Quadrant/octant sequencing and the role of coherent structures in bed load sediment entrainment

To permit the tracking of turbulent flow structures in an Eulerian frame from single-point measurements, we make use of a generalization of conventional two-dimensional quadrant analysis to three-dimensional octants. We characterize flow structures using the sequences of these octants and show how significance may be attached to particular sequences using statistical mull models. We analyze an example experiment and show how a particular dominant flow structure can be identified from the conditional probability of octant sequences. The frequency of this structure corresponds to the dominant peak in the velocity spectra and exerts a high proportion of the total shear stress. We link this structure explicitly to the propensity for sediment entrainment and show that greater insight into sediment entrainment can be obtained by disaggregating those octants that occur within the identified macroturbulence structure from those that do not. Hence, this work goes beyond critiques of Reynolds stress approaches to bed load entrainment that highlight the importance of outward interactions, to identifying and prioritizing the quadrants/octants that define particular flow structures. Key Points <list list-type=''bulleted'' id=''jgrf20196-list-0001''> <list-item id=''jgrf20196-li-0001''>A new method for analysing single point velocity data is presented <list-item id=''jgrf20196-li-0002''>Flow structures are identified by a sequence of flow states (termed octants) <list-item id=''jgrf20196-li-0003''>The identified structure exerts high stresses and causes bed-load entrainment

Identification and mutational analyses of phosphorylation sites of the calcineurin-binding protein CbpA and the identification of domains required for calcineurin binding in Aspergillus fumigatus.

Calcineurin is a key protein phosphatase required for hyphal growth and virulence in Aspergillus fumigatus, making it an attractive antifungal target. However, currently available calcineurin inhibitors, FK506 and cyclosporine A, are immunosuppressive, limiting usage in the treatment of patients with invasive aspergillosis. Therefore, the identification of endogenous inhibitors of calcineurin belonging to the calcipressin family is an important parallel strategy. We previously identified the gene cbpA as the A. fumigatus calcipressin member and showed its involvement in hyphal growth and calcium homeostasis. However, the mechanism of its activation/inhibition through phosphorylation and its interaction with calcineurin remains unknown. Here we show that A. fumigatus CbpA is phosphorylated at three distinct domains, including the conserved SP repeat motif (phosphorylated domain-I; PD-I), a filamentous fungal-specific domain (PD-II), and the C-terminal CIC motif (Calcipressin Inhibitor of Calcineurin; PD-III). While mutation of three phosphorylated residues (Ser208, Ser217, Ser223) in the PD-II did not affect CbpA function in vivo, mutation of the two phosphorylated serines (Ser156, Ser160) in the SP repeat motif caused reduced hyphal growth and sensitivity to oxidative stress. Mutational analysis in the key domains in calcineurin A (CnaA) and proteomic interaction studies confirmed the requirement of PxIxIT motif-binding residues (352-NIR-354) and the calcineurin B (CnaB)-binding helix residue (V371) for the binding of CbpA to CnaA. Additionally, while the calmodulin-binding residues (442-RVF-444) did not affect CbpA binding to CnaA, three mutations (T359P, H361L, and L365S) clustered between the CnaA catalytic and the CnaB-binding helix were also required for CbpA binding. This is the first study to analyze the phosphorylation status of calcipressin in filamentous fungi and identify the domains required for binding to calcineurin.

René-Théophile-Hyacinthe Laennec (1781-1826) and the description of metastatic pulmonary melanoma.

In 19th century, the anatomo-clinical school of Paris linked clinical signs with anatomical lesions establishing clinical medicine. One of the most enlightened promoters of this method was the French physician René-Théophile-Hyacinthe Laennec, known as the inventor of stethoscope. In our article, we reveal his work on pulmonary melanoma.

Natural vitamin C intake and the risk of head and neck cancer : a pooled analysis in the International Head and Neck Cancer Epidemiology Consortium

Evidence of associations between single nutrients and head and neck cancer (HNC) is still more limited and less consistent than that for fruit and vegetables. However, clarification of the protective mechanisms of fruit and vegetables is important to our understanding of HNC etiology. We investigated the association between vitamin C intake from natural sources and cancer of the oral cavity/pharynx and larynx using individual-level pooled data from ten case-control studies (5,959 cases and 12,248 controls) participating in the International Head and Neck Cancer Epidemiology (INHANCE) consortium. After harmonization of study-specific exposure information via the residual method, adjusted odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated using unconditional multiple logistic regression models on quintile categories of 'non-alcohol energy-adjusted' vitamin C intake. In the presence of heterogeneity of the estimated ORs among studies, we derived those estimates from generalized linear mixed models. Higher intakes of vitamin C were inversely related to oral and pharyngeal (OR = 0.54, 95% CI: 0.45-0.65, for the fifth quintile category versus the first one, p for trend<0.001) and laryngeal cancers (OR = 0.52, 95% CI: 0.40-0.68, p for trend = 0.006), although in the presence of heterogeneity among studies for both sites. Inverse associations were consistently observed for the anatomical subsites of oral and pharyngeal cancer, and across strata of age, sex, education, body mass index, tobacco, and alcohol, for both cancer sites. The inverse association of vitamin C intake from foods with HNC may reflect a protective effect on these cancers; however, we cannot rule out other explanations.

Loanword Phonology, Lexical Exceptions, Morphologically Driven Underapplication, and the Nature of Positionally Biased Constraints

In this paper we provide a formal account for underapplication of vowel reduction to schwa in Majorcan Catalan loanwords and learned words. On the basis of the comparison of these data with those concerning productive derivation and verbal inflection, which show analogous patterns, in this paper we also explore the existing and not yet acknowledged correlation between those processes that exhibit a particular behaviour in the loanword phonology with respect to the native phonology of the language, those processes that show lexical exceptions and those processes that underapply due to morphological reasons. In light of the analysis of the very same data and taking into account the aforementioned correlation, we show how there might exist a natural diachronic relation between two kinds of Optimality Theory constraints which are commonly used but, in principle, mutually exclusive: positional faithfulness and contextual markedness constraints. Overall, phonological productivity is proven to be crucial in three respects: first, as a context of the grammar, given that «underapplication» is systematically found in what we call the productive phonology of the dialect (including loanwords, learned words, productive derivation and verbal inflection); second, as a trigger or blocker of processes, in that the productivity or the lack of productivity of a specific process or constraint in the language is what explains whether it is challenged or not in any of the depicted situations, and, third, as a guiding principle which can explain the transition from the historical to the synchronic phonology of a linguistic variety.

Consistency and the core of multi-sided assignment markets

[cat] En aquest treball es demostra que en el domini dels jocs d’assignació equilibrats multisectorials (Quint, 1991), el core és l’única solució no buida que satisfà derived consistency i projection consistency. També es caracteritza el core en tota la classe dels jocs d’assignació multisectorials amb els axiomes de singleness best, individual antimonotonicity i derived consistency. Com a casos particulars, s’obtenen dues noves axiomàtiques del core per als jocs d’assignació bilaterals (Shapley and Shubik, 1972).

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

Background: The zona limitans intrathalamica (ZLI) and the isthmus organizer (IsO) are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians. Results: In this paper, we identified a conserved sequence motif (Fezf box) in all bilaterians. We report the expression pattern of Fezf in amphioxus and Drosophila and compare it with those of Gbx, Otx and Irx. We found that the relative expression patterns of these genes in vertebrates are fully conserved in amphioxus and flies, indicating that the genetic subdivisions defining the location of both secondary organizers in early vertebrate brain development were probably present in the last common ancestor of extant bilaterians. However, in contrast to vertebrates, we found that Irx-defective flies do not show an affected Fezf expression pattern. Conclusions: The absence of expression of the corresponding morphogens from cells at these conserved genetic boundaries in invertebrates suggests that the organizing properties might have evolved specifically in the vertebrate lineage by the recruitment of key morphogens to these conserved genetic locations.

Consistency and the core of multi-sided assignment markets

[cat] En aquest treball es demostra que en el domini dels jocs d’assignació equilibrats multisectorials (Quint, 1991), el core és l’única solució no buida que satisfà derived consistency i projection consistency. També es caracteritza el core en tota la classe dels jocs d’assignació multisectorials amb els axiomes de singleness best, individual antimonotonicity i derived consistency. Com a casos particulars, s’obtenen dues noves axiomàtiques del core per als jocs d’assignació bilaterals (Shapley and Shubik, 1972).

Ultrastructural study of spermiogenesis and the spermatozoon of the proteocephalidean cestode Barsonella lafoni de Chambrier et al., 2009, a parasite of the catfish Clarias gariepinus (Burchell, 1822) (Siluriformes, Clariidae)

Spermiogenesis in the proteocephalidean cestode Barsonella lafoni de Chambrier et al., 2009 shows typical characteristics of the type I spermiogenesis. These include the formation of distal cytoplasmic protrusions forming the differentiation zones, lined by cortical microtubules and containing two centrioles. An electron-dense material is present in the apical region of the differentiation zone during the early stages of spermiogenesis. Each centriole is associated to a striated rootlet, being separated by an intercentriolar body. Two free and unequal flagella originate from the centrioles and develop on the lateral sides of the differentiation zone. A median cytoplasmic process is formed between the flagella. Later these flagella rotate, become parallel to the median cytoplasmic process and finally fuse proximodistally with the latter. It is interesting to note that both flagellar growth and rotation are asynchronous. Later, the nucleus enlarges and penetrates into the spermatid body. Finally, the ring of arching membranes is strangled and the young spermatozoon is detached from the residual cytoplasm. The mature spermatozoon presents two axonemes of the 9 +"1" trepaxonematan pattern, crested body, parallel nucleus and cortical microtubules, and glycogen granules. Thus, it corresponds to the type II spermatozoon, described in almost all Proteocephalidea. The anterior extremity of the gamete is characterized by the presence of an apical cone surrounded by the lateral projections of the crested body. An arc formed by some thick and parallel cortical microtubules appears at the level of the centriole. They surround the centriole and later the first axoneme. This arc of electron-dense microtubules disorganizes when the second axoneme appears, and then two parallel rows of thin cortical microtubules are observed. The posterior extremity of the male gamete exhibits some cortical microtubules. This type of posterior extremity has never been described in proteocephalidean cestodes. The ultrastructural features of the spermatozoon/spermiogenesis of the Proteocephalidea species are analyzed and compared.

Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer

Background: The zona limitans intrathalamica (ZLI) and the isthmus organizer (IsO) are two major secondary organizers of vertebrate brain development. These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians. Results: In this paper, we identified a conserved sequence motif (Fezf box) in all bilaterians. We report the expression pattern of Fezf in amphioxus and Drosophila and compare it with those of Gbx, Otx and Irx. We found that the relative expression patterns of these genes in vertebrates are fully conserved in amphioxus and flies, indicating that the genetic subdivisions defining the location of both secondary organizers in early vertebrate brain development were probably present in the last common ancestor of extant bilaterians. However, in contrast to vertebrates, we found that Irx-defective flies do not show an affected Fezf expression pattern. Conclusions: The absence of expression of the corresponding morphogens from cells at these conserved genetic boundaries in invertebrates suggests that the organizing properties might have evolved specifically in the vertebrate lineage by the recruitment of key morphogens to these conserved genetic locations.

Ultrastructural study of spermiogenesis and the spermatozoon of the proteocephalidean cestode Barsonella lafoni de Chambrier et al., 2009, a parasite of the catfish Clarias gariepinus (Burchell, 1822) (Siluriformes, Clariidae)

Spermiogenesis in the proteocephalidean cestode Barsonella lafoni de Chambrier et al., 2009 shows typical characteristics of the type I spermiogenesis. These include the formation of distal cytoplasmic protrusions forming the differentiation zones, lined by cortical microtubules and containing two centrioles. An electron-dense material is present in the apical region of the differentiation zone during the early stages of spermiogenesis. Each centriole is associated to a striated rootlet, being separated by an intercentriolar body. Two free and unequal flagella originate from the centrioles and develop on the lateral sides of the differentiation zone. A median cytoplasmic process is formed between the flagella. Later these flagella rotate, become parallel to the median cytoplasmic process and finally fuse proximodistally with the latter. It is interesting to note that both flagellar growth and rotation are asynchronous. Later, the nucleus enlarges and penetrates into the spermatid body. Finally, the ring of arching membranes is strangled and the young spermatozoon is detached from the residual cytoplasm. The mature spermatozoon presents two axonemes of the 9 +"1" trepaxonematan pattern, crested body, parallel nucleus and cortical microtubules, and glycogen granules. Thus, it corresponds to the type II spermatozoon, described in almost all Proteocephalidea. The anterior extremity of the gamete is characterized by the presence of an apical cone surrounded by the lateral projections of the crested body. An arc formed by some thick and parallel cortical microtubules appears at the level of the centriole. They surround the centriole and later the first axoneme. This arc of electron-dense microtubules disorganizes when the second axoneme appears, and then two parallel rows of thin cortical microtubules are observed. The posterior extremity of the male gamete exhibits some cortical microtubules. This type of posterior extremity has never been described in proteocephalidean cestodes. The ultrastructural features of the spermatozoon/spermiogenesis of the Proteocephalidea species are analyzed and compared.