gebhart/patrepeval huggingface dataset:
Toxoplasmosis-Associated Neovascular Lesions Treated Successfully With Ranibizumab and Antiparasitic Therapy (2008)

With Ranibizumab and Antiparasitic TherapyChoroidal neovascular membranes (CNVMs) rarely complicate toxoplasmic chorioretinitis [1][2][3][4][5] and are managed by observation; antiparasitic, anti-inflammatory medication; laser photocoagulation; surgical excision; or photodynamic therapy, with variable outcomes.As occurs with CNVMs secondary to age-related macular degeneration, Toxoplasma gondii increases expression of hypoxia-inducible factor-1␣ in tissue cultures along with vascular endothelial growth factor (VEGF). 6Report of Cases.Two patients with prior ocular toxoplasmosis had active CNVMs with subretinal blood and fluid on clinical examination and ocular coherence tomography (OCT) and hyperfluorescence with leakage documented on fluorescein angiogram (FA).Each was treated with offlabel intravitreal injections of ranibizumab (Genentech, Inc, South San Francisco, California) and antiparasitic treatment, with responses documented with measurements of visual acuity, full fundus photographs, FA, and OCT.We reviewed courses and photographs of 187 persons with toxoplasmosis, 175 definitely congenitally acquired, followed up in the National Collaborative Chicagobased Congenital Toxoplasmosis Study to identify those who had recognized ocular neovascular disease.Three persons had a CNVM and 1 had a retinal angioma with exudation.Institutional review board approval was obtained for this study.Written informed consent was obtained from parents or legal guardians of participating children and directly from patients (if legal adult age).This study is in compliance with Health Insurance Portability and Accountability Act of 1996 regulations.
Protein corona formation around nanoparticles – from the past to the future (2013)

The protein adsorption layer (a.k.a. the “protein corona”) that forms on the surface of colloidal nanoparticles plays an important role in their interaction with living matter. Thus, characterization of the protein corona is of utmost importance for understanding how exposure to nanoparticles affects the biological responses of cells and organisms. Although a lot of experimental studies have been reported in this direction, a comprehensive picture is still missing, in particular due to the multitude of different scenarios under which experiments have been performed. In this review an analysis of existing experimental data about the protein corona, and an outline for required future work will be given. In particular we review how existing simple analytical models such as the adopted Hill model may help to extract quantitative data from such experiments such as equilibrium dissociation and kinetic coefficients. Careful quantitative assessment of equilibrium and kinetic properties would allow for a comparison of protein binding data from the vast array of engineered nanoparticles, so that basic principles could be revealed. This review outlines that the field is in dire need of more quantitative studies to further our understanding of protein corona formation and its biological consequences.
Rho Is Required for Gαq and α1-Adrenergic Receptor Signaling in Cardiomyocytes (1996)

G protein-coupled receptor agonists initiate a cascade of signaling events in neonatal rat ventricular myocytes that culminates in changes in gene expression and cell growth characteristic of hypertrophy. These responses have been previously shown to be dependent on Gq and Ras. Rho, a member of the Ras superfamily of GTPases, regulates cytoskeletal rearrangement and transcriptional activation of the c-fos serum response element. Immunofluorescence staining of cardiomyocytes shows that Rho is present and predominantly cytosolic. We used two inhibitors of Rho function, dominant negative N19RhoA and Clostridium botulinum C3 transferase, to examine the possible requirement for Rho in alpha1-adrenergic receptor-mediated hypertrophy. Both inhibitors markedly attenuated atrial natriuretic factor (ANF) reporter gene expression induced by alpha1-adrenergic receptor stimulation with phenylephrine, and virtually abolished the increase in ANF reporter gene expression induced by GTPase-deficient Galphaq. These effects were reproduced with the myosin light chain-2 reporter gene. Notably, N19RhoA did not block the ability of activated Ras to induce ANF and myosin light chain-2 reporter gene expression. Furthermore, activation of the extracellular signal-regulated kinase by phenylephrine was not blocked by N19RhoA, nor was it stimulated by an activated mutant of RhoA. Since activated RhoA and Ras produce a large synergistic effect on ANF-luciferase gene expression, we conclude that Rho functions in a pathway separate from but complementary to Ras. Our results provide direct evidence that Rho is an effector of Galphaq signaling and suggest for the first time that a low molecular weight GTPase other than Ras is involved in regulating myocardial cell growth and gene expression in response to heterotrimeric G protein-linked receptor activation.
Spatio-temporal combination of saliency maps and eye-tracking assessment of different strategies (2010)

The modeling of the human visual attention into a computational attention model leads to the split of visual features into several independent channels. Then, a difficult problem arises to combine these maps, having different dynamic ranges or distribution. When several maps are considered, such process is mandatory in order to compute a single measure of interest for each location, regardless of which features contributed to the salience. Several strategies of cue combination are proposed in this paper for the spatial cues as well as the temporal saliency. Finally, some user tests on still image and video databases leads to highlight one operator.
Mouse Models of Bleomycin‐Induced Pulmonary Fibrosis (2008)

Pulmonary fibrosis is a component of many interstitial lung diseases, including idiopathic pulmonary fibrosis, a chronic, progressive disease for which there is currently no effective therapy. Bleomycin has been widely used in rodents to model pulmonary fibrosis for the study of mechanisms involved in fibrogenesis and for evaluation of potential therapies. Bleomycin induces DNA strand breaks, resulting in pulmonary inflammation, injury, and subsequent interstitial fibrosis. This unit describes methods for delivering bleomycin, either directly into the lung or systemically, to create models of pulmonary fibrosis in rodents. Also described is a rapid and easy procedure for measuring lung collagen content to quantify the severity of fibrosis.
Human embryonic stem cell lines derived from single blastomeres of two 4-cell stage embryos (2009)

We report the successful derivation and characterization of two hESC lines from single blastomeres of four split 4-cell stage human embryos. These two hESC lines were derived from distinct embryos, proving that at least one of the 4-cell stage blastomeres is pluripotent.
COSMIC: somatic cancer genetics at high-resolution (2016)

COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website.
Ecdysteroid-dependent regulation of genes in mammalian cells by a Drosophila ecdysone receptor and chimeric transactivators. (1992)

Steroid receptors are members of a large family of transcription factors whose activity is tightly regulated by the binding of their cognate steroid ligand. Mammalian steroid hormone receptors have been exploited to obtain the regulated expression of heterologous genes in mammalian cells. However, the utility of these systems in cultured cells and transgenic animals is limited by the presence of endogenous steroids and their receptors. We show that a Drosophila ecdysone receptor can function in cultured mammalian cells as an ecdysteroid-dependent transcription factor. The activity of the ecdysone receptor was not induced by any of the mammalian steroid hormones tested. The DNA-binding and transactivation activities of viral, mammalian, or bacterial proteins were rendered ecdysteroid-dependent when fused to the ligand-binding domain of the ecdysone receptor. The ecdysone receptor may prove useful in selectively regulating the expression of endogenous or heterologous genes in mammalian cells.
Short-Text Topic Modeling via Non-negative Matrix Factorization Enriched with Local Word-Context Correlations (2018)

Being a prevalent form of social communications on the Internet, billions of short texts are generated everyday. Discovering knowledge from them has gained a lot of interest from both industry and academia. The short texts have a limited contextual information, and they are sparse, noisy and ambiguous, and hence, automatically learning topics from them remains an important challenge. To tackle this problem, in this paper, we propose a semantics-assisted non-negative matrix factorization (SeaNMF) model to discover topics for the short texts. It effectively incorporates the word-context semantic correlations into the model, where the semantic relationships between the words and their contexts are learned from the skip-gram view of the corpus. The SeaNMF model is solved using a block coordinate descent algorithm. We also develop a sparse variant of the SeaNMF model which can achieve a better model interpretability. Extensive quantitative evaluations on various real-world short text datasets demonstrate the superior performance of the proposed models over several other state-of-the-art methods in terms of topic coherence and classification accuracy. The qualitative semantic analysis demonstrates the interpretability of our models by discovering meaningful and consistent topics. With a simple formulation and the superior performance, SeaNMF can be an effective standard topic model for short texts.
Adrenal medullary responses to stimulation of the splanchnic nerve in the conscious calf. (1980)

1. Right adrenal medullary and various cardiovascular responses to stimulation of the peripheral end of the right splanchnic nerve have been investigated in conscious calves, 2--5 weeks after birth. 2. The output of both adrenaline and noradrenaline was linearly related to stimulus frequency over the range 2.0--10.0 Hz, 2 1/2 min after stimulation was initiated. Peak outputs of both amines were obtained in response to stimulation at 15.0 Hz. 3. The output of adrenaline invariably exceeded that of noradrenaline, roughly in the proportion 3:2. At all frequencies tested between 7.0 and 40.0 Hz this difference was statistically significant (P less than 0.1). 4. Continuous stimulation at either 4.0 or 10.0 Hz produced a small but significant rise in the output of dopamine-beta-monooxygenase (DBH) activity from the right adrenal gland. Mean maximal outputs were obtained after 10 min; the levels were closely similar at both 4.0 and 10.0 Hz and could not be related to stimulus frequency or to the output of either adrenaline or noradrenaline. 5. The results are discussed in relation to perfusion studies in vitro and experiments in anaesthetized animals. It is concluded that the levels of DBH in adrenal effluent plasma is an unreliable index of catecholamine exocytosis in the conscious calf.
Effect of Remdesivir vs Standard Care on Clinical Status at 11 Days in Patients With Moderate COVID-19 (2020)

ClinicalTrials.gov Identifier: NCT04292730.
Fertilization and early embryology: Intracytoplasmic sperm injection for Rhesus monkey fertilization results in unusual chromatin, cytoskeletal, and membrane events, but eventually leads to pronuclear development and sperm aster assembly (1996)

The disassembly and reorganization of sperm-derived structures are landmarks for the onset of embryonic development. Since complete information on these events is not yet available, we examined the disassembly of the sperm axoneme, the formation of the sperm aster, and the decondensation and development of the male and female pronuclei in inseminated Rhesus monkey oocytes conceived by in-vitro fertilization (IVF) or by intracytoplasmic sperm injection. During IVF, the spermatozoa lose their acrosomes after contacting the zona pellucida, and the plasma membrane and nuclear envelope disappear after fusion with the oolemma. Subsequently, a sperm aster of microtubules forms around the proximal centriole, which is bound to the sperm connecting piece. This process is then followed by the formation of both pronuclei, which single sperm centriole later duplicates and the bipolar mitotic apparatus is observed. Following sperm injection, the spermatozoa have both an intact plasma membrane and acrosome. Although the microtubules form the sperm aster in a fashion identical to that seen during IVF, the presence of an intact acrosome appears to be associated with a heterogeneity in the decondensation of sperm chromatin. While this may indicate an abnormal pattern of chromatin decondensation during the formation of the male pronucleus following sperm injection, the male pronucleus eventually fully decondenses, as during IVF. Sperm mitochondria are displaced as the sperm centriole is exposed. Annulate lamellae and a previously undescribed organelle which seems to contain annulate lamellae precursors, as well as maternal mitochondria, are found in association with the developing pronuclear envelopes. This information increases understanding of fertilization in primates, and may also be of significance for use in assisted human reproduction as well as in the preservation of endangered mammalian species. In addition, these results demonstrates the similarities between fertilization in Rhesus monkeys and humans, providing additional evidence for the use of this non-human primate as a model system in which to investigate the cellular and molecular biological basis of human reproduction.
Abstract 3669: IDH mutant glial cell resistance to natural killer cell cytotoxicity (2014)

Abstract Mutations in IDH 1 and 2 are common in gliomas. Methylation-related epigenetic repression of gene expression is a feature of IDH mutant (IDHmut) tumors. Epigenetic repression of NK cell ligands is a common occurrence in cancer, but it is unknown if this occurs in gliomas. Here, we demonstrate transcriptional repression of NKG2D activating ligands (NKG2DLs) in IDHmut tumors, and correlate this with decreased susceptibility to natural killer (NK) cell-mediated cytolysis in vitro We compared IDHmut and IDHwt gene expression values for annotated immune response genes and examined NKG2DL HM450 mean methylation values in glioma patients using TCGA data. cDNA was synthesized from cultured IDHwt or IDHmut astrocytes. NKG2DL expression was assayed using primers for NKG2D ligands ULBP1, ULBP2, ULBP3 and RAET1G. IDHwt astrocytes, U87 cells and IDHmut astrocytes were cultured with activated NK cells. Cytotoxicity was measured by flow cytometry. mRNA expression values for NKG2DLs ULBP1 and ULBP3 were significantly reduced in IDHmut gliomas. Conversely, methylation values were significantly increased. NKG2DL hierarchical clustering of gene expression of shows genotype-based expression clusters. IDHmt astrocytes expressed a two to eight-fold reduction in the relative gene expression of NKG2DLs compared with IDHwt astrocyte. Cytotoxicity is significantly lower in IDHmut astrocytes/NK cell co-cultures compared with IDHmut/NK or U87/NK co-cultures. Our data demonstrates evidence for the transcriptional repression of NKG2DLs in IDHmut gliomas in silico and in vitro. Reduced NKG2D levels in IDHmut cells correlates with impaired NK-mediated cytotoxicity and suggests a role for NK cell resistance in IDH mutant tumors. Further studies are in progress to utilize HSV vectors that express ULBP3 to determine whether restoration of ULBP3 expression in cancer cells will enhance susceptibility to NK activation and tumor cell killing. Results of these experiments will be reported. Citation Format: Xiaoran Zhang, Yigang Chang, Aofei Li, Joseph C. Glorioso, Paola Grandi, Mike Lotze, Nduka Amankulor. IDH mutant glial cell resistance to natural killer cell cytotoxicity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3669. doi:10.1158/1538-7445.AM2014-3669
Anion-conducting fluoride and oxyfluoride glasses (2001)

Main mechanisms of the anion (fluoride ion) transport in fluoride and oxyfluoride glasses are analysed. The variation in the transport number of F– ions depending on the glass composition is followed. Methods for optimisation of the conductivity characteristics of the glasses in question are considered. The prospects of using fluoride-conducting glasses in electrochemical devices are discussed. The bibliography includes 90 references.
Immune responses to gut microbiota-commensals and pathogens (2010)

The mammalian alimentary tract harbors hundreds of species of commensal microorganisms that intimately interact with the host immune system. Within the gut, the immune system actively reacts with potentially pathogenic microbes, while simultaneously remaining ignorant towards the vast majority of non-pathogenic microbiota. The disruption of this delicate balance results in inflammatory bowel diseases. In this review, we describe the recent advances in our understanding of how host-microbiota interactions shape the immune system and how they affect the responses against pathogenic bacteria.
Effect of HSP70 induced by warm ischemia to the liver on liver function after partial hepatectomy. (2001)

HSP70 induced by ischemic preconditioning prior to the partial hepatectomy was considered to protect the liver itself. In addition, the induced HSP70 may affect the Bcl-xL level after partial hepatectomy. Therefore, Bcl-xL seems to be involved in the reduction of liver damage after partial hepatectomy along with HSP.
Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity (2012)

Lubricin (or proteoglycan 4 (PRG4)) is an abundant mucin-like glycoprotein in synovial fluid (SF) and a major component responsible for joint lubrication. In this study, it was shown that O-linked core 2 oligosaccharides (Galβ1-3(GlcNAcβ1-6)GalNAcα1-Thr/Ser) on lubricin isolated from rheumatoid arthritis SF contained both sulfate and fucose residues, and SF lubricin was capable of binding to recombinant L-selectin in a glycosylation-dependent manner. Using resting human polymorphonuclear granulocytes (PMN) from peripheral blood, confocal microscopy showed that lubricin coated circulating PMN and that it partly co-localized with L-selectin expressed by these cells. In agreement with this, activation-induced shedding of L-selectin also mediated decreased lubricin binding to PMN. It was also found that PMN recruited to inflamed synovial area and fluid in rheumatoid arthritis patients kept a coat of lubricin. These observations suggest that lubricin is able to bind to PMN via an L-selectin-dependent and -independent manner and may play a role in PMN-mediated inflammation.
An improved aminoglycoside resistance gene cassette for use in Gram-negative bacteria andStreptomyces (1991)

A cloning cassette, carrying a modified amino-glycoside resistance gene (neo) from transposon Tn5 was constructed. Three restriction sites internal to the neo gene were eliminated by in vitro mutagenesis, allowing their use in designing new cloning vectors. The original, suboptimal transcription promoter was replaced with a synthetic sequence corresponding to the consensus for E. coli and Streptomyces promoters. The cassette has numerous restriction sites for easy subcloning of the promoter, the coding sequence or the whole gene.
Crystallization of a fragment of human fibronectin: Introduction of methionine by site‐directed mutagenesis to allow phasing via selenomethionine (1994)

Crystals of a fragment of human fibronectin encompassing the 7th through the RGD-containing 10th type III repeats (FN7-10) have been produced with protein expressed in E. coli. The crystals are monoclinic with one molecule in the asymmetric unit and diffract to beyond 2.0 A Bragg spacings. A mutant FN7-10 was produced in which three methionines, in addition to the single native methionine already present, have been introduced by site-directed mutagenesis. Diffraction-quality crystals of this mutant protein have been grown in which methionine was replaced with selenomethionine. The introduction of methionine by site-directed mutagenesis to allow phasing from selenomethionyl-substituted crystals is shown to be feasible by this example and is proposed as a general approach to solving the crystallographic phase problem. Strategies for selecting propitious sites for methionine mutations are discussed.
Misfit dislocations in nanowire heterostructures (2010)

The development of strain relaxation in lattice-mismatched semiconductor nanowire heterostructures is reviewed. Theoretical predictions for critical geometries for axial and core–shell structures are summarized and compared to experimental reports. All agree that nanowires can accommodate a greater elastic strain than is commonly seen with planar interfaces. Large mismatch as high as 10% has been elastically accommodated consistent with theoretical predictions. Elastically strained nanowire examples predominate, likely since nucleation is otherwise inhibited. A (maximum) critical radius is observed for epitaxial growth directly onto lattice-mismatched substrates. The few examples where strain relaxation via dislocations or roughening has been observed have been reported for core–shell geometries.
630-mV open circuit voltage, 12% efficient n-Si liquid junction (1984)

We report the first experimental observation of a semiconductor/liquid junction whose open circuit voltage Voc is controlled by bulk diffusion/recombination processes. Variation in temperature, minority-carrier diffusion length, and/or in majority-carrier concentration produces changes in the Voc of the n-Si/CH3OH interface in accord with bulk recombination/diffusion theory. Under AM2 irradiation conditions, the extrapolated intercept at 0 K of Voc vs T plots yields activation energies for the dominant recombination process of 1.1–1.2 eV, in accord with the 1.12-eV band gap of Si. A crucial factor in achieving optimum performance of the n-Si/CH3OH interface is assigned to photoelectrochemical oxide formation, which passivates surface recombination sites at the n-Si/CH3OH interface and minimizes deleterious effects of pinning of the Fermi level at the Si/CH3OH junction. Controlled Si oxide growth, combined with optimization of bulk crystal parameters in accord with diffusion theory, is found to yield improved photoelectrode output parameters, with 12.0±1.5% AM2 efficiencies and AM1 Voc values of 632–640 mV for 0.2-Ω cm Si materials.