bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractWe 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

ABSTRACTRNA 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

AbstractAortic 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

AbstractMalaria 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 SummaryMalaria 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

AbstractPhenotypic 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 summaryPhenotypic 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

PurposeThis 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/approachFirst, 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.FindingsThis 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/valueThis 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

PurposeThis 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/approachThe 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.FindingsThe 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/valueTo 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

PurposeThe 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/approachThe 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.FindingsThe 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/implicationsAs 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 implicationsThe 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/valueIn 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.
Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests
Authors: Lang Ashley K. , Pett‐Ridge Jennifer , McFarlane Karis J. , Phillips Richard P. 
Published: March 2023

Abstract

Identifying the primary controls of particulate (POM) and mineral‐associated organic matter (MAOM) content in soils is critical for determining future stocks of soil carbon (C) and nitrogen (N) across the globe. However, drivers of these soil organic matter fractions are likely to vary among ecosystems in response to climate, soil type and the composition of local biological communities.

We tested how soil factors, climate and plant–fungal associations influenced the distribution and concentrations of C and N in MAOM and POM in seven temperate forests in the National Ecological Observatory Network (NEON) across the eastern United States. Samples of upper mineral horizon soil within each forest were collected in plots representing a gradient of dominant tree–mycorrhizal association, allowing us to test how plant and microbial communities influenced POM and MAOM across sites differing in climate and soil conditions.

We found that concentrations of C and N in soil organic matter were primarily driven by soil mineralogy, but the relative abundance of MAOM versus POM C was strongly linked to plot‐level mycorrhizal dominance. Furthermore, the effect of dominant tree mycorrhizal type on the distribution of N among POM and MAOM fractions was sensitive to local climate: in cooler sites, an increasing proportion of ectomycorrhizal‐associated trees was associated with lower proportions of N in MAOM, but in warmer sites, we found the reverse. As an indicator of soil carbon age, we measured radiocarbon in the MAOM fraction but found that within and across sites, Δ14C was unrelated to mycorrhizal dominance, climate, or soil factors, suggesting that additional site‐specific factors may be primary determinants of long‐term SOM persistence.

Synthesis. Our results indicate that while soil mineralogy primarily controls SOM C and N concentrations, the distribution of SOM among density fractions depends on the composition of vegetation and microbial communities, with these effects varying across sites with distinct climates. We also suggest that within biomes, the age of mineral‐associated soil carbon is not clearly linked to the factors that control concentrations of MAOM C and N.