Clean Prediction of \CP violating processes ψ\psi, ϕ\phi and Υ(1S)\Upsilon(1S) decay to KsKs and KLKL

The ratio of $K_S K_S$ ($K_L K_L$) and $K_S K_L$ production rates is calculated by considering $K^0 - K^0bar$ oscillation in $J/\psi \to K^0K^0bar$ decay. The theoretical uncertainty due to strong interaction in $J/\psi$ decay is completely canceled in the ratio, therefore, the absolute branching fractions of the \CP violating processes of $J/\psi \to K_S K_S$ and $K_L K_L$ can be cleanly and model-independently determined in case that $J/\psi \to K_S K_L$ decay is precisely measured. In the future $\tau$-Charm factory, the expected \CP violating process of $J/\psi \to K_S K_S$ should be reached. It is important to measure $J/\psi$ to $K_S K_S$ and K_S K_L decays simultaneously, so that many systematic errors will be canceled. More precise measurements are suggested to examine the predicted isospin relation in $J/\psi \to KKbar$ decays. All results can be extended to decays of other vector quarkonia, $\phi$, $\psi(2S)$ and $\Upsilon(1S)$ and so on.Comment: Version 2 is the same as published one at PR

Modeling the iron oxides and oxyhydroxides for the prediction of environmentally sensitive phase transformations

Iron oxides and oxyhydroxides are challenging to model computationally as competing phases may differ in formation energies by only several kJ/mol, they undergo magnetization transitions with temperature, their structures may contain partially occupied sites or long-range ordering of vacancies, and some loose structures require proper description of weak interactions such as hydrogen bonding and dispersive forces. If structures and transformations are to be reliably predicted under different chemical conditions, each of these challenges must be overcome simultaneously, while preserving a high level of numerical accuracy and physical sophistication. Here we present comparative studies of structure, magnetization, and elasticity properties of iron oxides and oxyhydroxides using density functional theory calculations with plane-wave and locally-confined-atomic-orbital basis sets, which are implemented in VASP and SIESTA packages, respectively. We have selected hematite, maghemite, goethite, lepidocrocite, and magnetite as model systems from a total of 13 known iron oxides and oxyhydroxides; and use same convergence criteria and almost equivalent settings in order to make consistent comparisons. Our results show both basis sets can reproduce the energetic stability and magnetic ordering, and are in agreement with experimental observations. There are advantages to choosing one basis set over the other, depending on the intended focus. In our case, we find the method using PW basis set most appropriate, and combine our results to construct the first phase diagram of iron oxides and oxyhydroxides in the space of competing chemical potentials, generated entirely from first principlesComment: 46 pages - Accepted for publication in PRB (19 journal pages), January 201

Release of cholesterol-rich particles from the macrophage plasma membrane during movement of filopodia and lamellipodia.

Cultured mouse peritoneal macrophages release large numbers of ~30-nm cholesterol-rich particles. Here, we show that those particles represent fragments of the plasma membrane that are pulled away and left behind during the projection and retraction of filopodia and lamellipodia. Consistent with this finding, the particles are enriched in proteins found in focal adhesions, which attach macrophages to the substrate. The release of particles is abolished by blocking cell movement (either by depolymerizing actin with latrunculin A or by inhibiting myosin II with blebbistatin). Confocal microscopy and NanoSIMS imaging studies revealed that the plasma membrane-derived particles are enriched in 'accessible cholesterol' (a mobile pool of cholesterol detectable with the modified cytolysin ALO-D4) but not in sphingolipid-sequestered cholesterol [a pool detectable with ostreolysin A (OlyA)]. The discovery that macrophages release cholesterol-rich particles during cellular locomotion is likely relevant to cholesterol efflux and could contribute to extracellular cholesterol deposition in atherosclerotic plaques

Low temperature ordering and high (001) orientation of [Fe/Pt/Cu]\u3csub\u3e18\u3c/sub\u3e multilayer films

[Fe/Pt/Cu]18 multilayer films with different Cu thicknesses were prepared on thermally oxidized Si (111) substrates at room temperature using dc- and rf-magnetron sputtering. The magnetic proper-ties and microstructure of [Fe/Pt/Cu]18 multilayer films annealed at various temperatures have been investigated. Compared with pure [Fe/Pt]18 multilayer films low-temperature ordering and (001) ori-entation in the annealed films with Cu volume concentration below 20% can be obtained. During annealing process Cu atoms diffused into FePt lattice which enhanced the diffusion of Fe and Pt atoms and the grain growth of the films. The perpendicular anisotropy and hard magnetic properties of the films deteriorated with increasing Cu volume concentration due to the formation of L10 Fe-CuPt2 phase

Low temperature ordering and high (001) orientation of [Fe/Pt/Cu]\u3csub\u3e18\u3c/sub\u3e multilayer films

[Fe/Pt/Cu]18 multilayer films with different Cu thicknesses were prepared on thermally oxidized Si (111) substrates at room temperature using dc- and rf-magnetron sputtering. The magnetic proper-ties and microstructure of [Fe/Pt/Cu]18 multilayer films annealed at various temperatures have been investigated. Compared with pure [Fe/Pt]18 multilayer films low-temperature ordering and (001) ori-entation in the annealed films with Cu volume concentration below 20% can be obtained. During annealing process Cu atoms diffused into FePt lattice which enhanced the diffusion of Fe and Pt atoms and the grain growth of the films. The perpendicular anisotropy and hard magnetic properties of the films deteriorated with increasing Cu volume concentration due to the formation of L10 Fe-CuPt2 phase

Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin [preprint]

In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining Nucleolus Associated Domains (NADs) and Lamina Associated Domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurately than other peak-calling tools, due to its critical feature of chromosome-level local baseline correction. We detected two distinct classes of NADs. Type I NADs associate frequently with both the nucleolar periphery and with the nuclear lamina, and generally display characteristics of constitutive heterochromatin, including late DNA replication, enrichment of H3K9me3 and little gene expression. In contrast, Type II NADs associate with nucleoli but do not overlap with LADs. Type II NADs tend to replicate earlier, display greater gene expression, and are more often enriched in H3K27me3 than Type I NADs. The nucleolar associations of both classes of NADs were confirmed via DNA-FISH, which also detected Type I but not Type II probes enriched at the nuclear lamina. Interestingly, Type II NADs are enriched in distinct gene classes, notably factors important for differentiation and development. In keeping with this, we observed that a Type II NAD is developmentally regulated, present in MEFs but not in undifferentiated embryonic stem (ES) cells

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. RESULTS: We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. CONCLUSIONS: This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html

Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data

Background: Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig. Results: Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted proteincoding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5′ end extension, 3′ end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3′-RNAseq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in \u3e 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data. Conclusions: These validated results show significant improvement over current pig genome annotations

Fe-Al-rich tridymite-hercynite xenoliths with positive cerium anomalies: preserved lateritic paleosols and implications for Miocene climate

Abstract We report isotopic and chemical compositions of unusual tridymite -hercynite xenoliths in middle Miocene Niutoushan tholeiites from the southeast coastal area of China. These xenoliths are characterized by positive cerium (Ce) anomalies and extremely high Al 2 O 3 (32 -34 wt.%) and total iron oxide (20 -22%). . Their chemical and isotopic compositions suggest that these xenoliths represent preserved aluminous lateritic paleosols that are not genetically related to host tholeiites. These lateritic paleosols with strongly desilicated minerals were formed by intense chemical weathering under warm and humid tropical conditions (with annual average temperature of >19 jC and the annual rainfall of >165 cm) in SE China during the interval from 17 to 15 Ma. The formation age of the paleosols corresponds to a period characterized by slow uplift of the Himalayan -Tibetan Plateau region (and thus less consumption of CO 2 ) after 17 Ma, and eruptions of 17 -15 Ma Columbia River flood basalts, the Vogelsberg basalts, and eastern China basalts (and thus more input of CO 2 into the atmosphere). The tridymite -hercynite xenoliths in the Niutoushan basalts thus preserve evidence of extraordinary climatic greenhouse conditions in the middle Miocene that would otherwise have been lost by the erosion of paleosols.

Comparison of Hermetic Storage of Wheat with Traditional Storage Methods in India

India is among the countries experiencing high postharvest losses. Four hermetic bags, two metallic bins, and two gunny bag (also known as jute or burlap bag) piles each containing 1 tonne of wheat were instrumented with temperature, relative humidity, and carbon dioxide sensors. Representative samples from each structure were collected each month and tests for moisture, germination, insect-damaged grain, and milling yield were performed. After nine months, wheat stored in hermetic bags had higher germination (87%) and lower insect-damaged grain percentages (0% to 0.33% with a mean value of 0.2%). Hermetic bags with deliberately introduced Rhyzopertha dominica successfully eliminated the pests. Gunny bag piles had infestations; metallic bins also were infested. Wheat moisture content in all structures varied depending upon ambient conditions; moisture variation was largest in gunny bag piles. Milling yields were lowest for gunny bag piles. Hermetic bags can be an effective and environmentally friendly solution for reducing storage losses of wheat in India