Miracle-dz/UniFAR-FTUs huggingface dataset:
EL PAISAJE DEL BOSQUE ATLÁNTICO DEL ALTO PARANÁ Y SUS EFECTOS SOBRE LA DISTRIBUCIÓN Y ESTRUCTURA POBLACIONAL DEL JAGUAR (Panthera onca) Y EL PUMA (Puma concolor)

The Upper Parana Atlantic Forest (UPAF) is one of the planet’s most endangered environments on account of its being highly fragmented, a process that is threatening the largest natural predators of this area, the jaguar (Panthera onca) and the puma (Puma concolor). The main objective of this dissertation was to investigate the impact of the UPAF fragmentation and land use change on the survival of both predators. Analyses of satellite images were used to describe changes in land use. Agricultural expansion and the transformation of more than 75.000 km of native forest characterized the UPAF between 1973 and 2004, though the process of change was different in each of the three countries sharing this environment (Argentina, Brazil and Paraguay). A monitoring participative network was created and volunteers were trained to collect samples from big felids, such as feces and tracks, throughout the UPAF. From these samples I derived presence data for these species from which I mapped their current distribution in the UPAF. Puma, jaguar and big canid tracks collected at zoos were used to evaluate traditional track identification methods which proved to show high error rates. Morphometric variables measured on zoo tracks were used in discriminant function analysis (DFA) in order to improve differentiation between tracks of these species obtained by the participative network. Feces were identified by means of molecular techniques. Jaguar presence was confirmed in a large area of the Green Corridor in Misiones, and in the largest forest remnants of Brazil and Paraguay. Pumas showed a wider distribution, being recorded throughout Misiones province and including areas of Brazil and Paraguay where jaguars were not detected. An ecological niche factorial analysis showed that pumas and jaguars are mainly restricted to areas with native forest and avoid highly modified areas that are readily accessible to humans. The jaguar, however, proved to be a more sensitive species to landscape changes and anthropic pressures. Generalized lineal models indicate that jaguar persistence is determined not only by present conditions of this fragmented forest, but also by the fragmentation history of the landscape. Characteristics of surrounding land use and human pressure were also important to determinate jaguar presence in the forest remnants of the UPAF. A bidimensional model of habitat suitability allowed to determine the probable spatial structure of jaguar population and to detect priority areas to implement different management actions to preserve both this species and the UPAF.
Comparing landscape evolution models with quantitative field data at the millennial time scale in the Belgian loess belt

This study compares three landscape evolution models and their ability to correctly simulate measured 2500 year landscape evolution in two small catchments in the Belgian loess belt. WATEM LT and LAPSUS both model tillage and water erosion and deposition and have detachment‐limited descriptions for water erosion and deposition. Equations in LAPSUS are more mechanistic than those in WATEM LT. WATEM LTT resembles WATEM LT, but is a transport‐limited model. All three models are DEM‐based. Calibration and validation simulations were performed forward in time on (1D) transects for four spatial resolutions, and backward in time for (2D) catchments at 20 m resolution. For transects, model outputs were compared with discretized observations of transect shape. For catchments, outputs were compared with point observations of palaeo‐altitude, averaged over landscape element classes. For transects, the three models performed well, resulting in model efficiency factors of 0.92 to 0.99 for calibration and 0.62 to 0.96 for validation. However, for catchments, simulations showed that the transport‐limited WATEM LTT model could not realistically simulate long‐term landscape evolution. Performance of WATEM LT and LAPSUS at catchment scale was similar to that on transects, although LAPSUS has problems with backward calculation. Tests demonstrate that a transport‐limited approach cannot be used to model long‐term landscape evolution in the Belgian loess belt, which is in agreement with theoretical and empirical understanding of soil erosion processes in this environment. The difference in performance between transport‐limited and detachment‐limited models is clear only when the models are evaluated in a 2D catchment. The lack of such distinction when models were applied in a 1D transect highlights the importance of evaluating landscape evolution models in a 2D setting so that effects of flow convergence/divergence can be accounted for. Copyright © 2011 John Wiley & Sons, Ltd.
Outsourcing Medical Data Analyses: Can Technology Overcome Legal, Privacy, and Confidentiality Issues?

Background Medical data are gold mines for deriving the knowledge that could change the course of a single patient’s life or even the health of the entire population. A data analyst needs to have full access to relevant data, but full access may be denied by privacy and confidentiality of medical data legal regulations, especially when the data analyst is not affiliated with the data owner. Objective Our first objective was to analyze the privacy and confidentiality issues and the associated regulations pertaining to medical data, and to identify technologies to properly address these issues. Our second objective was to develop a procedure to protect medical data in such a way that the outsourced analyst would be capable of doing analyses on protected data and the results would be comparable, if not the same, as if they had been done on the original data. Specifically, our hypothesis was there would not be a difference between the outsourced decision trees built on encrypted data and the ones built on original data. Methods Using formal definitions, we developed an algorithm to protect medical data for outsourced analyses. The algorithm was applied to publicly available datasets (N=30) from the medical and life sciences fields. The analyses were performed on the original and the protected datasets and the results of the analyses were compared. Bootstrapped paired t tests for 2 dependent samples were used to test whether the mean differences in size, number of leaves, and the accuracy of the original and the encrypted decision trees were significantly different. Results The decision trees built on encrypted data were virtually the same as those built on original data. Out of 30 datasets, 100% of the trees had identical accuracy. The size of a tree and the number of leaves was different only once (1/30, 3%, P=.19). Conclusions The proposed algorithm encrypts a file with plain text medical data into an encrypted file with the data protected in such a way that external data analyses are still possible. The results show that the results of analyses on original and on protected data are identical or comparably similar. The approach addresses the privacy and confidentiality issues that arise with medical data and is adherent to strict legal rules in the United States and Europe regarding the processing of the medical data.
Comparisons of different semi-automated techniques for oil spill detection: A case study in Lebanon

Today, oil spills in the marine environment originated from land-based or sea-based sources are growing in all countries around the world and have serious biological and economic impacts. One of the most dangerous and hazardous effects on marine environment is the discharge of oil includingwith the tanker accidents. Besides oil pollution occurred recently in the Lebanon coast is one of the most hazardous land-based threats in the eastern Mediterranean coasts with an estimation of 110,000 barrels of oil. Due to not enough cleaning activities carried on, the oil pollution has spread 100 miles along the coast and effected also to Syria’s shoreline. Depending on thewind and current condition, the spilled oil could also be a big threat to other neighborhood countries such as Turkey, Greece, and Cyprus. In order to interfere the oil spill, it is important to identify the type, areal extent, position, (nearest ship position if any), the possibility percentage etc. For this purpose, satellite-based oil pollution monitoring systems are being used to take precautions and even to determine the possible polluter. Today, Synthetic Aperture Radar (SAR) satellites are often preferred to optical sensors due to the all-weather and all-day capabilities and being used to detect the oil spills discharged into the sea with sufficient accuracies. In this study, Radarsat-1 images covering Lebanon coasts acquired by ITU-CSCRS (Istanbul Technical University – Center of Satellite Communication and Remote Sensing) during the event were evaluated using both visual analysis and semi-automatic image processing techniques based on Artificial Intelligence. The urgent need for the establishment of an operational satellite-based oil spill monitoring system in the area and the effective role of a ground receiving station at ITU were also outlined.
Decadal variations of temperature and geopotential height over the Tibetan Plateau and their relations with Tibet ozone depletion

The Total Ozone Mapping Spectrometer/Solar Backscatter Ultraviolet (TOMS/SBUV) merged total ozone data, and the Tibetan Plateau radiosonde reports during the period from 1979 to 2002 are used in this paper, we study the decadal variations of temperature and geopotential height over the Tibetan Plateau and their relationship with changes of Tibet total ozone. It is found that temperature and geopotential height over the Tibetan Plateau have displayed declining trends in the stratosphere and positive trends in the troposphere since the late 1970s, well consistent with Tibet total ozone depletion. The possible role of ozone in long‐term changes of temperature and geopotential height is proposed.
On the relationship of peaks and troughs of the ellipticity (H/V) of Rayleigh waves and the transmission response of single layer over half-space models

SUMMARY One of the key challenges in the context of local site effect studies is the determination of frequencies where the shakeability of the ground is enhanced. In this context, the H/V technique has become increasingly popular and peak frequencies of H/V spectral ratio are sometimes interpreted as resonance frequencies of the transmission response. In the present study, assuming that Rayleigh surface wave is dominant in H/V spectral ratio, we analyse theoretically under which conditions this may be justified and when not. We focus on ‘layer over half-space’ models which, although seemingly simple, capture many aspects of local site effects in real sedimentary structures. Our starting point is the ellipticity of Rayleigh waves. We use the exact formula of the H/V-ratio presented by Malischewsky & Scherbaum (2004) to investigate the main characteristics of peak and trough frequencies. We present a simple formula illustrating if and where H/V-ratio curves have sharp peaks in dependence of model parameters. In addition, we have constructed a map, which demonstrates the relation between the H/V-peak frequency and the peak frequency of the transmission response in the domain of the layer's Poisson ratio and the impedance contrast. Finally, we have derived maps showing the relationship between the H/V-peak and trough frequency and key parameters of the model such as impedance contrast. These maps are seen as diagnostic tools, which can help to guide the interpretation of H/V spectral ratio diagrams in the context of site effect studies.
Control of small inhibitory RNA levels and RNA interference by doxycycline induced activation of a minimal RNA polymerase III promoter

RNA interference (RNAi) mediated by expression of short hairpin RNAs (shRNAs) is a powerful tool for efficiently suppressing target genes. The approach allows studies of the function of individual genes and may also be applied to human therapy. However, in many instances regulation of RNAi by administration of a small inducer molecule will be required. To date, the development of appropriate regulatory systems has been hampered by the few possibilities for modification within RNA polymerase III promoters capable of driving efficient expression of shRNAs. We have developed an inducible minimal RNA polymerase III promoter that is activated by a novel recombinant transactivator in the presence of doxycycline (Dox). The recombinant transactivator and the engineered promoter together form a system permitting regulation of RNAi by Dox-induced expression of shRNAs. Regulated RNAi was mediated by one single lentiviral vector, blocked the expression of green fluorescent protein (GFP) in a GFP-expressing HEK 293T derived cell line and suppressed endogenous p53 in wild-type HEK 293T, MCF-7 and A549 cells. RNA interference was induced in a dose- and time-dependent manner by administration of Dox, silenced the expression of both target genes by 90% and was in particular reversible after withdrawal of Dox.
A 117‐year long index of the Pacific‐Japan pattern with application to interdecadal variability

The Pacific‐Japan (PJ) pattern affects interannual variability in the East Asian and western North Pacific (WNP) summer monsoons. This teleconnection pattern is characterized by a meridional dipole of anomalous circulation and precipitation between the tropical WNP and the midlatitudes. This study develops a long index of the PJ pattern using station‐based atmospheric pressure data to track the PJ variability from 1897 to 2013. This index is correlated with a wide array of climate variables including air temperature, precipitation, Yangtze River flow, Japanese rice yield and the occurrence of tropical cyclones over the WNP (especially those that make landfall on the Chinese and Korean coast). For the recent three decades, the PJ index reproduces well‐known correlations with El Niño‐Southern Oscillation (ENSO) in the preceding boreal winter and Indian Ocean temperature in the concurrent summer. For the 117‐year period, this ENSO‐PJ relationship varies on interdecadal time scales, with low correlations in the 1920s and from the 1940s to 1970s, and recurrences of significant correlations at the beginning of the 20th century and the 1930s. In accordance with the modulation, the magnitude and regional climate effect of the PJ variability have changed. These results highlight the importance of interdecadal modulations of climate anomalies in the summer WNP and the need of long‐term observations to study such modulations.
Identification and Validation of Reference Genes for RT-qPCR Analysis in Reed Canary Grass during Abiotic Stress

Reed canary grass (Phalaris arundinacea L.) is known for its tolerance to drought, heavy metals, and waterlogging, making it a popular choice for forage production and wetland restoration in the Qinghai-Tibet Plateau (QTP). To accurately assess gene expression in reed canary grass under different abiotic stresses, suitable reference genes need to be identified and validated. Thirteen candidate reference gene sequences were selected and screened using RT-qPCR to detect their expression levels in reed canary grass leaves under drought, salt, cadmium, and waterlogging stresses. Four algorithms were used to assess the stability of the expression levels of the candidate reference genes. The most stably expressed genes were UBC and H3 under drought Cd, ETF and CYT under salt stress, and ETF and TUB under waterlogging stress. GAPDH was found to be less stable under abiotic stresses. PIP-1, PAL, NAC 90, and WRKY 72A were selected as response genes for quantitative expression assessment under drought, salt, Cd, and waterlogging stresses to confirm the accuracy of the selected stable reference genes. These results provide a theoretical reference for assessing gene expression in reed canary grass under abiotic stresses.
Bmc Medical Research Methodology Open Access Proportional Odds Ratio Model for Comparison of Diagnostic Tests in Meta-analysis

Background: Consider a meta-analysis where a 'head-to-head' comparison of diagnostic tests for a disease of interest is intended. Assume there are two or more tests available for the disease, where each test has been studied in one or more papers. Some of the papers may have studied more than one test, hence the results are not independent. Also the collection of tests studied may change from one paper to the other, hence incomplete matched groups.
Ridge-crossing seamount chains: A nonthermal approach

In this article we examine whether it is viable to form an age-progressive ridge-crossing seamount chain using a nonplume mechanism. Nonthermal melt sources considered include fertile mantle blobs and subsolidus mantle while lithospheric stresses generated at the ridge and at ridge-transform intersections (RTIs) are tapped to bring the mantle to the surface. Finite element models, analog models, and an analysis of the Tristan de Cunha chain all show that ridge-crossing seamount chains may be created using these mechanisms. Essentially, as a ridge migrates or reorganizes, excess magmatism may appear to switch sides of the ridge as areas of extensional stress at the RTI migrate with the ridge.
Shallow magma pathway geometry at Mt. Etna volcano

A fundamental goal of volcano seismology is to understand the dynamics of active magmatic systems in order to assess eruptive behavior and the associated hazard. Imaging of magma conduits, quantification of magma transport, and investigation of long‐period seismic sources, together with their temporal variations, are crucial for the comprehension of eruption‐triggering mechanisms. At Mt. Etna volcano, several intense episodes of tremor activity were recorded during 2007, in association with strombolian activity and/or intense fire fountaining episodes occurring from the South East Crater (SEC). The locations of the tremor sources and of the long‐period seismic events are used here to constrain both the area and the depth range of magma degassing, highlighting the geometry of the shallow conduits feeding SEC. The imaged conduits consist of two connected resonating dike‐like bodies, NNW‐SSE and NW–SE oriented, extending from sea level to the surface. In addition, we show how tremor, long‐period (LP), and very‐long‐period (VLP) event locations and signatures reflect pressure fluctuations in the plumbing system associated with the ascent/discharge of gas‐rich magma linked to the lava fountains. The evidence here reported, also corroborated by ground deformation variations, can help develop a better prediction and early warning system for those eruptions (effusive or explosive) that apparently manifest no clear precursors.
Software architecture for language engineering

This thesis defines the boundaries of Software Architecture for Language Engineering (SALE), an area formed by the intersection of human language computation and software engineering. SALE covers all areas of the provision of infrastructural systems to support research and development of language processing software. In order to demonstrate the theory developed in relation to SALE, we present the design, implementation and evaluation of GATE, a General Architecture for Text Engineering, which illustrates in practice many of the theoretical points made. The thesis represents the first discussion of software infrastructure for language computation that covers a large portion of the field. GATE is one of the most widely used such systems in existence, and very few other systems of similar design are freely available or in common use outside of their originating institutions.
Predicting Mandibular Third Molar Agenesis from Second Molar Formation

Objective: to describe the age of mandibular third molar (M3) crypt formation and investigate if root formation of the mandibular second molar (M2) can predict M3 agenesis. Materials and Methods: Mandibular M2 and M3 were categorised into developmental stages of Moorrees et al. (1963). The range and mean age of M3 crypt stage was calculated. Radiographs with M3 at crypt stage (N=150) were selected and the range of M2 formation stage described. The number and probability of M3 developing given M2 stage was calculated using 1749 radiographs. The odds ratio of M3 developing if M2 > R1/2 was calculated using logistic regression. Results: The average age of M3 crypt stage was 8.84 years [range 5.47 to 12.55]. No significant sex or ethnic differences were observed. When M3 was at crypt stage, the range of M2 stages was from crown half up to root three quarters, the most common being from crown complete to root one quarter. By the time M2 was R1/2, 99% of individuals had a visible M3 crypt. Odds ratio of M3 absence at M2 R3/4 or later stage was 0.03 [95% c.i. 0.02, 0.05]. Conclusion: The average age of M3 crypt was during the eighth year and most commonly occured when the adjacent M2 was at crown complete or early root stage. As the root of M2 developed, the likelihood of M3 crypt formation decreased. After M2 stage R1/2, the development of the M3 crypt was unlikely.
New precipitation and accumulation maps for Greenland

Abstract Annual total precipitation and the annual accumulation on the Greenland ice sheet are evaluated and presented in two maps. The maps are based on accumulation measurements of 251 pits and cores obtained from the upper accumulation zone and precipitation measurements made at 35 meteorological stations in the coastal region. To construct the accumulation map, the annual precipitation was split into solid and liquid precipitation components. Annual total precipitation exceeding 2500mmw.e. occurs on the southeastern tip of Greenland, while the minimum precipitation is estimated to occur on the northeastern slope of the ice sheet. The mean annual precipitation for all of Greenland is 340 mm w.e. The largest annual accumulation of about 1500 mm w.e. is found on the glaciers in the southeastern corner of Greenland, while the smallest accumulation is found on the northeastern slope of the ice sheet west of Danmarkshavn. The mean accumulation on the Greenland ice sheet is estimated at 310mmw.e. The regional difference in accumulation is examined with respect to the 850hPa(mbar) level circulation. The present surface topography is found to play an important role in determining regional accumulation on the ice sheet.
Thermo-hydro-mechanical Sand Production Model in Hydrate-bearing Sediments

A better understanding of the behavior of hydrate-bearing sediments during gas extraction is a vital step towards realization of commercially viable gas production for the future. In 2007, the world first trial of gas production from hydrate-bearing sediments by depressurization method was conducted at the Mallik gas hydrate site, located in the Mackenzie Delta of Northwest Territories, Canada. However, the operation encountered a large amount of sand migration into the well, a phenomenon known as sand production, and thus was terminated after 24 hours. This incident highlights the importance of development of hydro-mechanical sand production model within hydrate-bearing sediments and understanding of the behavior of hydrate-bearing sediments with the effect of sand production during gas extraction. This extended abstract provides a formulation for the sand production including grain flow and hydraulic dispersion effect. A formulation is fully-coupled such that the sand production affects fluid pressures, saturations and temperature. In addition, the effective stress reduction due to grain detachment is incorporated. This results in further deformation of hydrate-bearing sediments, which may need to be considered for stability of the wellbore.