Introduction to Python Dynamic Diffraction Toolkit (PyDDT): structural refinement of single crystals via X-ray phase measurements.

PyDDT is a free Python package of computer codes for exploiting X-ray dynamic multiple diffraction in single crystals. A wide range of tools are available for evaluating the usefulness of the method, planning feasible experiments, extracting phase information from experimental data and further improving model structures of known materials. Graphical tools are also useful in analytical methodologies related to the three-dimensional aspect of multiple diffraction. For general X-ray users, the PyDDT tutorials provide the insight needed to understand the principles of phase measurements and other related methodologies. Key points behind structure refinement using the current approach are presented, and the main features of PyDDT are illustrated for amino acid and filled skutterudite single crystals.

Superconductivity in Te-Deficient ZrTe2.

We present structural, electrical, and thermoelectric potential measurements on high-quality single crystals of ZrTe1.8 grown from isothermal chemical vapor transport. These measurements show that the Te-deficient ZrTe1.8, which forms the same structure as the nonsuperconducting ZrTe2, is superconducting below 3.2 K. The temperature dependence of the upper critical field (H c2) deviates from the behavior expected in conventional single-band superconductors, being best described by an electron-phonon two-gap superconducting model with strong intraband coupling. For the ZrTe1.8 single crystals, the Seebeck potential measurements suggest that the charge carriers are predominantly negative, in agreement with the ab initio calculations. Through first-principles calculations within DFT, we show that the slight reduction of Te occupancy in ZrTe2 unexpectedly gives origin to density of states peaks at the Fermi level due to the formation of localized Zr-d bands, possibly promoting electronic instabilities at the Fermi level and an increase at the critical temperature according to the standard BCS theory. These findings highlight that the Te deficiency promotes the electronic conditions for the stability of the superconducting ground state, suggesting that defects can fine-tune the electronic structure to support superconductivity.

Offshore decommissioning horizon scan: Research priorities to support decision-making activities for oil and gas infrastructure.

Thousands of oil and gas structures have been installed in the world's oceans over the past 70 years to meet the population's reliance on hydrocarbons. Over the last decade, there has been increased concern over how to handle decommissioning of this infrastructure when it reaches the end of its operational life. Complete or partial removal may or may not present the best option when considering potential impacts on the environment, society, technical feasibility, economy, and future asset liability. Re-purposing of offshore structures may also be a valid legal option under international maritime law where robust evidence exists to support this option. Given the complex nature of decommissioning offshore infrastructure, a global horizon scan was undertaken, eliciting input from an interdisciplinary cohort of 35 global experts to develop the top ten priority research needs to further inform decommissioning decisions and advance our understanding of their potential impacts. The highest research priorities included: (1) an assessment of impacts of contaminants and their acceptable environmental limits to reduce potential for ecological harm; (2) defining risk and acceptability thresholds in policy/governance; (3) characterising liability issues of ongoing costs and responsibility; and (4) quantification of impacts to ecosystem services. The remaining top ten priorities included: (5) quantifying ecological connectivity; (6) assessing marine life productivity; (7) determining feasibility of infrastructure re-use; (8) identification of stakeholder views and values; (9) quantification of greenhouse gas emissions; and (10) developing a transdisciplinary decommissioning decision-making process. Addressing these priorities will help inform policy development and governance frameworks to provide industry and stakeholders with a clearer path forward for offshore decommissioning. The principles and framework developed in this paper are equally applicable for informing responsible decommissioning of offshore renewable energy infrastructure, in particular wind turbines, a field that is accelerating rapidly.

Temperature Dependence of the Electrical Properties of Na2Ti3O7/Na2Ti6O13/POMA Composites.

The temperature dependence of the electrical properties of composites formed by biphasic sodium titanate and poly(o-methoxyaniline) (Na2Ti3O7/Na2Ti6O13/POMA) with different concentrations of POMA (0%, 1%, 10%, 15%, 35% and 50%) in the ceramic matrix was determined from measurements of complex impedance. The structural details were studied by means of X-ray diffraction, confirming the formation of the Na2Ti3O7/Na2Ti6O13/POMA composites. The displacement of the (200) reflection from 2θ = 10.45° to 11.15° in the composites with 10 and 15% of POMA suggested the partial replacement of H+ for Na+ in the Na2Ti3O7 structure. The thermal properties were investigated by Thermogravimetry and Differential Thermal Analysis. The Thermogravimetry curves of the composites with POMA content of 1, 10 and 15% presented profiles similar to that of pure sodium titanate sample. The composites with 35 and 50% of POMA showed a process at temperatures around 60-70 °C, which was associated with water absorbed by the polymer. The analysis of the complex impedance spectroscopy measurements revealed that the electrical resistivity of the composites in the range from 0 to 35% increased by two orders of magnitude, with different values for each concentration. This positive temperature coefficient of resistivity was less noticeable in the composite with highest POMA mass content (50%). The rapid increase in resistivity caused an increase in the relaxation time calculated from the time domain. The electrical response of the 50% of POMA compound changes in relation to what was observed in the other compounds, which suggests that there is a saturation limit in the increase in resistivity with POMA content.

Observed strong pervasive positive selection in the N-terminal domain, receptor-binding domain and furin-cleavage sites of SARS-CoV-2 Spike protein sampled from Zimbabwean COVID-19 patients.

Mutations primarily in the Spike (S) gene resulted in the emergence of many SARS-CoV-2 variants like Alpha, Beta, Delta and Omicron variants. This has also caused a number of COVID-19 pandemic waves which have impacted human lives in different ways due to restriction measures put in place to curb the spread of the virus. In this study, evolutionary patterns found in SARS-CoV-2 sequences of samples collected from Zimbabwean COVID-19 patients were investigated. High coverage SARS-CoV-2 whole genome sequences were downloaded from the GISAID database along with the GISAID S gene reference sequence. Biopython, NumPy and Pandas Data Science packages were used to load, slice and clean whole genome sequences outputting a fasta file with approximate Spike (S) gene sequences. Alignment of sliced dataset with GISAID reference sequence was done using Jalview 2.11.1.3 to find exact sequences of SARS-CoV-2 S gene. Evidence of recombination signals was investigated using RDP 4.1 and pervasive selection in the S gene was investigated using FUBAR algorithm hosted on the Datamonkey webserver. Matplotlib and Seaborn Python packages were used for Data Visualisation. A plot of Bayes factor hypothesizing non-synonymous substitution being greater than synonymous substitution ({beta} > ) in the S protein sites showed 3 peaks with evidence of strong divergence. These 3 diverging S protein sites were found to be D142G, D614G and P681R. No evidence of recombination was detected by 9 methods of RDP which use different approaches to detect recombination signals. This study is useful in guiding drug, vaccine and diagnostic innovations toward better control of the pandemic. Additionally, this study can guide other non-biological interventions as we better understand the changes in various viral characteristics driven by the observed evolutionary patterns.

Catalytic Transformation of Triglycerides to Biodiesel with SiO2-SO3H and Quaternary Ammonium Salts in Toluene or DMSO.

SiO2-SO3H, with a surface area of 115 m2·g-1, pore volumes of 0.38 cm3·g-1 and 1.32 mmol H+/g, was used as a transesterification catalyst. Triglycerides of waste cooking oil reacted with methanol in refluxing toluene to yield mixtures of diglycerides, monoglycerides and fatty acid methyl esters (FAMEs) in the presence of 20% (w/w) catalyst/oil using the hydrophilic sulfonated silica (SiO2-SO3H) catalyst alone or with the addition of 10% (w/w) co-catalyst/oil [(Bun4N)(BF4) or Aliquat 336]. The addition of the ammonium salts to the catalyst lead to a decrease in the amounts of diglycerides in the products, but the concentrations of monoglycerides increased. Mixtures of (Bun4N)(BF4)/catalyst were superior to catalyst alone or Aliquat 336/catalyst for promoting the production of mixtures with high concentrations of FAMEs. The same experiments were repeated using DMSO as the solvent. The use of the more polar solvent resulted in excellent conversion of the triglycerides to FAME esters with all three-catalyst media. A simplified mechanism is presented to account for the experimental results.

Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico.

This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.

From the 1990s climate change has decreased cool season catchment precipitation reducing river heights in Australia's southern Murray-Darling Basin.

The Murray-Darling Basin (MDB) is Australia's major agricultural region. The southern MDB receives most of its annual catchment runoff during the cool season (April-September). Focusing on the Murrumbidgee River measurements at Wagga Wagga and further downstream at Hay, cool season river heights are available year to year. The 27-year period April-September Hay and Wagga Wagga river heights exhibit decreases between 1965 and 1991 and 1992-2018 not matched by declining April-September catchment rainfall. However, permutation tests of means and variances of late autumn (April-May) dam catchment precipitation and net inflows, produced p-values indicating a highly significant decline since the early 1990s. Consequently, dry catchments in late autumn, even with average cool season rainfall, have reduced dam inflows and decreased river heights downstream from Wagga Wagga, before water extraction for irrigation. It is concluded that lower April-September mean river heights at Wagga Wagga and decreased river height variability at Hay, since the mid-1990s, are due to combined lower April-May catchment precipitation and increased mean temperatures. Machine learning attribute detection revealed the southern MDB drivers as the southern annular mode (SAM), inter-decadal Pacific oscillation (IPO), Indian Ocean dipole (IOD) and global sea-surface temperature (GlobalSST). Continued catchment drying and warming will drastically reduce future water availability.

Bremerella alba sp. nov., a novel planctomycete isolated from the surface of the macroalga Fucus spiralis.

A bacterial strain, designated FF15T, was isolated from the thallus surface of the macroalga Fucus spiralis sampled on a rocky beach in Porto, Portugal. Based on the 16S rRNA gene sequence, strain FF15T was affiliated to the phylum Planctomycetes. This strain forms white colonies on modified M13 medium and the cells are pear-shaped, can form rosettes, divide by polar budding and are motile. The novel isolate is mesophilic and neutrophilic with an optimum growth temperature of about 30 °C and an optimum pH for growth between 6.5 and 7.5. It showed growth over a broad range of salinities (0-9% NaCl - optimum at 1.5%). No additional vitamins are required for growth. It is cytochrome c oxidase and catalase positive. The major respiratory quinone was menaquinone 6 (MK-6). Genome sequencing revealed a genome size of 6.37 Mbp and a DNA G + C content of 54.2%. Analysis of phylogenetic markers, including similarities of the 16S rRNA gene sequence, rpoB gene sequence, as well as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI), suggest the affiliation of strain FF15T to "Bremerella", a recently described genus in the family Pirellulaceae. Based on the genotypic, phylogenetic, chemotaxonomic, physiological and biochemical characterization, we described a new species represented by strain FF15T (=CECT 8078T = LMG 31936T), for which we propose the name Bremerella alba snov.

A comparison of two remotely operated vehicle (ROV) survey methods used to estimate fish assemblages and densities around a California oil platform.

Offshore oil and gas platforms have a finite life of production operations. Once production ceases, decommissioning options for the platform are assessed. The role that a platform's jacket plays as fish habitat can inform the decommissioning decision. In this study, conducted along the crossbeams of a California platform jacket and using an ROV, we compared estimates of fish diversity and densities determined from a targeted "biological" survey with those from a replicated "structural" survey. We found that the water column fish species assemblages characterized by the two methods were similar. By contrast, the two survey methods yielded different species assemblages inhabiting the crossbeam at the platform jacket base. This difference occurred because, at least off California, the platform jacket base species diversity tends to be highest where the bottom crossbeam is undercut, creating sheltering sites for many species. Because the structural method inadequately imaged the seafloor-crossbeam interface, particularly where a gap occurred between crossbeam and seafloor, substantial numbers of fishes were not visible. While we cannot extrapolate from this study to all platforms' worldwide, it is clear that routine platform structural integrity surveys may be a valuable source for opportunistic marine community surveys. Intentional planning of the structural survey to incorporate relatively minor variations (e.g., maintaining fixed ROV distance from the infrastructure and consistent 90° camera angle) coupled with a deliberate consideration of the platform ecology (e.g., positioning the ROV to capture the seafloor-crossbeam interface) can substantially improve the effects on fish assemblage assessments from routine structural surveys without compromising the integrity assessment. We suggest that these biases should be both acknowledged and, understood when using routine structural surveys to inform platform ecology assessment. Additional consideration may be given to structural surveys that incorporate incremental adjustments to provide better data applicability to biological assessments.

A new maximum size for the family Nomeidae and the third record of a longfin cigarfish, Cubiceps paradoxus (Stromateoidei: Nomeidae) from California, USA.

We report the largest specimen from the stromateoid family Nomeidae. The specimen, measuring 1283 mm total length unpreserved, was caught on hook and line from shore in Port Hueneme, California, USA in June 2019. Despite scavenging damage, the specimen was identified as a longfin cigarfish, Cubiceps paradoxus, using morphological characters and molecular techniques. This is the third record of C. paradoxus from California. We also provide an account of a previously unreported C. paradoxus collected off the US-Mexico Border in 1999 that was examined but not preserved.

Alienimonas chondri sp. nov., a novel planctomycete isolated from the biofilm of the red alga Chondrus crispus.

The phylum Planctomycetes comprises bacteria with peculiar and very unique characteristics among prokaryotes. In marine environments, macroalgae biofilms are well known for harboring planctomycetal diversity. Here, we describe a novel isolate obtained from the biofilm of the red alga Chondrus crispus collected at a rocky beach in Porto, Portugal. The novel strain LzC2T is motile, rosette-forming with spherical- to ovoid-shaped cells. LzC2T forms magenta- to pinkish-colored colonies in M13 and M14 media. Transmission and scanning electron microscopy observations showed a division by polar and lateral budding. Mother cells are connected to the daughter cells by a tubular neck-like structure. The strain requires salt for growth. Vitamins are not required for growth. Optimal growth occurs from 15 to 30°C and within a pH range from 5.5 to 10.0. Major fatty acids are anteiso-C15:0 (54.2%) and iso-C15:0 (19.5%). Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid represent the main lipids and menaquinone 6 (MK-6) is the only quinone present. 16S rRNA gene-based phylogenetic analysis supports the affiliation to the phylum Planctomycetes and family Planctomycetaceae, with Alienimonas as the closest relative. Strain LzC2T shares 97% 16S rRNA gene sequence similarity with Alienimonas californiensis. LzC2T has a genome size of 5.3 Mb and a G+C content of 68.3%. Genotypic and phenotypic comparison with the closest relatives strongly suggest that LzC2T (=CECT 30038T=LMG XXXT) is a new species of the genus Alienimonas, for which we propose the name Alienimonas chondri sp. nov., represented by LzC2T as type strain. 16S rRNA gene accession number: GenBank=MN757873.1. Genome accession number: GenBank=WTPX00000000.

A Video-Based Framework for Automatic 3D Localization of Multiple Basketball Players: A Combinatorial Optimization Approach.

Sports complexity must be investigated at competitions; therefore, non-invasive methods are essential. In this context, computer vision, image processing, and machine learning techniques can be useful in designing a non-invasive system for data acquisition that identifies players' positions in official basketball matches. Here, we propose and evaluate a novel video-based framework to perform automatic 3D localization of multiple basketball players. The introduced framework comprises two parts. The first stage is player detection, which aims to identify players' heads at the camera image level. This stage is based on background segmentation and on classification performed by an artificial neural network. The second stage is related to 3D reconstruction of the player positions from the images provided by the different cameras used in the acquisition. This task is tackled by formulating a constrained combinatorial optimization problem that minimizes the re-projection error while maximizing the number of detections in the formulated 3D localization problem.

Forecasting the legacy of offshore oil and gas platforms on fish community structure and productivity.

There are currently thousands of offshore platforms in place for oil and gas extraction worldwide, and decommissioning efforts over the next three decades are estimated to cost more than US$200 billion. As platforms reach the end of their useful lifetime, operators and regulatory agencies will assess the environmental impact of potential decommissioning strategies. Among the many factors that will be weighed in preparation for these major economic and engineering challenges is the fate of the fish and invertebrate communities that inhabit the structures underwater. Offshore platforms act as inadvertent artificial reefs, and some are recognized among the most productive fish habitats in the global oceans. We present a model for forecasting changes to fish communities surrounding offshore installations following a series of decommissioning alternatives. Using 24 platforms off southern California, we estimate fish biomass and somatic production under three possible decommissioning scenarios: leave in place, partial removal at 26-m depth, and complete removal of the platform and underlying shell mound. We used fish density and size data from scuba and submersible surveys of the platforms from 1995-2013 to estimate biomass and annual somatic production. Bottom trawl surveys were used to characterize future fish assemblages at platform sites under the complete-removal decommissioning scenario. Based on a conservatively modeled extrapolation of the survey data, we found that complete removal of a platform resulted in 95% or more reduction in the average fish biomass and annual somatic production at the site, while partial removal resulted in far smaller losses, averaging 10% or less. In the event that all surveyed platforms are completely removed, we estimated a total loss of more than 28,000 kg of fish biomass in the Southern California Bight. Platform habitats, which attract reef-dwelling fish species, had minimal overlap in community composition with the surrounding soft-bottom habitat. To best serve the wide range of stakeholder interests, the site-specific biomass, productivity and species composition information provided in this study should be incorporated into strategic decommissioning planning. This approach could be used as a model for informing "rigs to reefs" discussions occurring worldwide.

Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov.

We performed high-quality genome sequencing of eight strains of the species of the genus Tepidimonas and examined the genomes of closely related strains from the databases to understand why Tepidimonas taiwanensis is the only strain of this genus that utilizes glucose and fructose for growth. We found that the assimilation of these hexoses by T. taiwanensis was due to the presence of two transporters that are absent in all other genomes of strains of members of the genus Tepidimonas examined. Some strains lack genes coding for glucokinase, but the Embden-Meyerhof-Parnas pathway appears to be otherwise complete. The pentose phosphate pathway has a complete set of genes, but genes of the Entner-Doudoroff pathway were not identified in the genomes of any of the strains examined. Genome analysis using average nucleotide identity (ANIb), digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and phylogenetic analysis of 400 conserved genes was performed to assess the taxonomic classification of the organisms. Two isolates of the genus Tepidimonas from the hot spring at São Pedro do Sul, Portugal, designated SPSP-6T and SPSPC-18 were also examined in this study. These organisms are mixotrophic, have an optimum growth temperature of about 50 ºC, utilize several organic acids and amino acids for growth but do not grow on sugars. Distinctive phenotypic, 16S rRNA gene sequence and genomic characteristics of strains SPSP-6T and SPSPC-18 lead us to propose a novel species based on strain SPSP-6T for which we recommend the name Tepidimonas charontis sp. nov. (=CECT 9683T=LMG 30884T).

High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria.

Gaiella occulta strain F2-233T (=CECT 7815 = LMG 26412), isolated from a 150 meter deep mineral water aquifer, was deemed a candidate for high-quality draft genome sequencing because of the rare environment from which it was isolated. The draft genome sequence (QQZY00000000) of strain F2-233T is composed of approximately 3 Mb, predicted 3,119 protein-coding genes of which 2,545 were assigned putative functions. Genome analysis was done by comparison with the other deep-branching Actinobacteria neighbors Rubrobacter radiotolerans, Solirubrobacter soli and Thermoleophilum album. The genes for the tricarboxylic acid cycle, gluconeogenesis and pentose phosphate pathway, were identified in G. occulta, R. radiotolerans, S. soli and T. album genomes. Genes of the Embden-Meyerhof-Parnas pathway and nitrate reduction were identified in G. occulta, R. radiotolerans and S. soli, but not in the T. album genome. Alkane degradation is precluded by genome analysis in G. occulta. Genes involved in myo-inositol metabolism were found in both S. soli and G. occulta genomes. A Calvin-Benson-Bassham (CBB) cycle with a type I RuBisCO was identified in G. occulta genome, as well. However, experimental growth under several conditions was negative and CO2 fixation could not be proven in G. occulta.

Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, Meiothermus roseus Ming et al. 2016, Meiothermus terrae Yu et al. 2014 and Meiothermus timidus Pires et al. 2005, to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus.

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus Meiothermuswith validly published names to reclassify this genus. The results indicate that the species of the genus Meiothermus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus Meiothermus to the species Meithermus ruber, Meiothermus cateniformans, Meiothermus taiwanensis, Meiothermus cerbereus, Meiothermus hypogaeus, Meiothermus luteus, Meiothermus rufus and Meiothermus granaticius, for which it is necessary to emend the genus Meiothermus. The species Meiothermus silvanus, which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species Meiothermus chliarophilus, Meiothermus timidus, Meiothermus roseus and Meiothermus terrae as species of a novel genus for which we propose the epithet Calidithermus gen. nov.