Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains

There are many reports of ancient DNA from bacteria of the Mycobacterium tuberculosis complex (MTBC) being present in skeletons with and without osteological indications of tuberculosis. A possible complication in these studies is that extracts might also contain DNA from the microbiome of the individual whose remains are being analysed and/or from environmental bacteria that have colonised the skeleton after death. These contaminants might include ‘mycobacteria other than tuberculosis’ (MOTT), which are common in the environment, but which are not normally associated with clinical cases of tuberculosis. In this paper we show that MOTT of various types, as well as bacteria of related genera, are present in most if not all archaeological remains. Our results emphasise the complications inherent in the biomolecular study of archaeological human tuberculosis. The specificity of any polymerase chain reaction directed at the MTBC cannot be assumed and, to confirm that an amplification is authentic, a sequencing strategy must be applied that allows characterisation of the PCR product. Any variations from the reference MTBC sequence must then be checked against sequence data for MOTT and other species to ensure that the product does actually derive from MTBC. Our results also illustrate the challenges faced when assembling MTBC genome sequences from ancient DNA samples, as misidentification of MOTT sequence reads as MTBC would lead to errors in the assembly. Identifying such errors would be particularly difficult, if not impossible, if the MOTT DNA content is greater than that of the authentic MTBC. The difficulty in identifying and excluding MOTT sequences is exacerbated by the fact that many MOTT are still uncharacterized and hence their sequence features are unknown

Some Properties of Noether Charge and a Proposal for Dynamical Black Hole Entropy

We consider a general, classical theory of gravity with arbitrary matter fields in $n$ dimensions, arising from a diffeomorphism invariant Lagrangian, \bL. We first show that \bL always can be written in a ``manifestly covariant" form. We then show that the symplectic potential current $(n-1)$-form, $\th$, and the symplectic current $(n-1)$-form, \om, for the theory always can be globally defined in a covariant manner. Associated with any infinitesimal diffeomorphism is a Noether current $(n-1)$-form, \bJ, and corresponding Noether charge $(n-2)$-form, \bQ. We derive a general ``decomposition formula" for \bQ. Using this formula for the Noether charge, we prove that the first law of black hole mechanics holds for arbitrary perturbations of a stationary black hole. (For higher derivative theories, previous arguments had established this law only for stationary perturbations.) Finally, we propose a local, geometrical prescription for the entropy, $S_{dyn}$, of a dynamical black hole. This prescription agrees with the Noether charge formula for stationary black holes and their perturbations, and is independent of all ambiguities associated with the choices of \bL, $\th$, and \bQ. However, the issue of whether this dynamical entropy in general obeys a ``second law" of black hole mechanics remains open. In an appendix, we apply some of our results to theories with a nondynamical metric and also briefly develop the theory of stress-energy pseudotensors.Comment: 30 pages, LaTe

The application of optical coherence tomography to image subsurface tissue structure of Antarctic krill Euphausia superba

Many small open ocean animals, such as Antarctic krill, are an important part of marine ecosystems. To discover what will happen to animals such as krill in a changing ocean, experiments are run in aquaria where conditions can be controlled to simulate water characteristics predicted to occur in the future. The response of individual animals to changing water conditions can be hard to observe, and with current observation techniques it is very difficult to follow the progress of an individual animal through its life. Optical coherence tomography (OCT) is an optical imaging technique that allows images at high resolution to be obtained from depths up to a few millimeters inside biological specimens. It is compatible with in vivo imaging and can be used repeatedly on the same specimens. In this work, we show how OCT may be applied to post mortem krill samples and how important physiological data such as shell thickness and estimates of organ volume can be obtained. Using OCT we find an average value for the thickness of krill exoskeleton to be (30±4) µm along a 1 cm length of the animal body. We also show that the technique may be used to provide detailed imagery of the internal structure of a pleopod joint and provide an estimate for the heart volume of (0.73±0.03) mm3

Kuru and its contribution to medicine

The solution of kuru led us to the solution of Creutzfeldt–Jakob disease and to the elucidation, in humans and other species, of previously unknown mechanisms of infection. These require very close three-dimensional matching, which determines infectious nucleant or prion activity. Evidence for nucleation processes is found widely in the organic and inorganic worlds and in the interactions between them: in the formation of amyloid fibrils; in the biochemistry of silicon; in cave formations deep in the Earth; and in outer space. Kuru in its location in Papua New Guinea has also led to an understanding of the cultural achievements of the Palaeo-Melanesians, with deep roots in human history

Spectral Statistics of the Two-Body Random Ensemble Revisited

Using longer spectra we re-analyze spectral properties of the two-body random ensemble studied thirty years ago. At the center of the spectra the old results are largely confirmed, and we show that the non-ergodicity is essentially due to the variance of the lowest moments of the spectra. The longer spectra allow to test and reach the limits of validity of French's correction for the number variance. At the edge of the spectra we discuss the problems of unfolding in more detail. With a Gaussian unfolding of each spectrum the nearest neighbour spacing distribution between ground state and first exited state is shown to be stable. Using such an unfolding the distribution tends toward a semi-Poisson distribution for longer spectra. For comparison with the nuclear table ensemble we could use such unfolding obtaining similar results as in the early papers, but an ensemble with realistic splitting gives reasonable results if we just normalize the spacings in accordance with the procedure used for the data.Comment: 11 pages, 7 figure

Black Hole Entropy is Noether Charge

We consider a general, classical theory of gravity in $n$ dimensions, arising from a diffeomorphism invariant Lagrangian. In any such theory, to each vector field, $\xi^a$, on spacetime one can associate a local symmetry and, hence, a Noether current $(n-1)$-form, ${\bf j}$, and (for solutions to the field equations) a Noether charge $(n-2)$-form, ${\bf Q}$. Assuming only that the theory admits stationary black hole solutions with a bifurcate Killing horizon, and that the canonical mass and angular momentum of solutions are well defined at infinity, we show that the first law of black hole mechanics always holds for perturbations to nearby stationary black hole solutions. The quantity playing the role of black hole entropy in this formula is simply $2 \pi$ times the integral over $\Sigma$ of the Noether charge $(n-2)$-form associated with the horizon Killing field, normalized so as to have unit surface gravity. Furthermore, we show that this black hole entropy always is given by a local geometrical expression on the horizon of the black hole. We thereby obtain a natural candidate for the entropy of a dynamical black hole in a general theory of gravity. Our results show that the validity of the ``second law" of black hole mechanics in dynamical evolution from an initially stationary black hole to a final stationary state is equivalent to the positivity of a total Noether flux, and thus may be intimately related to the positive energy properties of the theory. The relationship between the derivation of our formula for black hole entropy and the derivation via ``Euclidean methods" also is explained.Comment: 16 pages, EFI 93-4

Preschool hearing, speech, language, and vision screening

Child health surveillance is part of a broad set of activities, the objective of which is to reduce childhood disability by identifying and managing a multiplicity of conditions at an early stage.1 This includes several screening programmes which are focused on the detection of specific disorders. The value of surveillance and monitoring of child health, growth, and development used to be regarded as self evident. The Hall reports emphasised the importance of applying rigorous criteria for screening programmes in community child health and helped to produce a more coordinated national programme.2–4 However, there is still considerable variation both within and between health authorities in the content, timing, and delivery of child health surveillance. This paper summarises the research evidence presented in a recent issue of the Effective Health Care bulletin, Vol 4, No 2; April, 1998 about hearing, speech and language, and vision screening and is based on recent systematic reviews commissioned by the National Health Service (NHS) Health Technology Assessment Programme. Details of the methods and the results are available in the full reports.5–

Diversity of a wall-associated kinase gene in wild and cultivated barley

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour

Reconstructing the 3-D Trajectories of CMEs in the Inner Heliosphere

A method for the full three-dimensional (3-D) reconstruction of the trajectories of coronal mass ejections (CMEs) using Solar TErrestrial RElations Observatory (STEREO) data is presented. Four CMEs that were simultaneously observed by the inner and outer coronagraphs (COR1 and 2) of the Ahead and Behind STEREO satellites were analysed. These observations were used to derive CME trajectories in 3-D out to ~15Rsun. The reconstructions using COR1/2 data support a radial propagation model. Assuming pseudo-radial propagation at large distances from the Sun (15-240Rsun), the CME positions were extrapolated into the Heliospheric Imager (HI) field-of-view. We estimated the CME velocities in the different fields-of-view. It was found that CMEs slower than the solar wind were accelerated, while CMEs faster than the solar wind were decelerated, with both tending to the solar wind velocity.Comment: 17 pages, 10 figures, 1 appendi

Motion of Inertial Observers Through Negative Energy

Recent research has indicated that negative energy fluxes due to quantum coherence effects obey uncertainty principle-type inequalities of the form |\Delta E|\,{\Delta \tau} \lprox 1\,. Here $|\Delta E|$ is the magnitude of the negative energy which is transmitted on a timescale $\Delta \tau$. Our main focus in this paper is on negative energy fluxes which are produced by the motion of observers through static negative energy regions. We find that although a quantum inequality appears to be satisfied for radially moving geodesic observers in two and four-dimensional black hole spacetimes, an observer orbiting close to a black hole will see a constant negative energy flux. In addition, we show that inertial observers moving slowly through the Casimir vacuum can achieve arbitrarily large violations of the inequality. It seems likely that, in general, these types of negative energy fluxes are not constrained by inequalities on the magnitude and duration of the flux. We construct a model of a non-gravitational stress-energy detector, which is rapidly switched on and off, and discuss the strengths and weaknesses of such a detector.Comment: 18pp + 1 figure(not included, available on request), in LATEX, TUPT-93-