Vinculin binding angle in podosomes revealed by high resolution microscopy

Podosomes are highly dynamic actin-rich adhesive structures formed predominantly by cells of the monocytic lineage, which degrade the extracellular matrix. They consist of a core of F-actin and actin-regulating proteins, surrounded by a ring of adhesion-associated proteins such as vinculin. We have characterised the structure of podosomes in macrophages, particularly the structure of the ring, using three super-resolution fluorescence microscopy techniques: stimulated emission depletion microscopy, structured illumination microscopy and localisation microscopy. Rather than being round, as previously assumed, we found the vinculin ring to be created from relatively straight strands of vinculin, resulting in a distinctly polygonal shape. The strands bind preferentially at angles between 116° and 135°. Furthermore, adjacent vinculin strands are observed nucleating at the corners of the podosomes, suggesting a mechanism for podosome growth

Chasing Hypernyms in Vector Spaces with Entropy

In this paper, we introduce SLQS, a new entropy-based measure for the unsupervised identification of hypernymy and its directionality in Distributional Semantic Models (DSMs). SLQS is assessed through two tasks: (i.) identifying the hypernym in hyponym-hypernym pairs, and (ii.) discriminating hypernymy among various semantic relations. In both tasks, SLQS outperforms other state-of-the-art measures

Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus

<p>Abstract</p> <p>Background</p> <p>The dynamic geological and climatic histories of temperate South America have played important roles in shaping the contemporary distributions and genetic diversity of endemic freshwater species. We use mitochondria and nuclear sequence variation to investigate the consequences of mountain barriers and Quaternary glacial cycles for patterns of genetic diversity in the diadromous fish <it>Galaxias maculatus </it>in Patagonia (~300 individuals from 36 locations).</p> <p>Results</p> <p>Contemporary populations of <it>G. maculatus</it>, east and west of the Andes in Patagonia, represent a single monophyletic lineage comprising several well supported groups. Mantel tests using control region data revealed a strong positive relationship when geographic distance was modeled according to a scenario of marine dispersal. (<it>r </it>= 0.69, <it>P = 0.055</it>). By contrast, direct distance between regions was poorly correlated with genetic distance (<it>r </it>= -0.05, <it>P </it>= 0.463). Hierarchical AMOVAs using mtDNA revealed that pooling samples according to historical (pre-LGM) oceanic drainage (Pacific vs. Atlantic) explained approximately four times more variance than pooling them into present-day drainage (15.6% vs. 3.7%). Further <it>post-hoc </it>AMOVA tests revealed additional genetic structure between populations east and west of the Chilean Coastal Cordillera (coastal vs. interior). Overall female effective population size appears to have remained relatively constant until roughly 0.5 Ma when population size rapidly increased several orders of magnitude [100× (60×-190×)] to reach contemporary levels. Maximum likelihood analysis of nuclear alleles revealed a poorly supported gene tree which was paraphyletic with respect to mitochondrial-defined haplogroups.</p> <p>Conclusions</p> <p>First diversifying in the central/north-west region of Patagonia, <it>G. maculatus </it>extended its range into Argentina via the southern coastal regions that join the Pacific and Atlantic oceans. More recent gene flow between northern populations involved the most ancient and most derived lineages, and was likely facilitated by drainage reversal(s) during one or more cooling events of the late Pleistocene. Overall female effective population size represents the end result of a widespread and several hundred-fold increase over approximately 0.5 Ma, spanning several climatic fluctuations of the Pleistocene. The minor influence of glacial cycles on the genetic structure and diversity of <it>G. maculatus </it>likely reflects the access to marine refugia during repeated bouts of global cooling. Evidence of genetic structure that was detected on a finer scale between lakes/rivers is most likely the result of both biological attributes (i.e., resident non-migratory behavior and/or landlocking and natal homing in diadromous populations), and the Coastal Cordillera as a dispersal barrier.</p

Non-Compositional Term Dependence for Information Retrieval

Modelling term dependence in IR aims to identify co-occurring terms that are too heavily dependent on each other to be treated as a bag of words, and to adapt the indexing and ranking accordingly. Dependent terms are predominantly identified using lexical frequency statistics, assuming that (a) if terms co-occur often enough in some corpus, they are semantically dependent; (b) the more often they co-occur, the more semantically dependent they are. This assumption is not always correct: the frequency of co-occurring terms can be separate from the strength of their semantic dependence. E.g. "red tape" might be overall less frequent than "tape measure" in some corpus, but this does not mean that "red"+"tape" are less dependent than "tape"+"measure". This is especially the case for non-compositional phrases, i.e. phrases whose meaning cannot be composed from the individual meanings of their terms (such as the phrase "red tape" meaning bureaucracy). Motivated by this lack of distinction between the frequency and strength of term dependence in IR, we present a principled approach for handling term dependence in queries, using both lexical frequency and semantic evidence. We focus on non-compositional phrases, extending a recent unsupervised model for their detection [21] to IR. Our approach, integrated into ranking using Markov Random Fields [31], yields effectiveness gains over competitive TREC baselines, showing that there is still room for improvement in the very well-studied area of term dependence in IR

Characterizing response types and revealing noun ambiguity in German association norms

This paper presents an analysis of semantic association norms for German nouns. In contrast to prior studies, we not only collected associations elicited by written representations of target objects but also by their pictorial representations. In a first analysis, we identified systematic differences in the type and distribution of associate responses for the two presentation forms. In a second analysis, we applied a soft cluster analysis to the collected target-response pairs. We subsequently used the clustering to predict noun ambiguity and to discriminate senses in our target nouns

Nanopatterned sapphire substrates in deep UV LEDs is there an optical benefit?

Light emitting diodes LEDs in the deep ultra violet DUV offer new perspectives for multiple applications ranging from 3D printing to sterilization. However, insufficient light extraction severely limits their efficiency. Nanostructured sapphire substrates in aluminum nitride based LED devices have recently shown to improve crystal growth properties, while their impact on light extraction has not been fully verified. We present a model for understanding the impact of nanostructures on the light extraction capability of DUV LEDs. The model assumes an isotropic light source in the semiconductor layer stack and combines rigorously computed scattering matrices with a multilayer solver. We find that the optical benefit of using a nanopatterned as opposed to a planar sapphire substrate to be negligible, if parasitic absorption in the p side of the LED is dominant. If losses in the p side are reduced to 20 , then for a wavelength of 265 ,nm an increase of light extraction efficiency from 7.8 to 25.0 is possible due to nanostructuring. We introduce a concept using a diffuse Lambertian reflector as p contact, further increasing the light extraction efficiency to 34.2 . The results underline that transparent p sides and reflective p contacts in DUV LEDs are indispensable for enhanced light extraction regardless of the interface texture between semiconductor and sapphire substrate. The optical design guidelines presented in this study will accelerate the development of high efficiency DUV LEDs. The model can be extended to other multilayer opto electronic nanostructured devices such as photovoltaics or photodetector

Electrostatically gated membrane permeability in inorganic protocells

Although several strategies are now available to produce functional microcompartments analogous to primitive cell-like structures, little progress has been made in generating protocell constructs with self-controlled membrane permeability. Here we describe the preparation of water-dispersible colloidosomes based on silica nanoparticles and delineated by a continuous semipermeable inorganic membrane capable of self-activated, electrostatically gated permeability. We use crosslinking and covalent grafting of a pH-responsive copolymer to generate an ultrathin elastic membrane that exhibits selective release and uptake of small molecules. This behaviour, which depends on the charge of the copolymer coronal layer, serves to trigger enzymatic dephosphorylation reactions specifically within the protocell aqueous interior. This system represents a step towards the design and construction of alternative types of artificial chemical cells and protocell models based on spontaneous processes of inorganic self-organization

AlN overgrowth of nano-pillar-patterned sapphire with different offcut angle by metalorganic vapor phase epitaxy

We present overgrowth of nano-patterned sapphire with different offcut angles by metalorganic vapor phase epitaxy. Hexagonal arrays of nano-pillars were prepared via Displacement Talbot Lithography and dry-etching. 6.6 µm crack-free and fully coalesced AlN was grown on such substrates. Extended defect analysis comparing X-ray diffraction, electron channeling contrast imaging and selective defect etching revealed a threading dislocation density of about 109 cm-2. However, for c-plane sapphire offcut of 0.2° towards m direction the AlN surface shows step bunches with a height of 10 nm. The detrimental impact of these step bunches on subsequently grown AlGaN multi-quantum-wells is investigated by cathodoluminescence and transmission electron microscopy. By reducing the sapphire offcut to 0.1° the formation of step bunches is successfully suppressed. On top of such a sample an AlGaN-based UVC LED heterostructure is realized emitting at 265 nm and showing an emission power of 0.81 mW at 20 mA (corresponds to an external quantum efficiency of 0.86 %)

Microbotanical residues for the study of early hominin tools

More than 2 million years ago in East Africa, the earliest hominin stone tools evolved amidst changes in resource base, with pounding technology playing a key role in this adaptive process. Olduvai Gorge (now Oldupai) is a famed locality that remains paramount for the study of human evolution, also yielding some of the oldest battering tools in the world. However, direct evidence of the resources processed with these technologies is lacking entirely. One way to obtain this evidence is through the analysis of surviving residues. Yet, linking residues with past processing activities is not simple. In the case of plant exploitation, this link can only be established by assessing site-based reference collections inclusive of both anthropogenic and natural residues as a necessary first step and comparative starting point. In this paper, we assess microbotanical remains from rock clasts sourced at the same quarry utilized by Oldowan hominins at Oldupai Gorge. We mapped this signal and analysed it quantitatively to classify its spatial distribution objectively, extracting proxies for taxonomic identification and further comparison with freestanding soils. In addition, we used blanks to manufacture pounding tools for blind, controlled replication of plant processing. We discovered that stone blanks are in fact environmental reservoirs in which plant remains are trapped by lithobionts, preserved as hardened accretions. Tool use, on the other hand, creates residue clusters; however, their spatial distribution can be discriminated from purely natural assemblages by the georeferencing of residues and statistical analysis of resulting patterns. To conclude, we provide a protocol for best practice and a workflow that has the advantage of overcoming environmental noise, reducing the risk of false positive, delivering a firm understanding of residues as polygenic mixtures, a reliable use of controls, and most importantly, a stronger link between microbotanical remains and stone tool use. © 2022. The Author(s).Materials and methods Results - Blanks as environmental reservoirs - Utilization creates residue clusters - Anthropogenic residue distribution - Of lichen habitability, proxy palimpsests, and hardened accretions - A protocol to study plant residue from Oldowan pounding tool