Miracle-dz/UniFAR-FTUs huggingface dataset:
IDA-PBC for a class of underactuated mechanical systems with application to a rotary inverted pendulum

We develop a method to simplify the partial differential equations (PDEs) associated to the potential energy for interconnection and damping assignment passivity based control (IDA-PBC) of a class of underactuated mechanical systems. Solving the PDEs, also called the matching equations, is the main difficulty in the construction and application of the IDA-PBC. With the proposed method, a simplification to the potential energy PDE is achieved through a particular parametrization of the closed-loop inertia matrix that appears as a coupling term with the inverse of original inertia matrix. The results are applied to the Quanser rotary inverted pendulum and illustrated through numerical simulations.
Synaptophysin (p38) at the frog neuromuscular junction: its incorporation into the axolemma and recycling after intense quantal secretion

Recycling of synaptophysin (p38), a synaptic vesicle integral membrane protein, was studied by the use of antisera raised against the protein purified from frog brain. When frog cutaneous pectoris muscles were fixed at rest, a bright, specific immunofluorescent signal was observed in nerve-terminal regions only if their plasma membranes had been previously permeabilized. When muscles were fixed after they had been treated for 1 h with a low dose of alpha-latrotoxin in Ca2+-free medium, an equally intense fluorescence could be observed without previous permeabilization. Under this condition, alpha-latrotoxin depletes nerve terminals of their quantal store of acetylcholine and of synaptic vesicles. These results indicate that fusion of synaptic vesicles leads to the exposure of intravesicular antigenic determinants of synaptophysin on the outer surface of the axolemma, and provide direct support for the vesicle hypothesis of neurotransmitter release. After 1 h treatment with the same dose of alpha-latrotoxin in the presence of 1.8 mM extracellular Ca2+, immunofluorescent images were obtained only after permeabilization with detergents. Under this condition, the vesicle population was maintained by an active process of recycling and more than two times the initial store of quanta were secreted. Thus, despite the active turnover of synaptic vesicles and of quanta of neurotransmitter, no extensive intermixing occurs between components of the vesicle and presynaptic plasma membrane.
Soil available phosphorus by Mehlich-1, Mehlich-3 and anion exchange resin and its sensitivity to soil clay content.

Mehlich-1 is the most used chemical method to determine soil available P in Brazil, but its efficacy is affected by variations in clay contents due to the exhaustion of the extractants and readsorption of P by the soil particles. Thus, other methods have been tested in Southern Brazil to replace the Mehlich-1. The objective of this work was to evaluate the ability of Mehlich-1 (M1), Mehlich-3 (M3), and anion exchange resins in strip (AERst) or in sphere (AERsp) forms, to extract P from soils with a wide range of clay contents. Samples were collected from the B horizon of a Brazilian Oxisol were mixed with different amounts of sand in order to get artificial soil samples containing 200, 400 and 600 g/kg of clay, in addition to a pure sand (with no clay) and a pure soil (800 g/kg of clay). Phosphorus rates (0, 100, 200, 400 and 600 mg/kg) were applied to each one of these experimental soils that were subsequently incubated for 1, 30, 90 or 180 days. After each incubation period, available P was quantified by the four methods. All methods, extracted less P as the clay content of the samples increased. The amount of P extracted also decreased with increases on the incubation time. Thus, the evaluation of soil P availability to plants determined by all tested methods need to take into consideration the amount of clay.
Antiepileptic drugs and risk of suicide: a nationwide study

Patients with epilepsy or psychiatric diseases have increased risk of suicide, but whether the risk is influenced by antiepileptic drug (AED) treatment is unclear. Studies have suggested that AEDs in general increase the risk of suicidal behaviour shortly after initiation. This study investigated possible differences in suicide risk associated with different AEDs.
Microstructured index-guiding fibers with large cladding holes for evanescent field chemical sensing

Design, fabrication and application of small solid-core microstructured optical fibers with large cladding holes for evanescent field chemical sensing of gases and liquids will be presented. Such steering-wheel fiber structures give a high mode-field overlap in the holey region, they show low losses over a broad spectral range and they are easier to fabricate than hollow-core bandgap-guiding photonic crystal fibers.
ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity

The endoplasmic reticulum (ER) forms highly organized network structures composed of tubules and cisternae. Many plant species develop additional ER-derived structures, most of which are specific for certain groups of species. In particular, a rod-shaped structure designated as the ER body is produced by plants of the Brassicales order, which includes Arabidopsis thaliana. Genetic analyses and characterization of A. thaliana mutants possessing a disorganized ER morphology or lacking ER bodies have provided insights into the highly organized mechanisms responsible for the formation of these unique ER structures. The accumulation of proteins specific for the ER body within the ER plays an important role in the formation of ER bodies. However, a mutant that exhibits morphological defects of both the ER and ER bodies has not been identified. This suggests that plants in the Brassicales order have evolved novel mechanisms for the development of this unique organelle, which are distinct from those used to maintain generic ER structures. In A. thaliana, ER bodies are ubiquitous in seedlings and roots, but rare in rosette leaves. Wounding of rosette leaves induces de novo formation of ER bodies, suggesting that these structures are associated with resistance against pathogens and/or herbivores. ER bodies accumulate a large amount of β-glucosidases, which can produce substances that potentially protect against invading pests. Biochemical studies have determined that the enzymatic activities of these β-glucosidases are enhanced during cell collapse. These results suggest that ER bodies are involved in plant immunity, although there is no direct evidence of this. In this review, we provide recent perspectives of ER and ER body formation in A. thaliana, and discuss clues for the functions of ER bodies. We highlight defense strategies against biotic stress that are unique for the Brassicales order, and discuss how ER structures could contribute to these strategies.
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis

The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.
Dynamic nanomechanical response of nacre

Nacre, the shiny inner layer of mollusk shells is a model biomimetic nanocomposite system. Its exceptional mechanical properties have been the inspiration for materials scientists for several decades. Nacre exhibits a layered brick and mortar structure. It is composed of 95% inorganic (aragonitic CaCO_3) phase and 5% organic (mainly proteins and polysaccharides) phase that are arranged in interlocked brick and mortar architecture with the mineral as bricks and organics as the mortar. In the current work, we describe the dynamic nanomechanical behavior of nacre using dynamic nanoindentation (nano-DMA) experiments. Two sets of loads were applied to obtain the dynamic response from varying depths in nacre. These tests were performed at three different frequencies (25, 50, and 100 Hz) to study the effect of frequency on the dynamic properties of nacre. The loss modulus ( E ″) and the loss factor (tan δ) were measured. Both of these parameters were observed to increase with increase in depth. Significant increase in tan δ was observed with the increase in frequency. Photoacoustic Fourier transform infrared spectroscopic studies on nacre indicate the presence of water in nacre. This water may be present at nanograin interfaces in nacre platelets, at organic–inorganic interfaces, and also in the organic phase in nacre. We believe that water is one of the significant contributors to the viscoelasticity of nacre. Our results indicate that the aragonite platelets in nacre may also contribute to viscoelasticity.
A genome-wide screen for genes affecting eisosomes reveals Nce102 function in sphingolipid signaling

The protein and lipid composition of eukaryotic plasma membranes is highly dynamic and regulated according to need. The sphingolipid-responsive Pkh kinases are candidates for mediating parts of this regulation, as they affect a diverse set of plasma membrane functions, such as cortical actin patch organization, efficient endocytosis, and eisosome assembly. Eisosomes are large protein complexes underlying the plasma membrane and help to sort a group of membrane proteins into distinct domains. In this study, we identify Nce102 in a genome-wide screen for genes involved in eisosome organization and Pkh kinase signaling. Nce102 accumulates in membrane domains at eisosomes where Pkh kinases also localize. The relative abundance of Nce102 in these domains compared with the rest of the plasma membrane is dynamically regulated by sphingolipids. Furthermore, Nce102 inhibits Pkh kinase signaling and is required for plasma membrane organization. Therefore, Nce102 might act as a sensor of sphingolipids that regulates plasma membrane function.
A Probabilistic Framework for Recognizing Similar Actions using Spatio-Temporal Features

One of the challenges found in recent methods for action recognition has been to classify ambiguous actions successfully . In the case of methods that use spatio-temporal features this phenomenon is observed when two actions generate similar feature types. Ideally, a probabilistic c lassification method would be based on a model of the full joint distribution of features, but this is computationally intractable. In this paper we propose using an approximation of the full joint via first order dependencies between fe ature types using so-called Chow-Liu trees. We obtain promising results and achieve an improvement in the classification accuracy over naive Bayes an d other simple classifiers. Our implementation of the method makes use of a b inary descriptor for a video analogous to one previously used in location recognition for mobile robots. Because of the simplicity of the algorithm, once the offline learning phase is over, real-time action recognition is pos sible and we present an adaptation of this method that works in real-time.
Global-in-time Gevrey regularity solution for a class of bistable gradient flows

In this paper, we prove the existence and uniqueness of a Gevrey regularity solution for a class of nonlinear bistable gradient flows, where with the energy may be decomposed into purely convex and concave parts. Example equations include certain epitaxial thin film growth models and phase field crystal models. The energy dissipation law implies a bound in the leading Sobolev norm. The polynomial structure of the nonlinear terms in the chemical potential enables us to derive a local-in-time solution with Gevrey regularity, with the existence time interval length dependent on a certain $H^m$ norm of the initial data. A detailed Sobolev estimate for the gradient equations results in a uniform-in-time-bound of that $H^m$ norm, which in turn establishes the existence of a global-in-time solution with Gevrey regularity.
A Detailed Vth-Variation Analysis for Sub-100-nm Embedded SRAM Design

A Vth variation has large impact on SRAM operation. To predict an SRAM operating margin in design phase, a Vth window analysis is used. We propose an improved Vth window analysis, which considers a relationship between global and local Vth variation, and the analysis enables accurate operating margin prediction. This analysis predicts 7.7% larger yield deterioration than conventional method in 65-nm manufacturing process and gives a chance to introduce some operating margin enhancement circuits in design phase.
The capsian escargotieres.

Capsian occupation in the Cheria-Telidjene region of northeastern Algeria coinides with a phase of alluviation (about 9500 to 6500 years ago) with a semi-arid climate that was cooler and more humid than today. Capsian subsistence was based on a combination of hunting (gazelle, aurochs and hartebeest), land snail collecting, and presumably plant gathering. Partial excavation of the Ain Misteheya escargotiere has provided a number of insigths into Capsian subsistence, settlement and diet. The artifact assemblage from Ain Misteheyia falls within the established general parameters for the "Capsien superieur. " In sum, we interpret the Capsian subsistence adaptation as innovative, conservationist, and highly successful - so much so, in fact, that despite the appearance of Neolithic economic practices in neighboring regions by about 7000 years ago, the Capsian pattern in the Maghreb appears to have remained basically inchanged for a further two millenia.
Induced sputum genes associated with spirometric and radiological disease severity in COPD ex-smokers

Background Induced sputum is used to sample inflammatory cells, predominantly neutrophils and macrophages, from the airways of COPD patients. The author's aim was to identify candidate genes associated with the degree of airflow obstruction and the extent of emphysema by expression profiling, and then to confirm these findings for selected candidates using PCR and protein analysis. Methods Two sputum studies were performed in Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 2–4 COPD ex-smokers from the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) cohort. First, gene array profiling at baseline in samples from 148 patients. The findings were replicated in a separate population of 176 patients using real-time PCR. The findings for one selected gene IL-18R were further analysed using immunohistochemistry in lung tissue and induced sputum from patients outside the ECLIPSE cohort. Results Gene expression profiling revealed changes in 277 genes associated with GOLD stage 2 versus 3 and 4, and 198 genes with changes associated with the degree of emphysema (p<0.01 for each gene). Twelve of these candidate genes were analysed by PCR in the replication cohort, with significant changes (p<0.05) observed for 11 genes. IL-18R protein expression was higher on alveolar macrophages in lung tissue of COPD patients (mean 23.2%) compared to controls (mean ex-smokers 2% and non-smokers 2.5%). Conclusion Gene expression profiling in sputum cells identified candidate genes that may play roles in molecular mechanisms associated with COPD. The replication by PCR and protein in different studies confirms these findings, and highlights a potential role for IL-18R upregulation in severe COPD.
Parallel PWMs Based Fully Digital Transmitter with Wide Carrier Frequency Range

The carrier-frequency (CF) and intermediate-frequency (IF) pulse-width modulators (PWMs) based on delay lines are proposed, where baseband signals are conveyed by both positions and pulse widths or densities of the carrier clock. By combining IF-PWM and precorrected CF-PWM, a fully digital transmitter with unit-delay autocalibration is implemented in 180 nm CMOS for high reconfiguration. The proposed architecture achieves wide CF range of 2 M–1 GHz, high power efficiency of 70%, and low error vector magnitude (EVM) of 3%, with spectrum purity of 20 dB optimized in comparison to the existing designs.
A New Soft Sensor Based on Dynamic Principal Component Analysis and on-line Potential Fuzzy Clustering

In this paper, a new soft sensor methodology is proposed for estimation of product concentration in a chemical process. The new soft sensor utilizes dynamic principle component analysis (DPCA) method to select the optimum reduced process variables as the appropriate inputs. DPCA eliminates the high correlations among the process variable measurements, leading to a lower dimensional uncorrelated principle components of the process measurements. The DPCA transformed measurements are then used to train a global nonlinear fuzzy model, based on an on-line potential fuzzy clustering approach, for unmeasurable variable estimation. The developed soft sensor performance is demonstrated on a simulated distillation column benchmark problem.
Bi-criteria algorithm for scheduling jobs on cluster platforms

We describe in this paper a new method for building an efficient algorithm for scheduling jobs in a cluster. Jobs are considered as parallel tasks (PT) which can be scheduled on any number of processors. The main feature is to consider two criteria that are optimized together. These criteria are the makespan and the weighted minimal average completion time (minsum). They are chosen for their complementarity, to be able to represent both user-oriented objectives and system administrator objectives.We propose an algorithm based on a batch policy with increasing batch sizes, with a smart selection of jobs in each batch. This algorithm is assessed by intensive simulation results, compared to a new lower bound (obtained by a relaxation of ILP) of the optimal schedules for both criteria separately. It is currently implemented in an actual real-size cluster platform.
iPlane Nano: Path Prediction for Peer-to-Peer Applications

Many peer-to-peer distributed applications can benefit from accurate predictions of Internet path performance. Existing approaches either 1) achieve high accuracy for sophisticated path properties, but adopt an unscalable centralized approach, or 2) are lightweight and decentralized, but work only for latency prediction. In this paper, we present the design and implementation of iPlane Nano, a library for delivering Internet path information to peer-to-peer applications. iPlane Nano is itself a peer-to-peer application, and scales to a large number of end hosts with little centralized infrastructure and with a low cost of participation. The key enabling idea underlying iPlane Nano is a compact model of Internet routing. Our model can accurately predict end-to-end PoP-level paths, latencies, and loss rates between arbitrary hosts on the Internet, with 70% of AS paths predicted exactly in our evaluation set. Yet our model can be stored in less than 7MB and updated with approximately 1MB/day. Our evaluation of iPlane Nano shows that it can provide significant performance improvements for large-scale applications. For example, iPlane Nano yields near-optimal download performance for both small and large files in a P2P content delivery system.
Automatic 2-D gel registration using distance minimisation of image morphing

The necessity of applying image processing techniques to gel electrophoresis images is starting to appear. In particular, registering two gels for comparison purposes has emerged from the increasing popularity of gel databases distributed across the Internet. Current registration techniques are however cumbersome in the sense that they require user intervention for placing landmarks on both gels in order to define a mapping function. Current techniques also cannot account for distortions which are common to 2-D gels and non-reproducible by nature. Thus, the only method of choice is to make a side-by-side comparison of the gels. We propose an automatic registration method especially designed with electrophoresis gels in mind to give an optimal registration while still allowing human input. We think that an automated registration of 2-D gels, because of its non-intrusive nature, will lead to a wider acceptance of image vision technology in electrophoresis gel software. Potentially, other types of biomedical images could benefit from the technique.
Enhanced 3D Geolocation Algorithm for LTE Call Traces

Three dimensional location of users in indoor environments is highly desirable because it represents an extension to the Global Positioning System (GPS) where signals cannot penetrate within buildings. GPS-based positioning is reliable and accurate for outdoor situations, but it does not provide acceptable performance indoors. In indoor environments or when GPS functionality is turned off, fingerprinting geolocation techniques using available network measurements are a very promising alternative. In this paper, a 3D geolocation algorithm for Long Term Evolution (LTE) call traces is presented,one that enhances 2D geolocation methods and uses available measurement reports to locate mobile users in three dimensional space. The implemented 3D geolocation algorithm has on average a 45 meters positioning error, 15% smaller when compared to the 2D algorithm.
Selective retention of the fluorescent dye DASPEI in a larval gastropod mollusc after paraformaldehyde fixation

In the vertebrates, the vital mitochondrial dye DASPEI (2‐(4‐dimethylaminostyryl)‐N‐ethylpyridinium iodide) has been used for the rapid visualization of several distinct classes of epidermal cells in vivo and in vitro: epidermal electroreceptors, mechanoreceptors, and chloride cells in teleosts, and mechanoreceptors in amphibians. I used DASPEI in an attempt to locate a different type of sensory cell, namely, the chemosensory neurons that mediate the initiation of metamorphosis in veliger larvae of the prosobranch gastropod Ilyanassa obsoleta.
Fast k-Nearest Neighbour Search via Dynamic Continuous Indexing

Existing methods for retrieving k-nearest neighbours suffer from the curse of dimensionality. We argue this is caused in part by inherent deficiencies of space partitioning, which is the underlying strategy used by most existing methods. We devise a new strategy that avoids partitioning the vector space and present a novel randomized algorithm that runs in time linear in dimensionality of the space and sub-linear in the intrinsic dimensionality and the size of the dataset and takes space constant in dimensionality of the space and linear in the size of the dataset. The proposed algorithm allows fine-grained control over accuracy and speed on a per-query basis, automatically adapts to variations in data density, supports dynamic updates to the dataset and is easy-to-implement. We show appealing theoretical properties and demonstrate empirically that the proposed algorithm outperforms locality-sensitivity hashing (LSH) in terms of approximation quality, speed and space efficiency.