bluuebunny/crossref_metadata_2025 huggingface dataset:
Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps
Authors: Delgado Soledad , Somovilla Pilar , Ferrer-Orta Cristina , Martínez-González Brenda , Vázquez-Monteagudo Sergi , Muñoz-Flores Javier , Soria María Eugenia , García-Crespo Carlos , de Ávila Ana Isabel , Durán-Pastor Antoni , Gadea Ignacio , López-Galíndez Cecilio , Moran Federico , Lorenzo-Redondo Ramon , Verdaguer Nuria , Perales Celia , Domingo Esteban
Published: February 2024

Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
Evidence for the co-existence of separate strains or species of Ligula in Lough Neagh, Northern Ireland
Authors: Olson P.D. , Littlewood D.T.J. , Griffiths D. , Kennedy C.R. , Arme C.
Published: February 2024

Ligula (Cestoda: Pseudophyllidea) infections in gudgeon (Gobio gobio) and roach (Rutilus rutilus) differ markedly in the pathology that is observed in the host, particularly with respect to a tissue response and the extent of inhibition of gonadal development. The entire internal transcribed spacer (ITS) region (ITS-1, 5.8S and ITS-2) and the large subunit domains D1–D3 were sequenced and compared in parasites from these fish from Lough Neagh, Northern Ireland, together with a single specimen from minnow (Phoxinus phoxinus) from Wales. Sufficient differences were observed between parasites from R. rutilus and G. gobio to support the suggestion that they may represent different strains/species. In contrast, Ligula from P. phoxinus closely resembled those from R. rutilus. Ligula infections in G. gobio were recorded prior to the introduction of R. rutilus. The co-existence of separate strains or species of Ligula in Lough Neagh probably resulted from the introduction of R. rutilus to these waters, correlated with an increase in the number of great crested grebes (Podiceps cristatus).
Generation of interferometrically stable pulse pairs from a free-electron laser using a birefringent interferometer
Authors: Ardini B , Richter F , Uboldi L , Cinquegrana P , Danailov M , Demidovich A , Ganeshamandiram S D , Hartweg S , Kurdi G , Landmesser F , Michelbach M , Ngai A , Nikolov I , Rendler N , Stienkemeier F , Uhl D , Bruder L , Cerullo G , Manzoni C
Published: February 2024

We present a compact, intrinsically stable common path interferometer for the seeding of free-electron lasers (FELs). The interferometer can handle the required ultraviolet seed wavelengths and features an excellent phase stability of 10 mrad at 265 nm. By seeding the FEL FERMI, we demonstrate the generation of extreme ultraviolet (XUV) pulse pairs with tunable delay and a delay stability of 6 as at 52.5 nm. Prospective applications are Fourier transform spectroscopy, nonlinear spectroscopy and coherent control experiments in the XUV and x-ray domain.
Non-constant geometric curvature for tailored spin–orbit coupling and chirality in superconductor-magnet heterostructures
Authors: Johan Skarpeid Alv , Hugdal Henning G , Salamone Tancredi , Amundsen Morten , Jacobsen Sol H
Published: February 2024

We show that tailoring the geometric curvature profile of magnets can be used for bespoke design of an effective non-relativistic spin–orbit coupling, which may be used to control proximity effects if the magnet is coupled to a superconductor. We consider proximity-coupled one-dimensional magnetic wires with variable curvatures, specifically three distinct shapes classified as J-, C-, and S-type. We demonstrate a chirality-dependent spin polarization of the superconducting correlations, and show the role of curvature in determining the ground state of mixed-chirality junctions. We speculate on how this may be implemented in novel device design, and include analysis of its usage in a spin-triplet SQUID.
Effects of magnetic field and post-weld heat treatment on microstructure and properties of laser welded joints of 22MnB5-TRIP590 steel
Authors: Zhu Xiaoou , Liu Zhanqi , Yin Guili , Cui Nuonuo , Li Yu , Chen Yuhang
Published: February 2024

Laser welding without and with an auxiliary magnetic field (B = 30 mT) is performed on 22MnB5-TRIP590 steel. Subsequently, post-weld heat treatment, involving quenching at 800 °C followed by tempering at 200 °C, is carried out on the welded joints prepared by these two welding processes (B = 0 mT, B = 30 mT). This study examines the improvement of microstructures and mechanical properties of the welded joints by applying the magnetic field (B = 30 mT). Furthermore, this research investigates whether these enhanced characteristics of the welded joints persist after post-weld heat treatment. When the magnetic field is applied, the overall width of the welded joint is significantly reduced, and the microstructure of the weld is changed mainly from proeutectoid ferrite, granular bainite, and upper bainite to lath martensite and lower bainite. Furthermore, the grains in the coarse grain zone are refined, and the plasticity and overall hardness of the welded joint are considerably improved. After post-weld heat treatment, the weld and coarse grain zone of both welded joints (B = 0 mT, B = 30 mT) are mainly tempered martensite, and the tensile strength and overall hardness are significantly improved compared to those without post-weld heat treatment. Although the plasticity of two welded joints is lower than that of two unheated-treated welded joints, the fracture positions are all at the base metal and are both ductile fractures. The improved characteristics, such as optimized macro-morphology, refined grain morphology, improved plasticity, welded joint efficiency, and weld hardness of magnetic field-assisted laser welded joint, are all retained after post-weld heat treatment. A thorough comparison reveals that the magnetic field-assisted laser welded joint with post-weld heat treatment has better comprehensive mechanical properties.
Validating spatio-temporal environmental machine learning models: Simpson’s paradox and data splits
Authors: Boser Anna
Published: February 2024

Machine learning has revolutionized environmental sciences by estimating scarce environmental data, such as air quality, land cover type, wildlife population counts, and disease risk. However, current methods for validating these models often ignore the spatial or temporal structure commonly found in environmental data, leading to inaccurate evaluations of model quality. This paper outlines the problems that can arise from such validation methods and describes how to avoid erroneous assumptions about training data structure. In an example on air quality estimation, we show that a poor model with an r
2 of 0.09 can falsely appear to achieve an r
2 value of 0.73 by failing to account for Simpson’s paradox. This same model’s r
2 can further inflate to 0.82 when improperly splitting data. To ensure high-quality synthetic data for research in environmental science, justice, and health, researchers must use validation procedures that reflect the structure of their training data.
Acousto-optic deflectors in experimental neuroscience: overview of theory and applications
Authors: Ricci Pietro , Sancataldo Giuseppe , Gavryusev Vladislav , Pavone Francesco Saverio , Saggau Peter , Duocastella Martí
Published: February 2024

Cutting-edge methodologies and techniques are required to understand complex neuronal dynamics and pathological mechanisms. Among them, optical tools stand out due to their combination of non-invasiveness, speed, and precision. Examples include optical microscopy, capable of characterizing extended neuronal populations in small vertebrates at high spatiotemporal resolution, or all-optical electrophysiology and optogenetics, suitable for direct control of neuronal activity. However, these approaches necessitate progressively higher levels of accuracy, efficiency, and flexibility of illumination for observing fast entangled neuronal events at a millisecond time-scale over large brain regions. A promising solution is the use of acousto-optic deflectors (AODs). Based on exploiting the acousto-optic effects, AODs are high-performance devices that enable rapid and precise light deflection, up to MHz rates. Such high-speed control of light enables unique features, including random-access scanning or parallelized multi-beam illumination. Here, we survey the main applications of AODs in neuroscience, from fluorescence imaging to optogenetics. We also review the theory and physical mechanisms of these devices and describe the main configurations developed to accomplish flexible illumination strategies for a better understanding of brain function.
2D multifunctional devices: from material preparation to device fabrication and neuromorphic applications
Authors: Huang Zhuohui , Li Yanran , Zhang Yi , Chen Jiewei , He Jun , Jiang Jie
Published: February 2024

Neuromorphic computing systems, which mimic the operation of neurons and synapses in the human brain, are seen as an appealing next-generation computing method due to their strong and efficient computing abilities. Two-dimensional (2D) materials with dangling bond-free surfaces and atomic-level thicknesses have emerged as promising candidates for neuromorphic computing hardware. As a result, 2D neuromorphic devices may provide an ideal platform for developing multifunctional neuromorphic applications. Here, we review the recent neuromorphic devices based on 2D material and their multifunctional applications. The synthesis and next micro–nano fabrication methods of 2D materials and their heterostructures are first introduced. The recent advances of neuromorphic 2D devices are discussed in detail using different operating principles. More importantly, we present a review of emerging multifunctional neuromorphic applications, including neuromorphic visual, auditory, tactile, and nociceptive systems based on 2D devices. In the end, we discuss the problems and methods for 2D neuromorphic device developments in the future. This paper will give insights into designing 2D neuromorphic devices and applying them to the future neuromorphic systems.
Programmable cell unit arrangement of 3D printing mechanical metamaterial undergoing tailorable local instability
Authors: Li Zhenghong , Lu Haibao
Published: February 2024

3D printing mechanical metamaterial is one of the most popular research topics due to the advantages of rapidity, design, and programmable mechanical properties. Many previous studies had conducted on the 3D printing mechanical metamaterial using the holey column structure, however, there is few of reports on the effect of programmable cell unit arrangement on the mechanical metamaterials, of which the structural optimizations and designable strategies have not been understood yet. In this study, three types of holey column structures with a variety of rotation angles were designed and 3D printing manufactured. Effects of rotation angles of holes and their arrangements on mechanical properties and buckling modes were investigated using finite element analysis (FEA) simulations and experimental verifications for the 3D printing metamaterials. The compression-buckling behaviors can be tailorable by means of arrangement of the unit cells, i.e., auxeticity. Furthermore, a 3D printing mechanical metamaterial, which is made from the shape memory polymer (SMP), was fabricated to endow it with shape memory effect (SME) and designable mechanical behavior.
WATUNet: a deep neural network for segmentation of volumetric sweep imaging ultrasound
Authors: Khaledyan Donya , Marini Thomas J , O’Connell Avice , Meng Steven , Kan Jonah , Brennan Galen , Zhao Yu , Baran Timothy M , Parker Kevin J
Published: February 2024

Limited access to breast cancer diagnosis globally leads to delayed treatment. Ultrasound, an effective yet underutilized method, requires specialized training for sonographers, which hinders its widespread use. Volume sweep imaging (VSI) is an innovative approach that enables untrained operators to capture high-quality ultrasound images. Combined with deep learning, like convolutional neural networks, it can potentially transform breast cancer diagnosis, enhancing accuracy, saving time and costs, and improving patient outcomes. The widely used UNet architecture, known for medical image segmentation, has limitations, such as vanishing gradients and a lack of multi-scale feature extraction and selective region attention. In this study, we present a novel segmentation model known as Wavelet_Attention_UNet (WATUNet). In this model, we incorporate wavelet gates and attention gates between the encoder and decoder instead of a simple connection to overcome the limitations mentioned, thereby improving model performance. Two datasets are utilized for the analysis: the public ‘Breast Ultrasound Images’ dataset of 780 images and a private VSI dataset of 3818 images, captured at the University of Rochester by the authors. Both datasets contained segmented lesions categorized into three types: no mass, benign mass, and malignant mass. Our segmentation results show superior performance compared to other deep networks. The proposed algorithm attained a Dice coefficient of 0.94 and an F1 score of 0.94 on the VSI dataset and scored 0.93 and 0.94 on the public dataset, respectively. Moreover, our model significantly outperformed other models in McNemar’s test with false discovery rate correction on a 381-image VSI set. The experimental findings demonstrate that the proposed WATUNet model achieves precise segmentation of breast lesions in both standard-of-care and VSI images, surpassing state-of-the-art models. Hence, the model holds considerable promise for assisting in lesion identification, an essential step in the clinical diagnosis of breast lesions.
Online meta-learned gradient norms for active learning in science and technology
Authors: Dong Haiqi , Barnard Amanda S , Parker Amanda J
Published: February 2024

Acquisition of scientific data can be expensive and time-consuming. Active learning is a solution to reduce costs and time by guiding the selection of scientific experiments. Autonomous and automatic identification of the most essential samples to annotate by active learning can also help to mitigate human bias. Previous research has demonstrated that unlabelled samples causing the largest gradient norms of neural network models can promote active learning in classification. However, gradient norm estimation in regression is non-trivial because the continuous one-dimensional output of regression significantly differs from classification. In this study, we propose a new active learning method that uses meta-learning to estimate the gradient norm of the unlabelled sample in regression. Specifically, we use a separate model to be a selector that learns knowledge from the previous active learning results and is used to predict the gradient norms of unlabelled samples. In each active learning iteration, we estimate and select unlabelled samples with the largest gradient norms to annotate. Our method is evaluated on six regression data sets in various domains, which include costly scientific data.
Robust errant beam prognostics with conditional modeling for particle accelerators
Authors: Rajput Kishansingh , Schram Malachi , Blokland Willem , Alanazi Yasir , Ramuhalli Pradeep , Zhukov Alexander , Peters Charles , Vilalta Ricardo
Published: February 2024

Particle accelerators are complex and comprise thousands of components, with many pieces of equipment running at their peak power. Consequently, they can fault and abort operations for numerous reasons, lowering efficiency and science output. To avoid these faults, we apply anomaly detection techniques to predict unusual behavior and perform preemptive actions to improve the total availability. Supervised machine learning (ML) techniques such as siamese neural network models can outperform the often-used unsupervised or semi-supervised approaches for anomaly detection by leveraging the label information. One of the challenges specific to anomaly detection for particle accelerators is the data’s variability due to accelerator configuration changes within a production run of several months. ML models fail at providing accurate predictions when data changes due to changes in the configuration. To address this challenge, we include the configuration settings into our models and training to improve the results. Beam configurations are used as a conditional input for the model to learn any cross-correlation between the data from different conditions and retain its performance. We employ conditional siamese neural network (CSNN) models and conditional variational auto encoder (CVAE) models to predict errant beam pulses at the spallation neutron source under different system configurations and compare their performance. We demonstrate that CSNNs outperform CVAEs in our application.
Myosin F controls actin organization and dynamics in Toxoplasma gondii
Authors: Kellermeier Jacob A. , Heaslip Aoife T.
Published: February 2024

Intracellular cargo transport is a ubiquitous cellular process in all eukaryotes. In many cell types, membrane bound cargo is associated with molecular motors which transport cargo along microtubule and actin tracks. In Toxoplasma gondii ( T. gondii), an obligate intracellular parasite in the phylum Apicomplexa, organization of the endomembrane pathway depends on actin and an unconventional myosin motor, myosin F (MyoF). Loss of MyoF and actin disrupts vesicle transport, organelle positioning, and division of the apicoplast, a nonphotosynthetic plastid organelle. How this actomyosin system contributes to these cellular functions is still unclear. Using live-cell imaging, we observed that MyoF-EmeraldFP (MyoF-EmFP) displayed a dynamic and filamentous-like organization in the parasite cytosol, reminiscent of cytosolic actin filament dynamics. MyoF was not associated with the Golgi, apicoplast or dense granule surfaces, suggesting that it does not function using the canonical cargo transport mechanism. Instead, we found that loss of MyoF resulted in a dramatic rearrangement of the actin cytoskeleton in interphase parasites accompanied by significantly reduced actin dynamics. However, actin organization during parasite replication and motility was unaffected by the loss of MyoF. These findings revealed that MyoF is an actin organizing protein in Toxoplasma and facilitates cargo movement using an unconventional transport mechanism.
Modernizing Antiquity: Decadence and Futurism in Roman Africa
Authors: Agbamu Samuel
Published: February 2024

This chapter examines the imperial classicisms of two major cultural figures of early twentieth-century Italy: Gabriele D’Annunzio, and Filippo Tommaso Marinetti. The chapter suggests that the iconoclastic impetus of Futurism remained deeply rooted in Marinetti’s cultural and educational background. For Marinetti, Africa was a source of vigour, which he channelled into an aggressive imperial politics. D’Annunzio, this chapter suggests, represents a synthesis of conservative classicism and dynamic modernism, ingredients that would be central to Fascism’s aesthetic politics. The chapter looks at how the memory of Roman imperialism featured in these authors’ imperial discourse, and positions them as precursors to Fascist imperial classicism.
Carmine Gallone’s Scipione l’Africano: Restaging Rome, Reincarnating Romanità
Authors: Agbamu Samuel
Published: February 2024

This chapter examines the ideological potency of the Second Punic War for modern Italian imperialism by analysing Carmine Gallone’s 1937 film Scipione l’Africano. The chapter begins by outlining how the figure of Scipio has been appropriated in postclassical discourses to stand in for idealized constructions of masculinities. It moves on to argue that cinema had a unique capacity to promote this image rapidly, disseminating masculine, imperialist ideologies to diffuse audiences. After establishing the way in which Scipione constructs its own reality, the chapter investigates how the film promotes a distinctly Fascist imperial ideology. A key element of this is its representation of gender, which is deeply racialized. In exploring this aspect of the film’s ideology, the chapter draws on Black and postcolonial feminist theorists, bringing new perspectives to scholarship on this monumental film.
The Arco dei Fileni: The Realization of Romanità in Africa
Authors: Agbamu Samuel
Published: February 2024

This chapter focuses on a triumphal arch erected by Italian colonial authorities on the Strada Litoranea, in Libya in 1937. This road was continually represented as a Roman achievement in publications and media from the time, and was inaugurated during Mussolini’s spectacularized tour of Libya in 1937. The arch that marked the road’s midway point, designed by the architect Florestano Di Fausto, explicitly framed itself as a concrete manifestation of the legend of the Carthaginian Philaeni brothers, narrated most fully in a digression in Sallust’s Bellum Iugurthinum. This chapter suggests that if Roman integrity started to collapse with the destruction of Carthage, justifying Scipio Aemilianus’ tears over the ruins of the Punic city, Fascist imperialism was constantly foreshadowing its own downfall, by constantly excavating the absent presence of the city of Carthage.
Diagnostic utility of exome sequencing followed by research reanalysis in human brain malformations
Authors: Kooshavar Daniz , Amor David J , Boggs Kirsten , Baker Naomi , Barnett Christopher , de Silva Michelle G , Edwards Samantha , Fahey Michael C , Marum Justine E , Snell Penny , Bozaoglu Kiymet , Pope Kate , Mohammad Shekeeb S , Riney Kate , Sachdev Rani , Scheffer Ingrid E , Schenscher Sarah , Silberstein John , Smith Nicholas , Tom Melanie , Ware Tyson L , Lockhart Paul J , Leventer Richard J
Published: February 2024

This study aimed to determine the diagnostic yield of singleton exome sequencing and subsequent research-based trio exome analysis in children with a spectrum of brain malformations seen commonly in clinical practice. We recruited children ≤ 18 years old with a brain malformation diagnosed by magnetic resonance imaging and consistent with an established list of known genetic causes. Patients were ascertained nationally from eight tertiary paediatric centres as part of the Australian Genomics Brain Malformation Flagship. Chromosome microarray was required for all children, and those with pathogenic copy number changes were excluded. Cytomegalovirus polymerase chain reaction on neonatal blood spots was performed on all children with polymicrogyria with positive patients excluded. Singleton exome sequencing was performed through a diagnostic laboratory and analysed using a clinical exome sequencing pipeline. Undiagnosed patients were followed up in a research setting, including reanalysis of the singleton exome data and subsequent trio exome sequencing. A total of 102 children were recruited. Ten malformation subtypes were identified with the commonest being polymicrogyria (36%), pontocerebellar hypoplasia (14%), periventricular nodular heterotopia (11%), tubulinopathy (10%), lissencephaly (10%) and cortical dysplasia (9%). The overall diagnostic yield for the clinical singleton exome sequencing was 36%, which increased to 43% after research follow-up. The main source of increased diagnostic yield was the reanalysis of the singleton exome data to include newly discovered gene–disease associations. One additional diagnosis was made by trio exome sequencing. The highest phenotype-based diagnostic yields were for cobblestone malformation, tubulinopathy and lissencephaly and the lowest for cortical dysplasia and polymicrogyria. Pathogenic variants were identified in 32 genes, with variants in 6/32 genes occurring in more than one patient. The most frequent genetic diagnosis was pathogenic variants in TUBA1A. This study shows that over 40% of patients with common brain malformations have a genetic aetiology identified by exome sequencing. Periodic reanalysis of exome data to include newly identified genes was of greater value in increasing diagnostic yield than the expansion to trio exome. This study highlights the genetic and phenotypic heterogeneity of brain malformations, the importance of a multidisciplinary approach to diagnosis and the large number of patients that remain without a genetic diagnosis despite clinical exome sequencing and research reanalysis.
Fostering cardio-endometriosis: a call to action for a comprehensive understanding of cardiovascular disease in endometriosis
Authors: Marchandot Benjamin , Faller Emilie , Akladios Cherif , Matsushita Kensuke , Bäck Magnus , Jesel Laurence , Schini-Kerth Valérie , Morel Olivier
Published: February 2024

Recently, a growing body of evidence has highlighted a concerning link between endometriosis and cardiovascular disease. Endometriosis, a chronic, inflammatory, hormone-dependent condition affecting 5–10% of reproductive-aged women worldwide, has long been associated with reproductive and gynaecological consequences. However, emerging research has suggested that it may also contribute to adverse cardiovascular outcomes. This paper aims to shed light on the importance of recognizing cardio-endometriosis as a new and developing sphere of research in the field of cardiology, thereby urging the medical community to address this pressing issue.
Transferability of bone phenotyping and fracture risk assessment by μFRAC from first-generation high-resolution peripheral quantitative computed tomography to second-generation scan data
Authors: Bugbird Annabel R , Whittier Danielle E , Boyd Steven K
Published: February 2024

Introduction

The continued development of high-resolution peripheral quantitative computed tomography (HR-pQCT) has led to a second-generation scanner with higher resolution and longer scan region. However, large multicenter prospective cohorts were collected with first-generation HR-pQCT and have been used to develop bone phenotyping and fracture risk prediction (μFRAC) models. This study establishes whether there is sufficient universality of these first-generation trained models for use with second-generation scan data.

Methods

HR-pQCT data were collected for a cohort of 60 individuals, who had been scanned on both first- and second-generation scanners on the same day to establish the universality of the HR-pQCT models. These data were each used as input to first-generation trained bone microarchitecture models for bone phenotyping and fracture risk prediction, and their outputs were compared for each study participant. Reproducibility of the models were assessed using same-day repeat scans obtained from first-generation (n = 37) and second-generation (n = 74) scanners.

Results

Across scanner generations, the bone phenotyping model performed with an accuracy of 93.1%. Similarly, the 5-year fracture risk assessment by μFRAC was well correlated with a Pearson’s (r) correlation coefficient of r > 0.83 for the three variations of μFRAC (varying inclusion of clinical risk factors, finite element analysis, and dual X-ray absorptiometry). The first-generation reproducibility cohort performed with an accuracy for categorical assignment of 100% (bone phenotyping) and a correlation coefficient of 0.99 (μFRAC), whereas the second-generation reproducibility cohort performed with an accuracy of 96.4% (bone phenotyping) and a correlation coefficient of 0.99 (μFRAC).

Conclusion

We demonstrated that bone microarchitecture models trained using first-generation scan data generalize well to second-generation scans, performing with a high level of accuracy and reproducibility. Less than 4% of individuals’ estimated fracture risk led to a change in treatment threshold, and in general, these dissimilar outcomes using second-generation data tended to be more conservative.
Current and Emerging Antiviral Agents in the Prevention and Treatment of Cytomegalovirus in Pediatric Transplant Recipients
Authors: Valencia Deray Kristen G , Danziger-Isakov Lara A , Downes Kevin J
Published: February 2024

Despite current prophylaxis regimens, cytomegalovirus (CMV) is common in hematopoietic cell transplantation (HCT) and solid organ transplantation (SOT) and remains a significant cause of morbidity and mortality. Newer antiviral medications are reshaping the landscape for prevention and treatment of CMV DNAemia, infection, and disease. Letermovir is approved for CMV prevention in adult HCT patients and is attractive due to the absence of marrow suppression seen with ganciclovir/valganciclovir. Letermovir should not be routinely used for CMV treatment due to its low threshold for resistance. Maribavir is approved for the treatment of refractory or resistant CMV disease in HCT and SOT recipients ≥12 years of age, though it has no current role in CMV prevention. More research is needed to fully elucidate the roles, efficacy, and safety of these newer agents in prevention and treatment of CMV in pediatric transplant recipients.
The Microbiome and Pediatric Transplantation
Authors: Elgarten Caitlin W , Margolis Elisa B , Kelly Matthew S
Published: February 2024

The microbial communities that inhabit our bodies have been increasingly linked to host physiology and pathophysiology. This microbiome, through its role in colonization resistance, influences the risk of infections after transplantation, including those caused by multidrug-resistant organisms. In addition, through both direct interactions with the host immune system and via the production of metabolites that impact local and systemic immunity, the microbiome plays an important role in the establishment of immune tolerance after transplantation, and conversely, in the development of graft-versus-host disease and graft rejection. This review offers a comprehensive overview of the evidence for the role of the microbiome in hematopoietic cell and solid organ transplant complications, drivers of microbiome shift during transplantation, and the potential of microbiome-based therapies to improve pediatric transplantation outcomes.
A Focused Review of Epstein-Barr Virus Infections and PTLD in Pediatric Transplant Recipients: Guidance From the IPTA and ECIL Guidelines
Authors: Yamada Masaki , L'Huillier Arnaud G , Green Michael
Published: February 2024

Epstein-Barr Virus (EBV) diseases, including EBV-associated post-transplant lymphoproliferative disorder (PTLD) remain important causes of morbidity and mortality in children undergoing solid organ transplantation (SOT) and hematopoietic cell transplantation (HCT). Despite progress in the prevention of EBV disease including PTLD (EBV/PTLD) in HCT, key questions in the prevention, and management of these infectious complications remain unanswered. The goal of this manuscript is to highlight key points and recommendations derived from the consensus guidelines published by the International Pediatric Transplant Association and the European Conference on Infections in Leukemia for children undergoing SOT and HCT, respectively. Additionally, we provide background and guidance on the use of EBV viral load measurement in the prevention and management of these children.
Nontuberculous Mycobacterial Infections in Pediatric Solid Organ Transplant and Hematopoietic Cell Transplant Recipients
Authors: Albert Jonathan , Daley Charles L , Lin Philana Ling
Published: February 2024

The diagnosis of nontuberculous mycobacterial infections is challenging in pediatric solid organ transplant and hematopoietic cell transplant recipients due to the absence of specific clinical manifestations, limitations of sampling, prolonged times for culture and identification, and difficulty discerning colonization from clinical disease. Treatment is dependent on the nontuberculous mycobacterial species, disease type, and pattern of drug resistance. Treatment of nontuberculous mycobacterial infections involves prolonged durations of therapy using multiple medications, which are limited by toxicities and drug–drug interactions.
Management dampens seasonal variability in soil microclimates and alters its chemical and physical properties in a semi-arid region
Authors: Kurylo Jessica S , Le Jennifer T , Mehring Andrew , Ambrose Richard F
Published: February 2024

The urbanization process substantially alters every aspect of the soil environment. In this study, we compared soil microclimate, chemistry, and physical characteristics of unmanaged natural soils with managed soils of three common urban land uses (stormwater natural treatment systems, ornamentally landscaped areas, and lawns) across three University of California campuses. Over the course of 1-year, average monthly soil temperatures among land uses showed fewer than expected differences. Average monthly soil moisture reflected wet and dry seasonal changes, but this pattern was muted in managed land uses compared to natural soils due to irrigation. From April through December, lawns and landscaped areas were significantly wetter than natural soils (e.g. 1.5–3 times higher in August and September). Soil organic matter, total carbon, and total nitrogen were significantly higher in lawns compared to other land uses, while their bulk density was significantly lower. Principle component analysis confirmed that natural and lawn soil properties were distinct from each other. These differences in the managed soils, particularly lawns, are attributable to typical urban land management practices such as fertilization, irrigation, and the installation of organic-rich sod. As urbanization continues to change the native landscape of semi-arid regions, these changes to soil microclimate, chemistry, and physical characteristics are important to consider for urban best practices and sustainable development.
Patterns of water-wise residential landscaping in a drought-prone city
Authors: Green Jasmin C , Solins Joanna P , Brissette Logan E G , Benning Tracy L , Gould Kennedy , Bell Emily M , Cadenasso Mary L
Published: February 2024

The replacement of turf lawns with water-wise landscaping has become a common tactic for water conservation in drought-prone cities and is often incentivized through rebate programs that subsidize the cost of turf conversion. The impact of rebate programs increases if neighbors are inspired to adopt water-wise landscaping independently. However, turf conversion is expensive even with a rebate, and residents may have non-financial reasons for maintaining lawns or installing water-wise landscaping independently. We explored the distribution of water-wise yards and rebate recipients in relation to sociodemographic and biophysical landscape characteristics across the city of Sacramento, California, USA. For 100 census tracts in Sacramento, we visually assessed the landscaping in front of every single-family home to classify it as water-wise or conventional. We found that ∼10% of 109,062 sampled yards were water-wise, while only 0.3% were rebate recipients. We also found that water-wise yards were clustered, suggesting a neighborhood adoption effect. Water-wise yards and rebate recipients were positively correlated with educational attainment, white population, income, and tree canopy, and negatively correlated with July temperature and households with children. Our research shows that most water-wise landscaping in Sacramento has been installed without rebates, in areas with greater shading and socioeconomic status. Rebates did not appear to offset barriers to turf conversion, but may inspire neighborhood adoption. Our findings suggest that while water-wise landscaping is becoming more prevalent, it is not accessible or desirable for all residents, potentially contributing to uneven distributions of urban water use and ecosystem services.
Magnetic manipulation of the reactivity of singlet oxygen: from test tubes to living cells
Authors: Yang Zi-Shu , Gao Song , Zhang Jun-Long
Published: February 2024

Although magnetism undoubtedly influences life on Earth, the science behind biological magnetic sensing is largely a mystery, and it has proved challenging, especially in the life sciences, to harness the interactions of magnetic fields (MFs) with matter to achieve specific ends. Using the well-established radical pair (RP) mechanism, we here demonstrate a bottom-up strategy for the exploitation of MF effects in living cells by translating knowledge from studies of RP reactions performed in vitro. We found an unprecedented MF dependence of the reactivity of singlet oxygen (1O2) towards electron-rich substrates (S) such as anthracene, lipids and iodide, in which [S˙+ O2˙−] RPs are formed as a basis for MFs influencing molecular redox events in biological systems. The close similarity of the observed MF effects on the biologically relevant process of lipid peroxidation in solution, in membrane mimics and in living cells, shows that MFs can reliably be used to manipulate 1O2-induced cytotoxicity and cell-apoptosis-related protein expression. These findings led to a ‘proof-of-concept’ study on MF-assisted photodynamic therapy in vivo, highlighting the potential of MFs as a non-invasive tool for controlling cellular events.
Which Topics Drive Dissemination? Alternative Bibliometrics Analysis of the Highest-Ranking Articles in 3 Infectious Diseases Journals Before COVID-19
Authors: Marcelin Jasmine R , Goel Shipra , Niehaus William N , Messersmith Robert C , Cawcutt Kelly A
Published: February 2024

Dissemination of research is paramount to improving patient care. Historically, dissemination is reported in conventional bibliometrics. However, with the increased utilization of digital platforms for communication, alternative bibliometrics describe more real-time dissemination of information. This study documents dissemination of publication topics in infectious diseases journals prior to the COVID-19 pandemic.
Foreign-imposed Regime Change and the American War in Afghanistan
Authors: Brownlee Jason
Published: February 2024

Why did America's twenty-year war in Afghanistan fail to establish a self-sustaining non-Taliban government? Analysts have cited cultural obstacles in Afghanistan, bureaucratic inertia in Washington, and a lack of strategic commitment, in part because Iraq dominated national security policy. Such claims tend to draw evidence from Germany, Japan, and Iraq, places where the U.S. military achieved some measure of success establishing pro-American governments. The present article broadens the comparison to consider Afghanistan alongside Germany, Japan, Iraq, and two examples of post-Cold War regime-change success: Panama (1989–1990) and Haiti (1994–1995). The cases indicate that U.S. influence in the postwar environment has depended on the prospects for integrating old regime elites into the new government and on the strength of indigenous opposition forces. Both variables were unfavorable in Afghanistan, and they shaped the boundaries of political order—no matter how hard U.S. forces fought or how long they stayed.
On Thermal Transition in QCD
Authors: Hanada Masanori , Watanabe Hiromasa
Published: February 2024

We describe how the general mechanism of partial deconfinement applies to large-N QCD and a partially deconfined phase inevitably appears between completely confined and completely deconfined phases. Furthermore, we propose how partial deconfinement can be observed in real-world QCD with the SU(3) gauge group. For this purpose, we employ lattice configurations obtained by the WHOT-QCD Collaboration and examine our proposal numerically. In the discussion, the Polyakov loop plays a crucial role in characterizing the phases, without relying on center symmetry, and hence we clarify the meaning of the Polyakov loop in QCD at large N and finite N. At both large N and finite N, the complete confinement is characterized by the Haar-random distribution of the Polyakov line phases. Haar-randomness, which is stronger than unbroken center symmetry, indicates that Polyakov loops in any nontrivial representations have vanishing expectation values, and deviation from the Haar-random distribution at higher temperatures is quantified with the loops. We discuss that the transitions separating the partially deconfined phase are characterized by the behaviors of Polyakov loops in various representations. The lattice QCD data provide us with the signals exhibiting two different characteristic temperatures: deconfinement of the fundamental representation and deconfinement of higher representations. As a nontrivial test for our proposal, we also investigate the relation between partial deconfinement and instanton condensation and confirm the consistency with the lattice data. To make the presentation more easily accessible, we provide a detailed review of the previously known aspects of partial deconfinement.
Fabrication of a 3D bioprinting model for posterior capsule opacification using GelMA and PLMA hydrogel-coated resin
Authors: Liu Xin , Li Jiale , Liu Shuyu , Long Yan , Kang Ching , Zhao Chen , Wei Ling , Huang Shaoqi , Luo Yi , Dai Bo , Zhu Xiangjia
Published: February 2024

Posterior capsule opacification (PCO) remains the predominant complication following cataract surgery, significantly impairing visual function restoration. In this study, we developed a PCO model that closely mimics the anatomical structure of the crystalline lens capsule post-surgery. The model incorporated a threaded structure for accurate positioning and observation, allowing for opening and closing. Utilizing 3D printing technology, a stable external support system was created using resin material consisting of a rigid, hollow base and cover. To replicate the lens capsule structure, a thin hydrogel coating was applied to the resin scaffold. The biocompatibility and impact on cellular functionality of various hydrogel compositions were assessed through an array of staining techniques, including calcein-AM/PI staining, rhodamine staining, BODIPY-C11 staining and EdU staining in conjunction with transwell assays. Additionally, the PCO model was utilized to investigate the effects of eight drugs with anti-inflammatory and anti-proliferative properties, including 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR), THZ1, sorbinil, 4-octyl itaconate (4-OI), xanthohumol, zebularine, rapamycin and caffeic acid phenethyl ester, on human lens epithelial cells (HLECs). Confocal microscopy facilitated comprehensive imaging of the PCO model. The results demonstrated that the GelMA 60 5% + PLMA 2% composite hydrogel exhibited superior biocompatibility and minimal lipid peroxidation levels among the tested hydrogels. Moreover, compared to using hydrogel as the material for 3D printing the entire model, applying surface hydrogel spin coating with parameters of 2000 rpm × 2 on the resin-based 3D printed base yielded a more uniform cell distribution and reduced apoptosis. Furthermore, rapamycin, 4-OI and AICAR demonstrated potent antiproliferative effects in the drug intervention study. Confocal microscopy imaging revealed a uniform distribution of HLECs along the anatomical structure of the crystalline lens capsule within the PCO model, showcasing robust cell viability and regular morphology. In conclusion, the PCO model provides a valuable experimental platform for studying PCO pathogenesis and exploring potential therapeutic interventions.
Intensive support does not improve positive-airway pressure use in spinal cord injury/disease: a randomized clinical trial
Authors: Badr M Safwan , Martin Jennifer L , Sankari Abdulghani , Zeineddine Salam , Salloum Anan , Henzel M Kristina , Strohl Kingman , Shamim-Uzzaman Afifa , May Anna M , Fung Constance H , Pandya Nishtha , Carroll Sean , Mitchell Michael N
Published: February 2024

Study Objective

Treatment of sleep-disordered breathing (SDB) with positive airway pressure (PAP) therapy has unique clinical challenges in individuals living with spinal cord injuries and diseases (spinal cord injury [SCI]/D). Interventions focused on increasing PAP use have not been studied in this population. We aimed to evaluate the benefits of a program to increase PAP use among Veterans with SCI/D and SDB.

Methods

Randomized controlled trial comparing a behavioral Intervention (n = 32) and educational control (n = 31), both including one face-to-face and five telephone sessions over 3 months. The intervention included education about SDB and PAP, goal setting, troubleshooting, and motivational enhancement. The control arm included non-directive sleep education only.

Results

Primary outcomes were objective PAP use (nights ≥4 hours used within 90 days) and sleep quality (Pittsburgh Sleep Quality Index [PSQI] at 3 months). These did not differ between intervention and control (main outcome timepoint; mean difference 3.5 [−9.0, 15.9] nights/week for PAP use; p = .578; −1.1 [−2.8, 0.6] points for PSQI; p = .219). Secondary outcomes included fatigue, depression, function, and quality of life. Only fatigue improved significantly more in the intervention versus the control group (p = .025). Across groups, more PAP use was associated with larger improvements in sleep quality, insomnia, sleepiness, fatigue, and depression at some time points.

Conclusions

PAP use in Veterans with SCI/D and SDB is low, and a 3-month supportive/behavioral program did not show significant benefit compared to education alone. Overall, more PAP use was associated with improved symptoms suggesting more intensive support, such as in-home assistance, may be required to increase PAP use in these patients.

Clinical Trials Information

Title: “Treatment of Sleep Disordered Breathing in Patients with SCI.” Registration number: NCT02830074. Website: https://clinicaltrials.gov/study/NCT02830074?cond=Sleep%20Apnea&term=badr&rank=5