gebhart/patrepeval huggingface dataset:
Comparative effects of granulocyte-macrophage colony-stimulating factor (GM-CSF) and granulocyte colony-stimulating factor (G-CSF) on priming peripheral blood progenitor cells for use with autologous bone marrow after high-dose chemotherapy (1993)

Abstract Two hematopoietic colony-stimulating factors, granulocyte colony- stimulating factor (G-CSF) and granulocyte-macrophage CSF (GM-CSF), have been shown to accelerate leukocyte and neutrophil recovery after high-dose chemotherapy and autologous bone marrow (BM) support. Despite their use, a prolonged period of absolute leukopenia persists during which infections and other complications of transplantation occur. We collected large numbers of peripheral blood (PB) progenitors after CSF administration using either G-CSF or GM-CSF and tested their ability to affect hematopoietic reconstitution and resource utilization in patients undergoing high-dose chemotherapy and autologous BM support. Patients with breast cancer or melanoma undergoing high-dose chemotherapy and autologous BM support were studied in sequential nonrandomized trials. After identical high-dose chemotherapy, patients received either BM alone, with no CSF; BM with either G-CSF or GM-CSF; or BM with G-CSF or GM-CSF and G-CSF or GM-CSF primed peripheral blood progenitor cells (PBPC). Hematopoietic reconstitution, as well as resource utilization, was monitored in these patients. The use of CSF- primed PBPC led to a highly significant reduction in the duration of leukopenia with a white blood cell (WBC) count under 100 and 200 cells/mL, and neutrophil count under 100 and 200 cells/mL with both GM- and G-CSF primed PB progenitor cells, compared with the use of the CSF with BM or with historical controls using BM alone. In addition, the use of CSF-primed PBPC resulted in a significant reduction in median number of antibiotics used, days in the Bone Marrow Transplant Unit, and hospital resources used. Patients receiving G-CSF primed PBPC also experienced a reduction in the median number of days in the hospital, red blood cell (RBC) transfusions, platelet transfusions, days on antibiotics, and discounted hospital charges. Phenotypic analysis of the CSF-primed PBPC indicated the presence of cells bearing antigens associated with both early and late hematopoietic progenitor cells. The use of CSF-primed PBPC can significantly improve hematopoietic recovery after high-dose chemotherapy and autologous BM support. In addition, the use of G-CSF-primed PBPC was associated with a significant reduction in hospital resource utilization, and a reduction in hospital charges.
Elevation of a potassium current in differentiating human leukemic (HL‐60) cells (1987)

Abstract Human promyelocytic leukemia (HL‐60) cells display a novel voltage‐dependent outward current under voltage clamp. This current is present at low levels in the proliferative state and in granulocytes derived from HL‐60 cells which were induced to differentiate with retinoic acid. It is elevated in macrophages derived from HL‐60 cells after exposure to phorbol‐12‐myristate‐13‐acetate (PMA). The current is carried primarily by K + , is blocked by Cs + and by increased intracellular concentrations of Cl − . From a holding potential of −80 mV, significant activation required depolarization to +20 mV membrane potential. Activation was not influenced by intracellular Ca 2+ (1–2 × 10 −6 M). These properties appear to differ significantly from the Ca 2+ ‐activated K + channel and the delayed rectifier. The increase of this voltage‐activated current in differentiation toward the macrophage, but not the granulocyte, suggests that this current is correlated specifically with macrophage differentiation.
Apodisation of the spectral response of fibre Bragggratings using a phase maskwith variable diffraction efficiency (1995)

Bragg gratings with sidelobe levels 26 dB lower than the peak reflectivity have been fabricated in standard telecommunication optical fibres by exposure to ultraviolet light through a phase mask with a locally varying diffraction efficiency. This represents a reduction of 14 dB in the sidelobe levels compared to uniform gratings with the same bandwidth and reflectivity.
Expression of bacterial genes in plant cells. (1983)

Chimeric bacterial genes conferring resistance to aminoglycoside antibiotics have been inserted into the Agrobacterium tumefaciens tumor-inducing (Ti) plasmid and introduced into plant cells by in vitro transformation techniques. The chimeric genes contain the nopaline synthase 5' and 3' regulatory regions joined to the genes for neomycin phosphotransferase type I or type II. The chimeric genes were cloned into an intermediate vector, pMON120, and inserted into pTiB6S3 by recombination and then introduced into petunia and tobacco cells by cocultivating A. tumefaciens cells with protoplast-derived cells. Southern hybridization was used to confirm the presence of the chimeric genes in the transformed plant tissues. Expression of the chimeric genes was determined by the ability of the transformed cells to proliferate on medium containing normally inhibitory levels of kanamycin (50 micrograms/ml) or other aminoglycoside antibiotics. Plant cells transformed by wild-type pTiB6S3 or derivatives carrying the bacterial neomycin phosphotransferase genes with their own promoters failed to grow under these conditions. The significance of these results for plant genetic engineering is discussed.
STUDIES ON STREPTOCOCCAL BACTERIOPHAGES (1968)

Evidence has been presented that the burst size in the Group A and Group C streptococcal phage-host systems are in general similar producing approximately 13 phage particles per infected coccus. The exception was the C1 phage which produced 10 times more virus particles than all the other phages tested. The eclipse period for the A25 phage-host system was found to extend for 34 min, while the C1 phage were found as early as 10 min after infection. Conclusive evidence has been presented indicating that mercuric ions at 2.5 x 10(-6)M concentration have the ability to halt intracellular phage production at any point during the infective cycle of A25 bacteriophages. This blocking action can then be quickly reversed with the addition of reduced glutathione with subsequent completion of the viral cycle.
Measuring Clinical Performance To Provide Information for Quality Improvement (1996)

Measures of clinical performance summarize quality of care given to groups of patients by a practice, provider network, or plan. Clinical managers can use these measures to drive and track internal quality improvements, and purchasers and accreditors can provide benchmarks based on comparisons of performance in order to stimulate internal improvements. This article explains desired properties of such clinical performance measures and the AHCPR Typology of Clinical Performance Measures Project.
Phase-matched second-harmonic generation by periodic poling of fused silica (1994)

90° phase matching in periodically poled fused silica is achieved over approximately 2 mm at a wavelength of 1064 nm. Electrical poling was done at 5 kV for 120 min using photolithographed periodic electrodes on fused silica glass at 250 °C. A nonlinearity equivalent to d11/200 of quartz is estimated from measurements. Several phase-matched interactions are reported and the implications for device applications discussed.
Triggered self-assembly of magnetic nanoparticles (2016)

Colloidal magnetic nanoparticles are candidates for application in biology, medicine and nanomanufacturing. Understanding how these particles interact collectively in fluids, especially how they assemble and aggregate under external magnetic fields, is critical for high quality, safe, and reliable deployment of these particles. Here, by applying magnetic forces that vary strongly over the same length scale as the colloidal stabilizing force and then varying this colloidal repulsion, we can trigger self-assembly of these nanoparticles into parallel line patterns on the surface of a disk drive medium. Localized within nanometers of the medium surface, this effect is strongly dependent on the ionic properties of the colloidal fluid but at a level too small to cause bulk colloidal aggregation. We use real-time optical diffraction to monitor the dynamics of self-assembly, detecting local colloidal changes with greatly enhanced sensitivity compared with conventional light scattering. Simulations predict the triggering but not the dynamics, especially at short measurement times. Beyond using spatially-varying magnetic forces to balance interactions and drive assembly in magnetic nanoparticles, future measurements leveraging the sensitivity of this approach could identify novel colloidal effects that impact real-world applications of these nanoparticles.
THE LOCALIZATION OF CHOLINESTERASE ACTIVITY IN RAT CARDIAC MUSCLE BY ELECTRON MICROSCOPY (1964)

A method has been developed for localizing sites of cholinesterase activity in rat cardiac muscle by electron microscopy. The method utilizes thiocholine esters as substrates, and is believed to be dependent on the reduction of ferricyanide to ferrocyanide by thiocholine released by enzymatic activity. The ferrocyanide thus formed is captured by copper to form fine, electron-opaque deposits of copper ferrocyanide, which sharply delineate sites of enzymatic activity at the ultrastructural level. Cholinesterase activity in formalin-fixed heart muscle was localized: (a) in longitudinal elements of the sarcoplasmic reticulum, but not in the T, or transverse, elements; and (b) in the A band, with virtually no activity noted in the M band, or in the H zone. The I band was also negative. No activity was detected in the sarcolemma, or in invaginations of the sarcolemma at the level of the Z band. The perinuclear element of the sarcoplasmic (endoplasmic) reticulum was frequently strongly positive. Activity at all sites was completely abolished by omitting the substrates, or by inhibition with eserine 10(-4)M and diisopropylfluorophosphate 10(-5)M. Eserine 10(-5)M completely inhibited reaction in the sarcoplasmic reticulum, and virtually abolished that in the A band. These observations, together with the use of the relatively specific substrates and suitable controls to eliminate non-enzymatic staining, indicate that cholinesterase activity was being demonstrated. The activity in rat heart against different substrates was that of non-specific cholinesterases, in accordance with biochemical data. The activity in the A band was considered to be probably due to myosincholinesterase. It is proposed that the localization of cholinesterases in myocardium at the ultrastructural level should be taken into account in considering the possible functions of these myocardial enzymes, and it is hoped that knowledge of their localization will open up new avenues of approach in considering their physiological role in myocardium, which at present is not definitely known.
The Effect of Copper and Brass on Friction Stir Welded Dissimilar Aluminium Alloy When Used in Thin Sheet Form (2016)

In recent year’s aluminium and aluminium alloys are most widely used in many applications because of light weight, good formability and malleability, corrosion resistance, moderate strength and low cost. Friction Stir Welding (FSW) process is an efficient and cost-effective method for welding aluminium and aluminium alloys. FSW is a solid-state welding process that means the material is not melted during the process. Complete welding process accomplishes below the melting point of materials so it overcomes many welding defects that usually happens with conventional fusion welding technique which was initially used for low melting materials. Though this process is initially developed for low melting materials but now the process is widely used for a variety of other materials including titanium, steel and also for composites. The present butt jointed FSW experimental work has been done in two ways. Initially, a comparison of tensile properties of friction stir (FS) welded similar aluminium alloy (AA6351 with AA6351) and dissimilar aluminium alloy (AA6351 with AA5083) combinations. Later the effect of impurities (copper and brass) in sheet form (0.1 mm thick) when used as an insert in between two dissimilar aluminium (AA6351 with AA5083) alloy plates during FSW. Tensile tests were performed for these combinations and results were compared for with and without using strip material (copper and brass).
DNA Restriction and Modification Mechanisms in Bacteria (1971)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver (2011)

The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the detailed links between circadian regulators and downstream targets are poorly known. Using chromatin immunoprecipitation combined with deep sequencing we obtained a time-resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed us to identify over 2,000 binding sites, with peak binding narrowly centered around Zeitgeber time 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. Moreover, transcription regulators are largely overrepresented, several of which also exhibit circadian activity. Genes of the core circadian oscillator stand out as strongly bound, often at promoter and distal sites. Genomic sequence analysis of the sites identified E-boxes and tandem E1-E2 consensus elements. Electromobility shift assays showed that E1-E2 sites are bound by a dimer of BMAL1/CLOCK heterodimers with a spacing-dependent cooperative interaction, a finding that was further validated in transactivation assays. BMAL1 target genes showed cyclic mRNA expression profiles with a phase distribution centered at Zeitgeber time 10. Importantly, sites with E1-E2 elements showed tighter phases both in binding and mRNA accumulation. Finally, analyzing the temporal profiles of BMAL1 binding, precursor mRNA and mature mRNA levels showed how transcriptional and post-transcriptional regulation contribute differentially to circadian expression phase. Together, our analysis of a dynamic protein-DNA interactome uncovered how genes of the core circadian oscillator crosstalk and drive phase-specific circadian output programs in a complex tissue.
Microglia in Alzheimer’s disease (2017)

Microglia are brain-resident myeloid cells that mediate key functions to support the CNS. Microglia express a wide range of receptors that act as molecular sensors, which recognize exogenous or endogenous CNS insults and initiate an immune response. In addition to their classical immune cell function, microglia act as guardians of the brain by promoting phagocytic clearance and providing trophic support to ensure tissue repair and maintain cerebral homeostasis. Conditions associated with loss of homeostasis or tissue changes induce several dynamic microglial processes, including changes of cellular morphology, surface phenotype, secretory mediators, and proliferative responses (referred to as an "activated state"). Activated microglia represent a common pathological feature of several neurodegenerative diseases, including Alzheimer's disease (AD). Cumulative evidence suggests that microglial inflammatory activity in AD is increased while microglial-mediated clearance mechanisms are compromised. Microglia are perpetually engaged in a mutual interaction with the surrounding environment in CNS; thus, diverse microglial reactions at different disease stages may open new avenues for therapeutic intervention and modification of inflammatory activities. In this Review, the role of microglia in the pathogenesis of AD and the modulation of microglia activity as a therapeutic modality will be discussed.
Calnuc Function in Endosomal Sorting of Lysosomal Receptors (2016)

Calnuc is a ubiquitous Ca(2+)-binding protein present on the trans-Golgi network (TGN) and endosomes. However, the precise role of Calnuc in these organelles is poorly characterized. We previously highlighted the role of Calnuc in the transport of LRP9, a new member of a low-density lipoprotein (LDL) receptor subfamily that cycles between the TGN and endosomes. The objective of this study was to explore the role of Calnuc in the endocytic sorting of mannose-6-phosphate receptor (MPR) and Sortilin, two well-characterized lysosomal receptors that transit between the TGN and endosomes. Using biochemical and microscopy assays, we showed that Calnuc depletion [by small interfering RNA (siRNA)] causes the misdelivery to and degradation in lysosomes of cationic-independent mannose-6-phosphate receptor (CI-MPR) and Sortilin due to a defect in the endosomal recruitment of retromers, which are key components of the endosome-to-Golgi retrieval machinery. Indeed, we demonstrated that Calnuc depletion impairs the activation and membrane association of Rab7, a small G protein required for the endosomal recruitment of retromers. Overall, our data indicate a novel role for Calnuc in the endosome-to-TGN retrograde transport of lysosomal receptors through the regulation of Rab7 activity and the recruitment of retromers to endosomes.
Preposición + (artículo) + que relativo: análisis en la norma lingüística culta panhispánica (2004)

En este estudio se analiza la presencia/ausencia del articulo entre preposicion y el pronombre relativo que: “el nino con el que/con que jugabas”. El objetivo principal es conocer el funcionamiento de tales estructuras en la norma linguistica culta panhispanica y observar si existen criterios linguisticos y/o diatopicos que condicionen dicha alternancia. Los resultados de la investigacion han puesto de manifiesto que la variante con articulo no siempre es la mas empleada. Parece oportuno destacar el caso de la preposicion en, donde se utilizo mayoritariamente la opcion en que en todos los contextos sintacticos analizados. Finalmente se observaron situaciones diferentes a uno y otro lado del Atlantico. Mientras que en Hispanoamerica existe una importante representacion de la variante sin articulo, en Espana se advierte una mayor tendencia a su mantenimiento
Optical ptychography: a practical implementation with useful resolution (2010)

Quantitative phase microscopy offers a range of benefits over conventional phase-contrast techniques. For example, changes in refractive index and specimen thickness can be extrapolated and images can be refocused subsequent to their recording. In this Letter, we detail a lensless, quantitative phase microscope with a wide field of view and a useful resolution. The microscope uses the recently reported coherent diffractive imaging technique of ptychography to generate images from recorded diffraction patterns.
Comprehensive integration of single cell data (2018)

Single cell transcriptomics (scRNA-seq) has transformed our ability to discover and annotate cell types and states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, including high-dimensional immunophenotypes, chromatin accessibility, and spatial positioning, a key analytical challenge is to integrate these datasets into a harmonized atlas that can be used to better understand cellular identity and function. Here, we develop a computational strategy to “anchor” diverse datasets together, enabling us to integrate and compare single cell measurements not only across scRNA-seq technologies, but different modalities as well. After demonstrating substantial improvement over existing methods for data integration, we anchor scRNA-seq experiments with scATAC-seq datasets to explore chromatin differences in closely related interneuron subsets, and project single cell protein measurements onto a human bone marrow atlas to annotate and characterize lymphocyte populations. Lastly, we demonstrate how anchoring can harmonize in-situ gene expression and scRNA-seq datasets, allowing for the transcriptome-wide imputation of spatial gene expression patterns, and the identification of spatial relationships between mapped cell types in the visual cortex. Our work presents a strategy for comprehensive integration of single cell data, including the assembly of harmonized references, and the transfer of information across datasets. Availability: Installation instructions, documentation, and tutorials are available at: https://www.satijalab.org/seurat
A Novel Enzyme-Linked Immunosorbent Assay for Quantification of Soybean .BETA.-Conglycinin, a Major Soybean Storage Protein, in Soybean and Soybean Food Products (2005)

Soybean (Glycine max L.) storage proteins are composed of two major components, beta-conglycinin and glycinin, corresponding to 7S and 11S globulins, respectively. Recently, soybean beta-conglycinin (7S globulin) has been reported to show beneficial functions in animals and human. To date, there is no method for the precise quantification of soybean beta-conglycinin in processed food products or soybean seeds. We report here a novel method for this purpose. At first, antibodies specifically reactive to the subunits of beta-conglycinin were prepared. And then, a direct enzyme-linked immunosorbent assay (ELISA) for the quantification of soybean beta-conglycinin in processed foods and seeds was developed. In this assay, the sample was treated with sodium dodecyl sulfate sample buffer followed by dilution with phosphate-buffered saline. The diluted samples were poured and coated onto an ELISA plate and reacted with rabbit anti-beta-conglycinin antibody and peroxidase-labeled anti-rabbit IgG. Finally, the bound peroxidase-labeled antibody was detected by colorimetric reaction. By using this system, it has been possible to measure soybean beta-conglycinin concentrations in several processed food products. In addition, this simple quantification ELISA system was demonstrated to be adaptable for the quantification of beta-conglycinin contents of various soybean cultivars.
Online Contrastive Divergence with Generative Replay: Experience Replay without Storing Data (2016)

Conceived in the early 1990s, Experience Replay (ER) has been shown to be a successful mechanism to allow online learning algorithms to reuse past experiences. Traditionally, ER can be applied to all machine learning paradigms (i.e., unsupervised, supervised, and reinforcement learning). Recently, ER has contributed to improving the performance of deep reinforcement learning. Yet, its application to many practical settings is still limited by the memory requirements of ER, necessary to explicitly store previous observations. To remedy this issue, we explore a novel approach, Online Contrastive Divergence with Generative Replay (OCD_GR), which uses the generative capability of Restricted Boltzmann Machines (RBMs) instead of recorded past experiences. The RBM is trained online, and does not require the system to store any of the observed data points. We compare OCD_GR to ER on 9 real-world datasets, considering a worst-case scenario (data points arriving in sorted order) as well as a more realistic one (sequential random-order data points). Our results show that in 64.28% of the cases OCD_GR outperforms ER and in the remaining 35.72% it has an almost equal performance, while having a considerably reduced space complexity (i.e., memory usage) at a comparable time complexity.