gebhart/patrepeval huggingface dataset:
Dynamic Behavior of a Fluorescent Probe, a Swallow-tailed Perylene Derivative for Detecting Hydroperoxides (2008)

Abstract Dynamic behavior of a fluorescent probe, a swallow-tailed perylene derivative (Spy-Hp) for detecting hydroperoxides was studied by fluorescence lifetime and transient absorption measurements. The MO calculations suggest the intramolecular charge transfer for Spy-Hp. The excited state lifetime of Spy-Hp is shorter than that of the oxidized form, which was caused by intramolecular fluorescence quenching. These results elucidate the mechanism of Spy-Hp for detecting hydroperoxides in biosamples.
Phase I study of vorinostat, a histone deacetylase (HDAC) inhibitor, in combination with carboplatin (Cb) and paclitaxel (P) for patients with advanced solid malignancies (NCI #6922) (2006)

2077 Background: Vorinostat (SAHA) induces differentiation &amp; growth arrest in a variety of human carcinoma cell lines by inhibiting HDAC. It also enhances the efficacy of chemotherapy. We are conducting a phase I study to evaluate the combination of vorinostat, Cb &amp; P for patients with advanced solid malignancies. Methods: Patients with advanced solid malignancies who were candidates for combination therapy with Cb &amp; P were eligible. Vorinostat was given orally on d 1–14 of each 21-d-cycle, except in cycle 1 when begun on d -4 to facilitate PK studies. Cb &amp; P were given on d 1 of each cycle. Plasma concentrations of vorinostat, &amp; its 2 major metabolites were quantitated with a novel LC-MS/MS assay. Results: Dose level 4 has been determined as the recommended phase II dose (RP2D) for the combination, since the RP2D of single agent vorinostat is 400 mg on this schedule. Observed toxicities included nausea, vomiting, neutropenia &amp; thrombocytopenia, none of which were dose-limiting. Of 9 patients evaluable for response, 4 had PR (1 head &amp; neck cancer, 3 non-small cell lung cancer), &amp; 2 had stable disease. Vorinostat was rapidly absorbed &amp; AUC increased with dose. Vorinostat PK parameters included Tmax 0.5–2 h, t1/2 1.6 ± 0.5 h, &amp; CL/F 5.8 ± 1.7 l/min. Cb &amp; P did not alter vorinostat PK. 4-Anilino-4-oxobutanoic acid was the major, &amp; long-lived, vorinostat metabolite, with Cmax 1.5–7 fold &gt; vorinostat Cmax &amp; t ½ ∼6h. Vorinostat glucuronide Cmax was 1–5 fold &gt; vorinostat Cmax &amp; glucuronide t ½ ∼2h. The RP2D cohort is being expanded to 12 patients to obtain additional clinical &amp; PK data. Conclusions: Vorinostat can be safely administered in combination with Cb &amp; P at their recommended doses. Vorinostat PK are not altered by Cb &amp; P. Promising anti-cancer activity has been noted in patients with advanced NSCLC. Support: U01CA099168–01, U01CA62505, NIH/NCCR/GCRC grant 5M01RR 00056. [Table: see text] No significant financial relationships to disclose.
Prediction and prevention of autoimmune diseases: additional aspects of the mosaic of autoimmunity (2006)

Autoimmune connective tissue diseases are chronic, potentially life threatening complex multisystem disorders. Their etiology is unknown but genetic, hormonal and environmental factors are important. The clinical disease is preceded by a long period of time (sometimes many years) when the patients can be identified by characteristic antibodies in their serum. When such a patient is identified he is usually followed and treated if clinical disease manifests itself. However, other factors besides the existence of autoantibodies have a predictive value for those disorders; some of them hereditary or genetic, and can be used only to predict likelihood of future disease, and others, connected to lifestyle and environment, could be modified in order to try and prevent it. Several non-randomized small scale studies have suggested that autoimmune disease could be prevented if treated aggressively prior to manifestations of symptoms. However, if such is the case, criteria would have to be formalized for selection of patients for this preventive treatment. Only patients whose probability to develop clinical disease is higher then a certain threshold should be treated while asymptomatic. The aim of this article is to review the major risk factors for autoimmune disease, both hereditary and environmental, and so to help define those future criteria. Individuals who are at risk to develop an autoimmune disease should be advised to refrain from activities and lifestyle which endangers their health and quality of life.
Comparison between Conventional 4 L Polyethylene Glycol and Combination of 2 L Polyethylene Glycol and Sodium Phosphate Solution as Colonoscopy Preparation (2010)

Background/Aims: Effective bowel preparation is essential for accurate diagnosis of colon disease. We investigated efficacy and safety of 2 L polyethylene glycol (PEG) solution with 90 mL sodium phosphate (NaP) solution compared with 4 L PEG method. Methods: Between August 2009 and April 2010, 526 patients were enrolled who visited Seoul National University Bundang Hospital for colonoscopy. We allocated 249 patients to PEG 4 L group and 277 patients to PEG 2 L with NaP 90 mL group. Detailed questionnaires were performed to investigate compliance, satisfaction and preference of each method. Bowel preparation quality and segmental quality were evaluated. Success was defined as cecal intubation time less than 20 minutes without any help of supervisors. Results: Both groups revealed almost the same baseline characteristics except the experience of operation. PEG 4 L group's compliance was lower than PEG 2 L with NaP 90 mL group. Success rate and cecal intubation time was not different between two groups. Overall bowel preparation quality of PEG 2 L with NaP 90 mL group was better than PEG 4 L group. Segmental bowel preparation quality of PEG 2 L with NaP 90 mL group was also better than PEG 4 L group in all segments, especially right side colon. Occurrence of hyperphosphatemia was higher in PEG 2 L with NaP 90 mL group than PEG 4 L group. However, significant adverse event was not reported. Conclusions: PEG 2 L with NaP 90 mL method seems to be more effective bow-
S906 PRECLINICAL EVALUATION OF THE PRESERVATION OF RED BLOOD CELL CONCENTRATES IN HYPOXIA BY HYPOXIC STORAGE TECHNOLOGY FOR TRANSFUSION IN SICKLE CELL DISEASE. (2019)

Background: Sickle cell disease (SCD) is the most common genetic disease, due to a mutation of the sixth amino acid of gene coding for the Hemoglobin (Hb) beta chain. The mutated Hb, called HbS, is able to polymerize which entails red blood cell (RBC) sickling, leading to chronic hemolysis and painful vaso‐occlusive crisis. Transfusion exchange is one of the therapeutic strategies used for this pathology since it allows the replacement of sickle RBCs. The quality of the transfused RBCs is essential, both to improve the transfusion yield but also to limit the pathological interactions between RBCs and endothelial cells, damaged by hemolysis. RBC concentrates can be stored up to 42 days at 4°c, however, during their hypothermic storage, the quality of RBCs decreases, mainly because of oxidative damage. Hypoxic storage technology helps to keep RBC in hypoxia, improving the concentration of ATP, 2‐3DPG, hemolysis and deformability of RBCs. Aims: The purpose of our study was to compare the quality of conventionally conserved RBCs with those conserved with hypoxic storage technology. Methods: We assessed several parameters including sickle RBC flow adhesion to HUVEC (human umbilical vein endothelial cells), previously exposed to hemolysate, to mimic endothelial damage present in patients. We also evaluated hypoxic RBC senescence parameters by flow cytometry. In that purpose, we measured intracellular calcium and reactive oxygen species (ROS) concentration as well as phosphatidylserine exposure by annexin V staining in hypoxic RBCs and control RBCs, after incubation 24 h in plasma from healthy donors and SCD patients. RBC adherence on thrombospondin (TSP) under flow was also quantified, since RBC adhesion to TSP was shown to increase during storage and since TSP concentration is elevated in sickle cell disease patients during acute chest syndrome (ACS) or at risk of ACS. In addition, we assessed hemolysis in the bags by measuring free hemoglobin concentration in the supernatant by spectroscopy. Results: We found a reduction in the concentration of free Hb (produced by RBC lysis) in hypoxic storage bag, a decrease in RBC senescence (ROS and calcium intracellular concentrations) in hypoxic RBCs and a reduced adherence to thrombospondin when hypoxic RBCs are incubated during 24 h in plasma from healthy donors or SCD patients. There was no difference of RBC adhesion to endothelial cells. Summary/Conclusion: These results suggest that hypoxic storage technology meets the safety criteria for transfusion in SCD patients and may provide significant clinical benefits.
Application Specific NoC Design (2006)

Scalable networks on chips (NoCs) are needed to match the ever-increasing communication demands of large-scale multi-processor systems-on-chip (MPSoCs) for high-end wireless communications applications. The heterogeneous nature of on-chip cores and the energy efficiency requirements typical of wireless communications call for application-specific NoCs which eliminate much of the overheads connected with general-purpose communication architectures. However, application-specific NoCs must be supported by adequate design flows to reduce design time and effort. In this paper we survey the main challenges in application-specific NoC design, and we outline a complete NoC design flow and methodology. A case study on a high complexity SoC demonstrates that it is indeed possible to generate an application-specific NoC from a high level specification in a few hours. Comparison with a hand-tuned solution shows that the automatically generated one is very competitive from the area, performance and power viewpoint, while design time is reduced from days to hours
pH‐Controlled Fabrication of Polyelectrolyte Multilayers: Assembly and Applications (2002)

This chapter contains sections titled: Introduction Layer-by-Layer Assembly of Weak Polyelectrolyte Multilayers Light Emitting Thin Film Devices Microporous Thin Films Nanoreactors, Electroless Plating and Ink-jet Printing Surface Modification via Selective Adsorption of Block Copolymers Patterning of Weak Polyelectrolyte Multilayers Micro-Contact Printing Ink-jet Printing of Hydrogen-Bonded Multilayers Conclusions and Future Prospects
Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis) (2013)

This study illustrates the power of cDNA sequencing combined with MS profiling. The former quantifies transcript composition, allowing detection of novel proteins, but cannot indicate which proteins are actually secreted, as does MS. We show, for the first time, that transcript and peptide abundances are correlated. This means that MS can be used for quantitative, non-invasive venom profiling, which will be beneficial for studies of endangered species.
Improved Scalable Synthesis of Clinical Candidate KZR‐616, a Selective Immunoproteasome Inhibitor (2021)

Abstract KZR‐616 is a selective immunoproteasome inhibitor that is under clinical evaluation for the treatment of Systemic Lupus Erythematosus (SLE). KZR‐616 represents a first‐in‐class drug candidate for the treatment of autoimmune diseases targeting the immunoproteasome. Laboratory replication of the published synthetic route of KZR‐616 resulted in an inseparable mixture of enantiomers and diastereomers. Herein, we describe a stereoselective and scalable synthetic pathway for KZR‐616 that avoids laborious separation of enantiomeric mixtures of amino acids. Moreover, the new route provides KZR‐616 in higher overall yield (42.8 %), did not require a chiral chromatographic purification step, and the final product was obtained in high purity. The synthesized compound was evaluated for inhibition of human immunoproteasome and constitutive proteasome and found to target the β1 and β5 subunits of the immunoproteasome with higher potency than the equivalent subunits of the constitutive proteasome. Therefore, we have confirmed that KZR‐616, synthesized using this new method, is an immunoproteasome selective inhibitor.
Building Up a Chemical Proteomics Network in Europe and Beyond (2014)

ADVERTISEMENT RETURN TO ISSUEPREVIn FocusNEXTBuilding Up a Chemical Proteomics Network in Europe and BeyondMaja Köhn*†, Michael M. Meijler‡, and Markus Kaiser*§View Author Information† European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany‡ Department of Chemistry and National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er-Sheva 84105, Israel§ University of Duisburg-Essen, Chemical Biology, ZMB, Faculty of Biology, Universitätsstr. 2, 45117 Essen, Germany*Email: [email protected]*Email: [email protected]Cite this: ACS Chem. Biol. 2014, 9, 8, 1647–1648Publication Date (Web):August 15, 2014Publication History Published online15 August 2014Published inissue 15 August 2014https://pubs.acs.org/doi/10.1021/cb5005299https://doi.org/10.1021/cb5005299newsACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views382Altmetric-Citations-LEARN 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 SUBJECTS:Chemical probes,Immunology,Peptides and proteins,Probes,Proteomics Get e-Alerts
Pulse Shape Analysis on Mixed Beta Particle and Gamma-ray Source Measured by CdZnTe Semiconductor Detector by means of Digital-Analog Hybrid Signal Processing Method. (2001)

We present a study on pulse shapes of a CdZnTe semiconductor detector for beta particles and gamma-rays emitted by a 137Cs-90Sr mixed source. When beta and gamma radiations enter a semiconductor detector, two kinds of pulses are produced according to the type of radiations. The characteristics of the pulses are determined by their energy and depth of interaction. The energy deposited on the detector basically determines the pulse height and the depth of interaction affects the pulse shape. Because of the different characteristics of beta and gamma radiations, their pulse shapes are also different. The digital-analog hybrid signal processing method was applied to separation of the beta spectrum from the beta-gamma mixed one. The separation of beta spectrum was done based on a neural network algorithm, a leading edge area method, and a falling continuum tail value method. However, the perfect separation could not be obtained. The separation was also done by reconstructing the spectra on the basis of subtraction of gamma-ray component. The spectra of beta particles and gamma-rays from 137Cs-90Sr mixed source could be separated well by using the reconstruction method.
Soil Is Not a Reservoir for Phellinus noxius (2019)

<i>Phellinus noxius</i> causes brown root rot (BRR) of diverse trees. Basidiospores and diseased host tissues have been recognized as important sources of <i>P. noxius</i> inoculum. This study aimed to understand whether <i>P. noxius</i> could occur or survive in soil without host tissues in the natural environment. Soil was sampled before and after the removal of diseased trees at eight BRR infection sites (total of 44 samples). No <i>P. noxius</i> colonies were recovered in soil plating assays, suggesting that no or little viable <i>P. noxius</i> resided in the soil. To know whether <i>P. noxius</i> could disseminate from decayed roots to the surrounding soil, rhizosphere and non-rhizosphere soils were sampled from another two infection sites. Although <i>P. noxius</i> DNA was detectable with specific primers, no <i>P. noxius</i> could be isolated, even from the rhizosphere soils around decayed roots covered with <i>P. noxius</i> mycelial mats. The association between viable <i>P. noxius</i> and the presence of its DNA was also investigated using field soil mixed with <i>P. noxius</i> arthrospores. After <i>P. noxius</i> was exterminated by flooding or fumigation treatment, its DNA remained detectable for a few weeks. The potential of onsite soil as an inoculum was tested using the highly susceptible loquat (<i>Eriobotrya japonica</i>). Loquats replanted in an infection site that had been cleaned up by simply removing the diseased stump and visible residual roots remained healthy for a year. Taken together, <i>P. noxius</i> is not a soilborne pathogen, and diseased host tissues should be the focus of field sanitation and detection for BRR.
Defining the potential antidepressant mode of action of acetyl- l -carnitine (2016)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The CELF1 RNA-Binding Protein Regulates Decay of Signal Recognition Particle mRNAs and Limits Secretion in Mouse Myoblasts (2017)

We previously identified several mRNAs encoding components of the secretory pathway, including signal recognition particle (SRP) subunit mRNAs, among transcripts associated with the RNA-binding protein CELF1. Through immunoprecipitation of RNAs crosslinked to CELF1 in myoblasts and in vitro binding assays using recombinant CELF1, we now provide evidence that CELF1 directly binds the mRNAs encoding each of the subunits of the SRP. Furthermore, we determined the half-lives of the Srp transcripts in control and CELF1 knockdown myoblasts. Our results indicate CELF1 is a destabilizer of at least five of the six Srp transcripts and that the relative abundance of the SRP proteins is out of balance when CELF1 is depleted. CELF1 knockdown myoblasts exhibit altered secretion of a luciferase reporter protein and are impaired in their ability to migrate and close a wound, consistent with a defect in the secreted extracellular matrix. Importantly, similar defects in wound healing are observed when SRP subunit imbalance is induced by over-expression of SRP68. Our studies support the existence of an RNA regulon containing Srp mRNAs that is controlled by CELF1. One implication is that altered function of CELF1 in myotonic dystrophy may contribute to changes in the extracellular matrix of affected muscle through defects in secretion.
Genetic Variation Determines Mast Cell Functions in Experimental Asthma (2011)

Mast cell-deficient mice are a key for investigating the function of mast cells in health and disease. Allergic airway disease induced as a Th2-type immune response in mice is employed as a model to unravel the mechanisms underlying inception and progression of human allergic asthma. Previous work done in mast cell-deficient mouse strains that otherwise typically mount Th1-dominated immune responses revealed contradictory results as to whether mast cells contribute to the development of airway hyperresponsiveness and airway inflammation. However, a major contribution of mast cells was shown using adjuvant-free protocols to achieve sensitization. The identification of a traceable genetic polymorphism closely linked to the Kit(W-sh) allele allowed us to generate congenic mast cell-deficient mice on a Th2-prone BALB/c background, termed C.B6-Kit(W-sh). In accordance with the expectations, C.B6-Kit(W-sh) mice do not develop IgE- and mast cell-dependent passive cutaneous anaphylaxis. Yet, unexpectedly, C.B6-Kit(W-sh) mice develop full-blown airway inflammation, airway hyperresponsiveness, and mucus production despite the absence of mast cells. Thus, our findings demonstrate a major influence of genetic background on the contribution of mast cells in an important disease model and introduce a novel strain of mast cell-deficient mice.
Long-term Outcomes of Kidney Transplantation in Fabry Disease (2018)

We conclude that kidney transplantation has an excellent long-term outcome in FD.
Complex regional pain syndrome (2014)

Complex regional pain syndrome (CRPS) presents with clinical symptoms that can no longer be explained by the initial trauma, including pain, sensory, motor, and trophic symptoms, and impairment of autonomic control of the limb. These symptoms spread distally and go beyond single nerve innervation territories. Typically, the symptoms change through the course of CRPS as a result of the varying pathophysiology. Diagnosis is made clinically after the rigorous elimination of other possible causes, and 3-phase bone scintigraphy can be a useful tool for confirming CRPS. In acute stages, inflammatory symptoms prevail and should be treated with anti-inflammatory agents (steroids), bisphosphonates, or topical application of dimethyl sulfoxide. In chronic stages, many symptoms are related to so-called central neuroplasticity; these include hyperalgesia, sensory loss, motor symptoms, body perception disturbance, autonomic symptoms, and learned incorrect behavior such as nonuse. At this stage, the only medical treatment that is effective against pain without improving the function is ketamine infusions, but this has side effects. Physical therapy, graded motor imagery, and pain exposure/graded exposure in vivo therapy can help to overcome central reorganization. If a relevant mental comorbidity is present, the patient should be referred for psychotherapeutic treatment. Invasive treatment should be restricted to special cases and only offered after psychosomatic assessment. If these recommendations are followed, CRPS prognosis is not as poor as commonly assumed. Whether the patients can return to their previous life depends on particular individual factors.
A Low Cost Treadmill for Experimental Animals (1954)

Among physiologists in recent years, there has been a growing interest in the adaptive mechanisms of the normal or altered experimental animal to conditions of exertional stress.Such studies depend upon accurate assessment and reduplication of exercise conditions in the same or different animals.The treadmill, in which the parameters of travel rate, incline angle, and time can be controlled, has come to be a standard method of exercise measurement.Because most treadmills used for animal investigation are designed to accommodate human subjects as well, these instruments are usually large, expensive, and beyond the spatial or financial means of a small research unit.In the course of work in this laboratory a simple, inexpensive, small treadmill has been developed for use with dogs or other small animals.This treadmill has a continuously variable speed range of .8 to 7 mph, and readily accommodates dogs weighing from 5 to 25 kg.It has been used with satisfaction for many hundreds of hours, and because of the instrument's utility it was thought that it might be of value to present the construction in some detail.
Reconfigurable unit-cells for beam-scanning transmitarrays in X band (2013)

International audience
Supplementary File 10 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer (2023)

Supplementary File 10 from Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer