Abstract
Motivation
Next-generation sequencing (NGS) data frequently suffer from poor-quality cycles and adapter contaminations therefore need to be preprocessed before downstream analyses. With the ...ever-growing throughput and read length of modern sequencers, the preprocessing step turns to be a bottleneck in data analysis due to unmet performance of current tools. Extra-fast and accurate adapter- and quality-trimming tools for sequencing data preprocessing are therefore still of urgent demand.
Results
Ktrim was developed in this work. Key features of Ktrim include: built-in support to adapters of common library preparation kits; supports user-supplied, customized adapter sequences; supports both paired-end and single-end data; supports parallelization to accelerate the analysis. Ktrim was ∼2–18 times faster than current tools and also showed high accuracy when applied on the testing datasets. Ktrim could thus serve as a valuable and efficient tool for short-read NGS data preprocessing.
Availability and implementation
Source codes and scripts to reproduce the results descripted in this article are freely available at https://github.com/hellosunking/Ktrim/, distributed under the GPL v3 license.
Contact
sunkun@szbl.ac.cn
Supplementary information
Supplementary data are available at Bioinformatics online.
With the rapid development of the photovoltaic industry, the share of photovoltaic power generation in the power trading market is growing. The intermittent and uncontrollable characteristics of ...photovoltaic power generation have a huge impact on the stability of the power system. To reduce the occurrence of such conditions, it is necessary to improve the prediction accuracy of photovoltaic power generation. However, in the traditional modeling process, the accuracy of the model is often poor due to excessive noise in the original data or improper parameter adjustment. In this paper, Principal Component Analysis and K-means clustering algorithm combined with random forest algorithm optimized by Differential Evolution Grey Wolf Optimizer are used to model the photovoltaic power generation in three regions. Principal Component Analysis and K-means clustering are used to obtain the hourly point features similar to the predicted time points, and then the input data is filtered to reduce the noise data interference. At the same time, the popular optimization algorithm quickly selects the Random Forest parameters, which greatly avoids the artificial filtering factors and causes the error to be generated. Through the establishment of comparative experiments, it is found that the recommended model has higher prediction accuracy and robustness.
•An optimized hybrid method called PCA-K-means-HGWO-RF is proposed to forecast PV power.•Optimizing model parameters and input variables are the main ways to improve model accuracy.•A better combination of Principal Component Analysis and k-means can achieve better clustering results.•The Differential Evolution Grey Wolf Optimize algorithm is used to determine random forest model parameters.•The proposed method has the best performance compared with other methods.
We report the current density effect in controlling current-carrying friction of amorphous carbon (a-C) film sliding against steel ball. The current density at the sliding interface was set to a ...constant value or cyclic variation value by adjusting the current intensity and the contact area for exploring the current-carrying friction behavior. The results showed that when the current density enhanced from 0 to 0.196 mA/μm2, the friction coefficient decreased from 0.20 to 0.03 and the run-in cycle shortened from about 100 to few cycles. When the current density cyclically varied during the sliding, the friction coefficient had a very fast response and followed to the corresponding value which can be adjusted by the current density. Raman spectrum analysis and TEM observation confirmed that graphene nanosheets were formed at the sliding interface and the size of graphene nanosheets depended on the current density. The mechanism of current-carrying friction behavior of a-C film sliding against steel ball was the interactions of graphene to graphene and a-C to a-C at the contact area, which was controlled by the current density. This finding shed light on the great role of the current density in current-carrying friction of a-C film.
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SiOx is proposed as one of the most promising anodes for Li‐ion batteries (LIBs) for its advantageous capacity and stable Li uptake/release electrochemistry, yet its practical application is still a ...big challenge. Here encapsulation of SiOx nanoparticles into conductive graphene bubble film via a facile and scalable self‐assembly in solution is shown. The SiOx nanoparticles are closely wrapped in multilayered graphene to reconstruct a flake‐graphite‐like macrostructure, which promises uniform and agglomeration‐free distribution of SiOx in the carbon while ensures a high mechanical strength and a high tap density of the composite. The composites present unprecedented cycling stability and excellent rate capabilities upon Li storage, rendering an opportunity for its anode use in the next‐generation high‐energy LIBs.
SiOx nanoparticles are closely wrapped in multilayered graphene to reconstruct a macrostructure resembling flake graphite, which promises agglomeration‐free distribution of SiOx in the bulk while ensuring a high mechanical strength and a high tap density of the bubble film. By taking the advantages of the graphene network, the composites present unprecedented cycling stability and excellent rate capabilities upon Li storage.
Background: As the human lifespan increases, the number of people affected by agerelated
dementia is growing at an epidemic pace. Vascular pathology dramatically affects cognitive
profiles, resulting ...in dementia and cognitive impairment. While vascular dementia itself constitutes
a medical challenge, hypo-perfusion/vascular risk factors enhance amyloid toxicity and other memory-
damaging factors and hasten Alzheimer’s disease (AD) and other memory disorders’ progression,
as well as negatively affect treatment outcome.
Methods: Research and online content related to vascular cognitive impairment and dementia is
reviewed, specifically focusing on the potential treatment of the disorder.
Results: Few therapeutic options are currently available to improve the prognosis of patients with
vascular dementia and cognitive impairment, mixed AD dementia with vascular pathology, or other
memory disorders. Emerging evidence, however, indicates that, like AD and other memory disorders,
synaptic impairment underlies much of the memory impairment in the cognitive decline of
vascular cognitive impairment and vascular dementia.
Conclusion: Effective rescues of the memory functions might be achieved through synaptic and
memory therapeutics, targeting distinct molecular signaling pathways that support the formation of
new synapses and maintaining their connections. Potential therapeutic agents include: 1) memory
therapeutic agents that rescue synaptic and memory functions after the brain insults; 2) antipathologic
therapeutics and an effective management of vascular risk factors; and 3) preventative
therapeutic agents that achieve memory therapy through functional enhancement. These therapeutic
agents are also likely to benefit patients with AD and/or other types of memory disorders.
Pandemics have become more frequent and more complex during the twenty-first century. Posttraumatic stress disorder (PTSD) following pandemics is a significant public health concern. We sought to ...provide a reliable estimate of the worldwide prevalence of PTSD after large-scale pandemics as well as associated risk factors, by a systematic review and meta-analysis. We systematically searched the MedLine, Embase, PsycINFO, Web of Science, CNKI, WanFang, medRxiv, and bioRxiv databases to identify studies that were published from the inception up to August 23, 2020, and reported the prevalence of PTSD after pandemics including sudden acute respiratory syndrome (SARS), H1N1, Poliomyelitis, Ebola, Zika, Nipah, Middle Eastern respiratory syndrome coronavirus (MERS-CoV), H5N1, and coronavirus disease 2019 (COVID-19). A total of 88 studies were included in the analysis, with 77 having prevalence information and 70 having risk factors information. The overall pooled prevalence of post-pandemic PTSD across all populations was 22.6% (95% confidence interval (CI): 19.9-25.4%, I
: 99.7%). Healthcare workers had the highest prevalence of PTSD (26.9%; 95% CI: 20.3-33.6%), followed by infected cases (23.8%: 16.6-31.0%), and the general public (19.3%: 15.3-23.2%). However, the heterogeneity of study findings indicates that results should be interpreted cautiously. Risk factors including individual, family, and societal factors, pandemic-related factors, and specific factors in healthcare workers and patients for post-pandemic PTSD were summarized and discussed in this systematic review. Long-term monitoring and early interventions should be implemented to improve post-pandemic mental health and long-term recovery.
SiOx‐containing graphite composites have aroused great interests as the most promising alternatives for practical application in high‐performance lithium‐ion batteries. However, limited loading ...amount of SiOx on the surface of graphite and some inherent disadvantages of SiOx such as huge volume variation and poor electronic conductivity result in unsatisfactory electrochemical performance. Herein, a novel and facile fabrication approach is developed to synthesize high‐performance SiOx/C composites with graphite‐like structure in which SiOx particles are dispersed and anchored in the carbon materials by restoring original structure of artificial graphite. The multicomponent carbon materials are favorable for addressing the disadvantages of SiOx‐based anodes, especially for the formation of stable solid electrolyte interphase, maintaining structural integrity of electrode materials and improving electrical conductivity of electrode. The resultant SiOx/C anodes demonstrate high reversible capacities (645 mA h g−1), excellent cycling stability (≈90% capacity retention for 500 cycles), and superior rate capabilities. Even at high pressing density (1.3 g cm−3), SiOx/C anodes still present superior cycling performance due to the high tap density and structural integrity of electrode materials. The proposed synthetic method can also be developed to address other anode materials with inferior electronic conductivity and huge volume variation.
A blocky SiOx/C with graphite‐like structure is optimally designed and synthesized to load more SiOx materials and address the inherent disadvantages of SiOx‐based anodes by the synergistic effect of multicomponent carbon materials. The resultant SiOx/C anodes present superior electrochemical performance at high mass loading and pressing density.
Background： At present, a diagnostic tool with high specificity for impaired endometrial receptivity, which may lead to implantation failure, remains to be developed. We aimed to assess the different ...endometrial microRNA （miRNA） signatures for impaired endometrial receptivity by microarray analysis. Methods： A total of 12 repeated implantation failure （RIF） patients and I0 infertile patients, who conceived and delivered after one embryo transfer attempt, were recruited as RIF and control groups, respectively. Endometrial specimens from the window of implantation （WOI） were collected from these two groups. MiRNA microarray was conducted on seven and five samples from the RIF and control groups, respectively. Comparative, functional, and network analyses were performed for the microarray results. Quantitative real-time polymerase chain reaction （PCR） was performed on other samples to validate the expression of specific miRNAs. Results： Compared with those in the control group, the expression levels of 105 miRNAs in the RIF group were found to be significantly up- or down-regulated （at least 2-fold） by microarray analysis. The most relevant miRNA functional sets of these dysregulated miRNAs were miR-30 family, human embryonic stern cell regulation, epithelial-mesenchymal transition, and miRNA tumor suppressors by tool for annotations ofmicroRNA analysis. Network regulatory analysis found 176 miRNA-mRNA interactions, and the top 3 core miRNAs were has-miR-4668-5p, has-miR-429, and has-miR-5088. Expression levels of the 18 selected miRNAs in new samples by real-time PCR were found to be regulated with the same trend, as the result ofmicroarray analysis. Conclusions： There is a significant different expression of certain miRNAs in the WOI endometrium for RIF patients. These miRNAs may contribute to impaired endometrial receptivity.
•Cu/graphene interface can act as a resource of dislocation emission.•Dislocation propagations are confined by the impenetrable Cu/graphene interface.•Effects of Cu/graphene interface on dislocation ...evolutions are discussed deeply.
Molecular dynamics simulations are performed to investigate the effects of graphene on the mechanical properties in multilayer Cu/graphene composites under uniaxial tension. It is found that both of zigzag and armchair graphene can improve the mechanical strength of multilayer Cu/graphene composites. The enhanced efficiency is concerned with chirality and interlayer thickness of graphene. The Cu/graphene interface has a great effect on the dislocation nucleation and propagation in the plastic deformation. Firstly, the interface can act as a resource of dislocation emission. This is due to the high stress concentrated on the interface caused by lattice mismatch and shear modulus mismatch between Cu and graphene, which can reduce the energy of nucleation. The interface stress of armchair graphene is more evident than the zigzag graphene. Secondly, the dislocations are confined by the impenetrable interface during the propagation process, which leads to intense interaction between dislocations and interface. Both the confinements and interactions are responsible for high stress required during the propagation process. A confined layer slip (CLS) model is established to predict the strength of multilayer composites in quantification. After the fracture of graphene, the dislocations penetrate through the interface of Cu and graphene and the composites would neck and fracture around the region.
Cell-free circulating DNA (cfDNA) in plasma has gained global interest as a diagnostic material for noninvasive prenatal testing and cancer diagnosis, or the so-called "liquid biopsy". Recent studies ...have discovered a great number of valuable genetic and epigenetic biomarkers for cfDNA-based liquid biopsy. Considering that the genetic biomarkers, e.g., somatic mutations, usually vary from case to case in most cancer patients, epigenetic biomarkers that are generalizable across various samples thus possess certain advantages. In this study, we reviewed the most recent studies and advances on utilizing epigenetic biomarkers for liquid biopsies. We first reviewed more traditional methods of using tissue/cancer-specific DNA methylation biomarkers and digital PCR or sequencing technologies for cancer diagnosis, as well as tumor origin determination. In the second part, we discussed the emerging novel approaches for exploring the biological basis and clinical applications of cfDNA fragmentation patterns. We further provided our comments and points of view on the future directions on epigenetic biomarker development for cfDNA-based liquid biopsies.
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