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RNA aptamers are oligonucleotides with high binding affinity and specificity for target molecules and are expected to be a new generation of therapeutic molecules and targeted delivery materials. The tertiary structure of RNA molecules and RNA-protein interaction sites are increasingly important as potential targets for new drugs. The pathological mechanisms of diseases must be understood in detail to guide drug design. In developing RNA aptamers as drugs, information about the interaction mechanisms and structures of RNA aptamer-target protein complexes are useful. We constructed a database, RNA aptamer 3D-structural modeling (RNAapt3D), consisting of RNA aptamer data that are potential drug candidates. The database includes RNA sequences and computationally predicted RNA tertiary structures based on secondary structures and implements methods that can be used to predict unknown structures of RNA aptamer-target molecule complexes. RNAapt3D should enable the design of RNA aptamers for target molecules and improve the efficiency and productivity of candidate drug selection. RNAapt3D can be accessed at https://rnaapt3d.medals.jp.

The structure of the dinuclear Fe(II) complex [Fe2(Ph-bimp)(PhCO2)(CH3CN)](BF4)2·2CH3CN·3CH3CH2OH (1) was determined by X-ray crystallography, where Ph-bimp is 2,6-bis[bis{2-(1-methyl-4,5-diphenylimidazolyl)methyl}aminomethyl]-4-methylpenolate. The compound crystallizes in a monoclinic space group Cc with a = 15.5690(10), b = 23.8260(8), c = 24.821(1)Å, β = 95.3460(3)°, Z = 4, V = 9167.2(10)Å3. The R1 [I > 2σ(I)] and wR2 (all data) values are 0.0336 and 0.0850, respectively, for all 16812 independent reflections. The complex has a μ-phenoxo-μ-benzoate-bridged diiron(II) core structure.

In large-scale communication networks consisting of many end hosts and routers, accurate acquisition, measurement, and estimation of communication delays between node pairs are essential for providing high-quality communication services. In several QoS-related performance metrics such as metrics for efficiency, metrics for availability, metrics for reliability, communication delay is one of the key metrics to realize several traffic control mechanisms. Conventional instrumentation and measurement techniques are suitable when the size of the network to be measured is relatively small, or when the number of node pairs to be measured is relatively small. However, in evolving and complex networks, it is not trivial to acquire, measure, and estimate the communication quality at a huge number of routers and end hosts. In this paper, as an initial step toward the realization of estimating communication quality (especially communication delays between node pairs) in a large-scale network, we investigate the potential of graph neural networks with semi- supervised learning for estimating communication delays between node pairs. Our findings include that the average relative error of estimated communication delays is around 10-35% depending on the fraction of the number of measurement nodes, and that communication delays for large-scale networks can be estimated with a high accuracy even if the fraction of the number of measurement nodes is not so large.

Robustness against failure and attack is one of the essential properties of large-scale dynamical system such as power grids, transportation system, communication systems, and computer networks. Despite its popularity and intuitiveness, a major drawback of descriptive robustness metrics such as the size of the largest connected component and the diameter is its computational complexity. On the contrary, predictive metrics such as the spectral radius, the natural connectivity, and the algebraic connectivity are much easier to obtain than descriptive metrics, but the predictability of those measures against different levels and types of failures/attacks has not been well understood. In this paper, we therefore investigate how effectively predictive metrics (spectral measures) can estimate the robustness of a network against random node removal. Our finding includes that, among five types of spectral measures, the effective resistance is most suitable for predicting the largest cluster component size under low node removal ratio, and that the predictability of the effective resistance is stable for various networks generated with different network generation models.

Recently, Content-Centric Networking (CCN) has been extensively studied by networking researchers as a promising network architecture to realize an information-centric network. When a CCN router receives multiple Interest packets requesting identical content, it can aggregate those packets into a single Interest packet in order to reduce the amount of redundant Interest and Data packet transmission. In the literature, it is known that Interest packet aggregation significantly affects the performance of a CCN network. In this paper, we propose a method called Probabilistic Interest Packet Aggregation (PIPA). We investigate the fundamental characteristics of PIPA — in particular, the relation between its Interest packet aggregation probability and the average chunk delivery delay — through both simulation experiments and mathematical analyses. Our findings include that by appropriately aggregating Interest packets at a CCN router using PIPA, the average chunk delivery delay can be reduced by approximately 15% compared with the case without PIPA.

The present study has examined the effect of metals, such as iron and copper on the cytotoxicity of amyloid beta protein 1-40 (Abeta40). First, we showed that monomeric Abeta40 has stronger cytotoxicity than various type of aggregated Abeta40. Next we showed the addition of metals into the monomeric Abeta40 reduced the cytotoxicity of either monomeric Abeta40 or metals (iron and copper) although the addition of metals into monomeric Abeta40 resulted in a marked increase of aggregated form of Abeta40, which composed of beta-sheeted Abeta40 and Abeta40 aggregation not characterized by beta-sheet fibrils (coagrated Abeta40). Taken together, the metals and monomeric Abeta40 affect on each other and cause the reduction of their cell toxicity.

Repulsive guidance molecule (RGM) is a protein implicated in both axonal guidance and neural tube closure. We report RGMa as a potent inhibitor of axon regeneration in the adult central nervous system (CNS). RGMa inhibits mammalian CNS neurite outgrowth by a mechanism dependent on the activation of the RhoA–Rho kinase pathway. RGMa expression is observed in oligodendrocytes, myelinated fibers, and neurons of the adult rat spinal cord and is induced around the injury site after spinal cord injury. We developed an antibody to RGMa that efficiently blocks the effect of RGMa in vitro. Intrathecal administration of the antibody to rats with thoracic spinal cord hemisection results in significant axonal growth of the corticospinal tract and improves functional recovery. Thus, RGMa plays an important role in limiting axonal regeneration after CNS injury and the RGMa antibody offers a possible therapeutic agent in clinical conditions characterized by a failure of CNS regeneration.

Oxidative stress is a major risk factor for Alzheimer's disease (AD) and other neurodegenerative disorders. Metals are known to be one of the factors that contribute to oxidative stress. Recently, we reported that the aberrant splicing isoform (PS2V) generated by skipping exon5 of the presenilin-2 (PS2) gene is a diagnostic feature of sporadic AD (SAD). PS2V is inducible by exposure of human neuroblastoma to hypoxia. We examined whether this aberrant splicing was caused by metal-induced oxidative stress, such as exposure to aluminum. As a result, we demonstrated that exposure to aluminum accelerated PS2V production induced by hypoxia. This acceleration of the production of PS2V to hypoxia was caused by chronic aluminum exposure, but was not related to the intracellular content of aluminum. HMGA1a is a mediator of PS2V production, and it was induced by aluminum as well as by hypoxia. Induction of HMGA1a was increased by chronic exposure to aluminum, and a nuclear extract containing HMGA1a bound to a specific sequence on exon5 of PS2 pre-mRNA, as reported previously. Finally, the acceleration of PS2V production induced by aluminum under hypoxic conditions reflected, but has not yet been directly shown to cause, vulnerability to endoplasmic reticulum stress. These results suggest that exposure to some metals can accelerate and enhance PS2V generation, and that hypoxia plus chronic exposure to metals may promote the development of AD.

An alternative spliced form of the presinilin 2 (PS2) gene (PS2V) lacking exon 5 has previously been reported to be expressed in human brains in sporadic Alzheimer's disease (AD). PS2V encodes the amino-terminal portion of PS2, which contains residues Met1-Leu119 and 5 additional amino acid residues (SSMAG) at its carboxyl terminus. Here we report that PS2V protein impaired the signaling pathway of the unfolded protein response, similarly to familial AD-linked PS1 mutants and caused significant increases in the production of both amyloid beta40 and beta42. Interestingly, PS2V-encoding protein was expressed in neuropathologically affected neurons of the hippocampal CA1 region and temporal cortex in AD patients. These findings suggest that the aberrant splicing of the PS2 gene may be implicated in the neuropathology of sporadic AD.

A new dinucleating ligand containing a sterically bulky imidazolyl group, Ph-Htidp (N,N,N′,N′-tetrakis[(1-methyl-4,5-diphenyl-2-imidazolyl)methyl]-1,3-diamino-2-propanol), and its μ-alkoxo-diiron(II) complexes [Fe2(Ph-tidp)(RCO2)](ClO4)2, (RCO2 = C6H5CO2 (1), C6F5CO2 (2), CF3CO2 (3), and C2H5CO2 (4)), were synthesized. The structure of complex 1 was determined by X-ray crystallography. Complex 1 crystallizes in the monoclinic space group P21/c with a = 13.464(2), b = 19.223(4), c = 31.358(4) Å, β = 92.84(2)°, and Z = 4. The complex has a doubly-bridged structure with μ-alkoxo of Ph-tidp and μ-benzoate; the two iron centers have a distorted five-coordinate structure with N3O2 donor set. All the complexes showed fairly good reversible oxygenation below −30 °C in CH2Cl2, which was monitored by UV-vis and NMR spectroscopies, and dioxygen up-take measurements. Introduction of 4,5-diphenyl substituents into 2-imidazolyl group stabilized the μ-peroxo diiron species against irreversible oxidation, just as introduction of 6-methyl substituent into 2-pyridyl group did. Phenyl substituents appear to weaken the electron donor ability of a dinucleating ligand to stabilize divalent oxidation state of iron and to form a hydrophobic cavity for a O2 binding site, which would suppress the irreversible oxidation and facilitate the reversible oxygenation. Dioxygen affinities of the Ph-tidp and Me4-tpdp diiron(II), and the tpdp and bpmp dicobalt(II) complexes were measured, [Fe2(Me4-tpdp)(RCO2)]2+ (RCO2 = C6H5CO2 and RCO2 = CF3CO2) and [Co2(L)(RCO2)]2+ (L = tpdp, RCO2 = CH3CO2, and L = bpmp, RCO2 = C6F5CO2, and CF3CO2), where Me4-tpdp, tpdp, and bpmp are N,N,N′,N′-tetrakis[(6-methyl-2-pyridyl)methyl]-1,3-diamino-2-propanolate, N,N,N′,N′-tetrakis(2-pyridylmethyl)-1,3-diamino-2-propanolate, and 2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-methylphenolate, respectively. Within a series of the Ph-tidp diiron(II) complexes, dioxygen affinity is well correlated with electron donor ability of bridging carboxylates (1 (C6H5CO2) > 2 (C6F5CO2) > 3 (CF3CO2)). In contrast to the above trend, dioxygen affinities of the Ph-tidp complexes are lower than those of the Me4-tpdp complexes, although electron donor abilities of the Me4-tpdp complexes are weaker than those of the Ph-tidp complexes. Significant enhancement of dioxygen affinity was observed for both iron and cobalt complexes with 2,6-bis(aminomethyl)phenolate bridging skeleton compared to the complexes with a 1,3-diamino-2-propanolate bridging one. Thermodynamic study suggested that the observed enhancement is mainly attributable to a favorable entropy effect along with a steric effect.

Clarification of the pathogenesis and treatment of autism spectrum disorders is one of the challenges today. In this study, we examine scalp hair concentrations of 26 trace elements for 1,967 children with autistic disorders (1,553 males and 414 females). Five-hundred and eighty-four (29.7%), 347 (17.6%) and 114 (5.8%) subjects was found deficient in zinc, magnesium and calcium, respectively, and 2.0% or less in the other essential metals. The incidence rate of mineral deficiency was highly observed in infants aged 0-3 year-old. In contrast, 339 (17.2%), 168 (8.5%) and 94 (4.8%) individuals was found suffering from high burden of aluminium, cadmium and lead, and 2.8% or less from mercury and arsenic burden. These findings suggest that infantile zinc- and magnesium-deficiency and/or toxic metal burdens may epigenetically play principal roles as environmental factors in autistic disorders and that metallomics approach may lead to early screening and prevention of the neurodevelopment disorders.

Clarification of the pathogenesis and treatment of autism spectrum disorders is one of the challenges today. In this study, we examine scalp hair concentrations of 26 trace elements for 1,967 children with autistic disorders (1,553 males and 414 females). Five-hundred and eighty-four (29.7%), 347 (17.6%) and 114 (5.8%) subjects was found deficient in zinc, magnesium and calcium, respectively, and 2.0% or less in the other essential metals. The incidence rate of mineral deficiency was highly observed in infants aged 0-3 year-old. In contrast, 339 (17.2%), 168 (8.5%) and 94 (4.8%) individuals was found suffering from high burden of aluminium, cadmium and lead, and 2.8% or less from mercury and arsenic burden. These findings suggest that infantile zinc- and magnesium-deficiency and/or toxic metal burdens may epigenetically play principal roles as environmental factors in autistic disorders and that metallomics approach may lead to early screening and prevention of the neurodevelopment disorders.

Synthesis and cationic ring-opening polymerization of new 1,6-anhydro-β-lactose derivatives such as hexa-O-methylated (LSHME), tert-butyldimethylsilylated (LSHSE), and benzylated 1,6-anhydro-β-lactoses (LSHBE) were first investigated. The disaccharide monomers were prepared by methylation, tert-butyldimethylsilylation, and benzylation of 1,6-anhydro-β-lactose, respectively. It was found that LSHME was readily polymerized with such Lewis acid catalysts as PF5 and SbCl5 to give stereoregular 2,3-di-O-methyl-4-O-(2′,3′,4′,6′-tetra-O-methyl-β-D-galactopyranosyl)-(16)-β-D-glucopyranans which are comb-shaped polysaccharide derivatives. However, LSHSE and LSHBE had almost no polymerizability. It was revealed that the ring-opening polymerizability of the anhydrodisaccharide monomers was influenced by the steric hindrance of the hydroxyl-protective groups. Ring-opening copolymerization of LSHME with 1,6-anhydro-2,3,4-tri-O-benzyl-β-D-glucopyranose (LGTBE) in various ratios of monomer feeds was also examined to afford the corresponding copolymers. Structural analyses of the monomers and polymers were carried out by means of high resolution nuclear magnetic resonance spectroscopy.

In this study, the authors propose a new in situ degassing method by which only kicker magnets in the accelerator beam line are baked out without raising the temperature of the vacuum chamber to prevent unwanted thermal expansion of the chamber. By simply installing the heater and thermal radiation shield plates between the kicker magnet and the chamber wall, most of the heat flux from the heater directs toward the kicker magnet. The result of the verification test showed that each part of the kicker magnet was heated to above the target temperature with a small rise in the vacuum chamber temperature. A graphite heater was selected in this application to bake-out the kicker magnet in the beam line to ensure reliability and easy maintainability of the heater. The vacuum characteristics of graphite were suitable for heater operation in the beam line. A preliminary heat-up test conducted in the accelerator beam line also showed that each part of the kicker magnet was successfully heated and that thermal expansion of the chamber was negligibly small.

Such natural and nonnatural sugars as D- and L-glucoses and D- and L-mannose were reacted with curdlan to form branched curdlans, respectively. These structures were analyzed by means of 13 C NMR spectroscopy and methylation analysis. The branche curdlans were sulfated with piperidine-N-sulfonic acid in DMSO to give branched curdlan sulfates. It was revealed at these branched sulfates had high anti-AIDS virus activities in the EC 50 range of 0.3-1.2 μg/mL in vitro using MT-4 cells and exhibited low cytotoxicities as well as low anticoagulant activities. Furthermore, fon-glycosyl-branched curdlan states, retention times in rat in vivo calculating from their anticoagulant activities were a few hours

In order to investigate the body burden levels of toxic metals in Japanese, five toxic metal concentrations in scalp hair samples from 28,424 subjects from infant to elderly were determined with inductively coupled plasma mass spectrometry (ICP-MS). The geometric mean of hair mercury concentrations showed a high-significant age-correlated increase (r = 0.341, p0.0001) with a peak at the 6th decade of life and then decreased with further aging in both sexes. The mean mercury concentrations in male adults were significantly higher than those in female (p0.001), indicating the gender difference (malefemale) in mercury accumulation. Arsenic also showed a similar accumulation profile with age dependency and gender difference in adult subjects. In contrast, cadmium, lead and aluminium exhibited another type of accumulation profile: the highest burden level was observed in infants aged 0-3 years old for every element in both sexes. In addition, cadmium was found to have a character accumulating in aged females, with significant age-dependency (r = 0.134, p0.0001) and gender difference (femalemale). These findings suggest that toxic metals are classified into two families on the basis of their accumulation profiles, and that the three elements of mercury, arsenic and cadmium which accumulate age-dependently in adults, may play a role in aging process and higher burden with them may lead to acceleration of aging.

Oxidative stress is a major risk factor for Alzheimer's disease (AD) and other neurodegenerative disorders. Metals are known to be one of the factors that contribute to oxidative stress. Recently, we reported that the aberrant splicing isoform (PS2V) generated by skipping exon5 of the presenilin-2 (PS2) gene is a diagnostic feature of sporadic AD (SAD). PS2V is inducible by exposure of human neuroblastoma to hypoxia. We examined whether this aberrant splicing was caused by metal-induced oxidative stress, such as exposure to aluminum. As a result, we demonstrated that exposure to aluminum accelerated PS2V production induced by hypoxia. This acceleration of the production of PS2V to hypoxia was caused by chronic aluminum exposure, but was not related to the intracellular content of aluminum. HMGA1a is a mediator of PS2V production, and it was induced by aluminum as well as by hypoxia. Induction of HMGA1a was increased by chronic exposure to aluminum, and a nuclear extract containing HMGA1a bound to a specific sequence on exon5 of PS2 pre-mRNA, as reported previously. Finally, the acceleration of PS2V production induced by aluminum under hypoxic conditions reflected, but has not yet been directly shown to cause, vulnerability to endoplasmic reticulum stress. These results suggest that exposure to some metals can accelerate and enhance PS2V generation, and that hypoxia plus chronic exposure to metals may promote the development of AD.

Nucleoside analogues such as azidothymidine (AZT), dideoxyinosine (ddI), and dideoxycytidine (ddC) [1] inhibit the viral reverse transcriptase (RT) of human immunodeficiency virus (HIV) and terminate DNA chain synthesis from viral RNA inside the infected cells. However, these nucleosides manifest serious side-effects such as bonemarrow toxicity and the appearance of AZT-resistant viruses upon long-term treatment [2]. It is difficult to make an effective vaccine owing to the multiplicity of AIDS viruses. Therefore, anti-AIDS compounds having a different blocking mechanism are of interest. We have synthesized sulfated polysaccharides demonstrating high anti-AIDS virus activity by sulfation of synthetic and natural-occurring polysaccharides [3-6]. The mechanism of action of sulfated polysaccharides is assumed to be different from that of the nucleosides, that is, they bind to HIV virions and prevent them from penetrating into target cells [7-9]. However, sulfated polysaccharides such as dextran sulfate have high blood anticoagulant activity, leading to undesirable side-effects when used as anti-AIDS drugs [10].