On the Neocomian and the Wealden Rocks in the Jura and in England

In June, 1827, Dr. W. H. Fitton read before the Geological Society of London the following statement:—"It is obvious that, during a period of time sufficient for the accumulation of the Wealden, the deposition of matter in the adjacent seas could not have been inconsiderable; so that we might expect to find, interposed between the strata which then formed the bottom of the sea and the Lower Greensand, a series of beds coeval with the Wealden in point of date, but differing from it in possessing the characters of a marine deposit, and including marine shells and other productions of salt water; with which, near the shore, the productions of the land, or even the freshwater shells of the rivers, might be occasionally intermixed. . 1st. That the Wealden and its marine equivalent could not both be found in the same place; and consequently (since we have the former in England) that the marine beds of that date are not to be expected generally in this country; 2dl

Genetic variation in genes interacting with BRCA1/2 and risk of breast cancer in Cypriot population.

Inability to correctly repair DNA damage is known to play a role in the development of breast cancer. Single nucleotide polymorphisms (SNPs) of DNA repair genes have been identified, which modify the DNA repair capacity, which in turn may affect the risk of developing breast cancer. To assess whether alterations in DNA repair genes contribute to breast cancer, we genotyped 62 SNPs in 29 genes in 1,109 Cypriot women with breast cancer and 1,177 age-matched healthy controls. Five SNPs were associated with breast cancer. SNPs rs13312840 and rs769416 in the NBS1 gene were associated with a decrease in breast cancer risk (OR TT vs. TC/CC = 0.58; 95% CI, 0.37-0.92; P = 0.019 and OR GG vs. GT/TT = 0.23, 95% CI 0.06-0.85, P = 0.017, respectively). The variant allele of MRE11A rs556477 was also associated with a reduced risk of developing the disease (OR AA vs. AG/GG = 0.76; 95% CI, 0.64-0.91; P = 0.0022). MUS81 rs545500 and PBOV1 rs6927706 SNPs were associated with an increased risk of developing breast cancer (OR GG vs. GC/CC = 1.21, 95% CI, 1.02-1.45; P = 0.031; OR AA vs. AG/GG = 1.53, 95% CI, 1.07-2.18; P = 0.019, respectively). Finally, haplotype-based tests identified significant associations between specific haplotypes in MRE11A and NBS1 genes and breast cancer risk. Further large-scale studies are needed to confirm these results

Genesis of the alpha beta T-cell receptor

The T-cell (TCR) repertoire relies on the diversity of receptors composed of two chains, called $\alpha$ and $\beta$, to recognize pathogens. Using results of high throughput sequencing and computational chain-pairing experiments of human TCR repertoires, we quantitively characterize the $\alpha\beta$ generation process. We estimate the probabilities of a rescue recombination of the $\beta$ chain on the second chromosome upon failure or success on the first chromosome. Unlike $\beta$ chains, $\alpha$ chains recombine simultaneously on both chromosomes, resulting in correlated statistics of the two genes which we predict using a mechanistic model. We find that $\sim 28 \%$ of cells express both $\alpha$ chains. We report that clones sharing the same $\beta$ chain but different $\alpha$ chains are overrepresented, suggesting that they respond to common immune challenges. Altogether, our statistical analysis gives a complete quantitative mechanistic picture that results in the observed correlations in the generative process. We learn that the probability to generate any TCR$\alpha\beta$ is lower than $10^{-12}$ and estimate the generation diversity and sharing properties of the $\alpha\beta$ TCR repertoire

Inferring processes underlying B-cell repertoire diversity

We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, due to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.Comment: acknowledgement adde

Aspects of environmental impacts of seawater desalination : Cyprus as a case study

Acknowledgements The authors are grateful to the European Commission for supporting the activities carried out in the framework of the H2020 European project ZERO BRINE (project under grant agreement No. 730390). The authors would equally like to thank the TOTAL Foundation (Project “Diversity of brown algae in the Eastern Mediterranean”) and the UK Natural Environment Research Council for their support to FCK (program Oceans 2025 – WP 4.5 and grants NE/D521522/1 and NE/J023094/1). This work also received support from the Marine Alliance for Science and Technology for Scotland pooling initiative. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The authors would also like to thank representatives from competent authorities in Cyprus providing data, and specifically Nicoletta Kythreotou from the Department of Environment, George Ashikalis from the Transmission System Operator, Dr. DinosPoullis and Lia Georgiou from the Water Development Department.Peer reviewedPublisher PD

Predictive Models for the Free Energy of Hydrogen Bonded Complexes with Single and Cooperative Hydrogen Bonds

© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, WeinheimIn this work, we report QSPR modeling of the free energy ΔG of 1 : 1 hydrogen bond complexes of different H-bond acceptors and donors. The modeling was performed on a large and structurally diverse set of 3373 complexes featuring a single hydrogen bond, for which ΔG was measured at 298 K in CCl4. The models were prepared using Support Vector Machine and Multiple Linear Regression, with ISIDA fragment descriptors. The marked atoms strategy was applied at fragmentation stage, in order to capture the location of H-bond donor and acceptor centers. Different strategies of model validation have been suggested, including the targeted omission of individual H-bond acceptors and donors from the training set, in order to check whether the predictive ability of the model is not limited to the interpolation of H-bond strength between two already encountered partners. Successfully cross-validating individual models were combined into a consensus model, and challenged to predict external test sets of 629 and 12 complexes, in which donor and acceptor formed single and cooperative H-bonds, respectively. In all cases, SVM models outperform MLR. The SVM consensus model performs well both in 3-fold cross-validation (RMSE=1.50 kJ/mol), and on the external test sets containing complexes with single (RMSE=3.20 kJ/mol) and cooperative H-bonds (RMSE=1.63 kJ/mol)

QSPR MODELING OF TAUTOMERIC EQUILIBRIA USING LOCAL DESCRIPTORS

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