CP properties of symmetry-constrained two-Higgs-doublet models

The two-Higgs-doublet model can be constrained by imposing Higgs-family symmetries and/or generalized CP symmetries. It is known that there are only six independent classes of such symmetry-constrained models. We study the CP properties of all cases in the bilinear formalism. An exact symmetry implies CP conservation. We show that soft breaking of the symmetry can lead to spontaneous CP violation (CPV) in three of the classes.Comment: 14 pages, 2 tables, revised version adapted to the journal publicatio

Rapid movement and transcriptional re-localization of human cohesin on DNA

The spatial organization, correct expression, repair, and segregation of eukaryotic genomes depend on cohesin, ring-shaped protein complexes that are thought to function by entrapping DNA It has been proposed that cohesin is recruited to specific genomic locations from distal loading sites by an unknown mechanism, which depends on transcription, and it has been speculated that cohesin movements along DNA could create three-dimensional genomic organization by loop extrusion. However, whether cohesin can translocate along DNA is unknown. Here, we used single-molecule imaging to show that cohesin can diffuse rapidly on DNA in a manner consistent with topological entrapment and can pass over some DNA-bound proteins and nucleosomes but is constrained in its movement by transcription and DNA-bound CCCTC-binding factor (CTCF). These results indicate that cohesin can be positioned in the genome by moving along DNA, that transcription can provide directionality to these movements, that CTCF functions as a boundary element for moving cohesin, and they are consistent with the hypothesis that cohesin spatially organizes the genome via loop extrusion

Effective-Range Expansion of the Neutron-Deuteron Scattering Studied by a Quark-Model Nonlocal Gaussian Potential

The S-wave effective range parameters of the neutron-deuteron (nd) scattering are derived in the Faddeev formalism, using a nonlocal Gaussian potential based on the quark-model baryon-baryon interaction fss2. The spin-doublet low-energy eigenphase shift is sufficiently attractive to reproduce predictions by the AV18 plus Urbana three-nucleon force, yielding the observed value of the doublet scattering length and the correct differential cross sections below the deuteron breakup threshold. This conclusion is consistent with the previous result for the triton binding energy, which is nearly reproduced by fss2 without reinforcing it with the three-nucleon force.Comment: 21 pages, 6 figures and 6 tables, submitted to Prog. Theor. Phy

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.

BACKGROUND: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. RESULTS: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon. CONCLUSIONS: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community

The response of Plantago major ssp pleiosperma to elevated CO2 is modulated by the formation of secondary shoots

The effect of elevated CO2 on the relative growth rate (RGR) of Plantago major ssp. pleiosperma was studied during the vegetative stage, in relation to plant development, by growing plants at 350 mu l l(-1) or at 700 mu l l(-1) CO2 in non-limiting nutrient solution with nitrate. To minimize interference by the accumulation of non-structural carbohydrates in the interpretation of results, RGR was expressed on a f. wt basis (RGR(FW)), as were all plant weight ratios. Stimulation of the RGR(FW) Of the whole plant by elevated CO2 was transient, and did not last longer than 8 d. At the same time a transient increase in root weight ratio (RWR) was observed. In order to investigate whether the transient effect of elevated CO2 on RGR(FW) was size-dependent, the data were plotted versus total f. wt (log(e) transformed). The transient period of stimulation of RGR(FW) and of RWR by elevated CO2 was still found, but in both CO2 treatments RGR(FW) decreased after a certain plant size had been reached. This size coincided with the stage at which secondary shoots started to develop, and was reached earlier in plants grown at elevated CO2. The RGR of these secondary shoots (RGR(see)) was Still increased when the period of whole plant stimulation of RGR(FW) had ended, indicating that the development of these new sinks took priority over a continuation of the stimulation of RWR. It is hypothesized that in this Plantago subspecies the response of the RGR(FW) of the whole plants to elevated CO2 is modulated by the formation of secondary shoots. Apparently, partitioning of the extra soluble carbohydrates at elevated CO2 to this tissue takes precedence over partitioning to the roots. resulting in a cessation of stimulation of plant RGR(FW) by elevated CO2.info:eu-repo/semantics/publishedVersio

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Nucleic Acids Res 2018 Jan 4; 46(D1):D221-D228

Runoff sources and land cover change in the Amazon : an end-member mixing analysis from small watersheds

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Biogeochemistry 105 (2011): 7-18, doi:10.1007/s10533-011-9597-8.The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end member mixing analysis (EMMA) to ten small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27 to 28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45 to 57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60 to 89% in pasture watersheds 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.This work was supported by National Science Foundation (DEB-0315656, DEB-0640661), the NASA LBA Program (NCC5-686, NCC5-69, NCC5-705, NNG066E88A) and by grants from Brazilian agencies FAPESP (03/13172-2) and CNPq (20199/2005-5)

Symmetries and renormalisation in two-Higgs-doublet models

We discuss the classification of symmetries and the corresponding symmetry groups in the two-Higgs-doublet model (THDM). We give an easily useable method how to determine the symmetry class and corresponding symmetry group of a given THDM Higgs potential. One of the symmetry classes corresponds to a Higgs potential with several simultaneous generalised CP symmetries. Extending the CP symmetry of this class to the Yukawa sector in a straightforward way, the so-called maximally-CP-symmetric model (MCPM) is obtained. We study the evolution of the quartic Higgs-potential parameters under a change of renormalisation point. Finally we compute the so called oblique parameters S, T, and U, in the MCPM and we identify large regions of viable parameter space with respect to electroweak precision measurements. We present the corresponding allowed regions for the masses of the physical Higgs bosons. Reasonable ranges for these masses, up to several hundred GeV, are obtained which should make the (extra) Higgs bosons detectable in LHC experiments.Comment: 16 pages, 2 figure

Randomized controlled trial of postoperative exercise rehabilitation program after lumbar spine fusion: study protocol

Abstract Background Lumbar spine fusion (LSF) effectively decreases pain and disability in specific spinal disorders; however, the disability rate following surgery remains high. This, combined with the fact that in Western countries the number of LSF surgeries is increasing rapidly it is important to develop rehabilitation interventions that improve outcomes. Methods/design In the present RCT-study we aim to assess the effectiveness of a combined back-specific and aerobic exercise intervention for patients after LSF surgery. One hundred patients will be randomly allocated to a 12-month exercise intervention arm or a usual care arm. The exercise intervention will start three months after surgery and consist of six individual guidance sessions with a physiotherapist and a home-based exercise program. The primary outcome measures are low back pain, lower extremity pain, disability and quality of life. Secondary outcomes are back function and kinesiophobia. Exercise adherence will also be evaluated. The outcome measurements will be assessed at baseline (3 months postoperatively), at the end of the exercise intervention period (15 months postoperatively), and after a 1-year follow-up. Discussion The present RCT will evaluate the effectiveness of a long-term rehabilitation program after LSF. To our knowledge this will be the first study to evaluate a combination of strength training, control of the neutral lumbar spine position and aerobic training principles in rehabilitation after LSF. Trial registration ClinicalTrials.gov Identifier NCT00834015peerReviewe