Miracle-dz/UniFAR-FTUs huggingface dataset:
Butyrate inhibits inflammatory responses through NFκB inhibition: implications for Crohn's disease

BACKGROUND/AIM Proinflammatory cytokines are key factors in the pathogenesis of Crohn's disease (CD). Activation of nuclear factor kappa B (NFκB), which is involved in their gene transcription, is increased in the intestinal mucosa of CD patients. As butyrate enemas may be beneficial in treating colonic inflammation, we investigated if butyrate promotes this effect by acting on proinflammatory cytokine expression. METHODS Intestinal biopsy specimens, isolated lamina propria cells (LPMC), and peripheral blood mononuclear cells (PBMC) were cultured with or without butyrate for assessment of secretion of tumour necrosis factor (TNF) and mRNA levels. NFκB p65 activation was determined by immunofluorescence and gene reporter experiments. Levels of NFκB inhibitory protein (IκBα) were analysed by western blotting. The in vivo efficacy of butyrate was assessed in rats with trinitrobenzene sulphonic acid (TNBS) induced colitis. RESULTS Butyrate decreased TNF production and proinflammatory cytokine mRNA expression by intestinal biopsies and LPMC from CD patients. Butyrate abolished lipopolysaccharide (LPS) induced expression of cytokines by PBMC and transmigration of NFκB from the cytoplasm to the nucleus. LPS induced NFκB transcriptional activity was decreased by butyrate while IκBα levels were stable. Butyrate treatment also improved TNBS induced colitis. CONCLUSIONS Butyrate decreases proinflammatory cytokine expression via inhibition of NFκB activation and IκBα degradation. These anti-inflammatory properties provide a rationale for assessing butyrate in the treatment of CD.
Tropospheric cycle of nitrous acid

Measurements of the land surface exchange of nitrous acid over grass and sugar beet surfaces reveal both upward and downward fluxes with flux reversal occurring at an ambient concentration of nitrogen dioxide of about 10 ppb. This confirms earlier preliminary findings and strengthens the hypothesis that substantial production of nitrous acid can occur on land surfaces from reaction of nitrogen dioxide and water vapor. Detailed measurements of nitrous acid have been made in central urban, suburban, and rural environments. These measurements, in conjunction with a simple box model, indicate that the atmospheric concentrations of nitrous acid are explicable in terms of a small number of basic processes in which the most important are the surface production of nitrous acid from nitrogen dioxide, atmospheric production from the NO-OH reaction and loss of nitrous acid by photolysis and dry deposition. In the suburban atmosphere, concentrations of nitrous acid are strongly correlated with nitrogen dioxide. In the rural atmosphere a different behavior is seen, with much higher nitrous acid to nitrogen dioxide ratios occurring in more polluted air with nitrogen dioxide concentrations in excess of 10 ppb. At lower nitrogen dioxide concentrations, net deposition of nitrous acid at the ground leads to very low concentrations in advected air. The model study indicates that during daytime in the suburban atmosphere, production of HONO from the NO-OH reaction can compete with photolysis giving a HONO concentration of a few tenths of a part per billion. At the highest observed daytime concentrations of HONO, production of OH radical from its photolysis can proceed at a rate more than 10 times faster than from photolysis of ozone.
Stochastic Gene Expression: Dominance, Thresholds and Boundaries

Butterfly color patterns are built as finely tiles mosaics of colored scales, each the product of a single epidermal cell. The overall pattern is composed of a small number of pigments. Each scale appears to make an all-or-none “choice” to synthesize only one of this small set of alternative pigments. Gradual transitions from one color to another on the wing are accomplished by graded changes in the proportions of discretely colored scales, and areas of intermediate coloration are made up of a random salt-and-pepper mosaic of discretely colored scales. In transition regions, and at boundaries between colors, scales also exhibit stochastic patterns of pigment expression. A model for a stochastic mechanism for gene expression is presented that can account for the observed stochastic patterns of pigmentation. This model shows that stochastic gene expression provides a simple mechanism for establishing a step-like, or threshold, response to a spatially graded signal. Conditions that affect the steepness of the threshold are examined. It is shown that stochastic gene expression also results in the emergence of interesting patterns of dominance among the alleles of a gene.
Numerical model simulation of the Saharan dust event of 6-11 March 2006 using the Regional Climate Model version 3 (RegCM3)

The Sahara desert is the world's primary source of mineral dust aerosols and is known to be an important but poorly understood component of the climate system. Climate models which incorporate dust modules have the potential to improve our understanding of the climate impacts of dust. In this study, the performance of the Regional Climate Model version 3 (RegCM3) with an active dust scheme is evaluated, using a major dust event of 6? 11 March 2006 as a test case. To account for the distribution of preferential dust source regions, soil texture characteristics were modified in dust source regions identified from long-term SEVIRI satellite data. The dust event was associated with a pronounced cold outbreak of midlatitude air over the northern Sahara which produced anomalously strong northerly winds, which propagated from west to east over the Sahara during the study period. This resulted in dust mobilization from multiple dust sources across the domain. RegCM3 represents the space/time structure of near-surface meteorology well, although surface winds are underestimated in absolute terms. The experiment in which soils are modified provides a better representation of local dust sources and emission and resulting atmospheric optical thickness (AOT). In this experiment, model simulated dust flux exported from the Sahara to the Sahel and the tropical east Atlantic is estimated as 1.9 Tg d-1. The dust event had a profound impact on the surface solar radiation budget of ~-140 W m-2 per unit AOT (domain average). The shortwave radiative effect at the top of the atmosphere is~-10 W m-2 per unit AOT over the study domain. However, this is strongly dependent on surface albedo. The results also highlight how errors in model simulated circulation lead to errors in the position of the dust plume.
The last erythrosuchid—a revision of Chalishevia cothurnata from the late Middle Triassic of European Russia

Erythrosuchidae is a clade of early archosauriform reptiles that were large-bodied, hypercarnivorous, possibly apex predators in late Early and Middle Triassic ecosystems following the Permo-Triassic mass extinction. Chalishevia cothurnata from the late Middle Triassic (Ladinian) of Russia, is the stratigraphically youngest known erythrosuchid species, but the holotype and referred material of this taxon has received little study. Here, we provide the first detailed anatomical description of C. cothurnata , including comparisons to other erythrosuchids. Although known from relatively fragmentary material, the anatomy of C. cothurnata is distinctive, including an autapomorphic strongly slanted ventral border of the antorbital fossa. The presence of a large accessory opening (the “accessory antorbital fenestra”) in the skull between the premaxilla, nasal and maxilla, together with the inferred presence of a narrow postnarial process of the premaxilla that articulated with a slot on the nasal, provides strong evidence for a sister taxon relationship between C. cothurnata and the erythrosuchid Shansisuchus shansisuchus from the early Middle Triassic (Anisian) of China. The inferred basal skull length of C. cothurnata was approximately 80 cm, making it one of the largest erythrosuchids known.
The influence of resilience-based management on coral reef monitoring: A systematic review

With rapid changes taking place on coral reefs, managers and scientists are faced with prioritising interventions that might avoid undesirable losses in ecosystem health. The property of resilience captures how reefs react and respond to stressors and environmental changes. Therefore, in principle, management goals are more likely to be realised if resilience theory is used to inform decision making and help set realistic expectations for reef outcomes. Indeed, a new approach to reef management has been termed ‘resilience-based management’ (RBM). Yet, resilience concepts have often been criticised for being vague, difficult to operationalise, and beset by multiple definitions. Here, we evaluate how the advent of RBM has changed one aspect of reef management: assessment and monitoring. We compare the metrics used in conventional monitoring programs with those developed through resilience assessments and find that the latter have a stronger focus on ecological processes and exposure to environmental drivers. In contrast, monitoring tends to focus on metrics of reef state and has greater taxonomic resolution, which provides comprehensive information on the nature of changes but does not predict the future responses of reefs in part because it is difficult to extrapolate statistical trends of complex ecological systems. In addition, metrics measured by resilience studies are more diverse, owing in part to the reliance of state metrics as proxies of processes given the difficulty in quantifying key ecological processes directly. We conclude by describing practical ways of improving resilience assessments, and avenues for future research.
Drifter observations of coastal surface currents during CODE: The statistical and dynamical views

Observations of near-surface coastal currents were made off the Northern California coast during CODE by using 164 current-following drifters. These observations are used to describe the two-dimensional structure of the mean surface flow and the scales of its variability. The mean flow is a broad equatorward current, strongly sheared only within 10 km of the shore, and a mean offshore flow producing an average divergence ∇H·u ≈ 3 × 10−6 s−1. Divergence is uniformly distributed across the shelf, but variation of the alongshore flow causes an upwelling center near Point Arena. The spatial correlation scale is less than 40 km in both the alongshore and across-shelf directions, even though 55% of the surface kinetic energy is described by a single mode with gradual across-shelf variation and an alongshore wavelength of the order 200 km. The surface flow is well correlated with flow at 30-m depth. The Lagrangian time scale (≈1.5 day) is significantly shorter than the Eulerian time scale (≈5 days), indicating that the flow is dominated by highly nonlinear quasi-stationary eddies. Drifter displacements indicate that the mean lateral eddy transport of passive scalars can be described by an anisotropic and inhomogeneous eddy diffusivity, but this diffusivity cannot be used to relate eddy Reynolds stresses and the mean shear. Analysis of two-particle separations, which determine the size of dispersing property clouds, shows that dispersal cannot be described by a scale-dependent diffusivity and indicates the importance of small-scale convergences in retarding dispersal. Over the entire 100-km by 50-km region the surface layer heat budget is dominated by upwelling cooling and surface heating, with onshore eddy heat flux playing a smaller role. Substantial convergence of the alongshore eddy heat flux is apparently required to balance upwelling cooling in the upwelling center. Drifters are found to have a Lagrangian mean acceleration caused by eddy processes. Analysis of this acceleration and of the horizontal flow contributions to the eddy Reynolds stress allows examination of the importance of eddy processes in the mean momentum budget. While the alongshore flow must be in approximate geostrophic balance, there is a clear pattern to the eddy forcing, which appears to be important in the alongshore momentum equation.
Activation by NarL at the Escherichia coli ogt promoter

The Escherichia coli NarX/NarL two-component response-regulator system regulates gene expression in response to nitrate ions and the NarL protein is a global transcription factor, which activates transcript initiation at many target promoters. One such target, the E. coli ogt promoter, which controls the expression of an O6-alkylguanine-DNA-alkyltransferase, is dependent on NarL binding to two DNA targets centred at positions −44.5 and −77.5 upstream from the transcript start. Here, we describe ogt promoter derivatives that can be activated solely by NarL binding either at position −44.5 or position −77.5. We show that NarL can also activate the ogt promoter when located at position −67.5. We present data to argue that NarL-dependent activation of transcript initiation at the ogt promoter results from a direct interaction between NarL and a determinant in the C-terminal domain of the RNA polymerase α subunit. Footprinting experiments show that, at the −44.5 promoter, NarL and the C-terminal domain of the RNA polymerase α subunit bind to opposite faces of promoter DNA, suggesting an unusual mechanism of transcription activation. Our work suggests new organisations for activator-dependent transcription at promoters and future applications for biotechnology.
Stochastic convective rain‐field simulation using a high‐resolution synoptically conditioned weather generator (HiReS‐WG)

A new stochastic high‐resolution synoptically conditioned weather generator (HiReS‐WG) appropriate for climate regimes with a substantial proportion of convective rainfall is presented. The simulated rain fields are of high spatial (0.5 × 0.5 km2) and temporal (5 min) resolution and can be used for most hydrological applications. The WG is composed of four modules: the synoptic generator, the motion vector generator, the convective rain cell generator, and the low‐intensity rainfall generator. The HiReS‐WG was applied to a study region on the northwestern Israeli coastline in the Eastern Mediterranean, for which 12 year weather radar and synoptic data were extensively analyzed to derive probability distributions of convective rain cells and other rainfall properties for different synoptic classifications; these distributions were used as input to the HiReS‐WG. Simulated rainfall data for 300 years were evaluated for annual rain depth, season timing, wet‐/dry‐period durations, rain‐intensity distributions, and spatial correlations. In general, the WG well represented the above properties compared to radar and rain‐gauge observations from the studied region, with one limitation—an inability to reproduce the most extreme cases. The HiReS‐WG is a good tool to study catchments' hydrological responses to variations in rainfall, especially small‐size to medium‐size catchments, and it can also be linked to climate models to force the prevailing synoptic conditions.
Union Strategy and Optimal Income Taxation Union Strategy and Optimal Income Taxation

Any opinions expressed here are those of the author(s) and not those of the institute. Research disseminated by IZA may include views on policy, but the institute itself takes no institutional policy positions. The Institute for the Study of Labor (IZA) in Bonn is a local and virtual international research center and a place of communication between science, politics and business. IZA is an independent nonprofit company supported by Deutsche Post World Net. The center is associated with the University of Bonn and offers a stimulating research environment through its research networks, research support, and visitors and doctoral programs. IZA engages in (i) original and internationally competitive research in all fields of labor economics, (ii) development of policy concepts, and (iii) dissemination of research results and concepts to the interested public. IZA Discussion Papers often represent preliminary work and are circulated to encourage discussion. Citation of such a paper should account for its provisional character. A revised version may be available directly from the author. ABSTRACT Union Strategy and Optimal Income Taxation Restrictions on work hours are more important in countries with a large welfare state. We show that this empirical observation is consistent with the strategic effects of such restrictions in a welfare state in the context of optimal direct taxation in the tradition of Mirrlees (1971). Our results also apply to non-welfarist states which have income redistribution, but not in purely extortionary states.
An overview of the biological activity of polyacrylamide hydrogels

Background: Polyacrylamide hydrogels have emerged as a versatile class of materials with considerable potential within the domain of biomedicine. These hydrogels, comprising crosslinked polyacrylamide polymers, exhibit distinctive properties that render them highly appealing for a wide range of applications in tissue engineering, drug delivery, wound healing, and regenerative medicine. Objective: This article provides a comprehensive overview of polyacrylamide hydrogels and their properties . Discussion: Furthermore, it delves into the interactions between these hydrogels and living tissues, evaluates their biocompatibility, and underscores their diverse applications within the realm of biomedicine. Conclusion: By comprehending the intricate biological behavior and inherent potential of polyacrylamide hydrogels, researchers and practitioners can effectively explore their application in the development of advanced biomedical technologies.
Transient tracers and air‐sea gas transfer

This paper provides a review of the physics and chemistry associated with air-sea gas transfer of transient atmospheric trace gases and the available laboratory and field measurement techniques used to study air-water gas transfer. The mechanistic principles and their relation to the measurement techniques are used to show that the error associated with estimating air-sea transfer velocities of transient tracers from transfer velocities measured using proxy tracers can be significant if an incorrect dependence of the transfer velocity on molecular diffusivity is assumed. Bubble-mediated transfer processes are also demonstrated to have a significant effect on the parameterization of the transfer velocity.
Bacteroides thetaiotaomicron Growth Numbers Are Unchanged in the Presence of Yogurt

The microbiome is composed of microorganisms that prime the human immune system for proper functioning and aid in energy harvest and biomolecule production. Disruptions to the microbiome have been linked to the development of certain diseases such as diabetes and obesity. Recent phylogenetic analysis has shown that obese patients have an imbalance in the two major phyla, the Firmicutes and the Bacteroidetes that compose the gut microbiome. The obese gut has higher levels of Firmicute bacteria when compared to Bacteroidetes, which have reduced numbers. This is important because many probiotic foods and supplements are produced using bacteria that fall into the Firmicute phylum. This study explored whether or not Fage plain total 0% Greek yogurt, which contains live and active bacterial cultures belonging to the Firmicute phylum, could decrease the numbers of Bacteroides thetaiotaomicron, an organism found in the human gut that belongs to the Bacteroidetes phylum. B. thetaiotaomicron was grown in the presence of Fage plain total 0% Greek yogurt containing live and active cultures, and with re-pasteurized Fage plain total 0% Greek yogurt. ANOVA analysis indicated no statistically significant reduction in the numbers of B. thetaiotaomicron when grown in either yogurt condition. This study can be used to guide people in dietary measures meant to keep beneficial Bacteroidetes in the gut.
Integrated research in the Coniferous Forest Biome

Integrating the research effort for an analysis of ecosystems requiresa strong but flexible organization. The Coniferous Forest Biome's research groups reflect our changing perception of the major processes operating in both terrestrial and aquatic systems. They also reflect changing goals as our understanding increases and wider application and longer range predictions are desired. In addition, there is a geographic perspective expressing the concentration of effort on different processes and systems across the Biome. The evolution of field research and modeling are intimately linked. Directors and research committee chairmen take leading roles in designing and coordinating the research with the aid of workshops to measure progress, modify model structure, and identify critical data needs. Often a small task force is appointed to address particular problems that require shifting resources and personnel to meet a critical need. A key group of integrators has developed, consisting of people who have an ecosystem perspective and training in more than one discipline. Their contributions to the program are essential and their experience and talents make them capable of leading the next generation of ecosystem studies.
Mixing state of aerosols and direct observation of carbonaceous and marine coatings on African dust by individual particle analysis

[1] The mixing state of aerosols collected at M'Bour, Senegal, during the Special Observing Period conducted in January–February 2006 (SOP-0) of the African Monsoon Multidisciplinary Analysis project (AMMA), was studied by individual particle analysis. The sampling location on the Atlantic coast is particularly adapted for studying the mixing state of tropospheric aerosols since it is (1) located on the path of Saharan dust plumes transported westward over the northern tropical Atlantic, (2) influenced by biomass burning events particularly frequent from December to March, and (3) strongly influenced by anthropogenic emissions from polluted African cities. Particle size, morphology, and chemical composition were determined for 12,672 particles using scanning electron microscopy (automated SEM-EDX). Complementary analyses were performed using transmission electron microscopy combined with electron energy loss spectrometry (TEM-EELS) and Raman microspectrometry. Mineral dust and carbonaceous and marine compounds were predominantly found externally mixed, i.e., not present together in the same particles. Binary internally mixed particles, i.e., dust/carbonaceous, carbonaceous/marine, and dust/marine mixtures, accounted for a significant fraction of analyzed particles (from 10.5% to 46.5%). Western Sahara was identified as the main source of mineral dust. Two major types of carbonaceous particles were identified: “tar balls” probably coming from biomass burning emissions and soot from anthropogenic emissions. Regarding binary internally mixed particles, marine and carbonaceous compounds generally formed a coating on mineral dust particles. The carbonaceous coating observed at the particle scale on African dust was evidenced by the combined use of elemental and molecular microanalysis techniques, with the identification of an amorphous rather than crystallized carbon structure.
AMPc i neuroinflamació: Identificació de proteïnes implicades en la regulació dels nivells d’AMPc en l’encefalomielitis autoimmune experimental

Memoria presentada per optar al grau de Doctor en Biologia per la Universitat de Barcelona, dins del Programa de Docotorat en Biomedicina (Departament de Neurociencies, Facultat de Medicina, Universitat de Barcelona). -- Tesis elaborada en el Departament de Neuroquimica i Neurofarmacologia, Institut d'Investigacions Biomediques de Barcelona, Consejo Superior de Investigaciones Cientificas, Institut d'Investigacions Biomediques August Pi i Sunyer.