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

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

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

Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA)

The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage display random peptide library. After one round of prescreening and two rounds of screening, high-stringency screening at the third round of panning was performed to identify the highest affinity binders. Phages which had a specific binding activity to PSMA in human prostate cancer cells were isolated and the DNA corresponding to the 15-mers were sequenced to provide three consensus sequences: GDHSPFT, SHFSVGS and EVPRLSLLAVFL as well as other sequences that did not display consensus. Two of the peptide sequences deduced from DNA sequencing of binding phages, SHSFSVGSGDHSPFT and GRFLTGGTGRLLRIS were labeled with 5-carboxyfluorescein and shown to bind and co-internalize with PSMA on human prostate cancer cells by fluorescence microscopy. The high stringency requirements yielded peptides with affinities KD∼1 μM or greater which are suitable starting points for affinity maturation. While these values were less than anticipated, the high stringency did yield peptide sequences that apparently bound to different surfaces on PSMA. These peptide sequences could be the basis for further development of peptides for prostate cancer tumor imaging and therapy. © 2013 Shen et al

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

Early apoptosis of porcine alveolar macrophages limits avian influenza virus replication and proinflammatory dysregulation

Pigs are evidently more resistant to avian than swine influenza A viruses, mediated in part through frontline epithelial cells and alveolar macrophages (AM). Although porcine AM (PAM) are crucial in influenza virus control, their mode of control is unclear. To gain insight into the possible role of PAM in the mediation of avian influenza virus resistance, we compared the host effects and replication of two avian (H2N3 and H6N1) and three mammalian (swine H1N1, human H1N1 and pandemic H1N1) influenza viruses in PAM. We found that PAM were readily susceptible to initial infection with all five avian and mammalian influenza viruses but only avian viruses caused early and extensive apoptosis (by 6 h of infection) resulting in reduced virus progeny and moderated pro- inflammation. Full length viral PB1-F2 present only in avian influenza viruses is a virulence factor that targets AM for mitochondrial associated apoptotic cell death. With the use of reverse genetics on an avian H5N1 virus, we found that full length PB1-F2 contributed to increased apoptosis and pro-inflammation but not to reduced virus replication. Taken together, we propose that early apoptosis of PAM limits the spread of avian influenza viruses and that PB1-F2 could play a contributory role in the process

Benefits and risks of the hormetic effects of dietary isothiocyanates on cancer prevention

The isothiocyanate (ITC) sulforaphane (SFN) was shown at low levels (1-5 µM) to promote cell proliferation to 120-143% of the controls in a number of human cell lines, whilst at high levels (10-40 µM) it inhibited such cell proliferation. Similar dose responses were observed for cell migration, i.e. SFN at 2.5 µM increased cell migration in bladder cancer T24 cells to 128% whilst high levels inhibited cell migration. This hormetic action was also found in an angiogenesis assay where SFN at 2.5 µM promoted endothelial tube formation (118% of the control), whereas at 10-20 µM it caused significant inhibition. The precise mechanism by which SFN influences promotion of cell growth and migration is not known, but probably involves activation of autophagy since an autophagy inhibitor, 3-methyladenine, abolished the effect of SFN on cell migration. Moreover, low doses of SFN offered a protective effect against free-radical mediated cell death, an effect that was enhanced by co-treatment with selenium. These results suggest that SFN may either prevent or promote tumour cell growth depending on the dose and the nature of the target cells. In normal cells, the promotion of cell growth may be of benefit, but in transformed or cancer cells it may be an undesirable risk factor. In summary, ITCs have a biphasic effect on cell growth and migration. The benefits and risks of ITCs are not only determined by the doses, but are affected by interactions with Se and the measured endpoint

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