bluuebunny/crossref_metadata_2025 huggingface dataset:
The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes
Authors: Chen Juan , Cai Zhaokui , Bai Meizhu , Yu Xiaohua , Zhang Chao , Cao Changchang , Hu Xihao , Wang Lei , Su Ruibao , Wang Di , Wang Lei , Yao Yingpeng , Ye Rong , Hou Baidong , Yu Yang , Yu Shuyang , Li Jinsong , Xue Yuanchao
Published: August 2018

Activation-induced cytidine deaminase (AID) mediates class switching by binding to a small fraction of single-stranded DNA (ssDNA) to diversify the antibody repertoire. The precise mechanism for highly selective AID targeting in the genome has remained elusive. Here, we report an RNA-binding protein, ROD1 (also known as PTBP3), that is both required and sufficient to define AID-binding sites genome-wide in activated B cells. ROD1 interacts with AID via an ultraconserved loop, which proves to be critical for the recruitment of AID to ssDNA using bi-directionally transcribed nascent RNAs as stepping stones. Strikingly, AID-specific mutations identified in human patients with hyper-IgM syndrome type 2 (HIGM2) completely disrupt the AID interacting surface with ROD1, thereby abolishing the recruitment of AID to immunoglobulin (Ig) loci. Together, our results suggest that bi-directionally transcribed RNA traps the RNA-binding protein ROD1, which serves as a guiding system for AID to load onto specific genomic loci to induce DNA rearrangement during immune responses.
Reconciling glacial Antarctic water stable isotopes with ice sheet topography and the isotopic paleothermometer
Authors: Werner Martin , Jouzel Jean , Masson-Delmotte Valérie , Lohmann Gerrit
Published: August 2018

Stable water isotope records from Antarctica are key for our understanding of Quaternary climate variations. However, the exact quantitative interpretation of these important climate proxy records in terms of surface temperature, ice sheet height and other climatic changes is still a matter of debate. Here we report results obtained with an atmospheric general circulation model equipped with water isotopes, run at a high-spatial horizontal resolution of one-by-one degree. Comparing different glacial maximum ice sheet reconstructions, a best model data match is achieved for the PMIP3 reconstruction. Reduced West Antarctic elevation changes between 400 and 800 m lead to further improved agreement with ice core data. Our modern and glacial climate simulations support the validity of the isotopic paleothermometer approach based on the use of present-day observations and reveal that a glacial ocean state as displayed in the GLAMAP reconstruction is suitable for capturing the observed glacial isotope changes in Antarctic ice cores.
Density-functional fluctuation theory of crowds
Authors: Méndez-Valderrama J. Felipe , Kinkhabwala Yunus A. , Silver Jeffrey , Cohen Itai , Arias T. A.
Published: August 2018

A primary goal of collective population behavior studies is to determine the rules governing crowd distributions in order to predict future behaviors in new environments. Current top-down modeling approaches describe, instead of predict, specific emergent behaviors, whereas bottom-up approaches must postulate, instead of directly determine, rules for individual behaviors. Here, we employ classical density functional theory (DFT) to quantify, directly from observations of local crowd density, the rules that predict mass behaviors under new circumstances. To demonstrate our theory-based, data-driven approach, we use a model crowd consisting of walking fruit flies and extract two functions that separately describe spatial and social preferences. The resulting theory accurately predicts experimental fly distributions in new environments and provides quantification of the crowd “mood”. Should this approach generalize beyond milling crowds, it may find powerful applications in fields ranging from spatial ecology and active matter to demography and economics.
Identification of a novel anoikis signalling pathway using the fungal virulence factor gliotoxin
Authors: Haun Florian , Neumann Simon , Peintner Lukas , Wieland Katrin , Habicht Jüri , Schwan Carsten , Østevold Kristine , Koczorowska Maria Magdalena , Biniossek Martin , Kist Matthias , Busch Hauke , Boerries Melanie , Davis Roger J. , Maurer Ulrich , Schilling Oliver , Aktories Klaus , Borner Christoph
Published: August 2018

Anoikis is a form of apoptosis induced by cell detachment. Integrin inactivation plays a major role in the process but the exact signalling pathway is ill-defined. Here we identify an anoikis pathway using gliotoxin (GT), a virulence factor of the fungusAspergillus fumigatus, which causes invasive aspergillosis in humans. GT prevents integrin binding to RGD-containing extracellular matrix components by covalently modifying cysteines in the binding pocket. As a consequence, focal adhesion kinase (FAK) is inhibited resulting in dephosphorylation of p190RhoGAP, allowing activation of RhoA. Sequential activation of ROCK, MKK4/MKK7 and JNK then triggers pro-apoptotic phosphorylation of Bim. Cells in suspension or lacking integrin surface expression are insensitive to GT but are sensitised to ROCK-MKK4/MKK7-JNK-dependent anoikis upon attachment to fibronectin or integrin upregulation. The same signalling pathway is triggered by FAK inhibition or inhibiting integrin αV/β3 with Cilengitide. Thus, GT can target integrins to induce anoikis on lung epithelial cells.
Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation
Authors: Benzinger Dirk , Khammash Mustafa
Published: August 2018

Many natural transcription factors are regulated in a pulsatile fashion, but it remains unknown whether synthetic gene expression systems can benefit from such dynamic regulation. Here we find, using a fast-acting, optogenetic transcription factor in Saccharomyces cerevisiae, that dynamic pulsatile signals reduce cell-to-cell variability in gene expression. We then show that by encoding such signals into a single input, expression mean and variability can be independently tuned. Further, we construct a light-responsive promoter library and demonstrate how pulsatile signaling also enables graded multi-gene regulation at fixed expression ratios, despite differences in promoter dose-response characteristics. Pulsatile regulation can thus lead to beneficial functional behaviors in synthetic biological systems, which previously required laborious optimization of genetic parts or the construction of synthetic gene networks.
Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors
Authors: Pareja Fresia , Brandes Alissa H. , Basili Thais , Selenica Pier , Geyer Felipe C. , Fan Dan , Da Cruz Paula Arnaud , Kumar Rahul , Brown David N. , Gularte-Mérida Rodrigo , Alemar Barbara , Bi Rui , Lim Raymond S. , de Bruijn Ino , Fujisawa Sho , Gardner Rui , Feng Elvin , Li Anqi , da Silva Edaise M. , Lozada John R. , Blecua Pedro , Cohen-Gould Leona , Jungbluth Achim A. , Rakha Emad A. , Ellis Ian O. , Edelweiss Maria I. A. , Palazzo Juan , Norton Larry , Hollmann Travis , Edelweiss Marcia , Rubin Brian P. , Weigelt Britta , Reis-Filho Jorge S.
Published: August 2018

Granular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules. The genetic drivers of GCTs are currently unknown. Here, we apply whole-exome sequencing and targeted sequencing analysis to reveal mutually exclusive, clonal, inactivating somatic mutations in the endosomal pH regulatorsATP6AP1orATP6AP2in 72% of GCTs. Silencing of these genes in vitro results in impaired vesicle acidification, redistribution of endosomal compartments, and accumulation of intracytoplasmic granules, recapitulating the cardinal phenotypic characteristics of GCTs and providing a novel genotypic–phenotypic correlation. In addition, depletion of ATP6AP1 or ATP6AP2 results in the acquisition of oncogenic properties. Our results demonstrate that inactivating mutations ofATP6AP1andATP6AP2are likely oncogenic drivers of GCTs and underpin the genesis of the intracytoplasmic granules that characterize them, providing a genetic link between endosomal pH regulation and tumorigenesis.
Luciferase-induced photoreductive uncaging of small-molecule effectors
Authors: Lindberg Eric , Angerani Simona , Anzola Marcello , Winssinger Nicolas
Published: August 2018

Bioluminescence resonance energy transfer (BRET) is extensively used to study dynamic systems and has been utilized in sensors for studying protein proximity, metabolites, and drug concentrations. Herein, we demonstrate that BRET can activate a ruthenium-based photocatalyst which performs bioorthogonal reactions. BRET from luciferase to the ruthenium photocatalyst is used to uncage effector molecules with up to 64 turnovers of the catalyst, achieving concentrations >0.6 μM effector with 10 nM luciferase construct. Using a BRET sensor, we further demonstrate that the catalysis can be modulated in response to an analyte, analogous to allosterically controlled enzymes. The BRET-induced reaction is used to uncage small-molecule drugs (ibrutinib and duocarmycin) at biologically effective concentrations in cellulo.
Quantitative mappings between symmetry and topology in solids
Authors: Song Zhida , Zhang Tiantian , Fang Zhong , Fang Chen
Published: August 2018

The study of spatial symmetries was accomplished during the last century and had greatly improved our understanding of the properties of solids. Nowadays, the symmetry data of any crystal can be readily extracted from standard first-principles calculation. On the other hand, the topological data (topological invariants), the defining quantities of nontrivial topological states, are in general considerably difficult to obtain, and this difficulty has critically slowed down the search for topological materials. Here we provide explicit and exhaustive mappings from symmetry data to topological data for arbitrary gapped band structure in the presence of time-reversal symmetry and any one of the 230 space groups. The mappings are completed using the theoretical tools of layer construction and symmetry-based indicators. With these results, finding topological invariants in any given gapped band structure reduces to a simple search in the mapping tables provided.
Publisher Correction: Genomic instability in mutant p53 cancer cells upon entotic engulfment
Authors: Mackay Hannah L. , Moore David , Hall Callum , Birkbak Nicolai J. , Jamal-Hanjani Mariam , Karim Saadia A. , Phatak Vinaya M. , Piñon Lucia , Morton Jennifer P. , Swanton Charles , Le Quesne John , Muller Patricia A. J.
Published: August 2018

The original version of this article incorrectly omitted an affiliation of Patricia A. J. Muller: ‘Cancer Research UK Manchester Institute, The University of Manchester | Alderley Park, Manchester, SK10 4TG, UK’. This has been corrected in both the PDF and HTML versions of the Article.
Author Correction: Intracellular localization of nanoparticle dimers by chirality reversal
Authors: Sun Maozhong , Xu Liguang , Bahng Joong Hwan , Kuang Hua , Alben Silas , Kotov Nicholas A. , Xu Chuanlai
Published: August 2018

The original version of this Article contained an error in the spelling of the author Joong Hwan Bahng, which was incorrectly given as Joong Hwan Banhg. This has been corrected in both the PDF and HTML versions of the Article.
Publisher Correction: Single-shot condensation of exciton polaritons and the hole burning effect
Authors: Estrecho E. , Gao T. , Bobrovska N. , Fraser M. D. , Steger M. , Pfeiffer L. , West K. , Liew T. C. H. , Matuszewski M. , Snoke D. W. , Truscott A. G. , Ostrovskaya E. A.
Published: August 2018

The original PDF version of this Article had an incorrect Published online date of 25 December 2018; it should have been 9 August 2018. This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.
NF1 deficiency correlates with estrogen receptor signaling and diminished survival in breast cancer
Authors: Dischinger Patrick S. , Tovar Elizabeth A. , Essenburg Curt J. , Madaj Zachary B. , Gardner Eve E. , Callaghan Megan E. , Turner Ashley N. , Challa Anil K. , Kempston Tristan , Eagleson Bryn , Kesterson Robert A. , Bronson Roderick T. , Bowman Megan J. , Graveel Carrie R. , Steensma Matthew R.
Published: August 2018

The key negative regulatory gene of the RAS pathway, NF1, is mutated or deleted in numerous cancer types and is associated with increased cancer risk and drug resistance. Even though women with neurofibromatosis (germline NF1 mutations) have a substantially increased breast cancer risk at a young age and NF1 is commonly mutated in sporadic breast cancers, we have a limited understanding of the role of NF1 in breast cancer. We utilized CRISPR–Cas9 gene editing to create Nf1 rat models to evaluate the effect of Nf1 deficiency on tumorigenesis. The resulting Nf1 indels induced highly penetrant, aggressive mammary adenocarcinomas that express estrogen receptor (ER) and progesterone receptor (PR). We identified distinct Nf1 mRNA and protein isoforms that were altered during tumorigenesis. To evaluate NF1 in human breast cancer, we analyzed genomic changes in a data set of 2000 clinically annotated breast cancers. We found NF1 shallow deletions in 25% of sporadic breast cancers, which correlated with poor clinical outcome. To identify biological networks impacted by NF1 deficiency, we constructed gene co-expression networks using weighted gene correlation network analysis (WGCNA) and identified a network connected to ESR1 (estrogen receptor). Moreover, NF1-deficient cancers correlated with established RAS activation signatures. Estrogen-dependence was verified by estrogen-ablation in Nf1 rats where rapid tumor regression was observed. Additionally, Nf1 deficiency correlated with increased estrogen receptor phosphorylation in mammary adenocarcinomas. These results demonstrate a significant role for NF1 in both NF1-related breast cancer and sporadic breast cancer, and highlight a potential functional link between neurofibromin and the estrogen receptor.
Interrupted reprogramming of alveolar type II cells induces progenitor-like cells that ameliorate pulmonary fibrosis
Authors: Guo Li , Karoubi Golnaz , Duchesneau Pascal , Aoki Fabio Gava , Shutova Maria V. , Rogers Ian , Nagy Andras , Waddell Thomas K.
Published: August 2018

We describe here an interrupted reprogramming strategy to generate “induced progenitor-like (iPL) cells” from alveolar epithelial type II (AEC-II) cells. A carefully defined period of transient expression of reprogramming factors (Oct4, Sox2, Klf4, and c-Myc (OSKM)) is able to rescue the limited in vitro clonogenic capacity of AEC-II cells, potentially by activation of a bipotential progenitor-like state. Importantly, our results demonstrate that interrupted reprogramming results in controlled expansion of cell numbers yet preservation of the differentiation pathway to the alveolar epithelial lineage. When transplanted to the injured lungs, AEC-II-iPL cells are retained in the lung and ameliorate bleomycin-induced pulmonary fibrosis. Interrupted reprogramming can be used as an alternative approach to produce highly specified functional therapeutic cell populations and may lead to significant advances in regenerative medicine.
Understanding the effects of education through the lens of biology
Authors: Sokolowski H. Moriah , Ansari Daniel
Published: August 2018

Early educational interventions aim to close gaps in achievement levels between children. However, early interventions do not eliminate individual differences in populations and the effects of early interventions often fade-out over time, despite changes of the mean of the population immediately following the intervention. Here, we discuss biological factors that help to better understand why early educational interventions do not eliminate achievement gaps. Children experience and respond to educational interventions differently. These stable individual differences are a consequence of biological mechanisms that support the interplay between genetic predispositions and the embedding of experience into our biology. Accordingly, we argue that it is not plausible to conceptualize the goals of educational interventions as both a shifting of the mean and a narrowing of the distribution of a particular measure of educational attainment assumed to be of utmost importance (such as a standardized test score). Instead of aiming to equalize the performance of students, the key goal of educational interventions should be to maximize potential at the individual level and consider a kaleidoscope of educational outcomes across which individuals vary. Additionally, in place of employing short-term interventions in the hope of achieving long-term gains, educational interventions need to be sustained throughout development and their long-term, rather than short-term, efficacy be evaluated. In summary, this paper highlights how biological research is valuable for driving a re-evaluation of how educational success across development can be conceptualized and thus what policy implications may be drawn.
Publisher Correction: Effects of metformin on colorectal cancer stem cells depend on alterations in glutamine metabolism
Authors: Kim Jae Hyun , Lee Kyoung Jin , Seo Yoojeong , Kwon Ji-Hee , Yoon Jae Pil , Kang Jo Yeon , Lee Hyun Jung , Park Soo Jung , Hong Sung Pil , Cheon Jae Hee , Kim Won Ho , Il Kim Tae
Published: August 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Application of the fragment molecular orbital method to discover novel natural products for prion disease
Authors: Choi Jiwon , Kim Hyo-Jin , Jin Xuemei , Lim Hocheol , Kim Songmi , Roh In-Soon , Kang Hae-Eun , No Kyoung Tai , Sohn Hyun-Joo
Published: August 2018

Conformational conversion of the normal cellular isoform of the prion protein PrPC into an infectious isoform PrPSc causes pathogenesis in prion diseases. To date, numerous antiprion compounds have been developed to block this conversion and to detect the molecular mechanisms of prion inhibition using several computational studies. Thus far, no suitable drug has been identified for clinical use. For these reasons, more accurate and predictive approaches to identify novel compounds with antiprion effects are required. Here, we have applied an in silico approach that integrates our previously described pharmacophore model and fragment molecular orbital (FMO) calculations, enabling the ab initio calculation of protein-ligand complexes. The FMO-based virtual screening suggested that two natural products with antiprion activity exhibited good binding interactions, with hotspot residues within the PrPC binding site, and effectively reduced PrPSc levels in a standard scrapie cell assay. Overall, the outcome of this study will be used as a promising strategy to discover antiprion compounds. Furthermore, the SAR-by-FMO approach can provide extremely powerful tools in quickly establishing virtual SAR to prioritise compounds for synthesis in further studies.
A novel, non-invasive model for diagnosing liver fibrosis stage in patients with hepatocellular carcinoma
Authors: Ouyang Gao-Xiong , Zhang Yu-mei , Zhu Shao-Liang , Wang Peng , Ren Yuan , Li Jia-Hao , Liu Yu-Kai , Chen Jun , Xiang Bang-De , Li Le-Qun , Liu Jian-Yong , Zhang Zhi-Ming
Published: August 2018

The aim of this study was to investigate the diagnostic value of the platelet count-to-spleen volume ratio (PSR) for diagnosing hepatic fibrosis in patients with hepatocellular carcinoma (HCC). In this interim analysis of an on-going prospective study, 117 patients with HCC and with or without cirrhosis or fibrosis in different stages were analyzed. Fibrosis staging negatively correlated with PSR and the liver volume-to-spleen volume ratio (LSR), while it positively correlated with aspartate aminotransferase-to-platelet ratio index (APRI), Frons’ index, S-index and a fibrosis index based on four factors (FIB-4). The area under the receiver operating characteristic curve (AUROC) was significantly larger for PSR (0.777) than LSR (0.633, P = 0.002). Among patients with significant fibrosis, AUROC for PSR did not differ significantly from the AUROCs for APRI (0.789, P = 0.825), Frons’ index (0.674, P = 0.102), FIB-4 (0.704, P = 0.251) or S-index (0.696, P = 0.204). Among patients with severe fibrosis, AUROC was significantly higher for PSR (0.808) than for LSR (0.685, P = 0.003), Frons’ index (0.673, P = 0.014), FIB-4 (0.684, P = 0.029), or S-index (0.672, P = 0.016); in contrast, the AUROC for PSR was not significantly different from that for APRI (0.739, P = 0.215). Among patients with cirrhosis, AUROC was significantly higher for PSR (0.814) than for LSR (0.671, P = 0.001) or S-index (0.679, P = 0.022), while the AUROC for PSR did not differ significantly from those for APRI (0.711, P = 0.105), Frons’ index (0.722, P = 0.061) or FIB-4 (0.708, P = 0.079). Our results suggest that PSR may be a useful non-invasive model for diagnosing liver fibrosis stage in patients with HCC in China.
Exploring the potential of NTME/GC-MS, in the establishment of urinary volatomic profiles. Lung cancer patients as case study
Authors: Porto-Figueira Priscilla , Pereira Jorge , Miekisch Wolfram , Câmara José S.
Published: August 2018

The growing cancer incidence and mortality worldwide claims for the development of novel diagnostic strategies. In this study we aimed to explore the potential of an innovative methodology, based on a needle trap microextraction (NTME), combined with gas chromatography-mass spectrometry (GC-MS), as new approach to isolate and profile urinary volatile organic metabolites (VOMs) from lung cancer (LC) patients and healthy individuals (CTRL). In this context, different experimental parameters with influence of NTME extraction efficiency including, temperature, equilibration time, headspace volume, ionic strength, pH, effects of sample volume and stirring, were investigated and optimized. For the DVB/CarX/Car1000 needle trap device (NTD), the best results were obtained using 40 mL headspace of a 4-mL acidified (pH = 2) urine sample with 20% NaCl and an extraction temperature of 50 °C for 40 min of equilibration time. The stability of the isolated VOMs was investigated up to 72 h after extraction. From the VOMs identified, belonging namely to ketones, sulphur and benzene derivatives, 98 presented a frequency of occurrence above 90%. Data were processed by discriminant analysis, retrieving differentiated clusters for LC and CTRL groups. As far we are aware, this is the first study using NTME/GC-MS to establish urinary volatomic profiles. Preliminary results are very promising, as broad and comprehensive volatile profiles were obtained. Moreover, the extended storage stability of the NTD devices opens new opportunities for sampling other matrices in a wide range of applications.
Strengthening the efficacy of official food control improves Listeria monocytogenes prevention in fish-processing plants
Authors: Aalto-Araneda Mariella , Korkeala Hannu , Lundén Janne
Published: August 2018

Vacuum-packaged cold-salted and cold-smoked fish products are considered typical vehicles forListeria monocytogenes, the causative agent of the food-borne disease listeriosis, which is increasingly prevalent in the European Union. Efficacy of both the fish processing plant self-checking system and official food control conducted by authorities are crucial forL.monocytogenesprevention in the processing of these risky products. However, the impact of official control onL.monocytogenesprevention in the processing of fish products has not been extensively studied. We investigated the occurrence, control measures, and correction of non-compliances predisposing toL.monocytogenesin Finnish fish processing plants. The following features were associated withL.monocytogenesoccurrence: (a) frequency of non-compliances concerning processing machinery, (b) recurrence of non-compliances, and (c) frequency of non-compliances for which official control measures were requested by inspecting authorities. Official control of fish processing plants had focused on risky areas, but non-compliances were common and their correction exhibited deficiencies. We conclude thatL.monocytogenesprevention in fish processing can be enhanced by strengthening official food control measures and processing plant compliance. In particular, timely correction of all food safety violations must be improved.
Induction of Ptp2 and Cmp2 protein phosphatases is crucial for the adaptive response to ER stress in Saccharomyces cerevisiae
Authors: Mizuno Tomoaki , Nakamura Meyu , Irie Kenji
Published: August 2018

Expression control of the protein phosphatase is critically involved in crosstalk and feedback of the cellular signaling. In the budding yeast ER stress response, multiple signaling pathways are activated and play key roles in adaptive reactions. However, it remains unclear how the expression level of the protein phosphatase is modulated during ER stress response. Here, we show that ER stress increases expression of Ptp2 tyrosine phosphatase and Cmp2 calcineurin phosphatase. Upregulation of Ptp2 is due to transcriptional activation mediated by Mpk1 MAP kinase and Rlm1 transcription factor. This induction is important for Ptp2 to effectively downregulate the activity of Hog1 MAP kinase. The budding yeast genome possesses two genes, CMP2 and CNA1, encoding the catalytic subunit of calcineurin phosphatase. CMP2 is more important than CNA1 not only in ER stress response, but also in salt stress response. Higher promoter activity of CMP2 contributes to its relative functional significance in ER stress response, but is less important for salt stress response. Thus, our results suggest that expression control of Ptp2 and Cmp2 protein phosphatases at the promoter level is crucial for adaptive responses to ER stress.
Groupwise image registration based on a total correlation dissimilarity measure for quantitative MRI and dynamic imaging data
Authors: Guyader Jean-Marie , Huizinga Wyke , Poot Dirk H. J. , van Kranenburg Matthijs , Uitterdijk André , Niessen Wiro J. , Klein Stefan
Published: August 2018

The most widespread technique used to register sets of medical images consists of selecting one image as fixed reference, to which all remaining images are successively registered. This pairwise scheme requires one optimization procedure per pair of images to register. Pairwise mutual information is a common dissimilarity measure applied to a large variety of datasets. Alternative methods, called groupwise registrations, have been presented to register two or more images in a single optimization procedure, without the need of a reference image. Given the success of mutual information in pairwise registration, we adapt one of its multivariate versions, called total correlation, in a groupwise context. We justify the choice of total correlation among other multivariate versions of mutual information, and provide full implementation details. The resulting total correlation measure is remarkably close to measures previously proposed by Huizinga et al. based on principal component analysis. Our experiments, performed on five quantitative imaging datasets and on a dynamic CT imaging dataset, show that total correlation yields registration results that are comparable to Huizinga’s methods. Total correlation has the advantage of being theoretically justified, while the measures of Huizinga et al. were designed empirically. Additionally, total correlation offers an alternative to pairwise mutual information on quantitative imaging datasets.
Stationary log-normal distribution of weights stems from spontaneous ordering in adaptive node networks
Authors: Uzan Herut , Sardi Shira , Goldental Amir , Vardi Roni , Kanter Ido
Published: August 2018

Experimental evidence recently indicated that neural networks can learn in a different manner than was previously assumed, using adaptive nodes instead of adaptive links. Consequently, links to a node undergo the same adaptation, resulting in cooperative nonlinear dynamics with oscillating effective link weights. Here we show that the biological reality of stationary log-normal distribution of effective link weights in neural networks is a result of such adaptive nodes, although each effective link weight varies significantly in time. The underlying mechanism is a stochastic restoring force emerging from a spontaneous temporal ordering of spike pairs, generated by strong effective link preceding by a weak one. In addition, for feedforward adaptive node networks the number of dynamical attractors can scale exponentially with the number of links. These results are expected to advance deep learning capabilities and to open horizons to an interplay between adaptive node rules and the distribution of network link weights.
Yeast quality in juvenile diet affects Drosophila melanogaster adult life traits
Authors: Grangeteau Cédric , Yahou Fairouz , Everaerts Claude , Dupont Sébastien , Farine Jean-Pierre , Beney Laurent , Ferveur Jean-François
Published: August 2018

Diet quality is critical for animal development and survival. Fungi can provide nutrients that are essential to organisms that are unable to synthetize them, such as ergosterol in Drosophila melanogaster. Drosophila studies examining the influence of yeast quality in the diet have generally either provided the diet over the whole life span (larva to adult) or during the adult stage and have rarely focussed on the juvenile diet. Here, we tested the effect of yeast quality in the larval diet on pre-adult development and adult weight, survival, reproduction and food preference. The yeast Saccharomyces cerevisiae was added in three forms in three treatments—live, heated or dried—to food used as the juvenile diet or was not added (empty treatment). Adults resulting from the larvae raised on these four juvenile diets were all maintained on a similar standard laboratory food diet. Our data indicate that yeast quality in the juvenile diet affects larva-to-pupa—but not pupa-to-adult—development. Importantly, adult survival, food preference, mating behaviour and cuticular pheromones strongly varied with the juvenile diet. Therefore, the variation of yeast quality in the pre-adult Drosophila diet affects key adult life traits involved in food search, reproduction and survival.
Two-component marangoni-contracted droplets: friction and shape
Authors: Benusiglio Adrien , Cira Nate J. , Prakash Manu
Published: August 2018

We discuss in this paper the nature of the friction generated as a Marangoni-contracted drop glides on a slope.
Untargeted metabolomics-like screening approach for chemical characterization and differentiation of canopic jar and mummy samples from Ancient Egypt using GC-high resolution MS
Authors: Brockbals Lana , Habicht Michael , Hajdas Irka , Galassi Francesco M. , Rühli Frank J. , Kraemer Thomas
Published: August 2018

Canopic jarsvs.mummies: first time use of modern metabolomic techniques to unravel ancient embalming chemistry.
Mitochondria: promising organelle targets for cancer diagnosis and treatment
Authors: Hou Xiao-Shuang , Wang Huai-Song , Mugaka Benson Peter , Yang Gong-Jun , Ding Ya
Published: August 2018

Mitochondrial-mediated tumor monitoring provides a new perspective on mitochondria-based therapy.
Phosphine free Mn-complex catalysed dehydrogenative C–C and C–heteroatom bond formation: a sustainable approach to synthesize quinoxaline, pyrazine, benzothiazole and quinoline derivatives
Authors: Das Kalicharan , Mondal Avijit , Srimani Dipankar
Published: August 2018

Sustainable synthesis of quinoxalines, pyrazines, benzothiazoles and quinolines catalysed by a phosphine free Mn(i) complex.
Templated bipolar electrolysis for fabrication of robust Co and Pt nanorods
Authors: Koizumi Yuki , Nishiyama Hiroki , Tomita Ikuyoshi , Inagi Shinsuke
Published: August 2018

Robust, uniform and well-aligned arrays of Co and Pt nanorods were obtained by means of bipolar electrochemistry.
Expanding possibilities for solid-phase crystallization by exsolving tunable Pd–NiO core–shell nanostructures
Authors: Buharon Mariana , Singh Sarika , Komarala Eswaravara P. , Rosen Brian A.
Published: August 2018

The major drawbacks of solid-phase crystallization as a means of synthesizing catalysts are the lack of heterogeneous structural diversity and the comparatively low metal dispersion it affords.
Boron reagents for divergent radiochemistry
Authors: Wilson Thomas C. , Cailly Thomas , Gouverneur Véronique
Published: August 2018

This review discusses boron reagents as precursors for divergent radiolabelling with a focus on carbon-11, fluorine-18 and iodine-123, -125, -131.
Naphthalene containing amino-ether macrocycle based Cu(ii) templated [2]pseudorotaxanes and OFF/ON fluorescence switching via axle substitution
Authors: Bej Somnath , Ghosh Pradyut
Published: August 2018

A newly synthesized naphthalene containing macrocycle is employed towards the development of Cu(ii) templated [2]pseudorotaxanes. Furthermore, a fluorophoric axle threaded [2]pseudorotaxane is explored as an “OFF/ON” fluorescence switch through the axle substitution.
Impact of soil properties on the soil methane flux response to biochar addition: a meta-analysis
Authors: Cong Weiwei , Meng Jun , Ying Samantha C.
Published: August 2018

In an effort to optimize soil management practices that can help mitigate terrestrial carbon emissions, biochar has been applied to a wide range of soil environments to examine its effect on soil greenhouse gas emissions.
MoO2/Mo2N hybrid nanobelts doped with gold nanoparticles and their enhanced supercapacitive behavior
Authors: Tan Yongtao , Dong Wenju , Li Yuan , Muchakayala Ravi , Kong Lingbin , Kang Long , Ran Fen
Published: August 2018

AuNPMoON-nanobelts with a width of 200 nm and an Au content of 1.08 wt% show a capacitance of 348 F g−1.
Dinuclear iron(iii) complexes bearing phenylene-bridged bis(amino triphenolate) ligands as catalysts for the copolymerization of cyclohexene oxide with carbon dioxide or phthalic anhydride
Authors: Shi Zhan , Jiang Qingzhe , Song Zhaozheng , Wang Zhihui , Gao Canglong
Published: August 2018

Dinuclear iron(iii) complexes bearing rigid ortho-, meta-, and para-phenylene bridges as effective catalysts for CHO/CO2 and CHO/PA copolymerizations.
Tri-pillar[5]arene-based multi-stimuli-responsive supramolecular polymers for fluorescence detection and separation of Hg2+
Authors: Jiang Xiao-Mei , Huang Xiao-Juan , Song Shan-Shan , Ma Xiao-Qiang , Zhang You-Ming , Yao Hong , Wei Tai-Bao , Lin Qi
Published: August 2018

A novel tri-pillar[5]arene based supramolecular polymer (JP5G) shows multiple stimuli-response properties and could detect and remove Hg2+ from aqueous solution.
Conductive fullerene surfactants via anion doping as cathode interlayers for efficient organic and perovskite solar cells
Authors: Yan Kangrong , Liu Zhi-Xi , Li Xue , Chen Jiehuan , Chen Hongzheng , Li Chang-Zhi
Published: August 2018

Conductive fullerenes, with mild solution-processing capabilities, are developed as electron transporting materials for efficient organic and perovskite solar cells.
Nitrogen doped hierarchical activated carbons derived from polyacrylonitrile fibers for CO2 adsorption and supercapacitor electrodes
Authors: Zheng L. , Li W. B. , Chen J. L.
Published: August 2018

Nitrogen doped activated carbons with high surface area up to 3797 m2 g−1 exhibit specific capacitance of 231 F g−1 at a current density of 10 A g−1.
Ultrasensitive detection of low-ppm H2S gases based on palladium-doped porous silicon sensors
Authors: Eom Nu Si A. , Cho Hong-Baek , Lim Hyo-Ryoung , Hwang Tea-Yeon , Song Yoseb , Choa Yong-Ho
Published: August 2018

In this study, the sensing properties of palladium-doped porous silicon (Pd/p-Si) substrates for low-ppm level detection of toxic H2S gas are investigated.
TfOH mediated intermolecular electrocyclization for the synthesis of pyrazolines and its application in alkaloid synthesis
Authors: Annes Sesuraj Babiola , Vairaprakash Pothiappan , Ramesh Subburethinam
Published: August 2018

A metal free and green synthetic methodology employing aldehydes, phenylhydrazine and styrene mediated by TfOH has been developed to access 1,3,5-trisubstituted pyrazolines. The synthetic application of the methodology is demonstrated in the synthesis of a pyrazoline alkaloid.
Origin of the effects of PEG additives in electrolytes on the performance of quantum dot sensitized solar cells
Authors: Sun Yu , Jiang Guocan , Zhou Mengsi , Pan Zhenxiao , Zhong Xinhua
Published: August 2018

The origin for the effect of PEG additives in polysulfide electrolyte on the performance of both photoanode and counter electrode was explored, and a facile and general route for remarkably improving photovoltaic performance of QDSCs was offered.
Urea-assisted hydrothermal synthesis of a hollow hierarchical LiNi0.5Mn1.5O4 cathode material with tunable morphology characteristics
Authors: Qin Xing , Zhou Mushang , Zong Bo , Guo Jianling , Gong Jiajia , Wang Li , Liang Guangchuan
Published: August 2018

The particle morphology and size of LiNi0.5Mn1.5O4 material can be controlled by changing the precursors' morphology and size, which can be controlled by reactant concentration.
Synthesis and characterization of CdSxSe1−xalloy quantum dots with composition-dependent band gaps and paramagnetic properties
Authors: Chung Yueh-Chi , Yang Chien-Hsin , Zheng Hao-Wen , Tsai Ping-Szu , Wang Tzong-Liu
Published: August 2018

Both the fluorescence intensity and quantum yield of all the nanocrystals are much enhanced after the CdSxSe1−xQD cores are coated with a ZnS shell.
Preparation and investigation of novel SrCl2/DCMC-modified (via DOPA) decellularized arteries with excellent physicochemical properties and cytocompatibility for vascular scaffolds
Authors: Qi Hao , Cheng Can , Wang Xu , Yu Xixiun
Published: August 2018

A new method of fabricating vascular scaffolds was designed in this article by crosslinking the porcine arteries using dialdehyde carboxymethyl (DCMC) and further introducing the Sr element on the surface of modified arteries using DOPA.
Correction: Recent advances in surface plasmon-driven catalytic reactions
Authors: Ren Xin , Cao En , Lin Weihua , Song Yuzhi , Liang Wenjie , Wang Jingang
Published: August 2018

Correction for ‘Recent advances in surface plasmon-driven catalytic reactions’ by Xin Ren et al., RSC Adv., 2017, 7, 31189–31203.
A one-step method for covalent bond immobilization of biomolecules on silica operated in aqueous solution
Authors: Sim Yong-Kyun , Jung Heetae , Kim Su Hyun , Park Jung-Woo , Park Woo-Jin , Jun Chul-Ho
Published: August 2018

One-step covalent bond immobilization of biomolecules on silica in water is promoted by weak organic acid using bifunctional linker.
Luminescent mesoporous nanorods as photocatalytic enzyme-like peroxidase surrogates
Authors: Ortega-Liebana M. Carmen , Hueso Jose L. , Fernandez-Pacheco Rodrigo , Irusta Silvia , Santamaria Jesus
Published: August 2018

One-step synthesis of luminescent mesoporous rods with enhanced photocatalytic response as novel metal-free peroxidase-like nanozymes.
Will the competitive future of solid state Li metal batteries rely on a ceramic or a composite electrolyte?
Authors: Gutiérrez-Pardo Antonio , Pitillas Martinez Andrea I. , Otaegui Laida , Schneider Meike , Roters Andreas , Llordés Anna , Aguesse Frédéric , Buannic Lucienne
Published: August 2018

The industrial development of Li metal solid state batteries will be boosted not only by providing highly Li+ conductive electrolyte materials, but also by demonstrating their technical viability in the actual device.
To study surface and sub-surface nanomechanical properties of electrospun polyacrylonitrile (PAN) nanofibers/polydimethylsiloxane (PDMS) composites
Authors: Deshpande Tushar D. , Singh Yogesh R.G. , Patil Sandip , Joshi Yogesh M. , Sharma Ashutosh
Published: August 2018

We investigate surface and sub-surface nanomechanical properties of nanocomposites based on a crosslinked polydimethylsiloxane (PDMS) elastomer and electrospun polyacrylonitrile (PAN) nanofibers.
In-depth understanding of interfacial crystallization via Flash DSC and enhanced energy storage density in ferroelectric P(VDF-CTFE)/Au NRs nanocomposites for capacitor application
Authors: Chen Yingxin , Yao Lingyun , Yang Chengbiao , Zhang Lei , Zheng Peng , Liu Aiping , Shen Qun-Dong
Published: August 2018

Great improvements in energy density are attained in P(VDF-CTFE)/Au NRs nanocomposites, and interfacial crystallization kinetics are well revealed by Flash DSC.
Strong anchoring effect of ferric chloride-graphite intercalation compounds (FeCl3-GICs) with tailored epoxy groups for high-capacity and stable lithium storage
Authors: Zhang Chengzhi , Ma Jianmin , Han Fei , Liu Hongbo , Zhang Fuquan , Fan Changling , Liu Jinshui , Li Xuanke
Published: August 2018

FeCl3-intercalated graphite intercalation compounds are developed as stable anodes for optimized lithium storage based on a strong chemical anchoring effect.
Carbon dots with red emission as a fluorescent and colorimeteric dual-readout probe for the detection of chromium(vi) and cysteine and its logic gate operation
Authors: Gao Yifang , Jiao Yuan , Lu Wenjing , Liu Yang , Han Hui , Gong Xiaojuan , Xian Ming , Shuang Shaomin , Dong Chuan
Published: August 2018

A schematic illustration for assaying Cr(vi) and Cys activity by CDs with both fluorescent and colorimetric readouts.
Oxidase-mimicking activity of perovskite LaMnO3+δ nanofibers and their application for colorimetric sensing
Authors: Song Lifei , Zhu Yun , Yang Zezhou , Wang Ce , Lu Xiaofeng
Published: August 2018

Excellent oxidase-like mimics based on the ABX3-type perovskite structure and the corresponding sensitive colorimetric detection of l-cysteine have been developed.
Ultrasound induced phase-transition and invisible nanobomb for imaging-guided tumor sonodynamic therapy
Authors: Zhang Huijuan , Chen Jianjiao , Zhu Xing , Ren Yanping , Cao Fang , Zhu Ling , Hou Lin , Zhang Hongling , Zhang Zhenzhong
Published: August 2018

This ‘nanobomb’ can mechanically destroy tumor vessels, significantly relieve hypoxia within the tumor and reduce the microvessel density.
Versatile synthesis of α-fused BODIPY displaying intense absorption in the NIR region and high electron affinity
Authors: Huaulmé Quentin , Sutter Alexandra , Fall Sadiara , Jacquemin Denis , Lévêque Patrick , Retailleau Pascal , Ulrich Gilles , Leclerc Nicolas
Published: August 2018

A straightforward, highly regioselective and versatile chemical route allows the synthesis of α-fused boron dipyrromethene regioisomers.
A multi-state fluorescent switch with multifunction of AIE, methanol-responsiveness, photochromism and mechanochromism
Authors: Huang Lili , Qiu Yixin , Wu Chenyang , Ma Zhiyong , Shen Zhihao , Jia Xinru
Published: August 2018

In this article, we report a newly designed molecule, RhTPE, synthesized by fusing rhodamine with TPE, which realizes both emission color change and on/off switching.
Lactate transport facilitates neurite outgrowth
Authors: Chen Kun , Cheng Peng , Wang Huan , Gao Shutao , Li Xiao , Deng Zhenhan , Liu Jian , Sun Xuying
Published: August 2018

How glia affect neurite outgrowth during neural development has not been well elucidated. In the present study, we found that disruption of lactate production using 1,4-dideoxy-1,4-imino-D-arabinitol (DAB) and isofagomine significantly interfered with neurite outgrowth and that exogenous application of L-lactate rescued neurite growth failure. Monocarboxylate transporter-2-knockout, which blocked the lactate shuttle in neurons, showed a remarkable decrease in the length of axons and dendrites. We further demonstrated that Akt activity was decreased while glycogen synthase kinase 3β (GSK3β) activity was increased after astrocytic glycogen phosphorylase blockade. Additionally, GSK3βSer9 mutation reversed neurite growth failure caused by DAB and isofagomine. Our results suggested that lactate transportation played a critical role in neural development and disruption of the lactate shuttle in quiescent condition also affected neurite outgrowth in the central nervous system.
Robust filtering for uncertain two‐dimensional continuous‐discrete state‐delay systems in finite frequency domains
Authors: Wang Guopeng , Xu Huiling , Wang Lu , Yao Juan
Published: August 2018

In this work, the problem of robust filtering for uncertain two‐dimensional (2D) continuous‐discrete Roesser systems with state delays in finite frequency ranges is investigated. This study first develops the equivalence between a frequency domain inequality (FDI) and a linear matrix inequality. In particular, the proposed result covers FDIs in finite frequency intervals for 2D continuous/discrete/continuous‐discrete settings. Using the result, the existing finite frequency bounded ream lemmas and the finite frequency positive real lemmas have been generalised to uncertain 2D state‐delay Roesser systems. Then, a robust finite frequency filter design method for uncertain 2D continuous‐discrete state delay Roesser systems is given. Finally, examples are provided to clearly demonstrate the effectiveness of the proposed method.
Detecting TCP ACK storm attack: a state transition modelling approach
Authors: Hubballi Neminath , Santini Jonathan
Published: August 2018

Ack‐storm DoS attacks are injection attacks against an active Transmission Control Protocol (TCP) connection. These attacks can be generated by a very weak adversary and can generate amplification factor of orders of magnitude by exploiting a weakness in the TCP protocol specification. This attack requires sending two packets by the adversary with acknowledgement number greater than the sequence number used in each direction and the two end hosts will attempt to re‐synchronise the sequence numbers by sending duplicate acknowledgement and enter a loop. In this study, the authors propose a state transition model based detection scheme to detect these DoS attacks. This state transition machine called constrained counting automata (CCA) has the ability to count the number of times a state has been revisited and its transitions are constrained by invariant conditions to be satisfied. They model the chances of receiving a packet with acknowledgement number greater than the sequence number used by its peer as a probability distribution and use it to set appropriate value of threshold on revisits of a state for detecting attack. By experimenting within a local network and in Internet, they show that CCA can detect Ack‐storm DoS attacks.
Reinforcement learning‐based negotiation for spectrum micro‐trading framework
Authors: Paul Ayan , Mukherjee Devodyuti , Maitra Madhubanti
Published: August 2018

Spectrum trading has been permitted in most of the major wireless markets to facilitate better utilisation of spectrum. The authors have considered a spectrum trading framework in which a wireless service provider (WSP) leases its available channel(s) to another WSP for use at the designated base station (BS) of the latter for short duration. In their model, the agents of WSPs carry out the negotiation on the specifications of the channel usage such as transmission power, antenna height, spectrum band of the channel and price of the channel. In this work, they have modelled the negotiation as a multi‐issue bilateral negotiation problem. Initially, they have solved the problem with the help of the Bayesian learning‐based negotiation (BLBN) method. Furthermore, they have devised the novel reinforcement learning‐based technique namely, reinforcement learning‐based negotiation (RLBN) considering the adaptability of the BS to the new channel configuration. Surplus utility and convergence time of the negotiation process are considered as performance indices for the above techniques. The simulation results show that the RLBN outperforms BLBN and static negotiation technique as far as the objective of surplus utility is concerned.