Secondary cerebro-cerebellar and intracerebellar dysfunction in cerebellar mutism syndrome.

BACKGROUND: Cerebellar mutism syndrome (CMS) is characterized by deficits of speech, movement, and affect that can occur following tumor removal from the posterior fossa. The role of cerebrocerebellar tract injuries in the etiology of CMS remains unclear, with recent studies suggesting that cerebrocerebellar dysfunction may be related to chronic, rather than transient, symptomatology. METHODS: We measured functional connectivity between the cerebellar cortex and functional nodes throughout the brain using fMRI acquired after tumor removal but prior to adjuvant therapy in a cohort of 70 patients diagnosed with medulloblastoma. Surgical lesions were mapped to the infratentorial anatomy, and connectivity with cerebral cortex was tested for statistical dependence on extent of cerebellar outflow pathway injury. RESULTS: CMS diagnosis was associated with an increase in connectivity between the right cerebellar and left cerebral hemisphere, maximally between cerebellum and ventromedial prefrontal cortex (VM-PFC). Connectivity dependence on cerebellar outflow was significant for some speech nodes but not for VM-PFC, suggesting altered input to the cerebellum. Connectivity between posterior regions of cerebellar cortex and ipsilateral dentate nuclei was abnormal in CMS participants, maximally within the right cerebellar hemisphere. CONCLUSIONS: The functional abnormalities we identified are notably upstream of where causal surgical injury is thought to occur, indicating a secondary phenomenon. The VM-PFC is involved in several functions that may be relevant to the symptomatology of CMS, including emotional control and motor learning. We hypothesize that these abnormalities may reflect maladaptive learning within the cerebellum consequent to disordered motor and limbic function by the periaqueductal grey and other critical midbrain targets.

Engineering Site 228 of Streptomyces coelicolor Laccase for Optimizing Catalytic Activity.

Malachite green (MG) poses a formidable threat to ecosystems and human health. Laccase emerges as a promising candidate for MG degradation, prompting an investigation into the catalytic activity modulation of a small laccase (SLAC) from Streptomyces coelicolor, with a focus on amino acid position 228. Through saturation mutagenesis, five mutants with a 50% increase in the specific activity were generated. Characterization revealed notable properties, Km of E228F was 8.8% of the wild type (WT), and E288T exhibited a 133% kcat compared to WT. Structural analyses indicated improved hydrophobicity and electrostatic potential on the mutants' surfaces, with the stable E228F-ABTS complex exhibiting reduced flexibility, possibly contributing to the observed decrease in turnover rate. Mutants demonstrated enhanced MG decolorization, particularly E228G. Site 228 acts as a crucial functional control switch, suggesting its potential role in SLAC engineering. This study provides insights into laccase modulation and offers promising avenues for enzymatic bioremediation applications.

Equity-based carbon neutral plan induces cross-regional coal leakage and industrial relocation.

China as a major coal-consuming economy faces the challenge of balancing economic development and carbon neutrality goal. This paper incorporates both efficiency-based and equity-based carbon neutrality policies into a numerical model to quantitatively assess how coal reduction under various carbon-neutral policies affects energy mix, economic growth, and industrial structures by 2060. Results show the nationwide coal intensity will ultimately plunge by over 95% from 2017 to 2060, mainly attributed to the coal-phasing-out in most industries. National Gross Domestic Product losses reaches 4,951 billion USD in efficiency-based scenarios by 2060, and the economic losses are even more severe in less developed provinces, especially provinces in Northern China. Although the equity-based policy can reduce the economic burden for the Northern China, the equity-based policy is accompanied by a significant regional shift in coal across the country: eastern coal-intense industries will be relocated northward, leading to increases in embodied coal consumption.

Effects of collagen hydrolysates on UV-induced photoaging mice: Gly-Pro-Hyp as a potent anti-photoaging peptide.

This work aimed to investigate the protective effects of collagen hydrolysates containing different contents of Gly-Pro-Xaa tripeptides on UV-induced photoaging mice and to identify potent anti-photoaging peptides. Results showed that oral ingestion of collagen hydrolysates with a higher content of Gly-Pro-Xaa tripeptides (∼11.4%, HCH) dramatically enhanced the absorption of Pro-Hyp, Hyp-Gly, and Gly-Pro-Hyp into the body, which were 1.77-, 2.18-, and 65.07-fold higher in area under the concentration-time curve (AUC) values than that of collagen hydrolysates with a lower content of Gly-Pro-Xaa tripeptides (∼3.8%, LCH), respectively. Furthermore, the protective effects of HCH on the photo-aged skin of mice were significantly stronger than those of LCH in terms of increases in the contents of hyaluronic acid and collagen, improvement in skin elasticity and epidermal thickness, alleviation in inflammation, and decreases in the contents of matrix metalloproteinase-1 (MMP-1) and MMP-3. More importantly, Gly-Pro-Hyp displayed potent anti-photoaging activities comparable to HCH based on an equivalent amount of Hyp. Network pharmacology analysis for potential mechanisms further indicated that Gly-Pro-Hyp might interact with JUN and FOS and regulate IL-17 and TNF signaling pathways. Collectively, our results suggested that HCH had great potential to be applied in functional foods for skin health and Gly-Pro-Hyp was found to be a potent collagen-derived anti-photoaging peptide, which might contribute to the excellent anti-photoaging effects of HCH.

Isolation of Lactobacillus acidophilus strain and its anti-obesity effect in a diet induced obese murine model.

Intestinal microbiota is a potential determinant of obesity, with probiotic bile salt hydrolase (BSH) as one of the key mechanisms in the anti-obesity effects. In this study, we present a Lactobacillus acidophilus GOLDGUT-LA100 (LA100) with high BSH activity, good gastric acid and bile salt tolerance, and a potential anti-obesity effect. LA100's anti-obesity effects were evaluated in a high-fat diet-induced, obese mouse model. LA100 administration alleviates high-fat diet-induced pathophysiological symptoms, such as body weight gain, high serum glucose and cholesterol level, hepatic lipid accumulation, and adipose inflammation. These results demonstrate concrete anti-obesity benefit in animal models and show promising applications in future clinical studies.

A Bifidobacterium animalis subsp. lactis strain that can suppress Helicobacter pylori: isolation, in vitro and in vivo validation.

The administration of probiotics is an effective approach for treatment of Helicobacter pylori, which is associated with human gastrointestinal diseases and cancers. To explore more effective probiotics for H. pylori infection elimination, bacteria from infant feces were screened in this study. We successfully isolated the Bifidobacterium animalis subsp. lactis strains and evaluated its efficacy to inhibit H. pylori growth in vitro and in vivo. The results showed that a B. animalis strain (named BB18) sustained a high survival rate after incubation in gastric juice. The rapid urease test suggested that B. animalis BB18 reduced pathogen loads in H. pylori-infected Mongolian gerbils. Alleviation of H. pylori infection-induced gastric mucosa damage and decreased levels inflammatory cytokines were observed after the B. animalis BB18 administration. These findings demonstrated that B. animalis BB18 can inhibit H. pylori infection both in vitro and in vivo, suggesting its potential application for the prevention and eradication therapy of H. pylori infection.

Costs and health benefits of the rural energy transition to carbon neutrality in China.

The rural energy transition is critical in China's efforts to achieve carbon neutrality and improve air quality. However, the costs and health benefits associated with the transition to carbon neutrality remain unclear. Here we explore the cost-effective transition pathways and air quality-related health impacts using an integrated energy-air quality-health modeling framework. We find that decarbonizing rural cooking and heating would triple contemporary energy consumption from 2014 to 2060, considerably reducing energy poverty nationwide. By 2060, electric cooking ranges and air-to-air heat pumps should be widely integrated, costing an additional 13 billion USD nationally in transformation costs, with ~40% concentrated in Shandong, Heilongjiang, Shanxi and Hebei provinces. Rural residential decarbonization would remarkably improve air quality in northern China, yielding substantial health co-benefits. Notably, monetized health benefits in most provinces are projected to offset transformation costs, except for certain relatively lower-development southwestern provinces, implying more financial support for rural residents in these areas will be needed.

Beer-gut microbiome alliance: a discussion of beer-mediated immunomodulation via the gut microbiome.

As a long-established fermented beverage, beer is rich in many essential amino acids, vitamins, trace elements, and bioactive substances that are involved in the regulation of many human physiological functions. The polyphenols in the malt and hops of beer are also important active compounds that interact in both directions with the gut microbiome. This review summarizes the mechanisms by which polyphenols, fiber, and other beneficial components of beer are fermentatively broken down by the intestinal microbiome to initiate the mucosal immune barrier and thus participate in immune regulation. Beer degradation products have anti-inflammatory, anticoagulant, antioxidant, and glucolipid metabolism-modulating potential. We have categorized and summarized reported data on changes in disease indicators and in vivo gut microbiota abundance following alcoholic and non-alcoholic beer consumption. The positive effects of bioactive substances in beer in cancer prevention, reduction of cardiovascular events, and modulation of metabolic syndrome make it one of the candidates for microecological modulators.

Effect of a probiotic formula on gastrointestinal health, immune responses and metabolic health in adults with functional constipation or functional diarrhea.

Objective: Our aim was to determine the efficacy of four-week probiotic supplementation on gastrointestinal health. The secondary objectives were to assess probiotic effects on immune reaction, as well as weight control and metabolic health. Methods: We conducted two randomized sub-trials, respectively, among subjects who were diagnosed with functional constipation (FC) or functional diarrhea (FDr) according to the Rome IV criteria. In each sub-trial, 70 eligible Chinese adults were randomized to receive a multi-strain probiotic combination or a placebo. Gastrointestinal symptoms, defecation habits, stool characteristics, blood and fecal biochemistry markers, anthropometrics measures, stress-associated responses, and intestinal flora changes were assessed at baseline and after probiotics intervention. Results: Four weeks of probiotic supplementation reduced overall gastrointestinal symptoms scores in FC participants (p < 0.0001). Their mean weekly stool frequency increased from 3.3 times to 6.2 times; immune response and inflammation markers improved with increases in serum IgA, IFN-γ and fecal sIgA, and decrease in hsCRP; most components of lipid profile were significantly ameliorated, with increases in HDL-C and reductions in TC and TG; body weight, body mass index and basal metabolic rate decreased following probiotics consumption. For FDr participants, probiotics consumption markedly reduced overall gastrointestinal symptom scores (p < 0.0001); decreased stool frequency by 3 times per week; increased IgA, IFN-γ, sIgA concentrations, while lowered hsCRP and IL-4 levels. Both FC and FDr participants had improvement in the scores of defecation habits, anxiety or depression, and perceived stress. Probiotics supplementation promoted the production of all three major short-chain fatty acids. No changes were observed in LDL-C, IgG, IgM, IL-8, IL-10 and motilin. Conclusion: Supplementation with the probiotic formula over a four-week period could help relieving gastrointestinal symptoms, improving satisfaction with defecation habits, emotional state and immune response, and ameliorating dysbacteriosis in participants with FC or FDr. It also had beneficial effects on lipid metabolism and weight control for FC participants.

Regionally differentiated promotion of electric vehicles in China considering environmental and human health impacts.

Private passenger vehicles, with its high emissions of CO2 and air pollutants, poses a severe threat to global climate and human health, particularly for a large developing country like China. Although both energy efficiency improvement of internal combustion engine vehicles (ICEVs) and the wide adoption of electric vehicles (EVs) could contribute to reducing emissions, how they should be jointly implemented in provinces with a heterogeneous context to maximize their net benefits remains insufficiently explored. Here, based on an integrated modeling framework associated with one factual (REF) and four counterfactual scenarios to explore the priority and best-ranked ordering of both EVs' penetration and high energy-efficient ICEVs in 31 Chinese provinces to achieve the most environmental and human health benefits from 2011 to 2018. The results demonstrate that electrification of the passenger fleet, which is charged by a slightly cleaner power source relative to 2011, yields significant co-benefits of CO2 reduction and air quality improvement. Compared with REF, the fleet electrification scenario would lead to 3167 cases of avoided mortality and attain US$4.269 billion of health benefits in 2018, accounting for 0.03% of China's gross domestic product. Nonetheless, highly efficient ICEVs are found to harbor decarbonization potential and health benefits in northern China. Based on these results, Sichuan, Hebei and seven other provinces in east China should promote EVs imminently; conversely, eight provinces with a high share of thermal power must continually advance their implementation of ICEVs in the near future. Such prioritization of EVs and ICEV development at the provincial level provides timely insights for devising tailored policies regarding passenger car transition and for maximizing climate and health benefits based on regional heterogeneity.

Cerebellar mutism is linked to midbrain volatility and desynchronization from speech cortices.

Cerebellar mutism syndrome is a disorder of speech, movement and affect that can occur after tumour removal from the posterior fossa. Projections from the fastigial nuclei to the periaqueductal grey area were recently implicated in its pathogenesis, but the functional consequences of damaging these projections remain poorly understood. Here, we examine functional MRI data from patients treated for medulloblastoma to identify functional changes in key brain areas that comprise the motor system for speech, which occur along the timeline of acute speech impairment in cerebellar mutism syndrome. One hundred and twenty-four participants, all with medulloblastoma, contributed to the study: 45 with cerebellar mutism syndrome, 11 patients with severe postoperative deficits other than mutism, and 68 without either (asymptomatic). We first performed a data-driven parcellation to spatially define functional nodes relevant to the cohort that align with brain regions critical for the motor control of speech. We then estimated functional connectivity between these nodes during the initial postoperative imaging sessions to identify functional deficits associated with the acute phase of the disorder. We further analysed how functional connectivity changed over time within a subset of participants that had suitable imaging acquired over the course of recovery. Signal dispersion was also measured in the periaqueductal grey area and red nuclei to estimate activity in midbrain regions considered key targets of the cerebellum with suspected involvement in cerebellar mutism pathogenesis. We found evidence of periaqueductal grey dysfunction in the acute phase of the disorder, with abnormal volatility and desynchronization with neocortical language nodes. Functional connectivity with periaqueductal grey was restored in imaging sessions that occurred after speech recovery and was further shown to be increased with left dorsolateral prefrontal cortex. The amygdalae were also broadly hyperconnected with neocortical nodes in the acute phase. Stable connectivity differences between groups were broadly present throughout the cerebrum, and one of the most substantial differences-between Broca's area and the supplementary motor area-was found to be inversely related to cerebellar outflow pathway damage in the mutism group. These results reveal systemic changes in the speech motor system of patients with mutism, centred on limbic areas tasked with the control of phonation. These findings provide further support for the hypothesis that periaqueductal grey dysfunction (following cerebellar surgical injury) contributes to the transient postoperative non-verbal episode commonly observed in cerebellar mutism syndrome but highlights a potential role of intact cerebellocortical projections in chronic features of the disorder.

Automatic detection and segmentation of postoperative cerebellar damage based on normalization.

Background: Surgical resection is the gold standard in the treatment of pediatric posterior fossa tumors. However, surgical damage is often unavoidable and its association with postoperative complications is not well understood. A reliable localization and measure of cerebellar damage is fundamental to study the relationship between the damaged cerebellar regions and postoperative neurological outcomes. Existing cerebellum normalization methods are likely to fail on postoperative scans, therefore current approaches to measure postoperative damage rely on manual labelling. In this work, we develop a robust algorithm to automatically detect and measure cerebellum damage in postoperative 3D T1 magnetic resonance imaging (MRI). Methods: In our approach, normal brain tissues are first segmented using a Bayesian algorithm customized for postoperative scans. Next, the cerebellum is isolated by nonlinear registration of a whole-brain template to the native space. The isolated cerebellum is then normalized into the spatially unbiased atlas (SUIT) space using anatomical information derived from the previous step. Finally, the damage is detected in the atlas space by comparing the normalized cerebellum and the SUIT template. Results: We evaluated our damage detection tool on postoperative scans of 153 patients with medulloblastoma based on inspection by human experts. We also designed a simulation to evaluate performance without human intervention and with an explicitly controlled and defined ground truth. Our results show that the approach performs adequately under various realistic conditions. Conclusions: We develop an accurate, robust, and fully automatic localization and measurement of cerebellar damage in the atlas space using postoperative MRI.

Lipid accumulation and SNF1 transcriptional analysis of Mucor circinelloides on xylose under nitrogen limitation.

Sucrose non-fermenting 1 (SNF1) plays a crucial role in utilizing non-glucose carbon sources and regulating lipid metabolism. However, the mechanism by which SNF1 regulates lipid accumulation in oleaginous filamentous fungi in response to nutrient signals remains unclear. In the present study, by analysing the growth and lipid accumulation of M. circinelloides on xylose under nitrogen limitation, combined with the transcriptional changes of each subunit of SNF1, the regulation of SNF1 between nutrient signal and lipid accumulation was explored. The results showed that with the increase of carbon/nitrogen (C/N) ratio, the xylose consumption and cell growth of M. circinelloides decreased, and the lipid accumulation increased gradually. The optimal C/N ratio was 160:1, and the maximum lipid yield was 4.1 g/L. Two subunits of SNF1, Snf-α1 and Snf-ß, are related to the regulation of lipid metabolism in response to nutrient signals from different external nitrogen sources. This is the first report on the transcriptional analysis of SNF1 subunits on xylose metabolism under nitrogen limitation. This study provides a basis for further understanding of lipid synthesis mechanism on xylose in oleaginous fungi, and it also lays a foundation for the genetic engineering of high-lipid strain.

Fastigial nuclei surgical damage and focal midbrain disruption implicate PAG survival circuits in cerebellar mutism syndrome.

BACKGROUND: Pediatric postoperative cerebellar mutism syndrome (CMS) is a rare but well-known complication of medulloblastoma (Mb) resection with devastating effects on expressive language, mobility, cognition, and emotional regulation that diminishes quality of life for many Mb survivors. The specific anatomical and neuronal basis of CMS remains obscure. We address this issue by identifying patterns of surgical damage and secondary axonal degeneration in Mb survivors with CMS. METHODS: Children with Mb deemed high risk for CMS based on intraventricular location of the tumor had T1 images analyzed for location(s) of surgical damage using a specially developed algorithm. We used three complementary methods of spatial analysis to identify surgical damage linked to CMS diagnosis. Magnetization transfer ratio (MTR) images were analyzed for evidence of demyelination in anatomic regions downstream of the cerebellum, indicating neuronal dysfunction. RESULTS: Spatial analyses highlighted damage to the fastigial nuclei and their associated cerebellar cortices as the strongest predictors of CMS. CMS-related MTR decrease was greatest in the ventral periaqueductal gray (PAG) area and highly consistent in the left red nucleus. CONCLUSION: Our evidence points to disruption of output from the fastigial nuclei as a likely causal trigger for CMS. We propose that core CMS symptoms result from a disruption in the triggering of survival behaviors regulated by the PAG, including the gating of vocalization and volitional movement. The fastigial nuclei provide the densest output to the PAG from the cerebellum, thus sparing these structures may provide a greater likelihood of CMS prevention.

Essential oils of Zingiber officinale: Chemical composition, in vivo alleviation effects on TPA induced ear swelling in mice and in vitro bioactivities.

Zingiber officinale (ZO) is a traditional food condiment. The essential oils of Z. officinale (ZOEOs) are known to have multiple bioactivities. In this study, gas chromatography mass spectrometer (GC-MS) analytical method was used to identify active ingredient present in ZOEOs. A total of 41 compounds were identified in ZOEOs. Major components in ZOEOs were zingiberene (19.71%), (+)-ß-cedrene (12.85%), farnesene (12.17%), α-curcumene (10.18%) and ß-elemene (3.54%). Experimental results of 12-O-tetradecanoylphorbol-13 acetate (TPA) induced ear swelling validation mice model showed that ZOEOs treatment has better anti-inflammatory effect compared with ibuprofen (positive control) at high concentrations. Histological and immunohistochemical analysis showed that ZOEOs significantly decreased COX-2, IL-6 and NF-κB expression in a dose dependent manner. The mRNA levels of COX-2 and NF-κB were also down regulated by the application of ZOEOs. This indicated that ZOEOs exhibited positive effects in ear skin protection. Antibacterial experimental results showed that EOZOs had anti-bacterial effects on Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. DPPH radical scavenging, A549 cell line and LNCaP cell line inhibition results indicated that ZOEOs exhibited potential antioxidant and anti-tumor properties. The findings of these study provide scientific basis on therapeutic use of ZO in food, cosmetic and pharmaceutical industries.

Unified rhombic lip origins of group 3 and group 4 medulloblastoma.

Medulloblastoma, a malignant childhood cerebellar tumour, segregates molecularly into biologically distinct subgroups, suggesting that a personalized approach to therapy would be beneficial1. Mouse modelling and cross-species genomics have provided increasing evidence of discrete, subgroup-specific developmental origins2. However, the anatomical and cellular complexity of developing human tissues3-particularly within the rhombic lip germinal zone, which produces all glutamatergic neuronal lineages before internalization into the cerebellar nodulus-makes it difficult to validate previous inferences that were derived from studies in mice. Here we use multi-omics to resolve the origins of medulloblastoma subgroups in the developing human cerebellum. Molecular signatures encoded within a human rhombic-lip-derived lineage trajectory aligned with photoreceptor and unipolar brush cell expression profiles that are maintained in group 3 and group 4 medulloblastoma, suggesting a convergent basis. A systematic diagnostic-imaging review of a prospective institutional cohort localized the putative anatomical origins of group 3 and group 4 tumours to the nodulus. Our results connect the molecular and phenotypic features of clinically challenging medulloblastoma subgroups to their unified beginnings in the rhombic lip in the early stages of human development.

Sodium alginate and galactooligosaccharides ameliorate metabolic disorders and alter the composition of the gut microbiota in mice with high-fat diet-induced obesity.

We aimed to investigate the effects of sodium alginate (SA) and galactooligosaccharides (GOS) on the metabolism and gut microbiota of high-fat diet (HFD)-fed obese mice. GOS and SA delayed high-fat diet-induced obesity, reduced the epididymal fat and liver indices, and improved the circulating lipid profile. Low- and high-dose GOS reduced weight gain by 48.8 % and 35.3 %, and low- and high-dose SA reduced it by 37.7 % and 34.4 %, respectively. GOS and SA reduced blood glucose concentration, probably by increasing the expression of glucose transporter 4. GOS and SA increased the expression of tight junction proteins (ZO-1 and occludin), reduced the D-lactic acid (D-LA) and lipopolysaccharide concentrations, and reduced the expression of toll-like receptors, consistent with improved intestinal barrier function. GOS and SA also increased the abundance of Bacteroidota, Bifidobacterium, and Lactobacillus; and reduced that of Patescibacteria in the gut. The abundance of Parabacteroides positively correlated with the circulating low-density lipoprotein-cholesterol (LDL-C) concentration; that of Lactobacillus negatively correlated with LDL-C, D-LA, and tumor necrosis factor-α concentration; and that of Bifidobacterium positively correlated with high-density lipoprotein-cholesterol concentration, according to Spearman correlation analysis. In conclusion, SA and GOS ameliorate obesity and the associated metabolic disorders in mice, and also modulate their gut microbial composition.

Biogeographic Role of the Kuroshio Current Intrusion in the Microzooplankton Community in the Boundary Zone of the Northern South China Sea.

Kuroshio Current intrusion (KCI) has significant impacts on the oceanographic conditions and ecological processes of the Pacific-Asian marginal seas. Little is known to which extent and how, specifically, the microzooplankton community can be influenced through the intrusion. Here, we focused on ciliates that often dominated the microzooplankton community and investigated their communities using high-throughput sequencing of 18S rRNA gene transcripts in the northern South China Sea (NSCS), where the Kuroshio Current (KC) intrudes frequently. We first applied an isopycnal mixing model to assess the fractional contribution of the KC to the NSCS. The ciliate community presented a provincial distribution pattern corresponding to more and less Kuroshio-influenced stations. Structural equation modeling revealed a significant impact of the KCI on the community, while environmental variables had a marginal impact. KCI-sensitive OTUs were taxonomically diverse but mainly belonged to classes Spirotrichea and Phyllopharyngea, suggesting the existence of core ciliates responding to the KCI. KCI-sensitive OTUs were grouped into two network modules that showed contrasting abundance behavior with the KC fraction gradient, reflecting differential niches (i.e., winner and loser) in the ciliate community during the Kuroshio intrusion scenarios. Our study showed that the Kuroshio intrusion, rather than environmental control, was particularly detrimental to the oligotrophic microzooplankton community.

Estimating Feature-Label Dependence Using Gini Distance Statistics.

Identifying statistical dependence between the features and the label is a fundamental problem in supervised learning. This paper presents a framework for estimating dependence between numerical features and a categorical label using generalized Gini distance, an energy distance in reproducing kernel Hilbert spaces (RKHS). Two Gini distance based dependence measures are explored: Gini distance covariance and Gini distance correlation. Unlike Pearson covariance and correlation, which do not characterize independence, the above Gini distance based measures define dependence as well as independence of random variables. The test statistics are simple to calculate and do not require probability density estimation. Uniform convergence bounds and asymptotic bounds are derived for the test statistics. Comparisons with distance covariance statistics are provided. It is shown that Gini distance statistics converge faster than distance covariance statistics in the uniform convergence bounds, hence tighter upper bounds on both Type I and Type II errors. Moreover, the probability of Gini distance covariance statistic under-performing the distance covariance statistic in Type II error decreases to 0 exponentially with the increase of the sample size. Extensive experimental results are presented to demonstrate the performance of the proposed method.

A comparison of methods accounting for batch effects in differential expression analysis of UMI count based single cell RNA sequencing.

Accounting for batch effects, especially latent batch effects, in differential expression (DE) analysis is critical for identifying true biological effects. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for quantifying cell-to-cell variation in transcript abundance and characterizing cellular dynamics. Although many scRNA-seq DE analysis methods accommodate known batch variables, their performance has not been systematically evaluated. Moreover, the challenge of accounting for latent batch variables in scRNA-seq DE analysis is largely unmet. In contrast, many methods have been developed to account for batch variables (either known or latent) in other high-dimensional data, especially bulk RNA-seq. We extensively evaluate 11 methods for batch variables in different scRNA-seq DE analysis scenarios, with a primary focus on latent batch variables. We demonstrate that for known batch variables, incorporating them as covariates into a regression model outperformed approaches using a batch-corrected matrix. For latent batches, fixed effects models have inflated FDRs, whereas aggregation-based methods and mixed effects models have significant power loss. Surrogate variable based methods generally control the FDR well while achieving good power with small group effects. However, their performance (except that of SVA) deteriorated substantially in scenarios involving large group effects and/or group label impurity. In these settings, SVA achieves relatively good performance despite an occasionally inflated FDR (up to 0.2). Finally we make the following recommendations for scRNA-seq DE analysis: 1) incorporate known batch variables instead of using batch-corrected data; and 2) employ SVA for latent batch correction. However, better methods are still needed to fully unleash the power of scRNA-seq.