gebhart/patrepeval huggingface dataset:
Plasma vesicle miRNAs for therapy response monitoring in Hodgkin lymphoma patients (2016)

<b>BACKGROUND.</b> Cell-free circulating nucleic acids, including 22-nt microRNAs (miRNAs), represent noninvasive biomarkers for treatment response monitoring of cancer patients. While the majority of plasma miRNA is bound to proteins, a smaller, less well-characterized pool is associated with extracellular vesicles (EVs). Here, we addressed whether EV-associated miRNAs reflect metabolic disease in classical Hodgkin lymphoma (cHL) patients. <b>METHODS.</b> With standardized size-exclusion chromatography (SEC), we isolated EV-associated extracellular RNA (exRNA) fractions and protein-bound miRNA from plasma of cHL patients and healthy subjects. We performed a comprehensive small RNA sequencing analysis and validation by TaqMan qRT-PCR for candidate discovery. Fluorodeoxyglucose-PET (FDG-PET) status before treatment, directly after treatment, and during long-term follow-up was compared directly with EV miRNA levels. <b>RESULTS.</b> The plasma EV miRNA repertoire was more extensive compared with protein-bound miRNA that was heavily dominated by a few abundant miRNA species and was less informative of disease status. Purified EV fractions of untreated cHL patients and tumor EVs had enriched levels of miR24-3p, miR127-3p, miR21-5p, miR155-5p, and let7a-5p compared with EV fractions from healthy subjects and disease controls. Serial monitoring of EV miRNA levels in patients before treatment, directly after treatment, and during long-term follow-up revealed robust, stable decreases in miRNA levels matching a complete metabolic response, as observed with FDG-PET. Importantly, EV miRNA levels rose again in relapse patients. <b>CONCLUSION.</b> We conclude that cHL-related miRNA levels in circulating EVs reflect the presence of vital tumor tissue and are suitable for therapy response and relapse monitoring in individual cHL patients. <b>FUNDING.</b> Cancer Center Amsterdam Foundation (CCA-2013), Dutch Cancer Society (KWF-5510), Technology Foundation STW (STW Perspectief CANCER-ID).
MRA of the abdominal aorta and lower extremities (2000)

Atherosclerotic involvement of the aorta and lower extremity vessels is a common clinical problem, especially in developed countries. While x-ray angiography has been the method of choice for preoperative evaluation of patients with atherosclerotic disease, magnetic resonance angiography (MRA) is emerging as a powerful noninvasive tool that is capable of providing information critical to the care of these patients. The objective of this manuscript is to review the current state-of-the-art of MRA of the abdominal aorta and lower extremity vessels. The techniques are described, the clinical indications for MRA are discussed, and the diagnostic accuracy and pitfalls of the various methods are presented.
Implantable Cardioverter-Defibrillators: Implications for the Nonelectrophysiologist (1995)

Defibrillator therapy has become increasingly popular and complex. A basic understanding of these devices and skills in the short-term management of device-related problems is valuable for most physicians. These management guidelines will facilitate delivery of optimal care when specialized staff and material resources are not available.
High-performance photonic reservoir computer based on a coherently driven passive cavity (2015)

Reservoir computing is a recent bio-inspired approach for processing time-dependent signals. It has enabled a breakthrough in analog information processing, with several experiments, both electronic and optical, demonstrating state-of-the-art performances for hard tasks such as speech recognition, time series prediction and nonlinear channel equalization. A proof-of-principle experiment using a linear optical circuit on a photonic chip to process digital signals was recently reported. Here we present a photonic implementation of a reservoir computer based on a coherently driven passive fiber cavity processing analog signals. Our experiment has error rate as low or lower than previous experiments on a wide variety of tasks, and also has lower power consumption. Furthermore, the analytical model describing our experiment is also of interest, as it constitutes a very simple high performance reservoir computer algorithm. The present experiment, given its good performances, low energy consumption and conceptual simplicity, confirms the great potential of photonic reservoir computing for information processing applications ranging from artificial intelligence to telecommunications
Omega-3 Fatty Acids Supplementation: Therapeutic Potential in a Mouse Model of Stargardt Disease (2018)

Three months of ω3 supplementation (AA/EPA ∼1-1.5) reduces A2E levels, lipofuscin granules, and C3 levels in the ABCA4-/- mouse model of Stargardt disease, consistent with slowing of the disease.
Regulation of a nuclear export signal by an adjacent inhibitory sequence: The effector domain of the influenza virus NS1 protein (1998)

In the cell nucleus the NS1 protein of influenza A virus inhibits both pre-mRNA splicing and the nuclear export of mRNAs. Both the RNA-binding and effector domains of the protein are required for these nuclear functions. Here we demonstrate that the NS1 protein has a latent nuclear export signal (NES) that is located at the amino end of the effector domain. In uninfected, transfected cells the NS1 protein is localized in the nucleus because the NES is specifically inhibited by the adjacent amino acid sequence in the effector domain. Substitution of alanine residues for specific amino acids in the adjacent sequence abrogates its inhibitory activity, thereby unmasking the NES and causing the full-length NS1 protein to be localized to the cytoplasm. In contrast to uninfected cells, a substantial amount of the NS1 protein in influenza virus-infected cells is located in the cytoplasm. Consequently, the NES of these NS1 protein molecules is unmasked in infected cells, indicating that the NS1 protein most likely carries out functions in the cytoplasm as well as the nucleus. A dramatically different localization of the NS1 protein occurs in cells that are infected by a virus encoding an NS1 protein lacking the NES: the shortened NS1 protein molecules are almost totally in the nucleus. Because the NES of the full-length NS1 protein is unmasked in infected but not uninfected cells, it is likely that this unmasking results from a specific interaction of another virus-specific protein with the NS1 protein.
DSP Curve Surface Interpolator Research Based on Open Platform (2007)

For the improvement of the system real-time capability, the DSP Curve Surface interpolator has been designed to ensure high speed, high precision requirement for the machining of complexity curve surface. The hardware and software has been designed. The changeable feedrate interpolation algorithm of limit curve error has been studied. Furthermore, the algorithm has been applied to the interpolation and has well real-time capability to satisfy the requirement of high capability CNC by experimentation.
Does bioelectrochemical cell configuration and anode potential affect biofilm response? (2012)

Electrochemical gradients are the backbone of basic cellular functions, including chemo-osmotic transport and ATP synthesis. Microbial growth, terminal respiratory proteins and external electron transfer are major pathways competing for electrons. In BESs (bioelectrochemical systems), such as MFCs (microbial fuel cells), the electron flow can be via soluble inorganic/organic molecules or to a solid surface. The flow of electrons towards a solid surface can be via outer-membrane cytochromes or electron-shuttle molecules, mediated by conductive protein nanowires or extracellular matrices. In MECs (microbial electrolysis cells), the anode potential can vary over a wide range, which alters the thermodynamic energy available for bacteria capable of donating electrons to the electrode [termed EAB (electroactive bacteria)]. Thus the anode potential is an important electrochemical parameter determining the growth, electron distribution/transfer and electrical activity of films of these bacteria on electrodes. Different optimal applied potentials to anodes have been suggested in the literature, for selection for microbial growth, diversity and performance in biofilms on electrodes. In the present paper, we review the effects of anode potentials on electron-transfer properties of such biofilms, and report on the effect that electrochemical cell configuration may have on performance.
Acute promyelocytic leukemia: biology and treatment. (1997)

The discovery of the specific PML-RAR alpha gene rearrangement in acute promyelocytic leukemia (APL) and of the in vitro and in vivo differentiation of APL blasts by all transretinoic acid have allowed important advances in the pathophysiology and treatment APL. With a therapeutic strategy combining ATRA and anthracycline-AraC chemotherapy, about 70% of newly diagnosed APL cases can now be cured. ATRA syndrome--the major side effect of ATRA treatment--should, however, be prevented. Reverse transcription polymerase chain reaction of the PML-RAR alpha rearrangement is useful for the monitoring of minimal residual disease. Efforts are currently being made to treat patients that relapse and become resistant to ATRA.
Optofluidic ultrahigh-throughput detection of fluorescent drops (2015)

This paper describes an optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254,000 drops per second. To our knowledge, this rate is the highest interrogation rate published thus far. Our device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view in conventional microscopy. The interrogation rate of our device is currently limited by the acquisition speed of CMOS sensor, and is expected to increase further as high-speed sensors become increasingly available.
<b>Relationship between the age and histidinoalanine content of human aorta </b> (1987)

Human aorta specimens with no atherosclerotic lesions were obtained at autopsy from 126 individuals, and analyzed for the content of the cross-linking amino acid, histidinoalanine. The histidinoalanine content increased with an increase in age, although marked variability was seen in old age.
Utilizing query change for session search (2013)

Session search is the Information Retrieval (IR) task that performs document retrieval for a search session. During a session, a user constantly modifies queries in order to find relevant documents that fulfill the information need. This paper proposes a novel query change retrieval model (QCM), which utilizes syntactic editing changes between adjacent queries as well as the relationship between query change and previously retrieved documents to enhance session search. We propose to model session search as a Markov Decision Process (MDP). We consider two agents in this MDP: the user agent and the search engine agent. The user agent's actions are query changes that we observe and the search agent's actions are proposed in this paper. Experiments show that our approach is highly effective and outperforms top session search systems in TREC 2011 and 2012.
Ligand Effect on the Growth and the Digestion of Co Nanocrystals (2005)

The reaction product of cobalt carbonyl decomposition depends on the concentration of the oleic acid ligand. With a low concentration of ligand, nanocrystals nucleate and grow to large ferromagnetic particles through the process of Ostwald ripening and coalescence coarsening. With a high concentration of ligand, stable cluster complexes are formed. Addition or removal of ligand from the reaction products can interchange the formation of cluster complexes and nanocrystals.
CD 271 (P75 neurotrophin receptor). (2008)

P75NTR (or CD271) is a member of the Tumor Necrosis Factor receptor (TNFR) super family of transmembrane proteins that share significant homology in their extracellular domains. Subsets of TNF receptors, including CD271, have a cytoplasmic death domain, although CD271 has unique intracellular structure and downstream signaling partners. CD271 is also differentiated from other members of the TNFR receptor family in that it binds pro and mature neurotrophins and affects the growth, differentiation and death of the nervous system. The ligands for CD271 are neurotrophins, which are Nerve Growth Factor (NGF), Brain-Derived Growth factor (BDNF), Neurotrophin 3 (NT3) and Neurotrophin 4/5 (NT4/5). Recent studies have provided evidence that CD271 also serves as a receptor for the pro-forms of these neurotrophins.
Correction for geometric image distortion in the x‐ray imaging chain: Local technique versus global technique (1999)

The local technique to correct for geometric image distortion in the x-ray imaging chain has been implemented and compared with the global correction technique reported previously. Three local correction models were considered, all applied locally within each quadrilateral cell bounded by four adjacent points on a distorted 1.0 cm spaced rectilinear calibration grid. Model 1 uses bilinear interpolation between the correction vectors derived at the four vertices. In Models 2 and 3 a polynomial mapping from distorted to undistorted positions is applied, with Model 2 representing a linear six-parameter correction and Model 3 a nonlinear eight-parameter correction. Both techniques have been analyzed in depth concerning their accuracy. To this end, experimental (35 mm cine film and online video) and computer simulated distorted images of the calibration grid were used. Both radial and sigmoidal distortions were considered in the simulations. The main results are summarized as follows. The accuracy of the local technique depends upon the position within each quadrilateral cell and upon the local direction of the distortion gradient, contrary to the global technique. The accuracy of the local technique decreases with increasing radial as well as sigmoidal distortion. For the global technique only the latter dependency applies. The relationship of the accuracy with the pixel size is different for all models. Finally, the local technique is more sensitive to noise than the global technique. The reproducibility of the correction methods has been evaluated by means of imaging the calibration grid in various orientations with respect to the input screen of the image intensifier. The local technique turns out to reproduce a factor of 4-10 worse than the global technique. In summary, Model 1 is the worst method in all respects, whereas Model 3 is slightly better than Model 2. However, the global technique is to be preferred because it outperforms the local technique on all relevant issues.
Quantification of IFNγ- and IL17-producing cells after stimulation with citrullinated proteins in healthy subjects and RA patients (2012)

Antibodies against citrullinated proteins are highly specific for rheumatoid arthritis (RA) and are currently used as a diagnostic marker. In this study, we wanted to quantify the numbers of T cells that react to a wide range of citrullinated proteins in a wide range of HLA-DR subtypes in order to investigate whether citrullination might create T-cell neo-epitopes and could initiate a universal T-cell response. Therefore, PBMCs from healthy volunteers and RA patients were stimulated with a citrullinated and non-citrullinated cell extract on IFNγ-ELISpot. We found a significantly higher number of IFNγ-secreting cells after stimulation with citrullinated proteins compared to non-citrullinated proteins in RA patients (1:14,441 cells vs. 1:32,880 cells) as well as in healthy subjects (1:6,261 reactive cells compared to 1:16,212 cells). Additionally, a higher number of IL17-secreting cells were found after stimulation with citrullinated proteins compared to their non-citrullinated counterparts. Our data indicate that citrulline-dependent T-cell response is not restricted to RA patients but that citrullination as such gives rise to a universal break in tolerance.
The synthesis of [2‐<sup>3</sup>H<sub>2</sub>] taurine and [2‐<sup>3</sup>H<sub>2</sub>] hypotarine (1981)

Abstract The synthesis of [2‐ 3 H 2 ]‐2‐aminoethanesulfonate [2‐ 3 H]‐taurine by the reduction of cyanomethanesulfonic acid with tritium gas is described. The conversion of [2‐ 3 H]‐taurine and its 14 C and 35 S isotopic forms to 2‐aminoethanesulfinate (hypotaurine) was accomplished by converting taurine to its corresponding sulfonyl chloride and reducing the latter with metallic zinc.
Computer-assisted hip resurfacing surgery using the Acrobot® Navigation System (2007)

The authors have previously reported on the laboratory development of the Acrobot Navigation System for accurate computer-assisted hip resurfacing surgery. This paper describes the findings of using the system in the clinical setting and including the improvements that have been made to expedite the procedure. The aim of the present system is to allow accurate planning of the procedure and precise placement of the prosthesis in accordance with the plan, with a zero intraoperative time penalty in comparison to the standard non-navigated technique. At present the navigation system is undergoing final clinical evaluation prior to a clinical study designed to demonstrate the accuracy of outcome compared with the conventional technique. While full results are not yet available, this paper describes the techniques that will be used to evaluate accuracy by comparing pre-operative computed tomography (CT)-based plans with post-operative CT scans. Example qualitative clinical results are included based on visual comparison of the plan with post-operative X-rays.
Phenothiazines induce PP2A-mediated apoptosis in T cell acute lymphoblastic leukemia (2014)

T cell acute lymphoblastic leukemia (T-ALL) is an aggressive cancer that is frequently associated with activating mutations in NOTCH1 and dysregulation of MYC. Here, we performed 2 complementary screens to identify FDA-approved drugs and drug-like small molecules with activity against T-ALL. We developed a zebrafish system to screen small molecules for toxic activity toward MYC-overexpressing thymocytes and used a human T-ALL cell line to screen for small molecules that synergize with Notch inhibitors. We identified the antipsychotic drug perphenazine in both screens due to its ability to induce apoptosis in fish, mouse, and human T-ALL cells. Using ligand-affinity chromatography coupled with mass spectrometry, we identified protein phosphatase 2A (PP2A) as a perphenazine target. T-ALL cell lines treated with perphenazine exhibited rapid dephosphorylation of multiple PP2A substrates and subsequent apoptosis. Moreover, shRNA knockdown of specific PP2A subunits attenuated perphenazine activity, indicating that PP2A mediates the drug's antileukemic activity. Finally, human T-ALLs treated with perphenazine exhibited suppressed cell growth and dephosphorylation of PP2A targets in vitro and in vivo. Our findings provide a mechanistic explanation for the recurring identification of phenothiazines as a class of drugs with anticancer effects. Furthermore, these data suggest that pharmacologic PP2A activation in T-ALL and other cancers driven by hyperphosphorylated PP2A substrates has therapeutic potential.
Economic dismissal (2012)

This chapter examines the legal protections afforded to workers in the event of managerial decisions that require major changes in the business. The employer may become insolvent, or the business may be sold to a new owner. Changing market conditions and technologies may force the employer to seek to reduce the number of employees, to alter their contractual terms or to recruit new staff with different skills. Most restructuring exercises aim to improve, at least in the short term, the profits and the value of shares in solvent and successful companies. Whatever the cause of the restructuring, it is likely to have a significant adverse impact on the number of jobs or the terms and conditions of employment. What legal rights do employees have in respect of these decisions, and are these rights adequate to protect their interests?
Design of dual-mode substrate integrated hexagonal cavity (SIHC) filter for X-band application (2013)

A Dual-mode substrate integrated waveguide hexagonal cavity (SIHC) filter using hexagonal shaped cavity for X-Band application has been proposed in this paper. Use of perturbation technique to achieve dual mode response has been investigated. The field patterns of the degenerate modes and the mode splitting characteristics are also studied. The theoretical analysis with the help of coupling matrix is shown and experimental verification is also presented.
Development of Domino Processes by Using 7‐Silylcycloheptatrienes and Its Analogues (2012)

7-Silyl- and 7-silylmethylcycloheptatrienes were shown to react with acylnitroso reagents at room temperature, through their norcaradiene forms, to generate the corresponding cycloadducts 5 a-b and 6 a-b as single diastereomers. The course of the reaction was dramatically modified by changing the reaction conditions. Using a polar medium, functionalized cyclohexa-1,3-dienes 7 a-b and bicyclic compounds 13 a-b were instead generated, incorporating one or two amino groups. Similar behavior was observed by using other dienophiles, including triazolinedione, but also activated aldehydes and ketones. A tentative mechanism has been proposed to rationalize the formation of both classes of products that relies on a domino process involving four consecutive elementary steps, in this order: 1) electrocyclic process, 2) hetero-Diels-Alder reaction, 3) cyclopropane ring opening, and 4) hetero-Diels-Alder reaction. Trapping of the cationic intermediate and isolation of the primary cycloadduct provide support for this hypothesis. An enantioselective version of the cascade using cycloheptatriene 4 b and aldehydes and ketones, under copper(II) catalysis was also carried out, leading to cyclohexa-1,3-dienes 21, 28, and 30 with enantioselectivities up to 93 % ee. Finally, elaboration of the intermediates above has been carried out, opening a straightforward access to sugar mimics 42-43 and complex polycyclic systems 36 and 39.
A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human (2006)

Type 2 diabetes mellitus is the result of a combination of impaired insulin secretion with reduced insulin sensitivity of target tissues. There are an estimated 150 million affected individuals worldwide, of whom a large proportion remains undiagnosed because of a lack of specific symptoms early in this disorder and inadequate diagnostics. In this study, NMR-based metabolomic analysis in conjunction with multivariate statistics was applied to examine the urinary metabolic changes in two rodent models of type 2 diabetes mellitus as well as unmedicated human sufferers. The db/db mouse and obese Zucker (fa/fa) rat have autosomal recessive defects in the leptin receptor gene, causing type 2 diabetes. 1H-NMR spectra of urine were used in conjunction with uni- and multivariate statistics to identify disease-related metabolic changes in these two animal models and human sufferers. This study demonstrates metabolic similarities between the three species examined, including metabolic responses associated with general systemic stress, changes in the TCA cycle, and perturbations in nucleotide metabolism and in methylamine metabolism. All three species demonstrated profound changes in nucleotide metabolism, including that of N-methylnicotinamide and N-methyl-2-pyridone-5-carboxamide, which may provide unique biomarkers for following type 2 diabetes mellitus progression.