Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression

Multiple myeloma (MM) has two clinical precursor stages of disease: monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). However, the mechanism of progression is not well understood. Because gene co-expression network analysis is a well-known method for discovering new gene functions and regulatory relationships, we utilized this framework to conduct differential co-expression analysis to identify interesting transcription factors (TFs) in two publicly available datasets. We then used copy number variation (CNV) data from a third public dataset to validate these TFs. First, we identified co-expressed gene modules in two publicly available datasets each containing three conditions: normal, MGUS, and SMM. These modules were assessed for condition-specific gene expression, and then enrichment analysis was conducted on condition-specific modules to identify their biological function and upstream TFs. TFs were assessed for differential gene expression between normal and MM precursors, then validated with CNV analysis to identify candidate genes. Functional enrichment analysis reaffirmed known functional categories in MM pathology, the main one relating to immune function. Enrichment analysis revealed a handful of differentially expressed TFs between normal and either MGUS or SMM in gene expression and/or CNV. Overall, we identified four genes of interest (MAX, TCF4, ZNF148, and ZNF281) that aid in our understanding of MM initiation and progression

Categorizing resonances X(1835), X(2120) and X(2370) in the pseudoscalar meson family

Inspired by the newly observed three resonances X(1835), X(2120) and X(2370), in this work we systematically study the two-body strong decays and double pion decays of $\eta(1295)/\eta(1475)$, $\eta(1760)/X(1835)$ and $X(2120)/X(2370)$ by categorizing $\eta(1295)/\eta(1475)$, $\eta(1760)/X(1835)$, X(2120) and X(2370) as the radial excitations of $\eta(548)/\eta^\prime(958)$. Our numerical results indicate the followings: (1) The obtained theoretical strong decay widths of three pseudoscalar states $\eta(1295)$, $\eta(1475)$ and $\eta(1760)$ are consistent with the experimental measurements; (2) X(1835) could be the second radial excitation of $\eta^\prime(958)$; (3) X(2120) and X(2370) can be explained as the third and fourth radial excitations of $\eta(548)/\eta^\prime(958)$, respectively.Comment: 16 pages, 15 figures, 3 tables. Accepted for publication in Phys. Rev.

Strong Lensing Probabilities in a Cosmological Model with a Running Primordial Power Spectrum

The combination of the first-year Wilkinson Microwave Anisotropy Probe (WMAP) data with other finer scale cosmic microwave background (CMB) experiments (CBI and ACBAR) and two structure formation measurements (2dFGRS and Lyman $\alpha$ forest) suggest a $\Lambda$CDM cosmological model with a running spectral power index of primordial density fluctuations. Motivated by this new result on the index of primordial power spectrum, we present the first study on the predicted lensing probabilities of image separation in a spatially flat $\Lambda$CDM model with a running spectral index (RSI-$\Lambda$CDM model). It is shown that the RSI-$\Lambda$CDM model suppress the predicted lensing probabilities on small splitting angles of less than about 4$^{''}$ compared with that of standard power-law $\Lambda$CDM (PL-$\Lambda$CDM) model.Comment: 11 pages including 1 figures. Accepted for publication in Modern Physics Letters A (MPLA), minor revision

Semi-leptonic and Non-leptonic BB meson decays to charmed mesons

We study the semi-leptonic and non-leptonic $B$ weak decays which are governed by the $B\rightarrow D^{(*)}$ transitions. The branching ratios, CP asymmetries (CPA) and polarization fractions (FA) of non-leptonic decays are investigated in the factorization approximation. The $B\rightarrow D^{(*)}$ form factors are estimated in the Salpeter method. Our estimation on branching ratios generally agree with the existent experimental data. For CPA and polarizations, comparisons among the FA results, the perturbative QCD predictions and experimental data are made.Comment: 8 pages, 1 figures, 5 table

Kinematics of the Broad-line Region of 3C 273 from a Ten-year Reverberation Mapping Campaign

Despite many decades of study, the kinematics of the broad-line region of 3C~273 are still poorly understood. We report a new, high signal-to-noise, reverberation mapping campaign carried out from November 2008 to March 2018 that allows the determination of time lags between emission lines and the variable continuum with high precision. The time lag of variations in H$\beta$ relative to those of the 5100 Angstrom continuum is $146.8_{-12.1}^{+8.3}$ days in the rest frame, which agrees very well with the Paschen-$\alpha$ region measured by the GRAVITY at The Very Large Telescope Interferometer. The time lag of the H$\gamma$ emission line is found to be nearly the same as for H$\beta$. The lag of the Fe II emission is $322.0_{-57.9}^{+55.5}$ days, longer by a factor of $\sim$2 than that of the Balmer lines. The velocity-resolved lag measurements of the H$\beta$ line show a complex structure which can be possibly explained by a rotation-dominated disk with some inflowing radial velocity in the H$\beta$-emitting region. Taking the virial factor of $f_{\rm BLR} = 1.3$, we derive a BH mass of $M_{\bullet} = 4.1_{-0.4}^{+0.3} \times 10^8 M_{\odot}$ and an accretion rate of $9.3\,L_{\rm Edd}\,c^{-2}$ from the H$\beta$ line. The decomposition of its $HST$ images yields a host stellar mass of $M_* = 10^{11.3 \pm 0.7} M_\odot$, and a ratio of $M_{\bullet}/M_*\approx 2.0\times 10^{-3}$ in agreement with the Magorrian relation. In the near future, it is expected to compare the geometrically-thick BLR discovered by the GRAVITY in 3C 273 with its spatially-resolved torus in order to understand the potential connection between the BLR and the torus.Comment: 17 pages, 12 figures, 6 tables, accepted for publication in The Astrophysical Journa

Electronic specific heat and low energy quasiparticle excitations in superconducting state of La2−xSrxCuO4La_{2-x}Sr_xCuO_4 single crystals

Low temperature specific heat has been measured and extensively analyzed on a series of $La_{2-x}Sr_xCuO_4$ single crystals from underdoped to overdoped regime. From these data the quasiparticle density of states (DOS) in the mixed state is derived and compared to the predicted scaling law $C_{vol}/T\sqrt{H}=f(T/\sqrt{H})$ of d-wave superconductivity. It is found that the scaling law can be nicely followed by the optimally doped sample (x=0.15) in quite wide region of ($T/\sqrt{H} \leq 8 K /\sqrt{T}$). However, the region for this scaling becomes smaller and smaller towards more underdoped region: a clear trend can be seen for samples from x=0.15 to 0.069. Therefore, generally speaking, the scaling quality becomes worse on the underdoped samples in terms of scalable region of $T/\sqrt{H}$. This feature in the underdoped region is explained as due to the low energy excitations from a second order (for example, anti-ferromagnetic correlation, d-density wave, spin density wave or charge density wave order) that may co-exist or compete with superconductivity. Surprisingly, deviations from the d-wave scaling law have also been found for the overdoped sample (x=0.22). While the scaling law is reconciled for the overdoped sample when the core size effect is taken into account. An important discovery of present work is that the zero-temperature data follow the Volovik's relation $\Delta \gamma(T=0)=A\sqrt{H}$ quite well for all samples investigated here although the applicability of the d-wave scaling law to the data at finite temperatures varies with doped hole concentration. Finally we present the doping dependence of some parameters, such as, the residual linear term $\gamma_0$, the $\alpha$ value, etc. ...Comment: 15 pages, 24 figure

Gene Co-expression Network and Copy Number Variation Analyses Identify Transcription Factors Associated With Multiple Myeloma Progression

Multiple myeloma (MM) has two clinical precursor stages of disease: monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). However, the mechanism of progression is not well understood. Because gene co-expression network analysis is a well-known method for discovering new gene functions and regulatory relationships, we utilized this framework to conduct differential co-expression analysis to identify interesting transcription factors (TFs) in two publicly available datasets. We then used copy number variation (CNV) data from a third public dataset to validate these TFs. First, we identified co-expressed gene modules in two publicly available datasets each containing three conditions: normal, MGUS, and SMM. These modules were assessed for condition-specific gene expression, and then enrichment analysis was conducted on condition-specific modules to identify their biological function and upstream TFs. TFs were assessed for differential gene expression between normal and MM precursors, then validated with CNV analysis to identify candidate genes. Functional enrichment analysis reaffirmed known functional categories in MM pathology, the main one relating to immune function. Enrichment analysis revealed a handful of differentially expressed TFs between normal and either MGUS or SMM in gene expression and/or CNV. Overall, we identified four genes of interest (MAX, TCF4, ZNF148, and ZNF281) that aid in our understanding of MM initiation and progression

Environmental Effect on the Associations of Background Quasars with Foreground Objects: II. Numerical Simulations

Using numerical simulations of cluster formation in the standard CDM model (SCDM) and in a low-density, flat CDM model with a cosmological constant (LCDM), we investigate the gravitational lensing explanation for the reported associations between background quasars and foreground clusters. Under the thin-lens approximation and the unaffected background hypothesis , we show that the recently detected quasar overdensity around clusters of galaxies on scales of $\sim10$ arcminutes cannot be interpreted as a result of the gravitational lensing by cluster matter and/or by their environmental and projected matter along the line of sight, which is consistent with the analytical result based on the observed cluster and galaxy correlations (Wu, et al. 1996). It appears very unlikely that uncertainties in the modeling of the gravitational lensing can account for the disagreement between the theoretical predictions and the observations. We conclude that either the detected signal of the quasar-cluster associations is a statistical fluke or the associations are are generated by mechanisms other than the magnification bias.Comment: 15 pages, 5 figures, accepted for publication in Ap

Type-II Topological Dirac Semimetals: Theory and Materials Prediction (VAl3 family)

The discoveries of Dirac and Weyl semimetal states in spin-orbit compounds led to the realizations of elementary particle analogs in table-top experiments. In this paper, we propose the concept of a three-dimensional type-II Dirac fermion and identify a new topological semimetal state in the large family of transition-metal icosagenides, MA3 (M=V, Nb, Ta; A=Al, Ga, In). We show that the VAl3 family features a pair of strongly Lorentz-violating type-II Dirac nodes and that each Dirac node consists of four type-II Weyl nodes with chiral charge +/-1 via symmetry breaking. Furthermore, we predict the Landau level spectrum arising from the type-II Dirac fermions in VAl3 that is distinct from that of known Dirac semimetals. We also show a topological phase transition from a type-II Dirac semimetal to a quadratic Weyl semimetal or a topological crystalline insulator via crystalline distortions. The new type-II Dirac fermions, their novel magneto-transport response, the topological tunability and the large number of compounds make VAl3 an exciting platform to explore the wide-ranging topological phenomena associated with Lorentz-violating Dirac fermions in electrical and optical transport, spectroscopic and device-based experiments.Comment: 28 pages, 7 Figure