cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture.

Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD) boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits

The energy spectrum of all-particle cosmic rays around the knee region observed with the Tibet-III air-shower array

We have already reported the first result on the all-particle spectrum around the knee region based on data from 2000 November to 2001 October observed by the Tibet-III air-shower array. In this paper, we present an updated result using data set collected in the period from 2000 November through 2004 October in a wide range over 3 decades between $10^{14}$ eV and $10^{17}$ eV, in which the position of the knee is clearly seen at around 4 PeV. The spectral index is -2.68 $\pm$ 0.02(stat.) below 1PeV, while it is -3.12 $\pm$ 0.01(stat.) above 4 PeV in the case of QGSJET+HD model, and various systematic errors are under study now.Comment: 12 pages, 7 figures, accepted by Advances in space researc

Moon Shadow by Cosmic Rays under the Influence of Geomagnetic Field and Search for Antiprotons at Multi-TeV Energies

We have observed the shadowing of galactic cosmic ray flux in the direction of the moon, the so-called moon shadow, using the Tibet-III air shower array operating at Yangbajing (4300 m a.s.l.) in Tibet since 1999. Almost all cosmic rays are positively charged; for that reason, they are bent by the geomagnetic field, thereby shifting the moon shadow westward. The cosmic rays will also produce an additional shadow in the eastward direction of the moon if cosmic rays contain negatively charged particles, such as antiprotons, with some fraction. We selected 1.5 x10^{10} air shower events with energy beyond about 3 TeV from the dataset observed by the Tibet-III air shower array and detected the moon shadow at $\sim 40 \sigma$ level. The center of the moon was detected in the direction away from the apparent center of the moon by 0.23$^\circ$ to the west. Based on these data and a full Monte Carlo simulation, we searched for the existence of the shadow produced by antiprotons at the multi-TeV energy region. No evidence of the existence of antiprotons was found in this energy region. We obtained the 90% confidence level upper limit of the flux ratio of antiprotons to protons as 7% at multi-TeV energies.Comment: 13pages,4figures; Accepted for publication in Astroparticle Physic

The ARGO-YBJ Experiment Progresses and Future Extension

Gamma ray source detection above 30TeV is an encouraging approach for finding galactic cosmic ray origins. All sky survey for gamma ray sources using wide field of view detector is essential for population accumulation for various types of sources above 100GeV. To target the goals, the ARGO-YBJ experiment has been established. Significant progresses have been made in the experiment. A large air shower detector array in an area of 1km2 is proposed to boost the sensitivity. Hybrid detection with multi-techniques will allow a good discrimination between different types of primary particles, including photons and protons, thus enable an energy spectrum measurement for individual specie. Fluorescence light detector array will extend the spectrum measurement above 100PeV where the second knee is located. An energy scale determined by balloon experiments at 10TeV will be propagated to ultra high energy cosmic ray experiments

High Altitude test of RPCs for the ARGO-YBJ experiment

A 50 m**2 RPC carpet was operated at the YangBaJing Cosmic Ray Laboratory (Tibet) located 4300 m a.s.l. The performance of RPCs in detecting Extensive Air Showers was studied. Efficiency and time resolution measurements at the pressure and temperature conditions typical of high mountain laboratories, are reported.Comment: 16 pages, 10 figures, submitted to Nucl. Instr. Met

Single Spin Asymmetry ANA_N in Polarized Proton-Proton Elastic Scattering at s=200\sqrt{s}=200 GeV

We report a high precision measurement of the transverse single spin asymmetry $A_N$ at the center of mass energy $\sqrt{s}=200$ GeV in elastic proton-proton scattering by the STAR experiment at RHIC. The $A_N$ was measured in the four-momentum transfer squared $t$ range $0.003 \leqslant |t| \leqslant 0.035$ \GeVcSq, the region of a significant interference between the electromagnetic and hadronic scattering amplitudes. The measured values of $A_N$ and its $t$-dependence are consistent with a vanishing hadronic spin-flip amplitude, thus providing strong constraints on the ratio of the single spin-flip to the non-flip amplitudes. Since the hadronic amplitude is dominated by the Pomeron amplitude at this $\sqrt{s}$, we conclude that this measurement addresses the question about the presence of a hadronic spin flip due to the Pomeron exchange in polarized proton-proton elastic scattering.Comment: 12 pages, 6 figure

Are protons still dominant at the knee of the cosmic-ray energy spectrum?

A hybrid experiment consisting of emulsion chambers, burst detectors and the Tibet II air-shower array was carried out at Yangbajing (4,300 m a.s.l., 606 g/cm$^2$) in Tibet to obtain the energy spectra of primary protons and heliums. From three-year operation, these energy spectra are deduced between $10^{15}$ and $10^{16}$ eV by triggering the air showers associated with a high energy core and using a neural network method in the primary mass separation. The proton spectrum can be expressed by a single power-law function with a differential index of $-3.01 \pm 0.11$ and $-3.05 \pm 0.12$ based on the QGSJET+HD and SIBYLL+HD models, respectively, which are steeper than that extrapolated from the direct observations of $-2.74 \pm 0.01$ in the energy range below $10^{14}$ eV. The absolute fluxes of protons and heliums are derived within 30% systematic errors depending on the hadronic interaction models used in Monte Carlo simulation. The result of our experiment suggests that the main component responsible for the change of the power index of the all-particle spectrum around $3 \times 10^{15}$ eV, so-called ``knee'', is composed of nuclei heavier than helium. This is the first measurement of the differential energy spectra of primary protons and heliums by selecting them event by event at the knee energy region.Comment: This paper has been accepted for publication Physics Letters B on October 19th, 2005. This paper has been accepted for publication Physics Letters B on October 19th, 200

Study of J/Psi decays into eta Kstar Kstar-bar

We report the first observation of \mPJpsi \to \mPeta\mPKst\mAPKst decay in a \mPJpsi sample of 58 million events collected with the BESII detector. The branching fraction is determined to be $(1.15 \pm 0.13 \pm 0.22)\times 10^{-3}$. The selected signal event sample is further used to search for the \mPY resonance through \mPJpsi \to \mPeta \mPY, \mPY\to\mPKst\mAPKst. No evidence of a signal is seen. An upper limit of \mathrm{Br}(\mPJpsi \to \mPeta \mPY)\cdot\mathrm{Br}(\mPY\to\mPKst\mAPKst) < 2.52\times 10^{-4} is set at the 90% confidence level.Comment: 11 pages, 4 figure

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

ARGO-YBJ constraints on very high energy emission from GRBs

The ARGO-YBJ (Astrophysical Radiation Ground-based Observatory at YangBaJing) experiment is designed for very high energy $\gamma$-astronomy and cosmic ray researches. Due to the full coverage of a large area ($5600 m^2$) with resistive plate chambers at a very high altitude (4300 m a.s.l.), the ARGO-YBJ detector is used to search for transient phenomena, such as Gamma-ray bursts (GRBs). Because the ARGO-YBJ detector has a large field of view ($\sim$2 sr) and is operated with a high duty cycle ($>$90%), it is well suited for GRB surveying and can be operated in searches for high energy GRBs following alarms set by satellite-borne observations at lower energies. In this paper, the sensitivity of the ARGO-YBJ detector for GRB detection is estimated. Upper limits to fluence with 99% confidence level for 26 GRBs inside the field of view from June 2006 to January 2009 are set in the two energy ranges 10$-$100 GeV and 10 GeV$-$1 TeV.Comment: accepted for publication in Astroparticle Physic