SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data

Deep learning has been increasingly and widely used to solve numerous problems in various fields with state-of-the-art performance. It can also be applied in bioinformatics to reduce the requirement for feature extraction and reach high performance. This study attempts to use deep learning to predict SNARE proteins, which is one of the most vital molecular functions in life science. A functional loss of SNARE proteins has been implicated in a variety of human diseases (e.g., neurodegenerative, mental illness, cancer, and so on). Therefore, creating a precise model to identify their functions is a crucial problem for understanding these diseases, and designing the drug targets. Our SNARE-CNN model which uses two-dimensional convolutional neural networks and position-specific scoring matrix profiles could identify SNARE proteins with achieved sensitivity of 76.6%, specificity of 93.5%, accuracy of 89.7%, and MCC of 0.7 in cross-validation dataset. We also evaluate the performance of our model via an independent dataset and the result shows that we are able to solve the overfitting problem. Compared with other state-of-the-art methods, this approach achieved significant improvement in all of the metrics. Throughout the proposed study, we provide an effective model for identifying SNARE proteins and a basis for further research that can apply deep learning in bioinformatics, especially in protein function prediction. SNARE-CNN are freely available at https://github.com/khanhlee/snare-cnn

Current medical product development for diagnosis, surgical planning and treatment in the areas of Neurosurgery, Orthopeadic and Dental-Cranio-Maxillofacial surgery in Vietnam

With the population of 86 million and good GDP growth in recent decades, the medical market in Vietnam is growing fast. However, most of the medical technology products are imported, and the number of locally manufactured ones is limited and they do not have the high competition capability in term of quality, quantity and types. In this paper, the current product development in Vietnam for diagnosis, surgical planning and treatment in the areas of Rehabilitation, Neurosurgery, Orthopeadic and Dental-Cranio-Maxillofacial surgery is presented. A roadmap for medical technology development in Vietnam is propose

FIRST RECORD OF CANTHARELLUS MINOR IN VIETNAM

This species of mushroom with orange fruiting bodies and yellow flesh grows in clumps on the forest land in the coordinates 11o56'34.45" N, 108o28'33.56" E in the pine (Pinus kesiya) forest, Da Lat City, Lam Dong Province, Vietnam. The results of analysis on the morphology, both macro- and micro-morphological characteristics of this mushroom showed that, pileus: 5-15 mm wide, infundibuliform; yellowish to orange; margin incurred, wavy-liked margin, non-striate; Pileus surface: smooth, scaleless, yellowish; Lamellae: distant, decurrent, not intervenose, concolorous to pileus; Context: concolourous to the pileus, slight sweetness, aromatic flavor; Stipe: cylindrical shape, surface smooth, concolourous to pileus, 1-2 mm diameter, 20-50 mm length; Basidiospores: 6-11.5 x 4-6.5 μm, ovoid-ellipsoid with smooth surface; Basidia: 65 x 10 μm, cornuted 4-6 spores per basidium. Phylogenetic analysis of nrLSU sequence yielded consistent topology in different taxa of Cantharellus. The phylogenetic position of XC02 was obtained and accepted at sub-generic level: subgenus Parvocantharellus. This clade was suggested to be monophyletic, and separated from other sub-generic levels. Morphologically phylogenetically distinct from the other species of clade 4, such as C. appalachiensis, C. tabernensis, C. aff. Congolensis. The highly supported monophyletic group with referent Cantharellus minor was obtained with the bootstrap value of 99, indicated that XC02 was significant closely to Cantharellus minor. Phylogenetic of nrLSU analysis revealed clades with statistical support corresponding to morphological observation, thus, XC2 was concluded as Cantharellus minor

Comparison of the antibacterial activity against Escherichia coli of silver nanoparticle produced by chemical synthesis with biosynthesis

The synthesis of silver nanoparticles (Ag NPs) has been carried out using different methods, mainly by biological and chemical methods; however, comparing antibacterial activity of Ag NPs synthesized by these methods has not been conducted before. In this study, silver nanoparticles (Ag NPs) were synthesized by methods using reducing agent NaBH4/carboxymethyl cellulose (CMC) and fungal strain Trichoderma asperellum (T.asperellum). The formation of silver nanoparticles was observed visually by color change and identified by Ultraviolet-visible (UV – vis) spectroscopy. The transmission electron microscopy (TEM) image illustrated almost nanoparticles with spherical shape and average diameter of 4.1 ± 0.2 nm and 2.1 ± 0.2 nm of samples produced from chemical reduction and biosynthesis respectively. Both samples after 180 days storing have been separated lightly, but the agglomeration and absorbance peak shifting were not observed which proved the high stability of synthesized Ag NPs. Antimicrobial activity against human bacterial pathogen Escherichia coli (E. coli) showed that the inhibition zone produced by “biosynthesis” and “chemical reduction” Ag NPs were 3.17 cm and 2.42 cm respectively. With nanoparticles size smaller than 2 mm, antibacterial activity of “biosynthesis” Ag NPs against E. coli was 31 % higher than “chemical reduction” Ag NPs, although the concentration of Ag NPs produced by biosynthesis was about 10-fold less

Optimization of protein extraction from "Cam" rice bran by response surface methodology

"Cam" rice bran was considered a waste product from rice, which is rich in natural compounds and protein owing to its outstanding nutritional value. This study aimed to establish an optimization model for extracting protein from rice bran, with two responses: extraction yield (%) and protein content (%). The variable parameters included were pH (8.5-9.5), stirring time (3.5-4.5 h), and enzyme incubation temperature (85-95°C). The coefficient of determination for both models were above 0.95, indicating a high correlation between the actual and estimated values. The maximum extraction yield and protein content were achieved when the conditions were set at pH of 9.02, stirring time of 4.02 h, and extraction temperature of 90.6°C. Under these optimum conditions, the predicted protein extracted from rice bran was 43.03% (moisture <13.0%), with an extraction yield of 15.9%. The findings of this study suggested that this protocol can enhance the utilization of rice bran and might be employed on a large scale in the food industry to exploit the nutritional source

Genomic-Analysis-Oriented Drug Repurposing in the Search for Novel Antidepressants

From inadequate prior antidepressants that targeted monoamine neurotransmitter systems emerged the discovery of alternative drugs for depression. For instance, drugs targeted interleukin 6 receptor (IL6R) in inflammatory system. Genomic analysis-based drug repurposing using single nucleotide polymorphism (SNP) inclined a promising method for several diseases. However, none of the diseases was depression. Thus, we aimed to identify drug repurposing candidates for depression treatment by adopting a genomic-analysis-based approach. The 5885 SNPs obtained from the machine learning approach were annotated using HaploReg v4.1. Five sets of functional annotations were applied to determine the depression risk genes. The STRING database was used to expand the target genes and identify drug candidates from the DrugBank database. We validated the findings using the ClinicalTrial.gov and PubMed databases. Seven genes were observed to be strongly associated with depression (functional annotation score = 4). Interestingly, IL6R was auspicious as a target gene according to the validation outcome. We identified 20 drugs that were undergoing preclinical studies or clinical trials for depression. In addition, we identified sarilumab and satralizumab as drugs that exhibit strong potential for use in the treatment of depression. Our findings indicate that a genomic-analysis-based approach can facilitate the discovery of drugs that can be repurposed for treating depression

Multifunctional nanocarriers of Fe3O4@PLA-PEG/curcumin for MRI, magnetic hyperthermia and drug delivery

Background: Despite medicinal advances, cancer is still a big problem requiring better diagnostic and treatment tools. Magnetic nanoparticle (MNP)-based nanosystems for multiple-purpose applications were developed for these unmet needs. Methods: This study fabricated novel trifunctional MNPs of Fe3O4@PLA-PEG for drug release, MRI and magnetic fluid hyperthermia. Result: The MNPs provided a significant loading of curcumin (∼11%) with controllable release ability, a high specific absorption rate of 82.2 W/g and significantly increased transverse relaxivity (r2 = 364.75 mM-1 s-1). The in vivo study confirmed that the MNPs enhanced MRI contrast in tumor observation and low-field magnetic fluid hyperthermia could effectively reduce the tumor size in mice bearing sarcoma 180. Conclusion: The nanocarrier has potential for drug release, cancer treatment monitoring and therapy.The authors are grateful for the financial support by AOARD under award FA2386-17-1-4042. The Spanish government is acknowledged for the “Nanotechnology in translational hyperthermia (HIPERNANO)” research network (RED2018102626-T) and for funding under the project number MAT2017-83631-C3. NTK Thanh thanks EPSRC (EP/M015157/1). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed

FIRST - Flexible interactive retrieval SysTem for visual lifelog exploration at LSC 2020

Lifelog can provide useful insights of our daily activities. It is essential to provide a flexible way for users to retrieve certain events or moments of interest, corresponding to a wide variation of query types. This motivates us to develop FIRST, a Flexible Interactive Retrieval SysTem, to help users to combine or integrate various query components in a flexible manner to handle different query scenarios, such as visual clustering data based on color histogram, visual similarity, GPS location, or scene attributes. We also employ personalized concept detection and image captioning to enhance image understanding from visual lifelog data, and develop an autoencoderlike approach for query text and image feature mapping. Furthermore, we refine the user interface of the retrieval system to better assist users in query expansion and verifying sequential events in a flexible temporal resolution to control the navigation speed through sequences of images

Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection.

BACKGROUND: Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. METHODS: In this study, we investigated host gene expression profiles in nasopharyngeal (NP) swabs and whole blood samples during natural RSV and rhinovirus (hRV) infection (acute versus early recovery phase) in 83 hospitalized patients <2 years old with lower respiratory tract infections. RESULTS: Respiratory syncytial virus infection induced strong and persistent innate immune responses including interferon signaling and pathways related to chemokine/cytokine signaling in both compartments. Interferon-α/β, NOTCH1 signaling pathways and potential biomarkers HIST1H4E, IL7R, ISG15 in NP samples, or BCL6, HIST2H2AC, CCNA1 in blood are leading pathways and hub genes that were associated with both RSV load and severity. The observed RSV-induced gene expression patterns did not differ significantly in NP swab and blood specimens. In contrast, hRV infection did not as strongly induce expression of innate immunity pathways, and significant differences were observed between NP swab and blood specimens. CONCLUSIONS: We conclude that RSV induced strong and persistent innate immune responses and that RSV severity may be related to development of T follicular helper cells and antiviral inflammatory sequelae derived from high activation of BCL6