Miracle-dz/UniFAR-FTUs huggingface dataset:
Deferred Start: A Non-Work-Conserving Model for P-FRP Fixed Priority Task Scheduling

In real-time systems, FRP (Functional Reactive Programming) is playing and potentially going to play a more important role. Priority-based (preemptive) FRP (P-FRP), a variant of FRP with more real-time characteristics, demands more research in its scheduling and timing analysis. Its abort-and-restart nature indicates that reducing preemptions can be critical for improving system performance. In this paper, we present a non-work conserving scheduling model, Deferred Start, to reduce certain preemptions. Experiments show the improvement on schedulability and task response time.
REVERT: Runtime Verification for Real-Time Systems

Real-time systems are becoming more complex and open, thus increasing their development and verification costs. Although several static verification tools have been proposed over the last decades, they suffer from scalability and precision problems. As a result, the tools fail to cover all the necessary safety properties for realistic real-time applications involving a large number of components and tasks. Runtime verification (RV) is a formal technique that verifies properties during system execution with the support of monitors. The monitors are generated from formal languages using correct-by-construction generation methods. RV can thus be used as a complement or replacement for static verification approaches. The current state-of-the-art tools either do not have notion of time, or suffer from the potential blowup of states at run-time. In this paper, we propose REVERT, a framework developed with a focus on the verification of functional and non-functional properties with timing constraints. The contribution of this work is twofold: (i) a domain-specific specification language allowing the definition of requirements for real-time applications; (ii) a novel mechanism to generate monitors, with state-space and time guarantees, capable of identifying and reacting to timing properties defined with the proposed specification language.
Cyclic GMP-AMP Synthase Is an Innate Immune Sensor of HIV and Other Retroviruses

HIV Detection Is a (c)GAS Despite it being one of the most highly studied viruses, there are still many unknowns when it comes to HIV—including how it triggers the innate immune response. Gao et al. (p. 903, published 8 August) now demonstrate that the DNA sensor cyclic GMP-AMP synthase (cGAS) detects HIV infection. Reverse-transcribed HIV DNA triggers cGAS and downstream activation of antiviral immunity. Detection of HIV, as well as the retroviruses simian immunodeficiency virus and murine leukemia virus, was abrogated in mouse and human cells deficient in cGAS—suggesting that cGAS may be a critical activator of innate immunity in response to retroviral infection. Cell culture experiments suggest that detection of retroviral DNA activates cellular defense systems. Retroviruses, including HIV, can activate innate immune responses, but the host sensors for retroviruses are largely unknown. Here we show that HIV infection activates cyclic guanosine monophosphate–adenosine monophosphate (cGAMP) synthase (cGAS) to produce cGAMP, which binds to and activates the adaptor protein STING to induce type I interferons and other cytokines. Inhibitors of HIV reverse transcriptase, but not integrase, abrogated interferon-β induction by the virus, suggesting that the reverse-transcribed HIV DNA triggers the innate immune response. Knockout or knockdown of cGAS in mouse or human cell lines blocked cytokine induction by HIV, murine leukemia virus, and simian immunodeficiency virus. These results indicate that cGAS is an innate immune sensor of HIV and other retroviruses.
High-Performance Silicon Photoanodes Passivated with Ultrathin Nickel Films for Water Oxidation

Stabilizing Silicon Solar-driven water splitting has potential as an energy storage mechanism to supplement the direct conversion of sunlight to electricity. A submersed integrated device has been proposed both to absorb the light and to catalyze the reaction, but stability has been a problem. Kenney et al. (p. 836; see the Perspective by Turner) found that a nickel coating, thin enough to let light through, could protect a silicon absorber in the alkaline environment of a lithium/potassium borate electrolyte. The nickel also functioned as the oxidation catalyst, and the lithium ions helped to establish a protective film structure in situ. A nickel coating renders silicon stable in alkaline lithium borate electrolyte for solar water-splitting applications. [Also see Perspective by Turner] Silicon’s sensitivity to corrosion has hindered its use in photoanode applications. We found that deposition of a ~2-nanometer nickel film on n-type silicon (n-Si) with its native oxide affords a high-performance metal-insulator-semiconductor photoanode for photoelectrochemical (PEC) water oxidation in both aqueous potassium hydroxide (KOH, pH = 14) and aqueous borate buffer (pH = 9.5) solutions. The Ni film acted as a surface protection layer against corrosion and as a nonprecious metal electrocatalyst for oxygen evolution. In 1 M aqueous KOH, the Ni/n-Si photoanodes exhibited high PEC activity with a low onset potential (~1.07 volts versus reversible hydrogen electrode), high photocurrent density, and durability. The electrode showed no sign of decay after ~80 hours of continuous PEC water oxidation in a mixed lithium borate–potassium borate electrolyte. The high photovoltage was attributed to a high built-in potential in a metal-insulator-semiconductor–like device with an ultrathin, incomplete screening Ni/NiOx layer from the electrolyte.
Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells

Protecting Self-Replicating RNA? The potential for self-replication makes RNA an attractive candidate as a primordial catalysis in the origin of life. Catalysis may have occurred in some kind of compartment, possibly a fatty acid vesicle. However, RNA catalysis generally requires high levels of magnesium, which are incompatible with fatty acid vesicle integrity. Adamala and Szostak (p. 1098) screened magnesium chelators and found that several—including citrate, isocitrate, and oxalate—could maintain the membrane stability of fatty acid vesicles in the presence of Mg2+. Citrate also allowed Mg2+-dependent RNA synthesis within protocell-like vesicles, while at the same time protecting RNA from Mg2+-catalyzed degradation. Citrate can act as a partial magnesium chelator to facilitate the synthesis of RNA within a protocell-like vesicle. Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg2+ on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg2+ ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg2+-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles, which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides.
RNA Interference Functions as an Antiviral Immunity Mechanism in Mammals

Viral Defenses In plants and invertebrates, RNA interference (RNAi) functions as an innate antiviral defense mechanism. Viruses that infect plants and invertebrates have evolved viral suppressors of RNAi (VSRs) that disable the RNAi pathway. Whether mammals use RNAi as a defense against viruses has been less clear (see the Perspective by Sagan and Sarnow). Li et al. (p. 231) and Maillard et al. (p. 235) studied mammalian cell lines and baby mice productively infected with RNA viruses and observed the production of virus-derived small RNAs (vsRNAs). When the putative VSR proteins of the infecting viruses were disabled, host RNAi-derived vsRNAs were much increased and the viruses were rapidly cleared and unable to mount a full-blown infection. Thus, RNAi also has an innate antiviral function in mammals. Certain mammalian cells can use RNA interference in the innate defense against invading viruses. [Also see Perspective by Sagan and Sarnow] Diverse eukaryotic hosts produce virus-derived small interfering RNAs (siRNAs) to direct antiviral immunity by RNA interference (RNAi). However, it remains unknown whether the mammalian RNAi pathway has a natural antiviral function. Here, we show that infection of hamster cells and suckling mice by Nodamura virus (NoV), a mosquito-transmissible RNA virus, requires RNAi suppression by its B2 protein. Loss of B2 expression or its suppressor activity leads to abundant production of viral siRNAs and rapid clearance of the mutant viruses in mice. However, viral small RNAs detected during virulent infection by NoV do not have the properties of canonical siRNAs. These findings have parallels with the induction and suppression of antiviral RNAi by the related Flock house virus in fruit flies and nematodes and reveal a mammalian antiviral immunity mechanism mediated by RNAi.
A Homozygous Deletion in GRID2 Causes a Human Phenotype With Cerebellar Ataxia and Atrophy

GRID2 is a member of the ionotropic glutamate receptor family of excitatory neurotransmitter receptors. GRID2 encodes the glutamate receptor subunit delta-2, selectively expressed in cerebellar Purkinje cells. The phenotype associated with loss of GRID2 function was described only in mice until now, characterized by different degrees of cerebellar ataxia and usually relatively mild abnormalities of the cerebellum. This work describes for the first time the human phenotype associated with homozygous partial deletion of GRID2 in 3 children in one large consanguineous Turkish family. Homozygous deletion of exons 3 and 4 of GRID2 (94 153 589-94 298 037 bp) in the proband and similarly affected cousins, and heterozygous deletions in parental DNA were shown using Affymetrix® 6.0 single-nucleotide polymorphism array, confirmed by real-time polymerase chain reaction. The phenotype includes nystagmus, hypotonia with marked developmental delay in gross motor skills in early infancy followed by a static encephalopathy course with development of cerebellar ataxia, oculomotor apraxia, and pyramidal tract involvement.
Evolutionary motion inverse kinematics

In disciplines, such as robotics and computer graphics (CG) or industries such as, game development, various tasks involve the manipulation of articulated structures in interesting and complex ways. This may involve controlling robotic manipulators or perhaps posing the skeleton of a virtual human. When performed manually, the task of rotating each individual joint in order to produce a desired pose can be tedious and time consuming. The process of rotating each joint independently is known as forward kinematics (FK). One way to simplify this process is to automatically calculate the angles required for a given joint (known as the end-effector) to reach a goal position - this process is known as inverse kinematics (IK). In this paper an evolutionary algorithm (EA) is proposed as a solution to inverse kinematics. Several extensions are also proposed to allow extra constraints to be included, such as obstacle avoidance and angular joint limits. This approach is called Evolutionary Motion IK (E-MOTION IK).
Functional Connectivity of Corticostriatal Circuitry and Psychosis-like Experiences in the General Community

Background Psychotic symptoms are proposed lie on a continuum, ranging from isolated psychosis-like experiences (PLEs) in non-clinical populations to frank disorder. Here, we investigate neurobiological correlates of this symptomatologic continuum by examining whether functional connectivity of dorsal corticostriatal circuitry, which is disrupted in patients and high-risk individuals, is associated with the severity of subclinical PLEs. Methods A community sample of 672 adults with no history of psychiatric or neurological illnesses completed a battery of seven questionnaires spanning various PLE domains. Principal component analysis (PCA) estimated major dimensions of PLEs from the questionnaires. PCA dimension scores were then correlated with whole-brain voxelwise functional connectivity (FC) maps of the striatum in a subset of 353 participants who completed a resting-state neuroimaging protocol. Results PCA identified two dimensions of PLEs accounting for 62.57% of variance in the measures, corresponding to positive and negative PLEs. Reduced FC between the dorsal striatum and prefrontal cortex correlated with higher positive PLEs. Negative PLEs correlated with increased FC between the dorsal striatum and visual and sensorimotor areas. In the ventral corticostriatal system, positive and negative PLEs were both associated with FC between the ventro-rostral putamen and sensorimotor cortices. Conclusions Consistent with past findings in patients and high-risk individuals, subthreshold positive symptomatology is associated with reduced FC of the dorsal circuit. These findings suggest that the connectivity of this circuit tracks the expression of psychotic phenomena across a broad spectrum of severity, extending from the subclinical domain to clinical diagnosis.
Retaining the lessons from past for better performance in a dynamic multiple task environment

Human beings learn to do a task and then go on to learn some other task. However, they do not forget the previous learning. If need arises, they can call upon their previous learning and do not have to relearn from scratch again. In this paper, we build upon our earlier work in which we presented a mechanism for learning multiple tasks in a dynamic environment where the tasks can change arbitrarily without any warning to the learning agents. The main feature of the mechanism is that a percentage of the learning agents is periodically made to reset its previous learning and restart learning again. Thus, there is always a sub-population which can learn the new task, whenever there is a task change, without being hampered by previous learning. The learning then spreads to the other members of the population also. In our current work we experiment with the incorporation of archive for preserving those strategies which have performed well. The strategies in the archive are tested time to time in the current environment. If the current task is the same as the task for which the strategy was first discovered, then that strategy rapidly comes in vogue for the whole population. The criteria by which strategies are selected for storage in the archive, the deletion of some strategies because the archive has limited space and the mechanism for selecting strategies for utilization in the current environment are presented.
The effect of social influence on agent specialization in small-world social networks

Specialization, or division of labour, leads to increased productivity in systems. We study the effect of social influence on the level of agent specialization in complex systems connected via social networks. There are several methods that explain the emergence of specialization, with the most prominent being the genetic threshold model. This model posits that agents possess an inherent threshold for task stimulus, and when that threshold is exceeded, the agent will perform that task. The idea of social influence is that an agent's choice of which task to specialize in when multiple ones are availabe, is influenced by the choices of its neighbours. Using the threshold model and an established metric that quantifies the level of agent specialization, we found that social influence leads to an increase in the division of labour.
Low Coseismic Friction on the Tohoku-Oki Fault Determined from Temperature Measurements

Deep Drilling for Earthquake Clues The 2011 Mw 9.0 Tohoku-Oki earthquake and tsunami were remarkable in many regards, including the rupturing of shallow trench sediments with huge associated slip (see the Perspective by Wang and Kinoshita). The Japan Trench Fast Drilling Project rapid response drilling expedition sought to sample and monitor the fault zone directly through a series of boreholes. Chester et al. (p. 1208) describe the structure and composition of the thin fault zone, which is predominately comprised of weak clay-rich sediments. Using these same fault-zone materials, Ujiie et al. (p. 1211) performed high-velocity frictional experiments to determine the physical controls on the large slip that occurred during the earthquake. Finally, Fulton et al. (p. 1214) measured in situ temperature anomalies across the fault zone for 9 months, establishing a baseline for frictional resistance and stress during and following the earthquake. The Tohoku-Oki earthquake occurred along a thin, clay-rich fault zone in the basal strata of the subducting plate. The frictional resistance on a fault during slip controls earthquake dynamics. Friction dissipates heat during an earthquake; therefore, the fault temperature after an earthquake provides insight into the level of friction. The Japan Trench Fast Drilling Project (Integrated Ocean Drilling Program Expedition 343 and 343T) installed a borehole temperature observatory 16 months after the March 2011 moment magnitude 9.0 Tohoku-Oki earthquake across the fault where slip was ~50 meters near the trench. After 9 months of operation, the complete sensor string was recovered. A 0.31°C temperature anomaly at the plate boundary fault corresponds to 27 megajoules per square meter of dissipated energy during the earthquake. The resulting apparent friction coefficient of 0.08 is considerably smaller than static values for most rocks.
Is removal of weak connections necessary for graph-theoretical analysis of dense weighted structural connectomes from diffusion MRI?

Recent advances in diffusion MRI tractography permit the generation of dense weighted structural connectomes that offer greater insight into brain organization. However, these efforts are hampered by the lack of consensus on how to extract topological measures from the resulting graphs. Here we evaluate the common practice of removing the graphs’ weak connections, which is primarily intended to eliminate spurious connections and emphasize strong connections. Because this processing step requires arbitrary or heuristic-based choices (e.g., setting a threshold level below which connections are removed), and such choices might complicate statistical analysis and inter-study comparisons, in this work we test whether removing weak connections is indeed necessary. To this end, we systematically evaluated the effect of removing weak connections on a range of popular graph-theoretical metrics. Specifically, we investigated if (and at what extent) removal of weak connections introduces a statistically significant difference between two otherwise equal groups of healthy subjects when only applied to one of the groups. Using data from the Human Connectome Project, we found that removal of weak connections had no statistical effect even when removing the weakest ~70-90% connections. Removing yet a larger extent of weak connections, thus reducing connectivity density even further, did produce a predictably significant effect. However, metric values became sensitive to the exact connectivity density, which has ramifications regarding the stability of the statistical analysis. This pattern persisted whether connections were removed by connection strength threshold or connectivity density, and for connectomes generated using parcellations at different resolutions. Finally, we showed that the same pattern also applies for data from a clinical-grade MRI scanner. In conclusion, our analysis revealed that removing weak connections is not necessary for graph-theoretical analysis of dense weighted connectomes. Because removal of weak connections provides no practical utility to offset the undesirable requirement for arbitrary or heuristic-based choices, we recommend that this step is avoided in future studies. Declarations of interest none.
Determination of chemo-responses for osteosarcoma using a hybrid evolutionary algorithm

In this paper, a hybrid evolutionary algorithm (HEA) based on the approaches of the evolutionary algorithm and a local search (LS) is proposed to determine the gene signatures for predicting histologic response of chemotherapy on osteosarcoma patients, which is one of the most common malignant bone tumor in children. The HEA consists of a population of individuals but the evolution of individuals is conducted by a LS, rather than the crossover and mutation used in the traditional evolutionary algorithms. The proposed HEA can simultaneously optimize the feature subset and the classifier through a common solution coding mechanism. Experimental results indicate that HEA can obtain more accurate signatures than the other existing approaches in determining chemoresponse for osteosarcoma.
A Code Refactoring Dataset and Its Assessment Regarding Software Maintainability

It is very common in various fields that there is a gap between theoretical results and their practical applications. This is true for code refactoring as well, which has a solid theoretical background while being used in development practice at the same time. However, more and more studies suggest that developers perform code refactoring entirely differently than the theory would suggest. Our paper encourages the further investigation of code refactorings in practice by providing an excessive open dataset of source code metrics and applied refactorings through several releases of 7 open-source systems. As a first step of processing this dataset, we examined the quality attributes of the refactored source code classes and the values of source code metrics improved by those refactorings. Our early results show that lower maintainability indeed triggers more code refactorings in practice and these refactorings significantly decrease complexity, code lines, coupling and clone metrics. However, we observed a decrease in comment related metrics in the refactored code.
Computerized Cognitive Testing in the Management of Youth Sports-Related Concussion

Computerized neurocognitive testing has become a growing practice across medical populations, but particularly within sports medicine and the management of sports-related concussion. Although traditional neuropsychological measures are solely administered and interpreted by neuropsychologists, computerized cognitive tests are marketed to and utilized by a wide range of professionals involved in the management of sports-related concussions, many of whom lack specialized psychometric training. Although the benefits of computerized testing allow for many youth athletes to be evaluated quickly, professionals implementing their use should be aware of the potential pitfalls and the high potential for misuse. After briefly reviewing the recommended guidelines set forth by the American Academy of Clinical Neuropsychology and the National Academy of Neuropsychology, we review the benefits/limitations of computerized testing in the management of sports-related concussion and the basic psychometric properties of some of the more widely used computerized measures. Lastly, we discuss the practical application of these devices.