can be used to assess their effectiveness. To facilitate studies of these immunotherapies, we developed bioluminescent methods that could rapidly and sensitively measure target cell cytotoxicity. Two approaches were developed. The first method utilizes a bioluminescent enzymatic activity assay for a well-accepted cytotoxicity marker, lactate dehydrogenase (LDH), which is rapidly released from dead cells. With the improved sensitivity of the bioluminescent assay, lower levels of LDH can be measured, resulting in the detection of fewer dead cells (LOD&amp;lt; 10 cells). Cytotoxicity in both 2D and 3D cell cultures can be monitored over time by removing samples of medium at different time points. Here we present examples in which this assay was used to test the effectiveness of immunotherapeutic treatments including antibody-drug conjugates (ADC) and antibody-dependent cell-mediated cytotoxicity (ADCC). In ADCC models, cell killing was detectable at early time points (by 2 hours). Increases in the cytotoxicity of individual samples could be followed over time, from early time points to 24 hours. In the second approach we developed a novel bioluminescent assay based on the specific labeling of target cells. With this method, intracellular proteins in live target cells are covalently labeled. Upon target cell death, the labeled proteins are released from the cell and the label is quantitated using bioluminescence detection reagents. Using this assay, we were able to quantitate the killing of target cells in both ADCC and CAR-T applications. By adding the detection reagents directly to the medium at the start of the ADCC reaction, cell death was monitored in real-time for up to 6 hours. Neither assay requires genetic engineering and both involve no or minimal target cell preparation. They are applicable to multiple cell types and the non-lytic nature of these approaches provides kinetic capabilities and opportunities for multiplexing. The ability to rapidly quantitate cytotoxicity will facilitate the functional analysis of immunotherapies. Citation Format: Maggie L. Bach, Natasha Karassina, Peter Hofsteen, Donna Leippe, James Cali, Jolanta Vidugiriene. New bioluminescent strategies to measure kinetics of immune cell-mediated cytotoxicity [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 1182.
Deuterium Enrichment of PAHs by VUV Irradiation of Interstellar Ices (1998)

Laboratory results demonstrate that polycyclic aromatic hydrocarbons (PAHs) rapidly exchange their hydrogen atoms with those of nearby molecules when they are frozen into low-temperature ices and exposed to vacuum ultraviolet radiation. As a result, PAHs quickly become deuterium-enriched when VUV irradiated in D-containing ices. This mechanism has important consequences for several astrophysical issues owing to the ubiquitous nature of PAHs in the interstellar medium. For example, this process may explain the deuterium enrichments found in PAHs in meteorites and interplanetary dust particles. These results also provide general predictions about the molecular siting of the deuterium on aromatic materials in meteorites if this process produced a significant fraction of their D-enrichment.
Clinical activity of ONC201 in metastatic castrate resistant prostate cancer (mCRPC). (2016)

e16514 Background: Proteasome inhibitors that induce the integrated stress response are effective in preclinical models of hormone-refractory prostate cancer and have induced objective responses in prostate cancer patients in early phase clinical trials. ONC201 is a PERK-independent small molecule inducer of the integrated stress response that has compelling efficacy in preclinical advanced cancer models. In vitro sensitivity profiling has determined that prostate cancer is one of the most sensitive tumor types to ONC201 among solid tumors and that the drug is effective in hormone-refractory cancer cells. In addition, ONC201 shows excellent tolerability and can be given orally with infrequent dosing regimens. Methods: A phase I dose escalation trial recently established 625mg of ONC201 administered orally every three weeks (one cycle) as the recommended phase II dose. Metastatic castration-resistant prostate cancer patients were enriched in a dose expansion cohort based on the preclinical sensitivity profile of ONC201 in solid tumors. Results: Of the 28 patients in the phase I, 5 prostate cancer patients (age range 62-90) received 625mg ONC201 every three weeks; currently, 4 patients have recieved at least 2 cycles. One patient previously treated with sipuleucel-t, abiraterone, enzalutamide, and docetaxel exhibited stable disease after initiation of ONC201 therapy and remained on study for 6 months. A second patient previously treated with sipuleucel-t, abiraterone, enzalutamide, had a 25% decline in PSA after 2 cycles of ONC201 and remains on study after 4 cycles with radiographically stable disease. A third patient exhibited a mixed response, with overall stable disease after 4 cycles. A fourth patient had progression after 2 cycles and the fifth patient is in the first cycle of treatment. No drug related toxicity > grade 1 was observed. Conclusions: These results suggest that ONC201 is clinically active in prostate cancer patients and that investigation of more frequent dosing and/or combination therapy is warranted and enabled by its safety and pharmacokinetic/pharmacodynamic profile. Clinical trial information: NCT02324621.
3D-Printed Self-Folding Electronics (2017)

Self-transforming structures are gaining prominence due to their general ability to adopt programmed shapes each tailored for specific functions. Composites that self-fold have so far relied on using the stimuli-responsive mechanisms focusing on reversible shape change. Integrating additional functions within these composites can rapidly enhance their practical applicability; however, this remains a challenging problem. Here, we demonstrate a method for spontaneous folding of three-dimensional (3D)-printed composites with embedded electronics at room temperature. The composite is printed using a multimaterial 3D-printing process with no external processing steps. Upon peeling from the print platform, the composite self-shapes itself using the residual forces resulting from polymer swelling during the layer-by-layer fabrication process. As a specific example, electrochromic elements are printed within the composite and can be electrically controlled through its folded legs. Our shape-transformation scheme provides a route to transform planar electronics into nonplanar geometries containing the overhangs. Integrating electronics within complex 3D shapes can enable new applications in sensing and robotics.
In-Vivo Fusion of Human Cancer and Hamster Stromal Cells Permanently Transduces and Transcribes Human DNA (2014)

After demonstrating, with karyotyping, polymerase chain reaction (PCR) and fluorescence in-situ hybridization, the retention of certain human chromosomes and genes following the spontaneous fusion of human tumor and hamster cells in-vivo, it was postulated that cell fusion causes the horizontal transmission of malignancy and donor genes. Here, we analyzed gene expression profiles of 3 different hybrid tumors first generated in the hamster cheek pouch after human tumor grafting, and then propagated in hamsters and in cell cultures for years: two Hodgkin lymphomas (GW-532, GW-584) and a glioblastoma multiforme (GB-749). Based on the criteria of MAS 5.0 detection P-values ≤0.065 and at least a 2-fold greater signal expression value than a hamster melanoma control, we identified 3,759 probe sets (ranging from 1,040 to 1,303 in each transplant) from formalin-fixed, paraffin-embedded sections of the 3 hybrid tumors, which unambiguously mapped to 3,107 unique Entrez Gene IDs, representative of all human chromosomes; however, by karyology, one of the hybrid tumors (GB-749) had a total of 15 human chromosomes in its cells. Among the genes mapped, 39 probe sets, representing 33 unique Entrez Gene IDs, complied with the detection criteria in all hybrid tumor samples. Five of these 33 genes encode transcription factors that are known to regulate cell growth and differentiation; five encode cell adhesion- and transmigration-associated proteins that participate in oncogenesis and/or metastasis and invasion; and additional genes encode proteins involved in signaling pathways, regulation of apoptosis, DNA repair, and multidrug resistance. These findings were corroborated by PCR and reverse transcription PCR, showing the presence of human alphoid (α)-satellite DNA and the F11R transcripts in additional tumor transplant generations. We posit that in-vivo fusion discloses genes implicated in tumor progression, and gene families coding for the organoid phenotype. Thus, cancer cells can transduce adjacent stromal cells, with the resulting progeny having permanently transcribed genes with malignant and other gene functions of the donor DNA. Using heterospecific in-vivo cell fusion, genes encoding oncogenic and organogenic traits may be identified.
Applications of stabilized optical frequency combs (2013)

This paper will discuss optical frequency combs, techniques used for the stabilization of frequency combs and their applications.
Preclinical Characterization of Vadadustat (AKB-6548), an Oral Small Molecule Hypoxia-Inducible Factor Prolyl-4-Hydroxylase Inhibitor, for the Potential Treatment of Renal Anemia (2022)

Pharmacological inhibition of prolyl-4-hydroxylase domain (PHD) enzymes stabilizes hypoxia-inducible factors (HIFs), transcription factors that activate target genes that, among others, increase erythropoietin (EPO) synthesis, resulting in the production of new red blood cells (RBCs). Herein, we summarize the preclinical characteristics of the small molecule HIF prolyl-4-hydroxylase inhibitor vadadustat (AKB-6548), which is in development for the treatment of anemia in patients with chronic kidney disease (CKD). Vadadustat inhibits the enzyme activity of all three human PHD isozymes, PHD1, PHD2, and PHD3, with similar low nanomolar inhibitory constant values. PHD enzyme inhibition by vadadustat is competitive with endogenous cofactor 2-oxoglutarate and is insensitive to free iron concentration. In the human hepatocellular carcinoma cell line (Hep 3B) and human umbilical vein endothelial cells, PHD inhibition by vadadustat leads to the time- and concentration-dependent stabilization of HIF-1<i>α</i> and HIF-2<i>α</i> In Hep 3B cells, this in turn results in the synthesis and secretion of EPO; vascular endothelial growth factor is not measured at detectable levels. A single oral dose of vadadustat in rats potently increases circulating levels of EPO, and daily oral dosing for 14 days increases RBC indices in healthy rats and in the 5/6 nephrectomy model of CKD. In mice and dogs, once-daily repeat oral dosing increases hemoglobin and hematocrit. Vadadustat has a relatively short half-life in all nonclinical species evaluated and does not accumulate when administered as a single bolus dose (oral or intravenous) or upon repeat oral dosing. The pharmacological profile of vadadustat supports continued development for treatment of renal anemia. SIGNIFICANCE STATEMENT: Vadadustat (AKB-6548) is an orally bioavailable small molecule prolyl-4-hydroxylase inhibitor in development for anemia of chronic kidney disease. It is an equipotent inhibitor of the three human prolyl-4-hydroxylase domain isoforms, which activates erythropoiesis through stabilization of hypoxia-inducible factor (HIF)-1<i>α</i> and HIF-2<i>α</i>, increasing production of erythropoietin, without detectable stimulation of vascular endothelial growth factor.
Metal alkoxides: models for metal oxides. 16. Synthesis and characterization of a new class of homoleptic 12-electron molybdenum and tungsten alkoxide clusters of formula M4(OR)12: structural characterization of Mo4(OCH2-c-Bu)12.cntdot.(HOCH2-c-Bu) (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal alkoxides: models for metal oxides. 16. Synthesis and characterization of a new class of homoleptic 12-electron molybdenum and tungsten alkoxide clusters of formula M4(OR)12: structural characterization of Mo4(OCH2-c-Bu)12.cntdot.(HOCH2-c-Bu)M. H. Chisholm, K. Folting, C. E. Hammond, M. J. Hampden-Smith, and K. G. MoodleyCite this: J. Am. Chem. Soc. 1989, 111, 14, 5300–5312Publication Date (Print):July 1, 1989Publication History Published online1 May 2002Published inissue 1 July 1989https://pubs.acs.org/doi/10.1021/ja00196a040https://doi.org/10.1021/ja00196a040research-articleACS PublicationsRequest reuse permissionsArticle Views227Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Robotized stator cable winding (2018)

Automated stator winding assembly has been available for small and medium sized conventional electric machines for a long time. Cable winding is an alternative technology developed for medium and large sized machines in particular. In this paper we present, evaluate and validate the first fully automated stator cable winding assembly equipment in detail. A full-scale prototype stator cable winding robot cell has been constructed, based on extensive previous work and experience, and used in the experiments. While the prototype robot cell is adapted for the third design generation of the Uppsala University Wave Energy Converter generator stator, the winding method can be adapted for other stator designs. The presented robot cell is highly flexible and well prepared for future integration in a smart production line. Potential cost savings are indicated compared to manual winding, which is a backbreaking task. However, further work is needed to improve the reliability of the robot cell, especially when it comes to preventing the kinking of the winding cable during the assembly.
Assessment of the Safety and Efficacy of a Raft-Forming Alginate Reflux Suppressant (Liquid Gaviscon) for the Treatment of Heartburn during Pregnancy (2012)

Gastro-oesophageal reflux (GER) and the symptoms of heartburn and regurgitation are common in pregnancy. These symptoms are transient and mostly resolve postpartum but have a negative impact on quality of life. Here, we present a prospective clinical evaluation of the safety and efficacy of an alginate raft-forming oral suspension that is licensed for use in pregnancy. The study was a multicentre, prospective, open-label, and baseline-controlled study of Liquid Gaviscon (LG) in the treatment of heartburn in pregnant women with current symptoms of heartburn and/or reflux requiring treatment (recruited 144). The efficacy of the study medication was rated by the investigator (primary endpoint) and patient. Treatment was deemed to be a success in 91% of patients as judged by the investigator (95% CI 85.0-95.3) and 90% (95% CI 84.1-94.8) when assessed by the patient themselves. Very few adverse events or serious adverse events were reported that were considered to be related to the study medication, and these were consistent with the normal population incidences. Serum sodium levels remained unchanged. This prospective open-label study in a large number of pregnant women has shown that LG is both safe and highly efficacious in the treatment of heartburn and GER symptoms in pregnancy.
Free-standing ZnO–CuO composite nanowire array films and their gas sensing properties (2011)

A modified hydrothermal method was developed to synthesize ZnO-CuO composite nanostructures. A free-standing film made of ZnO-CuO nanostructures was assembled on the surface of the hydrothermal solution with a smooth surface on one side and a spherical surface on the other side. The structure, growth mechanism and the optical properties of the composite nanostructures were studied. Structural characterizations indicate that the composite nanostructure mainly consisted of two single-crystal phases of CuO and ZnO. The sensitivity for CO gas detection was significantly improved for the composite CuO-ZnO nanostructure film. This method offers a possible route for the fabrication of free-standing nanostructure films of different functional composite oxides.
The SH3 Domain of Amphiphysin Binds the Proline-rich Domain of Dynamin at a Single Site That Defines a New SH3 Binding Consensus Sequence (1997)

Amphiphysin is an SH3 domain-containing neuronal protein that is highly concentrated in nerve terminals where it interacts via its SH3 domain with dynamin I, a GTPase implicated in synaptic vesicle endocytosis. We show here that the SH3 domain of amphiphysin, but not a mutant SH3 domain, bound with high affinity to a single site in the long proline-rich region of human dynamin I, that this site was distinct from the binding sites for other SH3 domains, and that the mutation of two adjacent amino acids in dynamin I was sufficient to abolish binding. The dynamin I sequence critically required for amphiphysin binding (PSRPNR) fits in the novel SH3 binding consensus identified for the SH3 domain of amphiphysin via a combinatorial peptide library approach: PXRPXR(H)R(H). Our data demonstrate that the long proline-rich stretch present in dynamin I contained multiple SH3 domain binding sites that recognize interacting proteins with high specificity.
Bound Tris Confounds the Identification of Binding Site Residues in a Paraquat Single Chain Antibody (1997)

We produced an anti-paraquat single chain antibody (scFv) to investigate its potential use in immunotherapy for paraquat poisoning. However, this scFv was expressed in an insoluble form and only displayed moderate binding affinity. An earlier examination of the pH dependence of antigen binding by the parent paraquat-specific mAb (7D7-3) suggested that the electrostatic effects of a tyrosine residue were important. The aims of the current study were to obtain expression of a soluble scFv (D10) and to increase its binding affinity. The former was achieved by expression in a phagemid vector. Site-directed mutagenesis of tyrosine residues in CDR H3 did not result in improved affinity for paraquat, suggesting that the original pH dependence required re-examination. Nuclear magnetic resonance studies of 7D7-3 Fab revealed that the original observation of the pH-dependent paraquat binding with a mid-point of approximately pH 8.9 was due to tightly bound Tris. It appears that as Tris is titrated to a neutral species the energetically unfavourable juxtaposition of its positive charge with that of paraquat is reduced. These findings have broad implications in the interpretation of the pH or salt dependence of any antibody-antigen interaction which should be made cautiously and with regard to the possible interference of buffer components introduced during the preparation of the antibody.