Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Calibration of shielded microwave probes using bulk dielectrics

A stripline-type near-field microwave probe is microfabricated for microwave impedance microscopy. Unlike the poorly shielded coplanar probe that senses the sample tens of microns away, the stripline structure removes the stray fields from the cantilever body and localizes the interaction only around the focused-ion beam deposited Pt tip. The approaching curve of an oscillating tip toward bulk dielectrics can be quantitatively simulated and fitted to the finite-element analysis result. The peak signal of the approaching curve is a measure of the sample dielectric constant and can be used to study unknown bulk materials.Comment: 10 pages, 3 figure

Electronic structure induced reconstruction and magnetic ordering at the LaAlO3∣_3|SrTiO3_3 interface

Using local density approximation (LDA) calculations we predict GdFeO$_3$-like rotation of TiO$_6$ octahedra at the $n$-type interface between LaAlO$_3$ and SrTiO$_3$. The narrowing of the Ti $d$ bandwidth which results means that for very modest values of $U$, LDA$+U$ calculations predict charge and spin ordering at the interface. Recent experimental evidence for magnetic interface ordering may be understood in terms of the close proximity of an antiferromagnetic insulating ground state to a ferromagnetic metallic excited state

A Complete Year of User Retrieval Sessions in a Social Sciences Academic Search Engine

In this paper, we present an open data set extracted from the transaction log of the social sciences academic search engine sowiport. The data set includes a filtered set of 484,449 retrieval sessions which have been carried out by sowiport users in the period from April 2014 to April 2015. We propose a description of interactions performed by the academic search engine users that can be used in different applications such as result ranking improvement, user modeling, query reformulation analysis, search pattern recognition.Comment: 6 pages, 2 figures, accepted short paper at the 21st International Conference on Theory and Practice of Digital Libraries (TPDL 2017

Modeling of a Cantilever-Based Near-Field Scanning Microwave Microscope

We present a detailed modeling and characterization of our scalable microwave nanoprobe, which is a micro-fabricated cantilever-based scanning microwave probe with separated excitation and sensing electrodes. Using finite-element analysis, the tip-sample interaction is modeled as small impedance changes between the tip electrode and the ground at our working frequencies near 1GHz. The equivalent lumped elements of the cantilever can be determined by transmission line simulation of the matching network, which routes the cantilever signals to 50 Ohm feed lines. In the microwave electronics, the background common-mode signal is cancelled before the amplifier stage so that high sensitivity (below 1 atto-Farad capacitance changes) is obtained. Experimental characterization of the microwave probes was performed on ion-implanted Si wafers and patterned semiconductor samples. Pure electrical or topographical signals can be realized using different reflection modes of the probe.Comment: 7 figure

A SIFT approach for analysing failure by delamination and disbonding in composite structures

A strain invariant failure theory (SIFT) has been developed to predict resin failure in damaged and pristine composite structures The finite element (FE) analysis in this work uses shell elements consistent with common practice in the aeronautical industry. The new SIFT is similar in nature to a characteristic length method that requires a matched finite element mesh. It samples the strains in brick elements lofted between two layers of shell elements, each representing half of the damaged laminate in the failure critical zone. Experimental tests involving three laminate materials have been carried out to validate t he modified SIFT approach for notched laminates, including single and multiple level delamination tests, and stiffened panel tests under shear or compression load. These results are summarised in a table. Square and rectangle single delamination tests are presented in more detail and indicate that failure location and load predicted by the modified SIFT approach correlates well with the experimental results