Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of phylogeographic endemism in an environmentally complex biome

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.
Tree-Ring and Climate Relationships for Abies Alba in the Internal Alps

The relationships between the tree -rings of the white fir ( Abies alba Mill.) and climate in the French internal Alps are indicated by correlation functions. This fir shows an accurate response to climate as well as long term persistence for at least six years (MS =0.18, R1 =0.65, and R6= 0.27). Its growth is strongly influenced by the previous year's climate, especially by prior August rainfall, which enhances ring size, or by high temperatures, which show the opposite effect. The most critical period extends from prior July to prior September. This species responds positively to warm temperature from current January to April, followed by rainfall in May and June, which leads to a longer growth period. A favorable water balance seems to be decisive. Abies alba can be affected by frost and seems to prefer a low thermal amplitude as demonstrated by the analysis of the extreme temperature data. Moreover, even a few days of excessive heat can reduce its growth. Die Beziehungen zwischen den Jahresringen der Weistanne ( Abies alba Mill.) und das Klima in den zentralen franzosischen Alpen deuten Korrelationen an. Diese Tanne zeigt sowohl eine direkte Reaktion auf das Klima als auch langfristige Auswirkungen uber mindestens sechs Jahre (MS =0.18, R1 =0.65, und R6= 0.27). Ihr Wachstum ist stark durch das Klima des vorherigen Jahres beeinflust, vor allem durch Regenfalle vor dem ende des monats Juli, die zu einer erhohten Ringgrose fuhrt, oder durch hohe Temperaturen, die das Gegenteil bewirken. Die kritischste Periode erstreckt sich von ende Juni bis ende August. Diese Art reagiert positiv auf warme Temperaturen von Januar bis April, gefolgt von Regenfall im Mai und Juni, was zur einer verlangerten Wachstumsperiode fuhrt. Ein gunstiges Wasserverhaltnis scheint ausschlaggebend zu sein. Abies alba kann von Frost beeinflust werden und scheint eine niedrigere thermische Amplitude zu bevorzugen, wie die Analyse der extremen Temperaturdaten veranschaulicht. Auserdem kann ihr Wachstum schon durch wenige Tage ubermasiger Warme reduziert werden. On analyse les relations entre les cernes du Sapin pectine ( Abies alba Mill.) et le climat au moyen des fonctions de correlation. Le Sapin montre une bonne reponse au climat et une inertie a long terme sur au moins 6 ans (MS =0.18, R1 =0.65, and R6= 0.27). Sa croissance est fortement influencee par le climat de l'annee precedente, en particulier par les precipitations en Aoilt (n -1) qui augmentent les largeurs de cernes, ou par de fortes temperatures qui montrent simultanement un effet oppose. La periode la plus critique va de Juillet (n -1) a Septembre (n -1). Cette essence apprecie des temperatures chaudes de Janvier (n) a Avril (n), suivies de pluies en Mai (n) et Juin (n), ce qui conduit a une plus longue periode de vegetation. Un bilan hydrique favorable semble etre essentiel au Sapin. Il peut etre affecte par le gel et semble preferer une amplitude thermique reduite, comme le montre l'analyse des donnees de temperatures extremes. De plus, meme quelques jours trop chauds peuvent reduire sa croissance.
Mapping forest patches and scattered trees from SPOT images and testing their ecological importance for woodland birds in a fragmented agricultural landscape

Scattered trees represent an important element within the agricultural matrix for birds. The aims of this study were to develop methods for mapping isolated trees from satellite imagery and to assess the importance of isolated trees for bird species richness. Field sampling of birds and plants was conducted at 120 sites in south-east Australia. We mapped tree cover from Landsat and SPOT images using a combination of spectral and segmentation based methods. Mapping of isolated trees as point objects was highly accurate (80–90%). Tree cover at spatial extents of 3–28 ha around sites explained 60% of the variability in woodland–dependent bird species richness. However, isolated trees in agricultural areas made just a small contribution to explaining the spatial variability in overall avian richness. This approach can be used for more extensive assessment of avian habitat quality from high spatial resolution images across a range of human modified landscapes.
The use of resampling for estimating confidence intervals for single site and pooled frequency analysis / Utilisation d'un rééchantillonnage pour l'estimation des intervalles de confiance lors d'analyses fréquentielles mono et multi-site

Abstract A balanced resampling approach is presented for estimating confidence intervals for extreme flow quantiles determined from data at a single site. The approach is also adapted to provide resampled estimates for confidence intervals for extreme flow quantiles obtained from pooled frequency analysis. The balanced resampling approach does not require assumptions, in contrast to conventional approaches that are typically based on an asymptotic formula and require a distributional assumption. The approach is demonstrated to provide useful information in the context of both single site and pooled frequency analysis. The application of the approach also demonstrates the benefits of employing a pooled frequency analysis approach for estimating extreme flow quantiles.
An integrate and fire neural network to simulate epileptic patterns in intracortical EEG

Epilepsy is characterized by paradoxical patterns of neural activity, either localized within single regions of the cortex or spreading to large areas. These patterns may cause different types of EEG, which may dynamically change during the temporal evolution of seizure. It is generally assumed that these epileptic patterns may originate in a network of strongly interconnected neurons, in cases when excitation dominates over inhibition. The aim of this work is to use a neural network of integrate and fire neurons to analyze which parameter alterations (either at the neural level or at the level of synapses) may induce network instability and epileptic-like discharges. A signal representative of EEG is simulated by summing the membrane potential changes of all neurons. Model simulations show that an increase in the strength and in spatial extension of excitatory synapses vs. inhibitory synapses and/or an increase in the relative refractory period, may determine sustained patterns of uncontrolled activity, which propagate along the network. These propagating waves may have a different shape and frequency, depending on the particular parameter set used during the simulations and on initial random conditions. The resulting model EEG signals include isolated or repeated bursts, high-frequency low-amplitude waves or larger oscillations with lower frequency. A derangement in a few parameters of the model causes the transition from one pattern to another, thus generating a highly non-stationary signal which resembles that observed during intracortical EEG measurements in epilepsy. The obtained results may help to elucidate the mechanisms at the basis of some epileptic discharges, and to relate rapid changes in EEG patterns, often observed during seizure, with the underlying alterations at the neural and network levels.
Prediction with a short memory

We consider the problem of predicting the next observation given a sequence of past observations, and consider the extent to which accurate prediction requires complex algorithms that explicitly leverage long-range dependencies. Perhaps surprisingly, our positive results show that for a broad class of sequences, there is an algorithm that predicts well on average, and bases its predictions only on the most recent few observation together with a set of simple summary statistics of the past observations. Specifically, we show that for any distribution over observations, if the mutual information between past observations and future observations is upper bounded by I, then a simple Markov model over the most recent I/є observations obtains expected KL error є—and hence ℓ1 error √є—with respect to the optimal predictor that has access to the entire past and knows the data generating distribution. For a Hidden Markov Model with n hidden states, I is bounded by logn, a quantity that does not depend on the mixing time, and we show that the trivial prediction algorithm based on the empirical frequencies of length O(logn/є) windows of observations achieves this error, provided the length of the sequence is dΩ(logn/є), where d is the size of the observation alphabet. We also establish that this result cannot be improved upon, even for the class of HMMs, in the following two senses: First, for HMMs with n hidden states, a window length of logn/є is information-theoretically necessary to achieve expected KL error є, or ℓ1 error √є. Second, the dΘ(logn/є) samples required to accurately estimate the Markov model when observations are drawn from an alphabet of size d is necessary for any computationally tractable learning/prediction algorithm, assuming the hardness of strongly refuting a certain class of CSPs.
A Study Of Drivers For Agricultural LandAbandonment Using GIS AndData Mining Techniques

This paper examines the problem of agricultural land abandonment through knowledge of driving factors. First, we reach out a review of the concept of abandonment in order to define the negative and positive aspects of this process in the landscape. Then we focus on a real case study in the Marina Baja region (SE Spain). Finally, we propose, from a theoretical perspective, the use of a methodology to define the most important variables for studying the abandonment processes in this region. First of all, we performed various analyses using Geographical Information Systems (GIS) to create a geodatabase which stores the main factors generally associated with abandonment. The variables considered can be grouped into three groups: environmental (such as climate, soils or relief), socio-economic (such as demographic, accessibility or technology) and those related to cultural practices in the crop (such as irrigation or rain-fed stone walls). Considering over a hundred variables we need to answer two questions: (1) which of the variables are really driving factors in the abandonment process of an agricultural plot? and (2) how important is each of them alone or in combination with others? The authors advocate the use of GIS for the feature creation or management and Data Mining techniques to perform the feature selection. Specifically, we propose the use of a concrete metric, aci (Attribute Correlation Index), to answer the questions raised above.
Usability Comparisons of Seven Main Functions for Automated Teller Machine (ATM) Banking Service of Five Banks in Thailand

The objective of this research was to compare the seven main functions of ATM banking services from five banks in Thailand. The selection of the five ATM banks was based on the fact that they contained different hierarchical menu structures. In the research, four groups each with 200 participants were separated into two parts. The first group of participants was required to complete a questionnaire in order to identify the seven main tasks of ATM banking, whilst the second group was required to perform the experiment on the ATM simulator. The second group was subdivided into four groups; students, employees, government and state enterprises officers and agriculturists. To compare seven major functions, a simulator of each of the five banks’ ATM machines was developed and then tested in the laboratory environment. Usability was evaluated in terms of effectiveness, efficiency, satisfaction and the percentage difference. The results suggest that different menu structures will affect the usability of ATM banking. Moreover, the different types of user provide a different score based on usability measurement. Only one bank received the highest score on most of the usability criteria for all the different user groups.
Nymphalid eyespot serial homologues originate as a few individualized modules

Serial homologues are repeated traits that share similar development but occur in different parts of the body. Variation in number of repeats accounts for substantial diversity in animal form and considerable work has focused on identifying the factors accounting for this variation. Little is known, however, about how serial homologues originally become repeated, or about the relative timing of repeat individuation relative to repeat origin. Here, we show that the serially repeated eyespots on nymphalid butterfly wings most likely arose as a small cluster of units on the ventral hindwing that were later co-opted to the dorsal and anterior wing surfaces. Based on comparative analyses of over 400 species, we found support for a model of eyespot origin followed by redeployment, rather than by the conventional model, where eyespots arose as a complete row of undifferentiated units that later gained individuation. In addition, eyespots most likely evolved from simpler pattern elements, single-coloured spots, which were already individuated among different wing sectors. Finally, the late appearance of eyespots on the dorsal, hidden wing surface further suggests that these novel complex traits originally evolved for one function (thwarting predator attacks) and acquired a second function (sexual signalling) when moved to a different body location. This broad comparative analysis illustrates how serial homologues may initially evolve as a few units serving a particular function and subsequently become repeated in novel body locations with new functions.
Optimistic Active-Learning Using Mutual Information

An "active learning system" will sequentially decide which unlabeled instance to label, with the goal of efficiently gathering the information necessary to produce a good classifier. Some such systems greedily select the next instance based only on properties of that instance and the few currently labeled points -- e.g., selecting the one closest to the current classification boundary. Unfortunately, these approaches ignore the valuable information contained in the other unlabeled instances, which can help identify a good classifier much faster. For the previous approaches that do exploit this unlabeled data, this information is mostly used in a conservative way. One common property of the approaches in the literature is that the active learner sticks to one single query selection criterion in the whole process. We propose a system, MM+M, that selects the query instance that is able to provide the maximum conditional mutual information about the labels of the unlabeled instances, given the labeled data, in an optimistic way. This approach implicitly exploits the discriminative partition information contained in the unlabeled data. Instead of using one selection criterion, MM+M also employs a simple on-line method that changes its selection rule when it encounters an "unexpected label". Our empirical results demonstrate that this new approach works effectively.
Towards understanding spontaneous speech: word accuracy vs. concept accuracy

Describes an approach to the automatic evaluation of both the speech recognition and understanding capabilities of a spoken dialogue system for train timetable information. For performance judgement, we use word accuracy for recognition and concept accuracy for understanding. Both measures are calculated by comparing these modules' outputs with a correct reference answer. We report evaluation results for a spontaneous speech corpus with about 10,000 utterances. We observed a nearly linear relationship between word accuracy and concept accuracy.
Online discovery of AUV control policies to overcome thruster failures

We investigate methods to improve fault-tolerance of Autonomous Underwater Vehicles (AUVs) to increase their reliability and persistent autonomy. We propose a learning-based approach that is able to discover new control policies to overcome thruster failures as they happen. The proposed approach is a model-based direct policy search that learns on an on-board simulated model of the AUV. The model is adapted to a new condition when a fault is detected and isolated. Since the approach generates an optimal trajectory, the learned fault-tolerant policy is able to navigate the AUV towards a specified target with minimum cost. Finally, the learned policy is executed on the real robot in a closed-loop using the state feedback of the AUV. Unlike most existing methods which rely on the redundancy of thrusters, our approach is also applicable when the AUV becomes under-actuated in the presence of a fault. To validate the feasibility and efficiency of the presented approach, we evaluate it with three learning algorithms and three policy representations with increasing complexity. The proposed method is tested on a real AUV, Girona500.
Clinical utility of transdermal delivery of oxybutynin gel via a metered-dose pump in the management of overactive bladder

Oxybutynin is an efficacious treatment for overactive bladder, but its clinical utility is hampered by relative intolerability due to its side effect profile. Over the last few years, various attempts to enhance the tolerability of oxybutynin by varying the drug delivery mechanism have been introduced and have included extended release, rectal suppository, transdermal patch, and gel formulations. The recent introduction of a transdermal oxybutynin gel in a sachet form has been complemented by the administration of gel in a metered dose pump. This paper reviews the available evidence for transdermal oxybutynin gel and, where it exists, for the pump-based gel. The clinical utility of the pump-based gel is discussed.
Pitchfork and Gprasp2 Target Smoothened to the Primary Cilium for Hedgehog Pathway Activation

The seven-transmembrane receptor Smoothened (Smo) activates all Hedgehog (Hh) signaling by translocation into the primary cilia (PC), but how this is regulated is not well understood. Here we show that Pitchfork (Pifo) and the G protein-coupled receptor associated sorting protein 2 (Gprasp2) are essential components of an Hh induced ciliary targeting complex able to regulate Smo translocation to the PC. Depletion of Pifo or Gprasp2 leads to failure of Smo translocation to the PC and lack of Hh target gene activation. Together, our results identify a novel protein complex that is regulated by Hh signaling and required for Smo ciliary trafficking and Hh pathway activation.
Ceruloplasmin/Transferrin Ratio Changes in Alzheimer's Disease

The link between iron and Alzheimer's disease (AD) has been mainly investigated with a focus on the local accumulation of this metal in specific areas of the brain that are critical for AD. In the present study, we have instead looked at systemic variations of markers of iron metabolism. We measured serum levels of iron, ceruloplasmin, and transferrin and calculated the transferrin saturation and the ceruloplasmin to transferrin ratio (Cp/Tf). Cp/Tf and transferrin saturation increased in AD patients. Cp/Tf ratios also correlated positively with peroxide levels and negatively with serum iron concentrations. Elevated values of ceruloplasmin, peroxides, and Cp/Tf inversely correlated with MMSE scores. Isolated medial temporal lobe atrophy positively correlated with Cp/Tf and negatively with serum iron. All these findings indicate that the local iron accumulation found in brain areas critical for AD should be viewed in the frame of iron systemic alterations.
Pulmonary emphysema: objective quantification at multi-detector row CT--comparison with macroscopic and microscopic morphometry.

PURPOSE To prospectively compare pulmonary function tests and helical computed tomographic (CT) indexes for quantifying pulmonary emphysema with macroscopic and microscopic morphometry. MATERIALS AND METHODS The investigation was approved by the local ethics committee, and written informed consent was obtained from patients. Multi-detector row CT of the thorax was performed with simultaneous acquisition of four 1-mm sections in 80 patients (57 men, 23 women; age range, 38-79 years) referred for surgical resection of lung cancer. From the raw data, 1.25-mm-thick sections were reconstructed at 10-mm intervals. Relative areas of lung with attenuation coefficients lower than nine thresholds and eight percentiles of the distribution of attenuation coefficients were calculated. Relative areas and percentiles were compared with areas found macroscopically to have emphysema and with two microscopic indexes assessed on resected specimens. Pulmonary function tests were measured 24-48 hours before surgery. Spearman correlation coefficients were calculated between each set of CT data obtained with the nine tested thresholds and eight percentiles with macroscopic and microscopic measurements. RESULTS For relative lung areas, the strongest correlation with macroscopy was observed with a threshold of -970 HU (r = 0.543, P < .001) and that with microscopy was observed at -960 and -970 HU, depending on the index considered (r = 0.592, P < .001 and r = -0.546, P < .001, respectively). For percentiles, 1st percentile showed the strongest correlation with both macroscopy (r = -0.463, P < .001) and microscopy (r = -0.573, P < .001; and r = 0.523, P < .001 for each microscopic measurement). Forced expiratory volume in 1 second and vital capacity ratio, diffusing capacity of lung for carbon monoxide, and each of the three CT indexes were complementary to predict microscopic indexes. CONCLUSION Relative lung areas with attenuation coefficients lower than -960 or -970 HU and 1st percentile are valid indexes to quantify pulmonary emphysema on multi-detector row CT scans.
Formal Veri cation of a PowerPCTM MicroprocessorDavid

This paper presents the use of formal methods in the design of a PowerPC microprocessor. The chosen methodology employs two independently developed design views, a register-transfer level speciica-tion for eecient system simulation and a transistor-level implementation geared toward maximal processor performance. A BDD-based veriication tool is used to functionally compare the two views which essentially validates the transistor-level implementation with respect to any functional simulation/veriication performed at the register-transfer level. We show that a tight integration of the veriication approach into the overall design methodology allows the formal veriica-tion of complex microprocessor implementations without compromising the design process or performance of the resulting system.