Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct roles of PV and Sst interneurons in visually-induced gamma oscillations

Sensory processing relies on interactions between excitatory and inhibitory neurons, which are often coordinated by 30-80Hz gamma oscillations. However, the specific contributions of distinct interneurons to gamma synchronization remain unclear. We performed high-density recordings from V1 in awake mice and used optogenetics to identify PV+ (Parvalbumin) and Sst+ (Somatostatin) interneurons. PV interneurons were highly phase-locked to visually-induced gamma oscillations. Sst cells were heterogeneous, with only a subset of narrow-waveform cells showing strong gamma phase-locking. Interestingly, PV interneurons consistently fired at an earlier phase in the gamma cycle (≈6ms or 60 degrees) than Sst interneurons. Consequently, PV and Sst activity showed differential temporal relations with excitatory cells. In particular, the 1st and 2nd spikes in burst events, which were strongly gamma phase-locked, shortly preceded PV and Sst activity, respectively. These findings indicate a primary role of PV interneurons in synchronizing excitatory cells and suggest that PV and Sst interneurons control the excitability of somatic and dendritic neural compartments with precise time delays coordinated by gamma oscillations.
Single-cell transcriptome analysis reveals the cellular atlas of human intracranial aneurysm and highlights inflammation features associated with aneurysm rupture

Intracranial aneurysm (IA) is pouch-like pathological dilations of cerebral arteries, which often affects middle-aged people and culminates in life-threatening hemorrhagic stroke. A deeper knowledge of the cellular and gene expression perturbations in human IA tissue deepens our understanding of disease mechanisms and facilitates developing pharmacological targets for unruptured IA. In this study, 21,332 qualified cells were obtained from cell-sparse ruptured and unruptured human IA tissues and a detailed cellular profile was determined, including conventional endothelial cells, smooth muscle cells (SMC), fibroblasts and the newly identified pericytes. Notably, striking proportion of immune cells were identified in IA tissue, with the number of monocyte/macrophages and neutrophils being remarkably higher in ruptured IA. By leveraging external datasets and machine learning algorithms, a subset of macrophages characterized by high expression of CCL3 and CXCL3, and transcriptional activation of NF-κB and HIVEP2 was identified as the cell most associated with IA rupture. Further, the interactome of CCL3/CXCL3 macrophages disclosed their role in regulating vascular cell survival and orchestrating inflammation. In summary, this study illustrated the profile and interactions of vascular and immune cells in human IA tissue and the opportunities for targeting local chronic inflammation.
Classical Theory for Propagation Through Random Media

Overview: In this chapter we introduce the stochastic Helmholtz equation as the governing partial differential equation for the scalar field of an optical wave propagating through a random medium. However, we provide only the foundational material here for the classical methods of solving the Helmholtz equation. It is interesting that all such methods are based on the same set of simplifying assumptions - backscattering and depolarization effects are negligible, the refractive index is delta correlated in the direction of propagation (Markov approximation), and the paraxial approximation can be invoked. The Born and Rytov perturbation methods for solving the stochastic Helmholtz equation are introduced first. Whereas the Born approximation has limited utility in optical wave propagation, the Rytov approximation has successfully been used to predict all relevant statistical parameters associated with laser propagation throughout regimes featuring weak irradiance fluctuations. We also illustrate that the Rytov approximation can be generalized to include wave propagation through a train of optical elements that are all characterized by ABCD matrix representations. Methods applicable also under strong irradiance fluctuations are briefly discussed here but formulated in greater detail in Chap. 7. These methods are the parabolic equation method, which is based on the development of parabolic equations for each of the statistical moments of the field, and the extended Huygens-Fresnel principle. Early probability density function (PDF) models developed for the irradiance of the optical wave include the modified Rician distribution, which follows from the Born approximation, and the lognormal model, which follows directly from the first Rytov approximation. Of these two PDFs, only the lognormal PDF model compares well with the lower-order irradiance moments calculated from experimental data under weak fluctuation conditions. Hence, in this regime it has been the most often-used model for calculating fade statistics associated with a fading communications channel. Nonetheless, more recent investigations of the lognormal PDF suggest that it may be optimistic in predicting fade probabilities, even in weak fluctuation regimes. We end the chapter with a modification of the Rytov method called the extended Rytov theory that utilizes the two-scale behavior of the propagating wave encountered in regimes of strong irradiance fluctuations. The formalism of the method presented here permits the development of new models for beam wander and scintillation in subsequent chapters that are applicable under strong fluctuations.
Layer Dependence of Monocular and Binocular Responses in Human Ocular Dominance Columns at 7T using VASO and BOLD

The neurons located in the striate cortex (V1) preferentially respond to the input from one eye or another, forming a fingerprint-like pattern of ocular dominance columns (ODCs). At this mesoscopic scale, accessible by ultra-high field fMRI, V1 is supplied/drained by a network of surface (pial) vessels that connect to descending/ascending tangential vessels that penetrate the cortex and supply/drain a capillary bed whose density is also layer dependent. In this study, we measured the layer dependence of monocular and binocular responses of ocular dominance columns in V1 at 7T using Blood Oxygenation Level Dependent (BOLD) and VAscular Space Occupancy (VASO) contrasts. Our results indicate that the microvascular blood volume changes that give rise to VASO are well confined to the site of neural activity across the layers of the cortex and between the columns. Pial veins dominate the BOLD response and mix the signal between columns. When the GRE BOLD response was examined in only the VASO specific voxels (thus eliminating the pial vein signal), the laminar profile was very similar to VASO, however, the columnar response was still blurred. Caution needs to be exercised in the interpretation of signal changes in BOLD at the mesoscale both in terms of feedforward/feedback effects and inhibitory and excitatory effects. Highlights - VASO produced laminar profiles that were consistent with the known layer-dependent neuronal response to monocular and binocular stimulations. - VASO better differentiated the response between columns belonging to the left and right eyes. - GRE BOLD signal spatial specificity was poor in both laminar and columnar directions, however, when the pial veins were suppressed, the laminar BOLD signal was very similar to the VASO signal. - Caution needs to be exercised when interpreting cognitive neuroscience BOLD studies at the mesoscale level due to the confounding effects of pial and sub-pial veins and venules.
Global Profiling of Differentiating Macrophages Identifies Novel Functional Long Non-coding RNAs Regulating Polarization and Innate Immune Responses

Macrophages (Mφ) are functionally dynamic immune cells that bridge innate and adaptive immune responses. However, the underlying epigenetic mechanisms that control the macrophage plasticity and innate immune functions are not well-elucidated. Here we performed transcriptome profiling of differentiating M1Mφ and M2Mφ and identified thousands of previously known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs (LRRC75A-As1, GAPLINC and AL139099.5) with novel functions in Mφ differentiation, polarization and innate immunity. Knockdown of LRRC75A-As1, and GAPLINC downregulated Mφ differentiation markers CDw93 and CD68, and skewed macrophage polarization by decreasing M1 markers but had no significant impact on M2 markers. LRRC75A-As1, and GAPLINC RNAi in Mφ attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion supporting their functional role in potentiating innate immune functions. Mechanistically, lncRNA knockdown perturbed the expression of multiple cytoskeleton signaling thereby impairing Mφ migration suggesting their critical role in regulating macrophage polarity and motility. Together, our results show that Mφ acquire a unique repertoire of lncRNAs to shape differentiation, polarization and innate immune functions.
Coherent Mechanistic Patterns of Tropical Land Hydroclimate Changes

Changes in tropical (30 S–30 N) land hydroclimate following CO2‐induced global warming are organized according to climatological aridity index (AI) and daily soil moisture (SM) percentiles. The transform from geographical space to this novel process‐oriented phase space allows for interpretation of local, daily mechanistic relationships between key hydroclimatic variables in the context of time‐mean and/or global‐mean energetic constraints and the wet‐get‐wetter/dry‐get‐drier paradigm. Results from 16 CMIP models show coherent patterns of change in the AI/SM phase space that are aligned with the established soil‐moisture/evapotranspiration regimes. We introduce an active‐rain regime as a special case of the energy‐limited regime. Rainfall shifts toward larger rain totals in this active‐rain regime, with less rain on other days, resulting in an overall SM reduction. Consequently, the regimes where SM constrains evapotranspiration become more frequently occupied, and corresponding hydroclimatic changes align with the position of the critical SM value in the AI/SM phase space.
The dependent correlation between soil multifunctionality and bacterial community across different farmland soils

Introduction Microorganisms play a critical role in soil biogeochemical cycles, but it is still debated whether they influence soil biogeochemical processes through community composition and diversity or not. This study aims to investigate variation in bacterial community structure across different soils and its correlation to soil multifunctionality. Soil samples were collected from five typical farmland zones along distinct climatic gradients in China. Methods The high-throughput sequencing (Illumina MiSeq) of 16S rRNA genes was employed to analyze bacterial community composition in each soil sample. Multivariate analysis was used to determine the difference in soil properties, microbial community and functioning, and their interactions. Results Cluster and discrimination analysis indicated that bacterial community composition was similar in five tested soil samples, but bacterial richness combined with soil enzyme activities and potential nitrification rate (PNR) contributed most to the differentiations of soil samples. Mantel test analysis revealed that bacterial community composition and richness were more significantly shaped by soil nutrient conditions and edaphic variables than bacterial diversity. As for soil multifunctionality, soil microbial community level physiological profiles were little affected by abiotic and biotic factors, while soil enzymes and PNR were also significantly related to bacterial community composition and richness, in addition to soil N and P availability. Conclusion Cumulatively, soil enzymes’ activities and PNR were greatly dependent on bacterial community composition and richness not diversity, which in turn were greatly modified by soil N and P availability. Therefore, in the future it should be considered for the role of fertilization in the modification of bacterial community and the consequent control of nutrient cycling in soil.
Integrative analyses of biomarkers and pathways for diabetic nephropathy

Background: Diabetic nephropathy (DN) is a widespread diabetic complication and a major cause of terminal kidney disease. There is no doubt that DN is a chronic disease that imposes substantial health and economic burdens on the world’s populations. By now, several important and exciting advances have been made in research on etiopathogenesis. Therefore, the genetic mechanisms underlying these effects remain unknown. Methods: The GSE30122, GSE30528, and GSE30529 microarray datasets were downloaded from the Gene Expression Omnibus database (GEO). Analyses of differentially expressed genes (DEGs), enrichment of gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed. Protein-protein interaction (PPI) network construction was completed by the STRING database. Hub genes were identified by Cytoscape software, and common hub genes were identified by taking intersection sets. The diagnostic value of common hub genes was then predicted in the GSE30529 and GSE30528 datasets. Further analysis was carried out on the modules to identify transcription factors and miRNA networks. As well, a comparative toxicogenomics database was used to assess interactions between potential key genes and diseases associated upstream of DN. Results: Samples from 19 DNs and 50 normal controls were identified in the GSE30122 dataset. 86 upregulated genes and 34 downregulated genes (a total of 120 DEGs). GO analysis showed significant enrichment in humoral immune response, protein activation cascade, complement activation, extracellular matrix, glycosaminoglycan binding, and antigen binding. KEGG analysis showed significant enrichment in complement and coagulation cascades, phagosomes, the Rap1 signaling pathway, the PI3K-Akt signaling pathway, and infection. GSEA was mainly enriched in the TYROBP causal network, the inflammatory response pathway, chemokine receptor binding, the interferon signaling pathway, ECM receptor interaction, and the integrin 1 pathway. Meanwhile, mRNA-miRNA and mRNA-TF networks were constructed for common hub genes. Nine pivotal genes were identified by taking the intersection. After validating the expression differences and diagnostic values of the GSE30528 and GSE30529 datasets, eight pivotal genes (TYROBP, ITGB2, CD53, IL10RA, LAPTM5, CD48, C1QA, and IRF8) were finally identified as having diagnostic values. Conclusion: Pathway enrichment analysis scores provide insight into the genetic phenotype and may propose molecular mechanisms of DN. The target genes TYROBP, ITGB2, CD53, IL10RA, LAPTM5, CD48, C1QA, and IRF8 are promising new targets for DN. SPI1, HIF1A, STAT1, KLF5, RUNX1, MBD1, SP1, and WT1 may be involved in the regulatory mechanisms of DN development. Our study may provide a potential biomarker or therapeutic locus for the study of DN.
Spreading positive change: Societal benefits of meditation

Research over the past decades has revealed a variety of beneficial effects of meditation training. These beneficial effects span the levels of health and well-being, cognition, emotion, and social behavior. Around the same time, sociologists have shown that traits and outcomes on the individual level have the potential to spread in communities over three or more degrees. This means, for example, that changes can spread from one person to the next, and on to yet another person. Here, we propose that meditation-induced changes may likewise spread through the social networks of meditation practitioners. Such spreading may happen by positively influencing others through prosocial actions, improved cognitive functioning, and increased positive affect. Positive affective states and their underlying physiological correlates may also be shared in the literal sense. We argue that the spreading of positive meditation effects could provide the basis for collective responses to some of the urgent challenges we face in our current time and society and call for future meditation research to examine the phenomenon.
Microplastics in large marine herbivores: Florida manatees (Trichechus manatus latirostris) in Tampa Bay

Although there is growing concern about ingestion of microplastics by marine organisms, little research has been conducted on marine herbivores. This is the first study to document microplastic ingestion within the family Sirenia. Subsamples were collected from five locations in the gastrointestinal tracts (GI) of 26 dead manatees (Trichechus manatus latirostris) from Tampa Bay, Florida. During gross necropsies, macroplastic pieces were found in seven individuals (26.9%). Careful visual examination of the subsampled portions of the GI contents indicated that 19 individuals (73.1%) contained plastic particles. As five individuals had both macro and microplastic pieces, the overall frequency of occurrence of plastic ingestion was 76.9%. Due to the large volume of cellulose-rich ingested material, it was not feasible to analyze the entire gut contents, nor was it feasible to conduct chemical or enzymatic digestion; therefore, it is very likely that many microplastic pieces were not detected. Despite these technical challenges, it is clear that manatees in Tampa Bay are routinely consuming microplastics in addition to larger plastic pieces. Currently, nothing is known about the physiological effects of microplastic ingestion in sirenians, however environmental plastics could be concentrated by manatees through ingestion and the subsequent production of microplastics-laden feces.
Viscosity Model Data Fitting for Polymer Melt Based on Golden Section Method

The viscosity models of polymer melts are adopted popularly in the numerical simulation of plastic injection molding.The data fitting to these models is an important task. Based on golden section method, a kind of fitting method is proposed in order to reduce the restriction on initial values and to eliminate ill-conditioned matrixes. A direct search strategy is applied, with which the derivatives of an objective function need not be calculated. The search process is executed by round, and each round of search is carried out following a group of orthogonal feasible directions in turn. Based on golden section method, a one-dimensional nonlinear search is performed at a parametric interval in each feafible direction, so that a group of stage optimal solutions are attained. The convergence of a search process is guaranteed by continuously shrinking of the intervals and nonincreasing of the objective function values. Better extreme points can be found more easily by this kind of search method that make a current optimal point as the center of a searching interval, and fitting precision is enhanced accordingly. Moreover, a set of simple functions for calculating initial values is supplied for Cross-Arrhenius model. These functions can be employed in all kinds of fitting algorithms to this model. The fitting example shows that this method allows a wide range of feasible initial values, and its fitting precision is higher than Damped Newton's Method and Genetic Algorithm. It can engage in second optimization to the results made by other fitting methods. This fitting process can be accomplished in several seconds with a microcomputer for this example.
Flecainide induces a sustained countercurrent dependent effect on RyR2 in permeabilized WT ventricular myocytes but not in intact cells

Background and purpose: While flecainide is now an accepted treatment for arrhythmias associated with catecholaminergic polymorphic ventricular tachycardia (CPVT), its mechanism of action remains controversial. In studies on myocytes from CPVT mice, inhibition of proarrhythmic Ca2+ waves was initially attributed to a novel action on the type-2 ryanodine receptor (RyR2). However, subsequent work on wild type (WT) myocytes questioned the conclusion that flecainide has a direct action on RyR2. In the present study, the effects of flecainide were compared in intact and permeabilized WT myocytes. Experimental approach: Intracellular Ca2+ was measured using confocal microscopy in intact or saponin permeabilized adult rat ventricular myocytes (ARVM). In some experiments on permeabilized cells, flecainide was studied following partial inhibition of the sarcoplasmic reticulum (SR) counter-current. Key results: Flecainide induced sustained changes Ca2+ sparks and waves in permeabilized ARVM, which were comparable to those reported in intact or permeabilized myocytes from CPVT mice. However, a relatively high level of flecainide (25 μM) was required to induce these effects. Inhibition of the SR counter-current potentiated the effects of flecainide on SR Ca2+ waves. In intact field stimulated ARVM, prolonged exposure to 15 μM flecainide decreased wave frequency but RyR2 dependent effects on Ca2+ sparks were absent; higher drug concentrations blocked field stimulation, consistent with inhibition of Nav1.5. Conclusions and implications: In intact ARVM, the absence of effects on Ca2+ sparks suggests that the intracellular flecainide concentration was insufficient to influence RyR2. Wave inhibition in intact ARVM may reflect secondary effects of Nav1.5 inhibition. Potentiation of flecainide’s action by counter-current inhibition can be explained if transient polarization of the SR membrane during SR Ca2+ release facilitates its action on RyR2.
Ascorbate−glutathione cycle involving in response of Bangia fuscopurpurea (Bangiales, Rhodophyta) to hyposalinity

Bangia fuscopurpurea is a widespread intertidal seaweed that is commercially cultured in China. This seaweed is frequently exposed to hyposalinity stress, but little is known about the adaptation mechanisms. Ascorbate−glutathione (AsA−GSH) cycle plays important roles in many organisms under a variety of abiotic stress, including hyposaline stress. In this study, we investigated the response of key metabolites and enzymes involved in the AsA−GSH cycle of B. fuscopurpurea under hyposalinity, with the addition of exogenous GSH and Lbuthionine-sulfoximine (BSO). The quantification of BfAPX gene expression was assessed across varied treatment regimens. And the putative interaction proteins of BfAPX were screened by yeast two hybrid system. It was found that under hyposalinity (15 and/or 0 psu), the content of reduced glutathione (GSH), total glutathione (GSH+ oxidized glutathione, GSSG) and cysteine, the ratio of GSH/GSSG and ascorbic acid (AsA)/ dehydroascorbic acid (DHA), and the activity of ascorbic acid peroxidase (APX) and monodehydroascorbate reductase (MDHAR) was significantly up-regulated. The hyposality-promoted GSH/GSSG was weakened while the glutathione reductase (GR) activity was promoted by adding exogenous GSH and BSO. The hyposality-promoted AsA/DHA ratio was strengthened by exogenous GSH but weakened by BSO. The dehydroascorbate reductase (DHAR) activity had no significant changes either with or without exogenous GSH under all salinities, while DHAR activity together with DHA content was enhanced by BSO. The expression of APX gene markedly increased under hyposalinity+BSO treatment. Putative interacting proteins of APX, including glutamate dehydrogenase 1a and fructose diphosphate aldolase, were identified through screening. The results indicated that the AsA−GSH cycle was involved in response of B. fuscopurpurea to hyposalinity by means of increasing GSH/GSSG ratio (through promoting GSH biosynthesis pathway and GSH regeneration from GSSG by GR catalyzation) and AsA/DHA ratio (promoting AsA regeneration through MDHAR). These findings would contribute to improve the aquaculture of this promising economic species and unveil how intertidal seaweeds address the global climate challenges.