The Triassic-Jurassic boundary in eastern North America

Rift basins of the Atlantic passive margin in eastern North America are filled with thousands of meters of continental rocks termed the Newark Supergroup which provide an unprecedented opportunity to examine the fine scale structure of the Triassic-Jurassic mass extinction in continental environments. Time control, vital to the understanding of the mechanisms behind mass extinctions, is provided by lake-level cycles apparently controlled by orbitally induced climate change allowing resolution at the less than 21,000 year level. Correlation with other provinces is provided by a developing high resolution magnetostratigraphy and palynologically-based biostratigraphy. A large number of at least local vertebrate and palynomorph extinctions are concentrated around the boundary with survivors constituting the earliest Jurassic assemblages, apparently without the introduction of new taxa. The palynofloral transition is marked by the dramatic elimination of a relatively high diversity Triassic pollen assemblage with the survivors making up a Jurassic assemblage of very low diversity overwhelmingly dominated by Corollina. Based principally on palynological correlations, the hypothesis that these continental taxonomic transitions were synchronous with the massive Triassic-Jurassic marine extinctions is strongly corroborated. An extremely rapid, perhaps catastrophic, taxonomic turnover at the Triassic-Jurassic boundary, synchronous in continental and marine realms is hypothesized and discussed

Computation of the Transient in Max-Plus Linear Systems via SMT-Solving

This paper proposes a new approach, grounded in Satisfiability Modulo Theories (SMT), to study the transient of a Max-Plus Linear (MPL) system, that is the number of steps leading to its periodic regime. Differently from state-of-the-art techniques, our approach allows the analysis of periodic behaviors for subsets of initial states, as well as the characterization of sets of initial states exhibiting the same specific periodic behavior and transient. Our experiments show that the proposed technique dramatically outperforms state-of-the-art methods based on max-plus algebra computations for systems of large dimensions.Comment: The paper consists of 22 pages (including references and Appendix). It is accepted in FORMATS 2020 First revisio

Non-Abelian Chern-Simons Particles in an External Magnetic Field

The quantum mechanics and thermodynamics of SU(2) non-Abelian Chern-Simons particles (non-Abelian anyons) in an external magnetic field are addressed. We derive the N-body Hamiltonian in the (anti-)holomorphic gauge when the Hilbert space is projected onto the lowest Landau level of the magnetic field. In the presence of an additional harmonic potential, the N-body spectrum depends linearly on the coupling (statistics) parameter. We calculate the second virial coefficient and find that in the strong magnetic field limit it develops a step-wise behavior as a function of the statistics parameter, in contrast to the linear dependence in the case of Abelian anyons. For small enough values of the statistics parameter we relate the N-body partition functions in the lowest Landau level to those of SU(2) bosons and find that the cluster (and virial) coefficients dependence on the statistics parameter cancels.Comment: 35 pages, revtex, 3 eps figures include

Late Silurian plutons in Yucatan

This is the published version. Copyright 1996 American Geophysical Union. All Rights Reserved.U-Pb measurements of zircons from two composite plutons in the Maya Mountains of the Yucatan Block (Belize) give Late Silurian ages. Zircons from one of the five compositional phases of the Mountain Pine Ridge pluton yield an age of 418±3.6 Ma. A second compositional phase gives a minimum age of 404 Ma, and zircons from a third phase, although plagued with high common Pb, yield ages consistent with the other two. Zircons from one compositional phase of the Hummingbird-Mullins River pluton indicate an age of about 410–420 Ma. These data demonstrate that two of the three Maya Mountains plutons residing among the strata of the Late Pennsylvanian through Permian Santa Rosa Group are older than that sedimentation. Although the third pluton was not dated, both the similarity of sedimentary facies patterns adjacent to it to those adjacent to one of the plutons dated as Late Silurian and a published single Rb-Sr age of 428 ± 41 Ma suggest this third pluton also was emergent during Santa Rosa deposition. Thus the new U/Pb dates and other data suggest that all three Maya Mountains plutons pre-date Late Carboniferous sedimentation and that none intrude the Santa Rosa Group. Although very uniform ages of about 230 Ma amongst all plutons, derived from abundant earlier dating by the K-Ar system, led to the conclusion that intrusion mostly had occurred in the Late Triassic, the U-Pb ages (obtained from the same sites as the K-Ar dates) demonstrate that the K-Ar ages do not derive from a Late Triassic intrusive episode. The K-Ar dates probably are a signature of the rifting associated with Pangean breakup and formation of the Gulf of Mexico. In a reconstructed Pangea, the position of the Maya Mountains Late Silurian plutons suggests that the Late Silurian Acadian-Caledonian orogen of eastern North America extended through the region of the future Gulf of Mexico. Finally, the U-Pb ages of the Maya Mountains plutons are the same as those of a group of shocked zircons found in the Chicxulub impact structure and its fallout layer. The presence of these ages in both locations suggests that the Maya Mountains exposures may be representative of the basement of the Yucatan Block, hence of the basement impacted by the Chicxulub object

Male breast cancer: a report of 127 cases at a Moroccan institution

Background: Male breast cancer (MBC) is a rare disease representing less than 1% of all malignancies in men and only 1% of all incident breast cancers. Our study details clinico-pathological features, treatments and prognostic factors in a large Moroccan cohort. Findings: One hundred and twenty-seven patients were collected from 1985 to 2007 at the National Institute of Oncology in Rabat, Morocco. Median age was 62 years and median time for consultation 28 months. The main clinical complaint was a mass beneath the areola in 93, 5% of the cases. Most patients have an advanced disease. Ninety-one percent of tumors were ductal carcinomas. Management consisted especially of radical mastectomy; followed by adjuvant radiotherapy and hormonal therapy with or without chemotherapy. The median of follow-up was 30 months. The evolution has been characterized by local recurrence; in twenty two cases (17% of all patients). Metastasis occurred in 41 cases (32% of all patients). The site of metastasis was the bone in twenty cases; lung in twelve cases; liver in seven case; liver and skin in one case and pleura and skin in one case. Conclusion: Male breast cancer has many similarities to breast cancer in women, but there are distinct features that should be appreciated. Future research for better understanding of this disease at national or international level are needed to improve the management and prognosis of male patients

Biochemical markers of bone turnover and clinical outcome in patients with renal cell and bladder carcinoma with bone metastases following treatment with zoledronic acid: The TUGAMO study

Background: Levels of bone turnover markers (BTM) might be correlated with outcome in terms of skeletal-related events (SRE), disease progression, and death in patients with bladder cancer (BC) and renal cell carcinoma (RCC) with bone metastases (BM). We try to evaluate this possible correlation in patients who receive treatment with zoledronic acid (ZOL). Methods: This observational, prospective, and multicenter study analysed BTM and clinical outcome in these patients. Serum levels of bone alkaline phosphatase (BALP), procollagen type I amino-terminal propeptide (PINP), and beta-isomer of carboxyterminal telopeptide of type I collagen (b-CTX) were analysed. Results: Patients with RCC who died or progressed had higher baseline b-CTX levels and those who experienced SRE during follow-up showed high baseline BALP levels. In BC, a poor rate of survival was related with high baseline b-CTX and BALP levels, and new SRE with increased PINP levels. Cox univariate analysis showed that b-CTX levels were associated with higher mortality and disease progression in RCC and higher mortality in BC. Bone alkaline phosphatase was associated with increased risk of premature SRE appearance in RCC and death in BC. Conclusion: Beta-isomer of carboxy-terminal telopeptide of type I collagen and BALP can be considered a complementary tool for prediction of clinical outcomes in patients with BC and RCC with BM treated with ZOLNovartis Oncology Spain for supporting this stud

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome – NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome – NL interactions

Measuring Global Credibility with Application to Local Sequence Alignment

Computational biology is replete with high-dimensional (high-D) discrete prediction and inference problems, including sequence alignment, RNA structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical genetics. Even though prediction and inference in these settings are uncertain, little attention has been focused on the development of global measures of uncertainty. Regardless of the procedure employed to produce a prediction, when a procedure delivers a single answer, that answer is a point estimate selected from the solution ensemble, the set of all possible solutions. For high-D discrete space, these ensembles are immense, and thus there is considerable uncertainty. We recommend the use of Bayesian credibility limits to describe this uncertainty, where a (1−α)%, 0≤α≤1, credibility limit is the minimum Hamming distance radius of a hyper-sphere containing (1−α)% of the posterior distribution. Because sequence alignment is arguably the most extensively used procedure in computational biology, we employ it here to make these general concepts more concrete. The maximum similarity estimator (i.e., the alignment that maximizes the likelihood) and the centroid estimator (i.e., the alignment that minimizes the mean Hamming distance from the posterior weighted ensemble of alignments) are used to demonstrate the application of Bayesian credibility limits to alignment estimators. Application of Bayesian credibility limits to the alignment of 20 human/rodent orthologous sequence pairs and 125 orthologous sequence pairs from six Shewanella species shows that credibility limits of the alignments of promoter sequences of these species vary widely, and that centroid alignments dependably have tighter credibility limits than traditional maximum similarity alignments

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets

Abstract. In order to understand complex genetic regulatory networks researchers require automated formal modelling techniques that provide appropriate analysis tools. In this paper we propose a new qualitative model for genetic regulatory networks based on Petri nets and detail a process for automatically constructing these models using logic mini-mization. We take as our starting point the Boolean network approach in which regulatory entities are viewed abstractly as binary switches. The idea is to extract terms representing a Boolean network using logic minimization and to then directly translate these terms into appropri-ate Petri net control structures. The resulting compact Petri net model addresses a number of shortcomings associated with Boolean networks and is particularly suited to analysis using the wide range of Petri net tools. We demonstrate our approach by presenting a detailed case study in which the genetic regulatory network underlying the nutritional stress response in Escherichia coli is modelled and analysed.

Usefulness of bone turnover markers as predictors of mortality risk, disease progression and skeletal-related events appearance in patients with prostate cancer with bone metastases following treatment with zoledronic acid: TUGAMO study

Owing to the limited validity of clinical data on the treatment of prostate cancer (PCa) and bone metastases, biochemical markers are a promising tool for predicting survival, disease progression and skeletal-related events (SREs) in these patients. The aim of this study was to evaluate the predictive capacity of biochemical markers of bone turnover for mortality risk, disease progression and SREs in patients with PCa and bone metastases undergoing treatment with zoledronic acid (ZA). Methods: This was an observational, prospective and multicenter study in which ninety-eight patients were included. Patients were treated with ZA (4mg every 4 weeks for 18 months). Data were collected at baseline and 3, 6, 9, 12, 15 and 18 months after the beginning of treatment. Serum levels of bone alkaline phosphtase (BALP), aminoterminal propeptide of procollagen type I (P1NP) and beta-isomer of carboxiterminal telopeptide of collagen I (b-CTX) were analysed at all points in the study. Data on disease progression, SREs development and survival were recorded. Results: Cox regression models with clinical data and bone markers showed that the levels of the three markers studied were predictive of survival time, with b-CTX being especially powerful, in which a lack of normalisation in visit 1 (3 months after the beginning of treatment) showed a 6.3-times more risk for death than in normalised patients. Levels of these markers were also predictive for SREs, although in this case BALP and P1NP proved to be better predictors. We did not find any relationship between bone markers and disease progression. Conclusion: In patients with PCa and bone metastases treated with ZA, b-CTX and P1NP can be considered suitable predictors for mortality risk, while BALP and P1NP are appropriate for SREs. The levels of these biomarkers 3 months after the beginning of treatment are especially importantThis study was supported by Novartis Oncology Spai