Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.

Sources of gene expression variation in a globally diverse human cohort

Genetic variation influencing gene expression and splicing is a key source of phenotypic diversity. Though invaluable, studies investigating these links in humans have been strongly biased toward participants of European ancestries, diminishing generalizability and hindering evolutionary research. To address these limitations, we developed MAGE, an open-access RNA-seq data set of lymphoblastoid cell lines from 731 individuals from the 1000 Genomes Project spread across 5 continental groups and 26 populations. Most variation in gene expression (92%) and splicing (95%) was distributed within versus between populations, mirroring variation in DNA sequence. We mapped associations between genetic variants and expression and splicing of nearby genes (cis-eQTLs and cis-sQTLs, respective), identifying >15,000 putatively causal eQTLs and >16,000 putatively causal sQTLs that are enriched for relevant epigenomic signatures. These include 1310 eQTLs and 1657 sQTLs that are largely private to previously underrepresented populations. Our data further indicate that the magnitude and direction of causal eQTL effects are highly consistent across populations and that apparent "population-specific" effects observed in previous studies were largely driven by low resolution or additional independent eQTLs of the same genes that were not detected. Together, our study expands understanding of gene expression diversity across human populations and provides an inclusive resource for studying the evolution and function of human genomes.

The complete sequence of a human Y chromosome

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9  GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36  GeV/c^{2}, rejecting cross sections above 9.2×10^{-48}  cm at the 90% confidence level.

Characterization of large-scale genomic differences in the first complete human genome

BACKGROUND

The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet.

RESULTS

Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution.

CONCLUSION

Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.

A complete reference genome improves analysis of human genetic variation

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.

Local adaptation and archaic introgression shape global diversity at human structural variant loci

Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.

Psychological, social and everyday visual impact of diabetic macular oedema and diabetic retinopathy: a systematic review

AIMS

To synthesize the evidence on the impact of diabetic retinopathy and diabetic macular oedema from the patient perspective.

METHODS

A systematic literature review was conducted using MEDLINE Complete, PsycINFO, EMBASE and AMED. We included articles investigating the impact of the condition on quality of life, symptoms, visual functioning, activities of daily living, well-being, social functioning, and financial status. The studies evaluated were observational, including cross-sectional, prospective cohort and retrospective cohort designs. Outcome data were extracted and synthesized.

RESULTS

Searches yielded 5114 publications. After screening, 85 studies were included, measuring the following outcomes: visual functioning (n=46); quality of life (n=22); well-being (n=16); functional status (n=5); work (n=4); and visual task performance (n=2). Diabetic retinopathy has a considerable impact on visual functioning and this is greater in people with greater disease severity. Diabetic retinopathy significantly limits activities including working, driving, walking and reading, and has the potential to have a negative impact on psychological well-being.

CONCLUSIONS

Diabetic retinopathy is associated with poor self-reported visual functioning, well-being, and health-related quality of life. Ability to perform basic everyday tasks appears to diminish with disease severity. Some studies suggest impaired mobility and problems with work, but there are gaps in this evidence.

0399 The MSSA: A Novel Instrument to Assess Sleep and Sleep Disturbances in Military Men and Women

Introduction

Military personnel experience unique stressors (e.g., deployments, shift work, family separation) which can cause sleep disturbances. However, little is known regarding the general sleep quality of military personnel and how it changes throughout their service, what types of stressors precipitate sleep disturbances, and how this differs among military men and women. We present findings from a new self-report measure, the Military Service Sleep Assessment (MSSA), which was designed to assess (1) current primary problems with sleep, (2) sleep quality throughout military service (3) life events that may have impacted their sleep and (4) the specific events which most effected sleep.

Methods

A total of 69 military personnel (22 women and 47 men) completed the MSSA and 49 also completed a diagnostic polysomnogram (PSG). Chi-square tests were run to differences in responses between men and women.

Results

No significant differences were found between men and women. In general, sleep quality progressively decreased over a participant’s military career from 3 to 2 on a 5-point Likert scale (1=low, 5=high). For those with at least one deployment (n=52), 73% reported that deployment and 54% reported that a redeployment (return from deployment) negatively impacted sleep quality for 3 months. Women reported that permanent change of station (PCS) negatively impacted their sleep more frequently than men (36% vs. 28%). The reported events that most significantly impacted sleep quality were deployment, military service other than deployment and trauma.

Conclusion

The MSSA is a novel instrument that can be used to increase understanding of sleep disturbances in military men and women which can inform prevention and treatment strategies. This measure is being used to systematically evaluate the factors which may precipitate or perpetuate sleep disturbances in military men and women such as military service-associated factors, training, deployment history, changing stations, and exposure to trauma or other stressful life events.

Support

This study is supported by the Defense Health Agency, Defense Medical Research and Development Program, Clinical Research Intramural Initiative for Military Women’s Health.

0384 Do Nurses with High Blood Pressure Have More Sleep Disturbances Than Their Peers?

Introduction

Nurses work in stressful environments and often have rotating work schedules, which may put them at risk for disturbed sleep and health. Poor quality and short sleep duration are strong risk factors for high blood pressure (HBP). Yet few studies have examined these associations in nurses, who may be a particularly at-risk sample. To address this gap, we examined group differences in self-reported and actigraphy-assessed sleep among nurses with and without self-reported HBP.

Methods

Participants were 392 nurses (91.8% female; 77.8% white, mean age = 39.54) recruited for a parent study. Participants completed baseline questionnaires including the Pittsburgh Sleep Quality Index (PSQI), followed by 14 days of actigraphy and sleep diaries to prospectively assess 14-day mean total sleep time (TST) and sleep efficiency (SE). An independent samples t-tests was used to assess group differences in sleep variables by HBP status. Linear regression was used to further examine the association between HBP status on sleep variables when controlling for age, race, gender, ethnicity, and body mass index (BMI).

Results

Twenty-nine (7%) nurses endorsed having clinically-diagnosed HBP. Nurses with HBP had higher global PSQI scores (indicating worse sleep quality; t=2.71, p=0.007), compared to nurses who did not report HBP, with a mean difference of 1.24. When adjusting for covariates, the association between HBP and the PSQI became marginally significant (p=0.054). There were no group differences in sleep diary or actigraphy TST or SE by HBP status, nor did HBP predict these sleep variables when controlling for covariates.

Conclusion

We found that nurses who reported having clinically diagnosed HBP had poorer global sleep quality. Although limited by self-reported history of HBP diagnosis, and low endorsement of HBP in our sample, our results corroborate other findings which suggest there is a strong association between high blood pressure and disturbed sleep. Future studies should examine these associations in larger samples, assess blood pressure directly, and experimentally examine the effects of HBP treatment on sleep quality.

Support

NIH/NIAID R01AI128359-01

0225 Do Associations Between Daily Stress and Sleep Vary by Work Shift? A Within-Person Analysis in Nurses

Introduction

Longitudinal studies have shown daily stress and sleep are bidirectionally associated. Nurses are particularly likely to experience sleep disturbances and high stress due to demanding work environments. Night shift work may be a unique stressor for nurses that exacerbates associations between stress and sleep. Using a within-person design, we examined the daily bidirectional associations between stress and sleep and moderation by nightly work shift (day/off shift vs. night shift) in a large sample of nurses.

Methods

Participants were 393 nurses (91% female; 77% white, mean age = 38.4 years) recruited from two hospitals. Participants completed 14 days of sleep diaries and actigraphy to assess total sleep time (TST) and sleep efficiency (SE). They simultaneously completed assessments of stress on the previous day (0 = “not at all” to 4 = “extremely”) and daily work schedule (day/off shift vs. night shift [work between 9pm-6am]).

Results

Results indicated greater daily stress was associated with shorter diary TST (b = -9.49, p<.0001) and actigraphy TST (b = -4.48, p<.01), as well as lower diary SE (b = -0.56, p<.001). When examining reverse pathways of sleep predicting next day stress, both diary TST (b = -0.0004, p<.0001) and actigraphy TST (b = -0.0002, p = .03) predicted higher next-day stress. Lower diary SE predicted higher next-day stress (b = -0.005, p<.001). Only the association between daily stress and nightly diary SE was moderated by daily work shift: only when nurses worked a day or off shift did they have a negative association between daily stress and diary SE (b = -0.68, p<.0001).

Conclusion

Daily stress and sleep disturbances occurred in a bidirectional fashion for night- and day-shift working nurses. Most associations were similar regardless of daily type of work shift. Objective and subjective short TST and low subjective SE may contribute to a cycle of increased stress and are prime targets for a tailored sleep intervention in nurses. More research is needed to develop interventions to address the unique sleep health challenges faced by nurses.

Support

NIAID R01AI128359-01

0483 Predictors of Cognitive Behavioral Therapy for Insomnia (CBT) Outcomes in Active Duty U.S. Army Personnel

Introduction

Cognitive behavioral therapy for insomnia (CBTi) is well established as the first-line treatment for the management of chronic insomnia. Identifying predictors of response to CBTi should enable the field to efficiently utilize resources to treat those who are likely to respond and to personalize treatment approaches to optimize outcomes for those who are less likely to respond to traditional CBTi. Although a range of studies have been conducted, no clear pattern of predictors of response to CBTi has emerged.

Methods

The purpose of this study was to examine the impact and relative importance of a comprehensive group of pretreatment predictors of insomnia outcomes in 99 active duty service members who received in-person CBTi in a randomized clinical trial.

Results

Results indicated that higher levels of baseline insomnia severity and total sleep time predicted greater improvements on the Insomnia Severity Index (ISI) following treatment. Higher depression symptoms and a history of head injury predicted a worse response to treatment (i.e., smaller improvements on the ISI).

Conclusion

Clinically meaningful improvements, as measured by the reliable change index (RCI), were found in 59% of the sample. Over and above baseline insomnia severity, only depressive symptoms predicted this outcome. Future studies should examine if modifications to CBTi based on these predictors of response can improve outcomes.

Support

This study was conducted with support from the U.S. Department of Defense through the U.S. Army Medical Research and Materiel Command, Congressionally Directed Medical Research Programs, Psychological Health and Traumatic Brain Injury Research Program award W81XWH-10-1-0828 (PI: Dr Taylor).

0178 The Cycle of Daily Stress and Sleep: Sleep Measurement Matters

Introduction

Disturbed sleep can be both a cause and a consequence of increased stress. Yet intensive longitudinal studies have demonstrated that sleep assessed via sleep diaries and actigraphy is inconsistently associated with daily stress. We expanded this research by examining daily associations between sleep and stress using a three-fold approach to assess sleep: sleep diaries, actigraphy, and ambulatory single-channel electroencephalography [EEG].

Methods

Participants were 80 adults (M age = 32.65 years, 63% female) who completed 7 days of sleep and perceived stress assessments in a naturalistic setting (resulting in 560 possible measurement occasions). Multilevel models were used to examine bidirectional associations between daily stressor occurrence (0 = stressor did not occur, 1 = stressor occurred) and stressor severity (0 = not at all severe to 3 = very severe) and sleep parameters assessed via diary, actigraphy, and EEG (e.g. total sleep time [TST], sleep efficiency [SE], and sleep onset latency [SOL], wake after sleep onset [WASO]).

Results

Participants reported at least one stressor on 37% of days. Compared to days without a stressor experienced, days with a stressor were associated with a 14.4-minute reduction in actigraphy-determined TST the subsequent night (β = -0.24, p = 0.030). Nights with greater sleep-diary determined WASO were associated with greater next-day stressor severity (β = 0.01, p = .026). No EEG-determined sleep parameters were associated with next-day stressor occurrence or severity, or vice versa.

Conclusion

Daily stress and sleep disturbances occurred in a bidirectional fashion, though specific results varied by sleep measurement technique and sleep parameter. Together, our results highlight that type of sleep measurement matters for examining associations with daily stress. We urge future researchers to treat sleep diaries, actigraphy, and EEG as complementary — not redundant — sleep measurement approaches.

Support

Funding for this study included NIH/NIAID R01AI128359-01; DoD-VA 1I01CU000144-01; the Foundation for Rehabilitation Psychology; and General Sleep Corporation.

1110 Characteristics Of Untreated Sleep Disturbance During Intensive Outpatient Treatment For Substance Use Disorders: Preliminary Results From A Longitudinal Study

Introduction

Previous studies have shown that sleep problems are commonly reported during treatment for substance use disorders (SUDs) and sleep complaints have been linked to subsequent relapse. However, most of these findings were in well-controlled clinical trials and may not generalize to the public. Little is known about the natural progression of sleep complaints during treatment in community clinics, the most common treatment approach for SUDs. The aim of this study is to longitudinally assess prevalence of clinically significant sleep disturbance at baseline and post-treatment in a community-based intensive outpatient (IOP) SUD treatment program using a multi-method approach with well-validated measures of sleep.

Methods

Adults beginning IOP SUD treatment completed the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), Nightmare Disorder index (NDI), and one week of actigraphy and sleep diaries. Measures were repeated following treatment (approximately 5 weeks later).

Results

Preliminary analyses on 21 adults who have been enrolled thus far revealed 85.6% of participants experienced sleep disturbance (PSQI > 5) at baseline. 28.5% of participants reached cutoff for moderate-to-severe insomnia symptoms (ISI > 15) and 42.9% reported nightmares more than once per week. Sleep parameters taken from actigraphy and sleep diaries revealed mean sleep efficiency was 77.5% (TST M = 6.2 hours; TIB M = 7.9 hours). These variables did not improve from baseline to post-treatment. Further, most measures indicated a worsening of sleep, though this did not reach significance (all ps > .05).

Conclusion

This preliminary data show a high prevalence of self-reported sleep complaints and objectively measured poor sleep efficiency that do not improve over the course of treatment. Data collection is ongoing and expected to at least double. More robust analyses, including differences between SUD type (e.g., cannabis vs. opioid) and relationship to relapse at post-treatment, will then be completed.

Support

K12DA031794

Results of a Search for Sub-GeV Dark Matter Using 2013 LUX Data

The scattering of dark matter (DM) particles with sub-GeV masses off nuclei is difficult to detect using liquid xenon-based DM search instruments because the energy transfer during nuclear recoils is smaller than the typical detector threshold. However, the tree-level DM-nucleus scattering diagram can be accompanied by simultaneous emission of a bremsstrahlung photon or a so-called "Migdal" electron. These provide an electron recoil component to the experimental signature at higher energies than the corresponding nuclear recoil. The presence of this signature allows liquid xenon detectors to use both the scintillation and the ionization signals in the analysis where the nuclear recoil signal would not be otherwise visible. We report constraints on spin-independent DM-nucleon scattering for DM particles with masses of 0.4-5  GeV/c^{2} using 1.4×10^{4}  kg day of search exposure from the 2013 data from the Large Underground Xenon (LUX) experiment for four different classes of mediators. This analysis extends the reach of liquid xenon-based DM search instruments to lower DM masses than has been achieved previously.

Utilization of single-image normalized difference vegetation index (SI-NDVI) for early plant stress detection

PREMISE OF THE STUDY

An imaging system was refined to monitor the health of vegetation grown in controlled conditions using spectral reflectance patterns. To measure plant health, the single-image normalized difference vegetation index (SI-NDVI) compares leaf reflectance in visible and near-infrared light spectrums.

METHODS AND RESULTS

The SI-NDVI imaging system was characterized to assess plant responses to stress before visual detection during controlled stress assays. Images were analyzed using Fiji image processing software and Microsoft Excel to create qualitative false color images and quantitative graphs to detect plant stress.

CONCLUSIONS

Stress was detected in Arabidopsis thaliana seedlings within 15 min of salinity application using SI-NDVI analysis, before stress was visible. Stress was also observed during ammonium nitrate treatment of Eruca sativa plants before visual detection. Early detection of plant stress is possible using SI-NDVI imaging, which is both simpler to use and more cost efficient than traditional dual-image NDVI or hyper-spectral imaging.

First Searches for Axions and Axionlike Particles with the LUX Experiment

The first searches for axions and axionlike particles with the Large Underground Xenon experiment are presented. Under the assumption of an axioelectric interaction in xenon, the coupling constant between axions and electrons g_{Ae} is tested using data collected in 2013 with an exposure totaling 95 live days ×118  kg. A double-sided, profile likelihood ratio statistic test excludes g_{Ae} larger than 3.5×10^{-12} (90% C.L.) for solar axions. Assuming the Dine-Fischler-Srednicki-Zhitnitsky theoretical description, the upper limit in coupling corresponds to an upper limit on axion mass of 0.12  eV/c^{2}, while for the Kim-Shifman-Vainshtein-Zhakharov description masses above 36.6  eV/c^{2} are excluded. For galactic axionlike particles, values of g_{Ae} larger than 4.2×10^{-13} are excluded for particle masses in the range 1-16  keV/c^{2}. These are the most stringent constraints to date for these interactions.

Limits on Spin-Dependent WIMP-Nucleon Cross Section Obtained from the Complete LUX Exposure

We present experimental constraints on the spin-dependent WIMP-nucleon elastic cross sections from the total 129.5  kg yr exposure acquired by the Large Underground Xenon experiment (LUX), operating at the Sanford Underground Research Facility in Lead, South Dakota (USA). A profile likelihood ratio analysis allows 90% C.L. upper limits to be set on the WIMP-neutron (WIMP-proton) cross section of σ_{n}=1.6×10^{-41}  cm^{2} (σ_{p}=5×10^{-40}  cm^{2}) at 35  GeV c^{-2}, almost a sixfold improvement over the previous LUX spin-dependent results. The spin-dependent WIMP-neutron limit is the most sensitive constraint to date.

Results from a Search for Dark Matter in the Complete LUX Exposure

We report constraints on spin-independent weakly interacting massive particle (WIMP)-nucleon scattering using a 3.35×10^{4}  kg day exposure of the Large Underground Xenon (LUX) experiment. A dual-phase xenon time projection chamber with 250 kg of active mass is operated at the Sanford Underground Research Facility under Lead, South Dakota (USA). With roughly fourfold improvement in sensitivity for high WIMP masses relative to our previous results, this search yields no evidence of WIMP nuclear recoils. At a WIMP mass of 50  GeV c^{-2}, WIMP-nucleon spin-independent cross sections above 2.2×10^{-46}  cm^{2} are excluded at the 90% confidence level. When combined with the previously reported LUX exposure, this exclusion strengthens to 1.1×10^{-46}  cm^{2} at 50  GeV c^{-2}.

Results on the Spin-Dependent Scattering of Weakly Interacting Massive Particles on Nucleons from the Run 3 Data of the LUX Experiment

We present experimental constraints on the spin-dependent WIMP (weakly interacting massive particle)-nucleon elastic cross sections from LUX data acquired in 2013. LUX is a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility (Lead, South Dakota), which is designed to observe the recoil signature of galactic WIMPs scattering from xenon nuclei. A profile likelihood ratio analysis of 1.4×10^{4}  kg day of fiducial exposure allows 90% C.L. upper limits to be set on the WIMP-neutron (WIMP-proton) cross section of σ_{n}=9.4×10^{-41}  cm^{2} (σ_{p}=2.9×10^{-39}  cm^{2}) at 33  GeV/c^{2}. The spin-dependent WIMP-neutron limit is the most sensitive constraint to date.

Improved Limits on Scattering of Weakly Interacting Massive Particles from Reanalysis of 2013 LUX Data

We present constraints on weakly interacting massive particles (WIMP)-nucleus scattering from the 2013 data of the Large Underground Xenon dark matter experiment, including 1.4×10^{4}  kg day of search exposure. This new analysis incorporates several advances: single-photon calibration at the scintillation wavelength, improved event-reconstruction algorithms, a revised background model including events originating on the detector walls in an enlarged fiducial volume, and new calibrations from decays of an injected tritium β source and from kinematically constrained nuclear recoils down to 1.1 keV. Sensitivity, especially to low-mass WIMPs, is enhanced compared to our previous results which modeled the signal only above a 3 keV minimum energy. Under standard dark matter halo assumptions and in the mass range above 4  GeV c^{-2}, these new results give the most stringent direct limits on the spin-independent WIMP-nucleon cross section. The 90% C.L. upper limit has a minimum of 0.6 zb at 33  GeV c^{-2} WIMP mass.

Leadership in Obstetrics and Gynaecology and Contribution to the Millenium Development Goal 5

DOI: http://www.dx.doi.org/10.3126/njog.v7i2.11131 Nepal Journal of Obstetrics and Gynaecology / Vol 7 / No. 2 / Issue 14 / July-Dec, 2012 / 1-2

Spin density projection-assisted R2 magnetic resonance imaging of the liver in the management of body iron stores in patients receiving multiple red blood cell transfusions: an audit and retrospective study in South Australia

AIM

To assess the impact of non-invasive monitoring of liver iron concentration (LIC) on management of body iron stores in patients receiving multiple blood transfusions.

METHOD

A retrospective audit was conducted on clinical data from 40 consecutive subjects with haemolytic anaemias or ineffective haematopoiesis who had been monitored non-invasively for LIC over a period of at least 1 year. LIC was measured with spin density projection-assisted proton transverse relaxation rate-magnetic resonance imaging.

RESULTS

Nineteen clinical decisions were explicitly documented in the case notes as being based on LIC results. Decisions comprised initiation of chelation therapy, increasing chelator dose, decreasing chelator dose and change of mode of delivery of deferioxamine from subcutaneous to intravenous. The geometrical mean LIC for the cohort dropped significantly (P= 0.008) from 6.8 mg Fe/g dry tissue at initial measurement to 4.8 mg Fe/g dry tissue at final measurement. The proportion of subjects with LIC in the range associated with greatly increased risk of cardiac disease and death (>15 mg Fe/g dry tissue) dropped significantly (P= 0.01) from 14 of 40 subjects at initial measurement to 5 of 40 subjects at final measurement. No significant changes in the geometrical mean of serum ferritin or the proportion of subjects with serum ferritin above 2500 or 1500 µg/L were observed.

CONCLUSIONS

The data are consistent with previous observations that introduction of non-invasive monitoring of LIC can contribute to a decreased body iron burden through improved clinical decision making and improved feedback to patients and hence improved adherence to chelation therapy.

Serovars, bacteriophage types and antimicrobial sensitivities associated with salmonellosis in dogs in the UK (1954-2012)

Serovars and bacteriophage (phage) types were determined for 442 isolates of Salmonella enterica from dogs in the UK submitted to the Scottish Salmonella Reference Laboratory from 1954 to 2012. The most frequent serovars were Salmonella Typhimurium (196 isolates; 44.3 per cent), Dublin (40 isolates; 9.0 per cent), Enteritidis (28 isolates; 6.3 per cent), Montevideo (19 isolates; 4.3 per cent), Virchow (10 isolates; 2.3 per cent), Heidelberg (8 isolates; 1.8 per cent) and Derby (8 isolates; 1.8 per cent), along with 55 other recognised serovars among 127 other isolates, and six incompletely classified isolates. Serovars were frequently represented by strains commonly associated with poultry, cattle or pigs and their products. Among 196 Salmonella Typhimurium isolates from dogs, the most frequent phage types (definitive types) were the multiple antimicrobial-resistant strains DT104 (62 isolates), DT204c (18 isolates) and DT193 (8 isolates), along with antimicrobial sensitive wild finch strains DT40 (13 isolates) and DT56 variant (8 isolates). Eleven of 28 isolates of Salmonella Enteritidis were phage type 4. S enterica was frequently recovered from faecal or intestinal samples of dogs with diarrhoea, although many dogs had concurrent infection with other enteric pathogens. Salmonella Dublin was recovered from the brain and/or cerebrospinal fluid of two dogs with meningoencephalitis. Salmonella Kedougou was isolated from the joint fluid of a dog with septic arthritis. Salmonella Typhimurium and Salmonella Dublin were each recovered from the vaginas of bitches that had aborted. Isolates of Salmonella Enteritidis phage types 1, 4 and 8, Salmonella Typhimurium DT104, Salmonella Dublin and Salmonella Indiana were isolated from clinically healthy dogs in households where the same strains were recovered from human beings with diarrhoea. The pattern ampicillin-chloramphenicol-spectinomycin-streptomycin-sulfamethoxazole-tetracycline (ACSpSSuT) was the most frequent resistance phenotype and was observed in 44 (13.3 per cent) of 330 isolates. Dogs in the UK are exposed to a wide variety of serovars of S enterica, sometimes associated with clinical disease, and represent a zoonotic risk.

A field evaluation of a footbathing solution for the control of digital dermatitis in cattle

Footbathing is one of the most commonly used methods for controlling digital dermatitis (DD). A farm-based trial was undertaken using six dairy herds involving over 600 cubicle-housed Holstein-Friesian cattle. Split footbaths (length 2.2m) were used to compare the efficacy of two dips, namely, a positive control (5% copper sulphate) and a non-heavy metal-based proprietary dip. The dips were used from early January 2009 for a minimum of 103 days, bathing twice a day for 3 consecutive days every week, using one footbath (three herds) or two in line (three herds). The lesions of DD on the hind feet of cattle were scored by borescope while the animals were being milked, on three occasions (at approximately days 0, 55 and 110) and then compared both directly and by calculating the change in severity from the previous examination (when possible). Data from the 408 cows that had their feet examined for lesions on all three occasions were analysed separately. A reduction in lesion score was seen for both footbath products, but feet bathed in 5% copper sulphate improved more (OR=1.6, CI: 1.14-2.32; P<0.01), and, irrespective of solution, there was a significantly greater improvement in those herds where two footbaths were used (OR=3.39, CI: 2.07-5.19; P<0.001). Lesion improvement over time also increased with lactation number (OR=1.13, CI: 1.02-1.25; P<0.05).

Inflow boundary profile prescription for numerical simulation of nasal airflow

Knowledge of how air flows through the nasal passages relies heavily on model studies, as the complexity and relative inaccessibility of the anatomy prevents detailed in vivo measurement. Almost all models to date fail to incorporate the geometry of the external nose, instead employing a truncated inflow. Typically, flow is specified to enter the model domain either directly at the nares (nostrils), or via an artificial pipe inflow tract attached to the nares. This study investigates the effect of the inflow geometry on flow predictions during steady nasal inspiration. Models that fully replicate the internal and external nasal airways of two anatomically distinct subjects are used as a reference to compare the effects of common inflow treatments on physiologically relevant quantities including regional wall shear stress and particle residence time distributions. Inflow geometry truncation is found to affect flow predictions significantly, though slightly less so for the subject displaying more pronounced passage area contraction up to the internal nasal valve. For both subject geometries, a tapered pipe inflow provides a better approximation to the natural inflow than a blunt velocity profile applied to the nares. Computational modelling issues are also briefly outlined, by comparing quantities predicted using different surface tessellations, and by evaluation of domain-splitting techniques.

Practice observed: is speculum examination on admission a necessary procedure in the management of all cases of antepartum haemorrhage?

The objective of the study was to determine the justification or otherwise of admission speculum examination in women presenting with antepartum haemorrhage and the outcome/ benefits of the practice on women with antepartum haemorrhage presenting to the delivery suite of a UK teaching hospital. Factors studied included gestational age at presentation, associated factors with the bleeding, grade of medical/ midwifery staff performing the admission speculum examination, findings on speculum examination and ultrasound scan and the overall pregnancy outcome. Of the 564 (4.9%) women who presented with antepartum haemorrhage; 521 had an admission speculum examination; 94.4% of these were by senior house officers (SHOs). The findings were a normal cervix (69%) and ectopy (21.3%). Of the women, 14.4% had recurrent bleeding and 8.5% went into preterm labour. The complications of the pregnancies, timing of delivery and management were independent of speculum examination. Admission speculum examination did not influence the management of pregnancies and the complications thereafter. These results suggest that such an intrusive procedure may not be justifiable in women presenting with antepartum haemorrhage.

Assessment of subclinical venous catheter-related diseases in horses and associated risk factors

A total of 102 horses that had a catheter introduced intravenously to facilitate treatment had the catheterised jugular vein and contralateral vein examined by ultrasound every 48 hours. Subclinical complications were defined by thrombus formation or thickening of the venous wall, and the data were analysed to establish risk factors for the development of these complications. The horses with a rectal temperature above 38.5 degrees C when the catheter was introduced were four times more likely to develop complications, than the horses with a lower temperature. The administration of a NSAID while the catheter was in place reduced the risk of complications developing.

Assessing techniques for disinfecting sites for inserting intravenous catheters into the jugular veins of horses

The sites of insertion of catheters into the jugular veins of six horses were investigated to determine common isolates and to assess the effectiveness of two disinfection protocols with the hair coat left long, clipped or shaved. Skin commensals (Staphylococcus, Streptococcus and Micrococcus species) and environmental contaminants (Bacillus, Enterobacteriaceae, Aspergillus and Mucor species) were the microorganisms most frequently isolated. Chlorhexidine gluconate and povidone-iodine-based skin disinfection protocols resulted in significant reductions in the number of bacterial isolates from clipped sites. With chlorhexidine, there were no significant differences between the reductions observed at sites with the hair coat left long, clipped or shaved.

Childhood outcomes after prescription of antibiotics to pregnant women with preterm rupture of the membranes: 7-year follow-up of the ORACLE I trial

BACKGROUND

The ORACLE I trial compared the use of erythromycin and/or amoxicillin-clavulanate (co-amoxiclav) with that of placebo for women with preterm rupture of the membranes without overt signs of clinical infection, by use of a factorial randomised design. The aim of the present study--the ORACLE Children Study I--was to determine the long-term effects on children of these interventions.

METHODS

We assessed children at age 7 years born to the 4148 women who had completed the ORACLE I trial and who were eligible for follow-up with a structured parental questionnaire to assess the child's health status. Functional impairment was defined as the presence of any level of functional impairment (severe, moderate, or mild) derived from the mark III Multi-Attribute Health Status classification system. Educational outcomes were assessed with national curriculum test results for children resident in England.

FINDINGS

Outcome was determined for 3298 (75%) eligible children. There was no difference in the proportion of children with any functional impairment after prescription of erythromycin, with or without co-amoxiclav, compared with those born to mothers who received no erythromycin (594 [38.3%] of 1551 children vs 655 [40.4%] of 1620; odds ratio 0.91, 95% CI 0.79-1.05) or after prescription of co-amoxiclav, with or without erythromycin, compared with those born to mothers who received no co-amoxiclav (645 [40.6%] of 1587 vs 604 [38.1%] of 1584; 1.11, 0.96-1.28). Neither antibiotic had a significant effect on the overall level of behavioural difficulties experienced, on specific medical conditions, or on the proportions of children achieving each level in reading, writing, or mathematics at key stage one.

INTERPRETATION

The prescription of antibiotics for women with preterm rupture of the membranes seems to have little effect on the health of children at 7 years of age.

FUNDING

UK Medical Research Council.

Childhood outcomes after prescription of antibiotics to pregnant women with spontaneous preterm labour: 7-year follow-up of the ORACLE II trial

BACKGROUND

The ORACLE II trial compared the use of erythromycin and/or amoxicillin-clavulanate (co-amoxiclav) with that of placebo for women in spontaneous preterm labour and intact membranes, without overt signs of clinical infection, by use of a factorial randomised design. The aim of the present study--the ORACLE Children Study II--was to determine the long-term effects on children after exposure to antibiotics in this clinical situation.

METHODS

We assessed children at age 7 years born to the 4221 women who had completed the ORACLE II study and who were eligible for follow-up with a structured parental questionnaire to assess the child's health status. Functional impairment was defined as the presence of any level of functional impairment (severe, moderate, or mild) derived from the mark III Multi-Attribute Health Status classification system. Educational outcomes were assessed with national curriculum test results for children resident in England.

FINDINGS

Outcome was determined for 3196 (71%) eligible children. Overall, a greater proportion of children whose mothers had been prescribed erythromycin, with or without co-amoxiclav, had any functional impairment than did those whose mothers had received no erythromycin (658 [42.3%] of 1554 children vs 574 [38.3%] of 1498; odds ratio 1.18, 95% CI 1.02-1.37). Co-amoxiclav (with or without erythromycin) had no effect on the proportion of children with any functional impairment, compared with receipt of no co-amoxiclav (624 [40.7%] of 1523 vs 608 [40.0%] of 1520; 1.03, 0.89-1.19). No effects were seen with either antibiotic on the number of deaths, other medical conditions, behavioural patterns, or educational attainment. However, more children whose mothers had received erythromycin or co-amoxiclav developed cerebral palsy than did those born to mothers who received no erythromycin or no co-amoxiclav, respectively (erythromycin: 53 [3.3%] of 1611 vs 27 [1.7%] of 1562, 1.93, 1.21-3.09; co-amoxiclav: 50 [3.2%] of 1587 vs 30 [1.9%] of 1586, 1.69, 1.07-2.67). The number needed to harm with erythromycin was 64 (95% CI 37-209) and with co-amoxiclav 79 (42-591).

INTERPRETATION

The prescription of erythromycin for women in spontaneous preterm labour with intact membranes was associated with an increase in functional impairment among their children at 7 years of age. The risk of cerebral palsy was increased by either antibiotic, although the overall risk of this condition was low.

FUNDING

UK Medical Research Council.

Factors associated with cross-contamination of hides of Scottish cattle by Escherichia coli O157

The putative source of hide contamination for 236 cattle in Scotland followed from the farm through to slaughter was determined using phage and verocytotoxin type data. The majority of cattle (84%) were found to have subtypes of Escherichia coli O157 on their hide that had not been found previously in any animal from the farm of origin, strongly suggesting that contamination occurred once animals had left the farm of origin. Using logistic regression analysis, several variables and factors were found to be strongly associated (P < 0.01) with cross-contamination of cattle hides at the univariate level; commercial transport to slaughter, transport with other animals, use of a crush, line automation, and increasing slaughterhouse throughput were all risk factors, while feeding hay in lairage, processing an animal earlier in a slaughter cohort, and cleaning the landing area poststunning were protective. In the multivariable model, with the slaughterhouse and the farm group included as random effects, factors associated with the cross-contamination of cattle hides were identified. Transport to the slaughterhouse by a commercial hauler had a borderline-significant association with increased odds of an animal having a cross-contaminated hide (odds ratio [OR] [95% confidence interval (CI)] = 5.7 [0.99, 33.0]; P = 0.05). At the slaughterhouse, providing hay to cattle waiting in lairage (OR [95% CI] = 0.04 [<0.01, 1.04]; P = 0.05) and cleaning the landing area (OR [95% CI] = 0.03 [<0.01, 1.15,]; P = 0.06) also had a borderline-significant association with decreased odds of an animal having a cross-contaminated hide. Although the prevalence of carcass contamination remains very low, targeted intervention at the preslaughter stage may have the potential to reduce further the risk to public health.

Nasal architecture: form and flow

Current approaches to model nasal airflow are reviewed in this study, and new findings presented. These new results make use of improvements to computational and experimental techniques and resources, which now allow key dynamical features to be investigated, and offer rational procedures to relate variations in anatomical form. Specifically, both replica and simplified airways of a single subject were investigated and compared with the replica airways of two other individuals with overtly differing geometries. Procedures to characterize and compare complex nasal airway geometry are first outlined. It is then shown that coupled computational and experimental studies, capable of obtaining highly resolved data, reveal internal flow structures in both intrinsically steady and unsteady situations. The results presented demonstrate that the intimate relation between nasal form and flow can be explored in greater detail than hitherto possible. By outlining means to compare complex airway geometries and demonstrating the effects of rational geometric simplification on the flow structure, this work offers a fresh approach to studies of how natural conduits guide and control flow. The concepts and tools address issues that are thus generic to flow studies in other physiological systems.

Mechanics of airflow in the human nasal airways

The mechanics of airflow in the human nasal airways is reviewed, drawing on the findings of experimental and computational model studies. Modelling inevitably requires simplifications and assumptions, particularly given the complexity of the nasal airways. The processes entailed in modelling the nasal airways (from defining the model, to its production and, finally, validating the results) is critically examined, both for physical models and for computational simulations. Uncertainty still surrounds the appropriateness of the various assumptions made in modelling, particularly with regard to the nature of flow. New results are presented in which high-speed particle image velocimetry (PIV) and direct numerical simulation are applied to investigate the development of flow instability in the nasal cavity. These illustrate some of the improved capabilities afforded by technological developments for future model studies. The need for further improvements in characterising airway geometry and flow together with promising new methods are briefly discussed.