Recovery of the procedure of combined handling of elucidation methods for interpretable structure elucidation for decreasing frequencies of organic structure revision

Maybe more than one hundred papers on revision of organic structure appear every year. Most of them derive from unreasonable neglect of correct structures because of picking-up/angling methodology. Antithetically, the present paper recommends scooping-up/netting one as a proper systematic procedure in order to avoid such careless and unreasonable neglect as much as possible by indicating existence of informational homologues, which are answers matching with provided pieces of structure information. This was invented by a Japanese company JEOL for its commercial computer program for automated organic structure elucidation, Combined Handling of Elucidation Methods for Interpretable Chemical Structures (CHEMICS). But the basic policy of CHEMICS has been changed to kinds of picking-up methods by people who carried away the name without understanding importance of the policy. In order to aim to recover scooping-up methodology, the present paper shows four examples of our analysis, exemplifying neglected informational homologues, and demonstrating that scooping-up methodology is better.　　有機化合物の構造決定の誤りを修正する論文の数は年間おそらく100件を越す。これは構造データの解析の誤りによるよりは、つり法（拾い上げ法）手順採用による正しい構造の不当な無視による。つり法手順は見落としをしやすいので初心者が使うべきではない。このような正解の不当な無視をできるだけ減らすために標準的かつ系統的手順として本論文ではあみ法（囲い込みは法）手順を強く推奨する。この方法はもともと日本電子株式会社（JEOL）が自動構造解析システム、商品名Combined Handling of Elucidation Methods forInterpretable Chemical Structures （略称CHEMICS）（解析可能な化学構造のための複数の構造解析法の組み合わせ使用）のために最初に考えだしたものである。四つの事例でこの手順がきわめて有用であることを証明する（実際の文献から拾い出した構造決定の結果は誤まっていて真の正解を見落としている可能性があることを暗示し、真の正解の候補を提示した。）　　注：Appendix は「JEOL のCHEMICS の概念と名前がその基本方針を理解できなかった人たちによって他の機関に持ち出され、その方針が歪曲されてつり法に向いていく過程」を公表された文献で追っている。そこで本論文ではあみ法の復活を試みている

Genomic DNA sequences of non GT-AG introons in human mRNA genes

We searched human genome DNA sequences in the DDBJ/GenBank/EMBL for introns of mRNA genes which do not conform to the GT-AG rule, and collected 5791 fragments which do not form exon parts. Of these 159 are not of GT-AG form. Then we eliminated 19 because of non introns that were yielded by clerical error, frameshift, edition policy, and so on. Major part (94) of the 140 remaining sequences can be considered also to be GT-AG forms with alternative interpretation. There are several mRNAs carrying more than one intron where not GT-AG forms but non-GT-AG ones are chosen. This suggests easy usage of easy selection, even when there is more than one candidate, by easy computer software to infer an intron sequence as the logical difference between a gene and its corresponding cDNA

Effective procedure to develop alternative annotations of bacterial tRNA genes by means of deductive inference on the basis of characteristic tandems of tRNA genes

In a series of analysis of genomic DNA sequences, we have established an induction-deduction method to dig up hidden tRNA and rRNA genes from bacterial genome DNA sequences by means of a concept of a characteristic tRNA-gene tandem we have ldeveloped, and are accumulating information on positions of putative tRNA and rRNA genes to be proposed as alternative annotations to the DDBJ/GenBank/EMBL Database. We have searched the DNA sequences near the existing tRNA genes as golcondas for tRNA genes, and found mord than fifty genes, e.g. tRNA-Ser and tRNA-Met in [AB013377], and 5S rRNAs in [AE014192], [AE017000], and others. A part of miserable states of the Database was partly introduced, and it is discussd how such status will be disso1ved. In addition, we proposed some ideas to maintain and improve the DDBJ/GenBank/EMBL database

Subcellular localization of glucocorticoid receptor protein in the human kidney glomerulus

Subcellular localization of glucocorticoid receptor protein in the human kidney glomerulus.BackgroundThe detailed mechanisms of glucocorticoid action in idiopathic nephrotic syndrome and progressive glomerulonephritides have not been clearly elucidated. The pharmacological actions of glucocorticoids are mediated by their binding to an intracellular protein, the glucocorticoid receptor (GR). The determination of GR localization in normal glomerular cells is essential to elucidate the mechanisms of glucocorticoid action in various glomerular diseases.MethodsWe carried out an immunoblot examination using antihuman GR-specific antibody and homogenates of isolated normal human glomeruli and mesangial cells in culture. Immunohistochemical examinations were also performed on normal human kidney specimens at light and electron microscopic levels. The nuclear translocation of GRs elicited by ligand binding was further investigated by confocal laser-scanning microscopic inspection of freshly isolated glomeruli and mesangial cells cultured with dexamethasone.ResultsAn immunoblot examination demonstrated the presence of a 94 kDa protein, a molecular weight consistent with that of GRs, in the homogenates of glomeruli and cultured mesangial cells. By light microscopic examination, GRs were strongly detected in the nucleus and moderately in the cytoplasm of all glomerular cells, parietal and visceral epithelial cells, endothelial cells, and mesangial cells. By electron microscopic examination, the nuclear GRs of all glomerular cells were found to be diffusely distributed in the euchromatin. Additionally, the immunofluorescence intensities of nuclear GRs in isolated glomeruli and mesangial cells in culture became more intense by the addition of dexamethasone.ConclusionsOur findings suggest that all subsets of human glomerular cells definitely express the GR protein, which potentially undergoes translocation by glucocorticoids

A Role of Aromatase in Sjögren Syndrome

Several autoimmune diseases are known to develop in postmenopausal women. However, the mechanism by which estrogen deficiency influences autoimmunity is unknown. Aromatase is a converting enzyme from androgens to estrogens. In the present study, we used female aromatase gene knockout (ArKO) mice as a model of estrogen deficiency to investigate the molecular mechanism that underlies the onset and development of autoimmunity. Histological analyses showed that inflammatory lesions in the lacrimal and salivary glands of ArKO mice increased with age. Adoptive transfer of spleen cells or bone marrow cells from ArKO mice into recombination activating gene 2 knockout mice failed to induce the autoimmune lesions. Expression of mRNA encoding proinflammatory cytokines and monocyte chemotactic protein-1 (MCP-1) increased in white adipose tissue (WAT) of ArKO mice and was significantly higher than that in wild-type mice. Moreover, an increased number of inflammatory M-1 macrophage was observed in WAT of ArKO mice. A significantly increased MCP-1 mRNA expression of the salivary gland tissue in ArKO was found together with adiposity. Furthermore, the autoimmune lesions in a murine model of Sjögren’s syndrome (SS) were exacerbated by administration of an aromatase inhibitor. These results suggest that aromatase may play in a key role in the pathogenesis of SS-like lesions by controlling the target organ and adipose tissue-associated macrophage

Plasma levels of matrix metalloproteinase‐9 (MMP‐9) are associated with cognitive performance in patients with schizophrenia

Aim: Matrix metalloproteinase‐9 (MMP‐9) has been shown to modulate synaptic plasticity and may contribute to the pathophysiology of schizophrenia. This study investigated the peripheral levels of MMP‐9 and its association with cognitive functions in patients with schizophrenia to see the possible involvement of MMP‐9 in pathophysiology of schizophrenia, especially in cognitive decline. Methods: We measured the plasma levels of MMP‐9 in 257 healthy controls and 249 patients with schizophrenia, including antipsychotic drug–free patients. We also explored the possible association between plasma MMP‐9 levels and cognitive performance in healthy controls and patients with schizophrenia using the Wechsler Adult Intelligence Scale, Third Edition (WAIS‐ III), the Wechsler Memory Scale‐Revised (WMS‐R), and the Rey Auditory Verbal Learning Test (AVLT). Results: We found that the plasma levels of MMP‐9 were significantly higher in patients with schizophrenia, including antipsychotic drug–free patients, than in healthy controls. We found a significant negative association between plasma MMP‐9 levels and cognitive performance in controls and patients with schizophrenia. Conclusion: Together, these convergent data suggest a possible biological mechanism for schizophrenia, whereby increased MMP‐9 levels are associated with cognitive impairment

Plasma Levels of Soluble Tumor Necrosis Factor Receptor 2 (sTNFR2) Are Associated with Hippocampal Volume and Cognitive Performance in Patients with Schizophrenia

Background: An imbalance in the inflammatory tumor necrosis factor system, including soluble tumor necrosis factor receptor 2 (sTNFR2), may contribute to the pathophysiology of schizophrenia. Methods: We measured the plasma levels of sTNFR2 in 256 healthy controls and 250 patients with schizophrenia including antipsychotic drug-free patients and treatment-resistant patients. We also explored the possible association between plasma sTNFR2 levels and cognitive performance in healthy controls and patients with schizophrenia using the Wechsler Adult Intelligence Scale, Third Edition, the Wechsler Memory Scale-Revised, and the Rey Auditory Verbal Learning Test. An association between plasma sTNFR2 levels and hippocampal volume in controls and patients with schizophrenia was also investigated via MRI. Results: We found that the plasma levels of sTNFR2 were significantly higher in patients with schizophrenia, including both antipsychotic drug-free patients and treatment-resistant patients. We found a significant negative association between plasma sTNFR2 levels and cognitive performance in controls and patients with schizophrenia. Hippocampal volume was also negatively associated with plasma sTNFR2 levels in patients with schizophrenia. Conclusion: Together, these convergent data suggest a possible biological mechanism for schizophrenia, whereby increased sTNFR2 levels are associated with a smaller hippocampal volume and cognitive impairment

Effect of an Oral Adsorbent, AST-120, on Dialysis Initiation and Survival in Patients with Chronic Kidney Disease

The oral adsorbent AST-120 has the potential to delay dialysis initiation and improve survival of patients on dialysis. We evaluated the effect of AST-120 on dialysis initiation and its potential to improve survival in patients with chronic kidney disease. The present retrospective pair-matched study included 560 patients, grouped according to whether or not they received AST-120 before dialysis (AST-120 and non-AST-120 groups). The cumulative dialysis initiation free rate and survival rate were compared by the Kaplan-Meier method. Multivariate analysis was used to determine the impact of AST-120 on dialysis initiation. Our results showed significant differences in the 12- and 24-month dialysis initiation free rate (P < 0.001), although no significant difference was observed in the survival rate between the two groups. In conclusion, AST-120 delays dialysis initiation in chronic kidney disease (CKD) patients but has no effect on survival. AST-120 is an effective therapy for delaying the progression of CKD

Efficacy of SMART Stent Placement for Salvage Angioplasty in Hemodialysis Patients with Recurrent Vascular Access Stenosis

Vascular access stenosis is a major complication in hemodialysis patients. We prospectively observed 50 patients in whom 50 nitinol shape-memory alloy-recoverable technology (SMART) stents were used as salvage therapy for recurrent peripheral venous stenosis. Twenty-five stents each were deployed in native arteriovenous fistula (AVF) and synthetic arteriovenous polyurethane graft (AVG) cases. Vascular access patency rates were calculated by Kaplan-Meier analysis. The primary patency rates in AVF versus AVG at 3, 6, and 12 months were 80.3% versus 75.6%, 64.9% versus 28.3%, and 32.3% versus 18.9%, respectively. The secondary patency rates in AVF versus AVG at 3, 6, and 12 months were 88.5% versus 75.5%, 82.6% versus 61.8%, and 74.4% versus 61.8%, respectively. Although there were no statistically significant difference in patency between AVF and AVG, AVG showed poor tendency in primary and secondary patency. The usefulness of SMART stents was limited in a short period of time in hemodialysis patients with recurrent vascular access stenosis