bluuebunny/crossref_metadata_2025 huggingface dataset:
Infiltration of Tumor Spheroids by Activated Immune Cells
Authors: Mukherjee Mrinmoy , Chepizhko Oleksandr , Lionetti Maria Chiara , Zapperi Stefano , La Porta Caterina A. M. , Levine Herbert
Published: July 2022

Recent years have seen a tremendous growth of interest in understanding the role that the adaptive immune system could play in interdicting tumor progression. In this context, it has been shown that the density of adaptive immune cells inside a solid tumor serves as a favorable prognostic marker across different types of cancer. The exact mechanisms underlying the degree of immune cell infiltration is largely unknown. Here, we quantify the temporal dynamics of the density profile of activated immune cells around a solid tumor spheroid. We propose a computational model incorporating immune cells with active, persistent movement and a proliferation rate that depends on the presence of cancer cells, and show that the model able to reproduce quantitatively the experimentally measured infiltration profile. Studying the density distribution of immune cells inside a solid tumor can help us better understand immune trafficking in the tumor micro-environment, hopefully leading towards novel immunotherapeutic strategies.
Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals
Authors: Sohail Mashaal , Chong Amanda Y. , Quinto-Cortes Consuelo D. , Palma-Martínez María J. , Ragsdale Aaron , Medina-Muñoz Santiago G. , Barberena-Jonas Carmina , Delgado-Sánchez Guadalupe , Cruz-Hervert Luis Pablo , Ferreyra-Reyes Leticia , Ferreira-Guerrero Elizabeth , Mongua-Rodríguez Norma , Jimenez-Kaufmann Andrés , Moreno-Macías Hortensia , Aguilar-Salinas Carlos A. , Auckland Kathryn , Cortés Adrián , Acuña-Alonzo Víctor , Ioannidis Alexander G. , Gignoux Christopher R. , Wojcik Genevieve L. , Fernández-Valverde Selene L. , Hill Adrian V.S. , Tusié-Luna María Teresa , Mentzer Alexander J. , Novembre John , García-García Lourdes , Moreno-Estrada Andrés
Published: July 2022

Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories as well as complex trait architectures remain hidden due to the lack of Big Data. To fill this gap, the Mexican Biobank project genotyped 1.8 million markers in 6,057 individuals from 32 states and 898 sampling localities across Mexico with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Through a suite of state-of-the-art methods for ancestry deconvolution and inference of identity-by-descent (IBD) segments, we inferred detailed ancestral histories for the last 200 generations in different Mesoamerican regions, unraveling native and colonial/post-colonial demographic dynamics. We observed large variations in runs of homozygosity (ROH) among genomic regions with different ancestral origins reflecting their demographic histories, which also affect the distribution of rare deleterious variants across Mexico. We analyzed a range of biomedical complex traits and identified significant genetic and environmental factors explaining their variation, such as ROH found to be significant predictors for trait variation in BMI and triglycerides.
A New In-Silico Approach for PROTAC Design and Quantitative Rationalization of PROTAC mediated Ternary Complex Formation
Authors: Ben Geoffrey A S , Kulkarni Nagaraj M , Agrawal Deepak , Vetrivel Rajappan , Gurram Kishan
Published: July 2022

Proteolysis-Targeting Chimeric Molecules (PROTAC) is a rapidly emerging technology for drug target protein degradation and drugging undruggable drug targets. There is a growing literature on in-silico approaches to the complex problem of PROTAC design, specifically the advantages of AI/ in-silico methods in the PROTAC Design Make Test Analyze (DMTA) cycle. Our work presented here aims to contribute to the growing literature of in-silico approaches to PROTAC design by incorporating and demonstrating incremental advancement over previously published methods. We use AI based generative methods for PRTOAC design and Molecular Dynamics to evaluate the stability of the ternary complex formed and ability of the PROTAC to hold the target protein and E3 ligase together stably. To quantify the performance of the PROTAC candidate, we also estimate computationally the PROTAC performance metrics routinely measured by the experimentalists in PROTAC assays. We use highly accurate absolute binding free energy calculations used traditionally in protein-ligand space for the PROTAC system. We calculate (Gibbs free energy change) ΔG for binary complex formation and ternary complex formation mediated by the PROTAC using Free Energy Perturbation - Thermodynamics Integration (FEP-TI) method which is benchmarked in literature with a root mean square error of 0.8 kcal/mol. We calculate ΔG for ternary and binary complexes and estimate whether ΔG for ternary is lower than the ΔG estimated for binary complexes. When the ΔG for ternary is lower than the binary it is inferred that ternary complexation is favoured over binary. Therefore, through these methods we can theoretical estimate ΔG measured by experimentalists in PROTAC assays such as Isothermal titration calorimetry (ITC) and Surface plasmon resonance (SPR) which capture the ΔG for ternary and binary complex formation mediated by the PROTAC. This method will help reduce time as well as costs of the PROTAC DMTA cycle and will accelerate early stage PROTAC drug discovery. As an illustrative application of our in-silico PROTAC design approach, we chose the target Fibroblast growth factor receptor 1(FGFR-1) which is a target approved drug for colorectal cancer. We report the findings and conclude with future research directions.
Computational Enhanced Hi-C data reveals the function of structural geometry in genomic regulation
Authors: He Yueying , Xue Yue , Wang Jingyao , Huang Yupeng , Liu Lu , Huang Yanyi , Gao Yi Qin
Published: July 2022

High-throughput chromosome conformation capture (Hi-C) technique profiles the genomic structure in a genome-wide fashion. The reproducibility and consistency of Hi-C data are essential in characterizing dynamics of genomic structures. We developed a diffusion-based method, CTG (Hi-C To Geometry), to deal with the technical bias induced by insufficient sampling in sequencing and obtain reliable gemeotric information of the chromatin. CTG properly quantifies dubiously weak or even undetected interactions and produces a consistent and reproducible framework for the 3D genomic structure. CTG allows for a reliable genome-wide insight on the alteration of genomic structures under different cellular conditions and reveals correlations between genomic-proximal genes at both transcriptional and translational levels. Cell-specific correspondence between gene-gene and corresponding protein-protein physical interactions, as well as that with the transcription correlation reveals the coordinated inter-molecular structural and regulatory information passage in the central dogma.
Trim28 plays an indispensable role in maintaining functions and transcriptional integrity of hematopoietic stem cells
Authors: Silvestri Giovannino , Rathinam Chozha Vendan
Published: July 2022

Hematopoiesis is a complex process that is regulated at multiple levels and through both intrinsic and extrinsic regulators. Trim28 is a multidomain protein that functions as a transcription factor and E3 ubiquitin ligase. Recent studies have established the pivotal roles of Trim28 in a variety of pathophysiologic processes including inflammation, autoimmune disorders, viral pathogenesis, cancer, tumor microenvironment and epithelial-to- mesenchymal transition. However, importance of Trim28 in early hematopoiesis, particularly in the maintenance and functions of hematopoietic stem and progenitor cells (HSPCs), remains largely unknown. In the present study, we identified Trim28 as a critical regulator of self-renewal, quiescence, and functions of hematopoietic stem cells (HSC). Conditional ablation of Trim28 in HSCs leads to perinatal lethality, due to pancytopenia within the hematopoietic lineage. Loss of Trim28 in HSCs affects their differentiation into myeloid-, erythroid-, and lymphoid- lineages. Trim28 deletion leads to altered frequencies and absolute numbers of HSCs, Multipotent Progenitors (MPPs) and lineage committed progenitors in the bone marrow (BM). Primary- and secondary- BM transplantation studies identified an indispensable and a cell-intrinsic role for Trim28 in HSCs. Mechanistic studies identified hyperproliferation of HSPCs and deregulated expression of cell cycle regulators in HSPCs. Strikingly, gene expression studies demonstrated that Trim28 deficiency impairs the transcriptional landscape and transcription factors signatures of HSPCs. In essence, these studies highlight a previously unknown role for Trim28 in the maintenance, functions, and multi-lineage differentiation of HSPCs.
Neuronal glutamate transporters control reciprocal inhibition and gain modulation in D1 medium spiny neurons
Authors: Petroccione Maurice A. , D’Brant Lianna Y. , Affinnih Nurat , Wehrle Patrick H. , Todd Gabrielle C. , Zahid Shergil , Chesbro Haley E. , Tschang Ian L. , Scimemi Annalisa
Published: July 2022

Understanding the function of glutamate transporters has broad implications for explaining how neurons integrate information and relay it through complex neuronal circuits. Most of what is currently known about glutamate transporters, specifically their ability to maintain glutamate homeostasis and limit glutamate diffusion away from the synaptic cleft, is based on studies of glial glutamate transporters. By contrast, little is known about the functional implications of neuronal glutamate transporters. The neuronal glutamate transporter EAAC1 is widely expressed throughout the brain, particularly in the striatum, the primary input nucleus of the basal ganglia, a region implicated with movement execution and reward. Here, we show that EAAC1 limits synaptic excitation onto a population of striatal medium spiny neurons identified for their expression of D1 dopamine receptors (D1-MSNs). In these cells, EAAC1 also contributes to strengthen lateral inhibition from other D1-MSNs. Together, these effects contribute to reduce the gain of the input-output relationship and increase the offset at increasing levels of synaptic inhibition in D1-MSNs. By reducing the sensitivity and dynamic range of action potential firing in D1-MSNs, EAAC1 limits the propensity of mice to rapidly switch between behaviors associated with different reward probabilities.
Specialized metabolism by trichome-preferentially-expressed Rubisco and fatty acid synthase components
Authors: Ji Wangming , Mandal Sabyasachi , Rezenom Yohannes H. , McKnight Thomas D.
Published: July 2022

Acylsugars, specialized metabolites with defense activities, are secreted by trichomes of many solanaceous plants. Several acylsugar metabolic genes (AMGs) remain unknown. We previously reported multiple candidate AMGs. Here, using multiple approaches, we characterized additional AMGs. First, we identified differentially expressed genes between high- and low-acylsugar-producing F2 plants derived from a cross between Solanum lycopersicum and S. pennellii, which produce acylsugars ∼1% and ∼20% of leaf dry weight, respectively. Expression levels of many known and candidate AMGs positively correlated with acylsugar amounts in F2 individuals. Next, we identified lycopersicum-pennellii putative orthologs with higher nonsynonymous to synonymous substitutions. These analyses identified four candidate genes, three of which showed enriched expression in stem trichomes compared to underlying tissues (shaved stems). Virus-induced gene silencing confirmed two candidates, Sopen05g009610 [beta-ketoacyl-(acyl-carrier-protein) reductase; fatty acid synthase component] and Sopen07g006810 (Rubisco small subunit), as AMGs. Phylogenetic analysis indicated that Sopen05g009610 is distinct from specialized metabolic cytosolic reductases, but closely related to two capsaicinoid biosynthetic reductases, suggesting evolutionary relationship between acylsugar and capsaicinoid biosynthesis. Additionally, data mining revealed that orthologs of Sopen05g009610 are preferentially expressed in trichomes of several acylsugar-producing solanaceous species. Similarly, orthologs of Sopen07g006810 were identified as trichome-preferentially-expressed members, which form a phylogenetic clade distinct from those of mesophyll-expressed “regular” Rubisco small subunits. Furthermore, δ13C analyses indicated recycling of metabolic CO2 into acylsugars by Sopen07g006810 and shed light on how trichomes support high levels of specialized metabolite production. These findings have implications for genetic manipulation of trichome specialized metabolism in solanaceous crops, including tomato, potato, and tobacco.
Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein
Authors: Frenkel Alona , Zecharia Eli , Gómez-Pérez Daniel , Sendersky Eleonora , Yegorov Yevgeni , Jacobs Avi , Benichou Jennifer , Stierhof York-Dieter , Parnasa Rami , Golden Susan S , Kemen Eric , Schwarz Rakefet
Published: July 2022

Cyanobacterial biofilms are ubiquitous and play important roles in diverse environments, yet, understanding of the processes underlying development of these aggregates is just emerging. Here we report cell specialization in formation of Synechococcus elongatus PCC 7942 biofilms - a hitherto unknown characteristic of cyanobacterial multicellularity. We show that only a quarter of the cell population expresses at high levels the four-gene ebfG-operon that is required for biofilm formation. Almost all cells, however, are assembled in the biofilm. Detailed characterization of EbfG4 encoded by this operon revealed cell-surface localization as well as its presence in the biofilm matrix. Moreover, EbfG1-3 were shown to form amyloid structures such as fibrils and are thus likely to contribute to the matrix structure. These data suggest a beneficial ‘division of labour’ during biofilm formation where only some of the cells allocate resources to produce matrix proteins – ‘public goods’ that support robust biofilm development by the majority of the cells. Additionally, previous studies revealed the operation of a self-suppression mechanism that depends on an extracellular inhibitor, which supresses transcription of the ebfG-operon. Here we revealed inhibitor activity at an early growth stage and its gradual accumulation along the exponential growth phase in correlation with cell density. Data, however, do not support a threshold-like phenomenon known for quorum-sensing in heterotrophs. Together, data presented here demonstrate cell specialization and imply density-dependent regulation thereby providing novel insights into cyanobacterial communal behaviour.

Graphical Abstract
Structural and functional analysis of natural capsid variants reveals sialic-acid independent entry of BK polyomavirus
Authors: Sorin M.N. , Di Maio A. , Silva L.M. , Ebert D. , Delannoy C. , Nguyen N.-K. , Guerardel Y. , Chai W. , Halary F. , Renaudin-Autain K. , Liu Y. , Bressollette-Bodin C. , Stehle T. , McIlroy D.
Published: July 2022

BK Polyomavirus (BKPyV) is an opportunistic pathogen that causes nephropathy in kidney transplant recipients. The BKPyV major capsid protein, VP1, engages gangliosides, lipid-linked sialylated glycans at the cell surface, to gain entry into cells. Here, we characterise the influence of VP1 mutations observed in patients with persistent post-transplant BKPyV replication on ganglioside binding, VP1 protein structure, and the tropism of the virus in two renal cell lines: 293TT and immortalised renal tubular epithelial (RS) cells. Infectious entry of single mutants E73Q, E73A and the triple mutant A72V-E73Q-E82Q (VQQ) remained sialic acid-dependent. These three variants acquired binding to a-series gangliosides, including GD1a, although only E73Q was able to infect GD1a-supplemented LNCaP or GM95 cells. Crystal structures of the three mutants showed a clear shift of the BC2 loop in mutants E73A and VQQ that correlated with the inability of these VP1 variants to infect ganglioside complemented cells. On the other hand, the double mutant K69N-E82Q lost the ability to bind sialic acid, with the K69N mutation leading to a steric clash which precludes sialic acid binding. Nevertheless, this mutant retained significant infectivity in 293TT cells that was not dependent on heparan sulphate proteoglycans, implying that an unknown sialic acid-independent entry receptor for BKPyV exists.
Plan versus motion-referenced generalization of fast and slow processes in reach adaptation
Authors: Rudolph Judith L. , Selen Luc P.J. , Medendorp W. Pieter
Published: July 2022

Generalization in motor learning refers to the transfer of a learned compensation to other relevant contexts. The generalization function is typically assumed to be of Gaussian shape, centered on the planned motion, although more recent studies associate generalization with the actual motion. Because motor learning is thought to involve multiple adaptive processes with different time constants, we hypothesized that these processes have different time-dependent contributions to the generalization. Guided by a model-based approach, the objective of the present study was to experimentally examine these contributions. We first reformulated a validated two-state adaptation model as a combination of weighted motor primitives, each specified as a Gaussian-shaped tuning function. Adaptation in this model is achieved by updating individual weights of the primitives of the fast and slow adaptive process separately. Depending on whether updating occurred in a plan-referenced or a motion-referenced manner, the model predicted distinct contributions to the overall generalization by the slow and fast process. We tested 23 participants in a reach adaptation task, using a spontaneous recovery paradigm consisting of five successive blocks of a long adaptation phase to a viscous force field, a short adaptation phase with the opposite force, and an error-clamp phase. Generalization was assessed in eleven movement directions relative to the trained target direction. Results of our participant population fell within a continuum of evidence for plan-referenced to evidence for motion-referenced updating. This mixture may reflect the differential weighting of explicit and implicit compensation strategies among participants.
The influence of extrachromosomal elements in the anthrax “cross-over” strainBacillus cereusG9241
Authors: Taylor-Joyce Grace , Manoharan Shathviga , Brooker Thomas , Hernandez-Rodrıguez Carmen Sara , Baillie Les , Oyston Petra C. F. , Hapeshi Alexia , Waterfield Nicholas R.
Published: July 2022

Bacillus cereusG9241 was isolated from a welder who survived a pulmonary anthrax-like disease. Strain G9241 carries two virulence plasmids, pBCX01 and pBC210, as well as an extrachromosomal prophage, pBFH_1. pBCX01 has 99.6% sequence identity to pXO1 carried byBacillus anthracisand encodes the tripartite anthrax toxin genes andatxA, a mammalian virulence transcriptional regulator. This work looks at how the presence of pBCX01 and temperature may affect the lifestyle ofB. cereusG9241 using a transcriptomic analysis and by studying spore formation, an important part of theB. anthracislifecycle. Here we report that pBCX01 has a stronger effect on gene transcription at the mammalian infection relevant temperature of 37°C in comparison to 25°C. At 37°C, the presence of pBCX01 appears to have a negative effect on genes involved in cell metabolism, including biosynthesis of amino acids, whilst positively affecting the transcription of many transmembrane proteins. The study of spore formation showedB. cereusG9241 sporulated rapidly in comparison to theB. cereussensu stricto type strain ATCC 14579, particularly at 37°C. The carriage of pBCX01 did not affect this phenotype suggesting that other genetic elements were driving rapid sporulation. An unexpected finding of this study was that pBFH_1 is highly expressed at 37°C in comparison to 25°C and pBFH_1 expression leads to the production of Siphoviridae-like phage particles in the supernatant ofB. cereusG9241. This study provides an insight on how the extrachromosomal genetic elements inB. cereusG9241 has an influence in bacterial phenotypes.
High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates
Authors: Benman William , Datta Saachi , Gonzalez-Martinez David , Lee Gloria , Hooper Juliette , Qian Grace , Leavitt Gabrielle , Salloum Lana , Ho Gabrielle , Mhatre Sharvari , Magaraci Michael S. , Patterson Michael , Mannickarottu Sevile G. , Malani Saurabh , Avalos Jose L. , Chow Brian Y. , Bugaj Lukasz J.
Published: July 2022

The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression inE. coli. We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.
Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex
Authors: Mori Chinatsu , Nagatoishi Satoru , Matsunaga Ryo , Kuroda Daisuke , Nakakido Makoto , Tsumoto Kouhei
Published: July 2022

Interleukin-11 (IL-11) is a member of the interleukin-6 (IL-6) family of cytokines. IL-11 is a regulator of multiple events in hematopoiesis, and IL-11-mediated signaling is implicated in inflammatory disease, cancer, and fibrosis. All IL-6 family cytokines signal through the signal-transducing receptor, glycoprotein 130 (gp130), but these cytokines have distinct as well as overlapping biological functions. To understand IL-11 signaling at the molecular level, we performed a comprehensive interaction analysis of the IL-11 signaling complex, comparing it with the IL-6 complex, one of the best-characterized cytokine complexes. Our thermodynamic analysis revealed a clear difference between IL-11 and IL-6. Surface plasmon resonance analysis showed that the interaction between IL-11 and IL-11 receptor α (IL-11Rα) is entropy driven, whereas that between IL-6 and IL-6 receptor α (IL-6Rα) is enthalpy driven. Our analysis using isothermal titration calorimetry revealed that the binding of gp130 to the IL-11/IL-11Rα complex results in entropy loss, but that the interaction of gp130 with the IL-6/IL-6Rα complex results in entropy gain. Our hydrogen-deuterium exchange mass spectrometry experiments suggested that the D2 domain of gp130 was not involved in n IL-6-like interactions in the IL-11/IL-11Rα complex. It has been reported that IL-6 interaction with gp130 in the signaling complex was characterized through the hydrophobic interface located in its D2 domain of gp130. Our findings suggest that unique interactions of the IL-11 signaling complex with gp130 are responsible for the distinct biological activities of IL-11 compared to IL-6.
Cell cycle arrest explains the observed bulk 3D genomic alterations in response to long-term heat shock in K562 cells
Authors: Xu Bingxiang , Gao Xiaomeng , Li Xiaoli , Jia Yan , Li Feifei , Zhang Zhihua
Published: July 2022

Heat shock is a common environmental stress, although the response of the nucleus to it remains controversial in mammalian cells. Acute reaction and chronic adaptation to environmental stress may have distinct internal rewiring in the gene regulation networks. However, this difference remains largely unexplored. Here, we report that chromatin conformation and chromatin accessibility respond differently in short- and long-term heat shock in human K562 cells. We found that chromatin conformation in K562 cells was largely stable in response to short-term heat shock, whereas it showed clear and characteristic changes after long-term heat treatment with little alteration in chromatin accessibility during the whole process. We further show in silico and experimental evidence strongly suggesting that changes in chromatin conformation may largely stem from an accumulation of cells in the M stage of the cell cycle in response to heat shock. Our results represent a paradigm shift away from the controversial view of chromatin response to heat shock and emphasize the necessity of cell cycle analysis when interpreting bulk Hi-C data.
Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank
Authors: Kulik Marta , Chodkiewicz Michał Leszek , Dominiak Paulina Maria
Published: July 2022

The availability of atomic resolution experimental maps of electrostatic potential from 3D electron diffraction (3D ED) extends the possibility of investigating the electrostatic potential beyond the determination of non-H-atom positions. However, accurate tools to calculate this potential for macromolecules, without the use of expensive quantum calculations, are lacking. The University at Buffalo Data Bank (UBDB) gathers atom types that can be used to calculate accurate electrostatic potential maps via structure-factor calculations. Here, the transferable aspherical atom model (TAAM) is applied with UBDB to investigate theoretically obtained electrostatic potential maps of lysozyme and proteinase K, and compare them with experimental maps from 3D ED. UBDB better reproduces the molecular electrostatic potential of molecules within their entire volume compared with the neutral spherical models used in the popular independent atom model (IAM). Additionally, the theoretical electron-density maps of the studied proteins are shown and compared with the electrostatic potential maps. The atomic displacement parameters (B factors) may affect the electrostatic potential maps in a different way than in the case of electron-density maps. The computational method presented in this study could potentially facilitate the interpretation of the less resolved regions of cryo-electron microscopy density maps and pave the way for distinguishing between different ions/water molecules in the active sites of macromolecules in high-resolution structures, which is of interest for drug-design purposes.
Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure
Authors: Mou Tung-Chung , Zeng Baisen , Doukov Tzanko I. , Sprang Stephen R.
Published: July 2022

The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure, 27, 1137–1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103 kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77 Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, |Δano|/σΔano (d′′/sig), approaches 1.4 at 3.4 Å resolution. The highly redundant, 11 000 000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix, SHELXC/D and PRASA as implemented in the CRANK2 program suite were each employed to determine the sulfur substructure. All of these approaches were effective, although HySS, as a component of the phenix.autosol tool, required data from all crystals to find the positions of the sulfur atoms. Critical contributors in this case study to successful phase determination by SAD included (i) the high-flux FMX beamline, featuring helical-mode data collection and a helium-filled beam path, (ii) as recognized by many authors, a very highly redundant, multiple-crystal data set and (iii) the inclusion within that data set of data from crystals that were scanned over large ω ranges, yielding highly isomorphous and highly redundant intensity measurements.
Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals
Authors: Yabukarski Filip , Doukov Tzanko , Mokhtari Daniel A. , Du Siyuan , Herschlag Daniel
Published: July 2022

Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conformations that is at the heart of protein function and energetics. Room-temperature (RT) X-ray crystallography provides accurate ensemble information, and recent developments allow conformational heterogeneity (the experimental manifestation of ensembles) to be extracted from single-crystal data. Nevertheless, high sensitivity to X-ray damage at RT raises concerns about data reliability. To systematically address this critical issue, increasingly X-ray-damaged high-resolution data sets (1.02–1.52 Å resolution) were obtained from single proteinase K, thaumatin and lysozyme crystals at RT (277 K). In each case a modest increase in conformational heterogeneity with X-ray damage was observed. Merging data with different extents of damage (as is typically carried out) had negligible effects on conformational heterogeneity until the overall diffraction intensity decayed to ∼70% of its initial value. These effects were compared with X-ray damage effects in cryo-cooled crystals by carrying out an analogous analysis of increasingly damaged proteinase K cryo data sets (0.9–1.16 Å resolution). X-ray damage-associated heterogeneity changes were found that were not observed at RT. This property renders it difficult to distinguish real from artefactual conformations and to determine the conformational response to changes in temperature. The ability to acquire reliable heterogeneity information from single crystals at RT, together with recent advances in RT data collection at accessible synchrotron beamlines, provides a strong motivation for the widespread adoption of RT X-ray crystallography to obtain conformational ensemble information.
Art of using music-product congruence and lyrics in radio-ads
Authors: Vashisht Devika
Published: July 2022

Purpose

This research aims to exhibit the impacts of vocal music vs instrumental music on ad-recall from the perspectives of attention and elaboration.

Design/methodology/approach

A 2 music-product congruence (congruence vs incongruence) × 2 music lyrics (lyrics vs no lyrics) between-subject measures design is used. 180 management students participated in the study. A 2 × 2 between-subjects ANOVA is used to test the hypotheses.

Findings

Results showed that the instrumental rendition of an ad-song prompted higher ad-recall over the vocal variant. The instrumental rendition provoked the subjects to create the verses or lyrics in their minds, prompting superior recall. Further, it was found that a music-product congruent ad resulted into higher ad-recall than an incongruent ad. Moreover, for a congruent ad condition, the instrumental version of ad-song resulted into higher ad-recall than the vocal version of ad-song. On the other hand, for an incongruent ad condition, the instrumental version as well as the vocal version of ad-song resulted into same level of ad-recall.

Research limitations/implications

The study offers important implications for marketers and advertisers in terms of effective ad-designing and execution considering lyrics and music-product congruence as important factors in the context of radio advertising.

Originality/value

Since very little research has been done focusing on the combined effect of music lyrics and music-product congruence relationship on ad-recall from attention and elaboration perspectives, this paper scores as a pioneering study of its kind in India.
The high-temperature mechanical properties of HS110S steel and its corrosion behaviors in harsh downhole environment
Authors: Liu Wei , Zhou Zhiping , Li Zhaolin , Li Mingxing , Li Qiongwei , Ye Zhengrong , Yao Jinxing , Zhong Xiankang
Published: July 2022

Purpose

This paper aims to investigate the high-temperature mechanical properties of HS110S steel and its corrosion behaviors in harsh downhole environment.

Design/methodology/approach

In this work, mechanical property measurements were carried out from 25°C to 350°C and the scanning electron microscopy was used to observe the fracture morphology. The weight-loss measurements and surface characterization were used to evaluate the corrosion resistance of HS110S steel in harsh downhole environment.

Findings

Results show that the yield strength and tensile strength of HS110S steel at 350 °C are 779 and 861 MPa, respectively. Compared with room temperature, the reduction rate values are both less than 20%. At the high-temperature corrosion environment (350 °C), the static and dynamic corrosion rates are 0.9668 and 1.9236 mm/a, respectively. The generated corrosion products are mainly composed of FeSx, FeCO3and Fe3O4. Therefore, the HS110S steel applied under such conditions needs to take suitable protective measures.

Originality/value

In general, the HS110 steel has widely used in conventional development conditions (e.g. low H2S or high CO2environments). However, to the best of the authors’ knowledge, no studies have reported on its application at more than 250°C. Therefore, this work can be a reference to the application of HS110S steel in high-temperature corrosion conditions.
Empirical scrutiny of the behavioural intention of construction organisations to use unmanned aerial vehicles
Authors: Aghimien Douglas , Ikuabe Matthew , Aliu John , Aigbavboa Clinton , Oke Ayodeji Emmanuel , Edwards David John
Published: July 2022

Purpose

This paper aims to assess the behavioural intention of construction organisations to use unmanned aerial vehicles (UAVs) in the delivery of construction projects. Using the unified theory of technology adoption and use of technology (UTAUT) model, the study strives to improve project delivery by adopting beneficial digital technologies.

Design/methodology/approach

The study adopted a postpositivism philosophical stance through a quantitative research approach using a structured questionnaire administered to construction organisations in South Africa. Primary data gathered was analysed using frequency, percentage, mean item score, Mann–Whitney U-test and confirmatory factor analysis, where the latter sought to deductively confirm the variables within the UTAUT model.

Findings

Construction organisations were found to rarely use UAVs in the country and furthermore, most of the participating organisations are unsure about using UAVs for their project delivery. Factors impacting on an organisation’s intention to use UAVs were identified as social influence, performance expectancy, effort expectancy and facilitating conditions. However, factors surrounding resistance to using and perceived risk cannot be overlooked as they also proved to be significant (at p = 0.05) to the behavioural intention of organisations to use UAVs.

Practical implications

Practical guidance for industry practitioners is offered in terms of insight into the key factors that must be considered for the effective utilisation of UAVs and the realisation of concomitant benefits.

Originality/value

This study bridges the knowledge gap in extant literature by exploring the practitioner’s behavioural intention to use UAVs. As an aside, an emergent theoretical backdrop for future works on UAVs is provided (particularly in developing countries where such a study has not been previously explored).
How resilient safety culture correct unsafe behavior of new generation of construction workers: the mediating effects of job crafting and perceived work meaningfulness
Authors: Ni Guodong , Zhang Qi , Fang Yaqi , Zhang Ziyao , Qiao Yaning , Wang Wenshun , Deng Yongliang
Published: July 2022

Purpose

The purpose of this paper is to explore the correction mechanism of resilient safety culture on new generation of construction workers (NGCWs)' unsafe behavior and test the multiple mediation effects of job crafting and perceived work meaningfulness based on the context of Chinese construction industry in order to find a new way to effectively correct the NGCWs' unsafe behavior.

Design/methodology/approach

A theoretical model of correction mechanism was established based on literature research and theoretical deduction. An empirical study was employed based on confirmatory factor analysis and regression analysis with a sample of 404 NGCWs in China.

Findings

The results indicated that resilient safety culture can effectively correct NGCWs' unsafe behavior through job crafting and perceived work meaningfulness. Job crafting and perceived work meaningfulness can play independent and serial mediating roles between resilient safety culture and unsafe behavior.

Research limitations/implications

Research results only represent a short-term law about the correction mechanism of NGCWs' unsafe behavior based on a questionnaire study from China's construction industry. It is necessary to continue to implement a longitudinal study to test it in a relatively long period in future research. The findings also need to be verified based on the young construction workers in other countries.

Practical implications

This study provides a theoretical basis and feasible management reference for construction enterprises in China to correct NGCWs' unsafe behavior from the perspective of resilient safety culture. Furthermore, the construction of resilient safety culture in construction enterprises can help NGCWs better carry out job crafting and perceive the meaning of work.

Originality/value

This paper clarifies the correction mechanism of resilient safety culture on unsafe behavior of NGCWs, and further tests the independent mediating roles and a serial mediating role of job crafting and perceived work meaningfulness between resilient safety culture and unsafe behavior, which fills the research gap about the influence mechanism of resilient safety culture on young construction workers' unsafe behavior and enriches the theoretical system of unsafe behavior correction of construction workers.
Managing the complexity of green innovation
Authors: Abadzhiev Andrey , Sukhov Alexandre , Sihvonen Antti , Johnson Mikael
Published: July 2022

Purpose

Green innovation can promote both environmental sustainability and economic growth. However, its development and implementation can be complex due to the need to align innovation activities within and across companies. In this study, the authors examined how this complexity can be managed by analyzing how individual companies combine different innovation activities to develop green innovation, and how companies along the value chain align to implement these innovations.

Design/methodology/approach

The dataset comprises both interviews and a survey of senior executives from the Swedish wood construction industry. These data were first analyzed by using fuzzy set qualitative comparative analysis (fsQCA) to identify innovation activity configurations at the level of the individual company. The interviews were then analyzed to identify alignment mechanisms enabling the implementation of green innovation along the value chain.

Findings

At the company level, the authors found three innovation activity configurations with varying levels of complexity: (1) systemic innovation by proactive companies, (2) process innovation by reactive companies and (3) inaction by technology-independent companies. On the value chain level, the authors found three alignment mechanisms that facilitate the implementation of green innovation along the value chain. These mechanisms promote cooperation by increasing efficiency, opening up new market opportunities and increasing the level of servitization.

Originality/value

This paper analyzes the complexity of green innovation and provides novel insights into how complexity is managed at the level of both the individual company and the value chain.
Enhancing self-perceived employability via a curriculum intervention: a case of “The global marketing professional” module
Authors: Padgett Rebecca C. , Donald William E.
Published: July 2022

Purpose

Drawing on human capital and sustainable career theory, this paper aims to explore university students' views regarding their self-perceived employability following participation in a mandatory module titled “The Global Marketing Professional”.

Design/methodology/approach

Overall, 80 students studying a full-time postgraduate master's degree in international marketing management at a northern Russell Group university participated in a two-wave study by completing a questionnaire during Weeks 1 and 9 of the module in the 2021/2022 academic year. Descriptive statistics, paired samples t-tests and quantitative content analysis were subsequently applied to the data set.

Findings

Students' confidence in their self-perceived employability rose from 37.5% to 92.5%. This was supported by the paired samples t-tests’ findings of increases at the item and composite scale levels. The quantitative content analysis found benefits of the module to include increased confidence, interactive classes, skills development, knowledge of the recruitment process, CV development, proactive career ownership, interview guidance and networking. Suggestions for improvement included increasing the amount of lecture time provided, increased accessibility via subtitles and opportunities for real-world experience.

Originality/value

The contribution comes via the advancement of human capital and sustainable career theory by identifying empirically informed strategies for enhancing students' self-perceived employability within the university curriculum. Implications subsequently extend to universities, organisations and national economies.
Issues and challenges ofwaqfin providing healthcare resources
Authors: Sulistyowati  , Sukmana Raditya , Ratnasari Ririn Tri , Ascarya  , Widiastuti Tika
Published: July 2022

Purpose

This paper attempts to rejuvenatewaqfin the health sector by identifying and elaborating on its issues and challenges. The government budget for this sector is significant; thus, the present paper aims to provide a nongovernment budget to lessen the government's burden

Design/methodology/approach

This qualitative study uses structured in-depth interviews with 12 respondents to generate valuable insights and thoughts in order to frame recommendations.

Findings

The findings highlight the key themes: human resources, finance, collaboration and coordination, legal issues, basic healthcare insufficiency, data and digitalization, accountability and sustainability and infrastructure. The following are the proposed solutions: capacity building program (CBP), hybridwaqfscheme, big data connectivity, specific legal framework, refocusing and reallocating of resources for the health sector during and after the pandemic

Research limitations/implications

This study focuses on Indonesia and Malaysia as the authors believe that these two countries have a lot of practice in the field. Further studies may focus on other countries, such as Pakistan.

Practical implications

This paper proposes potential ways to embrace government policy consideration, optimize the elaboration among productivewaqfwith other kinds, improve governance of and coordination amongwaqfinstitutions and increase the awareness to improve significant development.

Social implications

By considering this paper's recommendations,waqfstakeholders in the healthcare system can improve the social benefits for poor and needy patients.

Originality/value

This study presents the latest strategic analysis ofwaqf, which is important for the government policy in developingwaqf.
Student retention in higher education: the influences of organizational identification and institution reputation on student satisfaction and behaviors
Authors: Al Hassani Amal Abdulla , Wilkins Stephen
Published: July 2022

Purpose

Universities worldwide struggle to retain students, so it is important to identify the factors that may improve retention levels. The research investigates key factors that have an impact upon student satisfaction and students' staying and supportive intentions. Of particular interest is the extent to which organizational identification and institution reputation influence student satisfaction and behaviors.

Design/methodology/approach

A conceptual model was developed and tested using covariance-based structural equation modeling. The data were obtained from a survey of 419 first year full-time undergraduate students in the United Arab Emirates.

Findings

Perceived quality of teaching, organizational identification and institution reputation were found to be significant predictors of student satisfaction in our model, with student satisfaction having both direct and mediating influences on students' staying and supportive intentions.

Practical implications

The findings suggest that universities should undertake activities that strengthen student-university identification and institution reputation, as these may strongly influence students' attitudes and behaviors. The paper discusses strategies that institutions may implement to develop and maintain organizational identification among students.

Originality/value

The research highlights that although perceived quality of teaching has an influence on student satisfaction, the influences of organizational identification and institution reputation are stronger.