共查询到20条相似文献,搜索用时 109 毫秒
1.
Background
A frontoparietal dome of a large pachycephalosaurid collected from the Upper Cretaceous Hell Creek Formation in 2001 is identified as Pachycephalosaurus wyomingensis. The specimen features two large oval depressions on the dorsal surface, accompanied by numerous circular pits on the margin and inner surface of the larger depressions.Methodology/Principal Findings
In order to identify the origin of these structures, computed tomography (CT) data and morphological characteristics of the specimen are analyzed and compared with similar osteological structures in fossil and extant archosaurs caused by taphonomic processes, non-pathologic bone resorption, and traumatic infection/inflammatory origins. The results of these analyses suggest that the structures are pathologic lesions likely resulting from a traumatic injury and followed by secondary infection at the site.Conclusions/Significance
The presence of lesions on a frontoparietal dome, and the exclusivity of their distribution along the dorsal dome surface, offers further insight into frontoparietal dome function and supports previously hypothesized agonistic behavior in pachycephalosaurids. 相似文献2.
Hui Miao Mikael Hartman Nirmala Bhoo-Pathy Soo-Chin Lee Nur Aishah Taib Ern-Yu Tan Patrick Chan Karel G. M. Moons Hoong-Seam Wong Jeremy Goh Siti Mastura Rahim Cheng-Har Yip Helena M. Verkooijen 《PloS one》2014,9(4)
Background
In Asia, up to 25% of breast cancer patients present with distant metastases at diagnosis. Given the heterogeneous survival probabilities of de novo metastatic breast cancer, individual outcome prediction is challenging. The aim of the study is to identify existing prognostic models for patients with de novo metastatic breast cancer and validate them in Asia.Materials and Methods
We performed a systematic review to identify prediction models for metastatic breast cancer. Models were validated in 642 women with de novo metastatic breast cancer registered between 2000 and 2010 in the Singapore Malaysia Hospital Based Breast Cancer Registry. Survival curves for low, intermediate and high-risk groups according to each prognostic score were compared by log-rank test and discrimination of the models was assessed by concordance statistic (C-statistic).Results
We identified 16 prediction models, seven of which were for patients with brain metastases only. Performance status, estrogen receptor status, metastatic site(s) and disease-free interval were the most common predictors. We were able to validate nine prediction models. The capacity of the models to discriminate between poor and good survivors varied from poor to fair with C-statistics ranging from 0.50 (95% CI, 0.48–0.53) to 0.63 (95% CI, 0.60–0.66).Conclusion
The discriminatory performance of existing prediction models for de novo metastatic breast cancer in Asia is modest. Development of an Asian-specific prediction model is needed to improve prognostication and guide decision making. 相似文献3.
4.
Background
Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies.Principal Findings
We present a novel heuristic algorithm, Pebble, which uses paired-end read information to resolve repeats and scaffold contigs to produce large-scale assemblies. In simulations, we can achieve weighted median scaffold lengths (N50) of above 1 Mbp in Bacteria and above 100 kbp in more complex organisms. Using real datasets we obtained a 96 kbp N50 in Pseudomonas syringae and a unique 147 kbp scaffold of a ferret BAC clone. We also present an efficient algorithm called Rock Band for the resolution of repeats in the case of mixed length assemblies, where different sequencing platforms are combined to obtain a cost-effective assembly.Conclusions
These algorithms extend the utility of short read only assemblies into large complex genomes. They have been implemented and made available within the open-source Velvet short-read de novo assembler. 相似文献5.
Background
Haloquadratum walsbyi represents up to 80 % of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid library and recovered seven novel version of its cell-wall associated genomic island. The fosmid inserts were sequenced and analysed.Results
The novel cell-wall associated islands delineated two major clades within H. walsbyi. The islands predominantly contained genes putatively involved in biosynthesis of surface layer, genes encoding cell surface glycoproteins and genes involved in envelope formation. We further found that these genes are maintained in the population and that the diversity of this region arises through homologous recombination but also through the action of mobile genetic elements, including viruses.Conclusions
The population of H. walsbyi in the studied saltern brine is composed of numerous clonal lineages that differ in surface structures including the cell wall. This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating viruses.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1794-8) contains supplementary material, which is available to authorized users. 相似文献6.
Songfeng Yu Feng Gao Jun Yu Sheng Yan Jian Wu Min Zhang Weilin Wang Shusen Zheng 《PloS one》2014,9(1)
Background
De novo cancers are a growing problem that has become one of the leading causes of late mortality after liver transplantation. The incidences and risk factors varied among literatures and fewer concerned the Eastern population.Aims
The aim of this study was to examine the incidence and clinical features of de novo cancers after liver transplantation in a single Chinese center.Methods
569 patients who received liver transplantation and survived for more than 3 months in a single Chinese center were retrospectively reviewed.Results
A total of 18 de novo cancers were diagnosed in 17 recipients (13 male and 4 female) after a mean of 41±26 months, with an overall incidence of 3.2%, which was lower than that in Western people. Of these, 8 (3.32%) cases were from 241 recipients with malignant liver diseases before transplant, while 10 (3.05%) cases were from 328 recipients with benign diseases. The incidence rates were comparable, p = 0.86. Furthermore, 2 cases developed in 1 year, 5 cases in 3 years and 11 cases over 3 years. The most frequent cancers developed after liver transplantation were similar to those in the general Chinese population but had much higher incidence rates.Conclusions
Liver transplant recipients were at increased risk for developing de novo cancers. The incidence rates and pattern of de novo cancers in Chinese population are different from Western people due to racial and social factors. Pre-transplant malignant condition had no relationship to de novo cancer. Exact risk factors need further studies. 相似文献7.
8.
9.
Background
Extended neoteny and late stage allometric growth increase morphological disparity between growth stages in at least some dinosaurs. Coupled with relatively low dinosaur density in the Upper Cretaceous of North America, ontogenetic transformational representatives are often difficult to distinguish. For example, many hadrosaurids previously reported to represent relatively small lambeosaurine species were demonstrated to be juveniles of the larger taxa. Marginocephalians (pachycephalosaurids + ceratopsids) undergo comparable and extreme cranial morphological change during ontogeny.Methodology/Principal Findings
Cranial histology, morphology and computer tomography reveal patterns of internal skull development that show the purported diagnostic characters for the pachycephalosaurids Dracorex hogwartsia and Stygimoloch spinifer are ontogenetically derived features. Coronal histological sections of the frontoparietal dome of an adult Pachycephalosaurus wyomingensis reveal a dense structure composed of metaplastic bone with a variety of extremely fibrous and acellular tissue. Coronal histological sections and computer tomography of a skull and frontoparietal dome of Stygimoloch spinifer reveal an open intrafrontal suture indicative of a subadult stage of development. These dinosaurs employed metaplasia to rapidly grow and change the size and shape of their horns, cranial ornaments and frontoparietal domes, resulting in extreme cranial alterations during late stages of growth. We propose that Dracorex hogwartsia, Stygimoloch spinifer and Pachycephalosaurus wyomingensis are the same taxon and represent an ontogenetic series united by shared morphology and increasing skull length.Conclusions/Significance
Dracorex hogwartsia (juvenile) and Stygimoloch spinifer (subadult) are reinterpreted as younger growth stages of Pachycephalosaurus wyomingensis (adult). This synonymy reduces the number of pachycephalosaurid taxa from the Upper Cretaceous of North America and demonstrates the importance of cranial ontogeny in evaluating dinosaur diversity and taxonomy. These growth stages reflect a continuum rather than specific developmental steps defined by “known” terminal morphologies. 相似文献10.
Gustavo A. Santa Cruz 《Reports of Practical Oncology and Radiotherapy》2016,21(2):135-139
Aim
to present the most important aspects of Microdosimetry, a research field in radiation biophysics.Background
microdosimetry is the branch of radiation biophysics that systematically studies the spatial, temporal and spectral aspects of the stochastic nature of the energy deposition processes in microscopic structures.Materials and Methods
we briefly review its history, the people, the formalism and the theories and devices that allowed researchers to begin to understand the true nature of radiation action on living matter.Results and Conclusions
we outline some of its applications, especially to Boron Neutron Capture Therapy, attempting to explain the biological effectiveness of the boron thermal neutron capture reaction. 相似文献11.
Background
Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders.Methodology
Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold''s surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space.Conclusions and Significance
This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor. 相似文献12.
Background
Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage.Results
Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes).Conclusions
Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa. 相似文献13.
Chauveau O Eggers L Raquin C Silvério A Brown S Couloux A Cruaud C Kaltchuk-Santos E Yockteng R Souza-Chies TT Nadot S 《Annals of botany》2011,107(8):1287-1312
Background and Aims
Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined.Methods
Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species.Key Results and Conclusions
Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paraná river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing. 相似文献14.
McDonald AT Kirkland JI DeBlieux DD Madsen SK Cavin J Milner AR Panzarin L 《PloS one》2010,5(11):e14075
Background
Basal iguanodontian dinosaurs were extremely successful animals, found in great abundance and diversity almost worldwide during the Early Cretaceous. In contrast to Europe and Asia, the North American record of Early Cretaceous basal iguanodonts has until recently been limited largely to skulls and skeletons of Tenontosaurus tilletti.Methodology/Principal Findings
Herein we describe two new basal iguanodonts from the Yellow Cat Member of the Cedar Mountain Formation of eastern Utah, each known from a partial skull and skeleton. Iguanacolossus fortis gen. et sp. nov. and Hippodraco scutodens gen. et sp. nov. are each diagnosed by a single autapomorphy and a unique combination of characters.Conclusions/Significance
Iguanacolossus and Hippodraco add greatly to our knowledge of North American basal iguanodonts and prompt a new comprehensive phylogenetic analysis of basal iguanodont relationships. This analysis indicates that North American Early Cretaceous basal iguanodonts are more basal than their contemporaries in Europe and Asia. 相似文献15.
Background and Aims
Asexual reproduction is a prominent evolutionary process within land plant lineages and especially in ferns. Up to 10 % of the approx. 10 000 fern species are assumed to be obligate asexuals. In the Asplenium monanthes species complex, previous studies identified two triploid, apomictic species. The purpose of this study was to elucidate the phylogenetic relationships in the A. monanthes complex and to investigate the occurrence and evolution of apomixis within this group.Methods
DNA sequences of three plastid markers and one nuclear single copy gene were used for phylogenetic analyses. Reproductive modes were assessed by examining gametophytic and sporophyte development, while polyploidy was inferred from spore measurements.Key Results
Asplenium monanthes and A. resiliens are confirmed to be apomictic. Asplenium palmeri, A. hallbergii and specimens that are morphologically similar to A. heterochroum are also found to be apomictic. Apomixis is confined to two main clades of taxa related to A. monanthes and A. resiliens, respectively, and is associated with reticulate evolution. Two apomictic A. monanthes lineages, and two putative diploid sexual progenitor species are identified in the A. monanthes clade.Conclusions
Multiple origins of apomixis are inferred, in both alloploid and autoploid forms, within the A. resiliens and A. monanthes clades. 相似文献16.
17.
18.
Pandya GA McEllistrem MC Venepally P Holmes MH Jarrahi B Sanka R Liu J Karamycheva SA Bai Y Fleischmann RD Peterson SN 《PloS one》2011,6(1):e15950
Background
While the pneumococcal protein conjugate vaccines reduce the incidence in invasive pneumococcal disease (IPD), serotype replacement remains a major concern. Thus, serotype-independent protection with vaccines targeting virulence genes, such as PspA, have been pursued. PspA is comprised of diverse clades that arose through recombination. Therefore, multi-locus sequence typing (MLST)-defined clones could conceivably include strains from multiple PspA clades. As a result, a method is needed which can both monitor the long-term epidemiology of the pneumococcus among a large number of isolates, and analyze vaccine-candidate genes, such as pspA, for mutations and recombination events that could result in ‘vaccine escape’ strains.Methodology
We developed a resequencing array consisting of five conserved and six variable genes to characterize 72 pneumococcal strains. The phylogenetic analysis of the 11 concatenated genes was performed with the MrBayes program, the single nucleotide polymorphism (SNP) analysis with the DNA Sequence Polymorphism program (DnaSP), and the recombination event analysis with the recombination detection package (RDP).Results
The phylogenetic analysis correlated with MLST, and identified clonal strains with unique PspA clades. The DnaSP analysis correlated with the serotype-specific diversity detected using MLST. Serotypes associated with more than one ST complex had a larger degree of sequence polymorphism than a serotype associated with one ST complex. The RDP analysis confirmed the high frequency of recombination events in the pspA gene.Conclusions
The phylogenetic tree correlated with MLST, and detected multiple PspA clades among clonal strains. The genetic diversity of the strains and the frequency of recombination events in the mosaic gene, pspA were accurately assessed using the DnaSP and RDP programs, respectively. These data provide proof-of-concept that resequencing arrays could play an important role within research and clinical laboratories in both monitoring the molecular epidemiology of the pneumococcus and detecting ‘vaccine escape’ strains among vaccine-candidate genes. 相似文献19.
20.