An Unstructured Phylogeographic Pattern with Extensive Gene Flow in an Endemic Bird of South China: Collared Finchbill (Spizixos semitorques)

Recent phylogeographical studies indicated that glacial oscillations played a key role on the phylogeographic pattern of extant species. As most studies have previously been carried out on heavily ice-covered regions, such as in European and North American regions, potential effects of climatic oscillations on species that are distributed on ice-free regions are less known. To address this, we investigated the phylogeographic pattern of an avian species endemic to South China, which was not glaciated during the Pleistocene glaciations. By using 2142 bp mitochondrial DNA, we identified 89 haplotypes defined by 39 polymorphic sites. A combination of high haplotype diversity (0.786–1.00) and low nucleotide diversity (0.00132–0.00252) was detected among geographic populations. Explicit genetic divergence was observed between S. s. semitorques and S. s. cinereicapillus but not detected among geographic populations of S. s. semitorques. Divergence time of the two subspecies was dated back to 87 Kyr which is congruent with the interglacial MIS 5. A weak phylogeographic structure due to strong gene flow among geographic populations was identified in this species, suggesting complex topography of South China has not formed barriers for this species

H5N1 avian influenza re-emergence of Lake Qinghai: phylogenetic and antigenic analyses of the newly isolated viruses and roles of migratory birds in virus circulation

Highly pathogenic avian influenza H5N1 virus has swept west across the globe and caused serious debates on the roles of migratory birds in virus circulation since the first large-scale outbreak in migratory birds of Lake Qinghai, 2005. In May 2006, another outbreak struck Lake Qinghai and six novel strains were isolated. To elucidate these QH06 viruses, the six isolates were subjected to whole-genome sequencing. Phylogenetic analyses show that QH06 viruses are derived from the lineages of Lake Qinghai, 2005. Five of the six novel isolates are adjacent to the strain A/Cygnus olor/Croatia/1/05, and the last one is related to the strain A/duck/Novosibirsk/02/05, an isolate of the flyway. Antigenic analyses suggest that QH06 and QH05 viruses are similar to each other. These findings implicate that QH06 viruses of Lake Qinghai may travel back via migratory birds, though not ruling out the possibility of local circulation of viruses of Lake Qinghai

The Survey of H5N1 Flu Virus in Wild Birds in 14 Provinces of China from 2004 to 2007

The highly pathogenic H5N1 avian influenza emerged in the year 1996 in Asia, and has spread to Europe and Africa recently. At present, effective monitoring and data analysis of H5N1 are not sufficient in Chinese mainland.)) were obviously higher than those in other 13 provinces. The results of sequence analysis indicated that the 17 strains isolated from wild birds were distributed in five clades (2.3.1, 2.2, 2.5, 6, and 7), which suggested that genetic diversity existed among H5N1 viruses isolated from wild birds. The five isolates from Qinghai came from one clade (2.2) and had a short evolutionary distance with the isolates obtained from Qinghai in the year 2005.We have measured the prevalence of H5N1 virus in 56 species of wild birds in 14 provinces of China. Continuous monitoring in the field should be carried out to know whether H5N1 virus can be maintained by wild birds

Establishment of porcine and human expanded potential stem cells.

We recently derived mouse expanded potential stem cells (EPSCs) from individual blastomeres by inhibiting the critical molecular pathways that predispose their differentiation. EPSCs had enriched molecular signatures of blastomeres and possessed developmental potency for all embryonic and extra-embryonic cell lineages. Here, we report the derivation of porcine EPSCs, which express key pluripotency genes, are genetically stable, permit genome editing, differentiate to derivatives of the three germ layers in chimeras and produce primordial germ cell-like cells in vitro. Under similar conditions, human embryonic stem cells and induced pluripotent stem cells can be converted, or somatic cells directly reprogrammed, to EPSCs that display the molecular and functional attributes reminiscent of porcine EPSCs. Importantly, trophoblast stem-cell-like cells can be generated from both human and porcine EPSCs. Our pathway-inhibition paradigm thus opens an avenue for generating mammalian pluripotent stem cells, and EPSCs present a unique cellular platform for translational research in biotechnology and regenerative medicine

Dual-energy CT for the detection of skull base invasion in nasopharyngeal carcinoma: comparison of simulated single-energy CT and MRI

Abstract Background Skull base invasion in nasopharyngeal carcinoma (NPC) was shown to be a poor negative prognostic factor, and dual-energy CT (DECT) has heralded a new approach to detect this condition. The study aims to evaluate the value of DECT for detection of skull base invasion in NPC and compare the diagnostic performance of DECT with those of simulated single-energy CT (SECT) and MRI. Methods The imaging findings of 50 NPC patients and 31 participants in control group which underwent DECT examinations were assessed in this retrospective study. The skull base invasions were evaluated using 5-point scale by two blind observers. ROC analysis, Mcnemar test, paired t test, weighted K statistics and intraclass correlation coefficient were performed to evaluate the diagnostic performance of simulated SECT, MRI and DECT. Results Quantitative analysis of DECT parameters showed higher normalized iodine concentration and effective atomic number values in sclerosis and lower values in erosion than those in normal bones (both p < 0.05). Compared with simulated SECT and MRI, the diagnostic sensitivity for DECT was significantly improved from 75% (simulated SECT) and 84.26% (MRI) to 90.74% (DECT) (both p < 0.001), specificity from 93.23% and 93.75% to 95.31 (both p < 0.001), accuracy from 86.67% and 90.33% to 93.67%, and AUC from 0.927 and 0.955 to 0.972 (both p < 0.05), respectively. Conclusions DECT demonstrates better diagnostic performance than simulated SECT and MRI for detecting skull base invasions in NPC, even those slight bone invasions in early stage, with higher sensitivity, specificity and accuracy. Graphical Abstrac

Schedulability analysis with CCSL specifications

International audienceThe Clock Constraint Specification Language (CCSL) is a formal polychronous language based on the notion of logical clock. It defines a set of kernel constraints that can represent both asynchronous and synchronous relations. It was originally developed as part of the UML Profile for MARTE to express causal and temporal constraints of Real-time and Embedded Systems. In this paper, we explore the use of CCSL for modeling scheduling requirements and to conduct schedulability analysis. For this purpose, a dedicated scheduling library of CCSL has been built. This library is endowed with a state-based operational semantics, and is applied to solve issues related to schedulability analysis and latency-insensitive design. We establish schedulability categories and latency-insensitiveness property in the context of the semantics, and solve those issues by using model checking techniques

Phylogeography of the <it>Alcippe morrisonia </it>(Aves: Timaliidae): long population history beyond late Pleistocene glaciations

<p>Abstract</p> <p>Background</p> <p>The role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, <it>Alcippe morrisonia</it>, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of <it>A. morrisonia </it>to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China.</p> <p>Results</p> <p>Mitochondrial genes cytochrome b (Cytb) and cytochrome c oxidase I (COI) were represented by 1236 nucleotide sites from 151 individuals from 29 localities. Phylogenetic analysis showed seven monophyletic clades congruent with the geographically separated groups, which were identified as major sources of molecular variance (90.92%) by AMOVA. TCS analysis revealed four disconnected networks, and that no haplotype was shared among the geographical groups. The common ancestor of these populations was dated to 11.6 Mya and several divergence events were estimated along the population evolutionary history. Isolation by distance was inferred by NCPA to be responsible for the current intra-population genetic pattern and gene flow among geographical groups was interrupted. A late Pleistocene demographic expansion was detected in the eastern geographical groups, while the expansion time (0.2–0.4 Mya) was earlier than the Last Glacial Maximum.</p> <p>Conclusion</p> <p>It is proposed that the complicated topology preserves high genetic diversity and ancient lineages for geographical groups of <it>A. morrisonia </it>in China mainland and its two major islands, and restricts gene exchange during climate oscillations. Isolation by distance seems to be an important factor of genetic structure formation within geographical populations. Although glacial influence to population fluctuation was observed in late Pleistocene, it seems that populations in eastern China were more susceptible to climate change, and all geographical groups were growing stably through the Last Glacial Maximum. Coalescence analysis suggested that the ancestor of <it>A. morrisonia </it>might be traced back to the late Miocene, and the current phylogeographical structure of <it>A. morrisonia </it>is more likely to be attributable to a series geological events than to Pleistocene glacial cycles.</p

Abnormal Topological Organization of White Matter Structural Networks in Normal Tension Glaucoma Revealed via Diffusion Tensor Tractography

Background: Normal tension glaucoma (NTG) is considered a neurodegenerative disease with glaucomatous damage extending to diffuse brain areas. Therefore, this study aims to explore the abnormalities in the NTG structural network to help in the early diagnosis and course evaluation of NTG. Methods: The structural networks of 46 NTG patients and 19 age- and sex-matched healthy controls were constructed using diffusion tensor imaging, followed by graph theory analysis and correlation analysis of small-world properties with glaucoma clinical indicators. In addition, the network-based statistical analysis (NBS) method was used to compare structural network connectivity differences between NTG patients and healthy controls. Results: Structural brain networks in both NTG and NC groups exhibited small-world properties. However, the small-world index in the severe NTG group was reduced and correlated with a mean deviation of the visual field (MDVF) and retinal nerve fiber layer (RNFL) thickness. When compared to healthy controls, degree centrality and nodal efficiency in visual brain areas were significantly decreased, and betweenness centrality and nodal local efficiency in both visual and nonvisual brain areas were also significantly altered in NTG patients (all p p < 0.05). Conclusions: NTG exhibited altered global properties and local properties of visual and cognitive-emotional brain areas, with enhanced structural connections within the occipitotemporal area. Moreover, the disrupted small-world properties of white matter might be imaging biomarkers for assessing NTG progression

Laminar Flame Characteristics and Kinetic Modeling Study of Ethyl Tertiary Butyl Ether Compared with Methyl Tertiary Butyl Ether, Ethanol, iso-Octane, and Gasoline

Laminar flame speeds of ethyl tertiary butyl ether (ETBE) were measured in a constant volume bomb at different initial temperatures (298 K, 373 K, 453 K) and pressures (1 atm, 3 atm, 5 atm). The laminar flame experiments were also conducted for methyl tertiary butyl ether (MTBE), ethanol, iso-octane, and gasoline for the comparison of laminar flame speeds and Markstein lengths. Experimental results show that laminar flame speeds peak at the equivalence ratio of 1.1 for all tested fuels. Ethanol has the fastest laminar flame speed and the other fuels have similar flame speeds, indicating replacing MTBE with ETBE in gasoline will not influence the laminar flame speed of present gasoline. The CRECK and Curran mechanisms were validated by experimental results of ETBE and neither could predict laminar flame speeds well. Curran mechanism was optimized by updating the underlying mechanism, and the Modified Curran mechanism has better prediction performance on the laminar flame speed. Sensitivity analyses were also provided to interpret the differences of laminar flame speeds and the major reason for better prediction performance for Modified Curran mechanism. The result of Markstein length shows that gasoline has the smallest Markstein lengths and its flame front is the most unstable. The Markstein lengths of ETBE and iso-octane differ little and are the largest under ϕ < 1.2. Ethanol has the largest Markstein lengths under ϕ > 1.2