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Few studies have used genomic epidemiology to understand tuberculosis (TB) transmission in rural and remote settings – regions often unique in history, geography and demographics. To improve our understanding of TB transmission dynamics in Yukon Territory (YT), a circumpolar Canadian territory, we conducted a retrospective analysis in which we combined epidemiological data collected through routine contact investigations with clinical and laboratory results. Mycobacterium tuberculosis isolates from all culture-confirmed TB cases in YT (2005–2014) were genotyped using 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) and compared to each other and to those from the neighbouring province of British Columbia (BC). Whole genome sequencing (WGS) of genotypically clustered isolates revealed three sustained transmission networks within YT, two of which also involved BC isolates. While each network had distinct characteristics, all had at least one individual acting as the probable source of three or more culture-positive cases. Overall, WGS revealed that TB transmission dynamics in YT are distinct from patterns of spread in other, more remote Northern Canadian regions, and that the combination of WGS and epidemiological data can provide actionable information to local public health teams.
For Brunei Darussalam, 2015 was primarily about the dilemma of maintaining domestic stability in the face of significant regional and global instability in areas of particular vulnerability for Southeast Asia's smallest country. Plummeting global energy prices saw the country's once extremely large current account surplus reverse into a large deficit. At the same time, as the smallest and weakest claimant in the South China Sea, Brunei has the fewest means to counter the effects of growing Chinese assertiveness, U.S.–China rivalry, and ASEAN ineffectiveness in relation to these disputed waters that lap on to the shores of the Sultanate. Aided by significant long-standing financial, political and diplomatic reserves, Brunei Darussalam was able to maintain an impressive level of social, political and diplomatic stability in these challenging times. On the economic and diplomatic fronts, Bandar Seri Begawan responded by enhancing existing relations and assets and seeking greater diversification. On the social and political fronts, the response was one of greater conservatism and centralization. As Brunei Darussalam's economic problems are significant and structural, the responses will have to pass the test of time for the country to overcome them.
More than Headwinds
Even a cursory glance at Table 1 shows how dramatically the Brunei economy was affected by falling energy prices. And yet, the growth estimates for 2015 are based on inflated price assumptions for both oil and liquefied natural gas, so the reality will likely be even worse. Likewise, current market movements suggest that the IMF price assumptions going forward err on the side of optimism.
The Sultan, His Majesty Haji Hassanal Bolkiah, is well aware that the country's hydrocarbon resources will eventually expire, possibly as early as 2025, and has tried to extend their life in recent years by capping production. The volume of oil production reportedly is now a full 40 per cent less than in 2006.1 In 2015 the scheduled and unscheduled maintenance of some of the most important energy projects has further hit production. However, the short-term costs of the policy have been exacerbated by the global collapse in the value of hydrocarbons with the price of crude oil having fallen from above US$100 in mid-2014 to less than US$30 per barrel by January 2016 and the value of natural gas per million Btu (British Thermal Unit) having fallen from over US$6 to nearly US$2 during the same period.
Excitable temperament disrupts physiological events required for reproductive development in cattle, but no research has investigated the impacts of temperament on growth and puberty attainment in Bos indicus females. Hence, this experiment evaluated the effects of temperament on growth, plasma cortisol concentrations and puberty attainment in B. indicus heifers. A total of 170 Nelore heifers, weaned 4 months before the beginning of this experiment (days 0 to 91), were managed in two groups of 82 and 88 heifers each (mean ± SE; initial BW=238±2 kg, initial age=369±1 days across groups). Heifer temperament was evaluated via exit velocity on day 0. Individual exit score was calculated within each group by dividing exit velocity into quintiles and assigning heifers with a score from 1 to 5 (1=slowest; 5=fastest heifer). Heifers were classified according to exit score as adequate (ADQ, n=96; exit score⩽3) or excitable temperament (EXC, n=74; exit score>3). Heifer BW, body condition score (BCS) and blood samples were obtained on days 0, 31, 60 and 91. Heifer exit velocity and score were recorded again on days 31, 60 and 91. Ovarian transrectal ultrasonography was performed on days 0 and 10, 31 and 41, 60 and 70, 81 and 91 for puberty evaluation. Heifer was declared pubertal at the first 10-day interval in which a corpus luteum was detected. Exit velocity and exit score obtained on day 0 were correlated (r⩾0.64, P<0.01) with evaluations on days 31, 60 and 91. During the experiment, ADQ had greater (P<0.01) mean BCS and BW gain, and less (P<0.01) mean plasma cortisol concentration compared with EXC heifers. Temperament × time interactions were detected (P<0.01) for exit velocity and exit score, which were always greater (P<0.01) in EXC v. ADQ heifers. A temperament × time interaction was also detected (P=0.03) for puberty attainment, which was delayed in EXC v. ADQ heifers. At the end of the experiment, a greater (P<0.01) proportion of ADQ were pubertal compared with EXC heifers. In summary, B. indicus heifers classified as EXC had reduced growth, increased plasma cortisol concentrations and hindered puberty attainment compared to ADQ heifers. Moreover, exit velocity may serve as temperament selection criteria to optimize development of B. indicus replacement heifers.
We propose here a generalization of the problem addressed by the SHGH conjecture. The SHGH conjecture posits a solution to the question of how many conditions a general union
of fat points imposes on the complete linear system of curves in
of fixed degree
, in terms of the occurrence of certain rational curves in the base locus of the linear subsystem defined by
. As a first step towards a new theory, we show that rational curves play a similar role in a special case of a generalized problem, which asks how many conditions are imposed by a general union of fat points on linear subsystems defined by imposed base points. Moreover, motivated by work of Di Gennaro, Ilardi and Vallès and of Faenzi and Vallès, we relate our results to the failure of a strong Lefschetz property, and we give a Lefschetz-like criterion for Terao’s conjecture on the freeness of line arrangements.
The slaughter of animals for human consumption leads to the production of a large quantity of materials which with further processing can be converted into a form suitable for use in animal feedingstuffs. Currently, much of this material goes to waste because of the fragmentation of the abattoir industry into many small units (1700). This means that it is often uneconomic to transport by-products to central points for further processing. However, more stringent control of effluents from abattoirs and the need for high capital investment to bring units up to newly imposed standards means that slaughterings will be concentrated into fewer and larger units (250) (Gerrard and Mallion, 1977), so making the collection and further processing of waste more attractive from both the economic and environmental standpoint. Within the UK, some 13 to 13.5 million cattle units are slaughtered per year (Table 1). (1 cattle unit = 1 beast or 2 pigs, or 3 calves, or 5 lambs).
Concentration data are reported for 18 trace elements in chalcopyrite from a suite of 53 samples from 15 different ore deposits obtained by laser-ablation inductively-coupled plasma-mass spectrometry. Chalcopyrite is demonstrated to host a wide range of trace elements including Mn, Co, Zn, Ga, Se, Ag, Cd, In, Sn, Sb, Hg, Tl, Pb and Bi. The concentration of some of these elements can be high (hundreds to thousands of ppm) but most are typically tens to hundreds of ppm. The ability of chalcopyrite to host trace elements generally increases in the absence of other co-crystallizing sulfides. In deposits in which the sulfide assemblage recrystallized during syn-metamorphic deformation, the concentrations of Sn and Ga in chalcopyrite will generally increase in the presence of co-recrystallizing sphalerite and/or galena, suggesting that chalcopyrite is the preferred host at higher temperatures and/or pressures. Trace-element concentrations in chalcopyrite typically show little variation at the sample scale, yet there is potential for significant variation between samples from any individual deposit. The Zn:Cd ratio in chalcopyrite shows some evidence of a systematic variation across the dataset, which depends, at least in part, on temperature of crystallization. Under constant physiochemical conditions the Cd:Zn ratios in co-crystallizing chalcopyrite and sphalerite are typically approximately equal. Any distinct difference in the Cd:Zn ratios in the two minerals, and/or a non-constant Cd:Zn ratio in chalcopyrite, may be an indication of varying physiochemical conditions during crystallization.
Chalcopyrite is generally a poor host for most elements considered harmful or unwanted in the smelting of Cu, suggesting it is rarely a significant contributor to the overall content of such elements in copper concentrates. The exceptions are Se and Hg which may be sufficiently enriched in chalcopyrite to exceed statutory limits and thus incur monetary penalties from a smelter.
The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source emission cooled from approximately 6 400 K to 2 100 K over a 7-d period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (~2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor.
We obtained radiocarbon (14C) dates with accelerator mass spectrometry (AMS) of vascular plant samples and a charcoal sample collected from peat deposits near the prehistoric village site informally designated CR-03 on Carlisle Island in the Islands of Four Mountains group, Alaska, to determine the eruption age of the CR-02 tephra. A fine vitric ash erupted from Okmok caldera, Umnak Island (ca. 2 ka BP) was also discovered in the bog. The ages of the CR-02 tephra and Okmok II ash are estimated to be 1050 and 2000 cal BP, respectively. Because both tephras are distinctive and widespread, these are important chronostratigraphic markers for archaeological sites in this island group. The 14C dates obtained from this bog are 800 years younger than the dates of the charcoal fragments from cultural layers in the Unit 3 of prehistoric village site CR-02 (AMK-0003).
TAOS II is a next-generation occultation survey with the goal of measuring the size distribution of the small end of the Kuiper Belt (objects with diameters 0.5–30 km). Such objects have magnitudes r > 30, and are thus undetectable by direct imaging. The project will operate three telescopes at San Pedro Mártir Observatory in Baja California, México. Each telescope will be equipped with a custom-built camera comprised of a focal-plane array of CMOS imagers. The cameras will be capable of reading out image data from 10,000 stars at a cadence of 20 Hz. The telescopes will monitor the same set of stars simultaneously to search for coincident occultation detections, thus minimising the false-positive rate. This talk described the project, and reported on the progress of the development of the survey infrastructure.
We explore the properties of sound and human sound recognition as a means to enhance and accelerate visual-only data analysis methods. The aim of this work is to enable and improve the analysis of large data sets, data requiring rapid analysis, multi-dimensional data, and signal detection in data with low signal-to-noise ratio. We present a prototype tool, StarSound, to sonify data such as astronomical transient light curves, spectra, and power spectra. Stereophonic sound is used to ‘visualise’ and localise the data under examination, and 3-D sound is discussed in conjunction with virtual reality technology, as a means to enhance analysis efficiency and efficacy, including rapid data assessment and training machine learning software. In addition, we explore the use of higher-order harmonics as a means to examine simultaneously multi-dimensional data sets. Such an approach can allow the data to be interpreted in a holistic manner and facilitates the discovery of previously unseen connections and relationships. Furthermore, we exploit the capability of the human brain for selective or focused hearing that enables the identification of desired signals in noisy data, or amidst similar or more significant signals. Finally, we provide research examples that benefit directly from data sonification. The work presented here aims to help tackle the challenges of the upcoming era of Big Data and help optimise, speed up and expand aspects of data analysis requiring human interaction.
Bone is frequently dated in archaeological studies and, especially for very old bones (more than 40,000 years old), it is critical to have an accurate and precise measure of the material-specific background value and its associated uncertainty. The SUERC Radiocarbon Laboratory has obtained a mammoth bone as a background bone standard and an appropriate number are now routinely prepared and measured in each AMS batch, resulting in the accumulation of a large number of background bone results over a two-year period. Additionally, information on which of the two accelerator mass spectrometry (AMS) instruments was used to make the radiocarbon (14C) measurements, and which sample pretreatment method (modified Longin or modified ultrafiltration) was used to extract and purify the collagen, is recorded for each sample. These data have been used to estimate the laboratory bone background (to be subtracted from each unknown bone sample prepared in the laboratory) and its associated analytical uncertainty. The statistical analysis of the bone results has made use of a linear mixed effects model to examine the variation, and to apportion the overall variation between and within batches on both AMS instruments, and the different pretreatment methods used at SUERC.
The SUERC Radiocarbon Laboratory employs a one-step “background subtraction” method when calculating 14C ages. An interglacial wood (VIRI Sample K) is employed as the non-bone organic background standard, while a mammoth bone (LQH12) from Latton Quarry is used as the bone background standard. Results over several years demonstrate that the bone background is consistently around a factor of two higher and more variable than the wood background. As a result, the uncertainty on routine bone measurements is higher than for other sample types. This study investigates the factors that may contribute to the difference in F14C values and the higher variability. Preparations of collagen using modified Longin or ultrafiltration methods show no significant difference, nor does eliminating the collagen dissolution step. Two bone samples of known infinite age with respect to radiocarbon are compared and again no significant difference is observed. Finally, the quantity and age of the organic matter in the water used during the pretreatment is investigated and it is shown that there is insufficient organic matter in the reverse osmosis water to influence background values significantly. The attention is now on determining if incomplete demineralization could lead to contaminants being retained by the phosphate in the hydroxyapatite.
The contribution to sea level to 2200 from the grounded, mainland Antarctic Peninsula ice sheet (APIS) was calculated using an ice-sheet model initialized with a new technique computing ice fluxes based on observed surface velocities, altimetry and surface mass balance, and computing volume response using a linearized method. Volume change estimates of the APIS resulting from surface mass-balance anomalies calculated by the regional model RACMO2, forced by A1B and E1 scenarios of the global models ECHAM5 and HadCM3, predicted net negative sea-level contributions between −0.5 and −12 mm sea-level equivalent (SLE) by 2200. Increased glacier flow due to ice thickening returned ∼15% of the increased accumulation to the sea by 2100 and ∼30% by 2200. The likely change in volume of the APIS by 2200 in response to imposed 10 and 20 km retreats of the grounding line at individual large outlet glaciers in Palmer Land, southern Antarctic Peninsula, ranged between 0.5 and 3.5 mm SLE per drainage basin. Ensemble calculations of APIS volume change resulting from imposed grounding-line retreat due to ice-shelf break-up scenarios applied to all 20 of the largest drainage basins in Palmer Land (covering ∼40% of the total area of APIS) resulted in net sea-level contributions of 7–16 mm SLE by 2100, and 10–25 mm SLE by 2200. Inclusion of basins in the northern peninsula and realistic simulation of grounding-line movement for AP outlet glaciers will improve future projections.
An automated method of estimating the spatial distribution of piglets within a pen was used to assess huddling behaviour under normal conditions and during a febrile response to vaccination. The automated method was compared with a manual assessment of clustering activity. Huddling behaviour was partly related to environmental conditions and clock time such that more huddling occurred during the night and at lower ambient air temperatures. There were no positive relationships between maximum pig temperatures and environmental conditions, suggesting that the narrow range of air temperatures in this study was not a significant factor for pig temperature. Spatial distribution affected radiated pig temperature measurements by IR thermography. Higher temperatures were recorded in groups of animals displaying huddling behaviour. Huddling behaviour was affected by febrile responses to vaccination with increased huddling occurring 3 to 8 h post-vaccination. The automated method of assessing spatial distribution from an IR image successfully identified periods of huddling associated with a febrile response, and to changing environmental temperatures. Infrared imaging could be used to quantify temperature and behaviour from the same images.
Among other zooarchaeological remains, terrestrial snails’ shells from the Thaumastus and Megalobulimus genera are found in some Brazilian shellmounds, presenting a potential substitute for charcoal in radiocarbon dating analyses, as reliable representatives of the atmospheric carbon isotopic ratio. In this paper, we present statistically similar results of both charcoal and land snails samples from the same archaeological contexts in three settlements on the coast of Rio de Janeiro. The Manitiba I shellmound results range from 4.2 to 3.7 ka cal BP (95.4%), contemporary with the Saquarema shellmound, occupied during the period from 4.3 to 3.6 ka cal BP (95.4%). For the Usiminas shellmound, two groups of samples revealed different periods of time for two occupational layers from 2.3 to 2.1 ka cal BP (95.4%) and from 1.6 and 1.3 ka cal BP (95.4%). A model constraining each group of samples to within a single phase has a general agreement of 97% with only two outliers out of 22 dates, yielding minimum individual agreement of 74% and 7% posterior outlier probability for Saquarema shells. These are good examples of sites in which the occupation chronology can be successfully obtained by the radiocarbon dating of land snails.
Dementia is a neurodegenerative syndrome that interferes with multiple aspects of life, including cognition, daily functioning, and behavior. Despite the large heterogeneity in symptom development, these three domains are seldom studied simultaneously. This study investigates how trajectories of these domains are interrelated within individuals over time, and how they in turn are related to dementia severity and quality of life (QoL).
We used data from a longitudinal clinical cohort study, including 331 dementia patients. Cognitive status was measured using the Mini-Mental State Examination, daily functioning was measured with the disability assessment for dementia and neuropsychiatric symptoms (NPS) were scored using the neuropsychiatric inventory. We investigated the relationships in the time course of the various dementia domains using random effects multilevel models and parallel-process growth models.
Changes in cognition and daily functioning were highly correlated over time (r = 0.85, p < 0.01), as were changes in NPS and functioning (r = −0.60, p < 0.01), while changes in cognition and NPS were not (r = −0.20, p = 0.06). All three domains were strongly associated with dementia severity over time (p < 0.01). Decreased functioning and increased NPS were both associated with decreased QoL (β = 2.97, p < 0.01 and β = −2.41, p < 0.01, respectively), while cognition was not (β = 0.01, p = 0.93).
This study demonstrates the heterogeneity of dementia progression between individuals and between different dementia domains within individuals. To improve our understanding of dementia progression, future research should embrace a broader perspective encompassing multiple outcome measures along with the patient's profile, including neurological factors as well as physical, social, and psychiatric health.
Computer models can be useful in planning interventions against novel strains of influenza. However such models sometimes make unsubstantiated assumptions about the relative infectivity of asymptomatic and symptomatic cases, or conversely assume there is no impact at all. Using household-level data from known-index studies of virologically confirmed influenza A infection, the relationship between an individual's infectiousness and their symptoms was quantified using a discrete-generation transmission model and Bayesian Markov chain Monte Carlo methods. It was found that the presence of particular respiratory symptoms in an index case does not influence transmission probabilities, with the exception of child-to-child transmission where the donor has phlegm or a phlegmy cough.
The high Antarctic plateau provides exceptional conditions for infrared observations on account of the cold, dry and stable atmosphere above the ice surface. This paper describes the scientific goals behind the first program to examine the time-varying universe in the infrared from Antarctica — the Kunlun Infrared Sky Survey (KISS). This will employ a 50cm telescope to monitor the southern skies in the 2.4μmKdark window from China's Kunlun station at Dome A, on the summit of the Antarctic plateau, through the uninterrupted 4-month period of winter darkness. An earlier paper discussed optimisation of the Kdark filter for sensitivity (Li et al. 2016). This paper examines the scientific program for KISS. We calculate the sensitivity of the camera for the extrema of observing conditions that will be encountered. We present the parameters for sample surveys that could then be carried out for a range of cadences and sensitivities. We then discuss several science programs that could be conducted with these capabilities, involving star formation, brown dwarfs and hot Jupiters, exoplanets around M dwarfs, the terminal phases of stellar evolution, fast transients, embedded supernova searches, reverberation mapping of AGN, gamma ray bursts and the detection of the cosmic infrared background.
We compared accelerator mass spectrometry (AMS) 14C ages of large (>150 μm) pelagic foraminifera with radiometric bulk carbonate 14C ages in two northeastern Atlantic cores. The foraminiferal ages are consistently older than those of the bulk sediment (by + 0.76 ka in Core 11881 and by + 1.1 ka in Core 11886), whereas corresponding fine (<5 μm) fraction ages are similar to those of the bulk sediment carbonate. We calculated near-identical sediment accumulation rates from both the foraminiferal and bulk sediment age/depth relations (3.0 cm ka−1 in Core 11881 and 5.9 cm ka−1 in Core 11886). Consideration of various factors that might produce such offsets leads us to believe that they are not artifacts, but were most probably caused by differential bioturbation of the different size-fractions in the sediment surface mixed layer. The importance of this finding is that many paleoceanographic records, such as the oxygen isotope record, also derive from analyses of large foraminifera, so that these records must be offset in time from the bulk of the sediments that they characterize.