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In lifecourse studies that encompass the adolescent period, the assessment of pubertal status is important, but can be challenging. We aimed to identify current methods for pubertal assessment and assess their appropriateness for population-based research by combining a review of the literature with the views of experts in the field. We searched bibliographic databases, extracted data and assessed study quality to inform a workshop with 21 experts. Acceptability of different approaches was explored with a panel of ten adolescents. We screened 11,935 abstracts, assessed 157 articles and summarised results from 38 articles. Combining these with the opinions of experts, self-assessment was found to be a practical method for use in studies where agreement with the gold standard of clinical assessment by physical examination to within one Tanner stage was acceptable. Serial measures of height and foot size accurately indicated timing of the pubertal growth spurt and age at peak height velocity, and were seen as feasible within longitudinal studies. Hormonal and radiological methods did not offer a practical means of assessing pubertal status. Assessment of voice maturation was promising, but needed validation. Young people thought that self-assessment, foot size and voice assessments were acceptable, and preferred an assessor of the same sex for clinical assessment. This review thus informs researchers working in lifecourse and adolescent health, and identifies future directions in order to improve validity of the methods.
Determining infectious cross-transmission events in healthcare settings involves manual surveillance of case clusters by infection control personnel, followed by strain typing of clinical/environmental isolates suspected in said clusters. Recent advances in genomic sequencing and cloud computing now allow for the rapid molecular typing of infecting isolates.
To facilitate rapid recognition of transmission clusters, we aimed to assess infection control surveillance using whole-genome sequencing (WGS) of microbial pathogens to identify cross-transmission events for epidemiologic review.
Clinical isolates of Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Klebsiella pneumoniae were obtained prospectively at an academic medical center, from September 1, 2016, to September 30, 2017. Isolate genomes were sequenced, followed by single-nucleotide variant analysis; a cloud-computing platform was used for whole-genome sequence analysis and cluster identification.
Most strains of the 4 studied pathogens were unrelated, and 34 potential transmission clusters were present. The characteristics of the potential clusters were complex and likely not identifiable by traditional surveillance alone. Notably, only 1 cluster had been suspected by routine manual surveillance.
Our work supports the assertion that integration of genomic and clinical epidemiologic data can augment infection control surveillance for both the identification of cross-transmission events and the inclusion of missed and exclusion of misidentified outbreaks (ie, false alarms). The integration of clinical data is essential to prioritize suspect clusters for investigation, and for existing infections, a timely review of both the clinical and WGS results can hold promise to reduce HAIs. A richer understanding of cross-transmission events within healthcare settings will require the expansion of current surveillance approaches.
Qualitative inorganic analysis is required for the identification of unknowns, the classification of type, and sometimes to decide what subsequent quantitative analysis is needed. The traditional way of performing qualitative XRF analysis on unknown materials is by subjecting the sample to a full spectral scan. This takes time and an experienced operator to interpret the spectra. Classifying the elements detected as major, minor or trace can also be person dependent. Round robin tests have confirmed this by showing considerable variation in results between laboratories.
Landraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.
Breakthrough Listen is a 10-yr initiative to search for signatures of technologies created by extraterrestrial civilisations at radio and optical wavelengths. Here, we detail the digital data recording system deployed for Breakthrough Listen observations at the 64-m aperture CSIRO Parkes Telescope in New South Wales, Australia. The recording system currently implements two modes: a dual-polarisation, 1.125-GHz bandwidth mode for single-beam observations, and a 26-input, 308-MHz bandwidth mode for the 21-cm multibeam receiver. The system is also designed to support a 3-GHz single-beam mode for the forthcoming Parkes ultra-wideband feed. In this paper, we present details of the system architecture, provide an overview of hardware and software, and present initial performance results.
We observed pediatric S. aureus hospitalizations decreased 36% from 26.3 to 16.8 infections per 1,000 admissions from 2009 to 2016, with methicillin-resistant S. aureus (MRSA) decreasing by 52% and methicillin-susceptible S. aureus decreasing by 17%, among 39 pediatric hospitals. Similar decreases were observed for days of therapy of anti-MRSA antibiotics.
The role that vitamin D plays in pulmonary function remains uncertain. Epidemiological studies reported mixed findings for serum 25-hydroxyvitamin D (25(OH)D)–pulmonary function association. We conducted the largest cross-sectional meta-analysis of the 25(OH)D–pulmonary function association to date, based on nine European ancestry (EA) cohorts (n 22 838) and five African ancestry (AA) cohorts (n 4290) in the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium. Data were analysed using linear models by cohort and ancestry. Effect modification by smoking status (current/former/never) was tested. Results were combined using fixed-effects meta-analysis. Mean serum 25(OH)D was 68 (sd 29) nmol/l for EA and 49 (sd 21) nmol/l for AA. For each 1 nmol/l higher 25(OH)D, forced expiratory volume in the 1st second (FEV1) was higher by 1·1 ml in EA (95 % CI 0·9, 1·3; P<0·0001) and 1·8 ml (95 % CI 1·1, 2·5; P<0·0001) in AA (Prace difference=0·06), and forced vital capacity (FVC) was higher by 1·3 ml in EA (95 % CI 1·0, 1·6; P<0·0001) and 1·5 ml (95 % CI 0·8, 2·3; P=0·0001) in AA (Prace difference=0·56). Among EA, the 25(OH)D–FVC association was stronger in smokers: per 1 nmol/l higher 25(OH)D, FVC was higher by 1·7 ml (95 % CI 1·1, 2·3) for current smokers and 1·7 ml (95 % CI 1·2, 2·1) for former smokers, compared with 0·8 ml (95 % CI 0·4, 1·2) for never smokers. In summary, the 25(OH)D associations with FEV1 and FVC were positive in both ancestries. In EA, a stronger association was observed for smokers compared with never smokers, which supports the importance of vitamin D in vulnerable populations.
Textural and chemical data are reviewed for amphiboles occurring in Cr-diopside series and Al-augite series xenoliths; as megacrysts in a variety of igneous environments; and also as minor phases in tectonic slices of upper-mantle peridotite. New data are given for pargasite and associated phases in a lherzolite from Tanzania and in kelyphite replacing garnet in a S. African kimberlite xenolith. It is concluded that only pargasites and titaniferous pargasites occurring in Cr-diopside series blocks have formed under upper-mantle conditions. Although amphibole is present in the upper mantle, as suggested by Oxburgh (1964), its relative paucity suggests it is not a major alkali and water storage site; phlogopite is a more likely candidate, particularly in the deeper parts of the upper mantle.
Svetlozarite, previously described as a new member of the mordenite group of zeolites, is reinterpreted as a multiply twinned and highly faulted dachiardite. X-ray diffraction study and transmission electron microscopy revealed (001) twins and (100) stacking faults. The former are attributed at least mainly to the insertion of a b glide plane between dachiardite sheets at each twin interface, which preserves the 5-ring linkages between the sheets. The latter are associated with loss of the C face-centring relation, and are attributed to replacement of shared 5-rings by linked 4-rings in the dachiardite sheets. Further study is needed to determine whether the structural faults in the dachiardite structures are chemically controlled.
Peridotite xenoliths 73–106 and 73–109 have coarse textures. All minerals in 73–106 are very Ti-rich, and include olivine (Fo 87.6), orthopyroxene (En 90.0), garnet (core TiO2 0.8, Cr2O3 7; rim 1.4, 4 wt. %), spinel (TiO2 5, Cr2O3 38), clinopyroxene (A12O3 1–8) secondary mica (TiO2 6, Cr2O3 2.5 near garnet 0.5 away from garnet), and serpentine (FeO 5–12) enclosing perovskite-rimmed ilmenite and minute apatites. All minerals in peridotite 73–109 are Ti-poor, and include olivine (Fo 92.6), orthopyroxene (En 93.6), garnet (Cr2O3 3.1–3.8), spinel (55), ureyitic diopside, primary mica (TiO2 0.06, Cr2O3 1.0, BaO 0.5, Cl 0.04), and serpentine (FeO 2–23). Various thermometers indicate ∼ 1350K (73–106) and 1100K (73–109). The low Al2O3 in the orthopyroxenes gives 39–47 kb for 73–109 from the Wood-Banno barometer. In 73–106, the spinel lies in secondary mica next to the garnet rim, whereas the spinel of 73–109 occurs in grains enclosed by garnet. The former assemblage indicates diffusion-dependent disequilibrium, whereas the latter is attributed to simultaneous growth of spinel and garnet, perhaps consequent upon exsolution from orthopyroxene. Complex behaviour was found for the Cr/Al distribution in published analyses of garnet and spinel. The 73–109 pair lies near the Thaba Putsoa trend, and the 73–106 assemblages are displaced towards the kelyphite region in which garnet and spinel have similar Cr/Al. Spinel and garnet may coexist over a 30 kb pressure interval ranging from ∼ 16 kb for low bulk Cr to ∼ 40 kb for high Cr.
Thirty-one natural olivines, of which 25 had been previously analysed by wet chemical methods, have been analysed for Mg, Fe, Mn, Ca, Ni, and Co by electron-microprobe techniques. The totals of the olivine molecules Fo, Fa, etc., calculated from the above metals vary from 97·6 to 101·5 with a mean of 99·6%. Twenty-one of the specimens had been used previously by Yoder and Sahama to prepare a determinative curve between mole per cent. Fo and the lattice spacing d130. Yoder and Sahama had found that the data for natural olivines showed large random displacements from a straight line, and that the best straight line deviated for low Fo values from that for synthetic olivines. A plot of Fo determined from the microprobe vs. d130 corrected for lattice expansion caused by Ca and Mn shows no systematic deviation between natural and synthetic specimens, and only small deviations from the best continuous curve (maximum 4% in Fo assuming no error in d130). The maximum contents found for Mn, Ca, Ni, and Co were 3·2, 0·54, 0·33, and 0·03%, respectively. For these minor constituents, some of the wet chemical analyses agreed very well with the microprobe results while others showed large deviations. Although the substitution of Ca is small, it can affect considerably the determination of mole per cent. Fo from d130.
After specimen preparation and calibration have been carried out, microprobe analyses for most major and minor (but not trace) elements in common silicates can be made with an accuracy of about 0·5 to 5% of the amount present in about one minute for each group of three elements. Although standard chemical methods applied to large homogeneous samples will retain their fundamental reference value, microprobe techniques with their high spatial resolution, relative freedom from contamination problems, high speed, and moderate to good accuracy promise to revolutionize analytical programmes in mineralogy and petrology.
The in situ dry matter disappearance technique (Ørskov and McDonald, 1979) evaluates forages for their rate and extent of degradation in the rumen. However, this method does not allow the evaluation of a large number of samples at one and the same time and therefore which limits screening of treatments applied to forages. The in vitro gas production method is faster and allows handling of many samples per batch; therefore, gas production could be an alternative to the use of nylon bags if the response to treatments between the two methods is similar among treated forages. The objective of this experiment was to compare results obtained with both the gas production and the nylon bag techniques for forages treated with four levels of maceration and conserved as hay or silage.
We examined risk factors associated with the intestinal acquisition of antimicrobial-resistant extraintestinal pathogenic Escherichia coli (ExPEC) and development of community-acquired urinary tract infection (UTI) in a case-control study of young women across Canada. A total of 399 women were recruited; 164 women had a UTI caused by E. coli resistant to ⩾1 antimicrobial classes and 98 had a UTI caused by E. coli resistant to ⩾3 antimicrobial classes. After adjustment for age, student health service (region of Canada) and either prior antibiotic use or UTI history, consumption of processed or ground chicken, cooked or raw shellfish, street foods and any organic fruit; as well as, contact with chickens, dogs and pet treats; and travel to Asia, were associated with an increased risk of UTI caused by antimicrobial resistant E. coli. A decreased risk of antimicrobial resistant UTI was associated with consumption of apples, nectarines, peppers, fresh herbs, peanuts and cooked beef. Drug-resistant UTI linked to foodborne and environmental exposures may be a significant public health concern and understanding the risk factors for intestinal acquisition of existing or newly emerging lineages of drug-resistant ExPEC is important for epidemiology, antimicrobial stewardship and prevention efforts.
Production from smallholder owned goats in the semi-arid tropics is constrained by dry season feed shortages. Kid mortality is high and low growth rate of kids weaned at the onset of the dry season delays slaughtering of males and breeding in females. Supplementation with purchased feed is unaffordable so only locally available, probably non-conventional feeds can be considered. In Southern Zimbabwe, the typical natural vegetation in communal grazing areas consists of annual and perennial grasses and trees and shrubs, many of which are Acacia species. In this project tree fruits, from Acacia and other available species were evaluated as dry season protein supplements for goats.
The mid-infrared range contains many spectral features associated with large molecules and dust grains such as polycyclic aromatic hydrocarbons and silicates. These are usually very strong compared to fine-structure gas lines, and thus valuable in studying the spectral properties of faint distant galaxies. In this paper, we evaluate the capability of low-resolution mid-infrared spectroscopic surveys of galaxies that could be performed by SPICA. The surveys are designed to address the question how star formation and black hole accretion activities evolved over cosmic time through spectral diagnostics of the physical conditions of the interstellar/circumnuclear media in galaxies. On the basis of results obtained with Herschel far-infrared photometric surveys of distant galaxies and Spitzer and AKARI near- to mid-infrared spectroscopic observations of nearby galaxies, we estimate the numbers of the galaxies at redshift z > 0.5, which are expected to be detected in the polycyclic aromatic hydrocarbon features or dust continuum by a wide (10 deg2) or deep (1 deg2) blind survey, both for a given observation time of 600 h. As by-products of the wide blind survey, we also expect to detect debris disks, through the mid-infrared excess above the photospheric emission of nearby main-sequence stars, and we estimate their number. We demonstrate that the SPICA mid-infrared surveys will efficiently provide us with unprecedentedly large spectral samples, which can be studied further in the far-infrared with SPICA.
Vitamin E and selenium have been reported to improve immune function across a range of species. Ewes lambing on poor-quality dry pasture in autumn in Western Australia are at risk of being deficient in vitamin E and selenium at lambing thus predisposing their lambs to deficiencies and increasing the risk of infection and disease. This study tested the hypotheses that (i) supplementation of autumn-lambing ewes with vitamin E plus selenium in late gestation will increase the concentrations of vitamin E and selenium in plasma in the ewe and lamb and (ii) that the increased concentrations of vitamin E and selenium in plasma in the lambs will improve their innate and adaptive immune responses and thus survival. Pregnant Merino ewes were divided into a control group (n=58) which received no supplementation or a group supplemented with vitamin E plus selenium (n=55). On days 111, 125 and 140 of pregnancy ewes in the vitamin E plus selenium group were given 4 g all-rac-α-tocopherol acetate orally. On day 111 the ewes were also given 60 mg of selenium as barium selenate by subcutaneous injection. The concentrations of α-tocopherol and selenium were measured in ewes and/or lambs from day 111 of pregnancy to 14 weeks of age±10 days (weaning). Immune function of the lamb was assessed by analysing the numbers and phagocytic capacities of monocytes and polymorphonuclear leucocytes and plasma IgG and anti-tetanus toxoid antibody concentrations between birth and 14 weeks of age±10 days. Maternal supplementation with vitamin E plus selenium increased the concentration of α-tocopherol in plasma (1.13 v. 0.67 mg/l; P<0.001) and selenium in whole blood (0.12 v. 0.07 mg/l; P<0.01) of the ewes at lambing compared with controls. Supplementation also increased the concentration of α-tocopherol (0.14 v. 0.08 mg/l; P<0.001) and selenium (0.08 v. 0.05 mg/l; P<0.01) in lambs at birth compared with controls. There was no significant effect of supplementation on immune function or survival in the lambs.
We present techniques for obtaining large (∼100 L STP) samples of ancient air for analysis of 14C of methane (14CH4)and other trace constituents. Paleoatmospheric 14CH4 measurements should constrain the fossil fraction of past methane budgets, as well as provide a definitive test of methane clathrate involvement in large and rapid methane concentration ([CH4]) increases that accompanied rapid warming events during the last deglaciation. Air dating to the Younger Dryas–Preboreal and Oldest Dryas–Bølling abrupt climatic transitions was obtained by melt extraction from old glacial ice outcropping at an ablation margin in West Greenland. The outcropping ice and occluded air were dated using a combination of δ15N of N2, δ18O of O2, δ18Oice and [CH4] measurements. The [CH4] blank of the melt extractions was <4 ppb. Measurements of δ18O and δ15N indicated no significant gas isotopic fractionation from handling. Measured Ar/N2, CFC-11 and CFC-12 in the samples indicated no significant contamination from ambient air. Ar/N2, Kr/Ar and Xe/Ar ratios in the samples were used to quantify effects of gas dissolution during the melt extractions and correct the sample [CH4]. Corrected [CH4] is elevated over expected values by up to 132 ppb for most samples, suggesting some in situ CH4 production in ice at this site.
Measurements of glacier ice cliff evolution are sparse, but where they do exist, they indicate that such areas of exposed ice contribute a disproportionate amount of melt to the glacier ablation budget. We used Structure from Motion photogrammetry with Multi-View Stereo to derive 3-D point clouds for nine ice cliffs on Khumbu Glacier, Nepal (in November 2015, May 2016 and October 2016). By differencing these clouds, we could quantify the magnitude, seasonality and spatial variability of ice cliff retreat. Mean retreat rates of 0.30–1.49 cm d−1 were observed during the winter interval (November 2015–May 2016) and 0.74–5.18 cm d−1 were observed during the summer (May 2016–October 2016). Four ice cliffs, which all featured supraglacial ponds, persisted over the full study period. In contrast, ice cliffs without a pond or with a steep back-slope degraded over the same period. The rate of thermo-erosional undercutting was over double that of subaerial retreat. Overall, 3-D topographic differencing allowed an improved process-based understanding of cliff evolution and cliff-pond coupling, which will become increasingly important for monitoring and modelling the evolution of thinning debris-covered glaciers.
Supernova (SN) 1987A has provided a unique opportunity to study how SN ejecta evolve in 30 years time scale. We report our ALMA spectral observations of SN 1987A, taken in 2014, 2015 and 2016, with detections of CO, 28SiO, HCO+ and SO, with weaker lines of 29SiO.
We find a dip in the SiO line profiles, suggesting that the ejecta morphology is likely elongated. The difference of the CO and SiO line profiles is consistent with hydrodynamic simulations, which show that Rayleigh-Taylor instabilities causes mixing of gas, with heavier elements much more disturbed, making more elongated structure.
Using 28SiO and its isotopologues, Si isotope ratios were estimated for the first time in SN 1987A. The estimated ratios appear to be consistent with theoretical predictions of inefficient formation of neutron rich atoms at lower metallicity, such as observed in the Large Magellanic Cloud (about half a solar metallicity).
The deduced large HCO+ mass and small SiS mass, which are inconsistent to the predictions of chemical model, might be explained by some mixing of elements immediately after the explosion. The mixing might have made some hydrogen from the envelope to sink into carbon and oxygen-rich zone during early days after the explosion, enabling the formation of a substantial mass of HCO+. Oxygen atoms may penetrate into silicon and sulphur zone, suppressing formation of SiS.
Our ALMA observations open up a new window to investigate chemistry, dynamics and explosive-nucleosynthesis in supernovae.
In August 2015 a gastroenteritis outbreak occurred following a wedding. An outbreak investigation was undertaken and a cohort study was conducted using an online survey. Of 140 guests, 134 received the survey and 113 responded (84·3% response rate). Seventy respondents met the case definition of vomiting and/or diarrhoea within 72 h of the wedding (61·9% attack rate). Fifteen exposures were associated with illness; on stratification, all were confounded by the ham hock starter. Multivariable analysis showed a significant association with exposure to ham hock (risk ratio 6·62, 95% confidence interval 2·19–20·03). Eight guests and two catering staff submitted stool samples. All tested positive for norovirus GI-6 infection, including a food handler who had vomiting less than 48 h before the wedding. A single genotype was detected among all samples, suggesting a single source of contamination. The transmission pattern suggested point-source exposure. The most plausible cause of the outbreak was transmission from an infected food handler via contaminated food. This highlights the importance of appropriate exclusions for symptomatic food handlers. Additionally, the food handler's stool sample was submitted 7 days after symptom resolution. The potential for extended viral excretion, and the extremely low infective dose of norovirus, may mean that current exclusion guidelines are not of sufficient duration.