bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmembrane region dimer structures of Type 1 receptors readily sample alternate configurations: MD simulations using the Martini 3 coarse grained model compared to AlphaFold2 Multimer
Authors: Sahoo Amita R. , Souza Paulo C. T. , Meng Zhiyuan , Buck Matthias 
Published: September 2021

SummaryDetermination of the structure and dynamics of transmembrane (TM) regions of single-transmembrane receptors is key to understanding their mechanism of signal transduction across the plasma membrane. Although many studies have been performed on isolated soluble extra- and intracellular receptor domains in aqueous solutions, limited knowledge exists on the lipid embedded TM domain. In this study, we examine the assembly of configurations of receptor TM region dimers using the Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. This recently published version of Martini has new bead types and sizes, which allows more accurate predictions of molecular interactions compared to the previous versions. At first glance our results with Martini 3 simulations show only a reasonable agreement withab initiopredictions using PREDDIMER (for TM domains only), AlphaFold2 Multimer and with available NMR derived structures for TM helix dimers. Specifically, 6 of 11 CG TM structures are similar to the NMR structures (within < 3.5 Å mainchain RMSD) compared to 10 of 11 and 9 of 11 using PREDDIMER and Alphafold, respectively (7 structures of the latter are within 1.5 Å) Surprisingly, AlphaFold2 predictions are more comparable with NMR structures when the database of 2001 (mainly composed of soluble proteins) instead of 2020 PDB structures are used. While there are some differences in the conditions used, the CG simulations primarily reveal that alternate configurations of the TM dimers that are sampled, which readily interconvert with a predominant population. The implications of these findings for our understanding of the signalling mechanism of TM receptors are discussed, including opportunities for the development of new pharmaceuticals, some of which are peptide based.
Prediction and validation of the three-dimensional structure of glucokinase-1 from Phytophthora infestans
Authors: Villalobos-Piña Liara , Rojas Ascanio , Acosta Héctor 
Published: September 2021

AbstractAccording to its primary structure, the [PITG_06016] gene encodes for one of the 7 glucokinases present in Phytophthora infestans (PiGlcK-1), the causal agent of late blight disease. Currently, there are no structural studies of any of its enzymes, being the determination of the three-dimensional (3D) structure of PiGlcK-1 a necessary contribution in the deduction of its functions, its interaction with ligands, and possible regulatory mechanisms. In this work we present the first structural model obtained by in silico tools for PiGlcK-1. For the prediction of this model, different algorithms were used to find the best annealing, refinement, and qualitative evaluation of them. A structural comparison of the predicted model with other structures of crystallized kinase enzymes allowed us to identify the regions of interaction with their classical substrates (glucose and ATP), as well as to identify the amino acid residues involved in the binding of other substrates such as fructose and ADP. In addition, we propose a possible recognition region of PPi, an activator of kinase activity that includes the GXGE motif, conserved in enzymes of the ribokinase (RK) family, which distinguishes this PiGlcK-1 from a classical glucokinase. Accordingly, these findings suggest PPi-binding motif as potential targets for the development of inhibitors of PiGlcK-1 activity.
AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement
Authors: Chai Lawrence , Zhu Ping , Chai Jin , Pang Changxu , Andi Babak , McSweeney Sean , Shanklin John , Liu Qun 
Published: September 2021

AbstractCrystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a dominant phasing method for the crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database for finding suitable templates for phasing. However, such sequence information is not always available such as when proteins are crystallized with unknown binding partner proteins or when the crystal is that of a contaminant. The recent development of AlphaFold has resulted in the availability of predicted protein structures for all proteins from twenty species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough for sequence-independent phasing of diffraction data from two crystallization contaminants for which we had not identified the protein. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained which allowed the identification and structure determination of both structures, YncE and YadF. Our results advocate a general utility of AlphaFold-predicted structure database with respect to crystallographic phasing.
Engineered bacteria detect tumor DNA
Authors: Cooper Robert M. , Wright Josephine A. , Ng Jia Q. , Goyne Jarrad M. , Suzuki Nobumi , Lee Young K. , Ichinose Mari , Radford Georgette , Ryan Feargal , Kumar Shalni , Thomas Elaine M. , Vrbanac Laura , Knight Rob , Woods Susan L. , Worthley Daniel L. , Hasty. Jeff 
Published: September 2021

SummaryAdvances in bacterial engineering have catalysed the development of living cell diagnostics and therapeutics1–3, including microbes that respond to gut inflammation4, intestinal bleeding5, pathogens6 and hypoxic tumors7. Bacteria can access the entire gastrointestinal tract8 to produce outputs measured in stool4 or urine7. Cellular memory, such as bistable switches4,9,10 or genomic rearrangements11, allows bacteria to store information over time. However, living biosensors have not yet been engineered to detect specific DNA sequences or mutations from outside the cell. Here, we engineer naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids and tumors. We characterize the functionality of the biosensors in vitro with co-culture assays and then validate in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observe horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. The sensor bacteria achieved 100% discrimination between mice with and without CRC. This Cellular Assay of Targeted, CRISPR-discriminated Horizontal gene transfer (CATCH), establishes a framework for biosensing of mutations or organisms within environments that are difficult to sample, among many other potential applications. Furthermore, the platform could be readily expanded to include production and delivery of antibiotic or antineoplastic therapeutic payloads at the detection site.
A case for glycerol as an acceptable additive for single particle cryoEM samples
Authors: Basanta Benjamin , Hirschi Marscha M. , Grotjahn Danielle A. , Lander Gabriel C. 
Published: September 2021

AbstractBuffer composition and sample preparation guidelines for cryo-electron microscopy are geared toward maximizing imaging contrast and reducing electron beam-induced motion. These pursuits often involve the minimization or complete removal of additives that are commonly used to facilitate proper protein folding and minimize aggregation. Among these admonished additives is glycerol, a widely used osmolyte that aids protein stability. In this work, we show that inclusion of glycerol does not preclude high-resolution structure determination by cryoEM, as demonstrated by a ∼2.3 Å reconstruction of mouse apoferritin (∼500 kDa) and a ∼3.3 Å reconstruction of rabbit muscle aldolase (∼160 kDa) in presence of 20% v/v glycerol. While we found that generating thin ice that is amenable for high-resolution imaging requires long blot times, the addition of glycerol did not result in increased beam-induced motion nor an inability to pick particles. Overall, our findings indicate glycerol should not be discounted as a cryoEM sample buffer additive, particularly for large, fragile complexes that are prone to disassembly or aggregation upon its removal.
The histone deacetylase activity of HDAC1/2 is required to safeguard zygotic genome activation in mice and cattle
Authors: Dang Yanna , Li Shuang , Zhao Panpan , Xiao Lieying , Wang Lefeng , Shi Yan , Luo Lei , Wang Shaohua , Wang Huanan , Zhang Kun 
Published: September 2021

ABSTRACTThe genome is transcriptionally inert at fertilization and must be activated through a remarkable developmental process called zygotic genome activation (ZGA). The gene expression pattern formed over the course of ZGA is required for establishing totipotency in early embryos and subsequent development. Substantial epigenetic reprogramming contributes significantly to the pronounced change in gene expression during ZGA, however the mechanism has yet to be resolved. Here, we find histone deacetylase 1 and 2 (HDAC1/2) are critical histone modifiers that regulate ZGA through the histone deacetylase activity. Notably, we show that H3K27ac level declines dramatically during ZGA with a dynamic change in its genome-wide distribution. In mouse embryos, ectopic expression of HDAC1/2 dominant negative mutant leads to a failure of H3K27ac removal and a developmental arrest at 2-cell stage. RNA-seq results reveal a remarkable transcriptomic change with 6565 differentially expressed genes identified. Further analysis shows 64% of down-regulated genes are ZGA genes and 49% of up-regulated genes are developmental genes. Low input ChIP-seq analysis exhibits an increase and decrease of H3K27ac enrichment at the promoter region of up- and down-regulated genes, respectively. Moreover, HDAC1 mutants prohibited removal of broad H3K4me3 domain via impeding the expression of Kdm5s during ZGA. Importantly, the developmental block can be greatly overcome through injection of Kdm5b mRNA and expression of the majority of dysregulated genes partially corrected. Similar functional significance of HDAC1/2 in ZGA is conserved in bovine embryos. Together, we propose that HDAC1/2 is indispensable for mouse and bovine ZGA via creating correct transcriptional repressive and active states.
Addressing Enzymatic-Independent Tumor-Promoting Function of NAMPT via PROTAC-Mediated Degradation
Authors: Zhu Xiaotong , Liu Haixia , Chen Li , Cang Yong , Jiang Biao , Yang Xiaobao , Fan Gaofeng 
Published: September 2021

AbstractThe rate-limiting enzyme of salvage pathway for NAD+ synthesis, NAMPT, is aberrantly overexpressed in a variety of tumor cells and is a poor prognosis factor for patient survival. NAMPT plays a major role in tumor cell proliferation, acting concurrently as an NAD+ synthase and unexpectedly, an extracellular ligand for several tumor-promoting signaling pathways. While previous efforts to modulate NAMPT activity were limited to enzymatic inhibitors with low success in clinical studies, protein degradation offers a possibility to simultaneously disrupt NAMPT’s enzyme activity and ligand capabilities. Here, we report the development of two highly selective NAMPT-targeted proteolysis-targeting chimeras (PROTACs), which promoted rapid and potent NAMPT degradation in a cereblon-dependent manner in multiple tumor cell lines. Notably, both PROTAC degraders outperform a clinical candidate, FK866, in killing effect on hematological tumor cells. These results emphasize the importance and feasibility of applying PROTACs as a better strategy for targeting proteins like NAMPT with dual tumor-promoting functions, which are not easily achieved by conventional enzymatic inhibitors.
Planning and optimization of robotic pick-and-place operations in highly constrained industrial environments
Authors: Tipary Bence , Kovács András , Erdős Ferenc Gábor 
Published: September 2021

Purpose
The purpose of this paper is to give a comprehensive solution method for the manipulation of parts with complex geometries arriving in bulk into a robotic assembly cell. As bin-picking applications are still not reliable in intricate workcells, first, the problem is transformed to a semi-structured pick-and-place application, then by collecting and organizing the required process planning steps, a methodology is formed to achieve reliable factory applications even in crowded assembly cell environments.

Design/methodology/approach
The process planning steps are separated into offline precomputation and online planning. The offline phase focuses on preparing the operation and reducing the online computational burdens. During the online phase, the parts laying in a semi-structured arrangement are first recognized and localized based on their stable equilibrium using two-dimensional vision. Then, the picking sequence and corresponding collision-free robot trajectories are planned and optimized.

Findings
The proposed method was evaluated in a geometrically complex experimental workcell, where it ensured precise, collision-free operation. Moreover, the applied planning processes could significantly reduce the execution time compared to heuristic approaches.

Research limitations/implications
The methodology can be further generalized by considering multiple part types and grasping modes. Additionally, the automation of grasp planning and the enhancement of part localization, sequence planning and path smoothing with more advanced solutions are further research directions.

Originality/value
The paper proposes a novel methodology that combines geometrical computations, image processing and combinatorial optimization, adapted to the requirements of flexible pick-and-place applications. The methodology covers each required planning step to reach reliable and more efficient operation.
Sulfide stress cracking inhibition of a supermartensitic stainless steel by using an imidazol obtained from palm oil
Authors: Gonzalez-Rodriguez Jose-Gonzalo , Carmona Hernandez Andres , Vázquez-Vélez E. , Contreras-Cuevas A. , Uruchurtu Chavarin Jorge 
Published: September 2021

Purpose
This paper aims to use an imidazole-based n-ionic Gemini surfactant derived from palm oil to inhibit the sulfide stress corrosion cracking of a supermartensitic stainless steel.

Design/methodology/approach
The slow strain rate testing technique, hydrogen permeation tests and potentiodynamic polarization curves have been used.

Findings
Addition of the inhibitor below the critical micelle concentration (CMC) decreased the corrosion current density (icorr), but not enough to avoid embrittlement due to the entry of hydrogen into the steel. Instead, the addition of the inhibitor close to the CMC decreased the icorr, suppressed the entry of hydrogen and inhibited the sulfide stress cracking of steel. Finally, the addition of inhibitor above the CMC led to a slight increase of icorr and promoted localized corrosion, however, the sulfide stress cracking of steel was inhibited.

Originality/value
A green sulfide stress corrosion cracking inhibitor of a supermartensitic stainless steel has been obtained.
Effect of Cu addition to low-alloy structural steel on the resistance against corrosion by the Pseudomonas aeruginosa biofilm
Authors: Li Zhong , Lei Qing , Huang Luyao , Liu Chao 
Published: September 2021

Purpose
Low-alloy structural steels (LASS) face severe microbiologically influenced corrosion (MIC) in their service environments. To mitigate this issue, Cu is often used as an alloying element owing to its intrinsic antimicrobial activity. However, the antibacterial performance and biofilm resistance of Cu-containing LASS (Cu-LASS) are still unclear. This study aims to analyze the effect of Cu addition to 420 MP LASS on its MIC by the Pseudomonas aeruginosa biofilm.

Design/methodology/approach
Scanning electron microscope, confocal laser scanning microscope and X-ray photoelectron spectroscopy were used to analyze the surface morphology and composition of corrosion products. The antibacterial activities of Cu-LASS were analyzed by the spread-plate method. In addition, electrochemical analysis was conducted to characterize the corrosion behavior of the produced alloy.

Findings
Bacterial analysis and morphological observation confirmed a reduced sessile cell count and inactivation of the P. aeruginosa biofilm on the surface of Cu-LASS coupons. Electrochemical measurements showed that Cu-LASS exhibited large polarization and charge-transfer resistances, which indicated excellent MIC resistance. This significantly enhanced resistance to MIC could be explained by the synergistic effect of released Cu2+ from the Cu-LASS surface and immediate contact to Cu-rich phase in the surface and the release of Cu2+ ions from the Cu-LASS surface.

Originality/value
The effect of Cu addition on the MIC resistance and antibacterial performance of LASS is seldom reported. It is necessary to investigate the corrosion resistance of Cu-LASS and clarify its antibacterial mechanism. This paper fulfills this need.
Big Five personality traits and green consumption: bridging the attitude-intention-behavior gap
Authors: Duong Cong Doanh 
Published: September 2021

PurposeThis study examines the roles of Big Five personality traits, including conscientiousness, agreeableness, extraversion, neuroticism and openness to experience, in shaping green consumption behavior, as well as bridging the attitude-intention-behavior gap in environmentally friendly consumption and testing the gender differences between these associations.Design/methodology/approachA dataset of 611 consumers was collected by means of mall-intercept surveys in major Vietnamese cities. Structural equation modeling (SEM) via AMOS 24.0 was employed to test the proposed conceptual framework and hypotheses, while the PROCESS approach was utilized to estimate mediation standardized regression coefficients.FindingsThe study revealed that in addition to extraversion, other personality traits (agreeableness, conscientiousness, openness to experience and neuroticism) were strongly associated with green consumption. Moreover, attitude towards green products and intention to buy environmentally friendly products were determined to have key roles in explaining consumers' pro-environmental behavior. There was also a notable difference in the impact of personality traits on men's and women's green consumption.Practical implicationsThis study provides useful recommendations for administrational practices seeking to understand consumer behavior, build appropriate marketing and communication campaigns and attract customers to buy environmentally friendly products.Originality/valueThis study makes efforts to resolve the attitude-intention-behavior gap, a recurring theme in the green consumption literature, as well as illustrates the significance of Big Five personality traits in explaining attitude, intention and behavior when purchasing green products. This research also demonstrates that Big Five personality traits have significantly different effects on green consumption attitudes and intention to carry out pro-behavioral consumption.
Benchmarking the outsourcing factors of third-party logistics services selection: analysing influential strength and building a sustainable decision model
Authors: Khan Sharfuddin Ahmed , Alkhatib Shahed , Ammar Zaina , Moktadir Md. Abdul , Kumar Anil 
Published: September 2021

PurposeOutsourcings always affect crucial supply chain functions concerning flexibility and cost. During the decision to outsource and consider third-party logistics service provider selection, decision-makers need to pay more attention to certain critical outsourcing factors such as coordination, integration and cooperation as these key factors are essential to improve overall supply chain performance. The main purpose of this work is to identify the inter-relations among outsourcing decision factors to highlight the most important and influential factors that should be considered and carefully thought through when making outsourcing sustainable decisions.Design/methodology/approachA two-phased methodology has been used in this study. In the first phase, outsourcing decision factors are identified from existing literature and validated by decision-makers from industry and academia. To understand the influential strength and build a sustainable model, the decision-making trial and evaluation laboratory method is used. A courier company in the UAE is considered for implementation.FindingsAll identified and validated factors are segregated into two categories (cause and effect). The result shows that the most influential factors are developing strategic alliances, uncertainty and risk mitigation and deficiency of internal resources for a service.Practical implicationsThere are several insights for industry managers and practitioners. The results of the study may help practitioners and logistics managers to make the logistics service sustainable and more efficient for businesses.Originality/valueThis study focusses on a courier company to understand the interdependencies among outsourcing decision factors; this is unique in this field of literature.
The effect of abusive supervision on safety behaviour of Chinese underground miners: a multi-level moderated mediation analysis
Authors: Ye Xinfeng , Cai Shaohan , Wang Zhining 
Published: September 2021

Purpose
Prior research has suggested that abusive supervision has negative impacts on various work outcomes. However, little attention has been paid to the relationship between abusive supervision and employees’ safety behaviour. The purpose of this study is, therefore, to address these limitations by developing and testing a theoretically based conceptual model that explicitly considers the underlying mechanism and boundary condition of the relationship between abusive supervision and safety behaviour of underground coal miners in China.

Design/methodology/approach
At Time 1, the authors conducted a survey of 630 employees to assess their supervisors’ abusive leadership behaviours, their own power distance beliefs and their self-reflection. At Time 2, the authros sent questionnaires to the leaders and invited them to evaluate employees’ safety behaviour in the workplace. After cleaning the survey data, the authors tested our model using a multi-level analysis on a sample (n = 458) of underground miners across 96 coal mining sites in China.

Findings
The authors propose that abusive supervision decreases employees’ safety compliance/participation by reducing reflection but strengthening rumination. The authors further find that the linkage from abusive supervision to reflection/rumination to safety compliance/participation is affected by power distance.

Originality/value
To the best of the authors’ knowledge, This is one of the first empirical studies to investigate the mediating effects of a deep cognitive processing variable – namely, self-reflection – and the moderating effects of power distance on the relationship between abusive supervision and safety behaviour.
Efficient partial product reduction for image processing application using approximate 4:2 compressor
Authors: Kattekola Naresh , Jawale Amol , Nath Pallab Kumar , Majumdar Shubhankar 
Published: September 2021

Purpose
This paper aims to improve the performance of approximate multiplier in terms of peak signal to noise ratio (PSNR) and quality of the image.

Design/methodology/approach
The paper proposes an approximate circuit for 4:2 compressor, which shows a significant amount of improvement in performance metrics than that of the existing designs. This paper also reports a hybrid architecture for the Dadda multiplier, which incorporates proposed 4:2 compressor circuit as a basic building block.

Findings
Hybrid Dadda multiplier architecture is used in a median filter for image de-noising application and achieved 20% more PSNR than that of the best available designs.

Originality/value
The proposed 4:2 compressor improves the error metrics of a Hybrid Dadda multiplier.