Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetic Allee effect: A unified framework for the genetics and demography of small populations

The Allee effect is a theoretical model predicting low growth rates and the possible extinction of small populations. Historically, studies of the Allee effect have focused on demography. As a result, underlying processes other than the direct effect of population density on fitness components are not generally taken into account. There has been heated debate about the potential of genetic processes to drive small populations to extinction, but recent studies have shown that such processes clearly impact small populations over short time scales, and some may generate Allee effects. However, as opposed to the ecological Allee effect, which is underpinned by cooperative interactions between individuals, genetically driven Allee effects require a change in genetic structure to link the decline in population size with a decrease in fitness components. We therefore define the genetic Allee effect as a two-step process whereby a decrease in population size leads to a change in population genetic structure, and in turn, to a decrease in individual fitness. We describe potential underlying mechanisms, and review the evidence for this original type of component Allee effect, using published examples from both plants and animals. The possibility of considering demogenetic feedback in light of genetic Allee effects clarifies the analysis and interpretation of demographic and genetic processes, and the interplay between them, in small populations.
Cargo-selective apical exocytosis in epithelial cells is conducted by Myo5B, Slp4a, Vamp7, and Syntaxin 3

The motor protein Myo5B and t-SNARE Stx3 drive cargo-selective apical exocytosis in polarized epithelial cells in a pathway dependent on v-SNARE–like Slp4a, v-SNARE Vamp7, Sec1/Munc18-like protein Munc18-2, and the Rab11/8 cascade.
The Olfactory Pathway of Adult and Larval Drosophila

Tracing of olfactory projections based on odorant receptor expression has led to an almost complete receptor‐to‐glomerulus map in adult Drosophila. While most of the glomeruli may be involved in processing of food odors, others appear to be more specialized, for example, responding to CO2 or to pheromonal cues. Recent studies have shed light on signal processing in the antennal lobe and in higher centers. Newly detected cholinergic excitatory local interneurons in the antennal lobe appear to provide substrates for the broad odor tuning properties of projection neurons. In the mushroom bodies, projection neurons establish an intricate divergence‐convergence network with their target cells, allowing complex modes of signal transfer. In the lateral horn, projection neurons innervating candidate pheromone glomeruli appear to segregate from those innervating “normal” glomeruli. Hence, pheromone and food information may be handled by separate channels, consistent with discrete behavioral meanings of the two kinds of signals. The olfactory pathway of the larva shares the general layout of its adult counterpart, with a number of simplifications. The presence of only 21 glomeruli suggests a reduction of primary olfactory “dimensions” compared to adults. The existence of a pheromone‐sensing subsystem is unlikely. Larval glomeruli are targets of single, unique sensory neurons rather than being sites of convergence as in the adult. Projection neuron outputs are restricted to single glomeruli in the mushroom body. Their target cells either innervate one or several of them creating substrates for elementary odor coding and coincidence detection. In conclusion, olfactory discrimination capacities of the larva are very likely reduced, consistent with the requirements of a substrate feeder.
A survey of the availability of state‐funded primary eye care in the UK for the very young and very old

Background: The National Health Service (NHS) provides General Ophthalmic Services (GOS) to eligible patients in the UK. Nearly all community optical practices have a contract with the NHS via local primary care organisations (primary care trusts in England) allowing the practices to provide NHS sight tests to eligible patients.
The Kaposi sarcoma-associated herpesvirus (KSHV) is present as an intact latent genome in KS tissue but replicates in the peripheral blood mononuclear cells of KS patients

Short DNA sequences have been identified, originally in association with Kaposi's sarcoma (KS) biopsies, that are highly homologous to oncogenic, lymphotropic herpesviruses. Recently a virus, Kaposi sarcoma associated herpesvirus (KSHV) or human herpesvirus-8 (HHV-8), bearing these sequences has been identified in a cell line derived from a body cavity-based lymphoma. In this report, we show that the same sequences are present in KS biopsies as DNA molecules of a form and size characteristic of latent herpesviruses-large, covalently closed, circular episomes. The genomes migrate with an apparent size larger than the herpesvirus Epstein-Barr virus (172 kb). This form of the viral genome was found in four of four biopsies and three of five peripheral blood samples from KS patients. Linear forms of the viral genome, characteristic of viral replication, were not detected in the biopsies, but were present in the peripheral blood of three out of five patients. The sequences for KSHV/HHV-8 were also detected in the blood of four of five allograft patients and three of five healthy donors without KS suggesting that the virus is widespread throughout the human population.
Motion planning under uncertainty for medical needle steering using optimization in belief space

We present an optimization-based motion planner for medical steerable needles that explicitly considers motion and sensing uncertainty while guiding the needle to a target in 3D anatomy. Motion planning for needle steering is challenging because the needle is a nonholonomic and underactuated system, the needle's motion may be perturbed during insertion due to unmodeled needle/tissue interactions, and medical sensing modalities such as ultrasound imaging and x-ray projection imaging typically provide only noisy and partial state information. To account for these uncertainties, we introduce a motion planner that computes a trajectory and corresponding linear controller in the belief space - the space of distributions over the state space. We formulate the needle steering motion planning problem as a partially observable Markov decision process (POMDP) that approximates belief states as Gaussians. We then compute a locally optimal trajectory and corresponding controller that minimize in belief space a cost function that considers avoidance of obstacles, penalties for unsafe control inputs, and target acquisition accuracy. We apply the motion planner to simulated scenarios and show that local optimization in belief space enables us to compute higher quality plans compared to planning solely in the needle's state space.
Memory deficits in abstinent MDMA (ecstasy) users: neuropsychological evidence of frontal dysfunction

Chronic administration of the common club drug 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) is associated with long-term depletion of serotonin (5-HT) and loss of 5-HT axons in the brains of rodents and non-human primates, and evidence suggests that recreational MDMA consumption may also affect the human serotonergic system. Moreover, it was consistently shown that abstinent MDMA users have memory de.cits. Recently, it was supposed that these de.cits are an expression of a temporal or rather hippocampal dysfunction caused by the serotonergic neurotoxicity of MDMA. The aim of this study is to examine the memory de.cits of MDMA users neuropsychologically in order to evaluate the role of different brain regions. Nineteen male abstinent MDMA users, 19 male abstinent cannabis users and 19 male drug-naive control subjects were examined with a German version of the Rey Auditory Verbal Learning Test (RAVLT). MDMA users showed widespread and marked verbal memory de.cits, compared to drug-naive controls as well as compared to cannabis users, whereas cannabis users did not differ from control subjects in their memory performance. MDMA users revealed impairments in learning, consolidation, recall and recognition. In addition, they also showed a worse recall consistency and strong retroactive interference whereby both measures were previously associated with frontal lobe function. There was a signi.cant correlation between memory performance and the amount of MDMA taken. These results suggest that the memory de.cits of MDMA users are not only the result of a temporal or hippocampal dysfunction, but also of a dysfunction of regions within the frontal cortex.
Etude expérimentale et théorique des propriétés optiques de nanocomposites plasmoniques fabriqués par irradiation laser et sous flux solaire concentré

Cette these porte sur l'etude de nanocomposites plasmoniques et, plus particulierement, sur des couches minces de polymere dopees en nanoparticules d'or et d'argent. Les travaux realises concernent le developpement de deux approches de fabrication originales fondees sur la synthese in situ de nanoparticules dans une matrice de polymere sous irradiation. La premiere methode envisagee etudie l’organisation de nanoparticules d’or dans les films de polymeres en les irradiant de maniere controlee dans l'espace par interferometrie laser. Ainsi, nous obtenons des reseaux de nanoparticules qui revelent des proprietes de diffraction atypiques dont la reponse spectrale depend fortement de la reponse plasmonique du systeme. Nous appelons ce phenomene diffraction amplifiee par plasmon. La seconde approche de fabrication developpee a pour but de realiser la synthese de nanoparticules in situ dans des films de polymere sous rayonnement solaire concentre. Nous nous sommes interesses, en particulier, a l'influence de l'irradiation solaire concentree sur les processus de formation des nanoparticules et sur leur morphologie finale, dans le but de controler les proprietes optiques du systeme. Nous avons notamment montre qu’il est possible de controler la taille des nanoparticules d’or formees in situ dans les films de polymere, en faisant varier le flux du rayonnement solaire. En parallele de ces travaux experimentaux, une approche semi-analytique combinant une description des materiaux en termes de milieux effectif a la methode RCWA (Rigorous Coupled Wave Analysis), a ete developpee pour calculer les proprietes optiques des nanocomposites.
ZML : Z Formal Specifications Using XML

This paper describes a project, the purpose of which was to determine the feasibility of using XML as a vehicle for carrying the contextual meaning of a Z formal specification. This paper describes a definition of the popular Z (pronounced z G), formal specification language, in terms of an eXtensible Markup Language (XML) Data Type Definition (DTD). Using the Sun JAXB tool, we wrote a Java program that supports building and processing a tree structure based on the DTD. Using that DTD, a small Z specification was rendered in XML. We then present a case study Java program written to demonstrate the ability to examine and process the Z specification as an internal tree structure. Finally, we describe some limitations encountered in the JAXB tool and suggestions for improving it. With the feasibility proven, we could then go on to use the XML vehicle to pass the Z specification to a theorem prover, a code generator, or other, as yet unforeseen tools. Z is a formal specification language, used for specifying requirements or designs, and to which formal proofs of correctness and completeness can be applied. XML allows us to define a Z schema, so it can be used with other software tools to contextually render the schema. We describe a complete Data Type Definition (DTD), denoted ZML, for the general Z schema format. While pursuing our primary purpose, we have found some limitations in JAXB, which we describe in this paper.
Finding collisions for MD4 hash algorithm using hybrid algorithm

The modication of message that meets the sucient conditions for collision is found in the last step of dierential attack proposed by Wang et all. (2005) on MD4 hash algorithm. Here we show how this attack phase, nding a collision starting from the list of sucient conditions for the collision, can be implemented using a combination of two algorithms - evolutionary algorithm and hill climbing. Hybridization of evolutionary algorithm and hill climbing is a well-known technique for improving solutions, but it isn’t applied to this domain (at least by information that author has collected).
Epithelial–mesenchymal transition in cancer development and its clinical significance

The epithelial–mesenchymal transition (EMT) plays a critical role in embryonic development. EMT is also involved in cancer progression and metastasis and it is probable that a common molecular mechanism is shared by these processes. Cancer cells undergoing EMT can acquire invasive properties and enter the surrounding stroma, resulting in the creation of a favorable microenvironment for cancer progression and metastasis. Furthermore, the acquisition of EMT features has been associated with chemoresistance which could give rise to recurrence and metastasis after standard chemotherapeutic treatment. Thus, EMT could be closely involved in carcinogenesis, invasion, metastasis, recurrence, and chemoresistance. Research into EMT and its role in cancer pathogenesis has progressed rapidly and it is now hypothesized that novel concepts such as cancer stem cells and microRNA could be involved in EMT. However, the involvement of EMT varies greatly among cancer types, and much remains to be learned. In this review, we present recent findings regarding the involvement of EMT in cancer progression and metastasis and provide a perspective from clinical and translational viewpoints. (Cancer Sci 2009)
Dovepress Open Access to Scientific and Medical Research Open Access Full Text Article the Use of Superparamagnetic Nanoparticles for Prosthetic Biofilm Prevention

As with all surgical procedures, implantation comes with the added risk of infection. The goal of this in vitro study was to explore the use of superparamagnetic iron oxide nanoparticles (SPION) as a multifunctional platform to prevent biofilm formation. Results showed for the first time decreased Staphylococcus epidermidis numbers when exposed to 100 µg/ml of SPION for 12 hours and this trend continued for up to 48 hours. Prevention of colony assembly, a prerequisite to biofilm formation, was also observed at lower SPION dosages of 10 µg/ml after 12 hours. Coupled with previous studies demonstrating enhanced bone cell functions in the presence of the same concentration of SPION, the present results provided much promise for the use of SPION for numerous anti-infection orthopedic applications.
Activity in older adults: cause or consequence of cognitive functioning? A longitudinal study on everyday activities and cognitive performance in older adults.

The impact of three types of everyday activities (i.e., social, experiential, and developmental) on four cognitive functions (i.e., immediate recall, learning, fluid intelligence, and information-processing speed) and one global indicator of cognitive functioning (Mini-Mental State Exam score) over a period of 6 years was studied in a large 55--85 year-old population-based sample (N = 2,076). A cross-lagged regression model with latent variables was applied to each combination of 1 cognitive function and 1 type of activity, resulting in 15 (3 x 5) different models. None of the activities were found to enhance cognitive functioning 6 years later when controlling for age, gender, level of education, and health, as well as for unknown confounding variables. Conversely, one cognitive function (i.e., information-processing speed) appeared to affect developmental activity. It is suggested that no specific activity, but rather socioeconomic status to which activities are closely connected, contributes to maintenance of cognitive functions.
Correction: Does the Chemotherapy Backbone Impact on the Efficacy of Targeted Agents in Metastatic Colorectal Cancer? A Systematic Review and Meta-Analysis of the Literature

1 Royal North Shore Hospital, Northern Clinical School, University of Sydney, St Leonards, New South Wales, Australia, 2 Department of Medical Oncology, Monash University, Victoria, Australia, 3 The Queen Elizabeth Hospital and University of Adelaide, South Australia, Australia, 4 Flinders University and Flinders Medical Centre, Flinders Centre for Innovation in Cancer, Bedford Park, South Australia, Australia, 5 Austin Health, Victoria, Australia, 6 St Vincent’s Clinical School, University of New South Wales, NSW, Australia
Robust Source Localization in Reverberant Environments Based on Weighted Fuzzy Clustering

Successful localization of sound sources in reverberant enclosures is an important prerequisite for many spatial signal processing algorithms. We investigate the use of a weighted fuzzy c-means cluster algorithm for robust source localization using location cues extracted from a microphone array. In order to increase the algorithm's robustness against sound reflections, we incorporate observation weights to emphasize reliable cues over unreliable ones. The weights are computed from local feature statistics around sound onsets because it is known that these regions are least affected by reverberation. Experimental results illustrate the superiority of the method when compared with standard fuzzy clustering. The proposed algorithm successfully located two speech sources for a range of angular separations in room environments with reverberation times of up to 600 ms.
Chapter 4 How does a dictation machine recognize speech ?

There is magic (or is it witchcraft? ) in a speech recognizer that transcribes continuous radio speech into text with a word accuracy of even not more than 50%. The extreme difficulty of this task, tough, is usually not perceived by the general public. This is because we are almost deaf to the infinite acoustic variations that accompany the production of vocal sounds, which arise from physiological constraints (co-articulation), but also from the acoustic environment (additive or convolutional noise, Lombard effect), or from the emotional state of the speaker (voice quality, speaking rate, hesitations, etc.). Our consciousness of speech is indeed not stimulated until after it has been processed by our brain to make it appear as a sequence of meaningful units: phonemes and words. In this Chapter we will see how statistical pattern recognition and statistical sequence recognition techniques are currently used for trying to mimic this extraordinary faculty of our mind (4.1). We will follow, in Section 4.2, with a MATLAB-based proof of concept of word-based automatic speech recognition (ASR) based on Hidden Markov Models (HMM), using a bigram model for modeling (syntactic-semantic) language constraints.
Modeling, refining and analyzing Incomplete Büchi Automata

Software development is an iterative process which includes a set of development steps that transform the initial high level specification of the system into its final, fully specified, implementation. This report discusses the theoretical foundations that allow Incomplete B\"uchi Automata (IBAs) to be used in the iterative development of a sequential system.
Terrain segmentation of high resolution satellite images using multi-class AdaBoost algorithm

Terrain segmentation is still a challenging issue in pattern recognition, especially in the application of high resolution satellite images. Among the various segmentation approaches are those based on graph partitioning, which present some drawbacks such as high processing time, low accuracy on detection of targets on the large scaled images such as high resolution satellite images. In this paper, we focus on the computational intelligence approach to classify and detect building, foliage, grass, bare-ground, and road of land cover. We propose a method, which has a high accuracy on classification and object detection by using multi-class AdaBoost algorithm based on a combination of two extracted features, which are cooccurrence and Haar-like features. With all features, multi-class Adaboost selects only critical features and performs as an extremely efficient classifier. Experimental results show that the classification accuracy is over 91% with a high resolution satellite image.
Transport in Two-Dimensional Maps

We study transport in the two-dimensional phase space of C r diffeomorphisms (r ~ 1) of two manifolds between regions of the phase space bounded by pieces of the stable and unstable manifolds of hyperbolic fixed points. The mechanism for the transport is associated with the dynamics of homoclinic and heteroclinic tangles, and the study of this dynamics leads to a general formulation for the transport rates in terms of distributions of small regions in phase space ("lobes"). It is shown how the method applies to three geometrical configurations, one of which corresponds to the geometry associated with the Kelvin-Stuart Cat's Eye flow undergoing a time-periodic perturbation. In this case the formulae imply, for example, that the evolution of only two lobes determines the mass transport from the upper to the lower half plane of the fluid flow. As opposed to previous studies this formulation takes into account the effect of re-entrainment of the lobes, i.e., the implications of the lobes leaving and re-entering the specified regions on the transport rates. The formulation is developed for both area-preserving and non-area-preserving two-dimensional diffeomorphisms and does not require the map to be near-integrable. The techniques involved in applying this formulation are discussed including the possible use of the generating function for computing the distributions of the Iobes in phase space, as well as the use of Poincar6 maps, which enable one to study the transport in continuous time systems using the above formalism. In particular, we demonstrate how the right choice of the Poincar6 section can reduce the labor of transport rate calculations.
Natural Selection Along an Environmental Gradient: A Classic Cline in Mouse Pigmentation

Abstract We revisited a classic study of morphological variation in the oldfield mouse (Peromyscus polionotus) to estimate the strength of selection acting on pigmentation patterns and to identify the underlying genes. We measured 215 specimens collected by Francis Sumner in the 1920s from eight populations across a 155-km, environmentally variable transect from the white sands of Florida's Gulf coast to the dark, loamy soil of southeastern Alabama. Like Sumner, we found significant variation among populations: mice inhabiting coastal sand dunes had larger feet, longer tails, and lighter pigmentation than inland populations. Most striking, all seven pigmentation traits examined showed a sharp decrease in reflectance about 55 km from the coast, with most of the phenotypic change occurring over less than 10 km. The largest change in soil reflectance occurred just south of this break in pigmentation. Geographic analysis of microsatellite markers shows little interpopulation differentiation, so the abrupt change in pigmentation is not associated with recent secondary contact or reduced gene flow between adjacent populations. Using these genetic data, we estimated that the strength of selection needed to maintain the observed distribution of pigment traits ranged from 0.0004 to 21%, depending on the trait and model used. We also examined changes in allele frequency of SNPs in two pigmentation genes, Mc1r and Agouti, and show that mutations in the cis-regulatory region of Agouti may contribute to this cline in pigmentation. The concordance between environmental variation and pigmentation in the face of high levels of interpopulation gene flow strongly implies that natural selection is maintaining a steep cline in pigmentation and the genes underlying it.