Safety and efficacy of ivacaftor in infants aged 1 to less than 4 months with cystic fibrosis.

BACKGROUND: Ivacaftor (IVA) has been shown to be safe and efficacious in children aged ≥4 months with cystic fibrosis (CF) and CFTR gating variants. We evaluated safety, pharmacokinetics (PK), and efficacy of IVA in a small cohort of infants aged 1 to <4 months with CF. METHODS: In this phase 3, open-label study, infants 1 to <4 months with CF and an IVA-responsive CFTR variant received an initial low dose of IVA based on age and weight. Because IVA is a sensitive CYP3A substrate and CYP3A maturation is uncertain in infants, doses were adjusted at day 15 to better match median adult exposures based on individual PK measurements taken on day 4. Primary endpoints were safety and PK measurements. RESULTS: Seven infants (residual function CFTR variants [n=5]; minimal function CFTR variants [n=2]) received ≥1 dose of IVA. Six infants had doses adjusted at day 15 and one infant did not require dose adjustment; subsequent PK analyses showed mean trough concentrations for IVA and metabolites were within range of prior clinical experience. Four infants (57.1%) had adverse events (AEs); no serious AEs were noted. One infant discontinued study drug due to a non-serious AE of elevated alanine aminotransferase >8x the upper limit of normal. Mean sweat chloride concentration decreased (-40.3 mmol/L [SD: 29.2]) through week 24. Improvements in biomarkers of pancreatic function and intestinal inflammation, as well as growth parameters, were observed. CONCLUSIONS: In this small, open-label study, IVA dosing in infants achieved exposures previously shown to be safe and efficacious. Because PK was predictable, a dosing regimen based on age and weight is proposed. IVA was generally safe and well tolerated, and led to improvements in CFTR function, markers of pancreatic function and intestinal inflammation, and growth parameters, supporting use in infants as young as 1 month of age.

Is the "Pandemic Diet" Nonlithogenic?

Introduction and Objective: The COVID-19 pandemic and worldwide quarantine resulted in major changes in individual lifestyles. In New York State, March 16, 2020, marked the end of in-restaurant dining and a reported shift to more cooking at home. We investigated the 24-hour urine of patients with known history of nephrolithiasis to see if changes during COVID-19 pandemic altered the risk of stone disease. Methods: Retrospectively, patients with history of nephrolithiasis seen for an outpatient visit from April 1, 2020, to December 31, 2020, were studied. All patients had a 24-hour urine study "pre-COVID" defined as before March 16, 2020, "during-COVID" from March 16, 2020, to December 31, 2020; if available, "post-COVID" from January 1, 2021, to October 31, 2022, was also included. Mean study values were compared using paired, two-tailed t-tests. Results: Ninety-three patients (M = 54, F = 39) with a mean age of 60 years were evaluated. Twenty-four-hour urine revealed a significant reduction in urinary sodium (uNa) levels from pre-COVID (166.15 ± 7.51 mEq/L) compared with during-COVID (149.09 ± 7.55 mEq/L) (p = 0.015) and urinary calcium (uCa) levels from pre-COVID (214.18 ± 13.05 mg) compared with during-COVID (191.48 ± 13.03 mg) (p = 0.010). Post-COVID 24-hour urine (N = 73) levels for uNa (138.55 ± 6.83 mEq/L, p = 0.0035) and uCa (185.33 ± 12.61 mg, p = 0.012) remained significantly reduced compared with pre-COVID values, but with no difference compared with during-COVID values. Upon age stratification, this significance was found only in patients younger than 65. There were no significant differences in 24-hour urine total volume, magnesium, or citrate levels. Conclusions: During the COVID-19 lockdown, dietary choices limited to home-cooked meals allowed patients to better identify their food choices. This study demonstrates that home-cooked meals improved urinary parameters minimizing lithogenic risk factors for stone formation, including hypernatriuria and hypercalciuria. That these changes persisted into the post-COVID period may indicate improved dietary practices after the lockdown ended.

Novel metagenomics analysis of stony coral tissue loss disease.

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared to a prior metagenome analysis of the same dataset.

Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolution.

Following prolonged cell division, mesenchymal stem cells enter replicative senescence, a state of permanent cell cycle arrest that constrains the use of this cell type in regenerative medicine applications and that in vivo substantially contributes to organismal ageing. Multiple cellular processes such as telomere dysfunction, DNA damage and oncogene activation are implicated in promoting replicative senescence, but whether mesenchymal stem cells enter different pre-senescent and senescent states has remained unclear. To address this knowledge gap, we subjected serially passaged human ESC-derived mesenchymal stem cells (esMSCs) to single cell profiling and single cell RNA-sequencing during their progressive entry into replicative senescence. We found that esMSC transitioned through newly identified pre-senescent cell states before entering into three different senescent cell states. By deconstructing this heterogeneity and temporally ordering these pre-senescent and senescent esMSC subpopulations into developmental trajectories, we identified markers and predicted drivers of these cell states. Regulatory networks that capture connections between genes at each timepoint demonstrated a loss of connectivity, and specific genes altered their gene expression distributions as cells entered senescence. Collectively, this data reconciles previous observations that identified different senescence programs within an individual cell type and should enable the design of novel senotherapeutic regimes that can overcome in vitro MSC expansion constraints or that can perhaps slow organismal ageing.

Practice Patterns Affecting Delays in Care of Testicular Torsion.

OBJECTIVES: To compare impact of day or on-call team, pediatric or adult attending, and patient age on testicular torsion management and outcomes. METHODS: A retrospective study of patients with testicular torsion between 2012 and 2022 at a single institution was conducted. Variables impacting management time were assessed using univariate analyses. RESULTS: One hundred and thirty-four patients were included: 49 underwent orchiectomies and 84 underwent orchiopexies. There was no significant difference between efficiency of on-call vs day team regarding time to ultrasound or time to operating room (OR). There were no significant differences between pediatric vs adult attending surgeons for time to surgery, intraoperative length of surgery, or testicular salvage rates. However, when patients were stratified by age greater or younger than 18years, older patients had significantly longer symptom duration (91.9 vs 20.0 minutes, P = .005), time to receive an ultrasound from emergency room registration (152 vs 87 minutes, P < .001), time to OR from emergency room registration (268 vs 185 minutes, P < .001), and time to OR from ultrasound read (187 vs 123 minutes, P = .03). Older patients also had lower rates of testicular salvage approaching significance (orchiectomy rate 48.8% vs 31.5%, P = .057). CONCLUSION: While no significant delays in testicular torsion management were detected between management by on-call vs day team nor pediatric vs adult attending, increased age of patient was associated with delays in definitive surgical management. Greater index of suspicion for testicular torsion diagnosis in adult patients may improve the rate of testicular salvage.

Surgical Drain-Related Small Bowel Obstruction After Open Radical Cystoprostatectomy: A Case Report.

Surgical drains are commonly used to manage intraperitoneal fluid after major surgeries, but their prophylactic use has been controversial due to potential complications. One rarely reported complication is small bowel obstruction (SBO), primarily seen in post-colorectal surgeries. We present a case of SBO following open radical cystectomy due to surgical drain placement, a complication not previously reported in urologic surgeries. The case highlights the importance of considering the risks and benefits of prophylactic drain placement. It emphasizes the need for a higher index of suspicion for SBO in patients with surgical drains who develop post-operative nausea and distention. Timely radiological imaging and clinical examination are crucial for accurate diagnosis and proper treatment.

Clinical significance of Nosocomiicoccus ampullae isolated from blood cultures.

IMPORTANCE: Nosocomiicoccus species are recently described as members of the Staphylococcaceae family. With their inclusion in commercial matrix-assisted laser desorption/ionization-time of flight mass spectrometry databases, Nosocomiicoccus species can now be identified when Gram-positive cocci in clusters are detected in positive blood cultures. However, their clinical significance is not known, making it difficult for the clinical microbiology laboratory to decide the extent of work-up. Based on our study, Nosocomiicoccus species demonstrate low pathogenicity and opportunistic potential. If isolated from a single blood culture set, limited work-up should be performed to an extent similar to other possible blood culture contaminants.

Major data analysis errors invalidate cancer microbiome findings.

IMPORTANCE: Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid.

Major data analysis errors invalidate cancer microbiome findings.

We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (1) errors in the genome database and the associated computational methods led to millions of false positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (2) errors in transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well.

Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids.

Objectives: Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. A better understanding of the molecular epidemiology and transmission dynamics of CRE is necessary to limit their dissemination within healthcare settings. We sought to investigate the mechanisms of resistance and spread of CRE within multiple hospitals in Maryland. Methods: From 2016 to 2018, all CRE were collected from any specimen source from The Johns Hopkins Medical Institutions. The isolates were further characterized using both phenotypic and genotypic approaches, including short- and/or long-read WGS. Results: From 2016 to 2018, 302 of 40 908 (0.7%) unique Enterobacterales isolates were identified as CRE. Of CRE, 142 (47%) were carbapenemase-producing CRE with KPC (80.3%) predominating among various genera. Significant genetic diversity was identified among all CRE with high-risk clones serving as major drivers of clonal clusters. Further, we found the predominance of pUVA-like plasmids, with a subset harbouring resistance genes to environmental cleaning agents, involved in intergenus dissemination of blaKPC genes. Conclusions: Our findings provide valuable data to understand the transmission dynamics of all CRE within the greater Maryland region. These data can help guide targeted interventions to limit CRE transmission in healthcare facilities.

Impacts of ruthenium valence state on the electrocatalytic activity of ruthenium ion-complexed graphitic carbon nitride/reduced graphene oxide nanosheets towards hydrogen evolution reaction.

Design and engineering of effective electrode catalysts represents a critical first step for hydrogen production by electrochemical water splitting. Nanocomposites based on ruthenium atomically dispersed within a carbon scaffold have emerged as viable candidates. In the present study, ruthenium metal centers are atomically embedded within graphitic carbon nitride/reduced graphene oxide nanosheets by thermal refluxing. Subsequent chemical reduction/oxidation leads to ready manipulation of the ruthenium valence state, as evidenced in microscopic and spectroscopic measurements, and hence enhancement/diminishment of the electrocatalytic activity towards hydrogen evolution reaction in both acidic and alkaline media. This is largely ascribed to the increased/reduced contribution of the Ru valence electrons to the density of state near the Fermi level which dictates the binding and reduction of hydrogen. Results from this study highlight the significance of the valence state of metal centers in the manipulation and optimization of the catalytic performance of single atom catalysts.

Stable Cuprous Hydroxide Nanostructures by Organic Ligand Functionalization.

Copper compounds have been extensively investigated for diverse applications. However, studies of cuprous hydroxide (CuOH) have been scarce due to structural metastability. Herein, a facile, wet-chemistry procedure is reported for the preparation of stable CuOH nanostructures via deliberate functionalization with select organic ligands, such as acetylene and mercapto derivatives. The resulting nanostructures are found to exhibit a nanoribbon morphology consisting of small nanocrystals embedded within a largely amorphous nanosheet-like scaffold. The acetylene derivatives are found to anchor onto the CuOH forming CuC linkages, whereas CuS interfacial bonds are formed with the mercapto ligands. Effective electronic coupling occurs at the ligand-core interface in the former, in contrast to mostly non-conjugated interfacial bonds in the latter, as manifested in spectroscopic measurements and confirmed in theoretical studies based on first principles calculations. Notably, the acetylene-capped CuOH nanostructures exhibit markedly enhanced photodynamic activity in the inhibition of bacteria growth, as compared to the mercapto-capped counterparts due to a reduced material bandgap and effective photocatalytic generation of reactive oxygen species. Results from this study demonstrate that deliberate structural engineering with select organic ligands is an effective strategy in the stabilization and functionalization of CuOH nanostructures, a critical first step in exploring their diverse applications.

Metagenome analysis using the Kraken software suite.

Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.

Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis.

In fragmented DNA, PCR-based methods quantify the number of intact regions at a specific amplicon length. However, the relationship between the population of DNA fragments within a sample and the likelihood they will amplify has not been fully described. To address this, we have derived a mathematical equation that relates the distribution profile of a stochastically fragmented DNA sample to the probability that a DNA fragment within that sample can be amplified by any PCR assay of arbitrary length. Two panels of multiplex PCR assays for quantifying fragmented DNA were then developed: a four-plex panel that can be applied to any human DNA sample and used to estimate the percentage of regions that are intact at any length; and a two-plex panel optimized for quantifying circulating cell-free DNA (cfDNA). For these assays, regions of the human genome least affected by copy number aberration were identified and selected; within these copy-neutral regions, each PCR assay was designed to amplify both genomic and bisulfite-converted DNA; and all assays were validated for use in both conventional qPCR and droplet-digital PCR. Finally, using the cfDNA-optimized assays we find evidence of universally conserved nucleosome positioning among individuals.

Poly(1,5-diaminonaphthalene)-Grafted Monolithic 3D Hierarchical Carbon as Highly Capacitive and Stable Supercapacitor Electrodes.

A holistic approach to fabricate a hierarchical electrode that consists of redox-active poly(1,5-diaminonaphthalene), 1,5 PDAN, uniformly and conformally grafted onto a 3D carbon nanotube (CNT-a-CC) electrode is set forth. The CNT-a-CC electrode was formed by direct growth of high-density CNTs on the surface of every individual microfiber, the constituent of activated carbon cloth (a-CC). Owing to the naphthalene backbone, conformal deposition of 1,5 PDAN on carbon surfaces has been readily attained via electropolymerization. This hierarchical platform with open and continuous nanochannels formed by CNTs coupled with excellent electrical connectivity between CNTs and the polymer provides a reproducible platform for electrochemical investigation. According to multiple sample analyses on CNT-a-CC, the gravimetric capacitance of 1,5 PDAN is up to 1250 F/g, and this value can be maintained up to 100 mV/s. Hierarchical organization provides a specific capacitance of 650 F/g at 2 mV/s at a 1,5 PDAN loading of 2.5 mg/cm2. The conjugated ladder structure of the polymer led to strong π-π interactions between the polymer and CNT-a-CC together with mechanically robust CNT-a-CC. A capacitance retention of 94% for 1,5 PDAN has been obtained after 25,000 cycles at 100 mV/s, a significant cycle stability improvement over conventional conductive polymers such as polyaniline. This new lightweight electrode that seamlessly integrates functional species with nanochannel-like CNT-a-CC opens up a new opportunity to harness electrochemical reactions in the 3D carbon electrode for energy storage and electrocatalysis as well as electrochemical sensing.

Directional, Low-Energy Driven Thermal Actuating Bilayer Enabled by Coordinated Submolecular Switching.

The authors reveal a thermal actuating bilayer that undergoes reversible deformation in response to low-energy thermal stimuli, for example, a few degrees of temperature increase. It is made of an aligned carbon nanotube (CNT) sheet covalently connected to a polymer layer in which dibenzocycloocta-1,5-diene (DBCOD) actuating units are oriented parallel to CNTs. Upon exposure to low-energy thermal stimulation, coordinated submolecular-level conformational changes of DBCODs result in macroscopic thermal contraction. This unique thermal contraction offers distinct advantages. It's inherently fast, repeatable, low-energy driven, and medium independent. The covalent interface and reversible nature of the conformational change bestow this bilayer with excellent repeatability, up to at least 70 000 cycles. Unlike conventional CNT bilayer systems, this system can achieve high precision actuation readily and can be scaled down to nanoscale. A new platform made of poly(vinylidene fluoride) (PVDF) in tandem with the bilayer can harvest low-grade thermal energy and convert it into electricity. The platform produces 86 times greater energy than PVDF alone upon exposure to 6 °C thermal fluctuations above room temperature. This platform provides a pathway to low-grade thermal energy harvesting. It also enables low-energy driven thermal artificial robotics, ultrasensitive thermal sensors, and remote controlled near infrared (NIR) driven actuators.

Prototypical Study of Double-Layered Cathodes for Aqueous Rechargeable Static Zn-I2 Batteries.

Aqueous rechargeable zinc-iodine batteries (ZIBs) are promising candidates for grid energy storage because they are safe and low-cost and have high energy density. However, the shuttling of highly soluble triiodide ions severely limits the device's Coulombic efficiency. Herein, we demonstrate for the first time a double-layered cathode configuration with a conductive layer (CL) coupled with an adsorptive layer (AL) for ZIBs. This unique cathode structure enables the formation and reduction of adsorbed I3- ions at the CL/AL interface, successfully suppressing triiodide ion shuttling. A prototypical ZIB using a carbon cloth as the CL and a polypyrrole layer as the AL simultaneously achieves outstanding Coulombic efficiency (up to 95.6%) and voltage efficiency (up to 91.3%) in the aqueous ZnI2 electrolyte even at high-rate intermittent charging/discharging, without the need of ion selective membranes. These findings provide new insights to the design and fabrication of ZIBs and other batteries based on conversion reactions.

Printing Porous Carbon Aerogels for Low Temperature Supercapacitors.

Maintaining fast charging capability at low temperatures represents a significant challenge for supercapacitors. The performance of conventional porous carbon electrodes often deteriorates quickly with the decrease of temperature due to sluggish ion and charge transport. Here we fabricate a 3D-printed multiscale porous carbon aerogel (3D-MCA) via a unique combination of chemical methods and the direct ink writing technique. 3D-MCA has an open porous structure with a large surface area of ∼1750 m2 g-1. At -70 °C, the symmetric device achieves outstanding capacitance of 148.6 F g-1 at 5 mV s-1. Significantly, it retains a capacitance of 71.4 F g-1 at a high scan rate of 200 mV s-1, which is 6.5 times higher than the non-3D printed MCA. These values rank among the best results reported for low temperature supercapacitors. These impressive results highlight the essential role of open porous structures for preserving capacitive performance at ultralow temperatures.

Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach.

Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. Methods: Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. Results: We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria ( Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), two cases with fungi ( Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. Conclusions: Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.