Changes in precipitation and river flow in northeast Turkey: associations with the North Atlantic Oscillation

This paper explores the relationships between the North Atlantic Oscillation (NAO) index and precipitation and river flow over northeast Turkey. Precipitation totals and maximum, mean and minimum river flow are analysed at the seasonal scale for 12 and 10 stations, respectively. Pearson’s and Mann-Kendall correlation tests are applied to assess relationships between the NAO index and precipitation and river flow metrics, and to detect trends in time-series. Autumn precipitation totals display significant increasing trends, especially for coastal stations, while inland stations show significant increasing trends for spring precipitation. Minimum and maximum river flow decreases significantly for spring and summer. This tendency implies varying conditions towards a drier regime. Seasonal precipitation patterns show a negative association with the NAO for December–January–February (DJF), March–April–May (MAM) and September–October–November (SON) for some stations. Positive associations between the NAO and winter-extended winter (December–March) river flows are detected for some stations in northeast Turkey

Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

BACKGROUND: The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF target genes is error prone, and has been shown to be improved by considering additional forms of evidence such as expression data. Previous expression based methods have not explicitly tried to associate TFs with their targets and therefore largely ignored the treatment specific and time dependent nature of transcription regulation. RESULTS: In this study we introduce CERMT, Covariance based Extraction of Regulatory targets using Multiple Time series. Using simulated and real data we show that using multiple expression time series, selecting treatments in which the TF responds, allowing time shifts between TFs and their targets and using covariance to identify highly responding genes appear to be a good strategy. We applied our method to published TF - target gene relationships determined using expression profiling on TF mutants and show that in most cases we obtain significant target gene enrichment and in half of the cases this is sufficient to deliver a usable list of high-confidence target genes. CONCLUSION: CERMT could be immediately useful in refining possible target genes of candidate TFs using publicly available data, particularly for organisms lacking comprehensive TF binding data. In the future, we believe its incorporation with other forms of evidence may improve integrative genome-wide predictions of transcriptional networks

Earthquake slip surfaces identified by biomarker thermal maturity within the 2011 Tohoku-Oki earthquake fault zone.

Extreme slip at shallow depths on subduction zone faults is a primary contributor to tsunami generation by earthquakes. Improving earthquake and tsunami risk assessment requires understanding the material and structural conditions that favor earthquake propagation to the trench. We use new biomarker thermal maturity indicators to identify seismic faults in drill core recovered from the Japan Trench subduction zone, which hosted 50 m of shallow slip during the Mw9.1 2011 Tohoku-Oki earthquake. Our results show that multiple faults have hosted earthquakes with displacement ≥ 10 m, and each could have hosted many great earthquakes, illustrating an extensive history of great earthquake seismicity that caused large shallow slip. We find that lithologic contrasts in frictional properties do not necessarily determine the likelihood of large shallow slip or seismic hazard

Robust High-Dynamic-Range Vector Magnetometry via Nitrogen-Vacancy Centers in Diamond

We demonstrate a robust, scale-factor-free vector magnetometer, which uses a closed-loop frequency-locking scheme to simultaneously track Zeeman-split resonance pairs of nitrogen-vacancy (NV) centers in diamond. Compared with open-loop methodologies, this technique is robust against fluctuations in temperature, resonance linewidth, and contrast; offers a three-order-of-magnitude increase in dynamic range; and allows for simultaneous interrogation of multiple transition frequencies. By directly detecting the resonance frequencies of NV centers aligned along each of the diamond's four tetrahedral crystallographic axes, we perform full vector reconstruction of an applied magnetic field

Southern expansion of the brown alga Colpomenia peregrina Sauvageau (Scytosiphonales) in the Northwest Atlantic Ocean

Blackler first recorded Colpomenia peregrina in the Northwest Atlantic based on collections from Nova Scotia, Canada. Five decades later we found large quantities of C. peregrina in Maine, USA, even though it was absent during earlier floristic studies in this region. Thus, C. peregrina has undergone a rapid southern expansion along the Northwest Atlantic coast. While the causes of such an expansion are unknown, it could have a major effect on both shellfish cultivation and native seaweeds within New England because of competitive interactions and increased drag

Why stellar feedback promotes disc formation in simulated galaxies

We study how feedback influences baryon infall onto galaxies using cosmological, zoom-in simulations of haloes with present mass $M_{vir}=6.9\times10^{11} M_{\odot}$ to $1.7\times10^{12} M_{\odot}$. Starting at z=4 from identical initial conditions, implementations of weak and strong stellar feedback produce bulge- and disc-dominated galaxies, respectively. Strong feedback favours disc formation: (1) because conversion of gas into stars is suppressed at early times, as required by abundance matching arguments, resulting in flat star formation histories and higher gas fractions; (2) because 50% of the stars form in situ from recycled disc gas with angular momentum only weakly related to that of the z=0 dark halo; (3) because late-time gas accretion is typically an order of magnitude stronger and has higher specific angular momentum, with recycled gas dominating over primordial infall; (4) because 25-30% of the total accreted gas is ejected entirely before z~1, removing primarily low angular momentum material which enriches the nearby inter-galactic medium. Most recycled gas roughly conserves its angular momentum, but material ejected for long times and to large radii can gain significant angular momentum before re-accretion. These processes lower galaxy formation efficiency in addition to promoting disc formation.Comment: 23 pages, 29 figures, accepted for publication in MNRA

The Combined Effect of Environmental and Host Factors on the Emergence of Viral RNA Recombinants

Viruses are masters of evolution due to high frequency mutations and genetic recombination. In spite of the significance of viral RNA recombination that promotes the emergence of drug-resistant virus strains, the role of host and environmental factors in RNA recombination is poorly understood. Here we report that the host Met22p/Hal2p bisphosphate-3′-nucleotidase regulates the frequency of viral RNA recombination and the efficiency of viral replication. Based on Tomato bushy stunt virus (TBSV) and yeast as a model host, we demonstrate that deletion of MET22 in yeast or knockdown of AHL, SAL1 and FRY1 nucleotidases/phosphatases in plants leads to increased TBSV recombination and replication. Using a cell-free TBSV recombination/replication assay, we show that the substrate of the above nucleotidases, namely 3′-phosphoadenosine-5′-phosphate pAp, inhibits the activity of the Xrn1p 5′-3′ ribonuclease, a known suppressor of TBSV recombination. Inhibition of the activity of the nucleotidases by LiCl and NaCl also leads to increased TBSV recombination, demonstrating that environmental factors could also affect viral RNA recombination. Thus, host factors in combination with environmental factors likely affect virus evolution and adaptation

Decision aids can support cancer clinical trials decisions: Results of a randomized trial

BACKGROUND. Cancer patients often do not make informed decisions regarding clinical trial participation. This study evaluated whether a web-based decision aid (DA) could support trial decisions compared with our cancer center’s website. METHODS. Adults diagnosed with cancer in the past 6 months who had not previously participated in a cancer clinical trial were eligible. Participants were randomized to view the DA or our cancer center’s website (enhanced usual care [UC]). Controlling for whether participants had heard of cancer clinical trials and educational attainment, multivariable linear regression examined group on knowledge, self-efficacy for finding trial information, decisional conflict (values clarity and uncertainty), intent to participate, decision readiness, and trial perceptions. RESULTS. Two hundred patients (86%) consented between May 2014 and April 2015. One hundred were randomized to each group. Surveys were completed by 87 in the DA group and 90 in the UC group. DA group participants reported clearer values regarding trial participation than UC group participants reported (least squares [LS] mean = 15.8 vs. 32, p < .0001) and less uncertainty (LS mean = 24.3 vs. 36.4, p = .025). The DA group had higher objective knowledge than the UC group’s (LS mean = 69.8 vs. 55.8, p < .0001). There were no differences between groups in intent to participate. CONCLUSIONS. Improvements on key decision outcomes including knowledge, self-efficacy, certainty about choice, and values clarity among participants who viewed the DA suggest web-based DAs can support informed decisions about trial participation among cancer patients facing this preference-sensitive choice. Although better informing patients before trial participation could improve retention, more work is needed to examine DA impact on enrollment and retention. IMPLICATIONS FOR PRACTICE: This paper describes evidence regarding a decision tool to support patients’ decisions about trial participation. By improving knowledge, helping patients clarify preferences for participation, and facilitating conversations about trials, decision aids could lead to decisions about participation that better match patients’ preferences, promoting patient-centered care and the ethical conduct of clinical research

Crossing Symmetry Violation of Unitarized Pion-Pion Amplitude in the Resonance Region

Pion-pion scattering amplitude obtained from one-loop Chiral Perturbation Theory (ChPT) is crossing symmetric, however the corresponding partial wave amplitudes do not respect exact unitarity relation. There are different approaches to get unitarized partial wave amplitudes from ChPT. Here we consider the inverse amplitude method (IAM) that is often used to fit pion-pion phase shifts to experimental data, by adjusting free parameters. We measure the amount of crossing symmetry violation (CSV) in this case and we show that crossing symmetry is badly violated by the IAM unitarized ChPT amplitude in the resonance region. Important CSV also occurs when all free parameters are set equal to zero.Comment: 6 pages, 4 figure