bluuebunny/crossref_metadata_2025 huggingface dataset:
A conserved SUMO-Ubiquitin pathway directed by RNF4/SLX5-SLX8 and PIAS4/SIZ1 drives proteasomal degradation of topoisomerase DNA-protein crosslinks
Authors: Sun Yilun , Jenkins Lisa M. Miller , Su Yijun P. , Nitiss Karin C. , Nitiss John L. , Pommier Yves
Published: July 2019

Topoisomerase cleavage complexes (TOPccs) can be stalled physiologically and by the anticancer drugs camptothecins (TOP1 inhibitors) and etoposide (TOP2 inhibitor), yielding irreversible TOP DNA-protein crosslinks (TOP-DPCs). Here we elucidate how TOP-DPCs are degraded via the SUMO-ubiquitin (Ub) pathway. We show that in human cells, TOP-DPCs are promptly and sequentially conjugated by SUMO-2/3, SUMO-1 and Ub. SUMOylation is catalyzed by the SUMO ligase PIAS4, which forms a complex with both TOP1 and TOP2α and β. RNF4 acts as the SUMO-targeted ubiquitin ligase (STUbL) for both TOP1- and TOP2-DPCs in a SUMO-dependent but replication/transcription-independent manner. This SUMO-Ub pathway is conserved in yeast with Siz1 the ortholog of PIAS4 and Slx5-Slx8 the ortholog of RNF4. Our study reveals a conserved SUMO-dependent ubiquitylation pathway for proteasomal degradation of both TOP1- and TOP2-DPCs and potentially for other DPCs.

Abstract Figure

In Brief

Topoisomerase DNA-protein crosslinks (TOP-DPCs) are the therapeutic mechanism of clinical TOP inhibitors (camptothecin and etoposide). TOP-DPCs induce rapid and sequential conjugation of SUMO-2/3- SUMO-1 and ubiquitin catalyzed by activation of PIAS4 through its DNA-binding SAP domain and RNF4 through its SIM domains. This SUMO-ubiquitin cascade triggers proteasomal degradation of TOP-DPCs.

HIGHLIGHTS

Abortive topoisomerase I (TOP1) and II (TOP2) cleavage complexes resulting in DNA-protein crosslinks (TOP-DPCs) are rapidly and sequentially modified by SUMO-2/3, SUMO-1 and ubiquitin before their proteasomal degradation.

PIAS4 SUMOylates TOP-DPCs via its DNA-binding SAP domain independently of DNA transactions and DNA damage responses.

RNF4 ubiquitylates SUMOylated TOP-DPCs and drives their proteasomal degradation.

TOP-DPC processing by the SUMO-Ub pathways is conserved in yeast and human cells.
SmartGraph: A Network Pharmacology Investigation Platform
Authors: Zahoránszky-Kőhalmi Gergely , Sheils Timothy , Oprea Tudor I.
Published: July 2019

Motivation

Drug discovery investigations need to incorporate network pharmacology concepts while navigating the complex landscape of drug-target and target-target interactions. This task requires solutions that integrate high-quality biomedical data, combined with analytic and predictive workflows as well as efficient visualization. SmartGraph is an innovative platform that utilizes state-of-the-art technologies such as a Neo4j graph-database, Angular web framework, RxJS asynchronous event library and D3 visualization to accomplish these goals.

Results

The SmartGraph framework integrates high quality bioactivity data and biological pathway information resulting in a knowledgebase comprised of 420,526 unique compound-target interactions defined between 271,098 unique compounds and 2,018 targets. SmartGraph then performs bioactivity predictions based on the 63,783 Bemis-Murcko scaffolds extracted from these compounds. Through several use-cases, we illustrate the use of SmartGraph to generate hypotheses for elucidating mechanism-of-action, drug-repurposing and off-target prediction.

Availability

https://smartgraph.ncats.io/
Designed Nanoparticles Elicit Cross-Reactive Antibody Responses To Conserved Influenza Virus Hemagglutinin Stem Epitopes
Authors: McCraw Dustin M. , Myers Mallory L. , Gulati Neetu M. , Gallagher John R. , Kim Alexander J. , Torian Udana , Harris Audray K.
Published: July 2019

Despite the availability of seasonal vaccines and antiviral medications, influenza virus continues to be a major health concern and pandemic threat due to the continually changing antigenic regions of the major surface glycoprotein, hemagglutinin (HA). One emerging strategy for the development of more efficacious seasonal and universal influenza vaccines is structure-guided design of nanoparticles that display conserved regions of HA, such as the stem. Using the H1 HA subtype to establish proof of concept, we found that an alpha-helical fragment (helix-A) from the conserved stem region can be displayed on nanoparticles. The stem region of HA on these nanoparticles is immunogenic and the nanoparticles are biochemically robust in that heat exposure did not destroy the particles and immunogenicity was retained. Furthermore, H1-nanoparticles protected mice from lethal challenge with H1N1 influenza virus. Importantly, antibodies elicited by these nanoparticles demonstrated homosubtypic and heterosubtypic cross-reactivity. The helix-A stem nanoparticle design represents a novel approach to display several hundred copies of non-trimeric conserved HA stem epitopes on vaccine nanoparticles. This design concept provides a new approach to universal influenza vaccine development strategies and opens up opportunities for the development of nanoparticles with broad coverage over many antigenically diverse influenza HA subtypes.

Significance

Influenza virus is a public health issue that affects millions of people globally each year. Commercial influenza vaccines are based on the hemagglutinin (HA) surface glycoprotein, which can change antigenically every year, demanding the manufacture of newly matched vaccines annually. HA stem epitopes have a higher degree of conservation than HA molecules contained in conventional vaccine formulations and we demonstrate that we are able to design nanoparticles that display hundreds of HA stem fragments on nanoparticles. These designed nanoparticles are heat-stable, elicit antibodies to the HA stem, confer protection in mouse challenge models, and show cross-reactivity between HA subtypes. This technology provides promising opportunities to improve seasonal vaccines, develop pandemic preparedness vaccines, and facilitate the development of a universal influenza vaccine.
Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC
Authors: Zhao Binhui , Chaturvedi Pankaj , Zimmerman David L. , Belmont Andrew S.
Published: July 2019

Achieving reproducible, stable, and high-level transgene expression in mammalian cells remains problematic. Previously, we attained copy-number-dependent, chromosome-position-independent expression of reporter minigenes by embedding them within a BAC containing the mouseMsh3-Dhfrlocus (DHFR BAC). Here we extend this “BAC TG-EMBED” approach. First, we report a toolkit of endogenous promoters capable of driving transgene expression over a 0.01-5 fold expression range relative to the CMV promoter, allowing fine-tuning of relative expression levels of multiple reporter genes expressed on a single BAC. Second, we show small variability in both the expression level and long-term expression stability of a reporter gene embedded in BACs containing either transcriptionally active or inactive genomic regions, making choice of BACs more flexible. Third, we describe an intriguing phenomenon in which BAC transgenes are maintained as episomes in a large fraction of stably selected clones. Finally, we demonstrate the utility of BAC TG-EMBED by simultaneously labeling three nuclear compartments in 94% of stable clones using a multi-reporter DHFR BAC, constructed with a combination of synthetic biology and BAC recombineering tools. Our extended BAC TG-EMBED method provides a versatile platform for achieving reproducible, stable simultaneous expression of multiple transgenes maintained either as episomes or stably integrated copies.
Atrial fibrillation associated common risk variants in SYNE2 lead to lower expression of nesprin-2α1 and increased nuclear stiffness
Authors: Liu Nana , Hsu Jeffrey , Mahajan Gautam , Sun Han , Barnard John , Van Wagoner David R. , Kothapalli Chandrasekhar R. , Chung Mina K. , Smith Jonathan D.
Published: July 2019

Rationale

Atrial fibrillation (AF) genome-wide association studies (GWAS) identified significant associations for rs1152591 and linked variants in the SYNE2 gene encoding the nesprin-2 protein that connects the nuclear membrane with the cytoskeleton

Objective

Determine the effects of the AF-associated rs1152591 and rs1152595, two linked intronic single nucleotide polymorphisms (SNPs), on SYNE2 expression and investigate the mechanisms for their association with AF.

Methods and Results

RNA sequencing of human left atrial appendage (LAA) tissues indicated that rs1152591 and rs1152595 were significantly associated with the expressions of SYNE2α1, a short mRNA isoform, without an effect on the expression of the full-length SYNE2 mRNA. SYNE2α1 mRNA uses an alternative transcription start site and encodes an N-terminal deleted 62 kDa nesprin-2α1 isoform, which can act as a dominant-negative on nuclear-cytoskeleton connectivity. Western blot and qPCR assays confirmed that AF risk alleles of both SNPs were associated with lower expression of nesprin-2α1 in human LAA tissues. Reporter gene transfections demonstrated that the risk vs. reference alleles of rs1152591 and rs1152595 had decreased enhancer activity. SYNE2 siRNA knockdown (KD) or nesprin-2α1 overexpression studies in human stem cell-derived induced cardiomyocytes (iCMs) resulted in ~12.5 % increases in the nuclear area compared to controls (p<0.001). Atomic force microscopy demonstrated that SYNE2 KD or nesprin-2α1 overexpression led to 57.5% or 33.2% decreases, respectively, in nuclear stiffness compared to controls (p< 0.0001).

Conclusions

AF-associated SNPs rs1152591 and rs1152595 downregulate the expression of SYNE2α1, increasing nuclear-cytoskeletal connectivity and nuclear stiffness. The resulting increase in mechanical stress may play a role in the development of AF.
α-carboxysome formation is mediated by the multivalent and disordered protein CsoS2
Authors: Oltrogge Luke M. , Chaijarasphong Thawatchai , Chen Allen W. , Bolin Eric R. , Marqusee Susan , Savage David F.
Published: July 2019

Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO2-concentrating mechanism, feeding high concentrations of CO2 to the enzyme Rubisco for fixation. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein-protein interactions which drive the assembly process. Here we show that the N-terminus of CsoS2, an intrinsically disordered protein found in the α-carboxysome, possesses a repeated peptide sequence that binds Rubisco. X-ray structural analysis of the peptide bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.
Selection against archaic hominin genetic variation in regulatory regions
Authors: Telis Natalie , Aguilar Robin , Harris Kelley
Published: July 2019

Traces of archaic hominin DNA persist in the human gene pool, but are systematically depleted around genes and other functionally important genomic regions. This suggests that many Neandertal and Denisovan alleles had harmful effects on hybrid fitness. We hypothesized that if some harmful effects were mediated by gene dysregulation in specific tissues, alleles previously flagged as archaic using a conditional random field (CRF) should be depleted from those tissues’ regulatory enhancers compared to “control” alleles matched for allele frequency and the strength of background selection. By this metric, both Neandertal and Denisovan variation appear depleted from enhancers, particularly enhancers that show pleiotropic activity across tissues. This depletion is driven by young archaic SNPs that the CRF confidently identifies as private to Neandertals or Denisovans; older variants that were likely present in both archaic species are not depleted from enhancers. We found that enhancer pleiotropy is not only a predictor of archaic SNP depletion, but also a predictor of intolerance to new mutations as measured by both phastCons scores and the frequency spectrum of African variation. In other respects, however, the landscape of selection against young archaic alleles appears qualitatively different from the landscape of ordinary purifying selection, suggesting that archaic alleles had a different distribution of fitness effects from ordinary new mutations. Most strikingly, fetal brain and muscle are the tissues most depleted of young archaic variation in their regulatory regions, but only brain enhancers appear commensurately intolerant to new mutations. In contrast, fetal muscle enhancers show no evidence of elevated purifying selection relative to other enhancers. This suggests that epistatic incompatibility between human and archaic alleles is needed to explain the degree of archaic variant depletion from fetal muscle enhancers, perhaps due to divergent selection for higher muscle mass in archaic hominins compared to humans.
Computational modeling of the photon transport, tissue heating, and cytochrome C oxidase absorption during transcranial near-infrared stimulation
Authors: Bhattacharya Mahasweta , Dutta Anirban
Published: July 2019

Transcranial near-infrared stimulation (tNIRS) has been proposed as a tool to modulate cortical excitability. However, the underlying mechanisms are not clear where the heating effects on the brain tissue needs investigation due to increased near-infrared (NIR) absorption by water and fat. Moreover, the risk of localized heating of tissues (including the skin) during optical stimulation of the brain tissue is a concern. The challenge in estimating localized tissue heating is due to the light interaction with the tissues’ constituents, which is dependent on the combination ratio of the scattering and absorption properties of the constituent. Here, apart from tissue heating that can modulate the cortical excitability (“photothermal effects”); the other mechanism reported in the literature is the stimulation of the mitochondria in the cells which are active in the adenosine triphosphate (ATP) synthesis. In the mitochondrial respiratory chain, the complex IV, also named as the cytochrome c oxidase(CCO), is the unit four with three copper atoms. The absorption peaks of CCO are in the visible (420-450nm and 600-700nm) and the near-infrared (760-980nm) spectral region which have been shown to be promising for low level light therapy (LLLT), also known as “photobiomodulation”. While much higher CCO absorption peaks in the visible spectrum can be used for the photobiomodulation of the skin, 810nm has been proposed for the non-invasive brain stimulation (using tNIRS) due to the optical window in the NIR spectral region. In this article, we applied a computational approach to delineate the “photothermal effects” from the “photobiomodulation,” i.e., to estimate the amount of light absorbed individually by each chromophore in the brain tissue (with constant scattering) and the related tissue heating. Photon migration simulations were performed for motor cortex tNIRS based on a prior work that used a 500mW cm−2light source placed on the scalp. We simulated photon migration at 630nm and 700nm (red spectral region) and 810nm (near-infrared spectral region). We found a temperature increase in the scalp below 0.25 ° C and a minimal temperature increase in the gray matter less than 0.04 ° C at 810nm. Similar heating was found for 630nm and 700nm used for LLLT, so photothermal effects are postulated to be unlikely in the brain tissue.
Developing a primary Paralichthys olivaceus gill epithelial cells as an in vitro model for propagation of VHSV show a corresponding increase in cell viability with increase in protein concentration in growth media
Authors: Han Sori , Hong Jimin , Seo Jong-pyo , Munang’andu Hetron Mweemba , Yeo In-kyu , Kim Sung-hyun
Published: July 2019

Background

Viral Hemorrhagic Septicemia Virus (VHSV) is a rhabdovirus that causes high mortalities linked to high economic losses in aquaculture. It has been grouped in four genotypes of which some do not easily propagate on continuous cell lines. As an alternative, the objectives of this study was to develop a primary gill epithelial cell (GEC) model from olive flounder (Paralichthys olivaceus) as an in vitro model for the propagation of VHSV.

Results

Our findings show that the primary GECs developed herein are highly permissive to replication of the JF-09 genotype IVa strain leading to high cytopathic effect observed within 96 hours post virus inoculation. Our findings also show that the viability GECs produced herein corresponded with increase in the concentration fetal bovine serum in growth medium. We envision that GECs produced herein will heighten our understanding of immune mechanisms associated with virus entry on gill mucosal surfaces in flounder.
Identifying the essential genes ofMycobacterium aviumsubsp.hominissuiswith Tn-Seq using a rank-based filter procedure
Authors: Matern William M. , Jenquin Robert L. , Bader Joel S. , Karakousis Petros C.
Published: July 2019

Mycobacterium avium(Mav) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying structural lung disease. Generally, Mav infection is treated with 2-3 antimicrobial drugs for at least 12 months. Identification of genes essential for Mav growth may yield novel strategies for improving curative therapy. We have generated saturating genome-wide transposon mutant pools in a commonly used laboratory strain ofMycobacterium aviumsubsp.hominissuis(MAC109) and developed a computational technique for classifying annotated genomic features as essential (ES), growth defect (GD), growth advantage (GA), or no-effect (NE) based on thein vitroeffect of disruption by transposon. We identified 270 features as ES with 230 of these overlapping with ES features inMycobacterium tuberculosis. These results may be useful for identifying drug targets or for informing studies requiring genetic manipulation ofMycobacterium avium, which should seek to avoid disrupting ES features to ensure bacterial viability.

Importance

Mycobacterium avium subsp. hominissuisis an emerging cause of morbidity in vulnerable populations in many countries. It is known to be particularly difficult to treat, often requiring years of antibiotic therapy. In this study we report the genes ofMycobacterium aviumsubsp.hominissuisthat are required for the organism to growin vitro. Our findings may help guide future research into identifying new drugs to improve the treatment of this serious infection.
kCSD-python, reliable current source density estimation with quality control
Authors: Chintaluri Chaitanya , Bejtka Marta , Średniawa Władysław , Czerwiński Michał , Dzik Jakub M. , Jędrzejewska-Szmek Joanna , Wójcik Daniel K.
Published: July 2019

Interpretation of the extracellular recordings can be difficult due to the long range of electric field but can be facilitated by estimating the density of current sources (CSD). Here we introducekCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method, and introduce several new techniques to facilitate CSD analysis of experimental data and interpretation of the results. We investigate the limitations imposed by noise and assumptions in the method itself.kCSD-pythonallows CSD estimation for arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter notebook tutorial to facilitate uptake by the community.
Metabolic stress is a primary pathogenic event in transgenic Caenorhabditis elegans expressing pan-neuronal human amyloid beta
Authors: Teo Emelyne , Ravi Sudharshan , Barardo Diogo , Kim Hyung-Seok , Fong Sheng , Cazenave-Gassiot Amaury , Tan Tsze Yin , Ching Jianhong , Kovalik Jean-Paul , Wenk Markus R , Gunawan Rudiyanto , Moore Philip K , Halliwell Barry , Tolwinski Nicholas , Gruber Jan
Published: July 2019

Alzheimer’s disease (AD) is the most common neurodegenerative disease affecting the elderly worldwide. Mitochondrial dysfunction has been proposed as a key event in the etiology of AD. We have previously modeled amyloid-beta (Aβ)-induced mitochondrial dysfunction in a transgenic Caenorhabditis elegans strain by expressing human Aβ peptide specifically in neurons (GRU102). Here, we focus on a deeper analysis of these metabolic changes associated with Aβ-induced mitochondrial dysfunction. Integrating metabolomics, transcriptomics, biochemical studies and computational modeling, we identify alterations in Tricarboxylic Acid (TCA) cycle metabolism following even low-level Aβ expression. In particular, GRU102 show reduced activity of a rate-limiting TCA cycle enzyme, alpha-ketoglutarate dehydrogenase. These defects are associated with elevation of protein carbonyl content specifically in mitochondria. Importantly, metabolic failure occurs before any significant increase in global protein aggregate is detectable. Treatment with an antidiabetes drug, Metformin, reverses Aβ-induced metabolic defects, reduces protein aggregation and normalizes the lifespan of GRU102. Our results point to metabolic dysfunction as an early and causative event in AD pathology and a promising target for intervention.
How Sampling-Based Overdispersion Undermines India’s Tiger Monitoring Orthodoxy
Authors: Gopalaswamy Arjun M. , Karanth K. Ullas , Delampady Mohan , Stenseth Nils Chr.
Published: July 2019

Conservation agencies entrusted with recovery of iconic mammals may exaggerate population trends without adequate scientific evidence. Recently, such populations were termed as ‘political populations’ in the conservation literature. We surmise that political populations emerge when agencies are pressured to report abundances at large spatial scales for species that are difficult to survey. Indian tiger conservation agencies use an experimental approach called double-sampling using index-calibration models. A recent, mathematical, study demonstrated the unreliability of this approach in the context of India’s tigers. Yet, this approach continues to be applied and even promoted by global tiger conservation agencies in other tiger range countries. In this article, we aim to: (1) discuss the ecological oddities emerging from results of India’s national tiger surveys, (2) demystify the mathematics underlying the problems of this survey methodology and (3) confront these findings with results from India’s recent national tiger survey of 2014. Our analyses show that the predictions of tiger abundance using sign-based indices reported in the 2014 survey in fact vary greatly and can be severely misleading and confirming the presence of high sampling-based overdispersion and parameter covariance. We call for species conservation initiatives to implement monitoring methods that are designed to clearly answer, a priori, scientific or management objectives instead of potentially implementing them as reactions to extraneous, social or fund raising pressures.
Neural ensemble activity depends on stimulus type in mouse primary visual cortex
Authors: Tolkiehn Marie , Schultz Simon R.
Published: July 2019

Early cortical processing of visual information has long been investigated by describing the response properties such as receptive fields or orientation selectivity of individual neurons to moving gratings. However, thanks to recent technological advances, it has been become easier to record from larger neuronal populations which allow us to analyse the population responses to probe visual information processing at the population level. In the end, it is unlikely that sensory processing is a single-neuron effort but that of an entire population. Here we show how different stimulus types evoke distinct binary activity patterns (words) of simultaneous events on different sites in the anaesthetised mouse. Spontaneous activity and natural scenes indicated lower word distribution divergences than each to drifting gratings. Accounting for firing rate differences, spontaneous activity was linked to more unique patterns than stimulus-driven responses. Multidimensional scaling conveyed that pattern probability distributions clustered for spatial frequencies but not for directions. Further, drifting gratings modulated the Shannon entropy estimated on spatial patterns in a similar fashion as classical directional and spatial frequency tuning functions of neurons. This was supported by a distinct sublinear relationship between Shannon entropy and mean population firing rate.
Nutritive diet becomes unhealthy if taken in a wrong ratio: Scientific validation of Ayurvedic concept of “incompatible diet” (Virrudh Aahar)
Authors: Aditi Prerana , Srivastva Shivani , pandey Harsh , Tripathi Y.B.
Published: July 2019

Honey and ghee is an important constituent of our diet. Honey contain about 200 components in its which play an important role as antioxidative, anti-inflammatory, antimicrobial, wound healing and sunburn, etc. Ghee has also many essential constituents such as phospholipids, PUFA, fat- soluble vitamins, etc. It is mention in Charak Samhita that equal ratio of honey and ghee when taken in food become toxic to health. This study was designed to explore the mechanism of toxicity through the biochemical and histological parameter. For this study, 24 Charles foster rats were taken and divided into four groups (n=6) normal, honey, ghee, and honey+ghee (1:1). After 60 days rats were sacrificed. Weight loss, Hair loss and red patches on ear were found on honey+ghee fed rats. LFT, amadori test, AGE, UV, glucose, DPP-4 and LPO were found significantly increased in honey+ghee group. SOD, Catalase, GSH, ABTS+, GLP-1, GIP-1, ACB and HB were found significantly decreased in honey+ghee group. No changes were found in RFT. H&E show normal morphology in kidney, intestine, and pancreas but mild inflammation was found in liver tissue. We conclude that the equal mixture of honey and ghee shows toxic effect. Increased formation of hydroxymethyl furfural, amadori product, DPP-4 activity and low incretins (GLP-1, GIP-1) activity resulting high postprandial hyperglycemic response are collectively responsible for oxidative stress-mediated toxicity of the mixture of honey and ghee in equal ratio.
Crystal structure of a low-spin poly[di-μ3-cyanido-di-μ2-cyanido-bis(μ2-2-ethylpyrazine)dicopper(I)iron(II)]
Authors: Partsevska Sofiia V. , Naumova Dina D. , Matushko Igor P. , Kucheriv Olesia I. , Gural'skiy Il'ya A.
Published: July 2019

In the title metal–organic framework, [Fe(C6H8N2)2{Cu(CN)2}2]
n
, the low-spin FeII ion lies at an inversion centre and displays an elongated octahedral [FeN6] coordination environment. The axial positions are occupied by two symmetry-related bridging 2-ethylpyrazine ligands, while the equatorial positions are occupied by four N atoms of two pairs of symmetry-related cyanide groups. The CuI centre is coordinated by three cyanide carbon atoms and one N atom of a bridging 2-ethylpyrazine molecule, which form a tetrahedral coordination environment. Two neighbouring Cu atoms have a short Cu...Cu contact [2.4662 (7) Å] and their coordination tetrahedra are connected through a common edge between two C atoms of cyanide groups. Each Cu2(CN)2 unit, formed by two neighbouring Cu atoms bridged by two carbons from a pair of μ-CN groups, is connected to six FeII centres via two bridging 2-ethylpyrazine molecules and four cyanide groups, resulting in the formation of a polymeric three-dimensional metal–organic coordination framework.
Crystal structures of an imidazo[1,5-a]pyridinium-based ligand and its (C13H12N3)2[CdI4] hybrid salt
Authors: Vassilyeva Olga Yu. , Buvaylo Elena A. , Kokozay Vladimir N. , Skelton Brian W. , Sobolev Alexandre N.
Published: July 2019

The monocation product of the oxidative condensation–cyclization between two molecules of pyridine-2-carbaldehyde and one molecule of CH3NH2·HCl in methanol, 2-methyl-3-(pyridin-2-yl)imidazo[1,5-a]pyridinium, was isolated in the presence of metal ions as bis[2-methyl-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium] tetraiodocadmate, (C13H12N3)2[CdI4], (I), and the mixed chloride/nitrate salt, bis[2-methyl-3-(pyridin-2-yl)imidazo[1,5-a]pyridin-2-ium] 1.5-chloride 0.5-nitrate trihydrate, 2C13H12N3
+·1.5Cl−·0.5NO3
−·3H2O, (II). Hybrid salt (I) crystallizes in the space group P21/n with two [L]2[CdI4] molecules in the asymmetric unit related by pseudosymmetry. In the crystal of (I), layers of organic cations and of tetrahalometallate anions are stacked parallel to the ab plane. Antiparallel L
+ cations disposed in a herring-bone pattern form π-bonded chains through aromatic stacking. In the inorganic layer, adjacent tetrahedral CdI4 units have no connectivity but demonstrate close packing of iodide anions. In the crystal lattice of (II), the cations are arranged in stacks propagating along the a axis; the one-dimensional hydrogen-bonded polymer built of chloride ions and water molecules runs parallel to a column of stacked cations.
catena-Poly[[diaquacadmium(II)]-μ2-3-(4-carboxylatophenyl)propionato]
Authors: Ezenyilimba Frederick C. , Staples Richard J. , LaDuca Robert L.
Published: July 2019

In the title compound, [Cd(C10H8O4)(H2O)2)]
n
, the CdII cation is coordinated in a distorted trigonal–prismatic fashion. 3-(4-Carboxyphenyl)propionate (cpp) ligands connect the CdII cations into zigzag [Cd(cpp)(H2O)2)]
n
coordination polymer chains, which are oriented parallel to [101]. The chains aggregate into supramolecular layers oriented parallel to (10\overline{1}) by means of O—H...O hydrogen bonding between bound water molecules and ligating cpp carboxylate O atoms. The layers stack in an ABAB pattern along [100] via other O—H...O hydrogen-bonding mechanisms also involving the bound water molecules. The crystal studied was an inversion twin.
(2,2-Bipyridine-κ2
N,N′)chlorido[η6-1-methyl-4-(propan-2-yl)benzene]ruthenium(II) tetraphenylborate
Authors: Thapa Rajesh , Kilyanek Stefan M.
Published: July 2019

The title complex, [RuCl(C10H14)(C10H8N2)](C24H20B), has monoclinic (P21) symmetry at 100 K. It was prepared by the reaction of the dichlorido[1-methyl-4-(propan-2-yl)benzene]ruthenium(II) dimer with 2,2′-bipyridine, followed by the addition of ammonium tetraphenylborate. The 1-methyl-4-(propan-2-yl)benzene group, the 2,2′-bipyridine unit and a chloride ion coordinate the ruthenium(II) atom, with the 1-methyl-4-(propan-2-yl)benzene ring and bipyridine moieties trans to each other. In the crystal, the complex cations are linked by C—H...Cl hydrogen bonds, forming chains parallel to [010]. These chains are linked by a number of C—H...π interactions, involving the phenyl rings of the tetraphenylborate anion and a pyridine ring of the bpy ligand, resulting in the formation of layers parallel to (10\overline{1}).
(1Z,2Z)-1,2-Bis{2-[3,5-bis(trifluoromethyl)phenyl]hydrazinylidene}-1,2-bis(4-methoxyphenyl)ethane including an unknown solvate
Authors: Akkurt Mehmet , Shikhaliyev Namiq Q. , Askerova Ulviyya F. , Mukhtarova Sevinc H. , Mammadova Gunay Z. , Toze Flavien A. A.
Published: July 2019

The complete molecule of the title compound, C32H22F12N4O2, is generated by a crystallographic twofold axis aligned parallel to [010]. The F atoms of one of the CF3 groups are disordered over three orientations in a 0.6: 0.2: 0.2 ratio. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming zigzag chains propagating along the a-axis direction. In addition, weak C—H...O and C—H...F bonds are observed. The contribution of the disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18] of PLATON. The solvent contribution is not included in the reported molecular weight and density.
6-Nitro-1,10-phenanthrolin-5-amine
Authors: Oosthuizen U. , Schutte-Smith M. , Visser Hendrik G.
Published: July 2019

In the title compound, C12H8N4O2, the dihedral angle between the phenanthroline ring system and the nitro group is 23.75 (14)°. The molecule features intramolecular N—H...O and C—H...O hydrogen bonds. In the crystal, N—H...(N,N), C—H...N and C—H...O hydrogen bonds link the molecules into [100] chains.
Investigation on cohesive zone model of bolted joint for water conveyance tunnel lining
Authors: Li Bingqi , Zhang Zhenyu , Wang Xiaogang , Liu Xiaonan
Published: July 2019

Purpose

The behavior of joints has a significant effect on the stability of water conveyance tunnel. The purpose of this paper is to study the contact and friction at the joint of the tunneling segment lining and establish its contact friction model. At the same time, the stress and deformation characteristics at the joint of the segment under hydrostatic load are analyzed.

Design/methodology/approach

In this study, the contact and friction in a bolted joint are examined using shear testing. The feasibility of the proposed model is verified by a numerical simulation of tests and a theoretical analysis. Accordingly, the effect of joints on the lining is explored under internal hydrostatic loading.

Findings

The results show that the openings of tunnel segments in joints gradually expand from the positions of the inner and outer edges to the location of the bolt. Moreover, the stress concentration zone is formed at the bolt. Under hydraulic loading, the opening displacement at the joint increases as the water pressure increases; nevertheless, it does not exceed engineering requirements. When the water pressure of the tunnel lining joint reaches 0.5 MPa, the opening of the joint slowly increases. When the water pressure exceeds 0.7 MPa, the opening of the joint rapidly and significantly increases.

Originality/value

Contact and friction in a bolted joint were examined using shear testing. A cohesive zone model of bolted joints was proposed based on test results. The influence of joint behavior on the stability of water conveyance tunnel was studied.
Analysis for center deviation of circular target under perspective projection
Authors: Sun Yu
Published: July 2019

Purpose

Accurate feature localization is a fundamental problem in computer vision and visual measurement. In a perspective projection model of the camera, the projected center of a spatial circle and the center of the projection ellipse are not identical. This paper aims to show how to locate the real projection center precisely in the perspective projection of a space circle target.

Design/methodology/approach

By analyzing the center deviation caused by projection transformation, a novel method is presented to precisely locate the real projection center of a space circle using projective geometry. Solution distribution of the center deviation is analyzed, and the quadratic equation for determining the deviation is derived by locating vanishing points. Finally, the actual projected center of the circular target is achieved by solving the deviation quadratic equations.

Findings

The procedures of the author’s method are simple and easy to implement. Experimental data calculated that maximum deviation occurs at approximately between 3π/10 and 2π/5 of the angle between the projection surface and the space target plane. The absolute reduction in error is about 0.03 pixels; hence, it is very significant for a high-accuracy solution of the position of the space circle target by minimizing systematic measurement error of the perspective projection.

Originality/value

The center deviation caused by the space circle projection transformation is analyzed, and the detailed algorithm steps to locate the real projection center precisely are described.
Corporate incubators as knowledge brokers between business units and ventures
Authors: Kötting Michael
Published: July 2019

Purpose

Through digitization and globalization, corporate incubators have gained new relevance as tool to foster innovation within established companies. Although many studies address business incubators in general, the specifics of corporate incubators are often neglected in the literature. The paper aims to discuss this issue.

Design/methodology/approach

The author systematically reviewed academic articles regarding corporate incubation, published in peer-reviewed journals. In the course of a subsequent analysis, open questions for further research were identified and addressed.

Findings

Corporate incubators differ significantly from business incubators. Based on an analysis of 45 academic papers, the main features of corporate incubators have been identified and addressed.

Originality/value

The present work suggests that it is one of the first that systematically analyze the literature on corporate incubation. Based on the literature review, a holistic framework was constructed that highlights the different elements of corporate incubation and also considers the incubator as knowledge broker between business units and ventures.
Relationship between gray directors and executive compensation in Indian firms
Authors: Prasad Krishna , Sankaran K. , Prabhu Nandan
Published: July 2019

Purpose

The purpose of this paper is to examine the empirical relationship between gray directors (non-executive non-independent directors) and executive compensation among companies listed in India’s National Stock Exchange (NSE). The paper also examines the possible interplay of relationships between controlling shareholder duality (controlling shareholder being the CEO), ownership category and executive compensation.

Design/methodology/approach

A sample of 438 firms listed in the NSE of India was studied using data spanning five financial years, 2012–2013 to 2016–2017.

Findings

Empirical evidence suggests that there is a positive association between the proportion of gray directors on the board and executive compensation. The sensitivity of executive compensation to gray directors is found to be higher among family controlled firms. This research has also found that CEOs who belong to controlling shareholder groups received higher pay than professional CEOs. The authors conjecture that these results suggest cronyism and may contribute to lower levels of corporate governance practices in the country.

Research limitations/implications

The hybrid board structure, which India has adopted with the desire to bring the best of Anglo Saxon and Japanese board philosophies, has paradoxically led to self-serving boards. Exploration of alternative thinking to bring about changes in the regulatory framework is, therefore, necessary.

Originality/value

Serious problems are identified with the philosophy behind board composition mandated by Listing Requirements for Indian firms with empirical evidence showing how the existing rules generate cronyism and unfairness to minority shareholders.
Numerical simulation of water/alumina nanofluid mixed convection in square lid-driven cavity
Authors: Toghraie Davood , Shirani Ehsan
Published: July 2019

Purpose

The purpose of this paper is to investigate the mixed convection of a two-phase water–aluminum oxide nanofluid in a cavity under a uniform magnetic field.

Design/methodology/approach

The upper wall of the cavity is cold and the lower wall is warm. The effects of different values of Richardson number, Hartmann number, cavitation length and solid nanoparticles concentration on the flow and temperature field and heat transfer rate were evaluated. In this paper, the heat flux was assumed to be constant of 10 (W/m2) and the Reynolds number was assumed to be constant of 300 and the Hartmann number and the volume fraction of solid nanoparticles varied from 0 to 60 and 0 to 0.06, respectively. The Richardson number was considered to be 0.1, 1 and 5. Aspect ratios were 1, 1.5 and 2.

Findings

Comparison of the results of this paper with the results of the numerical and experimental studies of other researchers showed a good correlation. The results were presented in the form of velocity and temperature profiles, stream and isotherm lines and Nusselt numbers. The results showed that by increasing the Hartmann number, the heat transfer rate decreases. An increase from 0 to 20 in Hartmann number results in a 20 per cent decrease in Nusselt numbers, and by increasing the Hartmann number from 20 to 40, a 16 per cent decrease is observed in Nusselt number. Accordingly, it is inferred that by increasing the Hartmann number, the reduction in the Nusselt number is decreased. As the Richardson number increased, the heat transfer rate and, consequently, the Nusselt number increased. Therefore, an increase in the Richardson number results in an increase of the Nusselt number, that is, an increase in Richardson number from 0.1 to 1 and from 1 to 5 results in 37 and 47 per cent increase in Nusselt number, respectively.

Originality/value

Even though there have been numerous investigations conducted on convection in cavities under various configurations and boundary conditions, relatively few studies are conducted for the case of nanofluid mixed convection in square lid-driven cavity under the effect of magnetic field using two-phase model.
A boundary determination problem in steady-state heat conduction – a solution and sensitivity analysis
Authors: Hożejowski Leszek
Published: July 2019

Purpose

The purpose of this paper is to propose a numerical procedure for discrete identification of the missing part of the domain boundary in a heat conduction problem. A new approach to sensitivity analysis is intended to give a better understanding of the influence of measurement error on boundary reconstruction.

Design/methodology/approach

The solution of Laplace’s equation is obtained using the Trefftz method, and then each of the sought boundary points can be derived numerically from a nonlinear equation. The sensitivity analysis comes down to the analytical evaluation of a sensitivity factor.

Findings

The proposed method very accurately recovers the unknown boundary, including irregular shapes. Even a very large number of the boundary points can be determined without causing computational problems. The sensitivity factor provides quantitative assessment of the relationship between the temperature measurement errors and boundary identification errors. The numerical examples show that some boundary reconstruction problems are error-sensitive by nature but such problems can be recognized with the use of a sensitive factor.

Originality/value

The present approach based on the Trefftz method separates, in terms of computation, specification of the coefficients appearing in the Trefftz method and missing coordinates of the sought boundary points. Due to introducing a sensitivity factor, a more profound sensitivity analysis was successfully conducted.
Heat flow model based on lattice Boltzmann method for modeling of heat transfer during phase transformation
Authors: Łach Łukasz , Svyetlichnyy Dmytro , Straka Robert
Published: July 2019

Purpose

A fundamental principle of materials engineering is that the microstructure of a material controls the properties. The phase transformation is an important phenomenon that determines the final microstructure. Recently, many analytical and numerical methods were used for modeling of phase transformation, but some limitations can be seen in relation to the choice of the shape of growing grains, introduction of varying grain growth rate and modeling of diffusion phenomena. There are also only few comprehensive studies that combine the final microstructure with the actual conditions of its formation. Therefore, the objective of the work is a development of a new hybrid model based on lattice Boltzmann method (LBM) and cellular automata (CA) for modeling of the diffusional phase transformations. The model has a modular structure and simulates three basic phenomena: carbon diffusion, heat flow and phase transformation. The purpose of this study is to develop a model of heat flow with consideration of enthalpy of transformation as one of the most important parts of the proposed new hybrid model. This is one of the stages in the development of the complex model, and the obtained results will be used in a combined solution of heat flow and carbon diffusion during the modeling of diffusion phase transformations.

Design/methodology/approach

Different values of overheating/overcooling affect different values in the enthalpy of transformation and thus the rate of transformation. CA and LBM are used in the hybrid model in part related to heat flow. LBM is used for modeling of heat flow, while CA is used for modeling of the microstructure evolution during the phase transformation.

Findings

The use of LBM and CA in one numerical solution creates completely new possibilities for modeling of phase transformations. CA and LBM in comparison with commonly used approaches significantly simplify interface and interaction between different parts of the model, which operates in a common domain. The CA can be used practically for all possible processes that consist of nucleation and grains growth. The advantages of the LBM method can be well used for the simulation of heat flow during the transformation, which is confirmed by numerical results.

Practical implications

The developed heat flow model will be combined with the carbon diffusion model at the next stage of work, and the new complex hybrid model at the final stage will provide new solutions in numerical simulation of phase transformations and will allow comprehensive modeling of the diffusional phase transformations in many processes. Heating, annealing and cooling can be considered.

Originality/value

The paper presents the developed model of heat flow (temperature module), which is one of the main parts of the new hybrid model devoted to modeling of phase transformation. The model takes into account the enthalpy of transformation, and the connection with the model of microstructure evolution was obtained.
Lattice Boltzmann simulation of convective flow and heat transfer in a nanofluid-filled hollow cavity
Authors: Pu Qiang , Aalizadeh Farhad , Aghamolaei Darya , Masoumnezhad Mojtaba , Rahimi Alireza , Kasaeipoor Abbas
Published: July 2019

Purpose

This paper aims to to simulate the flow and heat transfer during free convection in a square cavity using double-multi-relaxation time (MRT) lattice Boltzmann method.

Design/methodology/approach

The double-MRT lattice Boltzmann method is used, and the natural convection fluid flow and heat transfer under influence of different parameters are analyzed. The D2Q5 model and D2Q9 model are used for simulation of temperature field and flow field, respectively. The cavity is filled with CuO-water nanofluid; in addition, the thermo-physical properties of nanofluid and the effect of nanoparticles’ shapes are considered using Koo–Kleinstreuer–Li (KKL) model. On the other hand, the cavity is included with an internal active hollow with constant thermal boundary conditions at its walls and variable dimensions. It should be noted that the dimensions of the internal hollow will be determined by as aspect ratio.

Findings

The Rayleigh number, nanoparticle concentration and the aspect ratio are the governing parameters. The heat transfer performance of the cavity has direct relationship with the Rayleigh number and solid volume fraction of CuO-water nanofluid. Moreover, the configuration of the cavity is good controlling factor for changing the heat transfer performance and entropy generation.

Originality/value

The originality of this work is using double-MRT lattice Boltzmann method in simulating the free convection fluid flow and heat transfer.