bluuebunny/crossref_metadata_2025 huggingface dataset:
Core Amino Acid Residues in the Morphology-Regulating Protein, Mms6, for Intracellular Magnetite Biomineralization
Authors: Yamagishi Ayana , Narumiya Kaori , Tanaka Masayoshi , Matsunaga Tadashi , Arakaki Atsushi
Published: October 2016

Living organisms produce finely tuned biomineral architectures with the aid of biomineral-associated proteins. The functional amino acid residues in these proteins have been previously identified usingin vitroandin silicoexperimentation in different biomineralization systems. However, the investigation in living organisms is limited owing to the difficulty in establishing appropriate genetic techniques. Mms6 protein, isolated from the surface of magnetite crystals synthesized in magnetotactic bacteria, was shown to play a key role in the regulation of crystal morphology. In this study, we have demonstrated a defect in the specific region or substituted acidic amino acid residues in the Mms6 protein for observing their effect on magnetite biomineralizationin vivo. Analysis of the gene deletion mutants and transformants ofMagnetospirillum magneticumAMB-1 expressing partially truncated Mms6 protein revealed that deletions in the N-terminal or C-terminal regions disrupted proper protein localization to the magnetite surface, resulting in a change in the crystal morphology. Moreover, single amino acid substitutions at Asp123, Glu124, or Glu125 in the C-terminal region of Mms6 clearly indicated that these amino acid residues had a direct impact on magnetite crystal morphology. Thus, these consecutive acidic amino acid residues were found to be core residues regulating magnetite crystal morphology.
Prophylaxis of Diallyl Disulfide on Skin Carcinogenic Model via p21-dependent Nrf2 stabilization
Authors: Shan Yunlong , Wei Zhonghong , Tao Li , Wang Siliang , Zhang Feng , Shen Cunsi , Wu Hongyan , Liu Zhaoguo , Zhu Pingting , Wang Aiyun , Chen Wenxing , Lu Yin
Published: October 2016

Cancer prevention through intake of biologically active natural products appears to be an accessible way to reduce the risk of cancer. Diallyl disulfide (DADS), a major garlic derivative, has exhibited potential role in cancer therapy. The study is aimed to evaluate the prophylactic effect of DADS in chemically induced mouse skin carcinogenesis and investigate the molecular targets mediated by DADS. Two-stage chemically induced carcinogenesis model by cutaneous application of DMBA and subsequent TPA was established to study the prophylactic effect of DADS. As a result, we observed that DADS dose-dependently attenuated skin tumor incidence and multiplicity in the model mice, which was related to the up-regulation of a bunch of antioxidant enzymes activities and the nuclear accumulation of Nrf2. Furthermore, we developed skin carcinogenesis in Nrf2 knockout mice which could reverse the activity of DADS. Finally, we uncovered the underlying mechanism that DADS promoted the endogenous interaction between p21 and Nrf2, which was critical for impairing the Keap1-mediated degradation of Nrf2. Based on the results, we concluded that DADS was a promising cancer chemoprevention agent and suggested a garlic-rich diet might be beneficial to reduce the cancer risk in our daily life.
Effectiveness evaluation of organized screening for esophageal cancer: a case-control study in Linzhou city, China
Authors: Chen Qiong , Yu Liang , Hao Changqing , Wang Jinwu , Liu Shuzheng , Zhang Meng , Zhang Shaokai , Guo Lanwei , Quan Peiliang , Germain Patrick , Zhang Yawei , Sun Xibin
Published: October 2016

In China, esophageal cancer has remained a large burden, and endoscopic screening is expected to reduce esophageal cancer mortality. Therefore, a population-based case-control study was conducted to evaluate the effect of screening. Cases were defined as individuals who had died of esophageal cancer, and controls were residents from the same area (three per case) who had not died of esophageal cancer, matched by gender and birth year. The exposure status (whether cases and controls had ever attended the screening or not) was acquired by inspecting the well documented screening records. A conditional logistic regression model was used to estimate the odds ratios (OR) and their 95% confidence intervals (95% CI). There were 253 cases and 759 controls. The reduction in risk of esophageal cancer mortality in individuals who had ever attended screening was 47% (OR: 0.53, 95% CI: 0.37–0.77). Compared with never-screened subjects, the ORs for screened subjects within 36 and 48 months before the reference date were 0.59(0.39–0.89) and 0.59(0.40–0.87); the ORs for 50–59 year old subjects were 0.48(0.28–0.85). The results suggest a 47% reduction in esophageal cancer mortality risk due to endoscopic screening, which may have significant implications for esophageal cancer screening in China, especially in rural areas.
Accurate quantification of apoptosis progression and toxicity using a dielectrophoretic approach
Authors: Henslee Erin A. , Torcal Serrano Ruth M. , Labeed Fatima H. , Jabr Rita I. , Fry Christopher H. , Hughes Michael P. , Hoettges Kai F.
Published: October 2016

A rapid, low-cost and label-free method of cell analysis compares favorably to Annexin-V, MTT and trypan blue for assessment of apoptosis and IC50.
A UHPLC-MS/SRM method for analysis of phenolics from Camellia sinensis leaves from Nilgiri hills
Authors: Ramakrishnan Padma , Rangiah Kannan
Published: October 2016

Analysis of phenolics differentiates the top three leaves (Ist, IInd and IIIrd) in tea plants from Nilgiri hills.
Hot exciton cooling and multiple exciton generation in PbSe quantum dots
Authors: Kumar Manoj , Vezzoli Stefano , Wang Zilong , Chaudhary Varun , Ramanujan Raju V. , Gurzadyan Gagik G. , Bruno Annalisa , Soci Cesare
Published: October 2016

PbSe QDs show high multiple exciton generation (MEG) quantum yield. Here we have investigated the role of theΣtransition in slowing down the hot exciton cooling, which can help MEG to take over phonon relaxation.
Schottky barrier tuning of the single-layer MoS2on magnetic metal substrates through vacancy defects and hydrogenation
Authors: Yun Won Seok , Lee J. D.
Published: October 2016

The Schottky barrier and magnetism of the single-layer MoS2on magnetic metal substrates can be tuned by atomic vacancy defects and hydrogenation.
Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials
Authors: Briggs Beverly D. , Palafox-Hernandez J. Pablo , Li Yue , Lim Chang-Keun , Woehl Taylor J. , Bedford Nicholas M. , Seifert Soenke , Swihart Mark T. , Prasad Paras N. , Walsh Tiffany R. , Knecht Marc R.
Published: October 2016

Materials-binding peptides provide the basis for new nanoparticle assembly strategies.
Synthesis and structure of pseudo-three dimensional hybrid iodobismuthate semiconductors
Authors: Dennington Adam J. , Weller Mark T.
Published: October 2016

Semiconducting hybrid bismuth iodides, templated on piperizinium cations and their methylated derivatives, have pseudo three-dimensional connectivity reminiscent of the perovskite structure.
Grinding size-dependent mechanoresponsive luminescent Cd(ii) coordination polymer
Authors: Yan Yong , Chen Jun , Zhang Ning-Ning , Wang Ming-Sheng , Sun Cai , Xing Xiu-Shuang , Li Rong , Xu Jian-Gang , Zheng Fa-Kun , Guo Guo-Cong
Published: October 2016

A new mechanoresponsive luminescent Cd(ii) coordination polymer exhibits rare grinding size-dependent fluorescence and possesses good crystalline maintenance capability.
Blip-summed quantum–classical path integral with cumulative quantum memory
Authors: Makri Nancy
Published: October 2016

The quantum-classical path integral (QCPI) offers a rigorous methodology for simulating quantum mechanical processes in condensed-phase environments treated in full atomistic detail. This paper describes the implementation of QCPI on system–bath models, which are frequently employed in studying the dynamics of reactive processes. The QCPI methodology incorporates all effects associated with stimulated phonon absorption and emission as its crudest limit, thus can (in some regimes) converge faster than influence functional-based path integral methods specifically designed for system–bath Hamiltonians. It is shown that the QCPI phase arising from a harmonic bath can be summed analytically with respect to the discrete bath degrees of freedom and expressed in terms of precomputed influence functional coefficients, avoiding the explicit enumeration of forced oscillator trajectories, whose number grows exponentially with the length of quantum memory. Further, adoption of the blip decomposition (which classifies the system paths based on the time length over which their forward and backward components are not identical) and a cumulative treatment of the QCPI phase between blips allows elimination of the majority of system paths, leading to a dramatic increase in efficiency. The generalization of these acceleration techniques to anharmonic environments is discussed.
Catecholamine-functionalized graphene as a biomimetic redox shuttle for solar water oxidation
Authors: Son Eun Jin , Kim Jae Hong , Ko Jong Wan , Park Chan Beum
Published: October 2016

In natural photosynthesis, solar energy is converted to chemical energy through a cascaded, photoinduced charge transfer chain that consists of primary and secondary acceptor quinones (i.e., QA and QB). This leads to an exceptionally high near-unity quantum yield. Inspired by the unique multistep architecture of charge transfer in nature, we have synthesized a catecholamine-functionalized, reduced graphene oxide (RGO) film as a redox mediator that can mimic quinone acceptors in photosystem II. We used polynorepinephrine (PNE) as a redox-shuttling chemical. We also used it to coat graphene oxide (GO) and to reduce GO to RGO. The quinone ligands in PNE, which are characterized by a charge transfer involving two electrons and two protons, acted as electron acceptors that facilitated charge transfer in photocatalytic water oxidation. Furthermore, PNE-coated RGO film promoted fast charge separation in [Ru(bpy)3]2+ and increased the activity of cobalt phosphate on photocatalytic water oxidation more than two-fold. The results suggest that our bio-inspired strategy for the construction of a forward charge transfer pathway can provide more opportunities to realize efficient artificial photosynthesis.
Self-assembly of vascularized tissue to support tumor explants in vitro
Authors: Bazou Despina , Maimon Nir , Gruionu Gabriel , Munn Lance L.
Published: October 2016

Integration of tumor biopsies into a pre-formed vascularized supporting bed provides a new tool for studying tumor tissue ex vivo.
Synthesis and biological activity evaluation of novel peroxo-bridged derivatives as potential anti-hepatitis B virus agents
Authors: Jia Menglu , Zhao Rui , Xu Bing , Yan Wenqiang , Chu Fuhao , Gu Hongshun , Xie Tianxin , Xiang Hongjun , Ren Jian , Chen Dagang , Wang Penglong , Lei Haimin
Published: October 2016

Previous studies have demonstrated that natural steroid compounds containing a peroxide bridge exhibited potential anti-hepatitis B virus activity.
Synthesis and molecular structure of arene ruthenium(ii) benzhydrazone complexes: impact of substitution at the chelating ligand and arene moiety on antiproliferative activity
Authors: Mohamed Subarkhan Mohamed Kasim , Ramesh Rengan , Liu Yu
Published: October 2016

A series of ruthenium(ii) arene complexes have been synthesized and evaluated for their in vitro anticancer activities. The complexes exhibit promising anticancer activities in human cancer cells.
Pyranonaphthoquinones – isolation, biology and synthesis: an update
Authors: Naysmith Briar J. , Hume Paul A. , Sperry Jonathan , Brimble Margaret A.
Published: October 2016

The pyranonaphthoquinones are a diverse family of over one hundred natural products which exhibit promising biological activity, a review of the isolation and synthesis of pyranonaphthoquinones is provided.
Alcohol oxidation with H2O2 catalyzed by a cheap and promptly available imine based iron complex
Authors: Olivo Giorgio , Giosia Simone , Barbieri Alessia , Lanzalunga Osvaldo , Di Stefano Stefano
Published: October 2016

A cheap and easily available catalyst for alcohol oxidation with unexpected selectivity features.
Sol–gel reversible metallo-supramolecular hydrogels based on a thermoresponsive double hydrophilic block copolymer
Authors: Le Bohec Maël , Banère Manon , Piogé Sandie , Pascual Sagrario , Benyahia Lazhar , Fontaine Laurent
Published: October 2016

A new thermoresponsive double hydrophilic block copolymer bearing a terpyridine moiety formed a hydrogel with a sol–gel thermoreversible transition in the presence of Fe2+ ions.
Metal-free RAFT cationic polymerization of p-methoxystyrene with HCl·Et2O using a xanthate-type RAFT cationogen
Authors: Sugihara Shinji , Okubo Seiya , Maeda Yasushi
Published: October 2016

A xanthate-type RAFT cationogen (IBEX) mediates the metal-free cationic polymerization of pMOS with HCl·Et2O via the degenerative addition–fragmentation of cationic species, i.e. the RAFT mechanism.
Grafting of functional methacrylate polymer brushes by photoinduced SET-LRP
Authors: Vorobii Mariia , Pop-Georgievski Ognen , de los Santos Pereira Andres , Kostina Nina Yu. , Jezorek Ryan , Sedláková Zdeňka , Percec Virgil , Rodriguez-Emmenegger Cesar
Published: October 2016

The growth of polymer brushes from a variety of methacrylate monomers was accomplished using UV light as a polymerization trigger.
Utilization of a new gold/Schiff-base iron(iii) complex composite as a highly sensitive voltammetric sensor for determination of epinephrine in the presence of ascorbic acid
Authors: Gorczyński Adam , Kubicki Maciej , Szymkowiak Klaudia , Łuczak Teresa , Patroniak Violetta
Published: October 2016

A new voltammetric sensor based on an iron(iii) Schiff-base complex/Au composite is synthesized and applied for thein vitrodetection of epinephrine.
Structure, optical spectroscopy properties and thermochromism of Sm3Fe5O12 garnets
Authors: Liu Huanhuan , Yuan Long , Wang Shan , Fang Hairui , Zhang Yuan , Hou Changmin , Feng Shouhua
Published: October 2016

Inorganic compounds of Sm3−xCaxFe5O12 (x = 0, 0.1, 0.3, 0.5) samples can be used as a new family of thermochromic materials with the colour change from green (20 °C) to brown (240 °C) and the introduction of Ca2+ ions shows gradual changes in colour.
Effect of polymer rigidity on the phase behaviour of polymer adsorption on to planar surface
Authors: Yang Zhiyong , Chai Aihua , Zhou Peicong , Li Ping , Yang Yongfu
Published: October 2016

We study the process of a semiflexible polymer chain adsorption on to planar surface by the dynamic Monte Carlo (DMC) method, based on the 3D off-lattice model. Both the strength of attractive monomer–surface interaction (εa) and bending energy (b) have pronounced effect on the adsorption and shape of semiflexible polymer chain. The semiflexible polymer can just fully adsorb on to the surface at certain εa, which is defined as critical εa. The essential features of the semiflexible polymer adsorption on to surface are that (i) the critical εa increases with increase in b; (ii) the shape of the fully adsorbed semiflexible polymer chain is film-like toroid, and the toroid becomes more and more perfect with increase in b. In addition, the size of toroid and the number of turns of toroid can be controlled by the b and εa.
Attacking HIV-1 RNA versus DNA by sequence-specific approaches: RNAi versus CRISPR-Cas
Authors: Herrera-Carrillo Elena , Berkhout Ben
Published: October 2016

Human immunodeficiency virus type 1 (HIV-1) infection can be effectively controlled by potent antiviral drugs, but this never results in a cure. The patient should therefore take these drugs for the rest of his/her life, which can cause drug-resistance and adverse effects. Therefore, more durable therapeutic strategies should be considered, such as a stable gene therapy to protect the target T cells against HIV-1 infection. The development of potent therapeutic regimens based on the RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats (CRISPR-Cas) mechanisms will be described, which can be delivered by lentiviral vectors. These mechanisms attack different forms of the viral genome, the RNA and DNA, respectively, but both mechanisms act in a strictly sequence-specific manner. Early RNAi experiments demonstrated profound virus inhibition, but also indicated that viral escape is possible. Such therapy failure can be prevented by the design of a combinatorial RNAi attack on the virus and this gene therapy is currently being tested in a preclinical humanized mouse model. Recent CRISPR-Cas studies also document robust virus inhibition, but suggest a novel viral escape route that is induced by the cellular nonhomologous end joining DNA repair pathway, which is activated by CRISPR-Cas-induced DNA breaks. We will compare these two approaches for durable HIV-1 suppression and discuss the respective advantages and disadvantages. The potential for future clinical applications will be described.
Dawn of thein vivoRNA structurome and interactome
Authors: Kwok Chun Kit
Published: October 2016

RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo. For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure–function relationship on a transcriptomic scale. In this review, molecular tools and NGS methods used for RNA structure probing are presented, novel insights uncovered by RNA structurome and interactome studies are highlighted, and perspectives on current challenges and potential future directions are discussed. A more complete understanding of the RNA structures and interactions in vivo will help illuminate the novel roles of RNA in gene regulation, development, and diseases.
Role of the bone morphogenic protein pathway in developmental haemopoiesis and leukaemogenesis
Authors: Toofan Parto , Wheadon Helen
Published: October 2016

Myeloid leukaemias share the common characteristics of being stem cell-derived clonal diseases, characterised by excessive proliferation of one or more myeloid lineage. Chronic myeloid leukaemia (CML) arises from a genetic alteration in a normal haemopoietic stem cell (HSC) giving rise to a leukaemic stem cell (LSC) within the bone marrow (BM) ‘niche’. CML is characterised by the presence of the oncogenic tyrosine kinase fusion protein breakpoint cluster region-abelson murine leukaemia viral oncogene homolog 1 (BCR-ABL), which is responsible for driving the disease through activation of downstream signal transduction pathways. Recent evidence from our group and others indicates that important regulatory networks involved in establishing primitive and definitive haemopoiesis during development are reactivated in myeloid leukaemia, giving rise to an LSC population with altered self-renewal and differentiation properties. In this review, we explore the role the bone morphogenic protein (BMP) signalling plays in stem cell pluripotency, developmental haemopoiesis, HSC maintenance and the implication of altered BMP signalling on LSC persistence in the BM niche. Overall, we emphasise how the BMP and Wnt pathways converge to alter the Cdx–Hox axis and the implications of this in the pathogenesis of myeloid malignancies.
Primary cilia: a link between hormone signalling and endocrine-related cancers?
Authors: O'Toole Samuel M. , Chapple J. Paul
Published: October 2016

Primary cilia are sensory organelles that play a role as signalling hubs. Disruption of primary cilia structure and function is increasingly recognised in a range of cancers, with a growing body of evidence suggesting that ciliary disruption contributes to tumourigenesis. This review considers the role of primary cilia in the pathogenesis of endocrine-related cancers.
Computational protein design with backbone plasticity
Authors: MacDonald James T. , Freemont Paul S.
Published: October 2016

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process.
Genetic analysis of rare coding mutations of CELSR1–3 in congenital heart and neural tube defects in Chinese people
Authors: Qiao Xiaojin , Liu Yahui , Li Peiqiang , Chen Zhongzhong , Li Huili , Yang Xueyan , Finnell Richard H. , Yang Zhangmin , Zhang Ting , Qiao Bin , Zheng Yufang , Wang Hongyan
Published: October 2016

The planar cell polarity (PCP) pathway is critical for proper embryonic development of the neural tube and heart. Mutations in these genes have previously been implicated in the pathogenesis of neural tube defects (NTDs), but not in congenital heart defects (CHDs) in humans. We systematically identified the mutation patterns of CELSR1–3, one family of the core PCP genes, in human cohorts composed of 352 individuals with NTDs, 412 with CHDs and matched controls. A total of 72 disease-specific, rare, novel, coding mutations were identified, of which 37 were identified in patients with CHDs and 36 in patients with NTDs. Most of these mutations differed between the two cohorts, because only one novel missense mutation in CELSR1 (c.2609G>A p.P870L) was identified in both NTD and CHD patients. Both in vivo and in vitro assays revealed that CELSR1 P870L is a gain-of-function mutation. It up-regulates not only the PCP pathway, but also canonical WNT signalling in cells, and also induces both NTDs and CHDs in zebrafish embryos. As almost equal numbers of mutations were identified in each cohort, our results provided the first evidence that mutations in CELSR genes are as likely to be associated with CHDs as with NTDs, although the specific mutations differ between the two cohorts. Such differences in mutation panels suggested that CELSRs [cadherin, EGF (epidermal growth factor), LAG (laminin A G-type repeat), seven-pass receptors)] might be regulated differently during the development of these two organ systems.
Interference DOA estimation and suppression for GNSS receivers using fully augmentable arrays
Authors: Wang Xiangrong , Amin Moeness , Ahmad Fauzia , Aboutanios Elias
Published: October 2016

Multiple antenna receivers have been proposed for interference nulling in Global Navigation Satellite Systems (GNSS). An open‐loop anti‐jam approach is considered and an interference direction‐of‐arrival (DOA) estimation technique using fully augmentable non‐uniform linear arrays is introduced. The DOAs of incoming jammers are estimated utilising the minimum output power method applied to the GNSS receiver coarray and through two different approaches of spectrum sensing and polynomial rooting. Subsequently, the strong interferers are cancelled utilising a subspace projection approach, whereas the 30 dB despreading gain of GNSS receivers protects the satellite signals against weak jammers. Supporting simulation results demonstrate that DOA estimation based on polynomial rooting outperforms spectrum sensing and validate the effectiveness of the proposed anti‐jam strategy.
Low‐angle target tracking using frequency‐agile refined maximum likelihood algorithm
Authors: Zhu Yutang , Zhao Yongbo , Shui Penglang
Published: October 2016

An Low‐angle target tracking problem is investigated via the refined maximum likelihood (RML) algorithm. The results of the RML algorithm reveal that increasing the operating frequency of radar does not always reduce the mean‐squared error (MSE) of angle estimate and thus an appropriate selection of the operating frequency can improve the angle estimation accuracy. Here, a frequency‐agile RML algorithm is proposed, which adaptively adjusts the operating frequency during target tracking to minimize the MSEs of angle estimate. Theoretical analysis and simulation are made to verify the effectiveness of the frequency‐agile RML algorithm.
Uncertain measurement for student performance evaluation based on selection of boosted fuzzy rules
Authors: Darwish Saad Mohamed
Published: October 2016

Evaluation of student performance is one of the essential parts of educational systems that incorporated with uncertainty in human knowledge. Rating and predicting students’ educational achievement using arithmetical and statistical procedures may not explicitly advise the best route to estimate human acquisition of knowledge and experiences. Researchers in this field tended to adopt soft computing to defeat the challenges of analytical techniques in order to resolve this evaluation performance problem. Fuzzy logic is utilised to manage the intrinsic uncertainty associated with teachers’ subjective assessments and permits reproduction of student modelling in the linguistic form – the same form the human teachers do. The obstacle with existing fuzzy rule‐based systems is that the size of the rule base (the number of rules) grows exponentially with the expansion of the number of fuzzy sets included in the rules. This exponential increment in the size of the rule base enlarges the search time and the memory space needed. In this study, a fuzzy rule base compaction (densification) using genetic algorithm is suggested for uncertain measurement of student's performance. The proposed approach consists of three stages: knowledge recovery, coding, and compaction or optimisation. The comparative outcomes demonstrated that the recommended evaluator has a magnificent dynamic response than that of the traditional one.
Gearbox fault diagnosis under fluctuating load conditions with independent angular re‐sampling technique, continuous wavelet transform and multilayer perceptron neural network
Authors: Singh Amandeep , Parey Anand
Published: October 2016

Most research efforts in gearbox fault diagnosis thus far have focused on diagnosing gearbox faults under stationary conditions. Efforts in diagnosing gearbox faults under non‐stationary conditions have mostly involved an analysis of gearbox vibration signals under the speed‐up or run‐down processes. This paper attempts to diagnose faults in a single stage spur gearbox under non stationary conditions arising from fluctuating loads at the output of gearbox. The vibration signal corresponding to each independent revolution is synchronized from the revolution point of view by converting into the angular domain. This is accomplished experimentally by a simple process referred to as the independent angular re‐sampling (IAR) technique. The IAR technique is accomplished by employing a multiple pulse tachometer arrangement. Through the IAR process, non‐stationary signals in the time domain are converted into quasi‐stationary signals in the angular domain. The angular domain signals, each representing one revolution of the gearbox drive shaft, are then decomposed with continuous wavelet transform. Optimal scales are identified based on superior energy‐Shannon's entropy ratio of continuous wavelet coefficients (CWCs). The classification accuracy of a multilayer perceptron neural network is compared when CWCs from all scales and when CWCs from the optimal scales are fed to the neural network.
Parasites et cancer : existe-t-il un lien ?
Authors: Cheeseman Kevin , Certad Gabriela , Weitzman Jonathan B.
Published: October 2016

Le nombre de décès dus au cancer ne cesse d’augmenter. Plus de 20 % des cas de cancers sont d’origine infectieuse qu’elle soit virale, bactérienne ou parasitaire. Si la contribution de virus et de bactéries aux cancers d’origine infectieuse est clairement établie et acceptée, il n’en va pas de même pour les parasites eucaryotes intracellulaires. Ainsi, malgré l’accumulation de données épidémiologiques et cliniques indiquant un lien entre parasites et cancer, la contribution de ces derniers à la tumorigenèse reste floue et peu étudiée. Nous proposons ici un état des lieux sur les liens entre parasites intracellulaires eucaryotes et cancers, et montrons en prenant appui sur trois récentes études, comment les mécanismes des interactions hôtes-parasites peuvent conduire à l’apparition de cancers.
Next generation gamma-ray Cherenkov detectors for the National Ignition Facility
Authors: Herrmann H. W. , Kim Y. H. , McEvoy A. M. , Zylstra A. B. , Young C. S. , Lopez F. E. , Griego J. R. , Fatherley V. E. , Oertel J. A. , Stoeffl W. , Khater H. , Hernandez J. E. , Carpenter A. , Rubery M. S. , Horsfield C. J. , Gales S. , Leatherland A. , Hilsabeck T. , Kilkenny J. D. , Malone R. M. , Hares J. D. , Milnes J. , Shmayda W. T. , Stoeckl C. , Batha S. H.
Published: October 2016

The newest generation of Gas Cherenkov Detector (GCD-3) employed in Inertial Confinement Fusion experiments at the Omega Laser Facility has provided improved performance over previous generations. Comparison of reaction histories measured using two different deuterium-tritium fusion products, namely gamma rays using GCD and neutrons using Neutron Temporal Diagnostic (NTD), have provided added credibility to both techniques. GCD-3 is now being brought to the National Ignition Facility (NIF) to supplement the existing Gamma Reaction History (GRH-6m) located 6 m from target chamber center (TCC). Initially it will be located in a reentrant well located 3.9 m from TCC. Data from GCD-3 will inform the design of a heavily-shielded “Super” GCD to be located as close as 20 cm from TCC. It will also provide a test-bed for faster optical detectors, potentially lowering the temporal resolution from the current ∼100 ps state-of-the-art photomultiplier tubes (PMT) to ∼10 ps Pulse Dilation PMT technology currently under development.
Elastic X-ray scattering from state-selected molecules
Authors: Northey Thomas , Moreno Carrascosa Andrés , Schäfer Steffen , Kirrander Adam
Published: October 2016

The characterization of electronic, vibrational, and rotational states using elastic (coherent) X-ray scattering is considered. The scattering is calculated directly from complete active space self-consistent field level ab initio wavefunctions for H2 molecules in the ground-state X1Σg+ and first-excited EF1Σg+ electronic states. The calculated scattering is compared to recent experimental measurements [Y.-W. Liu et al., Phys. Rev. A 89, 014502 (2014)], and the influence of vibrational and rotational states on the observed signal is examined. The scaling of the scattering calculations with basis set is quantified, and it is found that energy convergence of the ab initio calculations is a good indicator of the quality of the scattering calculations.
Graphene grown out of diamond
Authors: Gu Changzhi , Li Wuxia , Xu Jing , Xu Shicong , Lu Chao , Xu Lifang , Li Junjie , Zhang Shengbai
Published: October 2016

Most applications of graphene need a suitable support substrate to present its excellent properties. But transferring graphene onto insulators or growing graphene on foreign substrates could cause properties diminishing. This paper reports the graphene growth directly out of diamond (111) by B doping, guided by first-principles calculations. The spontaneous graphene formation occurred due to the reconstruction of the diamond surface when the B doping density and profile are adequate. The resulting materials are defect free with high phase purity/carrier mobility, controllable layer number, and good uniformity, which can be potentially used directly for device fabrication, e.g., high-performance devices requiring good thermal conductivity.
Lagrangian analysis of the laminar flat plate boundary layer
Authors: Gabr Mohammad
Published: October 2016

The flow properties at the leading edge of a flat plate represent a singularity to the Blasius laminar boundary layer equations; by applying the Lagrangian approach, the leading edge velocity profiles of the laminar boundary layer over a flat plate are studied. Experimental observations as well as the theoretical analysis show an exact Gaussian distribution curve as the original starting profile of the laminar flow. Comparisons between the Blasius solution and the Gaussian curve solution are carried out providing a new insight into the physics of the laminar flow.
Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation
Authors: Sidler Dominik , Schwaninger Arthur , Riniker Sereina
Published: October 2016

In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which “envelopes” the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.
Spin-orbit coupling with approximate equation-of-motion coupled-cluster method for ionization potential and electron attachment
Authors: Cao Zhanli , Wang Fan , Yang Mingli
Published: October 2016

Various approximate approaches to calculate cluster amplitudes in equation-of-motion coupled-cluster (EOM-CC) approaches for ionization potentials (IP) and electron affinities (EA) with spin-orbit coupling (SOC) included in post self-consistent field (SCF) calculations are proposed to reduce computational effort. Our results indicate that EOM-CC based on cluster amplitudes from the approximate method CCSD-1, where the singles equation is the same as that in CCSD and the doubles amplitudes are approximated with MP2, is able to provide reasonable IPs and EAs when SOC is not present compared with CCSD results. It is an economical approach for calculating IPs and EAs and is not as sensitive to strong correlation as CC2. When SOC is included, the approximate method CCSD-3, where the same singles equation as that in SOC-CCSD is used and the doubles equation of scalar-relativistic CCSD is employed, gives rise to IPs and EAs that are in closest agreement with those of CCSD. However, SO splitting with EOM-CC from CC2 generally agrees best with that with CCSD, while that of CCSD-1 and CCSD-3 is less accurate. This indicates that a balanced treatment of SOC effects on both single and double excitation amplitudes is required to achieve reliable SO splitting.
Aberrant H3.3 dynamics in NAc promote vulnerability to depressive-like behavior
Authors: Lepack Ashley E. , Bagot Rosemary C. , Peña Catherine J. , Loh Yong-Hwee E. , Farrelly Lorna A. , Lu Yang , Powell Samuel K. , Lorsch Zachary S. , Issler Orna , Cates Hannah M. , Tamminga Carol A. , Molina Henrik , Shen Li , Nestler Eric J. , Allis C. David , Maze Ian
Published: October 2016

Significance

Human major depressive disorder is a chronic remitting syndrome that affects millions of individuals worldwide; however, the molecular mechanisms mediating this syndrome remain elusive. Here, using a unique combination of epigenome-wide and behavioral analyses, we demonstrate a role for histone variant dynamics in the nucleus accumbens (NAc)—a critical brain center of reward and mood—contributing to stress susceptibility in mice. These studies, which also demonstrate that molecular blockade of aberrant dynamics in the NAc promotes resilience to chronic stress, promise to aid in the identification of novel molecular targets (i.e., downstream genes displaying altered expression as the result of stress-induced histone dynamics) that may be exploited in the development of more effective pharmacotherapeutics.
Situating the default-mode network along a principal gradient of macroscale cortical organization
Authors: Margulies Daniel S. , Ghosh Satrajit S. , Goulas Alexandros , Falkiewicz Marcel , Huntenburg Julia M. , Langs Georg , Bezgin Gleb , Eickhoff Simon B. , Castellanos F. Xavier , Petrides Michael , Jefferies Elizabeth , Smallwood Jonathan
Published: October 2016

Significance

We describe an overarching organization of large-scale connectivity that situates the default-mode network at the opposite end of a spectrum from primary sensory and motor regions. This topography, based on the differentiation of connectivity patterns, is also embedded in the spatial distance along the cortical surface between these respective systems. In addition, this connectivity gradient accounts for the respective positions of canonical networks and captures a functional spectrum from perception and action to more abstract cognitive functions. These results suggest that the default-mode network consists of regions at the top of a representational hierarchy that describe the current cognitive landscape in the most abstract terms.
Cockayne syndrome group A and B proteins converge on transcription-linked resolution of non-B DNA
Authors: Scheibye-Knudsen Morten , Tseng Anne , Borch Jensen Martin , Scheibye-Alsing Karsten , Fang Evandro Fei , Iyama Teruaki , Bharti Sanjay Kumar , Marosi Krisztina , Froetscher Lynn , Kassahun Henok , Eckley David Mark , Maul Robert W. , Bastian Paul , De Supriyo , Ghosh Soumita , Nilsen Hilde , Goldberg Ilya G. , Mattson Mark P. , Wilson David M. , Brosh Robert M. , Gorospe Myriam , Bohr Vilhelm A.
Published: October 2016

Significance

In this paper we describe a possible pathogenesis for the accelerated aging disease Cockayne syndrome that entails defective transcription through DNA secondary structures leading to activation of the DNA damage response enzyme poly-ADP-ribose polymerase 1 and downstream mitochondrial derangement. These findings are important because they signify a possible new role of transcription in the resolution of DNA structures that form spontaneously and suggest a possible pathogenesis for this accelerated aging disease.
Structural and functional significance of water permeation through cotransporters
Authors: Zeuthen Thomas , Gorraitz Edurne , Her Ka , Wright Ernest M. , Loo Donald D. F.
Published: October 2016

Significance

Transport of water and polar solutes across membranes play an important physiological role, and it is widely appreciated that many membrane transport proteins are permeable to water. Molecular dynamics studies of sodium-coupled glucose cotransporters (SGLTs) indicate that water flows through the sugar transport pathway. We test this hypothesis by mutating residues lining the sugar transport pathway through SGLT1, and measuring the changes in the permeability of water and urea before and after their chemical modification. Mutation of outer and inner gate residues and residues involved in sugar binding confirms that water and urea permeate the glucose transport pathway, suggesting that water is involved in sugar transport. SGLT1 is physiologically important in determining osmotic flow across the small intestine.
Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice
Authors: Zhou Hongju , Wang Lijun , Liu Guifu , Meng Xiangbing , Jing Yanhui , Shu Xiaoli , Kong Xiangli , Sun Jian , Yu Hong , Smith Steven M. , Wu Dianxing , Li Jiayang
Published: October 2016

Significance

Resistant starch (RS) has the potential to protect against diabetes and reduce the incidence of diarrhea, inflammatory bowel disease, colon cancer, and chronic renal and hepatic diseases. In this study, we identified two critical starch synthase genes which together regulate RS biosynthesis in rice, and we explored their potential interactions as part of a network of starch biosynthetic enzymes. The findings hold promise for applications in breeding varieties with improvement of RS in hot cooked rice and may also have general implications for understanding RS biosynthesis in other major cereal crops.
Compactifications of splitting models of PEL-type Shimura varieties
Authors: Lan Kai-Wen
Published: October 2016

We construct toroidal and minimal compactifications, with expected properties concerning stratifications and formal local structures, for all integral models of PEL-type Shimura varieties defined by taking normalizations over the splitting models considered by Pappas and Rapoport. (These include, in particular, all the normal flat splitting models they considered.)
Removable singularities for degenerate elliptic equations without conditions on the growth of the solution
Authors: Vitolo Antonio
Published: October 2016

The aim of the paper is to state removable singularities results for solutions of fully nonlinear degenerate elliptic equations without any knowledge of the behaviour of the solution approaching the singular set and to obtain unconditional results of Brezis–Veron type for operators defined as the partial sum of the eigenvalues of the Hessian matrix.
HiLive: real-time mapping of illumina reads while sequencing
Authors: Lindner Martin S , Strauch Benjamin , Schulze Jakob M , Tausch Simon H , Dabrowski Piotr W , Nitsche Andreas , Renard Bernhard Y
Published: October 2016

Motivation

Next Generation Sequencing is increasingly used in time critical, clinical applications. While read mapping algorithms have always been optimized for speed, they follow a sequential paradigm and only start after finishing of the sequencing run and conversion of files. Since Illumina machines write intermediate output results, HiLive performs read mapping while still sequencing and thereby drastically reduces crucial overall sample analysis time, e.g. in precision medicine.

Methods

We present HiLive as a novel real time read mapper that implements a k-mer based alignment strategy. HiLive continuously reads intermediate BCL files produced by Illumina sequencers and then extends initial k-mer matches by increasingly produced data from the sequencer.

Results

We applied HiLive on real human transcriptome data to show that final read alignments are reported within few minutes after the end of a full Illumina HiSeq 1500 run, while already the necessary conversion to FASTQ files as the standard input to current read mapping methods takes roughly five times as long. Further, we show on simulated and real data that HiLive has comparable accuracy to recent read mappers.

Availability and Implementation

HiLive and its source code are freely available from https://gitlab.com/SimonHTausch/HiLive.

Supplementary information

Supplementary data are available at Bioinformatics online.
10. Freedom of Expression
Authors: Foster Steve
Published: October 2016

The Concentrate Questions and Answers series offer the best preparation for tackling exam questions. Each book includes typical questions, diagram answer plans, caution advice, suggested answers, illustrative diagrams and flowcharts and advice on gaining extra marks. Q&A Human Rights and Civil Liberties offers expert advice on what to expect from your human rights and civil liberties exam, how best to prepare, and guidance on what examiners are really looking for. Written by experienced examiners, it provides: clear commentary with each question and answer; bullet point and diagram answer plans; tips to make your answer really stand out from the crowd; and further reading suggestions at the end of every chapter. The book should help you to: identify typical law exam questions; structure a first-class answer; avoid common mistakes; show the examiner what you know; make your answer stand out from the crowd; and find relevant further reading.

This chapter covers freedom of speech and expression, including the scope of free speech and expression, its protection in domestic law and under the ECHR, and its application to areas such as public order, national security contempt of court, press freedom, and defamation law.
11. Freedom of Religion, Association, and Peaceful Assembly
Authors: Foster Steve
Published: October 2016

The Concentrate Questions and Answers series offer the best preparation for tackling exam questions. Each book includes typical questions, diagram answer plans, caution advice, suggested answers, illustrative diagrams and flowcharts and advice on gaining extra marks. Q&A Human Rights and Civil Liberties offers expert advice on what to expect from your human rights and civil liberties exam, how best to prepare, and guidance on what examiners are really looking for. Written by experienced examiners, it provides: clear commentary with each question and answer; bullet point and diagram answer plans; tips to make your answer really stand out from the crowd; and further reading suggestions at the end of every chapter. The book should help you to: identify typical law exam questions; structure a first-class answer; avoid common mistakes; show the examiner what you know; make your answer stand out from the crowd; and find relevant further reading.

This chapter covers freedom of religion, freedom of association, and the right to peaceful assembly, including the scope of those rights, their protection in domestic law and under the ECHR and their application to matters such as religious practices, trade unions, and political organisations, and the right to demonstrate.
3. Murder and Manslaughter
Authors: Allen Mischa
Published: October 2016

The Concentrate Questions and Answers series offers the best preparation for tackling exam questions. Each book includes typical questions, diagram answer plans, suggested answers, and author commentary. This chapter presents sample exam questions on murder and manslaughter and suggested answers. The key issues of direct and oblique intent as it applies to murder are considered. The chapter also deals with the changes to the partial defences to murder (loss of control and diminished responsibility) brought about by the statutory provisions in the Coroners and Justice Act 2009, and the differences between the types of involuntary manslaughter (by an unlawful act, by gross negligence, and by recklessness).