Miracle-dz/UniFAR-FTUs huggingface dataset:
Local adaptation under demographic and genetic fluctuations

Evolution frequently plays out over ecological timescales. Local adaptation under the joint action of evolutionary and ecological processes frequently leads to novel outcomes, as is evidenced by the theoretical work on adaptation at species’ borders. However, to date this body of work does not have a theory for the effect of stochastic processes on local adaptation. The primary goal of this thesis is to show that demographic and genetic fluctuations can significantly impact upon local adaptation. In addition, the effect of polygenic evolution is also analysed. Specifically, three types of models are considered. First a deterministic mainland-island, subject to hard directional selection, maladaptive gene flow and density regulation is solved for two different trait architectures: an explicit multilocus trait and a quantitative trait. The maladaptive and adaptive steady states can be bistable. This depends on the underlying architecture of the trait, as well as locus number and ploidy. Sourcesink structure can emerge, accompanied by a novel, upper critical threshold above which maladaptation occurs. The most favourable condition for local adaptation occurs for few loci and low migration. Second, a stochastic version of the mainland-island model is analysed as a diffusion process. This is the central premise of the thesis and is explored by examining properties of the stationary distributions of both trait architectures, and the first-passage properties of the single locus case. It is found that across a range of migration rates that depend on locus number and migrant polymorphism, local adaptation may be reversed or escape from maladaptation becomes possible at varying transition rates. The diffusion model is compared to a similar discrete model. The continuous model is in good qualitative agreement with the discrete model. Third, the stochastic model is generalised to the infinite island model, which evolves deterministically. Under deterministic dynamics a range of equilibria are possible, depending on whether habitat size varies or is fixed. Multilocus dynamics restrict the conditions for polymorphism. Stochastic dynamics can have potentially detrimental consequences for the persistence of the island population when drift is strong. The relevance of the stochastic model to border populations is discussed. Although the diffusion process imposes severe constraints on the permissible parameter ranges, it is still able to provide a good qualitative understanding of the impact demographic and genetic fluctuations have on local adaptation.
Estimación de evaporación y radiación solar en el valle del Yaqui Sonora usando datos de satélite

Para calcular la evaporacion potencial en el valle del Yaqui, usando la formula de Makkink, se utilizaron datos de dos estaciones meteorologicas automaticas. La mencionada formula se basa en la radiacion solar incidente observada y en ciertos valores climatologicos de temperatura del aire. Se evaluo la utilidad de esta formula, comparandola con las de Penman-Monteith, Penman y Priestley-Taylor; asi como con mediciones de radiacion neta. Se desarrollo una metodologia para estimar la radiacion solar incidente usando la banda visible del satelite GOES. Se hizo una comparacion con mediciones de dos piranometros instalados en el valle del Yaqui, obteniendose buenos resultados, principalmente en meses con poca nubosidad. Se utilizaron imagenes de agosto de 1993 para producir un mapa de la distribucion espacial de la evaporacion potencial.
The reappearance of the Huronian in Wyoming: rifting and drifting of ancient continents

Striking stratigraphic and sedimentological similarities between the Early Proterozoic Huronian Supergroup of the Canadian Shield and the Snowy Pass Supergroup of Wyoming suggest that they were deposited in a single, broad, epicratonic basin developed atop a large Archean continent that included the Superior and Wyoming geological provinces. Breakup of the continent after the 2.2 Ga intrusion of widespread gabbro sheets and dykes resulted in the separation of the Archean Superior and Wyoming cratons and their Early Proterozoic covers. These crustal fragments were subsequently reassembled during Early Proterozoic (~1.85 Ga) orogenesis, the end result being the present 2000 km separation of the Huronian and Snowy Pass supergroups and their Archean basements.
Trend analysis of medium- and coarse-resolution time series image data for burned area mapping in a Mediterranean ecosystem

In this study, the Breaks for Additive Seasonal and Trend (BFAST), a recently introduced trend analysis technique, was employed for the detection of fire-induced changes in a Mediterranean ecosystem. BFAST enables the decomposition of time series into trend, seasonal and noise components, resulting in the detection of gradual and rapid land cover changes. Normalised Difference Vegetation Index (NDVI) time series derived from the MODIS and VEGETATION (VGT) standard products were analysed. The time series decomposition resulted in the mapping of the burned area and the demonstration of the post-fire vegetation recovery trend. The observed gradual changes revealed an increase of NDVI values over time, indicating post-fire vegetation recovery. Spatial validation of the generated burned area maps with a higher resolution reference map was performed and probability statistics were derived. Both maps achieved a high probability of detection – 0.90 for MODIS and 0.87 for VGT – and a low probability of false alarms, 0.01 for MODIS and 0.02 for VGT. In addition, the Pareto boundary theory was implemented to account for the low-resolution bias of the maps. BFAST facilitated detection of fire-induced changes using image time series, without having to set thresholds, select specific seasons or adjust to certain land cover types. Further evaluation of the approach should focus on a more comprehensive assessment across regions and time.
Development of a Stepwise-Clustered Hydrological Inference Model

AbstractFlow prediction is one of the most important issues in modern hydrology. In this study, a statistical tool, stepwise-clustered hydrological inference (SCHI) model, was developed for daily streamflow forecasting. The SCHI model uses cluster trees to represent the nonlinear and complex relationships between streamflow and multiple factors related to climate and watershed conditions. It allows a great deal of flexibility in watershed configuration. The proposed model was applied to the daily streamflow forecasting in the Xiangxi River watershed, China. The correlation coefficient for calibration (1991–1995) was 0.881, and that for validation (1996–1998) was 0.771. Nash–Sutcliffe efficiencies for calibration and validation were 0.768 and 0.577, respectively. The results were compared to those of a conventional process-based model, and it was found that the SCHI model had a superior performance. The results indicate that the proposed model could provide not only reliable and efficient daily flow predic.
Importance of boundary layer mixing for the isotopic composition of surface vapor over the subtropical North Atlantic Ocean

During the summer 2012, we carried out continuous measurements of the isotopic composition (δ) of water vapor over the near‐surface subtropical North Atlantic Ocean (STRASSE cruise). In this region of excess evaporation, we investigate the control of evaporation and mixing with a lower troposphere‐derived, isotopically depleted air mass on the near‐surface δ. We use a simple model to simulate the near‐surface δ as the result of a two end‐member mixing of the evaporative flux with free tropospheric air. The evaporative flux δ was estimated by the Craig and Gordon equation while the δ of the lower troposphere was taken from the LMDZ‐iso global atmospheric circulation model. This simulation considers instantaneous mixing of lower tropospheric air with the evaporated flux and neglects lateral advection. Despite these simplifications, the simulations allow to identify the controls on the near‐surface δ. The d‐excess variability is largely a consequence of varying kinetic effects during evaporation, even during a convection event when the input of tropospheric vapor was strong. Kinetic effects and mixing processes affect simultaneously the near‐surface δ and result in the vapor occupying distinct domains in the δ18O‐δD space. The relative humidity‐d‐excess relationship shows that the closure assumption overestimates the d‐excess variability at short time scales (less than a day). We interpret this as due to an effect of the residence time of the near‐surface water vapor on the d‐excess. Finally, we highlight the importance of reproducing mixing processes in models simulating isotopes over the subtropical North Atlantic Ocean and propose an extension of the closure assumption for use in initial conditions of distillation calculations.
Focal Eosinophilic Necrosis of the Liver in Patients with Underlying Gastric or Colorectal Cancer: CT Differentiation from Metastasis

Objective To determine the helical CT findings which help differentiate between focal eosinophilic necrosis (FEN) of the liver and metastasis in patients with underlying gastric or colorectal cancer. Materials and Methods In 21 patients with underlying gastric and colorectal cancer examined during a recent 18-month period, the presence of FEN (n=90) was proven at CT. The diagnosis was verified by biopsy in eight patients and by the transient nature of the findings related to peripheral eosinophilia (>10%) in the remainder. For comparison, 20 consecutive patients with pathologically proven hepatic metastasis from gastric or colorectal cancer (n=158) were selected. Single-phase helical CT images (7-mm collimation, pitch 1:1) were independently analyzed in a random order by two blinded readers. The parameters evaluated included the margin (depicted border, fuzzy), shape (spherical, non-spherical), attenuation (subtle hypoattenuation, hypoattenuation), and the presence or absence of rim enhancement. Results FEN far more frequently showed a fuzzy margin (81%, 84%), subtle hypoattenuation (89%, 91%), and a non-spherical shape (84% for both readers) than metastasis, for which the respective findings were 6%, 22%; 20%, 39%; and 15%, 23%. Rim enhancement was seldom found in FEN (0%, 2%), but was recognized by both readers in 40% of metastases. For all parameters, the results were statistically significant (p < .01), and showed that both readers correctly differentiated FEN from metastasis in 78% of the patients (32/41). Interobserver agreement was, in addition, excellent (κ= 0.66). Conclusion When focal hepatic lesions with a fuzzy margin, non-spherical shape and subtle hypoattenuation without rim enhancement are found, the possibility of FEN should be considered even in patients with underlying gastrointestinal malignancy.
Direct use of the solid waste from oxytetracycline fermentation broth to construct Hf-containing catalysts for Meerwein–Ponndorf–Verley reactions

The oxytetracycline fermentation broth residue (OFR) is an abundant solid waste in the fermentation industry, which is hazardous but tricky to treat. The resource utilization of the waste OFR is still challenging. In this study, a novel route of using OFR was proposed that OFR was used as the organic ligands to construct a new hafnium based catalyst (Hf-OFR) for Meerwein–Ponndorf–Verley (MPV) reactions of biomass-derived platforms. The acidic groups in OFR were used to coordinate with Hf4+, and the carbon skeleton structures in OFR were used to form the spatial network structures of the Hf-OFR catalyst. The results showed that the synthesized Hf-OFR catalyst could catalyze the MPV reduction of various carbonyl compounds under relatively mild reaction conditions, with high conversions and yields. Besides, the Hf-OFR catalyst could be recycled at least 5 times with excellent stability in activity and structures. The prepared Hf-OFR catalyst possesses the advantages of high efficiency, a simple preparation process, and low cost in ligands. The proposed strategy of constructing catalysts using OFR may provide new routes for both valuable utilization of the OFR solid waste in the fermentation industry and the construction of efficient catalysts for biomass conversion.
A geosat altimeter wind speed algorithm and a method for altimeter wind speed algorithm development

A Geosat altimeter wind speed algorithm is derived by cross-calibrating Geosat and Seasat altimeter estimates of the normalized radar cross section σ0 and modifying an existing Seasat altimeter wind speed model function to obtain a model function appropriate for Geosat observations. It is argued that the σ0 distribution measured by an altimeter is relatively stable over a sufficiently large geographical region and a long enough time period. Systematic differences between σ0 estimates from two altimeters can therefore be identified based on comparisons of their σ0 histograms. Any such systematic differences can then be corrected using independent σ0 estimates. When this method is applied to the Geosat and Seasat altimeters, a systematic difference between the two σ0 histograms is shown to be consistent with differences between Seasat altimeter and nadir Seasat scatterometer estimates of σ0 deduced independently by a previous study. This supports the conclusions that (1) the σ0 distribution is stable, and (2) the Seasat altimeter estimates of σ0 were miscalibrated. After modifying the existing Seasat altimeter wind speed algorithm to account for this apparent σ0 error, the resulting Geosat estimates of wind speed agree with high-quality buoy observations to within an rms difference of less than 2 m/s.
Rapid diversification associated with a macroevolutionary pulse of developmental plasticity

Developmental plasticity has been proposed to facilitate phenotypic diversification in plants and animals, but the macroevolutionary potential of plastic traits remains to be objectively tested. We studied the evolution of feeding structures in a group of 90 nematodes, including Caenorhabditis elegans, some species of which have evolved a mouthpart polyphenism, moveable teeth, and predatory feeding. Comparative analyses of shape and form, using geometric morphometrics, and of structural complexity revealed a rapid process of diversification associated with developmental plasticity. First, dimorphism was associated with a sharp increase in complexity and elevated evolutionary rates, represented by a radiation of feeding-forms with structural novelties. Second, the subsequent assimilation of a single phenotype coincided with a decrease in mouthpart complexity but an even stronger increase in evolutionary rates. Our results suggest that a macroevolutionary ‘pulse’ of plasticity promotes novelties and, even after the secondary fixation of phenotypes, permits sustained rapid exploration of morphospace. DOI: http://dx.doi. org/10.7554/eLife.05463. 001
Evaluation of Landsat-7 SLC-off image products for forest change detection

Since July 2003, Landsat-7 ETM+ has been operating without the scan line corrector (SLC), which compensates for the forward motion of the satellite in the imagery acquired. Data collected in SLC-off mode have gaps in a systematic wedge-shaped pattern outside of the central 22 km swath of the imagery; however, the spatial and spectral quality of the remaining portions of the imagery are not diminished. To explore the continued use of Landsat-7 ETM+ SLC-off imagery to characterize change in forested environments, we compare the change detection results generated from a reference image pair (a 1999 Landsat-7 ETM+ image and a 2003 Landsat-5 TM image) with change detection results generated from the same 1999 Landsat-7 ETM+ image coupled with three different 2003 Landsat-7 SLC-off products: unremediated SLC-off (i.e., with gaps); histogram-based gap-filled; and segment-based gap-filled. The results are compared on both a pixel and polygon basis; on a pixel basis, the unremediated SLC-off product missed 35% of the change identified by the reference data, and the histogram- and segment-based gap-filled products missed 23% and 21% of the change, respectively. When using forest inventory polygons as a context for change (to reduce commission error), the amount of change missed was 31%, 14%, and 12% for the each of the unremediated, histogram-based gap-filled, and segment-based gap-filled products, respectively. Our results indicate that over the time period considered, and given the types and spatial distribution of change events within our study area, the gap-filled products can provide a useful data source for change detection in forested environments. The selection of which product to use is, however, very dependent on the nature of the application and the spatial configuration of change events.
A Randomized Trial of Closed-Loop Insulin Delivery Postpartum in Type 1 Diabetes

OBJECTIVE This study aimed to evaluate the efficacy of closed-loop insulin delivery postpartum. RESEARCH DESIGN AND METHODS In this open-label, randomized controlled trial, postpartum individuals with type 1 diabetes were randomized to hybrid closed-loop insulin delivery with the MiniMed 670G/770G system in automode or sensor-augmented pump therapy in the first 12-weeks postpartum followed by a continuation phase with closed-loop insulin delivery for all until 24 weeks postpartum. RESULTS Eighteen participants (mean ± SD age 32 ± 3.5 years, diabetes duration 22 ± 7.3 years, and early pregnancy HbA1c 52 ± 6.8 mmol/mol [6.9 ± 0.9%]) completed 24 weeks of postpartum follow-up. In the randomized phase, percent time in range 70–180 mg/dL (3.9–10 mmol/L) did not differ between groups (79.2 ± 8.7% vs. 78.2 ± 6.0%; P = 0.41). Participants randomized to closed-loop insulin delivery spent less time <70 mg/dL (3.9 mmol/L) and <54 mg/dL (3.0 mmol/L) (1.7 ± 0.8% vs. 5.5 ± 3.3% [P < 0.001] and 0.3 ± 0.2% vs. 1.1 ± 0.9% [P = 0.008]). Time >180 mg/dL (10 mmol/L) was not different between groups (18.7 ± 8.8% vs. 15.9 ± 7.7%; P = 0.21). In the continuation phase, those initially randomized to sensor-augmented pump therapy had less time <70 mg/dL after initiation of closed-loop insulin delivery (5.5 ± 3.3% vs. 3.3 ± 2.2%; P = 0.039). The closed-loop group maintained similar glycemic metrics in both study phases. There were no episodes of diabetic ketoacidosis or severe hypoglycemia in the randomized or continuation phase in either group. CONCLUSIONS Women randomized to closed-loop insulin delivery postpartum had less hypoglycemia than those randomized to sensor-augmented pump therapy. There were no safety concerns. These findings are reassuring for use of closed-loop insulin delivery postpartum because of its potential to reduce hypoglycemia.
Location of the photosynthetic carbon metabolism in microcompartments and separated phases in microalgal cells

Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid–liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin–Benson–Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.
Hg 0 trends in the North and South Atlantic

It was recently found that atmospheric Hg had decreased with 20-38% worldwide since the mid 1990s. However, the decrease is not supported by emission inventories that show rising global anthropogenic emissions over the past decades. We analyzed atmospheric data from 22 ship cruises in the North Atlantic (defined as 2°N-65°N), and 15 in the South Atlantic (defined as 70°S-8°N) between 1977 and 2010, as well as surface water Hg 0 from 10 cruises in the West Atlantic Ocean between 1998 and 2010. Linear regression analysis based on these cruise ensembles for each hemisphere will be discussed. We use the GEOS-Chem biogeochemical model to explore possible drivers of the Hg 0 trends found in this study and at previous studies at land based stations. These findings will also be discussed.
The Transposon-Like Correia Elements Encode Numerous Strong Promoters and Provide a Potential New Mechanism for Phase Variation in the Meningococcus

Neisseria meningitidis is the primary causative agent of bacterial meningitis. The genome is rich in repetitive DNA and almost 2% is occupied by a diminutive transposon called the Correia element. Here we report a bioinformatic analysis defining eight subtypes of the element with four distinct types of ends. Transcriptional analysis, using PCR and a lacZ reporter system, revealed that two ends in particular encode strong promoters. The activity of the strongest promoter is dictated by a recurrent polymorphism (Y128) at the right end of the element. We highlight examples of elements that appear to drive transcription of adjacent genes and others that may express small non-coding RNAs. Pair-wise comparisons between three meningococcal genomes revealed that no more than two-thirds of Correia elements maintain their subtype at any particular locus. This is due to recombinational class switching between elements in a single strain. Upon switching subtype, a new allele is available to spread through the population by natural transformation. This process may represent a hitherto unrecognized mechanism for phase variation in the meningococcus. We conclude that the strain-to-strain variability of the Correia elements, and the large number of strong promoters encoded by them, allows for potentially widespread effects within the population as a whole. By defining the strength of the promoters encoded by the eight subtypes of Correia ends, we provide a resource that allows the transcriptional effects of a particular subtype at a given locus to be predicted.