Late Miocene to early Pliocene biofacies of Wanganui and Taranaki Basins, New Zealand: Applications to paleoenvironmental and sequence stratigraphic analysis

The Matemateaonga Formation is late Miocene to early Pliocene (upper Tongaporutuan to lower Opoitian New Zealand Stages) in age. The formation comprises chiefly shellbeds, siliciclastic sandstone, and siltstone units and to a lesser extent non-marine and shallow marine conglomerate and rare paralic facies. The Matemateaonga Formation accumulated chiefly in shelf paleoenvironments during basement onlap and progradation of a late Miocene to early Pliocene continental margin wedge in the Wanganui and Taranaki Basins. The formation is strongly cyclothemic, being characterised by recurrent vertically stacked facies successions, bounded by sequence boundaries. These facies accumulated in a range of shoreface to mid-outer shelf paleoenvironments during conditions of successively oscillating sea level. This sequential repetition of facies and the biofacies they enclose are the result of sixth-order glacio-eustatic cyclicity. Macrofaunal associations have been identified from statistical analysis of macrofossil occurrences collected from multiple sequences. Each association is restricted to particular lithofacies and stratal positions and shows a consistent order and/or position within the sequences. This pattern of temporal paleoecologic change appears to be the result of lateral, facies-related shifting of broad biofacies belts, or habitat-tracking, in response to fluctuations of relative sea level, sediment flux, and other associated paleoenvironmental variables. The associations also show strong similarity in terms of their generic composition to biofacies identified in younger sedimentary strata and the modern marine benthic environment in New Zealand

Perceptions of 24/7 In‐house Attending Coverage on Fellow Education and Autonomy in a Pediatric Cardiothoracic Intensive Care Unit

BackgroundThe 24/7 in‐house attending coverage is emerging as the standard of care in intensive care units. Implementation costs, workforce feasibility, and patient outcomes resulting from changes in physician staffing are widely debated topics. Understanding the impact of staffing models on the learning environment for medical trainees and faculty is equally warranted, particularly with respect to trainee education and autonomy.ObjectiveThis study aims to elicit the perceptions of pediatric cardiology fellows and attendings toward 24/7 in‐house attending coverage and its effect on fellow education and autonomy.MethodsWe surveyed pediatric cardiology fellows and attendings practicing in the pediatric cardiothoracic intensive care unit (PCTU) of a large, university‐affiliated medical center, using structured Likert response items and open‐ended questions, prior to and following the transition to 24/7 in‐house attending coverage.ResultsAll (100%) trainees and faculty completed all surveys. Both prior to and following transition to 24/7 in‐house attending coverage, all fellows, and the majority of attendings agreed that the overnight call experience benefited fellow education. At baseline, trainees identified limited circumstances in which on‐site attending coverage would be critical. Preimplementation concerns that 24/7 in‐house attending coverage would negatively affect the education of fellows were not reflected following actual implementation of the new staffing policy. However, based upon open‐ended questions, fellow autonomy was affected by the new paradigm, with fellows and attendings reporting decreased “appropriateness” of autonomy after implementation.ConclusionsOur prospective study, showing initial concerns about limiting the learning environment in transitioning to 24/7 in‐house attending coverage did not result in diminished perceptions of the educational experience for our fellows but revealed an expected decrease in fellow autonomy. The study indirectly facilitated open discussions about methods to preserve fellow education and warranted autonomy in our PCTU; however, continued efforts are needed to achieve the optimal balance between supervised training and the transition to autonomous practice.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/111990/1/chd12261.pd

A single-copy IS5-like transposon in the genome of a bdelloid rotifer

Author Posting. © The Authors, 2009. This is the author's version of the work. It is posted here by permission of Oxford University for personal use, not for redistribution. The definitive version was published in Molecular Biology and Evolution 26 (2009): 1921-1929, doi:10.1093/molbev/msp104.In the course of sequencing telomeric chromosomal regions of the bdelloid rotifer Adineta vaga, we encountered an unusual DNA transposon. Unlike other bdelloid and, more generally, eukaryotic transposable elements (TEs), it exhibits similarity to prokaryotic insertion sequences (IS). Phylogenetic analysis indicates that this transposon, named IS5_Av, is related to the ISL2 group of the IS5 family of bacterial IS elements. Despite the apparent intactness of the single open reading frame coding for a DDE transposase and the perfect identity of its 213-bp terminal inverted repeats (TIRs), the element is present in only one copy per diploid genome. It does not exhibit any detectable levels of transcription, so that its transposase gene appears to be silent in the bdelloid host. While horizontal transfers of TEs between kingdoms are not known to happen in nature, it appears likely that IS5_Av underwent integration into the A. vaga genome relatively recently, but was not successful in adapting to the new host and failed to increase in copy number. Alternatively, it might be the only known member of a novel eukaryotic DNA TE superfamily which is so rare that its other members, if any, have not yet been identified in eukaryotic genomes sequenced to date.This research was supported by the U.S. National Science Foundation grant MCB- 0821956 to I.A

Why royalties ? Evidence from French distribution networks

Working paper GATE 2011-02This empirical note deals with the contractual design of relationships in distribution networks. In the framework of agency theory, I study the royalty rate as an incentive device for the upstream firm in maintaining brand-name value, using recent French data to estimate probit models. The results are consistent with the analytical framework

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

Distributions of epistasis in microbes fit predictions from a fitness landscape model.

How do the fitness effects of several mutations combine? Despite its simplicity, this question is central to the understanding of multilocus evolution. Epistasis (the interaction between alleles at different loci), especially epistasis for fitness traits such as reproduction and survival, influences evolutionary predictions "almost whenever multilocus genetics matters". Yet very few models have sought to predict epistasis, and none has been empirically tested. Here we show that the distribution of epistasis can be predicted from the distribution of single mutation effects, based on a simple fitness landscape model. We show that this prediction closely matches the empirical measures of epistasis that have been obtained for Escherichia coli and the RNA virus vesicular stomatitis virus. Our results suggest that a simple fitness landscape model may be sufficient to quantitatively capture the complex nature of gene interactions. This model may offer a simple and widely applicable alternative to complex metabolic network models, in particular for making evolutionary predictions

Farmer attitudes and livestock disease: exploring citizenship behaviour and peer monitoring across two BVD control schemes in the UK

The eradication of BVD in the UK is technically possible but appears to be socially untenable. The following study explored farmer attitudes to BVD control schemes in relation to advice networks and information sharing, shared aims and goals, motivation and benefits of membership, notions of BVD as a priority disease and attitudes toward regulation. Two concepts from the organisational management literature framed the study: citizenship behaviour where actions of individuals support the collective good (but are not explicitly recognised as such) and peer to peer monitoring (where individuals evaluate other’s behaviour). Farmers from two BVD control schemes in the UK participated in the study: Orkney Livestock Association BVD Eradication Scheme and Norfolk and Suffolk Cattle Breeders Association BVD Eradication Scheme. In total 162 farmers participated in the research (109 in-scheme and 53 out of scheme). The findings revealed that group helping and information sharing among scheme members was low with a positive BVD status subject to social censure. Peer monitoring in the form of gossip with regard to the animal health status of other farms was high. Interestingly, farmers across both schemes supported greater regulation with regard to animal health, largely due to the mistrust of fellow farmers following voluntary disease control measures. While group cohesiveness varied across the two schemes, without continued financial inducements, longer-term sustainability is questionabl

Changes in shell durability of common marine taxa through the Phanerozoic: evidence for biological rather than taphonomic drivers.

Abstract.-Phanerozoic trends in shell and life habit traits linked to postmortem durability were evaluated for the most common fossil brachiopod, gastropod, and bivalve genera in order to test for changes in taphonomic bias. Using the Paleobiology Database, we tabulated occurrence frequencies of genera for 48 intervals of ,11 Myr duration. The most frequently occurring genera, cumulatively representing 40% of occurrences in each time bin, were scored for intrinsic durability on the basis of shell size, reinforcement (ribs, folds, and spines), life habit, and mineralogy. Shell durability is positively correlated with the number of genera in a time bin, but durability traits exhibit different temporal patterns across higher taxa, with notable offsets in the timing of changes in these traits. We find no evidence for temporal decreases in durability that would indicate taphonomic bias at the Phanerozoic scale among commonly occurring genera. Also, all three groups show a remarkable stability in mean shell size through the Phanerozoic, an unlikely pattern if strong sizefiltering taphonomic megabiases were affecting the fossil record of shelly faunas. Moreover, small shell sizes are attained in the early Paleozoic in brachiopods and in the latest Paleozoic in gastropods but are steady in bivalves; unreinforced shells are common to all groups across the entire Phanerozoic; organophosphatic and aragonitic shells dominate only the oldest and youngest time bins; and microstructures having high organic content are most common in the oldest time bins. In most cases, the timing of changes in durability-related traits is inconsistent with a late Mesozoic Marine Revolution. The post-Paleozoic increase in mean gastropod reinforcement occurs in the early Triassic, suggesting either an earlier appearance and expansion of durophagous predators or other drivers. Increases in shell durability hypothesized to be the result of increased predation in the late Mesozoic are not evident in the common genera examined here. Infaunal life habit does increase in the late Mesozoic, but it does not become more common than levels already attained during the Paleozoic, and only among bivalves does the elevated late Mesozoic level persist through the Holocene. These temporal patterns suggest control on the occurrence of durability-related traits by individual evolutionary histories rather than taphonomic megabiases. Our findings do not mean taphonomic biases are absent from the fossil record, but rather that their effects apparently have had little net effect on the relative occurrence of shell traits generally thought to confer higher preservation potential over long time scales