bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolutionary fingerprints of EMT in pancreatic cancers
Authors: Perelli Luigi , Zhang Li , Mangiameli Sarah , Russell Andrew J. C. , Giannese Francesca , Peng Fuduan , Carbone Federica , Le Courtney , Khan Hania , Citron Francesca , Soeung Melinda , Lam Truong Nguyen Anh , Lundgren Sebastian , Zhu Cihui , Catania Desiree , Feng Ningping , Gurreri Enrico , Sgambato Alessandro , Tortora Giampaolo , Draetta Giulio F. , Tonon Giovanni , Futreal Andrew , Giuliani Virginia , Carugo Alessandro , Viale Andrea , Heffernan Timothy P. , Wang Linghua , Cittaro Davide , Chen Fei , Genovese Giannicola
Published: September 2023

Mesenchymal plasticity has been extensively described in advanced and metastatic epithelial cancers; however, its functional role in malignant progression, metastatic dissemination and therapy response is controversial. More importantly, the role of epithelial mesenchymal transition (EMT) and cell plasticity in tumor heterogeneity, clonal selection and clonal evolution is poorly understood. Functionally, our work clarifies the contribution of EMT to malignant progression and metastasis in pancreatic cancer. We leveragedad hocsomatic mosaic genome engineering, lineage tracing and ablation technologies and dynamic genetic reporters to trace and ablate tumor-specific lineages along the phenotypic spectrum of epithelial to mesenchymal plasticity. The experimental evidences clarify the essential contribution of mesenchymal lineages to pancreatic cancer evolution and metastatic dissemination. Spatial genomic analysis combined with single cell transcriptomic and epigenomic profiling of epithelial and mesenchymal lineages reveals that EMT promotes with the emergence of chromosomal instability (CIN). Specifically tumor lineages with mesenchymal features display highly conserved patterns of genomic evolution including complex structural genomic rearrangements and chromotriptic events. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross species analysis of pancreatic and other human epithelial cancers. Mechanistically, we discovered that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, which in turn results in delayed mitosis and catastrophic cell division. Therefore, EMT favors the emergence of high-fitness tumor cells, strongly supporting the concept of a cell-state, lineage-restricted patterns of evolution, where cancer cell sub-clonal speciation is propagated to progenies only through restricted functional compartments. Restraining those evolutionary routes through genetic ablation of clones capable of mesenchymal plasticity and extinction of the derived lineages completely abrogates the malignant potential of one of the most aggressive form of human cancer.
Evolution of cooperation in deme-structured populations on graphs
Authors: Moawad Alix , Abbara Alia , Bitbol Anne-Florence
Published: September 2023

Understanding how cooperation can evolve in populations despite its cost to individual cooperators is an important challenge. Models of spatially structured populations with one individual per node of a graph have shown that cooperation, modeled via the prisoner’s dilemma, can be favored by natural selection. These results depend on microscopic update rules, which determine how birth, death and migration on the graph are coupled. Recently, we developed coarse-grained models of spatially structured populations on graphs, where each node comprises a well-mixed deme, and where migration is independent from division and death, thus bypassing the need for update rules. Here, we study the evolution of cooperation in these models in the rare migration regime, within the prisoner’s dilemma. We find that cooperation is not favored by natural selection in these coarsegrained models on graphs where overall deme fitness does not directly impact migration from a deme. This is due to a separation of scales, whereby cooperation occurs at a local level within demes, while spatial structure matters between demes.
Determining the antiviral mechanism of MARCH2
Authors: Umthong Supawadee , Timilsina Uddhav , D’Angelo Mary , Stavrou Spyridon
Published: September 2023

Membrane-associated RING-CH (MARCH) 2 protein is a member of the MARCH protein family of RING-CH finger E3 ubiquitin ligases that have important functions in regulating the levels of proteins found on the cell surface. MARCH1, 2 and 8 inhibit HIV-1 infection by preventing the incorporation of the envelope glycoproteins in nascent virions. However, a better understanding on the mechanism utilized by MARCH proteins to restrict HIV-1 is needed. In this report, we identify an amino acid in human MARCH2, that is absent in mouse MARCH2, critical for its antiretroviral function. Moreover, we map the domains of human MARCH2 critical for restricting as well as binding to the HIV-1 envelope glycoproteins. Our findings reveal important new aspects of the antiviral mechanism utilized by human MARCH2 to restrict HIV-1 that have potential implications to all MARCH proteins with antiviral functions.
CRONOSOJA: a daily time-step hierarchical model predicting soybean development across maturity groups in the Southern Cone
Authors: Severini Alan D. , Álvarez-Prado Santiago , Otegui María E. , Kavanová Monika , Vega Claudia R. C. , Zuil Sebastián , Ceretta Sergio , Acreche Martín , Amarilla Fidencia , Cicchino Mariano , Fernández-Long María E. , Crespo Aníbal , Serrago Román , Miralles Daniel J.
Published: September 2023

Accurate prediction of phenology is the most critical aspect for the development of models aimed at estimating seed yield, particularly in species that exhibit variable sensitivity to environmental factors throughout the cycle and among genotypes. With this purpose, we evaluated the phenology of 34 soybean varieties in 43 field experiments located in Argentina, Uruguay, and Paraguay. Experiments covered a broad range of maturity groups (2.2-6.8), sowing dates (from spring to summer), and latitude range (24.9-35.6 °S), thus ensuring a wide range of thermo-photoperiodic conditions during the growing season. Based on the observed data, daily time-step models were developed and tested, first for each genotype, and then across maturity groups. We identified base temperatures specific for different developmental stages and an extra parameter for calculating the photoperiod effect after the R1 stage (flowering). Also, an optimum photoperiod length for each maturity group was found. Model selection showed that the determinants of phenology across maturity groups were mainly affecting the duration of vegetative and early reproductive stages. Even so, early phases of development were better predicted than later ones, particularly in locations with cool growing seasons, where the model tended to overestimate their duration. Overall, we developed a soybean phenology model that, owing to its process-based nature, is able to simulate phenology well across widespread locations and sowing dates yet, because of its simplicity, can be adopted by a wide audience. The final model was made available athttp://cronosoja.agro.uba.ar.
Structural and Functional Disparities within the Human Gut Virome in terms of Genome Topology and Representative Genome Selection
Authors: Veldsman Werner P , Yang Chao , Zhang Zhenmiao , Huang Yufen , Zhang Lu
Published: September 2023

Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. Yet, a shift away from morphology-based classification towards molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the ICTV operational definitions of viruses, particularly for those tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes, with taxonomic uncertainty prevailing at more granular taxa. In order to determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short read polishing, we show that circular and linear virus genomes differ remarkably in terms of genome quality, GC-skew, tRNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. The disparity profile furthermore changes during dereplication. In particular, our phage-host interaction results demonstrate that proportional abundances are incomparable without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome should report the ratio of circular to linear viral genomes (ΔCL) along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.
Auxin-mediated stress relaxation in pericycle and endoderm remodelling drive lateral root initiation
Authors: Ramos João R. D. , Reyes-Hernández Blanca Jazmin , Alim Karen , Maizel Alexis
Published: September 2023

Plant development relies on the precise coordination of cell growth, which is influenced by the mechanical constraints imposed by rigid cell walls. The hormone auxin plays a crucial role in regulating this growth by altering the mechanical properties of cell walls. During the post-embryonic formation of lateral roots, pericycle cells deep within the main root are triggered by auxin to resume growth and divide to form a new root. This growth involves a complex interplay between auxin, growth, and the resolution of mechanical conflicts with the overlying endodermis. However, the exact mechanisms by which this coordination is achieved are still unknown. Here, we propose a model that integrates tissue mechanics and auxin transport, revealing a connection between the auxin-induced relaxation of mechanical stress in the pericycle and auxin signalling in the endodermis. We show that the endodermis initially limits the growth of pericycle cells, resulting in a modest initial expansion. However, the associated stress relaxation is sufficient to redirect auxin to the overlying endodermis, which then actively accommodates the growth, allowing for the subsequent development of the lateral root. Our model uncovers that increased pericycle turgor and decreased endodermal resistance licence expansion of the pericycle and how the topology of the endodermis influences the formation of the new root. These findings highlight the interconnected relationship between mechanics and auxin flow during lateral root initiation, emphasizing the vital role of the endodermis in shaping root development through mechanotransduction and auxin signalling.
AI Algorithm Deployment and Utilization: Strategies to Facilitate Clinical Workflow Implementation and Integration
Authors: Erdal Barbaros Selnur , Laugerette Alexis , Fair Kimberly H. , Zimmermann Mathis , Demirer Mutlu , Gupta Vikash , O’Donnell Thomas P. , White Richard D.
Published: September 2023

Based on past experiences of the Center for Augmented Intelligence in Imaging (CAII) [Department of Radiology, Mayo Clinic Florida], depending on the project, 10 to 20 months has typically been required to realize the successful creation (data curation and algorithm development), and utilization (integration, testing, and operationalization) of an AI algorithm [Figure 1].

Abstract Figure

Figure 1:

AI algorithm evolution typically requires 10 to 20 months, consisting of four consecutive phases: 1. data identification and extraction; 2. data cleansing and labeling; 3. algorithm development with training and tuning; and 4. Implementation and integration with testing and operationalization.

This manuscript delineates the related challenges and opportunities for greater efficiency in completing the clinical workflow implementation and integration of an AI algorithm. Strategies exploiting conventional data standards in facilitating the completion of such deployment and utilization goals within the operations of a busy Radiology practice are described. Methodologies and techniques employed during this initial phase of the CAII-Siemens D&A AI collaboration to address the previously mentioned challenges and opportunities are depicted with use-case examples.
HumanPaenibacillusInfections: A Systematic Review with Comparison of Adult and Infant Cases
Authors: Smith Danielle , Bastug Kristen , Burgoine Kathy , Broach James R. , Hehnly Christine , Morton Sarah U. , Osman Marwan , Schiff Steven J. , Ericson Jessica E.
Published: September 2023

Neonatal infections due toPaenibacillus specieshave increasingly been reported over the last few years. We performed a structured literature review of humanPaenibacillusinfections in infants and adults to compare the epidemiology of infections between these distinct patient populations. Thirty-nine reports describing 176 infections met our inclusion criteria and were included. There were 37Paenibacillusinfections occurring in adults caused by 23 species. The clinical presentations of infections were quite variable. In contrast, infections in infants were caused by only 3 species:P. thiaminolyticus(112/139, 80%),P. alvei(2/139, 1%) andP. dendritiformis(2/139, 1%). All of the infants withPaenibacillusinfection presented with a sepsis syndrome or meningitis, often complicated by extensive cerebral destruction and hydrocephalus. Outcomes were commonly poor with 17% (24/139) mortality. Cystic encephalomalacia due to brain destruction was common in both Ugandan and American cases and 92/139 (66%) required surgical management of hydrocephalus following their infection.Paenibacillusinfections are likely underappreciated in infants and effective treatments are urgently needed.
Endozoicomonasprovides corals with steroid hormones during thermal stress
Authors: Ochsenkühn Michael A. , Mohamed Amin R. , Haydon Trent D. , Coe Lisa S.Y. , Abrego David , Amin Shady A.
Published: September 2023

Summary Paragraph

Rising temperatures are devastating coral populations throughout the globe1. The coral microbiome is believed to play a critical role in sustaining corals and enabling their adaptation to environmental changes, particularly thermal stress2–4. A ubiquitous group of coral-associated bacteria, known asEndozoicomonas, are hypothesized to provide their host with essential metabolites5. However, the nature of coral-Endozoicomonassymbiosis and the role these bacteria play in adaptation to thermal stress are largely unknown. Here, we show that symbioticEndozoicomonasadapt to the host environment by gaining the ability to degrade coral-derived steroids andSymbiodiniaceae-derived galactose while losing the ability to synthesize iron-binding siderophores, a common feature of free-living marine bacteria6. More importantly, under thermal stressEndozoicomonasutilizes coral-derived cholesterol partially as a carbon source while simultaneously converting it to the hormones testosterone and progesterone. Both steroids prime the innate immune system and inhibit pathogenic bacteria and fungi7. These findings highlight an unknown interaction between corals and their microbiome that may be critical to coral health as oceans warm up. The ability of bacteria to synthesize eukaryotic steroid hormones underscores the importance of these molecules in inter-kingdom interactions and suggests that their origin may have evolved as a result of eukaryogenesis.
Physical structure and interstitial flows govern microbial life in microenvironments
Authors: Shen Rachel , Borer Benedict , Ciccarese Davide , Salek M. Mehdi , Babbin Andrew R.
Published: September 2023

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection versus diffusion, and even a modest flow through a pore in the range of 10 µm s−1can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.
Agtrevirus phage AV101 infect diverse extended spectrum β-lactamaseE. coliby recognizing four different O-antigens
Authors: Sørensen Anders Nørgaard , Kalmar Dorottya , Lutz Veronika Theresa , Klein-Sousa Victor , Taylor Nicholas M. I. , Sørensen Martine C. Holst , Brøndsted Lone
Published: September 2023

Bacteriophages in theAgtrevirusgenus are known for expressing multiple tail spike proteins (TSPs), but little is known about their genetic diversity and host recognition apart from their ability to infect diverseEnterobacteriaceaespecies. Here we aim to determine the genetic differences that may account for the diverse host ranges ofAgrevirusphages. We performed comparative genomics of 14Agtrevirusand identified only a few genetic differences including genes involved in nucleotide metabolism. Most notably was the diversity of thetspgene cluster, specifically in the receptor binding domains that were unique among most of the phages. We further characterized agtrevirus AV101 infecting nine diverse Extended Spectrum β-lactamase (ESBL)E. coliand demonstrated that this phage encoded four unique TSPs amongAgtrevirus. Purified TSPs formed translucent zones and inhibited AV101 infection of specific hosts, demonstrating that TSP1, TSP2, TSP3, and TSP4 recognize O8, O82, O153, and O159 O-antigens of ESBLE. coli, respectively. BLASTp analysis showed that the receptor binding domain of TSP1, TSP2, TSP3 and TSP4 are similar to TSPs encoded byE. coliprophages and distant related virulent phages. Thus,Agtrevirusmay have gained their receptor binding domains by recombining with prophages or virulent phages. Overall, combining bioinformatic and biological data expands the understanding of TSP host recognition ofAgtrevirusand give new insight into the origin and acquisition of receptor binding domains ofAckermannviridaephages.

One sentence summary

Agtrevirus phage AV101 express four unique tail spike proteins that recognize different O-antigens of Extended Spectrum β-Lactamase producingE. coli.
Double-Strand Break Repair Pathways Differentially Affect Processing and Transduction by Dual AAV Vectors
Authors: Maurer Anna C. , Benyamini Brian , Fan Vinson B. , Whitney Oscar N. , Dailey Gina M. , Darzacq Xavier , Weitzman Matthew D. , Tjian Robert
Published: September 2023

Recombinant adeno-associated viral vectors (rAAV) are a powerful tool for gene delivery but have a limited DNA carrying capacity. Efforts to expand this genetic payload have focused on engineering the vector components, such as dual trans-splicing vectors which double the delivery size by exploiting the natural concatenation of rAAV genomes in host nuclei. We hypothesized that inefficient dual vector transduction could be improved by modulating host factors which affect concatenation. Since factors mediating concatenation are not well defined, we performed a genome-wide screen to identify host cell regulators. We discovered that Homologous Recombination (HR) is inhibitory to dual vector transduction. We demonstrate that depletion or inhibition of HR factors BRCA1 and Rad51 significantly increase reconstitution of a large split transgene by increasing both concatenation and expression from rAAVs. Our results define new roles for DNA damage repair in rAAV transduction and highlight the potential for pharmacological intervention to increase genetic payload of rAAV vectors.
Isolation and characterization of persisters of the pathogenic microorganismStaphylococcus aureus
Authors: Liu Shiqi , Laman Paul , Jensen Sean , van der Wel Nicole N. , Kramer Gertjan , Zaat Sebastian A. J. , Brul Stanley
Published: September 2023

Staphylococcus aureusis a notorious pathogen responsible for significant morbidity and mortality in both human society and animal husbandry. The presence ofS. aureuspersisters is also one of the leading causes of recurrent and chronic diseases. Persisters are a subset of growth-arrested bacteria within a susceptible bacterial population that are able to tolerate antibiotic treatment and resuscitate after stress removal. Consequently, investigating their formation and characteristics is of crucial importance to provide mechanism-based options for their eradication. However, one challenge in mechanistic research on persisters is the enrichment of pure persisters. In this work, we validated a proposed method to isolate persisters from vancomycin and enrofloxacin generated persistent populations. With this, we analyzed the proteome profile of pure persisters and revealed the distinct mechanisms associated with vancomycin and enrofloxacin induced persisters. Furthermore, morphological and metabolic characterizations were performed, indicating further differences between these two persister populations. Finally, we assessed the effect of ATP repression, protein synthesis inhibition and reactive oxygen species (ROS) level on persister formation. In conclusion, this work provides a comprehensive understanding ofS. aureusvancomycin and enrofloxacin induced persisters at the molecular, single cell and population levels, facilitating a better understanding of persisters and the development of effective strategies to combat them.
The Arabidopsis U1 snRNP regulates mRNA 3’-end processing
Authors: Mangilet Anchilie F. , Weber Joachim , Schüler Sandra , Droste-Borel Irina , Streicher Samuel , Schmutzer Thomas , Rot Gregor , Macek Boris , Laubinger Sascha
Published: September 2023

The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit of the spliceosome playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here, we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP, among them mRNA cleavage and polyadenylation factors. The loss of U1 core components is linked to premature cleavage and polyadenylation within gene bodies and alternative polyadenylation site selection in 3’-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3’-end processing in Arabidopsis, thus establishing the groundwork for a better understanding of non-canonical functions of plant U1 snRNPs.
Threatened and Priority listed Melaleuca species from Western Australia display high susceptibility toAustropuccinia psidiiin controlled inoculations
Authors: Martino A. M. , Park R. F. , Tobias P. A.
Published: September 2023

Austropuccinia psidiicauses rust disease on species within the family Myrtaceae and was first detected in Australia in 2010, with the first detection in Western Australia in 2022. While species within the genusMelaleucafrom Eastern Australia show variable responses to the pathogen, little is known of the response of species from Western Australia. This study established that 13 previously unscreened species ofMelaleuca, including Threatened and Priority species that were grown from seeds sourced from Western Australian populations, were susceptible to the pandemic strain of the pathogen. The proportion of highly susceptible plants within a single species ranged from 2% – 94%, with several species displaying highly variable levels of resistance toA. psidii. These results highlight the importance of disease screening and may direct conservation efforts.
Model-directed generation of CRISPR-Cas13a guide RNAs designs artificial sequences that improve nucleic acid detection
Authors: Mantena Sreekar , Pillai Priya P. , Petros Brittany A. , Welch Nicole L. , Myhrvold Cameron , Sabeti Pardis C. , Metsky Hayden C.
Published: September 2023

Generating maximally-fit biological sequences has the potential to transform CRISPR guide RNA design as it has other areas of biomedicine. Here, we introduce model-directed exploration algorithms (MEAs) for designing maximally-fit, artificial CRISPR-Cas13a guides—with multiple mismatches to any natural sequence—that are tailored for desired properties around nucleic acid diagnostics. We find that MEA-designed guides offer more sensitive detection of diverse pathogens and discrimination of pathogen variants compared to guides derived directly from natural sequences, and illuminate interpretable design principles that broaden Cas13a targeting.
Low-CO2inducible bestrophins in diatom thylakoid membranes sustain high photosynthetic efficacy at distant locations from the pyrenoid
Authors: Nigishi Minori , Shimakawa Ginga , Yamagishi Kansei , Amano Ryosuke , Ito Shun , Tsuji Yoshinori , Nagasato Chikako , Matsuda Yusuke
Published: September 2023

Anion transporters are important to sustain a variety of physiological states in cells. Bestrophins are a family of Cl−and/or HCO3−transporters conserved in bacteria, animals, algae, and plants. Recently, bestrophin paralogs were found in the green algaChlamydomonas reinhardtiias up- regulated components in low CO2conditions that play an essential role in the CO2- concentrating mechanism (CCM). Bestrophin orthologs are also conserved in diatoms, a group of secondary endosymbiotic algae harboring red-type plastids, but their physiological functions are not known yet. Here, we characterized the subcellular localization and expression profile of bestrophins in the marine diatomsPhaeodactylum tricornutum(PtBST1−4) andThalassiosira pseudonana(TpBST1 and 2). PtBST1 and PtBST2 were localized at the stromal thylakoid membrane outside of the pyrenoid, and PtBST3 was localized in the pyrenoid. Contrarily, TpBST1 and TpBST2 were both localized in the pyrenoid. These bestrophin proteins were accumulated in cells grown in atmospheric CO2but not in 1% CO2-grown cells. To assess the physiological functions, we generated knock-out mutants for PtBST1 by genome editing. The lack of PtBST1 decreased affinity of photosynthesis for dissolved inorganic carbon closer to that of the cells grown in 1% CO2. Additionally, non-photochemical quenching was 1.5–2.0 times higher in the mutants than that of the wild type cells. These data suggests that HCO3−transport at the stroma thylakoid membranes by PtBST1 is a critical part of the CO2evolving system of the pyrenoid in the fully induced CCM, and simultaneously that PtBST1 modulates photoprotection in response to CO2availability inP. tricornutum.

Significant statement

Marine diatoms are responsible for nearly half of oceanic primary production, owing to the high-affinity photosynthesis for dissolved inorganic carbon which is supported by CO2- concentrating mechanism (CCM). This study uncovered that a bestrophin family protein at the stoma thylakoid membrane operates to import HCO3−to the thylakoid lumen and mobilizes it towards the CO2evolving system at the pyrenoid-penetrating thylakoid in the diatomPhaeodactylum tricornutum. This HCO3−collecting system not only enhances the CCM but also down regulates the photoprotection capacity of photosystem II, presumably by affecting the thylakoid lumen acidification. This study experimentally demonstrates the molecular mechanism how diatoms optimize the use of CO2and light energy, giving an insight into the reason of ecological successfulness of marine diatoms.
Genetic features and genomic targets of human KRAB-zinc finger proteins
Authors: de Tribolet-Hardy Jonas , Thorball Christian W. , Forey Romain , Planet Evarist , Duc Julien , Coudray Alexandre , Khubieh Bara , Offner Sandra , Pulver Cyril , Fellay Jacques , Imbeault Michael , Turelli Priscilla , Trono Didier
Published: September 2023

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
Poly[diaqua[μ-1,4-bis(pyridin-4-ylmethyl)piperazine][μ-4-(carboxylatoethyl)benzoato]nickel(II)]
Authors: Gaskin Gabrielle J. , LaDuca Robert L.
Published: September 2023

The title compound, [Ni(C10H8O4)(C16H20N4)(H2O)2]
n
, contains NiII cations octahedrally surrounded within an [O4N2] coordination set. The cations are linked by 4-(carboxyethyl)benzoate (ceb) and 1,4-bis(pyridin-4-ylmethyl)piperazine (bpmp) ligands into tri-periodic diamondoid (dia) networks. The fivefold interpenetrated dia networks are held into the crystal structure by means of O—H...O hydrogen bonding between bound water molecules and unligated carboxylate O atoms of the ceb ligands.
Progress of research on gallic acid in corrosion inhibition and rust removal protection of metals
Authors: Li Jiaxin , Zhu Zhiyuan , Li Zhiwei , Zhao Yonggang , Lei Yun , Su Xuping , Wu Changjun , Peng Haoping
Published: September 2023

Purpose

Gallic acid is a substance that is widely found in nature. Initially, it was only used as a corrosion inhibitor to retard the rate of corrosion of metals. In recent years, with intensive research by scholars, the modification of coatings containing gallic acid has become a hot topic in the field of metal protection. This study aims to summarize the various preparation methods of gallic acid and its research progress in corrosion inhibitors and coatings, as well as related studies using quantum chemical methods to assess the predicted corrosion inhibition effects and to systematically describe the prospects and current status of gallic acid applications in the field of metal corrosion inhibition and protection.

Design/methodology/approach

First, the various methods of preparation of gallic acid in industry are understood. Second, the corrosion inhibition principles and research progress of gallic acid as a metal corrosion inhibitor are presented. Then, the corrosion inhibition principles and research progress of gallic acid involved in the synthesis and modification of various rust conversion coatings, nano-coatings and organic resin coatings are described. After that, studies related to the evaluation and prediction of gallic acid corrosion inhibition on metals by quantum chemical methods are presented. Finally, new research ideas on gallic acid in the field of corrosion inhibition and protection of metals are summarized.

Findings

Gallic acid can be used as a corrosion inhibitor or coating in metal protection.

Research limitations/implications

There is a lack of research on the synergistic improvement of gallic acid and other substances.

Practical implications

The specific application of gallic acid in the field of metal protection was summarized, and the future research focus was put forward.

Originality/value

To the best of the authors’ knowledge, this paper systematically expounds on the research progress of gallic acid in the field of metal protection for the first time and provides new ideas and directions for future research.
Sisterhood in academia: building a flock culture to cope and thrive
Authors: Hardie Geraldine , Almeida Shamika , Wijayawardena Kanchana , Frino Betty , Wang Hui-Ling , Rauf Afshan
Published: September 2023

Purpose

This paper examines the experiences of a team of female academics (teaching a large cohort of undergraduate students) and the coping mechanisms used to combat the challenges they confront in the Australian higher education sector.

Design/methodology/approach

Using a reflective autoethnographic method and strengths perspective, the authors share experiences as female professionals whose intersectional identities presented challenges that extend beyond those typically found in the current higher education setting.

Findings

The individualized nature of academic work exacerbates the systemic marginalization of female academics. Adopting a flock culture serves as a support network for addressing the various intersectional challenges. The authors liken the “flock cultural approach” to a “sisterhood” where individuals impacted by intersectional challenges build a strong and cohesive unit to support each other by utilizing their combined strengths to create positive synergy to cope with ongoing workplace challenges.

Research limitations/implications

The study highlights the benefit of the strengths perspective to understand how female academics with intersectional identities can overcome the challenges of their highly individualized profession.

Practical implications

This paper highlights the importance of building team-based work, cultivating collective achievement and high trust in a highly individualistic profession.

Social implications

Using the strength perspective, the authors disrupt the conventional and currently narrow usage of sisterhood to help develop strong, adaptive, flexible and responsive bonds among diverse female academics. The findings point to how using a “flock culture” – a membership-based philosophy – became the key support mechanism for the marginalized groups, empowering them to confront the systemic barriers within their profession.

Originality/value

First, the findings of this study are shaped by the intersections of factors such as ethnicity, age, race, religion and mode of employment, which all influences the participants’ lived experiences. Second, this study contributes to the transnational feminist movement by unveiling the contextualized barriers that junior academic females from various migrant backgrounds face and identify how they synergized their collective strengths to survive the challenging academic environment. Third, using the strength perspective, the authors disrupt the conventional and currently narrow usage of sisterhood to help develop strong, adaptive, flexible and responsive bonds among diverse female academics.
Financial development and growth nexus in Asian countries: mediating role of FDI, foreign aid and trade
Authors: Patra Biswajit , Sethi Narayan
Published: September 2023

Purpose

This paper analyzes the direct effect of financial development and the mediating impact of financial development through foreign direct investment (FDI), foreign aid and trade on economic growth for all Asian countries.

Design/methodology/approach

A fixed-effect model with Driscoll–Kraay panel corrected estimators was employed to find the direct and mediating impact of financial developments on growth for all 47 Asian economies from 1980 to 2020. The bootstrapped panel-quantile regression (BPQR) model is used to check how this effect varies for different income groups of countries.

Findings

The results demonstrated that financial development positively impacts countries' economic growth. The interaction effect of financial development with FDI, foreign aid and foreign trade negatively impacts economic growth. The BPQR results showed that FDI and foreign aid help in the growth of lower quantile economies; however, the impact is negative for middle- and upper-income countries. Trade impacts growth positively for all the quantiles of economies.

Research limitations/implications

The results suggest that the Asian economies must continue to provide thrust on the financial development of their own countries to achieve better growth. It also implied that the dependence on external finance is good for low-income countries and not advisable for middle- and upper-income countries.

Originality/value

To the best of the authors’ knowledge, the current study is the first to provide empirical evidence on analyzing both the direct and interaction effect of financial development on economic growth by considering all the Asian economies.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-09-2022-0587
Feeling stressed but in full flow? Leader mindfulness shapes subordinates' perseverative cognition and reaction
Authors: Xie Haoju , Feng Xingyu
Published: September 2023

Purpose

This study aims to illustrate the mechanisms underlying the effect of stress on flow states in the context of a multilevel organization, in which case employees' perseverative cognition and reactions to challenge–hindrance stressors are affected by leader mindfulness.

Design/methodology/approach

Study 1 employed a three-wave time-lag survey, and study 2 conducted a diary study across 10 workdays to replicate the results of study 1. Multilevel structural equation modeling and Monte Carlo simulation were performed using Mplus 8.0 software to test all hypotheses.

Findings

Problem-solving pondering transmits the nonlinear effect of challenge stressors on flow, and affective rumination mediates the negative effect of hindrance stressors on flow. Leader mindfulness amplifies the tendency of followers to ruminate on the positive aspects of challenge stressors, consequently increasing their positive reactions and flow. Although leader mindfulness fails to influence followers to ruminate less on hindrance stressors, it negates the harmful effect of affective rumination on the flow experience.

Originality/value

This study is one of the first to examine the associations between stressor types and flow in the workplace. The authors also develop a new theory that highlights the ability of leader mindfulness to shape subordinates' stress, cognitions and reactions through social modeling and the authors identify the boundaries of its beneficial effects.
Outcomes of hemorrhagic stroke in patients with autoimmune rheumatic diseases: An analysis of the US Nationwide Inpatient Sample
Authors: Chen Mao‐Yu , Chen Pin‐Yuan , Chang Chen‐Nen , Chen Bo‐An , Deng Wen‐Chun , Yan Jiun‐Lin
Published: September 2023

Aim

To determine whether and how rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic sclerosis (SSc) affect outcomes in patients admitted for hemorrhagic stroke.

Methods

This study screened the Nationwide Inpatient Sample database for adults aged ≥20 years admitted to US hospitals with a principal diagnosis of intracerebral hemorrhage (ICH) between 2005 and 2018. Diagnoses were determined using the International Classification of Diseases, 9th and 10th revisions (ICD‐9 and ICD‐10) diagnostic codes for ICH (ICD‐9: 431, 432; ICD‐10: I61, I62). Study outcomes were: (1) in‐hospital mortality; (2) unfavorable discharge, defined as transfer to nursing homes or long‐term care facilities; and (3) prolonged length of stay (LOS), defined as LOS >75th centile.

Results

Associations between comorbid RA, SLE, and SSc and clinical outcomes show a significantly lower risk of in‐hospital mortality and prolonged LOS in RA patients. After admissions for ICH, the risk for in‐hospital mortality and prolonged LOS was decreased in RA patients, and the risk for unfavorable discharge (long‐term care) was reduced in SLE patients.

Conclusions

Among patients admitted to US hospitals for hemorrhagic stroke, patients with RA had decreased risk for in‐hospital mortality and prolonged LOS.
Equalising the evidence base for adaptation and loss and damages
Authors: Otto Friederike E. L. , Fabian Frederick
Published: September 2023

Since the UNFCCC Paris Agreement came into force after 2015 international climate policy rests on three pillars: mitigation, adaptation and loss and damage. However, while there are clear agreed‐upon metrics to measure emissions, base mitigation goals against and hold countries and companies accountable to, the evidence base for the impacts of climate change to inform adaptation and loss and damage is very different. There are no agreed‐upon metrics, nor are there guidelines or criteria to delineate the impacts of climate change from other drivers of losses and damages. This imbalance is reflected in the lack of ability to set and enforce goals. With a new body of scientific evidence introduced in the IPCC, we argue that this can change. Especially with an increasing number of climate litigation cases being recognised as a legitimate root to justice, and thus being given due consideration in courts, the imbalance in evidence could change and put adaptation and loss and damage on more equal footing with mitigation.
Extracellular shuttling miR‐21 contributes to esophageal cancers and human umbilical vein endothelial cell communication in the tumor microenvironment and promotes tumor angiogenesis by targeting phosphatase and tensinhomolog
Authors: Zheng Shanbo , Liao Juan , Sun Mingjun , Liu Ran , Lv Junjie
Published: September 2023

Background

Cell‐cell communication by carcinoma‐derived exosomes can influence the tumor microenvironment (TME) and regulate cancer progression. Based on the overexpression of microRNA‐21‐5p (miR‐21) in plasma from patients diagnosed with esophageal squamous cell carcinoma (ESCC) and exosomes from ESCC cell lines identified earlier, this study aimed to explore the influence of exosomal miR‐21 within the TME.

Method

ScRNA‐Seq and Bulk RNA‐Seq were integrated to elucidate the communication between cancer and endothelial cells. The functionality and mechanisms by which exo‐miR‐21 derived from carcinoma regulate endothelial cell‐mediated angiogenesis were assessed using a cocultivation model of EC9706 cells and recipient human umbilical vein endothelial cells (HUVECs), through blood vessel formation experiments, luciferase reporter assays, RT‐qPCR, and western blot analysis.

Result

A total of 3842 endothelial cells were extracted from the scRNA‐seq data of ESCC samples and reclustered into five cell subtype. Cell‐cell communication analysis revealed cancer cells presented a strong interaction with angiogenesis‐like endothelial cells in secreted signaling. MiR‐21 was unregulated in ESCC and the carcinoma‐derived exo‐miR‐21 was significantly raised in HUVECs. The exo‐miR‐21 promoted the proliferation and migration of HUVECs while also enhancing, closed mesh count, and junction number in HUVECs. Mechanistically, dual‐luciferase reporter assay revealed that PTEN was the target of miR‐21. Meanwhile, p‐Akt was significantly increased and suppressed by inhibition of miR‐21 and PI3K inhibitor LY294002.

Conclusion

Exo‐miR‐21‐mediated communication between endothelial and cancer cells plays a pivotal role in promoting the angiogenesis of ESCC. Therefore, controlling exo‐miR‐21 could serve as a novel therapeutic strategy for ESCC by targeting angiogenesis.
The merits of securities litigation and corporate reputation
Authors: Donelson Dain C. , Kartapanis Antonis , Yust Christopher G.
Published: September 2023

We explore how securities litigation affects corporate reputation. Experts remain concerned that nonmeritorious securities class actions—those that will be dismissed or settled for nuisance amounts—cause reputational damage. Although several prior studies show reputational costs for nonmeritorious cases, they generally use indirect measures based on returns or total market losses, which are mechanically associated with securities litigation elements. In contrast, we use a relatively direct reputation measure from Fortune's “Most Admired Companies” list. We find significant reputational damage after meritorious litigation, with the strongest cases having the largest effects. However, we find no evidence of reputational damage after nonmeritorious litigation. We also find that Fortune's reputational damage measure is associated with more negative returns around the litigation filing date. We show possible mechanisms for our results, as initial legal filings contain information allowing market participants to assess case merits. Our results imply that reputational damage is primarily due to fraud, which securities litigation helps reveal to the market, rather than litigation itself. Thus, reputational damage is not an issue in over 70% of securities class actions due to the high frequency of nonmeritorious cases.
A comparison of the effect of patient‐specific versus weight‐based protocols to treat vaso‐occlusive episodes in the emergency department
Authors: Tanabe Paula , Ibemere Stephanie , Pierce Ava E. , Freiermuth Caroline E. , Bosworth Hayden B. , Yang Hongqui , Osunkwo Ifeyinwa , Paxton James H. , Strouse John J. , Miller Joseph , Paice Judith A. , Veeramreddy Padmaja , Kavanagh Patricia L. , Wilkerson R. Gentry , Hughes Robert , Barnhart Huiman X.
Published: September 2023

Background

Vaso‐occlusive crises (VOCs) cause debilitating pain and are a common cause of emergency department (ED) visits, for people with sickle cell disease (SCD). Strategies for achieving optimal pain control vary widely despite evidence‐based guidelines. We tested existing guidelines and hypothesized that a patient‐specific pain protocol (PSP) written by their SCD provider may be more effective than weight‐based (WB) dosing of parenteral opiate medication, in relieving pain.

Methods

This study was a prospective, randomized controlled trial comparing a PSP versus WB protocol for patients presenting with VOCs to six EDs. Patients were randomized to a PSP or WB protocol prior to an ED visit. The SCD provider wrote their protocol and placed it in the electronic health record for future ED visits with VOC exclusion criteria that included preexisting PSP excluding parenteral opioid analgesia or outpatient use of buprenorphine or methadone or highly suspected for COVID‐19. Pain intensity scores, side effects, and safety were obtained every 30 min for up to 6 h post–ED bed placement. The primary outcome was change in pain intensity score from placement in an ED space to disposition or 6 h.

Results

A total of 328 subjects were randomized; 104 participants enrolled (ED visit, target n = 230) with complete data for 96 visits. The study was unable to reach the target sample size and stopped early due to the impact of COVID‐19. We found no significant differences between groups in the primary outcome; patients randomized to a PSP had a shorter ED length of stay (p = 0.008), and the prevalence of side effects was low in both groups. Subjects in both groups experienced both a clinically meaningful and a statistically significant decrease in pain (27 mm on a 0‐ to 100‐mm scale).

Conclusions

We found a shorter ED length of stay for patients assigned to a PSP. Patients in both groups experienced good pain relief without significant side effects.