Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Transcription and Splicing of T-Type Channels Are Evolutionarily-Conserved Strategies for Regulating Channel Expression and Gating

T-type calcium channels operate within tightly regulated biophysical constraints for supporting rhythmic firing in the brain, heart and secretory organs of invertebrates and vertebrates. The snail T-type gene, LCav3 from Lymnaea stagnalis, possesses alternative, tandem donor splice sites enabling a choice of a large exon 8b (201 aa) or a short exon 25c (9 aa) in cytoplasmic linkers, similar to mammalian homologs. Inclusion of optional 25c exons in the III–IV linker of T-type channels speeds up kinetics and causes hyperpolarizing shifts in both activation and steady-state inactivation of macroscopic currents. The abundant variant lacking exon 25c is the workhorse of embryonic Cav3 channels, whose high density and right-shifted activation and availability curves are expected to increase pace-making and allow the channels to contribute more significantly to cellular excitation in prenatal tissue. Presence of brain-enriched, optional exon 8b conserved with mammalian Cav3.1 and encompassing the proximal half of the I–II linker, imparts a ∼50% reduction in total and surface-expressed LCav3 channel protein, which accounts for reduced whole-cell calcium currents of +8b variants in HEK cells. Evolutionarily conserved optional exons in cytoplasmic linkers of Cav3 channels regulate expression (exon 8b) and a battery of biophysical properties (exon 25c) for tuning specialized firing patterns in different tissues and throughout development.
Structure and Function of the Hypertension Variant A486V of G Protein-coupled Receptor Kinase 4*

Background: GRK4 mediates GPCR phosphorylation and is implicated in hypertension. Results: The crystal structure of human GRK4α A486V is presented. Phosphorylation assays highlight kinetic differences between wild-type GRK4α and GRK4α A486V. Conclusion: GRK4α has unusual features that help explain the effects of GRK4 mutations and GRK4 biology. Significance: This work provides a structural basis for GRK4 function. G-protein-coupled receptor (GPCR) kinases (GRKs) bind to and phosphorylate GPCRs, initiating the process of GPCR desensitization and internalization. GRK4 is implicated in the regulation of blood pressure, and three GRK4 polymorphisms (R65L, A142V, and A486V) are associated with hypertension. Here, we describe the 2.6 Å structure of human GRK4α A486V crystallized in the presence of 5′-adenylyl β,γ-imidodiphosphate. The structure of GRK4α is similar to other GRKs, although slight differences exist within the RGS homology (RH) bundle subdomain, substrate-binding site, and kinase C-tail. The RH bundle subdomain and kinase C-terminal lobe form a strikingly acidic surface, whereas the kinase N-terminal lobe and RH terminal subdomain surfaces are much more basic. In this respect, GRK4α is more similar to GRK2 than GRK6. A fully ordered kinase C-tail reveals interactions linking the C-tail with important determinants of kinase activity, including the αB helix, αD helix, and the P-loop. Autophosphorylation of wild-type GRK4α is required for full kinase activity, as indicated by a lag in phosphorylation of a peptide from the dopamine D1 receptor without ATP preincubation. In contrast, this lag is not observed in GRK4α A486V. Phosphopeptide mapping by mass spectrometry indicates an increased rate of autophosphorylation of a number of residues in GRK4α A486V relative to wild-type GRK4α, including Ser-485 in the kinase C-tail.
The event-related potential data processing using ART 2 network

The event-related potentials (ERPs) obtained by stimulation are much weaker than the continuous electro-encephalographic (EEG) signal. Therefore, the correct signal analysis is vital to detect the stimulation-driven signal components. This paper proposes the combination of matching pursuit for feature extraction and ART 2 neural network for clustering. Then, clusters are filtered and interpreted according to their statistical properties as ERP components or noise. The suggested method can be used to filter the EEG/ERP signal. Furthermore, its results lead to a method that improves averaging when compared to traditional approaches.
Comparison of TiAl‐Based Intermetallics Joints Brazed with Amorphous and Crystalline Ti–Zr–Cu–Ni–Co–Mo Fillers

Ti–25.65Zr–13.3Cu–12.35Ni–3Co–2Mo (wt%) alloy in amorphous or crystalline state is used as filler to vacuum braze Ti–47Al–2Nb–2Cr–0.15B (at%). Comparisons of microstructure and performance of the amorphous and crystalline fillers as well as the joints brazed with them are investigated. The amorphous filler shows more uniform microstructure, better spreadability, and narrower melting temperature interval compared with the crystalline filler. The shear strength of the joint brazed with the amorphous filler in the temperature range of 925–1 050 °C is always much higher than that with the crystalline filler, and the maximum joint shear strength is 202 MPa at a brazing temperature of 1 000 °C. The differences in performance of the joints are related to the microstructure characteristics of the brazing seams.
Expression of a gene encoding a glycine-rich protein in petunia

We have investigated the expression of a gene that codes for a glycine-rich structural protein (GRP1) in petunia. This gene is expressed as a single polyadenylated RNA of approximately 1,600 bases which was found to be present in leaves, stems, and flowers of petunia but not in roots. In the organs in which GRP1-specific mRNA was expressed, its steady-state levels were highest in stems and leaves and lowest in flowers. This analysis also revealed that the pattern of organ-specific expression for several of the GRP1-related genes was distinctly different. In addition, it was found that the levels of GRP1 RNA were significantly higher in young leaves and stems than in old, implying developmental regulation of the gene. GRP1-specific RNA in both old and young tissue that had been wounded was found to be increased at least 25-fold over that in young unwounded tissue. Increased levels of GRP1 mRNA were seen within 5 min after wounding, with substantial increases apparent by 30 min. Maximal levels of accumulation of GRP1 transcripts occurred 90 min after wounding. The enhancement of GRP1 mRNA levels by wounding appears to be one of the earliest events of the plant wound response and is distinct from that which we observed for the PAL gene in petunia. Using S1 analysis and RNA primer extension, we demonstrated that the same transcriptional start site was used by the GRP1 gene in all organs and in wounded and unwounded tissue. The potential significance of these data with regard to wound signal transduction is discussed.
Range-Max Queries on Uncertain Data

Let P be a set of n uncertain points in Red, where each point pi ∈ P is associated with a real value vi and a probability αi ∈ (0,1] of existence, i.e., each pi exists with an independent probability αi. We present algorithms for building an index on P so that for a d-dimensional query rectangle ρ, the expected maximum value or the most-likely maximum value in ρ can be computed quickly. The specific contributions of our paper include the following: (i) The first index of sub-quadratic size to achieve a sub-linear query time in any dimension d ≥ 1. It also provides a trade-off between query time and size of the index. (ii) A conditional lower bound for the most-likely range-max queries, based on the conjectured hardness of the set-intersection problem, which suggests that in the worst case the product (query time)2 x (index size) is Ω((n2}/polylog(n)). (iii) A linear-size index for estimating the expected range-max value within approximation factor 1/2 in O(logc n) time, for some constant c > 0; that is, if the expected maximum value is μ then the query procedure returns a value μ' with μ/2 ≤ μ' ≤ μ. (iv) Extensions of our algorithm to more general uncertainty models and for computing the top-k values of the range-max.
Effects of pedunculopontine nucleus stimulation on human bladder function

The pedunculopontine nucleus (PPN) is a deep brain stimulation target for Parkinson's disease (PD). Unilateral PPN stimulation has been described in a previous case report to provoke urinary frequency, urgency and detrusor overactivity, due to probable activation of the pontine micturition center. Our aim was to evaluate the effect of bilateral PPN DBS on urodynamic parameters and to investigate the likely mechanisms using probabilistic tractography.
Safety, immunogenicity, pharmacokinetics, and efficacy of degradation of anti‐HLA antibodies by IdeS (imlifidase) in chronic kidney disease patients

Safety, immunogenicity, pharmacokinetics, and efficacy of the IgG‐degrading enzyme of Streptococcus pyogenes (IdeS [imlifidase]) were assessed in a single‐center, open‐label ascending‐dose study in highly sensitized patients with chronic kidney disease. Eight patients with cytotoxic PRAs (median cytotoxic PRAs of 64%) at enrollment received 1 or 2 intravenous infusions of IdeS on consecutive days (0.12 mg/kg body weight ×2 [n = 3]; 0.25 mg/kg ×1 [n = 3], or 0.25 mg/kg ×2 [n = 2]). IgG degradation was observed in all subjects after IdeS treatment, with <1% plasma IgG remaining within 48 hours and remaining low up to 7 days. Mean fluorescence intensity values of HLA class I and II reactivity were substantially reduced in all patients, and C1q binding to anti‐HLA was abolished. IdeS also cleaved the IgG‐type B cell receptor on CD19+ memory B cells. Anti‐IdeS antibodies developed 1 week after treatment, peaking at 2 weeks. A few hours after the second IdeS infusion, 1 patient received a deceased donor kidney offer. At enrollment, the patient had a positive serum crossmatch (HLA‐B7), detected by complement‐dependent cytotoxicity, flow cytometry, and multiplex bead assays. After IdeS infusion (0.12 mg/kg ×2) and when the HLA‐incompatible donor (HLA‐B7+) kidney was offered, the HLA antibody profile was negative. The kidney was transplanted successfully.
Focus and Shoot: Exploring Auto-Focus in RFID Tag Identification Towards a Specified Area

With the rapid proliferation of RFID technologies, RFID has been introduced into applications such as inventory and sampling inspection. Conventionally, in RFID systems, the reader usually identifies all the RFID tags in the interrogation region with the maximum power. However, some applications may only need to identify the tags in a specified area, which is usually smaller than the reader's default interrogation region. An example could be identifying the tags in a box, while ignoring the tags out of the box. In this paper, we respectively present two solutions to identify the tags in the specified area. The principle of the solutions can be compared to the picture-taking process of an auto-focus camera, which firstly focuses on the target automatically and then takes the picture. Similarly, our solutions first focus on the specified area and then shoot the tags. The design of the two solutions is based on the extensive empirical study on RFID tags. Realistic experiment results show that our solutions can reduce the execution time by 44 percent compared to the baseline solution, which identifies the tags with maximum power. Furthermore, we improve the proposed solutions to make them work well in more complex environments.
Short‐term phytotoxicity in Brassica napus (L.) in response to pre‐emergently applied metazachlor: A microcosm study

In accordance with realistic application approaches, a short‐term 1‐factorial experiment was set up to investigate the phytotoxic impact of pre‐emergent application of the chloroacetamide herbicide metazachlor on Brassica napus. In addition to morphological parameters, the underlying processes that ultimately determine the extent of herbicide‐induced phytotoxicity (i.e., herbicide metabolization and cellular antioxidant defense) were examined. The present study demonstrated that metazachlor provoked fasciation of the leaves closely after emergence, which might be linked to its mode of action whereby cell division is impaired through the inhibition of very long chain fatty acid synthesis. The increased activities of antioxidative enzymes and metabolites in leaf tissue indicated the presence of reactive oxygen species under the influence of metazachlor. This resulted in oxidative damage in the form of membrane lipid peroxidation. Simultaneously, the increased activity of glutathione S‐transferase and the shift in glutathione redox state suggested activation of the detoxification metabolism. This occurred, however, at the expense of growth, with a temporary reduction in plant height and weight after application. The results indicated that metazachlor disappeared within 3 mo to 4 mo after application, which resulted in the recovery of the crop. In conclusion, metazachlor induces phytotoxicity in the short term, either directly through its mode of action or indirectly through the induction of oxidative stress, which resulted in a temporary reduction in growth. Environ Toxicol Chem 2017;36:59–70. © 2016 SETAC
The greatwall kinase is dominant over PKA in controlling the antagonistic function of ARPP19 in Xenopus oocytes

ABSTRACT The small protein ARPP19 plays a dual role during oocyte meiosis resumption. In Xenopus, ARPP19 phosphorylation at S109 by PKA is necessary for maintaining oocytes arrested in prophase of the first meiotic division. Progesterone downregulates PKA, leading to the dephosphorylation of ARPP19 at S109. This initiates a transduction pathway ending with the activation of the universal inducer of M-phase, the kinase Cdk1. This last step depends on ARPP19 phosphorylation at S67 by the kinase Greatwall. Hence, phosphorylated by PKA at S109, ARPP19 restrains Cdk1 activation while when phosphorylated by Greatwall at S67, ARPP19 becomes an inducer of Cdk1 activation. Here, we investigate the functional interplay between S109 and S67-phosphorylations of ARPP19. We show that both PKA and Gwl phosphorylate ARPP19 independently of each other and that Cdk1 is not directly involved in regulating the biological activity of ARPP19. We also show that the phosphorylation of ARPP19 at S67 that activates Cdk1, is dominant over the inhibitory S109 phosphorylation. Therefore our results highlight the importance of timely synchronizing ARPP19 phosphorylations at S109 and S67 to fully activate Cdk1.
Engineering Resilient Collective Adaptive Systems by Self-Stabilisation

Collective adaptive systems are an emerging class of networked computational systems particularly suited for application domains such as smart cities, complex sensor networks, and the Internet of Things. These systems tend to feature large-scale, heterogeneity of communication model (including opportunistic peer-to-peer wireless interaction) and require inherent self-adaptiveness properties to address unforeseen changes in operating conditions. In this context, it is extremely difficult (if not seemingly intractable) to engineer reusable pieces of distributed behaviour to make them provably correct and smoothly composable. Building on the field calculus, a computational model (and associated toolchain) capturing the notion of aggregate network-level computation, we address this problem with an engineering methodology coupling formal theory and computer simulation. On the one hand, functional properties are addressed by identifying the largest-to-date field calculus fragment generating self-stabilising behaviour, guaranteed to eventually attain a correct and stable final state despite any transient perturbation in state or topology and including highly reusable building blocks for information spreading, aggregation, and time evolution. On the other hand, dynamical properties are addressed by simulation, empirically evaluating the different performances that can be obtained by switching between implementations of building blocks with provably equivalent functional properties. Overall, our methodology sheds light on how to identify core building blocks of collective behaviour and how to select implementations that improve system performance while leaving overall system function and resiliency properties unchanged.
The ART of brain expression

When trying to find a mate, one might think about using a dating app. Imagine that someone else has installed the same app and tries to access the same potential mates that you have chosen, and that this someone uses false facts about himself/herself to increase the chance of dating someone before you or anyone else with honest status information does. Sounds familiar? It actually is, and in no way is such comportment restricted to human courtship behaviour. Alternative reproductive tactics (ARTs) are widespread in the animal kingdom. In this issue of Molecular Ecology, Cardoso, Gonçalves, Goesmann, Canário, and Oliveira ( ) investigate plastic ARTs of the peacock blenny (Salaria pavo), in which males occur in three morphs: nestholders, sneakers and transitionals between the two former. They apply transcriptome sequencing to answer the question how brain gene expression contributes to sex role‐specific behaviour and to intersex phenotypes.
Perceptual grouping via untangling Gestalt principles

Gestalt principles, a set of conjoining rules derived from human visual studies, have been known to play an important role in computer vision. Many applications such as image segmentation, contour grouping and scene understanding often rely on such rules to work. However, the problem of Gestalt confliction, i.e., the relative importance of each rule compared with another, remains unsolved. In this paper, we investigate the problem of perceptual grouping by quantifying the confliction among three commonly used rules: similarity, continuity and proximity. More specifically, we propose to quantify the importance of Gestalt rules by solving a learning to rank problem, and formulate a multi-label graph-cuts algorithm to group image primitives while taking into account the learned Gestalt confliction. Our experiment results confirm the existence of Gestalt confliction in perceptual grouping and demonstrate an improved performance when such a confliction is accounted for via the proposed grouping algorithm. Finally, a novel cross domain image classification method is proposed by exploiting perceptual grouping as representation.
Feedback from human posterior parietal cortex enables visuospatial category representations as early as primary visual cortex

Categorization is a fundamental cognitive process, whereby the brain assigns meaning to sensory stimuli. Previous studies have found category representations in prefrontal cortex and posterior parietal cortex (PPC). However, these higher‐order areas lack the fine‐scale spatial representations of early sensory areas, and it remains unclear what mechanisms enable flexible categorization based on fine‐scale features.
- 1-A QUALITY MODEL FOR QUALITY ASSURANCE OF ROAD INFORMATION

For future ITS-applications and many other areas a pan-European road data infrastructure of high quality is necessary. The EU-project EuroRoadS (Pan-European Road Data Solution) will lay the groundwork for the creation of such an infrastructure by national mapping agencies, road administrations, private enterprises and the research sector. The specific challenge regarding quality is to prepare a common model describing the quality assured data flow from acquisition and updating of the digital road map up to final application. This paper introduces a quality model of digital road maps for description of geographic data quality within acquisition and processing procedures. The quality model consists of a set of inherent quality characteristics and appropriate parameters, and is based on existing standards, like ISO 19100-series of ISO/TC211 and ISO 9000.
An Event Factuality Annotation Proposal for

Factuality information gives evidence on whether the events in texts have happened. This information can be relevant in natural language processing tasks such as timeline generation as it helps discriminating the events that are relevant to a certain timeline. We analysed some factuality annotation schemes and proposed a new scheme that aims at concise and easy annotation. We worked on a Basque corpus for the creation of the factuality annotation scheme as an additional layer to temporal information and we evaluated our annotation decisions through an inter-annotator agreement experiment.
Map-based localization in structured underwater environment using simulated hydrodynamic maps and an artificial lateral line

Flow sensing has recently gained attention of the robotics community, as it can complement the conventional sensing modalities of vision and sonar in underwater robotics. There is increasing literature in flow sensing for robotics focusing on performing tasks such as object detection and positioning, and robot's orientation estimation, most commonly under idealized laboratory conditions. In this paper, using recent advances and methodologies for bioinspired flow sensing, we propose a map-based localization technique that employs simulated hydrodynamic maps. The proposed conceptual idea could be an interesting complement to perform localization in those underwater environments with structural maps and a heterogeneous hydrodynamic, such as dams, harbour structures, fishways, caves, swers or any other drowned structure. To demonstrate its performance, computational fluid dynamic models are used to generate flow-speed maps of a structured underwater environment. Later, during off-line experiments, pressure data acquired using a flow sensing probe fitted on a Cartesian robot is transformed into speed information, and used inside a particle-filter to perform localization within the simulated flow-speed maps. The proposed technique has been tested using multiple scenarios with varying particle densities and motion command error levels. The results show filter convergence for all studied scenarios, inducing motion errors up to 0.20 m, suggesting that flow based information could be used to improve the navigation and localization abilities of underwater robots.
An OpenFlow-based performance-oriented multipath forwarding scheme in datacenters

Although dense interconnection datacenter networks (DCNs) (e.g., FatTree) provide multiple paths and high bisection bandwidth for each server pair, the widely used single-path Transmission Control Protocol (TCP) and equal-cost multipath (ECMP) transport protocols cannot achieve high resource utilization due to poor resource excavation and allocation. In this paper, we present LESSOR, a performance-oriented multipath forwarding scheme to improve DCNs’ resource utilization. By adopting an OpenFlow-based centralized control mechanism, LESSOR computes near-optimal transmission path and bandwidth provision for each flow according to the global network view while maintaining nearly real-time network view with the performance-oriented flow observing mechanism. Deployments and comprehensive simulations show that LESSOR can efficiently improve the network throughput, which is higher than ECMP by 4.9%–38.3% under different loads. LESSOR also provides 2%–27.7% improvement of throughput compared with Hedera. Besides, LESSOR decreases the average flow completion time significantly.