bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative reverse transcription PCR assay to detect pyrethroid resistance in Culex mosquitoes
Authors: Hager Kelli M. , Gaona Erick , Kistler Amy , Ratnasiri Kalani , Retallack Hanna , Barretto Miguel , Wheeler Sarah S. , Hoover Christopher M. , Haas-Stapleton Eric J.
Published: May 2021

Pyrethroid insecticides are widely used to control mosquitoes that transmit diseases such as West Nile virus (WNV) to humans. A single nucleotide polymorphism (SNP) in the knockdown resistance locus (kdr) of the voltage gated sodium channel (Vgsc) gene of Culex mosquitoes confers knockdown resistance to pyrethroids. PCR-based assays that detect these SNPs in Culex species are currently available for Culex pipiens Linnaeus and Culex quinquefasciatus Say. RNAseq was employed to sequence the coding region of Vgsc for Culex tarsalis Coquillett and Culex erythrothorax Dyar, two WNV vectors. We utilized the cDNA sequence to develop a quantitative reverse transcriptase PCR assay that detects the L1014F mutation in the kdr of Vgsc. Because this locus is conserved, the assay successfully detected the SNPs in multiple Culex spp. vectors of WNV in the United States. The resulting Culex RTkdr assay was validated using quantitative PCR, CDC bottle bioassays, and sequencing of PCR products. Using sequencing, we determined the accuracy of the Culex RTkdr assay was 99%. Pyrethroid resistance was more common among Cx. pipiens than other Culex spp. and co-occured with agriculture. We anticipate that public health and vector control agencies may utilize the Culex RTkdr assay to map the distribution of pyrethroid resistance in Culex species to more efficiently control mosquitoes and the diseases they transmit.
Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors
Authors: Pöll Gisela , Pilsl Michael , Griesenbeck Joachim , Tschochner Herbert , Milkereit Philipp
Published: May 2021

In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.
Inhibiting BCKDK in triple negative breast cancer suppress protein translation, impair mitochondrial function, and potentiate doxorubicin cytotoxicity
Authors: Biswas Dipsikha , Slade Logan , Duffley Luke , Mueller Neil , Dao Khoi Thien , Mercer Angella , Hiani Yassine El , Kienesberger Petra , Pulinilkunnil Thomas
Published: May 2021

Triple-negative breast cancers (TNBCs) are characterized by poor survival, prognosis and gradual resistance to cytotoxic chemotherapeutics, like doxorubicin (DOX), which is limited by its cardiotoxic and chemoresistant effects that manifest over time. TNBC growth and survival are fuelled by reprogramming branched-chain amino acids (BCAAs) metabolism, which rewires oncogenic gene expression and cell signaling pathways. A regulatory kinase of the rate-limiting enzyme of the BCAA catabolic pathway, branched-chain ketoacid dehydrogenase kinase (BCKDK), have recently been implicated in driving tumor cell proliferation and conferring drug resistance by activating RAS/RAF/MEK/ERK signaling. However it remains unexplored if BCKDK remodels TNBC proliferation, survival and susceptibility to DOX-induced genotoxic stress. TNBC cell lines exhibited reduced BCKDK expression in response to DOX. Genetic and pharmacological inhibition of BCKDK in TNBC cell lines displayed reduced intracellular and secreted BCKAs. Moreover, BCKDK inhibition with concurrent DOX treatment exacerbated apoptosis, caspase activity and loss of TNBC proliferation. Transcriptome analysis of BCKDK silenced cells confirmed a marked upregulation of the apoptotic signaling pathway with increased protein ubiquitylation and compromised mitochondrial metabolism. BCKDK silencing in TNBC downregulated mitochondrial metabolism genes, reduced electron complex protein expression, oxygen consumption and ATP production. Silencing BCKDK in TNBC upregulated sestrin 2 and concurrently decreased protein synthesis and mTORC1 signaling. Inhibiting BCKDK in TNBC remodel BCAA flux, reduces protein translation triggering cell death, ATP insufficiency and susceptibility to genotoxic stress.

Graphical abstract
An immature subset of neuroblastoma cells synthesizes retinoic acid and depends on this metabolite
Authors: van Groningen Tim , Niklasson Camilla U. , Chan Alvin , Akogul Nurdan , Westerhout Ellen M. , von Stedingk Kristoffer , Hamdi Mohamed , Valentijn Linda J. , Mohlin Sofie , Stroeken Peter , Hasselt Nancy E. , Haneveld Franciska , Lakeman Arjan , Zwijnenburg Danny A. , van Sluis Peter , Bexell Daniel , Adameyko Igor , Jansky Selina , Westermann Frank , Wigerup Caroline , Påhlman Sven , Koster Jan , Versteeg Rogier , van Nes Johan
Published: May 2021

Neuroblastoma is a pediatric tumor of the adrenergic sympathetic lineage. Most high risk neuroblastoma go in complete clinical remission by chemotherapy, which is subsequently complemented by retinoic acid (RA) maintenance therapy. However, by unresolved mechanisms most tumors ultimately relapse as therapy-resistant disease. Neuroblastoma cell lines were recently found to include, besides lineage committed adrenergic (ADRN) tumor cells, also immature mesenchymal (MES) tumor cells. Here, we report that MES-type cells synthesize RA and require this metabolite for proliferation and motility. MES cells are even resistant to RAin vitro. MES cells appear to resemble Schwann Cell Precursors (SCP), which are motile precursors of the adrenergic lineage. MES and SCP cells express shared RA-synthesis and RA-target genes. Endogenous RA synthesis and RA resistance thus stem from normal programs of lineage precursors that are maintained in an immature tumor cell fraction. These cells are fully malignant in orthotopic patient-derived xenograft models and may mediate development of drug-resistant relapses.
The draft genome sequence ofEucalyptus polybracteabased on hybrid assembly with short- and long-reads reads
Authors: Li Teng , Kainer David , Foley William J. , Rodrigo Allen , Külheim Carsten
Published: May 2021

Eucalyptus polybracteais a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of theE. polybracteagenome utilizing both short- and long-read technology. We generated 44 Gb of Illumina HiSeq short reads and 8 Gb of Nanopore long reads, representing approximately 83× and 15× genome coverage, respectively. The hybrid-assembled genome, after polishing, contained 24,864 scaffolds with an accumulated length of 523 Mb (N50 = 40.3 kb; BUSCO-calculated genome completeness of 94.3%). The genome contained 35,385 predicted protein-coding genes detected by combining homology-based and de novo approaches. We have provided the first assembled genome based on hybrid sequences from the highly diverseEucalyptussubgenusSymphyomyrtus, and revealed the value of including long-reads from Nanopore technology for enhancing the contiguity of the assembled genome, as well as for improving its completeness. We anticipate that theE. polybracteagenome will be an invaluable resource supporting a range of studies in genetics, population genomics and evolution of related species inEucalyptus.
Mechanosensitive calcium signaling in response to cell shape changes promotes epithelial tight junction remodeling by activating RhoA
Authors: Varadarajan Saranyaraajan , Stephenson Rachel E. , Misterovich Eileen R. , Wu Jessica L. , Erofeev Ivan S. , Goryachev Andrew B. , Miller Ann L.
Published: May 2021

Epithelia maintain an effective barrier by actively remodeling cell-cell junctions in response to mechanical stimuli. Cells often respond to mechanical stress through activation of RhoA and dynamic remodeling of actomyosin. Previously, we found that local leaks in the epithelial tight junction barrier are rapidly repaired by localized, transient activation of RhoA, a process we termed “Rho flares”, but how Rho flares are initiated remains unknown. Here, we discovered that intracellular calcium flashes occur in Xenopus laevis embryonic epithelial cells undergoing rapid remodeling of tight junctions via activation of Rho flares. Calcium flashes originate at the site of leaks and propagate into the cell. Depletion of intracellular calcium or inhibition of mechanosensitive calcium channels (MSC) reduced the amplitude of calcium flashes and diminished the activation of Rho flares. Furthermore, MSC-dependent calcium influx was necessary to maintain global barrier function by regulating repair of local tight junction proteins through efficient contraction of junctions. Collectively, we propose that MSC-dependent calcium flashes are an important mechanism allowing epithelial cells to sense and respond to local leaks induced by mechanical stimuli.
Rad52 oligomeric N-terminal domain stabilizes Rad51 nucleoprotein filaments and contributes to their protection against Srs2
Authors: Ma Emilie , Maloisel Laurent , Falher Léa Le , Guérois Raphaël , Coïc Eric
Published: May 2021

Homologous recombination (HR) depends on the formation of a nucleoprotein filament of the recombinase Rad51 to scan the genome and invade the homologous sequence used as template for DNA repair synthesis. Therefore, HR is highly accurate and crucial for genome stability. Rad51 filament formation is controlled by positive and negative factors. In Saccharomyces cerevisiae, the mediator protein Rad52 catalyzes Rad51 filament formation and stabilizes them, mostly by counteracting the disruptive activity of the translocase Srs2. Srs2 activity is essential to avoid the formation of toxic Rad51 filaments, as revealed by Srs2-deficient cells. We previously reported that Rad52 SUMOylation or mutations disrupting the Rad52-Rad51 interaction suppress Rad51 filament toxicity because they disengage Rad52 from Rad51 filaments and reduce their stability. Here, we found that mutations in Rad52 N-terminal domain also suppress the DNA damage sensitivity of Srs2-deficient cells. Structural studies showed that these mutations affect the Rad52 oligomeric ring structure. Overall, in vivo and in vitro analyzes of these mutants indicate that Rad52 ring structure is important for protecting Rad51 filaments from Srs2, but can increase Rad51 filament stability and toxicity in Srs2-deficient cells. This stabilization function is distinct from Rad52 mediator and annealing activities.
Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat
Authors: Chandran Vijayendran , Bermúdez Mei-Ling , Koka Mert , Chandran Brindha , Pawale Dhanashri , Vishnubhotla Ramana , Alankar Suresh , Maturi Raj , Subramaniam Balachundhar , Sadhasivam Senthilkumar
Published: May 2021

The positive impact of meditation on human wellbeing is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole blood gene expression profiling combined with multi-level bioinformatic analyses to characterize the co-expression, transcriptional, and protein-protein interaction networks to identify meditation-specific core network after an advanced 8-day Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were downregulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon (IFN) signaling were upregulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and potential implications to voluntarily and non-pharmacologically improve the immune response before immunotherapy for many conditions, including multiple sclerosis and COVID-19 vaccination.
Implications Derived from S-Protein Variants of SARS-CoV-2 from Six Continents
Authors: Hassan Sk. Sarif , Lundstrom Kenneth , Choudhury Pabitra Pal , Palu Giorgio , Uhal Bruce D. , Kandimalla Ramesh , Seyran Murat , Lal Amos , Sherchan Samendra P. , Azad Gajendra Kumar , Aljabali Alaa A. A. , Brufsky Adam M. , Serrano-Aroca Ángel , Adadi Parise , Abd El-Aziz Tarek Mohamed , Redwan Elrashdy M. , Takayama Kazuo , Barh Debmalya , Rezaei Nima , Tambuwala Murtaza , Uversky Vladimir N.
Published: May 2021

Spike (S) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are critical determinants of the infectivity and antigenicity of the virus. Several mutations in the spike protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, spike proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa (29.065%) had the highest percentage of unique S proteins. Notably, only North America had 87% (14046) of the total (16143) specific S proteins available in the NCBI database(across all continents). Based on the amino acid frequency distributions in the S protein variants from all the continents, the phylogenetic relationship implies that unique S proteins from North America were significantly different from those of the other five continents. Overtime, the unique variants originating from North America are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. Hence it is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.
Phenotypic and Kinetic Changes of Myeloid Lineage Cells in Innate Response to Chikungunya Infection in Cynomolgus Macaques
Authors: Beddingfield Brandon J. , Sugimoto Chie , Kuroda Marcelo J. , Wang Eryu , Weaver Scott C. , Russell-Lodrigue Kasi E. , Killeen Stephanie Z. , Roy Chad J.
Published: May 2021

Chikungunya is an emerging threat, spreading across multiple continents. The immune response to infection can lead to protection and convalescence, or result in long term sequelae such as arthritis. Early innate immune events during acute infection have been characterized for some cell types, but more must be elucidated with respect to cellular responses of monocytes and other myeloid lineage cells. In addition to their roles in protection and inflammation resolution, monocytes and macrophages are sites for viral replication and reservoirs for the virus. They are also found in joints post-infection, possibly playing a role in long term CHIKV-induced pathology. We examined kinetic and phenotypic changes in myeloid lineage cells, including monocytes, in cynomolgus macaques early after infection with CHIKV. We found increased turnover of monocytes and mDCs early during infection, with an accompanying decreases in both cell types, as well as a simultaneous increase in pDC number. An increase in CD16 and CD14 was seen along with a decrease in monocyte HLA-DR expression within 3 days of infection, potentially indicating monocyte deactivation. A transient decrease in T cells, B cells and NK cells correlates with lymphocytopenia observed during human infections with CHIKV. CD4+ T cell turnover decreased in blood, indicating relocation of cells to effector sites. This data indicates CHIKV influences turnover rates and kinetics of myeloid lineage cells early during infection, and may prove useful in development of therapeutics and evaluation of infection-induced pathogenesis.
3’HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression
Authors: Himadewi Pamela , David Wang Xue Qing , Feng Fan , Gore Haley , Liu Yushuai , Yu Lei , Liu Jie , Kurita Ryo , Nakamura Yukio , Pfeifer Gerd , Zhang Xiaotian
Published: May 2021

Mutations in the adult β-globin gene can lead to a variety of hemoglobinopathies, including sickle cell disease and β-thalassemia. An increase in fetal hemoglobin expression throughout adulthood, a condition named Hereditary Persistence of Fetal Hemoglobin (HPFH), has been found to ameliorate hemoglobinopathies. Deletional HPFH occurs through the excision of a significant portion of the 3’ end of the β-globin locus, including a CTCF binding site termed 3’HS1. Here, we show that the deletion of this CTCF site alone induces fetal hemoglobin expression in both adult CD34+ hematopoietic stem and progenitor cells and HUDEP-2 erythroid progenitor cells. This induction is driven by the ectopic access of a previously postulated distal enhancer located in the OR52A1 gene downstream of the locus, which can also be insulated by the inversion of the 3’HS1 CTCF site. This suggests that genetic editing of this binding site can have therapeutic implications to treat hemoglobinopathies.
Functional and structural modifications of influenza antibodies during pregnancy
Authors: Jennewein Madeleine F. , Kosikova Martina , Noelette Francesca J. , Radvak Peter , Boudreau Carolyn M. , Campbell James D. , Chen Wilbur H. , Xie Hang , Alter Galit , Pasetti Marcela F.
Published: May 2021

Pregnancy represents a unique tolerogenic immune state which may alter susceptibility to infection and vaccine-response. Here we characterized humoral immunity to seasonal influenza vaccine strains in pregnant and non-pregnant women. Pregnant women had reduced hemagglutinin subtype-1 (H1)-IgG, IgG1, and IgG2, hemagglutination inhibition and group 1 and 2 stem IgG. However, H1-specific avidity and FcγR1 binding increased. Influenza-antibodies in pregnancy had distinct Fc and Fab glycans characterized by di-galactosylation and di-sialylation. In contrast, agalactosylation and bisection were prominent outside of pregnancy. H1-specific Fc-functionality was moderately reduced in pregnancy, although likely compensated by stronger binding to cognate antigen and FcR. Multivariate analysis revealed distinct populations characterized by FcγR1 binding, H1-IgG levels, and glycosylation. Pooled sera from pregnant women exhibited longer retention in vivo. Our results demonstrate structural and functional modulation of humoral immunity during pregnancy in an antigen-specific manner towards reduced inflammation, increased retention in circulation, and efficient placental transport.
Hypertrophic Chondrocytes Serve as a Reservoir for Marrow Associated Skeletal Stem and Progenitor Cells, Osteoblasts, and Adipocytes During Skeletal Development
Authors: Long Jason T. , Leinroth Abigail , Liao Yihan , Ren Yinshi , Mirando Anthony J. , Nguyen Tuyet , Guo Wendi , Sharma Deepika , Rouse Douglas , Wu Colleen , Cheah Kathryn Song Eng , Karner Courtney M. , Hilton Matthew J.
Published: May 2021

Hypertrophic chondrocytes give rise to osteoblasts during skeletal development; however, the process by which these non-mitotic cells make this transition is not well understood. Prior studies have also suggested that skeletal stem and progenitor cells (SSPCs) localize to the surrounding periosteum and serve as a major source of marrow associated SSPCs, osteoblasts, osteocytes, and adipocytes during skeletal development. To further understand the cell transition process by which hypertrophic chondrocytes contribute to osteoblasts or other marrow associated cells, we utilized inducible and constitutive hypertrophic chondrocyte lineage tracing and reporter mouse models (Col10a1CreERT2; R26-tdTomatof/+andCol10a1Cre; R26-tdTomatof/+) in combination with aPDGFRa-H2B-GFPtransgenic line, single cell RNA-sequencing, bulk RNA-sequencing, immunofluorescence staining, and cell transplantation assays. Our data demonstrate that hypertrophic chondrocytes undergo a process of dedifferentiation to generate marrow associated SSPCs that serve as a primary source of osteoblasts during skeletal development. These hypertrophic chondrocyte derived SSPCs commit to a CXCL12-abundant reticular (CAR) cell phenotype during skeletal development and demonstrate unique abilities to recruit vasculature and promote bone marrow establishment, while also contributing to the adipogenic lineage.
Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection
Authors: Moses Melanie E. , Hofmeyr Steven , Cannon Judy L. , Andrews Akil , Gridley Rebekah , Hinga Monica , Leyba Kirtus , Pribisova Abigail , Surjadidjaja Vanessa , Tasnim Humayra , Forrest Stephanie
Published: May 2021

A key question in SARS-CoV-2 infection is why viral loads and patient outcomes vary dramatically across individuals. Because spatial-temporal dynamics of viral spread and immune response are challenging to study in vivo, we developed Spatial Immune Model of Coronavirus (SIMCoV), a scalable computational model that simulates hundreds of millions of lung cells, including respiratory epithelial cells and T cells. SIMCoV replicates viral growth dynamics observed in patients and shows how spatially dispersed infections can lead to increased viral loads. The model also shows how the timing and strength of the T cell response can affect viral persistence, oscillations, and control. By incorporating spatial interactions, SIMCoV provides a parsimonious explanation for the dramatically different viral load trajectories among patients by varying only the number of initial sites of infection, and the magnitude and timing of the T cell immune response. When the branching airway structure of the lung is explicitly represented, we find that virus spreads faster than in a 2D layer of epithelial cells, but much more slowly than in an undifferentiated 3D grid or in a well-mixed ODE model. These results illustrate how realistic spatially explicit computational models can improve understanding of within-host dynamics of SARS-CoV-2 infection.

A key question in SARS-CoV-2 infection is why viral loads and patient outcomes are so different across individuals. Because it’s difficult to see how the virus spreads in the lungs of infected people, we developed Spatial Immune Model of Coronavirus (SIMCoV), a computational model that simulates hundreds of millions of cells, including lung cells and immune cells. SIMCoV simulates how virus grows and then declines, and the simulations match data observed in patients. SIMCoV shows that when there are more initial infection sites, the virus grows to a higher peak. The model also shows how the timing of the immune response, particularly the T cell response, can affect how long the virus persists and whether it is ultimately cleared from the lungs. SIMCoV shows that the different viral loads in different patients can be explained by how many different places the virus is initially seeded inside their lungs. We explicitly add the branching airway structure of the lung into the model and show that virus spreads slightly faster than it would in a two-dimensional layer of lung cells, but much slower than traditional mathematical models based on differential equations. These results illustrate how realistic spatial computational models can improve understanding of how SARS-CoV-2 infection spreads in the lung.
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution
Authors: Amicone Massimo , Borges Vítor , Alves Maria João , Isidro Joana , Zé-Zé Líbia , Duarte Sílvia , Vieira Luís , Guiomar Raquel , Gomes João Paulo , Gordo Isabel
Published: May 2021

Background and objectives

To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV-2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures.

Methodology

We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains.

Results

From the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.25×10-6 nt-1 per infection cycle for both lineages of SARS-CoV-2. We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at rate five-fold higher than the genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein.

Conclusions and implications

These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome towards adaptation to new environments.

Lay summary

Mutation is the ultimate source of variation. We estimated how the SARS-COV-2 virus—cause of the COVID-19 pandemic—mutates. Upon infecting cells, its genome can change at a rate of 0.04 per replication. We also find that this rate can change and that its spike protein can adapt, even within few replications.
MAP2XANES: a Jupyter interactive notebook for elemental mapping and XANES speciation
Authors: Marini Carlo , Roqué-Rosell Josep , Campeny Marc , Toutounchiavval Shiva , Simonelli Laura
Published: May 2021

MAP2XANESis an intuitive Jupyter notebook that automatizes the analysis of synchrotron X-ray fluorescence imaging and X-ray absorption spectroscopy for the characterization of complex and heterogeneous samples. The notebook uses basic modules and functions from Numpy, Scipy, Pandas, iPywidgets and Matplotlib libraries for a powerful data reduction process that, in just a few clicks, guides the user through the visualization of elemental maps, space-resolved absorption spectra and their automatized analysis. In particular, by means of linear combination fit of the XANES spectra, the notebook determines the chemical species distribution in the sample under investigation. The direct output of the analysis process is the correlation between the different elemental distributions and the spatial localization of the chemical species detected. An application to mineralogy is thus presented, analyzing the Mn2+, Mn3+and Mn4+distribution in a mineral sample of hausmannite (Mn2+Mn23+O4), courtesy of the Museum of Natural Science of Barcelona.
Modelling covalent linkages in CCP4
Authors: Nicholls Robert A. , Joosten Robbie P. , Long Fei , Wojdyr Marcin , Lebedev Andrey , Krissinel Eugene , Catapano Lucrezia , Fischer Marcus , Emsley Paul , Murshudov Garib N.
Published: May 2021

In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.
Principal component analysis is limited to low-resolution analysis in cryoEM
Authors: Sorzano Carlos Oscar S. , Carazo Jose Maria
Published: May 2021

Principal component analysis (PCA) has been widely proposed to analyze flexibility and heterogeneity in cryo-electron microscopy (cryoEM). In this paper, it is argued that (i) PCA is an excellent technique to describe continuous flexibility at low resolution (but not so much at high resolution) and (ii) PCA components should be analyzed in a concerted manner (and not independently).
The impact of oncogenic mutations of the viral Src kinase on the structure and stability of the SH3 domain
Authors: Salinas-Garcia M. Carmen , Plaza-Garrido Marina , Camara-Artigas Ana
Published: May 2021

Src kinase belongs to the family of Src-related nonreceptor tyrosine kinases. Because of its physiological role in cell growth and proliferation, its activity is strictly controlled by several mechanisms. Nevertheless, in viral Src kinase (v-Src) some of these mechanisms fail, and its uncontrolled activity is responsible for the occurrence of cancer. Here, the crystal structures of three SH3-domain mutants of v-Src were determined to unveil the effects of these oncogenic mutations in this regulatory domain. Mutations in the n-Src and distal loops have a low impact on the overall structure of the domain and its capacity to form intertwined dimers. However, mutations in the RT loop compromise the stability of the domain and make the protein very prone to aggregation. Additionally, these mutations prevent the formation of intertwined dimers. The results show a synergistic effect between mutations in the RT loop and those in the n-Src and distal loops. Analysis of the structures of the v-Src SH3-domain mutants and the closed inactive conformation of cellular Src kinase (c-Src) point to a loss of the interactions that are required to establish the compact inactive form of the kinase. Nevertheless, an analysis of structures of the c-Src SH3 domain complexed with class I and II peptides points to minor changes in the interactions between the v-Src SH3 domain and these peptides. In this way, the structures reported here indicate that mutations in the RT loop might impair the kinase regulation mechanism without affecting the recognition of short proline-rich motifs in the target proteins of the kinase, thus explaining the oncogenic behaviour of the protein.
Intersectionality, vulnerability and resilience: why it is important to review the diversifications within groups at risk to achieve a resilient community
Authors: Chisty Musabber Ali , Dola Syeda Erena Alam , Khan Nesar Ahmed , Rahman Md Mostafizur
Published: May 2021

Purpose

The objective of this study was to assess the relationship among intersectionality, vulnerability and resilience with evidence. The conceptual framework developed by the study believed that intersectionality and vulnerabilities intersect and reduce the level of disaster resilience.

Design/methodology/approach

A qualitative approach was followed with relevant support from both primary and secondary data to conduct the study. The study focused on flood as a specific natural hazard to assess the relationship among the indicators of the objective. Focus group discussions (FGDs) were performed in two different flood-prone areas of Bangladesh. FGDs included young men, young women, men and women with disabilities and older people. Also, secondary literature helped to support ground-level data.

Findings

In the face of a flood, results showed that people with intersectional characteristics become more vulnerable within the at-risk groups. There are differences in people's level of vulnerabilities among the people of vulnerable groups. The results support the discussion that intersectionality exaggerates vulnerabilities, thus reducing the level of disaster resilience. The study summarizes that intersectionality needs to be addressed while supporting groups at risk to achieve a resilient community.

Research limitations/implications

The study is only based on qualitative and secondary data. For more generalized findings and implications, further research is needed. Also, this study will work as a guideline for future studies.

Originality/value

The study is one of the few works related to intersectionality. This study will open a new window to understand the importance of focusing on intersectional conditions while developing plans for disaster risk reduction (DRR).
Developing intrapreneurial self-efficacy through internships? Investigating agency and structure factors
Authors: Deprez Jana , Peeters Ellen R. , Gorgievski Marjan J.
Published: May 2021

Purpose

This paper seeks to identify how intrapreneurial self-efficacy (ISE) grows in a group of graduate students during their internship. We investigate which agency and structure factors shape their experience and stabilize or help grow their ISE and how this evolves in the course of their internship.

Design/methodology/approach

We conducted group interviews with 49 last year master students of a large Belgian university during their seven-month internship. We focused on those interns with low starter ISE to better understand which factors aid or hinder ISE development.

Findings

Our results show that students who did not experience ISE growth were less aware of their own agency factors, lacked supportive colleagues and experienced a misfit with their supervisors. Students who did grow their ISE did so mostly because of an initial experimentation phase, which was structured by their supervisor. This created a positive spiral where they started feeling increasingly better and able to act intrapreneurially.

Originality/value

With this study, we contribute to the extant literature in two main ways. First, we use a graduate employability lens to study the genesis of ISE. As such, we are amongst the first to investigate how education can nurture intrapreneurship and which agency and structure factors are particularly important for this. Second, we take a qualitative process approach, rather than a static and quantitative focus of most entrepreneurial education studies. As such, we gain better knowledge to the drivers of ISE at students first steps and during their internship.
The differentiated impacts of external and internal financing on export: the firm-level evidence
Authors: Meng Xiangyuan , Li Xue , Xiao Wenyan , Li Jie
Published: May 2021

Purpose

The authors provide firm-level evidence that external financing affects international trade in a way different from internal financing.

Design/methodology/approach

The authors separate new entrants from incumbent exporters and investigate the roles of external and internal financing in export market participation and export quantity.

Findings

The authors find that external financing is of particular importance, as well as internal financing, in helping a firm become a new exporter. By contrast, external financing, unlike internal financing, is not significantly important for an incumbent exporter to stay in the international market. Regarding export quantity, a firm's internal financing is positively associated with more export quantity, whereas external financing is not.

Originality/value

The authors’ findings are consistent with the existence of significant fixed cost for entering the export market and external financing is particularly needed to cover such cost. Meanwhile, the financial need for maintaining the export status is much less and can be satisfied via internal financing.
Last-mile logistics in the sharing economy: sustainability paradoxes
Authors: Moncef Btissam , Monnet Dupuy Marlène
Published: May 2021

Purpose

The purpose of this paper is to explore sustainability paradoxes in sharing economy initiatives by focusing on logistics management in last-mile logistics.

Design/methodology/approach

In this exploratory study, a total of 10 case studies were conducted in three categories of companies: anti-waste platforms, food delivery platforms and bicycle delivery companies. Twenty-seven face-to-face interviews with founders and/or managers and contractors (couriers, logistics service providers or volunteers) were the primary source of data collection. The heterogeneity of the sample enabled the authors to build an understanding of sustainability paradoxes in the logistics of sharing economy initiatives.

Findings

The findings indicate how logistics management impacts the sustainability of sharing economy initiatives in last-mile delivery. The authors identify seven paradoxical tensions (five of them social) generated by the contradictions between the organizations' promised environmental and social values and the impacts of their operations.

Research limitations/implications

This exploratory research is based on a qualitative study of 10 cases and 27 interviews from heterogeneous samples; further empirical research is needed to ensure generalization.

Practical implications

The paper increases the understanding of environmental and social paradoxical tensions and awareness of logistics challenges.

Social implications

The paper helps identify ways to reconcile promised values and impacts generated by sharing economy initiatives while managing last-mile delivery.

Originality/value

The results enrich the literature about the paradoxes in sharing economy initiatives by providing illustrations in last-mile logistics and exposing the underlying challenges for sharing economy logistics actors.
A novel framework for delivering static search capabilities to large textual corpora directly on the Web domain: an implementation for Migne’s Patrologia Graeca
Authors: Varthis Evagelos , Poulos Marios , Giarenis Ilias , Papavlasopoulos Sozon
Published: May 2021

Purpose

This study aims to provide a system capable of static searching on a large number of unstructured texts directly on the Web domain while keeping costs to a minimum. The proposed framework is applied to the unstructured texts of Migne’s Patrologia Graeca (PG) collection, setting PG as an implementation example of the method.

Design/methodology/approach

The unstructured texts of PG have automatically transformed to a read-only not only Structured Query Language (NoSQL) database with a structure identical to that of a representational state transfer access point interface. The transformation makes it possible to execute queries and retrieve ranked results based on a specialized application of the extended Boolean model.

Findings

Using a specifically built Web-browser-based search tool, the user can quickly locate ranked relevant fragments of texts with the ability to navigate back and forth. The user can search using the initial part of words and by ignoring the diacritics of the Greek language. The performance of the search system is comparatively examined when different versions of hypertext transfer protocol (Http) are used for various network latencies and different modes of network connections. Queries using Http-2 have by far the best performance, compared to any of Http-1.1 modes.

Originality/value

The system is not limited to the case study of PG and has a generic application in the field of humanities. The expandability of the system in terms of semantic enrichment is feasible by taking into account synonyms and topics if they are available. The system’s main advantage is that it is totally static which implies important features such as simplicity, efficiency, fast response, portability, security and scalability.
“I know it when I see it”: employing reflective practice for assessment and feedback of reflective writing in a makerspace classroom
Authors: Chen Ofer , Bergner Yoav
Published: May 2021

Purpose

In reflective writing, students are encouraged to examine their own setbacks and progress. With a shortage of guidance in how to provide feedback to students on this type of writing, teachers are often left to figure it out on the job. The central hypothesis in this paper is that the lens of reflective practice can help focus teacher efforts and ultimately improve both feedback and instruction. The purpose of this paper is not to produce a universal prescription for assessing reflective writing but rather a protocol for teacher reflective practice that can apply to challenging grading and feedback-giving situations.

Design/methodology/approach

Student assessment is a chance for teachers to learn about their students’ abilities and challenges and to provide feedback for improvement. Assessment and grading sessions can also become opportunities for teachers to examine their own instructional and assessment practices. This self-examination process, a cornerstone of reflective practice (Schön, 1984), is challenging, but it may be especially valuable when guidelines for feedback and assessment are hard to come by. Such may be said to be the case in student-centered learning environments such as school Fablabs and makerspaces, where stated goals commonly include cultivating learner self-regulation and resilience. These hard-to-measure constructs are typically assessed through analysis of student reflective journals. This in-depth case study uses mixed-methods to examine how a semester-long intervention affected the grading, feedback and instructional practices of a teacher in a hands-on design classroom. The intervention involved 10 grade-aloud sessions using a computer-based rubric tool (Gradescope) and a culminating card-sorting task. The lens of reflective practice was applied to understanding the teacher’s development of their own reflective capabilities.

Findings

During the intervention, the participating teacher grappled with grading and feedback-giving dilemmas which led to clarifications of assessment objectives; changes to instruction; and improved feedback-giving practices, many of which persisted after the intervention. The teacher perceived the intervention as adding both rigor and productive “soul-searching” to their professional practice. Lasting changes in feedback behaviors included a comprehensive rubric and an increase in the frequency, specificity and depth of feedback given to student written work.

Originality/value

Significant prior efforts have been directed separately at the use of reflective practice for teachers, in general, and on the feedback and grading of student process journals. This work combines these lines of inquiry in the reflective classroom assessment protocol, a novel on-the-job professional development opportunity that fosters reflective practice in times of assessment to improve instructional and feedback practices.
Impact of customer focus on technology leadership via technology development capability – a moderated mediation model
Authors: Husain Zafar , Dayan Mumin , Sushil Sushil , Di Benedetto C. Anthony
Published: May 2021

Purpose

This study aims to develop and empirically examine a model that investigates the mediating role of technology development capability (TDC) on the relationship between customer focus (CF) and technology leadership (TL).

Design/methodology/approach

The analysis and interpretation of a partial least square model include the following two stages: the first stage focuses on assessing the reliability and validity of the measurement model, while the second pertains to evaluating the structural model.

Findings

The general understanding prevailing in practice and literature is that management sponsorship (MS) has a positive impact on the relationship between CF and TDC. It is also generally understood that MS has a positive impact on TL initiatives. However, the findings of this study contradict these assumptions. Specifically, the study indicates that MS has a negative moderating effect on CF and technology development capabilities, and has no impact on CF and TL relationships.

Originality/value

CF, TDC and MS, and their interplay and impact in enhancing firms’ TL position, have not been explored thus far in an integrated manner in the context of the automobile industry in developing countries. The research relating to CF, technology development capabilities, technology innovation capabilities, MS and TL reported in the literature has drawn inferences from case studies, anecdotal evidence and experiences of industry leaders, experts and consultants. This study attempts to fill the gaps mentioned above by presenting and testing a new moderated mediation model that shows the relationship between CF, TDC, MS and TL.
How accurate and useful are published UK prevalence rates of intimate partner violence (IPV)? Rapid review and methodological commentary
Authors: Ali Parveen , Allmark Peter , Booth Andrew , Seedat Farah , Woods Helen B , McGarry Julie
Published: May 2021

Purpose

This paper aims to estimate the prevalence of intimate partner violence (IPV) in the UK general population and in the low-risk clinical population and to identify the methodological challenges presented by this task.

Design/methodology/approach

A rapid review of the evidence was conducted. Data were extracted with the help of pre-designed tools and were synthesised to answer the two study aims. The data extracted was both qualitative and quantitative.

Findings

In the general population, crime survey data gave a range of past-year IPV prevalence from 1.8% to 4.5%. This was higher in women than men (2.5%–6.3% vs 0.9%–2.7%). In both the general and low-risk clinical population, there was little data on pregnant women or gay men and lesbians. No significant relationships between IPV and ethnicity were found. Different surveys used different definitions of IPV and domestic violence, making it difficult to give an accurate estimate. There were also problems with data accuracy.

Originality/value

This research is original and contributes to the knowledge about IPV screening and if prevalence studies help.