Integrating multiple types of data to predict novel cell cycle-related genes

<p>Abstract</p> <p>Background</p> <p>Cellular functions depend on genetic, physical and other types of interactions. As such, derived interaction networks can be utilized to discover novel genes involved in specific biological processes. Epistatic Miniarray Profile, or E-MAP, which is an experimental platform that measures genetic interactions on a genome-wide scale, has successfully recovered known pathways and revealed novel protein complexes in <it>Saccharomyces cerevisiae</it> (budding yeast).</p> <p>Results</p> <p>By combining E-MAP data with co-expression data, we first predicted a potential cell cycle related gene set. Using Gene Ontology (GO) function annotation as a benchmark, we demonstrated that the prediction by combining microarray and E-MAP data is generally >50% more accurate in identifying co-functional gene pairs than the prediction using either data source alone. We also used transcription factor (TF)–DNA binding data (Chip-chip) and protein phosphorylation data to construct a local cell cycle regulation network based on potential cell cycle related gene set we predicted. Finally, based on the E-MAP screening with 48 cell cycle genes crossing 1536 library strains, we predicted four unknown genes (<it>YPL158C</it>, <it>YPR174C</it>, <it>YJR054W</it>, and <it>YPR045C</it>) as potential cell cycle genes, and analyzed them in detail.</p> <p>Conclusion</p> <p>By integrating E-MAP and DNA microarray data, potential cell cycle-related genes were detected in budding yeast. This integrative method significantly improves the reliability of identifying co-functional gene pairs. In addition, the reconstructed network sheds light on both the function of known and predicted genes in the cell cycle process. Finally, our strategy can be applied to other biological processes and species, given the availability of relevant data.</p

The Effect of Galaxy Interactions on Molecular Gas Properties

© 2018. The American Astronomical Society. All rights reserved.Galaxy interactions are often accompanied by an enhanced star formation rate (SFR). Since molecular gas is essential for star formation, it is vital to establish whether and by how much galaxy interactions affect the molecular gas properties. We investigate the effect of interactions on global molecular gas properties by studying a sample of 58 galaxies in pairs and 154 control galaxies. Molecular gas properties are determined from observations with the JCMT, PMO, and CSO telescopes and supplemented with data from the xCOLD GASS and JINGLE surveys at 12CO(1-0) and 12CO(2-1). The SFR, gas mass (), and gas fraction (f gas) are all enhanced in galaxies in pairs by ∼2.5 times compared to the controls matched in redshift, mass, and effective radius, while the enhancement of star formation efficiency (SFE ≡SFR/) is less than a factor of 2. We also find that the enhancements in SFR, and f gas, increase with decreasing pair separation and are larger in systems with smaller stellar mass ratio. Conversely, the SFE is only enhanced in close pairs (separation <20 kpc) and equal-mass systems; therefore, most galaxies in pairs lie in the same parameter space on the SFR- plane as controls. This is the first time that the dependence of molecular gas properties on merger configurations is probed statistically with a relatively large sample and a carefully selected control sample for individual galaxies. We conclude that galaxy interactions do modify the molecular gas properties, although the strength of the effect is dependent on merger configuration.Peer reviewedFinal Accepted Versio

Hard superconducting gap in PbTe nanowires

Semiconductor nanowires coupled to a superconductor provide a powerful testbed for quantum device physics such as Majorana zero modes and gate-tunable hybrid qubits. The performance of these quantum devices heavily relies on the quality of the induced superconducting gap. A hard gap, evident as vanishing subgap conductance in tunneling spectroscopy, is both necessary and desired. Previously, a hard gap has been achieved and extensively studied in III-V semiconductor nanowires (InAs and InSb). In this study, we present the observation of a hard superconducting gap in PbTe nanowires coupled to a superconductor Pb. The gap size ($\Delta$) is $\sim$ 1 meV (maximally 1.3 meV in one device). Additionally, subgap Andreev bound states can also be created and controlled through gate tuning. Tuning a device into the open regime can reveal Andreev enhancement of the subgap conductance, suggesting a remarkable transparent superconductor-semiconductor interface, with a transparency of $\sim$ 0.96. These results pave the way for diverse superconducting quantum devices based on PbTe nanowires

Ballistic PbTe Nanowire Devices

Disorder is the primary obstacle in current Majorana nanowire experiments. Reducing disorder or achieving ballistic transport is thus of paramount importance. In clean and ballistic nanowire devices, quantized conductance is expected with plateau quality serving as a benchmark for disorder assessment. Here, we introduce ballistic PbTe nanowire devices grown using the selective-area-growth (SAG) technique. Quantized conductance plateaus in units of $2e^2/h$ are observed at zero magnetic field. This observation represents an advancement in diminishing disorder within SAG nanowires, as none of the previously studied SAG nanowires (InSb or InAs) exhibit zero-field ballistic transport. Notably, the plateau values indicate that the ubiquitous valley degeneracy in PbTe is lifted in nanowire devices. This degeneracy lifting addresses an additional concern in the pursuit of Majorana realization. Moreover, these ballistic PbTe nanowires may enable the search for clean signatures of the spin-orbit helical gap in future devices

Modular analysis of the probabilistic genetic interaction network

Motivation: Epistatic Miniarray Profiles (EMAP) has enabled the mapping of large-scale genetic interaction networks; however, the quantitative information gained from EMAP cannot be fully exploited since the data are usually interpreted as a discrete network based on an arbitrary hard threshold. To address such limitations, we adopted a mixture modeling procedure to construct a probabilistic genetic interaction network and then implemented a Bayesian approach to identify densely interacting modules in the probabilistic network

Room-temperature ferromagnetism in Mn-doped CuCrO₂ nanopowders

Using the statefinder diagnostic,we discuss the torsion cosmology in the frame of Poincare gauge theory of gravity.We find that there are some different characteristic of the evolution of statefinder parameters for this model from the other cosmological model

Investigation of Phonon Scattering on the Tunable Mechanisms of Terahertz Graphene Metamaterials

The influences of different kinds of phonon scatterings (i.e., acoustic (AC) phonon, impurity, and longitudinal optical (LO) phonon scatterings) on the tunable propagation properties of graphene metamaterials structures have been investigated, also including the effects of graphene pattern structures, Fermi levels, and operation frequencies. The results manifested that, at room temperature, AC phonon scattering dominated, while with the increase in temperature, the LO phonon scattering increased significantly and played a dominate role if temperature goes beyond 600 K. Due to the phonon scatterings, the resonant properties of the graphene metamaterial structure indicated an optimum value (about 0.5&ndash;0.8 eV) with the increase in Fermi level, which were different from the existing results. The results are very helpful to understand the tunable mechanisms of graphene functional devices, sensors, modulators, and antennas

Nomograms predict long-term survival for patients with periampullary adenocarcinoma after pancreatoduodenectomy

Abstract Background The prognosis of patients with periampullary adenocarcinoma after pancreatoduodenectomy is diverse and not yet clearly illustrated. The aim of this study was to develop a nomogram to predict individual risk of overall survival (OS) and progression-free survival (PFS) in patients with periampullary adenocarcinoma after pancreatoduodenectomy. Methods A total of 205 patients with periampullary adenocarcinoma after pancreatoduodenectomy were retrospectively included. OS and PFS were evaluated by the Kaplan-Meier method. Two nomograms for predicting OS and PFS were established, and the predictive accuracy was measured by the concordance index (Cindex) and calibration plots. Results Lymph node ratio (LNR), carbohydrate antigen 19–9 (CA19–9) and anatomical location were incorporated into the nomogram for OS prediction and LNR, CA19–9; anatomical location and tumor differentiation were incorporated into the nomogram for PFS prediction. All calibration plots for the probability of OS and PFS fit well. The Cindexes of the nomograms for OS and PFS prediction were 0.678 and 0.68, respectively. The OS and PFS survival times were stratified significantly using the nomogram-predicted survival probabilities. Conclusions The present nomograms for OS and PFS prediction can provide valuable information for tailored decision-making for patients with periampullary adenocarcinoma after pancreatoduodenectomy