•A system that uses PCA, DWT and an optimized XGBoost classifier is proposed.•PCA is used to perform dimensionality reduction to the input data.•DWT performs a noise reduction to the input data.•The ...XGBoost classifier is optimized using a MOO-GA.•The proposed system outperforms the B&H strategy in different markets.
When investing in financial markets it is crucial to determine a trading signal that can provide the investor with the best entry and exit points of the financial market, however this is a difficult task and has become a very popular research topic in the financial area. This paper presents an expert system in the financial area that combines Principal Component Analysis (PCA), Discrete Wavelet Transform (DWT), Extreme Gradient Boosting (XGBoost) and a Multi-Objective Optimization Genetic Algorithm (MOO-GA) in order to achieve high returns with a low level of risk. PCA is used to reduce the dimensionality of the financial input data set and the DWT is used to perform a noise reduction to every feature. The resultant data set is then fed to an XGBoost binary classifier that has its hyperparameters optimized by a MOO-GA. The importance of the PCA is analyzed and the results obtained show that it greatly improves the performance of the system. In order to improve even more the results obtained in the system using PCA, the PCA and the DWT are then applied together in one system and the results obtained show that this system is capable of outperforming the Buy and Hold (B&H) strategy in three of the five analyzed financial markets, achieving an average rate of return of 49.26% in the portfolio, while the B&H achieves on average 32.41%.
New non-invasive approaches that can complement and improve on current strategies for colorectal cancer (CRC) screening and management are urgently needed. A growing number of publications have ...documented that components of tumors, which are shed into the circulation, can be detected in the form of liquid biopsies and can be used to detect CRC at early stages, to predict response to certain therapies and to detect CRC recurrence in a minimally invasive way. The analysis of circulating tumor DNA (ctDNA), tumor-derived cells (CTC, circulating tumor cells) or circulating microRNA (miRNA) in blood and other body fluids, have a great potential to improve different aspects of CRC management. The challenge now is to find which types of components, biofluids and detection methods would be the most suitable to be applied in the different steps of CRC detection and treatment. This chapter will provide an up to date review on ctDNA, CTCs and circulating miRNAs as new biomarkers for CRC, either for clinical management or early detection, highlighting their advantages and limitations.
We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations ...suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a 4 C 1 chair or 2 S O skew conformations, both of which can change to TS-like conformations characteristic of retaining glucosidases. Starting from four distinct enzyme:substrate complexes, umbrella sampling quantum mechanics/molecular mechanics simulations (converged within less than 1 kcal·mol–1 within a total simulation time of 1.6 ns) indicated that the reaction occurrs with a Gibbs barrier of 13.9 kcal·mol –1, in one asynchronous concerted step encompassing an acid–base reaction with Glu233 followed by a loose SN2-like nucleophilic substitution by the Asp197. The transition state is characterized by a 2 H 3 half-chair conformation of the buried glucoside that quickly changes to the E 3 envelope conformation preceding the attack of the anomeric carbon by the Asp197 nucleophile. Thermodynamic analysis of the reaction supported that a water molecule tightly hydrogen bonded to the glycosidic oxygen of the substrate at the reactant state (∼1.6 Å) forms a short hydrogen bond with Glu233 at the transition state (∼1.7 Å) and lowers the Gibbs barrier in over 5 kcal·mol–1. The resulting Asp197-glycosyl was mostly found in the 4 C 1 conformation, although the more endergonic B 3,O conformation was also observed. Altogether, the combination of short distances for the acid–base reaction with the Glu233 and for the nucleophilic attack by the Asp197 nucleophile and the availability of water within hydrogen bonding distance of the glycosidic oxygen provides a reliable criteria to identify reactive conformations of α-amylase complexes.
The derivation of a formula to compute the permeability coefficient in the commented paper assumes that the mass flow is homogeneous in a homogeneous layer of a specimen. This assumption is not ...correct when there is also, at least, one heterogeneous layer. Moreover, a mathematical lapse was found on one equation, that would prevent the right computation of the permeability coefficient, even if the assumption was correct. Although this does not invalidate the major conclusions of the study and has not an outstanding effect on the presented results, for the sake of rigor and sound background for future studies in this field, corrections to the published formulas and model are proposed.
Polyethylene terephthalate (PET) has been widely used to make disposable bottles, among others, leading to massive PET waste accumulation in the environment. The discovery of the Ideonella sakaiensis ...PETase and MHETase enzymes, which hydrolyze PET into its constituting monomers, opened the possibility of a promising route for PET biorecycling. We describe an atomistic and thermodynamic interpretation of the catalytic reaction mechanism of PETase using umbrella sampling simulations at the robust PBE/MM MD level with a large QM region. The reaction mechanism takes place in two stages, acylation and deacylation, each of which occurs through a single, associative, concerted and asynchronous step. Acylation consists of proton transfer from Ser131 to His208, concerted with a nucleophilic attack by Ser131 on the substrate, leading to a tetrahedral transition state, which subsequently results in the release of MHET after the breaking of the ester bond. Deacylation is driven by deprotonation of an active site water molecule by His208, with the resulting hydroxide attacking the acylated Ser131 intermediate and breaking its bond to the substrate. Subsequently, His208 transfers the water proton to Ser131, with ensuant formation of MHET and enzyme regeneration. The rate-limiting acylation has a free energy barrier of 20.0 kcal·mol–1, consistent with the range of experimental values of 18.0–18.7 kcal·mol–1. Finally, we identify residues whose mutation should increase the enzyme turnover. Specifically, mutation of Asp83, Asp89, and Asp157 by nonpositive residues is expected to decrease the barrier of the rate-limiting step. This work led to the understanding of the catalytic mechanism of PETase and opened the way for additional rational enzyme engineering.
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, ...the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme’s detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
Abstract
Background
Multiple technologies are available for detection of circulating tumor cells (CTCs), but standards to evaluate their technical performance are still lacking. This limits the ...applicability of CTC analysis in clinic routine. Therefore, in the context of the CANCER-ID consortium, we established a platform to assess technical validity of CTC detection methods in a European multi-center setting using non-small cell lung cancer (NSCLC) as a model.
Methods
We characterized multiple NSCLC cell lines to define cellular models distinct in their phenotype and molecular characteristics. Standardized tumor-cell-bearing blood samples were prepared at a central laboratory and sent to multiple European laboratories for processing according to standard operating procedures. The data were submitted via an online tool and centrally evaluated. Five CTC-enrichment technologies were tested.
Results
We could identify 2 cytokeratin expressing cell lines with distinct levels of EpCAM expression: NCI-H441 (EpCAMhigh, CKpos) and NCI-H1563 (EpCAMlow, CKpos). Both spiked tumor cell lines were detected by all technologies except for the CellSearch system that failed to enrich EpCAMlow NCI-H1563 cells. Mean recovery rates ranged between 49% and 75% for NCI-H411 and 32% and 76% for NCI-H1563 and significant differences were observed between the tested methods.
Conclusions
This multi-national proficiency testing of CTC-enrichment technologies has importance in the establishment of guidelines for clinically applicable (pre)analytical workflows and the definition of minimal performance qualification requirements prior to clinical validation of technologies. It will remain in operation beyond the funding period of CANCER-ID in the context of the European Liquid Biopsy Society (ELBS).
A methodology to compute the CO
2
uptake of recycled aggregate concrete is proposed in the commented paper. Besides some typos in several formulas, it is found that the approach to estimate the ...specific surface area of the recycled aggregates is not correct. This issue has some impact in the conclusions of the commented paper. Therefore, aiming to improve the understanding, accuracy and findings of the commented paper, an alternative approach to estimate the specific surface area of the recycled aggregates, as well as an erratum of the formulas and revised conclusions are suggested.
We explore the enzymatic mechanism of the reduction of glutathione disulfide (GSSG) by the reduced a domain of human protein disulfide isomerase (hPDI) with atomistic resolution. We use classical ...molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations at the mPW1N/6–311+G(2d,2p):FF99SB//mPW1N/6–31G(d): FF99SB level. The reaction proceeds in two stages: (i) a thiol-disulfide exchange through nucleophilic attack of the Cys53-thiolate to the GSSG-disulfide followed by the deprotonation of Cys56-thiol by Glu47-carboxylate and (ii) a second thiol-disulfide exchange between the Cys56-thiolate and the mixed disulfide intermediate formed in the first step. The Gibbs activation energy for the first stage was 18.7 kcal·mol−1, and for the second stage, it was 7.2 kcal·mol−1, in excellent agreement with the experimental barrier (17.6 kcal·mol−1). Our results also suggest that the catalysis by protein disulfide isomerase (PDI) and thiol-disulfide exchange is mostly enthalpy-driven (entropy changes below 2 kcal·mol−1 at all stages of the reaction). Hydrogen bonds formed between the backbone of His55 and Cys56 and the Cys56-thiol result in an increase in the Gibbs energy barrier of the first thiol-disulfide exchange. The solvent plays a key role in stabilizing the leaving glutathione thiolate formed. This role is not exclusively electrostatic, because an explicit inclusion of several water molecules at the density-functional theory level is a requisite to form the mixed disulfide intermediate. In the intramolecular oxidation of PDI, a transition state is only observed if hydrogen bond donors are nearby the mixed disulfide intermediate, which emphasizes that the thermochemistry of thiol-disulfide exchange in PDI is influenced by the presence of hydrogen bond donors.
The PETase enzyme from the bacterium
Ideonella sakaiensis
can degrade polyethylene terephthalate (PET) back into its polymeric constituents at room temperature, making it an ecologically friendly ...tool for reducing PET pollution. Computational enzyme optimization is a fundamental tool to accelerate enzyme engineering towards the "green revolution" promised by the introduction of enzymatic catalysis in industry. The Asp83Asn mutant generates a sub-optimal reactive conformation that the mutation-induced transition state stabilization does not compensate for, and the barrier is raised by 1.9 kcal mol
−1
. In contrast, the Asp89Asn mutant keeps a perfect reactive conformation, and the mutation stabilizes the transition state more than the reactants, lowering the barrier by 4.7 kcal mol
−1
. We show that computer-based well-chosen single-residue substitutions in PETase can decrease the activation barrier significantly, facilitating the development of highly-efficient PETase mutants. The results of this work encourage future studies that aim for rational enzyme engineering on PETase and other enzymes.
The PETase enzyme from the bacterium
Ideonella sakaiensis
can degrade polyethylene terephthalate (PET) back into its polymeric constituents at room temperature, making it an ecologically friendly tool for reducing PET pollution.
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