ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures

ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. These proteins are of interest to a wide range of biologists due to their diverse applications in medicine, neuroscience, pharmacology, drug discovery and agriculture. ArachnoServer currently manages 1078 protein sequences, 759 nucleic acid sequences and 56 protein structures. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface. The following significant improvements have been implemented in version 2.0: (i) the average and monoisotopic molecular masses of both the reduced and oxidized form of each mature toxin are provided; (ii) the advanced search feature now enables searches on the basis of toxin mass, external database accession numbers and publication date in ArachnoServer; (iii) toxins can now be browsed on the basis of their phyletic specificity; (iv) rapid BLAST searches based on the mature toxin sequence can be performed directly from the toxin card; (v) private silos can be requested from research groups engaged in venoms-based research, enabling them to easily manage and securely store data during the process of toxin discovery; and (vi) a detailed user manual is now available

A cognitive framework for object recognition with application to autonomous vehicles

Autonomous vehicles or self-driving cars are capable of sensing the surrounding environment so they can navigate roads without human input. Decisions are constantly made on sensing, mapping and driving policy using machine learning techniques. Deep Learning – massive neural networks that utilize the power of parallel processing – has become a popular choice for addressing the complexities of real time decision making. This method of machine learning has been shown to outperform alternative solutions in multiple domains, and has an architecture that can be adapted to new problems with relative ease. To harness the power of Deep Learning, it is necessary to have large amounts of training data that are representative of all possible situations the system will face. To successfully implement situational awareness in driverless vehicles, it is not possible to exhaust all possible training examples. An alternative method is to apply cognitive approaches to perception, for situations the autonomous vehicles will face. Cognitive approaches to perception work by mimicking the process of human intelligence – thereby permitting a machine to react to situations it has not previously experienced. This paper proposes a novel cognitive approach for object recognition. The proposed cognitive object recognition algorithm, referred to as Recognition by Components, is inspired by the psychological studies pertaining to early childhood development. The algorithm works by breaking down images into a series of primitive forms such as square, triangle, circle or rectangle and memory based aggregation to identify objects. Experimental results suggest that Recognition by Component algorithm performs significantly better than algorithms that require large amounts of training data

Post-operative Aspergillus mediastinitis in a man who was immunocompetent: a case report

<p>Abstract</p> <p>Introduction</p> <p><it>Aspergillus </it>spp. infections mainly affect patients who are immunocompromised, and are extremely rare in immunocompetent individuals.</p> <p>Case presentation</p> <p><it>Aspergillus </it>post-operative mediastinitis is considered to be a devastating infection, usually affecting patients undergoing cardiothoracic surgery with specific predisposing factors. We describe the case of an immunocompetent 68-year-old Caucasian man with severe chronic thromboembolic pulmonary hypertension, who underwent pulmonary thromboendarterectomy and developed post-operative mediastinitis due to <it>Aspergillus flavus</it>. The environmental control did not reveal the source of <it>A. flavus </it>infection and, despite combined antifungal therapy, our patient died as a result of septic shock and multiple organ failure.</p> <p>Conclusion</p> <p><it>Aspergillus </it>mediastinitis mainly affects patients after cardiosurgery operations with predisposing factors, and it is unusual in patients who are immunocompetent. The identification of the <it>Aspergillus </it>spp. source is often difficult, and there are no guidelines for the administration of pre-emptive therapy in this population of at-risk patients.</p

Lithic technological responses to Late Pleistocene glacial cycling at Pinnacle Point Site 5-6, South Africa

There are multiple hypotheses for human responses to glacial cycling in the Late Pleistocene, including changes in population size, interconnectedness, and mobility. Lithic technological analysis informs us of human responses to environmental change because lithic assemblage characteristics are a reflection of raw material transport, reduction, and discard behaviors that depend on hunter-gatherer social and economic decisions. Pinnacle Point Site 5-6 (PP5-6), Western Cape, South Africa is an ideal locality for examining the influence of glacial cycling on early modern human behaviors because it preserves a long sequence spanning marine isotope stages (MIS) 5, 4, and 3 and is associated with robust records of paleoenvironmental change. The analysis presented here addresses the question, what, if any, lithic assemblage traits at PP5-6 represent changing behavioral responses to the MIS 5-4-3 interglacial-glacial cycle? It statistically evaluates changes in 93 traits with no a priori assumptions about which traits may significantly associate with MIS. In contrast to other studies that claim that there is little relationship between broad-scale patterns of climate change and lithic technology, we identified the following characteristics that are associated with MIS 4: increased use of quartz, increased evidence for outcrop sources of quartzite and silcrete, increased evidence for earlier stages of reduction in silcrete, evidence for increased flaking efficiency in all raw material types, and changes in tool types and function for silcrete. Based on these results, we suggest that foragers responded to MIS 4 glacial environmental conditions at PP5-6 with increased population or group sizes, 'place provisioning', longer and/or more intense site occupations, and decreased residential mobility. Several other traits, including silcrete frequency, do not exhibit an association with MIS. Backed pieces, once they appear in the PP5-6 record during MIS 4, persist through MIS 3. Changing paleoenvironments explain some, but not all temporal technological variability at PP5-6.Social Science and Humanities Research Council of Canada; NORAM; American-Scandinavian Foundation; Fundacao para a Ciencia e Tecnologia [SFRH/BPD/73598/2010]; IGERT [DGE 0801634]; Hyde Family Foundations; Institute of Human Origins; National Science Foundation [BCS-9912465, BCS-0130713, BCS-0524087, BCS-1138073]; John Templeton Foundation to the Institute of Human Origins at Arizona State Universit

A bone grease processing station at the Mitchell Prehistoric Indian Village: archaeological evidence for the exploitation of bone fats

© Association for Environmental Archaeology 2015. Author's accepted manuscript version deposited in accordance with SHERPA RoMEO guidelines. The definitive version is available at http://www.maneyonline.com/doi/abs/10.1179/1749631414Y.0000000035.Recent excavations at the Mitchell Prehistoric Indian Village, an Initial Middle Missouri site in Mitchell, South Dakota have revealed a large, clay-lined feature filled with fractured and fragmented bison bones. Fracture and fragmentation analysis, along with taphonomic evidence, suggests that the bones preserved within the feature represent evidence of prehistoric bone marrow and bone grease exploitation. Further, the character of the feature suggests that it served as a bone grease processing station. Bone fat exploitation is an activity that is frequently cited as a causal explanation for the nature of many fractured and fragmented bone assemblages in prehistory, and zooarchaeological assemblages have frequently been studied as evidence of bone fat exploitation. The Mitchell example provides some of the first direct, in-situ archaeological evidence of a bone grease processing feature, and this interpretation is sustained by substantial analytical evidence suggesting bone fat exploitation. This new evidence provides a clearer concept of the nature of bone fat exploitation in prehistory as well as an indication of the scale and degree to which bone grease exploitation occurred at the Mitchell site. Finally, this research demonstrates the importance of careful zooarchaeological and taphonomic analysis for the interpretation of both artifactual remains as well as archaeological features

Human biogeography and faunal exploitation in Diamante River basin, central western Argentina

A biogeographic model used to describe human peopling of southern Mendoza, central western Argentina, proposed an intensification process activated by an increase in population growth rate during the Late Holocene. During this process, high-ranked resources at the surroundings of residential camps were depleted, and hunter–gatherers broadened their diet by incorporating a larger number of low-ranked prey and domesticated plant resources. In this paper, we evaluate an alternative hypothesis, focusing on zooarchaeological data from the Diamante River basin. The results show that faunal resource intensification does not appear to have occurred in the Diamante River basin during the Late Holocene. Faunal consumption in Diamante River basin mainly reflects the local fauna in each ecological zone. The data do not show a lack of higher ranked resources. We suggest it is more likely that the demographic increase was not significant enough to cause an impact on the faunal resources. The archaeological evidence should be improved and analysed in smaller scales to continue with the intensification debate.Fil: Otaola, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Giardina, Miguel Angel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales; ArgentinaFil: Franchetti, Fernando Ricardo. University of Pittsburgh at Johnstown; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Estimating population size, density and dynamics of Pre-Pottery Neolithic villages in the central and southern Levant: an analysis of Beidha, southern Jordan

The Pre-Pottery Neolithic (PPN) of the central and southern Levant played an integral role in the Neolithic Demographic Transition (NDT) from mobile hunter-gatherer to village-based, agro-pastoralist societies. An understanding of population dynamics is essential for reconstructing the trajectories of these early village societies. However, few investigations have produced absolute estimates of population parameters for these villages and those which have base estimates on a limited methodological framework. This research examines the methodological and theoretical basis for existing estimates, and explores a range of methodologies in order to derive more empirically-robust demographic data. Results reveal that commonly utilized methodologies and population density coefficients employed for estimating PPN village populations require re-evaluation. This article presents the application of methodologies to the PPNB site of Beidha in southern Jordan

Robustness assessment of the ‘cooperation under resource pressure’ (CURP) model: Insights on resource availability and sharing practices among hunter-gatherers

A well-known challenge in archaeological research is the exploration of the social mechanisms that hunter-gatherers may have implemented throughout history to deal with changes in resource availability. The agent-based model (ABM) ‘cooperation under resource pressure’ (CURP) was conceived to explore food stress episodes in societies lacking a food preservation technology. It was particularly aimed at understanding how cooperative behaviours in the form of food sharing practices emerge, increase and may become the prevailing strategy in relation to changes in resource availability and expectancy of reciprocity. CURP’s main outcome is the identification of three regimes of behaviour depending on the stress level. In this work, the model’s robustness to the original selection mechanism (random tournament) is assessed, as different dynamics can lead to different persistent regimes. For that purpose, three other selection mechanisms are implemented and evaluated, to identify the prevailing states of the system. Results show that the three regimes are robust irrespective of the analysed dynamics. We consequently examine in more detail the long-term archaeological implications that these results may have.Spanish Ministry of Economy and Competitiveness (former Ministry of Science and Innovation): SimulPast Project (CSD2010- 00034 CONSOLIDER-INGENIO 2010), HAR2009-06996 and CULM Project (HAR2016- 77672-P); from the Argentine National Scientific and Technical Research Council (CONICET): Project PIP-0706; from the Wenner-Gren Foundation for Anthropological Research: Project GR7846; from the project H2020 FET OPEN RIA IBSEN/662725 and from the European Social Fund as one of the authors is the recipient of a predoctoral grant from the Department of Education of Junta de Castilla y León (Spain)