Miracle-dz/UniFAR-FTUs huggingface dataset:
An algal photoenzyme converts fatty acids to hydrocarbons

Algal enzyme driven by blue light Microalgae make hydrocarbons. In searching for the enzyme responsible, Sorigué et al. found a glucose-methanolcholine oxidoreductase (see the Perspective by Scrutton). Expression of the enzyme in Escherichia coli showed that hydrocarbon production requires visible light. In fact, the enzyme requires a constant input of blue photons to carry out its catalytic reaction. A long hydrophobic tunnel in the enzyme stabilizes the fatty acid substrates in proximity to the flavin adenine dinucleotide cofactor. Science, this issue p. 903; see also p. 872 An algal flavoprotein uses blue light to catalyze decarboxylation of fatty acids to fuel-like molecules. Although many organisms capture or respond to sunlight, few enzymes are known to be driven by light. Among these are DNA photolyases and the photosynthetic reaction centers. Here, we show that the microalga Chlorella variabilis NC64A harbors a photoenzyme that acts in lipid metabolism. This enzyme belongs to an algae-specific clade of the glucose-methanol-choline oxidoreductase family and catalyzes the decarboxylation of free fatty acids to n-alkanes or -alkenes in response to blue light. Crystal structure of the protein reveals a fatty acid–binding site in a hydrophobic tunnel leading to the light-capturing flavin adenine dinucleotide (FAD) cofactor. The decarboxylation is initiated through electron abstraction from the fatty acid by the photoexcited FAD with a quantum yield >80%. This photoenzyme, which we name fatty acid photodecarboxylase, may be useful in light-driven, bio-based production of hydrocarbons.
Metamodelling for agent-based modelling: an application for posted pricing institutions

support from the project “Agent-based Modelling and Simulation of Complex Social Systems (SiCoSSys)”, supported by the Spanish Council for Science and Innovation, with grants TIN2008-06464- C03-01 and TIN2008-06464-C03-02, the Junta de Castilla y Leon with grant GREX251/2009 and Caja Burgos with grant 2009/00148/001.
Corpus-based Disambiguation for Machine Translation

This paper deals with problem of choosing a proper translation for polysemous words. We describe an original method for partial word sense disambiguation of such words using word sketches extracted from large-scale corpora and using simple English-Czech dictionary. Each word is translated from English to Czech and a word sketch for the word is compared with all word sketches of its appropriate Czech equivalents. These comparisons serve for choosing a proper translation of the word: given a context containing one of collocates from the English word sketch, result data can serve directly in the process of machine translation of the English word and at the same time it can be considered as a partial disambiguation of that word. Moreover, the results may be used for clustering word sketches according to distinct meanings of their headwords.
Managing real‐time risks and returns: The Thomson Reuters NewsScope Event Indices

As financial markets grow in size and complexity, risk management protocols must also evolve to address more challenging demands. One of the most difficult of these challenges is managing event risk, the risk posed by unanticipated news that causes major market moves over short time intervals. Often cited but rarely managed, event risk has been relegated to the domain of qualitative judgment and discretion because of its heterogeneity and velocity. In this chapter, we describe one initiative aimed at solving this problem. The Thomson Reuters NewsScope Event Indices Project is an integrated framework for incorporating real-time news from the Thomson Reuters NewsScope subscription service into systematic investment and risk management protocols. The framework consists of a set of real-time event indices—each one taking on numerical values between 0 and 100—designed to capture the occurrence of unusual events of a particular kind. Each index is constructed by applying disciplined pattern recognition algorithms to real-time news feeds, and validated using econometric methods applied to historical data. 3.
Systemic and vascular inflammation in an in-vitro model of central obesity

Metabolic disorders due to over-nutrition are a major global health problem, often associated with obesity and related morbidities. Obesity is peculiar to humans, as it is associated with lifestyle and diet, and so difficult to reproduce in animal models. Here we describe a model of human central adiposity based on a 3-tissue system consisting of a series of interconnected fluidic modules. Given the causal link between obesity and systemic inflammation, we focused primarily on pro-inflammatory markers, examining the similarities and differences between the 3-tissue model and evidence from human studies in the literature. When challenged with high levels of adiposity, the in-vitro system manifests cardiovascular stress through expression of E-selectin and von Willebrand factor as well as systemic inflammation (expressing IL-6 and MCP-1) as observed in humans. Interestingly, most of the responses are dependent on the synergic interaction between adiposity and the presence of multiple tissue types. The set-up has the potential to reduce animal experiments in obesity research and may help unravel specific cellular mechanisms which underlie tissue response to nutritional overload.
Oligopeptide Targeting Sortase A as Potential Anti-infective Therapy for Staphylococcus aureus

Sortase A (SrtA)-catalyzed anchorage of surface proteins in most Gram-positive bacteria is indispensable for their virulence, suggesting that this transpeptidase is a promising target for antivirulence therapy. Here, an oligopeptide, LPRDA, was identified as an effective inhibitor of SrtA via virtual screening based on the LPXTG substrate sequence, and it was found to inhibit SrtA activity in vitro and in vivo (IC50 = 10.61 μM) by competitively occupying the active site of SrtA. Further, the oligopeptide treatment had no anti-Staphylococcus aureus activity, but it provided protection against S. aureus-induced mastitis in a mouse model. These findings indicate that the oligopeptide could be used as an effective anti-infective agent for the treatment of infection caused by S. aureus or other Gram-positive bacteria via the targeting of SrtA.
pH homeostasis links the nutrient sensing PKA/TORC1/Sch9 ménage-à-trois to stress tolerance and longevity

The plasma membrane H+-ATPase Pma1 and the vacuolar V-ATPase act in close harmony to tightly control pH homeostasis, which is essential for a vast number of physiological processes. As these main two regulators of pH are responsive to the nutritional status of the cell, it seems evident that pH homeostasis acts in conjunction with nutrient-induced signalling pathways. Indeed, both PKA and the TORC1-Sch9 axis influence the proton pumping activity of the V-ATPase and possibly also of Pma1. In addition, it recently became clear that the proton acts as a second messenger to signal glucose availability via the V-ATPase to PKA and TORC1-Sch9. Given the prominent role of nutrient signalling in longevity, it is not surprising that pH homeostasis has been linked to ageing and longevity as well. A first indication is provided by acetic acid, whose uptake by the cell induces toxicity and affects longevity. Secondly, vacuolar acidity has been linked to autophagic processes, including mitophagy. In agreement with this, a decline in vacuolar acidity was shown to induce mitochondrial dysfunction and shorten lifespan. In addition, the asymmetric inheritance of Pma1 has been associated with replicative ageing and this again links to repercussions on vacuolar pH. Taken together, accumulating evidence indicates that pH homeostasis plays a prominent role in the determination of ageing and longevity, thereby providing new perspectives and avenues to explore the underlying molecular mechanisms.
Systemic Lupus Erythematosus: Definitions, Contexts, Conflicts, Enigmas

Systemic lupus erythematosus (SLE) is an inadequately defined syndrome. Etiology and pathogenesis remain largely unknown. SLE is on the other hand a seminal syndrome that has challenged immunologists, biologists, genetics, and clinicians to solve its nature. The syndrome is characterized by multiple, etiologically unlinked manifestations. Unexpectedly, they seem to occur in different stochastically linked clusters, although single gene defects may promote a smaller spectrum of symptoms/criteria typical for SLE. There is no known inner coherence of parameters (criteria) making up the disease. These parameters are, nevertheless, implemented in The American College of Rheumatology (ACR) and The Systemic Lupus Collaborating Clinics (SLICC) criteria to classify SLE. Still, SLE is an abstraction since the ACR or SLICC criteria allow us to define hundreds of different clinical SLE phenotypes. This is a major point of the present discussion and uses “The anti-dsDNA antibody” as an example related to the problematic search for biomarkers for SLE. The following discussion will show how problematic this is: the disease is defined through non-coherent classification criteria, its complexity is recognized and accepted, its pathogenesis is plural and poorly understood. Therapy is focused on dominant symptoms or organ manifestations, and not on the syndrome itself. From basic scientific evidences, we can add substantial amount of data that are not sufficiently considered in clinical medicine, which may change the paradigms linked to what “The Anti-DNA antibody” is—and is not—in context of the imperfectly defined syndrome SLE.
X-Ray Microtomograph Detection of Internal Defects for a UD Prepreg Composite

The current trend particularly in industrial and commercial sectors is to search for alternatives to the current structural materials made from new lightweight materials. One option is to use unconventional material composite structures which have a combined fibre/matrix. Analysis of UD prepregs with unidirectional carbon fibres was performed. These special unconventional materials can be used for both flat and shaped structural products. The extent and quality of the saturation of the fibre layers in the resulting composite are important features for the whole complex of its parameters and influence its quality and mechanical properties. The experimental study also included an exploration of the inner structure and interactions of the individual components and detection of internal defects in the carbon UD prepreg composite using an X-ray microtomograph. The results illustrated the detection of microcracks, which significantly influence the resulting synergy of the composite and which were previously undetected.
Characterization of Novel Plant Symbiosis Mutants Using a New Multiple Gene-Expression Reporter Sinorhizobium meliloti Strain

The formation of nitrogen fixing root nodules by Medicago truncatula and Sinorhizobium meliloti requires communication between both organisms and coordinated differentiation of plant and bacterial cells. After an initial signal exchange, the bacteria invade the tissue of the growing nodule via plant-derived tubular structures, called infection threads. The bacteria are released from the infection threads into invasion-competent plant cells, where they differentiate into nitrogen-fixing bacteroids. Both organisms undergo dramatic transcriptional, metabolic and morphological changes during nodule development. To identify plant processes that are essential for the formation of nitrogen fixing nodules after nodule development has been initiated, large scale mutageneses have been conducted to discover underlying plant symbiosis genes. Such screens yield numerous uncharacterized plant lines with nitrogen fixation deficient nodules. In this study, we report construction of a S. meliloti strain carrying four distinct reporter constructs to reveal stages of root nodule development. The strain contains a constitutively expressed lacZ reporter construct; a PexoY-mTFP fusion that is expressed in infection threads but not in differentiated bacteroids; a PbacA-mcherry construct that is expressed in infection threads and during bacteroid differentiation; and a PnifH-uidA construct that is expressed during nitrogen fixation. We used this strain together with fluorescence microscopy to study nodule development over time in wild type nodules and to characterize eight plant mutants from a fast neutron bombardment screen. Based on the signal intensity and the localization patterns of the reporter genes, we grouped mutants with similar phenotypes and placed them in a developmental context.
Preparation, Structural Characterization, and Application of Reduced Graphene Oxide-Based Hybrid Materials

X Part 1: Research Background for the Formation of Hybrid Materials Based on Graphene . 1 1.1 Importance of hybrid materials. 2 1.2 Development of graphene based hybrid materials . 5 1.2. 1 Methods for functionalization of graphene. 5 1.2. 1.1 Covalent functionalization of graphene . 6 1.2. 1.2 Non-covalent functionalization of graphene . 7 1.2. 1.3 Nanoparticles functionalized graphene . 10 1.2. 1.4 Substitutional doping . 10 1.3 Control of the electrical properties of graphene . 11 1.3. 1 p-type doped graphene . 11 1.3. 2 n-type doped graphene . 12 1.4 Application of graphene based hybrid materials . 15 1.5 Research objectives and approaches . 18 1.6 References . 20 Part 2. Functionalization of Graphene Oxide (GO) and Reduced Graphene Oxide (rGO) and Their Applications . 29 2.
Novel peptide binds EWS-FLI1 and reduces the oncogenic potential in Ewing tumors

Ewing tumor is driven by the oncogenic EWS-FLI1 fusion protein that functions as an aberrant transcription factor. The identification of EWS-FLI1 protein partners is essential to enhance its vulnerability as a therapeutic target. We utilized phage display library screening against recombinant EWS-FLI1 protein. We identified 27 unique Ewing sarcoma binding peptides. The cytotoxicity evaluation of these peptides with in EWS-FLI1 containing cell lines yielded one potent peptide called ESAP1 (TMRGKKKRTRAN). ESAP1 binds EWS-FLI1 with 0.202 micromolar affinity as measured in surface plasmon resonance. The minimal interaction region of ESAP1 is characterized and found that the lysine residues are critical for cellular cytotoxicity. ESAP1 reduces the transcriptional activity of EWS-FLI1 as well as disrupts cell cycle kinetics in Ewing Tumor cells. These findings provide both a novel experimental probe and a potential therapeutic scaffold for Ewing Tumor.
Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

Abstract The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host‐microbe associations under adverse environmental conditions. To gain insight into the stability of coral host‐microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora‐associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.
Overweight and obesity are associated with lower vitamin D status in Canadian children and adolescents.

Introduction There is evidence that 25-hydroxyvitamin D levels are lower in overweight and obese youth. This study examined the relationship between weight status and 25-hydroxyvitamin D, while controlling for confounders, in Canadian youth. Methods Plasma 25-hydroxyvitamin D from subjects aged 6 to 17 years from the Canadian Health Measures Survey cycles 1 (2007 to 2009) and 2 (2009 to 2011) was used. Sex-specific multiple linear regression and logistic regressions examined the relationship of overweight and obesity (body mass index ≥ 85th percentile) with 25-hydroxyvitamin D levels and the odds of 25-hydroxyvitamin D <40 nmol/L and <50 nmol/L. Results The prevalence of risk of vitamin D deficiency (25-hydroxyvitamin D < 30 nmol/L) was 6% (95% confidence interval [CI] 3.26% to 10.12%). Vitamin D inadequacy, estimated by levels <40 nmol/L, was 15% (95% CI 10.34% to 20.39%; 19% [95% CI 13.1 to 25.6] for teenagers). Seventy per cent (95% CI 63.59 to 75.17) had levels >50 nmol/L, consistent with achieving the Recommended Dietary Allowance. In adjusted analyses, overweight/obesity (1/3 of subjects) was independently associated with lower 25-hydroxyvitamin D for both sexes after adjustment for age, race, income, season, vitamin D supplementation and daily milk consumption. For 25-hydroxyvitamin D <40 nmol/L, the overweight/obese odds ratio for males was 2.63 (95% CI 1.34 to 5.18). For 25-hydroxyvitamin D <50 nmol/L, overweight/obese odds ratios were 2.19 (95% CI 1.46 to 3.28) for males and 1.39 (95% CI 1.05 to 1.84) for females. Conclusions This study confirms the inverse association between adiposity and serum concentrations of 25-hydroxyvitamin D in Canadian youth and the independent association of overweight/obesity to 25-hydroxyvitamin D level and vitamin D status after adjustment for other factors.
Cytological And Histochemical Studies On Rat Liver And Pancreas During Progression Of Streptozotocin Induced Diabetes And Possible Protection Using Certain Natural Antioxidants

Background: Diabetes mellitus is a major endocrine disorder and growing health problem in most countries. Diabetes manifested by experimental animal models exhibits high oxidative stress due to persistent and chronic hyperglycemia which increases the generation of free radicals, streptozotocin (STZ) provides an animal model of type 1 diabetes. Thereby depleting the activities of antioxidative defense systems with alteration of antioxidant activities of enzymes such as green tea and curcumin . Aim : Biochemical histological and histochemical investigations were carried on to revel the effect of STZ on the liver and pancreas cells. Natural antioxidants were used as a new way for ameliorating diabetic effect on the cells Material and methods: Diabetes was induced by a single intraperitoneal injection of freshly prepared STZ dissolved in 0.05M of sodium citrate buffer, pH = 4.6, (STZ; 45 mg/kg B.wt.). Three days after degeneration of beta cells, diabetes was induced in all animals. After induction of diabetes, diabetic and normal animals were kept in metabolic cages separately. Green tea (EGCG) and curcumin are used as natural antioxidants to improve the disorders and structural changes induced by STZ. Cellular and histochemical investigations were carried on the changes induced in the pancreatic and hepatic tissues.Body weight, level of serum glucose and insulin were calculated in the control and treated groups. For detecting the degeneration of both hepatocytes and pancreatic cells of diabetic rats, tissue samples from diabetic and treated rats were collected and pathologically examined. Results: The present investigations reveled that there was a detectable amelioration on the injures induced by STZ on both hepatocytes and pancreatic cells using green tea or curcumin with a detectable dose level. Also it can be observed that the ameliorated effect induced was a time dependant. Conformation of these results from histochemical detection of polysaccharides and DNA contents were detected by PAS and Feulgen reactions. Conclusion: Curcumin and green tea look to have a powerful effect against diabetic cell injury induced in both rat liver and pancreas. The ameliorating effect seem to be time dependant.
Acropetal Auxin Transport Inhibition Is Involved in Indeterminate But Not Determinate Nodule Formation

Legumes enter into a symbiotic relationship with nitrogen-fixing rhizobia, leading to nodule development. Two main types of nodules have been widely studied, indeterminate and determinate, which differ in the location of the first cell division in the root cortex, and persistency of the nodule meristem. Here, we compared the control of auxin transport, content, and response during the early stages of indeterminate and determinate nodule development in the model legumes Medicago truncatula and Lotus japonicus, respectively, to investigate whether differences in auxin transport control could explain the differences in the location of cortical cell divisions. While auxin responses were activated in dividing cortical cells during nodulation of both nodule types, auxin (indole-3-acetic acid) content at the nodule initiation site was transiently increased in M. truncatula, but transiently reduced in L. japonicus. Root acropetal auxin transport was reduced in M. truncatula at the very start of nodule initiation, in contrast to a prolonged increase in acropetal auxin transport in L. japonicus. The auxin transport inhibitors 2,3,5-triiodobenzoic acid and 1-N-naphthylphthalamic acid (NPA) only induced pseudonodules in legume species forming indeterminate nodules, but failed to elicit such structures in a range of species forming determinate nodules. The development of these pseudonodules in M. truncatula exhibited increased auxin responses in a small primordium formed from the pericycle, endodermis, and inner cortex, similar to rhizobia-induced nodule primordia. In contrast, a diffuse cortical auxin response and no associated cortical cell divisions were found in L. japonicus. Collectively, we hypothesize that a step of acropetal auxin transport inhibition is unique to the process of indeterminate nodule development, leading to auxin responses in pericycle, endodermis, and inner cortex cells, while increased auxin responses in outer cortex cells likely require a different mechanism during the formation of determinate nodules.