Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. ...However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been developed to date. The output data quality is very important for downstream analysis, whereas computing resources could limit the utility of some computing-intense tools. There is a lack of standardized assessments for these long-read error-correction methods.
Here, we present a comparative performance assessment of ten state-of-the-art error-correction methods for long reads. We established a common set of benchmarks for performance assessment, including sensitivity, accuracy, output rate, alignment rate, output read length, run time, and memory usage, as well as the effects of error correction on two downstream applications of long reads: de novo assembly and resolving haplotype sequences.
Taking into account all of these metrics, we provide a suggestive guideline for method choice based on available data size, computing resources, and individual research goals.
Abstract
Background
Osteoarthritis (OA) is a multifactorial joint degenerative disease with low-grade inflammation. The gut microbiome has recently emerged as an pathogenic factor of OA, and ...prebiotics supplementation could alleviate OA symptoms in animal models. However, the relationship between the gut microbiome and OA in the older female adults is hitherto not clear.
Results
Here we studied the gut microbiome of 57 OA patients and their healthy controls by metagenome-wide association study based on previously published data. A significant reduction in the richness and diversity of gut microbiome were observed in OA patients.
Bifidobacterium longum
and
Faecalibacterium prausnitzii
were decreased while
Clostridium
spp. was increased in the OA group. The functional modules, particularly the energetic metabolism and acetate production were also decreased in the OA patients. To evaluate the diagnostic value of identified species for elderly patients with OA, we constructed a set of random forest disease classifiers based on species differences between the two groups. Among them, 9 species reached the lowest classification error in the random forest cross validation, and the area under ROC of the model was 0.81.
Conclusions
Significant alterations in the gut microbial composition and function were observed between the older patients with OA and their controls, and a random forest classifier model for OA were constructed based on the differences in our study. Our study have identified several potential gut microbial targets in the elderly females with OA, which will facilitate the treatment of OA based on gut microbiota, is of great value in alleviating pain and improving the quality of life for them.
A bamboo-like nanomaterial composed of V2O5/polyindole (V2O5/PIn) decorated onto the activated carbon cloth was fabricated for supercapacitors. The PIn could effectively enhance the electronic ...conductivity and prevent the dissolution of vanadium. And the activation of carbon cloth with functional groups is conducive to anchoring the V2O5 and improving surface area, which results in an enhancement of electrochemical performance and leads to a high specific capacitance of 535.5 F/g. Moreover, an asymmetric flexible supercapacitor based on V2O5/PIn@activate carbon cloth and reduced graphene oxide (rGO)@activate carbon cloth exhibits a high energy density (38.7 W h/kg) at a power density of 900 W/kg and good cyclic stability (capacitance retention of 91.1% after 5000 cycles). And the prepared device is shown to power the light-emitting diode bulbs efficiently.
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•Synthesis method-resulting molecular structure stability/structure/reactivity relationships are discussed.•Diversity of sulfate zirconia preparation methods results in variety of the ...active site structures.•Hydrocarbon reaction mechanisms on sulfate zirconia mostly rely on homogeneous mechanisms.
This article critically reviews the literature on sulfated zirconia catalysts for variety of important hydrocarbon and oxygenate reactions including ethylene dimerization, isomerization, alkylation and esterification. The catalyst synthesis method-resulting molecular structure relationships, stability and reactive transformations of the active site in response to gas phase environment, reaction mechanisms, reaction intermediates, the corresponding kinetics and effect of some popular promoters are covered. Key structural features of the active sites have been extensively investigated but the conclusive structure is yet to be determined due to the diversity of the preparation methods (nature and crystallinity of the support, sulfate deposition method, sulfate coverage) as well as the diversity of the experimental conditions used during the spectroscopic determination. Similarly, the effect of the promoters and the synergistic effects of the promoter/sulfate sites in the presence of hydrocarbons are not well-defined. Finally, multiple theories exist for the reactive mechanisms on sulfated zirconia but most rely on the homogeneous reaction mechanisms, such as those for ethylene dimerization and butane alkylation with butane. Collectively, these show the lack of a fundamental understanding and the need of modern catalysis studies of this important catalytic system.
Hydrologic models are used to simulate natural phenomena while making different assumptions about the levels of complexity with which natural processes should be represented. Global Sensitivity ...Analysis is regularly applied to understand how the inputs (including forcing, parameters, and initial states) of these models control their outputs. A less widely explored strategy to support such diagnostic analysis is the assessment of direction of change (DOC), which addresses the question whether the increase (or decrease) of a model input leads to a positive (or negative) change in the model output. We propose a metric, called Direction Index, to quantitatively assess the DOC and develop an approach to calculate it. The basic idea of our approach is twofolded: (1) Estimate the zeroth and first‐order term of the High Dimensional Model Representation (HDMR) decomposition. (2) Calculate the derivatives of the first‐order term of the HDMR decomposition with respect to a given input. We demonstrate our approach on a widely used conceptual lumped hydrological model (Hymod) with a time‐varying analysis applied to the Leaf River Catchment in the USA. The results show that our approach provides new insights into the behavior of the model, which can be used to guide model structure improvement or to improve calibration efficiency.
Key Points
We bring attention to a diagnostic strategy—assessing the direction of change, which quantifies whether the increase (or decrease) of a model input leads to a positive (or negative) change in a model output variable
We developed a quantification and visualization approach to analyze the direction of change due to input variability within a Global Sensitivity Analysis context
We demonstrated our approach as a time‐varying analysis to diagnose how the parameters of a widely used hydrological model control the output's direction of change
Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs, ...has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3440 spiRNA species in mice and 4100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.
The error-prone third-generation sequencing (TGS) long reads can be corrected by the high-quality second-generation sequencing (SGS) short reads, which is referred to as hybrid error correction. We ...here investigate the influences of the principal algorithmic factors of two major types of hybrid error correction methods by mathematical modeling and analysis on both simulated and real data. Our study reveals the distribution of accuracy gain with respect to the original long read error rate. We also demonstrate that the original error rate of 19% is the limit for perfect correction, beyond which long reads are too error-prone to be corrected by these methods.
The fourth phase of water has garnered increased attention within the scientific community due to its distinct properties that differentiate it from regular water. This unique state seems to arise ...potentially from a liquid crystalline structure, which has been observed near various hydrophilic surfaces to possess the capability of excluding microspheres. Consequently, it has been labeled as exclusion zone (EZ) water. When in contact with hydrophilic surfaces, water could exhibit the ability to form organized layers of EZ water. In this study, we investigated the quick buildup of EZ water exposed to xylem vessels of four vegetable plants: cabbage, celery, asparagus, and pumpkin. Among them, pumpkin vessels showed larger EZs, up to 240 ± 56 μm in width. The width of EZ water found near the xylem vessels of the other plants ranged from 133 ± 22 to 142 ± 20 μm. EZ water generally excludes a wide range of particles, including polystyrene microspheres with various surface modifications, as well as silica microspheres. This implies that the formation of EZ water is not an artificial result of using specific microsphere types but rather demonstrates EZ's ability to exclude particles regardless of their composition. Inside single xylem vessels of the pumpkin, we could observe the dynamics of EZ buildup, growing from the inside edge of the vessel toward the center. The relationship between vessel diameter, vessel length, and salt concentration on EZ generation inside the xylem vessel was also explored. The results showed that EZ water can build up both inside and outside the xylem vessels. Our findings suggest that EZ generation inside xylem vessels is associated with water flow, likely driven by a proton gradient. Further research is warranted to elucidate the role of EZ water in the physiology of living plants, particularly considering the limitations of the current experiments conducted on cut-out xylem vessel samples.
Ammonia (NH3) is a common air pollutant, which poses a serious threat to farm animals. L-selenomethionine is organic selenium (Se), which can inhibit intracellular ROS generation, block ROS-dependent ...autophagy, promote mitochondrial energy metabolism, and enhance the body's immunity. Lung, as an important organ of the respiratory system, is highly susceptible to the toxic effects of NH3. However, there were few studies on the mechanism of toxic effects of NH3 on lung tissues. The aim of this study was to investigate the effect of NH3 on the lungs in pigs and the alleviating effect of L-selenomethionine. Twenty-four Large White*Duroc*Min pigs were randomly assigned to 4 groups: control group, NH3 group, Se group, and NH3 +Se group. The results showed that exposure to NH3 caused damage and inflammation in lung tissues and significantly increased blood NH3 concentration. NH3 induced changes of oxidative stress indexes (GSH, GSH-Px, SOD, MDA, Keap1, Nrf2, and HO-1) and expressions of energy metabolism related genes (HK1, HK2, PFK, PK, LDHA, and HIF-1α). Ultrastructure showed that mitochondrial damage and autophagosome increased significantly, and the expression levels of autophagy related genes (Beclin1, ATG5, ATG7, ATG10, and p62) changed. However, the addition of L-selenomethionine alleviated the above changes, but there was still a significant difference compared with the control group (P < 0.05). This finding can provide a new evidence for mitigation of NH3 toxicity.
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•Ammonia is a typical air pollutant, which has a strong toxic effect on respiratory system.•Ammonia exposure causes lung damage by oxidative stress and energy metabolism disorder.•ROS-mediated excessive autophagy is important mechanisms of ammonia toxicity.•L-selenomethionine can mitigate the toxic effect of ammonia exposure on lungs.
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