Zooarchaeology at the Niah Caves, Sarawak:Context and Research Issues INTRODUCTION

Extensive archaeological excavations in the Niah Caves (Sarawak, Malaysian Borneo) over the past 50 years have produced perhaps 750 000 fragments of vertebrate bone, one of the largest faunal assemblages in the region, This paper introduces a series of research studies examining different aspects of the Niah fauna, and discusses how they are contributing to, and shaping, regional research agendas relating to prehistoric environments and societies in Island Southeast Asia. Zooarchaeology has traditionally had a rather 'Cinderella' status here, but the ongoing programme of study of the Niah Caves fauna is demonstrating the remarkable potential of this material to address questions of Pleistocene and Holocene climate and environment, biodiversity, human activities within caves, people's engagement with the landscapes they inhabited as foragers and farmers, and the nature of the transition from foraging to farming. Copyright (C) 2009 John Wiley & Sons, Ltd.

The 'human revolution' in lowland tropical Southeast Asia:the antiquity and behavior of anatomically modern humans at Niah Cave (Sarawak, Borneo)

Recent research in Europe, Africa, and Southeast Asia suggests that we can no longer assume a direct and exclusive link between anatomically modern humans and behavioral modernity (the 'human revolution'), and assume that the presence of either one implies the presence of the other: discussions of the emergence of cultural complexity have to proceed with greater scrutiny of the evidence on a site-by-site basis to establish secure associations between the archaeology present there and the hominins who created it. This paper presents one such case study: Niah Cave in Sarawak on the island of Borneo, famous for the discovery in 1958 in the West Mouth of the Great Cave of a modern human skull, the 'Deep Skull,' controversially associated with radiocarbon dates of ca. 40,000 years before the present. A new chronostratigraphy has been developed through a re-investigation of the lithostratigraphy left by the earlier excavations, AMS-dating using three different comparative pre-treatments including ABOX of charcoal, and U-series using the Diffusion-Absorption model applied to fragments of bones from the Deep Skull itself. Stratigraphic reasons for earlier uncertainties about the antiquity of the skull are examined, and it is shown not to be an `intrusive' artifact. It was probably excavated from fluvial-pond-desiccation deposits that accumulated episodically in a shallow basin immediately behind the cave entrance lip, in a climate that ranged from times of comparative aridity with complete desiccation, to episodes of greater surface wetness, changes attributed to regional climatic fluctuations. Vegetation outside the cave varied significantly over time, including wet lowland forest, montane forest, savannah, and grassland. The new dates and the lithostratigraphy relate the Deep Skull to evidence of episodes of human activity that range in date from ca. 46,000 to ca. 34,000 years ago. Initial investigations of sediment scorching, pollen, palynomorphs, phytoliths, plant macrofossils, and starch grains recovered from existing exposures, and of vertebrates from the current and the earlier excavations, suggest that human foraging during these times was marked by habitat-tailored hunting technologies, the collection and processing of toxic plants for consumption, and, perhaps, the use of fire at some forest-edges. The Niah evidence demonstrates the sophisticated nature of the subsistence behavior developed by modern humans to exploit the tropical environments that they encountered in Southeast Asia, including rainforest. (c) 2006 Elsevier Ltd. All rights reserved.

Bone tool analysis

This article examines the osseous technologies that can be created from animal skeletons. 'Tool' status is accorded to a skeletal element or fragment that has been modified subsequent to its isolation from the carcass. Such anthropic adaptation may be deliberate (e.g., through manufacture) and/or appear as a result of utilization, and is granted in instances where these details cannot otherwise be ascribed to alternative nonanthropic causes. Implements can display a combination of traces from both human and natural sources and as such the study of them involves both zooarchaeological (i.e., via animal ecology, hunting, and butchery) and technological analysis.... As an exemplar of this, the following discussion will present some of the similarities and differences that exist between osseous and lithic raw materials and tool-blank production, and will situate both in an operational sequence of animal procurement and processing. It will then give an account of principal manufacturing techniques, methods for establishing tool function, and the phenomenon of 'pseudo tools'. © 2008 Copyright © 2008 Elsevier Inc.

The early exploitation of Southeast Asian mangroves:Bone technology from caves and open sites

This paper focuses on the contribution that the study of bone technology is making to the understanding of early tropical subsistence in Southeast Asia. Newly completed research suggests that during the period from the terminal Pleistocene to mid Holocene, bone tools may have featured prominently in coastal subsistence. There are indications that this technology may have had a particular association with hunting and gathering in the mangrove forests that proliferated along many coasts during this period. The study of these tools thus represents a rare chance to examine prehistoric extractive technologies, which are generally agreed to have been predominantly made on organic, nonpreserving media. The evidence presented also suggests that prehistoric foragers from this region possessed a good working understanding of the mechanical properties of bone and used bone implements where conditions and needs suited the parameters of this material. © 2005 by the University of Hawai'i Press.

Observational Constraints on the Progenitors of Core-Collapse Supernovae: The Case for Missing High-Mass Stars

Over the last 15 years, the supernova community has endeavoured to directly identify progenitor stars for core-collapse supernovae discovered in nearby galaxies. These precursors are often visible as resolved stars in high-resolution images from space-and ground-based telescopes. The discovery rate of progenitor stars is limited by the local supernova rate and the availability and depth of archive images of galaxies, with 18 detections of precursor objects and 27 upper limits. This review compiles these results (from 1999 to 2013) in a distance-limited sample and discusses the implications of the findings. The vast majority of the detections of progenitor stars are of type II-P, II-L, or IIb with one type Ib progenitor system detected and many more upper limits for progenitors of Ibc supernovae (14 in all). The data for these 45 supernovae progenitors illustrate a remarkable deficit of high-luminosity stars above an apparent limit of log L/L-circle dot similar or equal to 5.1 dex. For a typical Salpeter initial mass function, one would expect to have found 13 high-luminosity and high-mass progenitors by now. There is, possibly, only one object in this time-and volume-limited sample that is unambiguously high-mass (the progenitor of SN2009ip) although the nature of that supernovae is still debated. The possible biases due to the influence of circumstellar dust, the luminosity analysis, and sample selection methods are reviewed. It does not appear likely that these can explain the missing high-mass progenitor stars. This review concludes that the community's work to date shows that the observed populations of supernovae in the local Universe are not, on the whole, produced by high-mass (M greater than or similar to 18 M-circle dot) stars. Theoretical explosions of model stars also predict that black hole formation and failed supernovae tend to occur above an initial mass of M similar or equal to 18 M-circle dot. The models also suggest there is no simple single mass division for neutron star or black-hole formation and that there are islands of explodability for stars in the 8-120 M-circle dot range. The observational constraints are quite consistent with the bulk of stars above M similar or equal to 18 M-circle dot collapsing to form black holes with no visible supernovae.

Massive stars exploding in a He-rich circumstellar medium - VI. Observations of two distant Type Ibn supernova candidates discovered by La Silla-QUEST

We present optical observations of the peculiar stripped-envelope supernovae (SNe) LSQ12btw and LSQ13ccw discovered by the La Silla-QUEST survey. LSQ12btw reaches an absolute peak magnitude of M-g = -19.3 +/- 0.2, and shows an asymmetric light curve. Stringent pre-discovery limits constrain its rise time to maximum light to less than 4 d, with a slower post-peak luminosity decline, similar to that experienced by the prototypical SN Ibn 2006jc. LSQ13ccw is somewhat different: while it also exhibits a very fast rise to maximum, it reaches a fainter absolute peak magnitude (M-g =-18.4 +/- 0.2), and experiences an extremely rapid post-peak decline similar to that observed in the peculiar SN Ib 2002bj. A stringent pre-discovery limit and an early marginal detection of LSQ13ccw allow us to determine the explosion time with an uncertainty of +/- 1 d. The spectra of LSQ12btw show the typical narrow He I emission lines characterizing Type Ibn SNe, suggesting that the SN ejecta are interacting with He-rich circumstellar material. The He I lines in the spectra of LSQ13ccw exhibit weak narrow emissions superposed on broad components. An unresolved H alpha line is also detected, suggesting a tentative Type Ibn/IIn classification. As for other SNe Ibn, we argue that LSQ12btw and LSQ13ccw likely result from the explosions of Wolf-Rayet stars that experienced instability phases prior to core collapse. We inspect the host galaxies of SNe Ibn, and we show that all of them but one are hosted in spiral galaxies, likely in environments spanning a wide metallicity range.

Massive stars exploding in a He-rich circumstellar medium - IV. Transitional Type Ibn supernovae

We present ultraviolet, optical and near-infrared data of the Type Ibn supernovae (SNe) 2010al and 2011hw. SN 2010al reaches an absolute magnitude at peak of M-R = -18.86 +/- 0.21. Its early light curve shows similarities with normal SNe Ib, with a rise to maximum slower than most SNe Ibn. The spectra are dominated by a blue continuum at early stages, with narrow P-Cygni He I lines indicating the presence of a slow-moving, He-rich circumstellar medium. At later epochs, the spectra well match those of the prototypical SN Ibn 2006jc, although the broader lines suggest that a significant amount of He was still present in the stellar envelope at the time of the explosion. SN 2011hw is somewhat different. It was discovered after the first maximum, but the light curve shows a double peak. The absolute magnitude at discovery is similar to that of the second peak (M-R = -18.59 +/- 0.25), and slightly fainter than the average of SNe Ibn. Though the spectra of SN 2011hw are similar to those of SN 2006jc, coronal lines and narrow Balmer lines are clearly detected. This indicates substantial interaction of the SN ejecta with He-rich, but not H-free, circumstellar material. The spectra of SN 2011hw suggest that it is a transitional SN Ibn/IIn event similar to SN 2005la. While for SN 2010al the spectrophotometric evolution favours a H-deprived Wolf-Rayet progenitor (of WN-type), we agree with the conclusion of Smith et al. that the precursor of SN 2011hw was likely in transition from a luminous blue variable to an early Wolf-Rayet (Ofpe/WN9) stage.

LSQ14bdq: a type Ic Super-luminous Supernova with a double-peaked light curve

We present data for LSQ14bdq, a hydrogen-poor super-luminous supernova (SLSN) discovered by the La Silla QUEST survey and classified by the Public ESO Spectroscopic Survey of Transient Objects. The spectrum and light curve are very similar to slow-declining SLSNe such as PTF12dam. However, detections within ∼1 day after explosion show a bright and relatively fast initial peak, lasting for ∼15 days, prior to the usual slow rise to maximum light. The broader, main peak can be fit with either central engine or circumstellar interaction models. We discuss the implications of the precursor peak in the context of these models. It is too bright and narrow to be explained as a normal ⁵⁶Ni-powered SN, and we suggest that interaction models may struggle to fit the two peaks simultaneously. We propose that the initial peak may arise from the post-shock cooling of extended stellar material, and reheating by a central engine drives the second peak. In this picture, we show that an explosion energy of ∼2 × 10⁵² erg and a progenitor radius of a few hundred solar radii would be required to power the early emission. The competing engine models involve rapidly spinning magnetars (neutron stars) or fallback onto a central black hole. The prompt energy required may favor the black hole scenario. The bright initial peak may be difficult to reconcile with a compact Wolf-Rayet star as a progenitor since the inferred energies and ejected masses become unphysical.

On the progenitor of the Type Ic SN 2013dk in the Antennae galaxies

We report the results of our search for the progenitor candidate of SN 2013dk, a Type Ic supernova (SN) that exploded in the Antennae galaxy system. We compare pre-explosion Hubble Space Telescope (HST) archival images with SN images obtained using adaptive optics at the ESO Very Large Telescope. We isolate the SN position to within 3σ uncertainty radius of 0.02 arcsec and show that there is no detectable point source in any of the HST filter images within the error circle. We set an upper limit to the absolute magnitude of the progenitor to be MF555W ≳ -5.7, which does not allow Wolf-Rayet (WR) star progenitors to be ruled out. A bright source appears 0.17 arcsec away, which is either a single bright supergiant or compact cluster, given its absolute magnitude of MF555W = -9.02 ± 0.28 extended wings and complex environment. However, even if this is a cluster, the spatial displacement of SN 2013dk means that its membership is not assured. The strongest statement that we can make is that in the immediate environment of SN 2013dk (within 10 pc or so), we find no clear evidence of either a point source coincident with the SN or a young stellar cluster that could host a massive WR progenitor.

The death of massive stars - II. Observational constraints on the progenitors of Type Ibc supernovae

The progenitors of many Type II core-collapse supernovae (SNe) have now been identified directly on pre-discovery imaging. Here, we present an extensive search for the progenitors of Type Ibc SNe in all available pre-discovery imaging since 1998. There are 12 Type Ibc SNe with no detections of progenitors in either deep ground-based or Hubble Space Telescope archival imaging. The deepest absolute BVR magnitude limits are between -4 and - 5 mag. We compare these limits with the observed Wolf-Rayet population in the Large Magellanic Cloud and estimate a 16 per cent probability that we have failed to detect such a progenitor by chance. Alternatively, the progenitors evolve significantly before core-collapse or we have underestimated the extinction towards the progenitors. Reviewing the relative rates and ejecta mass estimates from light-curve modelling of Ibc SNe, we find both incompatible with Wolf-Rayet stars with initial masses >25 M⊙ being the only progenitors. We present binary evolution models that fit these observational constraints. Stars in binaries with initial masses ≲ 20 M⊙ lose their hydrogen envelopes in binary interactions to become low-mass helium stars. They retain a low-mass hydrogen envelope until ≈104 yr before core-collapse; hence, it is not surprising that Galactic analogues have been difficult to identify.

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH

BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples.

RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC outliers that might indicate microevents. These microevents were validated by the oligo platform results.

CONCLUSION: This article presents a genome-wide statistical validation of the oligo array platform on a large set of patient samples and demonstrates statistically its superiority over the BAC platform for the Identification of chromosomic events. Taking advantage of a large set of human samples treated by the two technologies, a statistical model has been developed to show that the BAC platform could also detect microevents.

Spatio-temporal feeding selection of red deer in a mountainous landscape

Understanding the dietary consumption and selection of wild populations of generalist herbivores is hampered by the complex array of factors. Here, we determine the influence of habitat, season, and animal density, sex, and age on the diet consumption and selection of 426 red deer (Cervus elaphus scoticus) culled in Fiordland National Park, New Zealand. Our site differs from studies elsewhere both in habitat (evergreen angiosperm-dominated forests) and the intensity of hunting pressures. We predicted that deer would not consume forage in proportion to its relative availability, and that dietary consumption would change among and within years in response to hunting pressures that would also limit opportunities for age and sex segregation. Using canonical correspondence analysis, we evaluated the relative importance of different drivers of variation in diet consumption assessed from gut content and related these to available forage in the environment. We found that altitude explained the largest proportion of variation in diet consumption, reflecting the ability of deer to alter their consumption and selection in relation to their foraging grounds. Grasses formed a high proportion of the diet consumption, even for deer culled several kilometres from the alpine grasslands. In the winter months, when the alpine grasslands were largely inaccessible, less grass was eaten and deer resorted to woody plants that were avoided in the summer months. Surprisingly, there were no significant dietary differences between adults and juveniles and only subtle differences between the sexes. Sex-based differences in diet consumption are commonly observed in ungulate species and we suggest that they may have been reduced in our study area owing to decreased heterogeneity in available forage as the diversity of palatable species decreased under high deer browsing pressures, or by intense hunting pressure. © 2009 The Authors. Journal compilation © 2009 Ecological Society of Australia.

Impacts of invasive browsers on demographic rates and forest structure in New Zealand

Background/Question/Methods

Assessing the large scale impact of deer populations on forest structure and composition is important because of their increasing abundance in many temperate forests. Deer are invasive animals and sometimes thought to be responsible for immense damage to New Zealand’s forests. We report demographic changes taking place among 40 widespread indigenous tree species over 20 years, following a period of record deer numbers in the 1950s and a period of extensive hunting and depletion of deer populations during the 1960s and 1970s.

Results/Conclusions

Across a network of 578 plots there was an overall 13% reduction in sapling density of our study species with most remaining constant and a few declining dramatically. The effect of suppressed recruitment when deer populations were high was evident in the small tree size class (30 – 80 mm dbh). Stem density decreased by 15% and species with the greatest annual decreases in small tree density were those which have the highest rates of sapling recovery in exclosures indicating that deer were responsible. Densities of large canopy trees have remained relatively stable. There were imbalances between mortality and recruitment rates for 23 of the 40 species, 7 increasing and 16 in decline. These changes were again linked with sapling recovery in exclosures; species which recovered most rapidly following deer exclusion had the greatest net recruitment deficit across the wider landscape, indicating recruitment suppression by deer as opposed to mortality induced by disturbance and other herbivores. Species are not declining uniformly across all populations and no species are in decline across their entire range. Therefore we predict that with continued deer presence some forests will undergo compositional changes but that none of the species tested will become nationally extinct.

Impacts of invasive browsers on demographic rates and forest structure in New Zealand. Available from: http://www.researchgate.net/publication/267285500_Impacts_of_invasive_browsers_on_demographic_rates_and_forest_structure_in_New_Zealand [accessed Oct 9, 2015].

Spitzer infrared spectrograph point source classification in the Small Magellanic Cloud

The Magellanic Clouds are uniquely placed to study the stellar contribution to dust emission. Individual stars can be resolved in these systems even in the mid-infrared, and they are close enough to allow detection of infrared excess caused by dust. We have searched the Spitzer Space Telescope data archive for all Infrared Spectrograph (IRS) staring-mode observations of the Small Magellanic Cloud (SMC) and found that 209 Infrared Array Camera (IRAC) point sources within the footprint of the Surveying the Agents of Galaxy Evolution in the Small Magellanic Cloud (SAGE-SMC) Spitzer Legacy programme were targeted, within a total of 311 staring-mode observations. We classify these point sources using a decision tree method of object classification, based on infrared spectral features, continuum and spectral energy distribution shape, bolometric luminosity, cluster membership and variability information. We find 58 asymptotic giant branch (AGB) stars, 51 young stellar objects, 4 post-AGB objects, 22 red supergiants, 27 stars (of which 23 are dusty OB stars), 24 planetary nebulae (PNe), 10 Wolf-Rayet stars, 3 H II regions, 3 R Coronae Borealis stars, 1 Blue Supergiant and 6 other objects, including 2 foreground AGB stars. We use these classifications to evaluate the success of photometric classification methods reported in the literature.