bluuebunny/crossref_metadata_2025 huggingface dataset:
Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
Authors: Jia Guangshuai , Preussner Jens , Chen Xi , Guenther Stefan , Yuan Xuejun , Yekelchyk Michail , Kuenne Carsten , Looso Mario , Zhou Yonggang , Teichmann Sarah , Braun Thomas
Published: November 2018

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood. Here, we comprehensively characterize mouse cardiac progenitor cells (CPCs) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing and transposase-accessible chromatin profiling (ATAC-seq). By leveraging on cell-to-cell transcriptome and chromatin accessibility heterogeneity, we identify different previously unknown cardiac subpopulations. Reconstruction of developmental trajectories reveal that multipotent Isl1+ CPC pass through an attractor state before separating into different developmental branches, whereas extended expression of Nkx2-5 commits CPC to an unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5. Our data provide a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.
Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions
Authors: Hoernes Thomas Philipp , Faserl Klaus , Juen Michael Andreas , Kremser Johannes , Gasser Catherina , Fuchs Elisabeth , Shi Xinying , Siewert Aaron , Lindner Herbert , Kreutz Christoph , Micura Ronald , Joseph Simpson , Höbartner Claudia , Westhof Eric , Hüttenhofer Alexander , Erlacher Matthias David
Published: November 2018

The precise interplay between the mRNA codon and the tRNA anticodon is crucial for ensuring efficient and accurate translation by the ribosome. The insertion of RNA nucleobase derivatives in the mRNA allowed us to modulate the stability of the codon-anticodon interaction in the decoding site of bacterial and eukaryotic ribosomes, allowing an in-depth analysis of codon recognition. We found the hydrogen bond between the N1 of purines and the N3 of pyrimidines to be sufficient for decoding of the first two codon nucleotides, whereas adequate stacking between the RNA bases is critical at the wobble position. Inosine, found in eukaryotic mRNAs, is an important example of destabilization of the codon-anticodon interaction. Whereas single inosines are efficiently translated, multiple inosines, e.g., in the serotonin receptor 5-HT2C mRNA, inhibit translation. Thus, our results indicate that despite the robustness of the decoding process, its tolerance toward the weakening of codon-anticodon interactions is limited.
A continuous-time MaxSAT solver with high analog performance
Authors: Molnár Botond , Molnár Ferenc , Varga Melinda , Toroczkai Zoltán , Ercsey-Ravasz Mária
Published: November 2018

Many real-life optimization problems can be formulated in Boolean logic as MaxSAT, a class of problems where the task is finding Boolean assignments to variables satisfying the maximum number of logical constraints. Since MaxSAT is NP-hard, no algorithm is known to efficiently solve these problems. Here we present a continuous-time analog solver for MaxSAT and show that the scaling of the escape rate, an invariant of the solver’s dynamics, can predict the maximum number of satisfiable constraints, often well before finding the optimal assignment. Simulating the solver, we illustrate its performance on MaxSAT competition problems, then apply it to two-color Ramsey number R(m, m) problems. Although it finds colorings without monochromatic 5-cliques of complete graphs on N ≤ 42 vertices, the best coloring for N = 43 has two monochromatic 5-cliques, supporting the conjecture that R(5, 5) = 43. This approach shows the potential of continuous-time analog dynamical systems as algorithms for discrete optimization.
Hidden diversity of soil giant viruses
Authors: Schulz Frederik , Alteio Lauren , Goudeau Danielle , Ryan Elizabeth M. , Yu Feiqiao B. , Malmstrom Rex R. , Blanchard Jeffrey , Woyke Tanja
Published: November 2018

Known giant virus diversity is currently skewed towards viruses isolated from aquatic environments and cultivated in the laboratory. Here, we employ cultivation-independent metagenomics and mini-metagenomics on soils from the Harvard Forest, leading to the discovery of 16 novel giant viruses, chiefly recovered by mini-metagenomics. The candidate viruses greatly expand phylogenetic diversity of known giant viruses and either represented novel lineages or are affiliated with klosneuviruses, Cafeteria roenbergensis virus or tupanviruses. One assembled genome with a size of 2.4 Mb represents the largest currently known viral genome in the Mimiviridae, and others encode up to 80% orphan genes. In addition, we find more than 240 major capsid proteins encoded on unbinned metagenome fragments, further indicating that giant viruses are underexplored in soil ecosystems. The fact that most of these novel viruses evaded detection in bulk metagenomes suggests that mini-metagenomics could be a valuable approach to unearth viral giants.
Author Correction: Bi-directional cell-pericellular matrix interactions direct stem cell fate
Authors: Ferreira Silvia A. , Motwani Meghna S. , Faull Peter A. , Seymour Alexis J. , Yu Tracy T. L. , Enayati Marjan , Taheem Dheraj K. , Salzlechner Christoph , Haghighi Tabasom , Kania Ewa M. , Oommen Oommen P. , Ahmed Tarek , Loaiza Sandra , Parzych Katarzyna , Dazzi Francesco , Varghese Oommen P. , Festy Frederic , Grigoriadis Agamemnon E. , Auner Holger W. , Snijders Ambrosius P. , Bozec Laurent , Gentleman Eileen
Published: November 2018

In the original version of this Article the dataset identifier in the Data Availability statement was incorrect. The correct dataset identifier is PXD009500. This has been corrected in the HTML and PDF versions of this Article.
Memory formation and long-term maintenance of IL-7Rα+ ILC1s via a lymph node-liver axis
Authors: Wang Xianwei , Peng Hui , Cong Jingjing , Wang Xuefu , Lian Zhexiong , Wei Haiming , Sun Rui , Tian Zhigang
Published: November 2018

Natural killer (NK) cells are reported to have immunological memory, with CD49a+ liver-resident NK cells shown to confer hapten-specific memory responses, but how this memory is induced or maintained is unclear. Here we show that memory type I innate lymphoid cells (ILC1s), which express IL-7Rα, are generated in the lymph nodes (LNs) and require IL-7R signaling to maintain their longevity in the liver. Hapten sensitization initiates CXCR3-dependent recruitment of IL-7Rα+ ILC1s into skin-draining LNs, where they are primed and acquire hapten-specific memory potential. Memory IL-7Rα+ ILC1s then exit draining LNs and are preferentially recruited, via CXCR6, to reside in the liver. Moreover, long-term blockade of IL-7R signaling significantly reduces ILC1-mediated memory responses. Thus, our results identify a memory IL-7Rα+ ILC1 population and reveal a LN-liver axis that is essential for ILC1 memory generation and long-term maintenance.
Decreased BDNF Release in Cortical Neurons of a Knock-in Mouse Model of Huntington’s Disease
Authors: Yu Chenglong , Li Chun Hei , Chen Sidong , Yoo Hanna , Qin Xianan , Park Hyokeun
Published: November 2018

Huntington’s disease (HD) is a dominantly inherited neurodegenerative disease caused by an increase in CAG repeats in the Huntingtin gene (HTT). The striatum is one of the most vulnerable brain regions in HD, and altered delivery of BDNF to the striatum is believed to underlie this high vulnerability. However, the delivery of BDNF to the striatum in HD remains poorly understood. Here, we used real-time imaging to visualize release of BDNF from cortical neurons cultured alone or co-cultured with striatal neurons. BDNF release was significantly decreased in the cortical neurons of zQ175 mice (a knock-in model of HD), and total internal reflection fluorescence microscopy revealed several release patterns of single BDNF-containing vesicles, with distinct kinetics and prevalence, in co-cultured cortical HD neurons. Notably, a smaller proportion of single BDNF-containing vesicles underwent full release in HD neurons than in wild-type neurons. This decreased release of BDNF in cortical neurons might lead to decreased BDNF levels in the striatum because the striatum receives BDNF mainly from the cortex. In addition, we observed a decrease in the total travel length and speed of BDNF-containing vesicles in HD neurons, indicating altered transport of these vesicles in HD. Our findings suggest a potential mechanism for the vulnerability of striatal neurons in HD and offer new insights into the pathogenic mechanisms underlying the degeneration of neurons in HD.
Access to high-impact mutations constrains the evolution of antibiotic resistance in soft agar
Authors: Ghaddar Nour , Hashemidahaj Mona , Findlay Brandon L.
Published: November 2018

Despite widespread resistance to many important antibiotics, the factors that govern the emergence and prevalence of antibiotic-resistant bacteria are still unclear. When exposed to antibiotic gradients in soft agar plates measuring as little as 1.25 × 11 cm we found that Escherichia coli rapidly became resistant to representatives from every class of antibiotics active against Gram-negative bacteria. Evolution kinetics were independent of the frequency of spontaneous mutations that confer antibiotic resistance or antibiotic dose-response curves, and were only loosely correlated to maximal antibiotic concentrations. Instead, rapid evolution required unrealized mutations that could markedly decrease antibiotic susceptibility. When bacteria could not evolve through these “high-impact” mutations, populations frequently bottlenecked, reducing the number of cells from which mutants could arise and prolonging evolution times. This effect was independent of the antibiotic’s mechanism of action, and may affect the evolution of antibiotic resistance in clinical settings.
Comparative genome-wide analysis of WRKY transcription factors in two Asian legume crops: Adzuki bean and Mung bean
Authors: Srivastava Richa , Kumar Sanjeev , Kobayashi Yasufumi , Kusunoki Kazutaka , Tripathi Prateek , Kobayashi Yuriko , Koyama Hiroyuki , Sahoo Lingaraj
Published: November 2018

The seminal participation of WRKY transcription factors in plant development, metabolism and in the governance of defense mechanism implicated their gaining importance for genomic and functional studies. The recent release of draft genome sequences of two legume crops, Adzuki bean (Vigna angularis) and Mung bean (Vigna radiata) has paved the way for characterization of WRKY gene family in these crops. We found 84WRKYgenes in Adzuki bean (VaWRKY) and 85WRKYgenes in Mung bean (VrWRKY). Based on the phylogenetic analysis,VaWRKYgenes were classified into three groups with 15 members in Group I, 56 members in Group II, and 13 members in Group III, which was comparable toVrWRKYdistribution in Mung bean, 16, 56 and 13 members in Group I, II and III, respectively. The few tandem and segmental duplication events suggested that recent duplication plays no prominent role in the expansionVaWRKYandVrWRKYgenes. The illustration of gene-structure and their encoded protein-domains further revealed the nature of WRKY proteins. Moreover, the identification of abiotic or biotic stress-responsivecis-regulatory elements in the promoter regions of someWRKYgenes provides fundamental insights for their further implementation in stress-tolerance and genetic improvement of agronomic traits.
Mavoglurant in Fragile X Syndrome: Results of two open-label, extension trials in adults and adolescents
Authors: Hagerman Randi , Jacquemont Sebastien , Berry-Kravis Elizabeth , Des Portes Vincent , Stanfield Andrew , Koumaras Barbara , Rosenkranz Gerd , Murgia Alessandra , Wolf Christian , Apostol George , von Raison Florian
Published: November 2018

Fragile X syndrome (FXS) is the most common monogenic cause of inherited intellectual and developmental disabilities. Mavoglurant, a selective metabotropic glutamate receptor subtype-5 antagonist, has shown positive neuronal and behavioral effects in preclinical studies, but failed to demonstrate any behavioral benefits in two 12-week, randomized, placebo-controlled, double-blind, phase IIb studies in adults and adolescents with FXS. Here we report the long-term safety (primary endpoint) and efficacy (secondary endpoint) results of the open-label extensions. Adolescent (n = 119, aged 12–19 years) and adult (n = 148, aged 18–45 years) participants received up to 100 mg bid mavoglurant for up to 34 months. Both extension studies were terminated prematurely due to lack of proven efficacy in the core studies. Mavoglurant was well tolerated with no new safety signal. Five percent of adults and 16.9 percent of adolescents discontinued treatment due to adverse events. Gradual and consistent behavioral improvements as measured by the ABC-CFX scale were observed, which were numerically superior to those seen in the placebo arm of the core studies. These two extension studies confirm the long-term safety of mavoglurant in FXS, but further investigations are required to determine whether and under which conditions the significant preclinical results obtained with mGluR5 inhibition can translate to humans.
A Novel Targeted Analysis of Peripheral Steroids by Ultra-Performance Supercritical Fluid Chromatography Hyphenated to Tandem Mass Spectrometry
Authors: de Kock Neil , Acharya Santosh R. , Ubhayasekera S. J. Kumari A. , Bergquist Jonas
Published: November 2018

Ultra-performance supercritical fluid chromatography–tandem mass spectrometry (UPSFC–MS/MS) is an alternative method for steroid analysis. Continuous development of analytical methodologies for steroid profiling is of major importance in the clinical environment to provide useful and more comprehensive data. The aim of this study was to identify and quantify a large number of endogenous steroids from the four major classes (estrogens, androgens, progestogens and corticosteroids) simultaneously within a short analytical time. This novel UPSFC–MS/MS method with electrospray in positive ionisation (ESI+) mode is robust, selective and present sufficiently high sensitivity to profile nineteen steroids in 50 µL human plasma. Under optimised conditions, nineteen different steroids were separated with high efficiency in the multiple reaction monitoring (MRM) mode. The linearity of the method was good with correlation coefficients (R2) in the range of 0.9983–0.9999 and with calibration range from 0.05–500 ng/mL in human plasma. The intraday and interday precision of the method, as RSD, was less than 15%. The accuracy of the nineteen analytes varied between 80 to 116%. Finally, the novel method was successfully applied for the determination of nineteen steroids within 5 minutes providing the possibility to use it for research as well as routine healthcare practice.
Human chemosignals of disgust facilitate food judgment
Authors: Zheng Yan , You Yuqi , Farias Ana R. , Simon Jessica , Semin Gün R. , Smeets Monique A. , Li Wen
Published: November 2018

Choosing food is not a trivial decision that people need to make daily, which is often subject to social influences. Here, we studied a human homolog of social transmission of food preference (STFP) as observed in rodents and other animals via chemosignals of body secretions. Human social chemosignals (sweat) produced during a disgust or neutral state among a group of donors were presented to participants undergoing a 2-alternative-forced-choice food healthiness judgment task during functional magnetic resonance imaging (fMRI). Response speed and two key signal detection indices—d’ (discrimination sensitivity) and β (response bias)—converged to indicate that social chemosignals of disgust facilitated food healthiness decisions, in contrast to primary disgust elicitors (disgust odors) that impaired the judgment. fMRI analyses (disgust vs. neutral sweat) revealed that the fusiform face area (FFA), amygdala, and orbitofrontal cortex (OFC) were engaged in processing social chemosignals of disgust during food judgment. Importantly, a double contrast of social signaling across modalities (olfactory vs. visual—facial expressions) indicated that the FFA and OFC exhibited preferential response to social chemosignals of disgust. Together, our findings provide initial evidence for human STFP, where social chemosignals are incorporated into food decisions by engaging social and emotional areas of the brain.
Molecular and isotopic evidence for the processing of starchy plants in Early Neolithic pottery from China
Authors: Shoda Shinya , Lucquin Alexandre , Sou Chi Ian , Nishida Yastami , Sun Guoping , Kitano Hiroshi , Son Joon-ho , Nakamura Shinichi , Craig Oliver E.
Published: November 2018

Organic residue analysis of ancient ceramic vessels enables the investigation of natural resources that were used in daily cooking practices in different part of the world. Despite many methodological advances, the utilization of plants in pottery has been difficult to demonstrate chemically, hindering the study of their role in ancient society, a topic that is especially important to understanding early agricultural practices at the start of the Neolithic period. Here, we present the first lipid residue study on the Chinese Neolithic pottery dated to 5.0 k - 4.7 k cal BC from the Tianluoshan site, Zhejiang province, a key site with early evidence for rice domestication. Through the identification of novel molecular biomarkers and extensive stable isotope analysis, we suggest that the pottery in Tianluoshan were largely used for processing starchy plant foods. These results not only highlight the significance of starchy plants in Neolithic southern China but also show a clear difference with other contemporary sites in northern Eurasia, where pottery is clearly orientated to aquatic resource exploitation. These differences may be linked with the early development of rice agriculture in China compared to its much later adoption in adjacent northerly regions.
Inverse Relationship between Metabolic Syndrome and 25-Hydroxyvitamin D Concentration in Elderly People without Vitamin D deficiency
Authors: Wang Chun-Min , Chang Chin-Sung , Chang Yin-Fan , Wu Shin-Jiuan , Chiu Ching-Ju , Hou Meng-Tzu , Chen Chuan-Yu , Liu Ping-Yen , Wu Chih-Hsing
Published: November 2018

Vitamin D status is inversely associated with the prevalence of metabolic syndrome (MetS). Whether this is true in the elderly without vitamin D deficiency is rarely investigated. Our data source is a cross-sectional survey of 1,966 community-dwelling elderly Taiwanese in 2012. An overnight fasting blood were obtained for biochemistry variables. Vitamin D deficiency was defined as serum 25-hydroxyvitamin D3 [25(OH)D] concentration <20 ng/mL. MetS is defined using modified ATP-III criteria. Of 523 participants without vitamin D deficiency (Men/Women = 269/254, age = 76.0 ± 6.2 years old [65–102 years old]), mean 25(OH)D was 44.0 ± 11.1 ng/mL, and the MetS prevalence of MS was 46.5%. Serum 25(OH)D was negatively associated with osteocalcin, the homeostatic model assessment insulin resistance (HOMA-IR) index, body mass index (BMI), and glycated hemoglobin A1c. Participants with more MetS features have lower serum 25(OH)D and osteocalcin. Binary logistic regression models showed that 25(OH)D, physical activity, and osteocalcin were negatively independent MetS factors, but that the HOMA-IR index, BMI, and being female were positively independent factors. The risk of MetS was progressively lower along with the increased 25(OH)D concentration, even above 60 ng/mL. In conclusion, a low 25(OH)D concentration is an independent risk factor for MetS in elderly people without vitamin D deficiency.
Crystalline structure, electronic and lattice-dynamics properties of NbTe2
Authors: Barajas-Aguilar Aarón Hernán , Irwin J. C. , Garay-Tapia Andrés Manuel , Schwarz Torsten , Paraguay Delgado Francisco , Brodersen P. M. , Prinja Rajiv , Kherani Nazir , Jiménez Sandoval Sergio J.
Published: November 2018

Layered-structure materials are currently relevant given their quasi-2D nature. Knowledge of their physical properties is currently of major interest. Niobium ditelluride possesses a monoclinic layered-structure with a distortion in the tellurium planes. This structural complexity has hindered the determination of its fundamental physical properties. In this work, NbTe2 crystals were used to elucidate its structural, compositional, electronic and vibrational properties. These findings have been compared with calculations based on density functional theory. The chemical composition and elemental distribution at the nanoscale were obtained through atom probe tomography. Ultraviolet photoelectron spectroscopy allowed the first determination of the work function of NbTe2. Its high value, 5.32 eV, and chemical stability allow foreseeing applications such as contact in optoelectronics. Raman spectra were obtained using different excitation laser lines: 488, 633, and 785 nm. The vibrational frequencies were in agreement with those determined through density functional theory. It was possible to detect a theoretically-predicted, low-frequency, low-intensity Raman active mode not previously observed. The dispersion curves and electronic band structure were calculated, along with their corresponding density of states. The electrical properties, as well as a pseudo-gap in the density of states around the Fermi energy are characteristics proper of a semi metal.
Integrated PTR-ToF-MS, GWAS and biological pathway analyses reveal the contribution of cow’s genome to cheese volatilome
Authors: Pegolo Sara , Bergamaschi Matteo , Gasperi Flavia , Biasioli Franco , Cecchinato Alessio , Bittante Giovanni
Published: November 2018

Volatile organic compounds (VOCs) are small molecules that contribute to the distinctive flavour of cheese which is an important attribute for consumer acceptability. To investigate whether cow’s genetic background might contribute to cheese volatilome, we carried out genome-wide association studies (GWAS) and pathway–based analyses for 173 spectrometric peaks tentatively associated with several VOCs obtained from proton-transfer-reaction mass spectrometry (PTR-ToF-MS) analyses of 1,075 model cheeses produced using raw whole-milk from Brown Swiss cows. Overall, we detected 186 SNPs associated with 120 traits, several of which mapped close to genes involved in protein (e.g. CSN3, GNRHR and FAM169A), fat (e.g. AGPAT3, SCD5, and GPAM) and carbohydrate (e.g. B3GNT2, B4GALT1, and PHKB) metabolism. Gene set enrichment analysis showed that pathways connected with proteolysis/amino acid metabolism (purine and nitrogen metabolism) as well as fat metabolism (long-term potentiation) and mammary gland function (tight junction) were overrepresented. Our results provide the first evidence of a putative link between cow’s genes and cheese flavour and offer new insights into the role of potential candidate loci and the biological functions contributing to the cheese volatilome.
Amplification of Mitochondrial Activity in the Healing Response Following Rotator Cuff Tendon Injury
Authors: Thankam Finosh G. , Chandra Isaiah S. , Kovilam Anuradha N. , Diaz Connor G. , Volberding Benjamin T. , Dilisio Matthew F. , Radwan Mohamed M. , Gross R. Michael , Agrawal Devendra K.
Published: November 2018

Mitochondrial function following rotator cuff tendon injury (RCI) influences the tendon healing. We examined the mitochondrial morphology and function under hypoxia in the shoulder tendon tissue from surgically-induced tenotomy-RCI rat model and cultured swine tenocytes. The tendon tissue was collected post-injury on 3–5 (Group-A), 10–12 (Group-B), and 22–24 (Group-C), days and the corresponding contralateral tendons were used as control for each group. There was higher protein expression of citrate synthase (P < 0.0001) [10.22 MFI (mean fluorescent intensity)] and complex-1 (P = 0.0008) (7.86 MFI) in Group-A and Group-B that decreased in Group-C [(P = 0.0201) (5.78 MFI and (P = 0.7915) (2.32 MFI), respectively] compared to control tendons. The ratio of BAX:Bcl2 (Bcl2 associated x protein:B cell lymphoma 2) in RCI tendons increased by 50.5% (Group-A) and 68.4% (Group-B) and decreased by 25.8% (Group-C) compared to normoxic controls. Hypoxia increased β-tubulin expression (P = 0067) and reduced PGC1-α (P = 0412) expression in the isolated swine tenocytes with no effect on the protein expression of Complex-1 (P = 7409) and citrate synthase (P = 0.3290). Also, the hypoxic tenocytes exhibited about 4-fold increase in mitochondrial superoxide (P < 0.0001), altered morphology and mitochondrial pore integrity, and increase in mitochondrial density compared to normoxic controls. These findings suggest the critical role of mitochondria in the RCI healing response.
Differential toxicities of fine particulate matters from various sources
Authors: Park Minhan , Joo Hung Soo , Lee Kwangyul , Jang Myoseon , Kim Sang Don , Kim Injeong , Borlaza Lucille Joanna S. , Lim Heungbin , Shin Hanjae , Chung Kyu Hyuck , Choi Yoon-Hyeong , Park Sun Gu , Bae Min-Suk , Lee Jiyi , Song Hangyul , Park Kihong
Published: November 2018

Fine particulate matters less than 2.5 µm (PM2.5) in the ambient atmosphere are strongly associated with adverse health effects. However, it is unlikely that all fine particles are equally toxic in view of their different sizes and chemical components. Toxicity of fine particles produced from various combustion sources (diesel engine, gasoline engine, biomass burning (rice straw and pine stem burning), and coal combustion) and non-combustion sources (road dust including sea spray aerosols, ammonium sulfate, ammonium nitrate, and secondary organic aerosols (SOA)), which are known major sources of PM2.5, was determined. Multiple biological and chemical endpoints were integrated for various source-specific aerosols to derive toxicity scores for particles originating from different sources. The highest toxicity score was obtained for diesel engine exhaust particles, followed by gasoline engine exhaust particles, biomass burning particles, coal combustion particles, and road dust, suggesting that traffic plays the most critical role in enhancing the toxic effects of fine particles. The toxicity ranking of fine particles produced from various sources can be used to better understand the adverse health effects caused by different fine particle types in the ambient atmosphere, and to provide practical management of fine particles beyond what can be achieved only using PM mass which is the current regulation standard.
Spontaneous activity emerging from an inferred network model captures complex spatio-temporal dynamics of spike data
Authors: Capone Cristiano , Gigante Guido , Del Giudice Paolo
Published: November 2018

Inference methods are widely used to recover effective models from observed data. However, few studies attempted to investigate the dynamics of inferred models in neuroscience, and none, to our knowledge, at the network level. We introduce a principled modification of a widely used generalized linear model (GLM), and learn its structural and dynamic parameters from in-vitro spike data. The spontaneous activity of the new model captures prominent features of the non-stationary and non-linear dynamics displayed by the biological network, where the reference GLM largely fails, and also reflects fine-grained spatio-temporal dynamical features. Two ingredients were key for success. The first is a saturating transfer function: beyond its biological plausibility, it limits the neuron’s information transfer, improving robustness against endogenous and external noise. The second is a super-Poisson spikes generative mechanism; it accounts for the undersampling of the network, and allows the model neuron to flexibly incorporate the observed activity fluctuations.
The different stratospheric influence on cold-extremes in Eurasia and North America
Authors: Kretschmer Marlene , Cohen Judah , Matthias Vivien , Runge Jakob , Coumou Dim
Published: November 2018

The stratospheric polar vortex can influence the tropospheric circulation and thereby winter weather in the mid-latitudes. Weak vortex states, often associated with sudden stratospheric warmings (SSW), have been shown to increase the risk of cold-spells especially over Eurasia, but its role for North American winters is less clear. Using cluster analysis, we show that there are two dominant patterns of increased polar cap heights in the lower stratosphere. Both patterns represent a weak polar vortex but they are associated with different wave mechanisms and different regional tropospheric impacts. The first pattern is zonally symmetric and associated with absorbed upward-propagating wave activity, leading to a negative phase of the North Atlantic Oscillation (NAO) and cold-air outbreaks over northern Eurasia. This coupling mechanism is well-documented in the literature and is consistent with the downward migration of the northern annular mode (NAM). The second pattern is zonally asymmetric and linked to downward reflected planetary waves over Canada followed by a negative phase of the Western Pacific Oscillation (WPO) and cold-spells in Central Canada and the Great Lakes region. Causal effect network (CEN) analyses confirm the atmospheric pathways associated with this asymmetric pattern. Moreover, our findings suggest the reflective mechanism to be sensitive to the exact region of upward wave-activity fluxes and to be state-dependent on the strength of the vortex. Identifying the causal pathways that operate on weekly to monthly timescales can pave the way for improved sub-seasonal to seasonal forecasting of cold spells in the mid-latitudes.
Top soil physical and chemical properties in Kazakhstan across a north-south gradient
Authors: Yapiyev Vadim , Gilman Charles P. , Kabdullayeva Tolganay , Suleimenova Akmaral , Shagadatova Aizhan , Duisembay Azat , Naizabekov Sanzhar , Mussurova Saule , Sydykova Kamilya , Raimkulov Ilyas , Kabimoldayev Ilyas , Abdrakhmanova Ainagul , Omarkulova Symbat , Nurmukhambetov Dastan , Kudarova Aliya , Malgazhdar Daniyar , Schönbach Christian , Inglezakis Vassilis
Published: November 2018

Kazakhstan’s soil properties have yet to be comprehensively characterized. We sampled 40 sites consisting of ten major soil types at spring (wet) and late-summer (dry) seasons. The sample locations range from semi-arid to arid with an annual mean air temperature from 1.2 to 10.7 °C and annual precipitation from less than 200 to around 400 mm. Overall topsoil total (STC), organic (SOC), and inorganic (SIC) carbon did not change significantly between spring and late summer. STC and SOC show a wave like pattern from north to south with two maxima in northern and southern Kazakhstan and one minimum in central Kazakhstan. With a few exceptions SIC content at northern sites is generally low, whereas at Lake Balkhash SIC can exceed 75% of STC. Independent of the seasons, SOC significantly differed among soil types. Total nitrogen content distribution among our sampling sites followed a similar pattern as SOC with significant differences between soil types occurring in northern, central and southern Kazakhstan.
A novel needle trap device coupled with gas chromatography for determination of five fatty alcohols in tea samples
Authors: Chen Jianxiong , Zhang Birong , Zheng Dongyun , Dang Xueping , Ai Youhong , Chen Huaixia
Published: November 2018

A novel needle trap device (NTD) was prepared by in situ electropolymerization, which inner wall was coated by polyaniline doped with proton-type ionic liquid and gold nanoparticles (PANI-HILs-Au).
Understanding the temperature effect on transport dynamics and structures in polyamide reverse osmosis system via molecular dynamics simulations
Authors: Li Ke , Liu Lifen , Wu Hao , Li Shanlong , Yu Chunyang , Zhou Yongfeng , Huang Wei , Yan Deyue
Published: November 2018

Molecular simulations could disclose the transport dynamics, membrane structures and temperature effect on reverse osmosis process.
Facile emission color tuning and circularly polarized light generation of single luminogen in engineering robust forms
Authors: Cheng Yanhua , Liu Shunjie , Song Fengyan , Khorloo Michidmaa , Zhang Haoke , Kwok Ryan T. K. , Lam Jacky W. Y. , He Zikai , Tang Ben Zhong
Published: November 2018

Versatile emissions are achieved by assembling crystalline and amorphous nano-aggregates of AIEgens with microstructure-engineered polymers.
Synthesis of dendrimer functionalized adsorbents for rapid removal of glyphosate from aqueous solution
Authors: Guo Dandan , Muhammad Nadeem , Lou Chaoyan , Shou Dan , Zhu Yan
Published: November 2018

Protonated PAMAM grafted adsorbents for rapid removal of glyphosate.
Distinct autophagy-inducing abilities of similar-sized nanoparticles in cell culture and liveC. elegans
Authors: Wang Qin , Zhou Yanfeng , Fu Rong , Zhu Yi , Song Bin , Zhong Yiling , Wu Sicong , Shi Yu , Wu Yanyan , Su Yuanyuan , Zhang Huimin , He Yao
Published: November 2018

Silicon nanoparticles, having the same size as the autophagy-inducing QDs, CDs and AuNPs, do not induce autophagyin vitroandin vivo.
Highly porous composite aerogel based triboelectric nanogenerators for high performance energy generation and versatile self-powered sensing
Authors: Mi Hao-Yang , Jing Xin , Cai Zhiyong , Liu Yuejun , Turng Lih-Sheng , Gong Shaoqin
Published: November 2018

A porous composite triboelectric nanogenerator (PCTENG) with excellent energy generation and sensing performances has been developed by introducing rabbit fur into a cellulose aerogel.
Polymer nanoparticles for the intravenous delivery of anticancer drugs: the checkpoints on the road from the synthesis to clinical translation
Authors: Ferrari R. , Sponchioni M. , Morbidelli M. , Moscatelli D.
Published: November 2018

The checkpoints for polymer nanoformulations from synthesis to clinic application are proposed as guidelines to develop safe and effective therapeutics.
Cathodoluminescence nanoscopy of open single-crystal aluminum plasmonic nanocavities
Authors: Li Li , Cai Wei , Du Chenglin , Guan Zhongyuan , Xiang Yinxiao , Ma Zenghong , Wu Wei , Ren Mengxin , Zhang Xinzheng , Tang Aiwei , Xu Jingjun
Published: November 2018

Using cathodoluminescence, the plasmonic modes of open triangle cavities patterned in single-crystal bulk aluminum are explored in deep subwavelengths from the UV to the visible, showing large Q factors.
Thermal insulation with 2D materials: liquid phase exfoliated vermiculite functional nanosheets
Authors: Janica Iwona , Del Buffa Stefano , Mikołajczak Agnieszka , Eredia Matilde , Pakulski Dawid , Ciesielski Artur , Samorì Paolo
Published: November 2018

Dispersions of high-quality 2D nanosheets are produced by liquid-phase exfoliation of vermiculite clay, resulting in thermally insulating printable inks.
Micro-flow nanocatalysis: synergic effect of TfOH@SPIONs and micro-flow technology as an efficient and robust catalytic system for the synthesis of plasticizers
Authors: Tashi Maryam , Shafiee Behnaz , Sakamaki Yoshie , Hu Ji-Yun , Heidrick Zachary , Khosropour Ahmad R. , Beyzavi M. Hassan
Published: November 2018

The combination of continuous flow technology with nanocatalyst for the synthesis of plasticizers.
Rhodamine B derivatives-modified upconversion nanoparticles as a fluorescent turn-off–on sensor for the highly sensitive detection of Cu2+ and pyrophosphate
Authors: Meng Zhipeng , Wu Suli , Zhong Linghua , Zeng Min , Sun Xiaoqian , Li Lu , Zhang Shufen
Published: November 2018

A new fluorescent turn-off–on sensor was developed based on the the rhodamine B derivatives (RBP) modified UCNPs to detect Cu2+ and pyrophosphate (PPi).
A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA
Authors: Hu Zheng-Li , Li Meng-Yin , Liu Shao-Chuang , Ying Yi-Lun , Long Yi-Tao
Published: November 2018

By developing lithium-ion-active aerolysin, for the first time we have achieved aerolysin detection of single-stranded DNA longer than 100 nt.
Colloidal stability dictates drop breakup under electric fields
Authors: Lanauze Javier A. , Sengupta Rajarshi , Bleier Blake J. , Yezer Benjamin A. , Khair Aditya S. , Walker Lynn M.
Published: November 2018

Suspension stability on time scales of drop deformation leads to rich and unexplored breakup phenomena.
Diffusiophoretic design of self-spinning microgears from colloidal microswimmers
Authors: Aubret Antoine , Palacci Jérémie
Published: November 2018

The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We show the self-assembly of self-spinning microgears from colloidal microswimmers and characterize the diffusiophoretic interactions using a novel optical technique.
Cell cycle and transmembrane mitochondrial potential analysis after treatment with chromium(iii), iron(iii), molybdenum(iii) or nickel(ii) and their mixtures
Authors: Terpilowska Sylwia , Siwicki Andrzej K.
Published: November 2018

The aim of this study was to examine the effect of chromium(iii), iron(iii), molybdenum(iii) and nickel(ii) and their combinations on the cell cycle and mitochondrial transmembrane potential (MTP) in BALB/3T3 and HepG2 cells.
Urinary angiotensinogen as a biomarker for acute to chronic kidney injury transition – prognostic and mechanistic implications
Authors: Connor Katie L. , Denby Laura
Published: November 2018

Accurate biomarkers that both predict the progression to, and detect the early stages of chronic kidney disease (CKD) are lacking, resulting in difficulty in identifying individuals who could potentially benefit from targeted intervention. In a recent issue [Clinical Science (2018) 132, 2121–2133], Cui et al. examine the ability of urinary angiotensinogen (uAGT) to predict the progression of acute kidney injury (AKI) to CKD. They principally employ a murine ischaemia reperfusion injury model to study this and provide data from a small prospective study of patients with biopsy proven acute tubular necrosis. The authors suggest that uAGT is a dynamic marker of renal injury that could be used to predict the likelihood of structural recovery following AKI. Here we comment on their findings, exploring the clinical utility of uAGT as a biomarker to predict AKI to CKD transition and perhaps more controversially, to discuss whether the early renin–angiotensin system blockade following AKI represents a therapeutic target.
Results on stability of switched discrete‐time systems with all subsystems unstable
Authors: Mao Xiang , Zhu Hui , Chen Wei , Zhang Hongbin
Published: November 2018

In this study, the stability problem of discrete‐time switched systems without stable subsystems is considered. Using the k ‐sample‐like method, the authors construct a Lyapunov function whose value at the switching instant is less than the value at the last switching instant when the corresponding dwell time belongs to a special time span. According to whether the dwell time belongs to the time span, switchings are divided into two categories: the switching without divergence time and the switching with divergence time. Based on that, a new less conservative exponential stability theorem is established with the bounded maximum average dwell time. Furthermore, by jointly considering the dynamic characteristics of the subsystems before and after switching instants, they also give the stability result via the dwell time with the floating lower and upper bounds. Finally, some numerical examples are given to illustrate the effectiveness of the theoretical results.
Personalised lane keeping assist strategy: adaptation to driving style
Authors: Rath Jagat Jyoti , Senouth Chouki , Popieul Jean Christophe
Published: November 2018

The research in advanced driver assistance systems (ADAS) has progressed to design architectures for driver specific performance. Personalised ADASs in this aspect have been developed with adaptation to driver attributes, state, style, behaviour, skill and so on. For the lane keeping task, the driver driving style while navigating a high/low curvature track plays an important part in the design of a lane keeping assist system. Considering this aspect, a robust co‐operative control approach is formulated to design a personalised lane keeping assist with adaptation to driver style. Based on statistical analysis of lateral jerk and steer feel, a fuzzy rule based identification procedure for the classification of the driver style as clam, moderate, aggressive or very aggressive is designed. Using the identified driving style, a modulation function is proposed to adapt the assist torque. The assist torque is generated based on a robust higher order sliding mode approach as a feedback control for the driver‐vehicle system. Closed‐loop stability of the proposed driver‐vehicle design in the presence of disturbances is established. Co‐operative control between human driver‐autonomous controller for the lane keeping task over the Satory test track with adaption to driver style is then shown for validation of the proposed architecture.
Pose detection in complex classroom environment based on improved Faster R‐CNN
Authors: Tang Lin , Gao Chenqiang , Chen Xu , Zhao Yue
Published: November 2018

Pose detection of small targets in poor imaging conditions like heavy occlusion and low resolution is still an open and challenging task in computer vision. For instance, detection of students' poses in classrooms that are even indistinguishable to human eyes remains a rather difficult task. Motivated by the success of convolutional feature merging and locality preserving, the authors propose a pose detection framework combining merged region of interest (ROI) pooling and locality preserving learning. Unlike usual object detection algorithms which use general top‐level convolutional features as inputs, their method uses a merged ROI pooling structure to merge semantic feature and high‐resolution feature from the last two levels of convolutional feature maps, so that this merged feature is made more expressive than the single‐level feature. In addition, the locality feature‐preserving learning is used in the last fully‐connected layer. Through locality preserving learning, features belonging to the same class would be forced to be closer in the feature space, which enables the model with stronger classification ability. Experimental results show that the proposed method outperforms the state‐of‐the‐art methods.
High step‐up single‐phase‐switched Z‐source inverter: steady‐state analysis and cost evaluation
Authors: Nozadian Mohsen Hasan Babayi , Babaei Ebrahim , Hosseini Seyed Hossein
Published: November 2018

This study presents a high step‐up switched Z‐source inverter. Only by using one more inductor and capacitor in comparison with switched boost inverter, the presented inverter reaches various advantages such as including high boost factor, reduced range of duty cycle and continuous input current. These features make it suitable to use in different applications such as photovoltaic system to increase the voltage level. In this study, a comprehensive analysis of the presented inverter in shoot through (ST) and non‐ST operation modes are given. This study also elaborates an appropriate switching pattern for the proposed inverter. There is also a comprehensive comparison and cost evaluation of the proposed structure with conventional structures. Cost and power efficiency comparisons are evaluated by the design considerations of ZSIs in the same condition. Finally, in order to reconfirm the analyses, the experimental results of the laboratory prototype are presented.
LOFAR observations of the XMM-LSS field
Authors: Hale C. L. , Williams W. , Jarvis M. J. , Hardcastle M. J. , Morabito L. K. , Shimwell T. W. , Tasse C. , Best P. N. , Harwood J. J. , Heywood I. , Prandoni I. , Röttgering H. J. A. , Sabater J. , Smith D. J. B. , van Weeren R. J.
Published: November 2018

We present observations of the XMM Large-Scale Structure (XMM-LSS) field observed with the LOw Frequency ARray (LOFAR) at 120–168 MHz. Centred at a J2000 declination of −4.5°, this is a challenging field to observe with LOFAR because of its low elevation with respect to the array. The low elevation of this field reduces the effective collecting area of the telescope, thereby reducing sensitivity. This low elevation also causes the primary beam to be elongated in the north-south direction, which can introduce side lobes in the synthesised beam in this direction. However the XMM-LSS field is a key field to study because of the wealth of ancillary information, encompassing most of the electromagnetic spectrum. The field was observed for a total of 12 h from three four-hour LOFAR tracks using the Dutch array. The final image presented encompasses ∼27 deg2, which is the region of the observations with a >50% primary beam response. Once combined, the observations reach a central rms of 280μJy beam−1at 144 MHz and have an angular resolution of 7.5 × 8.5″. We present our catalogue of detected sources and investigate how our observations compare to previous radio observations. This includes investigating the flux scale calibration of these observations compared to previous measurements, the implied spectral indices of the sources, the observed source counts and corrections to obtain the true source counts, and finally the clustering of the observed radio sources.
Ultra-steep spectrum emission in the merging galaxy cluster Abell 1914
Authors: Mandal S. , Intema H. T. , Shimwell T. W. , van Weeren R. J. , Botteon A. , Röttgering H. J. A. , Hoang D. N. , Brunetti G. , de Gasperin F. , Giacintucci S. , Hoekstra H. , Stroe A. , Brüggen M. , Cassano R. , Shulevski A. , Drabent A. , Rafferty D.
Published: November 2018

A number of radio observations have revealed the presence of large synchrotron-emitting sources associated with the intra-cluster medium. There is strong observational evidence that the emitting particles have been (re-)accelerated by shocks and turbulence generated during merger events. The particles that are accelerated are thought to have higher initial energies than those in the thermal pool but the origin of such mildly relativistic particles remains uncertain and needs to be further investigated. The galaxy cluster Abell 1914 is a massive galaxy cluster in which X-ray observations show clear evidence of merging activity. We carried out radio observations of this cluster with the LOw Frequency ARay (LOFAR) at 150 MHz and the Giant Metrewave Radio Telescope (GMRT) at 610 MHz. We also analysed Very Large Array (VLA) 1.4 GHz data, archival GMRT 325 MHz data, CFHT weak lensing data and Chandra observations. Our analysis shows that the ultra-steep spectrum source (4C38.39; α ≲ −2), previously thought to be part of a radio halo, is a distinct source with properties that are consistent with revived fossil plasma sources. Finally, we detect some diffuse emission to the west of the source 4C38.39 that could belong to a radio halo.