Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns

Cis-antisense gene pairs (CASGPs) can transcribe mRNAs from an opposite strand of a given locus. To classify and understand diverse CASGP phenomena in the human we compiled a genome-wide catalog of CASGPs and integrated these sequences with microarray, SAGE and miRNA data. Using the concept of overlapping regions and clustering of SA transcripts by chromosome coordinates, we identified up to 9000 overlapping antisense loci. Four thousand three hundred and seventy-four of these CASGPs form 1759 complex gene architectures. We found that ∼35% (6347/18160) of RefSeq genes are overlapped with the antisense transcripts. About 30% of Affymetrix U133 microarray initial sequences map transcripts of ∼35% CASGPs and reveal mostly concordant expression in CASGPs. We found strong significant overrepresentation of human miRNA genes in loci of CASGPs. We developed a data-driven model of cross-talk between co-expressed CASGPs and DICER1-mediated miRNA pathway in normal spermatogenesis and in severe teratozoospermia. Specifically, we revealed complex SA structural–functional gene module composing the protein-coding genes, WDR6, DALRD3, NDUFAF3 and ncRNA precursors, mir-425 and mir-191, which could provide downregulation of ncRNA pathway via direct targeting DICER1 and basonuclin 2 transcripts by mir-425 and mir-191 in normal spermatogenesis, but this mechanism is switched off in severe teratozoospermia. The database is available from http://globalisland.bii.a-star.edu.sg/∼jiangtao/sas/index3.php?link =abou

Diagnosis of glioma molecular markers by terahertz technologies

This review considers glioma molecular markers in brain tissues and body fluids, shows the pathways of their formation, and describes traditional methods of analysis. The most important optical properties of glioma markers in the terahertz (THz) frequency range are also presented. New metamaterial-based technologies for molecular marker detection at THz frequencies are discussed. A variety of machine learning methods, which allow the marker detection sensitivity and differentiation of healthy and tumor tissues to be improved with the aid of THz tools, are considered. The actual results on the application of THz techniques in the intraoperative diagnosis of brain gliomas are shown. THz technologies’ potential in molecular marker detection and defining the boundaries of the glioma’s tissue is discussed

Massive migration from the steppe is a source for Indo-European languages in Europe

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe

Demonstration of the temporal matter-wave Talbot effect for trapped matter waves

We demonstrate the temporal Talbot effect for trapped matter waves using ultracold atoms in an optical lattice. We investigate the phase evolution of an array of essentially non-interacting matter waves and observe matter-wave collapse and revival in the form of a Talbot interference pattern. By using long expansion times, we image momentum space with sub-recoil resolution, allowing us to observe fractional Talbot fringes up to 10th order.Comment: 17 pages, 7 figure

Pion, kaon, proton and anti-proton transverse momentum distributions from p+p and d+Au collisions at sNN=200\sqrt{s_{NN}} = 200 GeV

Identified mid-rapidity particle spectra of $\pi^{\pm}$, $K^{\pm}$, and $p(\bar{p})$ from 200 GeV p+p and d+Au collisions are reported. A time-of-flight detector based on multi-gap resistive plate chamber technology is used for particle identification. The particle-species dependence of the Cronin effect is observed to be significantly smaller than that at lower energies. The ratio of the nuclear modification factor ($R_{dAu}$) between protons $(p+\bar{p})$ and charged hadrons ($h$) in the transverse momentum range $1.2<{p_{T}}<3.0$ GeV/c is measured to be $1.19\pm0.05$(stat)$\pm0.03$(syst) in minimum-bias collisions and shows little centrality dependence. The yield ratio of $(p+\bar{p})/h$ in minimum-bias d+Au collisions is found to be a factor of 2 lower than that in Au+Au collisions, indicating that the Cronin effect alone is not enough to account for the relative baryon enhancement observed in heavy ion collisions at RHIC.Comment: 6 pages, 4 figures, 1 table. We extended the pion spectra from transverse momentum 1.8 GeV/c to 3. GeV/

Azimuthal anisotropy at RHIC: the first and fourth harmonics

We report the first observations of the first harmonic (directed flow, v_1), and the fourth harmonic (v_4), in the azimuthal distribution of particles with respect to the reaction plane in Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC). Both measurements were done taking advantage of the large elliptic flow (v_2) generated at RHIC. From the correlation of v_2 with v_1 it is determined that v_2 is positive, or {\it in-plane}. The integrated v_4 is about a factor of 10 smaller than v_2. For the sixth (v_6) and eighth (v_8) harmonics upper limits on the magnitudes are reported.Comment: 6 pages with 3 figures, as accepted for Phys. Rev. Letters The data tables are at http://www.star.bnl.gov/central/publications/pubDetail.php?id=3

3D Mueller Matrix Reconstruction of the Optical Anisotropy Parameters of Myocardial Histopathology Tissue Samples

Diseases affecting myocardial tissues are currently a leading cause of death in developed nations. Fast and reliable techniques for analysing and understanding how tissues are affected by disease and respond to treatment are fundamental to combating the effects of heart disease. A 3D Mueller matrix method that reconstructs the linear and circular birefringence and dichroism parameters has been developed to image the biological structures in myocardial tissues. The required optical data is gathered using a Stokes polarimeter and then processed mathematically to recover the individual optical anisotropy parameters, expanding on existing 2D Mueller matrix implementations by combining with a digital holography approach. Changes in the different optical anisotropy parameters are rationalised with reference to the general tissue structure, such that the structures can be identified from the anisotropy distributions. The first to fourth order statistical moments characterising the distribution of the parameters of the optical anisotropy of the polycrystalline structure of the partially depolarising layer of tissues in different phase sections of their volumes are investigated and analysed. The third and fourth order statistical moments are found to be the most sensitive to changes in the phase and amplitude anisotropy. The possibility of forensic medical differentiation of death in cases of acute coronary insufficiency (ACI) and coronary heart disease (CHD) is considered as a diagnostic application. The optimal phase plane ( θ ∗ = 0.7 r a d ) has been found, in which excellent differentiation accuracy is achieved ACI and CHD - A c ( Δ Z 4 ( θ ∗ , Φ L , Δ L ) ) = 93.05 % ÷ 95.8 % . A comparative analysis of the accuracy of the Mueller-matrix reconstruction of the parameters of the optical anisotropy of the myocardium in different phase planes ( θ = 0.9 r a d and θ = 1.2 r a d ), as well as the 2D Mueller-matrix reconstruction method was carried out. This work demonstrates that a 3D Mueller matrix method can be used to effectively analyse the optical anisotropy parameters of myocardial tissues with potential for definitive diagnostics in forensic medicine

EUNIS Habitat Classification: Expert system, characteristic species combinations and distribution maps of European habitats

Aim: The EUNIS Habitat Classification is a widely used reference framework for European habitat types (habitats), but it lacks formal definitions of individual habitats that would enable their unequivocal identification. Our goal was to develop a tool for assigning vegetation‐plot records to the habitats of the EUNIS system, use it to classify a European vegetation‐plot database, and compile statistically‐derived characteristic species combinations and distribution maps for these habitats. Location: Europe. Methods: We developed the classification expert system EUNIS‐ESy, which contains definitions of individual EUNIS habitats based on their species composition and geographic location. Each habitat was formally defined as a formula in a computer language combining algebraic and set‐theoretic concepts with formal logical operators. We applied this expert system to classify 1,261,373 vegetation plots from the European Vegetation Archive (EVA) and other databases. Then we determined diagnostic, constant and dominant species for each habitat by calculating species‐to‐habitat fidelity and constancy (occurrence frequency) in the classified data set. Finally, we mapped the plot locations for each habitat. Results: Formal definitions were developed for 199 habitats at Level 3 of the EUNIS hierarchy, including 25 coastal, 18 wetland, 55 grassland, 43 shrubland, 46 forest and 12 man‐made habitats. The expert system classified 1,125,121 vegetation plots to these habitat groups and 73,188 to other habitats, while 63,064 plots remained unclassified or were classified to more than one habitat. Data on each habitat were summarized in factsheets containing habitat description, distribution map, corresponding syntaxa and characteristic species combination. Conclusions: EUNIS habitats were characterized for the first time in terms of their species composition and distribution, based on a classification of a European database of vegetation plots using the newly developed electronic expert system EUNIS‐ESy. The data provided and the expert system have considerable potential for future use in European nature conservation planning, monitoring and assessment

Mid-rapidity anti-proton to proton ratio from Au+Au collisions at sNN=130 \sqrt{s_{NN}} = 130 GeV

We report results on the ratio of mid-rapidity anti-proton to proton yields in Au+Au collisions at \rts = 130 GeV per nucleon pair as measured by the STAR experiment at RHIC. Within the rapidity and transverse momentum range of $|y|<0.5$ and 0.4 $<p_t<$ 1.0 GeV/$c$, the ratio is essentially independent of either transverse momentum or rapidity, with an average of $0.65\pm 0.01_{\rm (stat.)} \pm 0.07_{\rm (syst.)}$ for minimum bias collisions. Within errors, no strong centrality dependence is observed. The results indicate that at this RHIC energy, although the $p$-\pb pair production becomes important at mid-rapidity, a significant excess of baryons over anti-baryons is still present.Comment: 5 pages, 3 figures, accepted by Phys. Rev. Let

Transverse-momentum ptp_t correlations on (η,ϕ)(\eta,\phi) from mean-ptp_{t} fluctuations in Au-Au collisions at sNN=\sqrt{s_{NN}} = 200 GeV

We present first measurements of the pseudorapidity and azimuth $(\eta,\phi)$ bin-size dependence of event-wise mean transverse momentum $$ fluctuations for Au-Au collisions at $\sqrt{s_{NN}} = 200$ GeV. We invert that dependence to obtain $p_t$ autocorrelations on differences $(\eta_\Delta,\phi_\Delta)$ interpreted to represent velocity/temperature distributions on ($\eta,\phi$). The general form of the autocorrelations suggests that the basic correlation mechanism is parton fragmentation. The autocorrelations vary strongly with collision centrality, which suggests that fragmentation is strongly modified by a dissipative medium in the more central Au-Au collisions relative to peripheral or p-p collisions. \\Comment: 7 pages, 3 figure