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The HEALthy Brain and Child Development (HBCD) Study, a multi-site prospective longitudinal cohort study, will examine human brain, cognitive, behavioral, social, and emotional development beginning prenatally and planned through early childhood. The acquisition of multimodal magnetic resonance-based brain development data is central to the study's core protocol. However, application of Magnetic Resonance Imaging (MRI) methods in this population is complicated by technical challenges and difficulties of imaging in early life. Overcoming these challenges requires an innovative and harmonized approach, combining age-appropriate acquisition protocols together with specialized pediatric neuroimaging strategies. The HBCD MRI Working Group aimed to establish a core acquisition protocol for all 27 HBCD Study recruitment sites to measure brain structure, function, microstructure, and metabolites. Acquisition parameters of individual modalities have been matched across MRI scanner platforms for harmonized acquisitions and state-of-the-art technologies are employed to enable faster and motion-robust imaging. Here, we provide an overview of the HBCD MRI protocol, including decisions of individual modalities and preliminary data. The result will be an unparalleled resource for examining early neurodevelopment which enables the larger scientific community to assess normative trajectories from birth through childhood and to examine the genetic, biological, and environmental factors that help shape the developing brain., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Tobias Kober and Tom Hilbert are employees of Siemens Healthineers International AG, Switzerland. Yulin Chang is an employee of Siemens Medical Solutions USA Inc. Dan Rettmann and Ralph Noeske are employed by GE HealthCare. Guillaume Gilbert, Yansong Zhao, Sandeep Ganji, and Maarten Versluis are employed by Philips Healthcare. Carina Lucena, Lucky Heisler-Roman, and Dhruman Goradia are employed by PrimeNeuro Inc. Under a license agreement between Philips and the Johns Hopkins University, Dr. van Zijl and the University are entitled to fees related to an imaging device used in the study discussed for publication. Dr. van Zijl also is a paid lecturer for Philips and receives research support from Philips. This arrangement has been reviewed and approved by the Johns Hopkins University in accordance with its conflict of interest policies. Damien Fair is a patent holder on the Framwise Integrated Real-Time Motion Monitoring (FIRMM) software. He is also a co-founder of Turing Medical Technologies, Inc. The nature of this financial interest and the design of the study have been reviewed by two committees at the University of Minnesota. They have put in place a plan to help ensure that this research is not affected by the financial interest. All other authors report no biomedical financial interests or potential conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Xanthomonas oryzae pv. oryzicola ( Xoc ) causes bacterial leaf streak (BLS) of rice. This disease represents a major constraint for rice production, a crop feeding more than half of the world's population. Xoc was first described in 1918 in the Philippines and is prevalent in Southeast Asia. Today, BLS is also omnipresent in both East and West Africa where the disease was first reported in the early 1980s. The appearance of Xoc in Africa decades after its first report in Asia suggests that the disease could have been introduced from Asia to Africa. Strict conservation of five Transcription Activator Like (TAL) effectors in whole-genome sequences of 10 strains of Xoc including 3 from West-Africa and 7 from Asia also support this hypothesis. East Africa, and especially Madagascar, where the disease was first described in 1985 is located at the interface between Asia and Africa, hence representing an interesting region to explore the link between strains from Asia and West-Africa. In this study, we i) reconstructed the genome of an historical Xoc strain from herbarium specimen of rice showing symptoms of BLS, sampled in Madagascar in 1931, 50 years before the first description of the disease, and ii) sequenced 9 new modern strains including 5 from Madagascar and East-Africa. The analysis of those new genomes along with previously published ones shed light within the evolutionary and epidemiological history of Xoc .

Background: Chronic obstructive pulmonary disease (COPD) is an inflammatory airway disease characterized by emphysema and chronic bronchitis and a leading cause of mortality worldwide. COPD is commonly associated with several comorbid diseases which contribute to exacerbated patient outcomes. Cigarette smoke (CS) is the most prominent risk factor for COPD development and progression and is known to be detrimental to numerous effector functions of lung resident immune cells, including phagocytosis and cytokine production. However, how CS mediates the various pathologies distant from the lung in COPD, and whether CS has a similar biological effect on systemic immune cells remains unknown., Methods: C57BL/6 mice were exposed to 8 weeks of CS as an experimental model of COPD. Bone marrow cells were isolated from both CS-exposed and room air (RA) control mice and differentiated to bone marrow-derived macrophages (BMDMs). Airspace macrophages (AMs) were isolated from the same CS-exposed and RA mice and bulk RNA-Seq performed. The functional role of differentially expressed genes was assessed through gene ontology analyses. Ingenuity Pathway Analysis was used to determine the activation states of canonical pathways and upstream regulators enriched in differentially expressed genes in both cell types, and to compare the differences between the two cell types., Results: CS induced transcriptomic changes in BMDMs, including an upregulation of genes in sirtuin signalling and oxidative phosphorylation pathways and a downregulation of genes involved in histone and lysine methylation. In contrast, CS induced decreased expression of genes involved in pathogen response, phagosome formation, and immune cell trafficking in AMs. Little overlap was observed in differentially expressed protein-coding genes in BMDMs compared to AMs and their associated pathways, highlighting the distinct effects of CS on immune cells in different compartments., Conclusions: CS exposure can induce transcriptomic remodelling in BMDMs which is distinct to that of AMs. Our study highlights the ability of CS exposure to affect immune cell populations distal to the lung and warrants further investigation into the functional effects of these changes and the ensuing role in driving multimorbid disease., (© 2024. The Author(s).)

Background: There is substantial literature supporting the use of cellular and/or tissue-based product (CTP) in managing Wagner grade 1 and 2 diabetic foot ulcers (DFUs) and, to a lesser extent, venous leg ulcers (VLUs). Several studies advocate CTP therapy as an effective method for promoting healing in chronic DFUs and VLUs., Objective: To evaluate how the number of CTP applications affect healing and wound area reduction (WAR) rates of DFUs and VLUs., Methods: A multicenter private wound care practice, electronic health record, and database were used to analyze Medicare patients receiving CTPs between January 1, 2018, and December 31, 2023. Wound treatments occurred in the nursing home, private office, and home settings, not in hospital outpatient department settings. This privately funded, non-vendor-sponsored, real-world retrospective analysis included wound closure and WAR rates after each CTP application. Analysis includes current (2024) aspects of proposed local coverage determination changes that limit the number of CTP applications to 4. A paired t test was used to compare mean wound area before CTP applications and after completing CTP applications over a 16-week period. Effect sizes were analyzed using Cohen d, and correlations between the number of CTP applications and WAR were determined using the Pearson correlation coefficient., Results: A total of 257 wounds were reviewed for analysis, of which 123 were DFUs and 134 were VLUs. For both DFUs and VLUs, there was a significant difference in the average initial wound areas (cm2) compared with the average wound areas after the CTP application series (P < .001)., Conclusion: This comprehensive retrospective real-world analysis of Medicare patients receiving CTP therapy in conjunction with standard of care treatment of DFUs and VLUs demonstrated significant reduction in the average wound area after completing a CTP application series. The results of this study could be used as a guide for the average number of CTP applications required for the effective treatment of DFUs and VLUs.

Bluetongue virus (BTV, Sedoreoviridae : Orbivirus ) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges ( Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.

Background: Constipation impacts 58% to 83% of critically ill patients and is associated with increased time on mechanical ventilation, delirium, and increased length of stay (LOS) in the intensive care unit (ICU)., Objective: The purpose of this study was to evaluate the efficacy of enteral naloxegol (NGL) versus subcutaneous methylnaltrexone (MNTX) for the management of opioid-induced constipation (OIC) in critically ill patients., Methods: A retrospective analysis was conducted on adult patients admitted to the ICU who received a parenteral opioid infusion for at least 4 hours and experienced no bowel movement (BM) within the 48-hour period preceding the administration of NGL or MNTX. The primary outcome was time to first BM from the start of NGL or MNTX therapy. Secondary outcomes included number of BMs 72 hours following NGL or MNTX administration, ICU LOS, and cost-effectiveness., Results: After exclusion criteria were applied, 110 and 51 patients were included in the NGL and MNTX groups, respectively. With a 10% noninferiority margin, NGL was noninferior to MNTX (Wald statistic = 1.67; P = 0.047). Median time to first BM was 23.7 hours for NGL and 18.3 hours for MNTX patients. Median LOS was 14 days (NGL) and 12 days (MNTX), and the average number of BMs in 72 hours was 3.9 for NGL and 3.8 for MNTX. Using wholesale acquisition cost (WAC), the cost per BM for NGL and MNTX was $21.74 and $170.00, respectively., Conclusion and Relevance: This study determined that NGL and MNTX had similar time to BM. NGL appears to be a safe and effective alternative with cost-saving potential in treating OIC in critically ill patients., Competing Interests: Declaration of Conflicting InterestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Long noncoding RNAs (lncRNAs) make up the largest portion of RNA produced from the human genome, but only a small fraction have any ascribed functions. Although the role of protein-coding genes in macrophage biology has been studied extensively, our understanding of the role played by lncRNAs in this context is still in its early stages. There are over 20,000 lncRNAs in the human genome therefore, attempting to select a lncRNA to characterize functionally can be a challenge. Here we describe two approaches to identify and functionally characterize lncRNAs involved in monocyte-to-macrophage differentiation. The first involves the use of RNA-seq to infer possible functions and the second involves a high throughput functional screen. We examine the advantages and disadvantages of these methodologies and the pipelines for validation that assist in determining functional lncRNAs., Competing Interests: Competing interests Carpenter is a paid consultant for NextRNA therapeutics.

We present CRISPRware, an efficient method for generating guide RNA (gRNA) libraries against transcribed, translated, and noncoding regions. CRISPRware leverages next-generation sequencing data to design context-specific gRNAs and accounts for genetic variation, which allows allele-specific guide design on a genome-wide scale. The latter ability holds promise for the development of gene therapy in the context of gene dosing and dominant negative mutations., Competing Interests: Competing interests Carpenter is a paid consultant for RNA therapeutics.

The Late Cretaceous of western North America supported diverse dinosaur assemblages, though understanding patterns of dinosaur diversity, evolution, and extinction has been historically limited by unequal geographic and temporal sampling. In particular, the existence and extent of faunal endemism along the eastern coastal plain of Laramidia continues to generate debate, and finer scale regional patterns remain elusive. Here, we report a new centrosaurine ceratopsid, Lokiceratops rangiformis , from the lower portion of the McClelland Ferry Member of the Judith River Formation in the Kennedy Coulee region along the Canada-USA border. Dinosaurs from the same small geographic region, and from nearby, stratigraphically equivalent horizons of the lower Oldman Formation in Canada, reveal unprecedented ceratopsid richness, with four sympatric centrosaurine taxa and one chasmosaurine taxon. Phylogenetic results show that Lokiceratops , together with Albertaceratops and Medusaceratops , was part of a clade restricted to a small portion of northern Laramidia approximately 78 million years ago. This group, Albertaceratopsini, was one of multiple centrosaurine clades to undergo geographically restricted radiations, with Nasutuceratopsini restricted to the south and Centrosaurini and Pachyrostra restricted to the north. High regional endemism in centrosaurs is associated with, and may have been driven by, high speciation rates and diversity, with competition between dinosaurs limiting their geographic range. High speciation rates may in turn have been driven in part by sexual selection or latitudinally uneven climatic and floral gradients. The high endemism seen in centrosaurines and other dinosaurs implies that dinosaur diversity is underestimated and contrasts with the large geographic ranges seen in most extant mammalian megafauna., Competing Interests: Andrew A. Farke is an Academic Editor for PeerJ. Brock A. Sisson is owner of Fossilogic LLC, which produces cast replicas of Lokiceratops elements., (© 2024 Loewen et al.)

Background: Culex pipiens L. is a principal vector of zoonotic arboviruses in Europe, acting in both an amplification role in enzootic transmission between avian hosts and as a bridge vector between avian hosts and mammals. The species consists of two forms which are indistinguishable using morphological methods but possess varying ecological and physiological traits that influence their vector capacity. In this study we validate methods that can be used to extract trace DNA from single pupal exuviae of Cx. pipiens for use in molecular speciation of samples. These DNA extraction methods are compared using measurement of the total yield and successful identification using a real-time polymerase chain reaction (PCR) assay., Results: Genomic DNA was initially extracted from colony-derived individuals using an ethanol precipitation method, two commercially available DNA extraction kits: DNeasy® Blood & Tissue Kit (Qiagen, UK) and Wizard® SV Genomic DNA Purification System (Promega, UK) and a direct real-time PCR method. Time elapsed between eclosion and processing of pupae significantly influenced Cx. pipiens form identification as nucleic acid concentration and PCR amplification success decreased with increased time elapsed. Real-time PCR amplification success, however, was not shown to vary significantly between the three extraction methods, with all methods successfully identifying all samples, but the direct real-time PCR method achieved a lesser amplification success rate of 70% (n = 20 for each treatment). More variable results were produced when field-derived exuviae were used, with no significant difference in real-time PCR amplification success found across the four methods and a lower overall rate of successful identification of 55-80%., Conclusions: This study shows that both colony and field derived Cx. pipiens pupal exuviae can be a useful non-invasive source of trace DNA permitting accurate biotype differentiation for at least twenty-four hours post-eclosion. The significance and utility of this technique in ecological and behavioural studies of Cx. pipiens is discussed and recommendations made for use according to experimental scenario., (© 2024. The Author(s).)

Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive genome profiling of 82 genes related to inherited retinal dystrophies. The PrismGuide IRD Panel System demonstrated 100% (n = 43) concordance with Sanger sequencing in detecting single-nucleotide variants, small insertions, and small deletions in the target genes and also in assessing their zygosity. It also identified copy-number loss in four out of five cases. When assessing precision, we evaluated the reproducibility of variant detection with 2,160 variants in 144 replicates and found 100% agreement in terms of single-nucleotide variants (n = 1,584) and small insertions and deletions (n = 576). Furthermore, the PrismGuide IRD Panel System generated sufficient read depth for variant calls across the purine-rich and highly repetitive open-reading frame 15 region of RPGR and detected all five variants tested. These results show that the PrismGuide IRD Panel System can accurately and consistently detect single-nucleotide variants and small insertions and deletions. Thus, the PrismGuide IRD Panel System could serve as useful tool that is applicable in clinical practice for identifying the causative genes based on the detection and interpretation of variants in patients with inherited retinal dystrophies and can contribute to a precise molecular diagnosis and targeted treatments., Competing Interests: The authors have the following interests. At the time of this research, JC, JH, JS, JR, GS, DM, VP, SC and EU were employed by Oxford Gene Technology Operations Limited, the founder of this study. TW and HS were employed by Riken Genesis Co. LTD, the founder of this study. YI, HN, YF, NA and TH were employed by Sysmex Corporation, the founder of this study. AM was employed by Kobe City Eye Hospital. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Chan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Long noncoding RNAs (lncRNAs) account for the largest portion of RNA from the transcriptome, yet most of their functions remain unknown. Here, we performed two independent high-throughput CRISPRi screens to understand the role of lncRNAs in monocyte function and differentiation. The first was a reporter-based screen to identify lncRNAs that regulate TLR4-NFkB signaling in human monocytes and the second screen identified lncRNAs involved in monocyte to macrophage differentiation. We successfully identified numerous noncoding and protein-coding genes that can positively or negatively regulate inflammation and differentiation. To understand the functional roles of lncRNAs in both processes, we chose to further study the lncRNA LOUP [lncRNA originating from upstream regulatory element of SPI1 (also known as PU.1)], as it emerged as a top hit in both screens. Not only does LOUP regulate its neighboring gene, the myeloid fate-determining factor SPI1 , thereby affecting monocyte to macrophage differentiation, but knockdown of LOUP leads to a broad upregulation of NFkB-targeted genes at baseline and upon TLR4-NFkB activation. LOUP also harbors three small open reading frames capable of being translated and are responsible for LOUP 's ability to negatively regulate TLR4/NFkB signaling. This work emphasizes the value of high-throughput screening to rapidly identify functional lncRNAs in the innate immune system., Competing Interests: Competing interests statement:S. Carpenter is a paid consultant for NextRNA Therapeutics.

We have previously experimentally observed high-power Stokes and second-order Stokes output from a mm-sized CaF 2 disk using stimulated Raman scattering. A pump laser at a wavelength of 1.06 µm was coupled via a tapered fiber to the whispering gallery modes (WGM) of the disk. In this Letter, we extend this work and demonstrate the production of the first anti-Stokes sideband at power levels as high as 60 µW in near continuous-wave (CW) operation. The result is a four-component Raman comb at the output, with a wavelength range covering from 1.023 to 1.14 µm. We discuss the threshold dependence of the observed Raman lines on the crystal orientation and provide experimental validation. These advances enable the use of such mm-sized resonators as compact, efficient sources for terahertz-level frequency modulation.

Abstract: Physical medicine and rehabilitation physicians often care for disabled patients, who comprise America's largest marginalized population. Despite medical students' and physicians' discomfort with caring for disabled patients and the pervasiveness of ableism in health care, medical education lacks disability-focused education. Kern's approach to curriculum development and disability community input were used to design a three-part, elective curriculum for first-year medical students. Part one introduced disability models and language. Part two described how to perform a comprehensive history and physical examination for a disabled patient using ADEPT-CARE. Part three provided an overview of disability history and the disability rights movement. The curriculum's goal was to improve students' attitudes regarding disability health and self-perceived knowledge and confidence in caring for patients with disabilities. The curriculum was evaluated through presurvey and postsurvey. Students favorably reviewed the curriculum. One hundred percent of students ( n = 21) agreed or strongly agreed that the curriculum improved their knowledge of disability health, increased their perceived confidence in caring for patients with disabilities, and enhanced their medical education. There were no statistically significant differences in students' attitudes toward patients with disabilities after curriculum completion. Our asynchronous module provides one potential curriculum for increasing preclinical medical students' self-perceived knowledge of disability health., Competing Interests: Financial disclosure statements have been obtained, and no conflicts of interest have been reported by the authors or by any individuals in control of the content of this article., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

To ensure a robust immune response to pathogens without risking immunopathology, the kinetics and amplitude of inflammatory gene expression in macrophages need to be exquisitely well controlled. There is a growing appreciation for stress-responsive membraneless organelles (MLOs) regulating various steps of eukaryotic gene expression in response to extrinsic cues. Here, we implicate the nuclear paraspeckle, a highly ordered biomolecular condensate that nucleates on the Neat1 lncRNA, in tuning innate immune gene expression in murine macrophages. In response to a variety of innate agonists, macrophage paraspeckles rapidly aggregate (0.5 h poststimulation) and disaggregate (2 h poststimulation). Paraspeckle maintenance and aggregation require active transcription and MAPK signaling, whereas paraspeckle disaggregation requires degradation of Neat1 via the nuclear RNA exosome. In response to lipopolysaccharide treatment, Neat1 KO macrophages fail to properly express a large cohort of proinflammatory cytokines, chemokines, and antimicrobial mediators. Consequently, Neat1 KO macrophages cannot control replication of Salmonella enterica serovar Typhimurium or vesicular stomatitis virus. These findings highlight a prominent role for MLOs in orchestrating the macrophage response to pathogens and support a model whereby dynamic assembly and disassembly of paraspeckles reorganizes the nuclear landscape to enable inflammatory gene expression following innate stimuli., Competing Interests: Competing interests statement:The authors declare no competing interest.

Introduction: Bluetongue virus (BTV) is an arthropod-borne Orbivirus that is almost solely transmitted by Culicoides biting midges and causes a globally important haemorrhagic disease, bluetongue (BT), in susceptible ruminants. Infection with BTV is characterised by immunosuppression and substantial lymphopenia at peak viraemia in the host., Methods: In this study, the role of cell-mediated immunity and specific T-cell subsets in BTV pathogenesis, clinical outcome, viral dynamics, immune protection, and onwards transmission to a susceptible Culicoides vector is defined in unprecedented detail for the first time, using an in vivo arboviral infection model system that closely mirrors natural infection and transmission of BTV. Individual circulating CD4 + , CD8 + , or WC1 + γδ T-cell subsets in sheep were depleted through the administration of specific monoclonal antibodies., Results: The absence of cytotoxic CD8 + T cells was consistently associated with less severe clinical signs of BT, whilst the absence of CD4 + and WC1 + γδ T cells both resulted in an increased clinical severity. The absence of CD4 + T cells also impaired both a timely protective neutralising antibody response and the production of IgG antibodies targeting BTV non-structural protein, NS2, highlighting that the CD4 + T-cell subset is important for a timely protective immune response. T cells did not influence viral replication characteristics, including onset/dynamics of viraemia, shedding, or onwards transmission of BTV to Culicoides . We also highlight differences in T-cell dependency for the generation of immunoglobulin subclasses targeting BTV NS2 and the structural protein, VP7., Discussion: This study identifies a diverse repertoire of T-cell functions during BTV infection in sheep, particularly in inducing specific anti-viral immune responses and disease manifestation, and will support more effective vaccination strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Newbrook, Khan, Fisher, Chong, Gubbins, Davies, Sanders, Busquets, Cooke, Corla, Ashby, Flannery, Batten, Stokes, Sanz-Bernardo, Carpenter, Moffat and Darpel.)

Competing Interests: We declare no competing interests. This paper was supported by the Natural Sciences and Engineering Research Council of Canada and Carleton University. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government. SJC is supported by the Natural Sciences and Engineering Research Council of Canada (319774) and Carleton University.