Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards an Open Data Set for Trace-Oriented Monitoring

Trace-oriented monitoring is one of the main methods for monitoring cloud systems. However, there is no free trace data set available, which hinders the development of trace-oriented monitoring. Therefore, we want to collect a trace data set in a real environment and make it free. During collection, many aspects are considered, including cluster sizes, user requests, workload speeds, injected faults, etc., to simulate different situations. The structure of this data set is well-designed. We believe that this data set will be helpful for the research of trace-oriented monitoring.
The 2016 Gyeongju earthquake sequence revisited: aftershock interactions within a complex fault system

Jeong-Ung Woo ,1 Junkee Rhie ,1 Seongryong Kim ,2 Tae-Seob Kang ,3 Kwang-Hee Kim4 and YoungHee Kim 1 1School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Korea. E-mail: rhie@snu.ac. kr 2Department of Geology and Earth Environmental Sciences, Chungnam National University, Daejeon 34134, Korea 3Department of Earth and Environmental Sciences, Pukyong National University, Busan 48513, Korea 4Department of Geological Sciences, Pusan National University, Busan 46241, Korea
Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals

Splice sites (SSs)—short nucleotide sequences flanking introns—are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.
Multiocular surveilance of wide dynamic environments based on optical vision, event modelling and end-to-end data encryption: A cloud-based monitoring approach of maritime activities

The success of contemporary surveillance systems depends on their cost and their ability to automatically and correctly interpret events that take place in an observed environment. Correct decisions enhance the situation awareness of an operator, while wrong ones lead to false or no alarms, damaging the system's credibility. In this paper a low-cost, secure, cloud-based surveillance system is described for monitoring wide dynamic environments. The focus of our current work is to present the system's overall architecture and discuss in detail the design and functionalities of its main modules: (a) the multiocular network of multispectral cameras for visual information gathering, (b) the intelligent segmentation, event modeling and anomaly detection module and (c) the end-to-end power-aware data encryption infrastructure. By following the proposed approach, different geographic areas can be successfully covered, high-level situations of interest can be modeled and secure data communication can be guaranteed, at a minimum necessary electrical and CPU power. Finally, an application scenario in the maritime domain is provided.
Swedish-Turkish Parallel Treebank

In this paper, we describe our work on building a parallel treebank for a less studied and typologically dissimilar language pair, namely Swedish and Turkish. The treebank is a balanced syntactically annotated corpus containing both fiction and technical documents. In total, it consists of approximately 160,000 tokens in Swedish and 145,000 in Turkish. The texts are linguistically annotated using different layers from part of speech tags and morphological features to dependency annotation. Each layer is automatically processed by using basic language resources for the involved languages. The sentences and words are aligned, and partly manually corrected. We create the treebank by reusing and adjusting existing tools for the automatic annotation, alignment, and their correction and visualization. The treebank was developed within the project supporting research environment for minor languages aiming at to create representative language resources for language pairs dissimilar in language structure. Therefore, efforts are put on developing a general method for formatting and annotation procedure, as well as using tools that can be applied to other language pairs easily.
Sarcoidosis in an Athlete

Background Sarcoidosis is a multisystem granulomatous disorder of unknown etiology, characterized by “noncaseating granulomas” in different organs. Clinical signs are variable and dependent on the organ involved. Although it is often asymptomatic in athletes, considering the high level of athletic performance and the related risks due to the potential heart involvement, a particular diagnostic flow-chart to consider some other diagnoses is required. The present case report aimed to focus on the clinical approach in case of a progressive weakness associated with a reduction in global performance of an athlete. Case Presentation Since October 2008 a 33-year-old Scandinavian professional soccer player has shown splitting headache, fever and impaired exercise tolerance. Despite some clinical aspects and symptoms that could address diagnosis of granulomatosis according to the current guidelines, the first hypothesis was indicative of a possible viral infection. Therefore, the athlete had received a drug-therapy resolving the headache and fever. However, because of the persisting weakness, several other clinical possibilities were evaluated following a more complete diagnostic flow-chart, blood and instrumental exams. Conclusion This case report focuses on the substantial absence of symptoms during the granulomatosis disease, which makes the differential diagnosis to be often complicating. Indeed, several additional exams are required in order to establish the presence of “Non-evolutive sarcoidosis- stage I”, for which the therapy is not mandatory.
On‐the‐Fly Processing of Generalized Lumigraphs

We introduce a flexible and powerful concept for reconstructing arbitrary views from multiple source images on the fly. Our approach is based on a Lumigraph structure with per‐pixel depth values, and generalizes the classical two‐plane parameterized light fields and Lumigraphs. With our technique, it is possible to render arbitrary views of time‐varying, non‐diffuse scenes at interactive frame rates, and it allows using any kind of sensor that yields images with dense depth information. We demonstrate the flexibility and efficiency of our approach through various examples.
Parawixin1: A Spider Toxin Opening New Avenues for Glutamate Transporter Pharmacology

Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system. After release from glutamatergic nerve terminals, glial and neuronal glutamate transporters remove glutamate from the synaptic cleft to terminate synaptic transmission and to prevent neuronal damage by excessive glutamate receptor activation. In this issue of Molecular Pharmacology, Fontana et al. (p. 1228) report on the action of a venom compound, Parawixin1, on excitatory amino acid transporters (EAATs). They demonstrate that this agent selectively affects a glial glutamate transporter, EAAT2, by specifically increasing one particular step of the glutamate uptake cycle. Disturbed glutamate homeostasis seems to be a pathogenetic factor in several neurodegenerative disorders. Because EAAT2 is a key player in determining the extracellular glutamate concentration in the mammalian brain, drugs targeting this protein could prevent glutamate excitotoxicity without blocking glutamatergic transmission. Its specificity and selectivity makes Parawixin1 a perfect starting point to design small molecules for the treatment of pathological conditions caused by alterations of glutamate homeostasis.
Late Holocene Structural Style and Seismicity of Highly Transpressional Faults in Southern Haiti

The devastating 2010 Haiti earthquake (Mw 7.0) was caused by rupture of the Léogâne, blind, thrust fault located 5 km north of the 1,200‐km‐long, left‐lateral, Enriquillo‐Plantain Garden fault zone (EPGFZ). Unexpectedly, the EPGFZ remained largely quiescent or slightly reactivated during the 2010 earthquake. Nevertheless, the EPGFZ still formed a major, crustal boundary between a coseismically uplifted lowland north of the EPGFZ and a subsided area in the highlands south of the fault. Here we use high‐resolution sonar data from two Haitian Lakes that straddle the EPGFZ to demonstrate the presence of a 10‐ to 15‐km‐wide, 120‐km‐long, late Holocene fold‐thrust belt which deforms clastic, lowland basins along the northern edge of the EPGFZ. In the eastern part of the study area, sonar results from Lake Azuey show that the linear trace of the EPGFZ cutting the Holocene lake bed is more deeply buried and less active than the adjacent, newly discovered, northwest striking, northeast dipping Jimani thrust fault that is part of the adjacent, transpressional belt of en echelon thrusts and folds. This structural relationship between a less active EPGFZ and more recently active, transpression‐related Jimani thrust is remarkably similar to the 2010 epicentral area 70 km to the west between the less active EPGFZ and seismogenic, northeast‐dipping, Léogâne thrust during the 2010 Haiti earthquake. In this complex transpressional zone, we propose that coseismic deformation alternates at recurrence intervals of centuries between oblique, transpression‐related structures (Léogâne, Jimani, and Trois Baies thrusts) and the main strike‐slip, plate boundary fault zone (EPGFZ).
Fundamental challenges in mobile computing

Abstract : This paper is an answer to the question: 'What is unique and conceptually different about mobile computing? ' The paper begins by describing a set of constraints intrinsic to mobile computing, and examining the impact of these constraints on the design of distributed systems. Next, it summarizes the key results of the Coda and Odyssey systems. Finally, it describes the research opportunities in five important topics relevant to mobile computing: caching metrics, semantic callbacks and validators, resource revocation, analysis of adaptation, and global estimation from local observations.
Effects of Polyamino Acids and Polyelectrolytes on Amyloid β Fibril Formation

The fibril formation of the neurodegenerative peptide amyloid β (Aβ42) is sensitive to solution conditions, and several proteins and peptides have been found to retard the process. Aβ42 fibril formation was followed with ThT fluorescence in the presence of polyamino acids (poly-glutamic acid, poly-lysine, and poly-threonine) and other polymers (poly(acrylic acid), poly(ethylenimine), and poly(diallyldimethylammonium chloride). An accelerating effect on the Aβ42 aggregation process is observed from all positively charged polymers, while no effect is seen from the negative or neutral polymers. The accelerating effect is dependent on the concentration of positive polymer in a highly reproducible manner. Acceleration is observed from a 1:500 polymer to Aβ42 weight ratio and up. Polyamino acids and the other polymers exert quantitatively the same effect at the same concentrations based on weight. Fibrils are formed in all cases as verified by transmission electron microscopy. The concentrations of polymers required for acceleration are too low to affect the Aβ42 aggregation process through increased ionic strength or molecular crowding effects. Instead, the acceleration seems to arise from the locally increased Aβ42 concentration near the polymers, which favors association and affects the electrostatic environment of the peptide.
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Motivation: An important step of "metagenomics" analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines employ a single-genome assembler with carefully optimized parameters and post-process the resulting scaffolds to correct assembly errors. Limitations of the use of a single-genome assembler for de novo metagenome assembly are that highly conserved sequences shared between different species often causes chimera contigs, and sequences of highly abundant species are likely mis-identified as repeats in a single genome, resulting in a number of small fragmented scaffolds. The metagenome assembly problem becomes harder when assembling from very short sequence reads. Method: We modified and extended a single-genome and de Bruijn-graph based assembler, known as "Velvet" [27], for short reads to metagenome assembly, called "MetaVelvet", for mixed short reads of multiple species. Our fundamental ideas are first decomposing de Bruijn graph constructed from mixed short reads into individual sub-graphs and second building scaffolds based on every decomposed de Bruijn sub-graph as isolate species genome. We make use of two features, graph connectivity and coverage (abundance) difference, for the decomposition of de Bruijn graph. Results: On simulated datasets, MetaVelvet succeeded to generate higher N50 scores and smaller chimeric scaffolds than any compared single-genome assemblers, produce high-quality scaffolds as well as the separate assembly using Velvet from isolated species sequence reads, and MetaVelvet reconstructed even relatively low-coverage genome sequences as scaffolds. On a real dataset of Human Gut microbial read data, MetaVelvet produced longer scaffolds, increased the number of predicted genes, and improved the assignments of a phylum-level taxonomy in the sense that the rate of predicted genes that cannot be assigned to any tanoxomy is reduced. Availability: The source code of MetaVelvet is freely available at http://metavelvet.dna. bio.keio. ac.jp under the GNU General Public License.
Complexities of service delivery and state-building

Approximately 4.75 billion USD of international aid money was spent in South Sudan between 2012 and 2014 alone. Yet despite the intense international engagement in institution-building, supposedly to help improve people’s perceptions of governance, South Sudan descended into armed conflict in 2013. The SLRC South Sudan programme has been working since 2012 to identify and understand the realities of access to basic services and perceptions of governance in post-independence South Sudan. This paper describes the findings from research carried out in several areas of South Sudan in the context of armed conflict and raiding. The findings show that despite state-building efforts, service delivery remained inadequate in remote areas and that the interface between service delivery and people’s perceptions of the state is complex. The authors recommend that the highly political nature of state-building and post-conflict transformation processes should be more systematically taken into account by external actors involved in South Sudan.
Modeling of the net ecosystem exchange, gross primary production, and ecosystem respiration for peatland ecosystems of Western Siberia

Observed and simulated carbon dioxide fluxes in oligotrophic peatlands of Western Siberia are discussed. Net ecosystem exchange, gross primary production, and ecosystem respiration are measured at a ridge-hollow complex in the South Taiga zone (Bakchar bog – field station “Vasjuganie”) and Middle Taiga zone (Mukhrino bog - field station “Mukhrino”). A model of net ecosystem exchange is used to study the influence of different environmental factors and to calculate daily the growing season carbon budget for an oligotrophic bog. The model uses the air and soil temperature, the incoming photosynthetically active radiation, and the leaf area index as the explanatory factors for gross primary production, heterotrophic and autotrophic respiration. The model coefficients are calibrated using data collected by an automated soil CO2 flux system with a clear long-term chamber. The studied ecosystems are sinks of carbon according to modelling and observation results.
Genetic and Genomic Discovery Using Family Studies

Genetic studies traditionally have been performed on sets of related individuals, that is, families. Mendel’s early studies in sweet peas ( Pisum sativum ) on the inheritance patterns of discrete traits from parents with specific mating types to offspring has shed light on the basic mechanisms of inheritance, including the fundamental laws of segregation of discrete factors (genes) from parents to offspring and the cosegregation of genes that are closely located on a chromosome (linkage). The distribution of traits within families exhibited mathematical segregation ratios in offspring from known mating types. These expected segregation ratios have been used as an important discovery tool in the study of human diseases in pedigrees, providing evidence for a multitude of single-gene disorders. Furthermore, in some cases, trait cosegregation with genetic markers with known positions provides mapping information that enables localization and, ultimately, identification of the relevant causative gene. Pedigree studies have been used fruitfully to identify genes influencing a wide range of monogenic, highly penetrant traits of biomedical importance, including a variety of inborn errors of metabolism and other genetic diseases (eg, cystic fibrosis, Duchenne muscular dystrophy, Huntington disease). These have been documented extensively in Mendelian Inheritance in Man (V.A. McKusick; http://www.ncbi.nlm. nih.gov/sites/entrez? db=OMIM). 1 In general, complex traits, such as coronary heart disease and its risk factors, are distinguished from these conditions in that (1) they are relatively common; (2) although they cluster in families, they do not demonstrate clean mendelian segregation patterns, suggesting the possibility of multiple underlying genes; (3) they are often influenced by >1 underlying pathway where several defects or mutations might contribute to phenotypic variation; (4) the marginal effect of any single gene on a relevant clinical end point such as atherosclerosis is likely to be small; and (5) alternative mechanisms or pathways may lead to a particular clinical outcome, that …
Dynamic remodeling of the dynamin helix during membrane constriction

Significance The GTPase dynamin catalyzes membrane fission and is essential in endocytosis and other events such as organelle division. Dynamin is a unique molecular motor with torsional and contractile abilities. Because these abilities involve a conformational change at the whole-polymer level, standard structural biology tools have not been able to fully unravel the mechanism by which it constricts and twists. Here we used high-speed atomic force microscopy to image the constriction and fission of dynamin-coated tubules with subnanometer and subsecond resolution. Our results provide important findings to establish the contribution of the various constriction mechanisms. Dynamin is a dimeric GTPase that assembles into a helix around the neck of endocytic buds. Upon GTP hydrolysis, dynamin breaks these necks, a reaction called membrane fission. Fission requires dynamin to first constrict the membrane. It is unclear, however, how dynamin helix constriction works. Here we undertake a direct high-speed atomic force microscopy imaging analysis to visualize the constriction of single dynamin-coated membrane tubules. We show GTP-induced dynamic rearrangements of the dynamin helix turns: the average distances between turns reduce with GTP hydrolysis. These distances vary, however, over time because helical turns were observed to transiently pair and dissociate. At fission sites, these cycles of association and dissociation were correlated with relative lateral displacement of the turns and constriction. Our findings show relative longitudinal and lateral displacements of helical turns related to constriction. Our work highlights the potential of high-speed atomic force microscopy for the observation of mechanochemical proteins onto membranes during action at almost molecular resolution.
Mobile ultrasound imaging on heterogeneous multi-core platforms

Ultrasound imaging is one of the most important medical diagnostic methods. The bulkiness of state-of-the-art high-quality ultrasound devices, however, drastically limits their usability in important application scenarios. In this paper, we show how a portable medical ultrasound device can be built using many-core technology and programmable logic, combining low power consumption with high flexibility. We discuss a typical ultrasound image reconstruction algorithm and howit can be parallelized using a pipelined design that efficiently partitions theworkload among heterogeneous processing elements. A special focus lies on the limited memory resources and data bandwidth between components. To tackle both problems, we use floating windowbuffers and approximate computations, and we minimize lookup table sizes using on-the-fly calculations. We evaluate the design on the Adapteva Parallella platform, which contains a power-efficient 16-core Epiphany coprocessor and a Zynq SoC including a dual-core ARM A9 processor and programmable logic. Experimental results show that parallel beamforming of 128 input channels to a 288x128 pixel ultrasound image can be achieved on the Parallella at a rate of 5.3 frames per second consuming only 2watt of dynamic power.
Requirements for the visualization of system-spanning business processes

The monitoring and visualization of enterprise-wide and cross-organizational business processes is an important, but also very complex task. The information needed for visualizing processes may be scattered over heterogeneous, distributed information systems. These systems may only support fragments of the process and may use different process meta models. Besides an integrated view on these process data, any process visualization must be flexibly and dynamically adaptable to the needs of different applications and user groups. This paper discusses requirements of a flexible process visualization in distributed environments. This includes process data integration issues as well as issues related to adaptable process visualization.