Miracle-dz/UniFAR-FTUs huggingface dataset:
The microbiota influences the Drosophila melanogaster life history strategy

Abstract Organismal life history traits are ideally adapted to local environments when an organism has a fitness advantage in one location relative to conspecifics from other geographies. Local adaptation has been best studied across, for example, latitudinal gradients, where organisms may tradeoff between investment in traits that maximize one, but not both, fitness components of somatic maintenance or reproductive output in the context of finite environmental resources. Latitudinal gradients in life history strategies are traditionally attributed to environmentally mediated selection on an animal’s genotype, without any consideration of the possible impact of associated microorganisms (‘microbiota’) on life history traits. Here we show that in Drosophila melanogaster, a key organism for studying local adaptation and life history strategies, associated microorganisms can drive life history variation. First, we reveal that an isogenic fly line reared with different bacteria vary the investment in early reproduction versus somatic maintenance, with little resultant variation in lifetime fitness. Next, we show that in wild Drosophila the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, and bacterial abundance was driven at least in part by host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota; but that the microbiota can override these host genetic adaptations. Taken together, these findings establish the microbiota as an essential consideration in local adaptation and life history evolution. Significance statement Explanations of local adaptation have historically focused on how animal genotypes respond to environmental selection. Although the impact of variation in host life histories on the composition of the microbiota has been investigated for many associations, the scale and pattern of microbial effects on host life history strategy are largely unknown. Here we demonstrate in the fruit fly Drosophila melanogaster that microbiota effects on host life history strategy in the laboratory are matched by patterns of microbiota composition in wild host populations. In particular, microbiota composition varies with latitude and the effects of the microbiota on life history traits are greater than host genetic adaptations. Together, these findings demonstrate that the microbiota plays an important role in local adaptation.
Rock weathering in engineering time

Abstract The paper attempts a comprehensive review of in situ weathering of rock used in civil engineering construction. It also presents some new data on weathered rock from Britain which have been used to develop a proposed tentative Rock Durability Indicator scheme. This is based on simple engineering tests to help assess the potential performance of the rock in service. It is concluded that weathering in geological time can have significant influence, under certain circumstances, on the durability of aggregate or stone in-service. Durability is defined as the rock material's ability to resist degradation during its working life and is considered to be dependent on a number of parameters; viz. the original stage of weathering of the rock mass; the degree of imposed stressing during winning, production, placing and service; the climatic; topographical and hydrological environments in-service. The production and construction procedures can have an important influence on the mechanical strength of the material. Physical weathering processes and imposed loading generally have the most significant effect on deterioration but chemical weathering could be of significance in-service, especially in hot, wet climates. No one engineering test can be used as an absolute predictor of performance. Combinations of common mechanical and physical tests such as water absorption, specific gravity, point load strength, modified AIV and magnesium sulphate soundness can be used in various combinations to help assess potential durability. For a more complete evaluation, environmental factors such as the climate, topography and hydrological regimes need to be taken into account.
Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease

Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn’s disease Short title: Mucosal microbiota of Crohn’s twins Ben Willing, *† , PhD, Jonas Halfvarson, ‡† , MD PhD, Johan Dicksved, * , PhD, Magnus Rosenquist, * , PhD, Gunnar Jarnerot, ‡ , MD PhD, Lars Engstrand, || , MD PhD, Curt Tysk ‡¶ , MD PhD, and Janet K Jansson ***†† , PhD Swedish University of Agricultural Sciences, Department of Microbiology, Uppsala, Sweden Division of Gastroenterology, Department of Medicine, Orebro University Hospital, Orebro, Sweden. Department of Oncology, Radiology and Clinical Immunology, Uppsala University Hospital, Uppsala, Sweden Swedish Institute for Infectious Disease Control, Department of Bacteriology, Solna, Sweden School of Health and Medical Sciences, Orebro University, Orebro, Sweden. Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA Authors contributed equally to this work Corresponding author: Janet K. Jansson, Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Road, MS 70A-3317D, Berkeley, CA 94720 USA, Phone number: +1 (510) 486-7487, Email: jrjansson@lbl.gov
Optimal Approach to Load Progressions during Strength Training in Older Adults: An Intent-to Treat Study

of a dissertation at the University of Miami. Dissertation supervised by Professor Joseph Signorile. No. of pages in text. (56) Regular participation in structured resistance training (RT) is one of the most effective interventions an individual can engage in to counter the progressive decline in muscle mass and physical function associated with normal aging. Researchers agree on the need for RT programs to progress at an appropriate speed, neither too slow to optimize compliance, nor too quickly to increase soreness and injury risk, however there is no consensus concerning the best method to use in an older population. The objective of this investigation was to compare three common and one unique progression models to determine if an optimal method exists for use with older adults. 83 healthy communitydwelling older adults (71.8 + 6.2 y) performed 9 weeks of structured RT (2.5 days/week) after a common two-week familiarization period designed to introduce the subjects to the exercise machines and allow collection of baseline measures. Treatment groups were identical except for the method used to determine increases in training loads. Multiple analyses of covariance (ANCOVA; controlling for baseline values) indicated no significant between-group differences on any maximal strength (chest press 1RM; leg press 1RM) or functional performance outcome (usual walking speed, maximum walking speed, 8 foot timed up-and-go, gallon jug transfer test, 30 second sit-to-stand). Results showed rating of perceived exertion (RPE) group found the progression to be significantly more tolerable and enjoyable than subjects in the repetitions in reserve (RiR), repetition maximum (RM), or percentage of one repetition max (%1RM groups) group. Given no significant differences were identified between the RM, RPE, %1RM, or RPE methods with respect to strength gain or functional performance, we conclude the RPE method is the best RT progression method to use for older adults because it is likely to be perceived as the most tolerable and enjoyable, which are two important factors determining older adults' continued participation in RT. Future researchers are directed to consider whether exercisers previous RT experience and personality factors influence which method is most appropriate to use.
Melt segregation and matrix compaction: the mush continuity equation, compaction/segregation time, implications

SUMMARY Two-phase aggregates, a special case of which is partially molten systems, are commonly modelled as an interpenetrating flow of two viscous liquids and are therefore described in terms of the fluid mechanics. The governing equation set of fluid mechanics describing a two-phase aggregate is incomplete as it consists of nine equations (momentum and mass conservation equations for each phase, and an energy conservation equation) in ten unknowns (six velocity components, two pressures, temperature and melt fraction). In this paper, the general equation closing the governing equation set is derived. It explicitly expresses the condition of the coupling between the liquid percolation and porosity volume change due to which the medium continuity is maintained. Therefore, the equation may be referred to as the mush continuity equation. The character of the closed set solutions is demonstrated using 1-D isothermal models by examples of melt segregation inside a bounded low-melting-degree zone and sediment compaction at the bottom of a reservoir. The compaction/segregation style and time are controlled by the compaction/segregation parameter γc= (L/δc)2 and compaction/segregation length depending on the mushy layer thickness, L, matrix permeability, k, characteristic porosity, φ0, and matrix, η, and fluid, μ, viscosities. At low γc, which approximately corresponds to low-viscosity liquids (kimberlites, carbonatites), the compaction/segregation time scales as L−1, which effectively constrains the molten region thickness at the moment of the segregation, and appears to explain the small volume and clustering of low viscosity magma eruptions characteristic of kimberlites. At high γc the porosity evolves through a formation of a series of isolated waves, which could provide an explanation for the rhythmicity observed in large layered plutons.
Quality of Care and Outcomes for In-Hospital Ischemic Stroke Findings From the National Get With The Guidelines-Stroke

stenosis, and heart failure ( P <0.0001), and experienced more severe strokes (median National Institutes of Health Stroke Score 9.0 versus 4.0; P <0.0001). Using GWTG-Stroke achievement measures, the proportion of patients with defect-free care was lower for in-hospital strokes (60.8% versus 82.0%; P <0.0001). After accounting for patient and hospital characteristics, patients with in-hospital strokes were less likely to be discharged home (adjusted odds ratio 0.37; 95% confidence intervals [0.35–0.39]) or be able to ambulate independently at discharge (adjusted odds ratio 0.42; 95% confidence intervals [0.39–0.45]). In-hospital mortality was higher for in-hospital stroke (adjusted odds ratio 2.72; 95% confidence intervals [2.57–2.88]). Conclusions —Compared with community-onset ischemic stroke, patients with in-hospital stroke experienced more severe strokes, received lower adherence to process-based quality measures, and had worse outcomes. These findings suggest there is an important opportunity for targeted quality improvement efforts for patients with in-hospital stroke. ( Stroke . 2014;45:231-238.) vascular disease, hypertension, dyslip- idemia, smoking, hospital region, hospital type, annual number of stroke discharges, and number of beds. Because stroke severity is a key prognostic factor but was not available in all patients, sensitivity analyses, adjusting for NIHSS, were performed on the subset of patients with complete NIHSS data available. All P values were 2-sided with P <0.05 considered significant. Analysis was performed using SAS version 9.2 (SAS Institute, Cary, NC). peripheral vascular disease, hypertension, dyslipidemia, smoking, hospital region, hospital type, annual number of stroke discharges, and number of beds. This analysis was limited to patients with NIHSS recorded.
Radiative forcing from tropospheric ozone calculated with a unified chemistry-climate model

We have developed a global model for the study of chemistry-climate interactions by incorporating a detailed simulation of tropospheric ozone-NOx-hydrocarbon chemistry within a general circulation model (GCM). We present a first application of the model to the calculation of radiative forcing from tropospheric ozone since preindustrial times. Longwave and shortwave radiation fluxes are computed every 5 hours in the GCM using the locally simulated ozone fields. In this manner, the model resolves synoptic-scale correlations between ozone and meteorological variables. A simulation for present-day conditions is compared to a preindustrial atmosphere (∼1800 A.D.) with no fossil fuel combustion, 10% of present-day biomass burning, and 0.7 ppm methane. The two simulations use the same meteorological fields; the radiative forcing does not feed back into the GCM. The model reproduces well the observed distributions of ozone and its precursors in the present-day atmosphere. Increases in ozone since preindustrial times are 20–200% depending on region and season. The global mean, instantaneous radiative forcing from anthropogenic ozone is 0.44 W m2 (0.35 longwave, 0.09 shortwave). The model reveals large shortwave forcings (0.3–0.7 W m2) over polar regions in summer. The total forcing is greater than 1.0 W m2 over large areas, including the Arctic, during Northern Hemisphere summer. The normalized radiative forcing per unit of added ozone column varies globally from −0.01 to 0.05 W m2. This variance can be explained in large part by the temperature difference between the surface and the tropopause; clouds are an additional factor, particularly at low latitudes. An off-line radiative calculation using the same ozone fields but averaged monthly shows nearly identical forcings, with differences less than ±2% over most of the Earth. The similarity between the off-line and on-line simulations suggests that the common use of off-line ozone fields is acceptable in radiative forcing calculations. Addition of the direct forcings from anthropogenic sulfate aerosol and tropospheric ozone computed with the same GCM shows compensating effects, with sulfate dominating at northern midlatitudes and ozone usually dominating elsewhere.
Three‐dimensional topographic and bathymetric effects on magnetotelluric responses in Jeju Island, Korea

SUMMARY Magnetotelluric (MT) surveys have been conducted to investigate the volcanic structure in Jeju Island in the South Sea of Korea. The island is oval in shape, 31 km wide and 73 km long, with a peak elevation of 1950 m at Mt. Halla, located in the centre of the island. MT data were obtained in a wide range of frequencies in a mid-mountain region and may be affected by distortion of electric fields due to topographic and bathymetric effects. The purpose of this paper is to investigate the topographic and bathymetric effects on MT data for a four-layered model having the topographic and bathymetric undulation of Jeju Island, using an edge finite-element method. The model effectively reproduces a general feature of MT sounding curves observed on the island. The topographic effect appears only at high frequencies, whereas the sea effect causes a split of apparent resistivity curves in different polarizations at low frequencies. Since the island has a gentle slope of less than 10° except in the close vicinity of Mt. Halla, it has a similar effect of a change in thickness in the top layer. In contrast, the sea effect can be observed as quasi-2-D rather than 3-D along the major axis of the island and generates a parallel shift of the log-apparent resistivity curve at low frequencies.
Morphology of sporadic E layer retrieved from COSMIC GPS radio occultation measurements: Wind shear theory examination

On the basis of the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC)‐measured fluctuations in the signal‐to‐noise ratio and excess phase of the GPS signal piercing through ionospheric sporadic E (Es) layers, the general morphologies of these layers are presented for the period from July 2006 to May 2011. It is found that the latitudinal variation in the Es layer occurrence is substantially geomagnetically controlled, most frequent in the summer hemisphere within the geomagnetic latitude region between 10° and 70° and very rare in the geomagnetic equatorial zone. Model simulations show that the summer maximum (winter minimum) in the Es layer occurrence is very likely attributed to the convergence of the Fe+ concentration flux driven by the neutral wind. In addition to seasonal and spatial distributions, the height‐time variations in the Es layer occurrence in the midlatitude (>30°) region in summer and spring are primarily dominated by the semidiurnal tides, which start to appear at local time around 6 and 18 h in the height range 110–120 km and gradually descend at a rate of about 0.9–1.6 km/h. In the low‐latitude (<30°) region, the diurnal tide dominates. The Horizontal Wind Model (HWM07) indicates that the height‐time distribution of Es layers at middle latitude (30°–60°) is highly coincident with the zonal neutral wind shear. However, Es layer occurrences in low‐latitude and equatorial regions do not correlate well with the zonal wind shear.
Molecular Carcinogenesis

Funding information National Research Service Award Institutional Training Grant, Grant/Award Number: T32CA174648; VA merit award, Grant/Award Number: I01 BX003232; NIH R01, Grant/ Award Number: DE024371; NIH R01s, Grant/ Award Numbers: DE027329, DE028420 Abstract SMAD4 is a potent tumor suppressor and a central mediator of the TGFß signaling pathway. SMAD4 genetic loss is frequent in squamous cell carcinomas (SCCs). Reports of SMAD4 expression in SCCs vary significantly possibly due to inter‐tumor heterogeneity or technical reasons. SMAD4 loss is an initiation event for SCCs. In tumor epithelial cells, SMAD4 loss causes increased proliferation, decreased apoptosis, and “Brca‐like” genomic instability associated with DNA repair defects. SMAD4 loss also plays a role in the expansion of cancer stem cells. Epithelial SMAD4 loss causes overexpression of TGFß that is released into the tumor microenvironment and contributes to SCC progression through proinflammatory and immune evasive mechanisms. SMAD4 loss, while not a direct therapeutic target, is associated with multiple targetable pathways that require further therapeutic studies. Altogether, SMAD4 loss is a potential biomarker in SCCs that should be further studied for its values in prognostic and therapeutic predictions. Such information will potentially guide future biomarker‐driven clinical trial designs and improve SCC patient outcomes.
The use of microtephra horizons to correlate Late-glacial lake sediment successions in Scotland

Evidence is presented to show that two measurable concentrations of microtephra particles can be detected in deposits of Late Devensian Late-glacial age in three sites in Scotland. One layer is attributed to the Vedde Ash, a marker horizon within the Younger Dryas chronozone. The second is a new tephra reported for the first time, which we name the Borrobol Tephra. This occurs consistently near the base of the Late-glacial Interstadial organic sediments at each site, and is thought to date to around 12.5 14C ka BP. Geochemical determinations using an electron microprobe confirm the identification of the Vedde Ash, suggest the Borrobol Tephra to have an Icelandic origin, and demonstrate the consistency of the geochemical signals at all three sites. © 1997 John Wiley & Sons, Ltd.
The pattern of expression of guanine nucleotide-binding protein β 3 (GNB3) in the retina is conserved across vertebrate species

Guanine nucleotide-binding protein β 3 (GNB3) is an isoform of the β subunit of the heterotrimeric G protein second messenger complex that is commonly associated with transmembrane receptors. The presence of GNB3 in photoreceptors, and possibly bipolar cells, has been confirmed in murine, bovine and primate retinas (Lee et al., 1992, Peng et al., 1992, Huang et al., 2003). Studies have indicated that a mutation in the GNB3 gene causes progressive retinopathy and globe enlargement (RGE) in chickens. The goals of this study were to 1) examine the expression pattern of GNB3 in wild-type and RGE mutant chickens, 2) characterize the types of bipolar cells that express GNB3 and 3) examine whether the expression of GNB3 in the retina is conserved across vertebrate species. We find that chickens homozygous for the RGE allele completely lack GNB3 protein. We find that the pattern of expression of GNB3 in the retina is highly conserved across vertebrate species, including teleost fish ( Carassius auratus) , frogs ( Xenopus laevis ), chickens ( Gallus domesticus ), mice ( Mus musculata ), guinea pigs ( Cavia porcellus ), dogs ( Canis familiaris ) and non-human primates ( Macaca fasicularis ). Regardless of the species, we find that GNB3 is expressed by Islet1-positive cone ON-bipolar cells and by cone photoreceptors. In some vertebrates, GNB3-immunoreactivity was observed in both rod and cone photoreceptors. A protein-protein alignment of GNB3 across different vertebrates, from fish to humans, indicates a high degree (>92%) of sequence conservation. Given that analogous types of retinal neurons express GNB3 in different species, we propose that the functions and the mechanisms that regulate the expression of GNB3 are highly conserved.
Estimating the basal melt rate at NorthGRIP using a Monte Carlo technique

Abstract From radio-echo sounding (RES) surveys and ice core data it can be seen that the ice sheet is melting at the base in a large area in Northern Greenland. The RES images reveal internal layers in the ice. The layers are former deposition surfaces and are thus isochrones. Undulations of the isochrones in regions where the base is smooth suggest that the basal melt rate changes over short distances. This indicates that the geothermal heat flux is very high and has large spatial variability in Northern Greenland. In this study, the basal melt rate at the NorthGRIP drill site in North-Central Greenland is calculated by inverse modelling. We use simple one- and two-dimensional flow models to simulate the ice flow along the NNW-trending ice ridge leading to NorthGRIP. The accumulation is calculated from a dynamical model. Several ice flow parameters are unknown and must be estimated along with the basal melt rate using a Monte Carlo method. The Monte Carlo inversion is constrained by the observed isochrones, dated from the timescale established for the NorthGRIP ice core. The estimates of the basal melt rates around NorthGRIP are obtained from both the one- and two-dimensional models. Combining the estimated basal melt rates with the observed borehole temperatures allows us to convert the basal melt rates to geothermal heat flow values. From the two-dimensional model we find the basal melt rate and geothermal heat flux at NorthGRIP to be 6.1 mma–1 and 129 mWm–2, respectively.