Simple and statistically sound recommendations for analysing physical theories

Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both of these categories. These issues are often sidestepped with statistically unsound ad hoc methods, involving intersection of parameter intervals estimated by multiple experiments, and random or grid sampling of model parameters. Whilst these methods are easy to apply, they exhibit pathologies even in low-dimensional parameter spaces, and quickly become problematic to use and interpret in higher dimensions. In this article we give clear guidance for going beyond these procedures, suggesting where possible simple methods for performing statistically sound inference, and recommendations of readily-available software tools and standards that can assist in doing so. Our aim is to provide any physicists lacking comprehensive statistical training with recommendations for reaching correct scientific conclusions, with only a modest increase in analysis burden. Our examples can be reproduced with the code publicly available at Zenodo.

Global analyses of Higgs portal singlet dark matter models using GAMBIT

We present global analyses of effective Higgs portal dark matter models in the frequentist and Bayesian statistical frameworks. Complementing earlier studies of the scalar Higgs portal, we use GAMBIT to determine the preferred mass and coupling ranges for models with vector, Majorana and Dirac fermion dark matter. We also assess the relative plausibility of all four models using Bayesian model comparison. Our analysis includes up-to-date likelihood functions for the dark matter relic density, invisible Higgs decays, and direct and indirect searches for weakly-interacting dark matter including the latest XENON1T data. We also account for important uncertainties arising from the local density and velocity distribution of dark matter, nuclear matrix elements relevant to direct detection, and Standard Model masses and couplings. In all Higgs portal models, we find parameter regions that can explain all of dark matter and give a good fit to all data. The case of vector dark matter requires the most tuning and is therefore slightly disfavoured from a Bayesian point of view. In the case of fermionic dark matter, we find a strong preference for including a CP-violating phase that allows suppression of constraints from direct detection experiments, with odds in favour of CP violation of the order of 100:1. Finally, we present DDCalc 2.0.0, a tool for calculating direct detection observables and likelihoods for arbitrary non-relativistic effective operators.

Status of the scalar singlet dark matter model

One of the simplest viable models for dark matter is an additional neutral scalar, stabilised by a Z 2 symmetry. Using the GAMBIT package and combining results from four independent samplers, we present Bayesian and frequentist global fits of this model. We vary the singlet mass and coupling along with 13 nuisance parameters, including nuclear uncertainties relevant for direct detection, the local dark matter density, and selected quark masses and couplings. We include the dark matter relic density measured by Planck, direct searches with LUX, PandaX, SuperCDMS and XENON100, limits on invisible Higgs decays from the Large Hadron Collider, searches for high-energy neutrinos from dark matter annihilation in the Sun with IceCube, and searches for gamma rays from annihilation in dwarf galaxies with the Fermi-LAT. Viable solutions remain at couplings of order unity, for singlet masses between the Higgs mass and about 300 GeV, and at masses above ∼ 1 TeV. Only in the latter case can the scalar singlet constitute all of dark matter. Frequentist analysis shows that the low-mass resonance region, where the singlet is about half the mass of the Higgs, can also account for all of dark matter, and remains viable. However, Bayesian considerations show this region to be rather fine-tuned.

Presence and interaction of inflammatory cells in the spleen of Atlantic cod, Gadus morhua L., infected with Francisella noatunensis

Serious infectious diseases, accompanied by macrophage-dominated chronic inflammation, are common in farmed Atlantic cod. To increase knowledge relating to morphological aspects of such inflammatory responses, cod were challenged with Francisella noatunensis, an important bacterial pathogen of this fish species. Tissue and cell dynamics in the spleen were examined sequentially over 60 days. Small clusters of mainly macrophage-like cells (MLCs) staining for non-specific esterase and acid phosphatase developed with time. These foci were transiently infiltrated by pleomorphic proliferating cells of unknown nature and by granulocyte-like cells (GCLCs) staining for peroxidase and lysozyme. The latter cell type, which appeared to be resident in the red pulp of control fish, migrated into the inflammatory foci of infected fish. Cells expressing genes encoding IFN-γ and IL-8 increased in number during the study period. Bacteria were detected only in the MLCs and their number increased despite the extensive inflammation. Our results demonstrate an intimate spatial relationship in inflammatory foci between at least three cell types. The presence of GCLCs, together with MLCs, suggests pyogranulomatous inflammation as a more appropriate descriptive term than granulomatous inflammation.

Microbial and pathological findings in farmed Atlantic salmon Salmo salar with proliferative gill inflammation

Proliferative gill inflammation (PGI) is an important cause of loss in seawater-farmed Atlantic salmon in Norway. Several microbes have been associated with PGI, including the commonly but not exclusively observed inclusions (epitheliocysts) within the gill lamellae related to infection with 'Candidatus Piscichlamydia salmonis'. Atlantic salmon transferred in the spring of 2004 to 12 seawater farms situated in mid- and southwest Norway were sampled throughout that year. Outbreaks of PGI, as evaluated by clinical examination, histology, and mortality data, were diagnosed in 6 of 7 farms in southwest Norway but not in the 5 farms studied in mid-Norway. Generally, mortality started 3 to 5 mo after seawater transfer and outbreaks lasted at least 1 to 3 mo. 'Ca. P. salmonis' was detected by real-time PCR only in fish from PGI-affected farms and our results indicate an association between 'Ca. P. salmonis' load and PGI severity. Likewise, although widely distributed in all 12 farms studied, epitheliocyst prevalence and number per fish as observed by histology appears associated with PGI prevalence and severity. However, the occurrence of epitheliocysts showed no association with molecular detection of 'Ca. P. salmonis', suggesting that at least 1 other organism is responsible for many of the observed inclusions. A microsporidian, Desmozoon lepeophtherii, was identified at high prevalence regardless of fish and farm PGI status, but at higher loads in fish with PGI. Our results support a multifactorial etiology for PGI in which 'Ca. P. salmonis', an unidentified epitheliocyst agent, and the microsporidian are contributing causes. No evidence for the involvement of Atlantic salmon paramyxovirus in PGI development was identified in the present study. High water temperatures and ectoparasites probably exacerbated mortality.

Nodavirus provokes subclinical encephalitis and retinochoroiditis in adult farmed Atlantic cod, Gadus morhua L

Viral nervous necrosis (VNN) caused by beta-nodavirus affects many species of farmed marine fish, in particular juveniles. Apparently healthy, normally feeding, adult farmed Atlantic cod, Gadus morhua, were sampled in a farm 14 months after an outbreak of VNN with clinical signs. Following necropsy, brain and eye tissues were examined by histology, immunohistochemistry and polymerase chain reaction (PCR). Nodavirus-provoked cell death and inflammation was detected in eye and brain, particularly in the retina and cerebellum and differed from that previously described in Atlantic cod during clinical stages of VNN. Virus was detected both by PCR and immunohistochemistry. This is, to the best of our knowledge, the first description of pathological changes associated with chronic subclinical nodavirus infection in Atlantic cod. Our observations suggest that severe infection and pathological changes may go undetected if investigations are restricted to clinical examination and macroscopic evaluation at necropsy.

Molecular characterisation of Atlantic salmon paramyxovirus (ASPV): a novel paramyxovirus associated with proliferative gill inflammation

Atlantic salmon paramyxovirus (ASPV) was isolated in 1995 from gills of farmed Atlantic salmon suffering from proliferative gill inflammation. The complete genome sequence of ASPV was determined, revealing a genome 16,968 nucleotides in length consisting of six non-overlapping genes coding for the nucleo- (N), phospho- (P), matrix- (M), fusion- (F), haemagglutinin-neuraminidase- (HN) and large polymerase (L) proteins in the order 3'-N-P-M-F-HN-L-5'. The various conserved features related to virus replication found in most paramyxoviruses were also found in ASPV. These include: conserved and complementary leader and trailer sequences, tri-nucleotide intergenic regions and highly conserved transcription start and stop signal sequences. The P gene expression strategy of ASPV was like that of the respiro-, morbilli- and henipaviruses, which express the P and C proteins from the primary transcript and edit a portion of the mRNA to encode V and W proteins. Sequence similarities among various features related to virus replication, pairwise comparisons of all deduced ASPV protein sequences with homologous regions from other members of the family Paramyxoviridae, and phylogenetic analyses of these amino acid sequences suggested that ASPV was a novel member of the sub-family Paramyxovirinae, most closely related to the respiroviruses.

First cases of amoebic gill disease (AGD) in Norwegian seawater farmed Atlantic salmon, Salmo salar L., and phylogeny of the causative amoeba using 18S cDNA sequences

Amoebic gill disease (AGD) was observed in seawater farmed Atlantic salmon at four geographically distant locations on the western coast of Norway. To the best of our knowledge, these are the first detected AGD outbreaks in Norway. The outbreaks lasted for 7-12 weeks in late autumn 2006 and were for the most part concurrent. The crude, cumulative mortality was in the range of 12-20% at three farms and 82% at a fourth. The histopathology showed uniform parasomal amoebae in lesions characteristic for AGD. Another gill disease, proliferative gill inflammation (PGI), was also present to a variable degree and the distinction between the two gill problems is discussed. Seawater temperatures were 3.5 degrees C higher than average before disease outbreaks, which subsided in early winter. The geographical and time pattern of these outbreaks strongly indicates simultaneous infection from the marine environment. Two contiguous 18S cDNA sequences, obtained by reverse transcriptase PCR from gill tissue with AGD-related lesions, showed highest similarity (99.2%) to a newly recognized species designated Neoparamoeba perurans and maximum likelihood analysis demonstrates that they represent Norwegian strains of this Neoparamoeba lineage.

Myocardial glycogen storage disease in farmed rainbow trout, Oncorhynchus mykiss (Walbaum)

This paper is the first description of a spontaneous glycogen-storage disease in a lower vertebrate, as previous descriptions deal with humans and other mammals, or fish where the condition has been experimentally induced. Affected farmed rainbow trout experienced increased mortality from 60 days post-startfeeding and displayed clinical signs of heart failure with abnormal behaviour, exophthalmia, distended abdomen and ventral skin petechiation. Necropsy revealed alterations in cardiac shape with distended atria and rounded ventricles. Microscopically, the compact wall of the ventricle was absent, uneven or thinner than normal. The cardiac myocytes contained extensive amounts of glycogen in cytoplasmic vacuoles as demonstrated by periodic acid-Schiff staining that was abolished by saliva-diastase pretreatment on serial sections. Associated lesions included conspicuous subepicardial and myocardial vascularization, epicardial thickening and necrosis of the ventricular compactum/spongiosum interphase. The lesions in cardiac myocytes had a striking resemblance to glycogenosis type II (Pompe disease), a rare autosomal recessive lysosomal storage disease in humans. This condition was more severe and mortality was higher in a replicate/parallel fish group treated perorally with 17alpha-methyltestosterone to produce all-female progeny, indicating that the hormone treatment aggravated the condition resulting in earlier and more severe manifestation of the disease in this group.

Platyspondyly and shortness of vertebral column in farmed Atlantic salmon Salmo salar in Norway--description and interpretation of pathologic changes

Body malformation due to shortness of the vertebral column, in most cases of unknown cause, has been observed in fish for more than 100 yr. It periodically occurs with high prevalence in farmed Atlantic salmon Salmo salar in Norway, and this paper describes the results of macroscopic, radiographic and histologic examination of parr and seawater-transferred fish. The vertebral bodies in both age groups did not acquire the length that they normally should due to a growth disturbance leading to the condition of platyspondyly and shortness in the column. The pathologic changes became visible at different ages in both groups and the process apparently starts in intervertebral tissues. There was proliferation of connective tissue and blood vessels, and sometimes infiltration with inflammatory cells, around affected vertebrae, especially in seawater-transferred fish. This is the first description of inflammation in abnormally short-spined fish, and it may indicate an infectious etiology, at least in farmed seawater-transferred salmon.

Male pseudohermaphroditism in a cat

A seven-month-old male pedigree cat was brought to the Norwegian College of Veterinary Medicine for routine castration. Visual examination of the external genitalia revealed a wide genital cleft with non-fused bilaterally located testicular pouches. A large clitoris, which was penis-like with small penile spines, was seen protruding dorsally from the ventral commissure of the genital cleft. During an exploratory coeliotomy, no intra-abdominal genital structures of müllerian origin were found. The skin pouches on either side of the vulvar cleft were incised and grossly normal testicles were removed. Histology of the removed gonads showed no or very sparse spermatogenesis. The chromosomal sex was determined by karyotyping to be a normal male 38XY. Based on these findings, the diagnosis of male pseudohermaphroditism was made. The aetiology of the condition in this cat was not determined.