café

Protein amino acid sequences can be used to determine the functions of the protein. However, determining the function of a single protein requires many resources and a tremendous amount of time. Computational Intelligence methods such as Deep learning have been shown to predict the proteins' functions. This paper proposes a hybrid deep neural network model to predict an unknown protein's functions from sequences. The proposed model is named Deep_CNN_LSTM_GO. Deep_CNN_LSTM_GO is an Integration between Convolutional Neural network (CNN) and Long Short-Term Memory (LSTM) Neural Network to learn features from amino acid sequences and outputs the three different Gene Ontology (GO)...

Our study aimed to synthesize and compare the mechanical properties and dentin interaction of two adhesives; experimental adhesive (EA) and EA containing 5 wt.% calcium fluoride (CaF2 ) nano-crystals (CaF2 adhesive-CAFA). CaF2 nano-crystals were synthesized by reacting two solutions (containing calcium and fluoride) in a glass chamber using a heated air system. The EA was produced using a mix of monomers, photo-initiators, camphorquinone, and electron initiators. The synthesized CaF2 nano-crystals were centrifuged to guarantee that inside the adhesive there is homogenized dispersion of the filler particles...

Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked...

MOTIVATION: Automated protein function prediction is a complex multi-class, multi-label, structured classification problem in which protein functions are organized in a controlled vocabulary, according to the Gene Ontology (GO). "Hierarchy-unaware" classifiers, also known as "flat" methods, predict GO terms without exploiting the inherent structure of the ontology, potentially violating the True-Path-Rule (TPR) that governs the GO, while "hierarchy-aware" approaches, even if they obey the TPR, do not always show clear improvements with respect to flat methods, or do not scale well when applied to the full GO...

An asymptomatic 75-year-old woman was identified with a 40-mm-sized, round-shaped lesion beside the pulmonary artery on computed tomography (CT). Coronary angiography showed a coronary artery fistula (CAF) with an aneurysm branching from the left anterior descending artery toward the pulmonary artery. The CAF aneurysm (CAFA) was resected and coronary artery bypass graft surgery using the left internal thoracic artery was performed successfully. Pathological analysis revealed that medial depletion similar to segmental arterial mediolysis (SAM) may contribute to aneurysm formation...

With the explosive growth of protein sequences, large-scale automated protein function prediction (AFP) is becoming challenging. A protein is usually associated with dozens of gene ontology (GO) terms. Therefore, AFP is regarded as a problem of large-scale multi-label classification. Under the learning to rank (LTR) framework, our previous NetGO tool integrated massive networks and multi-type information about protein sequences to achieve good performance by dealing with all possible GO terms (>44 000)...

Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments...

Interfacial engineering methods have been developed to solve defect issues of perovskite solar cells (PSCs). However, traditional surface passivation has limited effects on eliminating defect-forming residuals, while secondary grain growth (SGG) is restricted by limited choices of additives and intrinsic properties of perovskites. Here, a pincer strategy of taking advantages of surface passivation and SGG is proposed to modify both exterior and interior of CH3 NH3 PbI3 (MAPbI3 ) perovskite, by employing cyanoacetate-containing donor-acceptor compounds (CA-D-A) including 2-cyano-3-(3,4,5-trimethoxyphenyl)acrylic acid (CA), methanaminium 2-cyano-3-(3,4,5-trimethoxyphenyl)acrylate (CAMA), and aminomethaniminium (Z)-2-cyano-3-(3,4,5-trimethoxyphenyl)acrylate (CAFA)...

The number of available protein sequences in public databases is increasing exponentially. However, a significant percentage of these sequences lack functional annotation, which is essential for the understanding of how biological systems operate. Here, we propose a novel method, Quantitative Annotation of Unknown STructure (QAUST), to infer protein functions, specifically Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. QAUST uses three sources of information: structure information encoded by global and local structure similarity search, biological network information inferred by protein-protein interaction data, and sequence information extracted from functionally discriminative sequence motifs...

In fungi the β-class of carbonic anhydrases (β-CAs) are zinc metalloenzymes that are essential for growth, survival, differentiation, and virulence. Aspergillus fumigatus is the most important pathogen responsible for invasive aspergillosis and possesses two major β-CAs, CafA and CafB. Recently we reported the biochemical characterization and 1.8 Å crystal structure of CafA. Here, we report a crystallographic analysis of CafB revealing the mechanism of enzyme catalysis and establish the relationship of this enzyme to other β-CAs...

Predicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics. Both forward and reverse genetic screen are employed to identify the molecular mechanisms underlying phenotypes and disease, and these resulted in a large number of genotype-phenotype association being available for humans and model organisms. Combined with recent advances in machine learning, it may now be possible to predict human phenotypes resulting from particular molecular aberrations. We developed DeepPheno, a neural network based hierarchical multi-class multi-label classification method for predicting the phenotypes resulting from loss-of-function in single genes...

The long-term dynamics of fungicide resistance of the rice blast fungus Pyricularia oryzae was monitored by examining the reaction of the fungal field isolates, collected over a period of 26 years, to the active ingredients of commercially relevant fungicides. The in vitro sensitivity of all isolates was measured against quinone outside inhibitors (QoI), melanin biosynthesis inhibitors, and sterol demethylation inhibitor (DMI) fungicides, namely azoxystrobin (as a QoI), tricyclazole (as a melanin biosynthesis inhibitor), tebuconazole (as a DMI), and trifloxystrobin + tebuconazole (QoI + DMI)...

Potocki-Shaffer syndrome (PSS) is a rare non-recurrent contiguous gene deletion syndrome involving chromosome 11p11.2. Current literature implies a minimal region with haploinsufficiency of three genes, ALX4 (parietal foramina), EXT2 (multiple exostoses), and PHF21A (craniofacial anomalies, and intellectual disability). The rest of the PSS phenotype is still not associated with a specific gene. We report a systematic review of the literature and included two novel cases. Because deletions are highly variable in size, we defined three groups of patients considering the PSS-genes involved...

Ready-to-eat (RTE) artisanal foods are very popular, but they can be contaminated by Listeria monocytogenes . The aim was to determine the presence of L. monocytogenes in artisanal RTE foods and evaluate its food safety risk. We analyzed 400 RTE artisanal food samples requiring minimal (fresh products manufactured by a primary producer) or moderate processing (culinary products for sale from the home, restaurants such as small cafés, or on the street). Listeria monocytogenes was isolated according to the ISO 11290-1:2017 standard, detected with VIDAS equipment, and identified by real-time polymerase chain reaction (PCR)...

This study reports a facile preparation of black TiO2-x /CaFe2 O4 (Ti3+ self-doped titania coupled with calcium ferrite), an efficient photocatalyst for ibuprofen (IBP) oxidation under visible light irradiation. Compared with TiO2-x or CaFe2 O4 , TiO2-x /CaFe2 O4 heterojunction displayed better photo-oxidation performance, and their immobilization onto diatomaceous earth (DE) further increased the oxidation rate due to the adsorption ability of DE. The morphology, phase composition and other physicochemical properties of the composite were studied using different characterization methods...

Background: Clinical competency and professional growth amongst nursing students is the cornerstone of a nursing education programme. The demanding and complex training of nursing students requires various clinical teaching and learning strategies such as peer-group clinical mentoring. Aim: The objective of this research was to explore and describe the challenges that peer-mentees experience in an undergraduate peer-group clinical mentoring programme in one-specific nursing education institution in the North West Province...

In the current epidemic of African swine fever (ASF) in Europe, the maintenance and spread of the disease among wild boar populations remains the most important epidemiological challenge. Affected and at-risk countries have addressed this situation using a diversity of wild boar management methods with varying levels of success. The methods applied range from conventional animal disease intervention measures (zoning, stakeholder awareness campaigns, increased surveillance and biosecurity measures) to measures aimed at reducing wild boar population movements (fencing and baiting/feeding) or population numbers (intensive hunting)...

Tobacco smoke is known for releasing metals in indoor air of waterpipe/cigarette cafés. However, the worker exposure to metals, and its association with oxidative stress in these cafés are still unclear. To this end, 54 workers and 38 customers from waterpipe/cigarette cafés (the exposed group), 30 workers from non-smoking cafés (the control group 1 (CG_1)) and 32 individuals from the general population (the control group 2 (CG_2)) were selected and toenails samples were then taken from them. Our findings revealed a significant difference in terms of toenail-bounded metal levels between the exposure and control groups (CG_1 and CG_2) (Mann-Whitney U test, Pvalue  < 0...

Legius syndrome is characterized by numerous café-au-lait macules and intertriginous freckling, but typically lacks the distinctive tumor manifestations of neurofibromatosis type 1. We report two siblings with Legius syndrome and Lisch nodules illustrating the importance of eye surveillance in these patients.

Roasted coffee and many coffee flavorings emit volatile organic compounds (VOCs) including diacetyl and 2,3-pentanedione. Exposures to VOCs during roasting, packaging, grinding, and flavoring coffee can negatively impact the respiratory health of workers. Inhalational exposures to diacetyl and 2,3-pentanedione can cause obliterative bronchiolitis. This study summarizes exposures to and emissions of VOCs in 17 coffee roasting and packaging facilities that included 10 cafés. We collected 415 personal and 760 area full-shift, and 606 personal task-based air samples for diacetyl, 2,3-pentanedione, 2,3-hexanedione, and acetoin using silica gel tubes...