Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by ...their network features to infer their importance in the network, and it can help us identify central elements of biological networks.
We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network.
CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010.
Abstract
Photocatalytic water splitting is attracting considerable interest because it enables the conversion of solar energy into hydrogen for use as a zero-emission fuel or chemical feedstock. ...Herein, we present a universal approach for inserting hydrophilic non-conjugated segments into the main-chain of conjugated polymers to produce a series of discontinuously conjugated polymer photocatalysts. Water can effectively be brought into the interior through these hydrophilic non-conjugated segments, resulting in effective water/polymer interfaces inside the bulk discontinuously conjugated polymers in both thin-film and solution. Discontinuously conjugated polymer with 10 mol% hexaethylene glycol-based hydrophilic segments achieves an apparent quantum yield of 17.82% under 460 nm monochromatic light irradiation in solution and a hydrogen evolution rate of 16.8 mmol m
−2
h
−1
in thin-film. Molecular dynamics simulations show a trend similar to that in experiments, corroborating that main-chain engineering increases the possibility of a water/polymer interaction. By introducing non-conjugated hydrophilic segments, the effective conjugation length is not altered, allowing discontinuously conjugated polymers to remain efficient photocatalysis.
One major task in the post-genome era is to reconstruct proteomic and genomic interacting networks using high-throughput experiment data. To identify essential nodes/hubs in these interactomes is a ...way to decipher the critical keys inside biochemical pathways or complex networks. These essential nodes/hubs may serve as potential drug-targets for developing novel therapy of human diseases, such as cancer or infectious disease caused by emerging pathogens. Hub Objects Analyzer (Hubba) is a web-based service for exploring important nodes in an interactome network generated from specific small- or large-scale experimental methods based on graph theory. Two characteristic analysis algorithms, Maximum Neighborhood Component (MNC) and Density of Maximum Neighborhood Component (DMNC) are developed for exploring and identifying hubs/essential nodes from interactome networks. Users can submit their own interaction data in PSI format (Proteomics Standards Initiative, version 2.5 and 1.0), tab format and tab with weight values. User will get an email notification of the calculation complete in minutes or hours, depending on the size of submitted dataset. Hubba result includes a rank given by a composite index, a manifest graph of network to show the relationship amid these hubs, and links for retrieving output files. This proposed method (DMNC || MNC) can be applied to discover some unrecognized hubs from previous dataset. For example, most of the Hubba high-ranked hubs (80% in top 10 hub list, and >70% in top 40 hub list) from the yeast protein interactome data (Y2H experiment) are reported as essential proteins. Since the analysis methods of Hubba are based on topology, it can also be used on other kinds of networks to explore the essential nodes, like networks in yeast, rat, mouse and human. The website of Hubba is freely available at http://hub.iis.sinica.edu.tw/Hubba.
The feasibility of using deep learning in ultrasound imaging to predict the ambulatory status of patients with Duchenne muscular dystrophy (DMD) was previously explored for the first time. The ...present study further used clustering algorithms for the texture reconstruction of ultrasound images of DMD data sets and analyzed the difference in echo intensity between disease stages.
k-means (Kms) and fuzzy c-means (FCM) clustering algorithms were used to reconstruct the DMD data-set textures. Each image was reconstructed using seven texture-feature categories, six of which were used as the primary analysis items. The task of automatically identifying the ambulatory function and DMD severity was performed by establishing a machine-learning model.
The experimental results indicated that the Gaussian Naïve Bayes and k-nearest neighbors classification models achieved an accuracy of 86.78% in ambulatory function classification. The decision-tree model achieved an identification accuracy of 83.80% in severity classification. A deep convolutional neural network model was established as the main structure of the deep-learning model while automatic auxiliary interpretation tasks of ambulatory function and severity were performed, and data augmentation was used to improve the recognition performance of the trained model. Both the visual geometry group (VGG)-16 and VGG-19 models achieved 98.53% accuracy in ambulatory-function classification. The VGG-19 model achieved 92.64% accuracy in severity classification.
Regarding the overall results, the Kms and FCM clustering algorithms were used in this study to reconstruct the characteristic texture of the gastrocnemius muscle group in DMD, which was indeed helpful in quantitatively analyzing the deterioration of the gastrocnemius muscle group in patients with DMD at different stages. Subsequent combination of machine-learning and deep-learning technologies can automatically and accurately assist in identifying DMD symptoms and tracking DMD deterioration for long-term observation.
Conjugated copolymers (CCPs) are a class of polymers with excellent optical luminescent and electrical conducting properties because of their extensive π conjugation. CCPs have several advantages ...such as facile synthesis, structural tailorability, processability, and ease of device fabrication by compatible solvents. Electrospinning (ES) is a versatile technique that produces continuous high throughput nanofibers or microfibers and its appropriate synchronization with CCPs can aid in harvesting an ideal sensory nanofiber. The ES-based nanofibrous membrane enables sensors to accomplish ultrahigh sensitivity and response time with the aid of a greater surface-to-volume ratio. This review covers the crucial aspects of designing highly responsive optical sensors that includes synthetic strategies, sensor fabrication, mechanistic aspects, sensing modes, and recent sensing trends in monitoring environmental toxicants, pH, temperature, and humidity. In particular, considerable attention is being paid on classifying the ES-based optical sensor fabrication to overcome remaining challenges such as sensitivity, selectivity, dye leaching, instability, and reversibility.
Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening adverse drug reactions characterized by massive epidermal necrosis, in which the specific danger signals ...involved remain unclear. Here we show that blister cells from skin lesions of SJS-TEN primarily consist of cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells, and both blister fluids and cells were cytotoxic. Gene expression profiling identified granulysin as the most highly expressed cytotoxic molecule, confirmed by quantitative PCR and immunohistochemistry. Granulysin concentrations in the blister fluids were two to four orders of magnitude higher than perforin, granzyme B or soluble Fas ligand concentrations, and depleting granulysin reduced the cytotoxicity. Granulysin in the blister fluids was a 15-kDa secretory form, and injection of it into mouse skin resulted in features mimicking SJS-TEN. Our findings demonstrate that secretory granulysin is a key molecule responsible for the disseminated keratinocyte death in SJS-TEN and highlight a mechanism for CTL- or NK cell-mediated cytotoxicity that does not require direct cellular contact.
Conjugated polymers (CPs) have recently gained increasing attention as photocatalysts for sunlight-driven hydrogen evolution. However, they suffer from insufficient electron output sites and poor ...solubility in organic solvents, severely limiting their photocatalytic performance and applicability. Herein, solution-processable all-acceptor (A
-A
)-type CPs based on sulfide-oxidized ladder-type heteroarene are synthesized. A
-A
-type CPs showed upsurging efficiency improvements by two to three orders of magnitude, compared to their donor-acceptor -type CP counterparts. Furthermore, by seawater splitting, PBDTTTSOS exhibited an apparent quantum yield of 18.9% to 14.8% at 500 to 550 nm. More importantly, PBDTTTSOS achieved an excellent hydrogen evolution rate of 35.7 mmol h
g
and 150.7 mmol h
m
in the thin-film state, which is among the highest efficiencies in thin film polymer photocatalysts to date. This work provides a novel strategy for designing polymer photocatalysts with high efficiency and broad applicability.
Viruses are a key component of the colon microbiome, but the relationship between virome and colorectal cancer (CRC) remains poorly understood. We seek to identify alterations in the viral community ...that is characteristic of CRC and examine if they persist after surgery. Forty-nine fecal samples from 25 non-cancer (NC) individuals and 12 CRC patients, before and 6-months after surgery, were collected for metagenomic analysis. The fecal virome of CRC patients demonstrated an increased network connectivity as compared to NC individuals. Co-exclusion of influential viruses to bacterial species associated with healthy gut status was observed in CRC, suggesting an altered virome induced a change in the healthy gut bacteriome. Network analysis revealed lower connectivity within the virome and trans-kingdom interactions in NC. After surgery, the number of strong correlations decreased for trans-kingdom and within the bacteria and virome networks, indicating lower connectivity within the microbiome. Some co-occurrence patterns between dominant viruses and bacteria were also lost after surgery, suggesting a possible return to the healthy state of gut microbiome. Microbial signatures characteristic of CRC include an altered virome besides an altered bacterial composition. Elevated viral correlations and network connectivity were observed in CRC patients relative to healthy individuals, alongside distinct changes in the cross-kingdom correlation network unique to CRC patients. Some patterns of dysbiosis persist after surgery. Future studies should seek to verify if dysbiosis truly persists after surgery in a larger sample size with microbiome data collected at various time points after surgery to explore if there is field-change in the remaining colon, as well as to examine if persistent dysbiosis correlates with patient outcomes.
ABSTRACT
Yes‐associated protein (YAP) is a transcriptional coactivator in the Hippo pathway that regulates cell proliferation, differentiation, and apoptosis. The MEK5/ERK5 MAPK cascade is essential ...for the early step of myogenesis. In this study, we generated C2C12 stable cell lines that expressed YAP (C2C12‐YAP cells) and found that ERK5 and MEK5 were activated in C2C12‐YAP cells compared with control C2C12 (C2C12‐vector) cells. C2C12YAP stable cells also differentiated into myotubes better than C2C12‐vector cells, and expressed elevated levels of myogenin, a transcription factor that regulates myogenesis, as well as elevated levels of myosin heavy chain, a skeletal muscle marker. Western blot analysis revealed that Src and c‐Abl (Abelson murine leukemia viral oncogene homolog 1) activation were enhanced in C2C12‐YAP cells. Conversely, treatment of inhibitors of c‐Abl, Src, or MEK5 inhibited activation of MEK5 and ERK5 and myogenesis of C2C12 myoblasts. Specific interactions between YAP and proteins in the ERK5 pathway, such as MEK kinase 3 (MEKK3) and ERK5, were illustrated by coimmunoprecipitation experiments. MEKK3 contains the PPGY motif (aa 178–181), which may interact with YAP. Site‐directed mutagenesis experiments revealed that expression of MEKK3 Y181F mutant inhibited MEK5/ERK5 activation and myogenic differentiation. These results suggest that YAP promotes muscle differentiation by activating the Abl/Src/MEKK3/MEK5/ERK5 kinase cascade.—Chen, T.‐H., Chen, C.‐Y., Wen, H.‐C., Chang, C.‐C., Wang, H.‐D., Chuu, C.‐P., Chang, C.‐H. YAP promotes myogenic differentiation via the MEK5‐ERK5 pathway. FASEB J. 31, 2963–2972 (2017). www.fasebj.org
Tourette syndrome (TS) is associated with a variety of neuropsychiatric comorbidities. However, the relationship between TS and sleep disorders in children is less investigated. This nationwide ...population-based case-control study aimed to determine the correlation of TS and sleep disorders in children.
Patients aged less than 18 years with newly diagnosed TS from 2001 to 2007 were collected (n = 1124) using data from Taiwan's National Health Insurance Research Database and were compared with a comparison cohort (n = 3372). The adjusted hazard ratio (aHR) for developing sleep disorders was calculated by multivariate Cox proportional hazards model.
TS was more prevalent in boys, with a male to female ratio of 3.16:1. TS group also had significantly higher urbanization level of residence than controls (p < .001). The overall incidence rate of sleep disorders was 7.24‰ in children with TS, compared to 3.53‰ in controls. The TS group was associated with a significantly higher rate of sleep disorders, with a crude HR of 2.05 (95% confidence inerval CI = 1.43-2.95, p < .001). Among the comorbidities of TS, anxiety disorder was associated with the highest risk for sleep disorders (crude HR = 3.26, 95% CI = 1.52-7.00, p < .001). The aHR for TS cohort to develop sleep disorders was 1.72 (95% CI = 1.16-2.53, p = .007).
The increased risk of sleep disorders in children with TS cannot be fully attributed to its comorbidities, and TS is an independent risk factor for sleep disorders in children.
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