DOE JGI Metagenome Workflow.

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A.

Cementocyte alterations associated with experimentally induced cellular cementum apposition in Hyp mice.

Background: Cellular cementum, a mineralized tissue covering apical tooth roots, grows by apposition to maintain the tooth in its occlusal position. We hypothesized that resident cementocytes would show morphological changes in response to cementum apposition, possibly implicating a role in cementum biology.

Methods: Mandibular first molars were induced to super-erupt (EIA) by extraction of maxillary molars, promoting rapid new cementum formation.

Long-Term Care of the Pediatric Kidney Transplant Recipient.

Pediatric kidney transplant recipients are distinguished from adult recipients by the need for many decades of graft function, the potential effect of CKD on neurodevelopment, and the changing immune environment of a developing human. The entire life of an individual who receives a transplant as a child is colored by their status as a transplant recipient. Not only must these young recipients negotiate all of the usual challenges of emerging adulthood (transition from school to work, romantic relationships, achieving independence from parents), but they must learn to manage a life-threatening medical condition independently.

Effects of Active Vitamin D or FGF23 Antibody on Mice Dentoalveolar Tissues.

Mutations in the gene lead to X-linked hypophosphatemia (XLH), a form of inherited rickets featuring elevated fibroblast growth factor 23 (FGF23), reduced 1,25-dihydroxyvitamin D (1,25D), and hypophosphatemia. mutant mice replicate the XLH phenotype, including dentin, alveolar bone, and cementum defects. We aimed to compare effects of 1,25D versus FGF23-neutralizing antibody (FGF23Ab) monotherapies on mouse dentoalveolar mineralization.

A single-cell genomics pipeline for environmental microbial eukaryotes.

Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break.

Near-field airborne particle concentrations in young children undergoing high-flow nasal cannula therapy: a pilot study.

Background: High-flow nasal cannula therapy (HFNC) may increase aerosol generation, putting healthcare workers at risk, including from SARS-CoV-2.

Aim: To examine whether use of HFNC increases near-field aerosols and whether there is an association with flow rate.

Methods: Subjects aged four weeks to 24 months were recruited.

Deficiency of optineurin enhances osteoclast differentiation by attenuating the NRF2-mediated antioxidant response.

Abnormally increased resorption contributes to bone degenerative diseases such as Paget's disease of bone (PDB) through unclear mechanisms. Recently, the optineurin (OPTN) gene has been implicated in PDB, and global OPTN knockout mice (Optn) were shown to exhibit increased formation of osteoclasts (osteoclastogenesis). Growing evidence, including our own, has demonstrated that intracellular reactive oxygen species (ROS) stimulated by receptor activator of nuclear factor kappa-B ligand (RANKL) can act as signaling molecules to promote osteoclastogenesis.

Delivery of Alkaline Phosphatase Promotes Periodontal Regeneration in Mice.

Factors regulating the ratio of pyrophosphate (PP) to phosphate (P) modulate biomineralization. Tissue-nonspecific alkaline phosphatase (TNAP) is a key promineralization enzyme that hydrolyzes the potent mineralization inhibitor PP. The goal of this study was to determine whether TNAP could promote periodontal regeneration in bone sialoprotein knockout mice ( mice), which are known to have a periodontal disease phenotype.

Daptomycin-Induced Acute Eosinophilic Pneumonia.

Antibiotic use in pneumonia is a common practice globally when there is suspicion for bacterial involvement. However, there have been few instances where the treatment is the cause of pulmonary symptoms, manifesting as so-called "multifocal pneumonia." Daptomycin is one of the main antibiotics known to have several adverse effects, including drug-induced pulmonary eosinophila.

Guidelines for Micro-Computed Tomography Analysis of Rodent Dentoalveolar Tissues.

Micro-computed tomography (μCT) has become essential for analysis of mineralized as well as nonmineralized tissues and is therefore widely applicable in the life sciences. However, lack of standardized approaches and protocols for scanning, analyzing, and reporting data often makes it difficult to understand exactly how analyses were performed, how to interpret results, and if findings can be broadly compared with other models and studies. This problem is compounded in analysis of the dentoalveolar complex by the presence of four distinct mineralized tissues: enamel, dentin, cementum, and alveolar bone.

Adenomyosis in Pregnancy: Diagnostic Pearls and Pitfalls.

Adenomyosis is a common benign uterine disorder in which ectopic endometrial glands extend into the myometrium. Adenomyosis is increasingly diagnosed in young women, affecting 20%-35% of women of reproductive age. Features of adenomyosis can be seen with either US or MRI, especially with newer imaging technology.

An Unusual Presentation of COVID-19: Hemorrhagic Pericardial Effusion With Tamponade Physiology.

A 44-year-old woman with a history of factor V Leiden deficiency and recurrent pulmonary emboli was diagnosed with coronavirus disease 2019 (COVID-19) three weeks prior presented to her local ED with severe chest pain. She was found to have a large hemorrhagic pericardial effusion by cardiac MRI with echocardiographic signs of tamponade. She underwent the creation of a pericardial window and was treated with colchicine with improvement in symptoms.

An Integrated Clinical and Genetic Prediction Model for Tacrolimus Levels in Pediatric Solid Organ Transplant Recipients.

Background: There are challenges in achieving and maintaining therapeutic tacrolimus levels after solid organ transplantation (SOT). The purpose of this genome-wide association study was to generate an integrated clinical and genetic prediction model for tacrolimus levels in pediatric SOT.

Methods: In a multicenter prospective observational cohort study (2015-2018), children <18 years old at their first SOT receiving tacrolimus as maintenance immunosuppression were included (455 as discovery cohort; 322 as validation cohort).

In-Bore Versus Fusion MRI-Targeted Biopsy of PI-RADS Category 4 and 5 Lesions: A Retrospective Comparative Analysis Using Propensity Score Weighting.

Few published studies have compared in-bore and fusion MRI-targeted prostate biopsy, and the available studies have had conflicting results. The purpose of this study was to compare the target-specific cancer detection rate of in-bore prostate biopsy with that of fusion MRI-targeted biopsy. The records of men who underwent in-bore or fusion MRI-targeted biopsy of PI-RADS category 4 or 5 lesions between August 2013 and September 2019 were retrospectively identified.

Effect of vitrification on global gene expression dynamics of bovine elongating embryos.

Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming in the cryopreservation process. Many of these factors can potentially affect gene expression. In this study, invitro-produced bovine embryos at the blastocyst stage were subjected to vitrification.

Enhanced BMP signalling causes growth plate cartilage dysrepair in rats.

Growth plate cartilage injuries often result in bony repair at the injury site and premature mineralisation at the uninjured region causing bone growth defects, for which underlying mechanisms are unclear. With the prior microarray study showing upregulated bone morphogenetic protein (BMP) signalling during the injury site bony repair and with the known roles of BMP signalling in bone healing and growth plate endochondral ossification, this study used a rat tibial growth plate drill-hole injury model with or without systemic infusion of BMP antagonist noggin to investigate roles of BMP signalling in injury repair responses within the injury site and in the adjacent "uninjured" cartilage. At days 8, 14 and 35 post-injury, increased expression of BMP members and receptors and enhanced BMP signalling (increased levels of phosphorylated (p)-Smad1/5/8) were found during injury site bony repair.

Ultradeep sequencing differentiates patterns of skin clonal mutations associated with sun-exposure status and skin cancer burden.

In ultraviolet (UV) radiation-exposed skin, mutations fuel clonal cell growth. The relationship between UV exposure and the accumulation of clonal mutations (CMs) and the correlation between CMs and skin cancer risk are largely unexplored. We characterized 450 individual-matched sun-exposed (SE) and non-SE (NE) normal human skin samples.

The Expanding Scope, Inclusivity, and Integration of Music in Healthcare: Recent Developments, Research Illustration, and Future Direction.

This paper is in three sections. Section One presents a historical overview of international initiatives that have expanded the role of music in healthcare, from the initial formalization of music therapy to its more research-based rehabilitation focus to recent decades that have seen an increasing role for professional and community musicians, paraprofessional music services, music-oriented service organizations, and a very large increase in medical funding for music effects. "Music Care" is a particular and comprehensive concept promoted by the Room 217 Foundation in Canada, featuring an inclusive and integrated approach to optimizing the use of music in healthcare settings.

CD117/c-kit defines a prostate CSC-like subpopulation driving progression and TKI resistance.

Cancer stem-like cells (CSCs) are associated with cancer progression, metastasis, and recurrence, and may also represent a subset of circulating tumor cells (CTCs). In our prior study, CTCs in advanced prostate cancer patients were found to express CD117/c-kit in a liquid biopsy. Whether CD117 expression played an active or passive role in the aggressiveness and migration of these CTCs remained an open question.

A Phase II Trial of Imatinib Mesylate as Maintenance Therapy for Patients With Newly Diagnosed C-kit-positive Acute Myeloid Leukemia.

Introduction: Adults with acute myeloid leukemia (AML) have a high rate of remission; however, more than 50% relapse. C-kit is expressed in approximately 60% of patients with de novo AML and represents a potential therapeutic target.

Materials And Methods: Patients with newly diagnosed AML received 12 months of imatinib mesylate as maintenance therapy after the completion of post-remission therapy.

Age and sex determine conversion from immediate-release to extended-release tacrolimus in a multi-center cohort of Canadian pediatric renal transplant recipients.

ER-Tac, taken once per day, is associated with improved adherence. This study examined the potential patient and clinical factors that influence clinicians to convert pediatric patients from immediate-release to ER-Tac. This prospective multi-center observational study followed Canadian pediatric kidney transplant recipients up to 5 years post-transplant.

Ablation of Pyrophosphate Regulators Promotes Periodontal Regeneration.

Biomineralization is regulated by inorganic pyrophosphate (PP), a potent physiological inhibitor of hydroxyapatite crystal growth. Progressive ankylosis protein (ANK) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) act to increase local extracellular levels of PP, inhibiting mineralization. The periodontal complex includes 2 mineralized tissues, cementum and alveolar bone (AB), both essential for tooth attachment.