Using Coherence to Measure Regional Homogeneity of Resting-State fMRI Signal

In this study, we applied coherence to voxel-wise measurement of regional homogeneity of resting-state functional magnetic resonance imaging (RS-fMRI) signal. We compared the current method, regional homogeneity based on coherence (Cohe-ReHo), with previously proposed method, ReHo based on Kendall's coefficient of concordance (KCC-ReHo), in terms of correlation and paired t-test in a large sample of healthy participants. We found the two measurements differed mainly in some brain regions where physiological noise is dominant. We also compared the sensitivity of these methods in detecting difference between resting-state conditions [eyes open (EO) vs. eyes closed (EC)] and in detecting abnormal local synchronization between two groups [attention deficit hyperactivity disorder (ADHD) patients vs. normal controls]. Our results indicated that Cohe-ReHo is more sensitive than KCC-ReHo to the difference between two conditions (EO vs. EC) as well as that between ADHD and normal controls. These preliminary results suggest that Cohe-ReHo is superior to KCC-ReHo. A possible reason is that coherence is not susceptible to random noise induced by phase delay among the time courses to be measured. However, further investigation is still needed to elucidate the sensitivity and specificity of these methods

Application of operando X-ray diffraction and Raman spectroscopies in elucidating the behavior of cathode in lithium-ion batteries

With the advances in characterization techniques, various operando/in-situ methods were applied in studying rechargeable batteries in order to improve the electrochemical properties of electrode materials, prolonging the battery life and developing new battery materials. In the present review, we focus on the characterization of electrode materials with operando/in-situ X-ray diffraction and Raman spectroscopies. By correlating the results obtained via these two techniques in different electrode chemistry: (a) intercalation materials, such as layered metal oxides and (b) conversion materials, such as elemental sulfur. We demonstrate the importance of using operando/in-situ techniques in examining the microstructural changes of the electrodes under various operating conditions, in both macro and micro-scales. These techniques also reveal the working and the degradation mechanisms of the electrodes and the possible side reactions involved. The comprehension of these mechanisms is fundamental for ameliorating the electrode materials, enhancing the battery performance and lengthening its cycling life

Spontaneous Brain Activity in the Default Mode Network Is Sensitive to Different Resting-State Conditions with Limited Cognitive Load

BACKGROUND: Recent functional MRI (fMRI) studies have demonstrated that there is an intrinsically organized default mode network (DMN) in the resting brain, primarily made up of the posterior cingulate cortex (PCC) and the medial prefrontal cortex (MPFC). Several previous studies have found that the DMN is minimally disturbed during different resting-state conditions with limited cognitive demand. However, this conclusion was drawn from the visual inspection of the functional connectivity patterns within the DMN and no statistical comparison was performed. METHODOLOGY/PRINCIPAL FINDINGS: Four resting-state fMRI sessions were acquired: 1) eyes-closed (EC) (used to generate the DMN mask); 2) EC; 3) eyes-open with no fixation (EO); and 4) eyes-open with a fixation (EO-F). The 2-4 sessions were counterbalanced across participants (n = 20, 10 males). We examined the statistical differences in both functional connectivity and regional amplitude of low frequency fluctuation (ALFF) within the DMN among the 2-4 resting-state conditions (i.e., EC, EO, and EO-F). Although the connectivity patterns of the DMN were visually similar across these three different conditions, we observed significantly higher functional connectivity and ALFF in both the EO and the EO-F conditions as compared to the EC condition. In addition, the first and second resting EC conditions showed significant differences within the DMN, suggesting an order effect on the DMN activity. CONCLUSIONS/SIGNIFICANCE: Our findings of the higher DMN connectivity and regional spontaneous activities in the resting state with the eyes open suggest that the participants might have more non-specific or non-goal-directed visual information gathering and evaluation, and mind wandering or daydreaming during the resting state with the eyes open as compared to that with the eyes closed, thus providing insights into the understanding of unconstrained mental activity within the DMN. Our results also suggest that it should be cautious when choosing the type of a resting condition and designating the order of the resting condition in multiple scanning sessions in experimental design

An open science resource for establishing reliability and reproducibility in functional connectomics

Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals’ resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included

Characterizing ecosystem water-use efficiency of croplands with eddy covariance measurements and MODIS products

How to quantify the variability in ecosystem water use efficiency (WUE) of croplands is of vital importance. Especially in the context of changing hydrologic environment, much attention need to be paid on how to use limited water to improve crop yield. However, the biophysical performances of environmental/biological controls, crop types, and effects of diverse farming practices on WUE remain unclear. Therefore, this study aims to address these questions through tower-based measurements from eddy covariance and satellite-based estimates from MODIS GPP and ET products at the two annual soybean/corn rotation fields. The results exhibited that temperature and solar radiation are the most important meteorological factors. MODIS WUE estimates captured the broad trend of 8-day tower-based observations. However, ecosystem WUE was overpredicted at the seedling stage and after harvest, and was severely underestimated at the peak periods of maize, which was mainly ascribed to the uncertainties in MODIS GPP. Finally, we evaluated the effects of two farming practices (conventional vs alternative) on WUE and carbon sequence (NEE). On annual time scale, WUE of both soybean and maize are improved obviously under the alternative management whereas contrasting effects are observed on NEE. But the overall carbon balance for both treatments is nearly identical over 2-year rotation

Integrative analysis of co-expression pattern of solute carrier transporters reveals molecular subtypes associated with tumor microenvironment hallmarks and clinical outcomes in colon cancer

Recent findings have suggested that solute carrier (SLC) transporters play an important role in tumor development and progression, and alterations in the expression of individual SLC genes are critical for fulfilling the heightened metabolic requirements of cancerous cells. However, the global influence of the co-expression pattern of SLC transporters on the clinical stratification and characteristics of the tumor microenvironment (TME) remains unexplored. In this study, we identified five SLC gene subtypes based on transcriptome co-expression patterns of 187 SLC transporters by consensus clustering analysis. These subtypes, which were characterized by distinct TME and biological characteristics, were successfully employed for prognostic and chemotherapy response prediction in colon cancer patients, as well as demonstrated associations with immunotherapy benefits. Then, we generated an SLC score model comprising 113 genes to quantify SLC gene co-expression patterns and validated it as an independent prognostic factor and drug response predictor in several independent colon cancer cohorts. Patients with a high SLC score possessed distinct characteristics of copy number variation, genomic mutations, DNA methylation, and indicated an SLC-S2 subtype, which was characterized by strong stromal cell infiltration, stromal pathway activation, poor prognosis, and low predicted fluorouracil and immunotherapeutic responses. Furthermore, the analysis of the Cancer Therapeutics Response Portal database revealed that inhibitors targeting PI3K catalytic subunits could serve as promising chemosensitizing agents for individuals exhibiting high SLC scores. In conclusion, the co-expression patterns of SLC transporters aided the disease classification, and the SLC score proved to be a reliable tool for distinguishing SLC gene subtypes and guiding precise treatment in patients with colon cancer

Application of Operando X-ray Diffractometry in Various Aspects of the Investigations of Lithium/Sodium-Ion Batteries

The main challenges facing rechargeable batteries today are: (1) increasing the electrode capacity; (2) prolonging the cycle life; (3) enhancing the rate performance and (4) insuring their safety. Significant efforts have been devoted to improve the present electrode materials as well as to develop and design new high performance electrodes. All of the efforts are based on the understanding of the materials, their working mechanisms, the impact of the structure and reaction mechanism on electrochemical performance. Various operando/in-situ methods are applied in studying rechargeable batteries to gain a better understanding of the crystal structure of the electrode materials and their behaviors during charge-discharge under various conditions. In the present review, we focus on applying operando X-ray techniques to investigate electrode materials, including the working mechanisms of different structured materials, the effect of size, cycling rate and temperature on the reaction mechanisms, the thermal stability of the electrodes, the degradation mechanism and the optimization of material synthesis. We demonstrate the importance of using operando/in-situ XRD and its combination with other techniques in examining the microstructural changes of the electrodes under various operating conditions, in both macro and atomic-scales. These results reveal the working and the degradation mechanisms of the electrodes and the possible side reactions involved, which are essential for improving the present materials and developing new materials for high performance and long cycle life batteries

Requirement of microtubules for secretion of a micronemal protein CpTSP4 in the invasive stage of the apicomplexan Cryptosporidium parvum

ABSTRACTThe zoonotic Cryptosporidium parvum is a global contributor to infantile diarrheal diseases and opportunistic infections in immunocompromised or weakened individuals. Like other apicomplexans, it possesses several specialized secretory organelles, including micronemes, rhoptry, and dense granules. However, the understanding of cryptosporidial micronemal composition and secretory pathway remains limited. Here, we report a new micronemal protein in C. parvum, namely, thrombospondin (TSP)-repeat domain-containing protein-4 (CpTSP4), providing insights into these ambiguities. Immunostaining and enzyme-linked assays show that CpTSP4 is prestored in the micronemes of unexcysted sporozoites but secreted during sporozoite excystation, gliding, and invasion. In excysted sporozoites, CpTSP4 is also distributed on the two central microtubules unique to Cryptosporidium. The secretion and microtubular distribution could be completely blocked by the selective kinesin-5 inhibitors SB-743921 and SB-715992, resulting in the accumulation of CpTSP4 in micronemes. These support the kinesin-dependent microtubular trafficking of CpTSP4 for secretion. We also localize γ-tubulin, consistent with kinesin-dependent anterograde trafficking. Additionally, recombinant CpTSP4 displays nanomolar binding affinity to the host cell surface, for which heparin acts as one of the host ligands. A novel heparin-binding motif is identified and validated biochemically for its contribution to the adhesive property of CpTSP4 by peptide competition assays and site-directed mutagenesis. These findings shed light on the mechanisms of intracellular trafficking and secretion of a cryptosporidial micronemal protein and the interaction of a TSP-family protein with host cells.IMPORTANCECryptosporidium parvum is a globally distributed apicomplexan parasite infecting humans and/or animals. Like other apicomplexans, it possesses specialized secretory organelles in the zoites, in which micronemes discharge molecules to facilitate the movement and invasion of zoites. Although past and recent studies have identified several proteins in cryptosporidial micronemes, our understanding of the composition, secretory pathways, and domain-ligand interactions of micronemal proteins remains limited. This study identifies a new micronemal protein, namely, CpTSP4, that is discharged during excystation, gliding, and invasion of C. parvum sporozoites. The CpTSP4 secretion depends on the intracellular trafficking on the two Cryptosporidium-unique microtubes that could be blocked by kinesin-5/Eg5 inhibitors. Additionally, a novel heparin-binding motif is identified and biochemically validated, which contributes to the nanomolar binding affinity of CpTSP4 to host cells. These findings indicate that kinesin-dependent microtubular trafficking is critical to CpTSP4 secretion, and heparin/heparan sulfate is one of the ligands for this micronemal protein