gebhart/patrepeval huggingface dataset:
Neurogenic potential of human mesenchymal stem cells revisited: analysis by immunostaining, time-lapse video and microarray (2005)

The possibility of generating neural cells from human bone-marrow-derived mesenchymal stem cells (hMSCs) by simple in vitro treatments is appealing both conceptually and practically. However, whether phenotypic modulations observed after chemical manipulation of such stem cells truly represent a genuine trans-lineage differentiation remains to be established. We have re-evaluated the effects of a frequently reported biochemical approach, based on treatment with butylated hydroxyanisole and dimethylsulphoxide, to bring about such phenotypic conversion by monitoring the morphological changes induced by the treatment in real time, by analysing the expression of phenotype-specific protein markers and by assessing the modulation of transcriptome. Video time-lapse microscopy showed that conversion of mesenchymal stem cells to a neuron-like morphology could be reproduced in normal primary fibroblasts as well as mimicked by addition of drugs eliciting cytoskeletal collapse and disruption of focal adhesion contacts. Analysis of markers revealed that mesenchymal stem cells constitutively expressed multi-lineage traits, including several pertaining to the neural one. However, the applied ;neural induction' protocol neither significantly modulated the expression of such markers, nor induced de novo translation of other neural-specific proteins. Similarly, global expression profiling of over 21,000 genes demonstrated that gene transcription was poorly affected. Most strikingly, we found that the set of genes whose expression was altered by the inductive treatment did not match those sets of genes differentially expressed when comparing untreated mesenchymal stem cells and immature neural tissues. Conversely, by comparing these gene expression profiles with that obtained from comparisons between the same cells and an unrelated non-neural organ, such as liver, we found that the adopted neural induction protocol was no more effective in redirecting human mesenchymal stem cells toward a neural phenotype than toward an endodermal hepatic pathway.
Instability in a CO_2 sequence-band laser with a saturable absorber and vibration-to-vibration energy transfer processes (1993)

Several types of instability are observed in the passive Q-switching (PQS) pulsation of a CO2 sequence-band laser with a saturable absorber. The observed pulse shapes are different from those of a regular-band CO2 laser in detailed structure. We propose a novel model for the PQS instability of a CO2 sequence-band laser by considering two vibration-to-vibration energy-transfer processes. We find that the sequence-band PQS pulse width critically depends on the rate of vibrational relaxation in the ν3 mode. The vibration-to-vibration relaxation rate is estimated from the analysis of the pulse shapes.
Simplifying video editing using metadata (2002)

Digital video is becoming increasingly ubiquitous. However, editing video remains difficult for several reasons: it is a time-based medium, it has dual tracks of audio and video, and current tools force users to work at the smallest level of detail. Based on interviews with professional video editors, we developed a video editor, called Silver, that uses metadata to make digital video editing more accessible to novices. To help users visualize video, Silver provides multiple views with different semantic content and at different levels of abstraction, including storyboard, editable transcript, and timeline views. Silver offers smart editing operations that help users resolve the inconsistencies that arise because of the different boundaries in audio and video. We conducted a preliminary user study to investigate the effectiveness of the Silver smart editing. Participants successfully edited video after only a short tutorial, both with and without smart editing assistance. Our research suggests several ways in which video editing tools could use metadata to assist users in the reuse and composition of video.
Qualitative plus/versus quantitative: The last word (1994)

Abstract Neither methodological correctness nor paradigm purity offers an appropriate framework for evaluation practice.
Evaluation of the enantiomeric composition of amino acids in tobacco (1999)

Despite the fact that several studies have reported the concentrations of various free amino acids in tobacco, their enantiomeric composition is unknown. Both the absolute and enantiomeric compositions of proline, alanine, asparagine, aspartic acid, valine, methionine, leucine,and phenylalanine were determined for three strains of tobacco leaf, three types of smokeless tobacco, and six different blended filtered and nonfiltered reference cigarettes. Some of the highest levels of D-amino acids ever found in agricultural products were observed. Possible mechanisms for the production of these D-amino acids are considered. The relevance of D-amino acids in tobacco is discussed.
Elevated Alpha-Synuclein Impairs Innate Immune Cell Function and Provides a Potential Peripheral Biomarker for Parkinson's Disease (2013)

Alpha-synuclein protein is strongly implicated in the pathogenesis Parkinson's disease. Increased expression of α-synuclein due to genetic multiplication or point mutations leads to early onset disease. While α-synuclein is known to modulate membrane vesicle dynamics, it is not clear if this activity is involved in the pathogenic process or if measurable physiological effects of α-synuclein over-expression or mutation exist in vivo. Macrophages and microglia isolated from BAC α-synuclein transgenic mice, which overexpress α-synuclein under regulation of its own promoter, express α-synuclein and exhibit impaired cytokine release and phagocytosis. These processes were affected in vivo as well, both in peritoneal macrophages and microglia in the CNS. Extending these findings to humans, we found similar results with monocytes and fibroblasts isolated from idiopathic or familial Parkinson's disease patients compared to age-matched controls. In summary, this paper provides 1) a new animal model to measure α-synuclein dysfunction; 2) a cellular system to measure synchronized mobilization of α-synuclein and its functional interactions; 3) observations regarding a potential role for innate immune cell function in the development and progression of Parkinson's disease and other human synucleinopathies; 4) putative peripheral biomarkers to study and track these processes in human subjects. While altered neuronal function is a primary issue in PD, the widespread consequence of abnormal α-synuclein expression in other cell types, including immune cells, could play an important role in the neurodegenerative progression of PD and other synucleinopathies. Moreover, increased α-synuclein and altered phagocytosis may provide a useful biomarker for human PD.
EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections (2005)

Mycobacterium tuberculosis secretes ESAT-6, a virulence factor that triggers cell-mediated immune responses and IFN-gamma production during tuberculosis. ESAT-6 is transported across the bacterial envelope by a specialized secretion system with a FSD (FtsK-SpoIIIE domain) membrane protein. Although the presence of ESAT-6-like genes has been identified in the genomes of other microbes, the possibility that they may encode general virulence functions has hitherto not been addressed. Herein we show that the human pathogen Staphylococcus aureus secretes EsxA and EsxB, ESAT-6-like proteins, across the bacterial envelope. Staphylococcal esxA and esxB are clustered with six other genes and some of these are required for synthesis or secretion of EsxA and EsxB. Mutants that failed to secrete EsxA and EsxB displayed defects in the pathogenesis of S. aureus murine abscesses, suggesting that this specialized secretion system may be a general strategy of human bacterial pathogenesis.
Recent Advances in Clinical Applications of Circulating Cell-free DNA Integrity: Table 1 (2014)

Circulating DNA is an emerging biomarker in various types of cancer. It is generally believed that DNA released from apoptotic cells is uniformly truncated to small DNA fragments with 185-200 base pair (bp), whereas DNA produced by malignant cells varies in size (most of these are longer DNA fragments). Recently, the application of circulating DNA integrity indexes, represented by the ratio of the longer DNA fragments concentration to the shorter ones, has been reported in different cancers. This review will summarize the recently reported assays for detection of the circulating cell-free DNA (ccf-DNA) integrity and their clinical utility.
Flowers or a robot army? (2008)

Personal, mobile displays, such as those on mobile phones, are ubiquitous, yet for the most part, underutilized. We present results from a field experiment that investigated the effectiveness of these displays as a means for improving awareness of daily life (in our case, self-monitoring of physical activity). Twenty-eight participants in three experimental conditions used our UbiFit system for a period of three months in their day-to-day lives over the winter holiday season. Our results show, for example, that participants who had an awareness display were able to maintain their physical activity level (even during the holidays), while the level of physical activity for participants who did not have an awareness display dropped significantly. We discuss our results and their general implications for the use of everyday mobile devices as awareness displays.
Zwitterionic Ring-Opening Polymerization for the Synthesis of High Molecular Weight Cyclic Polymers (2013)

Cyclic polymers are an intriguing class of macromolecules. Because of the constraints of the cyclic topology and the absence of chain ends, the properties of these molecules differ from those of linear polymers in ways that remain poorly understood. Cyclic polymers present formidable synthetic challenges because the entropic penalty of coupling the chain ends grows exponentially with increasing molecular weight. In this Account, we describe recent progress in the application of zwitterionic ring-opening polymerization (ZROP) as a strategy for the synthesis of high molecular weight, cyclic polymers. Zwitterionic ring-opening polymerization involves the addition of neutral organic nucleophiles to strained heterocyclic monomers; under appropriate conditions, cyclization of the resultant macrozwitterions generates cyclic macromolecules. We discuss the mechanistic and kinetic features of these zwitterionic ring-opening reactions and the conditions that influence the efficiency of the initiation, propagation, and cyclization to generate high molecular weight cyclic polymers. N-Heterocyclic carbenes (NHC) are potent nucleophiles and relatively poor leaving groups, two features that are important for the generation of high molecular weight polymers. Investigations of the nature of the monomer and nucleophile have helped researchers understand the factors that govern the reactivity of these systems and their impact on the molecular weight and molecular weight distributions of the resulting cyclic polymers. We focus primarily on ZROP mediated by N-heterocyclic carbene nucleophiles but also discuss zwitterionic polymerizations with amidine, pyridine, and imidazole nucleophiles. The ZROP of N-carboxyanhydrides with N-hetereocyclic carbenes generates a family of functionalized cyclic polypeptoids. We can synthesize gradient lactone copolymers by exploiting differences in relative reactivity present in ZROP that differ from those of traditional metal-mediated polymerizations. These new synthetic methods have allowed us to investigate the influence of topology on the crystallization behavior, stereocomplexation, and solution properties of cyclic macromolecules.
Superoxide Radical and Iron Modulate Aconitase Activity in Mammalian Cells (1995)

Aconitase is a member of a family of iron-sulfur-containing (de)hydratases whose activities are modulated in bacteria by superoxide radical (O2-.)-mediated inactivation and iron-dependent reactivation. The inactivation-reactivation of aconitase(s) in cultured mammalian cells was explored since these reactions may impact important and diverse aconitase functions in the cytoplasm and mitochondria. Conditions which increase O2-. production including exposure to the redox-cycling agent phenazine methosulfate (PMS), inhibitors of mitochondrial ubiquinol-cytochrome c oxidoreductase, or hyperoxia inactivated aconitase in mammalian cells. Overproduction of mitochondrial Mn-superoxide dismutase protected aconitase from inactivation by PMS or inhibitors of ubiquinol-cytochrome c oxidoreductase, but not from normobaric hyperoxia. Aconitase activity was reactivated (t1/2 of 12 +/- 3 min) upon removal of PMS. The iron chelator deferoxamine impaired reactivation and increased net inactivation of aconitase by O2-.. The ability of ubiquinol-cytochrome c oxidoreductase-generated O2-. to inactivate aconitase in several cell types correlated with the fraction of the aconitase activity localized in mitochondria. Extracellular O2-. generated with xanthine oxidase did not affect aconitase activity nor did exogenous superoxide dismutase decrease aconitase inactivation by PMS. The results demonstrate a dynamic and cyclical O2-.-mediated inactivation and iron-dependent reactivation of the mammalian [4Fe-4S] aconitases under normal and stress conditions and provide further evidence for the membrane compartmentalization of O2-..
ALK-positive diffuse large B-cell lymphoma: two more cases and a brief literature review. (2005)

Anaplastic lymphoma kinase (ALK)-positive diffuse large B-cell lymphoma (DLBCL) is a rare, recently defined tumor distinct in many aspects from ALK-positive anaplastic large cell lymphoma (ALCL). We present two additional cases of ALK+DLBCL recently diagnosed in our department and a review of literature. A 48-year old man presented with a large upper neck mass growing slowly over 18 months. Histologically the tumor was diagnosed as an ALK-positive diffuse large B-cell lymphoma. with plasmablastic features. Large, frequently intrasinusoidal tumor cells expressed CD138, EMA, weakly IgA and kappa, but were negative for other B-cell markers, T-cell markers and CD30. The ALK staining was cytoplasmic with the increased intensity in the Golgi area. At the diagnosis the patient manifested with the stage IIIB. Three courses of CHOP resulted in partial and only transient remission. The patient died of massive bleeding from his decomposing tumor 3 months after the diagnosis. A 49-year old man complaining of abdominal pain revealed abdominal lymphadenomegaly and a gastric infiltrate, involving the deep portions of the gastric wall. The tumor showed immunoblastic/anaplastic morphology, with some Reed-Sternberg-like cells positive for ALK. ALK immunostaining was cytoplasmic, weak in a routine immunostain, enhanced with double (proteinase + pressure cooker) antigen retrieval. FISH was consistent with the t(2;5)/nucleophosmin(NPM)-ALK rearrangement. The tumor demonstrated similar "null" B/T phenotype with positivity for IgA, lambda, EMA and LCA. The patient (stage IVB) currently undergoes chemotherapy. ALK-positive DLBCL affects mostly middle-aged men, shows generally poor but stage-dependent prognosis (at least 60% mortality rate), presents typically as a lymph node-based disseminated disease, and very rarely involves the bone marrow. Genetic studies showed that the majority of ALK+DLBCL cases are characterized by the clathrin (CLTC)-ALK fusion and in a few cases the NPM-ALK rearrangement has been found.
Seasonal changes in fatty acids and leptin contents in the plasma of the European brown bear (Ursus arctos arctos) (1998)

The goal of this study was to examine whether or not the preparation of the bear to winter sleep requires changes in the composition of plasma fatty acids similar to those observed in deep hibernators. Seasonal changes in plasma fatty acids of six captive European brown bears (Ursus arctos arctos) were investigated between 1991 and 1996. Altogether fifty plasma samples were analysed chromatographically. The weight percentage of unsaturated to saturated fatty acids was 37.1% in winter but only 32.3% in summer. The proportions of palmitic (16:0), octadec-11-enoic (18:1n-7), arachidonic (20:4n-6), and docosahexaenoic (22:6n-3) acids increased significantly in the total fatty acid pool in winter. At the same time, a significant decrease in concentrations of heptadecanoic (17:0), stearic (18:0), oleic (18:1n-9), γ-linolenic (18:3n-6), α-linolenic (18:3n-3) and eicosapentaenoic (20:5n-3) acids was observed. Some fatty acids also act as precursors in the synthesis of specific tissue hormones. The leptin level reached its maximum just prior to winter sleep, i.e. when fat reserves were greatest.
US Trends in Prevalence, Awareness, Treatment, and Control of Hypertension, 1988-2008 (2010)

Blood pressure was controlled in an estimated 50.1% of all patients with hypertension in NHANES 2007-2008, with most of the improvement since 1988 occurring after 1999-2000. Hypertension control was significantly lower among younger than middle-aged individuals and older adults, and Hispanic vs white individuals.
Interleukin‐4 and ‐10 exacerbate candidiasis in mice (1995)

Neutralization of endogenous interleukin (IL)-4 or IL-10 in mice with Candida albicans infection initiates or accelerates development of a T helper (Th)1-associated protective response. Here, we report the effect of IL-4 and IL-10 administration on the course of systemic or gastrointestinal (GI) candidiasis and on the development of Th immunity using yeast/host combinations that result either in Th1-associated self-limiting infection (healer mice) or in Th2-associated progressive disease (nonhealer mice). Treatment with IL-4 or IL-10 greatly exacerbated the course of systemic infection in nonhealer mice and rendered healer mice, inoculated with attenuated yeast cells, susceptible to infection. Under the latter conditions of yeast challenge and IL-4/IL-10 administration, the development of a fatal disease was associated with inhibition of IL-12 production and detection of progressive Th2 cell dominance. In contrast, in healer mice allowed to resolve their infections and to develop long-lived anti-candidal resistance, the expression of this acquired resistance was not impaired by IL-4 and/or IL-10, as shown by the outcome of reinfection with virulent yeast cells. In the GI model of infection, both IL-4 and IL-10 were found to exacerbate the course of infection and to induce the appearance of CD4+ T cells producing high levels of IL-4 and IL-10 in Peyer's patches. These findings demonstrate that exogenous IL-4 and IL-10 may greatly affect the development of Th responses to C. albicans in vivo, but do not modify the expression of established and predominant Th1 cell reactivity.
Generating Images with Perceptual Similarity Metrics based on Deep Networks (2016)

Image-generating machine learning models are typically trained with loss functions based on distance in the image space. This often leads to over-smoothed results. We propose a class of loss functions, which we call deep perceptual similarity metrics (DeePSiM), that mitigate this problem. Instead of computing distances in the image space, we compute distances between image features extracted by deep neural networks. This metric better reflects perceptually similarity of images and thus leads to better results. We show three applications: autoencoder training, a modification of a variational autoencoder, and inversion of deep convolutional networks. In all cases, the generated images look sharp and resemble natural images.
Superoxide and peroxynitrite inatherosclerosis. (1994)

The role of reactive oxygen species in the vascular pathology associated with atherosclerosis was examined by testing the hypothesis that impaired vascular reactivity results from the reaction of nitric oxide (.NO) with superoxide (O2-), yielding the oxidant peroxynitrite (ONOO-). Contractility studies were performed on femoral arteries from rabbits fed a cholesterol-supplemented diet. Cholesterol feeding shifted the EC50 for acetylcholine (ACh)-induced relaxation and impaired the maximal response to ACh. We used pH-sensitive liposomes to deliver CuZn superoxide dismutase (SOD; superoxide:superoxide oxidoreductase, EC 1.15.1.1) to critical sites of .NO reaction with O2-. Intravenously injected liposomes (3000 units of SOD per ml) augmented ACh-induced relaxation in the cholesterol-fed group to a greater extent than in controls. Quantitative immunocytochemistry demonstrated enhanced distribution of SOD in both endothelial and vascular smooth muscle cells as well as in the extracellular matrix. SOD activity in vessel homogenates of liposome-treated rabbits was also increased. Incubation of beta very low density lipoprotein with ONOO- resulted in the rapid formation of conjugated dienes and thiobarbituric acid-reactive substances. Our results suggest that the reaction of O2- with .NO is involved in the development of atherosclerotic disease by yielding a potent mediator of lipoprotein oxidation, as well as by limiting .NO stimulation of vascular smooth muscle guanylate cyclase activity.
CLASSIFICATION OF EPSTEIN-BARR VIRUS-ASSOCIATED POSTTRANSPLANT LYMPHOPROLIFERATIVE DISEASES: Implications for Understanding their Pathogenesis and Developing Rational Treatment Strategies (1995)

The Epstein-Barr virus (EBV) is associated with a spectrum of B-cell lymphoproliferative diseases (LPD) that develop following organ transplantation. A classification scheme for these disorders has been developed based on the clinical, histologic, immunologic cell-typing, cytogenetic, immunoglobulin gene-rearrangement, and virologic characteristics of these LPD. Four disease groups have been identified: (a) uncomplicated posttransplant infectious mononucleosis, (b) benign polyclonal polymorphic B-cell hyperplasia, (c) early malignant transformation in polyclonal polymorphic B-cell lymphoma, and (d) monoclonal polymorphic B-cell lymphoma. This classification has furthered our understanding of the pathogenesis of these diverse LPD and has allowed the development of rational treatment protocols.
Temporal arteritis and Chlamydia pneumoniae: Failure to detect the organism by polymerase chain reaction in ninety cases and ninety controls (2002)

The results of this study using sensitive and specific PCR analyses do not support a role for C pneumoniae in the pathogenesis of TA.
A hypophosphorylated form of RPA34 is a specific component of pre-replication centers (2004)

Replication protein A (RPA) is a three subunit single-stranded DNA-binding protein required for DNA replication. In Xenopus, RPA assembles in nuclear foci that form before DNA synthesis, but their significance in the assembly of replication initiation complexes has been questioned. Here we show that the RPA34 regulatory subunit is dephosphorylated at the exit of mitosis and binds to chromatin at detergent-resistant replication foci that co-localize with the catalytic RPA70 subunit, at both the initiation and elongation stages of DNA replication. By contrast, the RPA34 phosphorylated form present at mitosis is not chromatin bound. We further demonstrate that RPA foci assemble on chromatin before initiation of DNA replication at sites functionally defined as initiation replication sites. Association of RPA with these sites does not require nuclear membrane formation, and is sensitive to the S-CDK inhibitor p21. We also provide evidence that RPA34 is present at initiation complexes formed in the absence of MCM3, but which contain MCM4. In such conditions, replication foci can form, and short RNA-primed nascent DNAs of discrete size are synthesized. These data show that in Xenopus, the hypophosphorylated form of RPA34 is a component of the pre-initiation complex.