Miracle-dz/UniFAR-FTUs huggingface dataset:
Electrostatic anchoring precedes stable membrane attachment of SNAP25/SNAP23 to the plasma membrane

The SNAREs SNAP25 and SNAP23 are proteins that are initially cytosolic after translation, but then become stably attached to the cell membrane through palmitoylation of cysteine residues. For palmitoylation to occur, membrane association is a prerequisite, but it is unclear which motif may increase the affinities of the proteins for the target membrane. In experiments with rat neuroendocrine cells, we find that a few basic amino acids in the cysteine-rich region of SNAP25 and SNAP23 are essential for plasma membrane targeting. Reconstitution of membrane-protein binding in a liposome assay shows that the mechanism involves protein electrostatics between basic amino acid residues and acidic lipids such as phosphoinositides that play a primary role in these interactions. Hence, we identify an electrostatic anchoring mechanism underlying initial plasma membrane contact by SNARE proteins, which subsequently become palmitoylated at the plasma membrane. DOI: http://dx.doi. org/10.7554/eLife.19394. 001
Surfing the Mouse Atlas 4th Year Project Report Artificial Intelligence and Computer Science

When you’re looking for the answer how to classify all cancer, proteins, microbes, fish and succulent legumes, You must know a little Latin tell a round fish from a flat one and have memory with lots and lots of room But, before we start alinking we should sit back and be thinking on our methods, clientele and on our goal, Lest we make a mammoth bank rarely used and rarely thanked just consuming funds and efforts: A BLACK HOLE.
Estimating the instantaneous frequencies of a multicomponent image by bidimensional empirical mode decomposition

An overview of AM-FM image presentation techniques is presented. Many nonstationary textures are multi-partite, and may be considered to comprise several locally narrowband components. The multicomponent AM-FM model is powerful in describing such images. The empirical mode decomposition is applied to processing textures, and proposed bidimensional empirical mode decomposition (BEMD) followed by a computationally efficient algorithm. It is shown that the components may be demodulated on a spatially local basis based on BEMD. The Burg linear predicting filter is used to reduce the decomposition error of BEMD. A practical approach, the direct method, is proposed for estimating the instantaneous frequencies of each component.
The social cognition and attentional preferences of autistic adults.

Attentional bias to faces can be seen from 9 minutes old in typical development (TD; Goren Sarty & Wu, 1975) and this is thought to underlie face processing expertise observed in adults (Johnson & Morton, 1991). In contrast people with Autistic Spectrum Disorders (ASDs) have deficits in orienting towards social information (e.g. Dawson et al., 2004). Novel methods, the Visual Dot Probe (VDP; Mathews, MacLeod & Tata, 1986) to measure automatic bias (at both sub and supra threshold presentation times) and Face-in-the-Crowd (FITC) to measure conscious bias (Hansen & Hansen, 1988), will be used to examine attentional bias for face stimuli in ASD and control participants.Experiments 1 and 3 examined attentional bias for faces (including emotional faces; Study Three) compared to non-face stimuli using the VDP task. In Study One neither group showed a sub-threshold bias. However at supra threshold durations the TD group had a bias for faces that was absent in the ASD group. In Study Three the TD group had a sub-threshold bias for neutral faces compared to non-face stimuli. However the ASD group showed no bias. Neither group had a supra-threshold bias.Experiments 2 and 4 used the FITC task to examine participants' attentional bias for faces (including emotional faces; Study Four) compared to non-face stimuli. In Study Two both groups showed an attentional bias for faces compared to non-face stimuli. However in Study Four neither group showed a bias for faces.Previous research has shown the social presentation of ASD to be heterogeneous (Wing & Attwood, 1987) and in the normative literature findings using the VDP and FITC tasks relate to personality variables (e.g. Mogg & Bradley, 1999a; b). In Chapter 7 the consistency of bias across tasks was relatively poor. In the ASD group bias for faces was found to relate to increased anxiety, reduced ASD severity, and increased intelligence. Psychometric variables did not to predict bias for faces in controls.In conclusion the control group show a bias for faces and there are some indications that the ASD group shows a face bias when under conscious control however this does not appear to be an automatic process. This suggests a potential cognitive model of ASD reliant on automatic social inattention as a key variable in ASD.
Effects of rTMS on an Auditory Oddball Task: A Pilot Study of Cortical Plasticity and the EEG

The objective of this study was to explore the effects of 1Hz repetitive transcranial magnetic stimulation (rTMS) applied to dorsal lateral prefrontal cortex (DLPFC) on both an EEG index of cortical excitation and inhibition, event-related desynchronization/synchronization (ERD/S) and on the P300 component of an auditory oddball-induced ERP. Eight normal participants received 15 minutes of 1Hz rTMS at 110% of the resting motor threshold to right DLPFC. ERD/S of alpha and beta bands was measured during an auditory oddball task immediately before and after stimulation. There was significantly less alpha desynchronization post-TMS, and this effect was widespread excepting posterior midline sites. No changes were found to oddball-P300 amplitudes or latencies. In conclusion, the findings of less alpha desynchronization post-TMS are compatible with notions of slow rTMS causing a decrease in cortical excitation.
HODGE-THEORETIC ATIYAH-MEYER FORMULAE AND THE STRATIFIED MULTIPLICATIVE PROPERTY

In this note we survey Hodge-theoretic formulae of Atiyah-Meyer type for genera and characteristic classes of complex algebraic varieties, and derive some new and interesting applications. We also present various exten- sions to the singular setting of the Chern-Hirzebruch-Serre signature formula.
Analysis of surface EMG signal morphology in Parkinson's disease

A novel approach is presented for the analysis of surface electromyogram (EMG) morphology in Parkinson's disease (PD). The method is based on histogram and crossing rate (CR) analysis of the EMG signal. In the method, histograms and CR values are used as high-dimensional feature vectors. The dimensionality of them is then reduced using the Karhunen–Loève transform (KLT). Finally, the discriminant analysis of feature vectors is performed in low-dimensional eigenspace. Histograms and CR values were chosen for analysis, because Parkinsonian EMG signals typically involve patterns of EMG bursts. Traditional methods of EMG amplitude and spectral analysis are not effective in analyzing impulse-like signals. The method, which was tested with EMG signals measured from 25 patients with PD and 22 healthy controls, was promising for discriminating between these two groups of subjects. The ratio of correct discrimination by augmented KLT was 86% for the control group and 72% for the patient group. On the basis of these results, further studies are suggested in order to evaluate the usability of this method in early stage diagnostics of PD.
Cognitive Reflection Effects on Time Discounting

In this work, we investigated individual differences in cognitive reflection effects on delay discounting – a preference for smaller sooner over larger later payoff. People are claimed to prefer more these alternatives they considered first – so-called reference point – over the alternatives they considered later. Cognitive reflection affects the way individuals process information, with less reflective individuals relying predominantly on the first information they consider, thus, being more susceptible to reference points as compared to more reflective individuals. In Experiment 1, we confirmed that individuals who scored high on the Cognitive Reflection Test discount less strongly than less reflective individuals, but we also show that such individuals are less susceptible to imposed reference points. Experiment 2 replicated these findings additionally providing evidence that cognitive reflection predicts discounting strength and (in)dependency to reference points over and above individual difference in numeracy.
ArrayStore: a storage manager for complex parallel array processing

We present the design, implementation, and evaluation of ArrayStore, a new storage manager for complex, parallel array processing. ArrayStore builds on prior work in the area of multidimensional data storage, but considers the new problem of supporting a parallel and more varied workload comprising not only range-queries, but also binary operations such as joins and complex user-defined functions. This paper makes two key contributions. First, it examines several existing single-site storage management strategies and array partitioning strategies to identify which combination is best suited for the array-processing workload above. Second, it develops a new and efficient storage-management mechanism that enables parallel processing of operations that must access data from adjacent partitions. We evaluate ArrayStore on over 80GB of real data from two scientific domains and real operators used in these domains. We show that ArrayStore outperforms previously proposed storage management strategies in the context of its diverse target workload.
Is Group Creativity ReallyAn Oxymoron? Some Thoughts on Bridging the Cohesion–Creativity Divide

The papers in this volume can be characterized by a “cohesion–creativity divide. ” On one side are scholars who describe the very nature of groups – its norms, interaction patterns, social influence, and hierarchy – as anathema to creativity. On the other side are advocates of cohesion and coordination, where the primary benefits of groups are to draw people together, form common ideas, and integrate knowledge into shared solutions. To bridge this “cohesion–creativity divide,” I have proposed four modes of resolution. They are: (1) searching for an overarching design that incorporates both integration and differentiation, (2) emphasizing dimensions of creativity most needed at a particular stage of the creative process, (3) promotion of a strong but creative culture, and (4) redefining creativity so that the tradeoffs inherent in the cohesion–creativity divide are drastically reduced. Each of these solutions is discussed in light of the papers in this volume as well as the creativity literature as a whole.
Geodesic exponential kernels: When curvature and linearity conflict

We consider kernel methods on general geodesic metric spaces and provide both negative and positive results. First we show that the common Gaussian kernel can only be generalized to a positive definite kernel on a geodesic metric space if the space is flat. As a result, for data on a Riemannian manifold, the geodesic Gaussian kernel is only positive definite if the Riemannian manifold is Euclidean. This implies that any attempt to design geodesic Gaussian kernels on curved Riemannian manifolds is futile. However, we show that for spaces with conditionally negative definite distances the geodesic Laplacian kernel can be generalized while retaining positive definiteness. This implies that geodesic Laplacian kernels can be generalized to some curved spaces, including spheres and hyperbolic spaces. Our theoretical results are verified empirically.
Using Metacognitive Strategy to Teach Learning Strategies: A Study of Indonesian Pre-Service Biology Teachers

Th e research aims at exploring Indonesian pre-service biology teachers’ metacognitive skills, measuring the development of learning strategies (LS) used by the teachers before and aft er the learning process, and describing the teachers’ responses aft erwards. Th ere were 25 subjects studied using a pretest-posttest design. Results showed that there was an increase in students’ metacognitive skills and their LS knowledge. Morever, they stated that they had got a lot of benefi ts aft er the learning process. Th is research concludes that metacognitive strategy can be used to teach LS so that students can broaden their LS understanding and thus enable to choose LS that fi ts them.
Synaptopathies: Dysfunction of Synaptic Function Synaptic Dysfunction in Parkinson's Disease

In neuronal circuits, memory storage depends on activity-dependent modifications in synaptic efficacy, such as LTD (long-term depression) and LTP (long-term potentiation), the two main forms of synaptic plasticity in the brain. In the nucleus striatum, LTD and LTP represent key cellular substrates for adaptive motor control and procedural memory. It has been suggested that their impairment could account for the onset and progression of motor symptoms of PD (Parkinson's disease), a neurodegenerative disorder characterized by the massive degeneration of dopaminergic neurons projecting to the striatum. In fact, a peculiar aspect of striatal plasticity is the modulation exerted by DA (dopamine) on LTP and LTD. Our understanding of these maladaptive forms of plasticity has mostly come from the electrophysiological, molecular and behavioural analyses of experimental animal models of PD. In PD, a host of cellular and synaptic changes occur in the striatum in response to the massive loss of DA innervation. Chronic l-dopa therapy restores physiological synaptic plasticity and behaviour in treated PD animals, but most of them, similarly to patients, exhibit a reduction in the efficacy of the drug and disabling AIMs (abnormal involuntary movements) defined, as a whole, as l-dopa-induced dyskinesia. In those animals experiencing AIMs, synaptic plasticity is altered and is paralleled by modifications in the postsynaptic compartment. In particular, dysfunctions in trafficking and subunit composition of NMDARs [NMDA (N-methyl-d-aspartate) receptors] on striatal efferent neurons result from chronic non-physiological dopaminergic stimulation and contribute to the pathogenesis of dyskinesias. According to these pathophysiological concepts, therapeutic strategies targeting signalling proteins coupled to NMDARs within striatal spiny neurons could represent new pharmaceutical interventions for PD and l-dopa-induced dyskinesia.
Improved feature decorrelation for HMM-based speech recognition

In most HMM-based recognition systems, a mixture of diagonal covariance gaussians is used to model the observation density functions in the states. The use of diagonal covariance gaussians however assumes that the underlying data vectors have uncorrelated vector components: if each gaussian is replaced with its full covariant counterpart, the off-diagonal elements in the covariance matrices should be small. To that end, most recognition systems have some kind of decorrelation matrix near the end of the preprocessing. Examples are the inverse cosine transform used with cepstral coefﬁcients, and principal component analysis (PCA) or linear discriminant analysis (LDA) of the features. However, none of these transforms is optimal if it comes to reducing the mismatch introduced by setting the off-diagonal elements in the covariance matrices to zero. The algorithm described in this paper reduces the local correlations between feature vector components inside the gaussians with a single global linear transform at the end of the preprocessing stage. The algorithm is optimal in the sense that we calculate the linear transformation that minimises the sum of the square of all off-diagonal elements over all gaussians. The algorithm is compared with principal component analysis, linear discriminant analysis and the recently published maximum likelihood modelling for semi-tied covariance matrices. The decorrelation method is also evaluated on two speech recognition tasks. A signiﬁcant relative improvement was achieved in both cases.
A Giant Pliosaurid Skull from the Late Jurassic of England

Pliosaurids were a long-lived and cosmopolitan group of marine predators that spanned 110 million years and occupied the upper tiers of marine ecosystems from the Middle Jurassic until the early Late Cretaceous. A well-preserved giant pliosaurid skull from the Late Jurassic Kimmeridge Clay Formation of Dorset, United Kingdom, represents a new species, Pliosaurus kevani. This specimen is described in detail, and the taxonomy and systematics of Late Jurassic pliosaurids is revised. We name two additional new species, Pliosaurus carpenteri and Pliosaurus westburyensis, based on previously described relatively complete, well-preserved remains. Most or all Late Jurassic pliosaurids represent a globally distributed monophyletic group (the genus Pliosaurus, excluding ‘Pliosaurus’ andrewsi). Despite its high species diversity, and geographically widespread, temporally extensive occurrence, Pliosaurus shows relatively less morphological and ecological variation than is seen in earlier, multi-genus pliosaurid assemblages such as that of the Middle Jurassic Oxford Clay Formation. It also shows less ecological variation than the pliosaurid-like Cretaceous clade Polycotylidae. Species of Pliosaurus had robust skulls, large body sizes (with skull lengths of 1.7–2.1 metres), and trihedral or subtrihedral teeth suggesting macropredaceous habits. Our data support a trend of decreasing length of the mandibular symphysis through Late Jurassic time, as previously suggested. This may be correlated with increasing adaptation to feeding on large prey. Maximum body size of pliosaurids increased from their first appearance in the Early Jurassic until the Early Cretaceous (skull lengths up to 2360 mm). However, some reduction occurred before their final extinction in the early Late Cretaceous (skull lengths up to 1750 mm).
Cognitive Impairment in Hospitalized Seniors

Cognitive disorders are highly prevalent in hospitalized seniors, and can be due to delirium, dementia, as well as other disorders. Hospitalization can have adverse cognitive effects, and cognitive dysfunction adversely affects hospital outcomes. In this article, the literature is reviewed on how hospitalization affects cognitive function and how cognitive impairment affects hospital outcomes. Possible interventions in cognitively impaired hospitalized seniors are reviewed.
Complex patterns of mitochondrial dynamics in human pancreatic cells revealed by fluorescent confocal imaging

Mitochondrial morphology and intracellular organization are tightly controlled by the processes of mitochondrial fission–fusion. Moreover, mitochondrial movement and redistribution provide a local ATP supply at cellular sites of particular demands. Here we analysed mitochondrial dynamics in isolated primary human pancreatic cells. Using real time confocal microscopy and mitochondria‐specific fluorescent probes tetramethylrhodamine methyl ester and MitoTracker Green we documented complex and novel patterns of spatial and temporal organization of mitochondria, mitochondrial morphology and motility. The most commonly observed types of mitochondrial dynamics were (i) fast fission and fusion; (ii) small oscillating movements of the mitochondrial network; (iii) larger movements, including filament extension, retraction, fast (0.1–0.3 μm/sec.) and frequent oscillating (back and forth) branching in the mitochondrial network; (iv) as well as combinations of these actions and (v) long‐distance intracellular translocation of single spherical mitochondria or separated mitochondrial filaments with velocity up to 0.5 μm/sec. Moreover, we show here for the first time, a formation of unusual mitochondrial shapes like rings, loops, and astonishingly even knots created from one or more mitochondrial filaments. These data demonstrate the presence of extensive heterogeneity in mitochondrial morphology and dynamics in living cells under primary culture conditions. In summary, this study reports new patterns of morphological changes and dynamic motion of mitochondria in human pancreatic cells, suggesting an important role of integrations of mitochondria with other intracellular structures and systems.
A new approach to GPS integrity monitoring using prior probability models and optimal threshold search

Current methods for GPS receiver autonomous integrity monitoring are limited by the assumptions they make. Using published studies of navigation system reliability, this paper develops a prior probability model for spacecraft and receiver anomalies based on non-ideal failure models and the uncertainty present in their failure distribution parameters. With this model, the thresholds for a residuals test statistic are found to optimize an arbitrary objective function based on relative costs for false alarm and missed detection errors. The outputs of Monte Carlo simulations allow thresholds to be computed for each geometry case using trial-and-error optimization. The simulation outputs suggest that the assumptions of traditional RAIM may be partially invalid. These results are useful for both snapshot RAIM tests as well as multi-step integrity algorithms which use Bayesian updating to generate posterior failure probabilities. Multi-step algorithms may be a valuable addition to the future GIC integrity structure. <<ETX>>
Designing minimal effective normative systems with the help of lightweight formal methods

Normative systems (i.e., a set of rules) are an important approach to achieving effective coordination among (often an arbitrary number of) agents in multiagent systems. A normative system should be effective in ensuring the satisfaction of a desirable system property, and minimal (i.e., not containing norms that unnecessarily over-constrain the behaviors of agents). Designing or even automatically synthesizing minimal effective normative systems is highly non-trivial. Previous attempts on synthesizing such systems through simulations often fail to generate normative systems which are both minimal and effective. In this work, we propose a framework that facilitates designing of minimal effective normative systems using lightweight formal methods. Given a minimal effective normative system which coordinates many agents must be minimal and effective for a small number of agents, we start with automatically synthesizing one such system with a few agents. We then increase the number of agents so as to check whether the same design remains minimal and effective. If it is, we manually establish an induction proof so as to lift the design to an arbitrary number of agents.
Change in ankle-brachial index over time and mortality in diabetics with proteinuria

Peripheral arterial disease is common in diabetic chronic kidney disease (CKD) and is characterized either by abnormally low or high ankle-brachial index (ABI). Whether low or high ABI carries similar prognostic value is unknown. The association of baseline ABI with all-cause mortality over 40 ± 21 months (mean ± SD) was ascertained in 167 proteinuric diabetics (age 57 ± 7 years; median urine protein-creatinine, 2.5 mg/mg). Association of change in ABI with all-cause mortality was determined in 75 subjects with normal ABI (0.9 – 1.3) at baseline. Among 167 participants, 41% had an abnormal ABI: < 0.9, 18%; and > 1.3 or non-compressible arteries, 23%. Only individuals with low ABI had a significantly higher risk for all-cause mortality (hazards ratio (95% confidence interval), HR: 2.23 (1.07, 4.65)). In subjects with normal ABI at baseline with follow-up measurement (n = 75), vascular disease worsened in 39% over 23 ± 6 months: 17% had either a decrease in ABI by ≥ 0.1 or a final ABI < 0.9, and 21% had a final ABI > 1.3 or non-compressible arteries. Only individuals who had a decrease in ABI over time had a significantly higher risk for death (adjusted HR, 7.41 (1.63, 33.65)). Peripheral arterial disease is not uncommon and progresses rapidly in individuals with diabetes and proteinuria. Low or declining ABI is a strong predictor of all-cause mortality. Routine measurement of ABI is a simple bed-side procedure that may permit easy risk-stratification in diabetic CKD patients.