Finding Top- k

Diagnostic genes are usually used to distinguish different disease phenotypes. Most existing methods for diagnostic genes finding are based on either the individual or combinatorial discriminative power of gene(s). However, they both ignore the common expression trends among genes. In this paper, we devise a novel sequence rule, namely, top-k irreducible covering contrast sequence rules (TopkIRs for short), which helps to build a sample classifier of high accuracy. Furthermore, we propose an algorithm called MineTopkIRs to efficiently discover TopkIRs. Extensive experiments conducted on synthetic and real datasets show that MineTopkIRs is significantly faster than the previous methods and is of a higher classification accuracy. Additionally, many diagnostic genes discovered provide a new insight into disease diagnosis

Few-photon single ionization of cold rubidium in the over-the-barrier regime

Photoionization of the rubidium (Rb) atoms cooled in a magneto-optical trap, characterized by the coexistence of the ground 5$S_{1/2}$ and the excited 5$P_{3/2}$ states, is investigated experimentally and theoretically with the 400 nm femtosecond laser pulses at intensities of $I=3\times10^9$ W/cm$^2$ - $4.5\times10^{12}$ W/cm$^2$. Recoil-ion momentum distribution (RIMD) of Rb$^+$ exhibits rich ring-like structures and their energies correspond to one-photon ionization of the 5$P_{3/2}$ state, two-photon and three-photon ionizations of the 5$S_{1/2}$ state, respectively. With the increasing of $I$, we find that experimental signals near zero-momentum (NZM) in RIMDs resulted from the 5$P_{3/2}$ state enhance dramatically and its peaked Rb$^+$ momenta dwindle obviously while that from the 5$S_{1/2}$ state is maintained. Meanwhile, the ion-yield ratio of the 5$S_{1/2}$ over the 5$P_{3/2}$ states varies from $I$ to $I^{1.5}$ as $I$ increases. These features indicate a transition from perturbative ionization to strong-perturbative ionization for the 5$P_{3/2}$ state. Numerical simulations by solving the time-dependent Schr\"odinger equation (TDSE) can qualitatively explain the measurements of RIMD, photoion angular distributions, as well as ion-yield ratio. However, some discrepancies still exist, especially for the NZM dip, which could stem from the electron-electron correlation that is neglected in the present TDSE simulations since we have adopted the single-active-electron approximation

Ellipticity-dependent sequential over-barrier ionization of cold rubidium

We perform high-resolution measurements of momentum distribution on Rb$^{n+}$ recoil ions up to charge state $n=4$, where laser-cooled rubidium atoms are ionized by femtosecond elliptically polarized lasers with the pulse duration of 35 fs and the intensity of 3.3$\times$10$^{15}$ W/cm$^2$ in the over-barrier ionization (OBI) regime. The momentum distributions of the recoil ions are found to exhibit multi-band structures as the ellipticity varies from the linear to circular polarizations. The origin of these band structures can be explained quantitatively by the classical OBI model and dedicated classical trajectory Monte Carlo simulations with Heisenberg potential. Specifically, with back analysis of the classical trajectories, we reveal the ionization time and the OBI geometry of the sequentially released electrons, disentangling the mechanisms behind the tilted angle of the band structures. These results indicate that the classical treatment can describe the strong-field multiple ionization processes of alkali atoms

Genome-wide analysis of the Tritipyrum WRKY gene family and the response of TtWRKY256 in salt-tolerance

IntroductionThe transcription factor WRKY is widespread in the plant kingdom and plays a crucial role in diverse abiotic stress responses in plant species. Tritipyrum, an octoploid derived from an intergeneric cross between Triticum aestivum (AABBDD) and Thinopyrum elongatum (EE), is a valuable germplasm resource for introducing superior traits of Th. elongatum into T. aestivum. The recent release of the complete genome sequences of T. aestivum and Th. elongatum enabled us to investigate the organization and expression profiling of Tritipyrum WRKY genes across the entire genome.ResultsIn this study, 346 WRKY genes, from TtWRKY1 to TtWRKY346, were identified in Tritipyrum. The phylogenetic analysis grouped these genes into three subfamilies (I-III), and members of the same subfamilies shared a conserved motif composition. The 346 TtWRKY genes were dispersed unevenly across 28 chromosomes, with 218 duplicates. Analysis of synteny suggests that the WRKY gene family may have a common ancestor. Expression profiles derived from transcriptome data and qPCR demonstrated that 54 TtWRKY genes exhibited relatively high levels of expression across various salt stresses and recovery treatments. Tel1E01T143800 (TtWRKY256) is extremely sensitive to salt stress and is on the same evolutionary branch as the salt-tolerant A. thaliana genes AtWRKY25 and AtWRKY33. From 'Y1805', the novel AtWRKY25 was cloned. The Pearson correlation analysis identified 181 genes that were positively correlated (R>0.9) with the expression of TtWRKY256, and these genes were mainly enriched in metabolic processes, cellular processes, response to stimulus, biological regulation, and regulation of biological. Subcellular localization and qRT-PCR analysis revealed that TtWRKY256 was located in the nucleus and was highly expressed in roots, stems, and leaves under salt stress.DiscussionThe above results suggest that TtWRKY256 may be associated with salt stress tolerance in plants and may be a valuable alien gene for improving salt tolerance in wheat

HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis

HD2 proteins are plant specific histone deacetylases. Four HD2 proteins, HD2A, HD2B, HD2C, and HD2D, have been identified in Arabidopsis. It was found that the expression of HD2A, HD2B, HD2C, and HD2D was repressed by ABA and NaCl. To investigate the function of HD2 proteins further, two HD2C T-DNA insertion lines of Arabidopsis, hd2c-1 and hd2c-3 were identified. Compared with wild-type plants, hd2c-1 and hd2c-3 plants displayed increased sensitivity to ABA and NaCl during germination and decreased tolerance to salt stress. These observations support a role of HD2C in the ABA and salt-stress response in Arabidopsis. Moreover, it was demonstrated that HD2C interacted physically with a RPD3-type histone deacetylase, HDA6, and bound to histone H3. The expression of ABA-responsive genes, ABI1 and ABI2, was increased in hda6, hd2c, and hda6/hd2c-1 double mutant plants, which was associated with increased histone H3K9K14 acetylation and decreased histone H3K9 dimethylation. Taken together, our results suggested that HD2C functionally associates with HDA6 and regulates gene expression through histone modifications

UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability

This study explored potential biomarkers associated with Lauren classification of gastric cancer. We screened microarray datasets on gastric cancer with information of Lauren classification in gene expression omnibus (GEO) database, and compared differentially expressing genes between intestinal-type or diffuse-type gastric cancer. Four sets of microarray data (GSE2669, GSE2680, GDS3438, and GDS4007) were enrolled into analysis. By differential gene analysis, UBE2C, CDH1, CENPF, ERO1L, SCD, SOX9, CKS1B, SPP1, MMP11, and ANLN were identified as the top genes related to intestinal-type gastric cancer, and MGP, FXYD1, FAT4, SIPA1L2, MUC5AC, MMP15, RAB23, FBLN1, ANXA10, and ADH1B were genes related to diffuse-type gastric cancer. We comprehensively validated the biological functions of the intestinal-type gastric cancer related gene UBE2C and evaluated its clinical significance on 1,868 cases of gastric cancer tissues from multiple medical centers of Shanghai, China. The gain of copy number on 20q was found in 4 out of 5 intestinal-type cancer cell lines, and no similar copy number variation (CNV) was found in any diffuse-type cancer cell line. Interfering UBE2C expression inhibited cell proliferation, migration and invasion in vitro, and tumorigenesis in vivo. Knockdown of UBE2C resulted in G2/M blockage in intestinal-type gastric cancer cells. Overexpression of UBE2C activated ERK signal pathway and promoted cancer cell proliferation. U0126, an inhibitor of ERK signaling pathway reversed the oncogenic phenotypes caused by UBE2C. Moreover, overexpression of UBE2C was identified in human intestinal-type gastric cancer. Overexpression of UBE2C protein predicted poor clinical outcome. Taken together, we characterized a group of Lauren classification-associated biomarkers, and clarified biological functions of UBE2C, an intestinal-type gastric cancer associated gene. Overexpression of UBE2C resulted in chromosomal instability that disturbed cell cycle and led to poor prognosis of intestinal-type gastric cancer

A Novel Intravital Method to Evaluate Cerebral Vasospasm in Rat Models of Subarachnoid Hemorrhage: A Study with Synchrotron Radiation Angiography

Precise in vivo evaluation of cerebral vasospasm caused by subarachnoid hemorrhage has remained a critical but unsolved issue in experimental small animal models. In this study, we used synchrotron radiation angiography to study the vasospasm of anterior circulation arteries in two subarachnoid hemorrhage models in rats. Synchrotron radiation angiography, laser Doppler flowmetry-cerebral blood flow measurement, [125I]N-isopropyl-p-iodoamphetamine cerebral blood flow measurement and terminal examinations were applied to evaluate the changes of anterior circulation arteries in two subarachnoid hemorrhage models made by blood injection into cisterna magna and prechiasmatic cistern. Using synchrotron radiation angiography technique, we detected cerebral vasospasm in subarachnoid hemorrhage rats compared to the controls (p<0.05). We also identified two interesting findings: 1) both middle cerebral artery and anterior cerebral artery shrunk the most at day 3 after subarachnoid hemorrhage; 2) the diameter of anterior cerebral artery in the prechiasmatic cistern injection group was smaller than that in the cisterna magna injection group (p<0.05), but not for middle cerebral artery. We concluded that synchrotron radiation angiography provided a novel technique, which could directly evaluate cerebral vasospasm in small animal experimental subarachnoid hemorrhage models. The courses of vasospasm in these two injection models are similar; however, the model produced by prechiasmatic cistern injection is more suitable for study of anterior circulation vasospasm