ARTEMIS: Ab initio restructuring tool enabling the modelling of interface structures (article)

This is the final version. Available on open access from Elsevier via the DOI in this recordThe software associated with this article is located in ORE at: http://hdl.handle.net/10871/121480A program, ARTEMIS, has been developed for the study of interface structures. This software allows for the generation of interfaces by identifying lattice matches between two parent crystal structures. To allow for further exploration of the energetic space of the interface, multiple surface terminations parallel to the Miller plane, interface alignments and intermixings are used to generate sets of potential interfaces for each lattice match. These interface structures can then be used in atomic simulations to determine the most energetically favourable interface. The software reported here can help to both drastically reduce the work of generating and exploring interfaces, and aid in understanding of how the interface structure influences the subsequent properties. Using several test cases, we demonstrate how ARTEMIS can both identify the location of an interface in existing structures, and also predict an optimum interface separation based upon the parents’ atomic structures, which aims to accelerate and inform the study of interface science.Engineering and Physical Sciences Research Council (EPSRC

Systemic delivery of microRNA-101 potently inhibits hepatocellular carcinoma in vivo by repressing multiple targets

Targeted therapy based on adjustment of microRNA (miRNA)s activity takes great promise due to the ability of these small RNAs to modulate cellular behavior. However, the efficacy of miR-101 replacement therapy to hepatocellular carcinoma (HCC) remains unclear. In the current study, we first observed that plasma levels of miR-101 were significantly lower in distant metastatic HCC patients than in HCCs without distant metastasis, and down-regulation of plasma miR-101 predicted a worse disease-free survival (DFS, P<0.05). In an animal model of HCC, we demonstrated that systemic delivery of lentivirus-mediated miR-101 abrogated HCC growth in the liver, intrahepatic metastasis and distant metastasis to the lung and to the mediastinum, resulting in a dramatic suppression of HCC development and metastasis in mice without toxicity and extending life expectancy. Furthermore, enforced overexpression of miR-101 in HCC cells not only decreased EZH2, COX2 and STMN1, but also directly down-regulated a novel target ROCK2, inhibited Rho/Rac GTPase activation, and blocked HCC cells epithelial-mesenchymal transition (EMT) and angiogenesis, inducing a strong abrogation of HCC tumorigenesis and aggressiveness both in vitro and in vivo. These results provide proof-of-concept support for systemic delivery of lentivirus-mediated miR-101 as a powerful anti-HCC therapeutic modality by repressing multiple molecular targets. © 2015 Zheng et al.published_or_final_versio

Computer simulation of syringomyelia in dogs

Syringomyelia is a pathological condition in which fluid-filled cavities (syringes) form and expand in the spinal cord. Syringomyelia is often linked with obstruction of the craniocervical junction and a Chiari malformation, which is similar in both humans and animals. Some brachycephalic toy breed dogs such as Cavalier King Charles Spaniels (CKCS) are particularly predisposed. The exact mechanism of the formation of syringomyelia is undetermined and consequently with the lack of clinical explanation, engineers and mathematicians have resorted to computer models to identify possible physical mechanisms that can lead to syringes. We developed a computer model of the spinal cavity of a CKCS suffering from a large syrinx. The model was excited at the cranial end to simulate the movement of the cerebrospinal fluid (CSF) and the spinal cord due to the shift of blood volume in the cranium related to the cardiac cycle. To simulate the normal condition, the movement was prescribed to the CSF. To simulate the pathological condition, the movement of CSF was blocked

Translation and validation of non-English versions of the Ankylosing Spondylitis Quality of Life (ASQOL) questionnaire

BACKGROUND: The Ankylosing Spondylitis Quality of Life (ASQOL) questionnaire is a unidimensional, disease-specific measure developed in the UK and the Netherlands. This study describes its adaptation into other languages. METHODS: The UK English ASQOL was translated into US English; Canadian French and English; French; German; Italian; Spanish; and Swedish (dual-panel methods). Cognitive debriefing interviews were conducted with AS patients. Psychometric/scaling properties were assessed using data from two Phase III studies of adalimumab. Baseline and Week-2 data were used to assess test-retest reliability. Validity was determined by correlation of ASQOL with SF-36 and BASFI and by discriminative ability of ASQOL based on disease severity. Item response theory (Rasch model) was used to test ASQOL's scaling properties. RESULTS: Cognitive debriefing showed the new ASQOL versions to be clear, relevant and comprehensive. Sample sizes varied, but were sufficient for: psychometric/scaling assessment for US English and Canadian English; psychometric but not scaling analyses for German; and preliminary evidence of these properties for the remaining languages. Test-retest reliability and Cronbach's alpha coefficients were high: US English (0.85, 0.85), Canadian English (0.87, 0.86), and German (0.77, 0.79). Correlations of ASQOL with SF-36 and BASFI for US English, Canadian English, and German measures were moderate, but ASQOL discriminated between patients based on perceived disease severities (p < 0.01). Results were comparable for the other languages. US English and Canadian English exhibited fit to the Rasch model (non-significant p-values: 0.54, 0.68), confirming unidimensionality. CONCLUSION: The ASQOL was successfully translated into all eight languages. Psychometric properties were excellent for US English, Canadian English, and German, and extremely promising for the other languages

Understanding charge transport in lead iodide perovskite thin-film field-effect transistors

Fundamental understanding of the charge transport physics of hybrid lead halide perovskite semiconductors is important for advancing their use in high-performance optoelectronics. We use field-effect transistors (FETs) to probe the charge transport mechanism in thin films of methylammonium lead iodide (MAPbI$_{3}$). We show that through optimization of thin-film microstructure and source-drain contact modifications, it is possible to significantly minimize instability and hysteresis in FET characteristics and demonstrate an electron field-effect mobility (μ$_{FET}$) of 0.5 cm$^{2}$/Vs at room temperature. Temperature-dependent transport studies revealed a negative coefficient of mobility with three different temperature regimes. On the basis of electrical and spectroscopic studies, we attribute the three different regimes to transport limited by ion migration due to point defects associated with grain boundaries, polarization disorder of the MA$^{+}$ cations, and thermal vibrations of the lead halide inorganic cages.S.P.S. acknowledges funding from the Royal Society London for a Newton Fellowship. B.Y. acknowledges support from China Council Scholarship and Cambridge Overseas Trust. A.S. and R.H.F. acknowledge funding and support from the Engineering and Physical Sciences Research Council (EPSRC) through the India-U.K. APEX project. P.D. acknowledges support from the European Union through the award of a Marie Curie Intra-European Fellowship. X.M. is grateful for the support from the Royal Society. B.N. is grateful for the support from Gates Cambridge and the Winton Program for the Physics of Sustainability. We acknowledge funding from the EPSRC through a program grant (EP/M005143/1). We acknowledge funding from the German Federal Ministry of Education and Research under agreement number 01162525/1. This work was performed in part on the SAXS/WAXS beamline of the Australian Synchrotron, Victoria, Australia (55, 56). C.R.M. acknowledges support from the Australian Research Council (DP13012616)

Atomic-scale combination of germanium-zinc nanofibers for structural and electrochemical evolution

Alloys are recently receiving considerable attention in the community of rechargeable batteries as possible alternatives to carbonaceous negative electrodes; however, challenges remain for the practical utilization of these materials. Herein, we report the synthesis of germanium-zinc alloy nanofibers through electrospinning and a subsequent calcination step. Evidenced by in situ transmission electron microscopy and electrochemical impedance spectroscopy characterizations, this one-dimensional design possesses unique structures. Both germanium and zinc atoms are homogenously distributed allowing for outstanding electronic conductivity and high available capacity for lithium storage. The as-prepared materials present high rate capability (capacity of similar to 50% at 20 C compared to that at 0.2 C-rate) and cycle retention (73% at 3.0 C-rate) with a retaining capacity of 546 mAh g(-1) even after 1000 cycles. When assembled in a full cell, high energy density can be maintained during 400 cycles, which indicates that the current material has the potential to be used in a large-scale energy storage system

Increased food availability raises eviction rate in a cooperative breeding mammal

In group-living mammals, the eviction of subordinate females from breeding groups by dominants may serve to reduce feeding competition or to reduce breeding competition. Here, we combined both correlational and experimental approaches to investigate whether increases in food intake by dominant females reduces their tendency to evict subordinate females in wild meerkats ($\textit{Suricata suricatta}$). We used 20 years of long-term data to examine the association between foraging success and eviction rate, and provisioned dominant females during the second half of their pregnancy, when they most commonly evict subordinates. We show that rather than reducing the tendency for dominants to evict subordinates, foraging success of dominant females is positively associated with the probability that pregnant dominant females will evict subordinate females and that experimental feeding increased their rates of eviction. Our results suggest that it is unlikely that the eviction of subordinate females serves to reduce feeding competition and that its principal function may be to reduce reproductive competition. The increase in eviction rates following experimental feeding also suggests that rather than feeding competition, energetic constraints may normally constrain eviction rates.The KMP is supported by the Universities of Cambridge, Zurich and Pretoria. Components of this research were supported by the Natural Environment Research Council (grant no. NE/G006822/1) and the European Research Council (grant no. 294494)

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Recent changes in populations of Critically Endangered Gyps vultures in India

SummaryPopulations of the White-rumped VultureGyps bengalensis, Indian VultureG. indicusand Slender-billed VultureG. tenuirostrisdeclined rapidly during the mid-1990s all over their ranges in the Indian subcontinent because of poisoning due to veterinary use of the non-steroidal anti-inflammatory drug diclofenac. This paper reports results from the latest in a series of road transect surveys conducted across northern, central, western and north-eastern India since the early 1990s. Results from the seven comparable surveys now available were analysed to estimate recent population trends. Populations of all three species of vulture remained at a low level. The previously rapid decline of White-rumped Vulture has slowed and may have reversed since the ban on veterinary use of diclofenac in India in 2006. A few thousand of this species, possibly up to the low tens of thousands, remained in India in 2015. The population of Indian Vulture continued to decline, though probably at a much slower rate than in the 1990s. This remains the most numerous of the three species in India with about 12,000 individuals in 2015 and a confidence interval ranging from a few thousands to a few tens of thousands. The trend in the rarest species, Slender-billed Vulture, which probably numbers not much more than 1,000 individuals in India, cannot be determined reliably.</jats:p