Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling species presence-only data with random forests

The Random Forest (RF) algorithm is an ensemble of classification or regression trees, and is a widely used and high-performing machine learning technique. It is increasingly used for species distribution modelling (SDM). Many researchers use implementations of RF in the R programming language with default parameters to analyse species presence-only data together with background samples. However, there is good evidence that RF with default parameters does not perform well with such species “presence-background” data. This is often attributed to the typical disparity between the number of presence and background samples also known as class imbalance, and several solutions have been proposed. Here, we first set the context: the background sample should be large enough to represent all environments in the region. We then aim to understand the drivers of poor performance of RF with presence-background data, and explain, test and evaluate suggested solutions. Using simulated and real species data, we compare performance of default RF with other weighting and sampling approaches. We show that class overlap is an important driver of poor performance, alongside class imbalance. The results demonstrate clear evidence of improvement in the performance of RFs when class imbalance is explicitly managed by sampling methods or when the overfitting commonly associated with overlapping classes is avoided by forcing shallow trees. Presence-background data is a particular version of class imbalance in which class overlap is highly likely and extreme imbalance exists. Without compromising the environmental representativeness of the sampled background, we show several approaches to fitting RF that ameliorate the effects of imbalance and overlap, and allow excellent predictive performance. Understanding the problems of RF in presence-background data allows new insights into how best to fit models, and should guide future efforts to best deal with such data.
Zeeman-resolved spectroscopy of the coronal optical lines of Fe ions

Zeeman-resolved spectroscopy of the coronal optical lines of Fe ions In this work, the following transitions are spectroscopically investigated: Fe13+ at 530 nm, Fe9+ at 637 nm, Fe12+ at 339 nm and Fe10+ at 789 nm. These transitions occur in the solar corona and other stars and are therefore of astrophysical interest. Reference wavelength values are needed to determine plasma movements and temperatures in those stars, but scarce laboratory measurements are available and theoretical calculations are not sufficiently precise. In our case, those highly charged ions are produced in the laboratory using an electron beam ion trap. The wavelengths and g-factors are determined: 530.42870(8) nm, 637.6277(4) nm, 338.8930(3) nm, 789.3915(8) nm. For the Fe13+ at 530 nm, Fe9+ at 637 nm and Fe10+ at 789 nm transitions, the Zeeman components are well resolved. For all the measured wavelength, the uncertainty is 5-14 times smaller than for the previous best measurement. Zeeman-auflösende Spektroskopie der koronalen optischen Linien von Fe Ionen In dieser Arbeit werden die folgenden Übergänge spektroskopisch untersucht: Fe13+ bei 530 nm, Fe9+ bei 637 nm, Fe12+ bei 339 nm und Fe10+ bei 789 nm. Diese Übergänge finden in der Korona der Sonne und anderer Sterne statt und sind somit von astrophysikalischem Interesse. Referenz-Wellenlängen werden benötigt um Plasma-Bewegungen und -Temperaturen zu bestimmen, aber wenige Labormessungen sind verfügbar und theoretische Berechnungen erreichen noch keine ausreichende Genauigkeit. Diese hochgeladenen Ionen wurden im Labor durch eine Elektronenstrahl-Ionenfalle produziert und gefangen. Die Wellenlängen und g-Faktoren wurden bestimmt: 530.42870(8) nm, 637.6277(4) nm, 338.8930(3) nm, 789.3915(8) nm. Für die Fe13+ bei 530 nm, Fe9+ bei 637 nm und Fe10+ bei 789 nm Linien sind die Zeeman-Komponenten gut aufgelöst. Für alle gemessenen Wellenlängen ist die Genauigkeit um 5 bis 14 mal besser als die vorherige beste Messung.
Stability of in-plane delocalized vibrational modes in triangular Morse lattice

Delocalized nonlinear vibrational modes (DNVMs) play a very important role in the study of the dynamics of a nonlinear lattice in solid state physics. Such modes are exact solutions to the equations of motion of atoms dictated by the lattice space symmetry. If the amplitude of DNVM is above the threshold value, it is modulationally unstable. In the present study, we consider the stability of DNVMs in a two-dimensional (2D) triangular lattice with atoms interacting via the Morse potential. Critical exponents are calculated numerically as functions of the DNVM amplitude. Extrapolation to the zero value of the critical exponent gives an estimation of the DNVM amplitude, below which it is stable.
Differences in gut microbiota between silkworms (Bombyx mori) reared on fresh mulberry (Morus alba var. multicaulis) leaves or an artificial diet

Artificial diets for silkworms have many potential applications and they are important in sericulture. However, the challenges of weak larvae and low silk protein synthesis efficiency in silkworms reared on artificial diets have not been resolved. Here, we used high-throughput sequencing to analyse the differences between the gut microbiota of 5th-instar larvae reared on mulberry leaves and larvae reared on an artificial diet. The results showed that at the phylum level, Cyanobacteria, Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria are the dominant bacteria in the intestines of silkworm larvae of all the strains. But the abundance of dominant bacteria in the gut microbiota differed between the silkworm strains that were reared on mulberry leaves, as well as between the silkworm strains that were reared on the artificial diet, while the gut microbiota diversity was lower in the silkworm strains that were reared on the artificial diet. Prediction of the functions of the gut microbiota in the hosts indicated that there was no significant difference between the silkworm strains that were reared on mulberry leaves, while there were significant differences between silkworm strains reared on the artificial diet. When the silkworm diet changed from mulberry leaves to the artificial diet, changes in gut microbiota in the silkworms affected host nutrient metabolism and immune resistance. These changes may be related to the adaptation of silkworms to their long evolutionary history of eating mulberry leaves.
Triangular Brushstrokes

This paper proposes a lossy image representation where a reference image is approximated by an evolved image, constituted of variable number of triangular brushstrokes. The parameters of each triangle brush are evolved using differential evolution, which self-adapts the triangles to the reference image, and also self-adapts some of the control parameters of the optimization algorithm, including the number of triangles. Experimental results show the viability of the proposed encoding and optimization results on a few sample reference images.
RESPONSE INEQUALITY OF OPPORTUNITY : REPLY TO PEDRO ROSA DIAS AND

de Barros RP et al. 2009. Measuring Inequality of Opportunities in Latin America and the Caribbean, World Bank: Washington DC. Fleurbaey M, Schokkaert E. 2009. Unfair inequalities in health and health care. Journal of Health Economics 28(1): 73–90. Fleurbaey M, Schokkaert E. 2012. Inequity in health and health care. Handbook of Health Economics, Barros P, McGuire T, Pauly M (eds.), vol. 2. Elsevier: New York; 1003–1092. Garcia-Gomez P, Schokkaert E, Van Ourti T, Bago d’ Uva T. 2014. Equity in the face of death. Health Economics. DOI: 10.1002/hec.3092. Lefranc A, Pistolesi N, Trannoy A. 2009. Equality of opportunity and luck: definitions and testable conditions, with an application to income in France. Journal of Public Economics 93: 1189–1207. Roemer J. 1998. Equality of Opportunity, Harvard University Press: Cambridge, Mass.
Effect of Stocking Density and Methionine Levels on Growth

Rearing poultry in intensive systems needs the birds with fast growth rate to be raised at high stocking density. Based on the investigations 85 to 90% of performance gains are due to genetic selection, while the 10 to 15% are the results of improvements in nutrition and other management practices (Havenstein et al. 2003). Meanwhile, selection for growth rate and feed efficiency cause to a number of negative effects that adversely influence welfare and productivity of poultry (Lara and Rostagno, 2013). Some research has shown that high stocking density demonstrates negative effects on growth and external carcass quality (Feddes et al. 2002). Dozier et al. (2005) evaluated performance of broilers grown to final body weight of 3.1 kg. By increasing stocking density from 30 to 45 kg/m, cumulative growth rate decreased by nearly 6%. Kestin et al. (1992) reported that by increasing stocking density lymphoid organs weight (spleen and bursa of fabricius) decreased that is an indication of stress caused by overcrowding. Heckert et al. (2002) studied the effect of stocking density on immune response, lymphoid organs weight, antibody titer against sheep red blood cells (SRBC), and heterophil to lymphocyte ratio at 32 and 42 days of age, they observed that increasing stocking density resulted in significant decreases in body weight and relative weight of bursa of fabricius. In combination with fast growth, the requirements for sulphur amino acids, especially methionine are high. The experiment was conducted to investigate the effect of stocking density and incremental methionine levels on performance, immune response, carcass traits, and digestive organs of broiler chicks. A total of 390 day-old broiler chicks (Ross 308) were allocated to six dietary treatments and five replicates base on 3 × 2 factorial arrangement in a completely randomized design. Experimental diets included three levels of stocking density (12, 16 and 18 birds/m) and two levels of methionine (100 and 120% requirement recommended for Ross 308) applied during 42 days of experiment. The results showed that 18 birds density decreased body weight and weight gain, feed intake and increased feed conversion ratio (P<0.05) in overall rearing period. The 120% methionine level tended to increase body weight at 42 day of age. Stocking density significantly (P<0.05) affected the relative weight of proventriculus, pancreas, gizzard and duodenum. The jejunum relative weight and ileum length of chicks received 120% methionine level significantly increased. Antibody titer against sheep red blood cells (SRBC), Influenza and Newcastle viruses, heterophil to lymphocyte ratio and lymphoid organs except spleen were not affected by dietary treatments (P<0.05). As a conclusion, broiler performance of chicks adversely affected by stocking density and methionine levels had no considerable effect on their performance.
Using reference radiosondes to characterise NWP model uncertainty for improved satellite calibration and validation

Abstract. The characterisation of errors and uncertainties in numerical weather prediction (NWP) model fields is a major challenge that is addressed as part of the Horizon 2020 Gap Analysis for Integrated Atmospheric ECV CLImate Monitoring (GAIA-CLIM) project. In that regard, observations from the GCOS (Global Climate Observing System) Reference Upper-Air Network (GRUAN) radiosondes are being used at the Met Office and European Centre for Medium-Range Weather Forecasts (ECMWF) to assess errors and uncertainties associated with model data. The software introduced in this study and referred to as the GRUAN processor has been developed to collocate GRUAN radiosonde profiles and NWP model fields, simulate top-of-atmosphere brightness temperature at frequencies used by space-borne instruments, and propagate GRUAN uncertainties in that simulation. A mathematical framework used to estimate and assess the uncertainty budget of the comparison of simulated brightness temperature is also proposed. A total of 1 year of GRUAN radiosondes and matching NWP fields from the Met Office and ECMWF have been processed and analysed for the purposes of demonstration of capability. We present preliminary results confirming the presence of known biases in the temperature and humidity profiles of both NWP centres. The night-time difference between GRUAN and Met Office (ECMWF) simulated brightness temperature at microwave frequencies predominantly sensitive to temperature is on average smaller than 0.1 K (0.4 K). Similarly, this difference is on average smaller than 0.5 K (0.4 K) at microwave frequencies predominantly sensitive to humidity. The uncertainty estimated for the Met Office–GRUAN difference ranges from 0.08 to 0.13 K for temperature-sensitive frequencies and from 1.6 to 2.5 K for humidity-sensitive frequencies. From the analysed sampling, 90 % of the comparisons are found to be in statistical agreement. This initial study has the potential to be extended to a larger collection of GRUAN profiles, covering multiple sites and years, with the aim of providing a robust estimation of both errors and uncertainties of NWP model fields in radiance space for a selection of key microwave and infrared frequencies.
Shelf-life Estimation of Mullet (Mugil cephalus) Fillets by Mathematical Models Based on Some Biochemical Parameters and Sensory Evaluation

This study aimed to estimate the shelf-life of mullet fillets stored in ice. Cadaverine, putrescine, total volatile base nitrogen (TVB-N), peroxide value (PV) and thiobarbituric acid reactive substances (TBARS) were evaluated together with sensory analyses. Empirical mathematical models were used to describe the data, and shelf-life was estimated by using acceptability limit and the model proposed for each parameter. The models proposed were all in agreement with the experimental data and can be safely used to estimate the shelf-life of mullet fillets. The lowest shelf-life was found as 5.2 days for the sensory analysis performed by trained panelist. Shelf-lives were determined as 6.5 and 7.5 days according to TBARS and PV, respectively. Lipid oxidation seemed to be the reason of the results since mullet is considered as a medium-fat fish. Highest shelf-life was calculated as 11.7 days according to cadaverine which is an indicator of late spoilage due to late formation. The results presented here revealed that predictive modeling can be used to describe the kinetic data for fish quality and further to estimate the shelf-life.
Purification and structural elucidation of chondroitin sulfate/dermatan sulfate from Atlantic bluefin tuna (Thunnus thynnus) skins and their anticoagulant and ACE inhibitory activities

Chondroitin sulfate/dermatan sulfate (CS/DS) was extracted from Atlantic bluefin tuna (Thunnus thynnus) skin (SGAT) and was purified and characterized. SGAT was characterized by acetate cellulose electrophoresis, FTIR spectroscopy, 13C NMR spectroscopy and SAX-HPLC. According to the results obtained for specific chondroitinases (ABC and AC) and the SAX-HPLC separation of generated unsaturated repeating disaccharides, the polymer was found to contain a disaccharide monosulfated in positions 6 and 4 of GalNAc and disulfated disaccharides in different percentages. These results were confirmed by 13C NMR experiments. The average molecular mass was 24.07 kDa, as determined by PAGE analysis. SGAT was evaluated for its in vitro anticoagulant activity via activated partial thromboplastin time, thrombin time and prothrombin time tests. The polymer showed strong inhibitory activity against angiotensin I-converting enzyme (IC50 = 0.25 mg mL−1). Overall, the results suggest that this newly extracted CS/DS can be useful for pharmacological applications.
Force Measurement System for Roller-Ski Skating

For a detailed biomechanical analysis of roller-ski skating a precise measurement of ground reaction forces is needed in addition to the measurement of the kinematic parameters. An innovative portable force measuring system was developed from processed roller-skis and ski poles equipped with strain gauges. The measuring system can measure normal (with respect to the upper surface of the roller-ski) and transverse forces (in the axial direction of the wheel) on each wheel, and axial forces in the ski poles. Force sensors are connected by cables to the data acquisition system carried in a backpack by the runner. In case of terrain usage, also a portable computer and a power supply are carried in the backpack. Calibration procedure for this measurement system is presented and measurement uncertainty of the sensors is calculated. The estimated measurement uncertainty of the entire measuring chain of individual roller-ski sensor, at a confidence level of 95 %, is up to ± 2,34 % of the maximum calibration forces. For the sensors of the poles this value makes up to ± 1,47 % of the maximum calibration force. Sample data from a roller-ski skating trial on a treadmill is presented and interpreted.
Verification of Aspergillus Niger as a Myco-remediation Agent of Lambda-Cyhalothrin and Associated Heavy Metals in Lactuca Sativa (L.) Leaf

Pesticide residue constitutes a danger to soil micro and macro fauna and flora and to humans. This study assessed the impact of the application of Aspergillus niger as a pesticide remediating agent on Lambda-cyhalothrin and some of its associated heavy metals translocated to the leaves of Lactuca sativa . A Complete Randomized Design (CRD) experiment using three Treatments was conducted. Lambda-cyhalothrin was extracted from the Samples using the multiple residue technique and its residue determined using Gas Chromatography with Pulsed Flame Photometric Detector (PFPD). The associated heavy metals were determined using the Atomic Absorption Spectrophotometric method. Data so generated were means from five replicates, and were subjected to a one way analysis of variance - ANOVA with Tukey HSD Test for differences between means at 99% confidence interval (P≤0.01). The results show that the highest mean value of Lambda-cyhalotrhrin residue in L. sativa leaves was found in Treatment A (1.50 mg/kg), a value which was significantly higher (P≤0.01) than the residue found in Treatments B (1.0 mg/kg) and C(0.02 mg/kg). Mean Lambda-cyhalothrin residue in Treatment A alone was above the Maximum Residue Level (MRL) of 1.0 mg/kg in vegetable set in the legal EU regulation.The application of A. niger also precipitated a significant reduction (P≤0.01) in the level of all the heavy metals evaluated except Arsenic. All the heavy metals evaluated were however below the WHO/FAO safe limit. The result from this study posits A. niger as a promising mycoremediation agent of pesticide pollution.
IFRS AND PROBABILITY OF REPUBLISHING: A STUDY OF BRAZILIAN COMPANIES LISTED ON BOVESPA

This study analyzed the transition and post-transition period of the adoption of the International Financial Reporting Standards (IFRS) in Brazil, and its main objective was to elucidate its implications both in republishing financial reports and in issuing an accounting audit opinion, with qualification or disapproval. This research analyzed 613 companies listed on BM&FBovespa from 2001 to 2016. The analysis was prepared through a Logit model, testing the hypotheses that the adoption of IFRS in Brazil would reduce both the probability of republishing and of issuing an opinion with qualification or disapproval. The results have indicated that both in the transition and in the post-IFRS periods there was a reduction in the probability of opinions with qualification or disapproval, with a stronger effect on the latter. These results indicate that the IFRS may have positively impacted reporting quality, but not as strongly as desired.
Strategyproof Social Decision Schemes on Super Condorcet Domains

One of the central economic paradigms in multi-agent systems is that agents should not be better off by acting dishonestly. In the context of collective decision-making, this axiom is known as strategyproofness and turns out to be rather prohibitive, even when allowing for randomization. In particular, Gibbard's random dictatorship theorem shows that only rather unattractive social decision schemes (SDSs) satisfy strategyproofness on the full domain of preferences. In this paper, we obtain more positive results by investigating strategyproof SDSs on the Condorcet domain, which consists of all preference profiles that admit a Condorcet winner. In more detail, we show that, if the number of voters $n$ is odd, every strategyproof and non-imposing SDS on the Condorcet domain can be represented as a mixture of dictatorial SDSs and the Condorcet rule (which chooses the Condorcet winner with probability $1$). Moreover, we prove that the Condorcet domain is a maximal connected domain that allows for attractive strategyproof SDSs if $n$ is odd as only random dictatorships are strategyproof and non-imposing on any sufficiently connected superset of it. We also derive analogous results for even $n$ by slightly extending the Condorcet domain. Finally, we also characterize the set of group-strategyproof and non-imposing SDSs on the Condorcet domain and its supersets. These characterizations strengthen Gibbard's random dictatorship theorem and establish that the Condorcet domain is essentially a maximal domain that allows for attractive strategyproof SDSs.
BEAN SEED QUALITY: ASSOCIATED GERMINABILITY

This work aimed to investigate the influence of different levels of bean seed quality on germinability (laboratory study), growth, yield and its components (green pod and dry seed yield) under field conditions. To achieve this study, the seed lot of bean (cv. Giza 3) was manually separated into three classes; light (33.79-38.02g 100 -1 seeds; in 2005 season) and (34.39-37.13g 100 1 seeds; in 2006 season); ungraded (37.70-42.85g 100 -1 seeds; in 2005 season) and (40.02-49.81g 100 -1 seeds; in 2006 season) and heavy (47.20-57.60g 100 -1 seeds; in 2005 season) and (48.7557.13g 100 -1 seeds; in 2006 season). Under field conditions, seeds of bean were sown during two summer successive seasons of 2005 and 2006 at the experimental station, Faculty of Agriculture, Fayoum University, Egypt. The obtained data could be summarized as follows: High-weight class of bean seeds usually exhibited faster and more uniform rates of radicle emergence (as indicator of germination) than low-weight and ungraded ones. Seedling produced from heavier seeds had greater rates of QI, VI, length of radical hypocotyl and accumulation of fresh and dry weights than those from light seeds. The water uptake%, EC and the quantity of materials leached from the seed (Na, K, Pi, sugars, free amino acids and A o 260 and A o 280 absorbing materials) during imbibition were inversely related to seed weight. It is suggesting that interferences existed during seed development or deterioration had occurred in the low weight seed. It can be noticed that seed quality of bean significantly affected field performance of bean plants and resulted in an increase of the studied plant growth traits (plant height, No. of leaves, No. of branches, leaf area leaf -1 , leaf area plant -1 , fresh and dry weights of leaves plant -1 , fresh and dry weights of branches plant -1 , and total fresh and dry weights of shoot plant -1 ) with increasing the level of seed quality class. It can be seen that there was a close relation between seed quality of bean and green pods yield and its components. In this respect, No. of green pods plant -1 , weight of green pod, green pod yield plant -1 and feddan -1 were increased as seed quality class was increased. It was found that bean dry seed yield and its components; empty and seeded pods plant -1 , total No. of pods plant -1 , grades of dry seeded pods, No. of seeds plant -1 , seed yield plant -1 and feddan -1 and seed index (100seed weight) was positively correlated with the class of sown seeds, the seeds which gave plants with high yield of dry seeds and its components were high in their quality and vice versa. It was shown that seed quality class markedly affected chemical constituents concentration of the different organs of bean plants