Predictive Value of Diaphragm Muscle Ultrasound for Ventilator Weaning Outcomes After Cervical Spinal Cord Injury: A Retrospective Case Series.

OBJECTIVES: Neuromuscular respiratory failure after cervical spinal cord injury (cSCI) can lead to dependence on an invasive mechanical ventilator. Ventilator-free breathing after cSCI is associated with improved morbidity, mortality, and quality of life. We investigated the use of diaphragm muscle ultrasound to predict ventilator weaning outcomes after cSCI. METHODS: This is a retrospective case series conducted at a university-affiliated freestanding inpatient rehabilitation facility. We identified patients with cSCI who had a tracheostomy and were dependent on an invasive mechanical ventilator at the time of admission to inpatient rehabilitation. A diaphragm muscle ultrasound was performed, which included measurements of the thickness of the diaphragm and a calculation of the thickening ratio (TR), which reflects diaphragm muscle contraction. The primary outcome measure was the need for mechanical ventilation at time of discharge from the inpatient rehabilitation facility. Successful ventilator weaning was defined as either daytime or full 24-hour ventilator-free breathing. RESULTS: Of the 21 patients enrolled, 11 (52%) were able to wean successfully (partially or fully) from the ventilator. Of the ultrasound measurements that were taken, the TR was the optimal predictor for ventilator weaning outcomes. A threshold of TR ≥ 1.2 as the maximum hemidiaphragm measurement had a sensitivity of 1.0 and specificity of 0.90 for predicting ventilator weaning. CONCLUSION: Normal diaphragm contractility (TR ≥ 1.2) as determined by diaphragm muscle ultrasound is a strong positive predictor for successful ventilator weaning in patients with cSCI. Utilizing diaphragm ultrasound, rehabilitation physicians can set precision rehabilitation goals regarding ventilator weaning for inpatients with respiratory failure after cSCI, potentially improving both outcomes and quality of life.

A secondary ß-hydroxybutyrate metabolic pathway linked to energy balance.

ß-hydroxybutyrate (BHB) is an abundant ketone body. To date, all known pathways of BHB metabolism involve interconversion of BHB and primary energy intermediates. Here we show that CNDP2 controls a previously undescribed secondary BHB metabolic pathway via enzymatic conjugation of BHB and free amino acids. This BHB-ylation reaction produces a family of endogenous ketone metabolites, the BHB-amino acids. Genetic ablation of CNDP2 in mice eliminates tissue amino acid BHB-ylation activity and reduces BHB-amino acid levels. Administration of BHB-Phe, the most abundant BHB-amino acid, to obese mice activates neural populations in the hypothalamus and brainstem and suppresses feeding and body weight. Conversely, CNDP2-KO mice exhibit increased food intake and body weight upon ketosis stimuli. CNDP2-dependent amino acid BHB-ylation and BHB-amino acid metabolites are also conserved in humans. Therefore, the metabolic pathways of BHB extend beyond primary metabolism and include secondary ketone metabolites linked to energy balance.

Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.

Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers of samples poses many challenges, with cross-contamination being the biggest obstacle. Contamination complicates analysis and results in sample loss, leading to higher costs and constraints on mixed sample type study designs. While many researchers opt for 96-well plates for their workflows, these plates present a significant issue: the shared seal and weak separation between wells leads to well-to-well contamination. To address this concern, we propose an innovative high-throughput approach, termed as the Matrix method, which employs barcoded Matrix Tubes for sample acquisition. This method is complemented by a paired nucleic acid and metabolite extraction, utilizing 95% (vol/vol) ethanol to stabilize microbial communities and as a solvent for extracting metabolites. Comparative analysis between conventional 96-well plate extractions and the Matrix method, measuring 16S rRNA gene levels via quantitative polymerase chain reaction, demonstrates a notable decrease in well-to-well contamination with the Matrix method. Metagenomics, 16S rRNA gene amplicon sequencing (16S), and untargeted metabolomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed that the Matrix method recovers reproducible microbial and metabolite compositions that can distinguish between subjects. This advancement is critical for large-scale study design as it minimizes well-to-well contamination and technical variation, shortens processing times, and integrates with automated infrastructure for enhancing sample randomization and metadata generation. IMPORTANCE: Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.

Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology.

BACKGROUND: The gut microbiome is a potentially modifiable factor in Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited. METHODS: Shallow-shotgun metagenomic data was used to analyze fecal microbiome from participants enrolled in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies. RESULTS: Gut microbiome composition and function differed between people with AD and cognitively unimpaired individuals. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies. DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

Investigating the Effect of Bacilli and Lactic Acid Bacteria on Water Quality, Growth, Survival, Immune Response, and Intestinal Microbiota of Cultured Litopenaeus vannamei.

Shrimp is one of the most important aquaculture industries. Therefore, we determined the effect of nitrifying-probiotic bacteria on water quality, growth, survival, immune response, and intestinal microbiota of Litopenaeus vannamei cultured without water exchange. In vitro, only Bacillus licheniformis used total ammonia nitrogen (TAN), nitrites, and nitrates since nitrogen bubbles were produced. TAN decreased significantly in the treatments with B. licheniformis and Pediococcus pentosaceus and Leuconostoc mesenteroides, but no differences were observed in nitrites. Nitrates were significantly higher in the treatments with bacteria. The final weight was higher only with bacilli and bacilli and LAB treatments. The survival of shrimp in the bacterial treatments increased significantly, and superoxide anion increased significantly only in lactic acid bacteria (LAB) treatment. The activity of phenoloxidase decreased significantly in the treatments with bacteria compared to the control. Shrimp treated with bacilli in the water showed lower species richness. The gut bacterial community after treatments was significantly different from that of the control. Linoleic acid metabolism was positively correlated with final weight and superoxide anion, whereas quorum sensing was correlated with survival. Thus, bacilli and LAB in the water of hyperintensive culture systems act as heterotrophic nitrifers, modulate the intestinal microbiota and immune response, and improve the growth and survival of shrimp. This is the first report on P. pentosaceus and L. mesenteroides identified as nitrifying bacteria.

Comparative Study of Bacillus-Based Plant Biofertilizers: A Proposed Index.

The market for bacteria as agricultural biofertilizers is growing rapidly, offering plant-growth stimulants; biofungicides; and, more recently, protectors against extreme environmental factors, such as drought. This abundance makes it challenging for the end user to decide on the product to use. In this work, we describe the isolation of a strain of Bacillus velezensis (belonging to the operational group Bacillus amyloliquefaciens) for use as a plant-growth-promoting rhizobacterium, a biofungicide, and a protector against drought. To compare its effectiveness with other commercial strains of the same operational group, Bacillus amyloliquefaciens, we analyzed its ability to promote the growth of pepper plants and protect them against drought, as well as its fungicidal activity through antibiosis and antagonism tests, its ability to solubilize potassium and phosphates, and its ability to produce siderophores. Finally, we used a probit function, a type of regression analysis used to model the outcomes of analyses, to quantify the biostimulatory effectiveness of the different plant-growth-promoting rhizobacteria, developing what we have called the Agricultural Protection Against Stress Index, which allowed us to numerically compare the four commercial strains of the operational group Bacillus amyloliquefaciens, based on a Delphi method-a type of regression analysis that can be used to model a cumulative normal distribution-and integrate the results from our panel of tests into a single value.

Enhancing Ecological Validity: Virtual Reality Assessment of Executive Functioning in Children and Adolescents with ADHD.

BACKGROUND: SmartAction-VR uses virtual reality to simulate daily life tasks and assess cognitive performance based on the multi-errand paradigm. This study explored whether this new task could provide insights into the executive functioning of children and adolescents with ADHD in their everyday activities. METHODS: A cross-sectional study was conducted between November 2021 and December 2022. It consisted of one session and was divided into two parts (cognitive tests; and SmartAction-VR). The sample comprised 76 children and adolescents with a median age (IQR) of 13 (11-14) years and an age range of 9-17 years. Of these participants, 60.50% (n = 46) were males. Out of this sample, 40 participants were in the ADHD group and 36 were in the neurotypical group. The following instruments were used: Waisman Activities of Daily Living Scale, Assessment of Sensory Processing and Executive Functioning, Pediatric Simulator Disease Questionnaire, Digit span subtest, Stroop test, NEPSY-II Subtest of Auditory Attention and Cognitive Flexibility, Trail Making Test, Zoo Map Test, and SmartAction-VR. RESULTS: The ADHD group demonstrated lower accuracy (U = 406, p = 0.010), higher values for total errors (U = 292, p = 0.001), more commissions (U = 417, p = 0.003), new actions (U = 470, p = 0.014), and forgetting actions (U = 406, p = 0.010), as well as fewer perseverations compared to the neurotypical group (U = 540.5, p = 0.029). Additionally, participants who forgot more actions were found to have lower independence in daily life (r = -0.281, p = 0.024). CONCLUSIONS: The correlations between the results of SmartAction-VR and activities of daily living, as well as cognitive tests, suggest that this new task could be useful for evaluating executive functioning in daily life.

Design and proof of concept of a double-panel TOF-PET system.

OBJECTIVE: Positron Emission Tomography (PET) is a well-known imaging technology for the diagnosis, treatment, and monitoring of several diseases. Most PET scanners use a Ring-Shaped Detector Configuration (RSDC), which helps obtain homogeneous image quality but are restricted to an invariable Field-of-View (FOV), scarce spatial resolution, and low sensitivity. Alternatively, few PET systems use Open Detector Configurations (ODC) to permit an accessible FOV adaptable to different target sizes, thus optimizing sensitivity. Yet, to compensate the lack of angular coverage in ODC-PET, developing a detector with high-timing performance is mandatory to enable Time-of-Flight (TOF) techniques during reconstruction. The main goal of this work is to provide a proof of concept PET scanner appropriate for constructing the new generation of ODC-PET suitable for biopsy guidance and clinical intervention during acquisition. The designed detector has to be compact and robust, and its requirements in terms of performance are spatial and time resolutions < 2 mm and < 200 ps, respectively. METHODS: The present work includes a simulation study of an ODC-PET based on 2-panels with variable distance. The image quality (IQ) and Derenzo phantoms have been simulated and evaluated. The phantom simulations have also been performed using a ring-shaped PET for comparison purposes of the ODC approach with conventional systems. Then, an experimental evaluation of a prototype detector that has been designed following the simulation results is presented. This study focused on tuning the ASIC parameters and evaluating the scintillator surface treatment (ESR and TiO2), and configuration that yields the best Coincidence Time Resolution (CTR). Moreover, the scalability of the prototype to a module of 64 × 64mm2 and its preliminary evaluation regarding pixel identification are provided. RESULTS: The simulation results reported sensitivity (%) values at the center of the FOV of 1.96, 1.63, and 1.18 for panel distances of 200, 250, and 300 mm, respectively. The IQ reconstructed image reported good uniformity (87%) and optimal CRC values, and the Derenzo phantom reconstruction suggests a system resolution of 1.6-2 mm. The experimental results demonstrate that using TiO2 coating yielded better detector performance than ESR. Acquired data was filtered by applying an energy window of ± 30% at the photopeak level. After filtering, best CTR of 230 ± 2 ps was achieved for an 8 × 8 LYSO pixel block with 2 × 2 × 12mm3 each. The detector performance remained constant after scaling-up the prototype to a module of 64 × 64mm2, and the flood map demonstrates the module's capabilities to distinguish the small pixels; thus, a spatial resolution < 2 mm (pixel size) is achieved. CONCLUSIONS: The simulated results of this biplanar scanner show high performance in terms of image quality and sensitivity. These results are comparable to state-of-the-art PET technology and, demonstrate that including TOF information minimizes the image artifacts due to the lack of angular projections. The experimental results concluded that using TiO2 coating provide the best performance. The results suggest that this scanner may be suitable for organ study, breast, prostate, or cardiac applications, with good uniformity and CRC.

Computerized Generation of Endodontic Files by Reproducing the Flute Grinding Manufacturing Process.

Background: File fracture during root canal treatment in endodontics is a major concern for clinicians. The strength of the file is strongly dependent on its geometry, material, and working conditions; finite element simulations are used to understand these failure mechanisms. One limitation of the models used for these simulations is the approximate geometric representation typically obtained by rotating and scaling a specific cross-section shape along the file length. Given the influence of file geometry on file strength, a more realistic representation based on the manufacturing method is needed. Methods: A computerized method was developed to generate the file geometry by simulating the flute grinding manufacturing process. This method generates the 3D geometry of the file starting from a blank and reproducing the motions of the file and grinding wheel. Results: The cross-section of the resulting geometry does not involve simple rotation and scaling but changes from the shank to the tip. The tilt angle of the grinding wheel affects the final geometry, thus altering the convexity of the cross-section. Several other parameters, such as the pitch and the radius of the grinding disc tip, impact the final geometry. Conclusions: The proposed computational method allows for the generation of endodontic file geometries that match those produced via the actual flute grinding method. This tool may help researchers and tool designers in the preparation of finite element models to assess the strength of realistic files.

House dust metagenome and pulmonary function in a US farming population.

BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together. RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait. CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.