bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in the 30-year span of Noninfectious Cardiovascular Implantable Electronic Device Complications in Olmsted County
Authors: Kowlgi Gurukripa N. , Vaidya Vaibhav , Dai Ming-Yan , Mishra Rahul , Hodge David O. , Deshmukh Abhishek J. , Mulpuru Siva K. , Friedman Paul A. , Cha Yong- Mei 
Published: May 2023

AbstractBackgroundCardiovascular implantable electronic devices (CIEDs) such as permanent pacemakers, implantable cardioverter-defibrillators, and cardiac resynchronization therapy devices alleviate morbidity and mortality in various diseases. There is a paucity of real-world data on CIED complications and trends.ObjectivesDescribe trends in noninfectious CIED complications over the past three decades in Olmsted County.MethodsThe Rochester Epidemiology Project is a medical records linkage system comprising records of over 500,000 residents of Olmsted County from 1966-current. CIED implants between 1988-2018 were determined. Trends in noninfectious complications within 30 days of implant were analyzed.Results175 out of 2536 (6.9%) patients who received CIED experienced device complications. 3.8% of the implants had major complications requiring intervention. Lead dislodgement was the most common (2.9%), followed by hematoma (2.1%). Complications went up from 1988 to 2005, then showed a downtrend until 2018, driven by a decline in hematomas in the last decade (p<0.01). Those with complications were more likely to have prosthetic valves. Obesity appeared to have a protective effect in a multivariate regression model. The mean Charlson comorbidity score has trended up over the 30 years.ConclusionsOur study describes a real-world trend of CIED complications over three decades. Lead dislodgements and hematomas were the most common complications. Complications have declined over the last decade due to safer practices and a better understanding of anticoagulant management.
Habituation to visual stimuli is personality-independent in a jumping spider
Authors: Beydizada Narmin Ilgar , Cannone Francesco , Pekár Stano , Baracchi David , De Agrò Massimo 
Published: May 2023

1AbstractJumping spiders display some of the richest visually-mediated behaviors in nature. Vision is indeed the most important sensory modality in these spiders where motion detection and response to visual stimuli allow key behaviors such as hunting, escaping from predators, and mating. These spiders have been used in various experiments demonstrating the existence of good associative learning and memory abilities, whose mechanism parallels that found in vertebrates. Here we focused on the habituation and dis-habituation (H/DH) paradigm, indicating either a gradual decrease in responsiveness to repeated visual stimuli (H), or a recovery of the habituated stimulus (DH). H is an elementary form of non-associative learning and memory, which is expected to vary from individual to individual. The link between personality and H/DH has been shown in many vertebrates, but rarely in invertebrates. To tackle this question we tested whether personality affects H/DH in the jumping spiderMenemerus semilimbatus.In our protocol, habituation was assessed by presenting repeatedly a visual stimulus on a screen to spiders tethered on a locomotor compensator. In the same individuals, personality (namely boldness) was assessed in a walking arena equipped with a shelter. We found thatM. semilimbatushabituated and dishabituated to our visual stimulus and that they differed in personality along a shy-bold axis. However, contrary to our expectations, personality was not related to learning. We discussed the results and speculated that the nature (neutral value) of the stimulus might have played a role in making learning independent from personality.
New parameters for the in vitro development of cell lines from fish species
Authors: de Oliveira Furo Ivanete , Nogueira Lygia S. , de Sousa Rodrigo Petry Corrêa , Silva-Oliveira Glaucia Caroline , Santos da Silva Diovanna Mirella dos , Costa-Malaquias Allan , de Oliveira Edivaldo H.C 
Published: May 2023

AbstractThe establishment of cell lines from fish species is becoming important because of the increase in interest of these cells for viral analysis, environmental monitoring and cytogenetic studies. However, there is some discussion about the best conditions for maintaining these cells. We describe here a protocol for primary cell lines which we have found to be reliable. Fin biopsies from two species,Geophagus proximusandAstyanax bimaculatus, were isolated and cultured. We used three culture media (Leibovitz-L15, Dulbecco s Modified Eagle Medium-DMEM and 199) with or without the addition of AmnioMax and a standard temperature of 29ºC. The results showed that 199 medium was less efficient for both species. However, the cells ofG. proximushad better proliferation in DMEM and L-15 media, whileA. bimaculatuscells fared better in DMEM medium. The high concentration of L-glutamine and branched-chain amino acids (BCAAs) in the DMEM and L15 media was probably important for better adaptation of these cells. Furthermore, the addition of AmnioMax, a supplement rich in L-glutamine, increased cell proliferation in both species. Thus, the protocol initially established was tested in other tissues (fin, gills and kidney) of other fish species from the Amazon region. The cells were maintained in L-15 medium supplemented with 20% FBS (Fetal Bovine Serum) and 5% AmnioMax. It was observed that the cells were successfully subcultured and had a good proliferation, also the morphological characteristics were preserved. Thus, the methodology described in this research represents an innovative tool for the establishing of fish cell.
Cardiomyopathy-Associated Variants Alter the Structure and Function of the α-Actinin-2 Actin-Binding Domain
Authors: Atang Alexandra E , Rebbeck Robyn T. , Thomas David D. , Avery Adam W. 
Published: May 2023

AbstractHypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy (RCM) are characterized by thickening, thinning, or stiffening, respectively, of the ventricular myocardium, resulting in diastolic or systolic dysfunction that can lead to heart failure and sudden cardiac death. Recently, variants in theACTN2gene, encoding the protein α-actinin-2, have been reported in HCM, DCM, and RCM patients. However, functional data supporting the pathogenicity of these variants is limited, and potential mechanisms by which these variants cause disease are largely unexplored. Currently, NIH ClinVar lists 34ACTN2missense variants, identified in cardiomyopathy patients, which we predict are likely to disrupt actin binding, based on their localization to specific substructures in the α-actinin-2 actin binding domain (ABD). We investigated the molecular consequences of three ABD localized, HCM-associated variants: A119T, M228T and T247M. Using circular dichroism, we demonstrate that the mutant ABD proteins can attain a well-folded state. However, thermal denaturation studies show that all three mutations are destabilizing, suggesting a structural disruption. Importantly, A119T decreased actin binding, and M228T and T247M cause increased actin binding. We suggest that altered actin binding underlies pathogenesis for cardiomyopathy mutations localizing to the ABD of α-actinin-2.
Computational framework for statistical epistasis supports XOR penetrance function in a living system
Authors: Batista Sandra , Madar Vered Senderovich , Freda Philip J. , Bhandary Priyanka , Ghosh Attri , Chitre Apurva S. , Palmer Abraham A. , Moore Jason H. 
Published: May 2023

AbstractStatistical epistasis has been studied extensively because of its potential to provide evidence for genetic interactions for phenotypes, but there have been methodological limitations to its exhaustive, widespread application. We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied encodings for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10000 loci and 1000 samples each, using the standard Cartesian encoding and the XOR penetrance function for the interactions, to test for evidence of statistical epistasis for the phenotype of body mass index. This study revealed that the XOR penetrance function found greater evidence for statistical epistasis in many more pairs of loci in both data sets and in the rat data set, those pairs of loci found using the XOR penetrance function are enriched for biologically relevant pathways.Author summaryEpistasis, the interaction between two or more genes, is likely integral to the study of genetics and present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects (such as GWAS), partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Many current methods for epistasis detection only consider a Cartesian encoding for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genes, some non-linear. In this work we describe computationally efficient algorithms for the detection of statistical epistasis that allow for varied interaction encodings for modeling epistasis. Our methodology efficiently detects pairwise and three-way epistatic interactions in two closely related species (rat and mouse) under both Cartesian and XOR interaction encodings. Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction encoding was applied providing evidence that more varied models for interaction may need to be applied to describe epistasis that occurs in living systems.
Functionally redundant formate dehydrogenases enable formate-dependent growth inMethanococcus maripaludis
Authors: Halim Mohd Farid Abdul , Fonseca Dallas R , Niehaus Thomas D , Costa Kyle C 
Published: May 2023

AbstractMethanogens are essential for the complete remineralization of organic matter in anoxic environments. Most cultured methanogens are hydrogenotrophic, using H2as an electron donor to reduce CO2to CH4, but in the absence of H2many can also use formate. Formate dehydrogenase (Fdh) is essential for formate oxidation, where it transfers electrons for reduction of coenzyme F420or to a flavin-based electron bifurcating reaction catalyzed by heterodisulfide reductase (Hdr), the terminal reaction of methanogenesis. How these competing reactions are coordinated is unknown. Furthermore, methanogens that use formate encode at least two isoforms of Fdh in their genomes, but how these different isoforms participate in methanogenesis is also unknown. UsingMethanococcus maripaludis, we undertook a biochemical characterization of both Fdh isoforms involved in methanogenesis. Both Fdh1 and Fdh2 interacted with Hdr to catalyze the flavin-based electron bifurcating reaction, and both reduced F420at similar rates. F420reduction preceded flavin-based electron bifurcation activity for both enzymes. In a Δfdh1mutant background, a suppressor mutation was required for Fdh2 activity. Genome sequencing revealed that this mutation resulted in loss of a specific molybdopterin transferase (moeA), allowing for Fdh2-dependent growth. This suggests that both isoforms of Fdh are functionally redundant, but their activitiesin vivomay be limited by gene regulation under different growth conditions. Together these results expand our understanding of formate oxidation and the role of Fdh in methanogenesis.
Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed inHydractiniaembryos
Authors: Ayers Taylor N. , Nicotra Matthew L. , Lee Miler T. 
Published: May 2023

AbstractEmbryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarianHydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities analogous to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far unique to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.
High-resolution molecular atlas of a lung tumor in 3D
Authors: Pentimalli Tancredi Massimo , Schallenberg Simon , León-Periñán Daniel , Legnini Ivano , Theurillat Ilan , Thomas Gwendolin , Boltengagen Anastasiya , Fritzsche Sonja , Nimo Jose , Ruff Lukas , Dernbach Gabriel , Jurmeister Philipp , Murphy Sarah , Gregory Mark T. , Liang Yan , Cordenonsi Michelangelo , Piccolo Stefano , Coscia Fabian , Woehler Andrew , Karaiskos Nikos , Klauschen Frederick , Rajewsky Nikolaus 
Published: May 2023

ABSTRACTCells live and interact in three-dimensional (3D) cellular neighborhoods. However, histology and spatial omics methods mostly focus on 2D tissue sections. Here we present a 3D spatial atlas of a routine clinical sample, an aggressive human lung carcinoma, by combiningin situquantification of 960 cancer-related genes across ∼340,000 cells with measurements of tissue-mechanical components. 3D cellular neighborhoods subdivided the tumor microenvironment into tumor, stromal, and immune multicellular niches. Interestingly, pseudotime analysis suggested that pro-invasive epithelial-to-mesenchymal transition (EMT), detected in stroma-infiltrating tumor cells, already occurred in one region at the tumor surface. There, myofibroblasts and macrophages specifically co-localized with pre-invasive tumor cells and their multicellular molecular signature identified patients with shorter survival. Moreover, cytotoxic T-cells did not infiltrate this niche but colocalized with inhibitory dendritic and regulatory T cells. Importantly, systematic scoring of cell-cell interactions in 3D neighborhoods highlighted niche-specific signaling networks accompanying tumor invasion and immune escape. Compared to 2D, 3D neighborhoods improved the characterization of immune niches by identifying dendritic niches, capturing the 3D extension of T-cell niches and boosting the quantification of niche-specific cell-cell interactions, including druggable immune checkpoints. We believe that 3D communication analyses can improve the design of clinical studies investigating personalized, combination immuno-oncology therapies.
Melanocytes Exhibit Distinct Cell States Governed by A Gene Regulatory Network Under Stochastic Influence
Authors: Aggarwal Ayush , Nasreen Ayesha , Sahoo Sarthak , Faruq Mohammed , Pandey Rajesh , Jolly Mohit K , Singh Abhyudai , Gokhale Rajesh S , Natarajan Vivek T 
Published: May 2023

SummaryMelanocytes serve as a protector of the skin against external stressors such as ultraviolet radiations. While melanocytes remain functional for nearly the entire lifespan of an individual, how they respond efficiently and survive such insults remain elusive. Here, we show the co-existence of multiple distinct states of normal human epidermal melanocytes (NHEMs). Using a progressive pigmentation model, we show that stochasticity in gene expression can lead to the co-existence of multiple melanocyte states. Using active enhancers and gene expression footprint, we identified state-specific transcription factors and constructed a gene regulatory network (GRN). The GRN couples pigmentation and cell cycle regulators and explains the co-existence and transitions of the melanocyte states. Finally, we show that NHEMs respond to external cues by altering the cell state dynamics. These results demonstrate that stochasticity in gene expression followed by epigenetic modification leads to the co-existence of multiple melanocyte states enabling an efficient response to environmental cues.
Life cycle-coupled evolution of mitosis in close relatives of animals
Authors: Shah Hiral , Olivetta Marine , Bhickta Chandni , Ronchi Paolo , Trupinić Monika , Tromer Eelco C. , Tolić Iva M. , Schwab Yannick , Dudin Omaya , Dey Gautam 
Published: May 2023

AbstractEukaryotes have evolved towards one of two extremes along a spectrum of strategies for remodelling the nuclear envelope (NE) during cell division: disassembling the NE in an open mitosis or constructing an intranuclear spindle in a closed mitosis. Both classes of mitotic remodelling involve key differences in the core division machinery, but the evolutionary reasons for adopting a specific mechanism are unclear. Here, we use an integrated comparative genomics and ultrastructural imaging approach to investigate mitotic strategies in Ichthyosporea, close relatives of animals and fungi. We show that species within this clade have diverged towards either a fungal-like closed or an animal-like open mitosis, most likely to support distinct multi- or uninucleated states. Our results suggest that multinucleated life cycles favour the evolution of closed mitosis.One-Sentence SummaryMitotic specialization in animal relatives reveal that multinucleated life cycles favor the evolution of closed mitosis
Exploring the influence of lean manufacturing and total quality management practices on environmental sustainability: the moderating role of quality culture
Authors: Jum’a Luay , Alkalha Ziad , Al Mandil Karam , Alaraj Maher 
Published: May 2023

Purpose
Organizations have released the importance of lean manufacturing practices (LMPs) and total quality management (TQM) in enhancing competitiveness. However, the implementation of LMPs and TQM becomes more complex when discerning the environmental sustainability position. The complexity stems from the fact that LMPs and TQM are more intricate because of cultural differences. Thus, this study aims to tackle the aforementioned phenomenon by investigating the impact of LMPs and TQM on environmental sustainability moderated by quality culture.

Design/methodology/approach
A survey was distributed among small and medium enterprises (SMEs) in Jordan; thus, 315 valid responses were received. Partial least square structural equation modelling was used to analyze the data and test hypotheses.

Findings
The findings showed that environmental sustainability was significantly impacted by all the LMP practices except Kanban and all the TQM practices except statistical process control. Moreover, quality culture significantly and negatively moderated the relationship between TQM and environmental sustainability. However, the influence of LMPs on environmental sustainability was not significantly moderated by quality culture.

Practical implications
This study has implications for policymakers in SMEs, supply chain managers and academics regarding the importance of LMPs and TQM systems for implementing environmental sustainability and the role of quality culture.

Social implications
This study provides guidelines for decision-makers on the pathways that enable them to sustain the environment to safeguard the natural ecosystem and natural resources for upcoming generations.

Originality/value
The originality of this study stems from the alignment of LMPs and TQM in enhancing environmental sustainability, taking into consideration the role of quality culture in SMEs, where previous studies failed short to investigate this phenomenon.
The isomorphism of educational providers in the New Zealand tertiary market
Authors: Wang Jenny Jing 
Published: May 2023

PurposeThe purpose of this paper is to explain how aspects of institutional theory can be used to explain how tertiary educational providers must necessarily adopt the same features while competing in the market for students. Using new institutional sociology (NIS), the authors seek to explain this phenomena and how such diverse private providers have borrowed from the polytechnics and universities to share the same institutional features.Design/methodology/approachThis paper employs NIS to explain how tertiary educational providers must necessarily adopt the same features while competing in the market for students. In the last few decades, the Auckland tertiary market for overseas students has enjoyed strong growth before Covid-19.FindingsDecoupling provides a link between NIS and legitimacy theory in that it explains how symbolic strategies are aimed at some kind of legitimization rather than directed at technical efficiencies. It is argued that the public tertiary providers are more prone to decoupling than PTEPs because they are less attentive to costs due to their more monopolistic position in the market.Originality/valueOriginally, the market was dominated by the local universities and polytechnics with few private providers. Currently, private providers cater for a large share of the certificate and diploma market and have a growing stake in the degree market. As these changes came about so, more diverse private providers entered the market. This paper explains how these diverse entrants came to share the same organizational features.