Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative assessment of motor functions post-stroke: Responsiveness of upper-extremity robotic measures and its task dependence

Technology aided measures offer a sensitive, accurate and time-efflcient approach for the assessment of sensorimotor function after neurological impairment compared to standard clinical assessments. This preliminary study investigated the relationship between task definition and its effect on robotic measures using a planar, two degree of freedom, robotic-manipulator (H-Man). Four chronic stroke participants (49.5±11.95 years, 2 Female, FMA: 37.5±13.96) and eight healthy control participants (26.25± 4.70 years, 2 Female) participated in the study. Motor functions were evaluated using line tracing and circle tracing tasks with dominant and nondominant hand of healthy and affected vs. non affected hand of stroke participants. The results show significant dependence of quantitative measures on investigated tasks.
Making the most of methods: the future for PCP?

It used to be the case that the Psychology of Personal Constructs was better known for its methods (or at least one of them: the repertory grid) than its theory. But now, in the UK at least, no personal construct methods are taught to undergraduates and few become familiar with PCP as a theoretical approach. Although we are focusing here on the UK as an example, we expect that the situation is similar in other countries. Some writers have previously tried to raise the profile of PCP by showing its compatibility with newer theoretical approaches. For example, given the obvious points of agreement between constructivism and social constructionism, some writers (e.g. Botella, 1995) have tried to bring these together in a synthesis. In this plenary we too will discuss the potential for raising the academic profile of Personal Construct Psychology but we will suggest that this can best be done by focussing once again on its methods. We argue that PCP is best ‘advertised’ to researchers using a variety of theoretical approaches by showing how its methods are sympathetic to these.
#Anorexia, #anarexia, #anarexyia: Characterizing online community practices with orthographic variation

Distinctive linguistic practices help communities build solidarity and differentiate themselves from outsiders. In an online community, one such practice is variation in orthography, which includes spelling, punctuation, and capitalization. Using a dataset of over two million Instagram posts, we investigate orthographic variation in a community that shares pro-eating disorder (pro-ED) content. We find that not only does orthographic variation grow more frequent over time, it also becomes more profound or “deep,” with variants becoming increasingly distant from the original: as, for example, #anarexyia is more distant than #anarexia from the original spelling #anorexia. We find that the these changes are driven by newcomers, who adopt the most extreme linguistic practices as they enter the community. Moreover, this behavior correlates with engagement with the community: the newcomers that adopt deeper variant orthography tend to remain active for longer in the community, and posts with deeper variation receive more positive feedback in the form of “likes. ” Previous work has linked community membership change with language change, and our work casts this connection in a new light, with newcomers driving an evolving practice rather than adapting to it. We also demonstrate the utility of orthographic variation as a new lens to study sociolinguistic change in online communities, particularly when the change results from an exogenous force such as a content ban.
Lack of Time-Delay Robustness for Stabilization of a Structural Acoustics Model

In this paper we consider a natural robustness question for a model for structural acoustics. This model, which has been of great interest in recent years, is represented by a wave equation in $\R^2$ coupled to a Kelvin--Voigt beam; the coupling is natural physically, and is represented mathematically by highly unbounded operators. We assume that the observation consists of point evaluation of the beam position, the beam velocity, and the wave velocity. We are interested in the effect of arbitrarily small delays in the feedback loop on a controller that uses these observations. We show that it is not possible to construct a dynamic stabilizer of a very general form---including static feedback---such that the stabilization is robust with respect to delays in the feedback loop. In order to do this we need to carefully analyze the input-to-output map. Finally, we relate these results to already existing numerical results obtained for a Galerkin approximation of the system.
Variational Inference on Deep Exponential Family by using Variational Inferences on Conjugate Models

In this paper, we propose a new variational inference method for deep exponentialfamily (DEF) models. Our method converts non-conjugate factors in a DEF model to easy-to-compute conjugate exponential-family messages. This enables local and modular updates similar to variational message passing, as well as stochastic natural-gradient updates similar to stochastic variational inference. Such updates make our algorithm highly suitable for large-scale learning. Our method exploits the structure of the deep network and can be useful to reduce the variance of stochastic methods for variational inference.
The role of ABA in triggering ethylene biosynthesis and ripening of tomato fruit

In order to understand more details about the role of abscisic acid (ABA) in fruit ripening and senescence of tomato, two cDNAs (LeNCED1 and LeNCED2) which encode 9-cis-epoxycarotenoid dioxygenase (NCED) as a key enzyme in ABA biosynthesis, two cDNAs (LeACS2 and LeACS4) which encode 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, and one cDNA (LeACO1) which encodes ACC oxidase involved in ethylene biosynthesis were cloned from tomato fruit using a reverse transcription-PCR (RT-PCR) approach. The relationship between ABA and ethylene during ripening was also investigated. Among six sampling times in tomato fruits, the LeNCED1 gene was highly expressed only at the breaker stage when the ABA content becomes high. After this, the LeACS2, LeACS4, and LeACO1 genes were expressed with some delay. The change in pattern of ACO activity was in accordance with ethylene production reaching its peak at the pink stage. The maximum ABA content preceded ethylene production in both the seeds and the flesh. The peak value of ABA, ACC, and ACC oxidase activity, and ethylene production all started to increase earlier in seeds than in flesh tissues, although they occurred at different ripening stages. Exogenous ABA treatment increased the ABA content in both flesh and seed, inducing the expression of both ACS and ACO genes, and promoting ethylene synthesis and fruit ripening, while treatment with fluridone or nordihydroguaiaretic acid (NDGA) inhibited them, delaying fruit ripening and softening. Based on the results obtained in this study, it was concluded that LeNCED1 initiates ABA biosynthesis at the onset of fruit ripening, and might act as an original inducer, and ABA accumulation might play a key role in the regulation of ripeness and senescence of tomato fruit.
Journal of Neuroengineering and Rehabilitation Open Access Using Non-invasive Brain Stimulation to Augment Motor Training-induced Plasticity

Therapies for motor recovery after stroke or traumatic brain injury are still not satisfactory. To date the best approach seems to be the intensive physical therapy. However the results are limited and functional gains are often minimal. The goal of motor training is to minimize functional disability and optimize functional motor recovery. This is thought to be achieved by modulation of plastic changes in the brain. Therefore, adjunct interventions that can augment the response of the motor system to the behavioural training might be useful to enhance the therapy-induced recovery in neurological populations. In this context, noninvasive brain stimulation appears to be an interesting option as an add-on intervention to standard physical therapies. Two non-invasive methods of inducing electrical currents into the brain have proved to be promising for inducing long-lasting plastic changes in motor systems: transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS). These techniques represent powerful methods for priming cortical excitability for a subsequent motor task, demand, or stimulation. Thus, their mutual use can optimize the plastic changes induced by motor practice, leading to more remarkable and outlasting clinical gains in rehabilitation. In this review we discuss how these techniques can enhance the effects of a behavioural intervention and the clinical evidence to date.
PROPERTIES OF A POLAR CORONAL HOLE DURING THE SOLAR MINIMUM IN 2007

We report measurements of a polar coronal hole during the recent solar minimum using the Extreme Ultraviolet Imaging Spectrometer on Hinode. Five observations are analyzed that span the polar coronal hole from the central meridian to the boundary with the quiet-Sun corona. We study the observations above the solar limb in the height range of 1.03–1.20 R☉. The electron temperature Te and emission measure (EM) are found using a geometric mean emission measure method. The EM derived from the elements Fe, Si, S, and Al are compared in order to measure relative coronal-to-photospheric abundance enhancement factors. We also studied the ion temperature Ti and the non-thermal velocity vnt using the line profiles. All these measurements are compared to polar coronal hole observations from the previous (1996–1997) solar minimum and to model predictions for relative abundances. There are many similarities in the physical properties of the polar coronal holes between the two minima at these low heights. We find that the electron density, Te, and Ti are comparable in both minima. Te shows a comparable gradient with height. Both minima show a decreasing Ti with increasing charge-to-mass ratio q/M. A previously observed upturn of Ti for ions above q/M>0.25 was not found here. We also compared relative coronal-to-photospheric elemental abundance enhancement factors for a number of elements. These ratios were ∼1 for both the low first ionization potential (FIP) elements Si and Al and the marginally high FIP element S relative to the low FIP element Fe, as is expected based on earlier observations and models for a polar coronal hole. These results are consistent with no FIP effect in a polar coronal hole.
Simulations of the NK Cell Immune Synapse Reveal that Activation Thresholds Can Be Established by Inhibitory Receptors Acting Locally

NK cell activation is regulated by a balance between activating and inhibitory signals. To address the question of how these signals are spatially integrated, we created a computer simulation of activating and inhibitory NK cell immunological synapse (NKIS) assembly, implementing either a “quantity-based” inhibition model or a “distance-based” inhibition model. The simulations mimicked the observed molecule distributions in inhibitory and activating NKIS and yielded several new insights. First, the total signal is highly influenced by activating complex dissociation rates but not by adhesion and inhibitory complex dissociation rates. Second, concerted motion of receptors in clusters significantly accelerates NKIS maturation. Third, when the potential of a cis interaction between Ly49 receptors and MHC class I on murine NK cells was added to the model, the integrated signal as a function of receptor and ligand numbers was only slightly increased, at least up to the level of 50% cis-bound Ly49 receptors reached in the model. Fourth, and perhaps most importantly, the integrated signal behavior obtained when using the distance-based inhibition signal model was closer to the experimentally observed behavior, with an inhibition radius of the order 3–10 molecules. Microscopy to visualize Vav activation in NK cells on micropatterned surfaces of activating and inhibitory strips revealed that Vav is only locally activated where activating receptors are ligated within a single NK cell contact. Taken together, these data are consistent with a model in which inhibitory receptors act locally; that is, that every bound inhibitory receptor acts on activating receptors within a certain radius around it.
Introducing Geometry in Active Learning for Image Segmentation

We propose an Active Learning approach to training a segmentation classifier that exploits geometric priors to streamline the annotation process in 3D image volumes. To this end, we use these priors not only to select voxels most in need of annotation but to guarantee that they lie on 2D planar patch, which makes it much easier to annotate than if they were randomly distributed in the volume. A simplified version of this approach is effective in natural 2D images. We evaluated our approach on Electron Microscopy and Magnetic Resonance image volumes, as well as on natural images. Comparing our approach against several accepted baselines demonstrates a marked performance increase.
Identification of Major Effect QTLs for Agronomic Traits and CSSLs in Rice from Swarna/Oryza nivara Derived Backcross Inbred Lines

Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass. BILs were genotyped using 111 polymorphic simple sequence repeats distributed across the genome. Fifteen QTLs including 10 novel QTLs were identified using composite interval mapping, Inclusive composite interval mapping and multiple interval mapping (MIM). O. nivara alleles were trait-enhancing in 26% of QTLs. Only 3 of 15 QTLs were also reported previously in BC2F2 of the same cross. These three included the two major effect QTLs for DM and PH detected in both years with 13 and 20% phenotypic variance. Further, a set of 74 CSSLs was identified using CSSL Finder and 22 of these showed significantly higher values than Swarna for five yield traits. CSSLs, 220S for panicle weight and 10-2S with consistent high yield in both years are worthy of large scale field evaluation. The major QTLs and 22 significantly different CSSLs are a useful resource for rice improvement and dissecting yield related traits.
HLA genotyping in the international Type 1 Diabetes Genetics Consortium

Background Although human leukocyte antigen (HLA) DQ and DR loci appear to confer the strongest genetic risk for type 1 diabetes, more detailed information is required for other loci within the HLA region to understand causality and stratify additional risk factors. The Type 1 Diabetes Genetics Consortium (T1DGC) study design included high-resolution genotyping of HLA-A, B, C, DRB1, DQ, and DP loci in all affected sibling pair and trio families, and cases and controls, recruited from four networks worldwide, for analysis with clinical phenotypes and immunological markers. Purpose In this article, we present the operational strategy of training, classification, reporting, and quality control of HLA genotyping in four laboratories on three continents over nearly 5 years. Methods Methods to standardize HLA genotyping at eight loci included: central training and initial certification testing; the use of uniform reagents, protocols, instrumentation, and software versions; an automated data transfer; and the use of standardized nomenclature and allele databases. We implemented a rigorous and consistent quality control process, reinforced by repeated workshops, yearly meetings, and telephone conferences. Results A total of 15,246 samples have been HLA genotyped at eight loci to four-digit resolution; an additional 6797 samples have been HLA genotyped at two loci. The genotyping repeat rate decreased significantly over time, with an estimated unresolved Mendelian inconsistency rate of 0.21%. Annual quality control exercises tested 2192 genotypes (4384 alleles) and achieved 99.82% intra-laboratory and 99.68% inter-laboratory concordances. Limitations The chosen genotyping platform was unable to distinguish many allele combinations, which would require further multiple stepwise testing to resolve. For these combinations, a standard allele assignment was agreed upon, allowing further analysis if required. Conclusions High-resolution HLA genotyping can be performed in multiple laboratories using standard equipment, reagents, protocols, software, and communication to produce consistent and reproducible data with minimal systematic error. Many of the strategies used in this study are generally applicable to other large multi-center studies. Clinical Trials 2010; 7: S75—S87. http:// ctj.sagepub. com
Nonparametric Modeling of Hierarchically Exchangeable Data

Hierarchically exchangeable data are characterized by the exchangeability of a population of units and the exchangeability of observations from each individual unit. A flexible model for such data is the hierarchical logistic-normal model, which provides unconstrained sampling distributions at the within-unit level and an unconstrained covariance structure at the betweenunit level. Also, the sampling distribution at the between-unit level is unimodal in a weak sense. Parameter estimation and inference for the hierarchical logistic-normal model is relatively straightforward via Markov chain Monte Carlo or an approximate EM algorithm. These and other features of the hierarchical logistic normal model are explored, and the model is applied to the analysis of tumor locations in a mammalian population. A comparison is made to a similar data analysis based on Dirichlet distributions. Some key words: nonparametric Bayes, logistic normal, multivariate normal, multinomial, Dirichlet distribution, repeated measures.
Modified Intracellular-Associated Phenotypes in a Recombinant Salmonella Typhi Expressing S. Typhimurium SPI-3 Sequences

A bioinformatics comparison of Salmonella Pathogenicity Island 3 sequences from S. Typhi and S. Typhimurium serovars showed that ten genes are highly conserved. However three of them are pseudogenes in S. Typhi. Our aim was to understand what functions are lost in S. Typhi due to pseudogenes by constructing a S. Typhi genetic hybrid carrying the SPI-3 region of S. Typhimurium instead of its own SPI-3. We observed that under stressful conditions the hybrid strain showed a clear impairment in resistance to hydrogen peroxide and decreased survival within U937 culture monocytes. We hypothesized that the marT-fidL operon, encoded in SPI-3, was responsible for the new phenotypes because marT is a pseudogen in S. Typhi and has a demonstrated role as a transcriptional regulator in S. Typhimurium. Therefore we cloned and transferred the S. Typhimurium marT-fidL operon into S. Typhi and confirmed that invasion of monocytes was dramatically decreased. Finally, our findings suggest that the genomic and functional differences between SPI-3 sequences have implications in the host specificity of Typhi and Typhimurium serovars.
Adaptive Framework for Load Balancing to Improve the Performance of Cloud Environment

Cloud computing is offering on demand services by providing virtualize and storage environment. Due to the sharing of resources in cloud, there is a chance of resource wastage which creates need for load balancing. To address this problem, this work proposes an adaptive solution which enhances the performance of the distributed systems and provides scalability desired in internet based computing environments. The proposed algorithm has been implemented and compared with the results of existing mechanisms and results of our proposed mechanism has been found promising.
SPIDER: Fault resilient SDN pipeline with recovery delay guarantees

When dealing with node or link failures in Software Defined Networking (SDN), the network capability to establish an alternative path depends on controller reachability and on the round trip times (RTTs) between controller and involved switches. Moreover, current SDN data plane abstractions for failure detection (e.g. OpenFlow “Fast-failover”) do not allow programmers to tweak switches' detection mechanism, thus leaving SDN operators still relying on proprietary management interfaces (when available) to achieve guaranteed detection and recovery delays. We propose SPIDER, an OpenFlow-like pipeline design that provides i) a detection mechanism based on switches' periodic link probing and ii) fast reroute of traffic flows even in case of distant failures, regardless of controller availability. SPIDER can be implemented using stateful data plane abstractions such as OpenState or Open vSwitch, and it offers guaranteed short (i.e. ms) failure detection and recovery delays, with a configurable trade off between overhead and failover responsiveness. We present here the SPIDER pipeline design, behavioral model, and analysis on flow tables' memory impact. We also implemented and experimentally validated SPIDER using OpenState (an OpenFlow 1.3 extension for stateful packet processing), showing numerical results on its performance in terms of recovery latency and packet losses.
Program insertion in real-time IP multicasts

We describe the design, implementation and operation of a prototype system which seamlessly mixes real-time audio and video streams originating from multiple, physically separated sources. Mixing is entirely decentralized, relying on new protocols to coordinate transfer of session control between IP multicast sources. The system is motivated by the desire to perform dynamic insertion of advertisements in active, real-time multimedia sessions. It permits content providers and viewers a far richer collection of relationships, opportunities, and features than possible with traditional broadcast media. Novel system features include 1) spontaneous meetings and business relationships between content providers, 2) program insertions from arbitrary locations on a multicast tree, 3) operation with no modifications to existing software players, 4) audience demographics from Real Time Control Protocol messages, and 5) mechanisms to allow users to select between multiple, simultaneous program transmissions. Additional system applications range from support of emergency broadcasts to the creation of novel virtual broadcasting networks.