jimnoneill/paper-to-field-training huggingface dataset:
Glycomic and Transcriptomic Response of GSC11 Glioblastoma Stem Cells to STAT3 Phosphorylation Inhibition and Serum-Induced Differentiation

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

A glioblastoma stem cell (GSC) line, GSC11, grows as neurospheres in serum-free media supplemented with EGF (epidermal growth factor) and bFGF (basic fibroblast growth factor), and, if implanted in nude mice brains, will recapitulate high-grade glial tumors. Treatment with a STAT3 (signal transducer and activator of transcription 3) phosphorylation inhibitor (WP1193) or 10% FBS (fetal bovine serum) both led to a decrease in expression of the stem cell marker CD133 in GSC11 cells, but differed in phenotype changes. Altered glycolipid profiles were associated with some differentially expressed glycogenes. In serum treated cells, an overall increase in glycosphingolipids may be due to increased expression of ST6GALNAC2, a sialyltransferase. Serum treated cells express more phosphatidylcholine (PC), short chain sphingomyelin (SM) and unsaturated long chain phosphatidylinositol (PI). Decrease of a few glycosphingolipids in the STAT3 phosphorylation inhibited cells may be linked to decreased transcripts of ST6GALNAC2 and UGCGL2, a glucosylceramide synthase. A rare 3-sulfoglucuronylparagloboside carrying HNK1 (human natural killer-1) epitope was found expressed in the GSC11 and the phenotypically differentiated cells. Its up-regulation correlates with increased transcripts of a HNK1 biosynthesis gene, B3GAT2 after serum treatment. Taken together with a quantitative phosphoproteomic study of the same GSC line (C. L. Nilsson, et al. J. Proteome Res. 2010, 9, 430-443), this report represents the most complete systems biology study of cancer stem cell (CSC) differentiation to date. The synergies derived by the combination of glycomic, transcriptomic and phosphoproteomic data may aid our understanding of intracellular and cell-surface events associated with CSC differentiation.
Effects of vitamin D and paricalcitol on murine cardiomyocytes

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Severe alterations of Cacium-Phospate metabolism are frequently associated with chronic kidney diseases. High levels of Phospate and low levels of vitamin D in subjects affected by chronic kidney disease are, in many cases, correlated with high risk of mortality. For this reason, administration of vitamin D represents the elective treatment. Nevertheless, vitamin D in itself induces a variety of side effects which in many cases can be avoided by the administration of vitamin D analogues. In this study we treated murine cardiomyocytes with different concentrations of vitamin D and paricalcitol (one of its analogues) for 48 hours. Cell morphology, cell proliferation, intracellular Calcium deposition, and cAMP level were investigated respectively by light microscopy, immunoenzymatic assay and Von Kossa staining. Results show that, in comparison to paricalcitol, vitamin D induces stronger side effects on cardiomyocytes (such as cell proliferation, morphological changes, activation of signal transduction pathways). From our data emerges that paricalcitol induces less stressful effects on murine cardiomyocytes in comparison to what observed with vitamin D treatment.
Proton Availability at the Air/Water Interface

Field: Chemistry (Physical Sciences)

The acidity of the water surface sensed by a colliding gas is determined in experiments in which the protonation of gaseous trimethylamine (TMA) on aqueous microjets is monitored by online electrospray mass spectrometry as a function of the pH of the bulk liquid (pH_(BLK)). TMAH^+ signal intensities describe a titration curve whose equivalence point at pH_(BLK) 3.8 is dramatically smaller than the acidity constant of trimethylammonium in bulk solution, pK_A(TMAH^+) = 9.8. Notably, the degree of TMA protonation above pH_(BLK) 4 is enhanced hundred-fold by submillimolar LiCl or NaCl and weakly inhibited at larger concentrations. Protonation enhancements are associated with the onset of significant direct kinetic solvent hydrogen isotope effects. Since TMA(g) can be protonated by H_2O itself only upon extensive solvent participation, we infer that H3O^+ emerges at the surface of neat water below pH_(BLK) 4.
The Modernity of Ecological Environment in Japanese Literature

Field: Arts and Humanities (Social Sciences)

The traditional study of modernity pays more attention to the time and historical dimension, but ignores the spatial dimension. The relationship between space and literature is that space is not only the premise and premise of literary creation, but also the object of literary creation. From the connotation of modernity, it includes secularization, rationality and rationalization, subjectivity, industrialism, capitalism and market economy. Karatani Kojin established the spatial view of the “origin” of modern literature, and pointed out its invisible end, reminding us that when the structure of spatial perception changes, it is also the “internal power” of literature that appears. From the perspective of environmental adjustment affecting the modernity of literary ecological environment, this study studies the literary creation itself, rationalization and refinement, as well as the interaction effect between rationalization and refinement. The results show that there is a U-shaped dynamic relationship between rationalization and refinement in the Japanese literature ecosystem.
Systems genetics approaches for understanding complex traits with relevance for human disease

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
What If There Are Only 30,000 Human Genes?

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The complete assembly of the entire human genome sequence by
Venter
et al.
confirms recent estimates that the total number of human protein coding genes might be less than 30,000--a mere one-third increase over the nematode
Caenorhabditis elegans. Such a low gene number constitutes a paradigm change, which could drastically modify our understanding of organism complexity and evolution, as well as our current interpretation of transcriptome analyses. It may also have severe consequences on the long-term sustainability of the biomedical industry in the postgenomic era.
Beyond FITT - How Density Can Improve the Understanding of the Dose-Response Relationship Between Physical Activity and Brain Health

Field: Medicine (Health Sciences)

Research on physical activity and health, including planned and structured forms such as acute and chronic physical exercise, has focused on understanding potential dose-response relationships. Traditionally, the variables of (i) Frequency, (ii) Intensity, (iii) Time, (iv) and Type (known as the FITT principle) have been used to operationalize the dose of physical activity. In this article, we describe the limitations of FITT and propose that it should be complemented by the underappreciated variable density, which defines the temporal distribution of physical activity stimuli within a single bout of physical activity or between successive bouts of physical activity relative to time spent resting (e.g., in napping/sleeping or sedentary behaviors). Using the field of physical activity and brain health as an example, we discuss challenges and opportunities for further research to use density to improve our understanding of dose-response relationships between physical activity and health-related outcomes.
New development: Philanthropy in networked governance—treading with care

Field: Social Sciences (Social Sciences)

While philanthropy is widely seen as a way of filling the void left by cuts in public services, reflective debates on philanthropy, its roles and challenges, are rare. The authors outline key facets of philanthropy, as expressed through philanthropic foundations and trusts, that require further exploration within networked governance debates: our limited understanding of philanthropy and of philanthropic foundations; the increasingly neoliberal discourse of and on philanthropy; and the extent of philanthropy's potential and achievements.
Data Analysis Approaches for the Risk-Informed Safety Margins Characterization Toolkit

Field: Decision Sciences (Social Sciences)

In the past decades, several numerical simulation codes have been employed to simulate accident dynamics (e.g., RELAP5-3D, RELAP-7, MELCOR, MAAP). In order to evaluate the impact of uncertainties into accident dynamics, several stochastic methodologies have been coupled with these codes. These stochastic methods range from classical Monte-Carlo and Latin Hypercube sampling to stochastic polynomial methods. Similar approaches have been introduced into the risk and safety community where stochastic methods (such as RAVEN, ADAPT, MCDET, ADS) have been coupled with safety analysis codes in order to evaluate the safety impact of timing and sequencing of events. These approaches are usually called Dynamic PRA or simulation-based PRA methods. These uncertainties and safety methods usually generate a large number of simulation runs (database storage may be on the order of gigabytes or higher). The scope of this paper is to present a broad overview of methods and algorithms that can be used to analyze and extract information from large data sets containing time dependent data. In this context, “extracting information” means constructing input-output correlations, finding commonalities, and identifying outliers. Some of the algorithms presented here have been developed or are under development within the RAVEN statistical framework.
A Novel Anionic Modification of N-Glycans on Mammalian Endothelial Cells Is Recognized by Activated Neutrophils and Modulates Acute Inflammatory Responses

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract We previously reported an unusual carboxylated modification on N-glycans isolated from whole bovine lung. We have now raised IgG mAbs against the modification by immunization with biotinylated aminopyridine-derivatized glycans enriched for the anionic species and screening for Abs whose reactivities were abrogated by carboxylate neutralization of bovine lung glycopeptides. One such Ab (mAb GB3.1) was inhibited by carboxylated bovine lung glycopeptides and other multicarboxylated molecules, but not by glycopeptides in which the carboxylate groups were modified. The Ab recognized an epitope constitutively expressed on bovine, human, and other mammalian endothelial cells. Stimulated, but not resting, neutrophils bound to immobilized bovine lung glycopeptides in a carboxylate-dependent manner. The binding of activated neutrophils to immobilized bovine lung glycopeptides was inhibited both by mAb GB3.1 and by soluble glycopeptides in a carboxylate-dependent manner. The Ab also inhibited extravasation of neutrophils and monocytes in a murine model of peritoneal inflammation. This inhibition of cell trafficking correlated with the increased sequestration but reduced transmigration of leukocytes that were found to be adherent to the endothelium of the mesenteric microvasculature. Taken together, these results indicate that these novel carboxylated N-glycans are constitutively expressed on vascular endothelium and participate in acute inflammatory responses by interaction with activated neutrophils.
Capital Adequacy in Insurance and Reinsurance

Field: Economics, Econometrics and Finance (Social Sciences)

Abstract This chapter considers capital adequacy and capital regulation of insurers and reinsurers. A basic theme is that capital standards should be less stringent for financial sectors characterized by greater market discipline and less systemic risk. Because market discipline is greater and systemic risk is lower for insurance than in banking, capital requirements should be less stringent for insurers than for banks. Similarly, because market discipline is generally greater in reinsurance (wholesale) markets than in direct insurance (retail) markets, capital requirements and related regulation plausibly need not be as stringent for reinsurers as for direct insurers. Current capital requirements and related solvency regulation for US and EU insurers and reinsurers are largely consistent with significant market discipline in the insurance and reinsurance sectors. Any federal regulation of US insurers/reinsurers, harmonized regulation of EU reinsurers, consolidated oversight of financial conglomerates, and increased centralization of regulatory authority to supervise insurance and other financial activities should be designed with full recognition of the limited systemic risk and strong market discipline in insurance/reinsurance and avoid undermining that discipline.
DEGRADATION OF AQUEOUS SOLUTIONS OF ALKANOLAMINE BLENDS AT HIGH TEMPERATURE, UNDER THE PRESENCE OF CO2AND H2S

Field: Chemical Engineering (Physical Sciences)

ABSTRACT ABSTRACT An experimental study on the degradation of aqueous solutions of alkanolamine blends, under the presence of carbon dioxide and hydrogen sulfide, was carried out. The studied alkanolamines were: diethanolamine (DEA), methyldiethanolamine (MDEA), and 2-amino-2-methyl-1-propanol (AMP). Degradation experiments were carried out at a temperature of 200°C. The mass fraction of DEA and MDEA in the studied aqueous solutions was 10% and 35%, respectively. AMP was incorporated into the MDEA-DEA aqueous solutions, with concentrations of (0–8) mass fraction. Partially degraded alkanolamine aqueous solutions were analyzed, after about 90 hours, by gas chromatography. It was found that in all the studied alkanolamine aqueous solutions the MDEA degrades more slowly than DEA under the same experimental conditions. Degradation of both alkanolamines was found to be almost independent of the AMP concentration. AMP exhibits an intermediate stability; it is more resistant to degradation than DEA but less than MDEA. In addition, thermal degradation of DEA and MDEA is minimal up to 200°C. Keywords: DiethanolamineMethyldiethanolamine2-Amino-2-methyl-1-propanolCarbon dioxideHydrogen sulfideAlkanolamine degradation Acknowledgments This work was supported by Instituto Mexicano del Petróleo under Research Projects D.00158, D.00127, and I.00102. We thank María Esther Rebolledo-Libreros for helping in the loading of the acid gases into the reactor during the experimental studies. We also thank Raúl Bocanegra Sánchez and Apolinar Jiménez Moreno for their constant help throughout the development of this research.
Carvedilol inhibits the cardiostimulant and thermogenic effects of MDMA in humans

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

We read with interest the study by Hysek and colleagues that investigated the cardiostimulant and thermogenic effects of carvedilol on 3,4-methylenedioxymethamphetamine (MDMA) (Hysek et al., 2012). Although we applaud the authors for performing a randomized placebo-controlled trial in humans, we have a concern about their study design. The study uses a relatively low dose of MDMA compared with those used by patients arriving to most hospitals. The average MDMA user often consumes greater doses than those used in this study, ranging up to 280 mg, whereas the study participants received a single oral dose of 125 mg (Morefield et al., 2011). Typical patients exhibit greater cardiostimulatory and thermogenic effects than the small changes noted in the study group. Additionally, it is unclear whether carvedilol would have an effect on severe hyperthermia as the temperature change reported in the placebo-MDMA group was no more than 0.5°C above baseline. This study's applicability would have been strengthened by demonstrating a more significant effect of MDMA prior to use of carvedilol. Because ethical considerations most likely prevent the ability of changing these parameters to reflect real-life patient presentations, the true utility of a clinically adequate dose of carvedilol given after a patient presents with significant MDMA toxicity remains unknown.
Contract model for agent mediated electronic commerce

Field: Computer Science (Physical Sciences)

In Agent Mediated Electronic Commerce, autonomy of agents is an important property. On one hand, it has to be favored to make the agents able to determine and adapt their own goals to the dynamic and open environment in which they are situated. On the other hand, it has to be con-trolled and limited to get a coherent and fruitful behavior in the system. In this paper we present a model of contract aiming at managing the cooperation between agents and at imposing a social order in the system: agents involved in a contract have to respect constraints related to others agents or to the society. This paper combines these notions with those of electronic contract in order to integrate agents within an eCommerce platform. 1.
Impact of feed ingredients and dietary protein level on microbial activity in the digestive tract of broilers

Field: Agricultural and Biological Sciences (Life Sciences)

Chicken diets have been supplemented with growth-promoting antibiotics for years. There are, however, increasing concerns regarding the use of those substances. Microbial activity and composition of microflora in the gastro-intestinal tract, intestinal health and mucosal function in broilers might be influenced by the choice of ingredients as well as by nutrient levels. Two experiments with male d old Ross 308 broilers following a 2 x 2 x 2 design were conducted using the experimental factors dietary protein level (19% or 25% in the starter diets and 18% or 24% in the grower diets), fish meal inclusion, and carbohydrate source (corn, wheat). Exp 1 was conducted to investigate the effects on performance and microbial activity in the digestive tract; Exp 2 was performed to examine the dietary effects under conditions of a combined challenge with E. acervulina and C. perfringens. In Exp 1, 1024 chicks were assigned to 64 floor pens resulting in 8 replicates per treatment with 16 birds per pen. At d 28 four birds per pen were selected to obtain digesta from the terminal ileum and the caeca. The remaining birds were fed until d 35. In Exp 2, 1408 chicks were distributed to 64 floor pens. Each treatment comprised 8 replicates with 22 birds per pen until d 35. Birds receiving the wheat based diets showed a higher feed intake than those fed corn based diets. Inclusion of fishmeal resulted in an improved performance at a high dietary protein level but not at low dietary protein. Both high dietary protein and fish meal addition resulted in an increased digesta ammonia content indicating a higher microbial breakdown of protein. Choice of cereals had no consistent effect on ammonia concentrations. Data suggest that microbial activity in the digestive tract can be manipulated by dietary means. Treatments did not affect the response towards a combined challenge with E. acervulina and C. perfringens. Other factors, such as hygiene or stress might have a much larger impact on the development of these diseases.
(Invited) Flexible Triboelectric Nanogenerator and Highly Sensitive Pressure Sensor

Field: Materials Science (Physical Sciences)

Transparent electronic devices built on flexible substrates are expected to meet emerging technological demands for the next generation of flexible electronic and optoelectronic devices. A suitable energy source is a vital part for realizing fully self-powered systems. Energy harvesting and conversion technology from environment in which the system will be deployed is a promising route. Recently, we have introduced a new concept on the basis of triboelectrification and electrostatic induction for successfully converting mechanical energy into electric energy at an energy conversion efficiency as high as 50%. Subsequently, transparent triboelectric nanogenerators (TENGs) using indium tin oxide (ITO) or graphene as electrodes have been demonstrated, which are the only possible power source that light can penetrate through. However, there is a need for a low-cost and large area compatible technology for producing transparent TENGs with high-output power supply, aiming for applications such as touch screens. In our previous work, we fabricated a transparent TENG and pressure sensor by using polyester (PET) and polydimethylsiloxane (PDMS) films as flexible substrates to integrate ITO electrodes. It has also been demonstrated that the patterned surface is an effective method to improve the output performance of the TENG. However, realizing such a structure is not trivial in mass production and the patterned structure will reduce the transparency of the device due to the light scattering effect. Here, we present a simple, cost-effective and large-scalable method for fabrication of highly transparent TENGs. Although triboelectric effect has been known for thousands years, the underlying mechanism is actually very complex and still under debating. The competing possible mechanisms appear to include electron transfer, ion transfer, bond dissociation, chemical changes, and material transfer, and it is likely that different mechanisms may be involved depending on the specific materials and environmental conditions. Usually, it needs specialized equipment to characterize the charged surface and study the mechanism. It is worth noting that the output performance of TENG can directly reflect the capacity of the triboelectrification. Herein, we use this feature to investigate the mechanism of the triboelectrification by examining various factors on the performance of TENG. Furthermore, another meaningful outcome of our study is that we explore the mechanism from the microscopic and molecular perspective using the methods for surface characterization, which would be beneficial to the improvementand application of TENG at a large scale. References F. R. Fan, Z. Q. Tian, Z. L. Wang, Nano Energy 2012, 1, 328-334. F. R. Fan, L. Lin, G. Zhu, W. Z. Wu, R. Zhang, Z. L. Wang, Nano Lett. 2012, 12, 3109-3114. F. R. Fan, J. J. Luo, W. Tang, C. Y. Li, C. P. Zhang, Z. Q. Tian, Z. L. Wang, J. Mater. Chem. A 2014, 2, 13219-13225.
Resistance of Cu(Aβ4–16) to Copper Capture by Metallothionein‐3 Supports a Function for the Aβ4–42 Peptide as a Synaptic CuII Scavenger

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract Aβ4‐42 is a major species of Aβ peptide in the brains of both healthy individuals and those affected by Alzheimer's disease. It has recently been demonstrated to bind Cu II with an affinity approximately 3000 times higher than the commonly studied Aβ1‐42 and Aβ1‐40 peptides, which are implicated in the pathogenesis of Alzheimer's disease. Metallothionein‐3, a protein considered to orchestrate copper and zinc metabolism in the brain and provide antioxidant protection, was shown to extract Cu II from Aβ1‐40 when acting in its native Zn 7 MT‐3 form. This reaction is assumed to underlie the neuroprotective effect of Zn 7 MT‐3 against Aβ toxicity. In this work, we used the truncated model peptides Aβ1‐16 and Aβ4‐16 to demonstrate that the high‐affinity Cu II complex of Aβ4‐16 is resistant to Zn 7 MT‐3 reactivity. This indicates that the analogous complex of the full‐length peptide Cu(Aβ4‐42) will not yield copper to MT‐3 in the brain, thus supporting the concept of a physiological role for Aβ4‐42 as a Cu II scavenger in the synaptic cleft.