Miracle-dz/UniFAR-FTUs huggingface dataset:
Some Geometric Methods for the Analysis of Images and Textures. (Approches géométriques pour l'analyse d'images et de textures)

This thesis focuses on the studies of the extraction and characterization of local image structures, in the context of images and texture analysis. Relying on the level lines of images or on the somehow dual and less structured notion of gradient orientation, the contributions of the thesis concentrate on following three themes: The first part of this thesis presents a new method for texture analysis that in spirit is similar to morphological granulometries, while allowing a high degree of geometrical and radiometric invariances. Also using the topographic map representation, the second part of this thesis develops a general approach for the abstraction of images, the aim of which is to automatically generate abstract images from realistic photographs. The subject of the last part of this thesis is the detection of junctions in natural images. The approach relies on the local directions of level lines through the orientation of image gradient. We introduce a generic junction analysis scheme. The first asset of the proposed procedure is an automatic criterion for the detection of junctions, permitting to deal with textured parts in which no detection is expected. Second, the method yields a characterization of L-, Y- and X- junctions, including a precise computation of their type, localization and scale. Contrary to classical approaches, scale characterization does not rely on the linear scale-space, therefore enabling geometric accuracy.
Plant Identification Based on Noisy Web Data: the Amazing Performance of Deep Learning (LifeCLEF 2017)

The 2017 fith edition of the LifeCLEF plant identification challenge is an important milestone towards automated plant identification systems working at the scale of continental floras with 10.000 plant species living mainly in Europe and North America illustrated by a total of 1.1M images. Nowadays, such ambitious systems are enabled thanks to the conjunction of the dazzling recent progress in image classification with deep learning and several outstanding international initiatives, such as the Encyclopedia of Life (EOL), aggregating the visual knowledge on plant species coming from the main national botany institutes. However, despite all these efforts the majority of the plant species still remain without pictures or are poorly illustrated. Outside the institutional channels, a much larger number of plant pictures are available and spread on the web through botanist blogs, plant lovers web-pages, image hosting websites and on-line plant retailers. The LifeCLEF 2017 plant challenge presented in this paper aimed at evaluating to what extent a large noisy training dataset collected through the web and containing a lot of labelling errors can compete with a smaller but trusted training dataset checked by experts. To fairly compare both training strategies, the test dataset was created from a third data source, i.e. the Pl@ntNet mobile application that collects millions of plant image queries all over the world. This paper presents more precisely the resources and assessments of the challenge, summarizes the approaches and systems employed by the participating research groups, and provides an analysis of the main outcomes. (Resume d'auteur)
Assessing the Effects of Changing Demographic and Consumption Patterns on Sea Tenure Regimes in the Roviana Lagoon, Solomon Islands

Abstract This paper investigates how sea tenure institutions in the Roviana Lagoon, Solomon Islands, mediate among population, consumption, and the environment. The focus is on explaining how growth in population and consumption alter sea tenure regimes, and the factors that shape either their institutional robustness or vulnerability. The paper also addresses the regional differences among sea tenure institutional arrangements, the processes that are producing them, and the social and environmental outcomes of these institutions as they engage external forces and internal changes. A major question is how existing forms of sea tenure respond comparatively when faced with parallel demographic and economic transformations? Two villages representing different sea tenure arrangements within the Roviana Lagoon are compared. Results show that inhabitants in these villages perceive their systems of sea tenure governance similarly; yet their managerial responses to changes brought about by growth in population and consumption differ, and the responses produce contrasting environmental effects.
Spectral-Domain Measurements of Birefringence and Sensing Characteristics of a Side-Hole Microstructured Fiber

We experimentally characterized a birefringent side-hole microstructured fiber in the visible wavelength region. The spectral dependence of the group and phase modal birefringence was measured using the methods of spectral interferometry. The phase modal birefringence of the investigated fiber increases with wavelength, but its positive sign is opposite to the sign of the group modal birefringence. We also measured the sensing characteristics of the fiber using a method of tandem spectral interferometry. Spectral interferograms corresponding to different values of a physical parameter were processed to retrieve the spectral phase functions and to determine the spectral dependence of polarimetric sensitivity to strain, temperature and hydrostatic pressure. A negative sign of the polarimetric sensitivity was deduced from the simulation results utilizing the known modal birefringence dispersion of the fiber. Our experimental results show that the investigated fiber has a very high polarimetric sensitivity to hydrostatic pressure, reaching −200 rad × MPa−1× m−1 at 750 nm.
The Vienna RNA Websuite

The Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. It provides a web interface to the most commonly used programs of the Vienna RNA package. Among them, we find folding of single and aligned sequences, prediction of RNA–RNA interactions, and design of sequences with a given structure. Additionally, we provide analysis of folding landscapes using the barriers program and structural RNA alignments using LocARNA. The web server together with software packages for download is freely accessible at http://rna.tbi. univie.ac. at/.
The Separation/Period Gap in the Distribution of Extrasolar Planets around Stars with Masses M ≥ 1.2 M☉

The evidence for a shortage of exosolar planets with semimajor axes -1.1 ≤ log(a/AU) ≤ -0.2 is investigated. It is shown that this valley results from a gap in the radial distribution of planets orbiting stars with masses M* ≥ 1.2 M☉ (the high-mass sample, HMS). No underabundance is found for planets orbiting stars with smaller masses. The observational data also indicate that within the HMS population, it is preferentially the more massive planets with M sin(i) ≥ 0.8 MJ that are missing. Monte Carlo simulations of planet formation and migration are presented that reproduce the observed shortage of planets in the observed radius regime. A dependence on the disk depletion timescale τdep is found. The gap is more pronounced for τdep = 106-107 yr than for τdep = 3 × 106-3 × 107 yr. This might explain the observed trend with stellar mass if disks around stars with masses M* ≥ 1.2 M☉ have shorter depletion timescales than those around less massive stars. Possible reasons for such a dependence are a decrease of disk size and an increase of stellar EUV flux with stellar mass.
Biased random-to-top shuffling

Recently Wilson [Ann. Appl. Probab. 14 (2004) 274--325] introduced an important new technique for lower bounding the mixing time of a Markov chain. In this paper we extend Wilson's technique to find lower bounds of the correct order for card shuffling Markov chains where at each time step a random card is picked and put at the top of the deck. Two classes of such shuffles are addressed, one where the probability that a given card is picked at a given time step depends on its identity, the so-called move-to-front scheme, and one where it depends on its position. For the move-to-front scheme, a test function that is a combination of several different eigenvectors of the transition matrix is used. A general method for finding and using such a test function, under a natural negative dependence condition, is introduced. It is shown that the correct order of the mixing time is given by the biased coupon collector's problem corresponding to the move-to-front scheme at hand. For the second class, a version of Wilson's technique for complex-valued eigenvalues/eigenvectors is used. Such variants were presented in [Random Walks and Geometry (2004) 515--532] and [Electron. Comm. Probab. 8 (2003) 77--85]. Here we present another such variant which seems to be the most natural one for this particular class of problems. To find the eigenvalues for the general case of the second class of problems is difficult, so we restrict attention to two special cases. In the first case the card that is moved to the top is picked uniformly at random from the bottom $k=k(n)=o(n)$ cards, and we find the lower bound $(n^3/(4\pi^2k(k-1)))\log n$. Via a coupling, an upper bound exceeding this by only a factor 4 is found. This generalizes Wilson's [Electron. Comm. Probab. 8 (2003) 77--85] result on the Rudvalis shuffle and Goel's [Ann. Appl. Probab. 16 (2006) 30--55] result on top-to-bottom shuffles. In the second case the card moved to the top is, with probability 1/2, the bottom card and with probability 1/2, the card at position $n-k$. Here the lower bound is again of order $(n^3/k^2)\log n$, but in this case this does not seem to be tight unless $k=O(1)$. What the correct order of mixing is in this case is an open question. We show that when $k=n/2$, it is at least $\Theta(n^2)$.
Frequencies of Apolipoprotein E Polymorphism in a Healthy Kurdish Population from Kermanshah, Iran

ABSTRACT The molecular polymorphism displayed by apolipoprotein E (APOE) has been listed as a risk factor for susceptibility to various disorders, such as those associated with lipid metabolism, arteriosclerosis, coronary artery disease (CAD), and Alzheimer disease. To evaluate the role of APOE genotypes as risk factors for Alzheimer disease, CAD, and atherosclerosis in the Kurdish population of Kermanshah, Iran, we studied the frequencies of APOE alleles *2, *3, and *4 and genotypes in 914 healthy Kurdish subjects (514 men and 400 women). The highest frequency of APOE in the Kurdish population was found for APOE*3 (87.87%). The APOE*2 and APOE*4 allele frequencies were 6.66% and 5.45%, respectively. Distribution of APOE genotypes and alleles was not significantly different between male and female subjects (p > 0.05). Interestingly, the order of the frequency of APOE alleles (*3 → *2 → *4) in the Kurdish population was quite different from that reported for most populations in the world (*3 → *4 → *2). The findings of the present study can be used to identify individuals with high risk of CAD and atherosclerosis and suggest a preventive measure to reduce their susceptibility.
Mapping intertidal eelgrass (Zostera marina L.) in three coastal estuaries of the Pacific Northwest USA using false colour near-infrared aerial photography

This study describes a hybrid technique of digitally classifying aerial photography used for mapping the intertidal habitat of eelgrass (Zostera marina L.) in Pacific Northwest USA estuaries. The large tidal range (2–3 m) in this region exposes most of this seagrass community at low tide, permitting the use of false colour near-infrared film that provides good contrast in imaging vegetated intertidal habitats. Three Oregon coastal estuaries in the USA were surveyed in 2004 or 2005 at photoscales of 1:10 000 or 1:20 000. Spatial resolution was 0.25 m and the minimum mapping unit was 2.5 × 2.5 m. Spatial accuracy was within 1.5 m. Comparison of the image classification and ground survey results yielded overall classification accuracies of 83% to 97%. This appears to be an effective technique for mapping intertidal eelgrass distributions in turbid coastal estuaries with large tidal ranges.
Drug Patents at the Supreme Court

Arguments for paying generic drug makers to abandon patent challenges may rest on dubious assumptions. U.S. pharmaceutical patent policy is poised for a major review by the U.S. Supreme Court. Later this month, the Court will hear a case, Federal Trade Commission (FTC) v. Actavis, Inc., about a tactic alleged to be illegal by U.S. regulators, so-called “reverse payment” settlements of patent litigation. A maker of a branded drug pays a “generic” drug maker offering a competing, unbranded version of a drug, to abandon its challenge of the branded firm's patent. This tactic has also received regulatory scrutiny in Europe (1, 2). The Court's ruling promises to reset the innovation/access balance for drugs, whatever the result. We explain the stakes of the case, and how settlements of “secondary” patents affect that balance.
Hydrology and near‐surface nutrient distribution along the South Otago continental shelf, New Zealand, in summer and winter 1986

Abstract The 3 Otago coastal water masses (Neritic water, subtropical Southland Current water, and Subantarctic Surface Water) defined in the literature were identified on 1 cruise in early summer and 1 in mid winter. Winter results showed that Neritic water is derived from the Clutha River. During winter the Southland Current was characterised by temperatures between 9.0 and 10.6°C and a salinity range of 34.4 to 34.9 × 10‐3. During summer a thermocline and pycnocline were observed at 30–50 m depth sloping down toward the coast. Low‐salinity Neritic water was less apparent than in winter. Summer nutrient levels were depleted over all of the continental shelf, relative to winter. This is probably caused by the enclosure of coastal surface waters inshore of the pycnocline. Reactive Si was conservative in winter regardless of water mass. Reactive P was approximately constant in Neritic water and Southland Current water. In summer, neither nutrient was conservative.
Comparison between the algebraic and the reduced-order extended state observer approaches for on-line load torque estimation in a speed control for PMSM system

This paper presents a passivity-based control for a Permanent Magnet Synchronous Motor; the torque is observed with a reduced-order extended state observer and a traditional reduced-order observer, which are compared with an online algebraic estimator. The Matlab-Simulink/PSIM simulation results show that the reduced-order extended state observer had a better performance in which the angular velocity was maintained at the desired reference value by the adapted controller, even under severe load changes on the motor shaft.
Systemic granulomatous and haemorrhagic syndrome in New Zealand dairy cattle

Abstract CASE HISTORY: Cases were obtained through passive surveillance reporting by veterinary pathologists, via the Ministry for Primary Industries Exotic Pest and Disease Hotline. They included ill or dead cows that had evidence of frank haemorrhage, petechial haemorrhages on mucous membranes, wasting or dermatitis of unknown cause, and were reported between 2009–2014. Affected cows (n=16) were from nine seasonally calving dairy farms, aged ≥3 years, and were predominantly in their mid-to-late non-lactating period. A brassica crop was identified in 15/16 cases as part of the current or recent ration. CLINICAL FINDINGS: Eight cows were found dead or died within 2 days of first signs. In eight cases death or euthanasia took place up to 3 weeks after signs were first observed. Cattle clinically examined prior to death (n=11) were generally inappetant, and recumbent or reluctant to move. Five cases had pale mucous membranes, three had petechiae and two were jaundiced. Rectal temperature was normal to sub-normal in eight cases. Evidence of melena or fresh blood at the anus or mouth was found in five cases. In three cases, alopecia and skin thickening was present, predominantly affecting the head and neck. PATHOLOGICAL FINDINGS: Petechiation of mucosal and internal serosal membranes, myocardium, subcutis and skeletal muscle was found in 10 cases. Frank haemorrhage was present in six cases, including haematomas of the subcutis, skeletal musculature, mesentery or omentum, and lumenal haemorrhage of the abomasum and/or intestine. In five cases pale nodules within myocardium and/or kidney, liver or spleen were present. Histopathologically, these were confirmed as granulomatous inflammatory lesions, which were also present within a wide range of tissues. Granulomatous foci typically comprised aggregates of macrophages, lymphocytes, plasma cells, prominent multinucleated giant cells and eosinophils. DIAGNOSIS: Idiopathic multisystemic granulomatous and haemorrhagic disease, occurring sporadically in dairy cattle, in the absence of feeds or feed additives previously associated with comparable syndromes. CLINICAL RELEVANCE: This is the first description of a novel systemic granulomatous and haemorrhagic syndrome seen in adult dairy cattle most often in their non-lactating period. The presentation can mimic important exotic disease differentials in New Zealand including anthrax, haemorrhagic septicaemia (associated with selected Pasteurella multocida strains) or infection with bovine viral diarrhoea virus type 2.
CT Scan Does Not Differentiate Patients with Hepatopulmonary Syndrome from Other Patients with Liver Disease

Background Hepatopulmonary syndrome (HPS) is defined by liver dysfunction, intrapulmonary vascular dilatations, and impaired oxygenation. The gold standard for detection of intrapulmonary vascular dilatations in HPS is contrast echocardiography. However, two small studies have suggested that patients with HPS have larger segmental pulmonary arterial diameters than both normal subjects and normoxemic subjects with cirrhosis, when measured by CT. We sought to compare CT imaging-based pulmonary vasodilatation in patients with HPS, patients with liver dysfunction without HPS, and matching controls on CT imaging. Methods We performed a retrospective cohort study at two quaternary care Canadian HPS centers. We analyzed CT thorax scans in 23 patients with HPS, 29 patients with liver dysfunction without HPS, and 52 gender- and age-matched controls. We measured the artery-bronchus ratios (ABRs) in upper and lower lung zones, calculated the “delta ABR” by subtracting the upper from the lower ABR, compared these measurements between groups, and correlated them with clinically relevant parameters (partial pressure of arterial oxygen, alveolar-arterial oxygen gradient, macroaggregated albumin shunt fraction, and diffusion capacity). We repeated measurements in patients with post-transplant CTs. Results Patients had significantly larger lower zone ABRs and delta ABRs than controls (1.20 +/- 0.19 versus 0.98 +/- 0.10, p<0.01; and 0.12 +/- 0.17 versus -0.06 +/- 0.10, p<0.01, respectively). However, there were no significant differences between liver disease patients with and without HPS, nor any significant correlations between CT measurements and clinically relevant parameters. There were no significant changes in ABRs after liver transplantation (14 patients). Conclusions Basilar segmental artery-bronchus ratios are larger in patients with liver disease than in normal controls, but this vasodilatation is no more severe in patients with HPS. CT does not distinguish patients with HPS from those with uncomplicated liver disease.
A Novel Approach to Genetic and Environmental Analysis of Cross-Lagged Associations Over Time: The Cross-Lagged Relationship Between Self-Perceived Abilities and School Achievement is Mediated by Genes as Well as the Environment

Using longitudinal cross-lagged analysis to infer causal directions of reciprocal effects is one of the most important tools in the developmental armamentarium. The strength of these analyses can be enhanced by analyzing the genetic and environmental aetiology underlying cross-lagged relationships, for which we present a novel approach here. Our approach is based on standard Cholesky decomposition. Standardized path coefficients are employed to assess genetic and environmental contributions to cross-lagged associations. We indicate how our model differs importantly from another approach that does not in fact analyze genetic and environmental contributions to cross-lagged associations. As an illustration, we apply our approach to the analysis of the cross-lagged relationships between self-perceived abilities and school achievement from age 9 to age 12. Self-perceived abilities of 3852 pairs of twins from the UK Twins Early Development Study were assessed using a self-report scale. School achievement was assessed by teachers based on UK National Curriculum criteria. The key cross-lagged association between self-perceived abilities at age 9 and school achievement at age 12 was mediated by genetic influences (28%) as well as shared (55%) and non-shared (16%) environment. The reverse cross-lagged association from school achievement at 9 to self-perceived abilities at 12 was primarily genetically mediated (73%). Unlike the approach to cross-lagged genetic analysis used in recent research, our approach assesses genetic and environmental contributions to cross-lagged associations per se. We discuss implications of finding that genetic factors contribute to the cross-lag between self-perceived abilities at age 9 and school achievement at age 12.
Automatic Synthesis of Behavioral Object Specifications from Scenarios

The use of scenarios has become a popular technique for requirements elicitation and specification building. Since scenarios capture only partial descriptions of system behavior, an approach for scenario composition and integration is needed to produce more complete specifications. The Unified Modeling Language (UML), which has become a standard notation for object-oriented modeling, provides a suitable framework for scenario acquisition using Use Case diagrams and Collaboration diagrams and for behavioral specification using Statechart diagrams; yet it does not propose any specific modeling process, let alone a process for transforming scenarios into behavioral specifications. In this paper, we suggest a four-step process for synthesizing behavioral specifications from scenarios. It automatically generates from a given set of Collaboration diagrams the Statechart diagrams of all the objects involved. An automatic analysis of specifications in respect to consistency and completeness is also provided. Our approach is incremental and is fully compliant with the UML. Furthermore, it provides an elegant solution to the problem of scenario interleaving. The underlying algorithms have been implemented and validated with several examples, and they are fit for integration into CASE tools supporting the UML.
Stratospheric ozone destruction: The importance of bromine relative to chlorine

The relative effectiveness of bromine compared to chlorine for destroying stratospheric ozone is explored. Two definitions previously used to quantify this relative effectiveness, typically referred to as α, are compared and a definition is presented to calculate α values applicable for column and global ozone loss. Calculations of α are made with a two-dimensional radiative/chemical/ dynamical model and suggest that bromine is roughly 45 times more effective than chlorine for global ozone destruction. The physical processes underlying this result are probed, and sensitivity studies are presented that show that relatively large changes invoked in the modeled transport and heterogeneous chemistry lead to changes in this value of <15%.