Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale and significant expression from pseudogenes in Sodalis glossinidius – a facultative bacterial endosymbiont

The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions, and demonstrate that pseudogenes are more complex than a simple degrading DNA sequence. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches. Importance Bacterial genomes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires – maintaining genome efficiency. In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.
Equity and Cash in Intercorporate Asset Sales: Theory and Evidence

We develop a two-sided asymmetric information model of asset sales that incorporates the key differences from mergers and allows the information held by each party to be impounded in the transaction. The buyer's information is conveyed through a first-stage competitive auction. A seller with unfavorable information about the asset accepts the cash offer of the highest bidder. A seller with favorable information proposes a take-it-or-leave-it counteroffer that entails buyer equity. Thus, the cash-equity decision reflects the seller's but not the buyer's information in contrast to the theoretical and empirical findings for mergers. The central prediction of our model is that there are large gains in wealth for both buyers and sellers in equity-based asset sales, whereas cash sales generate significantly smaller gains that typically accrue only to sellers. Our empirical results are consistent with the predictions of our theoretical model. The Author 2008. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org. , Oxford University Press.
Replacement of cereal grains by orange pulp and carob pulp in faba bean-based diets fed to lambs. Effects on growth performance and meat quality

Fourteen weaned lambs (43 days of age) were divided into two equal groups of seven animals and received two different diets. The experimental diet contained 10% of carob pulp and 10% of orange pulp associated to 54% of faba bean. The control diet contained 12% of maize meal and 12% of barley meal associated to 49.2% of faba bean. Both diets were pelletted and given ad libitum. The two diets had comparable contents of dry matter, ash, crude fat, fibre and crude protein. Control diet was relatively higher in soluble nitrogen than the experimental one. However, experimental diet was higher in fibre-bound nitrogen and in total and condensed tannins than control one. At the end of the feeding trial (120 d of age) growth and slaughter performance were comparable between treatments. Chemical analysis of meat samples did not show any significant difference between groups. Physical analysis of meat showed a higher ( P < 0.05) lightness (L*) value in experimental group than in the control one. Sensory analysis allowed the panellists to discriminate lamb meat from the two groups. Flavour, tenderness and juiciness were judged to be more intense ( P < 0.01) in the meat of control group; also overall acceptability was higher ( P < 0.05) in this group. It was concluded that the replacement of cereal grains with carob and orange pulp in lamb fattening diet is useful to reduce feeding costs. Nevertheless, we need further investigations on the level of inclusion in the diet, in order to avoid the negative effects on sensory attributes without detrimental effect on growth per- formance. cereal grains / orange pulp / carob pulp / growth / meat quality / sheep
' s personal copy A spectral index to monitor the head-emergence of wheat in semi-arid conditions

Harvesting wheat (Triticium aestivum L.) for forage or leaving it for grain is the main decision uncertainty growers face in semi-arid regions during mid-season. To facilitate decision-making, a decision support system (DSS) has recently been proposed that requires information about crop water and nutritional status during spike emergence. Though remote sensing has been used to provide site-specific crop status information, a spectral vegetation index is needed to ensure that the information has been acquired during spike emergence. The objective of this study was to propose a spectral index sensitive to spike emergence and validate its suitability across different commercial farm fields by using ground spectral measurements and multispectral satellite imagery. To develop the index, controlled experiments with commonly grown wheat varieties were conducted during the 2004/2005 and 2005/2006 growing season in the agricultural area of the northern Negev desert of Israel. The experiments showed that spike emergence correlated most strongly (r = 0.7, p < 0.05) with spectral changes near the 1.2 mm water absorption feature in contrast to the band at 1.1 mm which appeared to be only weakly correlated. Thus, the spike emergence sensitive band at 1.2 mm has been combined with the insensitive band at 1.1 mm as reference to form the ratio-based normalized heading index (NHI). Experimental data were then used to establish an index threshold that helps separate data acquired before and after spike emergence. The proposed NHI was able to identify spike emergence with a classification accuracy varying between 53 and 83%. Accuracy was influenced by season, and whether narrow or broad spectral bands were used. Validation of the index in commercial farm fields in Israel and the United States showed that the classification accuracy was similar for ground spectral measurements and the advanced land imager (ALI) satellite imagery. These results suggest that the NHI is suited for identifying the onset of heading throughout wheat-growing areas without the need for characterizing seasonal trends. 2008 Elsevier B.V. All rights reserved. * Corresponding author. Tel. : +972 8 9928654; fax: +972 8 9926485. E-mail address: bonfil@volcani.agri. gov.il (D.J. Bonfil).
Contribution Dairy-Food , Calcium , Magnesium , and Vitamin D Intake and Endometriosis : A Prospective Cohort Study

The etiology of endometriosis is poorly understood, and few modifiable risk factors have been identified. Dairy foods and some nutrients can modulate inflammatory and immune factors, which are altered in women with endometriosis. We investigated whether intake of dairy foods, nutrients concentrated in dairy foods, and predicted plasma 25-hydroxyvitamin D (25(OH)D) levels were associated with incident laparoscopically confirmed endometriosis among 70,556 US women in Nurses’ Health Study II. Diet was assessed via food frequency questionnaire. A score for predicted 25(OH)D level was calculated for each participant. During 737,712 person-years of followup over a 14-year period (1991–2005), 1,385 cases of incident laparoscopically confirmed endometriosis were reported. Intakes of total and low-fat dairy foods were associated with a lower risk of endometriosis. Women consuming more than 3 servings of total dairy foods per day were 18% less likely to be diagnosed with endometriosis than those reporting 2 servings per day (rate ratio = 0.82, 95% confidence interval: 0.71, 0.95; Ptrend = 0.03). In addition, predicted plasma 25(OH)D level was inversely associated with endometriosis. Women in the highest quintile of predicted vitamin D level had a 24% lower risk of endometriosis than women in the lowest quintile (rate ratio = 0.76, 95% confidence interval: 0.60, 0.97; Ptrend = 0.004). Our findings suggest that greater predicted plasma 25(OH)D levels and higher intake of dairy foods are associated with a decreased risk of endometriosis.
OBSERVER BASED DYNAMIC VISUAL FEEDBACK CONTROL FOR NONLINEAR ROBOTICS SYSTEMS

Abstract This paper investigates a robot motion control problem with visual information. Firstly the model of the relative rigid body motion (positions and rotations) and the method for the estimation of the relative rigid body motion are presented in order to derive the visual feedback system. Secondly we consider the velocity observer and derive the dynamic visual feedback system which contains the manipulator dynamics. Finally the main result with respect to stability for the proposed dynamic visual feedback control is discussed.
Limited‐Transpiration Trait May Increase Maize Drought Tolerance in the US Corn Belt

Yield loss due to water deficit is ubiquitous in maize (Zea mays L.) production environments in the United States. The impact of water deficits on yield depends on the cropping system management and physiological characteristics of the hybrid. Genotypic diversity among maize hybrids in the transpiration response to vapor pressure deficit (VPD) indicates that a limited-transpiration trait may contribute to improved drought tolerance and yield in maize. By limiting transpiration at VPD above a VPD threshold, this trait can increase both daily transpiration efficiency and water availability for lateseason use. Reduced water use, however, may compromise yield potential. The complexity associated with genotype X environment X management interactions can be explored in a quantitative assessment using a simulation model. A simulation study was conducted to assess the likely effect of genotypic variation in limited-transpiration rate on yield performance of maize at a regional scale in the United States. We demonstrated that the limited-transpiration trait can result in improved maize performance in drought-prone environments and that the impact of the trait on maize productivity varies with geography, environment type, expression of the trait, and plant density. The largest average yield increase was simulated for drought-prone environments (135 g m(-2)), while a small yield penalty was simulated for environments where water was not limiting (-33 g m(-2)). Outcomes from this simulation study help interpret the ubiquitous nature of variation for the limited-transpiration trait in maize germplasm and provide insights into the plausible role of the trait in past and future maize genetic improvement.
Coupling constants and the generalized Riemann problem for isothermal junction flow

We consider gas flow in pipe networks governed by the isothermal Euler equations. A set of coupling conditions is required to completely specify the Riemann problem at the junction. The momentum-related condition has no obvious expression and different approaches have been used in previous work. For the condition of equal momentum flux, Colombo and Garavello [A well posed Riemann problem for the p-system at a junction, Netw. Heterog. Media 1 (2006) 495–511] proved existence and uniqueness of solutions globally in time and locally in the subsonic region of the state space. If the entropy constraint is not considered, we are able to prove existence and uniqueness globally in the subsonic region for any momentum-related coupling constant satisfying a monotonicity requirement. The previously suggested conditions of equal pressure and equal momentum flux satisfy this requirement, but in general they both fail to fulfill the entropy constraint. The classical Bernoulli invariant is a natural scalar formulation o.
First Data Release of the COSMOS Lyα Mapping and Tomography Observations: 3D Lyα Forest Tomography at 2.05 < z < 2.55

Faint star-forming galaxies at z ∼ 2–3 can be used as alternative background sources to probe the Lyα forest in addition to quasars, yielding high sightline densities that enable 3D tomographic reconstruction of the foreground absorption field. Here, we present the first data release from the COSMOS Lyα Mapping And Tomography Observations (CLAMATO) Survey, which was conducted with the LRIS spectrograph on the Keck I telescope. Over an observational footprint of 0.157 deg2 within the COSMOS field, we used 240 galaxies and quasars at 2.17 < z < 3.00, with a mean comoving transverse separation of , as background sources probing the foreground Lyα forest absorption at 2.05 < z < 2.55. The Lyα forest data was then used to create a Wiener-filtered tomographic reconstruction over a comoving volume of with an effective smoothing scale of . In addition to traditional figures, this map is also presented as a virtual-reality visualization and manipulable interactive figure. We see large overdensities and underdensities that visually agree with the distribution of coeval galaxies from spectroscopic redshift surveys in the same field, including overdensities associated with several recently discovered galaxy protoclusters in the volume. Quantitatively, the map signal-to-noise is over a 3 h−1Mpc top-hat kernel based on the variances estimated from the Wiener filter. This data release includes the redshift catalog, reduced spectra, extracted Lyα forest pixel data, and reconstructed tomographic map of the absorption. These can be downloaded from Zenodo (10.5281/zenodo.1292459).
Decaying trees improve nesting opportunities for cavity‐nesting birds in temperate and boreal forests: A meta‐analysis and implications for retention forestry

Abstract Many studies have dealt with the habitat requirements of cavity‐nesting birds, but there is no meta‐analysis on the subject and individual study results remain vague or contradictory. We conducted a meta‐analysis to increase the available evidence for nest‐site selection of cavity‐nesting birds. Literature was searched in Web of Science and Google Scholar and included studies that provide data on the habitat requirements of cavity‐nesting birds in temperate and boreal forests of varying naturalness. To compare nest and non‐nest‐tree characteristics, the following data were collected from the literature: diameter at breast height (DBH) and its standard deviation (SD), sample size of trees with and without active nest, amount of nest and available trees described as dead or with a broken crown, and amount of nest and available trees that were lacking these characteristics. Further collected data included bird species nesting in the cavities and nest‐building type (nonexcavator/excavator), forest type (coniferous/deciduous/mixed), biome (temperate/boreal), and naturalness (managed/natural). From these data, three effect sizes were calculated that describe potential nest trees in terms of DBH, vital status (dead/alive), and crown status (broken/intact). These tree characteristics can be easily recognized by foresters. The results show that on average large‐diameter trees, dead trees, and trees with broken crowns were selected for nesting. The magnitude of this effect varied depending primarily on bird species and the explanatory variables forest type and naturalness. Biome had lowest influence (indicated by ΔAIC). We conclude that diameter at breast height, vitality, and crown status can be used as tree characteristics for the selection of trees that should be retained in selectively harvested forests.
Validation practices for satellite‐based Earth observation data across communities

Assessing the inherent uncertainties in satellite data products is a challenging task. Different technical approaches have been developed in the Earth Observation (EO) communities to address the validation problem which results in a large variety of methods as well as terminology. This paper reviews state‐of‐the‐art methods of satellite validation and documents their similarities and differences. First, the overall validation objectives and terminologies are specified, followed by a generic mathematical formulation of the validation problem. Metrics currently used as well as more advanced EO validation approaches are introduced thereafter. An outlook on the applicability and requirements of current EO validation approaches and targets is given.
Algebraic Topology – A Student's Guide: Vector fields on spheres

The question of vector fields on spheres arises in homotopy theory and in the theory of fibre bundles, and it presents a classical problem, which may be explained as follows. For each n, let Sn-I be the unit sphere in euclidean n-space Rn. A vector field on Sn-1 is a continuous function v assigning to each point x of Sn-1 a vector v(x) tangent to Sn-1 at x. Given r such fields v1, v2, . , Vr, we say that they are linearly independent if the vectors v1(x), v2(x), *--, vr(x) are linearly independent for all x. The problem, then, is the following: for each n, what is the maximum number r of linearly independent vector fields on Sn-i? For previous work and background material on this problem, we refer the reader to [1, 10, 11, 12, 13, 14, 15, 16]. In particular, we recall that if we are given r linearly independent vector fields vi(x), then by orthogonalisation it is easy to construct r fields wi(x) such that w1(x), w2(x), *I * , wr(x) are orthonormal for each x. These r fields constitute a cross-section of the appropriate Stiefel fibering. The strongest known positive result about the problem derives from the Hurwitz-Radon-Eckmann theorem in linear algebra [8]. It may be stated as follows (cf. James [13]). Let us write n = (2a + 1)2b and b = c + 4d, where a, b, c and d are integers and 0 < c < 3; let us define p(n) = 2c + 8d. Then there exist p(n) 1 linearly independent vector fields on Sn-1. It is the object of the present paper to prove that the positive result stated above is best possible.
3.6 AND 4.5 μm PHASE CURVES AND EVIDENCE FOR NON-EQUILIBRIUM CHEMISTRY IN THE ATMOSPHERE OF EXTRASOLAR PLANET HD 189733b

We present new, full-orbit observations of the infrared phase variations of the canonical hot Jupiter HD 189733b obtained in the 3.6 and 4.5 μm bands using the Spitzer Space Telescope. When combined with previous phase curve observations at 8.0 and 24 μm, these data allow us to characterize the exoplanet's emission spectrum as a function of planetary longitude and to search for local variations in its vertical thermal profile and atmospheric composition. We utilize an improved method for removing the effects of intrapixel sensitivity variations and robustly extracting phase curve signals from these data, and we calculate our best-fit parameters and uncertainties using a wavelet-based Markov Chain Monte Carlo analysis that accounts for the presence of time-correlated noise in our data. We measure a phase curve amplitude of 0.1242% ± 0.0061% in the 3.6 μm band and 0.0982% ± 0.0089% in the 4.5 μm band, corresponding to brightness temperature contrasts of 503 ± 21 K and 264 ± 24 K, respectively. We find that the times of minimum and maximum flux occur several hours earlier than predicted for an atmosphere in radiative equilibrium, consistent with the eastward advection of gas by an equatorial super-rotating jet. The locations of the flux minima in our new data differ from our previous observations at 8 μm, and we present new evidence indicating that the flux minimum observed in the 8 μm is likely caused by an overshooting effect in the 8 μm array. We obtain improved estimates for HD 189733b's dayside planet–star flux ratio of 0.1466% ± 0.0040% in the 3.6 μm band and 0.1787% ± 0.0038% in the 4.5 μm band, corresponding to brightness temperatures of 1328 ± 11 K and 1192 ± 9 K, respectively; these are the most accurate secondary eclipse depths obtained to date for an extrasolar planet. We compare our new dayside and nightside spectra for HD 189733b to the predictions of one-dimensional radiative transfer models from Burrows et al. and conclude that fits to this planet's dayside spectrum provide a reasonably accurate estimate of the amount of energy transported to the night side. Our 3.6 and 4.5 μm phase curves are generally in good agreement with the predictions of general circulation models for this planet from Showman et al., although we require either excess drag or slower rotation rates in order to match the locations of the measured maxima and minima in the 4.5, 8.0, and 24 μm bands. We find that HD 189733b's 4.5 μm nightside flux is 3. 3σ smaller than predicted by these models, which assume that the chemistry is in local thermal equilibrium. We conclude that this discrepancy is best explained by vertical mixing, which should lead to an excess of CO and correspondingly enhanced 4.5 μm absorption in this region. This result is consistent with our constraints on the planet's transmission spectrum, which also suggest excess absorption in the 4.5 μm band at the day–night terminator.
Effect of a single session exercise done twice a day on plasma lipids, lipoproteins, immun globulin and cortisol in elite karatekas

Introduction: There is a large body of research showing that aerobic based physical exercise has an effect on plasma lipid and lipoproteins. Relatively little attention, however, has been directed toward the lipid andlipoproteins responses to a single session of exercise in athletes. Furthermore, studies have shown that our bodies follow a daily cycle called the circadian rhythms, which regulate everything from body temperature, metabolism, blood pressure, hormone secretion and performance. Thus, the aim of this study was to examine whether a single session of exercise at different time of day affected lipid andlipoproteins levels before and after maximal karate exercise. Methods: twenty karate athlete (mean (SD) age 23 (3.4) years) volunteered to participate in the study and divided to trial and control groups. A trial group, with 36 hours between test sessions, performed two identical training sessions with %70-90 reserve heart rate at 07 and 19 hours in the same indoor place. plasma samples were taken pre and post exercise in all subjects. Results: significant decrease observed in the afternoon VLDL and TG and increase HDL in posttest versus pretest (P<0.05). Trial and control group comparison showed significant difference in posttest of TC and LDL (P≤0.05). Conclusion: These results suggest that a single session exercise affect cortisol, immunoglobulin, lipid andlipoproteins with circadian variation in some variables. © Idōkan Poland Association “IDO MOVEMENT FOR CULTURE. Journal of Martial Arts Anthropology”, Vol. 11, no. 3 (2011), pp. 42–46