An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data

1. Few examples of habitat-modelling studies of rare and endangered species exist in the literature, although from a conservation perspective predicting their distribution would prove particularly useful. Paucity of data and lack of valid absences are the probable reasons for this shortcoming. Analytic solutions to accommodate the lack of absence include the ecological niche factor analysis (ENFA) and the use of generalized linear models (GLM) with simulated pseudo-absences. 2. In this study we tested a new approach to generating pseudo-absences, based on a preliminary ENFA habitat suitability (HS) map, for the endangered species Eryngium alpinum. This method of generating pseudo-absences was compared with two others: (i) use of a GLM with pseudo-absences generated totally at random, and (ii) use of an ENFA only. 3. The influence of two different spatial resolutions (i.e. grain) was also assessed for tackling the dilemma of quality (grain) vs. quantity (number of occurrences). Each combination of the three above-mentioned methods with the two grains generated a distinct HS map. 4. Four evaluation measures were used for comparing these HS maps: total deviance explained, best kappa, Gini coefficient and minimal predicted area (MPA). The last is a new evaluation criterion proposed in this study. 5. Results showed that (i) GLM models using ENFA-weighted pseudo-absence provide better results, except for the MPA value, and that (ii) quality (spatial resolution and locational accuracy) of the data appears to be more important than quantity (number of occurrences). Furthermore, the proposed MPA value is suggested as a useful measure of model evaluation when used to complement classical statistical measures. 6. Synthesis and applications. We suggest that the use of ENFA-weighted pseudo-absence is a possible way to enhance the quality of GLM-based potential distribution maps and that data quality (i.e. spatial resolution) prevails over quantity (i.e. number of data). Increased accuracy of potential distribution maps could help to define better suitable areas for species protection and reintroduction.

Do stacked species distribution models reflect altitudinal diversity patterns?

The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed.

Scale effect in hazard assessment - application to daily rainfall

Daily precipitation is recorded as the total amount of water collected by a rain-gauge in 24h. Events are modelled as a Poisson process and the 24h precipitation by a Generalized Pareto Distribution (GPD) of excesses. Hazard assessment is complete when estimates of the Poisson rate and the distribution parameters, together with a measure of their uncertainty, are obtained. The shape parameter of the GPD determines the support of the variable: Weibull domain of attraction (DA) corresponds to finite support variables, as should be for natural phenomena. However, Fréchet DA has been reported for daily precipitation, which implies an infinite support and a heavy-tailed distribution. We use the fact that a log-scale is better suited to the type of variable analyzed to overcome this inconsistency, thus showing that using the appropriate natural scale can be extremely important for proper hazard assessment. The approach is illustrated with precipitation data from the Eastern coast of the Iberian Peninsula affected by severe convective precipitation. The estimation is carried out by using Bayesian techniques

Spontaneous viral clearance, viral load, and genotype distribution of hepatitis C virus (HCV) in HIV-infected patients with anti-HCV antibodies in Europe.

BACKGROUND: Variables influencing serum hepatitis C virus (HCV) RNA levels and genotype distribution in individuals with human immunodeficiency virus (HIV) infection are not well known, nor are factors determining spontaneous clearance after exposure to HCV in this population. METHODS: All HCV antibody (Ab)-positive patients with HIV infection in the EuroSIDA cohort who had stored samples were tested for serum HCV RNA, and HCV genotyping was done for subjects with viremia. Logistic regression was used to identify variables associated with spontaneous HCV clearance and HCV genotype 1. RESULTS: Of 1940 HCV Ab-positive patients, 1496 (77%) were serum HCV RNA positive. Injection drug users (IDUs) were less likely to have spontaneously cleared HCV than were homosexual men (20% vs. 39%; adjusted odds ratio [aOR], 0.36 [95% confidence interval {CI}, 0.24-0.53]), whereas patients positive for hepatitis B surface antigen (HBsAg) were more likely to have spontaneously cleared HCV than were those negative for HBsAg (43% vs. 21%; aOR, 2.91 [95% CI, 1.94-4.38]). Of patients with HCV viremia, 786 (53%) carried HCV genotype 1, and 53 (4%), 440 (29%), and 217 (15%) carried HCV genotype 2, 3, and 4, respectively. A greater HCV RNA level was associated with a greater chance of being infected with HCV genotype 1 (aOR, 1.60 per 1 log higher [95% CI, 1.36-1.88]). CONCLUSIONS: More than three-quarters of the HIV- and HCV Ab-positive patients in EuroSIDA showed active HCV replication. Viremia was more frequent in IDUs and, conversely, was less common in HBsAg-positive patients. Of the patients with HCV viremia analyzed, 53% were found to carry HCV genotype 1, and this genotype was associated with greater serum HCV RNA levels.

Combining Internet Monitoring Processes, Packaging and Isotopic Analyses to Determine The Market Structure: Example of Gamma Butyrolactone

The Internet is becoming more and more popular among drug users. The use of websites and forums to obtain illicit drugs and relevant information about the means of consumption is a growing phenomenon mainly for new synthetic drugs. Gamma Butyrolactone (GBL), a chemical precursor of Gamma Hydroxy Butyric acid (GHB), is used as a "club drug" and also in drug facilitated sexual assaults. Its market takes place mainly on the Internet through online websites but the structure of the market remains unknown. This research aims to combine digital, physical and chemical information to help understand the distribution routes and the structure of the GBL market. Based on an Internet monitoring process, thirty-nine websites selling GBL, mainly in the Netherlands, were detected between January 2010 and December 2011. Seventeen websites were categorized into six groups based on digital traces (e.g. IP addresses and contact information). In parallel, twenty-five bulk GBL specimens were purchased from sixteen websites for packaging comparisons and carbon isotopic measurements. Packaging information showed a high correlation with digital data confirming the links previously established whereas chemical information revealed undetected links and provided complementary information. Indeed, while digital and packaging data give relevant information about the retailers, the supply routes and the distribution close to the consumer, the carbon isotopic data provides upstream information about the production level and in particular the synthesis pathways and the chemical precursors. A three-level structured market has been thereby identified with a production level mainly located in China and in Germany, an online distribution level mainly hosted in the Netherlands and the customers who order on the Internet.

Comparison between land suitability and actual crop distribution in an irrigation district of the Ebro valley (Spain)

El objetivo de la presente investigación fue analizar la correspondencia entre los resultados de una evaluación de tierras con la distribución real de los cultivos. Para ello la aptitud biofísica de las tierras se comparó con diferentes tipologías de frecuencia de ocurrencia de los cultivos y rotaciones derivadas de mapas de cultivos multitemporales. La investigación fue llevada a cabo en el distrito de riego de Flumen (33.000 ha), localizado en el valle del Ebro (NE España). La evaluación de tierras se basó en una cartografía de suelos 1:100.000, según el esquema FAO, para los principales cultivos presentes en el área de estudio (alfalfa, cereales de invierno, maíz, arroz y girasol). Se utilizaron tres mapas de frecuencia de cultivos y un mapa de rotaciones, derivado de una serie temporal de imágenes Landsat TM y ETM+ del periodo 1993-2000, y se compararon con los mapas de aptitud de tierras para los diferentes cultivos. Se analizó estadísticamente (Pearson χ2, Cramer V, Gamma y Somers D) la relación entre los dos tipos de variables. Los resultados muestran la existencia de una relación significativa (P=0,001) entre la localización de los cultivos y la idoneidad de las tierras, excepto de cultivos oportunistas como el girasol, muy influenciado por las subvenciones en el periodo estudiado. Las rotaciones basadas en la alfalfa muestran los mayores porcentajes (52%) de ocupación en las tierras más aptas para la agricultura en el área de estudio. El presente enfoque multitemporal de análisis de la información ofrece una visión más real que la comparación entre un mapa de evaluación de tierras y un mapa de cultivos de una fecha determinada, cuando se valora el grado de acuerdo entre las recomendaciones sobre la aptitud de las tierras y los cultivos realmente cultivados por los agricultores.

MAGIC TeV Gamma-Ray Observations of Markarian 421 during Multiwavelength Campaigns in 2006

Wide-range spectral coverage of blazar-type active galactic nuclei is of paramount importance for understanding the particle acceleration mechanisms assumed to take place in their jets. The Major Atmospheric Gamma Imaging Cerenkov (MAGIC) telescope participated in three multiwavelength (MWL) campaigns, observing the blazar Markarian (Mkn) 421 during the nights of April 28 and 29, 2006, and June 14, 2006. Aims. We analyzed the corresponding MAGIC very-high energy observations during 9 nights from April 22 to 30, 2006 and on June 14, 2006. We inferred light curves with sub-day resolution and night-by-night energy spectra. Methods. MAGIC detects γ-rays by observing extended air showers in the atmosphere. The obtained air-shower images were analyzed using the standard MAGIC analysis chain. Results. A strong γ-ray signal was detected from Mkn 421 on all observation nights. The flux (E > 250 GeV) varied on night-by-night basis between (0.92±0.11) × 10-10 cm-2 s-1 (0.57 Crab units) and (3.21±0.15) × 10-10 cm-2 s-1 (2.0 Crab units) in April 2006. There is a clear indication for intra-night variability with a doubling time of 36± min on the night of April 29, 2006, establishing once more rapid flux variability for this object. For all individual nights γ-ray spectra could be inferred, with power-law indices ranging from 1.66 to 2.47. We did not find statistically significant correlations between the spectral index and the flux state for individual nights. During the June 2006 campaign, a flux substantially lower than the one measured by the Whipple 10-m telescope four days later was found. Using a log-parabolic power law fit we deduced for some data sets the location of the spectral peak in the very-high energy regime. Our results confirm the indications of rising peak energy with increasing flux, as expected in leptonic acceleration models.

Gamma-ray emission from massive young stellar objects

Context.Massive stars form in dense and massive molecular cores. The exact formation mechanism is unclear, but it is possible that some massive stars are formed by processes similar to those that produce the low-mass stars, with accretion/ejection phenomena occurring at some point of the evolution of the protostar. This picture seems to be supported by the detection of a collimated stellar wind emanating from the massive protostar IRAS 16547-4247. A triple radio source is associated with the protostar: a compact core and two radio lobes. The emission of the southern lobe is clearly non-thermal. Such emission is interpreted as synchrotron radiation produced by relativistic electrons locally accelerated at the termination point of a thermal jet. Since the ambient medium is determined by the properties of the molecular cloud in which the whole system is embedded, we can expect high densities of particles and infrared photons. Because of the confirmed presence of relativistic electrons, inverse Compton and relativistic Bremsstrahlung interactions are unavoidable. Aims.We aim to make quantitative predictions of the spectral energy distribution of the non-thermal spots generated by massive young stellar objects, with emphasis on the particular case of IRAS 16547-4247. Methods.We study the high-energy emission generated by the relativistic electrons which produce the non-thermal radio source in IRAS 16547-4247. We also study the result of proton acceleration at the terminal shock of the thermal jet and make estimates of the secondary gamma rays and electron-positron pairs produced by pion decay. Results.We present spectral energy distributions for the southern lobe of IRAS 16547-4247, for a variety of conditions. We show that high-energy emission might be detectable from this object in the gamma-ray domain. The source may also be detectable in X-rays through long exposures with current X-ray instruments. Conclusions.Gamma-ray telescopes such as GLAST, and even ground-based Cherenkov arrays of new generation can be used to study non-thermal processes occurring during the formation of massive stars.

High mass microquasars and low latitude gamma-ray sources

Population studies of unidentified EGRET sources suggest that there exist at least three different populations of galactic gamma-ray sources. One of these populations is formed by young objects distributed along the galactic plane with a strong concentration toward the inner spiral arms of the Galaxy. Variability, spectral and correlation analysis indicate that this population is not homogeneous. In particular, there is a subgroup of sources that display clear variability in their gamma-ray fluxes on timescales from days to months. Following the proposal by Kaufman Bernad\'o et al. (2002), we suggest that this group of sources might be high-mass microquasars, i.e. accreting black holes or neutron stars with relativistic jets and early-type stellar companions. We present detailed inhomogeneous models for the gamma-ray emission of these systems that include both external and synchrotron self-Compton interactions. We have included effects of interactions between the jet and all external photon fields to which it is exposed: companion star, accretion disk, and hot corona. We make broadband calculations to predict the spectral energy distribution of these objects from radio up to GeV energies. The results and predictions can be tested by present and future gamma-ray instruments like INTEGRAL, AGILE, and GLAST.

A nonparametric method for the measurement of size diversity with emphasis on data standardization

The most suitable method for estimation of size diversity is investigated. Size diversity is computed on the basis of the Shannon diversity expression adapted for continuous variables, such as size. It takes the form of an integral involving the probability density function (pdf) of the size of the individuals. Different approaches for the estimation of pdf are compared: parametric methods, assuming that data come from a determinate family of pdfs, and nonparametric methods, where pdf is estimated using some kind of local evaluation. Exponential, generalized Pareto, normal, and log-normal distributions have been used to generate simulated samples using estimated parameters from real samples. Nonparametric methods include discrete computation of data histograms based on size intervals and continuous kernel estimation of pdf. Kernel approach gives accurate estimation of size diversity, whilst parametric methods are only useful when the reference distribution have similar shape to the real one. Special attention is given for data standardization. The division of data by the sample geometric mean is proposedas the most suitable standardization method, which shows additional advantages: the same size diversity value is obtained when using original size or log-transformed data, and size measurements with different dimensionality (longitudes, areas, volumes or biomasses) may be immediately compared with the simple addition of ln k where kis the dimensionality (1, 2, or 3, respectively). Thus, the kernel estimation, after data standardization by division of sample geometric mean, arises as the most reliable and generalizable method of size diversity evaluation

Isotype distribution of anticardiolipin antibodies in systemic lupus erythematosus prospective analysis of a series of 100 patients

A prospective study of IgG and IgM isotypes of anticardiolipin antibodies (aCL) in a series of 100 patients with systemic lupus erythematosus was carried out. To determine the normal range of both isotype titres a group of 100 normal control serum samples was studied and a log-normal distribution of IgG and IgM isotypes was found. The IgG anticardiolipin antibody serum was regarded as positive if a binding index greater than 2.85 (SD 3.77) was detected and a binding index greater than 4.07 (3.90) was defined as positive for IgM anticardiolipin antibody. Twenty four patients were positive for IgG aCL, 20 for IgM aCL, and 36 for IgG or IgM aCL, or both. IgG aCL were found to have a significant association with thrombosis and thrombocytopenia, and IgM aCL with haemolytic anaemia and neutropenia. Specificity and predictive value for these clinical manifestations increased at moderate and high anticardiolipin antibody titres. In addition, a significant association was found between aCL and the presence of lupus anticoagulant. Identification of these differences in the anticardiolipin antibody isotype associations may improve the clinical usefulness of these tests, and this study confirms the good specificity and predictive value of the anticardiolipin antibody titre for these clinical manifestations.

Trolley R&D project for a small portal log yard crane

This master’s thesis was done for Andritz Inc. Atlanta Georgia. The purpose of the thesis was to develop a new trolley for a small portal log yard crane. In the beginning of the thesis the basic principles of the systematic design processes have been described, along which the design work of the trolley has proceeded. The second literature part consists of the design and dimensioning of the welded steel structures under fatigue loading. The design work of the trolley consists of the engineering and the selection of the mechanical components and the design of the load carrying structure for the trolley. The realization of the steel structure of the trolley is based on the fatigue and static dimensioning. The fatigue dimensioning is grounded in the life expectations estimated for the trolley and the static dimensioning is based on the CMAA guidelines. The computer aided element method was utilized in the design of the steel structure. The effective notch method and the hot spot method were used in the fatigue calculations. The trolley structure was carried out by using the sheet metal parts in order to manufacture the structure as effective and low cost way as possible. The corner stone of the dimensioning of the trolley structure was the utilization of the open profiles made of welded or cold formed sheet metals, which provide better weldability, weld inspection, access for repairs and corrosion protection. As a last part of the thesis a new trolley traveling system was developed. The distribution of the wheel loads of the trolley bogies on the main girder was also studied, which led to an innovative suspension arrangement between the trolley leg and the bogie. The new bogie solution increases the service life of the main girder of the crane and improves the stability of the bogies. The outcome of the thesis is an excellent trolley structure from the weight and the service life point of view.

Very High Energy Gamma-Rays emitting BL LAC's Population Study

Context: BL Lacs are the most numerous extragalactic objects which are detected in Very High Energy (VHE) gamma-rays band. They are a subclass of blazars. Large flux variability amplitude, sometimes happens in very short time scale, is a common characteristic of them. Significant optical polarization is another main characteristics of BL Lacs. BL Lacs' spectra have a continuous and featureless Spectral Energy Distribution (SED) which have two peaks. Among 1442 BL Lacs in the Roma-BZB catalogue, only 51 are detected in VHE gamma-rays band. BL Lacs are most numerous (more than 50% of 514 objects) objects among the sources that are detected above 10 GeV by FERMI-LAT. Therefore, many BL Lacs are expected to be discovered in VHE gamma-rays band. However, due to the limitation on current and near future technology of Imaging Air Cherenkov Telescope, astronomers are forced to predict whether an object emits VHE gamma-rays or not. Some VHE gamma-ray prediction methods are already introduced but still are not confirmed. Cross band correlations are the building blocks of introducing VHE gamma-rays prediction method. Aims: We will attempt to investigate cross band correlations between flux energy density, luminosity and spectral index of the sample. Also, we will check whether recently discovered MAGIC J2001+435 is a typical BL Lac. Methods: We select a sample of 42 TeV BL Lacs and collect 20 of their properties within five energy bands from literature and Tuorla blazar monitoring program database. All of the data are synchronized to be comparable to each other. Finally, we choose 55 pair of datasets for cross band correlations finding and investigating whether there is any correlation between each pair. For MAGIC J2001+435 we analyze the publicly available SWIFT-XRT data, and use the still unpublished VHE gamma-rays data from MAGIC collaboration. The results are compared to the other sources of the sample. Results: Low state luminosity of multiple detected VHE gamma-rays is strongly correlated luminosities in all other bands. However, the high state does not show such strong correlations. VHE gamma-rays single detected sources have similar behaviour to the low state of multiple detected ones. Finally, MAGIC J2001+435 is a typical TeV BL Lac. However, for some of the properties this source is located at the edge of the whole sample (e.g. in terms of X-rays flux). Keywords: BL Lac(s), Population study, Correlations finding, Multi wavelengths analysis, VHE gamma-rays, gamma-rays, X-rays, Optical, Radio

The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats

The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed) and BJs (sialic acid residues exposed) on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for 60 min after iv administration of 1 mg of each protein (7.4 MBq), as the intact proteins and also after carbohydrate oxidation. Images were obtained with a Siemens gamma camera with a high-resolution collimator and processed with a MicroDelta system. Hepatic and renal distribution were established and are reported as percent of injected dose. Liver uptake of BJg was significantly higher than liver uptake of BJs (94.3 vs 81.4%) (P<0.05). This contributed to its greater removal from the intravascular compartment, and consequently lower kidney accumulation of BJg in comparison to BJs (5.7 vs 18.6%) (P<0.05). After carbohydrate oxidation, there was a decrease in hepatic accumulation of both proteins and consequently a higher renal overload. The tissue distribution of periodate-treated BJg was similar to that of native BJs: 82.7 vs 81.4% in the liver and 17.3 vs 18.6% in the kidneys. These observations indicate the important role of sugar residues of Bence Jones proteins for their recognition by specific membrane receptors, which leads to differential tissue accumulation and possible toxicity

Topographic distribution of the tibial somatosensory evoked potential using coherence

The objective of the present study was to determine the adequate cortical regions based on the signal-to-noise ratio (SNR) for somatosensory evoked potential (SEP) recording. This investigation was carried out using magnitude-squared coherence (MSC), a frequency domain objective response detection technique. Electroencephalographic signals were collected (International 10-20 System) from 38 volunteers, without history of neurological pathology, during somatosensory stimulation. Stimuli were applied to the right posterior tibial nerve at the rate of 5 Hz and intensity slightly above the motor threshold. Response detection was based on rejecting the null hypothesis of response absence (significance level α= 0.05 and M = 500 epochs). The best detection rates (maximum percentage of volunteers for whom the response was detected for the frequencies between 4.8 and 72 Hz) were obtained for the parietal and central leads mid-sagittal and ipsilateral to the stimulated leg: C4 (87%), P4 (82%), Cz (89%), and Pz (89%). The P37-N45 time-components of the SEP can also be observed in these leads. The other leads, including the central and parietal contralateral and the frontal and fronto-polar leads, presented low detection capacity. If only contralateral leads were considered, the centro-parietal region (C3 and P3) was among the best regions for response detection, presenting a correspondent well-defined N37; however, this was not observed in some volunteers. The results of the present study showed that the central and parietal regions, especially sagittal and ipsilateral to the stimuli, presented the best SNR in the gamma range. Furthermore, these findings suggest that the MSC can be a useful tool for monitoring purposes.