Animal remains from Neolithic Lameiras, Sintra: the earliest domesticated sheep, goat, cattle and pigs in Portugal and some notes on their evolution

The fauna of Neolithic Lameiras includes abundant sheep. Many could be securely identified by applying criteria described by the late Joachim Boessneck as well as metrical methods. Sheep bones from Early Neolithic contexts, several dated directly via 14C, pinpoint the arrival here, 5450 cal BC, of this exotic animal three thousand years after its domestication 5000 km to the east. Thus sheep were transported at a rate of 1,6 km per year – considerably faster than suggested by the ‘wave of advance’ theory. It therefore seems probable that part of the journey was undertaken by ship. Most of the mammal remains identified at Lameiras belonged to domesticated forms and besides sheep and some goat, they include cattle and pig. Zooarchaeologically there is little difference between Early and Late Neolithic. However the Neolithic spectrum of species contrasts with that from a small assemblage in the underlying Mousterian level as well as other pre-Neolithic assemblages in Portugal. It is possible that in southern Portugal the adoption of animal husbandry was sudden. Measurements of the remains of Canis, Bos, Ovis, Capra and Sus compared with an increasingly large corpus of data from the South-Western part of the Iberian Peninsula indicate several occasions when these animals underwent size changes. Bos, Capra and Canis were considerably larger in the Pleistocene – a size difference now documented in other regions. Besides a Pleistocene-Holocene reduction in size, they underwent a further diminution associated with their domestication. It is possible that aurochs and wild boar recovered some of their former size after the Neolithic, perhaps due to a relaxation of hunting pressure after the Mesolithic. Domestic sheep, goats and cattle increased in size in more recent times perhaps reflecting Moslem and Christian improvements.La fauna neolítica de Lameiras incluye numerosas ovejas. Muchas pudieron ser identificadas al aplicar los criterios descritos por el fallecido J. Boessneck y por métodos métricos. Los huesos de oveja de los contextos del Neolítico temprano, algunos datados a través del C14, apuntan a la llegada de esta especie hacia el 5.450 cal. D.C. 3.000 años después de su domesticación a 5.000 km de distancia hacia el Oriente. De este modo, las ovejas fueron transportadas a un ritmo de 1,6 km al año lo cual es considerablemente más rápido que lo sugerido por la llamada teoría de la “ola de avance”. Por ello, parece probable que parte de este viaje se haya llevado a cabo en barco. La mayoría de los restos de mamíferos identificados en Lameiras representan formas domésticas que además de la oveja y alguna cabra incorporan vacuno y porcino. Desde un punto de vista zooarqueológico existe poca diferencia entre el Neolítico temprano y tardío. Sin embargo, el espectro de especies neolíticas contrasta con el de una pequeña muestra en el nivel musteriense que subyace a estos depósitos así como a otras muestras preneoliticas en Portugal. Es posible que en el sur de Portugal la adopción de la práctica ganadera haya sido rápida. Los valores de los restos de Canis, Bos, Ovis, Capra y Sus apuntan a varios momentos en los cuales los animales sufrieron cambios de tamaño, datos que encajan con el corpus osteométrico que se viene recopilando para el sector sudoccidental de la Península Ibérica. Bos, Capra y Canis eran considerablemente más grandes en el Pleistoceno, una diferencia de talla ahora documentada en otras regiones. Además de la reducción de tamaño durante la transición Pleistoceno-Holoceno estas especies sufrieron otra adicional asociada con su proceso de domesticación. Es posible que tanto uros como jabalíes recuperasen parte de sus antiguas tallas al concluir el Neolítico. Quizás ello se deba a una relajación en la presión de caza operada tras el Mesolítico. Las ovejas, cabras y vacas domésticas aumentaron de tamaño en épocas más recientes reflejando posiblemente mejoras en las prácticas pecuarias de musulmanes y cristianos.info:eu-repo/semantics/publishedVersio

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Massive Star Formation

This chapter reviews progress in the field of massive star formation. It focuses on evidence for accretion and current models that invoke high accretion rates. In particular it is noted that high accretion rates will cause the massive young stellar object to have a radius much larger than its eventual main sequence radius throughout much of the accretion phase. This results in low effective temperatures which may provide the explanation as to why luminous young stellar objects do not ionized their surroundings to form ultra-compact H II regions. The transition to the ultra-compact H II region phase would then be associated with the termination of the high accretion rate phase. Objects thought to be in a transition phase are discussed and diagnostic diagrams to distinguish between massive young stellar objects and ultra-compact H II regions in terms of line widths and radio luminosity are presented.Comment: 21 pages, 6 figures, chapter in Diffuse Matter from Star Forming Regions to Active Galaxies - A Volume Honouring John Dyson, Edited by T.W. Hartquist, J. M. Pittard, and S. A. E. G. Falle. Series: Astrophysics and Space Science Proceedings. Springer Dordrecht, 2007, p.6

General Overview of Black Hole Accretion Theory

I provide a broad overview of the basic theoretical paradigms of black hole accretion flows. Models that make contact with observations continue to be mostly based on the four decade old alpha stress prescription of Shakura & Sunyaev (1973), and I discuss the properties of both radiatively efficient and inefficient models, including their local properties, their expected stability to secular perturbations, and how they might be tied together in global flow geometries. The alpha stress is a prescription for turbulence, for which the only existing plausible candidate is that which develops from the magnetorotational instability (MRI). I therefore also review what is currently known about the local properties of such turbulence, and the physical issues that have been elucidated and that remain uncertain that are relevant for the various alpha-based black hole accretion flow models.Comment: To be published in Space Science Reviews and as hard cover in the Space Sciences Series of ISSI: The Physics of Accretion on to Black Holes (Springer Publisher

Cosmological perturbations in SFT inspired non-local scalar field models

We study cosmological perturbations in models with a single non-local scalar field originating from the string field theory description of the rolling tachyon dynamics. We construct the equation for the energy density perturbations of the non-local scalar field and explicitly prove that for the free field it is identical to a system of local cosmological perturbation equations in a particular model with multiple (maybe infinitely many) local free scalar fields.Comment: 21 pages, no figures, v3: presentation improved, results unchanged, references adde

Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic

Integrated motor drives: state of the art and future trends

With increased need for high power density, high efficiency and high temperature capabilities in Aerospace and Automotive applications, Integrated Motor Drives (IMD) offers a potential solution. However, close physical integration of the converter and the machine may also lead to an increase in components temperature. This requires careful mechanical, structural and thermal analysis; and design of the IMD system. This paper reviews existing IMD technologies and their thermal effects on the IMD system. The effects of the power electronics (PE) position on the IMD system and its respective thermal management concepts are also investigated. The challenges faced in designing and manufacturing of an IMD along with the mechanical and structural impacts of close physical integration is also discussed and potential solutions are provided. Potential converter topologies for an IMD like the Matrix converter, 2-level Bridge, 3-level NPC and Multiphase full bridge converters are also reviewed. Wide band gap devices like SiC and GaN and their packaging in power modules for IMDs are also discussed. Power modules components and packaging technologies are also presented

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy