Global Atlas of Methane Metabolism Marker Genes in Soil.

Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.

Subtle Radiographic Progression at Six Months Can Be Detected Using Automated Quantitative Software in Rheumatoid Arthritis While Receiving Tocilizumab.

OBJECTIVES: We investigated whether our in-house software equipped with partial image phase-only correlation (PIPOC) can detect subtle radiographic joint space narrowing (JSN) progression at six months and predict JSN progression in rheumatoid arthritis (RA) patients receiving Tocilizumab. METHODS: The study included 39 RA patients who were treated with Tocilizumab. Radiological progression of the metacarpophalangeal and the proximal interphalangeal joints was evaluated according to the Genant-modified Sharp score (GSS) at 0, 6, and 12 months. Automatic measurements were performed with the software. We validated the software in terms of accuracy in detecting the JSN progression. RESULTS: The success rate of the software for joint space width (JSW) measurement was 96.8% (449/464). The 0-12-month JSW change by the software was significantly greater in joints with the 0-6-month PIPOC (+) group than the 0-6-month PIPOC (-) group (p < 0.001). The 0-12-month JSW change by the software was 0-12-month GSS (+) than with 0-12-month GSS (-) (p = 0.02). Here, "(+)" indicates the JSN progression during the follow-up period. Meanwhile, "(-)" indicates no JSN progression during the follow-up period. Linear regression tests showed significant correlations between the 0-6-month and the 0-12-month PIPOC in the left 2nd and 3rd MCP joints (R2 = 0.554 and 0.420, respectively). CONCLUSIONS: Our in-house software equipped with PIPOC could predict subsequent JSN progression with only short-term observations.

Quantification of Joint Space Width Difference on Radiography Via Phase-Only Correlation (POC) Analysis: a Phantom Study Comparing with Various Tomographical Modalities Using Conventional Margin-Contouring.

Several visual scoring methods are currently used to assess progression of rheumatoid arthritis (RA) on radiography. However, they are limited by its subjectivity and insufficient sensitivity. We have developed an original measurement system which uses a technique called phase-only correlation (POC). The purpose of this study is to validate the system by using a phantom simulating the joint of RA patients.A micrometer measurement apparatus that can adjust arbitrary joint space width (JSW) in a phantom joint was developed to define true JSW. The phantom was scanned with radiography, 320 multi detector CT (MDCT), high-resolution peripheral quantitative CT (HR-pQCT), cone beam CT (CBCT), and tomosynthesis. The width was adjusted to the average size of a women's metacarpophalangeal joint, from 1.2 to 2.2 mm with increments of 0.1 mm and 0.01 mm. Radiographical images were analyzed by the POC-based system and manual method, and images from various tomographical modalities were measured via the automatic margin detection method. Correlation coefficients between true JSW difference and measured JSW difference were all strong at 0.1 mm intervals with radiography (POC-based system and manual method), CBCT, 320MDCT, HR-pQCT, and tomosynthesis. At 0.01 mm intervals, radiography (POC-based system), 320MDCT, and HR-pQCT had strong correlations, while radiography (manual method) and CBCT had low correlations, and tomosynthesis had no statistically significant correlation. The smallest detectable changes for radiography (POC-based system), radiography (manual method), 320MDCT, HR-pQCT, CBCT, and tomosynthesis were 0.020 mm, 0.041 mm, 0.076 mm, 0.077 mm, 0.057 mm, and 0.087 mm, respectively. We conclude that radiography analyzed with the POC-based system might sensitively detect minute joint space changes of the finger joint.

Overexpression of CD44 is associated with a poor prognosis in grade II/III gliomas.

PURPOSE: Overexpression of CD44 has been detected in many types of tumor tissues. Moreover, CD44 is recognized as a cancer stem cell marker for many cancers. However, the prognostic value of CD44 for glioma patients has not yet been clarified. The authors tried to explore the impact of CD44 expression on grade II/III glioma patients. METHODS: To assess the RNA expression levels of CD44 in glioma tissues and normal brain tissues, meta-analyses were conducted in the online Oncomine database. The mRNA expression levels of CD44, CD44s, and CD44v2-v10 in 112 grade II/III glioma patients in Hokkaido University Hospital (HUH) were detected by qPCR. The RNA-seq data and clinical data of grade II/III glioma patients were obtained from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases. RESULTS: Based on the Oncomine database, CD44 has significantly high expression in glioma tissues as compared with normal tissues. We explored the clinical relevance of CD44 mRNA expression based on the HUH cohorts, the TCGA cohorts, and the CGGA cohorts. In survival analysis, high mRNA expression of CD44 was correlated with poor overall survival and poor progression-free survival in grade II/III glioma patients. Multivariate Cox regression analyses confirmed CD44 as an independent prognostic factor for grade II/III glioma patients. CONCLUSIONS: The present study suggests that overexpression of CD44 is associated with a poor prognosis for grade II/III glioma patients. Moreover, our findings suggest that CD44 could serve as a prognostic biomarker in grade II/III glioma patients.

Corrections to "A Sub-Pixel Accurate Quantification of Joint Space Narrowing Progression in Rheumatoid Arthritis".

Presents corrections to the article "A Sub-Pixel Accurate Quantification of Joint Space Narrowing Progression in Rheumatoid Arthritis".

Fully automatic software for detecting radiographic joint space narrowing progression in rheumatoid arthritis: phantom study and comparison with visual assessment.

PURPOSE: We have developed an in-house software equipped with partial image phase-only correlation (PIPOC) which can automatically quantify radiographic joint space narrowing (JSN) progression. The purpose of this study was to evaluate the software in phantom and clinical assessments. MATERIALS AND METHODS: In the phantom assessment, the software's performance on radiographic images was compared to the joint space width (JSW) difference using a micrometer as ground truth. A phantom simulating a finger joint was scanned underwater. In the clinical assessment, 15 RA patients were included. The software measured the radiological progression of the finger joints between baseline and the 52nd week. The cases were also evaluated with the Genant-modified Sharp score (GSS), a conventional visual scoring method. We also quantitatively assessed these joints' synovial vascularity (SV) on power Doppler ultrasonography (0, 8, 20 and 52 weeks). RESULTS: In the phantom assessment, the PIPOC software could detect changes in JSN with a smallest detectable difference of 0.044 mm at 0.1 mm intervals. In the clinical assessment, the JSW change of the joints with GSS progression detected by the software was significantly greater than those without GSS progression (p = 0.004). The JSW change of joints with positive SV at baseline was significantly higher than those with negative SV (p = 0.024). CONCLUSION: Our in-house software equipped with PIPOC can automatically and quantitatively detect slight radiographic changes of JSW in clinically inactive RA patients.

A Sub-Pixel Accurate Quantification of Joint Space Narrowing Progression in Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is a chronic autoimmune disease that primarily affects peripheral synovial joints, like fingers, wrists and feet. Radiology plays a critical role in the diagnosis and monitoring of RA. Limited by the current spatial resolution of radiographic imaging, joint space narrowing (JSN) progression of RA for the same reason above can be less than one pixel per year with universal spatial resolution. Insensitive monitoring of JSN can hinder the radiologist/rheumatologist from making a proper and timely clinical judgment. In this paper, we propose a novel and sensitive method that we call partial image phase-only correlation which aims to automatically quantify JSN progression in the early RA. The majority of the current literature utilizes the mean error, root-mean-square deviation and standard deviation to report the accuracy at pixel level. Our work measures JSN progression between a baseline and its follow-up finger joint images by using the phase spectrum in the frequency domain. Using this study, the mean error can be reduced to 0.0130 mm when applied to phantom radiographs with ground truth, and 0.0519 mm standard deviation for clinical radiography. With the sub-pixel accuracy far beyond usual manual measurements, we are optimistic that the proposed work is a promising scheme for automatically quantifying JSN progression.

A deep registration method for accurate quantification of joint space narrowing progression in rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that leads to progressive articular destruction and severe disability. Joint space narrowing (JSN) has been regarded as an important indicator for RA progression and has received significant attention. Radiology plays a crucial role in the diagnosis and monitoring of RA through the assessment of joint space. A new framework for monitoring joint space by quantifying joint space narrowing (JSN) progression through image registration in radiographic images has emerged as a promising research direction. This framework offers the advantage of high accuracy; however, challenges still exist in reducing mismatches and improving reliability. In this work, we utilize a deep intra-subject rigid registration network to automatically quantify JSN progression in the early stages of RA. In our experiments, the mean-square error of the Euclidean distance between the moving and fixed images was 0.0031, the standard deviation was 0.0661 mm and the mismatching rate was 0.48%. Our method achieves sub-pixel level accuracy, surpassing manual measurements significantly. The proposed method is robust to noise, rotation and scaling of joints. Moreover, it provides misalignment visualization, which can assist radiologists and rheumatologists in assessing the reliability of quantification, exhibiting potential for future clinical applications. As a result, we are optimistic that our proposed method will make a significant contribution to the automatic quantification of JSN progression in RA. Code is available at https://github.com/pokeblow/Deep-Registration-QJSN-Finger.git.

Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.

Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.

Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway.

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood-Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.