ALBERT

Beschreibung: Hypercubes and star graphs are widespread topologies of interconnection networks. The class of hyper-stars was introduced as a new type of interconnection network to compete with both hypercubes and star graphs, and the class of folded hyper-stars is a strengthened variation of hyper-stars with additional links to connect nodes with complemented 0/1-strings. Constructing independent spanning trees (ISTs) has numerous applications in networks such as fault-tolerant broadcasting and secure message distribution. Recently, Yang and Chang [IST on folded hyper-stars, Networks 56 (2010), 272–281] proposed an algorithm to construct $k+1$ ISTs on folded hyper-star $FHS(2k,k)$ . For $k\geqslant 4$ , their constructions include $k$ ISTs with a height $2k-2$ and the other one with a height $k+1$ . In this paper, we refine their constructed rules on $FHS(2k,k)$ for $k\geqslant 3$ and provide a set of constructions including $k$ ISTs with a height $k+2$ and the other one with a height $k+1$ . As a by-product, we obtain an improvement on the upper bound of the fault diameter (respectively, the wide diameter) of $FHS(2k,k)$ .

Beschreibung: Aims To determine if an experimentally applied anomalous weather year could have effects on species composition and community structure that would carry over into the following year. Methods We conducted a field experiment applying two levels of temperature (ambient and +4°C) and two levels of precipitation (ambient and doubled) and followed cover of plant species during the treatment year and one post-treatment year. Data analysis included ordination analysis, examination of species frequency distributions and comparison of cover of functional groups and individual species. Important Findings A drought during the summer and fall of the treatment year resulted in significant differences in community structure between the 2 years. C 3 and winter annual species were depressed in the spring of the second year following the dry autumn. Species richness and legume cover increased in the second, wetter, year. Treatments caused no overall differences in community structure but did alter the dominance hierarchy of species among treatments as well as years. Warming decreased relative cover of winter annuals and early spring-flowering species but increased other annuals. Warming and double precipitation together increased cover of C 4 perennial graminoids. In particular, the warming and precipitation treatments both increased the abundance of Andropogon gerardii , not individually altering the dominance hierarchy but together nearly doubling the relative cover of A.gerardii , making it the most abundant species in the combined treatment, while the cover of Bromus arvensis , the former dominant, decreased by 25%. The following year, Andropogon relative cover increased further in the former warmed plots, becoming dominant in both the formerly warmed and warmed plus double precipitation treatments. The year following treatments also saw an increase in relative cover of summer-blooming species in the formerly warmed plots and differences among the former treatments in species richness of functional groups. If the effects of one anomalous year on plant abundance can carry over into the following year, several warm years could have a significant impact on plant community structure.

Beschreibung: Stochastic local search (SLS) algorithms are well known for their ability to efficiently find models of random instances of the Boolean satisfiability (SAT) problem. One of the most famous SLS algorithms for SAT is WalkSAT, which is an initial algorithm that has wide influence and performs very well on random 3-SAT instances. However, the performance of WalkSAT on random k -SAT instances with k 〉 3 lags far behind. Indeed, there are limited works on improving SLS algorithms for such instances. This work takes a good step toward this direction. We propose a novel concept namely multilevel make . Based on this concept, we design a scoring function called linear make , which is utilized to break ties in WalkSAT, leading to a new algorithm called WalkSAT lm . Our experimental results show that WalkSAT lm improves WalkSAT by orders of magnitude on random k -SAT instances with k 〉 3 near the phase transition. Additionally, we propose an efficient implementation for WalkSAT lm , which leads to a speedup of 100%. We also give some insights on different forms of linear make functions, and show the limitation of the linear make function on random 3-SAT through theoretical analysis.

Beschreibung: For hiding messages into multiple least significant bit (MLSB) planes, a new weighted stego-image (WS)\ steganalysis method is proposed to estimate the ratio of messages hidden into each bit plane. First, a new WS with multiple weights is constructed, and it is proved that when the squared Euclidean distance between the WS and the cover image is minimal, the weight parameters are equal to the embedding ratios in MLSB planes. Afterward, based on this result and an estimation of cover image, a simple estimation equation is derived to estimate the embedding ratio in each bit plane. Experimental results show that the new steganalysis method performs more stably with the change of embedding ratios than typical structural steganalysis, and outperforms the typical structural steganalysis method on the estimation accuracy when the embedding ratio in any bit plane is larger than 0.4.

Beschreibung: Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain composed of two alpha helices that physically tethers the C-terminal domain to the SF2 helicase core. We find that the Pincer plays an important role in mediating the enzymatic and signaling activities of RIG-I. We identify a series of mutations that additively decouple the Pincer motif from the ATPase core and show that this decoupling results in impaired signaling. Through enzymological and biophysical analysis, we further show that the Pincer domain controls coupled enzymatic activity of the protein through allosteric control of the ATPase core. Further, we show that select regions of the HEL1 domain have evolved to potentiate interactions with the Pincer domain, resulting in an adapted ATPase cleft that is now responsive to adjacent domains that selectively bind viral RNA.

Beschreibung: Aims Recent studies revealed convergent temperature sensitivity of ecosystem respiration ( R e ) within aquatic ecosystems and between terrestrial and aquatic ecosystems. We do not know yet whether various terrestrial ecosystems have consistent or divergent temperature sensitivity. Here, we synthesized 163 eddy covariance flux sites across the world and examined the global variation of the apparent activation energy (Ea), which characterizes the apparent temperature sensitivity of and its interannual variability (IAV) as well as their controlling factors. Methods We used carbon fluxes and meteorological data across FLUXNET sites to calculate mean annual temperature, temperature range, precipitation, global radiation, potential radiation, gross primary productivity and R e by averaging the daily values over the years in each site. Furthermore, we analyzed the sites with 〉8 years data to examine the IAV of Ea and calculated the standard deviation of Ea across years at each site to characterize IAV. Important Findings The results showed a widely global variation of Ea, with significantly lower values in the tropical and subtropical areas than in temperate and boreal areas, and significantly higher values in grasslands and wetlands than that in deciduous broadleaf forests and evergreen forests. Globally, spatial variations of Ea were explained by changes in temperature and an index of water availability with differing contribution of each explaining variable among climate zones and biomes. IAV and the corresponding coefficient of variation of Ea decreased with increasing latitude, but increased with radiation and corresponding mean annual temperature. The revealed patterns in the spatial and temporal variations of Ea and its controlling factors indicate divergent temperature sensitivity of R e , which could help to improve our predictive understanding of R e in response to climate change.

Beschreibung: The major histocompatibility complex (MHC) containing the classical human leukocyte antigen (HLA) Class I and Class II genes is among the most polymorphic and diverse regions in the human genome. Despite the clinical importance of identifying the HLA types, very few databases jointly characterize densely genotyped single nucleotide polymorphisms (SNPs) and HLA alleles in the same samples. To date, the HapMap presents the only public resource that provides a SNP reference panel for predicting HLA alleles, constructed with four collections of individuals of north-western European, northern Han Chinese, cosmopolitan Japanese and Yoruba Nigerian ancestry. Owing to complex patterns of linkage disequilibrium in this region, it is unclear whether the HapMap reference panels can be appropriately utilized for other populations. Here, we describe a public resource for the Singapore Genome Variation Project with: (i) dense genotyping across ~9000 SNPs in the MHC; (ii) four-digit HLA typing for eight Class I and Class II loci, in 96 southern Han Chinese, 89 Southeast Asian Malays and 83 Tamil Indians. This resource provides population estimates of the frequencies of HLA alleles at these eight loci in the three population groups, particularly for HLA-DPA1 and HLA-DPB1 that were not assayed in HapMap. Comparing between population-specific reference panels and a cosmopolitan panel created from all four HapMap populations, we demonstrate that more accurate imputation is obtained with population-specific panels than with the cosmopolitan panel, especially for the Malays and Indians but even when imputing between northern and southern Han Chinese. As with SNP imputation, common HLA alleles were imputed with greater accuracy than low-frequency variants.

Beschreibung: After carefully cross-identifying previously discovered – and selected by the Galaxy Evolution Explorer ( GALEX ) – Lyman break galaxy (LBG) candidates one-to-one with their optical counterparts in the field of the Chandra Deep Field South (CDF-S), we re-estimate their photometric redshifts using multiwavelength data from ultraviolet and optical to near-infrared. Considering their re-estimated photometric redshifts and spectral energy distributions, we refine a new updated sample of 383 LBGs at 0.7 z 1.4, with two confirmed active galactic nuclei being excluded. There are 260 and 111 LBGs classified as starburst and irregular types, respectively. The ages of the LBGs span from several Myr to 1.5 Gyr with a median of ~50 Myr. Their dust-corrected star formation rates (SFRs) and stellar masses ( M * ) are 4–220 M yr –1 and from 2.3  x 10 8 to 4  x 10 11 M , with median values of ~25 M yr –1 and ~10 10 M . The rest-frame far-ultraviolet luminosity function of the LBGs is presented with the best-fitting Schechter parameters of α = –1.61 ± 0.40, M * = –20.40 ± 0.22 and * = (0.89 ± 0.30)  x 10 –3 Mpc –3 dex –1 . LBGs of irregular types are mainly distributed along the main sequence of star-forming galaxies, while most LBGs of starburst types are located in the starburst region. Together with previous studies, we suggest that the star formation mode for LBGs at z 〉 3 is mainly starburst, and that it evolves to be more significant to the quenching mode after z  ~ 3. A downsizing effect is clearly found, and we discuss the physical implications and comparisons with previous studies in detail. LBGs with larger SFRs are, on average, more compact. In the rest-frame colour ( U – B )– M * diagram, LBGs are distributed in the ‘blue’ cloud. We suggest that LBGs might evolve along the blue cloud from later to earlier types. The Hubble Space Telescope images in F606W ( V band) and F850LP ( z band) are taken from the Galaxy Evolution from Morphology and SEDs (GEMS) survey and the Great Observatories Origins Deep Survey South (GOODS-S) for morphological studies of LBGs. sextractor and galfit are applied in order to obtain their morphological parameters. We establish an image gallery of 277 LBGs, commonly detected in both bands, by visually classifying individual LBGs into the following types: chain, spiral, tadpole, bulge and clump. We define a morphological sample of 142 LBGs with reliable results of Sérsic indices and sizes in both bands. We find that LBGs at z  ~ 1 are dominated by disc-like galaxies, with median sizes of 2.34 and 2.68 kpc in F606W and F850LP, respectively. The correlations between the photometric and morphological properties of LBGs are investigated. Strong correlations between their half-light radii and M * (i.e. size–stellar mass relations) are found in both bands. We discuss the physical connections between the correlations and the downsizing effect.

Beschreibung: Motivation: Long non-coding RNAs (lncRNAs) are essential in many molecular pathways, and are frequently associated with disease but the mechanisms of most lncRNAs have not yet been characterized. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome, including lncRNA gene regions. As the number of studies on lncRNAs grows rapidly, it is necessary to evaluate the effects of genetic variations on lncRNAs. Results: Here, we present LncVar, a database of genetic variation associated with long non-coding genes in six species. We collected lncRNAs from the NONCODE database, and evaluated their conservation. We systematically integrated transcription factor binding sites and m 6 A modification sites of lncRNAs and provided comprehensive effects of SNPs on transcription and modification of lncRNAs. We collected putatively translated open reading frames (ORFs) in lncRNAs, and identified both synonymous and non-synonymous SNPs in ORFs. We also collected expression quantitative trait loci of lncRNAs from the literature. Furthermore, we identified lncRNAs in CNV regions as prognostic biomarker candidates of cancers and predicted lncRNA gene fusion events from RNA-seq data from cell lines. The LncVar database can be used as a resource to evaluate the effects of the variations on the biological function of lncRNAs. Availability and Implementation: LncVar is available at http://bioinfo.ibp.ac.cn/LncVar . Contact: rschen@ibp.ac.cn Supplementary information: Supplementary materials are available at Bioinformatics online.

Beschreibung: Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.