A standard format and a graphical user interface for spin system specification

We introduce a simple and general XML format for spin system description that is the result of extensive consultations within Magnetic Resonance community and unifies under one roof all major existing spin interaction specification conventions. The format is human-readable, easy to edit and easy to parse using standard XML libraries. We also describe a graphical user interface that was designed to facilitate construction and visualization of complicated spin systems. The interface is capable of generating input files for several popular spin dynamics simulation packages.Comment: Submitted for publicatio

The Cosmic Graph: Optimal Information Extraction from Large-Scale Structure using Catalogues

We present an implicit likelihood approach to quantifying cosmological information over discrete catalogue data, assembled as graphs. To do so, we explore cosmological inference using mock dark matter halo catalogues. We employ Information Maximising Neural Networks (IMNNs) to quantify Fisher information extraction as a function of graph representation. We a) demonstrate the high sensitivity of modular graph structure to the underlying cosmology in the noise-free limit, b) show that networks automatically combine mass and clustering information through comparisons to traditional statistics, c) demonstrate that graph neural networks can still extract information when catalogues are subject to noisy survey cuts, and d) illustrate how nonlinear IMNN summaries can be used as asymptotically optimal compressed statistics for Bayesian implicit likelihood inference. We reduce the area of joint $\Omega_m, \sigma_8$ parameter constraints with small ($\sim$100 object) halo catalogues by a factor of 42 over the two-point correlation function, and demonstrate that the networks automatically combine mass and clustering information. This work utilises a new IMNN implementation over graph data in Jax, which can take advantage of either numerical or auto-differentiability. We also show that graph IMNNs successfully compress simulations far from the fiducial model at which the network is fitted, indicating a promising alternative to $n$-point statistics in catalogue-based analyses.Comment: 16 pages, 10 figures. To be submitted to RASTI. We provide code and a tutorial for the analysis and relevant software at https://github.com/tlmakinen/cosmicGraph

Energy status and HIF signalling in chorionic villi show no evidence of hypoxic stress during human early placental development.

Early human placental and embryonic development occurs in a physiologically low oxygen environment supported by histiotrophic secretions from endometrial glands. In this study, we compare the placental metabolomic profile in the first, second and third trimesters to determine whether the energy demands are adequately met in the first trimester. We investigated whether hypoxia-inducible factors, HIF-1α and/or HIF-2α, might regulate transcription during the first trimester. First and second trimester tissue was collected using a chorionic villus sampling-like (CVS) technique. Part of each villus sample was frozen immediately and the remainder cultured under 2 or 21% O2 ± 1 mM H2O2, and ±the p38 MAPK pathway inhibitor, PD169316. Levels of HIF-1α were assessed by western blotting and VEGFA, PlGF and GLUT3 transcripts were quantified by RT-PCR. Term samples were collected from normal elective Caesarean deliveries. There were no significant differences in concentrations of ADP, NAD(+), lactate, and glucose, and in the ATP/ADP ratio, across gestational age. Neither HIF-1α nor HIF-2α could be detected in time-zero CVS samples. However, culture under any condition (2 or 21% O2 ± 1 mM H2O2) increased HIF-1α and HIF-2α. HIF-1α and HIF-2α were additionally detected in specimens retrieved after curettage. HIF-1α stabilization was accompanied by significant increases in VEGFA and GLUT3 and a decrease in PlGF mRNAs. These effects were suppressed by PD169316. In conclusion, our data suggest that first trimester placental tissues are not energetically compromised, and that HIF-1α is unlikely to play an appreciable role in regulating transcriptional activity under steady-state conditions in vivo. However, the pathway may be activated by stress conditions.This work was supported by the Wellcome Trust (084804/2/08/Z). Funding to pay the Open Access publication charges for this article was provided by theWellcome Trust.This is the final published version. It originally appeared in Molecular Human Reproduction, at http://dx.doi.org/10.1093/molehr/gau105

Microbial Reduction of U(VI) under Alkaline Conditions: Implications for Radioactive Waste Geodisposal

Although there is consensus that microorganisms significantly influence uranium speciation and mobility in the subsurface under circumneutral conditions, microbiologically mediated U(VI) redox cycling under alkaline conditions relevant to the geological disposal of cementitious intermediate level radioactive waste, remains unexplored. Here, we describe microcosm experiments that investigate the biogeochemical fate of U(VI) at pH 10–10.5, using sediments from a legacy lime working site, stimulated with an added electron donor, and incubated in the presence and absence of added Fe(III) as ferrihydrite. In systems without added Fe(III), partial U(VI) reduction occurred, forming a U(IV)-bearing non-uraninite phase which underwent reoxidation in the presence of air (O2) and to some extent nitrate. By contrast, in the presence of added Fe(III), U(VI) was first removed from solution by sorption to the Fe(III) mineral, followed by bioreduction and (bio)magnetite formation coupled to formation of a complex U(IV)-bearing phase with uraninite present, which also underwent air (O2) and partial nitrate reoxidation. 16S rRNA gene pyrosequencing showed that Gram-positive bacteria affiliated with the Firmicutes and Bacteroidetes dominated in the post-reduction sediments. These data provide the first insights into uranium biogeochemistry at high pH and have significant implications for the long-term fate of uranium in geological disposal in both engineered barrier systems and the alkaline, chemically disturbed geosphere

Effect of melt composition on the reaction of uranium dioxide with hydrogen chloride in molten alkali chlorides

The reaction of uranium dioxide with excess hydrogen chloride in alkali chloride melts (LiCl, 3LiCl-2KCl, NaCl-KCl and NaCl-2CsCl) has been studied between 450 and 750°C, and the reaction products were characterized by electronic absorption and X-ray absorption spectroscopy. Uranium(V), [UO 2Cl4]3-, and uranium(IV), [UCl 6]2-, species were formed. They depended upon the temperature and the radius of the alkali cations present. Uranium(V) ions predominated in melts with small cations (LiCl and 3LiCl-2KCl). © 2007 Verlag der Zeitschrift für Naturforschung

A structural and biochemical model of processive chitin synthesis

Chitin synthases (CHS) produce chitin, an essential component of the fungal cell wall. The molecular mechanism of processive chitin synthesis is not understood, limiting the discovery of new inhibitors of this enzyme class. We identified the bacterial glycosyltransferase NodC as an appropriate model system to study the general structure and reaction mechanism of CHS. A high throughput screening-compatible novel assay demonstrates that a known inhibitor of fungal CHS also inhibit NodC. A structural model of NodC, on the basis of the recently published BcsA cellulose synthase structure, enabled probing of the catalytic mechanism by mutagenesis, demonstrating the essential roles of the DD and QXXRW catalytic motifs. The NodC membrane topology was mapped, validating the structural model. Together, these approaches give insight into the CHS structure and mechanism and provide a platform for the discovery of inhibitors for this antifungal target

RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first-second trimester transition.

The human placenta is exposed to major environmental changes towards the end of the first trimester associated with full onset of the maternal arterial placental circulation. Changes include a switch from histotrophic to hemotrophic nutrition, and a threefold rise in the intraplacental oxygen concentration. We evaluated their impact on trophoblast development and function using RNA-sequencing (RNA-Seq) and DNA-methylation analyses performed on the same chorionic villous samples at 7-8 (n=8) and 13-14 (n=6) weeks of gestation. Reads were adjusted for fetal sex. Most DEGs were associated with protein processing in the endoplasmic reticulum (ER), hormone secretion, transport, extracellular matrix, vasculogenesis, and reactive oxygen species metabolism. Transcripts higher in the first trimester were associated with synthesis and ER processing of peptide hormones, and glycolytic pathways. Transcripts encoding proteins mediating transport of oxygen, lipids, protein, glucose, and ions were significantly increased in the second trimester. The motifs of CBX3 and BCL6 were significantly overrepresented, indicating the involvement of these transcription factor networks in the regulation of trophoblast migration, proliferation and fusion. These findings are consistent with a high level of cell proliferation and hormone secretion by the early placenta to secure implantation in a physiological low-oxygen environment

Players’ Perceptions of the Talent Development Environment within the English Premier League and Football League

There is an increasing awareness of the importance of the environment in academy players’ development, yet limited research has investigated players’ perceptions of their talent development environments (TDEs). This study focused on academy soccer players’ perceptions of their TDE and compared perceptions across the English soccer academy categorization (CAT) system. A total of 136 U.K.-based male soccer players (M age = 17.7, SD = 1.03 years) representing all four categories (1 = highest to 4 = lowest) of soccer academies aligned to professional soccer clubs completed the TDE Questionnaire-5 (TDEQ-5). The players within the CAT1 academies had significantly more positive perceptions of their support network (p = .01) and holistic quality preparation (p = .03) than their CAT3 counterparts. Across CAT2–CAT3, holistic quality preparation was the least positively perceived subscale within the TDEQ-5, suggesting the need for additional coach education in this area. Soccer academies should consider how they ensure that all areas of their service are associated with optimal TDEs by offering a well-communicated and holistic development experience for their players to enhance effective personal and player development. The findings may have implications for player experience and associated progression rates of lower categorized soccer academies

Vascular endothelial growth factor-D is an independent prognostic factor in epithelial ovarian carcinoma.

We assessed the presence of vascular endothelial growth factor (VEGF)-C, VEGF-D and their receptor VEGFR-3 by immunohistochemistry in 59 epithelial ovarian carcinomas, 11 borderline tumours and 20 benign cystadenomas. VEGF-C and VEGF-D were generally expressed in tumour cells and also in endothelia adjacent to tumour nests which showed a strong staining for them. VEGFR-3 was expressed in lymphatic and vascular endothelial cells adjacent to tumour nests. Immunoreactivity was significantly more frequent as lesions progressed from a benign tumour to advanced carcinoma. A strong correlation was found between VEGF-C and VEGF-D detected in carcinoma and VEGFR-3 detected in neighbouring endothelial cells. Increased expression of VEGF-C, VEGF-D and VEGFR-3 was significantly associated with lymph node metastasis and peritoneal metastasis outside the pelvis. There was a significant correlation between the high levels of VEGF-C and VEGF-D proteins, and poor survival. The presence of VEGF-D was an independent prognostic indicator by multivariate analysis. We conclude that VEGF-C, VEGF-D and VEGFR-3 play an important role in lymphatic spread and intraperitoneal tumour development in ovarian carcinoma. Since VEGF-D was found to be an independent predictor of poor outcome, its measurement, together with other prognostic markers may improve prospective identification of patients with a poor prognosis