Wide-field LOFAR-LBA power-spectra analyses: Impact of calibration, polarization leakage and ionosphere

Contamination due to foregrounds (Galactic and Extra-galactic), calibration errors and ionospheric effects pose major challenges in detection of the cosmic 21 cm signal in various Epoch of Reionization (EoR) experiments. We present the results of a pilot study of a field centered on 3C196 using LOFAR Low Band (56-70 MHz) observations, where we quantify various wide field and calibration effects such as gain errors, polarized foregrounds, and ionospheric effects. We observe a `pitchfork' structure in the 2D power spectrum of the polarized intensity in delay-baseline space, which leaks into the modes beyond the instrumental horizon (EoR/CD window). We show that this structure largely arises due to strong instrumental polarization leakage ($\sim30\%$) towards {Cas\,A} ($\sim21$ kJy at 81 MHz, brightest source in northern sky), which is far away from primary field of view. We measure an extremely small ionospheric diffractive scale ($r_{\text{diff}} \approx 430$ m at 60 MHz) towards {Cas\,A} resembling pure Kolmogorov turbulence compared to $r_{\text{diff}} \sim3 - 20$ km towards zenith at 150 MHz for typical ionospheric conditions. This is one of the smallest diffractive scales ever measured at these frequencies. Our work provides insights in understanding the nature of aforementioned effects and mitigating them in future Cosmic Dawn observations (e.g. with SKA-low and HERA) in the same frequency window.Comment: 20 pages, 11 figures, accepted for publication in MNRA

Performance comparison of machine learning techniques in sleep scoring based on wavelet features and neighboring component analysis

Introduction: Sleep scoring is an important step in the treatment of sleep disorders. Manual annotation of sleep stages is time-consuming and experience-relevant and, therefore, needs to be done using machine learning techniques. Methods: Sleep-EDF polysomnography was used in this study as a dataset. Support vector machines and artificial neural network performance were compared in sleep scoring using wavelet tree features and neighborhood component analysis. Results: Neighboring component analysis as a combination of linear and non-linear feature selection method had a substantial role in feature dimension reduction. Artificial neural network and support vector machine achieved 90.30 and 89.93 accuracy, respectively. Discussion and Conclusion: Similar to the state of the art performance, the introduced method in the present study achieved an acceptable performance in sleep scoring. Furthermore, its performance can be enhanced using a technique combined with other techniques in feature generation and dimension reduction. It is hoped that, in the future, intelligent techniques can be used in the process of diagnosing and treating sleep disorders. © 2018 Alizadeh Savareh et al

Improving the Antioxidant Activities of Sweet Basil (Ocimum basilicum L.) under the Influence of Different Species of Mycorrhiza under Water Stress

Introduction  Medicinal plants have long had a special role in the traditional ‎agricultural system of Iran and the use of these plants as medicine to prevent and treat diseases has been considered by ‎traditional medicine experts since ancient times. Medicinal plants with rich sources of secondary metabolites provide the ‎basic active ingredients of many medicines. Although the biosynthesis of secondary metabolites is genetically controlled, ‎but their construction is strongly influenced by environmental factors. One of the important climatic factors that affect the ‎distribution of plants around the world and can cause morphological, physiological and biochemical changes in the plant is ‎the lack of available water. Basil seems to show little resistance to water stress. For this reason, there is a need for protective mechanisms for the ‎basil plant against stress due to water shortage. Plants are able to reduce or eliminate the effects of water shortage ‎stress by coexisting with a number of soil microorganisms. Inoculation of the plants with Arbuscular mycorrhizal fungi (AMF) has been exploited as an applicable strategy for reducing detrimental effects of water deficit stress. Present study was performed to evaluate the effects of three AMF on some physiological responses of Ocimum basilicum under water deficit stress.   Materials and Methods  The pot experiments were conducted as factorial based on completely randomized design blocks with three replications. The experimental factors were three AMF namely Glomus etunicatum, Glomus mosseae and Glomus intraradices and various soil moisture including severe stress, moderate stress, mild stress. Water stress was applied from the beginning to the end of flowering stage. After flowering stage, plants ‎were harvested and traits such as total phenols and flavonoids, antioxidant ‎capacity (DPPH), malondialdehyde (MDA), catalase and peroxidase enzymes were measured. To analyze the data, first the test of data normality and uniformity of variance within the treatment was performed and confirmed. The mean of treatments was compared by Duncan test at the level of 5% probability. SAS software (Ver. 9.3) was used to analyze the data and Excel software was used to draw the graphs.   Results and Discussion  The results of analysis of variance of the effect of mycorrhiza fungus and soil moisture on the studied parameters show that the effect of different levels of soil moisture on all traits was significant. The results of analysis of variance also showed that the effect of mycorrhiza on phenol and total flavonoids, antioxidant activity, catalase and peroxidase and malondialdehyde was significant at the level of one percent probability. According to the results of analysis of variance, the interaction effect of mycorrhiza on soil moisture on antioxidant activity was significant at 5% probability level and on total phenols and flavonoids, malondialdehyde, catalase and peroxidase at 1% probability level. Results showed that AMFs improve activity of catalase and peroxidase, antioxidant capacity and total phenols which led to decrease malondialdehyde content. Antioxidants as physiologically active compounds play an important role in plant resistance to stress. Increased oxygen species due to dehydration stress are a warning sign for plants and increase the activity of antioxidant enzymes. The plant's defense system increases the production of antioxidant enzymes to neutralize toxic oxygen forms, and fungi improve the intensity of this increase, which may be due to the chemical structure of the metal isoenzymes copper, zinc, and manganese. Factors sent to make antioxidant enzymes also contain the elements zinc and calcium. Mycorrhizal fungi increase the absorption of nutrients by sending more hormonal factors and increasing the activity of enzymes, all of which can be effective in increasing the activity of antioxidant enzymes.   Conclusion  When plants are exposed to dehydration stress, reactive oxygen species in them increase. The expression of antioxidant genes and the activity of antioxidants to eliminate reactive oxygen species are increased and the antioxidant defense system is improved and the tolerance to dehydration stress in the plant is increased. Scientists believe that peroxidase is involved in metabolic processes such as hormone catabolism, defense against pathogens, phenol oxidation, binding to cell structural proteins and cell wall polysaccharides. Present study revealed that application of AMFs can be good strategy for reducing harmful effects of water deficit stress in plants. Research has also shown that impregnating seeds with mycorrhiza increases antioxidants and reduces the amount of reactive oxygen species, a characteristic of resistance induction that occurs by this antagonist.   ‎   

The first power spectrum limit on the 21-cm signal of neutral hydrogen during the Cosmic Dawn at z=20-25 from LOFAR

Observations of the redshifted 21-cm hyperfine line of neutral hydrogen from early phases of the Universe such as Cosmic Dawn and the Epoch of Reionization promise to open a new window onto the early formation of stars and galaxies. We present the first upper limits on the power spectrum of redshifted 21-cm brightness temperature fluctuations in the redshift range z = 19.8-25.2 (54-68 MHz frequency range) using 14 h of data obtained with the LOFAR-Low Band Antenna (LBA) array. We also demonstrate the application of a multiple pointing calibration technique to calibrate the LOFAR-LBA dual-pointing observations centred on the North Celestial Pole and the radio galaxy 3C220.3, We observe an unexplained excess of similar to 30-50 per cent in Stokes / noise compared to Stokes V for the two observed fields, which decorrelates on greater than or similar to 12 s and might have a physical origin. We show that enforcing smoothness of gain errors along frequency direction during calibration reduces the additional variance in Stokes I compared Stokes V introduced by the calibration on sub-band level. After subtraction of smooth foregrounds, we achieve a 2 sigma upper limit on the 21-cm power spectrum of Delta(2)(21) &lt;(14561 mK)(2) at k similar to 0.038 h cMpc(-1) and Delta(2)(21) &lt;(14886 mK)(2) at k 0.038 h cMpc(-1) for the 3C220 and NCP fields respectively and both upper limits are consistent with each other. The upper limits for the two fields are still dominated by systematics on most k modes.</p

Inactivation of the nucl. Accumbens Core Exerts No Effect on Nicotine-Induced Conditioned Place Preference

Effects of transient inhibition of the core part of the nucl. accumbens (NAcC) by lidocaine on nicotine-induced conditioned place preference in male Wistar rats were examined. Lidocaine (2%) was injected into the NAcC of nicotine-conditioned animals before each nicotine i.p. injection. On the test day, behavior of the animals in a two-compartment apparatus was recorded during 10 min. Results revealed that i.p. injections of nicotine (1.0 or 1.5 mg/kg) induced place preference. Transient lidocaine-induced inhibition of one or both sides of the NAcC did not change place preference but changed the numbers of compartment crossings, rearings, and sniffings. Inhibition of the left part and both parts of the structure reduced sniffing and increased place preference; inhibition of the right part of the nucleus increased the intensity of this phenomena.Вивчали впливи тимчасової інактивації серцевинної частини nucl. accumbens (NAcC) за допомогою лідокаїну на індуковану нікотином умовнорефлекторну преференцію місця у самців щурів. Лідокаїн (2 %) ін’єкували в NAcC кондиційованих уведеннями нікотину тварин за 5 хв перед кожною тест-ін’єкцією нікотину. У день тестування поведінка тварин у двокомпартментному пристрої реєструвалася протягом 10 хв. Внутрішньоочеревинні ін’єкції нікотину (1.0 або 1.5 мг/кг) індукували виражену преференцію місця. Унілатеральна або білатеральна тимчасова інактивація NAcC не призводила до змін преференції, але зменшувала кількість стійок та перетинів межі компартментів. Гальмування лівої половини або обох частин NAcC зменшувало кількість епізодів принюхування та збільшувало інтенсивність преференції місця, тоді як гальмування тільки правої частини ядра посилювало принюхування та зменшувало рівень преференції. Отже, наші результати підтвердили, що як ліва, так і права частини NAcC залучені у формування нікотинової преференції місця, але їх ролі можуть бути відмінними

Background risk of breast cancer and the association between physical activity and mammographic density

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A Common Variant at the 14q32 Endometrial Cancer Risk Locus Activates AKT1 through YY1 Binding.

A recent meta-analysis of multiple genome-wide association and follow-up endometrial cancer case-control datasets identified a novel genetic risk locus for this disease at chromosome 14q32.33. To prioritize the functional SNP(s) and target gene(s) at this locus, we employed an in silico fine-mapping approach using genotyped and imputed SNP data for 6,608 endometrial cancer cases and 37,925 controls of European ancestry. Association and functional analyses provide evidence that the best candidate causal SNP is rs2494737. Multiple experimental analyses show that SNP rs2494737 maps to a silencer element located within AKT1, a member of the PI3K/AKT/MTOR intracellular signaling pathway activated in endometrial tumors. The rs2494737 risk A allele creates a YY1 transcription factor-binding site and abrogates the silencer activity in luciferase assays, an effect mimicked by transfection of YY1 siRNA. Our findings suggest YY1 is a positive regulator of AKT1, mediating the stimulatory effects of rs2494737 increasing endometrial cancer risk. Identification of an endometrial cancer risk allele within a member of the PI3K/AKT signaling pathway, more commonly activated in tumors by somatic alterations, raises the possibility that well tolerated inhibitors targeting this pathway could be candidates for evaluation as chemopreventive agents in individuals at high risk of developing endometrial cancer.The QIMR Berghofer groups were supported by a Rio Tinto Ride to Conquer Cancer (RTCC)/Weekend to End Women's Cancers (WEWC) Grant and NHMRC project grants 1058415 to SLE and 1031333 to ABS. ABS is supported by an NHMRC Senior Research Fellowship (1061779). DFE is a Principal Research Fellow of CR-UK.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by Cell Press

Prediction of post-operative necrosis after mastectomy: A pilot study utilizing optical diffusion imaging spectroscopy

<p>Abstract</p> <p>Introduction</p> <p>Flap necrosis and epidermolysis occurs in 18-30% of all mastectomies. Complications may be prevented by intra-operative detection of ischemia. Currently, no technique enables quantitative valuation of mastectomy skin perfusion. Optical Diffusion Imaging Spectroscopy (ViOptix T.Ox Tissue Oximeter) measures the ratio of oxyhemoglobin to deoxyhemoglobin over a 1 × 1 cm area to obtain a non-invasive measurement of perfusion (StO₂).</p> <p>Methods</p> <p>This study evaluates the ability of ViOptix T.Ox Tissue Oximeter to predict mastectomy flap necrosis. StO₂measurements were taken at five points before and at completion of dissection in 10 patients. Data collected included: demographics, tumor size, flap length/thickness, co-morbidities, procedure length, and wound complications.</p> <p>Results</p> <p>One patient experienced mastectomy skin flap necrosis. Five patients underwent immediate reconstruction, including the patient with necrosis. Statistically significant factors contributing to necrosis included reduction in medial flap StO₂(p = 0.0189), reduction in inferior flap StO₂(p = 0.003), and flap length (p = 0.009).</p> <p>Conclusion</p> <p>StO₂reductions may be utilized to identify impaired perfusion in mastectomy skin flaps.</p

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A&gt;T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Comprehensive genetic assessment of the ESR1 locus identifies a risk region for endometrial cancer

Excessive exposure to estrogen is a well-established risk factor for endometrial cancer (EC), particularly for cancers of endometrioid histology. The physiological function of estrogen is primarily mediated by estrogen receptor alpha, encoded by ESR1. Consequently, several studies have investigated whether variation at the ESR1 locus is associated with risk of EC, with conflicting results. We performed comprehensive fine-mapping analyses of 3633 genotyped and imputed single nucleotide polymorphisms (SNPs) in 6607 EC cases and 37 925 controls. There was evidence of an EC risk signal located at a potential alternative promoter of the ESR1 gene (lead SNP rs79575945, P=1.86x10(-5)), which was stronger for cancers of endometrioid subtype (P=3.76x10(-6)). Bioinformatic analysis suggests that this risk signal is in a functionally important region targeting ESR1, and eQTL analysis found that rs79575945 was associated with expression of SYNE1, a neighbouring gene. In summary, we have identified a single EC risk signal located at ESR1, at study-wide significance. Given SNPs located at this locus have been associated with risk for breast cancer, also a hormonally driven cancer, this study adds weight to the rationale for performing informed candidate fine-scale genetic studies across cancer types