An integrated analytical framework for carbon dioxide emission reduction potential in the water production and supply industry in China.

The Water Production and Supply (WP&S) industry faces the dual objectives of ensuring water supply security and achieving carbon neutrality. An integrated analytical framework (Measurement-Assessment-Identification) was developed to measure carbon dioxide emissions from the WP&S industry (WP&S-CO emissions), assess the CO emissions reduction potential of the WP&S industry (WP&S-CRP), and identify the key driving forces of WP&S-CRP. In the measurement module, a method for measuring CO emissions specific to the WP&S industry is proposed.

Technologies for investigating single-molecule chemical reactions.

Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam.

LL-37: Structures, Antimicrobial Activity, and Influence on Amyloid-Related Diseases.

Antimicrobial peptides (AMPs), as well as host defense peptides (HDPs), constitute the first line of defense as part of the innate immune system. Humans are known to express antimicrobial precursor proteins, which are further processed to generate AMPs, including several types of α/β defensins, histatins, and cathelicidin-derived AMPs like LL37. The broad-spectrum activity of AMPs is crucial to defend against infections caused by pathogenic bacteria, viruses, fungi, and parasites.

Topological Properties, Spectra Analysis, and Consensus Problems for a Class of Network Models Based on m-Fission Operation.

The network model, especially the network model constructed by network operation, is an important tool to study complex networks. Many topological and dynamic properties of complex networks can be studied in this way. In this article, the m -fission operation is constructed based on the phenomenon of node splitting in the network, which is quite common in complex networks.

An Improved Rapidly-Exploring Random Trees Algorithm Combining Parent Point Priority Determination Strategy and Real-Time Optimization Strategy for Path Planning.

In order to solve the problems of long path planning time and large number of redundant points in the rapidly-exploring random trees algorithm, this paper proposed an improved algorithm based on the parent point priority determination strategy and the real-time optimization strategy to optimize the rapidly-exploring random trees algorithm. First, in order to shorten the path-planning time, the parent point is determined before generating a new point, which eliminates the complicated process of traversing the random tree to search the parent point when generating a new point. Second, a real-time optimization strategy is combined, whose core idea is to compare the distance of a new point, its parent point, and two ancestor points to the target point when a new point is generated, choosing the new point that is helpful for the growth of the random tree to reduce the number of redundant points.

High-throughput 5' UTR engineering for enhanced protein production in non-viral gene therapies.

Despite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major technical challenge. Here, we develop a high-throughput strategy to design, screen, and optimize 5' UTRs that enhance protein expression from a strong human cytomegalovirus (CMV) promoter. We first identify naturally occurring 5' UTRs with high translation efficiencies and use this information with in silico genetic algorithms to generate synthetic 5' UTRs.

Spectral analysis for weighted iterated q-triangulation networks.

Deterministic weighted networks have been widely used to model real-world complex systems. In this paper, we study the weighted iterated q-triangulation networks, which are generated by iteration operation F(⋅). We add q(q∈N) new nodes on each old edge and connect them with two endpoints of the old edge.

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.

Despite large experimental and computational efforts aiming to dissect the mechanisms underlying disease risk, mapping cis-regulatory elements to target genes remains a challenge. Here, we introduce a matrix factorization framework to integrate physical and functional interaction data of genomic segments. The framework was used to predict a regulatory network of chromatin interaction edges linking more than 20 000 promoters and 1.

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

The aberrant activities of transcription factors such as the androgen receptor (AR) underpin prostate cancer development. While the AR -regulation has been extensively studied in prostate cancer, information pertaining to the spatial architecture of the AR transcriptional circuitry remains limited. In this paper, we propose a novel framework to profile long-range chromatin interactions associated with AR and its collaborative transcription factor, erythroblast transformation-specific related gene (ERG), using chromatin interaction analysis by paired-end tag (ChIA-PET).

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.

To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA.

[Stellate ganglion catheter retention with discontinuous block on efficacy and safety in the treatment of sudden deafness].

Objective: To investigate effect and safty evaluation of stellate ganglion catheter retention with discontinuous block on sudden deafness.

Method: One hundred and twenty-six patiens with sudden monaural deafness were randomly divided into Catheterp and block and control groups with 42 cases in each group. All patients' throats were given conventional blood activating drugs, hormone and hyperbaric oxygen therapy.

Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene.

Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB) and predict their off-target effects.

Integrative analysis of 111 reference human epigenomes.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.

The Brm-HDAC3-Erm repressor complex suppresses dedifferentiation in Drosophila type II neuroblast lineages.

The control of self-renewal and differentiation of neural stem and progenitor cells is a crucial issue in stem cell and cancer biology. Drosophila type II neuroblast lineages are prone to developing impaired neuroblast homeostasis if the limited self-renewing potential of intermediate neural progenitors (INPs) is unrestrained. Here, we demonstrate that Drosophila SWI/SNF chromatin remodeling Brahma (Brm) complex functions cooperatively with another chromatin remodeling factor, Histone deacetylase 3 (HDAC3) to suppress the formation of ectopic type II neuroblasts.

3D chromosome modeling with semi-definite programming and Hi-C data.

For a long period of time, scientists studied genomes while assuming they are linear. Recently, chromosome conformation capture (3C)-based technologies, such as Hi-C, have been developed that provide the loci contact frequencies among loci pairs in a genome-wide scale. The technology unveiled that two far-apart loci can interact in the tested genome.

Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.

Although de novo motifs can be discovered through mining over-represented sequence patterns, this approach misses some real motifs and generates many false positives. To improve accuracy, one solution is to consider some additional binding features (i.e.

Telomerase directly regulates NF-κB-dependent transcription.

Although elongation of telomeres is thought to be the prime function of reactivated telomerase in cancers, this activity alone does not account for all of the properties that telomerase reactivation attributes to human cancer cells. Here, we uncover a link between telomerase and NF-κB, a master regulator of inflammation. We observe that while blocking NF-κB signalling can inhibit effects of telomerase overexpression on processes relevant to transformation, increasing NF-κB activity can functionally substitute for reduced telomerase activity.

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions.

CENTDIST: discovery of co-associated factors by motif distribution.

Transcription factors (TFs) do not function alone but work together with other TFs (called co-TFs) in a combinatorial fashion to precisely control the transcription of target genes. Mining co-TFs is thus important to understand the mechanism of transcriptional regulation. Although existing methods can identify co-TFs, their accuracy depends heavily on the chosen background model and other parameters such as the enrichment window size and the PWM score cut-off.