An automata characterisation for multiple context-free languages

We introduce tree stack automata as a new class of automata with storage and identify a restricted form of tree stack automata that recognises exactly the multiple context-free languages.Comment: This is an extended version of a paper with the same title accepted at the 20th International Conference on Developments in Language Theory (DLT 2016

Population structure of island-associated dolphins: evidence from photo-identification of common bottlenose dolphins (Tursiops truncatus) in the main Hawaiian Islands

Management agencies often use geopolitical boundaries as proxies for biological boundaries. In Hawaiian waters a single stock is recognized of common bottlenose dolphins, Tursiops truncatus, a species that is found both in open water and near-shore among the main Hawaiian Islands. To assess population structure, we photo-identified 336 distinctive individuals from the main Hawaiian Islands, from 2000 to 2006. Their generally shallow-water distribution, and numerous within-year and between-year resightings within island areas suggest that individuals are resident to the islands, rather than part of an offshore population moving through the area. Comparisons of identifications obtained from Kaua‘i/Ni‘ihau, O‘ahu, the “4-island area,” and the island of Hawai‘i showed no evidence of movements among these island groups, although movements from Kaua‘i to Ni‘ihau and among the “4-islands” were documented. A Bayesian analysis examining the probability of missing movements among island groups, given our sample sizes for different areas, indicates that interisland movement rates are less than 1% per year with 95% probability. Our results suggest the existence of multiple demographically independent populations of island-associated common bottlenose dolphins around the main Hawaiian islands

New insights into Holocene hydrology and temperature from lipid biomarkers in western Mediterranean alpine wetlands

Alpine regions of the Mediterranean realm are among the most climatically sensitive areas in the world. Thus, alpine wetlands from the southern Iberian Peninsula, in the westernmost part of the Mediterranean region, are highly sensitive sensors of environmental changes. Difficulties have surfaced in separating controls by temperature and/or precipitation in previous paleoenvironmental studies from alpine environments in this area. We present a Holocene biomarker record (n-alkanes and long-chain diols) from a high elevation lake, Laguna de Río Seco (LdRS), in the south of the Iberian Peninsula, which contributes to the identification of these forcing mechanisms. The hydrological history of the area, primarily water availability and evapotranspiration, is reconstructed by means of the n-alkane record, including the indices of average chain length, portion aquatic, and carbon preference index, as well as hydrogen isotopes (δD) of aquatic (δDaq) and terrestrial (δDwax) n-alkanes. Temperatures are also estimated using the algae derived long-chain diols. We interpret δDaq and δDwax fluctuations as showing changes in the source and amount of precipitation throughout the LdRS record. An Atlantic precipitation source appears to have predominated during the early-middle Holocene, but an occasional Mediterranean influence with an isotopic enrichment in precipitation is detected in the middle-late Holocene that is likely related to the setting of the current atmospheric pattern in southeastern Iberia under the joint control of the North Atlantic Oscillation (NAO) and the Western Mediterranean dynamics, such as the Western Mediterranean Oscillation (WeMO). Our new record from LdRS is consistent with a generalized trend of a humid early-middle Holocene with low temperature variability, evolving towards an arid middle-late Holocene with abrupt temperature changes. In addition to these long-term trends during the last ∼10,500 years, two phases of climate instability, evidenced by abrupt depletions in δDaq, have been identified at the end of these periods, one between ∼6500 and 5500 cal yr BP and another in the last ∼500 years. These episodes would represent strengthened winter cold conditions that favoured the persistence of snowpack and frozen soil in the catchment, causing reduced terrestrial plant growth and low lake evaporation. According to the long-chain diol record, temperatures during these phases were relatively low, but experienced abrupt increases at the end of each period

Safety and feasibility of oral immunotherapy to multiple allergens for food allergy

BACKGROUND: Thirty percent of children with food allergy are allergic to more than one food. Previous studies on oral immunotherapy (OIT) for food allergy have focused on the administration of a single allergen at the time. This study aimed at evaluating the safety of a modified OIT protocol using multiple foods at one time. METHODS: Participants underwent double-blind placebo-controlled food challenges (DBPCFC) up to a cumulative dose of 182 mg of food protein to peanut followed by other nuts, sesame, dairy or egg. Those meeting inclusion criteria for peanut only were started on single-allergen OIT while those with additional allergies had up to 5 foods included in their OIT mix. Reactions during dose escalations and home dosing were recorded in a symptom diary. RESULTS: Forty participants met inclusion criteria on peanut DBPCFC. Of these, 15 were mono-allergic to peanut and 25 had additional food allergies. Rates of reaction per dose did not differ significantly between the two groups (median of 3.3% and 3.7% in multi and single OIT group, respectively; p = .31). In both groups, most reactions were mild but two severe reactions requiring epinephrine occurred in each group. Dose escalations progressed similarly in both groups although, per protocol design, those on multiple food took longer to reach equivalent doses per food (median +4 mo.; p < .0001). CONCLUSIONS: Preliminary data show oral immunotherapy using multiple food allergens simultaneously to be feasible and relatively safe when performed in a hospital setting with trained personnel. Additional, larger, randomized studies are required to continue to test safety and efficacy of multi-OIT. TRIAL REGISTRATION: Clinicaltrial.gov NCT0149017

Eotaxin and FGF enhance signaling through an Extracellular signal-related kinase (ERK)-dependent pathway in the pathogenesis of Eosinophilic Esophagitis

<p>Abstract</p> <p>Background</p> <p>Eosinophilic esophagitis (EoE) is characterized by the inflammation of the esophagus and the infiltration of eosinophils into the esophagus, leading to symptoms such as dysphagia and stricture formation. Systemic immune indicators like eotaxin and fibroblast growth factor were evaluated for possible synergistic pathological effects. Moreover, blood cells, local tissue, and plasma from EoE and control subjects were studied to determine if the localized disease was associated with a systemic effect that correlated with presence of EoE disease.</p> <p>Method</p> <p>Real-time polymerase chain reaction from peripheral blood mononuclear cells (PBMC), immunohistochemistry from local esophageal biopsies, fluid assays on plasma, and fluorescence-activated cell sorting on peripheral blood cells from subjects were used to study the systemic immune indicators in newly diagnosed EoE (n = 35), treated EoE (n = 9), Gastroesophageal reflux disease (GERD) (n = 8), ulcerative colitis (n = 5), Crohn's disease (n = 5), and healthy controls (n = 8).</p> <p>Result</p> <p>Of the transcripts tested for possible immune indicators, we found extracellular signal-regulated kinase (ERK), Bcl-2, bFGF (basic fibroblast growth factor), and eotaxin levels were highly upregulated in PBMC and associated with disease presence of EoE. Increased FGF detected by immunohistochemistry in esophageal tissues and in PBMC was correlated with low levels of pro-apoptotic factors (Fas, Caspase 8) in PBMC from EoE subjects. Plasma-derived bFGF was shown to be the most elevated and most specific in EoE subjects in comparison to healthy controls and disease control subjects.</p> <p>Conclusion</p> <p>We describe for the first time a possible mechanism by which increased FGF is associated with inhibiting apoptosis in local esophageal tissues of EoE subjects as compared to controls. Eotaxin and FGF signaling pathways share activation through the ERK pathway; together, they could act to increase eosinophil activation and prolong the half-life of eosinophils in local tissues of the esophagus in EoE subjects.</p

Hepatitis C virus-induced changes in microRNA 107 (miRNA-107) and miRNA-449a modulate CCL2 by targeting the interleukin-6 receptor complex in hepatitis

Hepatitis C virus (HCV)-mediated liver diseases are one of the major health issues in the United States and worldwide. HCV infection has been reported to modulate microRNAs (miRNAs) that control various cell surface receptors and gene-regulatory complexes involved in hepatic inflammation and liver diseases. We report here that specific downregulation of miRNA-107 and miRNA-449a following HCV infection in patients with HCV-mediated liver diseases modulates expression of CCL2, an inflammatory chemokine upregulated in patients with chronic liver diseases, by targeting components of the interleukin-6 receptor (IL-6R) complex. Computational analysis for DNA-bound transcription factors in the CCL2 promoter identified adjacent binding sites for CCAAT/CEBPα, spleen focus-forming virus, proviral integration oncogene (SPI1/PU.1), and STAT3. We demonstrate that CEBPα, PU.1, and STAT3 interacted with each other physically to cooperatively bind to the promoter and activate CCL2 expression. Analysis of IL-6R and JAK1 expression in HCV patients by quantitative PCR showed significant upregulation when there was impaired miRNA-107 and miRNA-449a expression, along with upregulation of PU.1 and STAT3, but not CEBPα. miRNA-449a and miRNA-107 target expression of IL-6R and JAK1, respectively, in vitro and also inhibit IL-6 signaling and impair STAT3 activation in human hepatocytes. Taken together, our results demonstrate a novel gene-regulatory mechanism in which HCV-induced changes in miRNAs (miRNA-449a and miRNA-107) regulate CCL2 expression by activation of the IL-6-mediated signaling cascade, which we propose will result in HCV-mediated induction of inflammatory responses and fibrosis. IMPORTANCE Hepatitis C virus (HCV)-induced hepatitis is a major health concern worldwide. HCV infection results in modulation of noncoding microRNAs affecting major cellular pathways, including inflammatory responses. In this study, we have identified a microRNA-regulated pathway for the chemokine CCL2 in HCV-induced hepatitis. Understanding microRNA-mediated transcriptional-regulatory pathways will result in development of noninvasive biomarkers for better disease prediction and development of effective therapeutics

Strong chemistry-climate feedbacks in the Pliocene

This is the final version. Available on open access from AGU via the DOI in this recordThe Pliocene epoch was the last sustained interval when global climate was significantly warmer than today but has been difficult to explain fully based on the external forcings from atmospheric carbon dioxide and surface albedo. Here we use an Earth system model to simulate terrestrial ecosystem emissions and atmospheric chemical composition in the mid-Pliocene (about 3 million years ago) and the preindustrial (∼1750s). Tropospheric ozone and aerosol precursors from vegetation and wildfire are ∼50% and ∼100% higher in the mid-Pliocene due to the spread of the tropical savanna and deciduous biomes. The chemistry-climate feedbacks contribute a net global warming that is +30-250% of the carbon dioxide effect and a net aerosol global cooling that masks 15-100% of the carbon dioxide effect. These large vegetation-mediated ozone and aerosol feedbacks operate on centennial to millennial timescales in the climate system and have not previously been included in paleoclimate sensitivity assessments.Funding for this research is provided by Yale University

Therapeutic Effect of a Poly(ADP-Ribose) Polymerase-1 Inhibitor on Experimental Arthritis by Downregulating Inflammation and Th1 Response

Poly(ADP-ribose) polymerase-1 (PARP-1) synthesizes and transfers ADP ribose polymers to target proteins, and regulates DNA repair and genomic integrity maintenance. PARP-1 also plays a crucial role in the progression of the inflammatory response, and its inhibition confers protection in several models of inflammatory disorders. Here, we investigate the impact of a selective PARP-1 inhibitor in experimental arthritis. PARP-1 inhibition with 5-aminoisoquinolinone (AIQ) significantly reduces incidence and severity of established collagen-induced arthritis, completely abrogating joint swelling and destruction of cartilage and bone. The therapeutic effect of AIQ is associated with a striking reduction of the two deleterious components of the disease, i.e. the Th1-driven autoimmune and inflammatory responses. AIQ downregulates the production of various inflammatory cytokines and chemokines, decreases the antigen-specific Th1-cell expansion, and induces the production of the anti-inflammatory cytokine IL-10. Our results provide evidence of the contribution of PARP-1 to the progression of arthritis and identify this protein as a potential therapeutic target for the treatment of rheumatoid arthritis