3,086 research outputs found
Changepoint detection in non-exchangeable data
Changepoint models typically assume the data within each segment are independent and identically distributed conditional on some parameters that change across segments. This construction may be inadequate when data are subject to local correlation patterns, often resulting in many more changepoints fitted than preferable. This article proposes a Bayesian changepoint model that relaxes the assumption of exchangeability within segments. The proposed model supposes data within a segment are m-dependent for some unknown m⩾0 that may vary between segments, resulting in a model suitable for detecting clear discontinuities in data that are subject to different local temporal correlations. The approach is suited to both continuous and discrete data. A novel reversible jump Markov chain Monte Carlo algorithm is proposed to sample from the model; in particular, a detailed analysis of the parameter space is exploited to build proposals for the orders of dependence. Two applications demonstrate the benefits of the proposed model: computer network monitoring via change detection in count data, and segmentation of financial time series
A case of TDP-43 type C pathology presenting as nonfluent variant primary progressive aphasia
We report a case of rapidly progressive nonfluent variant PPA (nfvPPA), age at onset 77 years old and disease duration 3.3 years, who came to post mortem and was found to have TDP-43 type C pathology, an unusual finding for nfvPPA. All prior TDP-43 type C cases from the UCL FTD cohort (n=25) had a semantic variant PPA (svPPA) phenotype, with all having a younger age at onset and longer disease duration than the nfvPPA case. Volumetric analysis of MRI from the nfvPPA case, twelve of the svPPA cases and ten age-matched controls was performed. Whilst left frontal and insular volumes were lower in the nfvPPA case compared with svPPA, cortical and medial temporal lobe volumes were lower (particularly on the right) in the svPPA group compared with the nfvPPA patient. Such anatomical involvement is likely to be consistent with the presence of a nonfluent aphasia (left frontal lobe and insula), and only mild semantic deficit early in the illness (left but not right temporal lobe). Such unique cases add to the heterogeneity of the FTD spectrum
Widespread horizontal transfer of mitochondrial genes in flowering plants
Horizontal gene transfer - the exchange of genes across mating barriers - is recognized as a major force in bacterial evolution(1,2). However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes(3-5). Although the human genome was initially reported(6) to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted(7,8). Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements(9-12). Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62688/1/nature01743.pd
Dissimilatory Fe(III) reduction controls on arsenic mobilisation: a combined biogeochemical and NanoSIMS imaging approach
This is the final version. Available on open access from Frontiers Media via the DOI in this recordMicrobial metabolism plays a key role in controlling the fate of toxic groundwater
contaminants such as arsenic. Dissimilatory metal reduction catalysed by subsurface bacteria
can facilitate the mobilisation of arsenic via the reductive dissolution of As(V)-bearing Fe(III)
mineral assemblages. The mobility of liberated As(V) can then be amplified via reduction to
the more soluble As(III) by As(V)-respiring bacteria. This investigation focused on the
reductive dissolution of As(V) sorbed onto Fe(III)-(oxyhydr)oxide by model Fe(III)- and
As(V)-reducing bacteria, to elucidate the mechanisms underpinning these processes at the
single cell scale. Axenic cultures of Shewanella sp. ANA-3 wild-type cells (able to respire both
Fe(III) and As(V)) were grown using C-labelled lactate on an arsenical Fe(III)-
(oxyhydr)oxide thin film, and after colonisation, the distribution of Fe and As in the solid phase
was assessed using nanoscale secondary ion mass spectrometry (NanoSIMS), complemented
with aqueous geochemistry analyses. Parallel experiments were conducted using an arrA
mutant, able to respire Fe(III) but not As(V). NanoSIMS imaging showed that most
metabolically active cells were not in direct contact with the Fe(III) mineral. Flavins were
released by both strains, suggesting that these cell-secreted electron shuttles mediated
extracellular Fe(III)-(oxyhydr)oxide reduction, but did not facilitate extracellular As(V)
reduction, demonstrated by the presence of flavins yet lack of As(III) in the supernatants of the
arrA deletion mutant strain. 3D reconstructions of NanoSIMS depth-profiled single cells
revealed that As and Fe were associated with the cell surface in the wild-type cells, whereas
for the arrA mutant only Fe was associated with the biomass. These data were consistent with
Shewanella sp. ANA-3 respiring As(V) in a multistep process; first the reductive dissolution
of the Fe(III) mineral released As(V), and once in solution, As(V) was respired by the cells to
As(III). As well as highlighting Fe(III) reduction as the primary release mechanism for arsenic,
our data also identified unexpected cellular As(III) retention mechanisms that require further
investigation.Mexican National Council for Science and Technology (CONACyT)Natural Environment Research Council (NERC
Homoeologous gene silencing in tissue cultured wheat callus
Abstract Background In contrast to diploids, most polyploid plant species, which include the hexaploid bread wheat, possess an additional layer of epigenetic complexity. Several studies have demonstrated that polyploids are affected by homoeologous gene silencing, a process in which sub-genomic genomic copies are selectively transcriptionally inactivated. This form of silencing can be tissue specific and may be linked to developmental or stress responses. Results Evidence was sought as to whether the frequency of homoeologous silencing in in vitro cultured wheat callus differ from that in differentiated organs, given that disorganized cells are associated with a globally lower level of DNA methylation. Using a reverse transcription PCR (RT-PCR) single strand conformation polymorphism (SSCP) platform to detect the pattern of expression of 20 homoeologous sets of single-copy genes known to be affected by this form of silencing in the root and/or leaf, we observed no silencing in any of the wheat callus tissue tested. Conclusion Our results suggest that much of the homoeologous silencing observed in differentiated tissues is probably under epigenetic control, rather than being linked to genomic instability arising from allopolyploidization. This study reinforces the notion of plasticity in the wheat epi-genome.</p
Surgery for fragility hip fracture—streamlining the process
published_or_final_versionSpringer Open Choice, 21 Feb 201
The Mitochondrial Genome of the Legume Vigna radiata and the Analysis of Recombination across Short Mitochondrial Repeats
The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes
A Brownian particle in a microscopic periodic potential
We study a model for a massive test particle in a microscopic periodic
potential and interacting with a reservoir of light particles. In the regime
considered, the fluctuations in the test particle's momentum resulting from
collisions typically outweigh the shifts in momentum generated by the periodic
force, and so the force is effectively a perturbative contribution. The
mathematical starting point is an idealized reduced dynamics for the test
particle given by a linear Boltzmann equation. In the limit that the mass ratio
of a single reservoir particle to the test particle tends to zero, we show that
there is convergence to the Ornstein-Uhlenbeck process under the standard
normalizations for the test particle variables. Our analysis is primarily
directed towards bounding the perturbative effect of the periodic potential on
the particle's momentum.Comment: 60 pages. We reorganized the article and made a few simplifications
of the conten
Unexpected Consequences: Women’s experiences of a self-hypnosis intervention to help with pain relief during labour.
Background
Self-hypnosis is becoming increasingly popular as a means of labour pain management. Previous studies have produced mixed results. There are very few data on women’s views and experiences of using hypnosis in this context. As part of a randomized controlled trial of self-hypnosis for intra-partum pain relief (the SHIP Trial) we conducted qualitative interviews with women randomized to the intervention arm to explore their views and experiences of using self-hypnosis during labour and birth.
Methods
Participants were randomly selected from the intervention arm of the study, which consisted of two antenatal self-hypnosis training sessions and a supporting CD that women were encouraged to listen to daily from 32 weeks gestation until the birth of their baby. Those who consented were interviewed in their own homes 8-12 weeks after birth. Following transcription, the interviews were analysed iteratively and emerging concepts were discussed amongst the authors to generate organizing themes. These were then used to develop a principal organizing metaphor or global theme, in a process known as thematic networks analysis.
Results
Of the 343 women in the intervention group, 48 were invited to interview, and 16 were interviewed over a 12 month period from February 2012 to January 2013.
Coding of the data and subsequent analysis revealed a global theme of ‘unexpected consequences’, supported by 5 organising themes, ‘calmness in a climate of fear’, ‘from sceptic to believer’, ‘finding my space’, ‘delays and disappointments’ and ‘personal preferences’. Most respondents reported positive experiences of self-hypnosis and highlighted feelings of calmness, confidence and empowerment. They found the intervention to be beneficial and used a range of novel strategies to personalize their self-hypnosis practice. Occasionally women reported feeling frustrated or disappointed when their relaxed state was misinterpreted by midwives on admission or when their labour and birth experiences did not match their expectations.
Conclusion
The women in this study generally appreciated antenatal self-hypnosis training and found it to be beneficial during labour and birth. The state of focused relaxation experienced by women using the technique needs to be recognized by providers if the intervention is to be implemented into the maternity service
Constipation preceding Parkinson's disease: a systematic review and meta-analysis
AJN is funded by Parkinson’s UK (grant reference F-1201). AJL has
received honoraria from Novartis, Teva, Meda, Boehringer Ingelheim, GSK, Ipsen,
Lundbeck, Allergan and Orion. AS has received grant money from GE Healthcare
and honoraria from UCB. AJN has received grants from Élan/Prothena
Pharmaceuticals and from GE Healthcare
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