Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

The number of interacting lipids regulates the diffusivity of a peripheral membrane protein bound on a membrane surface. Pleckstrin homology (PH) domains are membrane-binding lipid recognition proteins that interact with phosphatidylinositol phosphate (PIP) molecules in eukaryotic cell membranes. Diffusion of PH domains plays a critical role in biological reactions on membrane surfaces. Although diffusivity can be estimated by long-time measurements, it lacks information on the short-time diffusive nature. We reveal two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations. One is fractional Brownian motion, attributed to the motion of the lipids with which the PH domain interacts. The other is temporally fluctuating diffusivity; that is, the short-time diffusivity of the bound protein changes substantially with time. Moreover, the diffusivity for short-time measurements is intrinsically different from that for long-time measurements. This fluctuating diffusivity results from dynamic changes in interactions between the PH domain and PIP molecules. Our results provide evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces. Changes in the diffusivity of PH domains and related membrane-bound proteins may in turn contribute to the formation/dissolution of protein complexes in membranes.
SEAT-LA: a soft error analysis tool for combinational logic

Radiation induced soft errors in combinational logic is expected to become as important as directly induced errors on state elements. Consequently, it has become important to develop techniques to quickly and accurately predict soft error rates (SER) in logic circuits. In this paper, we propose a new approach, which can be applied to designs that use cell libraries characterized for soft error analysis and utilizes analytical equations to model the propagation of a voltage pulse to the input of a state element. The average error of the SER estimates using our approach compared to the estimates obtained using circuit level simulations is 6.5% while providing an average speed up of 15000. We have demonstrated the scalability of our approach using designs from the ISCAS-85 benchmarks.
Protocol S 1 : MPARobustness-Partial and Noisy Data

When applying MPA to biological systems, often not all multi-perturbation experiments are available. In such cases, the predicted MPA variant is used (as described in the main text). To demonstrate the stability of the MPA predicted Shapley value under partial and noisy data we performed two types of analysis; The first examines the experimental neural laser ablation data described in the main text and the second uses simulated data. Analyzing the simulated data has the advantage that we can compare the predicted contributions to the real contributions (whose knowledge we lack in the neural data). To test the stability of the predicted contributions in the neural ablation analysis, we repeated the process of calculating the predicted contributions using different subsets of the data, according to the leave-one-out scheme, where in each repetition one experiment is left out from the available experimental set. The result of this procedure provides 31 sets of predicted contributions (the dataset includes 31 experiments, and each time we apply the analysis to 30 of them). Figure 1 shows the results of the leave-one-out procedure. Evidently, the predicted contributions are similar to those calculated using all the data, and exhibit stability across the different repeats as noted by the relatively small standard deviations. In order to rigorously examine the stability and robustness of the MPA under noisy and partial data we used simulated data. In the simulation we assume a system with 8 elements (a,b,c,d,e,f,g,h) that perform a given function F , F = 0.35a − 0.1(a ∗ e ∗ d) + 0.15(a ∗ e) + 0.05d + 0.15(a ∗ d) + 0.25b − 0.15c+0.1g+0.1h+0.1(g∗h) (8 elements corresponds to the number of neuron pairs in the laser ablation experiments). The performance F is calculated by assigning one of two states to each of the elements (one if intact and zero if perturbed). Note that F is not a simple linear function, in which case a simple single-perturbation analysis would not be sufficient. Examining F shows that a is the most important element, c has a negative influence on the performance, f has no role at all and g and h are totally symmetric. Since we have 8 elements in the system there are 256 possible perturbation configurations. Performing these 256 experiments “in-silico” allows us to calculate the exact contribution of each element, which is further used as a benchmark to compare with the MPA outcome of partial and noisy experiments. To examine how sensitive our analysis is to noise, two types of noise were studied.
Relating Demographic Characteristics of a Small Mammal to Remotely Sensed Forest-Stand Condition

Many ecological systems around the world are changing rapidly in response to direct (land-use change) and indirect (climate change) human actions. We need tools to assess dynamically, and over appropriate management scales, condition of ecosystems and their responses to potential mitigation of pressures. Using a validated model, we determined whether stand condition of floodplain forests is related to densities of a small mammal (a carnivorous marsupial, Antechinus flavipes) in 60 000 ha of extant river red gum (Eucalyptus camaldulensis) forests in south-eastern Australia in 2004, 2005 and 2011. Stand condition was assessed remotely using models built from ground assessments of stand condition and satellite-derived reflectance. Other covariates, such as volumes of fallen timber, distances to floods, rainfall and life stages were included in the model. Trapping of animals was conducted at 272 plots (0.25 ha) across the region. Densities of second-year females (i.e. females that had survived to a second breeding year) and of second-year females with suckled teats (i.e. inferred to have been successful mothers) were higher in stands with the highest condition. There was no evidence of a relationship with stand condition for males or all females. These outcomes show that remotely-sensed estimates of stand condition (here floodplain forests) are relatable to some demographic characteristics of a small mammal species, and may provide useful information about the capacity of ecosystems to support animal populations. Over-regulation of large, lowland rivers has led to declines in many facets of floodplain function. If management of water resources continues as it has in recent decades, then our results suggest that there will be further deterioration in stand condition and a decreased capacity for female yellow-footed antechinuses to breed multiple times.
Verified Visualisation of Textual Modelling Languages

Many modelling languages have both a textual and a graphical form. The relationship between these two forms ought to be clear and concrete, but is instead commonly underspecified, weak, and informal. Further, processes and tool support for modelling often do not treat both forms as first-class citizens, instead choosing to favour one as the “real” representation and the other as a derivable representation. As textual and graphical forms have their individual strengths and weaknesses, ideally one should be able to view and edit a model in whichever form is most desirable at the moment. Furthermore, we should be able to do so without having to worry about semantic differences between what is seen in a graphical view versus what is seen in a textual view. If we are to develop tools that allow dual-editing—simultaneous editing of both the textual and graphical forms—then it is essential that their relationship is clearly and precisely defined. This paper details a formal relationship between the textual and graphical forms of a high-level modelling language called the Business Object Notation (BON). We describe the semantics of the graphical and textual representations and the relationship that holds between them. We also formally define a view on an underlying model as an extraction function, and model diffs as a means of tracking changes as a model evolves. This theoretical foundation provides a means by which tools guarantee consistency between textual and graphical notations, as well shows how to efficiently perform model updates, reason about model views, and interpret properties between modelling perspectives.
Motor Retraining in Virtual Reality: A Feasibility Study for Upper‐Extremity Rehabilitation in Individuals With Chronic Stroke

Background and Purpose. Individuals with stroke can improve upper‐extremity function in the chronic phase, providing rehabilitation is intensive, attended, and of sufficient duration. Virtual reality has been used in motor retraining; however, off‐the‐shelf game consoles may not be appropriate for those with marked motor impairment and high finger or arm spasticity. The objective of this study was to investigate the feasibility and effects of training in individuals with chronic stroke who are either high‐functioning or low‐functioning, and also spastic. Case Descriptions. Four volunteers, 3 men and 1 woman, were recruited from a local aphasia support group. All individuals were chronic post stroke with right‐side hemiplegia. Training took place at the Tele‐Rehabilitation Institute at Rutgers University. The intervention was performed on the Rutgers Arm II, a prototype training table that senses supported arm movement and grasp strength and tilts to resist or assist reach. Participants played games that adapted automatically to each individual's motor abilities. The games were practiced over 6 weeks, 3 sessions every week, with sessions lasting up to 1 hour. The 4 participants were evaluated by a senior physical therapist before, immediately following, and 6 weeks after the intervention. No occupational or physical therapist was present during the training sessions. Outcomes. The primary outcomes were changes in the affected upper‐extremity subset of the Fugl‐Meyer test and self‐reported changes in the participants' activities of daily living. Improvements in active range of motion and grasp strength were secondary outcomes. All individuals improved in Fugl‐Meyer scores and retained these gains (participant 1, 45 to 50; participant 2, 16 to 22; participant 3, 12 to 20; participant 4, 42 to 51). Participants 2 and 3, who presented with severe motor impairment, began using their affected arms in daily activities subsequent to training. All participants improved in their shoulder, elbow, and finger flexion active range of motion. Remarkably, participants 2 and 3, who were unable to exert force in grasping or pinching pre‐training, could now do so and retained these gains at 6 weeks following the intervention. Well‐being and mood seemed to improve in all participants. Discussion and Conclusion. Results show that motor retraining in virtual reality is feasible, well‐tolerated by participants, and benefitting them. The Rutgers Arm II system was able to train participants, who varied greatly in their degree of motor impairment, but without a clinician being present. The present study contributes to the body of knowledge on novel virtual rehabilitation interventions for the upper extremity.
Landscape-scale Spatial Distribution of the Lanner Falcon (Falco biarmicus feldeggii) Breeding Population in Italy

Abstract Falco biarmicus feldeggii is one of the most threatened taxa in Europe. Its global population is estimated at a few hundred pairs unequally scattered in a vast and fragmented area stretching from Sicily to the Caspian Sea. Most recent counts showed that Italy hosts a large part (>25%) of the whole population. Consequently, Italian authorities promoted a national action plan. In this framework, we carried out the first national survey for the Lanner Falcon in Italy (2003–2004). Our study area covered the whole breeding range, i.e., Sicily and the Italian peninsula (n = 2909 cells 10 × 10 km). When possible, we considered also additional information from previous regional investigations (1993–2001). First, we estimated size and distribution of each breeding subpopulation. Then, we tried to identify, at landscape level, the main environmental features linked to the spatial distribution of the nesting sites. We found the Lanner Falcon in 184 cells (6.4% of the total grid map), but we estimated no more than 140–172 pairs (70–80 of which are in Sicily) in the same breeding season. Higher levels of isolation characterize the continental breeding cells whereas in Sicily cells are much more clustered. Altitude is the main factor influencing cell aggregations in Italy; nevertheless, other environmental variables, such as climate, precipitation, and vegetation may be important. Our results show that the conservation measures adopted in Italy are somewhat inadequate given the low number of breeding pairs included in protected areas (23%–28%). Many small and scattered special areas of conservation (SAC) devoted to conserve priority habitats fit the irregular spatial aggregations of Lanner Falcon sites better than several large special protection areas (SPA).
Y‐chromosome Lineages from Portugal, Madeira and Açores Record Elements of Sephardim and Berber Ancestry

A total of 553 Y‐chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78–83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub‐populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum‐Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub‐clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre‐Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub‐Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex‐related gene flow, most likely mediated by the Atlantic slave trade.
Self-Similarity based Zebra-crossing Detection for Intelligent Vehicle

A zebra-crossing detection method for intelligent vehicle is proposed in this paper. The method is performed on a bird-eye view image called inverse perspective mapping image. The complete method includes two phrases. First, a morphological filer followed by horizontal projection is applied to fast extract candidate zebra-crossing regions, where the size and structure information of zebra-crossing are well utilized. Second, a recognition method which based on self- similarity is presented to identify the candidate regions. Given a seed region of a zebra-crossing, the recognition method can infer overall zebra-crossing region by matching and growing. Experiments on a great number of real images which consist of several challenge scenes demonstrate the effectiveness and efficiency of the proposed approach.
Building Better Test Functions

We introduce basic guidelines for developing test suites for evolutionary algorithms and examine common test functions in terms of these guidelines. Two methods of designing test functions are introduced which address speciic issues relevant to comparative studies of evolutionary algorithms. The rst method produces representation invariant functions. The second method constructs functions with diierent degrees of nonlinearity, where the interactions and the cost of evaluation scale with respect to the dimensionality of the search space.
Brain Tumor Detection in Conventional MR Images Based on Statistical Texture and Morphological Features

This paper presents a novel framework for brain tumor diagnosis and its grade classification based on higher order statistical texture features namely kurtosis and skewness along with selected morphological features. These features were extracted from segmented tumorous T2-weighted brain MR images, in order to distinguish high grade (HG) tumor from low grade (LG) tumor. Tumor classification is carried out using Support vector machine (SVM) classifier with k-fold crossvalidation. This work also compares the performance of the SVM with linear discriminant analysis (LDA) and Naives Bayes classifiers. Our proposed feature set achieved sensitivity, specificity and accuracy of 100% with SVM (linear kernel) while classifying brain tumor MR images as LG/HG.
Asticcacaulis solisilvae sp. nov., isolated from forest soil.

An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3EN(T), was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3-2.4 µm long by 0.30-0.75 µm wide) with single flagella. The strain grew at 10-37 °C (optimum 25-30 °C) and at pH 4.5-9.5 (optimum 5.0-7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3EN(T) was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3EN(T) was identified as Asticcacaulis biprosthecium DSM 4723(T) (97.2 % 16S rRNA gene sequence similarity) and the DNA-DNA hybridization value between strain CGM1-3EN(T) and A. biprosthecium DSM 4723(T) was less than 24.5 %. Strain CGM1-3EN(T) used d-glucose, d-fructose, sucrose, maltose, trehalose, d-mannose, d-mannitol, d-sorbitol, d-galactose, cellobiose, lactose, raffinose, fumarate, pyruvate, dl-alanine and glycerol as carbon sources. Based on data from the present polyphasic study, the forest soil isolate CGM1-3EN(T) is considered to represent a novel species of the genus Asticcacaulis, for which the name Asticcacaulis solisilvae sp. nov. is proposed. The type strain is CGM1-3EN(T) ( = AIM0088(T) = KCTC 32102(T) = JCM 18544(T)).
Blockade of Adenosine A2A Receptors Prevents Protein Phosphorylation in the Striatum Induced by Cortical Stimulation

Previous studies have shown that cortical stimulation selectively activates extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation and immediate early gene expression in striatal GABAergic enkephalinergic neurons. In the present study, we demonstrate that blockade of adenosine A2A receptors with caffeine or a selective A2A receptor antagonist counteracts the striatal activation of cAMP–protein kinase A cascade (phosphorylation of the Ser845 residue of the glutamate receptor 1 subunit of the AMPA receptor) and mitogen-activated protein kinase (ERK1/2 phosphorylation) induced by the in vivo stimulation of corticostriatal afferents. The results indicate that A2A receptors strongly modulate the efficacy of glutamatergic synapses on striatal enkephalinergic neurons.
Small but Powerful: Top Predator Local Extinction Affects Ecosystem Structure and Function in an Intermittent Stream

Top predator loss is a major global problem, with a current trend in biodiversity loss towards high trophic levels that modifies most ecosystems worldwide. Most research in this area is focused on large-bodied predators, despite the high extinction risk of small-bodied freshwater fish that often act as apex consumers. Consequently, it remains unknown if intermittent streams are affected by the consequences of top-predators’ extirpations. The aim of our research was to determine how this global problem affects intermittent streams and, in particular, if the loss of a small-bodied top predator (1) leads to a ‘mesopredator release’, affects primary consumers and changes whole community structures, and (2) triggers a cascade effect modifying the ecosystem function. To address these questions, we studied the top-down effects of a small endangered fish species, Barbus meridionalis (the Mediterranean barbel), conducting an enclosure/exclosure mesocosm experiment in an intermittent stream where B. meridionalis became locally extinct following a wildfire. We found that top predator absence led to ‘mesopredator release’, and also to ‘prey release’ despite intraguild predation, which contrasts with traditional food web theory. In addition, B. meridionalis extirpation changed whole macroinvertebrate community composition and increased total macroinvertebrate density. Regarding ecosystem function, periphyton primary production decreased in apex consumer absence. In this study, the apex consumer was functionally irreplaceable; its local extinction led to the loss of an important functional role that resulted in major changes to the ecosystem’s structure and function. This study evidences that intermittent streams can be affected by the consequences of apex consumers’ extinctions, and that the loss of small-bodied top predators can lead to large ecosystem changes. We recommend the reintroduction of small-bodied apex consumers to systems where they have been extirpated, to restore ecosystem structure and function.
Films as Graphical Comments in the Source Code of Programs

The author suggests using animated pictures (films) as graphical comments in the source code of programs. Such pictures can be played forwards and backwards in steps under the control of the user. They can have multiple branches, which lead to different pictures. Animation effects can be applied to show how a picture changes over time. This can be useful for visualizing the dynamic behavior of programs. He shows how to extend an object-oriented graphics editor so that it can be used for creating and viewing films. He also explains how such films can be embedded into the source code of programs using a text framework.
Functional electrical stimulation and ankle foot orthoses provide equivalent therapeutic effects on foot drop: A meta-analysis providing direction for future research.

OBJECTIVE To compare the randomized controlled trial evidence for therapeutic effects on walking of functional electrical stimulation and ankle foot orthoses for foot drop caused by central nervous system conditions. DATA SOURCES MEDLINE, CINAHL, Cochrane Central Register of Controlled Trials, REHABDATA, PEDro, NIHR Centre for Reviews and Dissemination, Scopus and clinicaltrials.gov. STUDY SELECTION One reviewer screened titles/abstracts. Two independent reviewers then screened the full articles. DATA EXTRACTION One reviewer extracted data, another screened for accuracy. Risk of bias was assessed by 2 independent reviewers using the Cochrane Risk of Bias Tool. DATA SYNTHESIS Eight papers were eligible; 7 involving participants with stroke and 1 involving participants with cerebral palsy. Two papes reporting different measures from the same trial were grouped, resulting in 7 synthesized randomized controlled trials (n= 464). Meta-analysis of walking speed at final assessment (p = 0.46), for stroke participants (p = 0.54) and after 4-6 weeks' use (p = 0.49) showed equal improvement for both devices. CONCLUSION Functional electrical stimulation and ankle foot orthoses have an equally positive therapeutic effect on walking speed in non-progressive central nervous system diagnoses. The current randomized controlled trial evidence base does not show whether this improvement translates into the user's own environment or reveal the mechanisms that achieve that change. Future studies should focus on measuring activity, muscle activity and gait kinematics. They should also report specific device details, capture sustained therapeutic effects and involve a variety of central nervous system diagnoses.