151 research outputs found
An evaluation of genotyping by sequencing (GBS) to map the <em>Breviaristatum-e (ari-e)</em> locus in cultivated barley
ABSTRACT: We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait Loci (QTL), the first in a region encompassing the spike architecture gene Vrs1 on chromosome 2H, the second in an uncharacterised centromeric region on chromosome 3H, and the third in a region of chromosome 5H coinciding with the previously described dwarfing gene Breviaristatum-e (Ari-e). BACKGROUND: Barley cultivars in North-western Europe largely contain either of two dwarfing genes; Denso on chromosome 3H, a presumed ortholog of the rice green revolution gene OsSd1, or Breviaristatum-e (ari-e) on chromosome 5H. A recessive mutant allele of the latter gene, ari-e.GP, was introduced into cultivation via the cv. ‘Golden Promise’ that was a favourite of the Scottish malt whisky industry for many years and is still used in agriculture today. RESULTS: Using GBS mapping data and phenotypic measurements we show that ari-e.GP maps to a small genetic interval on chromosome 5H and that alternative alleles at a region encompassing Vrs1 on 2H along with a region on chromosome 3H also influence plant height. The location of Ari-e is supported by analysis of near-isogenic lines containing different ari-e alleles. We explored use of the GBS to populate the region with sequence contigs from the recently released physically and genetically integrated barley genome sequence assembly as a step towards Ari-e gene identification. CONCLUSIONS: GBS was an effective and relatively low-cost approach to rapidly construct a genetic map of the GPMx population that was suitable for genetic analysis of row type and height traits, allowing us to precisely position ari-e.GP on chromosome 5H. Mapping resolution was lower than we anticipated. We found the GBS data more complex to analyse than other data types but it did directly provide linked SNP markers for subsequent higher resolution genetic analysis
Abelian Hidden Sectors at a GeV
We discuss mechanisms for naturally generating GeV-scale hidden sectors in
the context of weak-scale supersymmetry. Such low mass scales can arise when
hidden sectors are more weakly coupled to supersymmetry breaking than the
visible sector, as happens when supersymmetry breaking is communicated to the
visible sector by gauge interactions under which the hidden sector is
uncharged, or if the hidden sector is sequestered from gravity-mediated
supersymmetry breaking. We study these mechanisms in detail in the context of
gauge and gaugino mediation, and present specific models of Abelian GeV-scale
hidden sectors. In particular, we discuss kinetic mixing of a U(1)_x gauge
force with hypercharge, singlets or bi-fundamentals which couple to both
sectors, and additional loop effects. Finally, we investigate the possible
relevance of such sectors for dark matter phenomenology, as well as for low-
and high-energy collider searches.Comment: 43 pages, no figures; v2: to match JHEP versio
Community Occupational Therapy in Dementia intervention for people with mild to moderate dementia and their family carers in the UK: the VALID research programme including RCT
BACKGROUND: People with dementia find it increasingly difficult to carry out daily activities (activities of daily living), and may require increasing support from family carers. Researchers in the Netherlands developed the Community Occupational Therapy in Dementia intervention, which was delivered in 10 1-hour sessions over 5 weeks to people with dementia and their family carers at home. Community Occupational Therapy in Dementia was found to be clinically effective and cost-effective. OBJECTIVES: Translate and adapt Community Occupational Therapy in Dementia to develop the Community Occupational Therapy in Dementia - the UK version intervention and training programme and to optimise its suitability for use within the UK. To estimate the clinical effectiveness and cost-effectiveness of Community Occupational Therapy in Dementia - the UK version for people with mild to moderate dementia and their family carers compared with treatment as usual. DESIGN: The development phase used mixed methods to develop Community Occupational Therapy in Dementia - the UK version: translation, expert review, and adaptation of the manual and training materials; training occupational therapists; focus groups and interviews, including occupational therapists, managers, people with dementia and family carers; consensus conference; and an online survey of occupational therapists to scope UK practice. A multicentre, two-arm, parallel-group, single-blind individually randomised pragmatic trial was preceded by an internal pilot. Pairs were randomly allocated between Community Occupational Therapy in Dementia - the UK version and treatment as usual. A cost–utility analysis, fidelity study and qualitative study were also completed. SETTING: Community services for people with dementia across England. PARTICIPANTS: People with mild to moderate dementia recruited in pairs with a family carer/supporter. INTERVENTIONS: Community Occupational Therapy in Dementia - the UK version is an activity-based, goal-setting approach for people with dementia and family carers, and is delivered at home by an occupational therapist for 10 hours over 10 weeks. Treatment as usual comprised the usual local service provision, which may or may not include standard occupational therapy. MAIN OUTCOMES MEASURES: Data were collected through interviews conducted in person with dyads at baseline and at 12 and 26 weeks post randomisation, and then over the telephone with a reduced sample of just carers at 52 and 78 weeks post randomisation. The primary outcome was the Bristol Activities of Daily Living Scale at 26 weeks. The secondary outcomes were as follows: person with dementia – cognition, activities of daily living, quality of life and mood; carer – sense of competence, quality of life and mood; all participants – social contacts, leisure activities and serious adverse events. RESULTS: The Community Occupational Therapy in Dementia manual and training materials were translated and reviewed. In total, 44 occupational therapists were trained and delivered Community Occupational Therapy in Dementia to 130 pairs. A total of 197 occupational therapists completed the survey, of whom 138 also provided qualitative data. In total, 31 people attended the consensus conference. Community Occupational Therapy in Dementia - the UK version has more flexibility than Community Occupational Therapy in Dementia in terms of content and delivery; for example, occupational therapists can use the wider range of assessment tools that are already in regular use within UK practice and the time span for delivery is 10 weeks to better meet the needs of pairs and be more feasible for services to deliver. In total, 31 occupational therapists provided Community Occupational Therapy in Dementia - the UK version within the randomised controlled trial. A total of 468 pairs were randomised (249 pairs to Community Occupational Therapy in Dementia - the UK version, 219 pairs to treatment as usual). People with dementia ranged in age from 55 to 97 years (mean 78.6 years), and family carers ranged in age from 29 to 94 years (mean 69.1 years). The majority of those with dementia (74.8%) were married; 19.2% lived alone. Most family carers (72.6%) were spouses but 22.2% were adult children. At 26 weeks, 406 (87%) pairs remained in the trial, and the Bristol Activities of Daily Living Scale total score did not differ at the 5% level when comparing groups (adjusted mean difference estimate 0.35, 95% confidence interval –0.81 to 1.51; p = 0.55). The adjusted (for baseline Bristol Activities of Daily Living Scale total score and randomised group) intracluster correlation coefficient estimate at week 26 was 0.043. There were no significant differences in secondary outcomes. At 52 and 78 weeks, there were no differences between the two groups in Bristol Activities of Daily Living Scale total score and secondary outcomes. The probability that Community Occupational Therapy in Dementia - the UK version is cost-effective at a threshold of willingness to pay per quality-adjusted life-year of £20,000 is 0.02%. In the qualitative interviews, participants reported positive benefits and outcomes. Of the 249 pairs allocated to Community Occupational Therapy in Dementia - the UK version, 227 reached the goal-setting phase, and 838 of the 920 goals set (90.8%) were fully or partially achieved. LIMITATIONS: The development phase took longer than estimated because of translation time and organisational delays in delivering the intervention. Recruitment to the randomised controlled trial took longer than expected. Fidelity overall was moderate, with variation across sites and therapists. It is possible that Community Occupational Therapy in Dementia - the UK version did not work well in the UK service model in which usual care differs from that in the Netherlands. CONCLUSIONS: This programme used a rigorous process to develop Community Occupational Therapy in Dementia - the UK version but found no statistical evidence of clinical effectiveness or cost-effectiveness compared with usual care. Qualitative findings provided positive examples of how Community Occupational Therapy in Dementia - the UK version had enabled people to live well with dementia. FUTURE WORK: Developing tools to measure more meaningful outcomes, such as goals achieved or the quantity and quality of activity participation, with less reliance on proxy data, to collect the views and experiences of people with dementia themselves. TRIAL REGISTRATION: This trial was registered as ISRCTN10748953 (WP3 and WP4). FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Programme Grants for Applied Research programme and will be published in full in Programme Grants for Applied Research; Vol. 11, No. 5. See the NIHR Journals Library website for further project information
Candidates for Inelastic Dark Matter
Although we have yet to determine whether the DAMA data represents a true
discovery of new physics, among such interpretations inelastic dark matter
(IDM) can match the energy spectrum of DAMA very well while not contradicting
the results of other direct detection searches. In this paper we investigate
the general properties that a viable IDM candidate must have and search for
simple models that realize these properties in natural ways. We begin by
determining the regions of IDM parameter space that are allowed by direct
detection searches including DAMA, paying special attention to larger IDM
masses. We observe that an inelastic dark matter candidate with electroweak
interactions can naturally satisfy observational constraints while
simultaneously yielding the correct thermal relic abundance. We comment on
several other proposed dark matter explanations for the DAMA signal and
demonstrate that one of the proposed alternatives -- elastic scattering of dark
matter off electrons -- is strongly disfavored when the modulated and
unmodulated DAMA spectral data are taken into account. We then outline the
general essential features of IDM models in which inelastic scattering off
nuclei is mediated by the exchange of a massive gauge boson, and construct
natural models in the context of a warped extra dimension and supersymmetry.Comment: 44 pages, 6 figures, added reference
Nasal Iodophor Antiseptic vs Nasal Mupirocin Antibiotic in the Setting of Chlorhexidine Bathing to Prevent Infections in Adult ICUs: A Randomized Clinical Trial
IMPORTANCE: Universal nasal mupirocin plus chlorhexidine gluconate (CHG) bathing in intensive care units (ICUs) prevents methicillin-resistant Staphylococcus aureus (MRSA) infections and all-cause bloodstream infections. Antibiotic resistance to mupirocin has raised questions about whether an antiseptic could be advantageous for ICU decolonization.
OBJECTIVE: To compare the effectiveness of iodophor vs mupirocin for universal ICU nasal decolonization in combination with CHG bathing.
DESIGN, SETTING, AND PARTICIPANTS: Two-group noninferiority, pragmatic, cluster-randomized trial conducted in US community hospitals, all of which used mupirocin-CHG for universal decolonization in ICUs at baseline. Adult ICU patients in 137 randomized hospitals during baseline (May 1, 2015-April 30, 2017) and intervention (November 1, 2017-April 30, 2019) were included.
INTERVENTION: Universal decolonization involving switching to iodophor-CHG (intervention) or continuing mupirocin-CHG (baseline).
MAIN OUTCOMES AND MEASURES: ICU-attributable S aureus clinical cultures (primary outcome), MRSA clinical cultures, and all-cause bloodstream infections were evaluated using proportional hazard models to assess differences from baseline to intervention periods between the strategies. Results were also compared with a 2009-2011 trial of mupirocin-CHG vs no decolonization in the same hospital network. The prespecified noninferiority margin for the primary outcome was 10%.
RESULTS: Among the 801 668 admissions in 233 ICUs, the participants\u27 mean (SD) age was 63.4 (17.2) years, 46.3% were female, and the mean (SD) ICU length of stay was 4.8 (4.7) days. Hazard ratios (HRs) for S aureus clinical isolates in the intervention vs baseline periods were 1.17 for iodophor-CHG (raw rate: 5.0 vs 4.3/1000 ICU-attributable days) and 0.99 for mupirocin-CHG (raw rate: 4.1 vs 4.0/1000 ICU-attributable days) (HR difference in differences significantly lower by 18.4% [95% CI, 10.7%-26.6%] for mupirocin-CHG, P \u3c .001). For MRSA clinical cultures, HRs were 1.13 for iodophor-CHG (raw rate: 2.3 vs 2.1/1000 ICU-attributable days) and 0.99 for mupirocin-CHG (raw rate: 2.0 vs 2.0/1000 ICU-attributable days) (HR difference in differences significantly lower by 14.1% [95% CI, 3.7%-25.5%] for mupirocin-CHG, P = .007). For all-pathogen bloodstream infections, HRs were 1.00 (2.7 vs 2.7/1000) for iodophor-CHG and 1.01 (2.6 vs 2.6/1000) for mupirocin-CHG (nonsignificant HR difference in differences, -0.9% [95% CI, -9.0% to 8.0%]; P = .84). Compared with the 2009-2011 trial, the 30-day relative reduction in hazards in the mupirocin-CHG group relative to no decolonization (2009-2011 trial) were as follows: S aureus clinical cultures (current trial: 48.1% [95% CI, 35.6%-60.1%]; 2009-2011 trial: 58.8% [95% CI, 47.5%-70.7%]) and bloodstream infection rates (current trial: 70.4% [95% CI, 62.9%-77.8%]; 2009-2011 trial: 60.1% [95% CI, 49.1%-70.7%]).
CONCLUSIONS AND RELEVANCE: Nasal iodophor antiseptic did not meet criteria to be considered noninferior to nasal mupirocin antibiotic for the outcome of S aureus clinical cultures in adult ICU patients in the context of daily CHG bathing. In addition, the results were consistent with nasal iodophor being inferior to nasal mupirocin.
TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03140423
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Stewardship Prompts to Improve Antibiotic Selection for Urinary Tract Infection
ImportanceUrinary tract infection (UTI) is the second most common infection leading to hospitalization and is often associated with gram-negative multidrug-resistant organisms (MDROs). Clinicians overuse extended-spectrum antibiotics although most patients are at low risk for MDRO infection. Safe strategies to limit overuse of empiric antibiotics are needed.ObjectiveTo evaluate whether computerized provider order entry (CPOE) prompts providing patient- and pathogen-specific MDRO risk estimates could reduce use of empiric extended-spectrum antibiotics for treatment of UTI.Design, setting, and participantsCluster-randomized trial in 59 US community hospitals comparing the effect of a CPOE stewardship bundle (education, feedback, and real-time and risk-based CPOE prompts; 29 hospitals) vs routine stewardship (n = 30 hospitals) on antibiotic selection during the first 3 hospital days (empiric period) in noncritically ill adults (≥18 years) hospitalized with UTI with an 18-month baseline (April 1, 2017-September 30, 2018) and 15-month intervention period (April 1, 2019-June 30, 2020).InterventionsCPOE prompts recommending empiric standard-spectrum antibiotics in patients ordered to receive extended-spectrum antibiotics who have low estimated absolute risk (<10%) of MDRO UTI, coupled with feedback and education.Main outcomes and measuresThe primary outcome was empiric (first 3 days of hospitalization) extended-spectrum antibiotic days of therapy. Secondary outcomes included empiric vancomycin and antipseudomonal days of therapy. Safety outcomes included days to intensive care unit (ICU) transfer and hospital length of stay. Outcomes were assessed using generalized linear mixed-effect models to assess differences between the baseline and intervention periods.ResultsAmong 127 403 adult patients (71 991 baseline and 55 412 intervention period) admitted with UTI in 59 hospitals, the mean (SD) age was 69.4 (17.9) years, 30.5% were male, and the median Elixhauser Comorbidity Index count was 4 (IQR, 2-5). Compared with routine stewardship, the group using CPOE prompts had a 17.4% (95% CI, 11.2%-23.2%) reduction in empiric extended-spectrum days of therapy (rate ratio, 0.83 [95% CI, 0.77-0.89]; P < .001). The safety outcomes of mean days to ICU transfer (6.6 vs 7.0 days) and hospital length of stay (6.3 vs 6.5 days) did not differ significantly between the routine and intervention groups, respectively.Conclusions and relevanceCompared with routine stewardship, CPOE prompts providing real-time recommendations for standard-spectrum antibiotics for patients with low MDRO risk coupled with feedback and education significantly reduced empiric extended-spectrum antibiotic use among noncritically ill adults admitted with UTI without changing hospital length of stay or days to ICU transfers.Trial registrationClinicalTrials.gov Identifier: NCT03697096
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Stewardship Prompts to Improve Antibiotic Selection for Pneumonia
ImportancePneumonia is the most common infection requiring hospitalization and is a major reason for overuse of extended-spectrum antibiotics. Despite low risk of multidrug-resistant organism (MDRO) infection, clinical uncertainty often drives initial antibiotic selection. Strategies to limit empiric antibiotic overuse for patients with pneumonia are needed.ObjectiveTo evaluate whether computerized provider order entry (CPOE) prompts providing patient- and pathogen-specific MDRO infection risk estimates could reduce empiric extended-spectrum antibiotics for non-critically ill patients admitted with pneumonia.Design, setting, and participantsCluster-randomized trial in 59 US community hospitals comparing the effect of a CPOE stewardship bundle (education, feedback, and real-time MDRO risk-based CPOE prompts; n = 29 hospitals) vs routine stewardship (n = 30 hospitals) on antibiotic selection during the first 3 hospital days (empiric period) in non-critically ill adults (≥18 years) hospitalized with pneumonia. There was an 18-month baseline period from April 1, 2017, to September 30, 2018, and a 15-month intervention period from April 1, 2019, to June 30, 2020.InterventionCPOE prompts recommending standard-spectrum antibiotics in patients ordered to receive extended-spectrum antibiotics during the empiric period who have low estimated absolute risk (<10%) of MDRO pneumonia, coupled with feedback and education.Main outcomes and measuresThe primary outcome was empiric (first 3 days of hospitalization) extended-spectrum antibiotic days of therapy. Secondary outcomes included empiric vancomycin and antipseudomonal days of therapy and safety outcomes included days to intensive care unit (ICU) transfer and hospital length of stay. Outcomes compared differences between baseline and intervention periods across strategies.ResultsAmong 59 hospitals with 96 451 (51 671 in the baseline period and 44 780 in the intervention period) adult patients admitted with pneumonia, the mean (SD) age of patients was 68.1 (17.0) years, 48.1% were men, and the median (IQR) Elixhauser comorbidity count was 4 (2-6). Compared with routine stewardship, the group using CPOE prompts had a 28.4% reduction in empiric extended-spectrum days of therapy (rate ratio, 0.72 [95% CI, 0.66-0.78]; P < .001). Safety outcomes of mean days to ICU transfer (6.5 vs 7.1 days) and hospital length of stay (6.8 vs 7.1 days) did not differ significantly between the routine and CPOE intervention groups.Conclusions and relevanceEmpiric extended-spectrum antibiotic use was significantly lower among adults admitted with pneumonia to non-ICU settings in hospitals using education, feedback, and CPOE prompts recommending standard-spectrum antibiotics for patients at low risk of MDRO infection, compared with routine stewardship practices. Hospital length of stay and days to ICU transfer were unchanged.Trial registrationClinicalTrials.gov Identifier: NCT03697070
The USDA Barley Core Collection:Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections
Post-depositional fracturing and subsidence of pumice flow deposits: Lascar Volcano, Chile
Unconsolidated pyroclastic flow deposits of the
1993 eruption of Lascar Volcano, Chile, have, with time,
become increasingly dissected by a network of deeply
penetrating fractures. The fracture network comprises
orthogonal sets of decimeter-wide linear voids that form a
pseudo-polygonal grid visible on the deposit surface. In this
work, we combine shallow surface geophysical imaging
tools with remote sensing observations and direct field
measurements of the deposit to investigate these fractures
and their underlying causal mechanisms. Based on ground
penetrating radar images, the fractures are observed to have
propagated to depths of up to 10 m. In addition, orbiting radar interferometry shows that deposit subsidence of up to
1 cm/year occurred between 1993 and 1996 with continued
subsidence occurring at a slower rate thereafter. In situ
measurements show that 1 m below the surface, the 1993
deposits remain 5°C to 15°C hotter, 18 years after
emplacement, than adjacent deposits. Based on the observed
subsidence as well as estimated cooling rates, the fractures are
inferred to be the combined result of deaeration, thermal
contraction, and sedimentary compaction in the months to
years following deposition. Significant environmental factors,
including regional earthquakes in 1995 and 2007, accelerated
settling at punctuated moments in time. The spatially variable
fracture pattern relates to surface slope and lithofacies
variations as well as substrate lithology. Similar fractures
have been reported in other ignimbrites but are generally
exposed only in cross section and are often attributed to
formation by external forces. Here we suggest that such
interpretations should be invoked with caution, and deformation
including post-emplacement subsidence and fracturing of
loosely packed ash-rich deposits in the months to years postemplacement
is a process inherent in the settling of pyroclastic
material
Growth of a human mammary tumor cell line is blocked by galangin, a naturally occurring bioflavonoid, and is accompanied by down-regulation of cyclins D3, E, and A
INTRODUCTION: This study was designed to determine if and how a non-toxic, naturally occurring bioflavonoid, galangin, affects proliferation of human mammary tumor cells. Our previous studies demonstrated that, in other cell types, galangin is a potent inhibitor of the aryl hydrocarbon receptor (AhR), an environmental carcinogen-responsive transcription factor implicated in mammary tumor initiation and growth control. Because some current breast cancer therapeutics are ineffective in estrogen receptor (ER) negative tumors and since the AhR may be involved in breast cancer proliferation, the effects of galangin on the proliferation of an ER(-), AhR(high )line, Hs578T, were studied. METHODS: AhR expression and function in the presence or absence of galangin, a second AhR inhibitor, α-naphthoflavone (α-NF), an AhR agonist, indole-3-carbinol, and a transfected AhR repressor-encoding plasmid (FhAhRR) were studied in Hs578T cells by western blotting for nuclear (for instance, constitutively activated) AhR and by transfection of an AhR-driven reporter construct, pGudLuc. The effects of these agents on cell proliferation were studied by (3)H-thymidine incorporation and by flow cytometry. The effects on cyclins implicated in mammary tumorigenesis were evaluated by western blotting. RESULTS: Hs578T cells were shown to express high levels of constitutively active AhR. Constitutive and environmental chemical-induced AhR activity was profoundly suppressed by galangin as was cell proliferation. However, the failure of α-NF or FhAhRR transfection to block proliferation indicated that galangin-mediated AhR inhibition was either insufficient or unrelated to its ability to significantly block cell proliferation at therapeutically relevant doses (IC(50 )= 11 μM). Galangin inhibited transition of cells from the G(0)/G(1 )to the S phases of cell growth, likely through the nearly total elimination of cyclin D3. Expression of cyclins A and E was also suppressed. CONCLUSION: Galangin is a strong inhibitor of Hs578T cell proliferation that likely mediates this effect through a relatively unique mechanism, suppression of cyclin D3, and not through the AhR. The results suggest that this non-toxic bioflavonoid may be useful as a chemotherapeutic, particularly in combination with agents that target other components of the tumor cell cycle and in situations where estrogen receptor-specific therapeutics are ineffective
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