A Symmetric Prior for the Regularisation of Elastic Deformations: Improved anatomical plausibility in nonlinear image registration

Nonlinear registration is critical to many aspects of Neuroimaging research. It facilitates averaging and comparisons across multiple subjects, as well as reporting of data in a common anatomical frame of reference. It is, however, a fundamentally ill-posed problem, with many possible solutions which minimise a given dissimilarity metric equally well. We present a regularisation method capable of selectively driving solutions towards those which would be considered anatomically plausible by penalising unlikely lineal, areal and volumetric deformations. This penalty is symmetric in the sense that geometric expansions and contractions are penalised equally, which encourages inverse-consistency. We demonstrate that this method is able to significantly reduce local volume changes and shape distortions compared to state-of-the-art elastic (FNIRT) and plastic (ANTs) registration frameworks. Crucially, this is achieved whilst simultaneously matching or exceeding the registration quality of these methods, as measured by overlap scores of labelled cortical regions. Extensive leveraging of GPU parallelisation has allowed us to solve this highly computationally intensive optimisation problem while maintaining reasonable run times of under half an hour

togeny and Dynamics of the Gonadal Development, Embryogenesis, and Gestation in Xenotoca eiseni (Cyprinodontiformes, Goodeidae)

This is the author accepted manuscript. The final version is available from Karger via the DOI in this recordWe characterized the ontogeny and dynamics of gonadal development, embryogenesis, and gestation in captive stocks of the viviparous redtail splitfin, Xenotoca eiseni. Using histology, we showed that gonads were fully differentiated at the time of birth with a male:female sex ratio of 1:1 in the captive stock. External secondary sex features included a modified anal fin and a distinctive orange tail coloration. These features first appeared at 4 weeks after birth and were discriminative for males thereafter. There was no sex-related dichotomy in body size, and X. eiseni reached sexual maturity at approximately 12 weeks of age. We found no evidence for sperm storage in females. Gestation normally took 6 weeks, and there was a positive correlation between female body size and the number of offspring produced, with up to 27 offspring for a single pregnancy. Yolk is the main food source for developing embryos for the period up to 2 weeks, and thereafter, trophotaeniae in embryos act as nutrient exchange surfaces in the ovarian lumen, which subsequently undergo complete regression within 2 weeks of birth. In our final analysis, we discuss the great potential of X. eiseni as a model for studying the effects of chemicals on sexual development.University of Exete

Reconstructing pedigrees: some identifiability questions for a recombination-mutation model

Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.Comment: 40 pages, 9 figure

Effects of maternal exposure to environmentally relevant concentrations of 17α-ethinyloestradiol in a live bearing freshwater fish, Xenotoca eiseni (Cyprinodontiformes, Goodeidae)

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record The viviparous teleost redtail splitfin (Xenotoca eiseni) is a live bearing fish that presents a novel freshwater model for investigating the effects of maternally derived micropollutants on vulnerable early developmental life stages. Here, adult female X. eiseni were exposed to 17α-ethinyloestradiol (EE2), a potent a contraceptive oestrogen, at environmentally relevant concentrations, to investigate for effects on sex partitioning and development. Pregnant and non-pregnant females were exposed for four-weeks to EE2 at measured concentrations of 0.9 and 3.4 ng/L EE2 and offspring from gravid females kept in clean water for a further four weeks. Only pregnant females were seen to respond to 3.4 ng/L EE2 with an increase in the transcription of hepatic vitellogenins (vtgA, vtgB and vtgC). Offspring of exposed mothers showed no obvious effects on somatic growth, gonadal development, sex partitioning or development. However, there was a higher rate of deformities and developmental abnormalities in offspring of EE2-exposed females. The work presented provides the foundation for the development of X. eiseni as a new freshwater model for studies on maternal transfer of chemical pollutants in live bearing animals.University of Exete

Mental rotation task of hands: differential influence number of rotational axes

Various studies on the hand laterality judgment task, using complex sets of stimuli, have shown that the judgments during this task are dependent on bodily constraints. More specific, these studies showed that reaction times are dependent on the participant’s posture or differ for hand pictures rotated away or toward the mid-sagittal plane (i.e., lateral or medial rotation, respectively). These findings point to the use of a cognitive embodied process referred to as motor imagery. We hypothesize that the number of axes of rotation of the displayed stimuli during the task is a critical factor for showing engagement in a mental rotation task, with an increased number of rotational axes leading to a facilitation of motor imagery. To test this hypothesis, we used a hand laterality judgment paradigm in which we manipulated the difficulty of the task via the manipulation of the number of rotational axes of the shown stimuli. Our results showed increased influence of bodily constraints for increasing number of axes of rotation. More specifically, for the stimulus set containing stimuli rotated over a single axis, no influence of biomechanical constraints was present. The stimulus sets containing stimuli rotated over more than one axes of rotation did induce the use of motor imagery, as a clear influence of bodily constraints on the reaction times was found. These findings extend and refine previous findings on motor imagery as our results show that engagement in motor imagery critically depends on the used number of axes of rotation of the stimulus set

Annual report on surveillance of respiratory infectious diseases 2013, the Netherlands

Het griepseizoen (influenza) 2013/2014 was erg mild, na de uitzonderlijk langdurende epidemie in het seizoen 2012/2013. Ook was het een mild seizoen wat betreft het aantal mensen dat een longontsteking (pneumonie) opliep. In 2013 waren er geen grote uitbraken van de meldingsplichtige luchtweginfectieziekten legionellose (308 meldingen), papegaaienziekte (psittacose; 51 meldingen), Q-koorts (19 meldingen) en tuberculose (848 meldingen). Deze aantallen waren in het verslagjaar vergelijkbaar of lager dan het aantal meldingen in voorgaande jaren. Dit blijkt uit de jaarlijkse surveillance luchtweginfectieziekten 2013 van het RIVM. Griep en longontsteking leiden tot veel ziekenhuisopnames en sterfte in Nederland, waardoor het RIVM ze actief volgt. In vergelijking met griep komen de meldingsplichtige luchtweginfecties in Nederlands maar weinig voor. Ze zijn meldingsplichtig, omdat tijdige maatregelen, zoals de besmettingsbron opsporen, belangrijk kunnen zijn om uitbraken of verdere verspreiding van de ziekte te voorkomen. Het RIVM volgt ook potentieel gevaarlijke nieuwe luchtweginfecties die elders in de wereld voorkomen. In mei 2014 werden voor het eerst in Nederland twee patiënten gediagnostiseerd met het MERS coronavirus. In het seizoen 2013/2014 lag het aantal mensen dat met griepachtige klachten bij de huisarts kwam begin 2014 gedurende vier weken boven de grens waarmee een griepepidemie wordt geduid. Bij de patiënten met griepachtige klachten kwam naast influenzavirus vaak RSV (respiratoir syncytieel virus) en neusverkoudheid (rhinovirus) voor. Er kwamen minder mensen met een longontsteking bij de huisarts dan voorgaande seizoenen, maar het aantal longontstekingpatiënten in verpleeghuizen bleef gelijk.The 2013/2014 influenza season was extremely mild in the Netherlands, compared to the exceptionally long-lasting epidemic in 2012/2013. In addition, the number of pneumonia patients and overall mortality, possible complications of influenza, were low. In 2013, no major outbreaks of the notifiable respiratory infectious diseases legionellosis (308 notifications), psittacosis (51 notifications), Q-fever (19 notifications) and tuberculosis (848 notifications) occurred. These incidences are either comparable to or lower than preceding years. These are the outcomes of the annual report: 'Surveillance of respiratory infectious diseases 2013, the Netherlands', published by the Dutch National Institute for Public Health and the Environment (RIVM). Influenza and pneumonia are an important cause of hospital admissions and death in the Netherlands, a reason for the RIVM to actively monitor these diseases. In comparison to influenza, notifiable respiratory infectious diseases only rarely occur. These diseases are notifiable, as timely measures like source finding, are important for preventing outbreaks and/ or ongoing transmission of the disease. The RIVM also monitors potential threats to public health from new (worldwide) respiratory infections. In May 2014, the first two cases of MERS coronavirus were diagnosed in the Netherlands. During the 2013/2014 influenza-season, the number of patients with influenza-like illness (ILI) consulting a general practitioner, was above the threshold set for an influenza epidemic for four weeks at the beginning of 2014. In nose and throat samples of ILI-patients, RSV (respiratory syncytial virus) and rhinovirus were found in addition to the influenza virus. During the 2013/2014 influenza-season, fewer patients consulted the general practitioner for pneumonia than in previous years, however the number of pneumonia patients in nursing homes was similar.Ministerie van VW

A road to reality with topological superconductors

Topological states of matter are a source of low-energy quasiparticles, bound to a defect or propagating along the surface. In a superconductor these are Majorana fermions, described by a real rather than a complex wave function. The absence of complex phase factors promises protection against decoherence in quantum computations based on topological superconductivity. This is a tutorial style introduction written for a Nature Physics focus issue on topological matter.Comment: pre-copy-editing, author-produced version of the published paper: 4 pages, 2 figure

Recombination dynamics of a human Y-chromosomal palindrome:rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions

The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9-8.4×10(-4) events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages

On Glauber modes in Soft-Collinear Effective Theory

Gluon interactions involving spectator partons in collisions at hadronic machines are investigated. We find a class of examples in which a mode, called Glauber gluons, must be introduced to the effective theory for consistency.Comment: 19 pages, three figures. Uses JHEP3.cl

The Quantum Internet

Quantum networks offer a unifying set of opportunities and challenges across exciting intellectual and technical frontiers, including for quantum computation, communication, and metrology. The realization of quantum networks composed of many nodes and channels requires new scientific capabilities for the generation and characterization of quantum coherence and entanglement. Fundamental to this endeavor are quantum interconnects that convert quantum states from one physical system to those of another in a reversible fashion. Such quantum connectivity for networks can be achieved by optical interactions of single photons and atoms, thereby enabling entanglement distribution and quantum teleportation between nodes.Comment: 15 pages, 6 figures Higher resolution versions of the figures can be downloaded from the following link: http://www.its.caltech.edu/~hjkimble/QNet-figures-high-resolutio