Correction: Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling.

[This corrects the article DOI: 10.1371/journal.pone.

Development of method using language processing techniques for extracting information on drug-health food product interactions.

Aims: Health food products (HFPs) are foods and products related to maintaining and promoting health. HFPs may sometimes cause unforeseen adverse health effects by interacting with drugs. Considering the importance of information on the interactions between HFPs and drugs, this study aimed to establish a workflow to extract information on Drug-HFP Interactions (DHIs) from open resources.

EnzymeNet: residual neural networks model for Enzyme Commission number prediction.

Motivation: Enzymes are key targets to biosynthesize functional substances in metabolic engineering. Therefore, various machine learning models have been developed to predict Enzyme Commission (EC) numbers, one of the enzyme annotations. However, the previously reported models might predict the sequences with numerous consecutive identical amino acids, which are found within unannotated sequences, as enzymes.

Different Recognition of Protein Features Depending on Deep Learning Models: A Case Study of Aromatic Decarboxylase UbiD.

The number of unannotated protein sequences is explosively increasing due to genome sequence technology. A more comprehensive understanding of protein functions for protein annotation requires the discovery of new features that cannot be captured from conventional methods. Deep learning can extract important features from input data and predict protein functions based on the features.

Prediction of Metabolic Flux Distribution by Flux Sampling: As a Case Study, Acetate Production from Glucose in .

Omics data was acquired, and the development and research of metabolic simulation and analysis methods using them were also actively carried out. However, it was a laborious task to acquire such data each time the medium composition, culture conditions, and target organism changed. Therefore, in this study, we aimed to extract and estimate important variables and necessary numbers for predicting metabolic flux distribution as the state of cell metabolism by flux sampling using a genome-scale metabolic model (GSM) and its analysis.

Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling.

Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism.

Knowledge extraction from literature and enzyme sequences complements FBA analysis in metabolic engineering.

Flux balance analysis (FBA) using genome-scale metabolic model (GSM) is a useful method for improving the bio-production of useful compounds. However, FBA often does not impose important constraints such as nutrients uptakes, by-products excretions and gases (oxygen and carbon dioxide) transfers. Furthermore, important information on metabolic engineering such as enzyme amounts, activities, and characteristics caused by gene expression and enzyme sequences is basically not included in GSM.

Dynamic Flux Balance Analysis to Evaluate the Strain Production Performance on Shikimic Acid Production in .

Flux balance analysis (FBA) is used to improve the microbial production of useful compounds. However, a large gap often exists between the FBA solution and the experimental yield, because of growth and byproducts. FBA has been extended to dynamic FBA (dFBA), which is applicable to time-varying processes, such as batch or fed-batch cultures, and has significantly contributed to metabolic and cultural engineering applications.

Author Correction: Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids.

In the original version of this Article, the abbreviation of 3,4-dihydroxyphenylacetaldehyde synthase presented in the first paragraph of the Discussion section was given incorrectly as DYPAA. The correct abbreviation for this enzyme is DHPAAS. This error has been corrected in both the PDF and HTML versions of the Article.

Mechanism-based tuning of insect 3,4-dihydroxyphenylacetaldehyde synthase for synthetic bioproduction of benzylisoquinoline alkaloids.

Previous studies have utilized monoamine oxidase (MAO) and L-3,4-dihydroxyphenylalanine decarboxylase (DDC) for microbe-based production of tetrahydropapaveroline (THP), a benzylisoquinoline alkaloid (BIA) precursor to opioid analgesics. In the current study, a phylogenetically distinct Bombyx mori 3,4-dihydroxyphenylacetaldehyde synthase (DHPAAS) is identified to bypass MAO and DDC for direct production of 3,4-dihydroxyphenylacetaldehyde (DHPAA) from L-3,4-dihydroxyphenylalanine (L-DOPA). Structure-based enzyme engineering of DHPAAS results in bifunctional switching between aldehyde synthase and decarboxylase activities.

Kinetic modeling and sensitivity analysis for higher ethanol production in self-cloning xylose-using Saccharomyces cerevisiae.

We constructed a xylose-utilizing Saccharomyces cerevisiae strain using endogenous xylose-assimilating genes (strain K7-XYL). Such self-cloning yeast is expected to make a great contribution to cost reduction of ethanol production processes. However, it is difficult to modify self-cloning yeast for optimal performance because the available gene source is limited.

Transporter engineering in biomass utilization by yeast.

Biomass resources are attractive carbon sources for bioproduction because of their sustainability. Many studies have been performed using biomass resources to produce sugars as carbon sources for cell factories. Expression of biomass hydrolyzing enzymes in cell factories is an important approach for constructing biomass-utilizing bioprocesses because external addition of these enzymes is expensive.

[Compliance with FOLFOX4 for Stage III colon cancer in the adjuvant setting].

Aims: The usefulness of oxaliplatin(L-OHP)as adjuvant chemotherapy for Stage III colon cancer has been shown in clinical trials, such as the MOSAIC trial. The Leucovorin, fluorouracil, and oxaliplatin(FOLFOX)regimen has been recommended as adjuvant chemotherapy for colorectal cancer in Japan. In the MOSAIC trial, 74.

The clinical significance of breast MRI in the management of ductal carcinoma in situ diagnosed on needle biopsy.

Objective: To identify the factors associated with invasive disease in ductal carcinoma in situ diagnosed on needle biopsy by analyzing breast magnetic resonance imaging findings with the histopathological factors of biopsy specimens.

Methods: This was an institutional review board-approved, Health Insurance Portability and Accountability Act-compliant study. Seventy-five ductal carcinoma in situ patients diagnosed by needle biopsy who underwent preoperative magnetic resonance imaging were retrospectively reviewed.

Kinetic modeling and sensitivity analysis of acetone-butanol-ethanol production.

A kinetic simulation model of metabolic pathways that describes the dynamic behaviors of metabolites in acetone-butanol-ethanol (ABE) production by Clostridium saccharoperbutylacetonicum N1-4 was proposed using a novel simulator WinBEST-KIT. This model was validated by comparing with experimental time-course data of metabolites in batch cultures over a wide range of initial glucose concentrations (36.1-295 mM).

MRI accurately depicts underlying DCIS in a patient with Paget's disease of the breast without palpable mass and mammography findings.

Breast-conserving therapy must be carefully indicated among patients with Paget's disease of the breast, because the disease is often associated with an underlying in situ or invasive carcinoma, even when there are no palpable mass or mammography findings. We report a 52-year-old woman who complained of skin color change of her right nipple for 11 months. No mass was palpable in her breasts, and mammography did not show any density or calcification.

Central and peripheral activity of cholinesterase inhibitors as revealed by yawning and fasciculation in rats.

This study was designed to investigate the central and peripheral activity profile of cholinesterase inhibitors in rats. Intravenous injection of cholinesterase inhibitors caused fasciculation, a fine involuntary muscular movement. This peripheral cholinergic sign was tightly correlated with in vitro anti-acetylcholinesterase activity by cholinesterase inhibitors, suggesting that fasciculation is a valid index of peripheral cholinergic activation.

Comparison of inhibitory activities of donepezil and other cholinesterase inhibitors on acetylcholinesterase and butyrylcholinesterase in vitro.

This study was designed to compare the in vitro inhibitory effects on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) of donepezil and some other cholinesterase (ChE) inhibitors which have been developed for the treatment of Alzheimer's disease. The carbamate derivatives physostigmine and rivastigmine needed preincubation to exhibit appropriate anti-ChE activity. The maximum ChE inhibition by physostigmine developed within 30-60 min, while the inhibitory effect of rivastigmine on AChE and BuChE activities reached its peak after 48 and 6 h, respectively.

Donepezil, a centrally acting acetylcholinesterase inhibitor, alleviates learning deficits in hypocholinergic models in rats.

Donepezil is a member of a new class of centrally acting cholinesterase inhibitors which preferentially inhibit acetylcholinesterase rather than butyrylcholinesterase. The effects of donepezil on learning impairments were investigated in some hypocholinergic models in rats. In nucleus basalis magnocellularis (NBM)-lesioned rats, donepezil alleviated deficits in passive avoidance response at a dose of 0.

Inhibitory effect of orally administered donepezil hydrochloride (E2020), a novel treatment for Alzheimer's disease, on cholinesterase activity in rats.

Donepezil hydrochloride ((+/-)-2-[(1-benzylpiperidin-4-yl)methyl]-5, 6-dimethoxy-indan-1-one monohydrochloride: E2020: donepezil) is a potent and selective acetylcholinesterase inhibitor developed for the treatment of Alzheimer's disease. The present experiments were designed to compare the inhibitory effects of orally administered donepezil and other cholinesterase inhibitors, tacrine (9-amino-1,2, 3,4-tetrahydroacridine hydrochloride), (S)-N-ethyl-3-[(1-dimethyl-amino)ethyl]-N-methyl-phenylcarbamate hydrogentartrate (ENA-713, rivastigmine) and 3-[1-(phenylmethyl)-4-piperidinyl]-1-(2,3,4, 5-tetrahydro-1H-1-benzazepin-8-yl)-1-propanone fumarate (TAK-147), on the cholinesterase activity in the brain and plasma of rats. Moreover, in order to validate the cholinesterase inhibition data, we measured the brain and plasma concentrations of these drugs.

Inhibitory effects of donepezil hydrochloride (E2020) on cholinesterase activity in brain and peripheral tissues of young and aged rats.

Donepezil hydrochloride (donepezil: E2020: (+/-)-2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimethoxy-indan-1-one monohydrochloride)) is a centrally acting acetylcholinesterase inhibitor developed for the treatment of Alzheimer's disease. In the present study, its inhibitory effect on the activity of cholinesterase ex vivo was evaluated in the brain, plasma, erythrocytes, heart, small intestine, liver and pectoral muscle of young adult as well as aged rats, in comparison with that of tacrine (9-amino-1,2,3,4-tetrahydroacridine hydrochloride). In aged animals, cholinesterase activity in heart, small intestine and pectoral muscle was lower, whereas that in plasma and liver was higher than in young rats.

Effect of donepezil hydrochloride (E2020) on extracellular acetylcholine concentration in the cerebral cortex of rats.

Donepezil hydrochloride (donepezil), a potent and selective acetylcholinesterase inhibitor, has been developed for the treatment of Alzheimer's disease. We studied the effect of oral administration of this drug on the extracellular acetylcholine (ACh) concentration in the cerebral cortex of rats using microdialysis. We also observed fasciculation, a peripheral cholinergic sign induced by activation of neuromuscular transmission, after oral administration of the drug as an index of peripheral cholinergic activation.

Effect of donepezil hydrochloride (E2020) on basal concentration of extracellular acetylcholine in the hippocampus of rats.

The effects of oral administration of the centrally acting acetylcholinesterase (AChE) inhibitors, donepezil hydrochloride (donepezil: E2020: (+/-)-2-[(1-benzylpiperidin-4-yl)methyl]-5,6-dimethoxy-indan-1-one monohydrochloride), tacrine (9-amino-1,2,3,4-tetrahydroacridine hydrochloride) and ENA-713 (rivastigmine: (S)-N-ethyl-3-[(1-dimethyl-amino)ethyl]-N-methyl-phenylcarbamate hydrogentartrate), which have been developed for the treatment of Alzheimer's disease, on the extracellular acetylcholine concentration in the hippocampus of rats were evaluated by using a microdialysis technique without adding cholinesterase inhibitor to the perfusion solution. We also compared the inhibition of brain AChE and the brain concentrations of these drugs. Donepezil at 2.

Thoracoscopic en bloc total esophagectomy with radical mediastinal lymphadenectomy.

Objective: Total esophagectomy with en bloc mediastinal lymphadenectomy for cancer carries a substantial morbidity and mortality rate. To investigate the feasibility of thoracoscopic technique, we carried out an extensive laboratory study. Encouraged by our excellent results, we conducted a clinical trial.

[Cytophotometric DNA analysis of the early and superficial esophageal cancer].

Although it is widely known that early esophageal cancer (n-) patients have a favorable prognosis after surgery and the superficial esophageal cancer (n+) patients have a poor one, the differences between them have not been found out under the microscopic examination of the primary lesion. Cytophotometric DNA analysis of the primary lesion was done to search for the differences between early and superficial esophageal cancer. Significant differences were obtained in the mean DNA value (p less than 0.