Can AI Help Improve Water Quality? Towards the Prediction of Degradation of Micropollutants in Wastewater.

Micropollutants have become a serious environmental problem by threatening ecosystems and the quality of drinking water. This account investigates if advanced AI can be used to find solutions for this problem. We review background, the challenges involved, and the current state-of-the-art of quantitative structure-biodegradation relationships (QSBR). We report on recent progress combining experiment, quantum chemistry (QC) and chemoinformatics, and provide a perspective on potential future uses of AI technology to help improve water quality.

High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H5 C2 NO2.

High performance global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H5 C2 NO2 by using the scaled hypersphere search-anharmonic downward distortion following (SHS-ADDF) method. A multi-node operation, NeoGRRM, has achieved high performance exploration calculations for the large system by submitting SHS-ADDF sub-jobs into many cores in parallel and unifying the results of sub-jobs into the total lists of the main-job. Global exploration of equilibrium (EQ) and transition-state structures at the level of B3LYP/6-31G(d) gave 3210 EQs and 23278 TSs. Nine compounds were found in the low energy regions of 0-100 kJ/mol; the lowest energy compound is N-methylcarbamic acid, the second is methyl carbamate, and the third is glycine (the most fundamental amino acid). Interconversion pathways between the conformers of each of the low energy compounds were surveyed. Isomerization channels around glycine were explored in detail. The lowest energy barriers around some of the EQs turned to be negative after zero-point energy corrections. This indicates that those structures cannot exist as independent structures because they spontaneously collapse into more stable structures. The global PES search showed various interesting dissociating channels which indicate synthon reaction pathways in the reverse directions.

Exploration of Carbon Allotropes with Four-membered Ring Structures on Quantum Chemical Potential Energy Surfaces.

The existence of a new carbon allotrope family with four-membered rings as a key unit has been recently predicted with quantum chemical calculations. This family includes carbon allotropes in prism-, polymerized prism-, sheet-, tube-, and wavy-forms. An atypical bond property has been observed in this series of carbon structures, which differs from the typical sp3 , sp2 , and sp hybridizations. The lowest energy barrier from some of the equilibrium states of the carbon structures has been determined with the SHS-ADDF (scaled-hypersphere-search combined with the anharmonic downward distortion following) method within the GRRM software program package. The height of the barriers indicates that the well is deep enough for the carbon structures to exist. This class of carbon allotropes is expected to be energy-reservoirs with extra energy of 100-350 kJ mol-1 per one carbon atom. This article presents the structures, energies and reactivity of the carbon allotropes with four-membered ring structures as well as the background of the findings in the context of the global exploration of potential energy surfaces. © 2018 Wiley Periodicals, Inc.

Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3 CNO3.

Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H3 CNO3 using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. The molecular formula of H3 CNO3 includes functional groups of CH3 , OH, NH2 , COOH, NO, NO2 , and NO3 , which are very important in connection with amino acids and NOx. Geometrical structures and interconversion pathways are disclosed after 18719781 force calculations and 534726 Hessian calculations at the level of B3LYP/6-31G(d). The explored results are confirmed to be valid, especially for the important lower energy regions, by re-optimization at the higher level of B3LYP/6-311++G(d,p). A global reaction route-mapping using SHS-ADDF demonstrates the entire view and undeveloped landscapes on PES of H3 CNO3 . Typical compounds of H3 CNO3 , aminoxy formic acid, hydroxycarbamic acid, aminoperformic acid, hydroxymethyl nitrite, nitromethanol, methyl nitrate, methyl peroxynitrite, and dioxaziridine, are well separated from others by very high energy-barriers. The stable-most conformer of H3 CNO3 is difficult to be determined, because of seven structures existing with nearly the same energies within 5.7 kJ/mol at the level of CCSD(T)/aug-cc-pVTZ. © 2017 Wiley Periodicals, Inc.

Significant substituent effect on the anomerization of pyranosides: mechanism of anomerization and synthesis of a 1,2-cis glucosamine oligomer from the 1,2-trans anomer.

Aminoglycosides containing a 2,3-trans carbamate group easily undergo anomerization from the 1,2-trans glycoside to the 1,2-cis isomer under mild acidic conditions. The N-substituent of the carbamate has a significant effect on the anomerization reaction; in particular, an N-acetyl group facilitated rapid and complete α-anomerization. The differences in reactivity due to the various N-substituents were supported by the results of DFT calculations; the orientation of the acetyl carbonyl group close to the anomeric position was found to contribute significantly to the directing of the anomerization reaction. By exploiting this reaction, oligoaminoglycosides with multiple 1,2-cis glycosidic bonds were generated from 1,2-trans glycosides in a one-step process.

Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

A microarray analysis of urinary microRNAs in renal diseases.

BACKGROUND: MicroRNAs (miRNAs), a family of endogenous small non-coding RNAs, are associated with the development of renal diseases. To clarify whether urinary miRNAs (UmiRNAs) can be used for the evaluation of renal disease, we examined the profiles of UmiRNAs in various renal diseases. METHODS: We extracted miRNAs from urine specimens of 5 healthy controls and 71 patients with renal diseases, and we examined the correlation between clinical and histological parameters and the profile of UmiRNAs by microarray analysis. RESULTS: The urinary concentration of miRNAs increased in patients with renal disease compared with healthy controls, and the levels correlated with urinary protein and the degree of glomerular sclerosis. The microarray analysis detected 83-137 distinct UmiRNAs. We observed 80-99 % of the miRNAs in both the healthy controls and the renal disease patients. The majority of UmiRNAs displayed higher signal intensity in renal disease patients than in healthy controls, including 39 miRNAs exhibiting signal intensities 100 times greater than in healthy controls. A different pattern of UmiRNAs was observed in each type of renal disease. A comparison of renal tissue and UmiRNAs revealed that the sample profiles were similar and that their signal intensity was significantly correlated. CONCLUSION: This study demonstrated that UmiRNAs are correlated with renal pathological changes and that the profile of UmiRNAs presented different patterns corresponding to the type of renal disease. These results suggest that UmiRNAs can potentially be used as novel biomarkers for renal diseases.

Design of chemical glycosyl donors: does changing ring conformation influence selectivity/reactivity?

This tutorial review focuses on the design of glycosyl donors, especially on attempts to control selectivity/reactivity by employing bulky substituents, cyclic protecting groups, or bridged structures. These structural modifications are performed to change the conformational distributions of pyranoside/furanoside rings. We also briefly discuss this issue with regard to studies on furanosides and enzymatic glycosylation reactions. Readers will find that some of the designed glycosyl donors have been used to achieve total syntheses of natural products.

Miglitol, an anti-diabetic drug, inhibits oxidative stress-induced apoptosis and mitochondrial ROS over-production in endothelial cells by enhancement of AMP-activated protein kinase.

Endothelial dysfunction caused by oxidative stress plays a key role in atherogenesis. This study investigated whether the anti-diabetic drug miglitol, an α-glucosidase inhibitor, which is currently available in clinical practice, can prevent endothelial cell apoptosis and whether it might restore impaired vascular relaxation under oxidative stress. The bEnd.3 cells, a microvascular endothelial cell line, were pre-treated with various concentrations of miglitol and then were incubated with H(2)O(2) for 1 - 2 h. Treatment of bEnd.3 cells with miglitol resulted in the protection of cell viability, suppression of mitochondrial superoxide production, and DNA strand breakage under the oxidative stress. These effects of miglitol were associated with the activation of AMP-activated protein kinase (AMPK) and the phosphorylation of endothelial nitric oxide synthase (eNOS). In aortic rings with endothelium, acetylcholine (Ach)-induced relaxation was attenuated by H(2)O(2). We found that this impaired relaxation was restored by acute treatment with miglitol. Compound C, an AMPK inhibitor, inhibited the amelioration of vascular relaxations treated with miglitol. These results suggest that miglitol might protect against endothelial cells damage under oxidative stress via inhibition of endothelial cell apoptosis and mitochondrial superoxide production, which are mediated by the activation of AMPK and the phosphorylation of eNOS.

Endocyclic cleavage in glycosides with 2,3-trans cyclic protecting groups.

An endocyclic pathway is proposed as a reaction mechanism for the anomerization from the ß (1,2-trans) to the α (1,2-cis) configuration observed in glycosides carrying 2,3-trans cyclic protecting groups. This reaction occurs in the presence of a weak Lewis or Brønsted acid, while endocyclic cleavage (endocleavage) in typical glycosides was observed only when mediated by protic media or strong Lewis acids. To rationalize the behavior of this class of compounds, the reaction mechanism and the promoting factors of the endocleavage are investigated using quantum-mechanical (QM) calculations and experimental studies. We examine anomerization reactions of thioglycosides carrying 2,3-trans cyclic protecting groups, employing boron trifluoride etherate (BF(3)·OEt(2)) as a Lewis acid. The estimated theoretical reactivity, based on a simple model to predict transition state (TS) energies from the strain caused by the fused rings, is very close to the TS energies calculated by the TS search along the C1-C2 bond rotation after the endo C-O bond breaking. Excellent agreement is found between the predicted TS energies and the experimental reactivity ranking. The series of calculations and experiments strongly supports the predominance of the endocyclic rather than the exocyclic mechanism. Furthermore, these investigations suggest that the inner strain is the primary factor enhancing the endocleavage reaction. The effect of the cyclic protecting group in restricting the pyranoside ring to a (4)C(1) conformation, extensively discussed in conjunction with the stereoelectronic effect theory, is shown to be a secondary factor.

[MRI-CT fusion image navigation during surgery for inverted papilloma].

We report two cases of intraoperative computer-aided surgery using magnetic resonance imaging (MRI)/computed tomography (CT) fusion imaging for inverted papilloma (IP). Case 1: IP had spread to the frontal recess/sinus so we chose a combined endoscopic sinus surgery (ESS) and external approach. Case 2: For a maxillary sinus tumor, we combined ESS and the adjuvant external (Caldwell-Luc) procedure. This is helpful to surgeons when, shifting fusion imaging when opening the frontal sinus bone to obtain CT data, and shifting to MRI to detect the tumor pedicle, then approaching the bone defect using MRI-CT fusion imaging (50-50%).

Oral administration of tetrahydrobiopterin slows the progression of atherosclerosis in apolipoprotein E-knockout mice.

OBJECTIVE: Although it has been reported that oral administration of tetrahydrobiopterin (BH4) prevents endothelial dysfunction and vascular oxidative stress in various rat models, the effect of treatment with BH4 on atherogenesis remains unclear. METHODS AND RESULTS: In this study, we investigated whether oral BH4 treatment might slow the progression of atherosclerosis using hypercholesterolemic apolipoprotein E-knockout mice. We report that ingesting BH4 in drinking water is sufficient to inhibit atherogenesis in mice. Furthermore, we report that BH4 treatment improves endothelial dysfunction and attenuates increased mRNA expression of NADPH oxidase components, as well as a number of inflammatory factors, such as LOX-1 and MCP-1, in the aortas of apolipoprotein E- knockout mice. CONCLUSION: Strategies such as oral administration of BH4 to ensure continuous BH4 availability may be effective in restoring nitric oxide-mediated endothelial function and limiting vascular disease and the progression of atherosclerosis.

Tetrahydrobiopterin prevents endothelial dysfunction and restores adiponectin levels in rats.

Oxidative stress induces endothelial dysfunction and hypoadiponectinemia. We previously reported that supplementation with tetrahydrobiopterin (BH4), one of the most potent naturally occurring reducing agents and an essential cofactor of enzymatic NO synthase (NOS), ameliorates endothelial dysfunction and reverses hypoadiponectinemia as a result of oxidative stress in rats. To further confirm this hypothesis, we investigated the effects of treatment with BH4 on endothelium-dependent relaxation and adiponectin levels during oxidative stress in fructose-fed rats, which provide an animal model for the metabolic syndrome. Ingestion of a fructose diet for 8 weeks significantly impaired endothelium-dependent arterial relaxation in aortic strips and decreased plasma adiponectin levels, as well as adiponectin mRNA levels within adipose tissue. However, oral supplementation with BH4 (10 mg/kg day) over the final 4 weeks leads to a significant partial reversal of impaired endothelium-dependent arterial relaxation, as well as normalization of plasma adiponectin and fat adiponectin mRNA levels. Moreover, BH4 treatment of the fructose-fed rats significantly reduced the lipid peroxidation content of aorta, heart, liver, and kidney tissues, which were increased in fructose-fed rats. This effect of BH4 treatment may be due to its function as a cofactor for eNOS, as well as its anti-oxidative effects. Thus, BH4 might show promise for the treatment of oxidative stress-induced disorders, including the metabolic syndrome.

Globular adiponectin induces adhesion molecule expression through the sphingosine kinase pathway in vascular endothelial cells.

The signaling pathways that couple adiponectin receptors to functional, particularly inflammatory, responses have remained elusive. We report here that globular adiponectin induces endothelial cell activation, as measured by the expression of adhesion proteins such as vascular adhesion molecule-1 (VCAM-1), intracellular adhesion molecule-1 (ICAM-1), E-selectin and MCP-1, through the sphingosine kinase (SKase) signaling pathway. Treatment of human umbilical vein endothelial cells with globular adiponectin resulted in NF-kappaB activation and increased mRNA levels of VCAM-1, ICAM-1, E-selectin and MCP-1. Sphingosine 1-phosphate (S1P), but not ceramide or sphingosine, was a potent stimulator of adhesion protein expression. As S1P is generated from sphingosine by SKase, we treated cells with siRNA for SKase to silence the effects of S1P in the endothelial cells. Treatment with SKase siRNA inhibited globular adiponectin-induced NF-kappaB activation and markedly decreased the globular adiponectin-induced mRNA levels of adhesion protein. Thus, we demonstrated that the SKase pathway, through the generation of S1P, is critically involved in mediating globular adiponectin-induced endothelial cell activation.

Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.

This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for ß-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4C1 to 1C4 is lower than that of 1C4 to 4C1 (kinetic predominance).

The fetal dermal but not loose fascial mesenchymal cells possess regenerative activity of dermal structure.

Fetal skin possesses a regenerative activity until certain developmental stages. However, the origin of cells that regenerate dermis after wounding has not been clarified yet. In the present study we located the origin of cells that reconstruct fetal dermal structure by histological examination and by marking cells in the loose fascia. Next we evaluated the regenerative activity of fetal dermal mesenchymal cells by cotransplanting with fetal epidermal cells onto the skin defect of scid mice. We conclude that fetal dermal mesenchymal cells but not loose fascial cells possess regenerative activity even on the environment in scid mice.

Transplanted mesenchymal stem cells are effective for skin regeneration in acute cutaneous wounds.

Mesenchymal stem cells (MSCs) possess the capacity for site-specific differentiation of cell types in response to cues provided by different organs. This phenomenon suggests that MSCs participate in cutaneous wound regeneration. However, there are no prior reports on the influence of the local application of MSCs on cutaneous wound regeneration. To examine the effects of MSCs on wound regeneration, we cultured bone marrow cells of the femur of rats and treated the plastic adherent cells with a differentiation medium to induce differentiation. After treatment, we found that the bone marrow-derived plastic adherent cells possessed myogenesis, chondrogenesis, and adipogenesis capabilities, indicating that these cells are MSCs. The bone marrow-derived plastic adherent cells were injected intradermally into the skin of rats, and linear full-thickness incisional wounds were made immediately through the injected area. At 14 days after operation, wounds transplanted with bone marrow-derived plastic adherent cells had healed with very fine scars. Collagen architecture was thick and appeared to be similar to normal dermis. Histomorphologic scale analysis demonstrated significant differences between the control and the wounds transplanted with bone marrow-derived plastic adherent cells. These results indicate that transplanted MSCs can respond quite normally to wound healing and regenerate dermal structure.

Transplanted endothelial progenitor cells augment the survival areas of rat dorsal flaps.

Endothelial progenitor cells (EPCs) have been identified in peripheral blood, and have been reported to be incorporated into ischemic regions such as the ischemic hindlimb. In this study, we examined whether or not transplantation of EPCs is useful for salvaging surgical flaps in vivo. At the same time, we quantitatively compared the neovascularization ability of transplanted EPCs and that of mature endothelial cells (ECs). ECs obtained from the aorta of rats by explantation and passaged several times were used in the present study. EPCs were obtained from the blood of rat hearts. The blood samples were separated by density gradient centrifugation. Light-density mononuclear cells (MNCs) were collected and cultured on plastic plates coated with rat plasma vitronectin. Cells attached at day 7 of culture were deemed to be EPCs. Then PBS (control), ECs, or EPCs (3.0 x 10(5) suspended in 1.0 ml PBS) were injected at the middle of a flap. Seven days after surgery, the survival lengths of the flaps were evaluated. EPC-transplanted groups revealed statistically significant augmentation of survival length compared with the other two groups (p < 0.003). EPC-transplanted groups had significantly more angiographically detectable blood vessels (p < 0.003) and significantly higher capillary density (p < 0.03) than the other two groups. Confocal microscopy revealed that EPCs were incorporated into enhanced neovascularization. These results suggest that transplantation of EPCs may be useful for salvaging surgical flaps, and EPCs are superior to ECs in neovascularization ability.

Efficient and Selective Synthesis of Crownopaddlanes Possessing Two Cyclobutane Rings and Exclusive Complexation of Lithium.

A new type of crown compounds (crownopaddlanes) bearing two cyclobutane rings were efficiently and selectively prepared by means of intramolecular [2 + 2] photocycloaddition of appropriate styrene derivatives, which was successfully carried out in cyclohexane under irradiation through a Pyrex filter. Crownopaddlanes 4a, 5, and 6 exclusively and quantitatively extracted Li(+) on the solid-liquid extraction. Upon the competitive extraction, 4a showed the highest selectivity toward Li(+) over Na(+) and K(+) (Li(+)/Na(+) = 610, Li(+)/K(+) = 976). The structural factors working in the complexation of the crownopaddlane were examined by X-ray crystallographic analysis.

Substrate dependent inhibition profiles of fourteen drugs on CYP3A4 activity measured by a high throughput LCMS/MS method with four probe drugs, midazolam, testosterone, nifedipine and terfenadine.

The CYP3A4 enzyme is known for its atypical inhibition kinetics; ligand inhibition can differ depending upon the probe drug used. A high throughput-LCMS/MS CYP3A4 inhibition assay with four substrate drugs was developed to minimize the potential oversight of CYP3A4 inhibition. The assay uses a 96-well format, human liver microsomes, and four CYP3A4 substrate drugs, midazolam, testosterone, nifedipine and terfenadine. After incubation of the individual substrate with human liver microsomes, the reaction is stopped by solid phase extraction and the four probe metabolites produced are pooled and measured by LCMS/MS with multiple-ion-monitoring mode. Using this assay, the IC(50) values of fourteen compounds recognized as substrates/inhibitors of CYP3A4, were measured for the CYP3A4 catalyzed-metabolism of probe drugs. IC(50) values were also obtained for the common set of compounds by the microtiter plate fluorescent assays with cDNA-expressed CYP3A4. Comparison of the results from the two methods suggests that decision making should be cautiously executed to predict drug interaction potential caused by inhibition of CYP3A4 considering the gap between the two assays and various other factors.