Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Submesoscale Features on a Warm Core Ring of The Gulf Stream

Mixing and transport processes are very important in the dynamics of the oceans as they influence their physical, biological and chemical properties. From plankton to oil spills, there is a broad range of problems that can benefit from understanding these processes. Transport and mixing occur at all scales of motion, ranging from the scale of rings to the microscale of 3D turbulence. In the past many studies tried to discern the relative importance of the processes developing at different scales on transport and mixing reaching contrasting conclusions. The prevailing idea is that most of the transport and mixing are associated with meso/large scale features where most of the energy is stored. This vision is opposed to what suggested by recent studies where an important role on transport/mixing is given to submesoscale processes (SM) (Lumpkin and Elipot [1], Schroeder et al. [2]). The main objective of this work is to understand the role of SM features on the transport and mixing of large scale coherent structures (LCS) in the Gulf Stream (GS) region. Two numerical simulations in HYCOM are compared at different resolutions of a warm core ring in the northern branch of the GS. Diagnostics are computed for the winter season, when a strong submesoscale activity is observed in the mixed layer of the high resolution simulation.
Reputation-Enhanced QoS-based Web Services Discovery

With an increasing number of Web services providing similar functionalities, quality of service (QoS) is becoming an important criterion for selection of the best available service. Currently the problem is twofold. The Universal Description, Discovery and Integration (UDDI) registries do not have the ability to publish the QoS information, and the authenticity of the advertised QoS information available elsewhere may be questionable. We propose a model of reputation-enhanced QoS- based Web services discovery that combines an augmented UDDI registry to publish the QoS information and a reputation manager to assign reputation scores to the services based on customer feedback of their performance. A discovery agent facilitates QoS-based service discovery using the reputation scores in a service matching, ranking and selection algorithm. The novelty of our model lies in its simplicity and in its coordination of the above mentioned components. We present experiments to evaluate the effectiveness of our approach using a prototype implementation of the model.
Biosynthesis of 2-methylbacteriohopanepolyols by an anoxygenic phototroph

Sedimentary 2-methyhopanes have been used as biomarker proxies for cyanobacteria, the only known bacterial clade capable of oxygenic photosynthesis and the only group of organisms found thus far to produce abundant 2-methylbacteriohopanepolyols (2-MeBHPs). Here, we report the identification of significant quantities of 2-MeBHP in two strains of the anoxygenic phototroph Rhodopseudomonas palustris. Biosynthesis of 2-MeBHP can occur in the absence of O2, deriving the C-2 methyl group from methionine. The relative abundance of 2-MeBHP varies considerably with culture conditions, ranging from 13.3% of total bacteriohopanepolyol (BHP) to trace levels of methylation. Analysis of intact BHPs reveals the presence of methylated bacteriohopane-32,33,34,35-tetrol but no detectable methylation of 35-aminobacteriohopane-32,33,34-triol. Our results demonstrate that an anoxygenic photoautotroph is capable of generating 2-MeBHPs and show that the potential origins of sedimentary 2-methylhopanoids are more diverse than previously thought.
In black and white: an integrated approach to class-level testing of object-oriented programs

Because of the growing importance of object-oriented programming, a number of testing strategies have been proposed. They are based either on pure black-box or white-box techniques. We propose in this article a methodology to integrate the black- and white-box techniques. The black-box technique is used to select test cases. The white-box technique is mainly applied to determine whether two objects resulting from the program execution of a test care are observationally equivalent. It is also used to select test cases in some situations. We define the concept of a fundamental pair as a pair of equivalent terms that are formed by replacing all the variables on both sides of an axiom by normal forms. We prove that an implementation is consistent with respect to all equivalent terms if and only if it is consistent with respect to all fundamental pairs. In other words, the testing coverage of fundamental pairs is as good as that of all possible term rewritings, and hence we need only concentrate on the testing of fundamental pairs. Our strategy is based on mathematical theorems. According to the strategy, we propose an algorithm for selecting a finite set of fundamental pairs as test cases. Given a pair of equivalent terms as a test case, we should then determine whether the objects that result from executing the implemented program are observationally equivalent. We prove, however, that the observational equivalence of objects cannot be determined using a finite set of observable contexts (which are operation sequences ending with an observer function) derived from any black-box technique. Hence we supplement our approach with a “relevant observable context” technique, which is a heuristic white-box technique to select a relevant finite subset of the set of observable contexts for determining the observational equivalence. The relevant observable contezxts are constructed from a data member relevance graph (DRG), which is an abstraction of the given implementation for a given specificatin. A semiautomatic tool hass been developed to support this technique.
LTI Transceivers With Reduced Redundancy

This paper presents new linear time-invariant (LTI) block-based transceivers which employ a reduced amount of redundancy to eliminate the interblock interference. The proposals encompass both multicarrier and single-carrier systems with either zero-forcing or minimum mean-square error (MSE) equalizers. The amount of redundancy ranges from the minimum, [L/2], to the most commonly used value, L, assuming a channel-impulse response of order L. The resulting transceivers allow for superfast equalization of the received data blocks, since they only use fast Fourier transforms and single-tap equalizers in their structures. The paper also includes an MSE analysis of the proposed transceivers with respect to the amount of redundancy. Indeed, we demonstrate that larger amounts of transmitted redundant elements lead to lower MSE of symbols at the receiver end. Computer simulations indicate that, by choosing an appropriate amount of redundancy, our proposals can achieve higher throughputs than the standard superfast multicarrier and single-carrier systems, while keeping the same asymptotic computational complexity for the equalization process.
Botnet detection technology based on the on-line error model

Botnet is a serious information safety problem in the recent network. How to effectively find out the victim host and how to make the victim host free from the control of the botnet have become an urgent problem to be solved in the current network safety. In the paper, the use of the network online failure can distinguish the normal flow, P2P flow and the flow infected by the botnet. It can abstract the relevant characteristic values by observing the normal flow, the P2P flow and the online failure from the botnet intranet to the outer net, and then the characteristic values can create the detection model through the machine learning. The use of the detection model can distinguish the different kinds of flows.
Cloud Elasticity for Implementing an Agricultural Weather Service

In this paper, we describe a weather service dedicated to farming called CAP2020. The service involves interpolation operations accessing massive data. We explain the centralized implementation of this application and show the limits of this architecture. Then we present a Cloud-enabled distributed solution ensuring load balancing and data replication to take advantage of the elastic capabilities of Cloud solutions. Distributed implementation provides better quality of service and scalability for CAP2020 application in anticipation of increasing use and/or application data, but also to adapt to punctual and seasonal farming needs.
Semantic Web-Oriented Intelligent Information Retrieval System

The notion of ontology is introduced to information retrieval systems and semantic Web-oriented architecture of personalized intelligent information retrieval system is presented, and hierarchical tree model of local domain ontological repository of biomedical diseases system is constructed, in which the OWL language is used to detail annotate syntax and semantics of concepts, their attributes and relations among the concepts. Automatic acquirement of remote information on the Internet and pretreatment of local domain ontological repository are implemented by inference rules and information semantics-based intelligent clustering algorithm in the architecture, and preference database of doctors are managed logically according to their retrieval interests. Consequently, the system will meets the requirement of personalized intelligent information search for diseases diagnosis, and further improves recall and precision of information retrieval on biomedical diseases system.
FASTUS : Extracting Information from Natural-Language Texts

FASTUS is a system for extracting information from natural language text for entry into a database and for other applications. It works essentially as a cascaded, nondeterministic finite-state automaton. There are five stages in the operation of FASTUS. In Stage 1, names and other fixed form expressions are recognized. In Stage 2, basic noun groups, verb groups, and prepositions and some other particles are recognized. In Stage 3, certain complex noun groups and verb groups are constructed. Patterns for events of interest are identified in Stage 4 and corresponding ``event structures'' are built. In Stage 5, distinct event structures that describe the same event are identified and merged, and these are used in generating database entries. This decomposition of language processing enables the system to do exactly the right amount of domain-independent syntax, so that domain-dependent semantic and pragmatic processing can be applied to the right larger-scale structures. FASTUS is very efficient and effective, and has been used successfully in a number of applications.
Role of breast regression protein 39 (BRP-39)/chitinase 3-like-1 in Th2 and IL-13–induced tissue responses and apoptosis

Mouse breast regression protein 39 (BRP-39; Chi3l1) and its human homologue YKL-40 are chitinase-like proteins that lack chitinase activity. Although YKL-40 is expressed in exaggerated quantities and correlates with disease activity in asthma and many other disorders, the biological properties of BRP-39/YKL-40 have only been rudimentarily defined. We describe the generation and characterization of BRP-39−/− mice, YKL-40 transgenic mice, and mice that lack BRP-39 and produce YKL-40 only in their pulmonary epithelium. Studies of these mice demonstrated that BRP-39−/− animals have markedly diminished antigen-induced Th2 responses and that epithelial YKL-40 rescues the Th2 responses in these animals. The ability of interleukin13 to induce tissue inflammation and fibrosis was also markedly diminished in the absence of BRP-39. Mechanistic investigations demonstrated that BRP-39 and YKL-40 play an essential role in antigen sensitization and immunoglobulin E induction, stimulate dendritic cell accumulation and activation, and induce alternative macrophage activation. These proteins also inhibit inflammatory cell apoptosis/cell death while inhibiting Fas expression, activating protein kinase B/AKT, and inducing Faim 3. These studies establish novel regulatory roles for BRP-39/YKL-40 in the initiation and effector phases of Th2 inflammation and remodeling and suggest that these proteins are therapeutic targets in Th2- and macrophage-mediated disorders.
Connecting topics in document collections with stepping stones and pathways

In this paper, we present Stepping Stones and Pathways (SSP), an alternative model of building and presenting answers for the cases when queries on document collections cannot be answered just by a ranked list. Stepping Stones can handle questions like: "What is the relation of topics X and Y? " SSP addresses when the contents of a small set of related documents is needed as an answer rather than a single document, or when "query splitting" is required to satisfactorily explore a document space. Query results are networks of document groups representing topics, each group relating to and connecting (by documents) to other groups in the network. Thus, a network answers the user's information need. We devise new and more effective representations and techniques to visualize such answers, and to involve users as part of the answer-finding process. In order to verify the validity of our approach, and since the questions we aim to answer involve multiple topics, we performed a study involving a custom built broad collection of operating systems research papers, and evaluated the results with interested computer science students, using multiple measures.
TCP-CM: a transport protocol for TCP-friendly transmission of continuous media

We propose a new TCP friendly transport protocol, called TCP-CM, for continuous media applications over the Internet. TCP-CM is a direct modification of TCP to support continuous media applications without compromising the congestion control feature of TCP, which is critical to the stable functioning of the Internet. We design TCP-CM API to be compatible with the BSD socket interface, which requires minimum changes for applications to adopt TCP-CM. Continuous media applications that adopt TCP-CM as the transport protocol can be relieved from burdens such as rate control and scheduling for timely delivery, and hence can focus solely on advanced coding or compression techniques for adapting the content according to the available network bandwidth. We implement the TCP-CM in Linux 2.2. 15 TCP/IP protocol stack, and run extensive experiments on TCP-CM using emulated video flows. Our experiments show that TCP-CM can be used for the timely delivery of continuous media data within the constraints of the available network bandwidth and can compete with TCP connections fairly.
Collisions of matter-wave solitons

Supplementary Figure 1: Comparison between the expansion of a soliton and a repulsive condensate. a, A condensate with repulsive interactions is formed with N/Nc = +0.55, and suddenly transferred into a single-beam trap by turning off the beam perpendicular to the magnetic field axis. The new axial trap frequency is ωz2 = 8 Hz (τ2 = 125 ms). Images are taken at intervals of τ2/8. The condensate rapidly expands as a result of the repulsive interactions between atoms. The subsequent reformation of the condensate at τ2/2 and at τ2 indicates that a breathing mode has been excited. b, Similar to a, but with N/Nc = −0.53. Here, the soliton propagates without dispersion, as expected. The small displacement in time is due to a slight time-dependent displacement between trap centres. Note that the color mappings of Supplementary Figs. 1a and 1b differ to account for differences in density.
R-Type Calcium Channels Are Crucial for Semaphorin 3A–Induced DRG Axon Growth Cone Collapse

Semaphorin 3A (Sema3A) is a secreted protein involved in axon path-finding during nervous system development. Calcium signaling plays an important role during axonal growth in response to different guidance cues; however it remains unclear whether this is also the case for Sema3A. In this study we used intracellular calcium imaging to figure out whether Sema3A-induced growth cone collapse is a Ca2+ dependent process. Intracellular Ca2+ imaging results using Fura-2 AM showed Ca2+ increase in E15 mice dorsal root ganglia neurons upon Sema3A treatment. Consequently we analyzed Sema3A effect on growth cones after blocking or modifying intracellular and extracellular Ca2+ channels that are expressed in E15 mouse embryos. Our results demonstrate that Sema3A increased growth cone collapse rate is blocked by the non-selective R- and T- type Ca2+ channel blocker NiCl2 and by the selective R-type Ca2+ channel blocker SNX482. These Ca2+ channel blockers consistently decreased the Sema3A-induced intracellular Ca2+ concentration elevation. Overall, our results demonstrate that Sema3A-induced growth cone collapses are intimately related with increase in intracellular calcium concentration mediated by R-type calcium channels.
Sandbox System Based on Role and Virtualization

We present a sandbox system based on role and virtualization applied to intrusion detection, which overcomes some drawbacks of traditional sandbox system: heavy workload of administrating user’s access control information, imprecision of access control, security hidden and inconvenient trace record of intrusion in the event of denial of system call, low performance after being incorporated to the original system, etc. We define meta-permission and present role sandbox and virtualization sandbox based on introducing role. This ensures the strong function of intrusion detection based on host. The tests show that the sandbox system can protect system security effectively without imposing heavy performance impact upon operating system.
OPTIMAL DESIGN OF A MULTI-LEVEL VOLTAGE SOURCE INVERTER FOR SOLAR CELLS TO INCREASE OUTPUT POWER WITHOUT NEW SPENDING

Photovoltaic systems convert solar energy directly into electrical energy and do not cause environmental pollution compared with conventional systems of energy production. Therefore, photovoltaic systems are also called “green" or "clean” energy sources. Along with the increasing problems of environmental pollution and the reduction of fossil energy reserves, the use of photovoltaic systems has increased in recent years. Historically, due to their high costs, photovoltaic systems were generally used to provide the required electric power for satellites. But with the growth of the semiconductor industry in recent years and lower costs in the production of semiconductor devices, nowadays, solar arrays have found extensive applications one of which is grid-connected photovoltaic systems. In photovoltaic systems connected to the grid, the inverter is an important part of the system components whose optimal design is of high importance and there are various methods of modulation for it. A common method for the design of multi-level inverter is PWM modulation technique of stairs. In this paper, a new method is proposed through which the switching angles in a multilevel and multi-story inverter modulation step connected photovoltaic systems are calculated. Derived mathematically prove that the proposed algorithm is reduced by THD. To prove that THD is reduced by the proposed algorithm and the output power of solar cells is increased, the mathematical derivation is given. Compared with other methods, it is seen that the obtained THD in this method is the least of all and inverters have improved performances in converting the output voltage of the solar cell. Most importantly, the level of computational process is so low that the calculations can be performed in real time without a lookup table. The proposed method does not require any new spending.
Some GPU Algorithms for Graph Connected Components and Spanning Tree

Graphics Processing Units (GPU) are application specific accelerators which provide high performance to cost ratio and are widely available and used, hence places them as a ubiquitous accelerator. A computing paradigm based on the same is the general purpose computing on the GPU (GPGPU) model. The GPU due to its graphics lineage is better suited for the data-parallel, data-regular algorithms. The hardware architecture of the GPU is not suitable for the data parallel but data irregular algorithms such as graph connected components and list ranking. In this paper, we present results that show how to use GPUs efficiently for graph algorithms which are known to have irregular data access patterns. We consider two fundamental graph problems: finding the connected components and finding a spanning tree. These two problems find applications in several graph theoretical problems. In this paper we arrive at efficient GPU implementations for the above two problems. The algorithms focus on minimising irregularity at both algorithmic and implementation level. Our implementation achieves a speedup of 11-16 times over a corresponding best sequential implementation.
The Chromosomal Association of the Smc5/6 Complex Depends on Cohesion and Predicts the Level of Sister Chromatid Entanglement

The cohesin complex, which is essential for sister chromatid cohesion and chromosome segregation, also inhibits resolution of sister chromatid intertwinings (SCIs) by the topoisomerase Top2. The cohesin-related Smc5/6 complex (Smc5/6) instead accumulates on chromosomes after Top2 inactivation, known to lead to a buildup of unresolved SCIs. This suggests that cohesin can influence the chromosomal association of Smc5/6 via its role in SCI protection. Using high-resolution ChIP-sequencing, we show that the localization of budding yeast Smc5/6 to duplicated chromosomes indeed depends on sister chromatid cohesion in wild-type and top2-4 cells. Smc5/6 is found to be enriched at cohesin binding sites in the centromere-proximal regions in both cell types, but also along chromosome arms when replication has occurred under Top2-inhibiting conditions. Reactivation of Top2 after replication causes Smc5/6 to dissociate from chromosome arms, supporting the assumption that Smc5/6 associates with a Top2 substrate. It is also demonstrated that the amount of Smc5/6 on chromosomes positively correlates with the level of missegregation in top2-4, and that Smc5/6 promotes segregation of short chromosomes in the mutant. Altogether, this shows that the chromosomal localization of Smc5/6 predicts the presence of the chromatid segregation-inhibiting entities which accumulate in top2-4 mutated cells. These are most likely SCIs, and our results thus indicate that, at least when Top2 is inhibited, Smc5/6 facilitates their resolution.
SEX ALLOCATION ADJUSTMENT TO MATING GROUP SIZE IN A SIMULTANEOUS HERMAPHRODITE

Sex allocation theory is considered as a touchstone of evolutionary biology, providing some of the best supported examples for Darwinian adaptation. In particular, Hamilton's local mate competition theory has been shown to generate precise predictions for extraordinary sex ratios observed in many separate‐sexed organisms. In analogy to local mate competition, Charnov's mating group size model predicts how sex allocation in simultaneous hermaphrodites is affected by the mating group size (i.e., the number of mating partners plus one). Until now, studies have not directly explored the relationship between mating group size and sex allocation, which we here achieve in the simultaneously hermaphroditic flatworm Macrostomum lignano. Using transgenic focal worms with ubiquitous expression of green‐fluorescent protein (GFP), we assessed the number of wild‐type mating partners carrying GFP+ sperm from these focal worms when raised in different social group sizes. This allowed us to test directly how mating group size was related to the sex allocation of focal worms. We find that the proportion of male investment initially increases with increasing mating group size, but then saturates as predicted by theory. To our knowledge, this is the first direct test of the mating group size model in a simultaneously hermaphroditic animal.