Lithofacies analysis of the Catfish Creek till: Bradtville, Ontario

Sedimentologic and facies analyses are used to interpret a section of Catfish Creek till at Bradtville, Ontario. Repetitive passive lodgement of debris-rich ice and gradual melt-out beneath active ice produced four massive matrix-supported diamicts (Dmm) separated by sand (Sg) and gravel (Gm) horizons. This sequence was partly reworked by melt-water focused along sand horizons, depositing cross-cutting Dcm, Sg and Gm facies. Post-depositional faulting also occurred. Deposition and glaciofluvial reworking are inferred to have occurred at some distance behind an alternately floated and grounded margin of the late Wisconsinan Erie Lobe. RÉSUMÉ Une approche sédimentologique et une analyse des faciès sont utilisées pour interpréter une coupe du till du ruisseau Catfish à Bradville, en Ontario. La succession de la mise en place passive de glace riche en débris et de la fonte graduelle sous le glacier ont produit quatre diamictons à support par la matrice (Dmm), séparés par des horizons de sable (Sg) et de gravier (Gm). Cette séquence a été en partie remaniée par de l'eau de fonte concentrée le long d'horizons sableux, qui à dépose les faciès discordants Dcm, Sg et Gm. Des mouvements de failles postérieurs au dépôt se sont aussi produits. Il est déduit que le dépôt et le remaniement fluvio-glaciaire se seraient produits à une certaine distance de la marge du lobe Erié, du Wisconsinien tardif, laquelle était altérnativement flottante et échouée. [Traduit par le journal

Polyphase Glacigenic Deformation of Advance Glaciofluvial Sediments, Near Big Creek, British Colombia

Deformation structures were observed in glaciofluvial sediments near Big Creek, central British Columbia. These sediments record a sequence of polyphase deformation resulting from the advance and retreat of the Late Wisconsinan (Fraser Glaciation) Cordilleran Ice Sheet. Deformation is attributed to ductile then brittle failure resulting from: (a) horizontal compression and loading as ice advanced over saturated sediments; followed by (b) lateral extension then (c) compression under frozen conditions during glacier overriding; and finally (d) vertical extension during unloading upon déglaciation. Most deformation (a-c, above) appears to have occurred during the advance phase of the Fraser Glaciation.Des structures de déformation ont été observées dans des sédiments fluvioglaciaires, près de Big Creek. Ces sédiments comprennent la séquence d'une déformation polyphasée résultant de l'avancée et du retrait de l'Inlandsis de la Cordillère (Glaciation de Fraser) au Wisconsinien supérieur. La déformation est attribuée à des fractures d'abord de type ductile, puis cassant résultant : (a) d'une compression et d'une charge horizontales à mesure que la glace avançait sur les sédiments saturés; suivie (b) d'une extension latérale, puis (c) d'une compression en milieu gelé pendant la phase de chevauchement glaciaire; et enfin (d) d'une extension verticale pendant la décharge au moment de la déglaciation. La plus grande partie de la déformation (a-c) s'est produite au cours de la phase d'avancée de la Glaciation de Fraser.Nahe bei Big Creek im Zentrum von British Columbia hat man Verformungsstrukturen in fluvioglazialen Sedimenten beobachtet. Diese Sedimente belegen eine Sequenz mehrphasiger Verformung, welche durch den VorstoB und Rùckzug der Kordilleren-Eisdecke im spaten Wisconsin (Fraser-Vereisung) verursacht wurde. Die Verformung fuhrt man auf zunàchst geschmeidiges, dann sprodes Nachgeben zuruck, veranlaRt durch: (a) horizontale Verdichtung und Anhâufung wàhrend das Eis uber die saturierten Sedimente vordrang, darauf folgend (b) eine latérale Ausdehnung und dann (c) Verdichtung in vereistem Milieu wàhrend der Gletscherûberschiebung, und schlie&lich (d) vertikale Ausdehnung wàhrend der durch die Enteisung bewirkten Stromungen. Der grôRte TeN der Verformung (siehe a-c oben) scheint wàhrend der VorstoRphase der Fraser-Vereisung geschehen zu sein

King oil field, Jefferson County, Illinois

Includes bibliographical references

The experimental gas-phase structures of 1,3,5-trisilylbenzene and hexasilylbenzene and the theoretical structures of all benzenes with three or more silyl substituents

The structures of 1,3,5-trisilylbenzene and hexasilylbenzene in the gas phase have been determined by electron diffraction, and that of 1,3,5-trisilylbenzene by X-ray crystallography. The structures of three trisilylbenzene isomers, three tetrasilylbenzenes, pentasilylbenzene and hexasilylbenzene have been computed, ab initio and using Density Functional Theory, at levels up to MP2/6-31G*. The primary effect of silyl substituents is to narrow the ring angle at the substituted carbon atoms. Steric interactions between silyl groups on neighbouring carbon atoms lead first to displacement of these groups away from one another, and then to displacement out of the ring plane, with alternate groups moving to opposite sides of the ring. In the extreme example, hexasilylbenzene, the SiCCSi dihedral angle is 17.8(8)°

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats’ corresponding codons

Antibody response to SARS-CoV-2 infection in humans: A systematic review.

BACKGROUND: Progress in characterising the humoral immune response to Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) has been rapid but areas of uncertainty persist. Assessment of the full range of evidence generated to date to understand the characteristics of the antibody response, its dynamics over time, its determinants and the immunity it confers will have a range of clinical and policy implications for this novel pathogen. This review comprehensively evaluated evidence describing the antibody response to SARS-CoV-2 published from 01/01/2020-26/06/2020. METHODS: Systematic review. Keyword-structured searches were carried out in MEDLINE, Embase and COVID-19 Primer. Articles were independently screened on title, abstract and full text by two researchers, with arbitration of disagreements. Data were double-extracted into a pre-designed template, and studies critically appraised using a modified version of the Public Health Ontario Meta-tool for Quality Appraisal of Public Health Evidence (MetaQAT) tool, with resolution of disagreements by consensus. Findings were narratively synthesised. RESULTS: 150 papers were included. Most studies (113 or 75%) were observational in design, were based wholly or primarily on data from hospitalised patients (108, 72%) and had important methodological limitations. Few considered mild or asymptomatic infection. Antibody dynamics were well described in the acute phase, up to around three months from disease onset, but the picture regarding correlates of the antibody response was inconsistent. IgM was consistently detected before IgG in included studies, peaking at weeks two to five and declining over a further three to five weeks post-symptom onset depending on the patient group; IgG peaked around weeks three to seven post-symptom onset then plateaued, generally persisting for at least eight weeks. Neutralising antibodies were detectable within seven to 15 days following disease onset, with levels increasing until days 14-22 before levelling and then decreasing, but titres were lower in those with asymptomatic or clinically mild disease. Specific and potent neutralising antibodies have been isolated from convalescent plasma. Cross-reactivity but limited cross-neutralisation with other human coronaviridae was reported. Evidence for protective immunity in vivo was limited to small, short-term animal studies, showing promising initial results in the immediate recovery phase. CONCLUSIONS: Literature on antibody responses to SARS-CoV-2 is of variable quality with considerable heterogeneity of methods, study participants, outcomes measured and assays used. Although acute phase antibody dynamics are well described, longer-term patterns are much less well evidenced. Comprehensive assessment of the role of demographic characteristics and disease severity on antibody responses is needed. Initial findings of low neutralising antibody titres and possible waning of titres over time may have implications for sero-surveillance and disease control policy, although further evidence is needed. The detection of potent neutralising antibodies in convalescent plasma is important in the context of development of therapeutics and vaccines. Due to limitations with the existing evidence base, large, cross-national cohort studies using appropriate statistical analysis and standardised serological assays and clinical classifications should be prioritised

T cell response to SARS-CoV-2 infection in humans: A systematic review.

BACKGROUND: Understanding the T cell response to SARS-CoV-2 is critical to vaccine development, epidemiological surveillance and disease control strategies. This systematic review critically evaluates and synthesises the relevant peer-reviewed and pre-print literature published from 01/01/2020-26/06/2020. METHODS: For this systematic review, keyword-structured literature searches were carried out in MEDLINE, Embase and COVID-19 Primer. Papers were independently screened by two researchers, with arbitration of disagreements by a third researcher. Data were independently extracted into a pre-designed Excel template and studies critically appraised using a modified version of the MetaQAT tool, with resolution of disagreements by consensus. Findings were narratively synthesised. RESULTS: 61 articles were included. 55 (90%) studies used observational designs, 50 (82%) involved hospitalised patients with higher acuity illness, and the majority had important limitations. Symptomatic adult COVID-19 cases consistently show peripheral T cell lymphopenia, which positively correlates with increased disease severity, duration of RNA positivity, and non-survival; while asymptomatic and paediatric cases display preserved counts. People with severe or critical disease generally develop more robust, virus-specific T cell responses. T cell memory and effector function has been demonstrated against multiple viral epitopes, and, cross-reactive T cell responses have been demonstrated in unexposed and uninfected adults, but the significance for protection and susceptibility, respectively, remains unclear. CONCLUSION: A complex pattern of T cell response to SARS-CoV-2 infection has been demonstrated, but inferences regarding population level immunity are hampered by significant methodological limitations and heterogeneity between studies, as well as a striking lack of research in asymptomatic or pauci-symptomatic individuals. In contrast to antibody responses, population-level surveillance of the T cell response is unlikely to be feasible in the near term. Focused evaluation in specific sub-groups, including vaccine recipients, should be prioritised

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

BACKGROUND: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. METHODS AND RESULTS: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. CONCLUSIONS: We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects. Circ Genom Precis Med 2018 Feb; 11(2):e001813

Middle and Late Pleistocene environmental history of the Marsworth area, south-central England

To elucidate the Middle and Late Pleistocene environmental history of south-central England, we report the stratigraphy, sedimentology, palaeoecology and geochronology of some deposits near the foot of the Chiltern Hills scarp at Marsworth, Buckinghamshire. The Marsworth site is important because its sedimentary sequences contain a rich record of warm stages and cold stages, and it lies close to the Anglian glacial limit. Critical to its history are the origin and age of a brown pebbly silty clay (diamicton) previously interpreted as weathered till. The deposits described infill a river channel incised into chalk bedrock. They comprise clayey, silty and gravelly sediments, many containing locally derived chalk and some with molluscan, ostracod and vertebrate remains. Most of the deposits are readily attributed to periglacial and fluvial processes, and some are dated by optically stimulated luminescence to Marine Isotope Stage (MIS) 6. Although our sedimentological data do not discriminate between a glacial or periglacial interpretation of the diamicton, amino-acid dating of three molluscan taxa from beneath it indicates that it is younger than MIS 9 and older than MIS 5e. This makes a glacial interpretation unlikely, and we interpret the diamicton as a periglacial slope deposit. The Pleistocene history reconstructed for Marsworth identifies four key elements: (1) Anglian glaciation during MIS 12 closely approached Marsworth, introducing far-travelled pebbles such as Rhaxella chert and possibly some fine sand minerals into the area. (2) Interglacial environments inferred from fluvial sediments during MIS 7 varied from fully interglacial conditions during sub-stages 7e and 7c, cool temperate conditions during sub-stage 7b or 7a, temperate conditions similar to those today in central England towards the end of the interglacial, and cool temperate conditions during sub-stage 7a. (3) Periglacial activity during MIS 6 involved thermal contraction cracking, permafrost development, fracturing of chalk bedrock, fluvial activity, slopewash, mass movement and deposition of loess and coversand. (4) Fully interglacial conditions during sub-stage 5e led to renewed fluvial activity, soil formation and acidic weathering