Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium

An extreme diversity of substrates and catalytic reactions of cytochrome P450 (P450) enzymes is considered to be the consequence of evolutionary adaptation driven by different metabolic or environmental demands. Here we report the presence of numerous natural variants of P450 BM3 (CYP102A1) within a species of Bacillus megaterium. Extensive amino acid substitutions (up to 5% of the total 1049 amino acid residues) were identified from the variants. Phylogenetic analyses suggest that this P450 gene evolve more rapidly than the rRNA gene locus. It was found that key catalytic residues in the substrate channel and active site are retained. Although there were no apparent variations in hydroxylation activity towards myristic acid (C14) and palmitic acid (C16), the hydroxylation rates of lauric acid (C12) by the variants varied in the range of >25-fold. Interestingly, catalytic activities of the variants are promiscuous towards non-natural substrates including human P450 substrates. It can be suggested that CYP102A1 variants can acquire new catalytic activities through site-specific mutations distal to the active site

Pyruvate Dehydrogenase Kinase Is a Metabolic Checkpoint for Polarization of Macrophages to the M1 Phenotype

Metabolic reprogramming during macrophage polarization supports the effector functions of these cells in health and disease. Here, we demonstrate that pyruvate dehydrogenase kinase (PDK), which inhibits the pyruvate dehydrogenase-mediated conversion of cytosolic pyruvate to mitochondrial acetyl-CoA, functions as a metabolic checkpoint in M1 macrophages. Polarization was not prevented by PDK2 or PDK4 deletion but was fully prevented by the combined deletion of PDK2 and PDK4; this lack of polarization was correlated with improved mitochondrial respiration and rewiring of metabolic breaks that are characterized by increased glycolytic intermediates and reduced metabolites in the TCA cycle. Genetic deletion or pharmacological inhibition of PDK2/4 prevents polarization of macrophages to the M1 phenotype in response to inflammatory stimuli (lipopolysaccharide plus IFN-γ). Transplantation of PDK2/4-deficient bone marrow into irradiated wild-type mice to produce mice with PDK2/4-deficient myeloid cells prevented M1 polarization, reduced obesity-associated insulin resistance, and ameliorated adipose tissue inflammation. A novel, pharmacological PDK inhibitor, KPLH1130, improved high-fat diet-induced insulin resistance; this was correlated with a reduction in the levels of pro-inflammatory markers and improved mitochondrial function. These studies identify PDK2/4 as a metabolic checkpoint for M1 phenotype polarization of macrophages, which could potentially be exploited as a novel therapeutic target for obesity-associated metabolic disorders and other inflammatory conditions

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Global burden of 288 causes of death and life expectancy decomposition in 204 countries and territories and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND Regular, detailed reporting on population health by underlying cause of death is fundamental for public health decision making. Cause-specific estimates of mortality and the subsequent effects on life expectancy worldwide are valuable metrics to gauge progress in reducing mortality rates. These estimates are particularly important following large-scale mortality spikes, such as the COVID-19 pandemic. When systematically analysed, mortality rates and life expectancy allow comparisons of the consequences of causes of death globally and over time, providing a nuanced understanding of the effect of these causes on global populations. METHODS The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 cause-of-death analysis estimated mortality and years of life lost (YLLs) from 288 causes of death by age-sex-location-year in 204 countries and territories and 811 subnational locations for each year from 1990 until 2021. The analysis used 56 604 data sources, including data from vital registration and verbal autopsy as well as surveys, censuses, surveillance systems, and cancer registries, among others. As with previous GBD rounds, cause-specific death rates for most causes were estimated using the Cause of Death Ensemble model-a modelling tool developed for GBD to assess the out-of-sample predictive validity of different statistical models and covariate permutations and combine those results to produce cause-specific mortality estimates-with alternative strategies adapted to model causes with insufficient data, substantial changes in reporting over the study period, or unusual epidemiology. YLLs were computed as the product of the number of deaths for each cause-age-sex-location-year and the standard life expectancy at each age. As part of the modelling process, uncertainty intervals (UIs) were generated using the 2·5th and 97·5th percentiles from a 1000-draw distribution for each metric. We decomposed life expectancy by cause of death, location, and year to show cause-specific effects on life expectancy from 1990 to 2021. We also used the coefficient of variation and the fraction of population affected by 90% of deaths to highlight concentrations of mortality. Findings are reported in counts and age-standardised rates. Methodological improvements for cause-of-death estimates in GBD 2021 include the expansion of under-5-years age group to include four new age groups, enhanced methods to account for stochastic variation of sparse data, and the inclusion of COVID-19 and other pandemic-related mortality-which includes excess mortality associated with the pandemic, excluding COVID-19, lower respiratory infections, measles, malaria, and pertussis. For this analysis, 199 new country-years of vital registration cause-of-death data, 5 country-years of surveillance data, 21 country-years of verbal autopsy data, and 94 country-years of other data types were added to those used in previous GBD rounds. FINDINGS The leading causes of age-standardised deaths globally were the same in 2019 as they were in 1990; in descending order, these were, ischaemic heart disease, stroke, chronic obstructive pulmonary disease, and lower respiratory infections. In 2021, however, COVID-19 replaced stroke as the second-leading age-standardised cause of death, with 94·0 deaths (95% UI 89·2-100·0) per 100 000 population. The COVID-19 pandemic shifted the rankings of the leading five causes, lowering stroke to the third-leading and chronic obstructive pulmonary disease to the fourth-leading position. In 2021, the highest age-standardised death rates from COVID-19 occurred in sub-Saharan Africa (271·0 deaths [250·1-290·7] per 100 000 population) and Latin America and the Caribbean (195·4 deaths [182·1-211·4] per 100 000 population). The lowest age-standardised death rates from COVID-19 were in the high-income super-region (48·1 deaths [47·4-48·8] per 100 000 population) and southeast Asia, east Asia, and Oceania (23·2 deaths [16·3-37·2] per 100 000 population). Globally, life expectancy steadily improved between 1990 and 2019 for 18 of the 22 investigated causes. Decomposition of global and regional life expectancy showed the positive effect that reductions in deaths from enteric infections, lower respiratory infections, stroke, and neonatal deaths, among others have contributed to improved survival over the study period. However, a net reduction of 1·6 years occurred in global life expectancy between 2019 and 2021, primarily due to increased death rates from COVID-19 and other pandemic-related mortality. Life expectancy was highly variable between super-regions over the study period, with southeast Asia, east Asia, and Oceania gaining 8·3 years (6·7-9·9) overall, while having the smallest reduction in life expectancy due to COVID-19 (0·4 years). The largest reduction in life expectancy due to COVID-19 occurred in Latin America and the Caribbean (3·6 years). Additionally, 53 of the 288 causes of death were highly concentrated in locations with less than 50% of the global population as of 2021, and these causes of death became progressively more concentrated since 1990, when only 44 causes showed this pattern. The concentration phenomenon is discussed heuristically with respect to enteric and lower respiratory infections, malaria, HIV/AIDS, neonatal disorders, tuberculosis, and measles. INTERPRETATION Long-standing gains in life expectancy and reductions in many of the leading causes of death have been disrupted by the COVID-19 pandemic, the adverse effects of which were spread unevenly among populations. Despite the pandemic, there has been continued progress in combatting several notable causes of death, leading to improved global life expectancy over the study period. Each of the seven GBD super-regions showed an overall improvement from 1990 and 2021, obscuring the negative effect in the years of the pandemic. Additionally, our findings regarding regional variation in causes of death driving increases in life expectancy hold clear policy utility. Analyses of shifting mortality trends reveal that several causes, once widespread globally, are now increasingly concentrated geographically. These changes in mortality concentration, alongside further investigation of changing risks, interventions, and relevant policy, present an important opportunity to deepen our understanding of mortality-reduction strategies. Examining patterns in mortality concentration might reveal areas where successful public health interventions have been implemented. Translating these successes to locations where certain causes of death remain entrenched can inform policies that work to improve life expectancy for people everywhere. FUNDING Bill & Melinda Gates Foundation

Influence of Load Test Scale on Prediction of Ultimate Bearing Capacity of Aggregate Pier Reinforced Clay

Predicting the bearing capacity of spread footings on aggregate pier-reinforced soil is particularly important for ground improvement. Various methods for predicting the bearing capacity of spread footings supported on aggregate pier-reinforced clay have been proposed. In addition, many fields or laboratory load tests have been conducted to identify the improvement effects of aggregate pier. However, no study has quantitatively compared the effect of the experimental scale on the prediction of bearing capacity. In this study, multiple linear regression analyses were performed for field and laboratory load tests, and the effects of the load test scale on bearing capacity prediction were identified. The sensitivity analysis showed that the prediction model for the laboratory load test (MLRL) exhibited a higher sensitivity for the undrained shear strength than that of the field load test model (MLRF). However, the sensitivity of the area replacement ratio of MLRL was less than half that of the MLRF. As the undrained shear strength increased, the predicted bearing capacity of the MLRL was larger than that of the MLRF owing to the influence of boundary conditions on the experimental equipment

Evaluation of the Soil Thrust on Continuous Tracks Considering Independent Soil Shearing by Grousers

Soil thrust is a traction force of an off-road tracked vehicle. Existing soil thrust assessment methods assume that a continuous shear failure plane exists along the soil-track interface. However, recent experimental works revealed that the soil beneath the track is divided into soil blocks; each soil block is sheared independently. This study proposed a new total soil thrust assessment method based on the block-shaped failure mechanism, and the total soil thrust predicted by the proposed and the existing methods was compared. The results showed that the existing method showed a greater maximum soil thrust at a lower slip rate than the proposed method. When the soil exhibited a hardening behavior, the total soil thrust in the existing method was always greater than that in the proposed method. However, when the soil exhibited softening behavior or hump behavior, the total soil thrust in the existing method was greater than that in the proposed method until a specific slip ratio, after which the latter became greater. Unlike the existing method, the proposed method can consider the difference in soil thrust with the grouser shape ratio, showing that the total soil thrust increased as the grouser height increased and the shape ratio decreased

Evaluation of the Soil Thrust on Continuous Tracks Considering Independent Soil Shearing by Grousers

Soil thrust is a traction force of an off-road tracked vehicle. Existing soil thrust assessment methods assume that a continuous shear failure plane exists along the soil-track interface. However, recent experimental works revealed that the soil beneath the track is divided into soil blocks; each soil block is sheared independently. This study proposed a new total soil thrust assessment method based on the block-shaped failure mechanism, and the total soil thrust predicted by the proposed and the existing methods was compared. The results showed that the existing method showed a greater maximum soil thrust at a lower slip rate than the proposed method. When the soil exhibited a hardening behavior, the total soil thrust in the existing method was always greater than that in the proposed method. However, when the soil exhibited softening behavior or hump behavior, the total soil thrust in the existing method was greater than that in the proposed method until a specific slip ratio, after which the latter became greater. Unlike the existing method, the proposed method can consider the difference in soil thrust with the grouser shape ratio, showing that the total soil thrust increased as the grouser height increased and the shape ratio decreased

Deep Learning-Based Ultrasonic Testing to Evaluate the Porosity of Additively Manufactured Parts with Rough Surfaces

Ultrasonic testing (UT) has been actively studied to evaluate the porosity of additively manufactured parts. Currently, ultrasonic measurements of as-deposited parts with a rough surface remain problematic because the surface lowers the signal-to-noise ratio (SNR) of ultrasonic signals, which degrades the UT performance. In this study, various deep learning (DL) techniques that can effectively extract the features of defects, even from signals with a low SNR, were applied to UT, and their performance in terms of the porosity evaluation of additively manufactured parts with rough surfaces was investigated. Experimentally, the effects of the processing conditions of additive manufacturing on the resulting porosity were first analyzed using both optical and scanning acoustic microscopy. Second, convolutional neural network (CNN), deep neural network, and multi-layer perceptron models were trained using time-domain ultrasonic signals obtained from additively manufactured specimens with various levels of porosity and surface roughness. The experimental results showed that all the models could evaluate porosity accurately, even that of the as-deposited specimens. In particular, the CNN delivered the best performance at 94.5%. However, conventional UT could not be applied because of the low SNR. The generalization performance when using newly manufactured as-deposited specimens was high at 90%

Long-Term Compressive Strength Development of Steel Fiber Shotcrete from Cores Based on Accelerator Types at Tunnel Site

In this study, cement minerals, aluminates, and alkali-free accelerators incorporated with steel fiber were used to scrutinize the influence of accelerating agents on the long-term performance of tunneling shotcrete. Performance tests were identified based on the core compressive strength of mix shotcrete specimens with different types of accelerating agents throughout timeframes of 1, 3, 6, and 12 months. Here, 37 kg of steel fiber was incorporated into the cement mineral and aluminate mixes, and 40 kg of steel fiber was incorporated in an alkali-free mix for the shotcrete mix design. The KSF 2784 and ASTM 214 standards were followed for specimen fabrication and core cutting. For all specimens, shotcrete test panels of 250 × 600 × 500 mm were manufactured for core compressive strength tests conducted using 100, 75 and 55 mm diameter cylindrical molds and a length-to-diameter ratio of 2. The 1-month compressive strength of all test variables satisfied the Korea Expressway Co. standard of 21 MPa. The core compressive strength of the shotcrete specimens showed a tendency to increase with age, but a strength reduction occurred in 6 months and increased again at 12 months. Moreover, the impact of the diameter changes in the shotcrete core specimens was analyzed based on the mixing. For 12 months, a large increase in the core compressive strength occurred, particularly in the alkali-free specimens. The comparison also focused on the relative strength compared with a cast concrete mold and shotcrete core specimens. It is necessary to use alkali-free accelerators considering the long-term performance of tunnels and worker safety