Research highlights from Regional Studies in Marine Science

publisher: Elsevier articletitle: Research highlights from Regional Studies in Marine Science journaltitle: Regional Studies in Marine Science articlelink: http://dx.doi.org/10.1016/j.rsma.2016.05.008 content_type: simple-article copyright: © 2016 Published by Elsevier B.V

Predicting hip-knee-ankle and femorotibial angles from knee radiographs with deep learning

BACKGROUND: Knee alignment affects the development and surgical treatment of knee osteoarthritis. Automating femorotibial angle (FTA) and hip-knee-ankle angle (HKA) measurement from radiographs could improve reliability and save time. Further, if HKA could be predicted from knee-only radiographs then radiation exposure could be reduced and the need for specialist equipment and personnel avoided. The aim of this research was to assess if deep learning methods could predict FTA and HKA angle from posteroanterior (PA) knee radiographs. METHODS: Convolutional neural networks with densely connected final layers were trained to analyse PA knee radiographs from the Osteoarthritis Initiative (OAI) database. The FTA dataset with 6149 radiographs and HKA dataset with 2351 radiographs were split into training, validation, and test datasets in a 70:15:15 ratio. Separate models were developed for the prediction of FTA and HKA and their accuracy was quantified using mean squared error as loss function. Heat maps were used to identify the anatomical features within each image that most contributed to the predicted angles. RESULTS: High accuracy was achieved for both FTA (mean absolute error 0.8°) and HKA (mean absolute error 1.7°). Heat maps for both models were concentrated on the knee anatomy and could prove a valuable tool for assessing prediction reliability in clinical application. CONCLUSION: Deep learning techniques enable fast, reliable and accurate predictions of both FTA and HKA from plain knee radiographs and could lead to cost savings for healthcare providers and reduced radiation exposure for patients

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

Fitting Neutrino Physics with a U(1)_R Lepton Number

We study neutrino physics in the context of a supersymmetric model where a continuous R-symmetry is identified with the total Lepton Number and one sneutrino can thus play the role of the down type Higgs. We show that R-breaking effects communicated to the visible sector by Anomaly Mediation can reproduce neutrino masses and mixing solely via radiative contributions, without requiring any additional degree of freedom. In particular, a relatively large reactor angle (as recently observed by the Daya Bay collaboration) can be accommodated in ample regions of the parameter space. On the contrary, if the R-breaking is communicated to the visible sector by gravitational effects at the Planck scale, additional particles are necessary to accommodate neutrino data.Comment: 19 pages, 3 figures; v2: references added, constraints updated, overall conclusions unchange

Effects of Supersymmetric Threshold Corrections on High-Scale Flavor Textures

Integration of superpartners out of the spectrum induces potentially large contributions to Yukawa couplings. These corrections, the supersymmetric threshold corrections, therefore influence the CKM matrix prediction in a non-trivial way. We study effects of threshold corrections on high-scale flavor structures specified at the gauge coupling unification scale in supersymmetry. In our analysis, we first consider high-scale Yukawa textures which qualify phenomenologically viable at tree level, and find that they get completely disqualified after incorporating the threshold corrections. Next, we consider Yukawa couplings, such as those with five texture zeroes, which are incapable of explaining flavor-changing proceses. Incorporation of threshold corrections, however, makes them phenomenologically viable textures. Therefore, supersymmetric threshold corrections are found to leave observable impact on Yukawa couplings of quarks, and any confrontation of high-scale textures with experiments at the weak scale must take into account such corrections.Comment: 25 pages, submitted to JHE

Natural Islands for a 125 GeV Higgs in the scale-invariant NMSSM

We study whether a 125 GeV standard model-like Higgs boson can be accommodated within the scale-invariant NMSSM in a way that is natural in all respects, i.e., not only is the stop mass and hence its loop contribution to Higgs mass of natural size, but we do not allow significant tuning of NMSSM parameters as well. We pursue as much as possible an analytic approach which gives clear insights on various ways to accommodate such a Higgs mass, while conducting complementary numerical analyses. We consider both scenarios with singlet-like state being heavier and lighter than SM-like Higgs. With A-terms being small, we find for the NMSSM to be perturbative up to GUT scale, it is not possible to get 125 GeV Higgs mass, which is true even if we tune parameters of NMSSM. If we allow some of the couplings to become non-perturbative below the GUT scale, then the non-tuned option implies that the singlet self-coupling, kappa, is larger than the singlet-Higgs coupling, lambda, which itself is order 1. This leads to a Landau pole for these couplings close to the weak scale, in particular below ~10^4 TeV. In both the perturbative and non-perturbative NMSSM, allowing large A_lambda, A_kappa gives "more room" to accommodate a 125 GeV Higgs, but a tuning of these A-terms may be needed. In our analysis we also conduct a careful study of the constraints on the parameter space from requiring global stability of the desired vacuum fitting a 125 GeV Higgs, which is complementary to existing literature. In particular, as the singlet-Higgs coupling lambda increases, vacuum stability becomes more serious of an issue.Comment: 34 pages, 4 figures, references added, minor corrections to text and figures, version to be published in JHE

BSE Case Associated with Prion Protein Gene Mutation

Bovine spongiform encephalopathy (BSE) is a transmissible spongiform encephalopathy (TSE) of cattle and was first detected in 1986 in the United Kingdom. It is the most likely cause of variant Creutzfeldt-Jakob disease (CJD) in humans. The origin of BSE remains an enigma. Here we report an H-type BSE case associated with the novel mutation E211K within the prion protein gene (Prnp). Sequence analysis revealed that the animal with H-type BSE was heterozygous at Prnp nucleotides 631 through 633. An identical pathogenic mutation at the homologous codon position (E200K) in the human Prnp has been described as the most common cause of genetic CJD. This finding represents the first report of a confirmed case of BSE with a potential pathogenic mutation within the bovine Prnp gene. A recent epidemiological study revealed that the K211 allele was not detected in 6062 cattle from commercial beef processing plants and 42 cattle breeds, indicating an extremely low prevalence of the E211K variant (less than 1 in 2000) in cattle

Stimulation of Na⁺/H⁺ Exchanger Isoform 1 Promotes Microglial Migration

Regulation of microglial migration is not well understood. In this study, we proposed that Na+/H+ exchanger isoform 1 (NHE-1) is important in microglial migration. NHE-1 protein was co-localized with cytoskeletal protein ezrin in lamellipodia of microglia and maintained its more alkaline intracellular pH (pHi). Chemoattractant bradykinin (BK) stimulated microglial migration by increasing lamellipodial area and protrusion rate, but reducing lamellipodial persistence time. Interestingly, blocking NHE-1 activity with its potent inhibitor HOE 642 not only acidified microglia, abolished the BK-triggered dynamic changes of lamellipodia, but also reduced microglial motility and microchemotaxis in response to BK. In addition, NHE-1 activation resulted in intracellular Na+ loading as well as intracellular Ca2+ elevation mediated by stimulating reverse mode operation of Na+/Ca2+ exchange (NCXrev). Taken together, our study shows that NHE-1 protein is abundantly expressed in microglial lamellipodia and maintains alkaline pHi in response to BK stimulation. In addition, NHE-1 and NCXrev play a concerted role in BK-induced microglial migration via Na+ and Ca2+ signaling. © 2013 Shi et al

Bilinear R-parity violation with flavor symmetry

Bilinear R-parity violation (BRPV) provides the simplest intrinsically supersymmetric neutrino mass generation scheme. While neutrino mixing parameters can be probed in high energy accelerators, they are unfortunately not predicted by the theory. Here we propose a model based on the discrete flavor symmetry $A_4$ with a single R-parity violating parameter, leading to (i) correct Cabbibo mixing given by the Gatto-Sartori-Tonin formula, and a successful unification-like b-tau mass relation, and (ii) a correlation between the lepton mixing angles $\theta_{13}$ and $\theta_{23}$ in agreement with recent neutrino oscillation data, as well as a (nearly) massless neutrino, leading to absence of neutrinoless double beta decay.Comment: 16 pages, 3 figures. Extended version, as published in JHE

The generalised NMSSM at one loop: fine tuning and phenomenology

We determine the degree of fine tuning needed in a generalised version of the NMSSM that follows from an underlying Z4 or Z8 R symmetry. We find that it is significantly less than is found in the MSSM or NMSSM and extends the range of Higgs mass that have acceptable fine tuning up to Higgs masses of mh ~ 130 GeV. For universal boundary conditions analogous to the CMSSM the phenomenology is rather MSSM like with the singlet states typically rather heavy. For more general boundary conditions the singlet states can be light, leading to interesting signatures at the LHC and direct detection experiments.Comment: 20 pages, 9 figures, matches published versio