A comparison of different methods of estimating and testing the especification of rational expectation models with one endogeneus and one exogenus variable.

This article considers the theory of the estimation and testing of a model with one endogenous variable and one exogenous variable, where the structure of the model assumes a simple rational expectations hypothesis for the determination of the endogenous variable. Two methods of estimation are considered, the first the method of Maximum Likelihood, and the second the method of Instrumental Variables. The first is asymptotically efficient, the second may be relatively less asymptotically efficient. The first also has the advantage of suggesting suitable tests for the general form of the rational expectations model.Instrumental variables; Maximum likelihood estimation;

A comparison of different methods of estimating and testing the especification of rational expectation models with one endogeneus and one exogenus variable

This article considers the theory of the estimation and testing of a model with one endogenous variable and one exogenous variable, where the structure of the model assumes a simple rational expectations hypothesis for the determination of the endogenous variable. Two methods of estimation are considered, the first the method of Maximum Likelihood, and the second the method of Instrumental Variables. The first is asymptotically efficient, the second may be relatively less asymptotically efficient. The first also has the advantage of suggesting suitable tests for the general form of the rational expectations model

What Could a Trans Book History Look Like? Toward Trans Codicology

This article draws on critical trans studies and queer archival practice to propose a book historical mode that extends what we know about the premodern trans experience beyond the recovery of individual biographies. Instead of turning to textual sources for the identification of transness, the author looks to Susan Stryker’s call for the “recuperat[ion of] embodied knowing as a formally legitimated basis of knowledge production.” Bibliography, he suggests, makes claims of objectivity that engender a particular reluctance to respond to such calls. But the lived reality of archival research is one of affective embodiment. Affect theory is an area that, as yet, has seen little methodological uptake in bibliographical research. This article lays the ground for a trans book history that takes affective embodied response seriously as a source of trans connection to and through the past. (In the issue section Bibliographic Knowledge(s)

The spectral estimation of simultaneous equation systems with lagged endogenous variables

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Characterisation of Brachycephalic Obstructive Airway Syndrome in French Bulldogs Using Whole-Body Barometric Plethysmography.

Brachycephalic obstructive airway syndrome (BOAS) is an important health and welfare problem in several popular dog breeds. Whole-body barometric plethysmography (WBBP) is a non-invasive method that allows safe and repeated quantitative measurements of respiratory cycles on unsedated dogs. Here respiratory flow traces in French bulldogs from the pet population were characterised using WBBP, and a computational application was developed to recognise affected animals. Eighty-nine French bulldogs and twenty non-brachycephalic controls underwent WBBP testing. A respiratory functional grading system was used on each dog based on respiratory signs (i.e. respiratory noise, effort, etc.) before and after exercise. For development of an objective BOAS classifier, functional Grades 0 and I were considered to have insignificant clinical signs (termed here BOAS-) and Grades II and III to have significant signs (termed here BOAS+). A comparison between owner-perception of BOAS and functional grading revealed that 60 % of owners failed to recognise BOAS in dogs that graded BOAS+ in this study.WBBP flow traces were found to be significantly different between non-brachycephalic controls and Grade 0 French bulldogs; BOAS- and BOAS+ French bulldogs. A classifier was developed using quadratic discriminant analysis of the respiratory parameters to distinguish BOAS- and BOAS + French bulldogs, and a BOAS Index was calculated for each dog. A cut-off value of the BOAS Index was selected based on a receiver operating characteristic (ROC) curve. Sensitivity, specificity, positive predictive value, and negative predictive value of the classifier on the training group (n=69) were 0.97, 0.93, 0.95, and 0.97, respectively. The classifier was validated using a test group of French bulldogs (n=20) with an accuracy of 0.95. WBBP offers objective screening for the diagnosis of BOAS in French Bulldogs. The technique may be applied to other brachycephalic breeds affected by BOAS, and possibly to other respiratory disease in dogs.Funding was provided by (1) The Kennel Club Charitable Trust (KCCT), Grant no.: RG 71960, http://www.thekennelclub.org.uk/our-reso​urces/kennel-club-charitable-trust/, to DRS JFL; and (2) Cambridge Overseas Trust (Taiwan Cambridge Scholarship), https://www.cambridgetrust.org/about/cam​bridge-overseas-trust/, to NCL.This is the final published version. It first appeared at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130741

Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci

Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR) - or antigen receptor (AR) - gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes. This annotation was used to query 107 whole genome sequences from 19 breeds and identified over 5,500 alleles across the 550 genes of the seven AR loci: the IG heavy, kappa, and lambda loci; and the TR alpha, beta, gamma, and delta loci. Of note was the discovery that half of the IGK variable (V) genes were located downstream of, and inverted with respect to, the rest of the locus. Analysis of the germline sequences of all the AR V genes identified greater conservation between dog and human than mouse with either. This work brings our understanding of the genetic diversity and expression of AR in dogs to the same completeness as that of mice and men, making it the third species to have all AR loci comprehensively and accurately annotated. The large number of germline sequences serves as a reference for future studies, and has allowed statistically powerful conclusions to be drawn on the pressures that have shaped these loci.This work was supported by funding from the BBSRC and the Wellcome Trust

The Ghosts of Bindings Past: Micro-Computed X-Ray Tomography for the Study of Bookbinding

This essay describes the results of a new application of micro-computed X-ray tomography (µCT) to conduct nondestructive investigations of the binding structures of premodern books. This application addresses a twofold challenge in the study of historic bindings and their construction. Few premodern books survive in their original bindings. Moreover, until recently, when books were rebound, the original structures were rarely documented, and the remains were usually discarded. Where original bindings do remain in situ, much of their structure is, by design, hidden. Particulars of construction may be surmised; but without destructive disbinding, little can be proven. µCT enables an exploratory, multilinear approach to codicological investigations that makes bindings accessible in the form of tractable volumetric data

Canine genome assembly correction facilitates identification of a MAP9 deletion as a potential age of onset modifier for RPGRIP1-associated canine retinal degeneration.

Retinal degeneration (RD) in the Miniature Long Haired Dachshund (MLHD) is a cone-rod dystrophy resulting in eventual blindness in affected individuals. In a previous study, a 44-nucleotide insertion (ins44) in exon 2 of RPGRIP1 was associated with RD. However, results on an extended population of MLHD revealed a variable RD onset age for ins44 homozygous dogs. Further investigations using a genome-wide association study comparing early onset and late onset RD cases identified an age of onset modifying locus for RD, approximately 30 Mb upstream of RPGRIP1 on chr15. In this investigation, target enriched sequencing identified a MAP9 deletion spanning approximately 22 kb associated with early RD onset. Identification of the deletion required correction to the CanFam3.1 genome build as canine MAP9 is part of a historic tandem duplication, resulting in incomplete assembly of this genome region. The deletion breakpoints were identified in MAP9 intron 10 and in a downstream partial MAP9 pseudogene. The fusion of these two genes, which we have called MAP9 EORD (microtubule-associated protein, early onset retinal degeneration), is in frame and is expressed at the RNA level, with the 3' region containing several predicted deleterious variants. We speculate that MAP9 associates with α-tubulin in the basal body of the cilium. RPGRIP1 is also known to locate to the cilium, where it is closely associated with RPGR. RPGRIP1 mutations also cause redistribution of α-tubulin away from the ciliary region in photoreceptors. Hence, a MAP9 partial deficit is a particularly attractive candidate to synergise with a partial RPGRIP1 deficit to cause a more serious disease.This is the author accepted manuscript. The final version is available from Springer via http://dx.doi.org/10.1007/s00335-016-9627-

Rearranging Edgeworth-Cornish-Fisher Expansions

This paper applies a regularization procedure called increasing rearrangement to monotonize Edgeworth and Cornish-Fisher expansions and any other related approximations of distribution and quantile functions of sample statistics. Besides satisfying the logical monotonicity, required of distribution and quantile functions, the procedure often delivers strikingly better approximations to the distribution and quantile functions of the sample mean than the original Edgeworth-Cornish-Fisher expansions.Comment: 17 pages, 3 figure