Incomplete Transition Complexity of Basic Operations on Finite Languages

The state complexity of basic operations on finite languages (considering complete DFAs) has been in studied the literature. In this paper we study the incomplete (deterministic) state and transition complexity on finite languages of boolean operations, concatenation, star, and reversal. For all operations we give tight upper bounds for both description measures. We correct the published state complexity of concatenation for complete DFAs and provide a tight upper bound for the case when the right automaton is larger than the left one. For all binary operations the tightness is proved using family languages with a variable alphabet size. In general the operational complexities depend not only on the complexities of the operands but also on other refined measures.Comment: 13 page

HFST—Framework for Compiling and Applying Morphologies

HFST–Helsinki Finite-State Technology ( hfst.sf.net ) is a framework for compiling and applying linguistic descriptions with finite-state methods. HFST currently connects some of the most important finite-state tools for creating morphologies and spellers into one open-source platform and supports extending and improving the descriptions with weights to accommodate the modeling of statistical information. HFST offers a path from language descriptions to efficient language applications in key environments and operating systems. HFST also provides an opportunity to exchange transducers between different software providers in order to get the best out of each finite-state library.Peer reviewe

Elevated CO2induces a bloom of microphytobenthos within a shell gravel mesocosm

The geological storage of carbon dioxide (CO2) is expected to be an important component of future global carbon emission mitigation, but there is a need to understand the impacts of a CO2 leak on the marine environment and to develop monitoring protocols for leakage detection. In the present study, sediment cores were exposed to CO2-acidified seawater at one of five pH levels (8.0, 7.5, 7.0, 6.5 and 6.0) for 10 weeks. A bloom of Spirulina sp. and diatoms appeared on sediment surface exposed to pH 7.0 and 7.5 seawater. Quantitative PCR measurements of the abundance of 16S rRNA also indicated an increase within the pH 7.0 and 7.5 treatments after 10 weeks incubation. More detailed analysis of the microbial communities from the pH 7.0, 7.5 and 8.0 treatments confirmed an increase in the relative abundance of Spirulina sp. and Navicula sp. sequences, with changes in the relative abundance of major archaeal and bacterial groups also detected within the pH 7.0 treatment. A decreased flux of silicate from the sediment at this pH was also detected. Monitoring blooms of microphytobenthos may prove useful as an indicator of CO2 leakage within coastal area

The peripheral blood transcriptome in septic cardiomyopathy: an observational, pilot study.

BACKGROUND:Septic cardiomyopathy (SCM) is common in sepsis and associated with increased morbidity and mortality. Left ventricular global longitudinal strain (LV GLS), measured by speckle tracking echocardiography, allows improved identification of impaired cardiac contractility. The peripheral blood transcriptome may be an important window into SCM pathophysiology. We therefore studied the peripheral blood transcriptome and LV GLS in a prospective cohort of patients with sepsis. RESULTS:In this single-center observational pilot study, we enrolled adult patients (age > 18) with sepsis within 48 h of admission to the ICU. SCM was defined as LV GLS > - 17% based on echocardiograms performed within 72 h of admission. We enrolled 27 patients, 24 of whom had high-quality RNA results; 18 (75%) of 24 had SCM. The group was 50% female and had a median (IQR) age of 59.5 (48.5-67.0) years and admission APACHE II score of 21.0 (16.0-32.3). Forty-six percent had septic shock. After filtering for low-expression and non-coding genes, 15,418 protein coding genes were expressed and 73 had significantly different expression between patients with vs. without SCM. In patients with SCM, 43 genes were upregulated and 30 were downregulated. Pathway analysis identified enrichment in type 1 interferon signaling (adjusted p < 10-5). CONCLUSIONS:In this hypothesis-generating study, SCM was associated with upregulation of genes in the type 1 interferon signaling pathway. Interferons are cytokines that stimulate the innate and adaptive immune response and are implicated in the early proinflammatory and delayed immunosuppression phases of sepsis. While type 1 interferons have not been implicated previously in SCM, interferon therapy (for viral hepatitis and Kaposi sarcoma) has been associated with reversible cardiomyopathy, perhaps suggesting a role for interferon signaling in SCM

Adenosine metabolized from extracellular ATP ameliorates organ injury by triggering A2BR signaling

BACKGROUND: Trauma and a subsequent hemorrhagic shock (T/HS) result in insufficient oxygen delivery to tissues and multiple organ failure. Extracellular adenosine, which is a product of the extracellular degradation of adenosine 5' triphosphate (ATP) by the membrane-embedded enzymes CD39 and CD73, is organ protective, as it participates in signaling pathways, which promote cell survival and suppress inflammation through adenosine receptors including the A2BR. The aim of this study was to evaluate the role of CD39 and CD73 delivering adenosine to A2BRs in regulating the host's response to T/HS. METHODS: T/HS shock was induced by blood withdrawal from the femoral artery in wild-type, global knockout (CD39, CD73, A2BR) and conditional knockout (intestinal epithelial cell-specific deficient VillinCre-A2BRfl/fl) mice. At 3 three hours after resuscitation, blood and tissue samples were collected to analyze organ injury. RESULTS: T/HS upregulated the expression of CD39, CD73, and the A2BR in organs. ATP and adenosine levels increased after T/HS in bronchoalveolar lavage fluid. CD39, CD73, and A2BR mimics/agonists alleviated lung and liver injury. Antagonists or the CD39, CD73, and A2BR knockout (KO) exacerbated lung injury, inflammatory cytokines, and chemokines as well as macrophage and neutrophil infiltration and accumulation in the lung. Agonists reduced the levels of the liver enzymes aspartate transferase and alanine transaminase in the blood, whereas antagonist administration or CD39, CD73, and A2BR KO enhanced enzyme levels. In addition, intestinal epithelial cell-specific deficient VillinCre-A2BRfl/fl mice showed increased intestinal injury compared to their wild-type VillinCre controls. CONCLUSION: In conclusion, the CD39-CD73-A2BR axis protects against T/HS-induced multiple organ failure

The supportive care needs of women experiencing gynaecological cancer: a Western Australian cross-sectional study

Background: Women diagnosed with gynaecological cancer experience supportive care needs that require care provision to reduce the impact on their lives. International evidence suggests supportive care needs of women with gynaecological cancer are not being met and provision of holistic care is a priority area for action. Knowledge on gynaecological cancer supportive care needs is limited, specifically comparison of needs and cancer gynaecological subtype. Our aim was to identify supportive care needs of Western Australian women experiencing gynaecological cancer, their satisfaction with help and explore associations between participant’s demographic characteristics and identified needs. Methods: A cross-sectional design incorporating a modified version of the Supportive Care Needs Survey - short form (SCNS-SF34) assessed 37 supportive care needs under five domains in conjunction with demographic data. Three hundred and forty three women with gynaecological cancer attending a tertiary public referral hospital completed the survey over 12 months. Statistical analysis was performed using the R environment for statistical computing. A linear regression model was fitted with factor scores for each domain and demographic characteristics as explanatory variables. Results: Three hundred and three women (83%) identified at least one moderate or high level supportive care need. The five highest ranked needs were, ‘being informed about your test results as soon as feasible’ (54.8%), ‘fears about cancer spreading’ (53.7%), ‘being treated like a person not just another case’ (51.9%), ‘being informed about cancer which is under control or diminishing (that is, remission)’ (50.7%), and ‘being adequately informed about the benefits and side-effects of treatments before you choose to have them’ (49.9%). Eight of the top ten needs were from the ‘health system and information’ domain. Associations between supportive care items and demographic variables revealed ‘cancer type’, and ‘time since completion of treatment’ had no impact on level of perceived need for any domain. Conclusions: Western Australian women with gynaecological cancer identified a high level of supportive care needs. The implementation of a supportive care screening tool is recommended to ensure needs are identified and care is patient-centred. Early identification and management of needs may help to reduce the burden on health system resources for managing ongoing needs

Effects of biochar amendment on root traits and contaminant availability of maize plants in a copper and arsenic impacted soil

Biochar has been proposed as a tool to enhance phytostabilisation of contaminated soils but little data are available to illustrate the direct effect on roots in contaminated soils. This work aimed to investigate specific root traits and to assess the effect of biochar amendment on contaminant availability. Amendment with two different types of biochar, pine woodchip and olive tree pruning, was assessed in a rhizobox experiment with maize planted in a soil contaminated with significant levels of copper and arsenic. Amendment was found to significantly improve root traits compared to the control soil, particularly root mass density and root length density. Copper uptake to plants and ammonium sulphate extractable copper was significantly less in the biochar amended soils. Arsenic uptake and extractability varied with type of biochar used but was not considered to be the limiting factor affecting root and shoot development. Root establishment in contaminated soils can be enhanced by biochar amendment but choice of biochar is key to maximising soil improvement and controlling contaminant availability

Glucocorticoid resistance in T-lineage acute lymphoblastic leukaemia is associated with a proliferative metabolism

Glucocorticoids (GCs) are among the most important drugs for acute lymphoblastic leukaemia (ALL), yet despite their clinical importance, the exact mechanisms involved in GC cytotoxicity and the development of resistance remain uncertain. We examined the baseline profile of a panel of T-ALL cell lines to determine factors that contribute to GC resistance without prior drug selection. Transcriptional profiling indicated GC resistance in T-ALL is associated with a proliferative phenotype involving upregulation of glycolysis, oxidative phosphorylation, cholesterol biosynthesis and glutamate metabolism, increased growth rates and activation of PI3K/AKT/mTOR and MYC signalling pathways. Importantly, the presence of these transcriptional signatures in primary ALL specimens significantly predicted patient outcome. We conclude that in lymphocytes the activation of bioenergetic pathways required for proliferation may suppress the apoptotic potential and offset the metabolic crisis initiated by GC signalling. It is likely that the link between GC resistance and proliferation in T-ALL has not been fully appreciated to date because such effects would be masked in the context of current multiagent therapies. The data also provide the first evidence that altered expression of wild-type MLL may contribute to GC-resistant phenotypes. Our findings warrant the continued development of selective metabolic inhibitors for the treatment of ALL

Validation of a mouse xenograft model system for gene expression analysis of human acute lymphoblastic leukaemia

<p>Abstract</p> <p>Background</p> <p>Pre-clinical models that effectively recapitulate human disease are critical for expanding our knowledge of cancer biology and drug resistance mechanisms. For haematological malignancies, the non-obese diabetic/severe combined immunodeficient (NOD/SCID) mouse is one of the most successful models to study paediatric acute lymphoblastic leukaemia (ALL). However, for this model to be effective for studying engraftment and therapy responses at the whole genome level, careful molecular characterisation is essential.</p> <p>Results</p> <p>Here, we sought to validate species-specific gene expression profiling in the high engraftment continuous ALL NOD/SCID xenograft. Using the human Affymetrix whole transcript platform we analysed transcriptional profiles from engrafted tissues without prior cell separation of mouse cells and found it to return highly reproducible profiles in xenografts from individual mice. The model was further tested with experimental mixtures of human and mouse cells, demonstrating that the presence of mouse cells does not significantly skew expression profiles when xenografts contain 90% or more human cells. In addition, we present a novel <it>in silico </it>and experimental masking approach to identify probes and transcript clusters susceptible to cross-species hybridisation.</p> <p>Conclusions</p> <p>We demonstrate species-specific transcriptional profiles can be obtained from xenografts when high levels of engraftment are achieved or with the application of transcript cluster masks. Importantly, this masking approach can be applied and adapted to other xenograft models where human tissue infiltration is lower. This model provides a powerful platform for identifying genes and pathways associated with ALL disease progression and response to therapy <it>in vivo</it>.</p

COVID-19 and vertical transmission: assessing the expression of ACE2 / TMPRSS2 in the human fetus and placenta to assess the risk of SARS-CoV-2 infection

Background: While pregnant women have been identified as a potentially at-risk group concerning COVID-19 infection, little is known regarding the susceptibility of the fetus to infection. Co-expression of ACE2 and TMPRSS2 has been identified as a pre-requisite for infection, and expression across different tissues is known to vary between children and adults. However, the expression of these proteins in the fetus is unknown. Methods: We performed a retrospective analysis of single cell data repositories. This data was then validated at both gene and protein level by performing qRT-PCR and two-colour immunohistochemistry on a library of second-trimester human fetal tissues. Findings: TMPRSS2 is present at both gene and protein level in the predominantly epithelial fetal tissues analysed. ACE2 is present at significant levels, only in the fetal intestine and kidney and is not expressed in the fetal lung. The placenta is also negative for the two proteins both during development and at term. Interpretation: This dataset indicates that the lungs are unlikely to be a viable route of SARS-CoV2 fetal infection. The fetal kidney, despite presenting both the proteins required for the infection, is anatomically protected from the exposure to the virus. However, the GI tract is likely to be susceptible to infection due to its high co-expression of both proteins, as well as its exposure to potentially infected amniotic fluid