bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective G protein signaling driven by Substance P-Neurokinin Receptor structural dynamics
Authors: Harris Julian A. , Faust Bryan , Gondin Arisbel B. , Dämgen Marc André , Suomivuori Carl-Mikael , Veldhuis Nicholas A. , Cheng Yifan , Dror Ron O. , Thal David M. , Manglik Aashish 
Published: May 2021

AbstractThe neuropeptide Substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via Gqand Gsproteins. Neurokinin A also activates NK1R, but leads to selective Gqsignaling. How two stimuli yield distinct G-protein signaling at the same G-protein-coupled-receptor remains unclear. We determined cryo-EM structures of active NK1R bound to SP or the Gq-biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent Gssignaling but not Gqsignaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility deep in the NK1R pocket. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G-protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.
Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations
Authors: Othman Houcemeddine , da Rocha Jorge , Hazelhurst Scott 
Published: May 2021

AbstractPharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequencing showed that a large proportion of the variants for these genes are rare in African populations. This study investigates the impact of such variants on protein structure to assess their functional importance. We use genetic data of CYP3A5 from 458 individuals from sub-Saharan Africa to conduct a structural bioinformatics analysis. Five missense variants were modeled and microsecond scale molecular dynamics simulations were conducted for each, as well as for the CYP3A5 wildtype, and the Y53C variant, which has a known deleterious impact on enzyme activity. The binding of ritonavir and artemether to CYP3A5 variant structures was also evaluated. Our results showed different conformational characteristics between all the variants. No significant structural changes were noticed. However, the genetic variability acts on the plasticity of the protein. The impact on drug binding may be drug dependant. We conclude that rare variants hold relevance in determining the pharmacogenomics properties of populations. This could have a significant impact on precision medicine applications in sub-Saharan Africa.
Activation of thalamo-cortical circuits with posterior hypothalamic nucleus deep brain stimulation
Authors: Young Calvin K. , Bland Brian H. 
Published: May 2021

AbstractThe posterior hypothalamic nucleus (PH) has extensive anatomical connections to motor, cognitive, visceral, and homeostatic areas of the brain and serves as a crucial subcortical modulator of behaviour. Previous studies have demonstrated that deep brain stimulation (DBS) of this area can lead to powerful activation of motor behaviour, overcoming two rodent models of parkinsonian akinesia by increasing neocortical excitability. However, it is unclear how the PH may mediate this increase in neocortical excitability. In the present study, we examined the role of the thalamus in the PH-DBS mediated increase in neocortical excitability. In urethane anaesthetized animals, we demonstrate that PH-DBS elicits increased spiking activity in the motor thalamus (VL) that receives direct afferents from the PH that precedes the increase in spiking activity in the corresponding motor cortex. In contrast, in the somatosensory thalamus (VPM) where PH afferents are sparse at best, PH-DBS did not elicit an increase in thalamic activity despite of a slight increase in the corresponding somatosensory cortical spiking. Current source density analyses suggest a thalamo-cortical mechanism for motor cortex activation whereas a cortico-cortical activation mechanism is involved in somatosensory cortical activation. Inactivation of the VL resulted in the abolition of motor cortex spiking despite of the persistence of desynchronized field potential activity. Collectively, these data suggest indirect orthodromic activation of PH output fibres to the thalamus mediates increased neocortical excitation, which may spread through cortico-cortical connections and lead to an increase in integrated, non-stereotypical motor behaviour.
Metabolic Dynamics inEscherichia coli-based Cell-Free Systems
Authors: Miguez April M. , Zhang Yan , Piorino Fernanda , Styczynski Mark P. 
Published: May 2021

AbstractThe field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metabolic activity that is poorly understood yet has a significant impact on CFE productivity. Here, we use metabolomics to characterize the temporal metabolic changes in CFE systems and their constituent components, including significant metabolic activity in central carbon and amino acid metabolism. We find that while changing the reaction starting state via lysate pre-incubation impacts protein production, it has a comparatively small impact on metabolic state. We also demonstrate that changes to lysate preparation have a larger effect on protein yield and temporal metabolic profiles, though general metabolic trends are conserved. Finally, while we improve protein production through targeted supplementation of metabolic enzymes, we show that the endogenous metabolic activity is fairly resilient to these enzymatic perturbations. Overall, this work highlights the robust nature of CFE reaction metabolism as well as the importance of understanding the complex interdependence of metabolites and proteins in CFE systems to guide optimization efforts.Abstract FigureAbstract Figure
Arp2/3 mediated dynamic lamellipodia of the hPSC colony edges promote liposome-based DNA delivery
Authors: Surma Michelle , Anbarasu Kavitha , Das Arupratan 
Published: May 2021

AbstractCationic liposome-mediated delivery of drugs, DNA, or RNA plays a pivotal role in small molecule therapy, gene editing, and immunization. However, our current knowledge regarding the cellular structures that facilitate this process remains limited. Here, we used human pluripotent stem cells (hPSCs), which form compact colonies consisting of dynamically active cells at the periphery and epithelial-like cells at the core. We discovered that cells at the colony edges selectively got transfected by cationic liposomes through Arp2/3 dependent dynamic lamellipodia, which is augmented by myosin II inhibition. Conversely, cells at the core establish tight junctions at their apical surfaces, impeding liposomal access to the basal lamellipodia and thereby inhibiting transfection. In contrast, liposomes incorporating mannosylated lipids are internalized throughout the entire colony via receptor-mediated endocytosis. These findings contribute a novel mechanistic insight into enhancing therapeutic delivery via liposomes, particularly in cell types characterized by dynamic lamellipodia, such as immune cells, or those comprising the epithelial layer.Significance StatementDrug or gene delivery to human cells is essential for effective treatment. Cationic liposomes provide a safe delivery vehicle compared to viruses. However, the cellular structures required for internalizing liposomes are not yet fully understood. Using human stem cells which grow in compact colonies with more dynamic cells at the periphery and epithelial like cells at the center, here we discovered that Arp2/3 dependent dynamic lamellipodia promotes cationic liposome delivery in dynamic cells while receptor mediated endocytosis is required for epithelial cells. This is significant as it provides mechanisms for enhancing liposome delivery to both migratory and epithelial cells in our body.Abstract FigureGraphical AbstractMechanisms for liposome transfection to the lamellipodial or epithelial cells.Data shown here suggest cationic liposomes fuse with the negatively charged dynamic lamellipodia membrane in an Arp2/3 dependent manner and the process is enhanced by Myosin II inhibition, such as with the stem cell colony edge cells. However, cells more epithelial in nature such as those inside the stem cell colony center do not possess dynamic lamellipodia at the apical surface, rather they form tight junctions which inhibit cationic liposome transfection. Epithelial cells rely on receptor mediated endocytosis in both Myosin II dependent and independent manners to internalize liposomes with lipids that contain ligands for cell surface receptors such as mannose.
Restoration of DNA Integrity and Cell Cycle by Electric Stimulation in Planarian Tissues Damaged by Ionizing Radiation
Authors: Davidian Devon , LeGro Melanie , Barghouth Paul G. , Rojas Salvador , Ziman Benjamin , Maciel Eli Isael , Ardell David , Escobar Ariel L. , Oviedo Néstor J. 
Published: May 2021

AbstractExposure to high levels of ionizing γ-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally γ-irradiated tissues of the planarian flatwormSchmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse damaging effects of high dose γ-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.
High-throughput Raman-activated cell sorting in the fingerprint region
Authors: Lindley Matthew , de Pablo Julia Gala , Peterson Jorgen Walker , Isozaki Akihiro , Hiramatsu Kotaro , Goda Keisuke 
Published: May 2021

AbstractCell sorting is the workhorse of biological research and medicine. Cell sorters are commonly used to sort heterogeneous cell populations based on their intrinsic features. Raman-activated cell sorting (RACS) has recently received considerable interest by virtue of its ability to discriminate cells by their intracellular chemical content, in a label-free manner. However, broad deployment of RACS beyond lab-based demonstrations is hindered by a fundamental trade-off between throughput and measurement bandwidth (i.e., cellular information content). Here we overcome this trade-off and demonstrate broadband RACS in the fingerprint region (300 − 1,600 cm−1) with a record high throughput of ~50 cells per second. This represents a 100× throughput increase compared to previous demonstrations of broadband fingerprint-region RACS. To show the utility of our RACS, we demonstrate real-time label-free sorting of microalgal cells based on their accumulation of carotenoids and polysaccharide granules. These results hold promise for medical, biofuel, and bioplastic applications.
Lipid Bilayer Induces Contraction of the Denatured State Ensemble of a Helical-Bundle Membrane Protein
Authors: Gaffney Kristen A. , Guo Ruiqiong , Bridges Michael D. , Chen Daoyang , Muhammednazaar Shaima , Kim Miyeon , Yang Zhongyu , Schilmiller Anthony L. , Faruk Nabil F. , Peng Xiangda , Jones A. Daniel , Sun Liangliang , Hubbell Wayne L. , Sosnick Tobin R. , Hong Heedeok 
Published: May 2021

AbstractDefining the denatured state ensemble (DSE) and intrinsically disordered proteins is essential to understanding protein folding, chaperone action, degradation, translocation and cell signaling. While a majority of studies have focused on water-soluble proteins, the DSE of membrane proteins is much less characterized. Here, we reconstituted the DSE of a helical-bundle membrane protein GlpG of Escherichia coli in native lipid bilayers and measured the DSE’s conformation and compactness. The DSE was obtained using steric trapping, which couples spontaneous denaturation of a doubly biotinylated GlpG to binding of two bulky monovalent streptavidin molecules. Using limited proteolysis and mass spectrometry, we mapped the flexible regions in the DSE. Using our paramagnetic biotin derivative and double electron-electron resonance spectroscopy, we determined the dimensions of the DSE. Finally, we employed our Upside model for molecular dynamics simulations to generate the DSE including the collapsed and fully expanded states in a bilayer. We find that the DSE is highly dynamic involving the topology changes of transmembrane segments and their unfolding. The DSE is expanded relative to the native state, but only to 55–90% of the fully expanded condition. The degree of expansion depends on the chemical potential with regards to local packing and the lipid composition. Our result suggests that the E. coli’s native lipid bilayer promotes the association of helices in the DSE of membrane proteins and, probably in general, facilitating interhelical interactions. This tendency may be the outcome of a general lipophobic effect of proteins within the cell membranes.SignificanceHere, we delineate the conformation of the denatured state ensemble (DSE) of a membrane protein confined in a native lipid bilayer and assay whether the bilayer permits full expansion or nonspecific collapse of the DSE. Using the intramembrane protease GlpG as a model, we find that the denatured state is a dynamic ensemble involving topological changes and local unfolding of transmembrane segments. The bilayer tends to contract the DSE relative to the fully lipid-solvated, expanded conformations while the degree of compactness is determined by the balance between protein-lipid, lipid-lipid and protein-protein interactions. These findings provide new insights into the lipid bilayer as a solvent that mediates folding, chaperone action, turnover and protein-protein interactions in cell membranes.
Biochar alters soil properties, microbial community diversity, and enzyme activities, while decreasing conifer performance
Authors: Nash Jake , Miesel Jessica , Bonito Gregory , Sakalidis Monique , Ren Han , Warnock Daniel , Tiemann Lisa 
Published: May 2021

AbstractBiochars are porous charcoal-like materials that can enhance soil health and plant growth, but its use has not been adequately evaluated in woody cropping systems. We set up an experimental Christmas tree plantation on a Marlette series soil amended with two types of biochar and conducted two studies on the impacts of biochar on the agroecosystem over three years following establishment. The first study investigated the effects of biochar on plant performance, soil physicochemical properties and extracellular enzyme activities, while the second investigated the response of the root-associated fungal community. Both biochars stimulated five extracellular enzyme activities, with increases of between 67% and 446%. Structural equation modelling identified increases to dissolved organic carbon and soil moisture as potential mechanisms of biochar’s effects on enzyme activities. Tree growth and survival were negatively affected by biochar application, depending on the tree species and biochar applied, which may have been due to induced nitrogen limitation. High-throughput sequencing showed that biochar decreased the diversity of root-associated fungal communities, with the ectomycorrhizal species Wilcoxina mikolae reaching levels of hyper-dominance on balsam fir in response to one of the biochars. Further studies should investigate how biochar can be harnessed to remediate specific soil quality issues or restructure soil ecosystems in ways that improve crop performance.
M-GAN-XGBOOST model for sales prediction and precision marketing strategy making of each product in online stores
Authors: Wang Song , Yang Yang 
Published: May 2021

PurposeThe rapid development of e-commerce has brought not only great convenience to people but a great challenge to online stores. Phenomenon such as out of stock and slow sales has been common in recent years. These issues can be managed only when the occurrence of the sales volume is predicted in advance, and sufficient warnings can be executed in time. Thus, keeping in mind the importance of the sales prediction system, the purpose of this paper is to propose an effective sales prediction model and make digital marketing strategies with the machine learning model.Design/methodology/approachBased on the consumer purchasing behavior decision theory, we discuss the factors affecting product sales, including external factors, consumer perception, consumer potential purchase behavior and consumer traffic. Then we propose a sales prediction model, M-GNA-XGBOOST, using the time-series prediction that ensures the effective prediction of sales about each product in a short time on online stores based on the sales data in the previous term or month or year. The proposed M-GNA-XGBOOST model serves as an adaptive prediction model, for which the instant factors and the sales data of the previous period are the input, and the optimal computation is based on the proposed methodology. The adaptive prediction using the proposed model is developed based on the LSTM (Long Short-Term Memory), GAN (Generative Adversarial Networks) and XGBOOST (eXtreme Gradient Boosting). The model inherits the advantages among the algorithms with better accuracy and forecasts the sales of each product in the store with instant data characteristics for the first time.FindingsThe analysis using Jingdong dataset proves the effectiveness of the proposed prediction method. The effectiveness of the proposed method is enhanced and the accuracy that instant data as input is found to be better compared with the model that lagged data as input. The root means squared error and mean absolute error of the proposed model are found to be around 11.9 and 8.23. According to the sales prediction of each product, the resource can be arranged in advance, and the marketing strategy of product positioning, product display optimization, inventory management and product promotion is designed for online stores.Originality/valueThe paper proposes and implements a new model, M-GNA-XGBOOST, to predict sales of each product for online stores. Our work provides reference and enlightenment for the establishment of accurate sales-based digital marketing strategies for online stores.
A BIM-lean framework for digitalisation of premanufacturing phases in offsite construction
Authors: Barkokebas Beda , Khalife Salam , Al-Hussein Mohamed , Hamzeh Farook 
Published: May 2021

PurposeThe research introduces means for improving premanufacturing processes (design, procurement and bidding) by leveraging digitalisation in offsite construction. Specifically, this paper proposes a framework that provides measures for the planning and implementation of digitalisation in offsite construction by positioning building information modelling (BIM) as the key technology and lean principles to add value and reduce waste.Design/methodology/approachThe paper follows the design science research approach to develop the proposed framework and attain the aforementioned objective. The developed framework includes data collection, value-stream mapping and simulation to assess current processes, develop and propose improvements. An empirical implementation is employed to demonstrate the applicability of both the framework and the measures used to evaluate the outcomes.FindingsThe application of the proposed three-stage framework resulted in 9.45%–23.33%-time reduction per year for the various improvement categories in premanufacturing phases. Employing simulation and applying the developed measures provide incentive for upper management to adopt the suggested improvements. Additionally, while the empirical implementation was tested on a modular construction company, the methods used indicate that the framework, with its generic guidelines, could be applied and customized to any offsite company.Originality/valueWhile several studies propose that BIM-Lean integration offers an advantage in the context of production systems, this paper focuses on the initial design and planning phases, which are mostly overlooked in the literature. Moreover, the present study provides quantitative evidence of the benefits of data integration through BIM technology.
Planet Abled: can it sustain its first-mover advantage and scale-up?
Authors: Sharma Anita , Ghuman Karminder 
Published: May 2021

Learning outcomes
This paper aims to enable the application of Value Proposition Canvas and Business Model Canvas to evaluate an opportunity; understand the commonalities and differences between social and commercial enterprises; and recognize the challenges related to the paradox of the social mission and the financial/economic logic.

Case overview/synopsis
Neha Arora demonstrated exceptional capabilities of defying the social stigma associated with People with Disabilities (PwDs) to establish Planet Abled, a first in the world venture to provide accessible leisure excursions to PwDs. This entrepreneurial initiative enabling group and solo travel for PwDs as inclusive tourism has created the possibility of social sustainability by bringing change in the lives of PwDs and their family members by ignoring either the insensitive or overprotective societal attitudes and lack of infrastructure concerning travel for PwDs. Its potential growth qualifies for scaling-up, but it can also attract the existing big travel solution providers to enter this domain. Considering these facts, Neha faces multiple dilemmas: How can she sustain and scale up the early momentum created by her enterprise? How can she resolve the challenges related to the paradox of the social mission and the financial/ economic logic while scaling-up Planet Abled?

Complexity/Academic level
This case study is suitable for both undergraduate or graduate-level programs in the area of entrepreneurship.

Supplementary materials
Teaching Notes are available for educators only.

Subject code
CSS 3: Entrepreneurship