bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the Frequency of Drug Side effects
Authors: Galeano Diego , Paccanaro Alberto
Published: April 2019

Drug side effects are a leading cause of morbidity and mortality. Currently, the frequency of drug side effects is determined experimentally during human clinical trials through placebo-controlled studies. Here we present a novel framework to computationally predict the frequency of drug side effects. Our algorithm is based on learning a latent variable model for drugs and side effects by matrix decomposition. Extensive evaluations on held out test sets show that the frequency class is predicted with 67.8% to 94% accuracy in the neighborhood of the correct class. Evaluations on prospective data confirm the commonly held hypothesis that most post-marketing side effects are very rare in the population, with occurrences of less than 1 in a 10,000. Importantly, our model provides explanations of the biology underlying drug side effect relationships. We show that the drug latent representations in our model are related to distinct anatomical drug activities and that the similarity between these representations are predictive of the drug clinical activity as well as drug targets.

One summary sentence

novel explainable machine learning algorithm predicts the frequency of drug side effects in the population
Septins Coordinate with Microtubules and Actin to Initiate Cell Morphogenesis
Authors: Bogorodskaya Diana , Ligon Lee A.
Published: April 2019

Many organs are formed by a process of branching morphogenesis, which begins with the formation of cytoplasmic extensions from the basal surface of polarized cells in an epithelial sheet. To study this process, we used a system of polarized epithelial spheroids, which emit cytoplasmic extensions in response to treatment with hepatocyte growth factor. We found that these extensions contain both actin and microtubules, but also septins, which are localized to microtubule bundles and appear to be important in maintaining microtubule organization. We found that these extensions are highly dynamic and form at a non-linear rate. We also demonstrated that the coordinated activity of microtubules, actin, and septins is necessary for the formation and dynamic behavior of extensions. Each cytoskeletal system plays a district role in this process, with microtubules enabling persistent growth of the extensions, actin enabling extension dynamics, and septins organizing microtubules in the extensions and supporting the extension formation. Together, our data offer insights into the dynamics of early morphogenic extensions and the distinct, but coordinated, roles of cytoskeleton in early morphogenesis.
A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease
Authors: Emdin Connor A. , Haas Mary , Khera Amit V. , Aragam Krishna , Chaffin Mark , Jiang Lan , Wei Wei-Qi , Feng Qiping , Karjalainen Juha , Havulinna Aki , Kiiskinen Tuomo , Bick Alexander , Ardissino Diego , Wilson James G. , Schunkert Heribert , McPherson Ruth , Watkins Hugh , Elosua Roberto , Bown Matthew J , Samani Nilesh J , Baber Usman , Erdmann Jeanette , Gupta Namrata , Danesh John , Saleheen Danish , Daly Mark , Denny Joshua , Gabriel Stacey , Kathiresan Sekar
Published: April 2019

Analyzing 5770 all-cause cirrhosis cases and 572,850 controls from seven cohorts, we identify a missense variant in the Mitochondrial Amidoxime Reducing Component 1 gene (MARC1 p.A165T) that associates with protection from all-cause cirrhosis (OR 0.88, p=2.1*10−8). This same variant also associates with lower levels of hepatic fat on computed tomographic imaging and lower odds of physician-diagnosed fatty liver as well as lower blood levels of alanine transaminase (−0.012 SD, 1.4*10−8), alkaline phosphatase (−0.019 SD, 6.6*10−9), total cholesterol (−0.037 SD, p=1*10−18) and LDL cholesterol (−0.035 SD, p=7.3*10−16). Carriers of rare protein-truncating variants in MARC1 had lower liver enzyme levels, cholesterol levels, and reduced odds of liver disease (OR 0.19, p= 0.04) suggesting that deficiency of the MARC1 enzyme protects against cirrhosis.
Exploring Structural Aspects of the Human Golgi Matrix Protein GRASP55 in Solution
Authors: Thirupathi Reddy S. , Santos Mendes Luis Felipe , Fontana Natalia Aparecida , Costa-Filho Antonio José
Published: April 2019

In mammalian cells, the Golgi apparatus is a central hub for intracellular trafficking, sorting and post-translational modifications of proteins and lipids. The Golgi reassembly and stacking proteins (GRASPs) are somehow involved in the Golgi stacking, which is significant for the proper function of the Golgi apparatus, and also in unconventional protein secretion. However, the structural details on how GRASPs accomplish those tasks are still elusive. In this context, we have explored the biochemical and biophysical properties of the human full-length GRASP55 in solution. Sequence-based analyses and circular dichroism spectroscopy suggest that GRASP55 presents multiple intrinsically disordered sites, although keeping considerable contents of secondary structure. Size exclusion chromatography coupled with multiple-angle light scattering (SEC-MALS) studies show that GRASP55 are monomers in solution. Urea denaturation of GRASP55 suggests that the transition to the unfolded state is a cooperative process. Differential scanning calorimetry (DSC) analysis displays two endothermic transitions for GRASP55, indicating the existence of an intermediate state prior to unfolding. Thioflavin T fluorescence shows that GRASP55 can form protein aggregates/fibrils at the intermediate state. Transmission electron microscopy and fluorescence lifetime imaging microscopy prove that GRASP55 forms large amorphous aggregates but not amyloid-like fibrils in the intermediate state. The significance of these results could be helpful in discussing the proper function of human GRASP55 in the Golgi organization as well as unconventional secretion of proteins.
High-throughput single nucleotide polymorphism (SNP) discovery and validation through whole-genome resequencing of hundreds of individuals in Nile tilapia (Oreochromis niloticus)
Authors: Yáñez J.M. , Yoshida G. , Barria A. , Palma-Véjares R. , Travisany D. , Díaz D. , Cáceres G. , Cádiz M.I. , López M.E. , Lhorente J.P. , Jedlicki A. , Soto J. , Salas D. , Maass A.
Published: April 2019

Nile Tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world and so far, they are mainly based on conventional selection using genealogical and phenotypic information to estimate the genetic merit of breeders and make selection decisions. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure in the breeding goal. Thus, SNPs are required to investigate phenotype–genotype associations and determine the genomic basis of economically important traits. We performedde novoSNP discovery in three different populations of farmed tilapias. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps including removing SNP based on genotype and site quality, presence of Mendelian errors, and non unique position in the genome, a total of high quality 50,000 SNP were selected for validation purposes. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNP in HWE; 37,843 (76%) and 45,171(90%) SNP with a MAF higher than 0.05 and; 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The final list of 50K SNPs will be very useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection as well as supporting genetic studies in farmed populations Nile tilapia using dense genome-wide information.
DNA epigenetic marks are linked to reproductive aberrations in amphipods
Authors: Gorokhova Elena , Martella Giulia , Motwani Nisha H. , Tretyakova Natalia Y. , Sundelin Brita , Motwani Hitesh V.
Published: April 2019

Linking exposure to environmental contaminants with diseases is crucial for proposing preventive and regulatory actions. Upon exposure to anthropogenic chemicals, covalent modifications on the genome can drive developmental and reproductive disorders in wild populations, with subsequent effects on the population persistence. Hence, screening of chemical modifications on DNA can be used to provide information on the probability of such disorders in populations of concern. Using a high-resolution mass spectrometry methodology, we identified DNA nucleoside adducts in gravid females of the Baltic amphipodsMonoporeia affinis, and linked the adduct profiles to the frequency of embryo malformations in the broods. Twenty-three putative nucleoside adducts were detected in the females and their embryos, and eight modifications were structurally identified using high-resolution accurate mass data. To identify which adducts were significantly associated with embryo malformations, partial least squares regression (PLSR) modelling was applied. The PLSR model yielded three adducts as the key predictors: methylation at two different positions of the DNA (5-methyl-2’-deoxycytidine and N6-methyl-2’-deoxyadenosine) representing epigenetic marks, and a structurally unidentified nucleoside adduct. These adducts predicted the elevated frequency of the malformations with a high classification accuracy (84%). To the best of our knowledge, this is the first application of DNA adductomics for identification of contaminant-induced malformations in field-collected animals. The method can be adapted for a broad range of species and evolve as a new omics tool in environmental health assessment.
A comprehensive genome-scale model forRhodosporidium toruloidesIFO0880 accounting for functional genomics and phenotypic data
Authors: Dinh Hoang V. , Suthers Patrick F. , Chan Siu Hung Joshua , Shen Yihui , Xiao Tianxia , Deewan Anshu , Jagtap Sujit Sadashiv , Rabinowitz Joshua D. , Rao Christopher V. , Zhao Huimin , Maranas Costas D.
Published: April 2019

Background

Rhodosporidium toruloidesis a basidiomycetes yeast that can accumulate large amount of lipids and natively produce carotenoids. To better assess this non-model yeast’s metabolic capabilities, we reconstruct a genome-scale model ofR. toruloidesIFO0880’s metabolic network (iRhto1108) using recent functional genomics and phenotypic data in literature or generated herein.

Results

The modeliRhto1108 accounts for 2,203 reactions, 1,985 metabolites and 1,108 genes. In this work, we integrate and supplement the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism’s metabolic capabilities. Phenotype-genotype relationship predictions were improved through manual curation of gene-protein-reaction rules for 543 reactions and validations with gene essentiality data leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificity of 53.8%). Organism-specific macromolecular composition and ATP maintenance requirements were experimentally measured for two separate growth conditions: (i) carbon and (ii) nitrogen limitations. Overall,iRhto1108 reproducedR. toruloides’s utilization capabilities for 18 alternate substrates, matched measured wild-type growth yield, and recapitulated the viability of 772 out of 819 deletion mutants. As a demonstration to the model’s fidelity in guiding engineering interventions, the OptForce procedure was applied oniRhto1108 for the overproduction of triacylglycerol. Suggested interventions recapitulated many of the previously successfully implemented genetic modifications and put forth a few new ones.

Conclusion

iRhto1108 offers a highly curated model for a non-model yeast supported by multiple layers of experimental data that can be used to inform genetic interventions.
Tracking microbial evolution in the human gut using Hi-C
Authors: Yaffe Eitan , Relman David A.
Published: April 2019

Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota remains elusive. We used Hi-C (High-throughput chromosomal conformation capture), coupled with probabilistic modeling of experimental noise, to resolve 88 strain-level genomes of distal gut bacteria from two subjects, including 12,251 accessory elements. Comparisons of 2 samples collected 10 years apart for each of the subjects revealed extensive in situ exchange of accessory elements, as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult subjects. This work provides a foundation and approach for studying microbial evolution in natural environments.
STELAR: A statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency
Authors: Islam Mazharul , Sarker Kowshika , Das Trisha , Reaz Rezwana , Bayzid Md. Shamsuzzoha
Published: April 2019

Background

Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, estimating a species tree from a collection of gene trees can be complicated due to the presence of gene tree incongruence resulting from incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent process. Maximum likelihood and Bayesian MCMC methods can potentially result in accurate trees, but they do not scale well to large datasets.

Results

We present STELAR (Species Tree Estimation by maximizing tripLet AgReement), a new fast and highly accurate statistically consistent coalescent-based method for estimating species trees from a collection of gene trees. We formalized the constrained triplet consensus (CTC) problem and showed that the solution to the CTC problem is a statistically consistent estimate of the species tree under the multi-species coalescent (MSC) model. STELAR is an efficient dynamic programming based solution to the CTC problem which is highly accurate and scalable. We evaluated the accuracy of STELAR in comparison with SuperTriplets, which is an alternate fast and highly accurate triplet-based supertree method, and with MP-EST and ASTRAL – two of the most popular and accurate coalescent-based methods. Experimental results suggest that STELAR matches the accuracy of ASTRAL and improves on MP-EST and SuperTriplets.

Conclusions

Theoretical and empirical results (on both simulated and real biological datasets) suggest that STELAR is a valuable technique for species tree estimation from gene tree distributions.
A Human Tissue-Specific Transcriptomic Analysis Reveals that Ageing Hinders Cancer and Boosts Cellular Senescence
Authors: Chatsirisupachai Kasit , Palmer Daniel , Ferreira Susana , de Magalhães João Pedro
Published: April 2019

Ageing is the biggest risk factor for cancer, but the mechanisms linking these two processes remain unclear. We compared genes differentially expressed with age and genes differentially expressed in cancer among nine human tissues. In most tissues, ageing and cancer gene expression surprisingly changed in the opposite direction. These overlapping gene sets were related to several processes, mainly cell cycle and the immune system. Moreover, cellular senescence signatures derived from a meta-analysis changed in the same direction as ageing and in the opposite direction of cancer signatures. Therefore, transcriptomic changes in ageing and cellular senescence might relate to a decrease in cell proliferation, while cancer transcriptomic changes shift towards an increase in cell division. Our results highlight the complex relationship between ageing, cancer and cellular senescence and suggest that in most human tissues ageing processes and senescence act in tandem while being detrimental to cancer. Our work challenges the traditional view concerning the relationship between cancer and ageing and suggests that ageing processes may hinder cancer development.
Single subunit degradation of WIZ, a lenalidomide- and pomalidomide-dependent substrate of E3 ubiquitin ligase CRL4CRBN
Authors: Yu Helen H. , Reitsma Justin M. , Sweredoski Mike J. , Moradian Annie , Hess Sonja , Deshaies Raymond J.
Published: April 2019

Immunomodulators (IMiDs) are an effective class of drugs used to treat blood cancers. IMiDs are believed to work by recruiting protein targets containing a β-hairpin motif for ubiquitination by E3 ubiquitin ligase complexes composed of cereblon (CRBN), Cullin-4a (CUL4a), DNA Damage Binding protein-1 (DDB1), and Ring Box-1 (RBX1). The ubiquitinated protein is subsequently degraded by the proteasome. By characterizing the repertoire of proteins that show an increased physical association with CRBN after IMiD treatment, we identified a novel IMiD substrate, Widely Interspaced Zinc Finger Motifs (WIZ). WIZ contains a C2H2 zinc finger domain, like several other substrates that were previously characterized. We demonstrate that IMiDs stabilize physical association of WIZ with CRBN, deplete WIZ steady state protein levels in a way that is dependent on E3 ligase activity, and enhance the rate of its degradation. Notably, proteins that assemble with WIZ are co-recruited to CRBN by IMiDs but are not degraded, illustrating the potential of targeted protein degradation to eliminate individual subunits of a protein complex. These findings suggest that systematic characterization of the full repertoire of proteins that are targeted for degradation by IMiD compounds will be required to better understand their biological effects.

Synopsis

Proteolysis Targeting Chimeras (PROTACs) can be used to precisely target a subunit of a transcriptional complex for degradation in subpopulations of cells.
Alterations in Dynamic Spontaneous Network Microstates in Mild Traumatic Brain Injury: A MEG Beamformed Dynamic Connectivity Analysis
Authors: Antonakakis Marios , Dimitriadis Stavros I. , Zervakis Michalis , Papanicolaou Andrew C. , Zouridakis George
Published: April 2019

Dynamic functional connectivity (DFC) analysis has attracted interest in the last years for the characterization of brain electrophysiological activity at rest. In this work, we investigated changes in mild Traumatic Brain Injury (mTBI) patients using magnetoencephalographic (MEG) resting-state recordings and a DFC approach. The activity of several well-known brain rhythms was first beamformed using linearly constrained minimum norm variance of the MEG data to determine ninety anatomical brain regions of interest. A DFC graph was formulated using the imaginary part of phase lag value which were obtained from 30 mTBI patients and 50 normal controls. Filtering each quasi-static graph statistically and topologically, we estimated a normalized Laplacian transformation of every single quasistatic graph based on the degree of each node. Then, the related eigenvalues of the synchronization of each node were computed by incorporating the complete topology. Using the neural-gas algorithm, we modelled the evolution of the eigenvalues for each group, resulting in distinct FC microstates (FCμstates). Using the so-calledchronnectomics(transition rate, occupancy time of FCμstate, and Dwell time) and complexity index over the evolution of the FCμstates, we evaluated the level of discrimination and derived statistical differences between the two groups. In both groups, we detected equal number of FCμstates with statistically significant transitions in the δ, α, β, and γlowfrequency bands. The discrimination rate between the two groups was very high in the θ and γlowbands, followed by a statistically significant difference between the two groups in all the chronnectomics and the complexity index. Statistically significant differences in the degree of several anatomical subnetworks (BAN – brain anatomical networks: default mode network; frontoparietal; occipital; cingulo-opercular; and sensorimotor) were revealed in most FCμstates for the θ, α, β, and γlowbrain rhythms, indicating a higher level of communication within and between the BAN in the mTBI group. In our previous studies, we focused on intra- and inter-frequency couplings of static FC. Our current study summarizes a complete set of frequency-dependent connectomic markers of mTBI-caused alterations in brain connectivity that potentially could also serve as markers to assess the return of an injured subject back to normality.
Physical and data structure of 3D genome
Authors: Huang Kai , Li Yue , Shim Anne R. , Nap Rikkert J. , Agrawal Vasundhara , Virk Ranya K.A. , Eshein Adam , Almassalha Luay M. , Backman Vadim , Szleifer Igal
Published: April 2019

With the textbook view of chromatin folding based on the 30nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggested that such irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing 3D genome into tree data structures on top of, and in striking contrast to the linear topology of DNA double helix. Such functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi-self-similar manner as revealed by our electron and optical imaging. Our multi-scale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.
Molecular Dynamics Analysis of Mg2+-dependent Cleavage of a Pistol Ribozyme Reveals a Fail-safe Secondary Ion for Catalysis
Authors: Joseph Newlyn N. , Roy Raktim N. , Steitz Thomas A.
Published: April 2019

Pistol ribozymes comprise a class of small, self-cleaving RNAs discovered via comparative genomic analysis. Prior work in the field has probed the kinetics of the cleavage reaction, as well as the influence of various metal ion cofactors that accelerate the process. In the current study we perform unbiased and unconstrained molecular dynamics simulations from two current high-resolution pistol crystal structures, and we analyzed trajectory data within the context of the currently accepted ribozyme mechanistic framework. Root-mean-squared deviations (RMSDs), radial distribution functions (RDFs), and distributions of nucleophilic angle-of-attack reveal insights into the potential roles of three magnesium ions with respect to catalysis and overall conformational stability of the molecule. A series of simulation trajectories containingin-silicomutations reveal the relatively flexible and partially interchangeable roles of two particular magnesium ions within solvated hydrogen-bonding distances from the catalytic center.
Directed networks as a novel way to describe and analyze cardiac excitation: Directed Graph mapping
Authors: Vandersickel Nele , Van Nieuwenhuyse Enid , Van Cleemput Nico , Goedgebeur Jan , Haddad Milad El , Neve Jan De , Demolder Anthony , Strisciuglio Teresa , Duytschaever Mattias , Panfilov Alexander V.
Published: April 2019

Networks provide a powerful methodology with applications in a variety of biological, technological and social systems such as analysis of brain data, social networks, internet search engine algorithms, etc. To date, directed networks have not yet been applied to characterize the excitation of the human heart. In clinical practice, cardiac excitation is recorded by multiple discrete electrodes. During (normal) sinus rhythm or during cardiac arrhythmias, successive excitation connects neighboring electrodes, resulting in their own unique directed network. This in theory makes it a perfect fit for directed network analysis. In this study, we applied directed networks to the heart in order to describe and characterize cardiac arrhythmias. Proofof-principle was established using in-silico and clinical data. We demonstrated that tools used in network theory analysis allow to determine the mechanism and location of certain cardiac arrhythmias. We show that the robustness of this approach can potentially exceed the existing state-of-the art methodology used in clinics. Furthermore, implementation of these techniques in daily practice can improve accuracy and speed of cardiac arrhythmia analysis. It may also provide novel insights in arrhythmias that are still incompletely understood.
Quantification of microaerobic growth ofGeobacter sulfurreducens
Authors: Engel Christina E. A. , Vorländer David , Biedendieck Rebekka , Krull Rainer , Dohnt Katrin
Published: April 2019

Geobacter sulfurreducenswas originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate exposure to oxygen but also to use it as terminal electron acceptor. Research performed has so far only revealed the general ability ofG. sulfurreducensto reduce oxygen, but the oxygen uptake rate has not been quantified yet, nor has evidence been provided as to how the bacterium achieves oxygen reduction. Therefore, microaerobic growth ofG. sulfurreducenswas investigated here with better defined operating conditions as previously performed and a transcriptome analysis was performed to elucidate possible metabolic mechanisms important for oxygen reduction inG. sulfurreducens. The investigations revealed that cell growth with oxygen is possible to the same extent as with fumarate if the maximum specific oxygen uptake rate (sOUR) of 95 mgO2gCDW-1h-1is not surpassed. Hereby, the entire amount of introduced oxygen is reduced. When oxygen concentrations are too high, cell growth is completely inhibited and there is no partial oxygen consumption. Transcriptome analysis suggests a menaquinol oxidase to be the enzyme responsible for oxygen reduction. Transcriptome analysis has further revealed three different survival strategies, depending on the oxygen concentration present. When prompted with small amounts of oxygen,G. sulfurreducenswill try to escape the microaerobic area; if oxygen concentrations are higher, cells will focus on rapid and complete oxygen reduction coupled to cell growth; and ultimately cells will form protective layers if a complete reduction becomes impossible. The results presented here have important implications for understanding howG. sulfurreducenssurvives exposure to oxygen.
Prevalence and socioeconomic determinants of development delay among children in Ceará, Brazil: a population-based study
Authors: Correia Luciano L. , Rocha Hermano A. L. , Sudfeld Christopher R. , Rocha Sabrina G. M. O. , Leite Álvaro J. M. , Campos Jocileide S. , Silva Anamaria C. e
Published: April 2019

Objective

To assess the prevalence of child development delay and to identify socioeconomic determinants.

Study Design

We conducted a population-based cross-sectional study of children 2 to 72 months of age residing in the state of Ceará, Brazil. In total, 3200 households were randomly selected for participation in the study and had child development assessed with the Ages and Stages Questionnaire (ASQ) version 3. Development delay was defined as a score less than −2 standard deviations below the median of the Brazilian ASQ standard. We present population-level prevalence of delay in five development domains and assess socioeconomic determinants.

Results

A total of 3566 children completed the ASQ development assessment of which 9.2% (95% CI: 8.1-10.5) had at least one domain with development delay. The prevalence of delay increased with age in all domains and males were at higher risk for communication, gross motor and personal-social development delays as compared to females (p-values <0.05). We found robust associations of indicators of socioeconomic status with risk of development delay; increasing monthly income and higher social class were associated with reduced risk of delay across all domains (p-values <0.05). In addition, children in poor households that participated in conditional cash transfer (CCT) programs appeared to have reduced risk of delay as compared to children from households that were eligible, but did not participate, in CCT programs.

Conclusions

There is a relatively high population-level prevalence of development delay in at least one domain among children 0-6 years of age in Ceará, Brazil. Integrated child development, social support, and poverty reduction interventions may reduce the population-level prevalence of development delay in Ceará and similar settings.
Growth Patterns of birds, dinosaurs and reptiles: Are differences real or apparent?
Authors: Brunner Norbert , Kühleitner Manfred , Nowak Werner-Georg , Renner-Martin Katharina , Scheicher Klaus
Published: April 2019

Systematics of animals was done on their appearance or genetics. One can also ask about similarities or differences in the growth pattern. Quantitative studies of the growth of dinosaurs have made possible comparisons with modern animals, such as the discovery that dinosaurs grew in relation to their size faster than modern reptiles. However, these studies relied on only a few growth models. If these models are false, what about the conclusions? This paper fits growth data to a more comprehensive class of models, defined by the von Bertalanffy-Pütter differential equation. Applied to data about dinosaurs, reptiles and birds, the best fitting models confirmed that dinosaurs may have grown faster than alligators. However, compared to modern broiler chicken, this difference was small.
Fast three-dimensional phase retrieval in propagation-based X-ray tomography
Authors: Thompson Darren A. , Nesterets Yakov I. , Pavlov Konstantin M. , Gureyev Timur E.
Published: April 2019

The following article describes a method for 3D reconstruction of multi-material objects based on propagation-based X-ray phase-contrast tomography (PB-CT) with phase retrieval using the homogeneous form of the transport of intensity equation (TIE-Hom). Unlike conventional PB-CT algorithms that perform phase retrieval of individual projections, the described post-reconstruction phase-retrieval method is applied in 3D to a localized region of the CT-reconstructed volume. This work demonstrates, via numerical simulations, the accuracy and noise characteristics of the method under a variety of experimental conditions, comparing it with both conventional absorption tomography and 2D TIE-Hom phase retrieval applied to projection images. The results indicate that the 3D post-reconstruction method generally achieves a modest improvement in noise suppression over existing PB-CT methods. It is also shown that potentially large computational gains over projection-based phase retrieval for multi-material samples are possible. In particular, constraining phase retrieval to a localized 3D region of interest reduces the overall computational cost and eliminates the need for multiple CT reconstructions and global 2D phase retrieval operations for each material within the sample.
Crystallization of the human tetraspanin protein CD9
Authors: Umeda Rie , Nishizawa Tomohiro , Nureki Osamu
Published: April 2019

The tetraspanin family of proteins with four membrane-spanning proteins function in a wide range of physiological processes in higher organisms, including cell migration and proliferation, cell fusion, fertilization and virus infection. Although the recently reported structure of CD81 unveiled the basic architecture of this family for the first time, further structural and functional studies are required in order to understand the mechanistic details of the complicated functions of the tetraspanin-family proteins. In this study, attempts were made to crystallize human CD9, a representative member of the tetraspanin family, and it was demonstrated that the truncation of a variable region in the second long extracellular loop significantly improved crystal growth.
Crystal structure of hydroxy scandium nitrate chloride
Authors: Sears Jeremiah , Cramer Roger , Boyle Timothy
Published: April 2019

Each Sc3+ ion in the title salt, di-μ-hydroxido-bis[triaqua(nitrato-κ2
O,O′)scandium(III)] dichloride, [Sc2(NO3)2(OH)2(H2O)6]Cl2, is coordinated by a nitrate anion, two hydroxide ions and three water molecules to generate a distorted pentagonal–bipyramidal ScO7 coordination polyhedron. The complete {[(NO3)(μ-OH)Sc(H2O)3]2}2+ ion is generated by crystallographic inversion symmetry. The nitrate anion binds in a bidentate fashion whereas the hydroxide ions are bridged between two Sc centers. Two charge-balancing Cl− ions are located in the outer sphere. In the extended structure, O—H...O and O—H...Cl hydrogen bonds connect the components into a three-dimensional network.
Resilient cultural heritage: from global to national levels – the case of Bhutan
Authors: Minguez Garcia Barbara
Published: April 2019

Purpose

Cultural heritage is about people, their history and their identity. Protecting cultural heritage from natural hazards by connecting it with disaster risk management (DRM) directly benefits local communities. Cultural heritage also has a global dimension, and collaboration and support from the international community to protect it is vital. Culture and heritage differ among countries, as do natural hazards, but practitioners face some common challenges, such as the need to create awareness. The paper aims to discuss these issues.

Design/methodology/approach

This paper presents: a brief overview of the current connection between DRM and cultural heritage in the global context; an analysis of how international knowledge-exchange initiatives can help countries improve the resilience of their heritage sites, using Bhutan as an example; and a proposal to keep this topic moving forward in both the international and national agendas for sustainable development and resilience.

Findings

International knowledge exchanges may help to find solutions, and Bhutan is a good example. This small, hazard-prone country in the Himalayas, has strong traditions and heritage, and is aware of its vulnerabilities and risks. Learning from Japan’s extensive experience, Bhutan has been working with international experts to improve the resilience of its cultural heritage sites.

Originality/value

The ultimate aim is that this paper serves as an inspiration for other countries, as well as international organizations such as the World Bank, to keep strengthening ties between DRM and cultural heritage.
Understanding gender dimensions of climate-smart agriculture adoption in disaster-prone smallholder farming communities in Malawi and Zambia
Authors: Khoza Sizwile , Van Niekerk Dewald , Nemakonde Livhuwani David
Published: April 2019

Purpose

Through the application of traditional and contemporary feminist theories in gender mainstreaming, the purpose of this paper is to contribute to emergent debate on gender dimensions in climate-smart agriculture (CSA) adoption by smallholder farmers in disaster-prone regions. This is important to ensure that CSA strategies are tailored to farmer-specific gender equality goals.

Design/methodology/approach

An exploratory-sequential mixed methods research design which is qualitatively biased was applied. Key informant interviews and farmer focus group discussions in two study sites formed initial qualitative phase whose findings were explored in a quantitative cross-sectional household survey.

Findings

Findings shared in this paper indicate the predominant application of traditional gender mainstreaming approaches in CSA focusing on parochial gender dichotomy. Qualitative findings highlight perceptions that western gender approaches are not fully applicable to local contexts and realities, with gender mainstreaming in CSA seemingly to fulfil donor requirements, and ignorant of the heterogeneous nature of social groups. Quantitative findings establish that married men are majority adopters and non-adopters of CSA, while dis-adopters are predominantly de jure female household heads. The latter are more likely to adopt CSA than married women whose main role in CSA is implementers of spouse’s decisions. Access to education, intra-household power relations, productive asset and land ownership are socio-cultural dynamics shaping farmer profiles.

Originality/value

By incorporating African feminisms and intersectionality in CSA, value of this study lies in recommending gender policy reforms incorporating local gender contexts within the African socio-cultural milieu. This paper accentuates potential benefits of innovative blend of both contemporary and classic gender mainstreaming approaches in CSA research, practice and technology development in disaster-prone regions.
Conflicts in adaptation: case studies from Nepal and the Maldives
Authors: Lama Phu Doma , Becker Per
Published: April 2019

Purpose

Adaptation appears to be regarded as a panacea in policy circles to reduce the risk of impending crises resulting from contemporary changes, including but not restricted to climate change. Such conceptions can be problematic, generally assuming adaptation as an entirely positive and non-conflictual process. The purpose of this paper is to challenge such uncritical views, drawing attention to the conflictual nature of adaptation, and propose a theoretical framework facilitating the identification and analysis of conflicts in adaptation.

Design/methodology/approach

The study is based on case study research using first-hand narratives of adaptation in Nepal and the Maldives collected using qualitative interviews, participant observation and document analysis.

Findings

The findings identify conflicts between actors in, and around, communities that are adapting to changes. These conflicts can be categorized along three dimensions: qualitative differences in the type of conflict, the relative position of conflicting actors and the degree of manifestation of the conflict.

Originality/value

The three-dimensional Adaptation Conflict Framework facilitate analysis of conflicts in adaptation, allowing for a critical examination of subjectivities inherent in the adaptation discourses embedded in disaster risk reduction and climate change adaptation research and policy. Such an inquiry is crucial for interventions supporting community adaptation to reduce disaster risk.
A review of global lean construction during the past two decades: analysis and visualization
Authors: Li Long , Li Zhongfu , Li Xiaodan , Wu Guangdong
Published: April 2019

Purpose

The purpose of this paper is to provide comprehensive analysis and understanding of lean construction (LC) and to help researchers to find new gaps and research opportunities and develop potential collaboration chances.

Design/methodology/approach

The bibliographic data were obtained in peer-reviewed journals. The science mapping analysis and social network analysis (SNA) were used to conduct the analysis and visualization. Science mapping was performed to identify the research topics, evolution and the relationships between these topics. Also, the most influential LC-related articles in each topic were identified based on the concept of H-classics. SNA was also used to explore the collaboration status of authors and to identify the core authors in the LC field.

Findings

The results showed that topics in the LC field are consistently and continuously changing, which also reveals the fact that the lean concept system has evolved over time to a certain extent. The topics that could form the knowledge base of the LC research field in the future are related to two thematic areas: supply chain management (SCM) and planning and scheduling. SCM focuses on developing a system where supplier and client work together in coordination to deliver materials, works, equipment and labor and other resources. Moreover, prefabrication is a new hot topic, while BIM is a well-developed and isolated topic in the last five years. This result indicates that more studies need to be conducted in the future, to promote the integration of BIM and lean practices in the construction phase, as well as to explore the value of BIM in the reduction or elimination of waste and lean project delivery. As for global collaborations, LC research has been widely pursued throughout the world. The USA and the UK play the most dominant role in the international collaboration network.

Research limitations/implications

Since the analysis of data takes some time, the specific results of this paper are limited to articles published in peer-reviewed journals, which leads to a certain degree of research lag.

Practical implications

This paper provides insights (such as major journals, institutions, key scholars, the evolution of topics, highly indexed articles and the new LC trends in the last five years) for researchers in the LC field.

Originality/value

This paper gives a general review of the above-mentioned literature, including the number of LC-related articles published in each year, as well as the major journals and main contributors to the field of LC.
Creating social value within the delivery of construction projects: the role of lean approach
Authors: Daniel Emmanuel Itodo , Pasquire Christine
Published: April 2019

Purpose

The purpose of this paper is to present the current knowledge surrounding social value (SV) and show how lean approach supports SV realisation in the delivery of construction projects.

Design/methodology/approach

A critical literature review was adopted, to gather the current knowledge surrounding SV from mainstream management sciences, construction management and lean literature. A total of 70 studies were critically reviewed.

Findings

The study establishes that the current level of awareness on SV is still low and there is a dearth of scholarly publications on SV especially in the construction management literature. The investigation reveals the potentials of lean approach in supporting the delivery of SV on construction projects.

Social implications

This study conceptualises the community and the physical environment around where the construction project is executed as customers using lean production approach. It shows that the transformation, flow and value view supports smooth workflow, which enhances the achievement of SV objectives. This creates a new insight into how SV can be realised in construction project delivery.

Originality/value

This study extends the on-going debate around the need for SV in construction project delivery and contributes to construction management and lean construction literature on SV. Future studies could build on this to obtain empirical data and develop an approach/method that would support the evidencing of SV delivery on construction projects.
Adoption of building information modeling in Chinese construction industry
Authors: Chen Yilin , Yin Yilin , Browne Glenn J. , Li Dahui
Published: April 2019

Purpose

Building information modeling (BIM) is recognized as a major innovation in the architecture, engineering, and construction (AEC) industry. Understanding the factors that influence the AEC’s adoption of BIM will benefit the research and practice of BIM. The paper aims to discuss these issues.

Design/methodology/approach

This study provides empirical evidence for the accumulated knowledge of BIM adoption by examining the context of Chinese construction industry. Based on the technology-organization-environment (TOE) framework in the innovation diffusion literature, the authors develop a research model that integrates the critical success factors related to the technology of BIM, the construction company and the environment in Chinese construction industry. The authors collected two different data sets from engineering consulting firms and construction firms in China, and conducted rigorous analyses using a sophisticated statistical approach.

Findings

The authors found that the relative advantage of BIM was a major factor that enabled BIM adoption, while the complexity of BIM was an inhibiter. In addition, management support was also a significant antecedent of BIM adoption. However, organizational readiness was significant for engineering consulting firms but not for construction firms. Surprisingly, the authors did not find consistent significant impacts of any environmental factors. Last, younger firms were more likely to adopt BIM.

Originality/value

One of the first to apply the TOE framework to integrate three groups of factors that may explain BIM adoption in China. Such a comprehensive framework provides a much broader perspective of BIM adoption to evaluate the impacts of different antecedent factors. The authors conducted an empirical study based on survey data collected from two different types of companies, i.e., engineering consulting firms and construction firms, representing the two parties in the principal-agent relationship of a construction project. One of the first to apply a sophisticated statistical approach, i.e., partial least squares, to analyze the data in the BIM literature.
Cross-border acquisitions and family businesses
Authors: Ossorio Mario
Published: April 2019

Purpose

The purpose of this paper is to shed light on the propensity of family firms to join a cross-border acquisition as acquirers.

Design/methodology/approach

The present study analyzes a sample of 270 acquisitions in the period 2015–2017 whose acquiring firms are represented by family and nonfamily listed European firms.

Findings

The results point out that family firms are less likely to make a cross-border acquisition than nonfamily counterparts.

Research limitations/implications

Mergers and acquisitions (M&A) activity is cyclical by nature, represented by waves of concentrated intensity rather than necessarily by constant activity over time. Therefore, the main limitation is represented by the period analyzed (2015–2017), which restricts the possibility of seizing a greater number of transactions.

Practical implications

If careful evaluation leads to the consideration of M&A as the optimal mode of entry into a certain foreign market, family firms should broaden the pool from which managers are selected in order to access more qualified staff, who are able to face international M&As.

Originality/value

In recent years, a growing body of literature has focused on the effects of family ownership on the propensity of making an M&A, on the method of payment chosen by an acquired family firm, and on the reaction of the market at the announcement of a family business’ M&A. However, despite of the relevance of the entry modes of firms’ internationalization strategies, scant attention has been devoted to cross-border M&As conducted by family firms, which occur when a family firm acquires a firm located in a foreign country. In order to fill the research gap, this work investigates the likelihood of a family firm’s acquisition of a foreign target.