bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping lineage-traced cells across time points with moslin
Authors: Lange Marius , Piran Zoe , Klein Michal , Spanjaard Bastiaan , Klein Dominik , Junker Jan Philipp , Theis Fabian J. , Nitzan Mor
Published: April 2023

Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making beyond simpler pseudotime-based approaches. However, it is currently unclear how lineage and gene expression information across experimental time points can be combined in destructive experiments, which is particularly challenging for in-vivo systems. Here we present moslin, a Fused Gromov-Wasserstein-based model to couple matching cellular profiles across time points. In contrast to existing methods, moslin leverages both intra-individual lineage relations and inter-individual gene expression similarity. We demonstrate on simulated and real data that moslin outperforms state-of-the-art approaches that use either one or both data modalities, even when the lineage information is noisy. OnC. elegansembryonic development, we show how moslin, combined with trajectory inference methods, predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration. We anticipate moslin to play a crucial role in deciphering complex state change trajectories from lineage-traced single-cell data.
GraphPart: Homology partitioning for biological sequence analysis
Authors: Teufel Felix , Gíslason Magnús Halldór , Almagro Armenteros José Juan , Johansen Alexander Rosenberg , Winther Ole , Nielsen Henrik
Published: April 2023

When splitting biological sequence data for the development and testing of predictive models, it is necessary to avoid too closely related pairs of sequences ending up in different partitions. If this is ignored, performance estimates of prediction methods will tend to be exaggerated. Several algorithms have been proposed for homology reduction, where sequences are removed until no too closely related pairs remain. We present GraphPart, an algorithm for homology partitioning, where as many sequences as possible are kept in the dataset, but partitions are defined such that closely related sequences always end up in the same partition. Evaluation of GraphPart on Protein, DNA and RNA datasets shows that it is capable of retaining a larger number of sequences per dataset, while providing homology separation quality on par with reduction approaches.
Feasibility in MacArthur’s Consumer-Resource Model
Authors: Aparicio Andrea , Wang Tong , Saavedra Serguei , Liu Yang-Yu
Published: April 2023

Finding the conditions that ensure the survival of species has occupied ecologists for decades. Theoretically, for mechanistic models such as MacArthur’s consumer-resource model, most of the efforts have concentrated on proving the stability of an equilibrium assuming that it is feasible, but overlooking the conditions that ensure its feasibility. Here we address this gap by finding the range of conditions that lead to a feasible equilibrium of MacArthur’s consumer-resource model and study how changes in the system’s structural and parametric properties affect those ranges. We characterize the relationship between the loss of feasibility and the increase in complexity (measured by the system’s richness and connectance) by a power law that can be extended to random competition matrices. Focusing on the pool of consumers, we find that while the feasibility of the entire system decreases with the size of the pool, the expected fraction of feasible consumers increases —safety in consumer numbers. Focusing on the pool of resources, we find that if resources grow linearly, the larger the pool of resources, the lower the feasibility of the system and the expected fraction of feasible consumers —danger in resource numbers. However, if resources grow logistically, this pattern is reversed with a sublinear increase in feasibility, as it has been previously reported in experimental work. This work provides testable predictions for consumer-resource systems and is a gateway to exploring feasibility in other mechanistic models.
Total Chemical Synthesis of Glycosylated TREM2 Ectodomain
Authors: Wijegunawardena Gayani , Castillo Erika , Henrickson Brandy , Davis Regan , Condello Carlo , Wu Haifan
Published: April 2023

Mutations in a microglia-associated geneTREM2increase the risk of Alzheimer’s disease. Currently, structural and functional studies of TREM2 mainly rely on recombinant TREM2 proteins expressed from mammalian cells. However, using this method, it is difficult to achieve site-specific labeling. Here we present the total chemical synthesis of the 116 amino-acid TREM2 ectodomain. Rigorous structural analysis ensured correct structural fold after refolding. Treating microglial cells with refolded synthetic TREM2 enhanced microglial phagocytosis, proliferation, and survival. We also prepared TREM2 constructs with defined glycosylation patterns and found that glycosylation at N79 is critical to the thermal stability of TREM2. This method will provide access to TREM2 constructs with site-specific labeling, such as fluorescent labeling, reactive chemical handles, and enrichment handles, to further advance our understanding of TREM2 in Alzheimer’s disease.
Sexual Dimorphism in VEMP peak to trough Latency
Authors: Gattie Max , Lieven Elena V. M. , Kluk Karolina
Published: April 2023

The cervical vestibular-evoked myogenic potential (VEMP) was assessed in 24 women and 24 men having a mean age of 19.5 years (SD 0.7). Whilst there was no group difference in VEMP peak to trough (p1-n1) amplitude, VEMP p1-n1 latency was found to be shorter for women than for men by 2.4 ms (95% CI [–0.9, –3.9], chi squared (1) 9.6, p = 0.0020). This equates to 21% of the mean 11.4 ms VEMP p1-n1 latency across women and men. It is a reversal of findings in several prior studies, which are reviewed here. Statistical modelling based on the current study suggests some prior studies were underpowered to detect a sex difference in VEMP latency. Possible causes for sex difference in VEMPs are discussed. Candidate explanations include head resonance, superposition of motor unit action potentials and influence of sex hormones. These explanations are not mutually exclusive, and multiple factors may contribute to difference in VEMP measurement between women and men. This study used a methodology developed in Gattie et al. (2021), which addresses sound exposure concerns with the high amplitude air conducted stimuli necessary to evoke a VEMP response. It is suggested that body conducted stimuli may be preferable for VEMP testing in which ear-specific information is not required.
I-Spin live: An open-source software based on blind-source separation for real-time decoding of motor unit activity in humans
Authors: Rossato Julien , Hug François , Tucker Kylie , Gibbs Ciara , Lacourpaille Lilian , Farina Dario , Avrillon Simon
Published: April 2023

Decoding the activity of individual neural cells during natural behaviours allows neuroscientists to study how the nervous system generates and controls movements. Contrary to other neural cells, the activity of spinal motor neurons can be determined non-invasively (or minimally invasively) from the decomposition of electromyographic (EMG) signals into motor unit firing activities. For some interfacing and neuro-feedback investigations, EMG decomposition needs to be performed in real-time. Here, we introduce an open-source software that performs real-time decoding of motor neurons using a blind-source separation approach for multichannel EMG signal processing. Separation vectors (motor unit filters) are optimised for each motor unit from baseline contractions and then re-applied in real-time during test contractions. In this way, the firing activity of multiple motor neurons can be provided through different forms of visual feedback. We provide a complete framework with guidelines and examples of recordings to guide researchers who aim to study movement control at the motor neuron level. We first validated the software with synthetic EMG signals generated during a range of isometric contraction patterns. We then tested the software on data collected using either surface or intramuscular electrode arrays from five lower limb muscles (gastrocnemius lateralis and medialis, vastus lateralis and medialis, and tibialis anterior). We assessed how the muscle or variation of contraction intensity between the baseline contraction and the test contraction impacted the accuracy of the real-time decomposition. This open-source software provides a set of tools for neuroscientists to design experimental paradigms where participants can receive real-time feedback on the output of the spinal cord circuits.
SUMOylation of Bonus, theDrosophilahomolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes
Authors: Godneeva Baira , Ninova Maria , Fejes Tóth Katalin , Aravin Alexei A.
Published: April 2023

The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members,Drosophilaonly encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus’s repressive activity. SUMOylation influences Bonus’s subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
Characterizing the mechanical properties of low-profile prosthetic feet
Authors: Tacca Joshua R. , Colvin Zane A. , Grabowski Alena M.
Published: April 2023

Passive-elastic prosthetic feet are manufactured with different numerical stiffness categories that are prescribed based on the body mass and activity level of the user, but the mechanical properties, such as the stiffness values and hysteresis are not typically reported by the manufacturer. Since the mechanical properties of passive-elastic prosthetic feet can affect the walking biomechanics of people with transtibial or transfemoral amputation, characterizing these properties would provide objective values for comparison and aid the prescription of prosthetic feet. Therefore, we characterized the axial stiffness values, torsional stiffness values, and hysteresis of 33 different categories and sizes of a commercially available passive-elastic prosthetic foot model, the Össur low-profile (LP) Vari-flex with and without a shoe. We measured axial stiffness from compression and torsional stiffness from dorsiflexing and plantarflexing the prostheses. In general, a greater numerical prosthetic foot stiffness category resulted in increased heel, midfoot, and forefoot axial stiffness values, increased plantarflexion and dorsiflexion torsional stiffness values, and decreased heel, midfoot, and forefoot hysteresis. Moreover, a greater prosthetic foot size resulted in decreased heel, midfoot, and forefoot axial stiffness values, increased plantarflexion and dorsiflexion torsional stiffness values, and decreased heel and midfoot hysteresis. Finally, adding a shoe to the LP Vari-flex prosthetic foot resulted in decreased heel and midfoot axial stiffness values, decreased plantarflexion torsional stiffness values, and increased heel, midfoot, and forefoot hysteresis. In addition, we found that the force-displacement and torque-angle relationships were better described by curvilinear than linear equations. Ultimately, our results can be used to objectively compare LP Vari-flex prosthetic feet to other prosthetic feet in order to inform their prescription and design and use by people with a transtibial or transfemoral amputation.
Advances on sparse Dynamic Scanning in Spectromicroscopy through Compressive Sensing
Authors: Kourousias George , Billè Fulvio , Ippoliti Matteo , Guzzi Francesco , Bonanni Valentina , Gianoncelli Alessandra
Published: April 2023

Scanning microscopies and spectroscopies like X-ray Fluorescence (XRF), Scanning Transmission X-ray Microscopy (STXM), and Ptychography are of very high scientific importance as they can be employed in several research fields. Methodology and technology advances aim at analysing larger samples at better resolution, improved sensitivities and higher acquisition speeds. The frontiers of those advances are on detectors, radiation sources, motors, but also on acquisition and analysis software together with general methodology improvements. We’ve e recently introduced and fully implemented on a soft X-ray microscopy beamline an intelligent scanning methodology based on compressive sensing. This demonstrated sparse low energy XRF scanning of dynamically chosen regions of interest in combination with STXM. It resulted in a sparse megapixel-rage low energy XRF spectroimaging through dynamic scanning that was previously not feasible. This research has been further developed and has been applied in scientific applications in biology. The developments are mostly on the dynamic triggering decisional mechanism in order to incorporate modern Machine Learning and real-time XRF fitting but also on the suitable integration of the method in the control system making it available for other beamlines and imaging techniques. On the applications front, the method was successfully used on different samples, from lung and ovarian human tissues to plant root sections. This manuscript introduces the latest advances of the method and demonstrates applications in life and environmental sciences. Finally it highlights an auxiliary development of a mobile application that assists the selection of specific regions of interest in an easy way.
Loss of presenilin-1 in smooth muscle cells ameliorates elastin aortopathy
Authors: Saito Junichi , Dave Jui M. , Lau Freddy Duarte , Greif Daniel M.
Published: April 2023

Smooth muscle cell (SMC) accumulation is central to the pathogenesis of elastin-defective arterial diseases, such as atherosclerosis, pulmonary hypertension and supravalvular aortic stenosis (SVAS). We previously demonstrated that elastin insufficiency activates the Notch pathway in aortic SMCs, resulting in hypermuscularization. Activation of Notch is catalyzed by the enzyme gamma-secretase, but the role of specific catalytic subunits PSEN-1 or PSEN-2 in elastin aortopathy is not defined. This study utilizes genetic approaches to query the role of PSEN-1/2 in the pathogenesis of elastin mutant mice, which model human SVAS. Although endothelial cell-specificPsen1deletion does not improve elastin aortopathy, deletion of eitherPsen1in SMCs orPsen2globally attenuates Notch downstream gene expression and SMC proliferation, mitigating aortic disease. With SMC-specificPsen1deletion in elastin nulls, these rescue effects are more robust and in fact, survival is increased. On the background ofPsen1deletion in SMCs, globalPsen2deletion yields additional benefits in regard to elastin aortopathy. Finally, SMC deletion ofPsen1also attenuates hypermuscularization in newborns heterozygous for the elastin null gene, which genetically mimics SVAS. Taken together, these findings put forth SMC PSEN-1 as a potential therapeutic target in elastin aortopathy.
Bumble bees (Bombus terrestris) use time-memory to associate reward with color and time of day
Authors: Gonulkirmaz-Cancalar Ozlem , Shertzer Oded , Bloch Guy
Published: April 2023

Circadian clocks regulate ecologically important complex behaviors in honey bees but it is not clear to what extent these observations can be extended to other species of bees. One key behavior is time-memory allowing foraging bees to precisely time flower visitation to periods of maximal pollen or nectar availability and reducing the costs of arriving at a flower patch at the wrong time. It is unclear whether other bees such as bumble bees, who live in smaller societies and forage over shorter distances than honey bees, can similarly associate a reward with time of day. We trained individually marked bumble bee (Bombus terrestris) workers to forage for sugar syrup in a flight cage with yellow or blue feeders rewarding either during the morning or evening. After a two-weeks training session, we recorded all visitations to colored feeders filled with only water. We repeated this experiment twice, with different colonies. We found that bees tended to show higher foraging activity during the morning and evening training sessions compared to other times during the day. Trained bees were more likely to visit feeders with colors rewarding compared to non-rewarding at the same time of day during the training sessions and with relatively fewer mistakes. Our findings lend credence to the hypothesis that efficient time-memory is not limited to species such as honey bees that evolved sophisticated social foraging behaviors over large distances.
Conceptual representations in the default, control and attention networks are task-dependent and cross-modal
Authors: Kuhnke Philipp , Kiefer Markus , Hartwigsen Gesa
Published: April 2023

Conceptual knowledge is central to human cognition. Neuroimaging studies suggest that conceptual processing involves modality-specific and multimodal brain regions in a task-dependent fashion. However, it remains unclear (1) to what extent conceptual feature representations are also modulated by the task, (2) whether conceptual representations in multimodal regions are indeed cross-modal, and (3) how the conceptual system relates to the large-scale functional brain networks. To address these issues, we conducted multivariate pattern analyses on fMRI data. 40 participants performed three tasks—lexical decision, sound judgment, and action judgment—on written words. We found that (1) conceptual feature representations are strongly modulated by the task, (2) conceptual representations in several multimodal regions are cross-modal, and (3) conceptual feature retrieval involves the default, frontoparietal control, and dorsal attention networks. Conceptual representations in these large-scale networks are task-dependent and cross-modal. Our findings support theories that assume conceptual processing to rely on a flexible, multi-level architecture.
Natural forgetting reversibly modulates engram expression
Authors: O’Leary James D. , Bruckner Rasmus , Autore Livia , Ryan Tomás J.
Published: April 2023

Memories are stored as ensembles of engram neurons and their successful recall involves the reactivation of these cellular networks. However, significant gaps remain in connecting these cell ensembles with the process of forgetting. Here, we utilized a mouse model of object memory and investigated the conditions in which a memory could be preserved, retrieved, or forgotten. Direct modulation of engram activity via optogenetic stimulation or inhibition either facilitated or prevented the recall of an object memory. In addition, through behavioral and pharmacological interventions, we successfully prevented or accelerated forgetting of an object memory. Finally, we showed that these results can be explained by a computational model in which engrams that are subjectively less relevant for adaptive behavior are more likely to be forgotten. Together, these findings suggest that forgetting may be an adaptive form of engram plasticity which allows engrams to switch from an accessible state to an inaccessible state.
Tuning Minimum-Norm regularization parameters for optimal MEG connectivity estimation
Authors: Vallarino Elisabetta , Hincapié Ana Sofia , Jerbi Karim , Leahy Richard , Pascarella Annalisa , Sorrentino Alberto , Sommariva Sara
Published: April 2023

The accurate characterization of cortical functional connectivity from Magnetoencephalography (MEG) data remains a challenging problem due to the subjective nature of the analysis, which requires several decisions at each step of the analysis pipeline, such as the choice of a source estimation algorithm, a connectivity metric and a cortical parcellation, to name but a few. Recent studies have emphasized the importance of selecting the regularization parameter in minimum norm estimates with caution, as variations in its value can result in significant differences in connectivity estimates. In particular, the amount of regularization that is optimal for MEG source estimation can actually be suboptimal for coherence-based MEG connectivity analysis. In this study, we expand upon previous work by examining a broader range of commonly used connectivity metrics, including the imaginary part of coherence, corrected imaginary part of Phase Locking Value, and weighted Phase Lag Index, within a larger and more realistic simulation scenario. Our results show that the best estimate of connectivity is achieved using a regularization parameter that is 1 or 2 orders of magnitude smaller than the one that yields the best source estimation. This remarkable difference may imply that previous work assessing source-space connectivity using minimum-norm may have benefited from using less regularization, as this may have helped reduce false positives. Importantly, we provide the code for MEG data simulation and analysis, offering the research community a valuable open source tool for informed selections of the regularization parameter when using minimum-norm for source space connectivity analyses.

Highlights

The regularization parameter of the Minimum Norm Estimate of neural activity impacts connectivity estimation

We study empirically the optimal parameter for connectivity estimation using realistic synthetic datasets

We find the optimal parameter for connectivity estimation is systematically smaller than the optimal parameter for source imaging; different connectivity metrics yield the same result

Code and data are available open source.
A transient dermal niche and dual epidermal programs underlie sweat gland development
Authors: Dingwall Heather L. , Tomizawa Reiko R. , Aharoni Adam , Hu Peng , Qiu Qi , Kokalari Blerina , Martinez Serenity M. , Donahue Joan C. , Aldea Daniel , Mendoza Meryl , Glass Ian A. ,   Birth Defects Research Laboratory (BDRL), Wu Hao , Kamberov Yana G.
Published: April 2023

Eccrine glands are mammalian skin appendages indispensable for human thermoregulation. Like all skin-derived appendages, eccrine glands form from multipotent progenitors in the basal skin epidermis. It remains unclear how epidermal progenitors progressively specialize to specifically form eccrine glands, precluding efforts to regenerate these vital organs. Herein, we applied single nucleus transcriptomics to compare the expression content of wildtype, eccrine-forming mouse skin to that of mice harboring a skin-specific disruption ofEngrailed 1 (En1), a transcription factor that promotes the formation of eccrine glands in both humans and mice. We identify two concurrent epidermal transcriptomes in the earliest eccrine anlagen: a predominant transcriptome that is shared with hair follicles, and a vastly underrepresented transcriptome that isEn1-dependent and eccrine-specific. We demonstrate that differentiation of the eccrine anlage requires the induction of a transient and transcriptionally unique dermal niche that forms around each developing gland in humans and mice. Our study defines the transcriptional determinants underlying eccrine identity in the epidermis and uncovers the dermal niche required for eccrine developmental progression. By identifying these defining components of the eccrine developmental program, our findings set the stage for directed efforts to regenerate eccrine glands for comprehensive skin repair.
Type I IFN expression is inhibited during cell division by CDK4/6
Authors: Sumner Rebecca P. , Ellis Ailish , Lant Sian , Ashby Hannah , Towers Greg J. , Maluquer de Motes Carlos
Published: April 2023

Cells are equipped to defend themselves from invading pathogens through sensors such as cGAS, which upon binding DNA induces type I interferon (IFN) expression. Whilst IFNs are crucial for limiting viral infection and activating adaptive immunity, uncontrolled production causes excessive inflammation and autoimmunity. cGAS binds DNA of both pathogenic and cellular origin and its activity is therefore tightly regulated. This is particularly apparent during mitosis, where cGAS association with chromatin following nuclear membrane dissolution and phosphorylation by mitotic kinases negatively regulate enzymatic activity. Here we describe a novel mechanism by which DNA sensing and other innate immune pathways are regulated during cell division, dependent on cyclin dependent kinases (CDK) 4 and 6. Inhibition of CDK4/6 using chemical inhibitors, shRNA-mediated depletion, or overexpression of cellular CDK4/6 inhibitor p16INK4a, greatly enhanced DNA- or cGAMP-induced expression of cytokines and IFN-stimulated genes (ISG). Mechanistically, CDK4/6-dependent inhibition mapped downstream of cytoplasmic signalling events including STING and IRF3 phosphorylation, limiting innate immune induction at the level of IFNβ mRNA expression. This regulation was universal, occurring in primary and transformed cells of human and murine origin, and broad, as IFNβ expression was inhibited in a CDK4/6-dependent manner downstream of multiple pattern recognition receptors. Together these findings demonstrate that host innate responses are limited by multiple mechanisms during cell division, thus defining cellular replication as an innate immune privileged process that may be necessary to avoid aberrant self-recognition and autoimmunity.
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
Authors: Unneberg Per , Larsson Mårten , Olsson Anna , Wallerman Ola , Petri Anna , Bunikis Ignas , Vinnere Pettersson Olga , Papetti Chiara , Gíslason Ástþór , Glenner Henrik , Cartes Joan E. , Blanco-Bercial Leocadio , Eriksen Elena , Meyer Bettina , Wallberg Andreas
Published: April 2023

Krill is a vital food source for many marine animals but also strongly impacted by climate change. Genetic adaptation could support populations, but remains uncharacterized. We assembled the 19 Gb Northern krill genome and compared genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The genome is dominated by methylated transposable elements and contains many duplicated genes implied in molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect extreme divergence across hundreds of genes, governing ecophysiological functions like photoreception, circadian regulation, reproduction and thermal tolerance. Such standing variation may be essential for resilience in zooplankton, necessitating insight into adaptive variation to forecast their roles in future marine ecosystems and support ocean conservation.

One-Sentence Summary

Genome-scans of Northern krill link genes for photoreception, reproduction and thermal tolerance to ecological adaptation.
Incongruence between transcriptional and vascular pathophysiological cell states
Authors: Fernández-Chacón Macarena , Mühleder Severin , Regano Álvaro , Garcia-Ortega Lourdes , Torroja Carlos , Lytvyn Mariya , Sanchez-Muñoz Maria S , Casquero-Garcia Verónica , Camafeita Emilio , Vazquez Jesus , Benguría Alberto , Dopazo Ana , Sánchez-Cabo Fátima , Carter Hannah , Benedito Rui
Published: April 2023

The Notch pathway is a major regulator of transcriptional specification and vascular biology. Previous studies have suggested that targeting the ligand Dll4 or the Notch-receptors results in similar molecular and angiogenesis outcomes. Here, we analyzed single and compound genetic mutants for all Notch signaling members and found very significant differences in the way ligands and receptors regulate vascular homeostasis. Loss of Notch receptors, leads to minor vascular pathology featuring hypermitogenic MAPK-driven cell-cycle arrest and senescence. In contrast, loss of Dll4 triggers a strong Myc-driven switch towards cell proliferation and sprouting and major organ pathology. Targeting of Myc completely suppressed the proliferative and tip-cell angiogenic states induced by Dll4 loss-of-function, however, this did not avoid vascular pathology. Only VEGF blockade prevented the pathology induced by Dll4 loss, but without fully suppressing its transcriptional and metabolic programs. This study shows incongruence between single-cell transcriptional states and adult vascular phenotypes and related pathophysiology.
Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects
Authors: Liu Peng , Bo Ke , Ding Mingzhou , Fang Ruogu
Published: April 2023

Recent neuroimaging studies have shown that the visual cortex plays an important role in representing the affective significance of visual input. The origin of these affect-specific visual representations is debated: they are intrinsic to the visual system versus they arise through reentry from frontal emotion processing structures such as the amygdala. We examined this problem by combining convolutional neural network (CNN) models of the human ventral visual cortex pre-trained on ImageNet with two datasets of affective images. Our results show that (1) in all layers of the CNN models, there were artificial neurons that responded consistently and selectively to neutral, pleasant, or unpleasant images and (2) lesioning these neurons by setting their output to 0 or enhancing these neurons by increasing their gain led to decreased or increased emotion recognition performance respectively. These results support the idea that the visual system may have the intrinsic ability to represent the affective significance of visual input and suggest that CNNs offer a fruitful platform for testing neuroscientific theories.

Author Summary

The present study shows that emotion selectivity can emerge in deep neural networks trained to recognize visual objects and the existence of the emotion-selective neurons underlies the ability of the network to recognize the emotional qualities in visual images. Obtained using two affective datasets (IAPS and NAPS) and replicated on two CNNs (VGG-16 and AlexNet), these results support the idea that the visual system may have an intrinsic ability to represent the motivational significance of sensory input and CNNs are a valuable platform for testing neuroscience ideas in a way that is not practical in empirical studies.
Axon initial segment GABA inhibits action potential generation throughout periadolescent development
Authors: Lipkin Anna M , Bender Kevin J
Published: April 2023

Neurons are remarkably polarized structures: dendrites spread and branch to receive synaptic inputs while a single axon extends and transmits action potentials to downstream targets. Neuronal polarity is maintained by the axon initial segment (AIS), a region between the soma and axon proper that is also the site of action potential (AP) generation. This polarization between dendrites and axons extends to inhibitory neurotransmission. In adulthood, the neurotransmitter GABA hyperpolarizes dendrites but instead depolarizes axons. These differences in function collide at the AIS. Multiple studies have shown that GABAergic signaling in this region can share properties of either the mature axon or mature dendrite, and that these properties evolve over a protracted period encompassing periadolescent development. Here, we explored how developmental changes in GABAergic signaling affect AP initiation. We show that GABA at the axon initial segment inhibits action potential initiation in Layer 2/3 pyramidal neurons in prefrontal cortex from mice of either sex across GABA reversal potentials observed in periadolescence. These actions occur largely through current shunts generated by GABAA receptors and changes in voltage-gated channel properties that affected the number of channels that could be recruited for AP electrogenesis. These results suggest that GABAergic neurons targeting the axon initial segment provide an inhibitory “veto” across the range of GABA polarity observed in normal adolescent development, regardless of GABAergic synapse reversal potential.
Trilliumosides A-B, two novel steroidal saponins isolated from Rhizomes ofTrillium govanianumas potent anticancer agents targeting apoptosis in A-549 cancer cell line
Authors: Lone Bashir Ahmad , Tabassum Misbah , Bhushan Anil , Dhiman Urvashi , Rani Dixhya , Gupta Prem N. , Mondhe D. M. , Gairola Sumeet , Gupta Prasoon
Published: April 2023

Two novel steroidal saponins, Trilliumosides A (1) and B (2) were isolated from the rhizomes ofTrillium govanianumby bioactivity-guided phytochemical investigation along with seven known compounds protodioscin (3) govanoside B (4), borassoside E (5), 20-hydroxyecdysone (6), 5-20-hydroxyecdysone (7), govanic acid (8), and diosgenin (9). The structure of novel compounds 1-2 were established using spectroscopic methods such as 1D, 2D NMR data and HR-ESI-MS. The isolated compounds were evaluated forin-vitrocytotoxic activity against a panel of human cancer cell lines. Compound1showed significant cytotoxic activity against A-549 (Lung) and SW-620 (Colon) cell lines with IC50values of 1.83 and 1.85 µM, whereas compound (2) IC50value against A-549 cell line was found to be 1.79 µM. Among previously known compounds (3), (5) and (9) their cytotoxic IC50value was found to be in the range of 5-10 µM. In detailed anticancer analysis compound (2) was seen inhibiting colony forming potential andin-vitromigration in the A-549 cell line. Furthermore, the mechanistic study of compound (2) on the A-549 cell line revealed characteristic changes including nuclear morphology, increased ROS generation, and reduced levels of MMP. Above mentioned events eventually induce apoptosis, a key hallmark in cancer studies, by upregulating the pro-apoptotic protein BAX and downregulating the anti-apoptotic protein BCL-2 thereby activating Caspase-3. Our study reports the first mechanistic anticancer evaluation of the compounds isolated from the rhizomes ofTrillium govanianumwith remarkable activity in the desired micro molar range.

Graphical abstract
Photocatalytic setup for in situ and operando ambient-pressure X-ray photoelectron spectroscopy at MAX IV Laboratory
Authors: Klyushin Alexander , Ghosalya Manoj , Kokkonen Esko , Eads Calley , Jones Rosemary , Nalajala Naresh , Gopinath Chinnakonda S. , Urpelainen Samuli
Published: April 2023

The Ambient-Pressure X-ray Photoelectron Spectroscopy (APXPS) endstation at the SPECIES beamline at MAX IV Laboratory has been improved. The latest upgrades help in performing photo-assisted experiments under operando conditions in the mbar pressure range using gas and vapour mixtures whilst also reducing beam damage to the sample caused by X-ray irradiation. This article reports on endstation upgrades for APXPS and examples of scientific cases of in situ photocatalysis, photoreduction and photo-assisted atomic layer deposition (photo-ALD).
The rise of the food truck phenomenon: an integrated model of consumers' intentions to visit food trucks
Authors: Koay Kian Yeik , Cheah Chee Wei , Ganesan Natarsha
Published: April 2023

Purpose

In recent times, the market for food trucks has been growing due to customers seeking convenient food options. However, not many studies have been carried out to understand why consumers choose to visit food trucks. Hence, the purpose of this study is to understand consumers' intentions to visit food trucks through the theoretical lenses of the theory of planned behaviour (TPB) and the theory of consumption values (TCV).

Design/methodology/approach

A purposive sampling method was utilised to gather data from 203 food truck customers through a cross-sectional online survey. Data were evaluated using partial least squares structural equation modelling (PLS-SEM).

Findings

The findings indicate that attitudes, subjective norms and perceived behavioural control have a significant positive impact on consumers' intentions to visit food trucks. Furthermore, taste value, health value, emotional value and epistemic value have a significant positive effect on attitudes. However, neither price value nor interaction value has a significant impact on attitudes.

Originality/value

This study represents a pioneering effort in combining the theoretical perspectives of the TPB and the TCV to investigate consumers' intentions to visit food trucks. The resulting integrated model provides a more comprehensive understanding of the factors that influence consumers' decisions to visit food trucks. The findings are expected to furnish food truck vendors with valuable insights on crafting efficient marketing and operational tactics to retain their existing customer base and entice new consumers.
Convolutional neural network for fast adaptive beamforming of phased array weather radar
Authors: Sallam Tarek
Published: April 2023

Purpose

The purpose of this paper is to present a deep-learning-based beamforming method for phased array weather radars, especially whose antenna arrays are equipped with large number of elements, for fast and accurate detection of weather observations.

Design/methodology/approach

The beamforming weights are computed by a convolutional neural network (CNN), which is trained with input–output pairs obtained from the Wiener solution.

Findings

To validate the robustness of the CNN-based beamformer, it is compared with the traditional beamforming methods, namely, Fourier (FR) beamforming and Capon beamforming. Moreover, the CNN is compared with a radial basis function neural network (RBFNN) which is a shallow type of neural network. It is shown that the CNN method has an excellent performance in radar signal simulations compared to the other methods. In addition to simulations, the robustness of the CNN beamformer is further validated by using real weather data collected by the phased array radar at Osaka University (PAR@OU) and compared to, besides the FR and RBFNN methods, the minimum mean square error beamforming method. It is shown that the CNN has the ability to rapidly and accurately detect the reflectivity of the PAR@OU with even less clutter level in comparison to the other methods.

Originality/value

Motivated by the inherit advantages of the CNN, this paper proposes the development of a CNN-based approach to the beamforming of PAR using both simulated and real data. In this paper, the CNN is trained on the optimum weights of Wiener solution. In simulations, it is applied on a large 32 × 32 planar phased array antenna. Moreover, it is operated on real data collected by the PAR@OU.
Comparative analysis between different risk score calculation approaches
Authors: Youssefi Iman , Celik Tolga
Published: April 2023

Purpose

Total risk score (TRS) is considered one of the main indicators for risk evaluation. Several studies attempted to employ different types of risk indices for the evaluation of cost overrun causes. Hence, this study aims at performing a comparative analysis to evaluate the efficiency of three different approaches for TRS calculation.

Design/methodology/approach

Thirty-eight unique causes of cost overrun in urban-related construction projects were identified and a survey was conducted among construction professionals in Iran. The TRS for each cost overrun cause is calculated using single-attribute (SA), double-attribute (DA), and multiple-attribute (MA) approaches, and eventually, causes were ranked. Furthermore, principal component analysis (PCA), logistic regression analysis (LRA), and K-means clustering are utilized to compare the differences in the generated TRS using different approaches.

Findings

The results revealed that the TRS generated through the MA approach demonstrated the highest efficiency in terms of generating correlation between causes and their identified latent constructs, prediction capability, and classification of the influential causes in the same group.

Originality/value

The originality of this study primarily stems from the adoption of statistical approaches in the evaluation of the recently introduced TRS calculation approach in comparison to traditional ones. Additionally, this study proposed a modified application of the relative importance index (RII) for risk prioritization. The results from this study are expected to fulfill the gap in previous literature toward exploring the most efficient TRS calculation approach for those researchers and practitioners who seek to utilize them as a measure to identify the influential cost overrun causes.
Intermediate-level outside-in marketing capabilities, technological innovation, and management innovation
Authors: Han Chen , Liu Jiahui , Zhang Shuman , Nielsen Bo Bernhard
Published: April 2023

Purpose

This study aims to build a theoretical model including intermediate-level outside-in marketing capabilities (ILOIMC), radical and incremental technological innovations and management innovation.

Design/methodology/approach

This research used 272 pairs of survey questionnaires from Chinese firms’ managers to examine the hypotheses.

Findings

The results indicate that ILOIMC enhance management innovation by stimulating radical technological innovation. Furthermore, the mediating effect of incremental technological innovation depends on technological turbulence.

Research limitations/implications

This study may have several limitations which future research could try to overcome: cross-sectional data, Chinese samples, exclusive focus on ILOIMC, sociotechnical approach to innovation typology and measuring ILOIMC as a first-order variable.

Practical implications

ILOIMC can significantly improve innovations in technology and management systems by using customer value and market information.

Originality/value

This study proposes a new taxonomy to classify marketing capabilities into lower-level inside-out marketing capabilities, ILOIMC and higher-level outside-in marketing capabilities. It also provides an explicit discussion and examination of the influence of ILOIMC on technological and management innovations and the contingency effect of technological turbulence. Thus, it responds to Musarra and Morgan’s (2020) call for more research into the mechanism that explains when (the conditions under which) and how (the process by which) outside-in marketing capabilities could contribute to firm innovation.
Global overview of research data repositories: an analysis of re3data registry
Authors: Khan Aasif Mohammad , Loan Fayaz Ahmad , Parray Umer Yousuf , Rashid Sozia
Published: April 2023

Purpose

Data sharing is increasingly being recognized as an essential component of scholarly research and publishing. Sharing data improves results and propels research and discovery forward. Given the importance of data sharing, the purpose of the study is to unveil the present scenario of research data repositories (RDR) and sheds light on strategies and tactics followed by different countries for efficient organization and optimal use of scientific literature.

Design/methodology/approach

The data for the study is collected from registry of RDR (re3data registry) (re3data.org), which covers RDR from different academic disciplines and provides filtration options “Search” and “Browse” to access the repositories. Using these filtration options, the researchers collected metadata of repositories i.e. country wise contribution, content-type data, repository language interface, software usage, metadata standards and data access type. Furthermore, the data was exported to Google Sheets for analysis and visualization.

Findings

The re3data registry holds a rich and diverse collection of data repositories from the majority of countries all over the world. It is revealed that English is the dominant language, and the most widely used software for the creation of data repositories are “DataVerse”, followed by “Dspace” and “MySQL”. The most frequently used metadata standards are “Dublin Core” and “Datacite metadata schema”. The majority of repositories are open, with more than half of the repositories being “disciplinary” in nature, and the most significant data sources include “scientific and statistical data” followed by “standard office documents”.

Research limitations/implications

The main limitation of the study is that the findings are based on the data collected through a single registry of repositories, and only a few characteristic features were investigated.

Originality/value

The study will benefit all countries with a small number of data repositories or no repositories at all, with tools and techniques used by the top repositories to ensure long-term storage and accessibility to research data. In addition to this, the study provides a global overview of RDR and its characteristic features.
Untangling the influence of green human capital on green supply chain management practices through environmental education and internal environmental management
Authors: Murad Majid , Zou Shuli
Published: April 2023

Purpose

This paper aims to investigate the impact of green human capital (GHC) on green supply chain management (GSCM) practices (environmental education and internal environmental management) and sustainable supply chain performance.

Design/methodology/approach

This study used a survey method to collect data from 350 randomly selected manufacturing firms in China, including supply chain and human resource professionals from the period of December 2021 to June 2022.

Findings

The partial least squares-structural equation modeling version 4 is applied to assess the data and test the hypotheses. Under the notion of resource-based view theory, the findings demonstrate that GHC has a positive and significant relationship with GSCM practices (environmental education and internal environmental management) and that GSCM practices are positively associated with the sustainable supply chain performance.

Practical implications

This study offers implications for Chinese manufacturing firms to use GHC on dimensions of GSCM implementations for achieving environmental, financial and social performance.

Originality/value

This study finds that GHC as a critical enabler for implementing GSCM practices, resulting in more robust and better sustainable supply chain performance (environmental, financial and social performance).