bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in Gaps of Care for Congenital Heart Disease Patients: Implications for Social Determinants of Health and Child Opportunity Index
Authors: Zaidi Abbas H. , Alberts Adam , Chowdhury Devyani , Beaty Claude , Brewer Benjamin , Chen Ming Hui , de Ferranti Sarah D.
Published: February 2024

Background

Lifelong continuity of care is imperative for patients with congenital heart disease (CHD); unfortunately, gaps in care (GIC) are common.

Methods

All patients aged 0-34 years followed at a pediatric subspecialty hospital (primary location Delaware; satellites covering Pennsylvania, New Jersey, Maryland) with CHD who underwent surgery between January 2003 and May 2020 were included. Patients were categorized as simple, moderate, and complex CHD based on 2018 American Heart Association and American College of Cardiology guidelines. Social determinants of health factors such as age, race, ethnicity, sex, language, insurance status, and Child Opportunity Index based on home address zip code were analyzed.

Results

Of 2012 CHD patients, a GIC of ≥3 years was identified in 56% (n=1119). The proportion of patients with GIC per year increased for all patients. Multivariable longitudinal models with all CHD patients showed that GIC are increasing for patients who are ≥10.5 years old, have simple CHD, live out of state, live farther from a site of care (hospital or satellite clinics), receive public insurance and/or have less protection with additional insurance plans, and reside in low Child Opportunity Index neighborhoods. A separate model for only moderate/complex CHD patients showed similar findings. Neither longitudinal model showed race/ethnicity as significant for increasing GIC trends.

Conclusions

GIC have continued to increase with an aging CHD population with social determinants of health factors specifically related to insurance, access, and neighborhood opportunity. Attenuating GIC necessitates standardized practices while simultaneously addressing the impact of SDOH on all CHD patients.

Clinical Perspective

What is new?

This study is the first to examine gaps in care (GIC) trends over time in patients with repaired congenital heart disease (CHD) and found that almost half had GIC.

Over 2 decades, GIC are increasing for certain subpopulations of CHD patients based on social determinants of health, including being older, lacking insurance, and residing in low Child Opportunity Index neighborhoods.

What Are the Clinical Implications?

GIC are worsening in certain subpopulations of CHD patients, including those with low Child Opportunity Index, lack of insurance, or poor access to health care systems.

CHD programs must target social determinants of health factors to improve ongoing care and long-term outcomes for all patients.
Extensive distribution of β-1,2-glucanases: finding of new glycoside hydrolase families of β-1,2-glucanases
Authors: Nakajima Masahiro , Tanaka Nobukiyo , Motouchi Sei , Kobayashi Kaito , Shimizu Hisaka , Abe Koichi , Hosoyamada Naoya , Abara Naoya , Morimoto Naoko , Hiramoto Narumi , Nakata Ryosuke , Takashima Akira , Hosoki Marie , Suzuki Soichiro , Shikano Kako , Fujimaru Takahiro , Imagawa Shiho , Kawadai Yukiya , Wang Ziyu , Kitano Yoshinao , Nihira Takanori , Nakai Hiroyuki , Taguchi Hayao
Published: February 2024

β-1,2-Glucans are natural glucose polymers that play important physiological roles, including as symbiotic or pathogenic factors and in osmoregulation. Phylogenetically new glycoside hydrolase (GH) families have recently been identified from β-1,2-glucanase (SGL) sequences from bacteria (GH144) and a fungus (GH162). In this study, we identified four phylogenetically new groups (Groups 1–4), and determined that these families, together with GH144, GH162, and GH189, a family of transglycosylase domains in cyclic β-1,2-glucan synthases, form a superfamily. Biochemical analysis of six proteins in these groups revealed that the proteins in Groups 1–3 showed hydrolytic activity specific to β-1,2-glucan. The kinetic parameters of the enzymes of Groups 1–3 were similar to GH144 and GH162 SGLs, indicating that these enzymes were SGLs. Optical rotation analysis revealed that the SGLs followed an anomer-inverting mechanism. Structural analysis and prediction of the proteins in Groups 1–4, GH144, GH162, and GH189 suggested that Groups 1–3 and GH144 had the same reaction mechanism. Nevertheless, Groups 1–3 were dispersed irregularly in the superfamily. Overall, we determined that Groups 1–3 were new GH families, GHxxx, GHyyy, and GHzzz, respectively, and proposed that this superfamily be called an SGL superfamily because of the phylogenetical, functional, and structural relationships within the superfamily.

Highlights

Wide variety of glycoside hydrolases is far beyond our understanding.

Functional and structural analysis identified three new glycoside hydrolase families.

Molecular evolution with irregular changes in reaction mechanism was revealed.
Optogenetic control of pheromone gradients reveals functional limits of mating behavior in budding yeast
Authors: Banderas Alvaro , Hofmann Maud , Cordier Celine , Le Bec Matthias , Elizondo Carolina , Chiron Lionel , Pouzet Sylvain , Scolari Vittore , Hersen Pascal
Published: February 2024

Cell-cell communication through diffusible signals allows distant cells to coordinate biological functions. Such coordination depends on the signal landscapes generated by emitter cells and the sensory capacities of receiver cells. In contrast to morphogen gradients in embryonic development, microbial signal landscapes occur in open space with variable cell densities, spatial distributions, and physical environments. How do microbes shape signal landscapes to communicate robustly under such circumstances remains an unanswered question. Here we combined quantitative spatial optogenetics with biophysical theory to show that in the mating system of budding yeast— where two mates communicate to fuse—signal landscapes convey demographic or positional information depending on the spatial organization of mating populations. This happens becauseα-factor pheromone and its mate-produced protease Bar1 have characteristic wide and narrow diffusion profiles, respectively. Functionally, MATαpopulations signal their presence as collectives, but not their position as individuals, and Bar1 is a sink of alpha-factor, capable of both density-dependent global attenuation and local gradient amplification. We anticipate that optogenetic control of signal landscapes will be instrumental to quantitatively understand the spatial behavior of natural and engineered cell-cell communication systems.
Focal Deletions of a Promoter Tether Activate theIRX3Oncogene in T Cell Acute Lymphoblastic Leukemia
Authors: Rahman Sunniyat , Bloye Gianna , Farah Nadine , Demeulemeester Jonas , Costa Joana R. , O’Connor David , Pocock Rachael , Turna Adam , Wang Lingyi , Lee SooWah , Fielding Adele K. , Roels Juliette , Jaksik Roman , Dawidowska Malgorzata , Vlierberghe Pieter Van , Hadjur Suzana , Hughes Jim R. , Davies James O.J. , Gutierrez Alejandro , Kelliher Michelle A , Loo Peter Van , Dawson Mark A. , Mansour Marc R.
Published: February 2024

Oncogenes can be activated incisthrough multiple mechanisms including enhancer hijacking events and noncoding mutations that create enhancers or promotersde novo. These paradigms have helped parse somatic variation of noncoding cancer genomes, thereby providing a rationale to identify noncanonical mechanisms of gene activation. Here we describe a novel mechanism of oncogene activation whereby focal copy number loss of an intronic element within theFTOgene leads to aberrant expression ofIRX3, an oncogene in T cell acute lymphoblastic leukemia (T-ALL). Loss of this CTCF bound element downstream toIRX3(+224 kb) leads to enhancer hijack of an upstream developmentally active super-enhancer of theCRNDElong noncoding RNA (-644 kb). Unexpectedly, theCRNDEsuper-enhancer interacts with theIRX3promoter with no transcriptional output until it is untethered from theFTOintronic site. We propose that ‘promoter tethering’ of oncogenes to inert regions of the genome is a previously unappreciated biological mechanism preventing tumorigenesis.
Polyketide synthase-derived sphingolipids determine microbiota-mediated protection against pathogens inC. elegans
Authors: Peters Lena , Drechsler Moritz , Pees Barbara , Angelidou Georgia , Salzer Liesa , Moors Karlis Arturs , Paczia Nicole , Schulenburg Hinrich , Shi Yi-Ming , Kaleta Christoph , Witting Michael , Bode Helge B. , Dierking Katja
Published: February 2024

Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematodeCaenorhabditis elegansand its microbiota isolatePseudomonas fluorescensMYb115 that is known to protect againstBacillus thuringiensis(Bt) infection. We find that MYb115-mediated protection depends on sphingolipids that are derived from an iterative type I polyketide synthase (PKS), thereby describing a noncanonical pathway of bacterial sphingolipid production. We provide evidence that MYb115-derived sphingolipids affectC. eleganstolerance to Bt infection by altering host sphingolipid metabolism. This work establishes sphingolipids as structural outputs of bacterial PKS and highlights the role of microbiota-derived sphingolipids in host protection against pathogens.
A rapid, cost-effective, colorimetric LAMP assay (CLASS) for detecting invasive malaria vector,Anopheles stephensi
Authors: Rafferty Cristina , Raise Gloria , Scaife Jenyiah , Abongo Bernard , Omondi Seline , Milanoi Sylvia , Muchoki Margaret , Onyango Brenda , Ochomo Eric , Zohdy Sarah
Published: February 2024

Anopheles stephensi, an invasive malaria vector in Africa, has the potential to impact the landscape of malaria on the continent, threatening to put an additional 126 million people per year at risk of malaria, largely in peri-urban/urban areas. To accelerate the early detection and rapid response toAn. stephensiand ensure no gains made in malaria control and elimination are lost, it is critical to confirm the presence of the species and the geographic extent of its spread to inform control. However, morphological identification may be misinterpreted if specimens are damaged and existing molecular species confirmation assays require specialized laboratory equipment and training and may be challenging to interpret, requiring additional sequencing confirmation. A colorimetric rapid loop-mediated isothermal amplification (LAMP) assay for molecularAn. stephensispecies identification was developed and optimized. The colorimetric assay requires only a heat source and reagents and can be used with or without DNA extraction resulting in positive color change in 30-35 minutes. To determine analytical sensitivity, a 1:10 dilution series of the DNA extract was conducted showing 100% assay sensitivity down to 0.003 nanograms. To determine specificity, three differentAn. stephensilaboratory strains (STE2, SDA 500, UCI), 8 other Anopheles mosquito species, andAedes aegyptiwere compared, and the results indicated 100% specificity across these species. To determine use without the need for DNA extraction, samples evaluated included a single mosquito leg, whole adult or larval mosquitoes, and pooled DNA extract from several mosquito species. A total of 1687 individual reactions were tested during optimization and all LAMP assay results were compared against the conventional PCR assay and confirmed through Sanger sequencing. To validate the optimized assay on wild caught specimens, DNA extracted from 12 wild caught, sequence-confirmedAn. stephensifrom Marsabit, Kenya, were tested and the colorimetric assay was accurate in identifying all of the specimens asAn. stephensi. The assay described presents an opportunity to accelerateAn. stephensimolecular identification in new and existing locations in Africa, within its endemic range, and globally. These findings present a simple, rapid, unique alternative to existing PCR and sequencing-basedAn. stephensispecies identification and confirmation strategies. With additional field validation studies, molecular screening tools like the colorimetric LAMP-based An.stephensispecies identification (CLASS) assay fill an important gap of rapid confirmation of this invasive vector and presents an ideal opportunity to better understand the spread of the species in Africa and other recently invaded areas, thus accelerating a response to mitigate its long-term impacts on malaria on the continent.
Accumulation dynamics of defective genomes during experimental evolution of two betacoronaviruses
Authors: Hillung Julia , Olmo-Uceda María J. , Muñoz-Sánchez Juan C. , Elena Santiago F.
Published: February 2024

Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When coinfected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.
Motor adaptation to environment changes predicting object behaviour can be flexible and implicit
Authors: Modchalingam Shanaathanan , King Andrew , ’t Hart Bernard Marius , Henriques Denise Y. P.
Published: February 2024

Human motor behaviour can adapt in response to perturbations in the environment, either through updating existing motor control models or by creating context-specific motor memories or strategies. Context informed motor adaptation can allow for flexible motor behaviour in changing environments, albeit with costs associated with action selection. While our dynamic natural environments necessitates flexible motor behaviour, many studies of motor control and motor learning limit their focus to model-based motor adaptation. In this study, we investigate if motor adaptation is flexible when a perturbation is applied to either the acceleration of a rolling ball, or to the throw direction at release during a virtual throw-to-target task. We also determine if the tendency for model updating is influenced by immersive and informative visual cues indicating the presence of a perturbation, such as the slant of a surface on which thrown objects travel. Despite the visual slant allowing for more rapid performance change when adapting to both perturbation scenarios, our findings reveal that perturbations resembling accelerations enabled flexible motor adaptation regardless of the presence of the slant cue. Perturbations in the throw direction conversely predominantly led to internal model updating. Additionally, informative visual slant properties of the task surface elicited implicit, slant-specific changes in performance. Our findings underscore the role of visual properties of both perturbations and environments in flexible motor learning.
Mapping the soil microbiome functions shaping wetland methane emissions
Authors: Oliverio Angela M , Narrowe Adrienne B , Villa Jorge A , Rinke Christian , Hoyt David W , Liu Pengfei , McGivern Bridget B , Bechtold Emily K , Ellenbogen Jared B , Daly Rebecca A , Smith Garrett J , Angle Jordan C , Flynn Rory M , Freiburger Andrew P , Louie Katherine B , Stemple Brooke , Northen Trent , Henry Christopher , Miller Christopher , Morin Timothy H , Bohrer Gil , Borton Mikayla A , Wrighton Kelly C
Published: February 2024

Accounting for only 8% of Earth's land coverage, freshwater wetlands remain the foremost contributor to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with nearly half of the 72 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed in wetland soils. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more so than land coverage or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane cycling microorganisms, contrasting with theoretical expected responses to hydrological perturbations. Co-expression analyses coupled to depth resolved methane measurements exposed the metabolisms and trophic structures most predictive of methane hotspots. This compendium of biogeochemically-classified genomes and their spatiotemporal transcriptional patterns begins to untangle the microbial carbon, energy and nutrient processing contributing to soil methane production.
HDAC1/2 and HDAC3 play distinct roles in controlling adult Meibomian gland homeostasis
Authors: Zhu Xuming , Xu Mingang , Millar Sarah E.
Published: February 2024

Purpose

To investigate the roles of HDAC1/2 and HDAC3 in adult Meibomian gland (MG) homeostasis.

Methods

HDAC1/2 or HDAC3 were inducibly deleted in MG epithelial cells of adult mice. The morphology of MG was examined. Proliferation, apoptosis, and expression of MG acinus and duct marker genes, meibocyte differentiation genes, and HDAC target genes, were analyzed via immunofluorescence, TUNEL assay, and RNA in situ hybridization.

Results

Co-deletion of HDAC1/2 in MG epithelium caused gradual loss of acini and formation of cyst-like structures in the central duct. These phenotypes required homozygous deletion of both HDAC1 and HDAC2, indicating that they function redundantly in the adult MG. Short-term deletion of HDAC1/2 in MG epithelium had little effect on meibocyte maturation but caused decreased proliferation of acinar basal cells, excessive DNA damage, ectopic apoptosis, and increased p53 acetylation andp16expression in the MG. By contrast, HDAC3 deletion in MG epithelium caused dilation of central duct, atrophy of acini, defective meibocyte maturation, increased acinar basal cell proliferation, and ectopic apoptosis and DNA damage. Levels of p53 acetylation and p21 expression were elevated in HDAC3-deficient MGs, while the expression of the differentiation regulator PPARγ and the differentiation markers PLIN2 and FASN was downregulated.

Conclusions

HDAC1 and HDAC2 function redundantly in adult Meibomian gland epithelial progenitor cells and are essential for their proliferation and survival, but not for acinar differentiation, while HDAC3 is required to limit acinar progenitor cell proliferation and permit differentiation. HDAC1/2 and HDAC3 have partially overlapping roles in maintaining survival of MG cells.
Mean Dynamics Index: a useful tool to identify motor psychogenic non epileptic seizures
Authors: Winer Raz , Shahkoohi Shahram Shlomo , Herskovitz Moshe
Published: February 2024

Timely and accurate diagnosis of Psychogenic Non-Epileptic Seizures (PNES) is crucial. Aside from potential diagnostic delays, patients with PNES often undergo unnecessary pharmacological or invasive treatments. Presently, effective bedside tools for distinguishing PNES from epileptic seizures (ES) remain elusive, and the ‘gold standard’ diagnosis relies primarily on patient history and prolonged video EEG monitoring. In this study, we developed a simple clinical tool - the Mean Dynamic Index (MD) - to differentiate PNES from ES.

We divided the body into five anatomical regions: the head and face, two upper extremities, and two lower extremities. Due to limited movement potential, the trunk was excluded from consideration. Among these five areas, only actively involved regions were considered in the score calculation. Each distinct motor feature observed contributed a point to the regional summation, with each region’s score comprising the Regional Dynamic Index (RDI). The Mean Dynamic Index (MDI) represents the average of all RDIs.

Sixty consecutive patients admitted to the VEEG monitoring unit were evaluated. Of these, 15 patients presented primarily with motor symptoms. Eight were diagnosed with PNES, while seven had epileptic seizures. The mean MDI was 1.2±0.4 in the PNES group and 2.8±0.77 in the ES group (p<0.001). The mean MDI/duration ratio was 0.31±0.38 for PNES and 3.5±2.4 for ES (p < 0.003). An MDI score of 1.665 yielded a specificity of 87.5% and sensitivity of 100% for diagnosing ES. A low MDI score (<1.66) in motor seizures indicates limited variability in the movement profile of each body part, suggesting a PNES etiology. Additionally, as the MDI/time ratio decreases, PNES becomes more likely. Furthermore, we observed that an RDI of 3 or higher completely differentiated between PNES and ES. These findings offer a valuable bedside tool for distinguishing between the two conditions.
Competitive advantages of T-even phage lysis inhibition in response to secondary infection
Authors: Hvid Ulrik , Mitarai Namiko
Published: February 2024

T-even bacteriophages are known to employ lysis inhibition (LIN), where the lysis of an infected host is delayed in response to secondary adsorptions. Upon the eventual burst of the host, significantly more phage progenies are released. Here, we analysed the competitive advantage of LIN using a mathematical model. In batch culture, LIN provides a bigger phage yield at the end of the growth where all the hosts are infected due to an exceeding number of phage particles and, in addition, gives a competitive advantage against LIN mutants with rapid lysis by letting them adsorb to already infected hosts in the LIN state. By simulating plaque formation in a spatially structured environment, we show that, while LIN phages will produce a smaller zone of clearance, the area over which the phages spread is actually comparable to those without LIN. The analysis suggests that LIN induced by secondary adsorption is favourable in terms of competition, both in spatially homogeneous and inhomogeneous environments.

Author Summary

T-even bacteriophages can delay the lysis of their hosts when they detect more phages are adsorbing to the hosts, increasing the progeny production per host. Using a mathematical model, we provide a quantitative analysis of this strategy’s competitive advantages and disadvantages in different environments. The model predicts that phage adsorption to lysis-inhibited cells provides a significant competitive advantage to lysis-inhibiting phage against phages that quickly lyse the cells. We also find that secondary infection-triggered delay does not hinder the spreading of the phage in a lawn of uninfected cells, even though the apparent plaque size is small. The analysis suggests that lysis inhibition provides a robust competitive advantage for a virulent phage.
Dual action of sphinganine in the plant disease resistance to bacteria
Authors: Huby Eloïse , Villaume Sandra , Chemotti Catherine , Dorey Stéphan , Cordelier Sylvain , Crouzet Jérôme , Gilliard Guillaume , Terryn Christine , Berquand Alexandre , Herrfurth Cornelia , Feussner Ivo , Jacquard Cédric , Fontaine Florence , Clément Christophe , Baillieul Fabienne , Deleu Magali , Dhondt-Cordelier Sandrine
Published: February 2024

Sphingolipids are ubiquitous, highly diverse molecules constituting at least 40% of plant plasma membranes. Initially known as modulators of membrane integrity, they now emerge as important players in plant responses to (a)biotic stresses. The interaction betweenArabidopsis thalianaand the bacteriumPseudomonas syringaepv.tomatoDC3000AvrRpm1(Pst AvrRpm1) culminates in the activation of a programmed cell death known as the hypersensitive response, which is part of the plant immune response. In this study, we showed that the co-infiltration ofPst AvrRpm1and sphinganine (d18:0) inArabidopsisleaves suppress the hypersensitive response. This suppression phenotype is also observed with bacteria carrying the effectors AvrB and AvrPphB but not with the ones carrying AvrRpt2 and AvrRps4. Sphingolipid-induced hypersensitive response suppression byPst AvrRpm1is correlated with the down-regulation of the geneAtNMT1encoding aN-myristoyltransferase. d18:0 does not have a direct antibacterial effect and its co-infiltration in plants does not display typical signs of immune response such as activation of salicylic acid signaling pathway and extracellular reactive oxygen species production. Biophysical studies showed that d18:0 interacts with plant plasma membrane lipids. More specifically, d18:0 disturbs plant plasma membrane organization and mechanical properties. Our results demonstrate that sphingolipids play an important role in plant resistance, especially by interfering with the plasma membrane organization and effector localization and thus disturbing their function and subsequent immune responses.
PluMu - a Mu-like bacteriophage infectingActinobacillus pleuropneumoniae
Authors: Julia Bartsch L , Crespo Roberto Fernandez , Wang Yunfei , Skinner Michael A , Rycroft Andrew N , Cooley William , Everest David J , Li Yanwen , Bossé Janine T , Langford Paul R
Published: February 2024

Actinobacillus pleuropneumoniaeis the causative agent of pleuropneumonia, an economically important lung disease of pigs. In draft genomes of two Cypriot clinicalA. pleuropneumoniaeisolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence of active phage. Here, updated Phastest genomic analysis identified two loci in both MIDG3457 and MIDG3459 that were predicted to encode proteins with high homology to, and whose organization was characteristic of, Mu-like phages. Phylogenetically, the closest matches were withMannheimiaVb andGlaesserellaSuMu phages. Phastest scored the loci as “complete”, indicating they produced active phage. PCR amplification of the Mu-like phagecandtailgenes from DNase-treated polyethylene glycol 8000 (PEG)-precipitated supernatants of MIDG3457 and MIDG3459 (grown in either Brain Heart Infusion-NAD or Grace’s Insect Medium-NAD broth) indicated the presence of intact virions. The phages from MIDG3457 and MIDG3459 were named PluMu 3457-1, 3457-2, and PluMu 3459-1 and PluMu 3459-2, respectively. Transmission electron microscopy (TEM) of PEG-precipitated supernatants of broth-grown MIDG3459 identified virions with icosahedral heads and tails, consistent with other Mu-like phages. We conclude that MIDG3459 produces an active Mu- like phage.
Impact of Shifting University Policies During the COVID-19 Pandemic on Self-Reported Employee Social Networks
Authors: Johnson Stephanie S. , Jackson Katelin C. , Lofgren Eric T.
Published: February 2024

Objectives

To ascertain if faculty and staff were the link between the two COVID-19 outbreaks in a rural university county, and if the local university’s COVID-19 policies affected contact rates of their employees across all its campuses.

Methods

We conducted two anonymous, voluntary online surveys for faculty and staff of a PAC-12 university on their contact patterns both within and outside the university during the COVID-19 pandemic. One was asked when classes were virtual, and another when classes were in-person but masking. Participants were asked about the individuals they encountered, the type and location of the interactions, what COVID-19 precautions were taken – if any, as well as general questions about their location and COVID-19.

Results

We received 271 responses from the first survey and 124 responses from the second. The first survey had a median of 3 contacts/respondent, with the second having 7 contacts/respondent (p<0.001). During the first survey, most contacts were family contacts (Spouse, Children), with the second survey period having Strangers and Students having the most contact (p<0.001). Over 50% of the first survey contacts happened at their home, while the second survey had 40% at work and 35% at home. Both respondents and contacts masked 42% and 46% of the time for the two surveys respectively (p<0.01).

Conclusion

For future pandemics, it would be wise to take employees into account when trying to plan for the safety of university students, employees, and surrounding communities. The main places to be aware of and potentially push infectious disease precautions would be on campus, especially confined spaces like offices or small classrooms, and the home, as these tend to be the largest areas of non-masked close contact.
Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen
Authors: Sanchís-Calleja Fátima , Jain Akanksha , He Zhisong , Okamoto Ryoko , Rusimbi Charlotte , Rifes Pedro , Rathore Gaurav Singh , Santel Malgorzata , Janssens Jasper , Seimiya Makiko , Fleck Jonas Simon , Kirkeby Agnete , Camp J. Gray , Treutlein Barbara
Published: February 2024

Morphogens, secreted signalling molecules that direct cell fate and tissue development, are used to direct neuroepithelial progenitors towards discrete regional identities across the central nervous system. Neural tissues derived from pluripotent stem cells in vitro (neural organoids) provide new models for studying neural regionalization, however, we lack a comprehensive survey of how the developing human neuroepithelium responds to morphogen cues. Here, we produce a detailed map of morphogen-induced effects on the axial and regional specification of human neural organoids using a multiplexed single-cell transcriptomics screen. We find that the timing, concentration, and combination of morphogens strongly influence organoid cell type and regional composition, and that cell line and neural induction method strongly impact the response to a given morphogen condition. We apply concentration gradients in microfluidic chips or a range of static concentrations in multi-well plates to explore how human neuroepithelium interprets morphogen concentrations and observe similar dose-dependent induction of patterned domains in both scenarios. Altogether, we provide a detailed resource that supports the development of new regionalized neural organoid protocols and enhances our understanding of human central nervous system patterning.
Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation
Authors: Tang Qian , Xu Duorong , Lenzen Benjamin , Brachmann Andreas , Yapa Madhura M , Doroodian Paymon , Schmitz-Linneweber Christian , Masuda Tatsuru , Hua Zhihua , Leister Dario , Kleine Tatjana
Published: February 2024

Plastid biogenesis and the coordination of plastid and nuclear genome expression through anterograde and retrograde signaling are essential for plant development. GENOMES UNCOUPLED1 (GUN1) plays a central role in retrograde signaling during early plant development. The putative function of GUN1 has been extensively studied, but its molecular function remains controversial. Here, we evaluate published transcriptome data and generate our own data fromgun1mutants grown under signaling relevant conditions to show that editing and splicing are not relevant for GUN1-dependent retrograde signaling. Our study of the plastid (post)-transcriptome ofgun1seedlings with white and pale cotyledons demonstrates that GUN1 deficiency significantly alters the entire plastid transcriptome. By combining this result with a PPR code-based prediction and experimental validation by RNA immunoprecipitation experiments, several targets of GUN1 were identified, including 23S rRNA, tRNAs and RNAs derived fromycf1.2and thendhH-ndhA-ndhI-ndhG-ndhE-psaC-ndhDgene cluster. The absence of plastid rRNAs and the significant reduction of almost all plastid transcripts in whitegun1mutants account for the cotyledon phenotype. Our study identifies RNA binding and maturation as the long-sought molecular function of GUN1 and resolves long-standing controversies. We anticipate that our findings will serve as a basis for subsequent studies investigating the mechanism of plastid gene expression and will facilitate the elucidation of GUN1’s function in retrograde signaling.
Females extract multiple signals from male song in Java sparrows
Authors: Lewis Rebecca N. , Makioka Hiroharu , Gilman R. Tucker , Soma Masayo
Published: February 2024

Songs play an important role in mate choice for many bird species. Females of some species prefer mates with song characteristics such as familiarity, complexity, or specific temporal or note features. Different song characteristics may provide distinct information about the birds that produced those songs. For example, familiarity may be a signal of local adaptation, locally relevant information or learned behaviours, or genetic compatibility, while song complexity may be a signal of overall genetic quality. However, how song characteristics combine to affect female preferences remains poorly understood. We examined female preference for song familiarity and complexity using the Java sparrow (Padda oryzivora) as a model species. Females were presented with pairs of song stimuli; familiar and unfamiliar songs in familiarity trials, and songs differing in note repertoire or linearity in complexity trials. Females preferred their fathers’ songs over unfamiliar songs, but we did not find strong evidence that females generalized this preference to other socially related individuals. Females also preferred complex songs, specifically those with larger note repertoires and with lower linearity, even when controlling for familiarity. Our results suggest that female song preference in Java sparrows is multi-faceted, with different song characteristics potentially offering different information to choosy females.
Continuous-Variable Quantum State Designs: Theory and Applications
Authors: Iosue Joseph T. , Sharma Kunal , Gullans Michael J. , Albert Victor V.
Published: February 2024

We generalize the notion of quantum state designs to infinite-dimensional spaces. We first prove that, under the definition of continuous-variable (CV) state t-designs from [Blume-Kohout , ], no state designs exist for t≥2. Similarly, we prove that no CV unitary t-designs exist for t≥2. We propose an alternative definition for CV state designs, which we call rigged t-designs, and provide explicit constructions for t=2. As an application of rigged designs, we develop a design-based shadow-tomography protocol for CV states. Using energy-constrained versions of rigged designs, we define an average fidelity for CV quantum channels and relate this fidelity to the CV entanglement fidelity. As an additional result of independent interest, we establish a connection between torus 2-designs and complete sets of mutually unbiased bases.

Published by the American Physical Society
2024
Home organization and adaptive behavior in children with autism spectrum disorder
Authors: Ramey Arielle S. , Rainey Vanessa R. , Seals Samantha R.
Published: February 2024

Purpose

A chaotic home environment, marked by disorganization, noise and a lack of routine, has negative associations with language development, social competence and executive functioning. This study aims to investigate the mediating effect of chaotic homes on adaptive behaviors, or behaviors that allow independent functioning, in children diagnosed with autism spectrum disorder (ASD) compared to neurotypical (NT) children. Children with ASD have difficulties with adaptive functioning in their environment, and identifying factors in the home that may exacerbate these behaviors will help in understanding the larger family dynamics that may affect behavior.

Design/methodology/approach

In total, 251 primary caregivers completed questionnaires about their children’s adaptive behavior and the structure of the home environment.

Findings

The results of a mediation analysis found a significant indirect effect of ASD status leading to lower adaptive behaviors through home chaos. This suggests those with ASD experienced more household chaos than NT children, which influenced their lower adaptive behavior scores.

Originality/value

This research provides insights into the complex relationship between the home environment and child behavior in children with ASD.
When MNEs bribe more? The role of managerial discretion
Authors: Teng Da , Haj Youssef Moustafa Salman , Li Chengchun
Published: February 2024

Purpose

This paper builds upon managerial discretion literature to study the relationship between foreign ownership and bribery intensity.

Design/methodology/approach

Building on World Bank’s data of 9,386 firms from 125 countries over the period 2006–2018, this paper uses Tobit regression, ordered probit and logit models to empirically test the hypotheses.

Findings

This paper finds that firms have higher bribery intensity when executives have a higher level of managerial discretion. Smaller firms with slack financial resources tend to bribe more when they face more government intervention, munificent and uncertain industrial environment.

Originality/value

Extant corruption literature has addressed the effects of external institutional settings and internal corporate governance on bribery offering among multinational enterprises (MNEs). How much, and under what condition do top executives matter in bribery activities are yet to be answered. This paper integrates the concept of managerial discretion with corruption and bribery literature and offers a potential answer to the above question. In addition, prior corruption and bribery literature have primarily studied bribery through either micro- or macro-level analysis. This paper adopts multiple-level of analyses and elucidates the foreign ownership and bribery relationship from the organizational and industrial levels.
The effects of informal competition on firms’ innovation in Greece
Authors: Vlachos Vasileios
Published: February 2024

Purpose

Several empirical studies indicate that the existence of a large informal sector is a major obstacle to firms’ choices of innovation strategies. This paper aims to address this issue and investigates the effect of the informal sector on the innovation of formal firms in Greece.

Design/methodology/approach

Using the World Bank’s Enterprise Survey data, the impact of informal competition on formal firms’ innovation in Greece is investigated by testing whether formal firms use innovation as a tool to protect and sustain their competitive advantage vis-à-vis informal firms and whether overall and informal competition has an inverted-U relationship with the innovation of formal firms. The effects of bribing and other variables drawn from the empirical literature are also controlled for.

Findings

The findings fill a gap in the literature regarding the effects of the informal sector on formal economic activity in Greece, by indicating that the informal sector puts pressure on formal firms to innovate, in order to differentiate their product or service and enhance their productivity and by offering learnings to help policymakers to promote innovation in Greece.

Originality/value

The originality of this study is that it investigates the impact of informal competition on formal firms’ innovation in Greece, a developed economy with a large informal sector. It does so by focusing on the effects that formal firms’ informal practices have on their competitors’ innovation activities, and the role of informal competition in creating and sustaining a competitive advantage in Greece.
Revisiting the debt–growth nexus in sub-Saharan Africa: fresh evidence from panel nonlinear ARDL approach
Authors: Amoh John Kwaku , Abdul-Mumuni Abdallah , Amankwa Fosu Richard
Published: February 2024

Purpose

While some countries have used debt to drive economic growth, the asymmetric effect on sub-Saharan African (SSA) countries has received little attention in the empirical literature. This paper therefore examines the asymmetric effect of external debts on economic growth.

Design/methodology/approach

The panel nonlinear autoregressive distributed lag (NARDL) approach was employed in the study for 29 sub-Saharan African countries from 1990 to 2021. The cross-sectional dependence test was used to determine the presence of cross-sectional dependence, while the second-generation panel unit root tests was used to examine the unit-root properties.

Findings

The empirical results show that external debt has an asymmetric effect on economic growth in both the short and long run. In the long run, a positive shock in external debts of 1% triggers an upturn in economic growth by 0.216% while a negative shock triggers 0.354% decline in economic growth. This implies that the negative shock of external debts has a much stronger impact on economic growth than the positive shock. In the short run, a positive shock in external debts by 1% triggers a decline in economic growth by 0.641%, while a negative shock of 1% triggers a fall in economic growth of 0.170%.

Originality/value

The paper used the NARDL model to examine the asymmetric impact of external debt on the economic growth of SSA countries, which has not been extensively studied. It is recommended that governments in the selected countries in sub-Saharan Africa should drive economic growth by promoting domestic revenue mobilization since external debts impede economic growth.
How organizational readiness for green innovation, green innovation performance and knowledge integration affects sustainability performance of exporting firms
Authors: Ullah Sami , Ahmad Tooba , Kukreti Mohit , Sami Abdul , Shaukat Muhammad Rehan
Published: February 2024

Purpose

Consumers and businesses are becoming increasingly conscious of sustainable business practices and are often willing to pay a premium for responsibly sourced and manufactured products. Many countries and organizations have implemented regulations and standards for sustainability and companies face penalties or are barred from exporting for not meeting the requirements. Rooted in the resource-based view theory, this study aims to test a moderated mediation model to improve the sustainability performance of exporting firms.

Design/methodology/approach

Textile firms generating more than 25% of export revenues were targeted for this research. The data collected from 245 middle management-level employees were tested for reliability and validity. The structural equation modelling in AMOS 26 was used to test hypotheses.

Findings

Organizational readiness for green innovation (ORGI) has a direct positive effect on sustainability performance. The mediation analysis implies that ORGI translates into sustainability performance through improvement in green innovation performance. The moderating effect of knowledge integration highlights the importance of being prepared internally and actively seeking and incorporating external knowledge to improve green innovation performance.

Originality/value

The findings offer a solid foundation for informed decision-making, policy development and strategies to improve sustainability performance while aligning with the global nature of the textile industry and its inherent challenges. The proposed model and practical implications guide policymakers and managers of exporting firms to foster a culture of green innovation to leverage the effect of their readiness for green innovation on sustainability performance.
Dynamic capabilities and digitalization as antecedents of innovation and sustainable performance: empirical evidence from Vietnamese SMEs
Authors: Vo Thai Huy Cuong , Hong-Hue Trinh-Hoang , Tran My-Linh
Published: February 2024

Purpose

This study aims to investigate the relationship between dynamic capabilities and sustainable business performance in Vietnamese small- and medium-sized enterprises (SMEs), focusing on the mediating role of digitalization strategies. Specifically, the authors seek to explore whether and how the three critical characteristics of dynamic capabilities (DCs) – sensing, seizing and transforming capabilities – are linked to business model innovation (BMI) or sustained performance and what dimensions contribute to their development and adoption in digitalization strategies.

Design/methodology/approach

The authors analyse a sample of 596 Vietnamese SMEs using a validated measurement framework to explore the three clusters of DCs activities and their contributions to digitalization strategies, BMI and sustainable business performance across economic, social and environmental dimensions.

Findings

The study highlights the pivotal role of sensing, seizing and transforming capabilities in the adoption of digitalization strategies, BMI, as well as in promoting sustainable business performance. Firstly, sensing capability profoundly influences product digitalization strategy, whereas seizing capability has the greatest impact on process digitalization strategy. Secondly, sensing and transforming capabilities significantly contribute to BMI. Thirdly, both process and product digitalization strategies exert a significant positive influence on sustainable business performance, especially the environmental dimension. Finally, the study exhibits the indirect impacts of seizing and sensing capabilities on sustainable business performance through product and process digitization strategies.

Originality/value

This study extends recent research by investigating the DCs underlying a firm’s digitalization strategies and contribute to ongoing calls for further investigation in the DCs literature. This research design, which draws from a validated measurement framework, responds to recent calls to broaden the toolkit used in DCs research. The practical implications of this study can benefit SMEs in Vietnam and beyond as they seek to enhance their digitalization strategies and achieve sustainable competitive advantage.