Miracle-dz/UniFAR-FTUs huggingface dataset:
VOIQ: a practical high-performance architecture for the implementation of single-buffered routers

In order to find a more tractable and practical architecture for high-performance routers within current technology and market constraints, the High-Performance Networking Group (HPNG) of Stanford University proposed to build a router just with single stage of buffering, i.e. the scheme of single-buffered (SB) routers. Concretely, two different designs of SB routers were proposed by HPNG: one of which was parallel shared memory (PSM) router and the other was distributed shared memory (DSM) router. Although the notion of single-buffered routers deserves full credit, the results of HPNG seem just theoretical rather than practical. In this paper, we attempt to make high-performance SB routers practical by introducing a new architecture for the shared memories. We call the resulting SB router as virtual output and input queued (VOIQ) router. We show that the scheme of VOIQ can eliminate the need for centralized memory management algorithms and allow a fully distributed implementation of SB routers with rich QoS guarantees and the ability to support variable-length packets while retaining low total memory bandwidth and complexity of processing and communication
Genetically designed L3 photonic crystal nanocavities with measured quality factor exceeding one million

We report on the experimental realization of ultra-high quality factor (Q) designs of the L3-type photonic crystal nanocavity. Based on genetic optimization of the positions of few nearby holes, our design drastically improves the performance of the conventional L3 as experimentally confirmed by direct measurement of Q ≃ 2 × 106 in a silicon-based photonic crystal membrane. Our devices rank among the highest Q/V ratios ever reported in photonic crystal cavities, holding great promise for the realization of integrated photonic platforms based on ultra-high-Q resonators.
Imperative self-adjusting computation

Self-adjusting computation enables writing programs that can automatically and efficiently respond to changes to their data (e.g., inputs). The idea behind the approach is to store all data that can change over time in modifiable references and to let computations construct traces that can drive change propagation. After changes have occurred, change propagation updates the result of the computation by re-evaluating only those expressions that depend on the changed data. Previous approaches to self-adjusting computation require that modifiable references be written at most once during execution---this makes the model applicable only in a purely functional setting. In this paper, we present techniques for imperative self-adjusting computation where modifiable references can be written multiple times. We define a language SAIL (Self-Adjusting Imperative Language) and prove consistency, i.e., that change propagation and from-scratch execution are observationally equivalent. Since SAIL programs are imperative, they can create cyclic data structures. To prove equivalence in the presence of cycles in the store, we formulate and use an untyped, step-indexed logical relation, where step indices are used to ensure well-foundedness. We show that SAIL accepts an asymptotically efficient implementation by presenting algorithms and data structures for its implementation. When the number of operations (reads and writes) per modifiable is bounded by a constant, we show that change propagation becomes as efficient as in the non-imperative case. The general case incurs a slowdown that is logarithmic in the maximum number of such operations. We describe a prototype implementation of SAIL as a Standard ML library.
Wolbachia elevates host methyltransferase expression to block an RNA virus early during infection

Wolbachia pipientis is an intracellular endosymbiont known to confer host resistance against RNA viruses in insects. However, the causal mechanism underlying this antiviral defense remains poorly understood. To this end, we have established a robust arthropod model system to study the tripartite interaction involving Sindbis virus and Wolbachia strain wMel within its native host, Drosophila melanogaster. By leveraging the power of Drosophila genetics and a parallel, highly tractable D. melanogaster derived JW18 cell culture system, we determined that in addition to reducing infectious virus production, Wolbachia negatively influences Sindbis virus particle infectivity. This is further accompanied by reductions in viral transcript and protein levels. Interestingly, unchanged ratio of proteins to viral RNA copies suggest that Wolbachia likely does not influence the translational efficiency of viral transcripts. Additionally, expression analyses of candidate host genes revealed D. melanogaster methyltransferase gene Mt2 as an induced host factor in the presence of Wolbachia. Further characterization of viral resistance in Wolbachia–infected flies lacking functional Mt2 revealed partial recovery of virus titer relative to wild-type, accompanied by complete restoration of viral RNA and protein levels, suggesting that Mt2 acts at the stage of viral genome replication. Finally, knockdown of Mt2 in Wolbachia uninfected JW18 cells resulted in increased virus infectivity, thus demonstrating its previously unknown role as an antiviral factor against Sindbis virus. In conclusion, our findings provide evidence supporting the role of Wolbachia–modulated host factors towards RNA virus resistance in arthropods, alongside establishing Mt2’s novel antiviral function against Sindbis virus in D. melanogaster.
Monophyly, Distance and Character–Based Multigene Barcoding Reveal Extraordinary Cryptic Diversity in Nassarius: A Complex and Dangerous Community

Background Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity. Methodology/Principal Findings Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character–based barcoding methods were employed. Conclusions/Significance Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character–based barcoding methods are all very helpful in identification but the character-based method shows some advantages.
Moth tails divert bat attack: Evolution of acoustic deflection

Significance Bats and moths have been engaged in acoustic warfare for more than 60 million y. Yet almost half of moth species lack bat-detecting ears and still face intense bat predation. We hypothesized that the long tails of one group of seemingly defenseless moths, saturniids, are an anti-bat strategy designed to divert bat attacks. Using high-speed infrared videography, we show that the spinning hindwing tails of luna moths lure echolocating bat attacks to these nonessential appendages in over half of bat–moth interactions. Further we show that long hindwing tails have independently evolved multiple times in saturniid moths. This finding expands our knowledge of antipredator deflection strategies, the limitations of bat sonar, and the extent of a long-standing evolutionary arms race. Adaptations to divert the attacks of visually guided predators have evolved repeatedly in animals. Using high-speed infrared videography, we show that luna moths (Actias luna) generate an acoustic diversion with spinning hindwing tails to deflect echolocating bat attacks away from their body and toward these nonessential appendages. We pit luna moths against big brown bats (Eptesicus fuscus) and demonstrate a survival advantage of ∼47% for moths with tails versus those that had their tails removed. The benefit of hindwing tails is equivalent to the advantage conferred to moths by bat-detecting ears. Moth tails lured bat attacks to these wing regions during 55% of interactions between bats and intact luna moths. We analyzed flight kinematics of moths with and without hindwing tails and suggest that tails have a minimal role in flight performance. Using a robust phylogeny, we find that long spatulate tails have independently evolved four times in saturniid moths, further supporting the selective advantage of this anti-bat strategy. Diversionary tactics are perhaps more common than appreciated in predator–prey interactions. Our finding suggests that focusing on the sensory ecologies of key predators will reveal such countermeasures in prey.
Summarizing Datacubes: Semantic and Syntactic Approaches

Datacubes are especially useful for answering efficiently queries on data warehouses. Nevertheless the amount of generated aggregated data is huge with respect to the initial data which is itself very large. Recent research work has addressed the issue of summarizing Datacubes in order to reduce their size. In this chapter, we present three different approaches. They propose structures which make it possible to reduce the size of the data cube representation. The two former, the closed cube and the quotient cube, are said semantic and discard the redundancies captured within data cubes. The size of the underlying representations is especially reduced but the counterpart is an additional response time when answering the OLAP queries. The latter approach is rather syntactic since it enforces an optimization at the logical level. It is called Partition Cube and based on the concept of partition. We also give an algorithm to compute it. We propose a Relational Partition Cube, a novel R-Olap cubing solution for managing Partition Cubes using the relational technology. An analytical evaluation shows that the storage space of Partition Cubes is smaller than Datacubes. In order to confirm analytical comparison, experiments are performed in order to compare our approach with Datacubes and with two of the best reduction methods, the Quotient Cube and the Closed Cube.
EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing.

UNLABELLED Glioblastomas (GBM) with EGFR amplification represent approximately 50% of newly diagnosed cases, and recent studies have revealed frequent coexistence of multiple EGFR aberrations within the same tumor, which has implications for mutation cooperation and treatment resistance. However, bulk tumor sequencing studies cannot resolve the patterns of how the multiple EGFR aberrations coexist with other mutations within single tumor cells. Here, we applied a population-based single-cell whole-genome sequencing methodology to characterize genomic heterogeneity in EGFR-amplified glioblastomas. Our analysis effectively identified clonal events, including a novel translocation of a super enhancer to the TERT promoter, as well as subclonal LOH and multiple EGFR mutational variants within tumors. Correlating the EGFR mutations onto the cellular hierarchy revealed that EGFR truncation variants (EGFRvII and EGFR carboxyl-terminal deletions) identified in the bulk tumor segregate into nonoverlapping subclonal populations. In vitro and in vivo functional studies show that EGFRvII is oncogenic and sensitive to EGFR inhibitors currently in clinical trials. Thus, the association between diverse activating mutations in EGFR and other subclonal mutations within a single tumor supports an intrinsic mechanism for proliferative and clonal diversification with broad implications in resistance to treatment. SIGNIFICANCE We developed a novel single-cell sequencing methodology capable of identifying unique, nonoverlapping subclonal alterations from archived frozen clinical specimens. Using GBM as an example, we validated our method to successfully define tumor cell subpopulations containing distinct genetic and treatment resistance profiles and potentially mutually cooperative combinations of alterations in EGFR and other genes.
Student nurses’ perceptions of their educational environment at a school of nursing in Western Cape province, South Africa: A cross-sectional study

Background Educational environments have been found to bear a substantial relationship with the academic performance and success, as well as the retention, of students. Objectives The study objectives were to (1) evaluate the educational environment as perceived by undergraduate nursing students at a school of nursing (SON) in Western Cape province and (2) investigate whether the educational environment, or components thereof, is perceived negatively or positively among undergraduate nursing students of different year level, gender, home language and ethnicity. Method A quantitative research method with a cross-sectional design was implemented. Data were collected from 232 undergraduate nursing students from a SON at a university in Western Cape province, South Africa. The subscales and the items of the educational environment questionnaire were compared among undergraduate nursing students. Data were analysed by means of the IBM Statistical Package for Social Sciences (IBM SPSS-24) using analysis of variances (ANOVAs), independent-sample t-tests, mean scores, standard deviations and percentages. Results The mean score attained for the entire participant group was 195 (standard deviation [SD] = 24.2) out of 268 (equivalent to 72.8% of maximum score), which indicated that the educational environment was perceived substantially more positively than negatively. The overall mean score was significantly higher (p < 0.05) for male students (M = 202; SD = 21) and for black students (M = 202; SD = 21). The digital resources (DR) subscale was the only subscale with a statement or item that was rated as absolute negative (M = 1.9; SD = 0.9). Conclusion The educational environment at the institution concerned was perceived as predominantly positive by its undergraduate nursing students. Although the educational environment was predominantly perceived as positive, the results of this study also indicated that enhancements are required to improve the physical classroom conditions, skills laboratories, DR and the implemented teaching and learning strategies. It is vital for university management to prioritise the creation of an educational environment which would ensure that quality learning takes place. Keywords student’s perceptions; educational environment; nursing education; Western Cape; South Africa.
Performance analysis and evaluation of proposed algorithm for advance options of H.263 and H.264 video codec

This paper deals with the evaluation, analysis and algorithm of advance options of H.263 and H.264/AVC video codec. Analysis and evaluation of H.263 video codec is important because it enable us to determine output parameter, which is peak signal to noise ratio (PSNR) or quality of picture. In this paper, the performance of H.263 video codec is evaluated and analyzed for various advance options such as syntax based arithmetic coding (SBAC), advanced prediction mode, unrestricted motion vector mode etc. The H.264/AVC is an international video coding standard, jointly developed by groups from ISO/IEC and ITU-T, which aims at achieving improved compression performance. Various applications of H.264/AVC include conversational, storage, and streaming. For H.264 Video codec we proposed algorithm for advance options such as context adaptive binary arithmetic coding (CABAC). The improvement in video quality with the use of these advance options of H.263 is of the order of 0.8 dB or more. The compression efficiency of CABAC is 10-15% better as compared to context adaptive variable length coding (CAVLC) and it can be up to 32% better when compared to other entropy compression methods such as Huffman Coding.
Glacier Energy and Mass Balance in the Inland Tibetan Plateau: Seasonal and Interannual Variability in Relation to Atmospheric Changes

The Tibetan glaciers are greatly affected by the circulations of the westerlies and the Indian summer monsoon (ISM), but the mechanisms remain to be elucidated. In this project, we investigated the surface energy and mass balance of the Qiangtang No.1 Glacier in the inland Tibetan Plateau. Combining 4‐year mass balance and meteorological records near the equilibrium line altitude with an energy‐based mass balance model, we found that the meteorological conditions, which determined the glacier surface ablation and mass accumulation, are critically linked to changes in the intensity of the westerlies and the ISM. The 4‐year mass balance comparisons demonstrated that the enhancement of the ISM in June and July, especially June, greatly increases the mass accumulation but inhibits the glacial ablation in the melt season, shifting the mass balance in a positive direction. Moreover, the occurrence of the westerlies enhancement interrupts the dominance of the ISM in the melt season. The intensified westerlies in the early melt season (June) could not only reduce the mass accumulation but also enhance the mass loss in the following months. In addition, the enhancement of the westerlies in the main melt season (July) could also greatly influence the local meteorological conditions, with lower temperatures and humidity but higher wind speeds. Such meteorological changes significantly reduce glacial ablation because more energy is consumed by sublimation and/or evaporation, rather than surface melting. These findings will enhance our understanding of the mechanisms underlying glacier changes and their relationships with the westerlies and the ISM in the inland Tibetan Plateau.
Elasticity Measurements Show the Existence of Thin Rigid Cores Inside Mitotic Chromosomes

Chromosome condensation is one of the most critical steps during cell division. However, the structure of condensed mitotic chromosomes is poorly understood. In this paper we describe a new approach based on elasticity measurements for studying the structure of in vitro assembled mitotic chromosomes in Xenopus egg extract. The approach is based on a unique combination of measurements of both longitudinal deformability and bending rigidity of whole chromosomes. By using specially designed micropipettes, the chromosome force–extension curve was determined. Analysis of the curvature fluctuation spectrum allowed for the measurement of chromosome bending ridigity. The relationship between the values of these two parameters is very specific: the measured chromosome flexibility was found to be 2,000 times lower than the flexibility calculated from the experimentally determined Young modulus. This requires the chromosome structure to be formed of one or a few thin rigid elastic axes surrounded by a soft envelope. The properties of these axes are well-described by models developed for the elasticity of titin-like molecules. Additionally, the deformability of in vitro assembled chromosomes was found to be very similar to that of native somatic chromosomes, thus demonstrating the existence of an essentially identical structure.
Query Processing in a Mediator Based Framework for Linked Data Integration

In this paper, the authors present a three-level mediator based framework for linked data integration. In the approach, the mediated schema is represented by a domain ontology, which provides a conceptual representation of the application. Each relevant data source is described by a source ontology, published on the Web according to the Linked Data principles. Each source ontology is rewritten as an application ontology, whose vocabulary is restricted to be a subset of the vocabulary of the domain ontology. The main contribution of the paper is an algorithm for reformulating a user query into sub-queries over the data sources. The reformulation algorithm exploits inter-ontology links to return more complete query results. The approach is illustrated by an example of a virtual store mediating access to online booksellers.
Prenatal, but not early postnatal, exposure to a Western diet improves spatial memory of pigs later in life and is paired with changes in maternal prepartum blood lipid levels

Maternal obesity and perinatal high‐fat diets are known to affect cognitive development. We examined the effects of late prenatal and/or early postnatal exposure to a Western‐type diet, high in both fat and refined sugar, on the cognition of pigs (Sus scrofa) in the absence of obesity. Thirty‐six sows and their offspring were assigned to 1 of 4 treatments in a 2 × 2 factorial arrangement, with 8 wk prenatal and 8 wk postnatal exposure to a Western diet (enriched in fat, sucrose, and cholesterol) or control diets as factors. Compared to controls, piglets exposed to the prenatal Western diet showed enhanced working and reference memory during the acquisition and reversal phases of a spatial hole‐board task. Mothers fed the prenatal Western diet had higher prepartum blood cholesterol and free fatty acid levels. Postnatal exposure to the Western diet did not affect piglet cognitive performance, but it did increase postpartum maternal and postweaning piglet cholesterol levels. The Western diet had no effect on maternal or offspring insulin sensitivity or leptin levels. In conclusion, a prenatal Western diet improved memory function in pigs, which was paired with changes in prepartum maternal blood cholesterol levels. These findings highlight the key role of late fetal nutrition for long‐term programming of cognition. —Clouard, C. , Kemp, B. , Val‐Laillet, D. , Gerrits, W. J. J., Bartels, A. C. , Bolhuis, J. E. Prenatal, but not early postnatal, exposure to a Western diet improves spatial memory of pigs later in life and is paired with changes in maternal prepartum blood lipid levels. FASEB J. 30, 2466‐2475 (2016). www.fasebj. org
Markup and the GOLD Ontology

Figure 4. Upper taxonomy for the ontology For linguistics we are concerned with the grammatical qualities of instances of LINGUISTICUNIT, or those qualities which determine how instances of LINGUISTICUNIT behave in the grammar of a language. Instances of MORPHOSYNTACTICFEATURE include: TENSE, ASPECT, MOOD, NUMBER, PERSON, PARTOFSPEECH, etc. A MORPHOSYNTACTICUNIT is said to stand in a HASGRAMINFO relationship to particular instances of MORPHOSYNTACTICFEATURE. Features have as their values instances of the class FEATUREVALUE. That is, specific features have specific values associated with them, e.g., the feature TENSE has as its possible values {PAST, PRESENT, . , FUTURE}. Values can be thought of as points in a particular space or region, in philosophical terms feature values are known as ‘qualia’. Tense values are points in tense space which are represented in the ontology as the class TENSEVALUE, where TENSEVALUE defines all the allowable values for tense in human language (see Gärdenfors 2000 for a discussion of this notion). Subtypes in the value hierarchy do exist. Using TenseValue as an example, we may pose the following taxonomy, in Figure 5. MORPHOSYNTACTICVALUE