gebhart/patrepeval huggingface dataset:
THE CHEMICAL CYCLE AND BIOACCUMULATION OF MERCURY (1998)

▪ Abstract Because it is very toxic and accumulates in organisms, particularly in fish, mercury is an important pollutant and one of the most studied. Nonetheless we still have an incomplete understanding of the factors that control the bioconcentration of mercury. Elemental mercury is efficiently transported as a gas around the globe, and even remote areas show evidence of mercury pollution originating from industrial sources such as power plants. Besides elemental mercury, the major forms of mercury in water are ionic mercury (which is bound to chloride, sulfide, or organic acids) and organic mercury, particularly methylmercury. Methylmercury rather than inorganic mercury is bioconcentrated because it is better retained by organisms at various levels in the food chain. The key factor determining the concentration of mercury in the biota is the methylmercury concentration in water, which is controlled by the relative efficiency of the methylation and demethylation processes. Anoxic waters and sediments are an important source of methylmercury, apparently as the result of the methylating activity of sulfate-reducing bacteria. In surface waters, methylmercury may originate from anoxic layers or be formed through poorly known biological or chemical processes. Demethylation is effected both photochemically and biologically.
HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells (2011)

The availability of pluripotent stem cells offers the possibility of using such cells to model hepatic disease and development. With this in mind, we previously established a protocol that facilitates the differentiation of both human embryonic stem cells and induced pluripotent stem cells into cells that share many characteristics with hepatocytes. The use of highly defined culture conditions and the avoidance of feeder cells or embryoid bodies allowed synchronous and reproducible differentiation to occur. The differentiation towards a hepatocyte-like fate appeared to recapitulate many of the developmental stages normally associated with the formation of hepatocytes in vivo. In the current study, we addressed the feasibility of using human pluripotent stem cells to probe the molecular mechanisms underlying human hepatocyte differentiation. We demonstrate (1) that human embryonic stem cells express a number of mRNAs that characterize each stage in the differentiation process, (2) that gene expression can be efficiently depleted throughout the differentiation time course using shRNAs expressed from lentiviruses and (3) that the nuclear hormone receptor HNF4A is essential for specification of human hepatic progenitor cells by establishing the expression of the network of transcription factors that controls the onset of hepatocyte cell fate.
Small-Molecule CFTR Inhibitors Slow Cyst Growth in Polycystic Kidney Disease (2008)

Cyst expansion in polycystic kidney disease (PKD) involves progressive fluid accumulation, which is believed to require chloride transport by the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Herein is reported that small-molecule CFTR inhibitors of the thiazolidinone and glycine hydrazide classes slow cyst expansion in in vitro and in vivo models of PKD. More than 30 CFTR inhibitor analogs were screened in an MDCK cell model, and near-complete suppression of cyst growth was found by tetrazolo-CFTR(inh)-172, a tetrazolo-derived thiazolidinone, and Ph-GlyH-101, a phenyl-derived glycine hydrazide, without an effect on cell proliferation. These compounds also inhibited cyst number and growth by >80% in an embryonic kidney cyst model involving 4-d organ culture of embryonic day 13.5 mouse kidneys in 8-Br-cAMP-containing medium. Subcutaneous delivery of tetrazolo-CFTR(inh)-172 and Ph-GlyH-101 to neonatal, kidney-specific PKD1 knockout mice produced stable, therapeutic inhibitor concentrations of >3 microM in urine and kidney tissue. Treatment of mice for up to 7 d remarkably slowed kidney enlargement and cyst expansion and preserved renal function. These results implicate CFTR in renal cyst growth and suggest that CFTR inhibitors may hold therapeutic potential to reduce cyst growth in PKD.
Anti-cytokine and anti-inflammatory therapies for the treatment of severe sepsis: progress and pitfalls (2004)

The medical care of patients with sepsis or severe inflammatory response syndromes has seen tremendous technological advancements in recent years; yet, several clinical studies with anti-cytokine therapies targetted to this population have met with disappointing results. Four primary factors have been identified that represent potential pitfalls involving the use of biological response modifiers in critically-ill patients. First, the physiological response in the stressed patient is complex. Redundancy within this system may not allow a single intervention to produce a clinical response. Second, the critically-ill patient population is heterogenous and important factors including the age of the patient, associated co-morbidities, the nature of the original injury and the presence or absence of an ongoing injury can modulate the effectiveness of a specific therapy. Third, the timing of the therapeutic intervention can be difficult to standardize among patients and can often produce differing results. A greater understanding of the physiological response to injury has shown that there are both proinflammatory and anti-inflammatory processes ongoing simultaneously. Determining the optimal time to intervene within this framework can be problematic. Fourth, the presence of genetic polymorphisms within the general population has identified subsets of individuals who may have different physiological responses to similar stresses. The relative proportions of patients with these polymorphisms within clinical trials may affect outcome and data analysis. Thus, a better understanding of these issues will result in improvement of the experimental design of clinical trials involving anti-cytokine therapies and critically-ill patients. Avoidance of these pitfalls will enhance the quality and utility of outcomes research in this subset of patients.
CO-INERTIA ANALYSIS AND THE LINKING OF ECOLOGICAL DATA TABLES (2003)

Ecological studies often require studying the common structure of a pair of data tables. Co-inertia analysis is a multivariate method for coupling two tables. It is often neglected by ecologists who prefer the widely used methods of redundancy analysis and canonical correspondence analysis. We present the co-inertia criterion for measuring the adequacy between two data sets. Co-inertia analysis is based on this criterion as are canonical correspondence analysis or canonical correlation analysis, but the latter two have additional constraints. Co-inertia analysis is very flexible and allows many possibilities for coupling. Co-inertia analysis is suitable for quantitative and/or qualitative or fuzzy environmental variables. Moreover, various weighting of sites and various transformations and/or centering of species data are available for this method. Hence, more ecological considerations can be taken into account in the statistical procedures. Moreover, the principle of this method is very general and can be easily extended to the case of distance matrices or to the case of more than two tables. Simulated ecological data are used to compare the co-inertia approach with other available methods.
Conformationally Unbiased Macrocyclization Reactions by Ring Closing Metathesis (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTConformationally Unbiased Macrocyclization Reactions by Ring Closing MetathesisAlois Fürstner and Klaus LangemannView Author Information Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany Cite this: J. Org. Chem. 1996, 61, 12, 3942–3943Publication Date (Web):June 14, 1996Publication History Received23 April 1996Published online14 June 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo960733vhttps://doi.org/10.1021/jo960733vrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2381Altmetric-Citations252LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Carbene compounds,Lactones,Metathesis,Organic reactions,Post-translational modification Get e-Alerts
Magnetic Iron Oxide Nanoparticles for Biorecognition:  Evaluation of Surface Coverage and Activity (2006)

Modifying the surfaces of magnetic nanoparticles (MNPs) by the covalent attachment of biomolecules will enable their implementation as contrast agents for magnetic resonance imaging or as media for magnetically assisted bioseparations. In this paper we report both the surface coverage and the activity of IgG antibodies on MNPs. The antibodies were immobilized on γ-Fe2O3 nanoparticles by conventional methods using aminopropyltriethoxy silane and subsequent activation by glutaraldehyde. Novel fluorescence methods were used to provide a quantitative evaluation of this well-known approach. Our results show that surface coverage can be stoichiometrically adjusted with saturated surface coverage occurring at ∼36% of the theoretical limit. The saturated surface coverage corresponds to 34 antibody molecules bound to an average-sized MNP (32 nm diameter). We also show that the immobilized antibodies retain ∼50% of their binding capacity at surface-saturated levels.
FDA Approval Summary: Nivolumab for the Treatment of Metastatic Non-Small Cell Lung Cancer With Progression On or After Platinum-Based Chemotherapy (2016)

Based on the results from the CheckMate 057 clinical trial, nivolumab represents a new treatment option for patients requiring second-line treatment for metastatic non-small cell lung cancer. The role of nivolumab in patients with sensitizing epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) alterations is less clear. Until dedicated studies are performed to better characterize the role and sequence of programmed cell death 1 (PD-1) therapy, patients with EGFR or ALK alterations should have progressed on appropriate targeted therapy before initiating PD-1 inhibitor therapy. Some patients whose tumors lack programmed cell death ligand 1 (PD-L1) expression also appear to have durable responses. The U.S. Food and Drug Administration granted approval to Dako's PD-L1 test, PD-L1 IHC 28-8 pharmDx, which the applicant claimed as a nonessential complementary diagnostic for nivolumab use.
CD4+ type 1 and CD8+ type 2 T cell subsets in human leishmaniasis have distinct T cell receptor repertoires. (1993)

The mechanism of protective immunity and immunologic resistance against intracellular pathogens is believed to involve the activation of Ag-specific T cells. The T cells involved in protection/resistance to Leishmania can be studied using localized American cutaneous leishmaniasis (LCL) as a model, because the disease is often self-healing. Our study was undertaken to identify specific T cell populations that had accumulated in LCL lesions on the basis of TCR V beta gene usage. RNA was derived from skin lesions and blood of eight LCL patients, as well as from purified CD4+ and CD8+ subsets from the lesions and blood of three patients. After synthesis of cDNA, V beta gene usage was assessed by polymerase chain reaction. In all eight patients, several V beta gene families were overrepresented in lesions compared to blood. More importantly, the TCR V beta repertoires of both lesional CD4+ and CD8+ subsets were skewed compared to the repertoire of the respective subsets in the blood of the same donor. The overrepresented V beta s in the CD4+ and CD8+ subsets from lesions were in most instances disparate, particularly with the V beta 6 TCR skewed in the lesional CD8+ subset. Not only were the TCR repertoires of the overrepresented V beta in the lesional CD4+ and CD8+ subsets generally distinct, but the cytokine mRNA expressed by these subsets were also discrete. Strikingly, the CD4+ subset was characterized by IFN-gamma mRNA expression and the CD8+ subset by IL-4 and IL-10 mRNA expression. These data indicate that the pathogenesis of human leishmaniasis may be explained by the balance of CD4+ type 1 and CD8+ type 2 T cells, which probably recognize distinct sets of Ag.
1,25-Dihydroxyvitamin D3 reversibly blocks the progression of relapsing encephalomyelitis, a model of multiple sclerosis. (1996)

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune disease believed to be a model for the human disease multiple sclerosis (MS). Induced by immunizing B10.PL mice with myelin basic protein (MBP), EAE was completely prevented by the administration of 1,25-dihydroxyvitamin D3 [1,25-(OH)2D3]. 1,25-(OH)2D3 could also prevent the progression of EAE when administered at the appearance of the first disability symptoms. Withdrawal of 1,25-(OH)2D3 resulted in a resumption of the progression of EAE. Thus, the block by 1,25-(OH)2D3 is reversible. A deficiency of vitamin D resulted in an increased susceptibility to EAE. Thus, 1,25-(OH)2D3 or its analogs are potentially important for treatment of MS.
In Vitro and In Vivo Activities of Anti-Influenza Virus Compound T-705 (2002)

T-705 (6-fluoro-3-hydroxy-2-pyrazinecarboxamide) has been found to have potent and selective inhibitory activity against influenza virus. In an in vitro plaque reduction assay, T-705 showed potent inhibitory activity against influenza A, B, and C viruses, with 50% inhibitory concentrations (IC(50)s) of 0.013 to 0.48 microg/ml, while it showed no cytotoxicity at concentrations up to 1,000 microg/ml in Madin-Darby canine kidney cells. The selectivity index for influenza virus was more than 2,000. It was also active against a neuraminidase inhibitor-resistant virus and some amantadine-resistant viruses. T-705 showed weak activity against non-influenza virus RNA viruses, with the IC(50)s being higher for non-influenza virus RNA viruses than for influenza virus, and it had no activity against DNA viruses. Orally administered T-705 at 100 mg/kg of body weight/day (four times a day) for 5 days significantly reduced the mean pulmonary virus yields and the rate of mortality in mice infected with influenza virus A/PR/8/34 (3 x 10(2) PFU). These results suggest that T-705 may be a compound that is useful and highly selective against influenza virus infections and that has a mode of action different from those of commercially available drugs, such as amantadine, rimantadine, and neuraminidase inhibitors.
Epidermal Growth Factor Receptor Mutations, Small-Molecule Kinase Inhibitors, and Non–Small-Cell Lung Cancer: Current Knowledge and Future Directions (2005)

This information can guide practitioners and help them inform their patients about EGFR mutations and their impact on the treatment of NSCLC.
Anti‐gastrin antibodies raised by gastrimmune inhibit growth of the human colorectal tumour AP5 (1995)

The neutralising ability of rabbit anti-gastrin-17 (G17) antiserum raised by Gastrimmune, an immunogen constructed of the N-terminal portion of human G17 conjugated to diptheria toxoid (DT), was evaluated. The anti-serum (denoted anti-G17: DT) was shown to displace 125[I] G17 from the gastrin receptors on AR42J cells. The therapeutic effect of the rabbit anti-G17:DT anti-serum was evaluated on a freshly derived human colorectal cancer cell line, AP5, which was shown to express both gastrin receptors and gastrin immunoreactivity as assessed by immunocytochemistry. Rabbit anti-G17:DT anti-serum was shown to block basal in vitro growth of AP5 cells when used at an antigen binding capacity of 3.75 x 10(-9) M. The same dilution of anti-serum completely reversed growth stimulated by human G17 at concentrations of 1 x 10(-10) and 1 x 10(-9) M but did not inhibit growth at 1 x 10(-8) M G17. When AP5 was grown as a xenograft in nude mice, the sensitivity to the proliferative effect of human G17 was maintained. In addition, the basal growth of AP5 xenografts was significantly reduced by i.v. infusion of rabbit anti-G17:DT anti-serum when compared to treatment with rabbit anti:DT control anti-serum. Thus anti-G17:DT antibodies raised by Gastrimmune may be of clinical value in gastrin-sensitive tumours.
Synchrophasors: A primer and practical applications (2007)

Although the concept and definition of Synchrophasors dates back to 1980, the combination of 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> generation IED platforms and power system needs has brought the technology into high-visibility in the electric power industry. As synchrophasor technology has matured, nuances of the measurement of a synchronized phasor have been identified and the details of ldquohowrdquo a phasor is defined, synchronized to absolute time, reported, and communicated have subsequently been re-codified int he recently revised IEEE standard: Synchrophasors for Power Systems - C37.118. This paper reviews the concept of the synchronized phasor in light of the IEEE C37.118 standard. Specifically, details of an ldquoun-correctedrdquo Fourier based phasor during off-nominal frequency conditions are presented as well as techniques for correction to meet the Synchrophasor standard. The need for IED input transformer and filter characterization / correction is presented. Simulations of various system transients and their phasor response are presented - specifically, the response of synchrophasor calculation to dynamic system conditions. Finally, this paper reviews application of synchrophasors on the SRP system today as well as plans and needs in the future.
Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus (2013)

Person-to-person transmission of MERS-CoV can occur in health care settings and may be associated with considerable morbidity. Surveillance and infection-control measures are critical to a global public health response.
Mammalian neuronal differentiation: early expression of a neuronal phenotype from mouse neural crest cells in a chemically defined culture medium (1989)

We show that mouse neural crest cells cultured in a serum-deprived chemically defined medium on appropriate culture substrata can be induced to express a neuronal phenotype. The uncommitted neural crest cells express a mesenchymal intermediate filament protein such as vimentin, but not the usual neuronal markers such as receptor sites for tetanus toxin or neurofilaments. In the chemically defined medium, receptor sites for tetanus toxin or neurofilaments can be characterized after a few hours in culture. Furthermore, these cells acquire tetrodotoxin-sensitive voltage-dependent Na+ channels and can generate action potentials. Such an in vitro system should allow us to analyze and manipulate early stages of neuronal differentiation in a mammalian embryo, at a level so far restricted to lower vertebrate embryos.
Clinical Significance of Serum Mesothelin in Patients with Mesothelioma and Lung Cancer (2007)

Our data confirm that serum SMRP is a promising marker for the diagnosis, prognosis, and clinical monitoring of MM. We found that serum SMRP dosage may prove helpful in LC diagnosis as well. These data may also have positive repercussions on secondary preventive medical strategies for workers previously exposed to asbestos.
Predicting speech recognition confidence using deep learning with word identity and score features (2013)

Confidence classifiers for automatic speech recognition (ASR) provide a quantitative representation for the reliability of ASR decoding. In this paper, we improve the ASR confidence measure performance for an utterance using two distinct approaches: (1) to define and incorporate additional predictors in the confidence classifier including those based on the word identity and on the aggregated words, and (2) to train the confidence classifier built on deep learning architectures including the deep neural network (DNN) and the kernel deep convex network (K-DCN). Our experiments show that adding the new predictors to our multi-layer perceptron (MLP)-based baseline classifier provides 38.6% relative reduction in the correct-reject rate as our measure of the classifier performance. Further, replacing the MLP with the DNN and K-DCN provides an additional 14.5% and 47.5% in the relative performance gain, respectively.
O-glycosylation pattern of CD24 from mouse brain (2009)

The cell adhesion molecule CD24 is a highly glycosylated glycoprotein that plays important roles in the central nervous system, the immune system and in tumor biology. Since CD24 comprises only a short protein core of approximately 30 amino acids and low conservation among species, it has been proposed that the functions of CD24 are mediated by its glycosylation pattern. Our present study provides evidence that interaction of CD24 with the cell adhesion molecule L1 is mediated by O-linked glycans carrying alpha2,3-linked sialic acid. Furthermore, de-N-glycosylated CD24 was shown to promote or inhibit neurite outgrowth of cerebellar neurons or dorsal root ganglion neurons, respectively, to the same extent as untreated CD24. Therefore, this study is focused on the structural elucidation of the chemically released, permethylated CD24 O-glycans by electrospray ionization ion trap mass spectrometry. Our analyses revealed the occurrence of a diverse mixture of mucin-type and O-mannosyl glycans carrying, in part, functionally relevant epitopes, such as 3-linked sialic acid, disialyl motifs, Le(X), sialyl-Le(X) or HNK-1 units. Hence, our data provide the basis for further studies on the contribution of carbohydrate determinants to CD24-mediated biological activities.
High-Density Microarray-Mediated Gene Expression Profiling of Escherichia coli (2001)

A nearly complete collection of 4,290 Escherichia coli open reading frames was amplified and arrayed in high density on glass slides. To exploit this reagent, conditions for RNA isolation from E. coli cells, cDNA production with attendant fluorescent dye incorporation, DNA-DNA hybridization, and hybrid quantitation have been established. A brief isopropyl-beta-D-thiogalactopyranoside (IPTG) treatment elevated lacZ, lacY, and lacA transcript content about 30-fold; in contrast, most other transcript titers remained unchanged. Distinct RNA expression patterns between E. coli cultures in the exponential and transitional phases of growth were catalogued, as were differences associated with culturing in minimal and rich media. The relative abundance of each transcript was estimated by using hybridization of a genomic DNA-derived, fluorescently labeled probe as a correction factor. This inventory provided a quantitative view of the steady-state level of each mRNA species. Genes the expression of which was detected by this method were enumerated, and results were compared with the current understanding of E. coli physiology.
The Dual Function of Sugar Carriers: Transport and Sugar Sensing (1999)

Sucrose and its derivatives represent the major transport forms of photosynthetically assimilated carbon in plants. Sucrose synthesized in green leaves is exported via the phloem, the long-distance distribution network for assimilates, to supply nonphotosynthetic organs with energy and carbon