Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera , subsection Oenothera : I . Sequence evaluation and plastome evolution y

The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speciation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome– genome incompatibility. For evaluation of its molecular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163365bp (plastome IV) to 165 728bp (plastome I), display between 96.3% and 98.6% sequence similarity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, deletions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsectionspecific 56 kb inversion within the large single-copy segment. This inversion disrupted operon structures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I–III in one clade, while plastome IV appears to be closest to the common
The Ine ¢ ciency of Re nancing : Why Prepayment Penalties Are Good for Risky Borrowers

This paper explores the practice of mortgage re nancing in a dynamic competitive lending model with risky borrowers and costly default. We show that prepayment penalties improve welfare by ensuring longer-term lending contracts, which prevents the mortgage pools from becoming disproportionately composed of the riskiest borrowers over time (known in the insurance literature as reclassi cation risk). Mortgages with prepayment penalties allow lenders to lower mortgage rates and extend credit to the least creditworthy, with the largest bene ts going to the riskiest borrowers who have the highest reclassi cation risk. Empirical evidence from more than 21,000 non-agency securitized xed rate mortgages is consistent with the key predictions of our model. Our results suggest that regulations banning re nancing penalties might have the unintended consequence of restricting access to credit and raising rates for the least creditworthy borrowers.
1 DEVELOPMENT OF FLUID-SEDIMENT-SEABED INTERACTION MODEL AND ITS APPLICATION

To provide a computational framework for simulating fluid-sediment-seabed interactions, a three-dimensional coupled fluid-sediment-seabed interaction model was developed and applied to seabed response under regular waves and local scouring from tsunami run-up. For the seabed response under the regular waves, the validity of the model was verified from comparison with an analytical solution. For the seabed response under the tsunami-induced local scouring, numerical results showed that the model had sufficient computational capability to simulate the seabed response during the onset of the local scouring, and suggested that the model is a useful tool for analyzing and evaluating a general complex fluid-sediment-seabed interaction phenomenon in a marine environment.
Identification of the DEAD box RNA helicase DDX3 as a therapeutic target in colorectal cancer

Identifying druggable targets in the Wnt-signaling pathway can optimize colorectal cancer treatment. Recent studies have identified a member of the RNA helicase family DDX3 (DDX3X) as a multilevel activator of Wnt signaling in cells without activating mutations in the Wnt-signaling pathway. In this study, we evaluated whether DDX3 plays a role in the constitutively active Wnt pathway that drives colorectal cancer. We determined DDX3 expression levels in 303 colorectal cancers by immunohistochemistry. 39% of tumors overexpressed DDX3. High cytoplasmic DDX3 expression correlated with nuclear β-catenin expression, a marker of activated Wnt signaling. Functionally, we validated this finding in vitro and found that inhibition of DDX3 with siRNA resulted in reduced TCF4-reporter activity and lowered the mRNA expression levels of downstream TCF4-regulated genes. In addition, DDX3 knockdown in colorectal cancer cell lines reduced proliferation and caused a G1 arrest, supporting a potential oncogenic role of DDX3 in colorectal cancer. RK-33 is a small molecule inhibitor designed to bind to the ATP-binding site of DDX3. Treatment of colorectal cancer cell lines and patient-derived 3D cultures with RK-33 inhibited growth and promoted cell death with IC50 values ranging from 2.5 to 8 μM. The highest RK-33 sensitivity was observed in tumors with wild-type APC-status and a mutation in CTNNB1. Based on these results, we conclude that DDX3 has an oncogenic role in colorectal cancer. Inhibition of DDX3 with the small molecule inhibitor RK-33 causes inhibition of Wnt signaling and may therefore be a promising future treatment strategy for a subset of colorectal cancers.
Observational cosmology. IV. Perturbed spherically symmetric dust solutions

For pt.III see ibid., vol.9, p.509, (1992). The formulation and solution of the perturbed FLRW spherically symmetric field equations for dust are presented with observational data given on a past light cone. Observational coordinates are used. This follows from the treatment of the exact spherically symmetric observational solutions given in Stoeger et al (1992)-and is a preparation for formulating and solving the general FLRW perturbation equations in part V (ibid., vol.9, p.1725 (1992)). The authors explicitly write down both the first and second-order solutions to the perturbed field equations in terms of two unknown data functions r0+(z) and M0+(z), which represent the non-FLRW parts of the observer area distance-redshift and the mass-energy density-redshift relationships, respectively. These two functions are, in practice, given by fitting data sets by some functional form. Constructing concrete solutions using this scheme requires such functions-either presupposed or determined by actual data. Finally, on the basis of these perturbed solutions, a criterion for 'almost FLRW' observational spacetimes is proposed, and other issues, such as that of errors and gaps in the data and their evolution, are discussed.
SOIL MACROFAUNA COMMUNITY STRUCTURE ACROSS LAND USE SYSTEMS OF TAITA, KENYA

This paper presents data on diversity and abundance of soil macrofauna in various land use systems in Taita (natural forest, plantation forest, fallow, coffee, napier, and maize, Horticulture. Each was sampled for macrofauna using three sampling methods (monolith, transect and pitfall trapping). Seventy eight (78) genera/species were recorded across the different land use systems of Taita. Renyi diversity profile indicated no significant differences in species richness across land use systems as reflected by the very close diversity profiles at α = 0. However, the two diversity indices (Shannon index: α = 1 and Simpson’s index: α = 2) indicated that plantation forest was the most diverse of the land use systems, while fallow and maize were least diverse. Renyi evenness profile indicated that the plantation forest was most even in terms of species distribution which was least in maize. However because some of the profiles for some land use systems cross each other, they could not be ranked. The major macrofauna groups recorded in the Taita benchmark site included: Hymenoptera, Isoptera, Coleoptera, Oligochaeta and Orthoptera and Arenae. Generally Hymenoptera were the most abundant of the macrofauna groups constituting about 36% of the total followed by Isoptera (22%), Oligochaeta (16%), Coleoptera (10%). The other macrofauna (Arenae, Diplopoda, Diptera, Orthoptera, Blattidae, Isopoda, Chilopoda- Geopholomorpha, Hemiptera, Opiliones,Chiopoda-Scolopendromorpha, Lepidoptera, Dermaptera, Phasmidae, Blattelidae and Mantodea each constituted <10% of the total macrofauna recorded. Hymenoptera was ranked 1st as it had the highest total abundance (59,440 individuals m-2), while Mantodea was ranked 18th and had the lowest total abundance (6 individuals m-2). Generally macrofauna density was higher in arable systems than forests, although the differences were not always significant. Except for Chilopoda-Geopholomorpha, Chilopoda- Scolopendromorpha and Isopoda, all the other macroafauna groups were not significantly different across land use systems. The three groups (Chilopoda-Geopholomorpha, Chilopoda- Scolopendromorpha and Isopoda) were significantly highest in the forests than in all the other land use systems. These variation appear to be associated with management practices that consequently results in the destruction of nesting habitats, modification of soil microclimate within these habitats and removal of substrate, low diversity and availability of food sources for the associated macrofauna groups. The significant correlations between some soil macrofauna groups with selected soil chemical properties too show that, soil chemical characteristics may indirectly play a role in influencing the density, distribution and structure of macrofauna communities. This indicates the potential of using these fauna groups as bio-indicators of soil productivity.
Analyzing precipitationsheds to understand the vulnerability of rainfall dependent regions

It is well known that rivers connect upstream and downstream ecosystems within watersheds. Here we describe the concept of precipitationsheds to show how upwind terrestrial evaporation source areas contribute moisture for precipitation to downwind sink regions. We illustrate the importance of upwind land cover in precipitationsheds to sustain precipitation in critically water stressed downwind areas, specifically dryland agricultural areas. We first identify seven regions where rainfed agriculture is particularly vulnerable to reductions in precipitation, and then map their precipitationsheds. We then develop a framework for qualitatively assessing the vulnerability of precipitation for these seven agricultural regions. We illustrate that the sink regions have varying degrees of vulnerability to changes in upwind evaporation rates depending on the extent of the precipitationshed, source region land use intensity and expected land cover changes in the source region.
Exit Strategies ∗

We study alternative scenarios for exiting the post-crisis fiscal and monetary accommodation using the model of Angeloni and Faia (2010), that combines a standard DSGE framework with a fragile banking sector, suitably modified and calibrated for the euro area. Credibly announced and fast fiscal consolidations dominate – based on simple criteria – alternative strategies incorporating various degrees of gradualism and surprise. The fiscal adjustment should be based on spending cuts or else be relatively skewed towards consumption taxes. The phasing out of monetary accommodation should be simultaneous or slightly delayed. We also find that, contrary to widespread belief, Basel III may well have an expansionary macroeconomic effect. JEL classification: G01, E63, H12
Ground‐based detection of sprites and their parent lightning flashes over Africa during the 2006 AMMA campaign

Sprites have been detected in video camera observations from Niger over mesoscale convective systems in Nigeria during the 2006 AMMA (African Monsoon Multidisciplinary Analysis) campaign. The parent lightning flashes have been detected by multiple Extremely Low Frequency (ELF) receiving stations worldwide. The recorded charge moments of the parent lightning flashes are often in excellent agreement between different receiving sites, and are furthermore consistent with conventional dielectric breakdown in the mesosphere as the origin of the sprites. Analysis of the polarization of the horizontal magnetic field at the distant receivers provides evidence that the departure from linear magnetic polarization at ELF is caused primarily by the day–night asymmetry of the Earth–ionosphere cavity. Copyright © 2009 Royal Meteorological Society
Thermal growing season in Poland calculated by two different methods

Abstract Methods of identifying dates of passing determined threshold value are of significant importance in the study of thermal growing seasons. The difficulty to determine dates of beginning and end of growing season in a given year stems from the fact that daily mean air temperature changes irregularly on a day-to-day basis often crossing the threshold value (i.e. 5°C) multiple times. The most frequently used method to identify dates of threshold value crossing is the mathematical or graphical method proposed by Gumiński in 1950 which based on monthly mean air temperature values. In the 1970s, Huculak and Makowiec presented a method using daily mean values of air temperature. It is assumed that both methods give comparative results although calculations of daily mean air temperature render more accurate results. This paper presents the comparison of these two methods. Air temperatures measurements from 1966–2005 taken at 38 weather stations located in various physiographic conditions in Poland were used.
Pharmacologic Management of Overactive Bladder and Urge Incontinence: A Review of New and Old Treatment Options

Within the wall of the bladder is a rich network of parasympathetic efferent fibers and postganglionic cell bodies. There is little sympathetic innervation of the bladder; therefore the primary neurotransmitter involved in voluntary micturition is acetylcholine. In the male urinary tract, the neck of the bladder does contain sympathetic innervation to prevent retrograde ejaculation, thus responds to adrenergic stimulation as well [3,4]. The afferent nerve fibers in the bladder are activated by increased intra-vesical pressure, bladder stretch, as well as existing urine flow. These fibers initiate signals to urinate when the bladder is full, as well as to continue urinating until the bladder is empty [3].
From Turmoil to Crisis: Dislocations in the FX Swap Market Before and After the Failure of Lehman Brothers

This paper investigates dislocations in the foreign exchange (FX) swap market between the US dollar and three major European currencies. After the failure of Lehman Brothers in September 2008, deviations from covered interest parity (CIP) were negatively associated with the creditworthiness of US financial institutions (as well as that of European institutions), consistent with the deepening of a dollar liquidity problem into a global phenomenon. US dollar term funding auctions by the ECB, SNB, and BoE, as well as the US Federal Reserve commitment to provide unlimited dollar swap lines are found to have ameliorated the FX swap market dislocations.
In Search of the First Hominids

BECOMING HUMANThanks to an astonishing series of fossil discoveries, researchers are at last glimpsing our earliest ape ancestors, back beyond 4 million years ago. The finds are shifting attention from the savanna to the woods--and changing ideas about what it means to be a hominid. Indeed, they may end up displacing Lucy, who for 2 decades has stood alone as the first known human ancestor. The faces and many features of these earliest hominids remain shadowy, but their outlines can be discerned, revealing apes the size of chimpanzees that walked upright through African forests. The second story in this special Focus section explores more recent prehistory, namely the birth of our own species, Homo sapiens .
Section properties of palm petioles , Part 1 : The influence of section shape on the flexural and torsional properties of selected palm petioles

Shape factors have been used to calculate the shape efficiency of palm leaf petiole sections in order to understand how palms compensate for the torsional and bending forces put upon them by their environment. That part of the palm leaf that is similar in form to the leaf stalk (petiole) in dicot leaves will be referred to as a petiole in this paper, whilst recognising that it is probably not an exact homologue. Wind and rain on the blade generate combined flexural and torsion loads on the petiole and a question arises as to how the section properties of the petiole deal with this loading. By isolating the shape from the size of the sections through the use of shape factors, the effects of the petiole section shape can be analysed on its own. Thus micro structural and material factors become a separate issue and will be discussed in a later paper. Cross section profiles from seven palm petioles are modelled, independent of their sizes, in order to calculate and plot the flexural and torsional coupling efficiencies for comparison with other plants and typical engineering cross sections.
Wide Variability in Emergency Physician Admission Rates: A Target to Reduce Costs Without Compromising Quality

Introduction Attending physician judgment is the traditional standard of care for emergency department (ED) admission decisions. The extent to which variability in admission decisions affect cost and quality is not well understood. We sought to determine the impact of variability in admission decisions on cost and quality. Methods We performed a retrospective observational study of patients presenting to a university-affiliated, urban ED from October 1, 2007, through September 30, 2008. The main outcome measures were admission rate, fiscal indicators (Medicaid-denied payment days), and quality indicators (15- and 30-day ED returns; delayed hospital admissions). We asked each Attending to estimate their inpatient admission rate and correlated their personal assessment with actual admission rates. Results Admission rates, even after adjusting for known confounders, were highly variable (15.2%–32.0%) and correlated with Medicaid denied-payment day rates (p=0.038). There was no correlation with quality outcome measures (30-day ED return or delayed hospital admission). There was no significant correlation between actual and self-described admission rate; the range of mis-estimation was 0% to 117%. Conclusion Emergency medicine attending admission rates at this institution are highly variable, unexplained by known confounding variables, and unrelated to quality of care, as measured by 30-day ED return or delayed hospital admission. Admission optimization represents an important untapped potential for cost reduction through avoidable hospitalizations, with no apparent adverse effects on quality.
Soil production and hillslope transport in mid‐latitudes during the last glacial–interglacial cycle: a combined data and modelling approach in northern Ardennes

The relative efficiency of various hillslope processes through Quaternary glacial–interglacial cycles in the mid‐latitudes is not yet well constrained. Based on a unique set of topographic and soil thickness data in the Ardennes (Belgium), we combine the new CLICHE model of climate‐dependent hillslope evolution with an inversion algorithm in order to get deeper insight into the ways and timing of hillslope dynamics under one such climatic cycle. We simulate the evolution of a synthetic hill reproducing the slope, curvature, and contributing area distributions of the hillslopes of a ~ 2500 km2 real area under a simple two‐stage 120‐kyr‐long climatic scenario with linear transitions between cold and warm stages. The inversion method samples a misfit function in the model parameter space, based on estimates of the fit of topographic derivative distributions in classes of soil thickness and of the relative frequencies of the predicted soil thickness classes. Though the inversion results show remarkable convergence patterns for most parameters, no unique solution emerges. We obtain five clusters of good fits, whose centroids are taken as acceptable model solutions. Based on the predicted time series of average denudation rate and soil thickness, plus snapshots of the soil distribution at characteristic times, we discuss these solutions and, comparing them with independent data not involved in the misfit function, we identify the most realistic scenario. Beyond providing first‐order estimates of several parameters that compare well with published data, our results show that denudation rates increase dramatically for a short time at both warm–cold and cold–warm transitions, when the mean annual temperature passes through the [0, −5 °C] range. We also point to the overwhelming importance of solifluction in shaping hillslopes and transporting soil, and the role of depth‐dependent creep (including frost creep) throughout the climatic cycle, whereas the contributions of simple creep and overland flow are minor. Copyright © 2016 John Wiley & Sons, Ltd.
Community and regional scale patterns of native and exotic plant species in sand beaches of Vancouver Island, British Columbia

ii List of Tables.iv List of Figures . v Acknowledgements . vi Chapter 1. General Introduction Spatial Patterns of Vegetation Development . 2 Are Native and Exotic Species Ecologically Different? 3 Thesis Structure . 3 References.4 Chapter 2. Description and Classification of Plant Associations in Sand Beaches of the West Coast of Vancouver Island Introduction.7 Methods . 8 Study Area . 8 Field Sampling.9 Data Analyses . 13 Results . 15 Discussion.24 References.29 Chapter 3. Spatial Patterns of Native and Exotic Plant Richness in Sand Beaches Introduction.33 Methods . 35 Plant Species Richness and Plant Cover.35 Environmental Variables . 36 Seedling Experiment.37 Statistical and Comparative Analyses . 37 Results . 39 Discussion.48 Management Implications . 52 References.53 Chapter 4. Do Native and Exotic Plants Have Different Distribution–Abundance Relationships in Regional Patch Networks? Introduction.59 Methods . 60 Summary of Datasets.60 Regional Distribution: Patches and Patch Occupancy.62 Local Abundance.63 Statistical Analyses.64 Results . 65 Discussion.71 Management Implications . 72 References.75
Benthic Microalgal and Phytoplankton Production in Barnegat Bay, New Jersey (USA): Microcosm Experiments and Data Synthesis

p < 0.05). A synthesis of data from a range of coastal systems showed that benthic microalgal production could best be predicted by a combination of bottom light levels and rates of benthic respiration (a proxy for nutrient supply from the sediments) (r2 = 0.79, p < 0.05). The current and previous studies have shown that benthic algae can assimilate some or all of the nutrients mineralized in sediments, and thus can decrease the magnitude of N and P recycled to the water column. A synthesis of data across a range of shallow coastal systems revealed that little or no ammonium is released from sediments when rates of benthic photosynthesis exceed rates of benthic respiration. However, when rates of benthic respiration exceed rates of benthic photosynthesis, ammonium is recycled to the overlying water at a rate consistent with the imbalance in respiration (N mineralization) and photosynthesis (N assimilation).
Interactive comment on “ Diurnal variations of residential particulate wood burning emissions and their contribution to the concentration of Polycyclic Aromatic Hydrocarbons ( PAHs ) ” by L .

estimate the contribution of the emission sources to the aerosol organic concentration and several tracers were included to help identifying the different sources. The contribution of the wood combustion to the highly-resolved PAH concentrations was also discussed. Due to the renewed interest in residential wood combustion as alternative of fossil fuel and nuclear power consumption and its high impact on air quality, the topic of the manuscript by Poulain et al. is relevant. The manuscript is recommended for publication in the Atmospheric Physics and Chemistry Journal after a major review. The authors should address all comments and modify the manuscript accordingly. The manuscript should be also improved from the grammatical point of view.