Significance: Functional near-infrared spectroscopy (fNIRS) has been widely used to probe human brain function during task state and resting state. However, the existing analysis toolboxes mainly focus on task activation analysis, few software packages can assist resting-state fNIRS studies. Aim:We aimed to provide a versatile and easy-to-use toolbox to perform analysis for both resting state and task fNIRS.Approach: We developed a MATLAB toolbox called NIRS-KIT that works for both restingstate analysis and task activation detection.Results: NIRS-KIT implements common and necessary processing steps for performing fNIRS data analysis, including data preparation, quality control, preprocessing, individual-level analysis, group-level statistics with several popular statistical models, and multiple comparison correction methods, and finally results visualization. For resting-state fNIRS analysis, functional connectivity analysis, graph theory-based network analysis, and amplitude of low-frequency fluctuations analysis are provided. Additionally, NIRS-KIT also supports activation analysis for task fNIRS.Conclusions: NIRS-KIT offers an open source tool for researchers to analyze resting-state and/ or task fNIRS data in one suite. It contains several key features: (1) good compatibility, supporting multiple fNIRS recording systems, data formats of NIRS-SPM and Homer2, and the shared near-infrared spectroscopy format data format recommended by the fNIRS society; (2) flexibility, supporting customized preprocessing scripts; (3) ease-to-use, allowing processing fNIRS signals in batch manner with user-friendly graphical user interfaces; and (4) feature-packed data viewing and result visualization. We anticipate that this NIRS-KIT will facilitate the development of the fNIRS field.

Somatic cell nuclear transfer (SCNT) has shown tremendous potential for understanding the mechanisms of reprogramming and creating applications in the realms of agriculture, therapeutics, and regenerative medicine, although the efficiency of reprogramming is still low. Somatic nucleus reprogramming is triggered in the short time after transfer into recipient cytoplasm, and therefore, this period is regarded as a key stage for optimizing SCNT. Here we report that CBHA, a histone deacetylase inhibitor, modifies the acetylation status of somatic nuclei and increases the developmental potential of mouse cloned embryos to reach pre-and post-implantation stages. Furthermore, the cloned embryos treated by CBHA displayed higher efficiency in the derivation of nuclear transfer embryonic stem cell lines by promoting outgrowths. More importantly, CBHA increased blastocyst quality compared with trichostatin A, another prevalent histone deacetylase inhibitor reported previously. Use of CBHA should improve the productivity of SCNT for a variety of research and clinical applications, and comparisons of cells with different levels of pluripotency and treated with CBHA versus trichostatin A will facilitate studies of the mechanisms of reprogramming.Reprogramming of a terminally differentiated nucleus is successfully achieved in many species through somatic cell nuclear transfer (SCNT) 3 technology. However, its efficiency remains very low, limiting its application in agriculture to well bred livestock propagation and in species preservation (1) and regenerative medicine. The reprogramming process remains largely unknown; at the time of its transfer into an enucleated oocyte the somatic donor nucleus is in a configuration very different from a germ cell or an embryonic nucleus. Its own specific program of gene expression will have to be turned on, and the specific epigenetic modifications and chromatin configuration were erased (2). Extensive chromatin remodeling takes place as soon as the somatic nucleus is in contact with the oocyte cytoplasm, and two main types of epigenetic marks are directly involved in gene expression regulation; that is, methylation of histones or DNA and acetylation of histones (3-5). During normal pre-implantation development, the embryonic genome is progressively demethylated up to the early blastocyst stage. This is followed by differential remethylation in the two lineages of the blastocyst, the pluripotent inner cell mass and the trophoblast (6), but this process has been shown to be errorprone in SCNT embryos (7,8).Attempts to improve reprogramming during nuclear transfer have, therefore, focused primarily on modifying the epigenetic configuration of the donor nuclei before nuclear transfer. Therefore, treating donor cells with pharmacological agents to remove some epigenetic marks before NT may improve the ability of the donor cells to be fully reprogrammed by the recipient ooplasm. Pretreatment of bovine fibroblast donor cells by DNA demethylation agents such as 5-aza-2Ј-deoxycytidine or S-adenosy...

Cholinergic projections from the basal forebrain and brainstem are thought to play important roles in rapid eye movement (REM) sleep and arousal. Using transgenic mice in which channelrhdopsin-2 is selectively expressed in cholinergic neurons, we show that optical stimulation of cholinergic inputs to the thalamic reticular nucleus (TRN) activates local GABAergic neurons to promote sleep and protect non-rapid eye movement (NREM) sleep. It does not affect REM sleep. Instead, direct activation of cholinergic input to the TRN shortens the time to sleep onset and generates spindle oscillations that correlate with NREM sleep. It does so by evoking excitatory postsynaptic currents via α7-containing nicotinic acetylcholine receptors and inducing bursts of action potentials in local GABAergic neurons. These findings stand in sharp contrast to previous reports of cholinergic activity driving arousal. Our results provide new insight into the mechanisms controlling sleep.DOI: http://dx.doi.org/10.7554/eLife.10382.001