420 research outputs found
The Generalized Makeev Problem Revisited
No full textBased on a result of Makeev, in 2012 Blagojevi\'c and Karasev proposed the
following problem: given any positive integers and , find
the minimum dimension such that for any mass
distributions on , there exist hyperplanes, any of
which equipartition each mass. The case is a central question in
geometric and topological combinatorics which remains open except for few
values of and . For and arbitrary , we establish new upper
bounds on when (1) and is arbitrary and (2)
and . When and is a power of two these bounds
are nearly optimal and are exponentially smaller than the current best upper
bounds when . Similar remarks apply to our upper bounds when the
hyperplanes are prescribed to be pairwise orthogonal. Lastly, we provide
transversal extensions of our results along the lines recently established by
Frick et al.: given families of compact convex sets in such
that no members of any family are pairwise disjoint, we show that
every member of each family is pierced by the union of any of some
collection of hyperplanes.Comment: 17 pages. Final version, corrects typo
Age determinations at sites Reshet, Balyk, Drag and Priam on Kotelny Island
No full textAge determinations at sites Reshet, Balyk, Drag and Priam on Kotelny Islan
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease.
No full textBACKGROUND: Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated with autoimmune diseases. We aimed to investigate VDR binding in primary CD4+ cells from healthy volunteers. METHODS: We extracted CD4+ cells from nine healthy volunteers. Each sample underwent VDR ChIP-seq. Our results were analyzed in relation to published ChIP-seq and RNA-seq data in the Genomic HyperBrowser. We used MEMEChIP for de novo motif discovery. 25-Hydroxyvitamin D levels were measured using liquid chromatography-tandem mass spectrometry and samples were divided into vitamin D sufficient (25(OH)D ≥75 nmol/L) and insufficient/deficient (25(OH)D <75 nmol/L) groups. RESULTS: We found that the amount of VDR binding is correlated with the serum level of 25-hydroxyvitamin D (r = 0.92, P= 0.0005). In vivo VDR binding sites are enriched for autoimmune disease associated loci, especially when 25-hydroxyvitamin D levels (25(OH)D) were sufficient (25(OH)D ≥75: 3.13-fold, P<0.0001; 25(OH)D <75: 2.76-fold, P<0.0001; 25(OH)D ≥75 enrichment versus 25(OH)D <75 enrichment: P= 0.0002). VDR binding was also enriched near genes associated specifically with T-regulatory and T-helper cells in the 25(OH)D ≥75 group. MEME ChIP did not identify any VDR-like motifs underlying our VDR ChIP-seq peaks. CONCLUSION: Our results show a direct correlation between in vivo 25-hydroxyvitamin D levels and the number of VDR binding sites, although our sample size is relatively small. Our study further implicates VDR binding as important in gene-environment interactions underlying the development of autoimmunity and provides a biological rationale for 25-hydroxyvitamin D sufficiency being based at 75 nmol/L. Our results also suggest that VDR binding in response to physiological levels of vitamin D occurs predominantly in a VDR motif-independent manner
Study of degradation processes kinetics in ohmic contacts of resonant tunneling diodes based on nanoscale AlAs/GaAs heterostructures under influence of temperature
No full textSingle cell analyses of ES cells reveal alternative pluripotent cell states and molecular mechanisms that control self-renewal
No full textAnalyses of gene expression in single mouse embryonic stem cells (mESCs) cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM). In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN) reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP) data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB) suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations
No full textKeilwagen J, Baumbach J, Kohl TA, Grosse I. MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology. 2009;10(5):R46.Valuable binding-site annotation data are stored in databases. However, several types of errors can, and do, occur in the process of manually incorporating annotation data from the scientific literature into these databases. Here, we introduce MotifAdjuster http://dig.ipk-gatersleben.de/MotifAdjuster.html webcite, a tool that helps to detect these errors, and we demonstrate its efficacy on public data sets
Seedlings' growth in response to drought stress and 2,4-dichlorophenoxyacetic acid (2,4-D)
No full textThe aim of this work was to study the effect of the herbicide, 2,4-D on a mono- cot (Lolium temulentum Linn.) and a dicot (Raphanus sativus Linn.) in relation to drought stress, in order to elucidate if the combined treatments altered the survival of the plants. Herbicide effects were investigated on a number of plant developmental stages; germination, seedling growth, mature leaves and root function, and were combined with various water stress regimes.2,4-D did not alter the germination percentage in either species when applied singly or with polyethylene glycol (PEG) induce water stress. However, rate of seedling emergence and accumulation of chlorophyll, protein and proline were inhibited. Foliar application of 2,4-D at selective concentrations showed that in addition to induced growth distortion the herbicide reduced the survivial capacity of radish but enhanced that of rye grass to later drought stress. Analysis of the content of proline (a stress metabolite) in both species indicated that the accumulation of this compound was reduced in radish but enhanced in rye grass. In contrast, when 2,4-,VJ)&^Dlapplied via the roots, from water culture, the selectivity of effect was lost since proline accumulation was reduced in both species. Use of (^14)C-2,4-D showed that the herbicide remained in the roots when applied in water culture and that since a major response was seen in the roots this implied that some signalling was occuring between the two organs. From the results it would appear that the use of low doses of herbicides such as 2,4-D may be valuable in protecting certain plants from drought stress, whilst the susceptability of other plants could be increased hence making the herbicide more effective at low concentrations
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