Deciphering hierarchical organization of topologically associated domains through change-point testing.

BACKGROUND: The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them. RESULTS: We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions. CONCLUSIONS: HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions

Analyzing the Study of Using Acupuncture in Delivery in the Past Ten Years in China

The use of acupuncture in inducing delivery has a long history in China. With progress over time, it has been applied in many aspects. For further study of acupuncture in delivery, this paper analyzed the papers using acupuncture in delivery in the past ten years in mainland China. 87 literatures were picked out by searching relevant electronic databases and bibliographies of relevant journals. The analysis showed randomized controlled trials that were the major type of research, while preclinical researches and literature reviews only account for around ten percent, respectively. Clinical researches indicated that acupuncture can relieve labor pain, promote maternal uterine contraction, shorten birth process, and treat postpartum disorders. Preclinical researches found that acupuncture can adjust certain hormones and improve uterus contraction of late-stage pregnant rats. However, due to lack of large multicenter randomized controlled clinical trials, standardized evaluations of clinical effects in clinical researches and detailed mechanism study in preclinical researches and unequivocal conclusions about the effectiveness, efficacy, and mechanisms of acupuncture in this field cannot be obtained from those researches yet. Further clinical and preclinical studies about the use of acupuncture in delivery with improved methodology is still needed

Analyzing the Study of Using Acupuncture in Delivery in the Past Ten Years in China

The use of acupuncture in inducing delivery has a long history in China. With progress over time, it has been applied in many aspects. For further study of acupuncture in delivery, this paper analyzed the papers using acupuncture in delivery in the past ten years in mainland China. 87 literatures were picked out by searching relevant electronic databases and bibliographies of relevant journals. The analysis showed randomized controlled trials that were the major type of research, while preclinical researches and literature reviews only account for around ten percent, respectively. Clinical researches indicated that acupuncture can relieve labor pain, promote maternal uterine contraction, shorten birth process, and treat postpartum disorders. Preclinical researches found that acupuncture can adjust certain hormones and improve uterus contraction of late-stage pregnant rats. However, due to lack of large multicenter randomized controlled clinical trials, standardized evaluations of clinical effects in clinical researches and detailed mechanism study in preclinical researches and unequivocal conclusions about the effectiveness, efficacy, and mechanisms of acupuncture in this field cannot be obtained from those researches yet. Further clinical and preclinical studies about the use of acupuncture in delivery with improved methodology is still needed

Utilization of cotton byproduct-derived biochar : A review on soil remediation and carbon sequestration

Biochar can improve soil health and fix CO2 by altering soil microenvironment, thus impacting the global carbon cycle and the change of soil ecological environment. Recent studies show that cotton byproduct-derived biochar is a potential effective amendment for soil improvement so that it could play an important role in agricultural and environmental conservation. In this work, research topics on cotton byproduct-derived biochar in soil in last decade and so are systematically reviewed for better understanding of the progresses of cotton byproduct-derived biochar in (i) the morphologic and physicochemical characterization, (ii) latest research hotspots and trends, (iii) the roles in soil reclamation, and (iv) relevant carbon sequestration mechanisms. Finally, the future research directions regarding cotton byproduct-derived biochar mingled to soil environment are discussed. Insight derived from this work would provide scientific basis for promoting more applications of cotton byproduct-derived biochar in soil ecological restoration and carbon fixation

Clinical characteristics and work-up of small to intermediate-sized pulmonary nodules in a Chinese dedicated cancer hospital

Objectives: To evaluate the characteristics and work-up of small to intermediate-sized pulmonary nodules in a Chinese dedicated cancer hospital. Methods: Patients with pulmonary nodules 4-25 mm in diameter detected via computed tomography (CT) in 2013 were consecutively included. The analysis was restricted to patients with a histological nodule diagnosis or a 2-year follow-up period without nodule growth confirming benign disease. Patient information was collected from hospital records. Results: Among the 314 nodules examined in 299 patients, 212 (67.5%) nodules in 206 (68.9%) patients were malignant. Compared to benign nodules, malignant nodules were larger (18.0 mm vs. 12.5 mm, P < 0.001), more often partly solid (16.0% vs. 4.7%, P < 0.001) and more often spiculated (72.2% vs. 41.2%, P < 0.001), with higher density in contrast-enhanced CT (67.0 HU vs. 57.5 HU, P = 0.015). Final diagnosis was based on surgery in 232 out of 314 (73.9%) nodules, 166 of which were identified as malignant [30 (18.1%) stage III or IV] and 66 as benign. In 36 nodules (11.5%), diagnosis was confirmed by biopsy and the remainder verified based on stability of nodule size at follow-up imaging (n = 46, 14.6%). Among 65 nodules subjected to gene (EGFR) mutation analyses, 28 (43.1%) cases (EGFR19 n = 13; EGFR21 n = 15) were identified as EGFR mutant and 37 (56.9%) as EGFR wild-type. Prior to surgery, the majority of patients [n = 194 (83.6%)] received a contrast-enhanced CT scan for staging of both malignant [n = 140 (84.3%)] and benign [n = 54 (81.8%)] nodules. Usage of positron emission tomography (PET)-CT was relatively uncommon [n = 38 (16.4%)]. Conclusions: CT-derived nodule assessment assists in diagnosis of small to intermediate- sized malignant pulmonary nodules. Currently, contrast-enhanced CT is commonly used as the sole diagnostic confirmation technique for pre-surgical staging, often resulting in surgery for late-stage disease and unnecessary surgery in cases of benign nodules

A review on modelling methods, tools and service of integrated energy systems in China

An integrated energy system (IES) is responsible for aggregating various energy carriers, such as electricity, gas, heating, and cooling, with a focus on integrating these components to provide an efficient, low-carbon, and reliable energy supply. This paper aims to review the modeling methods, tools, and service modes of IES in China to evaluate opportunities for improving current practices. The models reviewed in this paper are classified as demand forecasting or energy system optimization models based on their modeling progress. Additionally, the main components involved in the IES modeling process are presented, and typical domestic tools utilized in the modeling processes are discussed. Finally, based on a review of several demonstration projects of IES, future development directions of IES are summarized as the integration of data-driven and engineering models, improvements in policies and mechanisms, the establishment of regional energy management centers, and the promotion of new energy equipment