bluuebunny/crossref_metadata_2025 huggingface dataset:
Delivery mode impacts newborn gut colonization efficiency
Authors: Mitchell Caroline , Hogstrom Larson , Bryant Allison , Bergerat Agnes , Cher Avital , Pochan Shawna , Herman Penelope , Carrigan Maureen , Sharp Karen , Huttenhower Curtis , Lander Eric S. , Vlamakis Hera , Xavier Ramnik J. , Yassour Moran
Published: January 2020

Delivery mode is the variable with the greatest influence on the infant gut microbiome composition in the first few months of life. Children born by Cesarean section (C-section) lack species from theBacteroidesgenus in their gut microbial community, and this difference can be detectable until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome, as children born by C-section do not pass through the birth canal; however,Bacteroidesspecies are not common members of the vaginal microbiome, thus this explanation seems inadequate. Here, we set out to re-evaluate this hypothesis by collecting rectal and vaginal samples before delivery from 73 mothers with paired stool from their infants in the first two weeks of life. We compared microbial profiles of infants born by planned, pre-labor C-section to those born by emergent, post-labor surgery (where the child was in the birth canal, but eventually delivered through an abdominal incision), and found no significant differences in the microbiome between these two groups. Both groups showed the characteristic signature lack ofBacteroidesspecies, despite their difference in exposure to the birth canal. Surprisingly, this signature was only evident in samples from week two of life, but not in the first week. Children born by C-section often had high abundance ofBacteroidesin their first few days of life, but these were not stable colonizers of the infant gut, as they were not detectable by week two. Finally, we used metagenomic sequencing to compare microbial strains in maternal vaginal and rectal samples and samples from their infants; we found evidence for mother-to-child transmission of rectal rather than vaginal strains. These results challenge birth canal exposure as the dominant factor in infant gut microbiome establishment and implicate colonization efficiency rather than exposure as a dictating factor of the newborn gut microbiome composition.
Creative destruction: a basic computational model of cortical layer formation
Authors: Bauer Roman , Clowry Gavin J , Kaiser Marcus
Published: January 2020

One of the most characteristic properties of many vertebrate neural systems is the layered organization of different cell types. This cytoarchitecture exists in the cortex, the retina, the hippocampus and many other parts of the central nervous system. The developmental mechanisms of neural layer formation have been subject to substantial experimental efforts. Here, we provide a general computational model for cortical layer formation in 3D physical space. We show that this multi-scale, agent-based model comprising two distinct stages of apoptosis, can account for the wide range of neuronal numbers encountered in different cortical areas and species. Our results demonstrate the phenotypic richness of a basic state diagram structure, and suggest a novel function for apoptosis. Moreover, slightly changed gene regulatory dynamics recapitulate characteristic properties observed in neurodevelopmental diseases. Overall, we propose a novel computational model using gene-type rules, exhibiting many characteristics of normal and pathological cortical development.
Potential inhibitors for 2019-nCoV coronavirus M protease from clinically approved medicines
Authors: Liu Xin , Wang Xiu-Jie
Published: January 2020

Starting from December 2019, a novel coronavirus, named 2019-nCoV, was found to cause Severe Acute Respiratory (SARI) symptoms and rapid pandemic in China. With the hope to identify candidate drugs for 2019-nCoV, we adopted a computational approach to screen for available commercial medicines which may function as inhibitors for the Mproof 2019-nCoV. Up to 10 commercial medicines that may form hydrogen bounds to key residues within the binding pocket of 2019-nCoV Mprowere identified, which may have higher mutation tolerance than lopinavir/ritonavir and may also function as inhibitors for other coronaviruses with similar Mprobinding sites and pocket structures.
Landscape of transcript isoforms in single T cells infiltrating in non-small cell lung cancer
Authors: Li Jiesheng , Zhang Zemin , Ren Xianwen
Published: January 2020

Single cell RNA-seq has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes. However, analyses at the transcript isoform level are rarely reported. As alternative splicing is critical to T cell differentiation and activation, here we proposed a computational method named as IDEA to comprehensively detect and annotate differentially used isoforms across cell subtypes. We applied IDEA on a scRNA-seq dataset of 12,346 T cells from non-small cell lung cancer. We found most genes tend to dominantly express one isoform in single T cells, enabling typing T cells according to the isotypes given a gene. Isotype analysis suggested that tumor-infiltrating T cells significantly preferred specific isotypes for 245 genes in CD8+ T cells and 456 genes in CD4+ T cells. Functional annotation suggests that the preferred isoforms involved in coding/non-coding switches, transcription start site changes, gains/losses of domains and subcellular translocation. Clonal analysis revealed that isoform switching occurred during T cell activation/differentiation. Our analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and sheds new lights into the regulatory mechanisms of tumor-infiltrating T cells.
TrkB induced metastatic potential of cancer by suppression of BMP mediated tumor inhibitory activity
Authors: Kim Min Soo , Jin Wook
Published: January 2020

Our previous observations also demonstrate that TrkB expression in breast cancer induces metastatic potential by both JAK2/STAT3 and PI3K/AKT activation and induced metastasis of breast cancer mediated suppression of RUNX3 and KEAP1 expression by TrkB. Also, TrkB induced metastatic potential of cancer and suppressed the growth inhibitory activity in response to BMP signaling by preventing BMRRI/BMPRII complex formation. The previous report BMP-2 and BMP4 trigger tumor inhibitory activity in colorectal cancer by upregulation of RUNX3 expression. Although TrkB may regulate tumor inhibitory activity by BMP-induced upregulation of RUNX3, it is not still fully understood how TrkB signaling adjusts to inhibit BMP signaling-mediated tumor suppression.Our findings provide important molecular insights into TrkB-mediated modulation of BMP signaling has remained unknown, and none of the studies still reported a correlation between TrkB and BMP signaling. Our current study surprisingly showed that unique role of TrkB in the regulation of BMP-induced tumor inhibitory activity and BMP-2-induced RUNX3 expression.
Obesity-driven changes in ECM composition promote local invasion and metastasis of breast tumors
Authors: Wishart Andrew , Peng Yifan , Conner Sydney , Guarin Justinne , Crews Rebecca , Fatherree Jackson , Greenberg Andrew S. , Oudin Madeleine J.
Published: January 2020

The extracellular matrix (ECM) is a major component of the tumor microenvironment that supports cellular growth, promotes local invasion from the primary tumor, and contributes to metastatic outgrowth in sites of colonization. Obesity is a systemic disease that causes chronic inflammation which can lead to ECM deposition and ultimately fibrosis in adipose tissues such as the mammary gland. Overweight breast cancer patients have increased metastasis to the lung and liver, exhibit resistance to chemotherapy and have worse outcomes. We found that ECM isolated from the mammary gland of both tumor-bearing and obese mice increased invasion of breast cancer cells and set out to investigate whether obesity-driven changes in ECM could identify novel drivers of invasion and metastasis in breast cancer. We performed proteomics of the mammary fat pads of both lean and obese mice and identified the entire landscape of obesity-driven ECM changes. In particular, we focused on Collagen VI, an ECM protein secreted by adipocytes in mammary tissues. Collagen VI is upregulated in the ECM of obese and tumor-bearing mice and is associated with poor outcome in human breast cancer. We found that Collagen VI drives adhesion, migration and invasion of several human breast cancer cell lines via crosstalk between the adhesion receptor NG2 and the receptor tyrosine kinase EGFR, and activation of MAPK signaling. Overall, these studies demonstrate that obesity can have profound effects on the ECM composition of tissues, which in turn can promote local invasion and metastasis.
Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria
Authors: Moya Andrés , Oliver José L. , Verdú Miguel , Delaye Luis , Arnau Vicente , Bernaola-Galván Pedro , de la Fuente Rebeca , Díaz Wladimiro , Gómez-Martín Cristina , González Francisco M. , Latorre Amparo , Lebrón Ricardo , Román-Roldán Ramón
Published: January 2020

Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.
Reducing FASN expression sensitizes acute myeloid leukemia cells to differentiation therapy
Authors: Humbert Magali , Seiler Kristina , Mosimann Severin , Rentsch Vreni , McKenna Sharon L. , Tschan Mario P.
Published: January 2020

Fatty acid synthase (FASN) is the only human lipogenic enzyme available for de novo fatty acid synthesis and is often highly expressed in cancer cells. We found that FASN mRNA levels were significantly higher in acute myeloid leukemia (AML) patients than in healthy granulocytes or CD34+ hematopoietic progenitors. Accordingly, FASN levels decreased during all-trans retinoic acid (ATRA)-mediated granulocytic differentiation of acute promyelocytic leukemia (APL) cells, partially via autophagic degradation. Furthermore, our data suggests that inhibition of FASN expression levels using RNAi or (-)-epigallocatechin-3-gallate (EGCG), accelerates the differentiation of APL cell lines and significantly re-sensitized ATRA refractory non-APL AML cells. FASN reduction promoted translocation of transcription factor EB (TFEB) to the nucleus, paralleled by activation of CLEAR network genes and lysosomal biogenesis. Lysosomal biogenesis was activated, consistent with TFEB transcriptional activation of CLEAR network genes.

Together, our data demonstrate that inhibition of FASN expression in combination with ATRA treatment facilitates granulocytic differentiation of APL cells and may extend differentiation therapy to non-APL AML cells.
Mechanism of DNA surface exploration and operator bypassing during target search
Authors: Marklund E. , van Oosten B. , Mao G. , Amselem E. , Kipper K. , Sabantsev A. , Emmerich A. , Globisch D. , Zheng X. , Lehmann L. C. , Berg O. , Johansson M. , Elf J. , Deindl S.
Published: January 2020

Many proteins that bind specific DNA sequences search the genome by combining three dimensional (3D) diffusion in the cytoplasm with one dimensional (1D) sliding on non-specific DNA1–5. Here we combine resonance energy transfer and fluorescence correlation measurements to characterize how individuallacrepressor (LacI) molecules explore DNA during the 1D phase of target search. To track the rotation of sliding LacI molecules on the microsecond time scale during DNA surface search, we use real-time single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy (SMCT-FCS). The fluorescence signal fluctuations are accurately described by rotation-coupled sliding, where LacI traverses ~40 base pairs (bp) per revolution. This distance substantially exceeds the 10.5-bp helical pitch of DNA, suggesting that the sliding protein frequently hops out of the DNA groove, which would result in frequent bypassing of target sequences. Indeed, we directly observe such bypassing by single-molecule fluorescence resonance energy transfer (smFRET). A combined analysis of the smFRET and SMCT-FCS data shows that LacI at most hops one to two grooves (10-20 bp) every 250 μs. Overall, our data suggest a speed-accuracy trade-off during sliding; the weak nature of non-specific protein-DNA interactions underlies operator bypassing but also facilitates rapid sliding. We anticipate that our SMCT-FCS method to monitor rotational diffusion on the microsecond time scale while tracking individual molecules with millisecond time resolution will be applicable to the real-time investigation of many other biological interactions and effectively extends the accessible time regime by two orders of magnitude.
WISP2/CCN5gene knockdown in vitro and in vivo exhibits proliferation promotion of breast cancer through targeting Skp2 and p27Kip1
Authors: Lv Yan , Zhang Chang , Li Xiao Jiang , Gao Shan , Zheng Xu , Han Yan Yan , Li Chong , Geng Qiang
Published: January 2020

Background

Emerging evidence has demonstrated that WISP2/CCN5 is critically involved in tumorigenesis. However, the function of WISP2/CCN5 in breast cancer carcinogenesis is largely unclear.

Methods

we aim to explore the effects and potential mechanisms of WISP2/CCN5 on proliferation of breast cancer cells and carcinogenesis of breast cancer xenograft. Lentivirus vector with WISP2/CCN5shRNA was transfected into MCF-7, and breast cancer cells and xenograft were conducted. Effect of WISP2/CCN5 on growth and carcinogenesis of breast cancer cells and xenografts was evaluated by MTT assay and tumor volume. The relationship between WISP2/CCN5, Skp2 and p27Kip1 was detected in vitro and in vivo by RT-PCR at mRNA level and Western blotting at protein level.

Results

The result of MTT assay indicated that MCF-7 cell growth viability in WISP2/CCN5 gene knockdown group was significantly higher than negative vector group(P<0.05) or control group (P<0.05). It suggested that knockdown ofWISP2/CCN5gene by shRNA lentivirus plasmid promoted proliferation of MCF-7 cells. The growth curves of breast cancer xenograft showed that xenografts in WISP2/CCN5 knockdown group grew more quickly than negative vector group(P< 0.05) or control group (P< 0.05). Subsequently, the results of RT-PCR and Western blotting revealed thatWISP2/CCN5gene knockdown led to increased Skp2 and decreased p27Kip1 at mRNA and protein levels. WISP2/CCN5 exerts its inhibition on proliferation of MCF-7 cell line and suppressive functions on growth of breast carcinoma via regulation of Skp2 and p27Kip1at mRNA and protein levels. However,WISP2/CCN5gene knockdown resulted in loss of inhibition effect on MCF-7 and breast cancer.

Conclusions

Our findings suggest that WISP2/CCN5 could be a useful therapeutic strategy for the treatment of breast cancer through targeting Skp2 and p27Kip1.
The histone variant macroH2A1.1 regulates RNA Polymerase II paused genes within defined chromatin interaction landscapes
Authors: Recoules Ludmila , Heurteau Alexandre , Raynal Flavien , Karasu Nezih , Moutahir Fatima , Bejjani Fabienne , Jariel-Encontre Isabelle , Cuvier Olivier , Sexton Thomas , Lavigne Anne-Claire , Bystricky Kerstin
Published: January 2020

The histone variant macroH2A1.1 (mH2A1.1) plays a role in cancer development and metastasis-related processes. To determine the underlying molecular mechanisms, we mapped genome-wide localization of endogenous mH2A1.1 in the human breast cancer cell MDA-MB 231. We demonstrate that mH2A1.1 specifically binds to active promoters and enhancers in addition to facultative heterochromatin. Selective knock-down of mH2A1.1 deregulates expression of hundreds of highly active genes. Depending on the chromatin landscape, mH2A1.1 acts through two distinct molecular mechanisms. The first is to limit excessive transcription in a predefined environment and relies on domain recruitment of mH2A1.1 at the promoter and gene body. The second mechanism is specific to RNA Pol II (Pol II) paused genes. It requires recruitment of mH2A1.1 restricted to the TSS of these genes. Moreover, we show that these processes occur in a predefined local 3D genome organization and are largely independent of enhancer-promoter looping. Among the genes activated by mH2A1.1, genes regulating mammary tumor cell migration are mostly dependent on Pol II release for their expression level, unlike other categories of mH2A1.1-regulated genes. We thus identified an intriguing new mode of transcriptional regulation by mH2A1.1 and propose that mH2A1.1 serves as a transcriptional modulator with a potential role in assisting the conversion of promoter-locked RNA polymerase II into a productive and elongated Pol II.
Seasonal and social factors associated with spacing in a wild territorial electric fish
Authors: Zubizarreta Lucía , Quintana Laura , Hernández Daniel , de Mello Franco Teixeira , Meerhoff Mariana , Honji Renato Massaaki , Moreira Renata Guimarães , Silva Ana C.
Published: January 2020

The expression of territorial behavior in wild species is especially suited to explore how animals integrate individual traits with dynamic environmental and social contexts. In this study, we focused on the seasonal variation of the determinants of territory size in the weakly electric fishGymnotus omarorum. This species is a seasonal breeder that displays year-long territorial aggression, in which female and male dyads exhibit indistinguishable non-breeding territorial agonistic behavior and the only significant predictor of contest outcome is body size. We carried out field surveys across seasons that included the identification of individual location, measurements of water physico-chemical variables, characterization of individual morphometric and physiological traits, and their correlation to spatial distribution. AlthoughGymnotus omarorumtolerates a wide range of dissolved oxygen concentration, territory size correlated with dissolved oxygen in both seasons. In the non-breeding season, we show that territory size is sexually monomorphic and explained only by body size. In the breeding season, while body size no longer correlated with territory size, evidence of sexual differences in territory size determinants emerged. First, the overall spatial arrangement adopted a sexual bias. Second, territory size depended on gonadal hormones in both sexes, which was expected for males, but not previously reported in females. Third, females’ territory size correlated with gonadal size and females showed relatively larger territories than males, probably to meet sexually dimorphic energetic requirements. This study provides evidence of seasonal changes in factors correlated with territory size and contributes to the understanding of the mechanisms underlying behavioral plasticity.
Telomere damage induces internal loops that generate telomeric circles
Authors: Mazzucco Giulia , Huda Armela , Galli Martina , Piccini Daniele , Giannattasio Michele , Pessina Fabio , Doksani Ylli
Published: January 2020

Extrachromosomal telomeric circles are commonly invoked as important players in telomere maintenance, but their origin has remained elusive. Using electron microscopy analysis on purified telomeres we show that, apart from known structures, telomeric repeats accumulate internal loops (i-loops), that occur in proximity of nicks and single-stranded DNA gaps. I-loops are induced by single-stranded damage at normal telomeres and represent the majority of telomeric structures detected in ALT (Alternative Lengthening of Telomeres) tumor cells. Our data indicate that i-loops form as a consequence of the exposure of single-stranded DNA at telomeric repeats. Finally, we show that these damage-induced i-loops can be excised to generate extrachromosomal telomeric circles resulting in loss of telomeric repeats. Our results identify damage-induced i-loops as a new intermediate in telomere metabolism and reveal a simple mechanism that links telomere damage with the accumulation of extrachromosomal telomeric circles and telomere erosion.
Sapling: Accelerating Suffix Array Queries with Learned Data Models
Authors: Kirsche Melanie , Das Arun , Schatz Michael C.
Published: January 2020

Motivation

As genomic data becomes more abundant, efficient algorithms and data structures for sequence alignment become increasingly important. The suffix array is a widely used data structure to accelerate alignment, but the binary search algorithm used to query it requires widespread memory accesses, causing a large number of cache misses on large datasets.

Results

Here we present Sapling, an algorithm for sequence alignment which uses a learned data model to augment the suffix array and enable faster queries. We investigate different types of data models, providing an analysis of different neural network models as well as providing an open-source aligner with a compact, practical piecewise linear model. We show that Sapling outperforms both an optimized binary search approach and multiple existing read aligners on a wide collection of genomes, including human, bacteria, and plants, speeding up the algorithm by more than a factor of two while adding less than 1% to the suffix array’s memory footprint.

Availability and implementation

The source code and tutorial are available open-source athttps://github.com/mkirsche/sapling.

Supplementary Information

Supplementary notes and figures are available online.
Li-ion half-cells studied operando during cycling by small-angle neutron scattering
Authors: Hattendorff Johannes , Seidlmayer Stefan , Gasteiger Hubert A. , Gilles Ralph
Published: January 2020

Small-angle neutron scattering (SANS) was recently applied to the in situ and operando study of the charge/discharge process in Li-ion battery full-cells based on a pouch cell design. Here, this work is continued in a half-cell with a graphite electrode cycled versus a metallic lithium counter electrode, in a study conducted on the SANS-1 instrument of the neutron source FRM II at the Heinz Maier-Leibnitz Zentrum in Garching, Germany. It is confirmed that the SANS integrated intensity signal varies as a function of graphite lithiation, and this variation can be explained by changes in the squared difference in scattering length density between graphite and the electrolyte. The scattering contrast change upon graphite lithiation/delithiation calculated from a multi-phase neutron scattering model is in good agreement with the experimentally measured values. Due to the finite coherence length, the observed SANS contrast, which mostly stems from scattering between the (lithiated) graphite and the electrolyte phase, contains local information on the mesoscopic scale, which allows the development of lithiated phases in the graphite to be followed. The shape of the SANS signal curve can be explained by a core–shell model with step-wise (de)lithiation from the surface. Here, for the first time, X-ray diffraction, SANS and theory are combined to give a full picture of graphite lithiation in a half-cell. The goal of this contribution is to confirm the correlation between the integrated SANS data obtained during operando measurements of an Li-ion half-cell and the electrochemical processes of lithiation/delithiation in micro-scaled graphite particles. For a deeper understanding of this correlation, modelling and experimental data for SANS and results from X-ray diffraction were taken into account.
Quantifying nanoparticles in clays and soils with a small-angle X-ray scattering method
Authors: Tsukimura Katsuhiro , Suzuki Masaya
Published: January 2020

Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3–10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and α-aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.
Bragg-edge attenuation spectra at voxel level from 4D wavelength-resolved neutron tomography
Authors: Carminati Chiara , Strobl Markus , Minniti Triestino , Boillat Pierre , Hovind Jan , Morgano Manuel , Holm Rod Thomas , Polatidis Efthymios , Valsecchi Jacopo , Mannes David , Kockelmann Winfried , Kaestner Anders
Published: January 2020

4D wavelength-resolved neutron tomography of a reference sample made of several polycrystalline materials, namely nickel, iron, titanium, lead, copper and aluminium, is presented. Data were acquired using the time-of-flight transmission imaging method at the IMAT beamline at the ISIS pulsed neutron source. Wavelength-dispersive tomography reconstruction was computed using filtered back projection, allowing wavelength-resolved total-cross-section retrieval for each voxel in the reconstructed volume of the sample. The need for background correction to enable quantitative results and analysis is discussed, and the achieved 3D spatial resolution with respect to the obtained Bragg-edge pattern quality is investigated.
Effect of relative humidity on corrosion of Q235 carbon steel under thin electrolyte layer in simulated marine atmosphere
Authors: Song Qingqing , Wang Xudong , Pan Boyang , Wan Lei
Published: January 2020

Purpose

The purpose of this paper is to obtain the environmental factor, which has the greatest effect on the corrosion rate of Q235 carbon steel under thin electrolyte layer, and to analyze the effect of this factor on the corrosion morphology, corrosion products and polarization process of Q235 carbon steel.

Design/methodology/approach

An electrochemical device, which can be used under thin electrolyte layer is designed to measure the corrosion current in different environments. Response surface methodology (RSM) is introduced to analyze the effect of environmental factors on corrosion rate. Scanning electron microscope (SEM) and X-ray diffraction (XRD) technique are used to analyze the results. The Tafel slopes of anode and cathode in different humidity and solution are calculated by least square method.

Findings

The three environmental factors are ranked according to importance, namely, humidity, temperature and chloride ion deposition rate. In a high humidity environment, the relative content ofα-FeOOH in the corrosion product is high and the relative content ofβ-FeOOH is low. The higher the humidity, the lower the degree of anodic blockage, whereas the degree of cathodic blockage is independent of humidity. The above experiments confirm the effectiveness and efficiency of the device, indicating it can be used for the screening of corrosive environmental factors.

Originality/value

In this paper, an electrochemical device under thin film is designed, which can simulate atmospheric corrosion well. Subsequent SEM and XRD confirmed the reliability of the data measured by this device. The introduction of a scientific RSM can overcome the limitations of orthogonal experiments and more specifically and intuitively analyze the effects of environmental factors on corrosion rates.
Corporate foresight for strategic innovation management: the case of a Russian service company
Authors: Calof Jonathan , Meissner Dirk , Vishnevskiy Konstantin
Published: January 2020

Purpose

This paper aims to provide a detailed case study of a corporate foresight for innovation (CFI) project done by the Higher School of Economics’ (HSE) (Moscow, Russia) corporate foresight (CF) unit for a large state-owned Russian service company. It demonstrates how CFI methods lead to recommendations and how these recommendations result in decisions.

Design/methodology/approach

Drawing from being part of the project team, review of the project documents and interviews, the case describes a multi-phased CFI project which incorporated several CF methods. Techniques used for the project itself included grand challenges and trend analysis, analysis of best practices through use of benchmarking and horizon scanning, interviews, expert panels, wild card and weak signals analysis, cross impact analysis, SWOT and backcasting. The project used a broad-base of secondary information, expert panels consisting of company experts and HSE CF team personnel, interviews with senior management and an extensive literature review using HSE’s propriety iFORA system.

Findings

In all 17 CFI recommendation and over 100 implementation recommendations were made; 94 per cent of the CFI recommendations were accepted with most implemented at the time this case was written. The case also identifies five enabling factors that collectively both helped the CFI project and led to a high rate of recommendation acceptance and one factor that hindered CFI project success.

Practical implications

The case study provides detailed information and insight that can help others in conducting CF for innovation projects and establishes a link between CF methods and innovation-based recommendations and subsequent decisions.

Originality/value

In-depth case studies that show academe and practitioners how CFI leads to recommendations and is linked to subsequent decisions have been identified as a gap in the literature. This paper therefore seeks to address this need by presenting a detailed CF case for a corporate innovation project.
Choice of the regularization parameter for the Cauchy problem for the Laplace equation
Authors: Joachimiak Magda
Published: January 2020

Purpose

In this paper, the Cauchy-type problem for the Laplace equation was solved in the rectangular domain with the use of the Chebyshev polynomials. The purpose of this paper is to present an optimal choice of the regularization parameter for the inverse problem, which allows determining the stable distribution of temperature on one of the boundaries of the rectangle domain with the required accuracy.

Design/methodology/approach

The Cauchy-type problem is ill-posed numerically, therefore, it has been regularized with the use of the modified Tikhonov and Tikhonov–Philips regularization. The influence of the regularization parameter choice on the solution was investigated. To choose the regularization parameter, the Morozov principle, the minimum of energy integral criterion and the L-curve method were applied.

Findings

Numerical examples for the function with singularities outside the domain were solved in this paper. The values of results change significantly within the calculation domain. Next, results of the sought temperature distributions, obtained with the use of different methods of choosing the regularization parameter, were compared. Methods of choosing the regularization parameter were evaluated by the normNmax.

Practical implications

Calculation model described in this paper can be applied to determine temperature distribution on the boundary of the heated wall of, for instance, a boiler or a body of the turbine, that is, everywhere the temperature measurement is impossible to be performed on a part of the boundary.

Originality/value

The paper presents a new method for solving the inverse Cauchy problem with the use of the Chebyshev polynomials. The choice of the regularization parameter was analyzed to obtain a solution with the lowest possible sensitivity to input data disturbances.
Appraising conjugate heat transfer, heatlines visualization and entropy generation of Ag-MgO/H2O hybrid nanofluid in a partitioned medium
Authors: Ferhi Mokhtar , Djebali Ridha
Published: January 2020

Purpose

This paper aims to perform the lattice Boltzmann simulation of conjugate natural convection heat transfer, heat flow visualization via heatlines approach and entropy generation in a partitioned medium filled with Ag-MgO (15-85%)/water.

Design/methodology/approach

The lattice Boltzmann method (LBM) is used to predict the dynamic and thermal behaviors. Experimental correlations for dynamic viscosity and thermal conductivity versus solid volume fraction are used. The study is conducted for the ranges of Rayleigh number 103 ≤ Ra ≤ 106, the partitioner thickness 0.01 ≤ δ ≤ 0.9, its position 0.15 ≤ Xs ≤ 0.85 and the hybrid nano-suspensions volume fraction 0% ≤ ϕ ≤ 2%.

Findings

The effects of varying of controlling parameters on the convective flow patterns, temperature contours, heat transfers, the heatlines and the entropy generation are presented. It has been found that the maximum rate of heat transfer enhancement occurs for low Ra numbers (103) and is close to 13.52%. The solid thickness d and its horizontal position Xs have a substantial influence on the heat transfer rate, flow structure, heatline, total entropy generation and Bejan number. Besides, the maximum heat transfer is detected for high Ra and δ ≈ 1 and the percentage of augmentation is equal to 65.55% for ϕ = 2%. According to the horizontal position, the heat transfer remains invariant for Ra = 103 and takes a maximum value near the active walls for Ra ≥ 104. The total entropy generation increases with Ra and decreases with ϕ for Ra = 106. The increase of ϕ from 0 to 2% leads to a reduction in close to 40.76%. For this value of Ra, the entropy is the maximum for δ = 0.4 and Xs = 0.35 and Xs = 0.65%. Moreover, as the Ra increases the Bejan number undergoes a decrease. The Bejan number is the maximum for Ra = 103 independently to δ and Xs. The superior thermal performance manifests at low Ra and high value of δ independently to the positions of the conducting body.

Originality/value

The originality of this paper is to analyze the hybrid nano-additive effects on the two-dimensional conjugate natural convection in a partitioned medium using the LBM. The experimental correlations used for the effective thermal conductivity and dynamic viscosity give credibility to our study. Different approaches such as heatlines and entropy generation are used.
Analysis of factors influencing AM application in food sector using ISM
Authors: Palaniappan Arun , Vinodh S. , Ranganathan Rajesh
Published: January 2020

Purpose

The purpose of this paper is to report the analysis of factors influencing additive manufacturing (AM) application in the food domain.

Design/methodology/approach

Based on literature review, 16 factors are being considered in the study. Interpretive structural modelling is used as a modelling approach. The derived structural model indicates the dominant factors. Matriced’ impacts croises-multipication applique and classment (cross-impact matrix multiplication applied to classification) (MICMAC) analysis is being done to group the factors.

Findings

Based on the study, it has been found that raw material usage, the shelf life of food, demand for the food and accuracy are dominant factors. MICMAC analysis indicated that number of driving, dependent and linkage factors are 6, 4 and 4, respectively.

Research limitations/implications

In the present study, 16 factors are being considered. In future, additional factors could be considered to deal with advancements in the food domain.

Practical implications

The study has been executed in discussion with practitioners in AM, and hence derived inferences have practical validity. Food making has become more agile with 3D printer and has become sensitive to customer demand.

Social implications

Social implications are primarily highlighted by the aspect of controlling the exact amount of nutrients corresponding to the application of food. In certain commercial applications, people can customize their shape and ingredients to be injected into the food.

Originality/value

The development of a model for the analysis of factors influencing AM in the food domain is the original contribution of the authors.
Multigenerational exposure to elevated temperatures leads to a reduction in standard metabolic rate in the wild
Authors: Pilakouta Natalie , Killen Shaun S. , Kristjánsson Bjarni K. , Skúlason Skúli , Lindström Jan , Metcalfe Neil B. , Parsons Kevin J.
Published: January 2020

In light of global climate change, there is a pressing need to understand and predict the capacity of populations to respond to rising temperatures. Metabolic rate is a key trait that is likely to influence the ability to cope with climate change. Yet, empirical and theoretical work on metabolic rate responses to temperature changes has so far produced mixed results and conflicting predictions.

Our study addresses this issue using a novel approach of comparing fish populations in geothermally warmed lakes and adjacent ambient‐temperature lakes in Iceland. This unique ‘natural experiment’ provides repeated and independent examples of populations experiencing contrasting thermal environments for many generations over a small geographic scale, thereby avoiding the confounding factors associated with latitudinal or elevational comparisons. Using Icelandic sticklebacks from three warm and three cold habitats, we measured individual metabolic rates across a range of acclimation temperatures to obtain reaction norms for each population.

We found a general pattern for a lower standard metabolic rate (SMR) in sticklebacks from warm habitats when measured at a common temperature, as predicted by Krogh's rule. Metabolic rate differences between warm‐ and cold‐habitat sticklebacks were more pronounced at more extreme acclimation temperatures, suggesting the release of cryptic genetic variation upon exposure to novel conditions, which can reveal hidden evolutionary potential. We also found a stronger divergence in metabolic rate between thermal habitats in allopatry than sympatry, indicating that gene flow may constrain physiological adaptation when dispersal between warm and cold habitats is possible.

In sum, our study suggests that fish may diverge toward a lower SMR in a warming world, but this might depend on connectivity and gene flow between different thermal habitats.

A free Plain Language Summary can be found within the Supporting Information of this article.
Consumption of red maple in anticipation of beech mast‐seeding drives reproduction in eastern chipmunks
Authors: Tissier Mathilde L. , Réale Denis , Garant Dany , Bergeron Patrick
Published: January 2020

Understanding the determinants of reproduction is a central question in evolutionary ecology. In pulsed‐resource environments, the reproduction and population dynamics of seed consumers are driven by pulsed production of seeds by trees or mast‐seeding. In Southern Québec, eastern chipmunks Tamias striatus exclusively reproduce during the summer before and the spring after a mast‐seeding event of American beech. They thus seem to anticipate beech mast by reproducing during early summer, so that juveniles can emerge at the time of maximum beechnut abundance during late summer.

However, the cues allowing chipmunks to anticipate beech mast remain unknown, and the existence of the anticipation process itself has been questioned. To tackle those issues, we investigated the links between the nutritional ecology and reproduction of adult chipmunks and compared their spring diet in mast‐ versus post‐mast years.

We monitored female reproductive status (N = 446), analysed cheek pouch contents at capture (n = 3,761 captures) and recorded seed production by deciduous trees on three different sites in Mont‐Sutton from 2006 to 2018.

Results revealed a systematic shift in chipmunk diet towards red maple seeds in springs preceding a beech mast, with red maple seeds composing more than 77% of chipmunk diet. However, red maple consumption was unrelated to red maple production, but was related to beech seed production in the upcoming fall. We also found that red maple consumption best predicted the proportion of females in summer oestrus.

Our results confirm that chipmunks anticipate beech mast‐seeding and highlight a key role of red maple consumption in that anticipation. Results also suggest that red maple seeds may contain nutrients or secondary plant components essential to sustain or trigger the summer reproduction in chipmunks, which allow them to remain synchronized with pulsed productions of both red maple and beech and improve their fitness.
Combining species distribution models and value of information analysis for spatial allocation of conservation resources
Authors: Raymond Calla V. , McCune Jenny L. , Rosner‐Katz Hanna , Chadès Iadine , Schuster Richard , Gilbert Benjamin , Bennett Joseph R.
Published: January 2020

Managers often have incomplete information to make decisions about threatened species management, and lack the time or funding needed to obtain complete information. Value of information (VOI) analysis can assist managers in deciding whether to manage using current information or monitor to reduce uncertainty before managing. However, VOI analysis has not yet been applied to spatial allocation of monitoring resources across a landscape.

Here, we demonstrate how to make the best use of data from species distribution models (SDMs) and VOI analysis to assess the value of land protection decisions for single and multiple‐species objectives across a heterogeneous landscape. Our method determines the situations where one should monitor before protecting the land, and those where one should act based on current incomplete information. Further, we prioritize land planning units based on cost‐effectiveness (expected number of occurrences protected per dollar spent) and identify properties to target for monitoring or immediate conservation.

In a single species case study, we found that the optimal decision was to act based on current information when the prior probability of detecting an occurrence in a survey was low. When probability of detection was high, it was most effective to monitor the majority of units. In a multi‐species case study, monitoring was only optimal in 50% of cases, due to high inferred probability of at least one occurrence of a threatened species in many units. When compared to a simulation where units were monitored by default, using VOI to determine which units were monitored or prioritized for immediate conservation led to an increase in the expected number of occurrences protected.

Synthesis and applications. Using a combination of species distribution models and value of information analysis can assist managers in efficiently distributing limited resources for protected area allocation. Our results suggest that if managers can use value of information to monitor more efficiently, it can lead to protecting a greater number of threatened species occurrences.
A newly recorded Rickettsia of the Torix group is a recent intruder and an endosymbiont in the whitefly Bemisia tabaci
Authors: Wang Hua‐Ling , Lei Teng , Wang Xiao‐Wei , Maruthi M. N. , Zhu Dan‐Tong , Cameron Stephen L. , Rao Qiong , Shan Hong‐Wei , Colvin John , Liu Yin‐Quan , Liu Shu‐Sheng
Published: January 2020

The bacterium Rickettsia is found widely in phytophagous insects and often exerts profound effects on the phenotype and fitness of its hosts. Here, we decrypt a new, independent, phylogenetically ancient Torix Rickettsia endosymbiont found constantly in a laboratory line of an economically important insect Asia II 7, a putative species of the Bemisia tabaci whitefly complex (Hemiptera: Aleyrodidae), and occasionally in field whitefly populations. This new Rickettsia distributes throughout the body of its whitefly host. Genetically, compared to Rickettsia_bellii_MEAM1 found earlier in whiteflies, the new Rickettsia species has more gene families and pathways, which may be important factors in shaping specific symbiotic relationships. We propose the name ‘Candidatus Rickettsia_Torix_Bemisia_tabaci (RiTBt)’ for this new endosymbiont associated with whiteflies. Comparative genomic analyses indicate that RiTBi may be a relatively recent intruder in whiteflies given its low abundance in the field and relatively larger genome compared to Rickettsia_bellii_MEAM1.
The Base Rate Study: Developing Base Rates for Risk Factors and Indicators for Engagement in Violent Extremism
Authors: Clemmow Caitlin , Schumann Sandy , Salman Nadine L. , Gill Paul
Published: January 2020

Improvements have been made in identifying the prevalence of risk factors/indicators for violent extremism. A consistent problem is the lack of base rates. How to develop base rates is of equal concern. This study has two aims: (i) compare two methods for developing base rates; the Unmatched Count Technique (UCT) and direct questioning, (ii) generate base rates in a general population sample and compare these to a sample of lone‐actor terrorists (n = 125). We surveyed 2108 subjects from the general population. Participants were recruited from an online access panel and randomly assigned to one of three conditions; direct survey, control, or UCT. Survey items were based on a lone‐actor terrorist codebook developed from the wider literature. Direct questioning was more suitable under our study conditions where UCT resulted in deflation effects. Comparing the base rates identified a number of significant differences: (i) lone‐actor terrorists demonstrated propensity indicators related to a cognitive susceptibility, and a crime‐ and/or violence‐supportive morality more often; the general sample demonstrated protective factors more often, (ii) lone‐actor terrorists demonstrated situational indicators related to a crime‐ and/or violence‐supportive morality more often, whereas the general sample experienced situational stressors more often, (iii) lone‐actor terrorists demonstrated indicators related to exposure to extremism more often. Results suggest there are measurable differences in the prevalence of risk factors between lone‐actor terrorists and the general population. However, no single factor “predicts” violent extremism. This bears implications for our understanding of the interrelation of risk and protective factors, and for the risk assessment of violent extremism.