bluuebunny/crossref_metadata_2025 huggingface dataset:
Size-dependent sex allocation and the expression of andromonoecy in a protogynous perennial herb: both size and timing matter
Authors: Chen Kai-Hsiu , Pannell John R
Published: March 2023

The optimal life history and sex allocation of perennial hermaphrodites should depend on both their size and the relative costs and benefits of reproducing through male versus female functions. Theory predicts that insect-pollinated perennials should increase their allocation to female function with size, while the ‘mating environment’ hypothesis predicts that allocation to male function should track mating opportunities over the course of flowering. We test these two predictions by inferring male and female reproductive success in the protogynous perennial herbPulsatilla alpinaby tracking the patterns and dynamics of sex allocation over time for marked individuals over a range of sizes. We found that small individuals tend to produce only male flowers and that both small and larger individuals produced male flowers at the beginning of the flowering season when mating opportunities were high. By considering within-population variation in life history and phenology jointly rather than separately, and by considering both the tradeoff costs and benefits of allocation to male versus female functions, our results provide new insights into the evolution of both gender diphasy and andromonoecy in perennial plants that are constrained by a dichogamous flowering strategy.
Transcending Markov: Non-Markovian Rate Processes of Thermosensitive TRP Ion Channels
Authors: Ben-Abu Yuval , Tucker Stephen J , Contera Sonia
Published: March 2023

The Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. A MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does not depend on the history of state occupancy within the system, i.e., it only includes reversible, non-dissipative processes. However, this requires knowledge of the precise conformational state of the protein and is not predictive when those details are not known. In the case of ion channels, this simple description fails in real (non-equilibrium) situations, for example when local temperature changes, or when energy losses occur during channel gating. Here, we show it is possible to use non-Markovian equations (i.e. offer a general description that includes the MSM as a particular case) to develop a relatively simple analytical model that describes the non-equilibrium behavior of the temperature-sensitive TRP ion channels, TRPV1 and TRPM8. This model accurately predicts asymmetrical opening and closing rates, infinite processes, and the creation of new states, as well as the effect of temperature changes throughout the process. This approach therefore overcomes the limitations of the MSM and allows us to go beyond a mere phenomenological description of the dynamics of ion channel gating towards a better understanding of the physics underlying these processes.

Significance Statement

Modeling ion channel processes has long relied on the Markovian assumption. However, Markov theory cannot translate situations in which the physical state of an ion channel changes during its gating process. By using a non-Markovian approach, we develop a simple analytical model that describes the non-equilibrium behavior of two temperature-sensitive TRP channels, TRPV1 and TRPM8. This model accurately describes and predicts their biophysical behavior as well as their temperature dependence. This approach therefore provides a better understanding of the physics underlying dynamic conformational changes such as those that occur during ion channel gating.
Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry
Authors: Phulphagar Kshiti Meera , Ctortecka Claudia , Vaca Jacome Alvaro Sebastian , Klaeger Susan , Verzani Eva K. , Hernandez Gabrielle M. , Udeshi Namrata , Clauser Karl , Abelin Jennifer , Carr Steven A
Published: March 2023

Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare, clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of sample. While immunopeptidome depth can be increased by off-line fractionation prior to MS, its use is impractical when analyzing limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high throughput, sensitive, single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight mass spectrometry on the Bruker timsTOF SCP. We demonstrate >2-fold improved coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the timsTOF SCP maintains high coverage, eliminates the need for off-line fractionation and reduces input requirements to as few as 1e6 A375 cells for > 800 distinct HLA-I peptides. This depth is sufficient to identify HLA-I peptides derived from cancer-testis antigen, and novel/unannotated open reading frames. We also apply our optimized single-shot SCP acquisition methods to tumor derived samples, enabling sensitive, high throughput and reproducible immunopeptidome profiling with detection of clinically relevant peptides from less than 4e7 cells or 15 mg wet weight tissue.
A versatile multimodal optical modality based on Brillouin light scattering and photoacoustic effect
Authors: Shi Chenjun , Yan Yan , Mehrmohammadi Mohammad , Zhang Jitao
Published: March 2023

Multimodal optical imaging techniques are useful for various applications, including imaging biological samples for providing comprehensive material properties. In this work, we developed a new modality that can measure a set of mechanical, optical, and acoustical properties of a sample at microscopic resolution, which is based on the integration of Brillouin (Br) and photoacoustic (PA) microscopy. The proposed multimodal imaging technique not only can acquire co-registered Br and PA signals but also allows us to utilize the sound speed measured by PA to quantify the sample’s refractive index, which is a fundamental property of the material and cannot be measured by either technique individually. We demonstrated the colocalization of Br and time-resolved PA signals in a synthetic phantom made of kerosene and CuSO4aqueous solution. In addition, we measured the refractive index of saline solutions and validated the result against published data with a relative error of 0.3 %. This multimodal Br-PA modality could open a new way for characterizing biological samples in physiological and pathological conditions.
Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding
Authors: Badiee Mohsen , Kenet Adam L. , Ganser Laura R. , Paul Tapas , Myong Sua , Leung Anthony K. L.
Published: March 2023

Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.

Significance

Poly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.
Modulating Nucleic Acid Phase Transitions as a Mechanism of Action for Cell-Penetrating Antimicrobial Peptides
Authors: Sneideris Tomas , Erkamp Nadia A. , Ausserwöger Hannes , Saar Kadi L. , Welsh Timothy J. , Qian Daoyuan , Johncock Margaret L. L. Y. , Krainer Georg , Borodavka Alexander , Knowles Tuomas P. J.
Published: March 2023

Antimicrobial peptides (AMPs) are a vital part of the immune system that helps combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we have discovered that a significant number of AMPs have a strong tendency to form liquid-like condensates in the presence of nucleic acids, a process known as phase separation. We have demonstrated that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. We propose that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. These findings open up exciting possibilities for the development of antimicrobials that target nucleic acid phase transitions.
Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility
Authors: Rana Ushnish , Xu Ke , Narayanan Amal , Walls Mackenzie T. , Panagiotopoulos Athanassios Z. , Avalos José L. , Brangwynne Clifford P.
Published: March 2023

Endogenous biomolecular condensates, comprised of a multitude of proteins and RNAs, can organize into multiphasic structures, with compositionally-distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here, we utilizein vivocondensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein region (IDR) results in enhanced immiscibility and multiphase formation. Interestingly, we found that oligomerization tunes the miscibility of IDRs in an asymmetric manner, with the effect being more pronounced when the IDR exhibiting stronger homotypic IDR interactions is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism which cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.
Unsupervised discovery of family specific vocal usage in the Mongolian gerbil
Authors: Peterson Ralph E. , Choudhri Aman , Mitelut Catalin , Tanelus Aramis , Capo-Battaglia Athena , Williams Alex H. , Schneider David M. , Sanes Dan H.
Published: March 2023

In nature, animal vocalizations can provide crucial information about identity, including kinship and hierarchy. However, lab-based vocal behavior is typically studied during brief interactions between animals with no prior social relationship, and under environmental conditions with limited ethological relevance. Here, we address this gap by establishing long-term acoustic recordings from Mongolian gerbil families, a core social group that uses an array of sonic and ultrasonic vocalizations. Three separate gerbil families were transferred to an enlarged environment and continuous 20-day audio recordings were obtained. Using a variational autoencoder (VAE) to quantify 583,237 vocalizations, we show that gerbils exhibit a more elaborate vocal repertoire than has been previously reported and that vocal repertoire usage differs significantly by family. By performing gaussian mixture model clustering on the VAE latent space, we show that families preferentially use characteristic sets of vocal clusters and that these usage preferences remain stable over weeks. Furthermore, gerbils displayed family-specific transitions between vocal clusters. Since gerbils live naturally as extended families in complex underground burrows that are adjacent to other families, these results suggest the presence of a vocal dialect which could be exploited by animals to represent kinship. These findings position the Mongolian gerbil as a compelling animal model to study the neural basis of vocal communication and demonstrates the potential for using unsupervised machine learning with uninterrupted acoustic recordings to gain insights into naturalistic animal behavior.
Brain fingerprinting using EEG graph inference
Authors: Miri Maliheh , Abootalebi Vahid , Amico Enrico , Saeedi-Sourck Hamid , Van De Ville Dimitri , Behjat Hamid
Published: March 2023

Taking advantage of the human brain functional connectome as an individual’s fingerprint has attracted great research in recent years. Conventionally, Pearson correlation between regional time-courses is used as a pairwise measure for each edge weight of the connectome. Building upon recent advances in graph signal processing, we propose here to estimate the graph structure as a whole by considering all time-courses at once. Using data from two publicly available datasets, we show the superior performance of such learned brain graphs over correlation-based functional connectomes in characterizing an individual.
Metabolic energetics underlying attractors in neural models
Authors: Buxton Richard B. , Wong Eric C.
Published: March 2023

Neural population modeling, including the role of neural attractors, is a promising tool for understanding many aspects of brain function. We propose a modeling framework to connect the abstract variables used in modeling to recent cellular level estimates of the bioenergetic costs of different aspects of neural activity, measured in ATP consumed per second per neuron. Based on recent work, an empirical reference for brain ATP use for the awake resting brain was estimated as ∼2×109ATP/s-neuron across several mammalian species. The energetics framework was applied to the Wilson-Cowan (WC) model of two interacting populations of neurons, one excitatory (E) and one inhibitory (I). Attractors were considered exhibiting steady-state behavior and limit cycle behavior, both of which end when the excitatory stimulus ends, and sustained activity that persists after the stimulus ends. The general finding was that the energy cost essentially follows the firing rate (average spikes/s) of theE-population, and firing rates of 8-10 spikes/s are in good agreement with the empirical reference value of ATP use. Self-sustained firing driven by recurrent excitation, though, involves higher firing rates and a higher energy cost. By considering a network in which each node is a WC model, we found that a combination of three nodes can serve as a circuit element that turns on when input passes a threshold and then persists after the input ends (an ‘on-switch’), with moderate overall ATP use. The proposed framework can serve as a guide for anchoring neural population models to plausible bioenergetics requirements.
Assessment and validation of enrichment and target capture approaches to improveMycobacterium tuberculosisWGS from direct patient samples
Authors: Mann B.C. , Jacobson K.R. , Ghebrekristos Y. , Warren R.M. , Farhat M.R.
Published: March 2023

Background

Within-hostM. tuberculosis(Mtb) diversity may capture antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here we compared three sample preprocessing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples.

Design/Methods

Mtb positive NALC - NaOH treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I or Benzonase digestion. Levels of contaminating host DNA and target Mtb DNA was assessed by Quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment.

Results

The pre-treatment sample has a high host-to-target ratio of DNA (6 168 ± 1 638 host copies/ng to 212,3 ± 59,4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3 422 ± 2 162 host copies/ng to 11 721 ± 7 096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum after benzonase treatment the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb to 90,95% from 1,18 % compared with benzonase treatment without enrichment.

Conclusion

We demonstrate a low limit of detection (LoD) for a new custom dsDNA Mtb target enrichment panel that has a favourable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
An interpretable ML model to characterize patient-specific HLA-I antigen presentation
Authors: Liang Shaoheng , Jiang Xianli , Chiu Yulun , Xu Haodong , Kim Kun Hee , Lizee Gregory , Chen Ken
Published: March 2023

Personalized immunotherapy holds the promise of revolutionizing cancer prevention and treatment. However, selecting HLA-bound peptide targets that are specific to patient tumors has been challenging due to a lack of patient-specific antigen presentation models. Here, we present epiNB, a white-box, positive-example-only, semi-supervised method based on Naive Bayes formulation, with information content-based feature selection, to achieve accurate modeling using Mass Spectrometry data eluted from mono-allelic cell lines and patient-derived cell lines. In addition to achieving state-of-the-art accuracy, epiNB yields novel insights into the structural properties, such as interactions of peptide positions, that appear important for modeling personalized, tumor-specific antigen presentation. epiNB uses substantially less parameters than neural networks, does not require hyperparameter tweaking and can efficiently train and run on our web portal (https://epinbweb.streamlit.app/) or a regular PC/laptop, making it easily applicable in translational settings.
First report of a successful development of yam hybrids (Dioscorea alataL.) from lyophilized and long-term stored pollens
Authors: Malédon Erick , Nudol Elie , Perrot Christophe , Gravillon Marie-claire , Rivallan Ronan , Cornet Denis , Chair Hâna , Dossa Komivi
Published: March 2023

Background

Greater yam,Dioscorea alataL., is a significant food security crop in tropical areas. However, low genetic diversity and various biological constraints, including susceptibility to viruses, ploidy, erratic and low flowering intensity, and asynchronous flowering hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate genetic material exchanges, artificial pollinations and to increase the genetic gains in breeding programs. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from twoD. alatamales, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24-25 °C) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties.

Results

Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12 to 21% compared to 21-31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse.

Conclusions

The results signify the importance of pollen lyophilization for yam breeding programs.
Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer
Authors: Panda Aniruddha , Giska Fabian , Duncan Anna L. , Welch Alexander J. , Brown Caroline , McAllister Rachel , Parameswaran Hariharan , Goder Jean N. D. , Coleman Jeff , Ramakrishnan Sathish , Pincet Frédéric , Guan Lan , Krishnakumar Shyam , Rothman James E. , Gupta Kallol
Published: March 2023

Hierarchical organization of integral membrane proteins (IMP) and lipids at the membrane is essential for regulating myriad downstream signaling. A quantitative understanding of these processes requires both detections of oligomeric organization of IMPs and lipids directly from intact membranes and determination of key membrane components/properties that regulate them. Addressing this, we have developed a platform that enables native mass spectrometry (nMS) analysis of IMP-lipid complexes directly from intact and customizable lipid membranes. Both the lipid composition and membrane properties (such as curvature, tension, fluidity) of these bilayers can be precisely customized to a target membrane. Subsequent direct nMS analysis of these intact proteo-lipid vesicles can yield the oligomeric states of the embedded IMPs, identify bound lipids, and determine the membrane properties that can regulate the observed IMP-lipid organization. Applying this, we show how lipid binding regulates neurotransmitter release and how membrane composition regulates the functional oligomeric state of a transporter.
Dimensionality reduction reveals separate translation and rotation populations in the zebrafish hindbrain
Authors: Feierstein Claudia E. , de Goeij Michelle H.M. , Ostrovsky Aaron D. , Laborde Alexandre , Portugues Ruben , Orger Michael B. , Machens Christian K.
Published: March 2023

In many brain areas, neuronal activity is associated with a variety of behavioral and environmental variables. In particular, neuronal responses in the zebrafish hindbrain relate to oculomotor and swimming variables, as well as sensory information. However, the precise functional organization of the neurons has been difficult to unravel since neuronal responses are heterogeneous. Here we used dimensionality reduction methods on neuronal population data to reveal the role of the hindbrain in visually-driven oculomotor behavior and swimming. We imaged neuronal activity in zebrafish expressing GCaMP6s in the nucleus of almost all neurons, while monitoring the behavioral response to gratings that rotated with different speeds. We then used reduced-rank regression, a method that condenses the sensory and motor variables into a smaller number of ‘features’, to predict the fluorescence traces of all ROIs (regions of interest). Despite the potential complexity of the visuo-motor transformation, our analysis revealed that the bulk of population activity can be explained by only two features. Based on the contribution of these features to each ROI’s activity, ROIs formed three clusters. One cluster was related to vergent movements and swimming, whereas the other two clusters related to leftward and rightward rotation. Voxels corresponding to these clusters were segregated anatomically, with leftward and rightward rotation clusters located selectively to the left and right hemispheres, respectively. Just as described in many cortical areas, our analysis revealed that single neuron complexity co-exists with a simpler population-level description, thereby providing insights into the organization of visuo-motor transformations in the hindbrain.
Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays
Authors: Chiang Timothy K. , Kimchi Ofer , Dhaliwal Herman K. , Villarreal Daniel A. , Vasquez Fernando F. , Manoharan Vinothan N. , Brenner Michael P. , Garmann Rees F.
Published: March 2023

We describe a simple method to infer intramolecular connections in a population of long RNA molecules in vitro. First we add DNA oligonucleotide “patches” that perturb the RNA connections, then we use a microarray containing a complete set of DNA oligonucleotide “probes” to record where perturbations occur. The pattern of perturbations reveals couplings between different regions of the RNA sequence, from which we infer connections as well as their prevalences in the population. We validate this patch-probe method using the 1,058-nucleotide RNA genome of satellite tobacco mosaic virus (STMV), which has previously been shown to have multiple long-range connections. Our results not only indicate long duplexes that agree with previous structures but also reveal the prevalence of competing connections. Together, these results suggest that globally-folded and locally-folded structures coexist in solution. We show that the prevalence of connections changes when pseudouridine, an important component of natural and synthetic RNA molecules, is substituted for uridine in STMV RNA.
A high-resolution view of RNA endonuclease cleavage inBacillus subtilis
Authors: Taggart James C. , Dierksheide Julia , LeBlanc Hannah , Lalanne Jean-Benoît , Durand Sylvain , Braun Frédérique , Condon Ciarán , Li Gene-Wei
Published: March 2023

RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studiedBacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity amongB. subtilisendoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificityin vivo.
Failure properties and microstructure of porcine aortic adventitia: fiber level damage vs tissue failure
Authors: Ayyalasomayajula Venkat , Pierrat Baptiste , Badel Pierre
Published: March 2023

Aortic aneurysm rupture is a sudden local event with high mortality. It is generally accepted that the adventitia acts as the final barrier protecting the aorta from over-expansion. Currently, the knowledge of microscopic structural determinants of the tissue’s mechanical response and failure is very limited. The purpose of this study is to provide data on the directional failure properties of the adventitia, combined with micro-structural imaging and structure based constitutive modeling to quantify fiber-scale rupture criteria. Eleven healthy porcine aortas were used in this study. Cylindrical portions of the abdominal section were excised, cut-open longitudinally, the medial and adventitial layers separated methodically. Picrosirius red staining was used to image the collagen fiber morphology via an optical microscope. Subsequently, dog-bone shaped specimens were subjected to uniaxial testing until failure while being recorded by a Nikon digital camera. A fiber-scale damage model was utilized to explain the tissue-scale failure. The ultimate tensile stress in the circumferential and longitudinal directions were recorded to be 0.96 ± 0.29MPaand 0.85 ± 0.36MParespectively. Meanwhile, the ultimate stretch to failure in the circumferential and longitudinal directions were recorded to be 1.72 ± 0.16 and 1.88 ± 0.13 respectively. Further, correlation between the failure properties of the tissue and mean fiber orientation have been reported. Finally, the critical fiber stretch for damage initiation and eventual tissue failure were identified to be 1.19 ± 0.07 and 1.24 ± 0.05 for circumferential and longitudinal specimens respectively. Our approach provides valuable insight into the (patho)physiological mechanical role of collagen fibers at different loading states. This study is useful in enhancing the utilization of structurally motivated material models for predicting arterial tissue failure.
A malaria parasite phospholipase facilitates efficient asexual blood stage egress
Authors: Ramaprasad Abhinay , Burda Paul-Christian , Koussis Konstantinos , Thomas James A , Pietsch Emma , Calvani Enrica , Howell Steven A , MacRae James I , Snijders Ambrosius P. , Gilberger Tim-Wolf , Blackman Michael J
Published: March 2023

Malaria parasite release (egress) from host red blood cells involves parasite-mediated membrane poration and rupture, thought to involve membrane-lytic effector molecules such as perforin-like proteins and/or phospholipases. With the aim of identifying these effectors, we disrupted the expression of twoPlasmodium falciparumperforin-like proteins simultaneously and showed that they have no essential roles during blood stage egress. Proteomic profiling of parasite proteins discharged into the parasitophorous vacuole (PV) just prior to egress detected the presence in the PV of a lecithin:cholesterol acyltransferase (LCAT; PF3D7_0629300). Conditional ablation of LCAT resulted in abnormal egress and a reduced replication rate. Lipidomic profiles showed drastic changes in several phosphatidylserine and acylphosphatidylglycerol species during egress. We thus show that, in addition to its previously demonstrated role in liver stage merozoite egress, LCAT is required to facilitate efficient egress in asexual blood stage malaria parasites.

Author Summary

Malaria kills over half a million people every year worldwide. It is caused by a single-celled parasite calledPlasmodium falciparumthat grows and multiplies within a bounding vacuole, inside red blood cells of the infected individuals. Following each round of multiplication, the infected cell is ruptured in a process known as egress to release a new generation of parasites. Egress is required for the disease to progress and is orchestrated by the parasite. The parasite sends out various molecules to puncture and destroy the membranes of the vacuole and the red blood cell. However, little is known about these molecules. In this work, we set out to identify these molecules by using genetic and proteomics approaches. We screened the molecules the parasite sends out during egress and identified a parasite enzyme called LCAT present in the vacuole. Our experiments found that mutant parasites that were unable to make LCAT clumped together and could not escape the infected cell properly. As a result, we saw a reduction in the rate at which these parasites spread through the red blood cells. Taken together, our findings suggest thatP. falciparumneeds LCAT to efficiently break out of red blood cells.
Costs of phenotypic plasticity can undermine its benefits for evolvable digital organisms
Authors: Miras Karine
Published: March 2023

Phenotypic plasticity is usually defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. While the benefits of plasticity for adaptation are well established, the costs associated with plasticity remain somewhat obscure. Understanding both why and how these costs occur could help us explain and predict the behaviour of living creatures as well as allow us to design more adaptable robotic systems. One of the challenges of conducting such investigations concerns the difficulty in isolating the effects of different types of costs and the lack of control over environmental conditions. The present study tackles these challenges by using virtual worlds (software) to investigate the environmentally regulated phenotypic plasticity of digital organisms: the experimental setup guarantees that possibly incurred genetic costs of plasticity are isolated from other plasticity-related costs. The hypothesis put forward here is that despite the potential benefits of plasticity, these benefits might be undermined by the genetic costs related to plasticity itself. This hypothesis was subsequently confirmed to be true.

Author summary

Phenotypic plasticity is usually defined as a property of individual DNA that produces different bodies and brains when exposed to different environmental conditions. While the benefits of plasticity for adaptation are well established, there are also potential costs associated with plasticity: “Jack of all trades, master of none.” Understanding both why and how these costs occur could help us explain and predict the behaviour of living creatures as well as allow us to design more adaptable robotic systems. While some studies have reported strong evidence for such costs, many other studies have observed no costs. One of the challenges associated with conducting such investigations concerns the difficulty of isolating the effects of the different types of costs. Artificial life (ALife) involves the design and investigation of artificial living systems in different levels of organisation and mediums. Importantly, ALife allows for the customisation of multiple properties of an artificial living system. In the present study, I investigate the environmentally regulated phenotypic plasticity of evolvable digital organisms using an ALife system. The experimental setup guarantees that possibly incurred genetic costs of plasticity are isolated from other plasticity-related costs. The hypothesis put forward here is that despite the potential benefits of plasticity, these benefits might be undermined by the genetic costs related to plasticity itself. This hypothesis was subsequently confirmed to be true.
Effect of silane on corrosion resistance and aerodynamic performance of 6063 Al alloy inertial air–water separator
Authors: Wan Lei , Xu Jian , Li Yulai , Sun Haiou , Zhang Tao
Published: March 2023

Purpose

The purpose of this paper is to improve the corrosion resistance of anodized 6063 Al alloy inertial air–water separator by means of silane technology and to investigate the effect of corrosion-generated surface roughness changes on aerodynamic performance.

Design/methodology/approach

The BTSE-KH560 double-layer silane film treatment technique is used to close micropores on the anodic oxide film surface. The microstructure of the coating is observed by scanning electron microscopy, the coating structure of the specimens is determined by X-ray diffraction (XPS) and the corrosion resistance is determined by electrochemical and salt-spray tests. Computational fluid dynamics is also used to calculate the effect of roughness and analyse the change in separator performance.

Findings

The silane film deposited on the surface of the anodic oxide film acts as a good seal against microporous defects on the surface of the anodic oxide film and reduces the surface roughness. Electrochemical and salt-spray tests show that the silane film improved the corrosion resistance of the anodized film. The roughness produced by the corrosion deteriorates the performance of the separator.

Originality/value

The porous structure of the anodized coating makes it easier for corrosive ions to enter the substrate and cause pitting corrosion. Therefore, in this study, the corrosion behaviour of the coating in the marine environment and its effect on aerodynamic performance are investigated using a BTSE-KH560 double-layer silane coating with a sealing effect.
Does venture-backed innovation support carbon neutrality?
Authors: Li Donghui , Liu Yingdong , Sun Minxing , Wang Xinjie , Xu Weike
Published: March 2023

Purpose

This paper aims to answer three questions: (1) Which countries invest more capital in green firms? (2) What kind of industries do venture capitals (VCs) invest in? (3) Do VCs invest more capital in green firms?

Design/methodology/approach

First, the authors provide summary statistics of the key variables for green and non-green firms. Then the authors use figures to plot the growth of green firms over time. Next, the authors use descriptive data to study VC-invested firms for the top 10 countries and industries for all firms, green firms and non-green firms. Finally, the authors compare the VC investors' characteristics and investment behavior between green and non-green firms.

Findings

This study documents that venture-backed investments in clean technologies have increased dramatically in the number of deals and in the total amount of dollar volume over time. This paper provides evidence that VC firms invest more in green firms in each deal than in non-green firms. The United States and European countries play an important role in funding clean technologies across countries, and this study’s results suggest that VC investors play a considerable role in shaping the development of green finance.

Originality/value

This paper makes the first attempt to investigate the role of VCs in clean technologies to support carbon neutrality, providing initial evidence on venture capitalists' investment efforts towards carbon neutrality. The paper also has practical implications for start-up firms that raise capital and venture capitalists who finance green start-ups.
Extended reality (XR) technologies in the construction safety: systematic review and analysis
Authors: Zoleykani Mohammad Javad , Abbasianjahromi Hamidreza , Banihashemi Saeed , Tabadkani Seyed Amir , Hajirasouli Aso
Published: March 2023

Purpose

Extended reality (XR) is an emerging technology, with its popularity rising in different industry sectors, where its application has been recently considered in construction safety. This study aims to investigate the applications of XR technologies in the safety of construction through projects lifecycle perspective.

Design/methodology/approach

Scientometric analysis was conducted to discover trends, keywords, contribution of countries and publication outlets in the literature. The content analysis was applied to categorize previous studies into three groups concerning the phase of lifecycle in which they used XR.

Findings

Results of the content analysis showed that the application of XR in the construction safety is mostly covered in two areas, namely, safety training and risk management. It was found that virtual reality was the most used XR tool with most of its application dedicated to safety training in the design phase. The amount of research on the application of augmented reality and mixed reality in safety training, and risk management in all phases of lifecycle is still insignificant. Finally, this study proposed three main areas for using the XR technologies regarding the safety issues in future research, namely, control of safety regulations and safety coordination in construction phase, and safety reports in the operation phase.

Originality/value

This paper inspected the utilization of all types of XR for safety in each phase of construction lifecycle and proposed future directions for research by addressing the safety challenges in each phase.
Corporate governance, voluntary disclosure and firm valuation relationship: evidence from top listed Indian firms
Authors: Saha Rupjyoti
Published: March 2023

Purpose

This study aims to examine the relationship between corporate governance (CG) voluntary disclosure (VD) and firm valuation (FV). Moreover, the study also investigates whether VD mediates the impact of CG on FV or not.

Design/methodology/approach

The study is based on a panel data set of top 100 listed firms on Bombay Stock Exchange (BSE) over the period of 2014–2018 and develops CG index and VD index (VDI) in order to capture both the constructs respectively. The author adopts suitable panel data model to examine the relationship between CG, VD and FV as well as indirect impact of CG on FV through mediation of VD. Further, the author uses instrumental variables regression model for robustness check.

Findings

The author's findings reveal significant positive impact of CG on FV. Likewise, VD also exhibits significant positive impact on FV. Notably, the interaction of CG and VD complements each other in making positive contribution towards FV. In addition, the author observes that VD partially mediates the impact of CG on FV. Specifically, the outcome suggests that CG apart from having direct impact on FV also influences the same through the mediation of VD. Moreover, as the direction of indirect impact coincide with direct impact, such indirect impact has complementary relationship with the direct impact, implying that when CG makes direct contribution towards improving FV, CG's contribution toward FV through mediation of VD also increases.

Originality/value

To the best of the author's knowledge, this is the first endeavor in the extant literature that examines the interaction performance impact of CG and VD. Further, the author also provides primary evidence on the mediating impact of VD in the relationship between CG and FV.
Waving the flames of fan engagement: strategies for coping with the digital transformation in sports organizations
Authors: Pandita Deepika , Vapiwala Fatima
Published: March 2023

Purpose

The purpose of this study is to understand the factors responsible for social media fan engagement and experience. The research study also attempts to analyze the significance of adopting digital strategies with a fan-centric approach for sports organizations.

Design/methodology/approach

The authors conducted 18 semi-structured interviews with managers in different sports organizations and fans of various popular sports leagues and clubs in India. The authors used a qualitative exploratory approach by applying coding and thematic analysis to arrive at findings and conclusions.

Findings

The responses led to the emergence of three major themes comprising effective planning, harnessing fan participation and boosting the quality of experience. Building on these themes, the authors recommended the “PRIME” model for sports organizations.

Research limitations/implications

As this study explores the growing importance of fan engagement from the top three sports leagues in India, future researchers can focus on obtaining data from multiple countries and multiple leagues to enhance fan engagement's generalizability. Also with the growing popularity of eSports, the scope of the present study may be expanded based on eSports.

Practical implications

The authors' study acts as an eye-opener for managers revealing that to get active participation from fans, sports organizations will have to be active in social media initiatives. In addition to this, the authors also propose the PRIME model, which elaborates on the aspects of Planning social media programs, Regularization of content creation, increased Interaction with the fan base, Motivation through rewards and Enriching fan experience for effectively harnessing fan engagement and experience.

Originality/value

In the pandemic era, engaging with fans on social media can enable sports organizations to thrive. The authors suggest a “PRIME” model which can aid sports managers in effectively harnessing fan engagement and experience for the managers of sports organizations. The model can also be applied beyond the sports context in anchoring customer engagement and experience through the social media of other business organizations.
Enhanced task parameterized dynamic movement primitives by GMM to solve manipulation tasks
Authors: Li Jinzhong , Cong Ming , Liu Dong , Du Yu
Published: March 2023

Purpose

Under the development trend of intelligent manufacturing, the unstructured environment requires the robot to have a good generalization performance to adapt to the scene changes. The purpose of this paper aims to present a learning from demonstration (LfD) method (task parameterized [TP]-dynamic movement primitives [DMP]-GMR) that combines DMPs and TP-LfD to improve generalization performance and solve object manipulation tasks.

Design/methodology/approach

The dynamic time warping algorithm is applied to processing demonstration data to obtain a more standard learning model in the proposed method. The DMPs are used to model the basic trajectory learning model. The Gaussian mixture model is introduced to learn the force term of DMPs and solve the problem of learning from multiple demonstration trajectories. The robot can learn more local geometric features and generalize the learned model to unknown situations by adding task parameters.

Findings

An evaluation criterion based on curve similarity calculated by the Frechet distance was constructed to evaluate the model’s interpolation and extrapolation performance. The model’s generalization performance was assessed on 2D virtual data sets, and first, the results show that the proposed method has better interpolation and extrapolation performance than other methods.

Originality/value

The proposed model was applied to the axle-hole assembly task on real robots, and the robot’s posture in grasping and placing the axle part was taken as the task parameter of the model. The experiment results show that The proposed model is competitive with other models.