Impact of Ground Truth Annotation Quality on Performance of Semantic Image Segmentation of Traffic Conditions

Preparation of high-quality datasets for the urban scene understanding is a labor-intensive task, especially, for datasets designed for the autonomous driving applications. The application of the coarse ground truth (GT) annotations of these datasets without detriment to the accuracy of semantic image segmentation (by the mean intersection over union - mIoU) could simplify and speedup the dataset preparation and model fine tuning before its practical application. Here the results of the comparative analysis for semantic segmentation accuracy obtained by PSPNet deep learning architecture are presented for fine and coarse annotated images from Cityscapes dataset. Two scenarios were investigated: scenario 1 - the fine GT images for training and prediction, and scenario 2 - the fine GT images for training and the coarse GT images for prediction. The obtained results demonstrated that for the most important classes the mean accuracy values of semantic image segmentation for coarse GT annotations are higher than for the fine GT ones, and the standard deviation values are vice versa. It means that for some applications some unimportant classes can be excluded and the model can be tuned further for some classes and specific regions on the coarse GT dataset without loss of the accuracy even. Moreover, this opens the perspectives to use deep neural networks for the preparation of such coarse GT datasets.Comment: 10 pages, 6 figures, 2 tables, The Second International Conference on Computer Science, Engineering and Education Applications (ICCSEEA2019) 26-27 January 2019, Kiev, Ukrain

Peatlands and Climate Change

This is the author's manuscript version and this version is free to view and download for personal use only. Not for re-distribution, re-sale or use in derivative works.This material is forthcoming in Peatland Restoration and Ecosystem Services Science, Policy and Practice, 9781107619708, © Cambridge University PressThe fundamental reason for the presence of peatlands is a positive balance between plant production and decomposition. Organic matter accumulates in these systems because prolonged waterlogged conditions result in soil anoxia (i.e., exclusion of oxygen), and under these conditions decomposition rates can be lower than those of primary production. Climate therefore plays an important role in peat accumulation, both directly by affecting productivity and decomposition processes, and indirectly through its effects on hydrology/water balance and vegetation (for a summary, refer to Yu, Beilman & Jones 2009). Climate provides broad-scale constraints or controls on peatland extent, types and vegetation, and ultimately, ecosystem functioning, carbon accumulation, greenhouse gas exchange and all of the other ecosystem services that peatlands provide. Peatlands can play a vital role in helping society mitigate and adapt to climate change, because of their carbon and water regulating functions, while at the same time, the climate sensitivity of peatlands makes them potentially vulnerable to future global warming and changes in spatial and temporal patterns of precipitation, especially if they are in a degraded state. Climate change is likely to alter the hydrology and soil temperature of peatlands, with far- reaching consequences for their biodiversity, ecology and biogeochemistry. Their involvement in the global carbon cycle will also be affected, with the possibility of drier conditions allowing peatland erosion and increases in CO2 emissions that would result in a positive feedback to climate change (Turetsky 2010). This highlights all the more the need for restoration to ensure peatlands are resilient to change so that they continue to deliver ecosystem services for human well-being. This chapter describes the interactions between climate and peatlands, in three sections. The first section explains how present climate influences peatlands, by documenting how climate limits peatland geographical extent globally, and how bioclimatic envelope models can predict peatland extent. We indicate how each type of peatland is linked to a specific climate range, and introduce the concept of ecosystem function in relation to climate. The second section looks into the past. It describes how peat preserves a record of past climates and environmental conditions that can be deciphered to reveal the history of peatland vegetation, hydrology and carbon accumulation changes in relation to past changes in climate. We highlight lessons that can be learned from the palaeorecord preserved in peat. The final section discusses the potential effects of present and future climate change on peatlands, their extent, carbon accumulation rates, fire frequency, water table and greenhouse gas exchanges. We also consider how increases in sea level and CO2 concentration, and decreases in the extent of permafrost, are likely to affect peatlands

Morphine modulation of pain processing in medial and lateral pain pathways

<p>Abstract</p> <p>Background</p> <p>Despite the wide-spread use of morphine and related opioid agonists in clinic and their powerful analgesic effects, our understanding of the neural mechanisms underlying opioid analgesia at supraspinal levels is quite limited. The present study was designed to investigate the modulative effect of morphine on nociceptive processing in the medial and lateral pain pathways using a multiple single-unit recording technique. Pain evoked neuronal activities were simultaneously recorded from the primary somatosensory cortex (SI), ventral posterolateral thalamus (VPL), anterior cingulate cortex (ACC), and medial dorsal thalamus (MD) with eight-wire microelectrode arrays in awake rats.</p> <p>Results</p> <p>The results showed that the noxious heat evoked responses of single neurons in all of the four areas were depressed after systemic injection of 5 mg/kg morphine. The depressive effects of morphine included (i) decreasing the neuronal response magnitude; (ii) reducing the fraction of responding neurons, and (iii) shortening the response duration. In addition, the capability of cortical and thalamic neural ensembles to discriminate noxious from innocuous stimuli was decreased by morphine within both pain pathways. Meanwhile, morphine suppressed the pain-evoked changes in the information flow from medial to lateral pathway and from cortex to thalamus. These effects were completely blocked by pre-treatment with the opiate receptor antagonist naloxone.</p> <p>Conclusion</p> <p>These results suggest that morphine exerts analgesic effects through suppressing both sensory and affective dimensions of pain.</p

Type 2 diabetes genetic association database manually curated for the study design and odds ratio

<p>Abstract</p> <p>Background</p> <p>The prevalence of type 2 diabetes has reached epidemic proportions worldwide, and the incidence of life-threatening complications of diabetes through continued exposure of tissues to high glucose levels is increasing. Advances in genotyping technology have increased the scale and accuracy of the genotype data so that an association genetic study has expanded enormously. Consequently, it is difficult to search the published association data efficiently, and several databases on the association results have been constructed, but these databases have their limitations to researchers: some providing only genome-wide association data, some not focused on the association but more on the integrative data, and some are not user-friendly. In this study, a user-friend database of type 2 diabetes genetic association of manually curated information was constructed.</p> <p>Description</p> <p>The list of publications used in this study was collected from the HuGE Navigator, which is an online database of published genome epidemiology literature. Because type 2 diabetes genetic association database (T2DGADB) aims to provide specialized information on the genetic risk factors involved in the development of type 2 diabetes, 701 of the 1,771 publications in the type 2 Diabetes case-control study for the development of the disease were extracted.</p> <p>Conclusions</p> <p>In the database, the association results were grouped as either positive or negative. The gene and SNP names were replaced with gene symbols and rsSNP numbers, the association p-values were determined manually, and the results are displayed by graphs and tables. In addition, the study design in publications, such as the population type and size are described. This database can be used for research purposes, such as an association and functional study of type 2 diabetes related genes, and as a primary genetic resource to construct a diabetes risk test in the preparation of personalized medicine in the future.</p

Wall Crossing and Instantons in Compactified Gauge Theory

We calculate the leading weak-coupling instanton contribution to the moduli-space metric of N=2 supersymmetric Yang-Mills theory with gauge group SU(2) compactified on R^3 x S^1. The results are in precise agreement with the semiclassical expansion of the exact metric recently conjectured by Gaiotto, Moore and Neitzke based on considerations related to wall-crossing in the corresponding four-dimensional theory.Comment: 24 pages, no figure

Two real parton contributions to non-singlet kernels for exclusive QCD DGLAP evolution

Results for the two real parton differential distributions needed for implementing a next-to-leading order (NLO) parton shower Monte Carlo are presented. They are also integrated over the phase space in order to provide solid numerical control of the MC codes and for the discussion of the differences between the standard $\bar{MS}$ factorization and Monte Carlo implementation at the level of inclusive NLO evolution kernels. Presented results cover the class of non-singlet diagrams entering into NLO kernels. The classic work of Curci-Furmanski-Pertonzio was used as a guide in the calculations.Comment: 34 pages, 3 figure

Small inhibitor of Bcl-2, HA14-1, selectively enhanced the apoptotic effect of cisplatin by modulating Bcl-2 family members in MDA-MB-231 breast cancer cells

Inhibition or downregulation of Bcl-2 represents a new therapeutic approach to by-pass chemoresistance in cancer cells. Therefore, we explored the potential of this approach in breast cancer cells. Cisplatin and paclitaxel induced apoptosis in a dose-dependent manner in MCF-7 (drug-sensitive) and MDA-MB-231 (drug-insensitive) cells. Furthermore, when we transiently silenced Bcl-2, both cisplatin and paclitaxel induced apoptosis more than parental cells. Dose dependent induction of apoptosis by drugs was enhanced by the pre-treatment of these cells with HA14-1, a Bcl-2 inhibitor. Although the effect of cisplatin was significant on both cell lines, the effect of paclitaxel was much less potent only in MDA-MB-231 cells. To further understand the distinct role of drugs in MDA-MB-231 cells pretreated with HA14-1, caspases and Bcl-2 family proteins were studied. The apoptotic effect of cisplatin with or without HA14-1 pre-treatment is shown to be caspase-dependent. Among pro-apoptotic Bcl-2 proteins, Bax and Puma were found to be up-regulated whereas Bcl-2 and Bcl-x(L) were down-regulated when cells were pretreated with HA14-1 followed by paclitaxel or cisplatin. Enforced Bcl-2 expression in MDA-MB-231 cells abrogated the sensitizing effect of HA14-1 in cisplatin induced apoptosis. These results suggest that the potentiating effect of HA14-1 is drug and cell type specific and may not only depend on the inhibition of Bcl-2. Importantly, alteration of other pro-apoptotic or anti-apoptotic Bcl-2 family members may dictate the apoptotic response when HA14-1 is combined with chemotherapeutic drugs

Hendra Virus Infection Dynamics in Australian Fruit Bats

Hendra virus is a recently emerged zoonotic agent in Australia. Since first described in 1994, the virus has spilled from its wildlife reservoir (pteropid fruit bats, or ‘flying foxes’) on multiple occasions causing equine and human fatalities. We undertook a three-year longitudinal study to detect virus in the urine of free-living flying foxes (a putative route of excretion) to investigate Hendra virus infection dynamics. Pooled urine samples collected off plastic sheets placed beneath roosting flying foxes were screened for Hendra virus genome by quantitative RT-PCR, using a set of primers and probe derived from the matrix protein gene. A total of 1672 pooled urine samples from 67 sampling events was collected and tested between 1 July 2008 and 30 June 2011, with 25% of sampling events and 2.5% of urine samples yielding detections. The proportion of positive samples was statistically associated with year and location. The findings indicate that Hendra virus excretion occurs periodically rather than continuously, and in geographically disparate flying fox populations in the state of Queensland. The lack of any detection in the Northern Territory suggests prevalence may vary across the range of flying foxes in Australia. Finally, our findings suggest that flying foxes can excrete virus at any time of year, and that the apparent seasonal clustering of Hendra virus incidents in horses and associated humans (70% have occurred June to October) reflects factors other than the presence of virus. Identification of these factors will strengthen risk minimization strategies for horses and ultimately humans

Increased entropy of signal transduction in the cancer metastasis phenotype

Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of networks in the context of cancer genomics. However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes. Based on the observation that frequent genomic alterations underlie a more aggressive cancer phenotype, we asked if such an effect could be detectable as an increase in the randomness of local gene expression patterns. Using a breast cancer gene expression data set and a model network of protein interactions we derive constrained weighted networks defined by a stochastic information flux matrix reflecting expression correlations between interacting proteins. Based on this stochastic matrix we propose and compute an entropy measure that quantifies the degree of randomness in the local pattern of information flux around single genes. By comparing the local entropies in the non-metastatic versus metastatic breast cancer networks, we here show that breast cancers that metastasize are characterised by a small yet significant increase in the degree of randomness of local expression patterns. We validate this result in three additional breast cancer expression data sets and demonstrate that local entropy better characterises the metastatic phenotype than other non-entropy based measures. We show that increases in entropy can be used to identify genes and signalling pathways implicated in breast cancer metastasis. Further exploration of such integrated cancer expression and protein interaction networks will therefore be a fruitful endeavour.Comment: 5 figures, 2 Supplementary Figures and Table

Properties of small molecular drug loading and diffusion in a fluorinated PEG hydrogel studied by ^1H molecular diffusion NMR and ^(19)F spin diffusion NMR

R_f-PEG (fluoroalkyl double-ended poly(ethylene glycol)) hydrogel is potentially useful as a drug delivery depot due to its advanced properties of sol–gel two-phase coexistence and low surface erosion. In this study, ^1H molecular diffusion nuclear magnetic resonance (NMR) and ^(19)F spin diffusion NMR were used to probe the drug loading and diffusion properties of the R_f-PEG hydrogel for small anticancer drugs, 5-fluorouracil (FU) and its hydrophobic analog, 1,3-dimethyl-5-fluorouracil (DMFU). It was found that FU has a larger apparent diffusion coefficient than that of DMFU, and the diffusion of the latter was more hindered. The result of ^(19)F spin diffusion NMR for the corresponding freeze-dried samples indicates that a larger portion of DMFU resided in the R_f core/IPDU intermediate-layer region (where IPDU refers to isophorone diurethane, as a linker to interconnect the R_f group and the PEG chain) than that of FU while the opposite is true in the PEG–water phase. To understand the experimental data, a diffusion model was proposed to include: (1) hindered diffusion of the drug molecules in the R_f core/IPDU-intermediate-layer region; (2) relatively free diffusion of the drug molecules in the PEG-water phase (or region); and (3) diffusive exchange of the probe molecules between the above two regions. This study also shows that molecular diffusion NMR combined with spin diffusion NMR is useful in studying the drug loading and diffusion properties in hydrogels for the purpose of drug delivery applications