Tainted ores and the rise of tin bronzes in Eurasia, c. 6500 years ago

The earliest tin bronze artefacts in Eurasia are generally believed to have appeared in the Near East in the early third millennium BC. Here we present tin bronze artefacts that occur far from the Near East, and in a significantly earlier period. Excavations at Pločnik, a Vinča culture site in Serbia, recovered a piece of tin bronze foil from an occupation layer dated to the mid fifth millennium BC. The discovery prompted a reassessment of 14 insufficiently contextualised early tin bronze artefacts from the Balkans. They too were found to derive from the smelting of copper-tin ores. These tin bronzes extend the record of bronze making by c. 1500 years, and challenge the conventional narrative of Eurasian metallurgical development

Genetic variation and relationships among spring camelina (Camelina sativa, Brassicaceae) accessions of different origin

Camelina sativa L. is one of the oldest crops of the Brassicaceae family, first domesticated in the region of south-eastern Europe. It has regained interest as a very promising alternative oilseed crop with broad adaptability, a wide range of tolerances to pests and diseases, and low-input requirements. The genetic diversity in spring camelina proved to be limited, so the identification and characterization of genetic variations is considered very useful for development of efficient breeding programmes. The aim of the study was to use SSR markers in order to investigate genetic variation of twenty spring camelina accessions and their relatedness. Forty-five individual samples were taken from each accession and used for amplification of SSR markers P4C11, P6E4 and LIB19. The accessions expressed different levels of genetic variation, AMOVA (analysis of molecular variance) showed that 64% of the total genetic variation was attributed to variance within accessions. Genetic distance analysis indicated that there was overlapping in certain breeding programs and exchange of breeding germplasm

Incidence and molecular characterization of flavescence dorée and stolbur phytoplasmas in grapevine cultivars from different viticultural areas of Serbia

The presence and distribution of grapevine phytoplasmas was investigated from 2003 to 2005 in some of the most important viticultural areas of Serbia, considering in particular the susceptibility and sensitiveness of both local and imported grapevine cultivars. Both flavescence dorée (FD) and bois noir (BN) phytoplasmas were detected using molecular techniques. The presence of FD phytoplasma at the moment seems limited, while BN phytoplasma appears to be present in the majority of grape growing regions in Serbia. Field surveys demonstrate that grapevine yellows (GY) epidemics in the vineyards inspected in Serbia spread very fast, indeed the incidence of symptomatic plants increased considerably year by year. In particular, the average rate of FD diffusion increased from 45.5 to 93.0 % in the Sićevačko region, while the spread of BN resulted lower. The local cultivar 'Plovdina' appeared to be extremely sensitive to FD phytoplasma showing a percentage of infected plants ranging from 91 to 100 %. PCR-RFLP and phylogenetic analyses based on ribosomal protein (rp) and secY gene sequences performed on Serbian FD grapevine strains demonstrated their close relationship with the Italian FD-C strain present in north-east Italy. Based on both phylogenetic markers, Serbian FD strains represent a new distinct lineage and together with the FD-C strain form a major phylogenetic group within the elm yellows group.

Strong coupling regime of semiconductor quantum dot embedded in the nano-cavity

Photonic lattices represent suitable systems for investigation of wave propagation in periodic structures [1]. However, different unavoidable defects may arise either during their process of fabrication or as result of misusage, accidental damage, etc. Although undesirable in the first place, these imperfections enable the existence of different types of stable, localized defect modes [2]. In this paper, we investigate light propagation through composite photonic lattice composed of two identical linear and lossless lattices. The interface between them represents a geometric defect, while each lattice contains a single nonlinear defect that is placed symmetrically with respect to the interface. Depending on the input light beam parameters (its position, width and transverse tilt), the width of geometric defect, strength and position of the nonlinear defects, different dynamical regimes have been identified. These dynamical regimes are caused by the balance of photonic lattice potentials’ contributions originating from the presence of the geometric and two nonlinear defects. We have found numerically conditions under which dynamically stable bounded modes can exist in the area between nonlinear defects or between a nonlinear and a geometric defect. Various types of localized modes such as: two-hump, multi-hump, one- and multicomponent moving breathers localized at a certain area among defects have been observed. The parameters can be adjusted to capture light and to prevent light launched inside the area among defects to leave it, i.e. this corresponds to the appearance of the modes trapped inside this area. Since the configuration of the lattice prevents transmission of the light through the area confined by defects, these modes can formally be related to Fano resonances and Fano- blockade [3, 4]. When light is launched outside the area among defects, different dynamical regimes have been distinguished: total reflection, single and double partial reflection and full transmission through the area among defects. These numerical findings may lead to interesting applications such as blocking, filtering and transporting light beams through the optical medium. Photonic devices based on resonant tunneling such as waveguides interacting through the area between defects, may be applied as add-drop filters.V International School and Conference on Photonics and COST actions: MP1204, BM1205 and MP1205 and the Second international workshop "Control of light and matter waves propagation and localization in photonic lattices" : PHOTONICA2015 : book of abstracts; August 24-28, 2015; Belgrad

Machine learning integrates genomic signatures for subclassification beyond primary and secondary acute myeloid leukemia

Although genomic alterations drive the pathogenesis of acute myeloid leukemia (AML), traditional classifications are largely based on morphology, and prototypic genetic founder lesions define only a small proportion of AML patients. The historical subdivision of primary/de novo AML and secondary AML has shown to variably correlate with genetic patterns. The combinatorial complexity and heterogeneity of AML genomic architecture may have thus far precluded genomic-based subclassification to identify distinct molecularly defined subtypes more reflective of shared pathogenesis. We integrated cytogenetic and gene sequencing data from a multicenter cohort of 6788 AML patients that were analyzed using standard and machine learning methods to generate a novel AML molecular subclassification with biologic correlates corresponding to underlying pathogenesis. Standard supervised analyses resulted in modest cross-validation accuracy when attempting to use molecular patterns to predict traditional pathomorphologic AML classifications. We performed unsupervised analysis by applying the Bayesian latent class method that identified 4 unique genomic clusters of distinct prognoses. Invariant genomic features driving each cluster were extracted and resulted in 97% cross-validation accuracy when used for genomic subclassification. Subclasses of AML defined by molecular signatures overlapped current pathomorphologic and clinically defined AML subtypes. We internally and externally validated our results and share an open-access molecular classification scheme for AML patients. Although the heterogeneity inherent in the genomic changes across nearly 7000 AML patients was too vast for traditional prediction methods, machine learning methods allowed for the definition of novel genomic AML subclasses, indicating that traditional pathomorphologic definitions may be less reflective of overlapping pathogenesis

Atypical emotional anticipation in high-functioning autism

"Background: Understanding and anticipating others’ mental or emotional states relies on the processing of social cues, such as dynamic facial expressions. Individuals with high-functioning autism (HFA) may process these cues differently from individuals with typical development (TD) and purportedly use a ‘mechanistic’ rather than a ‘mentalistic’ approach, involving rule- and contingency-based interpretations of the stimuli. The study primarily aimed at examining whether the judgments of facial expressions made by individuals with TD and HFA would be similarly affected by the immediately preceding dynamic perceptual history of that face. A second aim was to explore possible differences in the mechanisms underpinning the perceptual judgments in the two groups. Methods: Twenty-two adults with HFA and with TD, matched for age, gender and IQ, were tested in three experiments in which dynamic, ‘ecologically valid’ offsets of happy and angry facial expressions were presented. Participants evaluated the expression depicted in the last frame of the video clip by using a 5-point scale ranging from slightly angry via neutral to slightly happy. Specific experimental manipulations prior to the final facial expression of the video clip allowed examining contributions of bottom-up mechanisms (sequential contrast/ context effects and representational momentum) and a top-down mechanism (emotional anticipation) to distortions in the perception of the final expression. Results: In experiment 1, the two groups showed a very similar perceptual bias for the final expression of joy-to-neutral and anger-to-neutral videos (overshoot bias). In experiment 2, a change in the actor’s identity during the clip removed the bias in the TD group, but not in the HFA group. In experiment 3, neutral-to-joy/anger-to-neutral sequences generated an undershoot bias (opposite to the overshoot) in the TD group, whereas no bias was observed in the HFA group. Conclusions: We argue that in TD individuals the perceptual judgments of other’s facial expressions were underpinned by an automatic emotional anticipation mechanism. In contrast, HFA individuals were primarily influenced by visual features, most notably the contrast between the start and end expressions, or pattern extrapolation. We critically discuss the proposition that automatic emotional anticipation may be induced by motor simulation of the perceived dynamic facial expressions and discuss its implications for autism.

GFAP-Driven GFP Expression in Activated Mouse Muller Glial Cells Aligning Retinal Blood Vessels Following Intravitreal Injection of AAV2/6 Vectors

Background: Muller cell gliosis occurs in various retinal pathologies regardless of the underlying cellular defect. Because activated Muller glial cells span the entire retina and align areas of injury, they are ideal targets for therapeutic strategies, including gene therapy.Methodology/Principal Findings: We used adeno-associated viral AAV2/6 vectors to transduce mouse retinas. The transduction pattern of AAV2/6 was investigated by studying expression of the green fluorescent protein (GFP) transgene using scanning-laser ophthalmoscopy and immuno-histochemistry. AAV2/6 vectors transduced mouse Muller glial cells aligning the retinal blood vessels. However, the transduction capacity was hindered by the inner limiting membrane (ILM) and besides Muller glial cells, several other inner retinal cell types were transduced. To obtain Muller glial cell-specific transgene expression, the cytomegalovirus (CMV) promoter was replaced by the glial fibrillary acidic protein (GFAP) promoter. Specificity and activation of the GFAP promoter was tested in a mouse model for retinal gliosis. Mice deficient for Crumbs homologue 1 (CRB1) develop gliosis after light exposure. Light exposure of Crb1(-/-) retinas transduced with AAV2/6-GFAP-GFP induced GFP expression restricted to activated Muller glial cells aligning retinal blood vessels.Conclusions/Significance: Our experiments indicate that AAV2 vectors carrying the GFAP promoter are a promising tool for specific expression of transgenes in activated glial cells

Origins and genetic legacy of prehistoric dogs

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry

Organotypic Culture of Physiologically Functional Adult Mammalian Retinas

BACKGROUND: The adult mammalian retina is an important model in research on the central nervous system. Many experiments require the combined use of genetic manipulation, imaging, and electrophysiological recording, which make it desirable to use an in vitro preparation. Unfortunately, the tissue culture of the adult mammalian retina is difficult, mainly because of the high energy consumption of photoreceptors. METHODS AND FINDINGS: We describe an interphase culture system for adult mammalian retina that allows for the expression of genes delivered to retinal neurons by particle-mediated transfer. The retinas retain their morphology and function for up to six days— long enough for the expression of many genes of interest—so that effects upon responses to light and receptive fields could be measured by patch recording or multielectrode array recording. We show that a variety of genes encoding pre- and post-synaptic marker proteins are localized correctly in ganglion and amacrine cells. CONCLUSIONS: In this system the effects on neuronal function of one or several introduced exogenous genes can be studied within intact neural circuitry of adult mammalian retina. This system is flexible enough to be compatible with genetic manipulation, imaging, cell transfection, pharmacological assay, and electrophysiological recordings