Accurate autocorrelation modeling substantially improves fMRI reliability
Accurate autocorrelation modeling substantially improves fMRI reliability, Published online: 25 December 2019; doi:10.1038/s41467-019-09230-wThere has been recent controversy over the validity of commonly-used software packages for functional MRI (fMRI) data analysis. Here, the authors compare the performance of three leading packages (AFNI, FSL, SPM) in terms of temporal autocorrelation modeling, a key statistical step in fMRI analysis.
In a continuing effort to address high rates of maternal mortality in the United States, the American College of Obstetrics...
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Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10377-9Phase gradient metagratings suffer from limits on conversion efficiency. Here, the authors show a refractive-type metagrating which can enable anomalous reflection and refraction with almost unity efficiency over a wide incident range and uncover how integer parity plays a role in higher order diffraction.
Poly(bis-arylimidazoliums) possessing high hydroxide ion exchange capacity and high alkaline stability
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10292-zThe hydroxide anion exchange polymers are key materials of solid polymer electrolyte devices that operate under alkaline conditions. Here the authors show the rational design of such polymers that exhibit high ion exchange capacity and exceptional stability under highly caustic conditions.
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10283-0It has been predicted theoretically that the density of self-propelled particles whose speed is spatially dependent should be inversely proportional to the local speed. Here the authors present a systematic check of this prediction in a system of light-activated E. coli.
qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10332-8Measuring relative frequencies of DNA double-strand breaks between loci does not provide the full physiological relevance of those breaks. Here Rowicka and colleagues present qDSB-Seq method which uses spike-in double-strand breaks induced by a restriction enzyme to accurately quantify DNA damage.
Collective cell migration and metastases induced by an epithelial-to-mesenchymal transition in <i>Drosophila</i> intestinal tumors
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10269-yModelling and visualizing tumor metastasis in Drosophila has been a challenge. Here, the authors show that constitutive expression of Sna in primary adult Drosophila intestinal tumors drives EMT and dissemination of tumor cells, induces collective cell migration and formation of polyclonal metastases.
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10370-2Habitat loss could affect ecological communities in variable ways depending on its structure. Here, the authors show that contiguous rather than random loss is more damaging to the stability of multitrophic communities, regardless of the fraction of mutualistic interactions within the community.
<i>Schistosoma mansoni</i> treatment reduces HIV entry into cervical CD4+ T cells and induces IFN-I pathways
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-09900-9Schistosoma mansoniinfection has been linked with an increased risk of HIV acquisition in women. Here, the authors show that standard S. mansoniinfection treatment causes a reduction of HIV entry into cervical and blood CD4+ T cells, which is sustained for up to two months and is associated with de-repression of IFN-I signaling.
Absorbable hemostatic hydrogels comprising composites of sacrificial templates and honeycomb-like nanofibrous mats of chitosan
Nature Communications, Published online: 24 May 2019; doi:10.1038/s41467-019-10290-1Sacrificial templates are used for a range of different applications. Here, the authors synthesise a hyperbranched cyclodextrin polyester template with large void spaces, which is degraded in physiological conditions, and use it to create high surface area chitosan scaffolds for haemostatic applications.
Genetics in Medicine, Published online: 24 May 2019; doi:10.1038/s41436-019-0550-xChromosomal microarray vs. NIPS: analysis of 5541 low-risk pregnancies
An 84-year-old man becomes oldest living kidney donor in the United States at Houston Methodist Hospital
An 84-year-old Texas man recently became the oldest living kidney donor in the country after donating one of his kidneys...
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Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans [RESOURCES]
Long-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated within a species, we sequenced a C. elegans strain, CB4856, which is one of the most genetically divergent strains compared to the N2 reference strain. For this comparison, we used the Pacific Biosciences (PacBio) RSII platform (80x, N50 read length 11.8 kb) and generated de novo genome assembly to the level of pseudochromosomes containing 76 contigs (N50 contig = 2.8 Mb). We identified structural variations that affected as many as 2694 genes, most of which are at chromosome arms. Subtelomeric regions contained the most extensive genomic rearrangements, which even created new subtelomeres in some cases. The subtelomere structure of Chromosome VR implies that ancestral telomere damage was repaired by alternative lengthening of telomeres even in the presence of a functional telomerase gene and that a new subtelomere was formed by break-induced replication. Our study demonstrates that substantial genomic changes including structural variations and new subtelomeres can be tolerated within a species, and that these changes may accumulate genetic diversity within a species.
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution [RESOURCES]
We have used RNA-seq in Caenorhabditis elegans to produce transcription profiles for seven specific embryonic cell populations from gastrulation to the onset of terminal differentiation. The expression data for these seven cell populations, covering major cell lineages and tissues in the worm, reveal the complex and dynamic changes in gene expression, both spatially and temporally. Also, within genes, start sites and exon usage can be highly differential, producing transcripts that are specific to developmental periods or cell lineages. We have also found evidence of novel exons and introns, as well as differential usage of SL1 and SL2 splice leaders. By combining this data set with the modERN ChIP-seq resource, we are able to support and predict gene regulatory relationships. The detailed information on differences and similarities between gene expression in cell lineages and tissues should be of great value to the community and provides a framework for the investigation of expression in individual cells.
Cell-Type Heterogeneity in Adipose Tissue Is Associated with Complex Traits and Reveals Disease-Relevant Cell-Specific eQTLs
HOUSTON – (May 23, 2019) – Years of home-schooling don’t appear to influence the general health of children, according to...
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