Miracle-dz/UniFAR-FTUs huggingface dataset:
The Borgs, a New Family of Cdc42 and TC10 GTPase-Interacting Proteins

ABSTRACT The Rho family of GTPases plays key roles in the regulation of cell motility and morphogenesis. They also regulate protein kinase cascades, gene expression, and cell cycle progression. This multiplicity of roles requires that the Rho GTPases interact with a wide variety of downstream effector proteins. An understanding of their functions at a molecular level therefore requires the identification of the entire set of such effectors. Towards this end, we performed a two-hybrid screen using the TC10 GTPase as bait and identified a family of putative effector proteins related to MSE55, a murine stromal and epithelial cell protein of 55 kDa. We have named this family the Borg (binder of Rho GTPases) proteins. Complete open reading frames have been obtained for Borg1 through Borg3. We renamed MSE55 as Borg5. Borg1, Borg2, Borg4, and Borg5 bind both TC10 and Cdc42 in a GTP-dependent manner. Surprisingly, Borg3 bound only to Cdc42. An intact CRIB (Cdc42, Rac interactive binding) domain was required for binding. No interaction of the Borgs with Rac1 or RhoA was detectable. Three-hemagglutinin epitope (HA3)-tagged Borg3 protein was mostly cytosolic when expressed ectopically in NIH 3T3 cells, with some accumulation in membrane ruffles. The phenotype induced by Borg3 was reminiscent of that caused by an inhibition of Rho function and was reversed by overexpression of Rho. Surprisingly, it was independent of the ability to bind Cdc42. Borg3 also inhibited Jun kinase activity by a mechanism that was independent of Cdc42 binding. HA3-Borg3 expression caused substantial delays in the spreading of cells on fibronectin surfaces after replating, and the spread cells lacked stress fibers. We propose that the Borg proteins function as negative regulators of Rho GTPase signaling.
Coached for the Classroom

Scholars typically view class socialization as an implicit process. This study instead shows how parents actively transmit class-based cultures to children and how these lessons reproduce inequalities. Through observations and interviews with children, parents, and teachers, I found that middle- and working-class parents expressed contrasting beliefs about appropriate classroom behavior, beliefs that shaped parents’ cultural coaching efforts. These efforts led children to activate class-based problem-solving strategies, which generated stratified profits at school. By showing how these processes vary along social class lines, this study reveals a key source of children’s class-based behaviors and highlights the efforts by which parents and children together reproduce inequalities.
Lexical relations: enhancing effectiveness of information retrieval systems

One of the essential features of the "Meaning <=> Text" model (MTM) developed by I. A. Mel'chuk et. al. is the special lexicon or ECD ('explanatory and combinatory' dictionary). This component can be thought of as a collection independent thesaurus, and can be applied to improve the effectiveness of an information retrieval system.After outlining the MTM and related work, this paper briefly describes the SMART type of information retrieval system. Applicability of the above-mentioned lexicon to such a system is discussed. In particular, the list of lexical relations included in the ECD is expanded and organized to be more effective for retrieval, partially along the lines suggested by Evens and Smith.Finally, an experimental analysis of the utility of lexical relations in an information retrieval system is discussed. It is shown that lexical relations generally enhance system performance. When all lexical relations are considered in the comparison, the resulting performance is shown, by statistical methods, to make a significant improvement (up to 16.5% at a single recall level); when all lexical relations except for antonyms are considered, the improvement is even greater (up to 20.2% at a single recall level).
A DDoS Attack Detection Method Based on Hybrid Heterogeneous Multiclassifier Ensemble Learning

The explosive growth of network traffic and its multitype on Internet have brought new and severe challenges to DDoS attack detection. To get the higher True Negative Rate (TNR), accuracy, and precision and to guarantee the robustness, stability, and universality of detection system, in this paper, we propose a DDoS attack detection method based on hybrid heterogeneous multiclassifier ensemble learning and design a heuristic detection algorithm based on Singular Value Decomposition (SVD) to construct our detection system. Experimental results show that our detection method is excellent in TNR, accuracy, and precision. Therefore, our algorithm has good detective performance for DDoS attack. Through the comparisons with Random Forest, -Nearest Neighbor (-NN), and Bagging comprising the component classifiers when the three algorithms are used alone by SVD and by un-SVD, it is shown that our model is superior to the state-of-the-art attack detection techniques in system generalization ability, detection stability, and overall detection performance.
National identity: A comparison of Sweden, Germany and Australia

Abstract This article compares three countries with different policy regimes in the area of citizenship and immigration, namely Australia, Germany and Sweden. Australia is here defined as multicultural, Germany as ‘ethnic’ and Sweden as semi‐multicultural. The aim is to see, first, if differences in policy regimes are reflected in the attitudes of national identity amongst the citizens, and second, to assess the effects different forms of national identity have on xenophobia. The conclusions are, first, that in spite of different policy regimes, national identity is constituted in similar ways in the three countries and, second, that the common subdivision of national identity into an ‘ethnic’ and a civic part may warrant reconsideration. Third, different types of national identity appear to affect xenophobia similarly in all the three countries under examination, namely in a way which supports the common assumption that civic identities are preferable to ethnic ones.
Alteplase at 0.6 mg/kg for Acute Ischemic Stroke Within 3 Hours of Onset: Japan Alteplase Clinical Trial (J-ACT)

Background and Purpose— Based on previous studies comparing different recombinant tissue plasminogen activator (rt-PA) doses, we performed a clinical trial with 0.6 mg/kg, which is lower than the internationally approved dosage of 0.9 mg/kg, aiming to assess the efficacy and safety of alteplase in acute ischemic stroke for the Japanese. Methods— Our prospective, multicenter, single-arm, open-label trial was designed with a target sample size of 100 patients. The primary end points were the proportion of patients with a modified Rankin Scale (mRS) score of 0 to 1 at 3 months and the incidence of symptomatic intracranial hemorrhage (sICH) within 36 hours. Thresholds for these end points were determined by calculating 90% CIs of weighted averages derived from published reports. The protocol was defined according to the National Institute of Neurological Disorders and Stroke (NINDS) rt-PA stroke study with slight modifications. Results— Among the 103 patients enrolled, 38 had an mRS of 0 to 1 at 3 months; this proportion (36.9%) exceeded the predetermined threshold of 33.9%. sICH within 36 hours occurred in 6 patients; this incidence (5.8%) was lower than the threshold of 9.6%. Conclusions— In patients receiving 0.6 mg/kg alteplase, the outcome and the incidence of sICH were comparable to published data for 0.9 mg/kg. These findings indicate that alteplase, when administered at 0.6 mg/kg to Japanese patients, might offer a clinical efficacy and safety that are compatible with data reported in North America and the European Union for a 0.9 mg/kg dose.
Combinatory Categorial Grammar

Combinatory Categorial Grammar is a generalization of classical Categorial Grammar that is at the least greater level of expressive power than context-free grammar that has yet been identified. The paper reviews its use for the explanatory analysis of natural language grammar, particularly with respect to bounded and unbounded constructions, multiple dependencies, relativization, and coordination.
A general framework integrating exploration, self-assembly and locomotion control for swarm robots

In this paper, we proposed a general control framework for the swarm robots with self-assembly in real environments. There are three tasks: exploration task, self-assembly task and locomotion task. At the start, the swarm robots explore the environment using their sensors and make decision to form some robotic structures to finish the task. Then the swarm robots execute the self-assembly task to construct the corresponding configuration. For the locomotion, a unified CPG controller model as well as unity configuration representation is combined to generate locomotive motions for robotic structure and improve self-adaptation according to any configuration. Based on Sambot simulation platform, we demonstrate simulation experiments that the swarm robots form different robotic structures to adapt to the different environments. Finally, the effectiveness and scalability of the framework are discussed.
A distinct trans-Golgi network subcompartment for sorting of synaptic and granule proteins in neurons and neuroendocrine cells

Golgi-to-plasma-membrane trafficking of synaptic-like microvesicle (SLMV) proteins, vesicular acetylcholine transporter (VAChT) and synaptophysin (SYN), and a large dense-core vesicle (LDCV) protein, chromogranin A (CgA), was investigated in undifferentiated neuroendocrine PC12 cells. Live cell imaging and 20°C block–release experiments showed that VAChT–GFP, SYN–GFP and CgA–RFP specifically and transiently cohabitated in a distinct sorting compartment during cold block and then separated into synaptic protein transport vesicles (SPTVs) and LDCVs, after release from temperature block. We found that in this trans-Golgi subcompartment there was colocalization of SPTV and LDCV proteins, most significantly with VAMP4 and Golgin97, and to some degree with TGN46, but not at all with TGN38. Moreover, some SNAP25 and VAMP2, two subunits of the exocytic machinery, were also recruited onto this compartment. Thus, in neuroendocrine cells, synaptic vesicle and LDCV proteins converge briefly in a distinct trans-Golgi network subcompartment before sorting into SPTVs and LDCVs, ultimately for delivery to the plasma membrane. This specialized sorting compartment from which SPTVs and LDCVs bud might facilitate the acquisition of common exocytic machinery needed on the membranes of these vesicles.
Effect of endocrine and paracrine factors on protein synthesis and cell proliferation in bovine hoof tissue culture

Laminitis is a major cause of lameness in dairy cattle, and is widely attributed to a defect in the horny tissue that gives the hoof its mechanical strength. Defective horn is associated with, and may be preceded by, impaired keratin deposition in the hoof epidermis. The cause of abnormal keratin deposition is not easily identified but, like epidermal keratinization in other tissues, is likely to be controlled by hormones and the paracrine action of locally produced growth factors. The hormonal regulation of keratin synthesis and cell proliferation in the bovine hoof was studied using tissue explants in organ culture. As the highest incidence of laminitis is in early lactation, the study focused on insulin, cortisol and prolactin, three hormones implicated in lactogenesis and galactopoiesis. Incubation of tissue explants for 24 h in medium containing insulin (10–5000 ng/ml) stimulated protein synthesis measured by incorporation of 35 S-labelled amino acids. Histochemical examination showed that insulin binding co-localized with the site of protein synthesis. Insulin also stimulated DNA synthesis, an index of cell proliferation, which was measured by incorporation of [3H]methyl thymidine. Cortisol (10–5000 ng/ml) decreased protein synthesis, whereas prolactin (10–5000 ng/ml) had no significant effect on protein or DNA synthesis. Epidermal growth factor (10–200 ng/ml), a potent inhibitor of keratinization in other tissues, stimulated protein synthesis compared with untreated controls. Epidermal growth factor binding was located microscopically to the germinal and differentiating epidermal layers. SDS-PAGE and fluorography showed that the population of proteins synthesized in the presence of any hormone or growth factor combination did not differ from that in untreated controls and included the keratins involved in horn deposition. The results show that bovine hoof keratinization is under endocrine and growth factor control, and suggest that systemic changes in lactogenic hormones may act to inhibit keratin deposition.
Energy efficient hybrid-powered communication systems using joint adaptive power allocation and energy exchange

The spread in the use of wireless services resulted in a remarkable growth of power consumption for telecommunication systems to satisfy the continuous growth of data demand. On the other hand, the emergence of smart grids and the expansion of low-cost distributed powering solutions represented an opportunity to enhance the energy efficiency and improve communication systems' costs. In this paper, we propose to enhance the energy efficiency of self-powered wireless networks by exploiting the possibility of energy exchange between different micro-grids. The objective is to exploit the flexibility and non homogeneity of communication services' demand to maximize the global utility. Cooperation between cells is exploited to exchange additional/needed power as function of their respective users' demands and energy availabilities. While taking into consideration the power losses due to this exchange, we propose an efficient approach to allocate the available resources across the different cells. Numerical simulations show the gains that can be achieved due to this approach as a function of the demand and energy availability variations.
Modeling and performance analysis of the VEGA grid system

In this paper, we propose four general queueing models based on input and server distributions, to analyze a special grid system, VEGA grid system version 1.1 (VEGA1.1). The mean queue lengths and mean waiting times of these models are deduced. The two classic applications, the computing-oriented application (blast computing) and online transaction processing application (air booking service) are employed to analyze and evaluate the grid system and the models. Meanwhile, we validate VEGA's four prominent characteristics, versatile services, enabling intelligence, global uniformity and autonomous control. Finally, we analyze the experiment results, predict the behavior of VEGA1.1 in equilibrium and point out the bottlenecks of the system
Hierarchical time-dependent shortest path algorithms for vehicle routing under ITS

ABSTRACT The development of efficient algorithms for vehicle routing on time-dependent networks is one of the major challenges in routing under intelligent transportation systems. Existing vehicle routing navigation systems, whether built-in or portable, lack the ability to rely on online servers. Such systems must compute the route in a stand-alone mode with limited hardware processing/memory capacity given an origin/destination pair and departure time. In this article, we propose a computationally efficient, yet effective, hierarchical algorithm to solve the time-dependent shortest path problem. Our proposed algorithm exploits community-based hierarchical representations of road networks, and it recursively reduces the search space in each level of the hierarchy by using our proposed search strategy algorithm. Our proposed algorithm is efficient in terms of finding shortest paths in milliseconds for large-scale road networks while eliminating the need to store preprocessed shortest paths, shortcuts, lower bounds, etc. We demonstrate the performance of the proposed algorithm using data from Detroit, New York, and San Francisco road networks.
Diverse Effects on Mitochondrial and Nuclear Functions Elicited by Drugs and Genetic Knockdowns in Bloodstream Stage Trypanosoma brucei

Background The options for treating the fatal disease human African trypanosomiasis are limited to a few drugs that are toxic or facing increasing resistance. New drugs that kill the causative agents, subspecies of Trypanosoma brucei, are therefore urgently needed. Little is known about the cellular mechanisms that lead to death of the pathogenic bloodstream stage. Methodology/Principal Findings We therefore conducted the first side by side comparison of the cellular effects of multiple death inducers that target different systems in bloodstream form parasites, including six drugs (pentamidine, prostaglandin D2, quercetin, etoposide, camptothecin, and a tetrahydroquinoline) and six RNAi knockdowns that target distinct cellular functions. All compounds tested were static at low concentrations and killed at high concentrations. Dead parasites were rapidly quantified by forward and side scatter during flow cytometry, as confirmed by ethidium homodimer and esterase staining, making these assays convenient for quantitating parasite death. The various treatments yielded different combinations of defects in mitochondrial potential, reactive oxygen species, cell cycle, and genome segregation. No evidence was seen for phosphatidylserine exposure, a marker of apoptosis. Reduction in ATP levels lagged behind decreases in live cell number. Even when the impact on growth was similar at 24 hours, drug-treated cells showed dramatic differences in their ability to further proliferate, demonstrating differences in the reversibility of effects induced by the diverse compounds. Conclusions/Significance Parasites showed different phenotypes depending on the treatment, but none of them were clear predictors of whether apparently live cells could go on to proliferate after drugs were removed. We therefore suggest that clonal proliferation assays may be a useful step in selecting anti-trypanosomal compounds for further development. Elucidating the genetic or biochemical events initiated by the compounds with the most profound effects on subsequent proliferation may identify new means to activate death pathways.
Elevated substitution rates estimated from ancient DNA sequences

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which are not directly accessible via modern DNA. They are particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing the difficult task of choosing independent calibration points. The substitution rates obtained from such datasets have typically been high, falling between the rates estimated from pedigrees and species phylogenies. Many of these estimates have been made using a Bayesian phylogenetic method that explicitly accommodates heterochronous data. Stimulated by recent criticism of this method, we present a comprehensive simulation study that validates its performance. For datasets of moderate size, it produces accurate estimates of rates, while appearing robust to assumptions about demographic history. We then analyse a large collection of 749 ancient and 727 modern DNA sequences from 19 species of animals, plants and bacteria. Our new estimates confirm that the substitution rates estimated from ancient DNA sequences are elevated above long-term phylogenetic levels.
Continuous Three-Dimensional Control of a Virtual Helicopter Using a Motor Imagery Based Brain-Computer Interface

Brain-computer interfaces (BCIs) allow a user to interact with a computer system using thought. However, only recently have devices capable of providing sophisticated multi-dimensional control been achieved non-invasively. A major goal for non-invasive BCI systems has been to provide continuous, intuitive, and accurate control, while retaining a high level of user autonomy. By employing electroencephalography (EEG) to record and decode sensorimotor rhythms (SMRs) induced from motor imaginations, a consistent, user-specific control signal may be characterized. Utilizing a novel method of interactive and continuous control, we trained three normal subjects to modulate their SMRs to achieve three-dimensional movement of a virtual helicopter that is fast, accurate, and continuous. In this system, the virtual helicopter's forward-backward translation and elevation controls were actuated through the modulation of sensorimotor rhythms that were converted to forces applied to the virtual helicopter at every simulation time step, and the helicopter's angle of left or right rotation was linearly mapped, with higher resolution, from sensorimotor rhythms associated with other motor imaginations. These different resolutions of control allow for interplay between general intent actuation and fine control as is seen in the gross and fine movements of the arm and hand. Subjects controlled the helicopter with the goal of flying through rings (targets) randomly positioned and oriented in a three-dimensional space. The subjects flew through rings continuously, acquiring as many as 11 consecutive rings within a five-minute period. In total, the study group successfully acquired over 85% of presented targets. These results affirm the effective, three-dimensional control of our motor imagery based BCI system, and suggest its potential applications in biological navigation, neuroprosthetics, and other applications.
Correcting Smartphone orientation for accelerometer-based analysis

A method was developed for rotating a Smartphone accelerometer coordinate system from an offset to a predetermined three-dimensional position to improve accelerometer-based activity identification. A quaternion-based rotation matrix was constructed from an axis-angle pair, produced via algebraic manipulations of the gravity acceleration components in the device's body-fixed frame of reference with the desired position of the vector. The rotation matrix is constructed during quiet standing and then applied to all subsequent accelerometer readings thereafter, transforming their values in this new fixed frame. This method provides a consistent accelerometer orientation between people, thereby reducing Smartphone orientation variability that can adversely affect activity classification algorithms.
Towards fast hardware memory integrity checking with skewed Merkle trees

Protection of a computer's memory's integrity is crucial in situations where physical attacks on the computer system are a threat. Such attacks can happen during physical break in into a data center or when a mobile device is lost or stolen. Since the memory modules can be easily removed or manipulated, the integrity of their contents cannot be trusted under threat of physical attacks. To counter this, hardware memory integrity checking schemes have been proposed, and realized in a number of security microprocessor architectures. At the core of these schemes is usually some form of a Merkle tree. All previous work on security architectures, however, uses full, balanced Merkle trees. In this paper, we propose a new solution to hardware memory integrity checking based on skewed Merkel trees. Because not all memory locations are accessed equally frequently in a modern computer system, a skewed Merkle three offers better performance as the frequently accessed memory locations can be located on the leaves of the skewed Merkle tree that have shorter path to the root -- thus fewer nodes of the tree have to be accessed during integrity checks. Skewed Merkle trees offer better system performance when considering realistic memory access patterns where some page are accessed more frequently than others, they do not impact caches as much as full Merkle trees, and they do not require more storage than full, balanced Merkle trees.