Detecting long-term occupancy changes in Californian odonates from natural history and citizen science records

In a world of rapid environmental change, effective biodiversity conservation and management relies on our ability to detect changes in species occurrence. While long-term, standardized monitoring is ideal for detecting change, such monitoring is costly and rare. An alternative approach is to use historical records from natural history collections as a baseline to compare with recent observations. Here, we combine natural history collection data with citizen science observations within a hierarchical Bayesian occupancy modeling framework to identify changes in the occupancy of Californian dragonflies and damselflies (Odonata) over the past century. We model changes in the probability of occupancy of 34 odonate species across years and as a function of climate, after correcting for likely variation in detection probability using proxies for recorder effort and seasonal variation. We then examine whether biological traits can help explain variation in temporal trends. Models built using only opportunistic records identify significant changes in occupancy across years for 14 species, with eight of those showing significant declines and six showing significant increases in occupancy in the period 1900–2013. These changes are consistent with estimates obtained using more standardized resurvey data, regardless of whether resurvey data are used individually or in conjunction with the opportunistic dataset. We find that species increasing in occupancy over time are also those whose occupancy tends to increase with higher minimum temperatures, which suggests that these species may be benefiting from increasing temperatures across California. Furthermore, these species are also mostly habitat generalists, whilst a number of habitat specialists display some of the largest declines in occupancy across years. Our approach enables more robust estimates of temporal trends from opportunistic specimen and observation data, thus facilitating the use of these data in biodiversity conservation and management

Breast cancer histologic grading using digital microscopy: concordance and outcome association

Aims: Virtual microscopy utilising digital whole slide imaging (WSI) is increasingly used in breast pathology. Histologic grade is one of the strongest prognostic factors in breast cancer (BC). This study aims at investigating the agreement between BC grading using traditional light microscopy (LM) and digital whole slide imaging (WSI) with consideration of reproducibility and impact on outcome prediction. Methods: A large (n=1675) well-characterised cohort of BC originally graded by LM was re-graded using WSI. Two separate virtual-based grading sessions (V1 and V2) were performed with a three months washout period. Outcome was assessed using breast cancer specific and distant metastasis free survival. Results: The concordance between LM grading and WSI was strong (LM/SWI Cramer’s V: V1=0.576, and V2=0.579). The agreement regarding grade components was as follows: Tubule formation=0.538, Pleomorphism=0.422 and Mitosis=0.514. Greatest discordance was observed between adjacent grades whereas high/low grade discordance was uncommon (1.5%). The intra-observer agreement for the two WSI sessions was substantial for grade (V1/V2 Cramer’s V=0.676; kappa=0.648) and grade components (Cramer’s V T=0.628, P=0.573 and M=0.580). Grading using both platforms showed strong association with outcome (All p-value <0.001). Although mitotic scores assessed using both platforms were strongly associated with outcome, WSI tends to underestimate mitotic counts. Conclusions: Virtual microscopy is a reliable and reproducible method for assessing BC histologic grade. Regardless of the observer or assessment platform, histologic grade is a significant predictor of outcome. Continuing advances in imaging technology could potentially provide improved performance of WSI BC grading and in particular mitotic count assessment

Untangling the ATR-CHEK1 network for prognostication, prediction and therapeutic target validation in breast cancer

Background: ATR-Chk1 signalling network is critical for genomic stability. ATR-Chk1 may be deregulated in breast cancer and have prognostic, predictive and therapeutic significance. Patients and methods: We investigated ATR and phosphorylated CHK1Ser345 protein (pChk1) expression in 1712 breast cancers (Nottingham Tenovus series). ATR and Chk1 mRNA were evaluated in 1950 breast cancers (METABRIC cohort). Pre-clinically, biological consequences of ATR gene knockdown or ATR inhibition by small molecule inhibitor (VE-821) were investigated in MCF-7 and MDA-MB-231 breast cancer cell lines and in non-tumorigenic breast epithelial cells (MCF10A). Results: High ATR and high cytoplasmic pChk1 expression was significantly associated with higher tumour stage, higher mitotic index, pleomorphism and lymphovascular invasion. In univariate analysis, high ATR and high cytoplasmic pChk1 protein expression was associated with shorter breast cancer specific survival (BCSS). In multivariate analysis, high ATR remains an independent predictor of adverse outcome. At the mRNA level, high Chk1 remains associated with aggressive phenotypes including lymph node positivity, high grade, Her-2 overexpression, triple-negative phenotype and molecular classes associated with aggressive behaviour and shorter survival.. Pre-clinically, Chk1 phosphorylation at serine 345 following replication stress (induced by gemcitabine or hydroxyurea treatment) was impaired in ATR knockdown and in VE-821 treated breast cancer cells. Doxycycline inducible knockdown of ATR suppressed growth, which was restored when ATR was re-expressed. Similarly, VE-821 treatment resulted in a dose dependent suppression of cancer cell growth and survival (MCF7 and MDA-MB-231) but had no effect on non-tumorigenic breast epithelial cells (MCF10A). Conclusions: We provides evidence that ATR and Chk1 are promising biomarkers and rational drug target for personalized therapy in breast cancer

Parameter estimators of random intersection graphs with thinned communities

This paper studies a statistical network model generated by a large number of randomly sized overlapping communities, where any pair of nodes sharing a community is linked with probability $q$ via the community. In the special case with $q=1$ the model reduces to a random intersection graph which is known to generate high levels of transitivity also in the sparse context. The parameter $q$ adds a degree of freedom and leads to a parsimonious and analytically tractable network model with tunable density, transitivity, and degree fluctuations. We prove that the parameters of this model can be consistently estimated in the large and sparse limiting regime using moment estimators based on partially observed densities of links, 2-stars, and triangles.Comment: 15 page

On the nonthermal X-ray emission in blazar jets

We consider particle acceleration to high energy via diffusive shock acceleration in a simple, self-consistent shock in jet model for blazars. Electrons are assumed to be accelerated at a shock front in relativistic jets and radiate synchrotron emission in a post-shock region. The full time, space and momentum dependence of the electron distribution function is used for a calculation of the nonthermal synchrotron spectra. We discuss the evolution of the spectral index by varying the rate at which particles enter the acceleration process. The results indicate that the synchrotron spectral index displays a characteristic looplike behaviour with intensity (as has been observed in several blazars), where the orientation of the loop depends on whether the acceleration time scale is comparable to the synchrotron cooling time scale or not. We show that our model provides a good fit to the observed evolution of the spectral index of Mkn 421 during a flare in 1994.Comment: 6 pages, 3 figures, conference proceedin

First-trimester or second-trimester screening, or both, for Down's syndrome

BACKGROUND: It is uncertain how best to screen pregnant women for the presence of fetal Down's syndrome: to perform first-trimester screening, to perform second-trimester screening, or to use strategies incorporating measurements in both trimesters.METHODS: Women with singleton pregnancies underwent first-trimester combined screening (measurement of nuchal translucency, pregnancy-associated plasma protein A [PAPP-A], and the free beta subunit of human chorionic gonadotropin at 10 weeks 3 days through 13 weeks 6 days of gestation) and second-trimester quadruple screening (measurement of alpha-fetoprotein, total human chorionic gonadotropin, unconjugated estriol, and inhibin A at 15 through 18 weeks of gestation). We compared the results of stepwise sequential screening (risk results provided after each test), fully integrated screening (single risk result provided), and serum integrated screening (identical to fully integrated screening, but without nuchal translucency).RESULTS: First-trimester screening was performed in 38,167 patients; 117 had a fetus with Down's syndrome. At a 5 percent false positive rate, the rates of detection of Down's syndrome were as follows: with first-trimester combined screening, 87 percent, 85 percent, and 82 percent for measurements performed at 11, 12, and 13 weeks, respectively; with second-trimester quadruple screening, 81 percent; with stepwise sequential screening, 95 percent; with serum integrated screening, 88 percent; and with fully integrated screening with first-trimester measurements performed at 11 weeks, 96 percent. Paired comparisons found significant differences between the tests, except for the comparison between serum integrated screening and combined screening.CONCLUSIONS: First-trimester combined screening at 11 weeks of gestation is better than second-trimester quadruple screening but at 13 weeks has results similar to second-trimester quadruple screening. Both stepwise sequential screening and fully integrated screening have high rates of detection of Down's syndrome, with low false positive rates

Two remarks on generalized entropy power inequalities

This note contributes to the understanding of generalized entropy power inequalities. Our main goal is to construct a counter-example regarding monotonicity and entropy comparison of weighted sums of independent identically distributed log-concave random variables. We also present a complex analogue of a recent dependent entropy power inequality of Hao and Jog, and give a very simple proof.Comment: arXiv:1811.00345 is split into 2 papers, with this being on

Is Task-Irrelevant Learning Really Task-Irrelevant?

In the present study we address the question of whether the learning of task-irrelevant stimuli found in the paradigm of task-irrelevant learning (TIPL) [1]–[9] is truly task irrelevant. To test the hypothesis that associations that are beneficial to task-performance may develop between the task-relevant and task-irrelevant stimuli, or the task-responses and the task-irrelevant stimuli, we designed a new procedure in which correlations between the presentation of task-irrelevant motion stimuli and the identity of task-targets or task-responses were manipulated. We found no evidence for associations developing between the learned (task-irrelevant) motion stimuli and the targets or responses to the letter identification task used during training. Furthermore, the conditions that had the greatest correlations between stimulus and response showed the least amount of TIPL. On the other hand, TIPL was found in conditions of greatest response uncertainty and with the greatest processing requirements for the task-relevant stimuli. This is in line with our previously published model that suggests that task-irrelevant stimuli benefit from the spill-over of learning signals that are released due to processing of task-relevant stimuli

Is Task-Irrelevant Learning Really Task-Irrelevant?

In the present study we address the question of whether the learning of task-irrelevant stimuli found in the paradigm of task-irrelevant learning (TIPL) [1]–[9] is truly task irrelevant. To test the hypothesis that associations that are beneficial to task-performance may develop between the task-relevant and task-irrelevant stimuli, or the task-responses and the task-irrelevant stimuli, we designed a new procedure in which correlations between the presentation of task-irrelevant motion stimuli and the identity of task-targets or task-responses were manipulated. We found no evidence for associations developing between the learned (task-irrelevant) motion stimuli and the targets or responses to the letter identification task used during training. Furthermore, the conditions that had the greatest correlations between stimulus and response showed the least amount of TIPL. On the other hand, TIPL was found in conditions of greatest response uncertainty and with the greatest processing requirements for the task-relevant stimuli. This is in line with our previously published model that suggests that task-irrelevant stimuli benefit from the spill-over of learning signals that are released due to processing of task-relevant stimuli

A smog chamber comparison of a microfluidic derivatisation measurement of gas-phase glyoxal and methylglyoxal with other analytical techniques

A microfluidic lab-on-a-chip derivatisation technique has been developed to measure part per billion (ppbV) mixing ratios of gaseous glyoxal (GLY) and methylglyoxal (MGLY), and the method is compared with other techniques in a smog chamber experiment. The method uses-(2, 3, 4, 5, 6-pentafluorobenzyl) hydroxylamine (PFBHA) as a derivatisation reagent and a microfabricated planar glass micro-reactor comprising an inlet, gas and fluid splitting and combining channels, mixing junctions, and a heated capillary reaction microchannel. The enhanced phase contact area-to-volume ratio and the high heat transfer rate in the micro-reactor resulted in a fast and highly efficient derivatisation reaction, generating an effluent stream ready for direct introduction to a gas chromatograph-mass spectrometer (GC-MS). A linear response for GLY was observed over a calibration range 0.7 to 400 ppbV, and for MGLY of 1.2 to 300 ppbV, when derivatised under optimal reaction conditions. The analytical performance shows good accuracy (6.6% for GLY and 7.5% for MGLY), suitable precision (<12.0%) with method detection limits (MDLs) of 75 pptV for GLY and 185 pptV for MGLY, with a time resolution of 30 min. These MDLs are below or close to typical concentrations of these compounds observed in ambient air. The feasibility of the technique was assessed by applying the methodology to quantify α-dicarbonyls formed during the photo-oxidation of isoprene in the EUPHORE chamber. Good correlations were found between microfluidic measurements and Fourier Transform InfraRed spectroscopy (FTIR) with a correlation coefficient (2) of 0.84, Broadband Cavity Enhanced Absorption Spectroscopy (BBCEAS) (2 Combining double low line 0.75), solid phase micro extraction (SPME) (2 Combining double low line 0.89), and a photochemical chamber box modelling calculation (2 Combining double low line 0.79) for GLY measurements. For MGLY measurements, the microfluidic technique showed good agreement with BBCEAS (2 Combining double low line 0.87), SPME (2 Combining double low line 0.76), and the modeling simulation (2 Combining double low line 0.83), FTIR (2 Combining double low line 0.72) but displayed a discrepancy with Proton-Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) with 2 value of 0.39