bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of prolines and glycine in the transmembrane domain of LAT
Authors: Glatzová Daniela , Mavila Harsha , Saija Maria Chiara , Chum Tomáš , Cwiklik Lukasz , Brdička Tomáš , Cebecauer Marek 
Published: August 2020

ABSTRACTLAT is a critical regulator of T cell development and function. It organises signalling events at the plasma membrane. However, the mechanism, which controls LAT localisation at the plasma membrane is not fully understood. Here, we studied the impact of helix-breaking amino acids, two prolines and one glycine, in the transmembrane segment on localisation and function of LAT. Using in silico analysis, confocal and superresolution imaging and flow cytometry we demonstrate that central proline residue destabilises transmembrane helix by inducing a kink. The helical structure and dynamics is further regulated by glycine and another proline residue in the luminal part of LAT transmembrane domain. Replacement of these residues with aliphatic amino acids reduces LAT dependence on palmitoylation for sorting to the plasma membrane. However, surface expression of these mutants is not sufficient to recover function of non-palmitoylated LAT in stimulated T cells. These data indicate that geometry and dynamics of LAT transmembrane segment regulate its localisation and function in immune cells.
Myogenin is an Essential Regulator of Adult Myofibre Growth and Muscle Stem Cell Homeostasis
Authors: Ganassi Massimo , Badodi Sara , Wanders Kees , Zammit Peter S. , Hughes Simon M. 
Published: August 2020

AbstractGrowth and maintenance of skeletal muscle fibres depend on coordinated activation and return to quiescence of resident muscle stem-cells (MuSCs). The transcription factor Myogenin (Myog) regulates myocyte fusion during development, but its role in adult myogenesis remains unclear. In contrast to mice,myog−/−zebrafish are viable, but have hypotrophic muscles. By isolating adult myofibres with associated MuSCs we found thatmyog−/−myofibres have severely reduced nuclear number, but increased myonuclear domain size. Expression of fusogenic genes is decreased,pax7upregulated, MuSCs are fivefold more numerous and mis-positioned throughout the length ofmyog−/−myofibers instead of localising at myofibre ends as in wild-type. Loss of Myog dysregulates mTORC1 signalling, resulting in an ‘alerted’ state of MuSCs, which display precocious activation and faster cell cycle entry ex vivo, concomitant withmyodupregulation. Thus, beyond controlling myocyte fusion, Myog influences the MuSC:niche relationship, demonstrating a multi-level contribution to muscle homeostasis throughout life.
Structure-function analyses of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation
Authors: Bryant J. A. , Morris F. C. , Knowles T. J. , Maderbocus R. , Heinz E. , Boelter G. , Alodaini D. , Colyer A. , Wotherspoon P. J. , Staunton K. A. , Jeeves M. , Browning D. F. , Sevastsyanovich Y. R. , Wells T. J. , Rossiter A. E. , Bavro V. N. , Sridhar P. , Ward D. G. , Chong Z-S. , Icke C. , Teo A. , Chng S-S. , Roper D. I. , Lithgow T. , Cunningham A. F. , Banzhaf M. , Overduin M. , Henderson I. R. 
Published: August 2020

AbstractThe Gram-negative outer membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here we reveal DolP is a lipoprotein functionally conserved among Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds to anionic phospholipids through an extensive membrane:protein interface providing evidence of subcellular localization of these phospholipids within the outer membrane. This interaction is essential for DolP function and is required for sub-cellular localization of the protein to the cell division site. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.
The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins
Authors: Jaroszewski Lukasz , Iyer Mallika , Alisoltani Arghavan , Sedova Mayya , Godzik Adam 
Published: August 2020

AbstractFast evolution of the SARS-CoV-2 virus provides us with unique information about the patterns of genetic changes in a single pathogen in the timescale of months. This data is used extensively to track the phylodynamic of the pandemic’s spread and its split into distinct clades. Here we show that the patterns of SARS-CoV-2 virus mutations along its genome are closely correlated with the structural features of the coded proteins. We show that the foldability of proteins’ 3D structures and conservation of their functions are the universal factors driving evolutionary selection in protein-coding genes. Insights from the analysis of mutation distribution in the context of the SARS-CoV-2 proteins’ structures and functions have practical implications including evaluating potential antigen epitopes or selection of primers for PCR-based COVID-19 tests.
On the complexity of haplotyping a microbial community
Authors: Nicholls Samuel M. , Aubrey Wayne , De Grave Kurt , Schietgat Leander , Creevey Christopher J. , Clare Amanda 
Published: August 2020

AbstractMotivationPopulation-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes), but for an unknown number of individuals.ResultsThe problem of single individual haplotyping (SIH) was first formalised by Lanciaet alin 2001. Now, nearly two decades later, we discuss the complexity of “haplotyping” metagenomic samples, with a new formalisation of Lanciaet al‘s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample: which we term the metagenomic individual haplotyping (MIH) problem. We also provide software implementations of our proposed pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm.Availability and implementationOur reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) are open source, MIT licensed and freely available online atgithub.com/samstudio8/hanselandgithub.com/samstudio8/gretel, respectively.Contacts.nicholls.1@bham.ac.uk
Crystal structures of Arabidopsis and Physcomitrella CR4 reveal the molecular architecture of CRINKLY4 receptor kinases
Authors: Okuda Satohiro , Hothorn Ludwig A. , Hothorn Michael 
Published: August 2020

AbstractPlant-unique receptor kinases harbor conserved cytoplasmic kinase domains and sequence-diverse ectodomains. Here we report crystal structures of CRINKLY4-type ectodomains from Arabidopsis ACR4 andPhyscomitrella patensPpCR4 at 1.95 Å and 2.70 Å resolution, respectively. Monomeric CRINKLY4 ectodomains harbor a N-terminal WD40 domain and a cysteine-rich domain (CRD) connected by a short linker. The WD40 domain forms a seven-bladed β-propeller with the N-terminal strand buried in its center. Each propeller blade is stabilized by a disulfide bond and contributes to the formation of a putative ligand binding groove. The CRD forms a β-sandwich structure stabilized by six disulfide bonds and shares low structural homology with tumor necrosis factor receptor domains. Quantitative binding assays reveal that ACR4 is not a direct receptor for the peptide hormone CLE40. An ACR4 variant lacking the entire CRD can rescue the knownacr4-2mutant phenotype, as can expression of PpCR4. Together, an evolutionary conserved signaling function for CRINKLY4 receptor kinases is encoded in its WD40 domain.
Identifiability analysis for stochastic differential equation models in systems biology
Authors: Browning Alexander P , Warne David J , Burrage Kevin , Baker Ruth E , Simpson Matthew J 
Published: August 2020

AbstractMathematical models are routinely calibrated to experimental data, with goals ranging from building predictive models to quantifying parameters that cannot be measured. Whether or not reliable parameter estimates are obtainable from the available data can easily be overlooked. Such issues ofparameter identifiabilityhave important ramifications for both the predictive power of a model, and the mechanistic insight that can be obtained. Identifiability analysis is well-established for deterministic, ordinary differential equation (ODE) models, but there are no commonly-adopted methods for analysing identifiability in stochastic models. We provide an accessible introduction to identifiability analysis and demonstrate how existing ideas for analysis of ODE models can be applied to stochastic differential equation (SDE) models through four practical case studies. To assessstructural identifiability, we study ODEs that describe the statistical moments of the stochastic process using open-source software tools. Using practically-motivated synthetic data and Markov-chain Monte Carlo (MCMC) methods, we assess parameter identifiability in the context of available data. Our analysis shows that SDE models can often extract more information about parameters than deterministic descriptions. All code used to perform the analysis is available on Github.
Facultative chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California
Authors: Goffredi Shana K , Motooka Cambrie , Fike David A. , Gusmão Luciana C , Tilic Ekin , Rouse Greg W , Rodríguez Estefanía 
Published: August 2020

AbstractBackgroundNumerous deep-sea invertebrates have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to most animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain one of the only phyla without a clear dependence on hydrothermal vents and reliance on chemosynthetic bacterial symbionts specifically.ResultsA new chemosynthetic symbiosis between the sea anemoneOstiactis pearseae(Daly & Gusmão, 2007) and intracellular bacteria was discovered at ~3700 m deep hydrothermal vents in the southern Pescadero Basin, Gulf of California. Unlike most sea anemones observed from chemically-reduced habitats, this species was observed in and amongst vigorously venting fluids, side-by-side with the chemosynthetic tubewormOasisiaaff.alvinae.Individuals ofO. pearseaedisplayed carbon, nitrogen, and sulfur tissue isotope values (average δ13C −29.1‰, δ15N 1.6‰, and δ34S −1.1‰) suggestive of a distinct nutritional strategy from conventional Actiniaria suspension feeding or prey capture. Molecular and microscopic evidence confirmed the presence of intracellular SUP05-related bacteria housed in the tentacle epidermis ofO. pearseaespecimens collected from 5 hydrothermally-active structures within two vent fields ~2 km apart. SUP05 bacteria dominated theO. pearseaebacterial community (64-96% of the total bacterial community based on 16S rRNA sequencing), but were not recovered from other nearby anemones, and were generally rare in the surrounding water (< 7% of the total community). Further, the specificOstiactis-associated SUP05 phylotypes were not detected in the environment, indicating a specific association. Two unusual candidate bacterial phyla (the OD1 and BD1-5 groups) also appeared to associate exclusively withO. pearseaeand may play a role in symbiont sulfur cycling.ConclusionOstiactis pearseaerepresents the first member of Cnidaria described to date to have a physical and nutritional alliance with chemosynthetic bacteria. The facultative nature of this symbiosis is consistent with the dynamic relationships formed by both the SUP05 bacterial group and Anthozoa. The advantages gained by appropriating metabolic and structural resources from each other presumably contribute to their striking abundance in the Pescadero Basin, at the deepest known hydrothermal vents in the Pacific Ocean.
Metabolomics dissection of depression heterogeneity and related cardiometabolic risk
Authors: Alshehri Tahani , Mook-Kanamori Dennis O , van Dijk Ko Willems , Dinga Richard , Penninx Brenda WJH , Rosendaal Frits R , Cessie Saskia le , Milaneschi Yuri 
Published: August 2020

AbstractBackgroundA recent hypothesis postulates the existence of an “immune-metabolic depression” (IMD) dimension characterized by metabolic dysregulations. Combining data on metabolomics and depressive symptoms, we aimed to identify depressions associated with an increased risk of adverse metabolic alterations.MethodClustering data were from 1094 individuals with current major depressive disorder and measures of 149 metabolites from a 1H-NMR platform and 30 depressive symptoms (IDS-SR30). Canonical correlation analyses (CCA) were used to identify main independent metabolite-symptom axes of variance. Then, for the replication, we examined the association of the identified dimensions with metabolites from the same platform and cardiometabolic endpoints in an independent population-based cohort (n=6572).ResultsCCA identified an overall depression dimension and a dimension resembling IMD, in which symptoms such as sleeping too much, increased appetite, and low energy level had higher relative loading. In the independent sample, the overall depression dimension was associated with lower levels of metabolites linked to cardiometabolic risk, such as HOMA-1B −0.09 (95% CI:-0.13--0.06), and visceral adipose tissue −0.15 cm2 (95% CI:-0.20--0.10). In contrast, the IMD dimension was associated with well-known adverse cardiometabolic metabolites such as higher visceral adipose tissue 0.11 cm2 (95% CI:0.06-0.16), HOMA-1B 0.08 (95% CI: 0.05-0.12), and lower HDL levels −0.04 mmol/L (95% CI:-0.07--0.01).ConclusionsCombining metabolomics and clinical symptoms we identified a replicable depression dimension associated with adverse metabolic alterations, in line with the IMD hypothesis. Patients with IMD may be at higher cardiometabolic risk and may benefit from specific treatment targeting underlying metabolic dysregulations.
An investigation of hydrogen embrittlement of 12Cr2Mo1R(H) steel by slow strain rate tests and first-principles calculation
Authors: Kang Qin , Fan Yicheng , Zhang Kun , Chen Xiaolang , San Hongyu , Chen Yiqing , Zhao Heming 
Published: August 2020

Purpose
With excellent mechanic properties and hydrogen embrittlement (HE) resistance, 12Cr2Mo1R(H) steel is suitable to make hot-wall hydrogenation reactors. However, longtime exposure to a harsh environment of high-pressure hydrogen at medium temperature in practical application would still induce severe hydrogen uptake and eventually damage the mechanical properties of the steel. The study aims to evaluate the HE resistance of the steel under different tensile strain rates after hydrogen charging and analyze the hydrogen effect from atomic level.

Design/methodology/approach
This research studied the HE properties of 12Cr2Mo1R(H) steel by slow strain rate tests. Meanwhile, the effect of hydrogen on the structures and the mechanical properties of the simplified models of the steel was also investigated by first-principle calculations.

Findings
Experimental results showed that after hydrogen pre-charging in this work, hydrogen had little effect on the microstructure of the steel. The elongations and reduction of cross-sectional area of the samples reduced a lot, by contrast, the yield and tensile strengths changed slightly. The 12Cr2Mo1R(H) steel was not very susceptible to HE with a maximum embrittlement index of about 20.00%. First principles calculation results showed that after H dissolution, lattice distortion occurred and interstitial H atoms would preferentially occupy the tetrahedral interstitial site in bcc-Fe crystal and increase the stability of the supercells. With the increase of H atoms added into the simplified model, the steel still possessed a good ductility and toughness at a low hydrogen concentration, while the material would become brittle as the concentration of hydrogen continued to increase.

Originality/value
These finds can provide valuable information for subsequent HE studies on this steel.
Phosphate-doped polyaniline/Al2O3 nanocomposite coating for protection of stainless steel
Authors: Hermas Abou-Elhagag A. , Wahdan Mostafa H. , Ahmed Eatemad M. 
Published: August 2020

Purpose
This work aims to prepare and characterize of protective anticorrosion phosphate-doped polyaniline (PANI) nanocomposite coatings for stainless steel (SS) in chloride solution.

Design/methodology/approach
PANI composite coatings were electrodeposited from aqueous sulfuric acid solution containing monomer and Al2O3 nanoparticles using cyclic voltammetry technique. Doping by phosphate was done by aging the coated steels for different periods (1–168 h) in phosphate solution. The polymer film composite was investigated by Fourier-transform infrared spectroscopy and scanning electron microscopy techniques. Potential-time, anodic polarization and electrochemical impedance spectroscopy were used to study the protection efficiency of the coatings.

Findings
The Al2O3 nanoparticles were incorporated into the deposited PANI layer but they decreased the deposition of polymer. The nanoparticles and the phosphate anions enhanced the protective PANI layer for passivation and protection of SS in the chloride solution.

Originality/value
The replacement of counter anions by phosphate ions improved significantly the PANI and its nanocomposite as protective coating of SS in chloride solution.
Worldwide role of women entrepreneurs in economic development
Authors: Sajjad Muhammad , Kaleem Nishat , Chani Muhammad Irfan , Ahmed Munir 
Published: August 2020

Purpose
The contribution of women entrepreneurs is still invisible and needs to be properly investigated. The purpose of this paper is to investigate this relationship by measuring women entrepreneurship and economic development at global level.

Design/methodology/approach
Secondary data has been retrieved from Female Entrepreneurship Index Report 2015, Human Development Report 2015 and KOF Index of Globalization 2015. Cross-sectional data is used from 69 countries of the world. Multiple regression is applied to estimate the data.

Findings
The results explained the significant impact of women entrepreneurship on the economies of the world. It was observed that women participation in entrepreneurial activities not only supports to their family income but also plays a significant role in economic development and social well-being of the society.

Research limitations/implications
There is no information about total output of women entrepreneurs in terms of new enterprises setups and established businesses of women except for year 2015. So, to measure the real contribution of women entrepreneurs around the globe is still a challenge.

Practical implications
It is reality that when women would be empowered as entrepreneurs then whole society gets benefits from it, as women entrepreneurs are beneficial for not only economic development but also social development of society.

Originality/value
This study uniquely addresses the contribution of women entrepreneurs in the world economy which is still an unseen but a powerful benefactor of development.
Improving clients’ satisfaction in construction projects: the case of Saudi Arabia
Authors: Alshihre Fawaz , Chinyio Ezekiel , Nzekwe-Excel Chinny , Daniel Emmanuel I. 
Published: August 2020

PurposeClients’ satisfaction is often associated with performance in the construction industry. Organisations that achieve very high ratings of clients’ satisfaction improve their positions in the marketplace. Many clients are often dissatisfied with their project outcomes. Hence, a research study was carried out to examine the ways project managers and/or contractors perceive the subject of clients’ satisfaction.Design/methodology/approachThe study applied qualitative research methods and followed the interpretivist paradigm and inductive research approach. A total of 30 interviews were conducted with construction project managers and evaluated by a thematic analysis.FindingsThe study identified five prominent factors which the project managers perceived to impact on clients’ satisfaction, which are as follows: effective financial management; use of skilled workers; use of advanced technology; customer relation and time management. Other contributors to clients’ satisfaction include effective team leadership, project monitoring, communication and adequate knowledge and skills.Research limitations/implicationsData collection was limited to Saudi Arabia, but the general methodology used and some of the findings may be applicable beyond this country.Practical implicationsThe findings provide a more informed basis of attaining greater clients’ satisfaction by contractors, especially within and possibly beyond Saudi Arabia. Also, contractors can directly enquire from clients about their satisfaction following project completion.Originality/valueA project manager's perspective and Saudi Arabian orientation of clients’ satisfaction are presented. Also, insight into the multifaceted nature of the factors influencing clients’ satisfaction is provided.
Access to justice as a human right, organizational entitlement and precursor to diversity and inclusion
Authors: Roberson Quinetta 
Published: August 2020

PurposeIn the wake of the death of George Floyd in the United States, many corporate leaders have released statements condemning racism and police brutality and committed their organizations to focus on diversity and inclusion. While such statements, intentions, and goals are laudable, they evade the phenomenon at the crux of the current social movement: access to justice.Design/methodology/approachThis essay draws upon theory and research across a variety of disciplines to examine the accessibility of justice for African Americans in society and in work organizations.FindingsAs corporate leaders have made statements decrying racism and police brutality and offered their support to civil rights groups and organizations fighting for racial justice, there is a need for that same level of scrutiny and support within their own organizations. As a precursor to diversity and inclusion initiatives, corporate leaders need to take actions to ensure the fairness of outcomes, policies and practices, and treatment by others for African Americans within their organizations.Practical implicationsStrategies for reviewing and revising organizational policies and practices to preserve fairness in the work experiences of African Americans and for creating and maintaining cultures of fairness are offered.Originality/valueThe author integrates historical documents, research, opinion, and literary devices to understand the meaning and practice of justice in society and organizations.