Towards dynamically configured databases for CIFs: the new modulated structures open database at the Bilbao Crystallographic Server.

This article presents a web-based framework to build a database without in-depth programming knowledge given a set of CIF dictionaries and a collection of CIFs. The framework consists of two main elements: the public site that displays the information contained in the CIFs in an ordered manner, and the restricted administrative site which defines how that information is stored, processed and, eventually, displayed. Thus, the web application allows users to easily explore, filter and access the data, download the original CIFs, and visualize the structures via JSmol. The modulated structures open database B-IncStrDB, the official International Union of Crystallography repository for this type of material and available through the Bilbao Crystallographic Server, has been re-implemented following the proposed framework.

Free tools for crystallographic symmetry handling and visualization.

Online courses and innovative teaching methods have triggered a trend in education, where the integration of multimedia, online resources and interactive tools is reshaping the view of both virtual and traditional classrooms. The use of interactive tools extends beyond the boundaries of the physical classroom, offering students the flexibility to access materials at their own speed and convenience and enhancing their learning experience. In the field of crystallography, there are a wide variety of free online resources such as web pages, interactive applets, databases and programs that can be implemented in fundamental crystallography courses for different academic levels and curricula. This paper discusses a variety of resources that can be helpful for crystallographic symmetry handling and visualization, discussing four specific resources in detail: the Bilbao Crystallographic Server, the Cambridge Structural Database, VESTA and Jmol. The utility of these resources is explained and shown by several illustrative examples.

Meteorological Approach in the Identification of Local and Remote Potential Sources of Radon: An Example in Northern Iberian Peninsula.

This paper presents a meteorological approach to identify local and remote sources driving the variability of surface daily radon concentrations. To this purpose, hourly 222Rn concentration and surface meteorological measurements, and air mass trajectories at Bilbao station (northern Iberian Peninsula) during the period 2017-2018 have been taken as reference. To investigate the potential transport pathways and potential 222Rn sources, the backward trajectory cluster analysis, trajectory sector analysis (TSA), and potential source contribution function (PSCF) are applied. On average, the diurnal 222Rn cycle shows the expected behaviour, with larger concentrations during the night and minimum concentrations during the daylight hours, with differences in the seasonal amplitudes. According to daily differences between maximum and baseline values, 222Rn daily cycles were grouped into six groups to identify meteorological conditions associated with each amplitude, and potential source areas and transport routes of 222Rn over Bilbao. The trajectory cluster and the TSA method show that the main airflow pathways are from the south, with small displacement, and the northeast, while the analysis of surface wind speed and direction indicates that the highest amplitudes of 222Rn concentrations are registered under the development of sea-land breezes. The PSCF method identified south-western and north-eastern areas highly contributing to the 222Rn concentration. These areas are confirmed by comparing with the radon flux map and the European map of uranium concentration in soil. The results have demonstrated the need in combining the analysis of local and regional/synoptic factors in explaining the origin and variability of 222Rn concentrations.

Layer groups: Brillouin-zone and crystallographic databases on the Bilbao Crystallographic Server.

The section of the Bilbao Crystallographic Server (https://www.cryst.ehu.es/) dedicated to subperiodic groups contains crystallographic and Brillouin-zone databases for the layer groups. The crystallographic databases include the generators/general positions (GENPOS), Wyckoff positions (WYCKPOS) and maximal subgroups (MAXSUB). The Brillouin-zone database (LKVEC) offers k-vector tables and Brillouin-zone figures of all 80 layer groups which form the background of the classification of their irreducible representations. The symmetry properties of the wavevectors are described applying the so-called reciprocal-space-group approach and this classification scheme is compared with that of Litvin & Wike [(1991), Character Tables and Compatibility Relations of the Eighty Layer Groups and Seventeen Plane Groups. New York: Plenum Press]. The specification of independent parameter ranges of k vectors in the representation domains of the Brillouin zones provides a solution to the problems of uniqueness and completeness of layer-group representations. The Brillouin-zone figures and k-vector tables are described in detail and illustrated by several examples.

Naturally growing grimmiaceae family mosses as passive biomonitors of heavy metals pollution in urban-industrial atmospheres from the Bilbao Metropolitan area.

In analytical chemistry, biomonitoring is known as the methodology, which consider the use of living organisms to monitor and assess the impact of different contaminants in a known area. This type of monitoring is a relatively inexpensive method and easy to implement, being a viable alternative to be developed in sites where there is no infrastructure/instruments for a convenctional air quality monitoring. These organisms, having the capability to monitor the pollution, are also known as passive biomonitors (PBs), since they are able to identify possible contamination sources without the need of any additional tool. In this work, a multianalytical methodology was applied to verify the usefulness of naturally growing Grimmia genus mosses as PBs of atmospheric heavy metals pollution. Once mosses were identified according to their morphology and taxonomy, thei ability to accumulate particulate matter (PM) was determined by SEM. EDS coupled to SEM also allowed to identify the main metallic particles deposited and finally, an acid digestion of the mosses and a subsequent ICP-MS study define more precisely the levels of metals accumulated on each collected moss. The study was focused on six sampling locations from the Bilbao Metropolitan area (Biscay, Basque Country, north of Spain). The experimental evidences obtained allowed to propose naturally growing Grimmia genus as PB of atmospheric heavy metals pollution and to identify the anthropogenic sources that contribute to the emission of the airborne particulate matter rich in metals, evaluating in this sense the atmospheric heavy metals pollution of the selected locations.

Multi-annual survey of health status disturbance in the Bilbao estuary (Bay of Biscay) based on sediment chemistry and juvenile sole (Solea spp.) histopathology.

The Bilbao estuary (SE Bay of Biscay) is a recovering ecosystem whose sediments are still contaminated. They represent a potential risk for the biota including benthic and demersal species living in direct contact with the sediment. In this context, the present study aims to survey trends of the health status of the Bilbao estuary based on sediment chemistry and sole (Solea spp.) histopathology. Monitoring campaigns were carried out every autumn from 2011 to 2017 along the estuary. Contaminant levels were measured in sediments; liver, gills and gonads of juvenile fish were collected for histopathology. Overall, contaminant levels fluctuated throughout the years, with highest values recorded in the earlier years of the study period. Sole histopathology showed alterations of mild severity. Results permitted to assess the environmental health status of the Bilbao estuary during 7 years, although no clear temporal trend was detected. Longer-term monitoring programmes are necessary to confirm the ecosystem recovery.

The site-symmetry induced representations of layer groups on the Bilbao Crystallographic Server.

The section of the Bilbao Crystallographic Server (http://www.cryst.ehu.es) dedicated to subperiodic groups includes a new tool called LSITESYM for the study of materials with layer and multilayer symmetry. This new program, based on the site-symmetry approach, establishes the symmetry relations between localized and extended crystal states using representations of layer groups. The efficiency and utility of the program LSITESYM is demonstrated by illustrative examples, which include the analysis of phonon symmetry in Aurivillius compounds and in van der Waals layered crystals MoS2 and WS2.

Environmental regeneration processes in the Anthropocene: The Bilbao estuary case (northern Spain).

This work tackles a multidisciplinary study on the recent sedimentary record of the Bilbao estuary (northern Spain), which is the backbone of a city that was primarily industrial and now is widely recognized as a successful example of urban transformation. Although hotspots of heavily polluted materials still remain at the mouth of the two main tributaries (Galindo and Gobelas), the data obtained confirm the ongoing formation of a new layer of sediments (here called "postindustrial zone") covering historically polluted and azoic deposits. It is characterized by largely variable levels of metals and magnetic susceptibility and moderate-to-high abundances of benthic foraminifera. Monitoring of the evolution of this layer appears a key factor to assess environmental improvement and decision-making in polluted estuaries.

Evaluation of black crust formation and soiling process on historical buildings from the Bilbao metropolitan area (north of Spain) using SEM-EDS and Raman microscopy.

In the present work, several building materials suffering from black crusts and soiled surfaces were evaluated by scanning electron microscopy energy dispersive X-ray spectrometry (SEM-EDS) and micro-Raman spectroscopy. The goal was to examine the elemental and molecular composition, the distribution on the samples, and the morphology of endogenous and exogenous compounds on those black crusts and soiled surfaces. The black crusts were deposited over different building materials such as limestone, sandstone, and brick that constitute a small construction called "malacate" as well as over a limestone substrate of a cemetery gate. Both constructions are dated back to the beginning of the twentieth century. The samples of soiling were taken from the façade of a building constructed in the 1980s. The analytical evaluation allowed in a first stage the determination of the composition and the observation of the morphology of soiling and black crusts. In addition, the evaluation of the compositions of the soiling and black crusts of different grade and formation allowed the assessment of the main weathering phenomena that the buildings have suffered, which were found to be sulfate impact, marine aerosol impact, depositions of metallic particles, crustal particulate matter depositions, carbonaceous particles, biodeterioration, and vandalism.

Numerical assessment of the dispersion of overspilled sediment from a dredge barge and its sensitivity to various parameters.

Marine dredging operations are not uncommon in coastal waters since they are necessary for several beneficial uses, such as harbour maintenance, beach nourishment or removal/capping of pollutants, amongst others. They also constitute a significant risk for the environment, changing its physical, chemical and biological characteristics, as evidenced by many authors. In this study, two numerical models are used to simulate the dispersion pattern of fine suspended sediment spilled from a dredge barge, considering different hydrodynamic scenarios, particle sizes and dredging tracks in a mesotidal environment. The results show that, in this particular case, the currents (largely induced by the tide) are the main responsible for the final disposition of the settled particles, being the other variables of secondary importance.

Brillouin-zone database on the Bilbao Crystallographic Server.

The Brillouin-zone database of the Bilbao Crystallographic Server (http://www.cryst.ehu.es) offers k-vector tables and figures which form the background of a classification of the irreducible representations of all 230 space groups. The symmetry properties of the wavevectors are described by the so-called reciprocal-space groups and this classification scheme is compared with the classification of Cracknell et al. [Kronecker Product Tables, Vol. 1, General Introduction and Tables of Irreducible Representations of Space Groups (1979). New York: IFI/Plenum]. The compilation provides a solution to the problems of uniqueness and completeness of space-group representations by specifying the independent parameter ranges of general and special k vectors. Guides to the k-vector tables and figures explain the content and arrangement of the data. Recent improvements and modifications of the Brillouin-zone database, including new tables and figures for the trigonal, hexagonal and monoclinic space groups, are discussed in detail and illustrated by several examples.

The genus Pseudo-nitzschia (Bacillariophyceae) in a temperate estuary with description of two new species: Pseudo-nitzschia plurisecta sp. nov. and Pseudo-nitzschia abrensis sp. nov.

The genus Pseudo-nitzschia contains potentially toxic species of problematic taxonomy, making it one of the most intensively studied diatom genera. The study of 35 clonal strains isolated from the Bilbao estuary, an area that experiences recurrent blooms of Pseudo-nitzschia, revealed the presence of two new species, P. abrensis and P. plurisecta, differing from their congeners in both morphology and gene sequence. The morphological features were analyzed by LM and EM, whereas molecular analyses were based on the internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA. P. plurisecta appears closely related to P. cuspidata/P. pseudodelicatissima in the phylogenetic tree, whereas P. abrensis forms a moderately supported clade with P. heimii/P. subpacifica and P. caciantha/P. circumpora. Comparison of the secondary structure of ITS2 regions reveals marked differences in the most highly conserved regions among related taxa. Morphologically, the new species differ from their closest congeners in the arrangement of the poroid sectors and the density of valve striae and fibulae. The two species share similar pigment composition, and belong to the group of Pseudo-nitzschia species containing only chlorophyll c2 and c3 .