Sudden changes in local mean values demarcate geophysical regimes

Sudden changes occur where the mean values associated with two adjacent non-overlapping windows of data are anomalously different, and the transition between the window means occurs over a scale that is small relative to the scale of the windows. Positions of sudden changes can be economically retrieved. The sudden change positions demarcate the data in a manner that can be physically interpreted. Associated with this thesis, are data analyses in terms of the scales, positions, and magnitudes of sudden changes in local (window) mean data values. A sudden change ideally includes an anomalously steep small scale gradient that is associated with change on a much larger scale. Preserving this structure when filtering small scale variance requires an adaptive cutoff scale, as constructed in the third study. The filter adapts a local cutoff scale to the scales, locations and relative magnitudes of the local extremes in the Haar transform, which ideally responds to sudden changes. In the fourth study a filter using a variable cutoff scale is applied in order to partition a nine hour time series of wind velocity. The variable cutoff scale filter separated a transport mode from an isotropic small scale mode more cleanly, in terms of traditional statistics, than did a constant cutoff scale filter. Generally, the positions of sudden changes distinguish windows of data. Windows can be centered on the sudden changes or between them. In the fifth study the sudden changes define boundaries of data windows. The within-window data then contains less variance associated with sudden changes, which deterministically occur between adjacent windows. A sampling procedure based on the locations of the sudden changes is applied in the sixth study in an analysis of surface layer measurements. The "non-random" sampling helps to clarify spatial and temporal patterns in samples of the mean wind and the turbulence stress; the "mesoscale effect" is less ambiguous

Speckle Imaging of Gamma2 Velorum: The Inner Wind Possibly Resolved

Accurately quantifying the rates dM/dt at which massive stars lose mass is essential to any understanding of their evolution. All dM/dt estimates to date assume wind clumping factors; not allowing for clumping leads to overestimates of dM/dt and underestimates of lifetimes and masses when these stars explode as supernovae. Mid-IR spectroscopy suggested that the wind of the nearest Wolf-Rayet star, Gamma2 Vel, is resolved with a Full Width at 10 per cent intensity of 0.5 arcsec, or 171 AU at the 342 pc distance of the star. As the Zorro speckle imager on Gemini-South is capable of 0.02 arcsec resolution, we have used it to image Gamma2 Vel at two orbital phases (0.30 and 0.44) with two narrowband and two intermediate-band filters in an attempt to resolve its wind. Our observations demonstrate that the wind of Gamma2 Vel may be resolved as a 0.07 arcsec westward elongation through an 832 nm filter at orbital phase 0.3 . If confirmed, this is the smallest scale (24 AU) at which a WR star wind asymmetry has been directly imaged. Similar imaging at multiple phases is needed to determine if the asymmetry is due to stochastic wind clumping, co-rotating interaction regions or colliding-wind, cone-shaped shocks.Comment: 7 pages, 4 Figures, in press in MNRA

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture for long-term genetic gains in wheat

Cereal crop breeders have achieved considerable genetic gain in genetically complex traits, such as grain yield, while maintaining genetic diversity. However, focus on selection for yield has negatively impacted other important traits. To better understand multi-trait selection within a breeding context, and how it might be optimized, we analysed genotypic and phenotypic data from a genetically diverse, 16-founder wheat multi-parent advanced generation inter-cross population. Compared to single-trait models, multi-trait ensemble genomic prediction models increased prediction accuracy for almost 90 % of traits, improving grain yield prediction accuracy by 3–52 %. For complex traits, non-parametric models (Random Forest) also outperformed simplified, additive models (LASSO), increasing grain yield prediction accuracy by 10–36 %. Simulations of recurrent genomic selection then showed that sustained greater forward prediction accuracy optimized long-term genetic gains. Simulations of selection on grain yield found indirect responses in related traits, involving optimized antagonistic trait relationships. We found multi-trait selection indices could effectively optimize undesirable relationships, such as the trade-off between grain yield and protein content, or combine traits of interest, such as yield and weed competitive ability. Simulations of phenotypic selection found that including Random Forest rather than LASSO genetic models, and multi-trait rather than single-trait models as the true genetic model accelerated and extended long-term genetic gain whilst maintaining genetic diversity. These results (i) suggest important roles of pleiotropy and epistasis in the wider context of wheat breeding programmes, and (ii) provide insights into mechanisms for continued genetic gain in a limited genepool and optimization of multiple traits for crop improvement

Cataclysmic Variables from SDSS II. The Second Year

The first full year of operation following the commissioning year of the Sloan Digital Sky Survey has revealed a wide variety of newly discovered cataclysmic variables. We show the SDSS spectra of forty-two cataclysmic variables observed in 2002, of which thirty-five are new classifications, four are known dwarf novae (CT Hya, RZ Leo, T Leo and BZ UMa), one is a known CV identified from a previous quasar survey (Aqr1) and two are known ROSAT or FIRST discovered CVs (RX J09445+0357, FIRST J102347.6+003841). The SDSS positions, colors and spectra of all forty-two systems are presented. In addition, the results of follow-up studies of several of these objects identify the orbital periods, velocity curves and polarization that provide the system geometry and accretion properties. While most of the SDSS discovered systems are faint (>18th mag) with low accretion rates (as implied from their spectral characteristics), there are also a few bright objects which may have escaped previous surveys due to changes in the mass transfer rate.Comment: Accepted for publication in The Astronomical Journal, Vol. 126, Sep. 2003, 44 pages, 25 figures (now with adjacent captions), AASTeX v5.

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

Background Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination. Results We bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders’ genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders’ genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling. Conclusions Our results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations

SN 2016coi/ASASSN-16fp: An example of residual helium in a type Ic supernova?

The optical observations of Ic-4 supernova (SN) 2016coi/ASASSN-16fp, from $\sim 2$ to $\sim450$ days after explosion, are presented along with analysis of its physical properties. The SN shows the broad lines associated with SNe Ic-3/4 but with a key difference. The early spectra display a strong absorption feature at $\sim 5400$ \AA\ which is not seen in other SNe~Ic-3/4 at this epoch. This feature has been attributed to He I in the literature. Spectral modelling of the SN in the early photospheric phase suggests the presence of residual He in a C/O dominated shell. However, the behaviour of the He I lines are unusual when compared with He-rich SNe, showing relatively low velocities and weakening rather than strengthening over time. The SN is found to rise to peak $\sim 16$ d after core-collapse reaching a bolometric luminosity of Lp $\sim 3\times10^{42}$ \ergs. Spectral models, including the nebular epoch, show that the SN ejected $2.5-4$ \msun\ of material, with $\sim 1.5$ \msun\ below 5000 \kms, and with a kinetic energy of $(4.5-7)\times10^{51}$ erg. The explosion synthesised $\sim 0.14$ \msun\ of 56Ni. There are significant uncertainties in E(B-V)host and the distance however, which will affect Lp and MNi. SN 2016coi exploded in a host similar to the Large Magellanic Cloud (LMC) and away from star-forming regions. The properties of the SN and the host-galaxy suggest that the progenitor had $M_\mathrm{ZAMS}$ of $23-28$ \msun\ and was stripped almost entirely down to its C/O core at explosion.Comment: Accepted for publication in MNRAS. Updated to reflect the published version, minor typographical changes onl

Preoperative behavioural intervention to reduce drinking before elective orthopaedic surgery: the PRE-OP BIRDS feasibility RCT.

Background Heavy alcohol consumption is associated with an increased risk of postoperative complications and extended hospital stay. Alcohol consumption therefore represents a modifiable risk factor for surgical outcomes. Brief behavioural interventions have been shown to be effective in reducing alcohol consumption among increased risk and risky drinkers in other health-care settings and may offer a method of addressing preoperative alcohol consumption. Objectives To investigate the feasibility of introducing a screening process to assess adult preoperative drinking levels and to deliver a brief behavioural intervention adapted for the target population group. To conduct a two-arm (brief behavioural intervention plus standard preoperative care vs. standard preoperative care alone), multicentre, pilot randomised controlled trial to assess the feasibility of proceeding to a definitive trial. To conduct focus groups and a national web-based survey to establish current treatment as usual for alcohol screening and intervention in preoperative assessment. Design A single-centre, qualitative, feasibility study was followed by a multicentre, two-arm (brief behavioural intervention vs. treatment as usual), individually randomised controlled pilot trial with an embedded qualitative process evaluation. Focus groups and a quantitative survey were employed to characterise treatment as usual in preoperative assessment. Setting The feasibility study took place at a secondary care hospital in the north-east of England. The pilot trial was conducted at three large secondary care centres in the north-east of England. Participants Nine health-care professionals and 15 patients (mean age 70.5 years, 86.7% male) participated in the feasibility study. Eleven health-care professionals and 68 patients (mean age 66.2 years, 80.9% male) participated in the pilot randomised trial. An additional 19 health-care professionals were recruited to one of three focus groups, while 62 completed an electronic survey to characterise treatment as usual. Interventions The brief behavioural intervention comprised two sessions. The first session, delivered face to face in the preoperative assessment clinic, involved 5 minutes of structured brief advice followed by 15–20 minutes of behaviour change counselling, including goal-setting, problem-solving and identifying sources of social support. The second session, an optional booster, took place approximately 1 week before surgery and offered the opportunity to assess progress and boost self-efficacy. Main outcome measures Feasibility was assessed using rates of eligibility, recruitment and retention. The progression criteria for a definitive trial were recruitment of ≥ 40% of eligible patients and retention of ≥ 70% at 6-month follow-up. Acceptability was assessed using themes identified in qualitative data. Results The initial recruitment of eligible patients was low but improved with the optimisation of recruitment processes. The recruitment of eligible participants to the pilot trial (34%) fell short of the progression criteria but was mitigated by very high retention (96%) at the 6-month follow-up. Multimethod analyses identified the methods as acceptable to the patients and professionals involved and offers recommendations of ways to further improve recruitment. Conclusions The evidence supports the feasibility of a definitive trial to assess the effectiveness of brief behavioural intervention in reducing preoperative alcohol consumption and for secondary outcomes of surgical complications if recommendations for further improvements are adopted. Trial registration Current Controlled Trials ISRCTN36257982. Funding This project was funded by the National Institute for Health Research Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 12. See the National Institute for Health Research Journals Library website for further project information

Epidemiologic investigation of immune-mediated polyradiculoneuropathy among abattoir workers exposed to porcine brain

Background In October 2007, a cluster of patients experiencing a novel polyradiculoneuropathy was identified at a pork abattoir (Plant A). Patients worked in the primary carcass processing area (warm room); the majority processed severed heads (head-table). An investigation was initiated to determine risk factors for illness. Methods and Results Symptoms of the reported patients were unlike previously described occupational associated illnesses. A case-control study was conducted at Plant A. A case was defined as evidence of symptoms of peripheral neuropathy and compatible electrodiagnostic testing in a pork abattoir worker. Two control groups were used - randomly selected non-ill warm-room workers (n = 49), and all non-ill head-table workers (n = 56). Consenting cases and controls were interviewed and blood and throat swabs were collected. The 26 largest U.S. pork abattoirs were surveyed to identify additional cases. Fifteen cases were identified at Plant A; illness onsets occurred during May 2004–November 2007. Median age was 32 years (range, 21–55 years). Cases were more likely than warm-room controls to have ever worked at the head-table (adjusted odds ratio [AOR], 6.6; 95% confidence interval [CI], 1.6–26.7), removed brains or removed muscle from the backs of heads (AOR, 10.3; 95% CI, 1.5–68.5), and worked within 0–10 feet of the brain removal operation (AOR, 9.9; 95% CI, 1.2–80.0). Associations remained when comparing head-table cases and head-table controls. Workers removed brains by using compressed air that liquefied brain and generated aerosolized droplets, exposing themselves and nearby workers. Eight additional cases were identified in the only two other abattoirs using this technique. The three abattoirs that used this technique have stopped brain removal, and no new cases have been reported after 24 months of follow up. Cases compared to controls had higher median interferon-gamma (IFNγ) levels (21.7 pg/ml; vs 14.8 pg/ml, P<0.001). Discussion This novel polyradiculoneuropathy was associated with removing porcine brains with compressed air. An autoimmune mechanism is supported by higher levels of IFNγ in cases than in controls consistent with other immune mediated illnesses occurring in association with neural tissue exposure. Abattoirs should not use compressed air to remove brains and should avoid procedures that aerosolize CNS tissue. This outbreak highlights the potential for respiratory or mucosal exposure to cause an immune-mediated illness in an occupational setting

Epidemiologic investigation of immune-mediated polyradiculoneuropathy among abattoir workers exposed to porcine brain

Background In October 2007, a cluster of patients experiencing a novel polyradiculoneuropathy was identified at a pork abattoir (Plant A). Patients worked in the primary carcass processing area (warm room); the majority processed severed heads (head-table). An investigation was initiated to determine risk factors for illness. Methods and Results Symptoms of the reported patients were unlike previously described occupational associated illnesses. A case-control study was conducted at Plant A. A case was defined as evidence of symptoms of peripheral neuropathy and compatible electrodiagnostic testing in a pork abattoir worker. Two control groups were used - randomly selected non-ill warm-room workers (n = 49), and all non-ill head-table workers (n = 56). Consenting cases and controls were interviewed and blood and throat swabs were collected. The 26 largest U.S. pork abattoirs were surveyed to identify additional cases. Fifteen cases were identified at Plant A; illness onsets occurred during May 2004–November 2007. Median age was 32 years (range, 21–55 years). Cases were more likely than warm-room controls to have ever worked at the head-table (adjusted odds ratio [AOR], 6.6; 95% confidence interval [CI], 1.6–26.7), removed brains or removed muscle from the backs of heads (AOR, 10.3; 95% CI, 1.5–68.5), and worked within 0–10 feet of the brain removal operation (AOR, 9.9; 95% CI, 1.2–80.0). Associations remained when comparing head-table cases and head-table controls. Workers removed brains by using compressed air that liquefied brain and generated aerosolized droplets, exposing themselves and nearby workers. Eight additional cases were identified in the only two other abattoirs using this technique. The three abattoirs that used this technique have stopped brain removal, and no new cases have been reported after 24 months of follow up. Cases compared to controls had higher median interferon-gamma (IFNγ) levels (21.7 pg/ml; vs 14.8 pg/ml, P<0.001). Discussion This novel polyradiculoneuropathy was associated with removing porcine brains with compressed air. An autoimmune mechanism is supported by higher levels of IFNγ in cases than in controls consistent with other immune mediated illnesses occurring in association with neural tissue exposure. Abattoirs should not use compressed air to remove brains and should avoid procedures that aerosolize CNS tissue. This outbreak highlights the potential for respiratory or mucosal exposure to cause an immune-mediated illness in an occupational setting