Miracle-dz/UniFAR-FTUs huggingface dataset:
First 100 ms of a long-lived magnetized neutron star formed in a binary neutron star merger

The recent multimessenger observation of the short gamma-ray burst (SGRB) GRB 170817A together with the gravitational wave (GW) event GW170817 provides evidence for the long-standing hypothesis associating SGRBs with binary neutron star (BNS) mergers. The nature of the remnant object powering the SGRB, which could have been either an accreting black hole (BH) or a long-lived magnetized neutron star (NS), is, however, still uncertain. General relativistic magnetohydrodynamic (GRMHD) simulations of the merger process represent a powerful tool to unravel the jet launching mechanism, but so far most simulations focused the attention on a BH as the central engine, while the long-lived NS scenario remains poorly investigated. Here, we explore the latter by performing a GRMHD BNS merger simulation extending up to ~100 ms after merger, much longer than any previous simulation of this kind. This allows us to (i) study the emerging structure and amplification of the magnetic field and observe a clear saturation at magnetic energy $E_\mathrm{mag} \sim 10^{51}$ erg, (ii) follow the magnetically supported expansion of the outer layers of the remnant NS and its evolution into an ellipsoidal shape without any surrounding torus, and (iii) monitor density, magnetization, and velocity along the axis, observing no signs of jet formation. We also argue that the conditions at the end of the simulation disfavor later jet formation on subsecond timescales if no BH is formed. Furthermore, we examine the rotation profile of the remnant, the conversion of rotational energy associated with differential rotation, the overall energy budget of the system, and the evolution of the GW frequency spectrum. Finally, we perform an additional simulation where we induce the collapse to a BH ~70 ms after merger, in order to gain insights on the prospects for massive accretion tori in case of a late collapse. We find that.
A Novel Routing Scheme for Creating Opportunistic Context-Virtual Networks in IoT Scenarios †

The massive amount of traffic required by the emerging Internet of Things (IoT) paradigm can be supported by the imminent arrival of 5G next-generation networks. However, the limited capacity of resources in IoT nodes, e.g., battery lifetime or buffer space, opens a challenge to be taken into account when proposing new routing solutions on IoT scenarios with intermittent connectivity. In this paper, we propose the concept of Opportunistic Context-Virtual Networks (OCVNs). The novelty of this approach is to create virtual groups of nodes that share interests in common for routing purposes. Therefore, only the nodes that are interested in the content of the messages that are flowing throughout the network are used as relaying nodes, providing their own resources for the sake of the communication. By leveraging the use of store-carry-and-forward mechanisms, a novel routing algorithm is proposed and evaluated over two realistic scenarios. Experimental results reveal that our solution outperforms other well-known opportunistic routing algorithms in terms of delivery probability and overhead ratio, while resource usage of relaying nodes is significantly reduced.
Deficits in Quadriceps Force Control After Anterior Cruciate Ligament Injury: Potential Central Mechanisms.

CONTEXT Poor quadriceps force control has been observed after anterior cruciate ligament (ACL) reconstruction but has not been examined after ACL injury. Whether adaptations within the central nervous system are contributing to these impairments is unknown. OBJECTIVE To examine quadriceps force control in individuals who had sustained a recent ACL injury and determine the associations between cortical excitability and quadriceps force control in these individuals. DESIGN Cross-sectional study. SETTING Research laboratory. PATIENTS OR OTHER PARTICIPANTS Eighteen individuals with a recent unilateral ACL injury (6 women, 12 men; age = 29.6 ± 8.4 years, height = 1.74 ± 0.07 m, mass = 76.0 ± 10.4 kg, time postinjury = 69.5 ± 42.5 days) and 18 uninjured individuals (6 women, 12 men; age = 29.2 ± 6.8 years, height = 1.79 ± 0.07 m, mass = 79.0 ± 8.4 kg) serving as controls participated. MAIN OUTCOME MEASURE(S) Quadriceps force control was quantified as the root mean square error between the quadriceps force and target force during a cyclical force-matching task. Cortical excitability was measured as the active motor threshold and cortical silent period. Outcome measures were determined bilaterally in a single testing session. Group and limb differences in quadriceps force control were assessed using mixed analyses of variance (2 × 2). Pearson product moment correlations were performed between quadriceps force control and cortical excitability in individuals with an ACL injury. RESULTS Individuals with an ACL injury exhibited greater total force-matching error with their involved (standardized mean difference [SMD] = 0.8) and uninvolved (SMD = 0.9) limbs than did controls (F1,27 = 11.347, P = .03). During the period of descending force, individuals with an ACL injury demonstrated greater error using their involved (SMD = 0.8) and uninvolved (SMD = 0.8) limbs than uninjured individuals (F1,27 = 4.941, P = .04). Greater force-matching error was not associated with any cortical excitability measures (P > .05). CONCLUSIONS Quadriceps force control was impaired bilaterally after recent ACL injury but was not associated with selected measures of cortical excitability. The findings highlight a need to incorporate submaximal-force control tasks into rehabilitation and "prehabilitation," as the deficits were present before surgery.
A Flexible Framework for Parallel Multi-Dimensional DFTs

Multi-dimensional discrete Fourier transforms (DFT) are typically decomposed into multiple 1D transforms. Hence, parallel implementations of any multi-dimensional DFT focus on parallelizing within or across the 1D DFT. Existing DFT packages exploit the inherent parallelism across the 1D DFTs and offer rigid frameworks, that cannot be extended to incorporate both forms of parallelism and various data layouts to enable some of the parallelism. However, in the era of exascale, where systems have thousand of nodes and intricate network topologies, flexibility and parallel efficiency are key aspects all multi-dimensional DFT frameworks need to have in order to map and scale the computation appropriately. In this work, we present a flexible framework, built on the Redistribution Operations and Tensor Expressions (ROTE) framework, that facilitates the development of a family of parallel multi-dimensional DFT algorithms by 1) unifying the two parallelization schemes within a single framework, 2) exploiting the two different parallelization schemes to different degrees and 3) using different data layouts to distribute the data across the compute nodes. We demonstrate the need of a versatile framework and thus a need for a family of parallel multi-dimensional DFT algorithms on the K-Computer, where we show almost linear strong scaling results for problem sizes of 1024^3 on 32k compute nodes.
Twenty-Five Years of Structural Parvovirology

Parvoviruses, infecting vertebrates and invertebrates, are a family of single-stranded DNA viruses with small, non-enveloped capsids with T = 1 icosahedral symmetry. A quarter of a century after the first parvovirus capsid structure was published, approximately 100 additional structures have been analyzed. This first structure was that of Canine Parvovirus, and it initiated the practice of structure-to-function correlation for the family. Despite high diversity in the capsid viral protein (VP) sequence, the structural topologies of all parvoviral capsids are conserved. However, surface loops inserted between the core secondary structure elements vary in conformation that enables the assembly of unique capsid surface morphologies within individual genera. These variations enable each virus to establish host niches by allowing host receptor attachment, specific tissue tropism, and antigenic diversity. This review focuses on the diversity among the parvoviruses with respect to the transcriptional strategy of the encoded VPs, the advances in capsid structure-function annotation, and therapeutic developments facilitated by the available structures.
Acute Effect of Drop-Set, Traditional, and Pyramidal Systems in Resistance Training on Neuromuscular Performance in Trained Adults.

Costa, BDV, Ferreira, MEC, Gantois, P, Kassiano, W, Paes, ST, de Lima-Júnior, D, Cyrino, ES, and Fortes, LS. Acute effect of drop-set, traditional, and pyramidal systems in resistance training on neuromuscular performance in trained adults. J Strength Cond Res XX(X): 000-000, 2019-The aim of this study was to analyze the acute effects of resistance training (RT) systems on lower- and upper-limb performance in trained adults. Eighteen male young adults with experience in RT aged from 18 to 26 years underwent the 3 experimental conditions (drop-set [DS], decrescent pyramid [DP], and traditional [TR]). The participants performed 2 exercises (bench press and leg press 45°). In the DS condition, they underwent 2 sets of 10 repetitions at 12RM, followed by 5 additional repetitions with an intensity of 15RM with 6-minute interval rest between sets. In the DP, it was performed 3 sets of 10 repetitions at 10RM, 12RM, and 15RM, respectively, and the rest interval was 3 minutes between sets. In the TR, the participants performed 3 sets of 10 repetitions at 12RM with 3 minutes of rest between sets. Countermovement jump, peak power (Wpeak), and force (Fpeak) in the bench press were evaluated in the baseline, before, and 30 minutes after the experimental sessions. Countermovement jump performance decreased significantly only after the DS and DP conditions (-6.7 and -1.9%, respectively). The groups were significantly different in the post-intervention; the DS condition presented lower values when compared with the DP (p = 0.01) and TR (p = 0.001). According to Fpeak and Wpeak, only DS condition significantly decreased the performance (-3.8 and -4.1%, respectively). The results indicate the DS and DP conditions impair the neuromuscular performance of the lower limbs, whereas for upper limbs, only DS condition negatively affect upper-limb performance.
Discovery of an RmlC/D fusion protein in the microalga Prymnesium parvum and its implications for NDP-β-l-rhamnose biosynthesis in microalgae

The 6-deoxy sugar l-rhamnose (l-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host–pathogen interactions often means that l-Rha plays an essential role in many organisms. l-Rha is most commonly biosynthesized as the activated sugar nucleotide uridine 5′-diphospho-β-l-rhamnose (UDP-β-l-Rha) or thymidine 5′-diphospho-β-l-rhamnose (TDP-β-l-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of l-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated l-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-β-l-Rha biosynthesis, from P. parvum. Using this new sequence and also others, we explored l-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like l-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate β-l-Rha (NDP-β-l-Rha) pathways among algae.
Sequence capture across large phylogenetic scales by using pooled PCR‐generated baits: A case study of Lepidoptera

Sequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR‐generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein‐coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well‐resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade‐representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection.
IGF1R as druggable target mediating PI3K-δ inhibitor resistance in a murine model of chronic lymphocytic leukemia.

Targeted therapy is currently revolutionizing the treatment of cancers, but resistance evolves against these therapies and derogates their success. The PI3K-δ inhibitor idelalisib has been approved for CLL and NHL treatment, but the mechanisms conferring resistance in a subset of patients are unknown. Here, we modelled resistance to PI3K-δ inhibitor in vivo using a serial tumor transfer and treatment scheme in mice. Whole exome sequencing identified no recurrent mutation explaining resistance to PI3K-δ inhibitor. In the murine model resistance to PI3K-δ inhibitor occurred due to a signalling switch mediated by consistent and functionally relevant activation of Insulin-like growth factor 1 receptor (IGF1R), resulting in enhanced MAPK signalling in the resistant tumors. Overexpression of IGF1R in vitro demonstrated its prominent role in PI3K-δ inhibitor resistance. IGF1R upregulation in PI3K-δ inhibitor resistant tumors was mediated by functional activation and enhanced nuclear localization of forkhead box protein O1 (FOXO1) transcription factors and glycogen synthase kinase 3 beta (GSK3B). In human CLL, high IGF1R expression was associated with trisomy-12. CLL cells from an idelalisib treated patient showed decreased sensitivity to idelalisib in vitro concomitant with enhanced MAPK signalling and strong upregulation of IGF1R upon idelalisib exposure. Our results thus highlight that alternative signalling cascades are playing a predominant role in the resistance and survival of cancer cells under PI3K-δ inhibition. We also demonstrate that these pathway alterations can serve as therapeutic targets, as inhibition of IGF1R offered efficacious salvage treatment for PI3K-δ inhibitor resistant tumors in vitro and in vivo.
Comparison of optical projection tomography and light‐sheet fluorescence microscopy

We present a numerical analysis and experimental characterisation of spatial resolution in optical projection tomography (OPT) and light‐sheet fluorescence microscopy (LSFM) using their ‘standard’ systems. Although both techniques provide spatial resolution at the micrometre scale for mesoscopic (millimetre to centimetre) samples, LSFM provides higher lateral (∼3 μm, ∼34% of OPT) but lower axial (∼25.8 μm, 295% of OPT) resolution as compared to OPT (∼8.75 μm, 100%) when imaging the same sample (∼2 mm). Moreover, OPT provides isotropic spatial resolution due to its rotational scanning which may reduce the ambiguity in 3D analysis, so it is more practically appropriate for relatively large samples. We also demonstrate the application performances of both techniques by imaging various biological tissues, illustrating their imaging ability at different spatial scales.
Conformal prediction of HDAC inhibitors

ABSTRACT The growing interest in epigenetic probes and drug discovery, as revealed by several epigenetic drugs in clinical use or in the lineup of the drug development pipeline, is boosting the generation of screening data. In order to maximize the use of structure–activity relationships there is a clear need to develop robust and accurate models to understand the underlying structure–activity relationship. Similarly, accurate models should be able to guide the rational screening of compound libraries. Herein we introduce a novel approach for epigenetic quantitative structure–activity relationship (QSAR) modelling using conformal prediction. As a case study, we discuss the development of models for 11 sets of inhibitors of histone deacetylases (HDACs), which are one of the major epigenetic target families that have been screened. It was found that all derived models, for every HDAC endpoint and all three significance levels, are valid with respect to predictions for the external test sets as well as the internal validation of the corresponding training sets. Furthermore, the efficiencies for the predictions are above 80% for most data sets and above 90% for four data sets at different significant levels. The findings of this work encourage prospective applications of conformal prediction for other epigenetic target data sets.
Pole placement control of a ball and beam system a graphical user interface (GUI) approach

The ball and beam (B&B) system is widely used as a laboratory equipment to study control systems engineering since it represents one of the most easy to understand and important system. In this work, a step by step Lagrangian model for the B&B system has been obtained. Afterward, a pole placement controller has been designed for trajectory tracking and disturbance rejection purpose. The derived model and the controller has been demonstrated in Simulink environment. The paper also investigates the controller robustness in the existence of sensor noise and external disturbances. For the purpose of better understanding of the relationship between the set of placed poles, the system response plot and the physical system behavior, a visualized model for the B&B system has been built using Matlab graphical user interface (GUI) platform. The GUI platform present a helpful tool in understanding the ball and beam system mechanical behavior with different placed poles' positions. It will also minify the need for an actual B&B laboratory experimental set.
Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

The concept of information has emerged as a language in its own right, bridging several disciplines that analyze natural phenomena and man-made systems. Integrated information has been introduced as a metric to quantify the amount of information generated by a system beyond the information generated by its elements. Yet, this intriguing notion comes with the price of being prohibitively expensive to calculate, since the calculations require an exponential number of sub-divisions of a system. Here we introduce a novel framework to connect algorithmic randomness and integrated information and a numerical method for estimating integrated information using a perturbation test rooted in algorithmic information dynamics. This method quantifies the change in program size of a system when subjected to a perturbation. The intuition behind is that if an object is random then random perturbations have little to no effect to what happens when a shorter program but when an object has the ability to move in both directions (towards or away from randomness) it will be shown to be better integrated as a measure of sophistication telling apart randomness and simplicity from structure. We show that an object with a high integrated information value is also more compressible, and is, therefore, more sensitive to perturbations. We find that such a perturbation test quantifying compression sensitivity provides a system with a means to extract explanations--causal accounts--of its own behaviour. Our technique can reduce the number of calculations to arrive at some bounds or estimations, as the algorithmic perturbation test guides an efficient search for estimating integrated information. Our work sets the stage for a systematic exploration of connections between algorithmic complexity and integrated information at the level of both theory and practice.
Some Functional Properties of khambir, an Ethnic Fermented Cereal-Based Food of Western Himalayas

Traditional leavened wheat-based flat bread khambir is a staple food for the high-altitude people of the Western Himalayan region. The health promoting abilities of two types of khambir, yeast added khambir (YAK) and buttermilk added khambir (BAK), were evaluated. A group of microbes like yeast, mold, lactic acid bacteria (LAB), and Bifidobacterium sp. were abundant in both khambir but in varied proportions. Both are enriched with phenolics and flavonoids. The aqueous extracts of both breads strongly inhibited the growth of enteropathogens. Molecular docking experiments showed that phenolic acid, particularly p-coumaric acid, blocked the active sites of β-glucosidase and acetylcholine esterase (AChE), thereby inhibiting their activities. YAK and BAK showed antiradical and antioxidant activity ranging from 46 to 67% evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), and ferric reducing/antioxidant power (FRAP) assays. The aqueous extract of both khambir samples protected the arsenic toxicity when examined under an in situ rat intestinal loop model study. The arsenic induced elevated levels of superoxide dismutase (SOD), catalase (CAT), reduced glutathione, lipid peroxidation (LPO) and DNA fragmentation, and transmembrane mitochondrial potential was alleviated by khambir extract. These results scientifically supported its age-old health benefit claims by the consumer at high altitude and there are enough potentialities to explore khambir as a medicinal food for human welfare.
Feel Safe to Take More Risks? Insecure Attachment Increases Consumer Risk-Taking Behavior

Attachment styles, originated from early childhood experience, have been documented to influence human behaviors among adults. Drawing on life history theory, we examined whether or not, and how, attachment styles impact risk-taking behaviors beyond evolutionary valid domains, and explored the moderation role of parental status. In the consumer behavior context, three correlational studies provide convergent evidence that insecurely attached (vs. securely attached) consumers are more risk-taking in consumption situations like dining in a toilet-themed restaurant or buying genetically modified products. Specifically, insecurely attached consumers were more likely to take risks in two experiential purchase scenarios (Study 1) and this effect was not domain-specific (Study 2). In Study 3, we showed that safety perception mediated the relationship between attachment insecurity and risk-taking, which was manifested by purchase intentions toward genetically modified products. Specifically, insecurely attached individuals perceived genetically modified products to be safer and were more willing to make a purchase. Additionally, parental status moderates the relationship (Studies 2 and 3). We conclude with a discussion on the implications of attachment theory on consumer risk-taking behaviors from a life history perspective.