bluuebunny/crossref_metadata_2025 huggingface dataset:
Evapotranspiration Trends (1979–2015) in the Central Valley of California, USA: Contrasting Tendencies During 1981–2007
Authors: Szilagyi Jozsef , Jozsa Janos
Published: August 2018

Trends in monthly evapotranspiration (ET) rates across three watersheds covering the Central Valley in California were calculated by the latest calibration‐free version of the complementary relationship of evaporation for 1979–2015. While a recent study concluded that ET rates of the irrigated fields in the Central Valley were declining in 1981–2007, here an ET trend of about 2.6 ± 12 mm per decade was found over the same period in spite of a drop in precipitation (−22 ± 30 mm per decade) and ET rates (−9.5 ± 10 mm per decade) for the rest of the watersheds, none of them statistically significant. After 2007, the precipitation decline accelerated causing a sharp drop in both irrigated and nonirrigated ET rates across the watersheds. Observations from the California Irrigation Management Information System support the present findings: Under increasing air temperatures, both dew point temperature and relative humidity values increased (at a statistically significant rate) during 1983–2007, while they reversed afterwards, in agreement with the estimated sharp irrigation ET trend decline for the remainder of the study period. Actual (in this case over irrigated fields) and reference ET rates complement each other, that is, they express opposite tendencies, as was demonstrated with California Irrigation Management Information System data, yielding a statistically significant plot‐scale irrigation ET rate increase of 31 to 41 (±17) millimeters per decade for 1983–2007 in accordance with a similar drop in reference ET rates of −28 to −50 (±16) millimeters per decade, depending on whether published monthly or daily values (aggregated to monthly ones after leaving out spurious measurements) were employed.
A Structure Function Model Recovers the Many Formulations for Air‐Water Gas Transfer Velocity
Authors: Katul Gabriel , Mammarella Ivan , Grönholm Tiia , Vesala Timo
Published: August 2018

Two ideas regarding the structure of turbulence near a clear air‐water interface are used to derive a waterside gas transfer velocity kL for sparingly and slightly soluble gases. The first is that kL is proportional to the turnover velocity described by the vertical velocity structure function Dww(r), where r is separation distance between two points. The second is that the scalar exchange between the air‐water interface and the waterside turbulence can be suitably described by a length scale proportional to the Batchelor scale lB=ηSc−1/2, where Sc is the molecular Schmidt number and η is the Kolmogorov microscale defining the smallest scale of turbulent eddies impacted by fluid viscosity. Using an approximate solution to the von Kármán‐Howarth equation predicting Dww(r) in the inertial and viscous regimes, prior formulations for kL are recovered including (i)
, vK is the Kolmogorov velocity defined by the Reynolds number vKη/ν = 1 and ν is the kinematic viscosity of water; (ii) surface divergence formulations; (iii)
, where u∗ is the waterside friction velocity; (iv)
for Keulegan numbers exceeding a threshold needed for long‐wave generation, where the proportionality constant varies with wave age, g is the gravitational acceleration; and (v)
in free convection, where qo is the surface heat flux and βo is the thermal expansion of water. The work demonstrates that the aforementioned kL formulations can be recovered from a single structure function model derived for locally homogeneous and isotropic turbulence.
Insights From Unsteady Flow Analysis of Underdamped Slug Tests in Fractured Rock
Authors: Quinn P. M. , Klammler H. , Cherry J. A. , Parker B. L.
Published: August 2018

Slug tests generating oscillating (underdamped) responses are common in high‐transmissivity (T) zones, and the nature of the response depends on the plumbing of the test equipment and the formation properties. The standard approach for obtaining T is to measure pressure shallow in the riser pipe to obtain an accurate estimate of flow and then predict the formation response from this shallow measurement by accounting for friction and acceleration assuming steady flow conditions (parabolic radial velocity profile). In this study a mathematical solution is developed for unsteady oscillatory laminar flow that shows non‐parabolic radial velocity profiles resulting in larger frictional losses, which are out of phase with the average flow velocity, indicating that errors are introduced when using the standard approach for underdamped slug test analysis. The unsteady flow model produces correction factors that can be used to improve the standard approach for predicting the formation pressure; however, not all errors are eliminated. Consequently, a new procedure is presented and applied to underdamped slug tests observed in fractured rock that avoids errors associated with quantifying inertial and frictional effects along the test equipment. This is achieved through the use of two transducers, where one is placed shallow in the water column to infer flow, and one is placed inside the test interval to represent the formation pressure. Comparison of T estimated by the new procedure to T derived from constant head step tests show better agreement than T obtained when predicting the formation pressure from a shallow pressure measurement.
The Development of Wormholes in Laboratory‐Scale Fractures: Perspectives From Three‐Dimensional Simulations
Authors: Starchenko Vitaliy , Ladd Anthony J. C.
Published: August 2018

We investigate the development of wormholes in laboratory‐scale fractures using three‐dimensional numerical simulations. Well‐controlled initial conditions, involving a small perturbation near the inlet of an otherwise flat fracture aperture field, were used to make a systematic study of the effects of flow rate and reaction rate on the aperture evolution. We find at least two characteristic wormhole shapes, which can be grouped within a phase diagram in the space of Péclet and Damköhler numbers. We investigate how this phase diagram depends on fracture geometry, specifically the length (L) and width (W) in comparison to the initial aperture (h0). This information is used to determine an effective Damköhler number that leads to a Péclet and length‐independent phase boundary between wormholes and uniform dissolution. We relate these observations to experimental studies of wormhole formation in dissolving fractures.
Six Centuries of Upper Indus Basin Streamflow Variability and Its Climatic Drivers
Authors: Rao Mukund Palat , Cook Edward R. , Cook Benjamin I. , Palmer Jonathan G. , Uriarte Maria , Devineni Naresh , Lall Upmanu , D'Arrigo Rosanne D. , Woodhouse Connie A. , Ahmed Moinuddin , Zafar Muhammad Usama , Khan Nasrullah , Khan Adam , Wahab Muhammad
Published: August 2018

Our understanding of the full range of natural variability in streamflow, including how modern flow compares to the past, is poorly understood for the Upper Indus Basin because of short instrumental gauge records. To help address this challenge, we use Hierarchical Bayesian Regression with partial pooling to develop six centuries long (1394–2008 CE) streamflow reconstructions at three Upper Indus Basin gauges (Doyian, Gilgit, and Kachora), concurrently demonstrating that Hierarchical Bayesian Regression can be used to reconstruct short records with interspersed missing data. At one gauge (Partab Bridge), with a longer instrumental record (47 years), we develop reconstructions using both Bayesian regression and the more conventionally used principal components regression. The reconstructions produced by principal components regression and Bayesian regression at Partab Bridge are nearly identical and yield comparable reconstruction skill statistics, highlighting that the resulting tree ring reconstruction of streamflow is not dependent on the choice of statistical method. Reconstructions at all four reconstructions indicate that flow levels in the 1990s were higher than mean flow for the past six centuries. While streamflow appears most sensitive to accumulated winter (January–March) precipitation and summer (May–September) temperature, with warm summers contributing to high flow through increased melt of snow and glaciers, shifts in winter precipitation and summer temperatures cannot explain the anomalously high flow during the 1990s. Regardless, the sensitivity of streamflow to summer temperatures suggests that projected warming may increase streamflow in coming decades, though long‐term water risk will additionally depend on changes in snowfall and glacial mass balance.
The Resazurin‐Resorufin System: Insights From a Decade of “Smart” Tracer Development for Hydrologic Applications
Authors: Knapp Julia L. A. , González‐Pinzón Ricardo , Haggerty Roy
Published: August 2018

The resazurin‐resorufin tracer system has been used to quantify surface water‐sediment interactions and microbial metabolic activity in stream ecosystems for one decade. This review describes the evolution of the tracer technique and summarizes how it has been used by the hydrologic and stream ecology communities. We highlight major hydrologic applications and milestones in the advancement of the reactive tracer system on scales ranging from cells to river reaches and catchments. We discuss the advantages and limitations of the resazurin‐resorufin system for hydrologic applications and suggest new directions of research, including how to address existing knowledge gaps. Beyond the goal of summarizing information that is specific to the development of the resazurin‐resorufin system, this review seeks to inform on the development of new “smart” tracer techniques as they, very likely, will face the same or similar challenges and opportunities encountered in the development of the resazurin‐resorufin system. The supporting information furthermore contains a detailed manual for the application of the resazurin‐resorufin system as hydrologic tracer and MATLAB codes for the analysis of their reactive transport.
Self-organization of active particles by quorum sensing rules
Authors: Bäuerle Tobias , Fischer Andreas , Speck Thomas , Bechinger Clemens
Published: August 2018

Many microorganisms regulate their behaviour according to the density of neighbours. Such quorum sensing is important for the communication and organisation within bacterial populations. In contrast to living systems, where quorum sensing is determined by biochemical processes, the behaviour of synthetic active particles can be controlled by external fields. Accordingly they allow to investigate how variations of a density-dependent particle response affect their self-organisation. Here we experimentally and numerically demonstrate this concept using a suspension of light-activated active particles whose motility is individually controlled by an external feedback-loop, realised by a particle detection algorithm and a scanning laser system. Depending on how the particles’ motility varies with the density of neighbours, the system self-organises into aggregates with different size, density and shape. Since the individual particles’ response to their environment is almost freely programmable, this allows for detailed insights on how communication between motile particles affects their collective properties.
Bifidobacterium breve MRx0004 protects against airway inflammation in a severe asthma model by suppressing both neutrophil and eosinophil lung infiltration
Authors: Raftis Emma J. , Delday Margaret I. , Cowie Philip , McCluskey Seánín M. , Singh Mark D. , Ettorre Anna , Mulder Imke E.
Published: August 2018

Asthma is a phenotypically heterogeneous disease. In severe asthma, airway inflammation can be predominantly eosinophilic, neutrophilic, or mixed. Only a limited number of drug candidates are in development to address this unmet clinical need. Live biotherapeutics derived from the gut microbiota are a promising new therapeutic area. MRx0004 is a commensal Bifidobacterium breve strain isolated from the microbiota of a healthy human. The strain was tested prophylactically and therapeutically by oral gavage in a house dust mite mouse model of severe asthma. A strong reduction of neutrophil and eosinophil infiltration was observed in lung bronchoalveolar lavage fluid following MRx0004 treatment. Peribronchiolar and perivascular immunopathology was also reduced. MRx0004 increased lung CD4+CD44+ cells and CD4+FoxP3+ cells and decreased activated CD11b+ dendritic cells. Cytokine analysis of lung tissue revealed reductions of pro-inflammatory cytokines and chemokines involved in neutrophil migration. In comparison, anti-IL-17 antibody treatment effectively reduced neutrophilic infiltration and increased CD4+FoxP3+ cells, but it induced lung eosinophilia and did not decrease histopathology scores. We have demonstrated that MRx0004, a microbiota-derived bacterial strain, can reduce both neutrophilic and eosinophilic infiltration in a mouse model of severe asthma. This novel therapeutic is a promising next-generation drug for management of severe asthma.
The impact of non-alcoholic fatty liver disease and metabolic syndrome on the progression of coronary artery calcification
Authors: Cho Yun Kyung , Kang Yu Mi , Yoo Jee Hee , Lee Jiwoo , Lee Seung Eun , Yang Dong Hyun , Kang Joon-Won , Park Joong-Yeol , Jung Chang Hee , Kim Hong-Kyu , Lee Woo Je
Published: August 2018

It is unclear whether non-alcoholic fatty liver disease (NAFLD) is an independent risk factor for cardiovascular disease. We examined the independent impact of NAFLD on the progression of the coronary artery calcification (CAC) score, a well-known marker of atherosclerosis progression. We examined 1,173 asymptomatic participants who underwent repeated CAC score measurement during routine health examinations. The subjects were categorised into four groups based on the presence (+) or absence (−) of NAFLD and metabolic syndrome (MetS). The progression of CAC score was defined as either incident CAC in a CAC-free population at baseline or an increase of ≥2.5 units between the baseline and the final square roots of the CAC scores of participants with detectable CAC at baseline. CAC progression was seen in 18.6% (98/526), 28.3% (77/272), 29.1% (30/103) and 32.0% (87/272) of the subjects with NAFLD(−)/MetS(−), NAFLD(+)/MetS(−), NAFLD(−)/MetS(+) and NAFLD(+)/MetS(+), respectively. The subjects with NAFLD(+)/MetS(+) and NAFLD(+)/MetS(−) had a significantly higher risk of CAC progression than those with NAFLD(−)/MetS(−) (multivariate-adjusted odds ratio [OR]: 1.76; 95% confidence interval [CI]: 1.18–2.62 and multivariate-adjusted OR: 1.53, 95% CI: 1.05–2.23, respectively). NAFLD is an independent risk factor for CAC progression, irrespective of the presence of MetS.
Effect of storage conditions on salivary polyamines quantified via liquid chromatography-mass spectrometry
Authors: Tomita Atsumi , Mori Masayo , Hiwatari Kana , Yamaguchi Eri , Itoi Takao , Sunamura Makoto , Soga Tomoyoshi , Tomita Masaru , Sugimoto Masahiro
Published: August 2018

Salivary polyamines are potential non-invasive tools for screening various types of cancers. For clinical use, the reproducibility of these metabolites should be evaluated under various storage conditions, including duration and temperature, to establish standard operating protocols. Polyamines and amino acids in unstimulated whole saliva were quantified via liquid chromatography-mass spectrometry. Concentrations of time course samples were analysed after short-term storage for up to 240 min and long-term storage for up to 8 days under various storage conditions. As expected, storage at the lowest temperature (−18 °C) exerted the least pronounced effects on the quantified values in both tests. At a higher temperature, polyamines were more stable than amino acids, as evident from polyamine profiling. Addition of ethanol significantly stabilized polyamine profiles even at a higher temperature. Comparative processing of saliva revealed a minor effect of the solvent, whereas drying had a more prominent effect on polyamine profiles. Computational analyses evaluated the ability of polyamines to discriminate pancreatic cancer from controls. Repeated noise added tests were designed on the basis of the results of the storage tests; these analyses confirmed that the discriminative abilities were robust. These data contribute to the standardization of salivary storage conditions, thereby highlighting the clinical utility of saliva.
IL-1β, IL-6, TNF- α and CRP in Elderly Patients with Depression or Alzheimer’s disease: Systematic Review and Meta-Analysis
Authors: Ng Ada , Tam Wilson W. , Zhang Melvyn W. , Ho Cyrus S. , Husain Syeda F. , McIntyre Roger S. , Ho Roger C.
Published: August 2018

We carried out systematic review and meta-analysis to evaluate whether peripheral levels of pro-inflammatory markers including Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumor Necrosis Factor-α (TNF- α) and C-Reactive Protein (CRP) are significantly higher in elderly with depression and Alzheimer’s disease. We searched Pubmed, PsycINFO and Embase, and thirty-four relevant studies (2609 with Depression, 1645 with Alzheimer’s disease and 14363 Controls) were included. Compared with controls, IL-1β (pooled standardized mean difference [SMD]: 0.642; 95% confidence interval [CI]: 0.078–1.206; significant heterogeneity: I2 = 86.28%) and IL-6 (pooled SMD: 0.377; 95% CI: 0.156–0.598; significant heterogeneity: I2 = 88.75%) were significantly elevated in depression. There was no difference in TNF-α (p = 0.351) and CRP (p = 0.05) between those with depression and controls. Compared with controls, IL-1β (pooled SMD: 1.37, 95% CI: 0.06–2.68, significant heterogeneity: I2 = 96.01%) was significantly elevated in Alzheimer’s disease. There were no differences in IL-6 (p = 0.138), TNF-α (p = 0.451) and CRP (p = 0.07) between elderly with Alzheimer’s disease and controls. After Bonferroni adjustment, only IL-6 remained significantly higher in depression. Elderly with depression have higher IL-6 than controls, while those with Alzheimer’s disease did not have higher peripheral inflammatory markers.
The Gpr1-regulated Sur7 family protein Sfp2 is required for hyphal growth and cell wall stability in the mycoparasite Trichoderma atroviride
Authors: Atanasova Lea , Gruber Sabine , Lichius Alexander , Radebner Theresa , Abendstein Leoni , Münsterkötter Martin , Stralis-Pavese Nancy , Łabaj Paweł P. , Kreil David P. , Zeilinger Susanne
Published: August 2018

Mycoparasites, e.g. fungi feeding on other fungi, are prominent within the genus Trichoderma and represent a promising alternative to chemical fungicides for plant disease control. We previously showed that the seven-transmembrane receptor Gpr1 regulates mycelial growth and asexual development and governs mycoparasitism-related processes in Trichoderma atroviride. We now describe the identification of genes being targeted by Gpr1 under mycoparasitic conditions. The identified gene set includes a candidate, sfp2, encoding a protein of the fungal-specific Sur7 superfamily, whose upregulation in T. atroviride upon interaction with a fungal prey is dependent on Gpr1. Sur7 family proteins are typical residents of membrane microdomains such as the membrane compartment of Can1 (MCC)/eisosome in yeast. We found that GFP-labeled Gpr1 and Sfp2 proteins show partly overlapping localization patterns in T. atroviride hyphae, which may point to shared functions and potential interaction during signal perception and endocytosis. Deletion of sfp2 caused heavily altered colony morphology, defects in polarized growth, cell wall integrity and endocytosis, and significantly reduced mycoparasitic activity, whereas sfp2 overexpression enhanced full overgrowth and killing of the prey. Transcriptional activation of a chitinase specific for hyphal growth and network formation and strong downregulation of chitin synthase-encoding genes were observed in Δsfp2. Taken together, these findings imply crucial functions of Sfp2 in hyphal morphogenesis of T. atroviride and its interaction with prey fungi.
Drug-based perturbation screen uncovers synergistic drug combinations in Burkitt lymphoma
Authors: Tomska K. , Kurilov R. , Lee K. S. , Hüllein J. , Lukas M. , Sellner L. , Walther T. , Wagner L. , Oleś M. , Brors B. , Huber W. , Zenz T.
Published: August 2018

Burkitt lymphoma (BL) is a highly aggressive B-cell lymphoma associated with MYC translocation. Here, we describe drug response profiling of 42 blood cancer cell lines including 17 BL to 32 drugs targeting key cancer pathways and provide a systematic study of drug combinations in BL cell lines. Based on drug response, we identified cell line specific sensitivities, i.e. to venetoclax driven by BCL2 overexpression and partitioned subsets of BL driven by response to kinase inhibitors. In the combination screen, including BET, BTK and PI3K inhibitors, we identified synergistic combinations of PI3K and BTK inhibition with drugs targeting Akt, mTOR, BET and doxorubicin. A detailed comparison of PI3K and BTKi combinations identified subtle differences, in line with convergent pathway activity. Most synergistic combinations were identified for the BET inhibitor OTX015, which showed synergistic effects for 41% of combinations including inhibitors of PI3K/AKT/mTOR signalling. The strongest synergy was observed for the combination of the CDK 2/7/9 inhibitor SNS032 and OTX015. Our data provide a landscape of drug combination effects in BL and suggest that targeting CDK and BET could provide a novel vulnerability of BL.
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Authors: Escobar-Zepeda Alejandra , Godoy-Lozano Elizabeth Ernestina , Raggi Luciana , Segovia Lorenzo , Merino Enrique , Gutiérrez-Rios Rosa María , Juarez Katy , Licea-Navarro Alexei F. , Pardo-Lopez Liliana , Sanchez-Flores Alejandro
Published: August 2018

Metagenomics research has recently thrived due to DNA sequencing technologies improvement, driving the emergence of new analysis tools and the growth of taxonomic databases. However, there is no all-purpose strategy that can guarantee the best result for a given project and there are several combinations of software, parameters and databases that can be tested. Therefore, we performed an impartial comparison, using statistical measures of classification for eight bioinformatic tools and four taxonomic databases, defining a benchmark framework to evaluate each tool in a standardized context. Using in silico simulated data for 16S rRNA amplicons and whole metagenome shotgun data, we compared the results from different software and database combinations to detect biases related to algorithms or database annotation. Using our benchmark framework, researchers can define cut-off values to evaluate the expected error rate and coverage for their results, regardless the score used by each software. A quick guide to select the best tool, all datasets and scripts to reproduce our results and benchmark any new method are available at https://github.com/Ales-ibt/Metagenomic-benchmark. Finally, we stress out the importance of gold standards, database curation and manual inspection of taxonomic profiling results, for a better and more accurate microbial diversity description.
A factor VII-based method for the prediction of anticoagulant response to warfarin
Authors: Ooi Qing-Xi , Wright Daniel F. B. , Isbister Geoffrey K. , Duffull Stephen B.
Published: August 2018

Warfarin dosing methods based on existing models for warfarin and the international normalised ratio (INR) give biased maintenance dose predictions at the upper and lower quantiles of dose requirements. The aim of this work is to propose a conceptually different approach to predict INR after warfarin dosing. Factor VII concentration was proposed as the principal driving force for the INR. The time to steady-state INR (tSS,INR) was determined based on the INR response to changes in factor VII concentrations following warfarin initiation, and from this the steady-state INR (INRSS) was derived. The proposed method requires timed, paired blood samples of INR and factor VII. At different simulated warfarin dose rates, the prediction error associated with the proposed method was shown to be within clinically acceptable limits for both the tSS,INR (±2 days) and INRSS (±0.2). The use of the method was demonstrated in two patients who were initiated with 5 mg of warfarin daily. The difference in predicted versus actual steady-state INR were 0.0 and −0.4. The proposed method represents a unique approach to predict the INR. It considers factor VII as the main driver for INR and provides valuable information about the time to steady state INR.
Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure
Authors: Zhang Hong , Li Xintong , He Fan , Zhao Mingqin , Ling Liansheng
Published: August 2018

A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2′-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2−) by H2O2 to generate green ABTS•− radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2−. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0–250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.
Comparative toxicity of synchrotron and conventional radiation therapy based on total and partial body irradiation in a murine model
Authors: Smyth Lloyd M. L. , Donoghue Jacqueline F. , Ventura Jessica A. , Livingstone Jayde , Bailey Tracy , Day Liam R. J. , Crosbie Jeffrey C. , Rogers Peter A. W.
Published: August 2018

Synchrotron radiation can facilitate novel radiation therapy modalities such as microbeam radiation therapy (MRT) and high dose-rate synchrotron broad-beam radiation therapy (SBBR). Both of these modalities have unique physical properties that could be exploited for an improved therapeutic effect. While pre-clinical studies report promising normal tissue sparing phenomena, systematic toxicity data are still required. Our objective was to characterise the toxicity of SBBR and MRT and to calculate equivalent doses of conventional radiation therapy (CRT). A dose-escalation study was performed on C57BLJ/6 mice using total body and partial body irradiations. Dose-response curves and TD50 values were subsequently calculated using PROBIT analysis. For SBBR at dose-rates of 37 to 41 Gy/s, we found no evidence of a normal tissue sparing effect relative to CRT. Our findings also show that the MRT valley dose, rather than the peak dose, best correlates with CRT doses for acute toxicity. Importantly, longer-term weight tracking of irradiated animals revealed more pronounced growth impairment following MRT compared to both SBBR and CRT. Overall, this study provides the first in vivo dose-equivalence data between MRT, SBBR and CRT and presents systematic toxicity data for a range of organs that can be used as a reference point for future pre-clinical work.
Determining Relative Dynamic Stability of Cell States Using Boolean Network Model
Authors: Joo Jae Il , Zhou Joseph X. , Huang Sui , Cho Kwang-Hyun
Published: August 2018

Cell state transition is at the core of biological processes in metazoan, which includes cell differentiation, epithelial-to-mesenchymal transition (EMT) and cell reprogramming. In these cases, it is important to understand the molecular mechanism of cellular stability and how the transitions happen between different cell states, which is controlled by a gene regulatory network (GRN) hard-wired in the genome. Here we use Boolean modeling of GRN to study the cell state transition of EMT and systematically compare four available methods to calculate the cellular stability of three cell states in EMT in both normal and genetically mutated cases. The results produced from four methods generally agree but do not totally agree with each other. We show that distribution of one-degree neighborhood of cell states, which are the nearest states by Hamming distance, causes the difference among the methods. From that, we propose a new method based on one-degree neighborhood, which is the simplest one and agrees with other methods to estimate the cellular stability in all scenarios of our EMT model. This new method will help the researchers in the field of cell differentiation and cell reprogramming to calculate cellular stability using Boolean model, and then rationally design their experimental protocols to manipulate the cell state transition.
Dislocation driven nanosample plasticity: new insights from quantitative in-situ TEM tensile testing
Authors: Samaee Vahid , Gatti Riccardo , Devincre Benoit , Pardoen Thomas , Schryvers Dominique , Idrissi Hosni
Published: August 2018

Intrinsic dislocation mechanisms in the vicinity of free surfaces of an almost FIB damage-free single crystal Ni sample have been quantitatively investigated owing to a novel sample preparation method combining twin-jet electro-polishing, in-situ TEM heating and FIB. The results reveal that the small-scale plasticity is mainly controlled by the conversion of few tangled dislocations, still present after heating, into stable single arm sources (SASs) as well as by the successive operation of these sources. Strain hardening resulting from the operation of an individual SAS is reported and attributed to the decrease of the length of the source. Moreover, the impact of the shortening of the dislocation source on the intermittent plastic flow, characteristic of SASs, is discussed. These findings provide essential information for the understanding of the regime of ‘dislocation source’ controlled plasticity and the related mechanical size effect.
Novel clinical device tracking and tissue event characterization using proximally placed audio signal acquisition and processing
Authors: Illanes Alfredo , Boese Axel , Maldonado Iván , Pashazadeh Ali , Schaufler Anna , Navab Nassir , Friebe Michael
Published: August 2018

We propose a new and complementary approach to image guidance for monitoring medical interventional devices (MID) with human tissue interaction and surgery augmentation by acquiring acoustic emission data from the proximal end of the MID outside the patient to extract dynamical characteristics of the interaction between the distal tip and the tissue touched or penetrated by the MID. We conducted phantom based experiments (n = 955) to show dynamic tool/tissue interaction during tissue needle passage (a) and vessel perforation caused by guide wire artery perforation (b). We use time-varying auto-regressive (TV-AR) modelling to characterize the dynamic changes and time-varying maximal energy pole (TV-MEP) to compute subsequent analysis of MID/tissue interaction characterization patterns. Qualitative and quantitative analysis showed that the TV-AR spectrum and the TV-MEP indicated the time instants of the needle path through different phantom objects (a) and clearly showed a perforation versus other generated artefacts (b). We demonstrated that audio signals acquired from the proximal part of an MID could provide valuable additional information to surgeons during minimally invasive procedures.
A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator
Authors: Heller Philip , Casaletto James , Ruiz Gregory , Geller Jonathan
Published: August 2018

The Cytochrome C Oxidase subunit I gene (“COI”) is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD’s submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive. Midori, derived from GenBank, has more sequences but less stringent standards than BOLD, resulting in higher error rates. To address the need for a comprehensive and accurate COI database, we adapted the ARBitrator algorithm, which classifies based only on sequence properties and has successfully auto-curated bacterial genes mined from GenBank. The adapted algorithm, which we call CO-ARBitrator, built a database of over a million metazoan COI sequences. Sensitivity and specificity are significantly higher than Midori. Specificity is comparable to what BOLD achieves with data quality prerequisites. Results and software are publicly available.
Photochemical activation of SF6 by N-heterocyclic carbenes to provide a deoxyfluorinating reagent
Authors: Tomar Pooja , Braun Thomas , Kemnitz Erhard
Published: August 2018

A photochemical activation of SF6 provides access to difluoroimidazolidine derivatives, which can serve as intermediates to shuttle fluorides to alcohols by deoxyfluorination.
Evolving mechanism of organotemplate-free hierarchical FAU zeolites with house-of-card-like structures
Authors: Liu Lijia , Wang Hongbin , Wang Ziqi , Zhu Liangkui , Huang Lin , Yu Liang , Fan Jinya , Yao Yuechao , Liu Shiyu , Zou Jizhao , Zeng Xierong
Published: August 2018

The evolution mechanism of organotemplate-free FAU zeolites with house-of-card-like (HCL) structures is determined to follow a nucleation and skeleton crystal growth model, which is different from those of traditional HCL zeolites obtained using organic templates.
Improved model for the refractive index: application to potential components of ambient aerosol
Authors: Bouteloup Rémi , Mathieu Didier
Published: August 2018

Understanding the impact of atmospheric aerosols on the global radiative balance requires knowing the refractive index (RI) of their components.
Electrochemical tuning of capacitive response of graphene oxide
Authors: Gutić Sanjin J. , Kozlica Dževad K. , Korać Fehim , Bajuk-Bogdanović Danica , Mitrić Miodrag , Mirsky Vladimir M. , Mentus Slavko V. , Pašti Igor A.
Published: August 2018

The capacitance of graphene oxide can be maximized by precise control of the conditions of electrochemical reduction to balance the oxygen concentration and conductivity.
State-of-the-art computation of the rotational and IR spectra of the methyl-cyclopropyl cation: hints on its detection in space
Authors: Puzzarini Cristina , Tasinato Nicola , Bloino Julien , Spada Lorenzo , Barone Vincenzo
Published: August 2018

A route toward the detection of the methyl-cyclopropenyl cation in space: a spectroscopic characterization by state-of-the-art computational approaches.
A printable voltammetric genosensor for tumour suppressor gene screening based on a nanocomposite of Ceria NPs–GO/nano-PANI
Authors: Eskandari Mahboubeh , Faridbod Farnoush
Published: August 2018

A specific sequence of the adenomatous polyposis coli (APC) gene is detected electrochemically using a new nanomaterial based bio-sensing platform.
Red-emitting fluorescent organic@silicate core–shell nanoparticles for bio-imaging
Authors: Shenoi-Perdoor Shridevi , Cattoën Xavier , Bretonnière Yann , Eucat Gwenaëlle , Andraud Chantal , Gennaro Béatrice , Kodjikian Stéphanie , Dubois Fabien , Ibanez Alain
Published: August 2018

Original core–shell nanoparticles featuring a fluorescent organic nanocrystalline core emitting in the red region are described.
Correction: Chiral NHC-catalyzed 1,3-dipolar [3 + 2] cycloaddition of azomethine imines with α-chloroaldehydes for the synthesis of bicyclic pyrazolidinones
Authors: Yang Limin , Lv Yunbo , Wang Fei , Zhong Guofu
Published: August 2018

Correction for ‘Chiral NHC-catalyzed 1,3-dipolar [3 + 2] cycloaddition of azomethine imines with α-chloroaldehydes for the synthesis of bicyclic pyrazolidinones’ by Limin Yang, et al., Org. Biomol. Chem., 2018, 16, 4433–4438.
Temporal–spatial-resolved mapping of the electrical double layer changes by surface plasmon resonance imaging
Authors: Luo Xueyi , Deng Shijie , Wang Peng
Published: August 2018

This paper provides a novel method for temporal–spatial-resolved mapping of the electrical double layer changes at the heterogeneous interface.
Synthesis of a cationic polyacrylamide by a photocatalytic surface-initiated method and evaluation of its flocculation and dewatering performance: nano-TiO2 as a photo initiator
Authors: Liu Yongzhi , Zheng Huaili , Wang Yili , Zheng Xinyu , Wang Moxi , Ren Jie , Zhao Chuanliang
Published: August 2018

In the face of complex water quality changes, the application of existing cationic polyacrylamide has been largely limited.
An efficient reduced graphene-oxide filter for PM2.5 removal
Authors: Jung Wonji , Lee Jeong Seok , Han Seonggeun , Ko Seung Hwan , Kim Taewoo , Kim Yong Hyup
Published: August 2018

The most efficient 3-D reduced graphene oxide filter that can simultaneously remove outdoor PM and purify indoor PM.
High performance low-bandgap perovskite solar cells based on a high-quality mixed Sn–Pb perovskite film prepared by vacuum-assisted thermal annealing
Authors: Liu Meiyue , Chen Ziming , Xue Qifan , Cheung Sin Hang , So Shu Kong , Yip Hin-Lap , Cao Yong
Published: August 2018

Vacuum-assisted thermal annealing not only could improve film morphology and crystallinity, but also could accelerate the sublimation of undesired MACl. With the help of this process, we obtain a highly efficient low-bandgap CH3NH3Sn0.5Pb0.5IxCl3−xperovskite solar cell with a power conversion efficiency of 12.3%.
Elucidating the energy storage mechanism of ZnMn2O4 as promising anode for Li-ion batteries
Authors: Zhao Zijian , Tian Guiying , Sarapulova Angelina , Trouillet Vanessa , Fu Qiang , Geckle Udo , Ehrenberg Helmut , Dsoke Sonia
Published: August 2018

Promising ZnMn2O4 anode provides high capacity in Li-ion batteries and the capacity increase during cycling due to the reversible Li storage in SEI and the extra redox reaction of Mn(ii)/Mn(iii).
Bulk linearisation of the MOS resistor
Authors: Arnaud A. , Miguez M.
Published: August 2018

A bulk‐linearised composite MOSFET is presented, with an extended linear range and an equivalent saturation voltage of up to several hundred mV even in weak inversion. Some preliminary measurements are presented as well as a 300 MΩ equivalent resistor, with almost a 1 V quasi‐linear range. A low frequency, 28 dB gain, biomedical bandpass filter/amplifier is also shown, taking advantage of the linearised MOSFETs to consume only 16 nA of supply current.
Two-dimensional simulations of mixing in classical novae: The effect of white dwarf composition and mass
Authors: Casanova Jordi , José Jordi , Shore Steven N.
Published: August 2018

Context. Classical novae are explosive phenomena that take place in stellar binary systems. They are powered by mass transfer from a low-mass main sequence star onto either a CO or ONe white dwarf. The material accumulates for 104–105yr until ignition under degenerate conditions, resulting in a thermonuclear runaway. The nuclear energy released produces peak temperatures of ∼0.1–0.4 GK. During these events, 10−7−10−3M⊙enriched in intermediate-mass elements, with respect to solar abundances, are ejected into the interstellar medium. However, the origin of the large metallicity enhancements and the inhomogeneous distribution of chemical species observed in high-resolution spectra of ejected nova shells is not fully understood.

Aims. Recent multidimensional simulations have demonstrated that Kelvin-Helmholtz instabilities that operate at the core-envelope interface can naturally produce self-enrichment of the accreted envelope with material from the underlying white dwarf at levels that agree with observations. However, such multidimensional simulations have been performed for a small number of cases and much of the parameter space remains unexplored.

Methods. We investigated the dredge-up, driven by Kelvin-Helmholtz instabilities, for white dwarf masses in the range 0.8–1.25M⊙and different core compositions, that is, CO-rich and ONe-rich substrates. We present a set of five numerical simulations performed in two dimensions aimed at analyzing the possible impact of the white dwarf mass, and composition, on the metallicity enhancement and explosion characteristics.

Results. At the time we stop the simulations, we observe greater mixing (∼30% higher when measured in the same conditions) and more energetic outbursts for ONe-rich substrates than for CO-rich substrates and more massive white dwarfs.
Random vibration based damage detection for a composite beam under environmental and operational variability via a stochastic Functional Model based method
Authors: Aravanis Tryfon-Chrysovalantis , Kolovos Spiros , Sakellariou John , Fassois Spilios
Published: August 2018

The problem of random vibration response based damage detection for a composite beam under non-measurable environmental and operational variability, presently temperature and tightening torque, is considered via a Functional Model based method. The method is based on proper representation of the healthy structural dynamics under any environmental/operating conditions via a data based Functional Model obtained in the method’s baseline phase and used to define a ‘healthy subspace’. Damage detection is, in the method’s inspection phase, achieved by examining whether or not the current dynamics belongs to the healthy subspace. The experimental results obtained for damage detection on a composite beam indicate excellent detection performance, with correct detection rate of 100% for false alarm rate as small as 1%. The superiority of the proposed method is confirmed via comparisons with a state-of-the-art Principal Component Analysis based method.
Composite cylindrical shells under combined loading
Authors: Charitidis Panagiotis , Zacharopoulos Dimitrios
Published: August 2018

The structural design of a cylindrical shell made of a unidirectional glass/epoxy fiber composite and subjected to torsional moment and internal pressure is studied. An anisotropic model for analysis of composite material is applied. The minimum wall thickness of the shell, with the use of the Tsai-Hill failure criterion, is derived. In this connection, the strain energy density criterion (SED) is applied, by which the critical crack length is determined. In this paper, we illustrate the fracture methodology towards the design of a cylindrical shell structure for determining safe operation. Finite element analysis and analytical method were also established.
Effect of interlaminar flaw on composite panel behaviour under acoustic loading
Authors: Běhal Jiří , Zděnek Pavel
Published: August 2018

A design of airframe structures has to be accompanied by material properties testing. Special focus has to be laid on high frequency fatigue behaviour. The acoustic fatigue test equipment for grazing wave’s incidence was designed based on the FE analyses. Flat composite panels were designed and manufactured using the Hexply 8552/AGP193-PW prepreg with different fiber lay-ups and with simulation of production imperfections or operational damage. Dynamic behaviour of panels was tested using three regimes of acoustic loading: white noise spectrum, engine noise spectrum and discrete harmonic frequencies loading. Rayleigh damping coefficients were evaluated for later use in FE models. Panel health was checked periodically through a power spectral density response on white noise signal. The ultrasonic NDT instruments were used for monitoring of relevant delamination increment. No increments of delamination were detected. The available acoustic power was below the fatigue limit of the tested structure.
Ballistic impact response of steel fiber-metal laminates
Authors: Bikakis George , Tsigkros Nikolaos , Sideridis Emilios , Savaidis Alexander
Published: August 2018

In this article, the ballistic impact response of square clamped fiber-metal laminates and monolithic plates consisting of different metal alloys is investigated using the ANSYS LS-DYNA explicit nonlinear analysis software. The panels are subjected to central normal high velocity ballistic impact by a cylindrical projectile. Using validated finite element models, the influence of the mechanical properties of the constituent metal alloy on the ballistic resistance of the fiber-metal laminates and the monolithic plates is studied. Six steel alloys are examined, namely 304 stainless steel, 1010, 1080, 4340, A36 steel and DP 590 dual phase steel. A comparison with the response of GLARE plates is also implemented. It is found that the ballistic limits of the panels can be substantially affected by the constituent alloy. The stainless steel based panels offer the highest ballistic resistance followed by the A36 steel based panels which in turn have higher ballistic resistance than the 2024-T3 aluminum based panels. The A36 steel based panels have higher ballistic limit than the 1010 steel based panels which in turn have higher ballistic limit than the 1080 steel based panels. The behavior of characteristic impact variables during the ballistic impact phenomenon is analyzed.
A model of low-velocity impact damage assessment of laminated composite structures
Authors: Stamoulis Konstantinos P. , Georgantzinos Stylianos K. , Giannopoulos Georgios I.
Published: August 2018

Laminated composites have important applications in modern aeronautical structures due to their extraordinary mechanical and environmental behaviour. Nevertheless, aircraft composite structures are highly vulnerable to impact damage, either by low-velocity sources during maintenance or high-velocity sources during in-flight events. Even barely visible impact damage induced by low-velocity loading, substantially reduces the residual mechanical performance and the safe-service life of the composites structures. Despite the extensive research already carried out, impact damage of laminated composite structures is still not well understood and it is an area of on-going research. Numerical modelling is considered as the most efficient tool as compared to the expensive and time-consuming experimental testing. In this paper, a finite element model based on explicit dynamics formulations is adopted. Hashin criterion is applied to predict the intra-laminar damage initiation and evolution. The numerical analysis is performed using the ABAQUS® programme. The employed modelling approach is validated using numerical results found in the literature and the presented results show an acceptable correlation to the available literature data. It is demonstrated that the presented model is able to capture force-time response as well as damage evolution map for a range of impact energies.
Finite element modelling of air cavities effect on GnP/epoxy nanocomposite thermal response and its full-field validation
Authors: Manta Asimina , Gresil Matthieu , Soutis Constantinos
Published: August 2018

The manufacturing process of GnP/polymer nanocomposites exhibits important challenges regarding the material quality and how to reduce or eliminate fabrication induced defects. In this work, the effect of air cavities (voids) on the thermal response of nanocomposites is studied by means of finite element analysis on a multi-scale scheme. The proposed model is validated with experimental data by performing generic and full-field comparisons.