bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictors of hinge effect in patients with Peyronie’s disease
Authors: Roadman Daniel , Wang Vinson , Langbo William , Paddock David , Levine Laurence
Published: July 2023

Background

Patients with Peyronie’s disease present with a variety of penile deformities. Those with hinge effect can experience bothersome buckling of the erection and instability during penetrative sex; however, the actual characteristics and clinical implications are not fully understood.

Aim

To determine the factors that cause hinge effect and to assess the role on surgical intervention.

Methods

This retrospective review included 1223 consecutive patients who were examined by a single surgeon and had a complete penile duplex evaluation with curvature and hinge assessment. Baseline demographics, penile duplex findings, and clinical outcomes were used to assess for predictors of hinge effect.

Outcomes

Analyses were performed to assess preoperative predictors of hinge effect and surgical intervention.

Results

Hinge effect was observed at the time of penile duplex Doppler examination in 33% of patients. Circumferential girth discrepancy at point of indentation (odds ratio [OR] 1.82; P < .001), rigidity of erection (OR, 0.82; P = .002), and degree of primary curvature (OR, 1.03; P < .001) predicted the presence of hinge effect. When controlling for rigidity, a girth discrepancy >1 cm did appear to be associated with a hinge.

Clinical Implications

Circumferential girth discrepancy >1 cm, regardless of erectile rigidity, can be associated with hinge effect.

Strengths and Limitations

As a strength, this study included the largest cohort of patients with Peyronie’s disease, all of whom were examined in a rigorous and uniform manner via the same operative counseling. However, the study is limited by its retrospective nature and potential for selection and observer bias, given that the treating physician was also assessing all penile deformities as well as performing operative intervention.

Conclusions

The presence of hinge effect can cause instability of erections during penetrative sex. Multiple factors may predispose patients to a hinge effect, including the quality of erection and severity of curvature. But when controlling for rigidity, a girth discrepancy >1 cm did appear to be associated with a hinge. While many factors, such as baseline erectile dysfunction and severity of curvature, are important in determining the optimal surgical intervention, assessing for preoperative hinge effect also influenced the surgical approach.
Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses
Authors: Olabode Abayomi S , Mumby Mitchell J , Wild Tristan A , Muñoz-Baena Laura , Dikeakos Jimmy D , Poon Art F Y
Published: July 2023

Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
Ncs2* mediates in vivo virulence of pathogenic yeast through sulphur modification of cytoplasmic transfer RNA
Authors: Alings Fiona , Scharmann Karin , Eggers Cristian , Böttcher Bettina , Sokołowski Mikołaj , Shvetsova Ekaterina , Sharma Puneet , Roth Joël , Rashiti Leon , Glatt Sebastian , Brunke Sascha , Leidel Sebastian A
Published: July 2023

Fungal pathogens threaten ecosystems and human health. Understanding the molecular basis of their virulence is key to develop new treatment strategies. Here, we characterize NCS2*, a point mutation identified in a clinical baker's yeast isolate. Ncs2 is essential for 2-thiolation of tRNA and the NCS2* mutation leads to increased thiolation at body temperature. NCS2* yeast exhibits enhanced fitness when grown at elevated temperatures or when exposed to oxidative stress, inhibition of nutrient signalling, and cell-wall stress. Importantly, Ncs2* alters the interaction and stability of the thiolase complex likely mediated by nucleotide binding. The absence of 2-thiolation abrogates the in vivo virulence of pathogenic baker's yeast in infected mice. Finally, hypomodification triggers changes in colony morphology and hyphae formation in the common commensal pathogen Candida albicans resulting in decreased virulence in a human cell culture model. These findings demonstrate that 2-thiolation of tRNA acts as a key mediator of fungal virulence and reveal new mechanistic insights into the function of the highly conserved tRNA-thiolase complex.
W. E. B. Du Bois and Rural Sociology
Authors: Bailey Conner , Zimmerman Julie N.
Published: July 2023

Among W. E. B. Du Bois’s many intellectual contributions were his studies of rural Black Americans and the social milieu in which they lived one generation removed from enslavement. These studies, conducted at the end of the nineteenth century and during early years of the twentieth, were groundbreaking theoretically and methodologically, beginning with detailed rural community studies that provided the basis for broader work on race and the class distinctions that quickly emerged among Black farmers and artisans. The focus here is on Du Bois’s work as a rural scholar and his connections with the emergence of rural sociology as a discipline over the first decades of the twentieth century through interactions rural sociologists had with Du Bois and other Black sociologists. Two central insights from Du Bois’s work have continuing relevance to rural sociologists: the centrality of race and the importance of a moral purpose guiding scholarly pursuits.
Songs, Rites, and Identity in the Religious Folklore of Latvia and Lithuania
Authors: Strmiska Michael , Ozoliņš Gatis , Rudling Odeta , Ūdre Digne
Published: July 2023

This chapter examines the enduring presence of pre-Christian, Pagan religious elements in Baltic folklore—the related but distinct folk traditions of Lithuania and Latvia—and the purposes these remnants of Baltic Paganism serve as expressions of ethnic and/or national identity. Particular attention is paid to a genre of folk songs known as dainasin Latvia and dainos in Lithuania, solstice celebrations, ancestral rites, and folk symbols. The Indo-European background of Baltic languages and mythology is also discussed along with the utilization of Pagan gods, symbols, and traditions in national independence movements and their continuing resonance in post-Soviet Baltic society and culture.
Israel in Deuteronomy
Authors: Crouch C. L.
Published: July 2023

The book of Deuteronomy is engaged in an intensive project of Israelite identity formation, provoked initially by an increased exposure to alternative cultural matrices in the southern Levant in the long seventh century bce and then reinforced by the global scope of Israelite experience in the wake of the destruction of the kingdom of Judah in the early sixth century. Although the construction of a distinctively Israelite religious and cultural identity is not the book’s sole concern, it accounts for a number of the book’s preoccupations and constitutes one of its most significant contributions to the theology of the Hebrew Bible and associated religious traditions. This chapter discusses some of the most important features of Israelite identity developed in Deuteronomy’s legislative and exhortatory core, including the distinctively Israelite cultural characteristics of exclusive Yahwism, centralized worship, and a shared mythology of Israel’s origins in an exodus from Egypt, as well as examining ways in which this Deuteronomic material seeks to protect the distinctive Israelite identity it constructs. A final section discusses some of the ways that this construction of Israelite identity was adjusted in response to Israel’s deportation, displacement, and long-term diaspora.
Ancient Ireland
Authors: Parsons Geraldine
Published: July 2023

The places and times to which Cuchulain and Oisin alike belonged were conceptualized by William Butler Yeats as ‘ancient Ireland’. This chapter seeks to illuminate some sources underpinning Yeats’s long and fruitful engagement with—as he saw it—the literary output of Ireland’s ancient past, born of his desire to forge a national, anglophone literature for Ireland. It shows how Yeats’s ancient Ireland was built on foundations laid in the 1880s and 1890s, using materials from the 1850s and 1860s, and how those foundations were broader than is sometimes acknowledged. It argues that Yeats made greater use of the work of Eugene O’Curry than has hitherto been acknowledged.
Yeats in the Media
Authors: Morin Emilie
Published: July 2023

Yeats’s world was always the world of mass media, and his work was widely reproduced from early on, via official as well as unofficial channels: he was the solemn poet published by Macmillan and one of the dramatists of the American Little Leather Library; his poetry was presented to the readers of The New York Times, the New Statesman, and a wide range of newspapers and magazines of different political persuasions; he was a prolific journalist and reviewer, his opinions on literature appearing across the political spectrum, from The Irish Homestead to The Manchester Playgoer through to Harper’s Weekly; he was also an easily irritated Irish citizen who enjoyed crafting letters to the editor of The Irish Times, and a poet courted by the BBC, who transformed his lifelong reflection on the performance of poetry into a broadcasting success. His engagement with modern media was a large-scale rhetorical experiment: he transferred his experience from one medium to another, taking his experience as poetry anthologist, public reader and jack-of-all-trades journalist into the radio studio, a poet who was transformed into a gifted and prominent mass communicator.
‘Knights of the Air’
Authors: Brearton Fran
Published: July 2023

This essay explores Yeats’s relationship to the growing ‘air-mindedness’ of Ireland and the increasing prevalence of flight in the aftermath of the First World War. It investigates Gogarty’s improbable claim to have taken Yeats up in a plane in the 1920s, in the context of Ireland’s increasing emphasis on the perceived political, economic and physical benefits of flight. The essay traces Yeats’s Romantic inheritance, notably the Romantic conception of aerial vision and ascent, and his resistance to the ‘machine age’, as it informs his own aesthetics of ascent in the early decades of the 20th century. As one of the earliest authors of a ‘flight’ poem, ‘An Irish Airman Foresees His Death’ (1918), written without experience of flying, Yeats’s influence on the aviation poetry that became more prevalent after World War I is also delineated, alongside the extent to which he captured in his work some of the essence of how the ‘Knights of the Air’ were perceived.
Developing and Implementing a Father-Friendly Neonatal Intensive Care Unit Improved Nurses' Self-Efficacy
Authors: Noergaard Betty , Kofoed Poul-Erik
Published: July 2023

Background:

The need for paternal support is rarely addressed in neonatal intensive care units (NICUs). Neonatal nurses often primarily focus on the needs of the mother and infant and may not be trained in support of fathers.

Purpose:

To investigate nurses' self-efficacy (SE) in guiding and supporting fathers after implementing a father-friendly NICU.

Methods:

Nurses from the intervention NICU and 13 control NICUs were included in a before-and-after intervention study. Questionnaires measuring nurses' SE regarding support of fathers and mothers were obtained when starting the development process, before and 18 months after the implementation. The primary outcome was the difference between nurses' SE scores for father and mother questions in the intervention group compared with the control group.

Results:

In total, 294, 330, and 288 nurses responded to the first, second, and third questionnaires, respectively. From the first to third questionnaires, the intervention group showed a significantly higher increase in SE scores for father questions compared with the control group (0.53 vs 0.20, P = .005) and a nonsignificantly higher increase for mother questions (0.30 vs 0.09, P = .13). In the third questionnaire, the intervention group showed a higher SE score for father questions compared with the control group (9.02 vs 8.45, P = .002) and the first questionnaire (9.02 vs 8.49, P = .02).

Implications for Practice and Research:

By implementing a father-friendly NICU, nurses' SE for providing support to fathers increased significantly. Training in a father-friendly approach increases nurses' ability to support both parents.
Visualizing the (Causal) Effect of a Continuous Variable on a Time-To-Event Outcome
Authors: Denz Robin , Timmesfeld Nina
Published: July 2023

Visualization is a key aspect of communicating the results of any study aiming to estimate causal effects. In studies with time-to-event outcomes, the most popular visualization approach is depicting survival curves stratified by the variable of interest. This approach cannot be used when the variable of interest is continuous. Simple workarounds, such as categorizing the continuous covariate and plotting survival curves for each category, can result in misleading depictions of the main effects. Instead, we propose a new graphic, the survival area plot, to directly depict the survival probability over time and as a function of a continuous covariate simultaneously. This plot utilizes g-computation based on a suitable time-to-event model to obtain the relevant estimates. Through the use of g-computation, those estimates can be adjusted for confounding without additional effort, allowing a causal interpretation under the standard causal identifiability assumptions. If those assumptions are not met, the proposed plot may still be used to depict noncausal associations. We illustrate and compare the proposed graphics to simpler alternatives using data from a large German observational study investigating the effect of the Ankle-Brachial Index on survival. To facilitate the usage of these plots, we additionally developed the contsurvplot R-package, which includes all methods discussed in this paper.
The Enduring Power of Magnet®
Authors: Lal M. Maureen
Published: July 2023

More than 3 decades have passed since an enterprising team of nurse researchers unearthed groundbreaking findings that led to the creation of the American Nurses Credentialing Center's Magnet Recognition Program®. Over time, the program has grown bigger and broader than anyone could predict, making a significant impact on nurses, the nursing profession, and healthcare delivery around the world. After the recent upheavals caused by the COVID-19 pandemic, is Magnet® still relevant today? This month's Magnet Perspectives column examines the program's enduring significance and proven value in supporting nurses and helping healthcare organizations navigate the financial, labor, and regulatory challenges of the post-COVID era.
Supporting Advanced Practice Nurses to Work at the Top of Their License
Authors: Kapu April , Rodgers Jennifer
Published: July 2023

This month's column highlights the value of nurse executive leaders in leveraging their experience, role, and partnership in empowering advanced practice RNs to work at the top of their education, clinical training, and license, optimizing the triple aim, even quadruple aim, in healthcare.
Nursing's Critical Role in Driving Toward Health Equity
Authors: Ridling Debra , Finch Christina , Moore J. Mari , Ofamen Juliette , Price Wendy
Published: July 2023

In the last decade, there has been active discourse within nursing communities regarding healthcare disparities associated with racism. To address this critical problem, a multidisciplinary team at a pediatric healthcare setting identified 33 projects across 4 key drivers of health equity. The drivers of health equity include: 1) developing a diverse nursing workforce; 2) creating a nursing culture with a strong sense of belonging; 3) providing learning and growth opportunities; and 4) providing equitable nursing care. This article describes 1 organization's approach to addressing healthcare disparities associated with racism through a nursing program to address equity, diversity, inclusion, and antiracism.
Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose
Authors: Nong Daguan , Haviland Zachary K. , Zexer Nerya , Pfaff Sarah J. , Cosgrove Daniel J. , Tien Ming , Anderson Charles T. , Hancock William O.
Published: July 2023

Degrading cellulose is a key step in the processing of lignocellulosic biomass into bioethanol. Cellobiose, the disaccharide product of cellulose degradation, has been shown to inhibit cellulase activity, but the mechanisms underlying product inhibition are not clear. We combined single-molecule imaging and biochemical investigations with the goal of revealing the mechanism by which cellobiose inhibits the activity ofTrichoderma reeseiCel7A, a well-characterized exo-cellulase. We find that cellobiose slows the processive velocity of Cel7A and shortens the distance moved per encounter; effects that can be explained by cellobiose binding to the product release site of the enzyme. Cellobiose also decreases the binding rate of Cel7A to immobilized cellulose but does not slow the binding rate of an isolated carbohydrate-binding module, suggesting that cellobiose inhibits binding of the catalytic domain of Cel7A to cellulose. In support of this, cellopentaose, which is considerably larger than cellobiose, also slows the binding rate of Cel7A to cellulose without affecting the velocity and run length. Together, these results suggest that cellobiose inhibits Cel7A activity both by binding to the ‘back door’ product release site to slow activity and to the ‘front door’ substrate binding tunnel to inhibit interaction with cellulose. These findings point to new strategies for engineering cellulases to reduce product inhibition and enhance cellulose degradation, supporting the growth of a sustainable bioeconomy.

Significance

Cellulose, a polymer of repeating glucose subunits, is the primary component of plant cell walls. A promising route to reducing petrochemical use is digesting plant biomass to glucose and fermenting glucose to bioethanol. Cel7A is a model cellulase enzyme that degrades cellulose from one end to generate the disaccharide product, cellobiose. Because industrial-scale bioethanol generation generates high concentrations of cellobiose, product inhibition is a significant concern. We investigated product inhibition of Cel7A by cellobiose at the single-molecule level and found that cellobiose both slows the movement of Cel7 along cellulose and inhibits the initial binding of Cel7 to cellulose. These results suggest that cellobiose binds to the enzyme at more than one site and achieves its inhibition by multiple mechanisms.
EasyEyes — Accurate fixation for online vision testing of crowding and beyond
Authors: Kurzawski Jan W. , Pombo Maria , Burchell Augustin , Hanning Nina M. , Liao Simon , Majaj Najib J. , Pelli Denis G.
Published: July 2023

Online methods allow testing of larger, more diverse populations, with much less effort than in-lab testing. However, many psychophysical measurements, including visual crowding, require accurate eye fixation, which is classically achieved by testing only experienced observers who have learned to fixate reliably, or by using a gaze tracker to restrict testing to moments when fixation is accurate. Alas, both approaches are impractical online since online observers tend to be inexperienced, and online gaze tracking, using the built-in webcam, has a low precision (±4 deg, Papoutsaki et al., 2016). The EasyEyes open-source software reliably measures peripheral thresholds online with accurate fixation achieved in a novel way, without gaze tracking. EasyEyes tells observers to use the cursor to track a moving crosshair. At a random time during successful tracking, a brief target is presented in the periphery. The observer responds by identifying the target. To evaluate EasyEyes fixation accuracy and thresholds, we tested 12 naive observers in three ways in a counterbalanced order: first, in the lab, using gaze-contingent stimulus presentation (Kurzawski et al., 2023; Pelli et al., 2016); second, in the lab, using EasyEyes while independently monitoring gaze; third, online at home, using EasyEyes. We find that crowding thresholds are consistent (no significant differences in mean and variance of thresholds across ways) and individual differences are conserved. The small root mean square (RMS) fixation error (0.6 deg) during target presentation eliminates the need for gaze tracking. Thus, EasyEyes enables fixation-dependent measurements online, for easy testing of larger and more diverse populations.
Assimilation efficiencies and elimination rates of silver, cadmium and zinc accumulated by trophic pathway inGammarus fossarum
Authors: Gestin Ophélia , Lopes Christelle , Delorme Nicolas , Garnero Laura , Geffard Olivier , Lacoue-Labarthe Thomas
Published: July 2023

To improve the assessment of metal toxicity in aquatic organisms, it is important to consider the different uptake pathways (i.e. trophic or aqueous). The bioaccumulation of dissolved metals such as Cd and Zn in gammarids is beginning to be well described. However, there are very few data on the contribution of the dietary pathway, and its associated toxicokinetic parameters. Among these, the assimilation efficiency (AE) is an essential parameter for the implementation of models that take the trophic pathway into account. This study aims to estimate the assimilation efficiencies and elimination rates of two types of food, i.e. alder leaves and chironomid larvae, contaminated with three metals (Ag, Cd and Zn) of major concern for the Water Framework Directive (WFD). The pulse-chase-feeding method was used. Gammarids were fed with alder leaves or chironomid larvae previously contaminated with110mAg,109Cd or65Zn, for a short period of time (1 to 5 hours), followed by an elimination phase of 14 days. At different time points, the gammarids were placed alive on the gamma detector to individually quantify whole body concentrations of110mAg,109Cd or65Zn. Our results indicate that: i) Cd has the highest assimilation efficiency (39% for leaves and 19% for larvae), followed by Zn (15% for leaves and 9% for larvae) and Ag (5% for leaves); ii) for Cd and Zn, the AE were higher when gammarids were fed with leaves than with larvae; iii) the elimination rates of metals seem to depend more on the food matrix than on the metal assimilated; and thus iv) the biological half-life calculated from the kesis 5.1 days for Ag, between 4.9 and 13 days for Cd and between 3.8 and 13 days for Zn.
Assessment of technical and clinical utility of a bead-based flow cytometry platform for multiparametric phenotyping of CNS-derived extracellular vesicles
Authors: Brahmer Alexandra , Geiß Carsten , Lygeraki Andriana , Neuberger Elmo , Tzaridis Theophilos , Nguyen Tinh Thi , Luessi Felix , Régnier-Vigouroux Anne , Hartmann Gunther , Simon Perikles , Endres Kristina , Bittner Stefan , Reiners Katrin S , Krämer-Albers Eva-Maria
Published: July 2023

Extracellular vesicles (EVs) derived from the CNS are potential liquid-biopsy markers for early detection and monitoring of neurodegenerative diseases and brain tumors. This study assessed the performance of a bead-based flow cytometry assay (EV Neuro) for multiparametric detection of CNS-derived EVs and identification of disease-specific markers. Different sample materials and EV isolation methods were compared. Glioblastoma- and primary human astrocyte-derived EVs exhibited distinct EV profiles, with signal intensities increasing with higher EV input. Analysis of serum or plasma from glioblastoma, multiple sclerosis, Alzheimer’s Disease patients and healthy controls showed varying marker signal intensities. Notably, data normalization improved marker identification. Specific EV populations, such as CD36+EVs in glioblastoma and GALC+EVs in multiple sclerosis, were significantly elevated in disease compared to controls. Clustering analysis techniques effectively differentiated glioblastoma patients from controls. A potential correlation between CD107a+EVs and neurofilament levels in the blood was identified in multiple sclerosis patients. Together, the semi-quantitative EV Neuro assay demonstrated its utility for EV profiling in complex samples. However, reliable statistical results in biomarker studies require large sample cohorts and high effect sizes. Nonetheless, this exploratory trial confirmed the feasibility of discovering EV-associated biomarkers and monitoring circulating EV profiles in CNS diseases using the EV Neuro assay.
Proteomic analysis reveals APOE isoform-specific regulation of ribosomes in neural precursor cells
Authors: Srividya M , Paul Pradip , Ramakrishna Sarayu , Ghose Vivek , Dey Gourav , Muddashetty Ravi S , Jain Sanjeev , Purushottam Meera , Viswanath Biju , Sud Reeteka
Published: July 2023

ApoE4 isoform contributes to increased risk for Alzheimer’s Disease (AD) over the life course of individuals. Much remains unknown about the biological pathways that connectAPOE4genotype with the development of pathology that eventually leads to AD, nor do we know how early in life these cellular alterations begin. To answer these questions, we derived neural precursor cells (NPCs) from induced pluripotent stem cells (IPSCs) that were CRISPR-edited at theAPOElocus. We intended to characterize the protein expression landscape in the NPCs subsequent to targeted deletion of E4 from a parent IPSC line ofAPOE3/4genotype. Differentially expressed proteins (DEPs) following mass spectrometric analysis were determined from the protein abundance fold change values obtained for each protein. Proteins which showed >1.5-fold difference with FDR adjusted P-value < 0.05 were considered differentially expressed. DEPs were mapped to the STRING database (v11.5) for retrieval of interacting proteins and functional enrichment. CRISPR-editing of E4 from the parent line revealed 98 differential expressed proteins. Of these, 54 were upregulated, and 44 were downregulated. Further analysis of the DEPs via STRING database showed that these changes primarily affect pathways linked to RNA processing, plasma membrane repair, and cytoskeleton organization. Indeed, we find the effects of E4 extend beyond proteins considered central to AD pathology. Knowing more about the protein interactions regulated by ApoE, in an isoform-specific manner, can reveal new mechanistic insights into development of AD.
A single cell atlas of sexual development inPlasmodium falciparum
Authors: Dogga Sunil Kumar , Rop Jesse C. , Cudini Juliana , Farr Elias , Dara Antoine , Ouologuem Dinkorma , Djimde Abdoulaye A. , Talman Arthur M. , Lawniczak Mara K.N.
Published: July 2023

The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short and long-read single-cell transcriptomes of over 37,000Plasmodium falciparumcells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development, and expanded it to include malaria parasites collected from a Malian individual naturally infected with multipleP. falciparumstrains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at a single-cell level for the first time, finding considerable differential expression between different strains even within the same host. This work is a key addition to the Malaria Cell Atlas, enabling a deeper understanding of the biology and diversity of transmission stages.

One sentence summary

This addition to the Malaria Cell Atlas presents an analysis of sexual development and uses it to explore a natural infection.
Correlative superresolution microscopy with deep UV reactivation
Authors: Prakash Kirti
Published: July 2023

Correlative superresolution microscopy has the potential to accurately visualize and validate new biological structures past the diffraction limit. However, combining different superresolution modalities, such as deterministic stimulated emission depletion (STED) and stochastic single-molecule localization microscopy (SMLM), is a challenging endeavor. For correlative STED and SMLM, the following poses a significant challenge: (1) the photobleaching of the fluorophores in STED; (2) the subsequent reactivation of the fluorophores for SMLM; and (3) finding the right fluorochrome and imaging buffer for both imaging modalities. Here, we highlight how the deep ultraviolet (DBUE) wavelengths of the Mercury (Hg) arc lamp can help recover STED bleaching and allow for the reactivation of single molecules for SMLM imaging. We also show that Alexa Fluor 594 and the commercially available Prolong Diamond turn out to be excellent fluorophores and imaging media for correlative STED and SMLM.
Amphibian segmentation clock models suggest mechanisms of slowed development across increasing genome size and nuclear volume
Authors: Taylor Alexandra Nicole , Mueller Rachel Lockridge , Prasad Ashok
Published: July 2023

Evolutionary increases in genome size, cell volume, and nuclear volume have been observed across the tree of life, with positive correlations documented between all three traits. Developmental tempo slows as genomes, nuclei, and cells increase in size, yet the driving mechanisms are poorly understood. To bridge this gap, we use a mathematical model of the somitogenesis clock to link slowed developmental tempo with changes in intra-cellular gene expression kinetics induced by increasing genome size and nuclear volume. We adapt a well-known somitogenesis clock model to two model amphibian species that vary ten-fold in genome size:Xenopus laevis(3.2 Gb) andAmbystoma mexicanum(32 Gb). Based on simulations and backed by analytical derivations, we identify parameter changes originating from increased genome and nuclear size that slow gene expression kinetics. We simulate biological scenarios for which these parameter changes mathematically recapitulate slowed gene expression inA. mexicanumrelative toX. laevis, and we consider scenarios for which additional alterations in gene product stability and chromatin packing are necessary. Results suggest that slowed degradation rates as well as changes induced by increasing nuclear volume, which remain relatively unexplored, are significant drivers of slowed developmental tempo.
Multi-monoubiquitination controls VASP-mediated actin dynamics
Authors: McCormick Laura E. , Suarez Cristian , Herring Laura E. , Cannon Kevin S. , Kovar David R. , Brown Nicholas G. , Gupton Stephanie L.
Published: July 2023

The actin cytoskeleton performs multiple cellular functions, and as such, actin polymerization must be tightly regulated. We previously demonstrated that reversible, non-degradative ubiquitination regulates the function of the actin polymerase VASP in developing neurons. However, the underlying mechanism of how ubiquitination impacts VASP activity was unknown. Here we show that mimicking multi-monoubiquitination of VASP at K240 and K286 negatively regulates VASP interactions with actin. Using in vitro bio-chemical assays, we demonstrate the reduced ability of multi-monoubiquitinated VASP to bind, bundle, and elongate actin fil-aments. However, multi-monoubiquitinated VASP maintained the ability to bind and protect barbed ends from capping protein. Lastly, we demonstrate the introduction of recombinant multi-monoubiquitinated VASP protein altered cell spreading morphology. Collectively, these results suggest a mechanism in which ubiquitination controls VASP-mediated actin dynamics.
Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition
Authors: Wei Janet , Wood Thomas W.P. , Flaherty Kathleen , Enny Alyssa , Andrescavage Ali , Brazer Danielle , Navon Dina , Stewart Thomas A. , Cohen Hannah , Shanabag Anusha , Kuroda Shunya , Braasch Ingo , Nakamura Tetsuya
Published: July 2023

The mechanisms of the pectoral girdle transformation at the origin of terrestrial locomotion in vertebrates remains an outstanding problem in evolutionary biology1. The loss of dermal bones and the enlargement of endochondral bones resulted in the disarticulation of the pectoral girdle from the skull and the formation of the neck during the fish-to-tetrapod transition2–5. Despite the functional implications of this skeletal shift in the emergence of terrestrial vertebrates, the underlying genetic-developmental alterations have remained enigmatic. Here, we discovered that in zebrafish pectoral girdle mesodermal cells expressinggli3, a transcription factor in the Hedgehog signaling pathway, contribute to both dermal and endochondral bones. We show that Gli3 regulates expression ofactivin A receptor type 1-like, a BMP type 1 receptor lost in tetrapod lineages, and thereby determines endochondral and dermal ossification. Intriguingly, Gli and Hedgehog compound knockout fish exhibited an unexpected combination of actinopterygian fish and stem-tetrapod pectoral girdle characteristics. These ontogenetic and anatomical data suggest that a trade-off between the two distinct ossification pathways is a deeply embedded developmental program in bony fishes, with potential for tuning of this trade-off to generate novel pectoral girdle forms akin to stem-tetrapods at the dawn of vertebrate terrestrialization.
Decoding familiar visual object categories in the mu rhythm oscillatory response
Authors: Bailey Kerri M , Sami Saber , Smith Fraser W
Published: July 2023

Whilst previous research has linked attenuation of the mu rhythm to the observation of specific visual categories, and even to a potential role in action observation via a putative mirror neuron system, much of this work has not considered what specific type of information might be coded in this oscillatory response when triggered via vision. Here, we sought to determine whether the mu rhythm contains content-specific information about the identity of familiar (and also unfamiliar) graspable objects. In the present study, right-handed participants (N=27) viewed images of both familiar (apple, wine glass) and unfamiliar (cubie, smoothie) graspable objects, whilst performing an orthogonal task at fixation. Multivariate pattern analysis (MVPA) revealed significant decoding of familiar, but not unfamiliar, visual object categories in the mu rhythm response. Thus, simply viewing familiar graspable objects may automatically trigger activation of associated tactile and/or motor properties in sensorimotor areas, reflected in the mu rhythm. In addition, we report significant attenuation in the central beta band for both familiar and unfamiliar visual objects, but not in the mu rhythm. Our findings highlight how analysing two different aspects of the oscillatory response – either attenuation or the representation of information content – provide complementary views on the role of the mu rhythm in response to viewing graspable object categories.

Highlights

The Mu Rhythm oscillation contains fine-grained information about the identity of familiar, graspable objects (but not unfamiliar)

This study offers evidence of a possible oscillatory marker for cross-sensory effects involving sensorimotor and visual cortices

Different analysis techniques (univariate vs multivariate) imply different conclusions about the role of specific oscillations in the perception of graspable objects

The alpha rhythm at occipital sites shows greater attenuation for unfamiliar objects but better representation for familiar objects consistent with sharpening accounts of Predictive Processing
From Asymptomatic to Symptomatic: Multiomics profiling of the temporal response of grapevine viral-mixed infection
Authors: Fall M.L. , Poursalavati A. , Sidibé A. , Xu D. , Lemoyne P. , Martins G.S. , Javaran V.J. , Moffett P. , Odile Carisse
Published: July 2023

Mixed viral infections are common in grapevines. However, our understanding of the factors and signaling pathways that influence the expression of viral symptoms in mixed infections is still incomplete. In a previous study, we revealed that the presence of grapevine leafroll-associated virus species in mixed infections was randomly associated with the devel-opment of virus-like symptoms. To understand what drives the timing of these virus-like symptoms in mixed infections, we used dsRNA and total RNA sequencing and metabolomic analysis to profile the viromes, metabolites, and transcripts of grapevine leaves collected at two different times of the year (summer and autumn). We demonstrated that neither viral titre nor virome composition changes were associated with symptom expression in autumn. The total phenolic content and antioxidant capacity increased in most plants except for those with early onset symptoms. According to the results of differential gene expression analysis, cell wall biosynthesis pathways were significantly downregulated in all grapevine plants infected with grapevine leafroll-associated virus 3, grapevine asteroid mosaic-associated virus, and grape-vine Pinot gris virus. In addition, polyketide pathways were significantly upregulated in all cultivars, while flavonoid precursor (e.g. abscisic acid) production was significantly reduced in plants that expressed strong virus-like symptoms. In the ‘Vidal’ cultivar, an uncharacterized double-stranded RNA-binding protein (DRB) appears to play a critical role in the plant’s an-tiviral defences, supporting the recent hypothesis that DRBs make an important contribution to dominant antiviral responses in plants. The seasonality of the expression virus-like symptoms appears to be a consequence of the dynamic interactions between antiviral factors and viral counter-defences that occur at different developmental stages of grapevine.
Structural insights into complex I deficiency and assembly from the disease-relatedndufs4-/-mouse
Authors: Yin Zhan , Agip Ahmed-Noor A. , Bridges Hannah R. , Hirst Judy
Published: July 2023

Respiratory complex I (NADH:ubiquinone oxidoreductase) is essential for cellular energy production and NAD+homeostasis. Complex I mutations cause neuromuscular, mitochondrial diseases, such as Leigh Syndrome, but their molecular-level consequences remain poorly understood. Here, we use a popular complex I-linked mitochondrial disease model, thendufs4-/-mouse, to define the structural, biochemical and functional consequences of the absence of subunit NDUFS4. Cryo-EM analyses of mouse-heartndufs4-/-complex I revealed a loose association of the NADH-dehydrogenase module, and discrete classes containing either assembly factor NDUFAF2 or subunit NDUFS6. Subunit NDUFA12 (that replaces its paralogue NDUFAF2 in mature complex I) is absent from all classes, compounding the deletion of NDUFS4 and preventing maturation of an NDUFS4-free but otherwise complete enzyme. We propose NDUFAF2 as the recruiter of the NADH dehydrogenase module during assembly of the complex. Our results provide new molecular level understanding of thendufs4-/-mouse model and complex I-linked mitochondrial disease.
Combining Magnetoencephalography with Telemetric Streaming of Intracranial Recordings and Deep Brain Stimulation – a Feasibility Study
Authors: Hnazaee Mansoureh Fahimi , Sure Matthias , O’Neill George , Leogrande Gaetano , Schnitzler Alfons , Florin Esther , Litvak Vladimir
Published: July 2023

The combination of subcortical Local Field Potential (LFP) recordings and stimulation with Magnetoencephalography (MEG) in Deep Brain Stimulation (DBS) patients enables the investigation of cortico-subcortical communication patterns and provides insights into DBS mechanisms. Until now, these recordings have been carried out in post-surgical patients with externalised leads. However, a new generation of telemetric stimulators makes it possible to record and stream LFP data in chronically implanted patients. Nevertheless, whether such streaming can be combined with MEG has not been tested.

In the present study, we tested the most commonly implanted telemetric stimulator – Medtronic Percept PC with a phantom in three different MEG systems: two cryogenic scanners (CTF and MEGIN) and an experimental Optically Pumped Magnetometry (OPM)-based system.

We found that when used in combination with the new SenSight segmented leads, Percept PC telemetric streaming only generates band-limited interference in the MEG at 123Hz and harmonics. However, the ‘legacy streaming mode’ used with older lead models generates multiple, dense artefact peaks in the physiological range of interest (below 50Hz).

The effect of stimulation on MEG critically depends on whether it is done in bipolar (between two contacts on the lead) or monopolar (between a lead contact and the stimulator case) mode. Monopolar DBS creates severe interference in the MEG as previously reported. However, we found that the OPM system is more resilient to this interference and could provide artefact-free measurements at least for limited frequency ranges.

A resting measurement in the MEGIN system from a Parkinson’s patient implanted with Percept PC and subthalamic SenSight leads revealed artefact patterns consistent with our phantom recordings. Moreover, analysis of LFP-MEG coherence in this patient showed oscillatory coherent networks consistent in their frequency and topography with those described in published group studies done with externalised leads.

In conclusion, Percept PC telemetric streaming with SenSight leads is compatible with MEG. Furthermore, OPM sensors could provide additional new opportunities for studying DBS effects.
Bacteroidalesas a Fecal Contamination Indicator in Fresh Produce Industry: A Baseline Measurement
Authors: Wang Jiangshan , Ranjbaran Mohsen , Verma Mohit S.
Published: July 2023

Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of “buffer zones” between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the backgroundBacteroidalesconcentration, as a quantitative fecal contamination indicator, in California’s Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. TheBacteroidalesconcentration was very low (0 – 2.00 copies/cm2). Furthermore, we established a practical methodology for evaluating the risk of fecal contamination in a real-world setting, complementing the current environmental assessment practices. This method can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their fields. We anticipate this work can encourage the use ofBacteroidalesin the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.
The equilibrium theory of biodiversity dynamics: a general framework for scaling species richness and community abundance along environmental gradients
Authors: Okie Jordan G , Storch David
Published: July 2023

Large-scale temporal and spatial biodiversity patterns have traditionally been explained by multitudinous particular factors and a few theories. However, these theories lack sufficient generality and do not address fundamental interrelationships and coupled dynamics between resource availability, community abundance, and species richness. We propose the Equilibrium Theory of Biodiversity Dynamics (ETBD) to address these linkages. According to the theory, equilibrium levels of species richness and community abundance emerge at large spatial scales due to the population size-dependence of speciation and/or extinction rates, modulated by resource availability and the species abundance distribution. In contrast to other theories, ETBD includes the effect of biodiversity on community abundance and thus addresses phenomena such as niche complementarity, facilitation, and ecosystem engineering. It reveals how alternative stable states in both diversity and community abundance emerge from these nonlinear biodiversity effects. The theory predicts how the strength of these effects alters scaling relationships between species richness, (meta)community abundance, and resource availability along different environmental gradients. Using data on global-scale variation in tree species richness, we show how the general framework is useful for clarifying the role of speciation, extinction and resource availability in driving macroecological patterns in biodiversity and community abundance, such as the latitudinal diversity gradient.
Conformational dynamics underlying Atypical Chemokine Receptor 3 activation
Authors: Otun Omolade , Aljamous Christelle , Nero Elise Del , Arimont-Segura Marta , Bosma Reggie , Zarzycka Barbara , Girbau Tristan , Leyrat Cédric , de Graaf Chris , Leurs Rob , Durroux Thierry , Granier Sebastien , Cong Xiaojing , Bechara Cherine
Published: July 2023

Atypical Chemokine Receptor 3 (ACKR3) is a G protein-coupled receptor that does not signal through G proteins. It is known as a chemokine scavenger involved in various pathologies, making it an appealing yet intriguing therapeutic target. Indeed, the structural properties that govern ACKR3 functional selectivity and the overall conformational dynamics of ACKR3 activation are poorly understood. Here we combined Hydrogen/Deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics simulations to examine the binding mode and mechanism of action of various small-molecule ACKR3 ligands of different efficacy for β-arrestin recruitment. Our results show that activation or inhibition of ACKR3 is largely governed by intracellular conformational changes of helix 6, intracellular loop 2 and helix 7, while the DRY motif becomes protected during both processes. Moreover, HDX-MS identifies the binding sites and the allosteric modulation of ACKR3 upon β-arrestin 1 binding. In summary, this study highlights the structure-function relationship of small-molecule ligands, the overall activation dynamics of ACKR3, the binding mode of β-arrestin 1 and the atypical dynamic features in ACKR3 that may contribute to its inability to activate G proteins.