The Consequences of Non-Classical Measurement Error for Distributional Analysis

This paper analyzes the consequences of non-classical measurement error for distributional analysis. We show that for a popular set of distributions negative correlation between the measurement error (u) and the true value (y) may reduce the bias in the estimated distribution at every value of y. For other distributions the impact of non-classical measurement di¤ers throughout the support of the distribution. We illustrate the practical importance of these results using models of unemployment duration and income.Distribution functions,Non-classical measurement error,

Pterosaurs of the Wessex Formation (Early Cretaceous, Barremian) of the Isle of Wight, southern England: a review with new data

Micropalaeontological processing of vertebrate-bearing horizons within the Early Cretaceous (Barremian) Wessex Formation of the Isle of Wight, southern England, reveals a rare, but diverse assemblage of pterosaurs. Besides the previously known euornithocheiran Caulkicephalus, the new material demonstrates the presence of three species of istiodactylid, a ctenochasmatid, and a distinct form that cannot easily be placed in a higher taxon. This elevated diversity is in keeping with pterosaur diversity from other Early Cretaceous localities, having some similarities with assemblages from the Early Cretaceous of Brazil, China and Spain. The apparent absence of toothless forms in the Wessex Formation may represent a preservation bias or collecting artefact.El análisis micropaleontológico de los niveles estratigráficos ricos en vertebrados del Barremiense (Cretácico Inferior) de la Formacion Wessex en la Isla de Wight al sur de Inglaterra, demuestra la presencia de una escasa aunque diversa asociacion de pterosaurios. Ademas del conocido euornitoqueriaceo Caulkicephalus los nuevos hallazgos han revelado la presencia de tres especies pertenecientes a las familias Istiodactylidae, un taxon de Ctenochasmatidae, y un taxon singular de difícil atribucion a nivel taxonomico superior. Esta gran diversidad es coherente con la de otras localidades del Cretacico Inferior, y tiene algunas semejanzas con asociaciones del Cretacico Inferior de Brasil, China y Espana. La aparente ausencia de formas edentadas en la Formacion Wessex puede ser debida a un sesgo de conservacion o a un artefacto relacionado con la colecta de ejemplares

Has phytodetritus processing by an abyssal soft-sediment community recovered 26 years after an experimental disturbance?

The potential harvest of polymetallic nodules will heavily impact the abyssal, soft sediment ecosystem by removing sediment, hard substrate, and associated fauna inside mined areas. It is therefore important to know whether the ecosystem can recover from this disturbance and if so at which rate. The first objective of this study was to measure recovery of phytodetritus processing by the benthic food web from a sediment disturbance experiment in 1989. The second objective was to determine the role of holothurians in the uptake of fresh phytodetritus by the benthic food web. To meet both objectives, large benthic incubation chambers (CUBEs; 50 × 50 × 50 cm) were deployed inside plow tracks (with and without holothurian presence) and at a reference site (holothurian presence, only) at 4100 m water depth. Shortly after deployment, 13C- and 15N-labeled phytodetritus was injected in the incubation chambers and during the subsequent 3-day incubation period, water samples were taken five times to measure the production of 13C-dissolved inorganic carbon over time. At the end of the incubation, holothurians and sediment samples were taken to determine biomass, densities and incorporation of 13C and 15N into bacteria, nematodes, macrofauna, and holothurians. For the first objective, the results showed that biomass of bacteria, nematodes and macrofauna did not differ between reference sites and plow track sites when holothurians were present. Additionally, meiofauna and macrofauna taxonomic composition was not significantly different between the sites. In contrast, total 13C uptake by bacteria, nematodes and holothurians was significantly lower at plow track sites compared to reference sites, though the number of replicates was low. This result suggests that important ecosystem functions such as organic matter processing have not fully recovered from the disturbance that occurred 26 years prior to our study. For the second objective, the analysis indicated that holothurians incorporated 2.16 × 10−3 mmol labile phytodetritus C m−2 d−1 into their biomass, which is one order of magnitude less as compared to bacteria, but 1.3 times higher than macrofauna and one order of magnitude higher than nematodes. Additionally, holothurians incorporated more phytodetritus carbon per unit biomass than macrofauna and meiofauna, suggesting a size-dependence in phytodetritus carbon uptake

MicroRNA regulation of the paired-box transcription factor Pax3 confers robustness to developmental timing of myogenesis

Commitment of progenitors in the dermomyotome to myoblast fate is the first step in establishing the body musculature. Pax3 is a crucial transcription factor, important for skeletal muscle development and expressed in myogenic progenitors in the dermomyotome of developing somites and in migratory muscle progenitors that populate the limb buds. Down-regulation of Pax3 is essential to ignite the myogenic program, including up-regulation of myogenic regulators, Myf-5 and MyoD. MicroRNAs (miRNAs) confer robustness to developmental timing by posttranscriptional repression of genetic programs that are related to previous developmental stages or to alternative cell fates. Here we demonstrate that the muscle-specific miRNAs miR-1 and miR-206 directly target Pax3. Antagomir-mediated inhibition of miR-1/miR-206 led to delayed myogenic differentiation in developing somites, as shown by transient loss of myogenin expression. This correlated with increased Pax3 and was phenocopied using Pax3-specific target protectors. Loss of myogenin after antagomir injection was rescued by Pax3 knockdown using a splice morpholino, suggesting that miR-1/miR-206 control somite myogenesis primarily through interactions with Pax3. Our studies reveal an important role for miR-1/miR-206 in providing precision to the timing of somite myogenesis. We propose that posttranscriptional control of Pax3 downstream of miR-1/miR-206 is required to stabilize myoblast commitment and subsequent differentiation. Given that mutually exclusive expression of miRNAs and their targets is a prevailing theme in development, our findings suggest that miRNA may provide a general mechanism for the unequivocal commitment underlying stem cell differentiation

Actin depolymerization is associated with meiotic acceleration in cycloheximide-treated ovine oocytes

Oocytes treated with the protein synthesis inhibitor cycloheximide (CHX) arrest at the germinal vesicle (GV) stage and undergo accelerated GV breakdown (GVBD) after CHX is removed. However, little is known about the underlying mechanism of accelerated meiotic maturation. Here, we investigated this mechanism and found that oocytes released from CHX arrest have higher amounts of cyclin B1 (CCNB1) and phosphorylated mitogen-activated protein kinase (pMAPK) proteins. Increased levels of these factors were not associated with mRNA polyadenylation or increased transcription rates of CCNB1 and MOS (Moloney murine sarcoma viral oncogene homolog) during CHX arrest. We found that treatment of CHX-arrested oocytes with the actin filament-stabilizing agent Jasplakinolide (Jasp) delayed GVBD following release from CHX arrest and that this was correlated with reduced maturation-promoting factor (MPF) activity. These results suggest that CCNB1 mRNAs released from actin filaments during CHX arrest increase CCNB1 transcripts available for translation after release from CHX arrest, leading to the precocious activation of MPF and accelerated meiotic progression

Ovine induced pluripotent stem cells are resistant to reprogramming after nuclear transfer

Induced pluripotent stem cells (iPSCs) share similar characteristics of indefinite in vitro growth with embryonic stem cells (ESCs) and may therefore serve as a useful tool for the targeted genetic modification of farm animals via nuclear transfer (NT). Derivation of stable ESC lines from farm animals has not been possible, therefore, it is important to determine whether iPSCs can be used as substitutes for ESCs in generating genetically modified cloned farm animals. We generated ovine iPSCs by conventional retroviral transduction using the four Yamanaka factors. These cells were basic fibroblast growth factor (bFGF)- and activin A-dependent, showed persistent expression of the transgenes, acquired chromosomal abnormalities, and failed to activate endogenous NANOG. Nonetheless, iPSCs could differentiate into the three somatic germ layers in vitro. Because cloning of farm animals is best achieved with diploid cells (G1/G0), we synchronized the iPSCs in G1 prior to NT. Despite the cell cycle synchronization, preimplantation development of iPSC-NT embryos was lower than with somatic cells (2% vs. 10% blastocysts, p<0.01). Furthermore, analysis of the blastocysts produced demonstrated persistent expression of the transgenes, aberrant expression of endogenous SOX2, and a failure to activate NANOG consistently. In contrast, gene expression in blastocysts produced with the parental fetal fibroblasts was similar to those generated by in vitro fertilization. Taken together, our data suggest that the persistent expression of the exogenous factors and the acquisition of chromosomal abnormalities are incompatible with normal development of NT embryos produced with iPSCs

The distribution of Polychlorinated Biphenyls (PCBs) in the River Thames Catchment under the scenarios of climate change

Measurements have shown low levels of PCBs in water but relatively high concentrations in the resident fish of the River Thames (UK). To better understand the distribution and behaviour of PCBs in the Thames river basin and their potential risks, a level III fugacity model was applied to selected PCB congeners (PCB 52, PCB 118 and PCB 153). The modelling results indicated that fish and sediments represent environmental compartments with the highest PCB concentrations; but the greatest mass of PCBs (over 70%) is likely to remain in the soil. As emissions decline, soil could then act as a significant secondary source of PCBs with the river bed-sediment functioning as a long-term reservoir of PCBs. The predicted changes in temperature and rainfall forecast in the UK Climate Projections 2009 (UKCP09) over the next 80 years had only a modest influence on PCB fate in the model. The most significant result was a tendency for climate change to enhance the evaporation of PCBs from soil to air in the Thames catchment. (C) 2015 Elsevier B.V. All rights reserved

How Group Members Appraise Collective History: Appraisal Dimensions of Collective History and Their Role in In-Group Engagement

This is the final version. Available on open access from PsychOpen via the DOI in this recordData Availability: For this article, a data set is freely available (Makanju, Livingstone, & Sweetman, 2022).Group members’ appraisals of their in-group’s collective history have been found to shape their engagement with the in-group and its collective goals. We add to this research by examining the complexity and dimensionality of how group members appraise collective history, and how different forms of appraisals relate to different forms of in-group engagement. We do so by (1) outlining four key dimensions – richness, clarity, valence and subjective importance – of how an in-group’s collective history can be appraised, and (2) examining how these appraisal dimensions relate to group members’ engagement with the in-group. Focussing on the African in-group category, we tested these ideas using a qualitative, essay writing approach. Analysis of responses (N = 33) indicated varied use of each of these dimensions of collective history appraisal, and that they relate to in-group engagement in differing ways. Two specific rhetorical strategies were identified: deploying the in-group’s history as a contrast; and deploying the in-group’s history as an inspiration. When collective history was appraised as rich, complex, negatively-valenced and unimportant, it was characterised as something from which the in-group should break away (history-as-contrast). Conversely, when collective history was appraised as rich, complex, positively-valenced and important, history was characterised as something to be used as a resource for the in-group (history-as-inspiration). Our findings build a fuller and more nuanced picture of how collective history shapes in-group engagement in a non-western setting

Annotation of gene function in citrus using gene expression information and co-expression networks

BACKGROUND: The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world's most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a "guilt-by-association" principle whereby genes encoding proteins involved in similar and/or related biological processes may exhibit similar expression patterns across diverse sets of experimental conditions. While bioinformatics resources such as GCN analysis are widely available for efficient gene function prediction in model plant species including Arabidopsis, soybean and rice, in citrus these tools are not yet developed. RESULTS: We have constructed a comprehensive GCN for citrus inferred from 297 publicly available Affymetrix Genechip Citrus Genome microarray datasets, providing gene co-expression relationships at a genome-wide scale (33,000 transcripts). The comprehensive citrus GCN consists of a global GCN (condition-independent) and four condition-dependent GCNs that survey the sweet orange species only, all citrus fruit tissues, all citrus leaf tissues, or stress-exposed plants. All of these GCNs are clustered using genome-wide, gene-centric (guide) and graph clustering algorithms for flexibility of gene function prediction. For each putative cluster, gene ontology (GO) enrichment and gene expression specificity analyses were performed to enhance gene function, expression and regulation pattern prediction. The guide-gene approach was used to infer novel roles of genes involved in disease susceptibility and vitamin C metabolism, and graph-clustering approaches were used to investigate isoprenoid/phenylpropanoid metabolism in citrus peel, and citric acid catabolism via the GABA shunt in citrus fruit. CONCLUSIONS: Integration of citrus gene co-expression networks, functional enrichment analysis and gene expression information provide opportunities to infer gene function in citrus. We present a publicly accessible tool, Network Inference for Citrus Co-Expression (NICCE, http://citrus.adelaide.edu.au/nicce/home.aspx), for the gene co-expression analysis in citrus.Darren CJ Wong, Crystal Sweetman and Christopher M For

Testing the effect of historical representations on collective identity and action

This is the final version. Available from Public Library of Science via the DOI in this record. Data Availability: All data and research material files are available from the Open Science Framework database (https://osf.io/esnb4/?view_only=0be6351ee8b34ea8b9543afa101e5824).Historical representation of collective identity offer means of influencing the extent to which group members engage in activities in line with the collective interests of their group vs. their own individual interests. This research tested the effect of different historical representations of the African people on Africans’ perceptions of African social identity and engagement in identity management strategies across two studies. In Study 1 (N = 162), we tested the effect of two historical representations: positive (prestigious precolonial African history and resistance to the colonial power) and negative (inhumane practices of precolonial Africans). In Study 2 (N = 431), we tested the effect of two historical representations: positive (prestigious precolonial African history) and negative factual (inhuman practices of precolonial Africans) while also making salient the ubiquitous historical representation of the African people (negative colonial-perspective) across all history conditions. We predicted that positive (vs. negative) historical representation would lead to more positive perceptions of African identity, which in turn would predict more collectively-oriented identity management strategies. Altogether, results provided no support for these predictions. We highlight methodological (and by extension theoretical) features–such as, psychological reactance and outgroup audience effect–which may have limited the effect of the manipulations to help inform the interpretation of the null findings obtained. We conclude by discussing other limitations and the theoretical implications of our work, before pointing out various avenues for future research to help us better test, and understand, the role of historical representation in the African context