Size-Change Abstraction and Max-Plus Automata

Max-plus automata (over ℕ ∪ − ∞) are finite devices that map input words to non-negative integers or − ∞. In this paper we present (a) an algorithm allowing to compute the asymptotic behaviour of max-plus automata, and (b) an application of this technique to the evaluation of the computational time complexity of programs

Containment and equivalence of weighted automata: Probabilistic and max-plus cases

This paper surveys some results regarding decision problems for probabilistic and max-plus automata, such as containment and equivalence. Probabilistic and max-plus automata are part of the general family of weighted automata, whose semantics are maps from words to real values. Given two weighted automata, the equivalence problem asks whether their semantics are the same, and the containment problem whether one is point-wise smaller than the other one. These problems have been studied intensively and this paper will review some techniques used to show (un)decidability and state a list of open questions that still remain

Generalized β\beta-conformal change and special Finsler spaces

In this paper, we investigate the change of Finslr metrics $$L(x,y) \to\bar{L}(x,y) = f(e^{\sigma(x)}L(x,y),\beta(x,y)),$$ which we refer to as a generalized $\beta$-conformal change. Under this change, we study some special Finsler spaces, namely, quasi C-reducible, semi C-reducible, C-reducible, $C_2$-like, $S_3$-like and $S_4$-like Finsler spaces. We also obtain the transformation of the T-tensor under this change and study some interesting special cases. We then impose a certain condition on the generalized $\beta$-conformal change, which we call the b-condition, and investigate the geometric consequences of such condition. Finally, we give the conditions under which a generalized $\beta$-conformal change is projective and generalize some known results in the literature.Comment: References added, some modifications are performed, LateX file, 24 page

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Identifying human diamine sensors for death related putrescine and cadaverine molecules

Pungent chemical compounds originating from decaying tissue are strong drivers of animal behavior. Two of the best-characterized death smell components are putrescine (PUT) and cadaverine (CAD), foul-smelling molecules produced by decarboxylation of amino acids during decomposition. These volatile polyamines act as 'necromones', triggering avoidance or attractive responses, which are fundamental for the survival of a wide range of species. The few studies that have attempted to identify the cognate receptors for these molecules have suggested the involvement of the seven-helix trace amine-associated receptors (TAARs), localized in the olfactory epithelium. However, very little is known about the precise chemosensory receptors that sense these compounds in the majority of organisms and the molecular basis of their interactions. In this work, we have used computational strategies to characterize the binding between PUT and CAD with the TAAR6 and TAAR8 human receptors. Sequence analysis, homology modeling, docking and molecular dynamics studies suggest a tandem of negatively charged aspartates in the binding pocket of these receptors which are likely to be involved in the recognition of these small biogenic diamines

Corrosion of gold by a nanoscale gold and copper beltlike structure

We report the observation of corrosion of gold at the nanoscale, in which nanometer-sized gold can be corroded in the air in the presence of copper at room temperature during ageing to form a compound of gold with residual copper. The compound is a nanoscale beltlike two-dimensional structure that grows from gold nanoparticles. Using high-resolution electron microscopy and chemical analyses, we show that the structure consists of alternating rows of gold and copper atoms. The atomic columns of gold are arranged in rows separated by 0.5 nm, and the structure extends in a perpendicular direction to these. Density functional theory calculations of an atomic model of this two-dimensional material consisting of gold, copper, and oxygen suggest that it is a narrow bandgap semiconductor. This beltlike structure, growing around Au fine wire bonding in nanodevices, may cause their failure in the electric contact in nanodevices. Thus, this study has direct relevance to the use of gold as a contact material in semiconductor devices. In addition, possible future applications of the observed structures as additives in organic solar cells are discussed

The ErbB signalling pathway: protein expression and prognostic value in epithelial ovarian cancer

Ovarian cancer is the most frequent cause of death from gynaecological cancer in the Western world. Current prognostic factors do not allow reliable prediction of response to chemotherapy and survival for individual ovarian cancer patients. Epidermal growth factor receptor (EGFR) and HER-2/neu are frequently expressed in ovarian cancer but their prognostic value remains unclear. In this study, we investigated the expression and prognostic value of EGFR, EGFR variant III (EGFRvIII), HER-2/neu and important downstream signalling components in a large series of epithelial ovarian cancer patients. Immunohistochemical staining of EGFR, pEGFR, EGFRvIII, Her-2/neu, PTEN (phosphatase and tensin homologue deleted on chromosome 10), total and phosphorylated AKT (pAKT) and phosphorylated ERK (pERK) was performed in 232 primary tumours using the tissue microarray platform and related to clinicopathological characteristics and survival. In addition, EGFRvIII expression was determined in 45 tumours by RT–PCR. Our results show that negative PTEN immunostaining was associated with stage I/II disease (P=0.006), non-serous tumour type (P=0.042) and in multivariate analysis with a longer progression-free survival (P=0.015). Negative PTEN staining also predicted improved progression-free survival in patients with grade III or undifferentiated serous carcinomas (P=0.011). Positive pAKT staining was associated with advanced-stage disease (P=0.006). Other proteins were expressed only at low levels, and were not associated with any clinicopathological parameter or survival. None of the tumours were positive for EGFRvIII. In conclusion, our results indicate that tumours showing negative PTEN staining could represent a subgroup of ovarian carcinomas with a relatively favourable prognosis

Study of parameters in focus simulation functions of virtual slide

As a special function of Virtual Slide (VS) for thick specimens like cytology slides, multilayer (Z-stack) simulated focus and focus fusion were introduced. From the standpoint of surgical pathologist, the optimum parameters for multilayer focus simulation were examined. First, minimal thickness of the layer was checked by measuring thickness of small cells counting the number of the layers that come into focus. Then the optimal number of layers to scan, total thickness, was tried. Small-sized cell nuclei showed around 2μm or less thickness. As minimal thickness of one layer for focus simulation, less than 2 μm is required. Papillary cell mass of urothelial carcinoma, aspiration cytology specimen of breast or thyroid, and uterine cervical smear showed different optimal thickness. Cells piling up more than 4 to 5 layer are difficult to make close up observation. Total 15 (to 30) μm thick scan was enough for most specimens. The “focus fusion” image is single layer image synthesized from multiple layer images. Several layer thicknesses were examined, and there was negligible difference between the focus fusion image synthesized from 0.25 and 1μm thick layers. In the focus fusion image synthesized from 3μm thick layers, some cells not to come into focus. The “focus fusion” seems to contain all the cells in one plane, and easy for screening. To emphasize the existence of myoepithelial cells in fibroadenoma of breast, or to clarify the 3-dimensional tissue structure, multilayer image was better. From our results, 10 layers with 1.5μm thick each provide sufficient information in most specimens

The triggering receptor expressed on myeloid cells (TREM) in inflammatory bowel disease pathogenesis

The Triggering Receptors Expressed on Myeloid cells (TREM) are a family of cell-surface molecules that control inflammation, bone homeostasis, neurological development and blood coagulation. TREM-1 and TREM-2, the best-characterized receptors so far, play divergent roles in several infectious diseases. In the intestine, TREM-1 is highly expressed by macrophages, contributing to inflammatory bowel disease (IBD) pathogenesis. Contrary to current understanding, TREM-2 also promotes inflammation in IBD by fueling dendritic cell functions. This review will focus specifically on recent insights into the role of TREM proteins in IBD development, and discuss opportunities for novel treatment approaches