Statistical and Biological Evaluation of Different Gene Set Analysis Methods

AbstractGene-set analysis (GSA) methods have been widely used in microarray data analysis. Owing to the unusual characteristics of microarray data, such as multi-dimension, small sample size and complicated relationship between genes, no generally accepted methods have been used to detect differentially expressed gene sets (DEGs) up to now. Our group assessed the statistical performance of some commonly used methods through Monte Carlo simulation combined with the analysis of real-world microarray data sets. Not only did we discover a few novel features of GSA methods during experiences, but also we find that some GSA methods are effective only if genes were assumed to be independent. And we also detected that model-based methods (GlobalTest and PCOT2) performed well when analyzing our simulated data sets in which the inter-gene correlation structure was incorporated into each gene set separately for more reasonable. Through analysis of real-world microarray data, we found GlobalTest is more effective. Then we concluded that GlobalTest is a more effective gene set analysis method, and recommended using it with microarray data analysis

Effects of Surface Modification of Nanotube Arrays on the Performance of CdS Quantum-Dot-Sensitized Solar Cells

CdS-sensitized TiO2 nanotube arrays have been fabricated using the method of successive ionic layer adsorption and reaction and used as a photoanode for quantum-dot-sensitized solar cells. Before being coated with CdS, the surface of TiO2 nanotube arrays was treated with TiCl4, nitric acid (HNO3), potassium hydroxide (KOH), and methyltrimethoxysilane (MTMS), respectively, for the purpose of reducing the interface transfer resistance of quantum-dot-sensitized solar cells. The surfaces of the modified samples represented the characteristics of superhydrophilic and hydrophobic which directly affect the power conversion efficiency of the solar cells. The results showed that surface modification resulted in the reduction of the surface tension, which played a significant role in the connectivity of CdS and TiO2 nanotube arrays. In addition, the solar cells based on CdS/TiO2 electrode treated by HNO3 achieved a maximum power conversion efficiency of 0.17%, which was 42% higher than the reference sample without any modification

Energy bands, conductance and thermoelectric power for ballistic electrons in a nanowire with spin-orbit interaction

We calculated the effects of spin-orbit interaction (SOI) on the energy bands, ballistic conductance and the electron-diffusion thermoelectric power of a nanowire by varying the temperature, electron density and width of the wire. The potential barriers at the edges of the wire are assumed to be very high. A consequence of the boundary conditions used in this model is determined by the energy band structure, resulting in wider plateaus when the electron density is increased due to larger energy-level separation as the higher subbands are occupied by electrons. The nonlinear dependence of the transverse confinement on position with respect to the well center excludes the "pole-like feature" in the conductance which is obtained when a harmonic potential is employed for confinement. At low temperature, the electron diffusion thermoelectric power increases linearly with T but deviates from the linear behavior for large values of T.Comment: Updated corrected version of the original submissio

Tunable Band Structure Effects on Ballistic Transport in Graphene Nanoribbons

Graphene nanoribbons (GNR) in mutually perpendicular electric and magnetic fields are shown to exhibit dramatic changes in their band structure and electron transport properties. A strong electric field across the ribbon induces multiple chiral Dirac points, closing the semiconducting gap in armchair GNR's. A perpendicular magnetic field induces partially formed Landau levels as well as dispersive surface-bound states. Each of the applied fields on its own preserves the even symmetry $E_{k} = E_{-k}$ of the subband dispersion. When applied together, they reverse the dispersion parity to be odd and gives $E_{e,k} = -E_{h,-k}$ and mix the electron and hole subbands within the energy range corresponding to the change in potential across the ribbon. This leads to oscillations of the ballistic conductance within this energy range

Performing group-level functional image analyses based on homologous functional regions mapped in individuals

Functional MRI (fMRI) studies have traditionally relied on intersubject normalization based on global brain morphology, which cannot establish proper functional correspondence between subjects due to substantial intersubject variability in functional organization. Here, we reliably identified a set of discrete, homologous functional regions in individuals to improve intersubject alignment of fMRI data. These functional regions demonstrated marked intersubject variability in size, position, and connectivity. We found that previously reported intersubject variability in functional connectivity maps could be partially explained by variability in size and position of the functional regions. Importantly, individual differences in network topography are associated with individual differences in task-evoked activations, suggesting that these individually specified regions may serve as the localizer to improve the alignment of task-fMRI data. We demonstrated that aligning task-fMRI data using the regions derived from resting state fMRI may lead to increased statistical power of task-fMRI analyses. In addition, resting state functional connectivity among these homologous regions is able to capture the idiosyncrasies of subjects and better predict fluid intelligence (gF) than connectivity measures derived from group-level brain atlases. Critically, we showed that not only the connectivity but also the size and position of functional regions are related to human behavior. Collectively, these findings suggest that identifying homologous functional regions across individuals can benefit a wide range of studies in the investigation of connectivity, task activation, and brain-behavior associations. Author summary No two individuals are alike. The size, shape, position, and connectivity patterns of brain functional regions can vary drastically between individuals. While interindividual differences in functional organization are well recognized, to date, standard procedures for functional neuroimaging research still rely on aligning different subjects' data to a nominal average brain based on global brain morphology. We developed an approach to reliably identify homologous functional regions in each individual and demonstrated that aligning data based on these homologous functional regions can significantly improve the study of resting state functional connectivity, task-fMRI activations, and brain-behavior associations. Moreover, we showed that individual differences in size, position, and connectivity of brain functional regions are dissociable, and each can provide nonredundant information in explaining human behavior

Disseminated varicella-zoster virus infection in an aplastic anemia- paroxysmal nocturnal hemoglobinuria syndrome patient: A case report

BackgroundVaricella-zoster virus (VZV) is a common and widespread human-restricted pathogen. It is famous for its dermatological manifestations, such as varicella and herpes zoster. Patients with aplastic anemia-paroxysmal nocturnal hemoglobinuria (AA-PNH) syndrome complicated with fatal disseminated varicella zoster virus infection are very rare and in danger.Patient concernsA 26-year-old man with a history of AA-PNH syndrome was receiving cyclosporine and corticosteroid treatment in the hematology department. During his hospitalization in our hospital, he developed fever, abdominal pain, and lower back pain, and his face, penis, trunk, and limbs developed itchy rash. Subsequently, the patient had to undergo cardiopulmonary resuscitation because of sudden cardiac arrest, and be transferred to ICU for treatment. It was presumed that the cause is unknown severe sepsis. The patient’s condition quickly progressed to multiple organ failure, accompanied by liver, respiratory, and circulatory failure, and signs of disseminated intravascular coagulation. Unfortunately, the patient died after 8 h of active treatment. Finally, we collected all the evidence and concluded that the patient died of AA-PNH syndrome combined with poxzoster virus.ConclusionAA-PNH syndrome patients treated with steroids and immunosuppressants are prone to various infections, considering that herpes virus infection with chickenpox and rash as the initial manifestations is characterized by rapid progress and often accompanied by serious complications. It is more difficult to distinguish it from AA-PNH syndrome with skin bleeding points. If it is not identified in time, it may delay the treatment opportunity, make the condition worse, and cause serious adverse prognosis. Therefore, clinicians need to pay attention to it

CRISPR-Cas13 in malaria parasite: Diagnosis and prospective gene function identification

Malaria caused by Plasmodium is still a serious public health problem. Genomic editing is essential to understand parasite biology, elucidate mechanical pathways, uncover gene functions, identify novel therapeutic targets, and develop clinical diagnostic tools. Recent advances have seen the development of genomic diagnostic technologies and the emergence of genetic manipulation toolbox comprising a host of several systems for editing the genome of Plasmodium at the DNA, RNA, and protein level. Genomic manipulation at the RNA level is critical as it allows for the functional characterization of several transcripts. Of notice, some developed artificial RNA genome editing tools hinge on the endogenous RNA interference system of Plasmodium. However, Plasmodium lacks a robust RNAi machinery, hampering the progress of these editing tools. CRISPR-Cas13, which belongs to the VI type of the CRISPR system, can specifically bind and cut RNA under the guidance of crRNA, with no or minimal permanent genetic scar on genes. This review summarizes CRISPR-Cas13 system from its discovery, classification, principle of action, and diagnostic platforms. Further, it discusses the application prospects of Cas13-based systems in Plasmodium and highlights its advantages and drawbacks