bluuebunny/crossref_metadata_2025_split huggingface dataset:
SP2G: an imaging and analysis pipeline revealing the inter and intra-patient migratory diversity of glioblastoma
Authors: Crestani Michele , Kakogiannos Nikolaos , Iannelli Fabio , Dini Tania , Maderna Claudio , Giannotta Monica , Pelicci Giuliana , Maiuri Paolo , Monzo Pascale , Gauthier Nils C. 
Published: February 2023

AbstractGlioblastomas are heterogeneous, primary brain tumors hiding several sub-populations. Patient-derived xenografts are considered gold-standards to study glioblastoma invasion. However, they present many disadvantages, including time consumption, complex standardization, high cost. To counteract these issues and rapidly identify the most invasive sub-populations, we developed anin vivomimicry platform named SP2G (SPheroid SPreading on Grids). Live imaging of tumor-derived spheroids spreading on gridded micro patterns mimicking the brain vasculature recapitulated 3D motility features observed in brain or 3D matrices. Using patient-derived samples coupled with a semi-automated macro suite, SP2G easily characterized and sorted differences in cell migration and motility modes. Moreover, SP2G exposed the hidden intra-patient heterogeneity in cell motility that correlated molecularly to specific integrins. Thus, SP2G constitute a versatile and potentially pan-cancer workflow to identify the diverse invasive tumor sub-populations in patient-derived specimens. SP2G includes an integrative tool, available as open-source Fiji macro suite, for therapeutic evaluations at single patient level.TeaserCracking the inter and intra-patient diversity in Glioblastoma migration profiles
Evaluation of Known Human PDE Inhibitors Against Nematode PDE4s
Authors: Anindya Clianta S , Hoffman Charles S 
Published: February 2023

AbstractParasitic nematodes are responsible for more than one and a half billion infections world-wide. The drugs developed against these infections only target a few different proteins. As drug resistance is becoming more common, there is a need to develop new drugs against new targets. Cyclic Nucleotide Phosphodiesterases (PDEs), are enzymes that hydrolyze the cyclic molecules of cyclic AMP and cyclic GMP. Physical properties of mammalian PDEs have led them to become well-established as drug targets. Mammals possess 11 families of PDEs, many of which are the target of selective and potent drugs. Nematodes have 6 PDE genes representing 6 families, which have not been well-studied;C. elegans, is a model organism nematode that would allow people to assess the therapeutic benefit of targeting PDEs. The Hoffman Lab has developed a platform for discovering PDE inhibitors and has carried out high-throughput screens (HTS) to help identify inhibitors of mammalian PDE4, PDE7, PDE8, and PDE11 families. The PDE4 family inC. elegansis of particular interest as work inC. eleganssuggests that it may be involved in neuronal function. However, research has shown that two compounds developed against mammalian PDE4s generally do not work onC. elegansPDE4. Therefore, the goal of this project is to screen a collection of compounds discovered by the Hoffman Lab to identify the compounds that will affectC. elegansor parasitic nematode PDE4s to find compounds that could then be tested for their effect onC. elegansand parasitic nematodes. This research could then identify an effective new target for drug development to treat infections by parasitic nematodes.SummaryParasitic nematodes are the soil worms responsible for more than one and a half billion infections around the world. While drugs are being developed against them, these drugs are designed against relatively few proteins, which is a problem as drug resistance becomes more common. Therefore, there is a need for new drugs. PDEs are enzymes that hydrolyze the signaling molecules cAMP and cGMP. Mammalian PDEs have been well-established as drug targets. In nematodes, there are 6 PDE genes representing 6 families of the 11 families found in mammals. Additionally, a free-living model organism nematode,Caenorhabditis elegans(C. elegans) can be used to assess the impact of PDE inhibition on nematode biology. In the Hoffman Lab, they have developed a platform for discovering PDE inhibitors and have used these in high throughput screens to identify inhibitors of mammalian PDE4, PDE7, PDE8, and PDE11 families. The PDE4 family inC. elegansis of particular interest as work inC. eleganssuggests that it may be involved in neuronal function. However, research has shown that compounds developed against mammalian PDE4s generally do not work onC. elegansPDE4. Therefore, by the end of this project we hope to identify the compounds that do work on nematode PDE4s that could be used to test whether they have the potential to treat these infections.
What confidence and the eyes can tell about interacting with a partner
Authors: Sanchez Rémi , Tomei Anne-Catherine , Mamassian Pascal , Vidal Manuel , Desantis Andrea 
Published: February 2023

AbstractPerceptual confidence reflects the ability to evaluate the evidence that supports perceptual decisions. It is thought to play a critical role in guiding decision-making, but only a few empirical studies have actually investigated the function of confidence. To address this issue, we designed a perceptual task in which participants provided a confidence judgment on the accuracy of their perceptual decision. Then, they viewed the response of a machine or human partner, and they were instructed to decide whether to keep or change their initial response. We observed that confidence predicted participants’ decision to keep or change their initial responses more than task difficulty and perceptual accuracy. This suggests that confidence, as a subjective evaluation of uncertainty, enables us to weigh our decisions, driving the interaction with a partner. Furthermore, confidence judgments could be predicted by pre-response pupil dynamics, suggesting that arousal changes are linked to confidence computations. This study contributes to our understanding of the function of confidence in decision-making and highlights the possibility of using pupil dynamics as a proxy of confidence.
PhageDPO: Phage Depolymerase Finder
Authors: Vieira Maria , Duarte José , Domingues Rita , Oliveira Hugo , Dias Oscar 
Published: February 2023

AbstractBacteriophages are the most predominant and genetically diverse biological entities on Earth. They are bacterial viruses which encode numerous proteins with potential antibacterial activity. However, most bacteriophage-encoded proteins have no assigned function, hindering the discovery of novel antibacterial agents. In particular, there has been a growing interest in exploring recombinant bacteriophage depolymerases from the fundamental standpoint, but mostly for biotechnological applications to control bacterial pathogens. Due to the lack of efficient identification tools, we developedPhageDPO, the first developed tool that predicts depolymerases in bacteriophage genomes using machine learning methods.Availability and implementationPhageDPOwas integrated into a Galaxy framework available online at: bit.ly/phagedpo.
The level of Nck rather than N-WASP determines the rate of actin-based motility of Vaccinia
Authors: Basant Angika , Way Michael 
Published: February 2023

ABSTRACTVaccinia virus exiting from host cells activates Src/Abl kinases to phosphorylate A36, an integral membrane viral protein. Phosphorylated A36 binds the adaptors Nck and Grb2 which recruit N-WASP to activate Arp2/3-driven actin polymerisation to promote viral spread. A36 also recruits intersectin, which enhances actin polymerization via AP-2/clathrin and Cdc42. How many viral and host molecules does vaccinia hijack to induce actin polymerization? To advance our quantitative understanding of this process, we now determined absolute numbers of the essential molecules in the vaccinia signalling network using fluorescent molecule counting approaches in live cells. There are 1156±120 A36 molecules on virus particles inducing actin polymerization in HeLa cells. This number, however, is over 2000 in mouse embryonic fibroblasts (MEFs), suggesting that A36 levels on the virion are not fixed. In MEFs, viruses recruit 1032±200 Nck and 434±10 N-WASP molecules, suggesting a ratio of 4:2:1 for the A36:Nck:N-WASP signalling network. Loss of A36 binding to either secondary adaptors Grb2 or intersectin results in a 1.3- and 2.5-fold reduction in Nck respectively. Curiously, despite recruiting comparable numbers of the Arp2/3 activator, N-WASP (245±26 and 276±66), these mutant viruses move at different speeds that inversely correlate with the number of Nck molecules. Our analysis has uncovered two unexpected new aspects of Vaccinia virus egress, numbers of the viral protein A36 can vary in the virion membrane and the velocity of virus movement depends on the levels of the adaptor protein Nck.
mTORC1-mediated acquisition of reward-related spatial representations by hippocampal somatostatin interneuronsa
Authors: Michon François-Xavier , Laplante Isabel , Bosson Anthony , Robitaille Richard , Lacaille Jean-Claude 
Published: February 2023

AbstractPlasticity of principal cells and inhibitory interneurons underlies hippocampal memory. Bidirectional modulation of somatostatin cell mTORC1 activity, a crucial translational control mechanism in synaptic plasticity, causes parallel changes in hippocampal CA1 somatostatin interneuron (SOM-IN) long-term potentiation and hippocampus-dependent memory, indicating a key role in learning. However, SOM-IN activity changes and behavioral correlates during learning, and the role of mTORC1 in these processes, remain ill-defined. To address these questions, we used two-photon Ca2+imaging from SOM-INs during a virtual reality goal-directed spatial memory task in head-fixed control mice (SOM-IRES-Cre mice) or in mice with conditional knockout ofRptor(SOM-Rptor-KO mice) to block mTORC1 activity in SOM-INs. We found that control mice learn the task, but SOM-Raptor-KO mice exhibit a deficit. Also, SOM-IN Ca2+activity became increasingly related to reward localization during learning in control mice but not in SOM-Rptor-KO mice. Four types of SOM-IN activity patterns related to reward location were observed, “reward off sustained”, “reward off transient”, “reward on sustained” and “reward on transient”, and these responses showed global remapping after reward relocation in control but not SOM-Rptor-KO mice. Thus, SOM-INs develop mTORC1-dependent spatial coding related to learning reward localization. This coding may bi-directionally interact with pyramidal cells and other structures to represent and consolidate reward location.
A Recombinant Approach For Stapled Peptide Discovery Yields Inhibitors of the RAD51 Recombinase
Authors: Pantelejevs Teodors , Zuazua-Villar Pedro , Koczy Oliwia , Counsell Andrew , Walsh Stephen J. , Robertson Naomi S. , Spring David R. , Downs Jessica , Hyvönen Marko 
Published: February 2023

AbstractStapling is a macrocyclisation method that connects amino acid side chains of a peptide to improve its pharmacological properties. We describe an approach for stapled peptide preparation and biochemical evaluation that combines recombinant expression of fusion constructs of target peptides and cysteine-reactive divinyl-heteroaryl chemistry, as an alternative to solid-phase synthesis. We then employ this workflow to prepare and evaluate BRC-repeat-derived inhibitors of the RAD51 recombinase, showing that a diverse range of secondary structure elements in the BRC repeat can be stapled without compromising binding and function. Using X-ray crystallography, we elucidate the atomic-level features of the staple moieties. We then demonstrate that BRC-repeat-derived stapled peptides can disrupt RAD51 function in cells following ionising radiation treatment.
Themisto: a scalable coloredk-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes
Authors: Alanko Jarno N. , Vuohtoniemi Jaakko , Mäklin Tommi , Puglisi Simon J. 
Published: February 2023

AbstractMotivationHuge data sets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these data sets, efficient indexing data structures — that are both scalable and provide rapid query throughput — are paramount.ResultsHere, we present Themisto, a scalable coloredk-mer index designed for large collections of microbial reference genomes, that works for both short and long read data. Themisto indexes 179 thousandSalmonella entericagenomes in 9 hours. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 thousand genomes in the same time. In pseudoalignment, these other tools were either an order of magnitude slower than Themisto, or used an order of magnitude more memory. Themisto also offers superior pseudoalignment quality, achieving a higher recall than previous methods on Nanopore read sets.Availability and implementationThemisto is available and documented as a C++ package athttps://github.com/algbio/themistoavailable under the GPLv2 license.Contactjarno.alanko@helsinki.fiSupplementary informationSupplementary data are available atBioinformaticsonline.
Multi-modal Proteomic Characterization of Lysosomal Function and Proteostasis in Progranulin-Deficient Neurons
Authors: Hasan Saadia , Fernandopulle Michael S. , Humble Stewart W. , Frankenfield Ashley M. , Li Haorong , Prestil Ryan , Johnson Kory R. , Ryan Brent J. , Wade-Martins Richard , Ward Michael E. , Hao Ling 
Published: February 2023

AbstractProgranulin (PGRN) is a lysosomal protein implicated in various neurodegenerative diseases. Over 70 mutations discovered in theGRNgene all result in reduced expression of PGRN protein. However, the detailed molecular function of PGRN within lysosomes and the impact of PGRN deficiency on lysosomal biology remain unclear. Here we leveraged multifaceted proteomic techniques to comprehensively characterize how PGRN deficiency changes the molecular and functional landscape of neuronal lysosomes. Using lysosome proximity labeling and immuno-purification of intact lysosomes, we characterized lysosome compositions and interactomes in both human induced pluripotent stem cell (iPSC)-derived glutamatergic neurons (i3Neurons) and mouse brains. Using dynamic stable isotope labeling by amino acids in cell culture (dSILAC) proteomics, we measured global protein half-lives in i3Neurons for the first time and characterized the impact of progranulin deficiency on neuronal proteostasis. Together, this study indicated that PGRN loss impairs the lysosome’s degradative capacity with increased levels of v-ATPase subunits on the lysosome membrane, increased catabolic enzymes within the lysosome, elevated lysosomal pH, and pronounced alterations in neuron protein turnover. Collectively, these results suggested PGRN as a critical regulator of lysosomal pH and degradative capacity, which in turn influences global proteostasis in neurons. The multi-modal techniques developed here also provided useful data resources and tools to study the highly dynamic lysosome biology in neurons.
Prediction of failure in reorganization agreements under Colombia's Corporate Insolvency Act
Authors: Abinzano Isabel , Bonilla Harold , Muga Luis 
Published: February 2023

PurposeThe aim of this paper is to provide an overview of the impact of the implementation of Colombian Corporate Insolvency Act 1116 of 2006 in the period 2008–2018 and to assess the relevance of a broad set of financial predictors, as well as variables related to the economic context or the characteristics of the process itself, in explaining the failure of reorganization processes.Design/methodology/approachBoth logit and probit models are estimated, starting from a large number of variables proposed in the literature which are then narrowed down to a final selection based on their individual significance and machine learning.FindingsThe results show the prevalence of a limited number of financial variables related to equity, indebtedness, profits and liquidity as predictors of the failure of reorganization processes. The use of financial information from the year prior to the completion of the reorganization improves predictive accuracy and reliability. The debt-to-equity indicator provides no significant explanatory power, while voluntary entry into a reorganization process favors its success.Originality/valueWhile financial and accounting information is used across the literature to predict insolvency events, it is used here to predict success or failure in reorganization processes under the conditions imposed by a specific legislative act in a Latin American context.
Design of service network for containerized export by multimodal transportation: with quality concept
Authors: Dua Aman , Chhabra Rishika , Sinha Deepankar 
Published: February 2023

PurposeThe first purpose is to assess the quality of containerized multimodal export and the second is to develop and demonstrate the design of a service network with quality approach.Design/methodology/approachThe article used the structural equation model to develop a model to measure the quality of multimodal transportation for containerized exports and finalized the model with an alternative approach. The evolutionary algorithm had been used to design a service network based on quality.FindingsProvided factors affecting quality of multimodal transportation and reverse to one hypothesis, the construct variation in cost, time shape and quantity did not affect the quality of multimodal transportation for containerized exports. The model without variation construct was finalized by exploring causality.Research limitations/implicationsThis research had scope till container loading onto the vessel and assessed the quality for containerized cargo only, and second research purpose is limited by assumed values of fitness function and the limited number of nodes, in service network design demonstration.Practical implicationsThis research provided a tool to measure the quality of multimodal transportation for containerized exports and demonstrated the field application of the model developed in service network design. This approach included all factors applicable across the container movement. The integrated approach of the article provided an organized method to design a service network for containerized exports.Originality/valueThis work provided the tool to assess the quality of multimodal transportation for containerized exports and developed an approach to design a service network of multimodal transportation based on quality. This approach has considered the factors of multimodal transportation comprehensively in contrast to the optimization approaches based on operation research techniques.
Modern-day marketing concepts based on face recognition and neuro-marketing: a review and future research directions
Authors: Srivastava Gautam , Bag Surajit 
Published: February 2023

PurposeData-driven marketing is replacing conventional marketing strategies. The modern marketing strategy is based on insights derived from customer behavior information gathered from their facial expressions and neuro-signals. This study explores the potential for face recognition and neuro-marketing in modern-day marketing.Design/methodology/approachThe study conducts an in-depth examination of the extant literature on neuro-marketing and facial recognition marketing. The articles for review are downloaded from the Scopus database, and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) is then used to screen and choose the relevant papers. The systematic literature review method is applied to conduct the study.FindingsAn extensive review of the literature reveals that the domains of neuro-marketing and face recognition marketing remain understudied. The authors’ review of selected papers delivers five neuro-marketing and facial recognition marketing themes that are essential to modern marketing concepts.Practical implicationsNeuro-marketing and facial recognition marketing are artificial intelligence (AI)-enabled marketing techniques that assist in gaining cognitive insights into human behavior. The findings would be of use to managers in designing marketing strategies to enhance their marketing approach and boost conversion rates.Originality/valueThe uniqueness of this study lies in that it provides an updated review on neuro-marketing and face recognition marketing.
Sustainability study of electric vehicles performance in the UAE: moderated by blockchain
Authors: Sundarakani Balan , Rajamani Haile-Selassie , Madmoune Anas 
Published: February 2023

PurposeThe UAE has set an ambitious target to become one of the most sustainable countries in the world. In addition, the country's infrastructure is playing a pivotal role in terms of electric vehicle (EV) usability with regard to its roads, power generation capacity, availability of charging stations and the drive towards customer adoption. The readiness for EVs in the UAE is assessed in this study as part of its development towards its sustainable target. This research aims to study EV readiness among the UAE car users from a sustainability perspective.Design/methodology/approachThe proposed methodology follows with a comprehensive literature review to identify the various drivers of EV readiness and their contribution to sustainability. A list of hypotheses was developed based on the identified drivers to EV readiness. A questionnaire survey was designed to validate the hypothesis, and data were collected from consumers in the UAE. In total, 140 complete responses were received across different consumers and the results were studied using partial least square based structural equation modeling (PLS-SEM) method.FindingsAn initial framework for EV readiness was developed, and analyses of the variables that are driving the relationships was done. The analysis confirmed that quality of service, power quality and infrastructure are positively linked to EV readiness in the UAE. However, the role of blockchain as a moderator to enhance the relationship between power quality, infrastructure and sustainability is not significant, indicating blockchain adoption in the UAE is still nascent in nature. However, its adoption has some potential to save energy.Research limitations/implicationsThe research is limited to the UAE region in terms of sample collection and respondents' profile. Further, research on EV readiness seemed to be early at present and therefore this research on EV readiness and its associated variables could set future research directions.Originality/valueLogistics industry and automotive industries will benefit from the outcomes of the study especially while operating in the UAE. Also, the research recommends EV makers to understand the relationship between quality of service, power quality, infrastructure, EV readiness and sustainability in order to move towards a more sustainable transportation future.