Miracle-dz/UniFAR-FTUs huggingface dataset:
Birth Weight, Genetic Susceptibility, and Adulthood Risk of Type 2 Diabetes

OBJECTIVE Both stressful intrauterine milieus and genetic susceptibility have been linked to later-life diabetes risk. The current study aims to examine the interaction between low birth weight, a surrogate measure of stressful intrauterine milieus, and genetic susceptibility in relation to risk of type 2 diabetes in adulthood. RESEARCH DESIGN AND METHODS The analysis included two independent, nested case-control studies of 2,591 type 2 diabetic case subjects and 3,052 healthy control subjects. We developed two genotype scores: an obesity genotype score based on 32 BMI-predisposing variants and a diabetes genotype score based on 35 diabetes-predisposing variants. RESULTS Obesity genotype scores showed a stronger association with type 2 diabetes risk in individuals with low birth weight. In low–birth weight individuals, the multivariable-adjusted odds ratio (OR) was 2.55 (95% CI 1.34–4.84) by comparing extreme quartiles of the obesity genotype score, while the OR was 1.27 (1.04–1.55) among individuals with birth weight >2.5 kg (P for interaction = 0.017). We did not observe significant interaction between diabetes genotype scores and birth weight with regard to risk of type 2 diabetes. In a comparison of extreme quartiles of the diabetes gene score, the multivariable-adjusted OR was 3.80 (1.76–8.24) among individuals with low birth weight and 2.27 (1.82–2.83) among those with high birth weight (P for interaction = 0.16). CONCLUSIONS Our data suggest that low birth weight and genetic susceptibility to obesity may synergistically affect adulthood risk of type 2 diabetes.
Flying shells: historical dispersal of marine snails across Central America

The geological rise of the Central American Isthmus separated the Pacific and the Atlantic oceans about 3 Ma, creating a formidable barrier to dispersal for marine species. However, similar to Simpson's proposal that terrestrial species can ‘win sweepstakes routes’—whereby highly improbable dispersal events result in colonization across geographical barriers—marine species may also breach land barriers given enough time. To test this hypothesis, we asked whether intertidal marine snails have crossed Central America to successfully establish in new ocean basins. We used a mitochondrial DNA genetic comparison of sister snails (Cerithideopsis spp.) separated by the rise of the Isthmus. Genetic variation in these snails revealed evidence of at least two successful dispersal events between the Pacific and the Atlantic after the final closure of the Isthmus. A combination of ancestral area analyses and molecular dating techniques indicated that dispersal from the Pacific to the Atlantic occurred about 750 000 years ago and that dispersal in the opposite direction occurred about 72 000 years ago. The geographical distribution of haplotypes and published field evidence further suggest that migratory shorebirds transported the snails across Central America at the Isthmus of Tehuantepec in southern Mexico. Migratory birds could disperse other intertidal invertebrates this way, suggesting the Central American Isthmus may not be as impassable for marine species as previously assumed.
STACKING OF P-SV SEISMIC REFLECTION DATA USING DIP MOVEOUT1

The moveout of P-SV mode-converted seismic reflection events in a common-midpoint gather is non-hyperbolic. This is true even if the medium has constant P- and SV-wave velocities. Furthermore, reflection-point smear occurs even along horizontal reflectors. These effects reduce the resolution of the zero-offset stack. In such a medium, the generalization of the dip moveout transformation to P-SV data can be calculated analytically. The resulting P-SV dip moveout operators solve the problem of reflection-point smear, and image any reflector regardless of dip or depth. The viability of this technique is demonstrated on synthetic and field data.
Structures génétique et démographique des populations de deux espèces d'ophiures aux caractéristiques biologiques contrastées, Acrocnida brachiata et Ophiothrix fragilis, en Atlantique Nord-Est

La distribution des especes depend de leur histoire evolutive et de leur capacite a disperser et coloniser de nouveaux territoires. En milieu marin, cette capacite de dispersion est conditionnee par la duree de la phase larvaire et la repartition plus ou moins continue de leur habitat. Afin de mieux comprendre la part respective de ces differents facteurs, l’histoire passee et contemporaine des populations a ete etudiee, par le biais de la genetique et de la dynamique des populations, pour deux especes d’ophiures de l’Atlantique Nord-Est, A. brachiata et O.fragilis, qui presentent des caracteristiques biologiques contrastees. L’espece A. brachiata est constituee de deux lignees ecotypiques dont la speciation aurait ete de nature allopatrique a la transition Mio-Pliocene (5 MA). Chaque lignee se repartit preferentiellement a un etage bathymetrique, l’une en milieu subtidal et l’autre en milieu intertidal, avec une histoire de colonisation de l’habitat propre a chaque lignee, depuis des refuges glaciaires differents. Les echanges entre populations sont tres faibles, en raison de la fragmentation de l’habitat sablo-vaseux et de la phase dispersive courte (quatre jours). Des phenomenes d’hybridation rares sont observes entre lignees et apparaissent fortement contre-selectionnes par l’habitat lors de la phase de recrutement. Des mecanismes de migration d’adultes semblent homogeneiser les populations a micro-echelle. Le fonctionnement des populations d’A. brachiata ne semble pas suivre un rythme de renouvellement annuel mais plutot se faire par des episodes de recrutement plus consequents certaines annees. L’espece O. fragilis est egalement constituee de deux lignees genetiques dont l’une est infeodee a la Mediterranee et aux cotes de la peninsule iberique tandis que l’autre est presente sur les cotes bretonnes et de la Manche. Cette seconde lignee se subdivise en deux varietes ecotypiques, l’une vraisemblablement adaptee a une vie subtidale gregaire et l’autre a des habitats intertidaux. L’existence de ces varietes induit un premier niveau de structure genetique relativement faible. En depit du fait que l’espece vit majoritairement sur des fonds caillouteux qui forment un continuum d’habitats favorables en Manche et que la duree de sa phase larvaire soit longue (environ 21 jours), la structure des populations d’O. fragilis semble etre le reflet de processus locaux, tels que des effets Walhund temporels, plutot que celui des processus d’isolement geographique. Le fonctionnement demographique d’O. fragilis montre d’importantes disparites entre sites, qui peuvent egalement contribuer a la structure globale de l’espece. L’ensemble de ces resultats, mis en parallele, souligne l’importance des processus historiques dans la repartition globale de l’espece et celle des processus locaux dans la structure contemporaine des populations.
The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo

The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme the ability to initiate promoter-specific transcription. Although σ factors are generally classified as initiation factors, σ can also remain associated with, and modulate the behavior of, RNAP during elongation. Here we establish that the primary σ factor in Escherichia coli, σ70, can function as an elongation factor in vivo by loading directly onto the transcription elongation complex (TEC) in trans. We demonstrate that σ70 can bind in trans to TECs that emanate from either a σ70-dependent promoter or a promoter that is controlled by an alternative σ factor. We further demonstrate that binding of σ70 to the TEC in trans can have a particularly large impact on the dynamics of transcription elongation during stationary phase. Our findings establish a mechanism whereby the primary σ factor can exert direct effects on the composition of the entire transcriptome, not just that portion that is produced under the control of σ70-dependent promoters. DOI: http://dx.doi. org/10.7554/eLife.10514. 001
Effects of Soil Properties and Flooding on the Mobility and Transformation of Mercury in a Temperate Riparian Wetland

Three fractions of mercury (mobile, semi-mobile, and non-mobile mercury) were detected in the soil of an estuarine wetland in Nansi Lake, which is on the east route of China's South-to-North Water Transfer Project. The correlations between these mercury fractions and soil properties were examined under different levels of toxicity. Furthermore, the effects of two flooding conditions (permanent flooding and seasonal flooding) on mercury mobility were analyzed. Results showed that soil pH was negatively correlated with mobile mercury, whereas semi-mobile mercury was positively correlated with total aluminum, iron, and manganese. Moreover, free alumina was positively correlated with all three fractions of mercury. Our study suggests that high contents of soil acid and free alumina might promote wetlands as “sinks” for mercury sequestration, along with low concentrations of organic matter and manganese. In addition, seasonally flooded wetland might limit the production of toxic mobile mercury more than permanently flooded wetland. Large areas of seasonally flooded wetlands in the watershed are permanently flooded by the water transfer project, which elevates the water level during the dry season. As a result, the potential toxicity of mercury may increase in the watershed during water transfer, which should gain more attention.
Monitoring of ambient fine particulate matter concentrations from space: application to European and African cities

Air pollution is a major issue for global environment as well as human health and well-being. Recently, satellites which are equipped with relevant air quality instruments have been placed into orbit. In this paper, we first present a review on satellite remote sensing of particulate pollution. We then present new results for Europe and on African cities particulate air pollutants using POLDER satellite data. Based on satellite AOD observations, we show that the number of days exceeding the 15.4 μg/m3 threshold is twice frequent in Ouagadougou, Burkina- Faso than in Paris, France. At the regional scale, we observe that the northern coast of the golf of Guinea is dramatically impacted by poor air quality.
Population-size history inferences from the coho salmon (Oncorhynchus kisutch) genome

Abstract Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this trend. To assist in stock management and conservation efforts, we generated a chromosome-level genome assembly. We also resequenced the genomes of 83 coho salmon across the North American range to identify nucleotide variants and understand the demographic histories of these salmon by modeling effective population size from genome-wide data. From demographic history modeling, we observed reductions in effective population sizes between 3,750 and 8,000 years ago for several northern sampling sites, which may correspond to bottleneck events during recolonization after glacial retreat.
Major and trace element geochemistry and isotope (Sr, Nd, Pb, O) systematics of an Archaean basement involved in a 2.0 Ga very high-temperature (1000oC) metamorphic event: In Ouzzal Massif, Hoggar, Algeria

The In Ouzzal granulitic massif is composed mainly of various meta-igneous rocks which, in spite of Rb, U, Th, Cs and some K and Sr mobility, can be dated and generally classified according to their chemical composition as follows. Basic and ultrabasic granulites interlayered with the metasediments correspond to (1) ultrabasic cumulates from dislocated tholeiitic bodies, (2) ancient komatiitic to high-Mg tholeiitic basalts similar to the suites found in Archaean greenstone belts and (3) calcalkaline protoliths of high-K andesitic composition. No geochronological constraints are available apart from the depositional age of some associated sediments which is younger than 2.70 Ga detrital zircons, and the Nd model age of the andesitic granulites of c. 3.4 Ga. In spite of the high-grade metamorphism, the acidic magmatic precursors of the charnockites can be divided in three groups. (1) The most juvenile acid orthogneisses are trondhjemitic or tonalitic in composition, being similar to the TTG suites which are classically considered to be formed by partial melting of mantle-derived protoliths. The 3.3–3.2 Ga TDM indicates a possible age of separation from the mantle reservoir while the plutons may have been emplaced between 3.3 and 2.7 Ga (U–Pb zircon & Nd ages). (2) A group of alkaline granitic gneisses, similar in composition to rift-related-granites, were emplaced at 2650±10 Ma (U–Pb & Rb–Sr ages) in a thick continental crust. (3) Calcalkaline granodioritic and monzogranitic suites derived from the partial melting of continental precursors (3.5–3.3 Ga), in lower to middle levels of the continental crust. They were emplaced close to 2.5 Ga during crustal thickening. The very high-temperature metamorphism occurred at 2002±7 Ma from the age of synfoliation intrusions and was probably related to major overthrusting. Retrogressive metamorphism is dated at 1.95 Ga from garnet-Nd ages. In spite of the very high-temperature conditions, partial melting during granulite facies metamorphism may be restricted to scarce cordierite-bearing monzogranitic gneisses. The 2.0 Ga VHT metamorphism could be related to overthrusting, extensional or underplating processes.
Methodological approaches in estimating anomalous geochemical field structure

Mathematical statistic methods were applied to analyze the core samples from vertical expendable wells in Chertovo Koryto gold ore field. The following methods were used to analyse gold in samples: assay tests and atomic absorption method (AAS), while emission spectrum semiquantative method was applied to identify traces. The analysis of geochemical association distribution in one central profile demonstrated that bulk metasomatic aureoles are characteristic of concentric zonal structure. The distribution of geochemical associations is correlated to the hydrothermal stages of mineral formation identified in this deposit. It was proved that the processed geochemical data by factor and cluster analyses provided additional information on the anomalous geochemical field structure in gold- bearing black-shale strata. Such methods are effective tools in interpretating specific features of geochemical field structures in analogous potential ore-bearing areas.
Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages

Innate immune activation is a hallmark of HIV-1 pathogenesis. Thus, it is critical to understand how HIV-1 infection elicits innate immune responses. ABSTRACT HIV-1 replicates in cells that express a wide array of innate immune sensors and may do so simultaneously with other pathogens. How a coexisting innate immune stimulus influences the outcome of HIV-1 sensing, however, remains poorly understood. Here, we demonstrate that the activation of a second signaling pathway enables a cyclic GMP-AMP synthase (cGAS)-dependent type I interferon (IFN-I) response to HIV-1 infection. We used RNA sequencing to determine that HIV-1 alone induced few or no signs of an IFN-I response in THP-1 cells. In contrast, when supplemented with suboptimal levels of bacterial lipopolysaccharide (LPS), HIV-1 infection triggered the production of elevated levels of IFN-I and significant upregulation of interferon-stimulated genes. LPS-mediated enhancement of IFN-I production upon HIV-1 infection, which was observed in primary macrophages, was lost by blocking reverse transcription and with a hyperstable capsid, pointing to viral DNA being an essential immunostimulatory molecule. LPS also synergistically enhanced IFN-I production by cyclic GMP-AMP (cGAMP), a second messenger of cGAS. These observations suggest that the DNA sensor cGAS is responsible for a type I IFN response to HIV-1 in concert with LPS receptor Toll-like receptor 4 (TLR4). Small amounts of a TLR2 agonist also cooperate with HIV-1 to induce type I IFN production. These results demonstrate how subtle immunomodulatory activity renders HIV-1 capable of eliciting an IFN-I response through positive cross talk between cGAS and TLR sensing pathways. IMPORTANCE Innate immune activation is a hallmark of HIV-1 pathogenesis. Thus, it is critical to understand how HIV-1 infection elicits innate immune responses. In this work, we show that HIV-1 infection of macrophages leads to a robust type I interferon (IFN) production only when a second signaling event is initiated by a coexisting immunostimulatory molecule. Our results show that HIV-1 infection alone is not sufficient for triggering a strong IFN response. We find that bacterial membrane components, which are recognized by endosomal innate sensors, enable production of elevated levels of IFNs and significant upregulation of interferon-stimulated genes upon HIV-1 infection. This IFN response is dependent on viral DNA synthesis and prevented by a stable capsid, pointing to an essential role for a DNA sensing molecule. These observations provide new insights into how different innate immune recognition pathways synergize during HIV-1 infection and determine the outcome of innate responses.
Geology and Exploration Potential of the Gorontalo Basin, Central Indonesia – Eastern Extension of the North Makassar Basin?

Prior to 2005 no seismic data coverage or offshore wells existed for the Gorontalo Basin, and consequently, the hydrocarbon potential was poorly understood. In 2006, following encouraging interpretation of the 2005 ‘NewLook’ deep recording 2D reconnaissance non-exclusive seismic survey, some 5800 line kilometres of 2D nonexclusive seismic data was acquired. Subsequent interpretation of this data revealed a new geological picture that challenges pre-existing ideas about tectonic development and the hydrocarbon prospectivity of the region. The Pliocene to Recent spreading along the southern Palau ridge combined with the Upper Miocene to Pliocene spreading within the Banda Sea has resulted in the westerly migration of the significant portion of eastern Indonesia and surrounds that included SE Halmahera, Philippines, Banggai-Sula-Obi, Offshore Eastern Sulawesi and Offshore Buton terrains. The Gorontalo Basin is underlain by Eocene rift grabens similar in geometry to the fluvio-lacustrine source rock-rich megasequences that underlie many oil-prone petroleum systems in Indonesia. An active petroleum system is suggested by east-west oriented depocentres with thicknesses locally exceeding 10 kilometres, the mostly southward focussed hydrocarbon migration routes, and the presence of numerous onshore oil seeps along the southern edge of the Gorontalo Basin. Numerous Amplitude with Offset (AVO) anomalies observed on newly acquired seismic sections also suggest the presence of hydrocarbons at a variety of stratigraphic levels. The new seismic data indicate the following prePaleogene to Recent plays, some of which may * Fugro ** Ministry of Energy and Mineral Resources Republic of Indonesia contain stacked reservoir–seal pairs sourced by several Tertiary source rocks: • Older rift fault blocks associated with the Australian plate rifting, and subsequent collision with Borneo in the Cretaceous • Eocene rift fault-blocks • Oligocene to Middle Miocene platform carbonates • Late Miocene to Pliocene biohermal build-ups • Late Miocene to Recent lowstand deltas and turbidites • Late Miocene to Recent compressional folds associated with the progressive collision of Sundaland with the northern margin of the Australian plate
Remote detection and recognition of bio-aerosols by laser-induced fluorescense lidar: practical implementation and field tests

Recognition of aerosol clouds material at some significant distance is now a key requirement for the wide range of applications. The elastic backscatter lidar have demonstrated high capabilities in aerosol remote detection, cloud real-time mapping at very long distances for low-concentration natural aerosols as well as artificial ones [1]. However, recognition ability is required to make them more relevant. Laser-induced fluorescence (LIF) looks very promising with respect to the recognition problem. New approach based on mobile lidar complex [2] equipped by spectrally-and range-resolved LIF-sensor is described as well as some results of field tests. The LIF-sensor consists of four-harmonics Nd:YAG laser equipped by an output expander to provide final beam divergence <1 mrad, 500-mm aspheric Cassegrain-type multi-wavelength receiving telescope, set of single-element receivers for measurement of the elastic backscatter radiation, and multi-element receiver with monochromator for spectrally-resolved LIF measurements. The system is equipped by 2-axis scanning mirror and variable-FOV video-camera collimated with the lidar scanning direction. The LIF-lidar is mounted on a truck-based platform (20-feet container) as a part of multi-purpose mobile lidar complex and adjusted for field conditions.