Miracle-dz/UniFAR-FTUs huggingface dataset:
Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory

Significance We combined molecule counting and superresolution microscopy to observe the size, shape, and biomolecular composition of vesicles in the endocytic pathway. From a large number of steady-state snapshots, we follow the maturation of vesicles to endosomes. First, phosphatidylinositol 3-phosphate (PI3P) is generated on newly formed vesicles, principally after they shed their clathrin coat. Next, PI3P sites increase (∼100-fold) on small vesicles whose size is tightly regulated. Finally, the GTPase Vps21 (Rab5 homolog) is associated with small endosomal structures during the initial phase of PI3P production, whereas Ypt7 (Rab7 homolog) localizes to larger endosomal structures, which exhibit saturating levels of PI3P.This new technique opens up the possibility of accurately measuring molecular stoichiometries across several orders of magnitude while resolving subdiffraction-limit organelles. Cells tightly regulate trafficking of intracellular organelles, but a deeper understanding of this process is technically limited by our inability to track the molecular composition of individual organelles below the diffraction limit in size. Here we develop a technique for intracellularly calibrated superresolution microscopy that can measure the size of individual organelles as well as accurately count absolute numbers of molecules, by correcting for undercounting owing to immature fluorescent proteins and overcounting owing to fluorophore blinking. Using this technique, we characterized the size of individual vesicles in the yeast endocytic pathway and the number of accessible phosphatidylinositol 3-phosphate binding sites they contain. This analysis reveals a characteristic vesicle maturation trajectory of composition and size with both stochastic and regulated components. The trajectory displays some cell-to-cell variability, with smaller variation between organelles within the same cell. This approach also reveals mechanistic information on the order of events in this trajectory: Colocalization analysis with known markers of different vesicle maturation stages shows that phosphatidylinositol 3-phosphate production precedes fusion into larger endosomes. This single-organelle analysis can potentially be applied to a range of small organelles to shed light on their precise composition/structure relationships, the dynamics of their regulation, and the noise in these processes.
Optimal Feedback Control for anthropomorphic manipulators

We study target reaching tasks of redundant anthropomorphic manipulators under the premise of minimal energy consumption and compliance during motion. We formulate this motor control problem in the framework of Optimal Feedback Control (OFC) by introducing a specific cost function that accounts for the physical constraints of the controlled plant. Using an approximative computational optimal control method we can optimally control a high-dimensional anthropomorphic robot without having to specify an explicit inverse kinematics, inverse dynamics or feedback control law. We highlight the benefits of this biologically plausible motor control strategy over traditional (open loop) optimal controllers: The presented approach proves to be significantly more energy efficient and compliant, while being accurate with respect to the task at hand. These properties are crucial for the control of mobile anthropomorphic robots, that are designed to interact safely in a human environment. To the best of our knowledge this is the first OFC implementation on a high-dimensional (redundant) manipulator.
An efficient protocol for private iris-code matching by means of garbled circuits

Biometric-based access control is receiving increasing attention due to its security and ease-of-use. However, concerns are often raised regarding the protection of the privacy of enrolled users. Signal processing in the encrypted domain has been proposed as a viable solution to protect biometric templates and the privacy of the users. In particular, several solutions have been proposed to protect the privacy of the biometric probe during the authentication process. In this paper we focus on privacy-preserving iris-based authentication. The main innovations compared to the prior art include: i) an iris masking technique that simplifies the operations on the encrypted data without sacrificing the recognition rate; ii) the adoption of a matching protocol based only on garbled circuits which offers longer term security over existing solutions based on homomorphic encryption or hybrid techniques. The computational and communication complexity of the on-line phase of the proposed protocol is extremely low, thus opening the way to its exploitation in practical applications.
Multimodal addressee detection in multiparty dialogue systems

Addressee detection answers the question, “Are you talking to me? ” When multiple users interact with a dialogue system, it is important to know when a user is speaking to the computer and when he or she is speaking to another person. We approach this problem from a multimodal perspective, using lexical, acoustic, visual, dialog state, and beam-forming information. Using data from a multiparty dialogue system, we demonstrate the benefit of using multiple modalities over using a single modality. We also assess the relative importance of the various modalities in predicting the addressee. In our experiments, we find that acoustic features are by far the most important, that ASR and system-state information are useful, and that visual and beamforming features provide little additional benefit. Our study suggests that acoustic, lexical, and system state information are an effective, economical combination of modalities to use in addressee detection.
Molecular and Functional Diversity of GABA-A Receptors in the Enteric Nervous System of the Mouse Colon

The enteric nervous system (ENS) provides the intrinsic neural control of the gastrointestinal tract (GIT) and regulates virtually all GI functions. Altered neuronal activity within the ENS underlies various GI disorders with stress being a key contributing factor. Thus, elucidating the expression and function of the neurotransmitter systems, which determine neuronal excitability within the ENS, such as the GABA-GABAA receptor (GABAAR) system, could reveal novel therapeutic targets for such GI disorders. Molecular and functionally diverse GABAARs modulate rapid GABAergic-mediated regulation of neuronal excitability throughout the nervous system. However, the cellular and subcellular GABAAR subunit expression patterns within neurochemically defined cellular circuits of the mouse ENS, together with the functional contribution of GABAAR subtypes to GI contractility remains to be determined. Immunohistochemical analyses revealed that immunoreactivity for the GABAAR gamma (γ) 2 and alphas (α) 1, 2, 3 subunits was located on somatodendritic surfaces of neurochemically distinct myenteric plexus neurons, while being on axonal compartments of submucosal plexus neurons. In contrast, immunoreactivity for the α4–5 subunits was only detected in myenteric plexus neurons. Furthermore, α-γ2 subunit immunoreactivity was located on non-neuronal interstitial cells of Cajal. In organ bath studies, GABAAR subtype-specific ligands had contrasting effects on the force and frequency of spontaneous colonic longitudinal smooth muscle contractions. Finally, enhancement of γ2-GABAAR function with alprazolam reversed the stress-induced increase in the force of spontaneous colonic contractions. The study demonstrates the molecular and functional diversity of the GABAAR system within the mouse colon providing a framework for developing GABAAR-based therapeutics in GI disorders.
An Unsupervised Morpheme-Based HMM for Hebrew Morphological Disambiguation

Morphological disambiguation is the process of assigning one set of morphological features to each individual word in a text. When the word is ambiguous (there are several possible analyses for the word), a disambiguation procedure based on the word context must be applied. This paper deals with morphological disambiguation of the Hebrew language, which combines morphemes into a word in both agglutinative and fusional ways. We present an unsupervised stochastic model ‐ the only resource we use is a morphological analyzer ‐ which deals with the data sparseness problem caused by the axational morphology of the Hebrew language. We present a text encoding method for languages with axational morphology in which the knowledge of word formation rules (which are quite restricted in Hebrew) helps in the disambiguation. We adapt HMM algorithms for learning and searching this text representation, in such a way that segmentation and tagging can be learned in parallel in one step. Results on a large scale evaluation indicate that this learning improves disambiguation for complex tag sets. Our method is applicable to other languages with ax morphology.
Double Lip Surgical Correction in Ascher’s Syndrome: Diagnosis and Treatment of a Rare Condition

Ascher’s syndrome is a rare disease first described in 1920 by Ascher, an ophthalmologist from Prague.1 The disease is characterized by a double upper lip, blepharochalasis, and nontoxic thyroid enlargement, though the thyroid enlargement may be evident in only 10% to 50% of patients.2,3 These deformities, though not posing functional problems, may cause severe psychological distress to the affected person because of the disfiguring effect on smiling.4 Prompt recognition of this syndrome can prevent unnecessary tests and diagnostic delays, and allow for quicker scheduling of appropriate surgical treatment.5
Enhancement of existing clustering algorithm for tracking online community in social network

Social networks provide a powerful abstraction of the structure and dynamics of diverse kinds of people or people-to-technology interaction. The increasing achievement of the Web has led people to exploit collaborative technologies in order to encourage partnerships among different groups. The problem of tracking community in social networks inferred from online interactions by tracking evolution of known subgroups over time. Finding subgroups within social networks is important for understanding and possibly influencing the formation and evolution of online communities. The focus of present paper is enhancement of clustering methods for tracking online community interaction.
Softening Discrete Relaxation

This paper describes a new framework for relational graph matching. The starting point is a recently reported Bayesian consistency measure which gauges structural differences using Hamming distance. The main contributions of the work are threefold. Firstly, we demonstrate how the discrete components of the cost function can be softened. The second contribution is to show how the softened cost function can be used to locate matches using continuous non-linear optimisation. Finally, we show how the resulting graph matching algorithm relates to the standard quadratic assignment problem.
Modeling tidal current around Mokpo, the South Western coastal zone of Korea

This study provide modeling of tidal circulation around the Mokpo coastal zone (MC) using unstructured triangular horizontal grid by which high resolution is concentrated in the local region that reaches to 100 m. For this simulation, the 3D finite-volume ocean model FVCOM is applied for the numerical simulation. Only the astronomical tidal constituent M2 and its harmonic M4 are considered. By expanding open boundary to the shelf break of the East China Sea, only M2 elevation was specified on the open boundaries, and the generation of M4 tide around MC was observed, which is the representative criteria for the accuracy of the shallow water tide simulation. Around the intertidal zone of MC, wet/dry point treatment method incorporated in FVCOM was also used and tested its applicability in the level of resolution of this model.
Analysis of morphological features of thalamocortical neurons from the ventroposterolateral nucleus of the cat

Morphological features of the dendritic arborization can affect neuronal responses and thus the input‐output function of a particular neuron. In this study, morphological data of eight fully reconstructed thalamocortical (TC) neurons from the ventroposterolateral (VPL) nucleus of adult cats have been analyzed. We examined several geometrical and topological parameters, which have been previously shown to have a high impact on the neuron firing pattern and propagation of signals in the dendritic tree. In addition to well‐known morphological parameters such as number of dendritic trees (8.3 ± 1.5) and number of branching points (80–120), we investigated the distribution of dendritic membrane area, branching points, geometrical ratio, asymmetry index, and mean path length for all subtrees of the TC neurons. We demonstrate that due to extensive branching in proximal and middle dendritic sections, the maximum value of the dendritic area distribution is reached at 120–160 μm from the soma. Our analysis reveals that TC neurons are highly branched cells and their dendritic branching pattern does not follow Rall's 3/2 power rule; average values at proximal vs. distal dendritic sections were different. We also found that the dendritic branching pattern of each subtree of the cell had a wide range in symmetry index, whereas the mean path length did not show a large variation through the dendritic arborizations. J. Comp. Neurol. 518:3541–3556, 2010. © 2010 Wiley‐Liss, Inc.
Automating software evolution

Software maintenance and evolution are the most expensive activities in the software process, consuming 60% to 80% of the total time spent on a software system. However our understanding of maintenance activities has barely developed beyond arbitrary change to arbitrary things. The standard categories of maintenance are based on subjective characteristics (purpose), rather than objective attributes. Only by understanding the relationships and dependencies between entities in the software process (such as specification, design and implementation) can we begin to objectively categorise and potentially automate aspects of software evolution.
Glottal features for speech-based cognitive load classification

Cognitive load measurement is important when designing adaptive interfaces that optimize the performance of users working on high mental load tasks. Recent research on automatic speech-based measurement system indicates that cognitive load information is more prominent in the frequency region below 1 kHz. This study investigates the effects of cognitive load on glottal parameters (open quotient, normalized amplitude quotient and speed quotient), and proposes a system employing these parameters as features for cognitive load classification. Analysis of the glottal parameter distributions suggests that an increase in cognitive load can be related to a more creaky voice quality. Additionally, three-class classification results show that score-level fusion of systems based on the glottal features and baseline features (MFCCs, pitch, intensity and shifted delta cepstra) improves the baseline accuracy from 79% to 84%.
Using ADOPT Algorithm and Operational Data to Discover Precursors to Aviation Adverse Events

In this paper, we describe a data mining method called ADOPT (Automatic Discovery of Precursors in Time series data) to identify precursors to aviation adverse events. An adverse event may refer to any unsafe event ranging from a negligible safety hazard to a catastrophic accident, depending on the scope of the analysis. A precursor is an early indicator of an increasing likelihood of the adverse event. Identifying precursors is important in the context of a proactive safety management because precursors detect the increasing severity of the underlying hazard much earlier, giving sufficient time to identify, analyze and implement corrective actions. ADOPT analyzes large volumes of historical data to find complex trends among several sensory variables simultaneously to find precursors. ADOPT’s data mining approach captures real-world effects such as human factors, weather, geographic constraints, operating procedures, airline strategies etc that are difficult to capture using first-principle models. This paper describes the algorithm using two case studies including a take-off stall hazard and RNAV adherence. While the case studies are not intended to discuss the critical safety risks in aviation, they are used to demonstrate the various steps involved in ADOPT including data preparation, variable selection, parameter tuning, experiment setup and analyzing the results. The results show that ADOPT can be a powerful tool to identify and analyze performance and safety issues in Aviation.
Small Molecules with Similar Structures Exhibit Agonist, Neutral Antagonist or Inverse Agonist Activity toward Angiotensin II Type 1 Receptor

Small differences in the chemical structures of ligands can be responsible for agonism, neutral antagonism or inverse agonism toward a G-protein-coupled receptor (GPCR). Although each ligand may stabilize the receptor conformation in a different way, little is known about the precise conformational differences. We synthesized the angiotensin II type 1 receptor blocker (ARB) olmesartan, R239470 and R794847, which induced inverse agonism, antagonism and agonism, respectively, and then investigated the ligand-specific changes in the receptor conformation with respect to stabilization around transmembrane (TM)3. The results of substituted cysteine accessibility mapping studies support the novel concept that ligand-induced changes in the conformation of TM3 play a role in stabilizing GPCR. Although the agonist-, neutral antagonist and inverse agonist-binding sites in the AT1 receptor are similar, each ligand induced specific conformational changes in TM3. In addition, all of the experimental data were obtained with functional receptors in a native membrane environment (in situ).
Time-Delay Signature Suppression of Polarization-Resolved Chaos Outputs from Two Mutually Coupled VCSELs

Time-delay (TD) signature performances of polarization-resolved chaos outputs from two mutually coupled vertical-cavity surface-emitting lasers (MC VCSELs) are investigated through detailed simulations by means of self-correlation function (SF) and permutation entropy (PE). The results show that, under suitable coupling strength (η) and frequency detuning (Δf) between the two MC VCSELs, the TD signatures of two polarization modes from each VCSEL can be suppressed simultaneously. Furthermore, based on the map of TD signature evolution in the parameter space of Δf and η, the optimal parameter region of TD signature suppression has been determined.
The Impact of Reader Skill on Phonological processing in visual Word Recognition

There has been much debate about the role of phonology in reading. This debate has been fuelled, in part, by mixed findings for phonological effects in lexical decision tasks. In the present research we investigated the impact of reader skill on three phonological effects (homophone, homograph, and regularity effects) in a lexical decision task and in a phonological lexical decision task. In both tasks, the more skilled readers showed different patterns of phonological effects from those of the less skilled readers; in particular, less skilled readers showed regularity effects in both tasks whereas more skilled readers did not. We concluded that more skilled readers activate phonology in these tasks but do so more efficiently, with less spurious phonological activation.
Epidemiology of tattoo skin disease in captive common bottlenose dolphins (Tursiops truncatus): Are males more vulnerable than females?

ABSTRACT Clinical and epidemiological features of tattoo skin disease (TSD) are reported for 257 common bottlenose dolphins held in 31 facilities in the Northern Hemisphere. Photographs and biological data of 146 females and 111 males were analyzed. Dolphins were classified into three age classes: 0–3 years, 4–8 years, and older than 9 years. From 2012 to 2014, 20.6% of the 257 dolphins showed clinical TSD. The youngest dolphins with tattoo lesions were 14 and 15 months old. TSD persisted from 4 to 65 months in 30 dolphins. Prevalence varied between facilities from 5.6% to 60%, possibly reflecting variation in environmental factors. Unlike in free-ranging Delphinidae, TSD prevalence was significantly higher in males (31.5%) than in females (12.3%). Infection was age-dependent only in females. Prevalence of very large tattoos was also higher in males (28.6%) than in females (11.1%). These data suggest that male T. truncatus are more vulnerable to TSD than females, possibly because of differences in immune response and susceptibility to captivity-related stress.
Is Leadership a Reliable Concept in Animals? An Empirical Study in the Horse

Leadership is commonly invoked when accounting for the coordination of group movements in animals, yet it remains loosely defined. In parallel, there is increased evidence of the sharing of group decisions by animals on the move. How leadership integrates within this recent framework on collective decision-making is unclear. Here, we question the occurrence of leadership in horses, a species in which this concept is of prevalent use. The relevance of the three main definitions of leadership – departing first, walking in front travel position, and eliciting the joining of mates – was tested on the collective movements of two semi-free ranging groups of Przewalski horses (Equus ferus przewalskii). We did not find any leader capable of driving most group movements or recruiting mates more quickly than others. Several group members often displayed pre-departure behaviours at the same time, and the simultaneous departure of several individuals was common. We conclude that the decision-making process was shared by several group members a group movement (i.e., partially shared consensus) and that the leadership concept did not help to depict individual departure and leading behaviour across movements in both study groups. Rather, the different proxies of leadership produced conflicting information about individual contributions to group coordination. This study discusses the implications of these findings for the field of coordination and decision-making research.
Effects of stimulation frequency, amplitude, and impulse width on muscle fatigue

Introduction: We investigated the effect of stimulation intensity (in percent of maximal tolerated stimulation current, mTSC), frequency, and impulse width on muscle fatigue. Methods: Using a randomized crossover design, 6 parameter combinations (80% mTSC, 80 Hz, 400 μs; 60% mTSC, 80 Hz, 400 μs; 80% mTSC, 20 Hz, 400 μs; 60% mTSC, 20 Hz, 400 μs; 80% mTSC, 80 Hz, 150 μs; 60% mTSC, 80 Hz, 150 μs) were tested in both legs of 13 athletic men (age 26 ± 2.3). The slope of the linear regression line over all tetani (FIS) and the number of tetani whose force was above 50% of the initial tetanus (FIN) were used to quantify fatigue. Results: FIS and FIN were significantly lower in high‐frequency protocols. No effects on FIS and FIN were found for intensity and impulse width. Conclusions: Stimulation frequency, but not impulse width or intensity, affected fatigue kinetics. Muscle Nerve 53: 608–616, 2016