gebhart/patrepeval huggingface dataset:
Synthesis-dependent microhomology-mediated end joining accounts for multiple types of repair junctions (2010)

Ku or DNA ligase 4-independent alternative end joining (alt-EJ) repair of DNA double-strand breaks (DSBs) frequently correlates with increased junctional microhomology. However, alt-EJ also produces junctions without microhomology (apparent blunt joins), and the exact role of microhomology in both alt-EJ and classical non-homologous end joining (NHEJ) remains unclear. To better understand the degree to which alt-EJ depends on annealing at pre-existing microhomologies, we examined inaccurate repair of an I-SceI DSB lacking nearby microhomologies of greater than four nucleotides in Drosophila. Lig4 deficiency affected neither frequency nor length of junctional microhomology, but significantly increased insertion frequency. Many insertions appeared to be templated. Based on sequence analysis of repair junctions, we propose a model of synthesis-dependent microhomology-mediated end joining (SD-MMEJ), in which de novo synthesis by an accurate non-processive DNA polymerase creates microhomology. Repair junctions with apparent blunt joins, junctional microhomologies and short indels (deletion with insertion) are often considered to reflect different repair mechanisms. However, a majority of each type had structures consistent with the predictions of our SD-MMEJ model. This suggests that a single underlying mechanism could be responsible for all three repair product types. Genetic analysis indicates that SD-MMEJ is Ku70, Lig4 and Rad51-independent but impaired in mus308 (POLQ) mutants.
Dual Atrioventricular Nodal Pathways Physiology: A Review of Relevant Anatomy, Electrophysiology, and Electrocardiographic Manifestations (2014)

More than half a century has passed since the concept of dual atrioventricular (AV) nodal pathways physiology was conceived. Dual AV nodal pathways have been shown to be responsible for many clinical arrhythmia syndromes, most notably AV nodal reentrant tachycardia. Although there has been a considerable amount of research on this topic, the subject of dual AV nodal pathways physiology remains heavily debated and discussed. Despite advances in understanding arrhythmia mechanisms and the widespread use of invasive electrophysiologic studies, there is still disagreement on the anatomy and physiology of the AV node that is the basis of discontinuous antegrade AV conduction. The purpose of this paper is to review the concept of dual AV nodal pathways physiology and its varied electrocardiographic manifestations.
Dynamics of the cytosolic chelatable iron pool of K562 cells (1996)

The labile iron pool of cells (LIP) constitutes the primary source of metabolic and catalytically reactive iron in the cytosol. We studied LIP homeostasis in K562 cells using the fluorescent metal-sensitive probe calcein. Following brief exposure to iron(II) salts or to oxidative or reductive stress, LIP rose by up to 120% relative to the normal level of 350nM. However, the rate of recovery to normal LIP level differed markedly with each treatment (respective t1/2s of 27, 65-88 and < or = 17 min). We show that the capacity of K562 cells to adjust LIP levels is highly dependent on the origin of the LIP increase and on the pre-existing cellular iron status.
Instant Ligand Libraries. Parallel Synthesis of Monodentate Phosphoramidites and in Situ Screening in Asymmetric Hydrogenation (2004)

Chiral phosphoramidites have been identified as excellent ligands for various metal-catalyzed enantioselective transformations. Taking advantage of their easy preparation and modular nature, we designed a fully automated protocol for the parallel preparation of a library of 32 phosphoramidites and its screening in asymmetric hydrogenation of amino acid precursors. This initial study led to the discovery of a new ligand for the preparation of an enantiopure beta(3)-homoalanine precursor. [structure--see text]
End group removal and modification of RAFT polymers (2009)

This paper describes both well-established routes and recent advances in the end group modification of polymers synthesised by reversible addition–fragmentation chain transfer (RAFT) polymerisation. The lability of the thiocarbonylthio group, which facilitates the RAFT mechanism, allows for ready post-polymerisation functionalisation of RAFT polymers by a number of techniques. In particular, end group thermolysis, radical induced reduction, hetero-Diels–Alder reactions and reaction with nucleophiles are discussed as are the applications and limitations of each method. The versatility of RAFT as a polymerisation tool for the synthesis of polymers with functional end groups for a range of applications is demonstrated.
Limitations of Voltage-Oriented PI Current Control of Grid-Connected PWM Rectifiers With $LCL$ Filters (2008)

Voltage-oriented PI control of three-phase grid-connected pulsewidth-modulation rectifiers with <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filters is addressed. <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filters require resonance damping. Active resonance damping is state of the art to face the problem, but it is still under investigation because of the manifold solutions. It is often realized using many sensors and/or complex control algorithms. In contrast, pure PI control requires only one set of current sensors, and its implementation and design are rather simple and well known from the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</i> filter control. PI control has already been shown to be a suitable solution also for <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filters, but there are limitations. These are investigated in this paper. System stability is analyzed with respect to different ratios of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filter resonance and control frequencies. The latter are important parameters for system design and control. Both line and converter current control are analyzed. For a certain range of frequency ratios, the voltage-oriented PI control gives stable performance without additional feedback, but for ratios outside this range, stable operation is impossible. Experimental tests validate the theoretical results. In addition, an experimentally determined <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LCL</i> filter transfer function is shown in this paper, which shows a lower resonance peak as expected from commonly used filter models.
Chemotaxis in Neutrophil-Like HL-60 Cells (2009)

Asymmetric localization of intracellular proteins and signals directs movement during axon guidance, endothelial cell invasion, and immune cell migration. In these processes, cell movement is guided by external chemical cues in a process known as chemotaxis. In particular, leukocyte migration in the innate immune system has been studied in the human neutrophil-like cell line (HL-60). Here, we describe the maintenance and transfection of HL-60 cells and explain how to analyze their behavior with two standard chemotactic assays. Finally, we demonstrate how to fix and stain the actin cytoskeleton of polarized cells for fluorescent microscopy imaging.
Polymer-Encapsulated PC12 Cells: Long-Term Survival and Associated Reduction in Lesion-Induced Rotational Behavior (1992)

Intrastriatal implantation of a dopaminergic cell line surrounded by a permeable, thermoplastic membrane was investigated as a method of long-term dopamine (DA) delivery within the central nervous system (CNS). An increase in DA release from PC12 cell-loaded capsules maintained in vitro was associated with an increase in mitotic activity of the encapsulated cell line. A significant reduction in apomorphine-induced rotational behavior was observed after PC12 cell-containing capsules were implanted into unilaterally 6-hydroxydopamine (6-OHDA) lesioned rats, which was sustained for 24 wk. Four wk after implantation, microdialysis studies revealed the presence of DA near PC12 cell-containing capsules, which was comparable to extracellular striatal levels of unlesioned controls. Extracellular striatal DA was undetectable by microdialysis in lesioned animals near empty polymer capsules. Histological analysis after 24 wk in vivo demonstrated that encapsulated PC12 cells survived, continued to express tyrosine hydroxylase, and that encapsulation prevented tumorigenesis. The data suggested that the release of a diffusible substance, most likely DA, from an implant is sufficient to exert a long-term functional influence upon 6-OHDA unilaterally lesioned rats and that capsules containing DA-secreting cells may be an effective method of long-term DA delivery in the CNS.
The Utility of Near-Infrared Fluorescence and Indocyanine Green During Robotic Pulmonary Resection (2019)

During minimally invasive pulmonary resection, it is often difficult to localize pulmonary nodules that are small (<2cm), low-density/subsolid on imaging, or deep to the visceral pleura. The use of near-infrared fluorescence imaging for localizing pulmonary nodules using indocyanine green (ICG) contrast is an emerging technology that is increasingly utilized during pulmonary resection. When administered via electromagnetic navigational bronchoscopy (ENB), ICG can accurately localize pulmonary nodules. When injected intravenously (IV), ICG can also help delineate the intersegmental plane. Research is ongoing regarding the utility of ICG for identification of the sentinel lymph node in lung cancer.
Enhanced Myeloid Progenitor Cell Cycling and Apoptosis in Mice Lacking the Chemokine Receptor, CCR2 (1999)

Chemokines regulate hematopoiesis in part by influencing the proliferative status of myeloid progenitor cells (MPC). Human MCP-1/murine JE, a myelosuppressive chemokine, specifically binds C-C chemokine receptor 2 (CCR2). Transgenic mice containing a targeted disruption in CCR2 that prevents expression of CCR2 mRNA and protein and have MPC that are insensitive to inhibition by MCP-1 and JE in vitro were assessed for potential abnormalities in growth of bone marrow (BM) and spleen MPC. MPC in both unseparated and c-kit+lin− populations of BM from CCR2-deficient (−/−) mice were in a greatly increased proliferation state compared with CCR2 littermate control (+/+) mice, an effect not apparent with progenitors from spleens of CCR2 (−/−) mice. Increased cycling status of CCR2 (−/−) BM MPC did not result in increased numbers of nucleated cells or MPC in BM or spleens of CCR2 (−/−) mice. Possible reasons for this apparent discrepancy were highlighted by flow cytometric analysis of c-kit+lin− BM cells and colony formation by MPC subjected to delayed addition of growth factors. The c-kit+lin− population of BM cells from CCR2 (−/−) mice had a significantly higher percentage of apoptotic cells than those from CCR2 (+/+) BM. However, elevated apoptosis was not associated with decreased numbers of c-kit+lin− cells. The increased percentage of apoptotic c-kit+lin− cells was due to elevated apoptosis within the c-kitdimlin−, but not the c-kitbrightlin−, subpopulations of cells. Consistent with enhanced apoptosis of phenotypically defined cells, MPC from CCR2 (−/−) BM and purified c-kit+lin− cells demonstrated decreased cell survival in vitro upon delayed addition of growth factors. The data suggest that signals received by CCR2 limit proliferation of progenitor cells in the BM, but also enhance survival of these cells.
Neurology: A Queen Square Textbook (2009)

Neurology: A Queen Square Textbook is a remarkable fusion of modern neuroscience with traditional neurology that will inform and intrigue trainee and experienced neurologists alike. Modern neuroscience has penetrated exciting and diverse frontiers into the causes, diagnosis, and treatment of neurological disease. Clinical neurology, whilst greatly enhanced by dramatic advances in molecular biology, genetics, neurochemistry and physiology, remains deeply rooted in practical traditions: the history from the patient and the elicitation of physical signs. Neurologists, neuroscientists and neurosurgeons working at Queen Square, and advised by an international editorial team, have combined their expertise and experience to produce this unique text. The synthesis of clinical neurology with translational research provides a fresh perspective which is * Practical; * Multidisciplinary; * Translational; * Integrative. The blend of new science and proven practice underpins this creative approach towards investigating and improving the care of patients suffering from neurological diseases.
Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs (2007)

MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding their roles in specific cells and tissues. However, gel-based assays currently used to detect miRNAs are very limited in terms of throughput, sensitivity and specificity. Here we provide protocols for detection and quantification of miRNAs by RT-PCR. We describe an end-point and real-time looped RT-PCR procedure and demonstrate detection of miRNAs from as little as 20 pg of plant tissue total RNA and from total RNA isolated from as little as 0.1 mul of phloem sap. In addition, we have developed an alternative real-time PCR assay that can further improve specificity when detecting low abundant miRNAs. Using this assay, we have demonstrated that miRNAs are differentially expressed in the phloem sap and the surrounding vascular tissue. This method enables fast, sensitive and specific miRNA expression profiling and is suitable for facilitation of high-throughput detection and quantification of miRNA expression.
Acceptorless, Reversible Dehydrogenation and Hydrogenation of N-Heterocycles with a Cobalt Pincer Catalyst (2015)

Acceptorless, reversible dehydrogenation and hydrogenation reactions involving N-heterocycles are reported with a well-defined cobalt complex supported by an aminobis(phosphine) [PN(H)P] pincer ligand. Several N-heterocycle substrates have been evaluated under dehydrogenation and hydrogenation conditions. The cobalt-catalyzed amine dehydrogenation step, a key step in the dehydrogenation process, has been independently verified. Control studies with related cycloalkanes suggest that a direct acceptorless alkane dehydrogenation pathway is unlikely. The metal–ligand cooperativity is probed with the related [PN(Me)P] derivative of the cobalt catalyst. These results suggest a bifunctional dehydrogenation pathway and a nonbifunctional hydrogenation mechanism.
Floating Points: A Method for Computing Stipple Drawings (2000)

We present a method for computer generated pen‐and‐ink illustrations by the simulation of stippling. In a stipple drawing, dots are used to represent tone and also material of surfaces. We create such drawings by generating an initial dot set which is then processed by a relaxation method based on Voronoi diagrams. The point patterns generated are approximations of Poisson disc distributions and can also be used for integrating functions or the positioning of objects. We provide an editor similar to paint systems for interactively creating stipple drawings. This makes it possible to create such drawings within a matter of hours, instead of days or even weeks when the drawing is done manually.
Lipid clearance from fatty streak lesions by foam cell migration. (1980)

Dietary-induced hypercholesterolemia in swine produces fatty streak lesions in the aortic arch within 15 wks. These lesions, though becoming more extensive in area, do not progress beyond the fatty streak stage up to 30 wks on the diet. The stabilization of these lesions may be attributed, in part, to the extensive migration of foam cells from the lesion into the aortic lumen. Morphological evidence indicates a lumenal movement of these cells. Previous studies (1) indicate that foam cells in these lesions are monocyte-derived. The combined evidence suggests the existence of a monocyte lipid clearance mechanism which may represent an initial response of the blood-vascular system to atherogenesis.
Expression of Insulin-Like Growth Factor-2 Can Predict the Prognosis of Human Colorectal Cancer Patients: Correlation with Tumor Progression, Proliferative Activity and Survival (1998)

Expression of insulin-like growth factor-2 (IGF-2) has been reported in tissue specimens and cell lines of human colorectal cancers. However, the effects of IGF-2 in colorectal cancer patients are not well known. In this study, IGF-2 staining was performed on tissue samples from 92 patients with colorectal cancer, and the relationship of IGF-2 staining to clinicopathological variables, proliferating cell nuclear antigen (PCNA) staining and patient survival was analyzed. IGF-2 staining was correlated with tumor progression, PCNA staining and patient survival. Our results suggest that IGF-2 plays an important role in tumor progression and that IGF-2 staining is useful as a prognostic factor in colorectal cancer patients.
Influence of physical and chemical parameters on wood pyrolysis (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfluence of physical and chemical parameters on wood pyrolysisOlivier Beaumont and Yvan SchwobCite this: Ind. Eng. Chem. Process Des. Dev. 1984, 23, 4, 637–641Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/i200027a002https://doi.org/10.1021/i200027a002research-articleACS PublicationsRequest reuse permissionsArticle Views864Altmetric-Citations122LEARN 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 options Get e-Alerts
Ligand Binding and Hydration in Protein Misfolding: Insights from Studies of Prion and p53 Tumor Suppressor Proteins (2009)

Protein misfolding has been implicated in a large number of diseases termed protein- folding disorders (PFDs), which include Alzheimer's disease, Parkinson's disease, transmissible spongiform encephalopathies, familial amyloid polyneuropathy, Huntington's disease, and type II diabetes. In these diseases, large quantities of incorrectly folded proteins undergo aggregation, destroying brain cells and other tissues. The interplay between ligand binding and hydration is an important component of the formation of misfolded protein species. Hydration drives various biological processes, including protein folding, ligand binding, macromolecular assembly, enzyme kinetics, and signal transduction. The changes in hydration and packing, both when proteins fold correctly or when folding goes wrong, leading to PFDs, are examined through several biochemical, biophysical, and structural approaches. Although in many cases the binding of a ligand such as a nucleic acid helps to prevent misfolding and aggregation, there are several examples in which ligands induce misfolding and assembly into amyloids. This occurs simply because the formation of structured aggregates (such as protofibrillar and fibrillar amyloids) involves decreases in hydration, formation of a hydrogen-bond network in the secondary structure, and burying of nonpolar amino acid residues, processes that also occur in the normal folding landscape. In this Account, we describe the present knowledge of the folding and misfolding of different proteins, with a detailed emphasis on mammalian prion protein (PrP) and tumoral suppressor protein p53; we also explore how ligand binding and hydration together influence the fate of the proteins. Anfinsen's paradigm that the structure of a protein is determined by its amino acid sequence is to some extent contradicted by the observation that there are two isoforms of the prion protein with the same sequence: the cellular and the misfolded isoform. The cellular isoform of PrP has a disordered N-terminal domain and a highly flexible, not-well-packed C-terminal domain, which might account for its significant hydration. When PrP binds to biological molecules, such as glycosaminoglycans and nucleic acids, the disordered segments appear to fold and become less hydrated. Formation of the PrP-nucleic acid complex seems to accelerate the conversion of the cellular form of the protein into the disease-causing isoform. For p53, binding to some ligands, including nucleic acids, would prevent misfolding of the protein. Recently, several groups have begun to analyze the folding-misfolding of the individual domains of p53, but several questions remain unanswered. We discuss the implications of these findings for understanding the productive and incorrect folding pathways of these proteins in normal physiological states and in human disease, such as prion disorders and cancer. These studies are shown to lay the groundwork for the development of new drugs.
Effect of fluvastatin on proteinuria in patients with immunoglobulin A nephropathy (2000)

3-Hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors are established drugs for the treatment of hypercholesterolemia, but several studies have shown that benefits obtained with these drugs are not causally related only to regression of cholesterol lowering. Moreover, in experimental models of progressive renal disease, statins have reduced the extent of glomerulosclerosis. This study evaluated the antiproteinuric effect of a daily dose of 40 mg fluvastatin for 6 months in moderately proteinuric patients with immunoglobulin A nephropathy, stable renal function, and no indicators of poor long-term prognosis. The effects of therapy were evaluated on the basis of 24-hour proteinuria (total proteinuria and albuminuria), albuminemia, creatinine clearance, cholesterol, and triglyceride values. Renal function remained stable in all patients. A significant decrease in proteinuria was observed after 6 months of therapy and persisted for all the observations. An increase in serum albumin was observed after 6 months of therapy. This study suggests that there is an antiproteinuric effect of HMG-CoA reductase inhibitors in moderately proteinuric patients with immunoglobulin A nephropathy.