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Phylobone: a comprehensive database of bone extracellular matrix proteins in human and model organisms

Bone Research 2023年第3期11卷 617-624页

作者： Margalida Fontcuberta-Rigo miho nakamura Pere Puigbò Medicity Research Laboratory Faculty of MedicineUniversity of TurkuTykistökatu 620520 TurkuFinland Institute of Biomaterials and Bioengineering Tokyo Medical and Dental University2-3-10 Kanda-SurugadaiChiyodaTokyo 1010062Japan Graduate School of Engineering Tohoku University6-6 Aramaki Aza AobaAoba-kuSendaiMiyagi 9808579Japan Department of Biology University of Turku20500 TurkuFinland Eurecat Technology Center of Catalonia.Nutrition and Health UnitReus 43204 CataloniaSpain Department of Biochemistry and Biotechnology University Rovira i Virgili43007 TarragonaCataloniaSpain

The bone extracellular matrix(ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of noncollagenous proteins. Some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways,and play important regulatory and structural roles. However, the complete list of bone extracellular matrix proteins, their roles, and the extent of individual and cross-species variations have not been fully captured in both humans and model organisms. Here, we introduce the most comprehensive resource of bone extracellular matrix(ECM) proteins that can be used in research fields such as bone regeneration, osteoporosis, and mechanobiology. The Phylobone database(available at https://***) includes 255proteins potentially expressed in the bone extracellular matrix(ECM) of humans and 30 species of vertebrates. A bioinformatics pipeline was used to identify the evolutionary relationships of bone ECM proteins. The analysis facilitated the identification of potential model organisms to study the molecular mechanisms of bone regeneration. A network analysis showed high connectivity of bone ECM proteins. A total of 214 functional protein domains were identified, including collagen and the domains involved in bone formation and resorption. Information from public drug repositories was used to identify potential repurposing of existing drugs. The Phylobone database provides a platform to study bone regeneration and osteoporosis in light of(biological) evolution,and will substantially contribute to the identification of molecular mechanisms and drug targets.

关键词： drugs matrix database

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Reading impairment after neonatal hypoglycemia with parietotemporo-occipital injury without cortical blindness:A case report

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World Journal of Clinical Cases 2023年第16期11卷 3899-3906页

作者： Naoko Kurahashi Shunsuke Ogaya Yuki Maki Norie Nonobe Sumire Kumai Yosuke Hosokawa Chikako Ogawa Keitaro Yamada Koichi Maruyama Kiyokuni Miura miho nakamura Department of Pediatric Neurology Central HospitalAichi Developmental Disability CenterKasugai 480-0392AichiJapan Department of Pediatrics Nagoya University Graduate School of MedicineNagoya 466-8560AichiJapan Division of Neonatology Center for Maternal-Neonatal Care Nagoya University HospitalNagoya 466-8560AichiJapan Department of Pediatrics Tokyo Metropolitan Fuchu Medical Center for the DisabledFuchu 183-0042TokyoJapan Department of Functioning and Disability Institute for Developmental ResearchAichi Developmental Disability CenterKasugai 480-0392AichiJapan Okazaki Medical Center for Child Development Okazaki 444-0011AichiJapan

BACKGROUND Perinatal brain injury may lead to later neurodevelopmental disorders,whose outcomes may vary due to neuroplasticity in young *** neuroimaging studies have shown that the left parietotemporal area(which includes the left inferior parietal lobe)is associated with phonological awareness and decoding skills,which are essential skills for reading acquisition in ***,the literature on the effect of perinatal cerebral injury on the development of phonological awareness or decoding ability in childhood is *** SUMMARY We report the case of an 8-year-old boy who presented with reading difficulty following a perinatal injury in the parieto-temporal-occipital *** patient was born at term and was treated for hypoglycemia and seizures during the neonatal ***-weighted brain magnetic resonance imaging on postnatal day 4 revealed cortical and subcortical hyperintensities in the parieto-temporo-occipital *** the age of 8 years,physical examination was unremarkable,aside from mild *** occipital lobe injury,the patient had adequate visual acuity,normal eye movement,and no visual field ***-scale intelligence quotient and verbal comprehension index on Wechsler Intelligence Scale for Children-Fourth Edition were 75 and 90,*** assessment revealed adequate recognition of Japanese Hiragana ***,he had significantly slower reading speed in the Hiragana reading test than control *** phonological awareness test revealed significant errors(standard deviation+2.7)in the mora reversal *** Patients with perinatal brain injuries in the parietotemporal area require attention and may benefit from additional reading instructions.

关键词： Brain diseases Hypoglycemia Dyslexia Long-term care Education Case report

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A comparative study on crash-influencing factors by facility types on urban expressway

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Journal of Modern Transportation 2013年第4期21卷 224-235页

作者： Yong Wu Hideki nakamura miho Asano Department of Civil Engineering Nagoya University

This study aims at identifying crash-influencing factors by facility type of Nagoya Urban Expressway, considering the interaction of geometry, traffic flow, and ambient conditions. Crash rate （CR） model is firstly developed separately at four facility types： basic, merge, and diverge segments and sharp curve. Traffic flows are thereby categorized, and based on the traffic categories, the significances of factors affecting crashes are analyzed by principal component analysis. The results reveal that, the CR at merge segment is significantly higher than those at basic and diverge segments in uncongested flow, while the value is not significantly different at the three facility types in congested flow. In both un- and congested flows, sharp curve has the worst safety performance in view of its highest CR. Regarding influencing factors, geometric design and traffic flow are most significant in un- and congested flows, respectively. As mainline flow increases, the effect of merging ratio affecting crash is on the rise at basic and merge segments as opposed to the decreasing significance of diverging ratio at diverge segment. Mean- while, longer acceleration and deceleration lanes are adverse to safety in uncongested flow, while shorter acceleration and deceleration lanes are adverse in congested flow. Due to its special geometric design, crashes at sharp curve are highly associated with the large centrifugal force and heavy restricted visibility.

关键词： Crash-influencing factors Crash rates Principal component analysis - Facility types Urbanexpressway

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Excited state calculations using variational quantum eigensolver with spin-restricted ansätze and automatically-adjusted constraints

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npj Computational Materials 2023年第1期9卷 2204-2212页

作者： Shigeki Gocho Hajime nakamura Shu Kanno Qi Gao Takao Kobayashi Taichi Inagaki miho Hatanaka School of Fundamental Science and Technology Faculty of Science and TechnologyKeio UniversityYokohama 223-8522Japan Quantum Computing Center Keio UniversityYokohama 223-8522Japan IBM Quantum–IBM Research Tokyo Tokyo 103-8510Japan Mitsubishi Chemical Corporation Science&Innovation CenterYokohama 227-8502Japan

The ground and excited state calculations at key geometries, such as the Frank–Condon (FC) and the conical intersection (CI)geometries, are essential for understanding photophysical properties. To compute these geometries on noisy intermediate-scalequantum devices, we proposed a strategy that combined a chemistry-inspired spin-restricted ansatz and a new excited statecalculation method called the variational quantum eigensolver under automatically-adjusted constraints (VQE/AC). Unlike theconventional excited state calculation method, called the variational quantum deflation, the VQE/AC does not require the pre-determination of constraint weights and has the potential to describe smooth potential energy surfaces. To validate this strategy,we performed the excited state calculations at the FC and CI geometries of ethylene and phenol blue at the complete active spaceself-consistent field (CASSCF) level of theory, and found that the energy errors were at most 2 kcal mol−1 even on the ibm_kawasakidevice.

关键词： properties quantum variational

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Current status and future perspectives for the treatment of resectable locally advanced esophagogastric junction cancer:A narrative review

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World Journal of Gastroenterology 2023年第24期29卷 3758-3769页

作者： Yoshiaki Shoji Kazuo Koyanagi Kohei Kanamori Kohei Tajima Mika Ogimi Kentaro Yatabe miho Yamamoto Akihito Kazuno Kazuhito Nabeshima Kenji nakamura Takayuki Nishi Masaki Mori Department of Gastroenterological Surgery Tokai University School of MedicineIsehara 259-1193Japan

Incidence rates for esophagogastric junction cancer are rising rapidly worldwide possibly due to the economic development and demographic ***,increased attention has been paid to the prevention,diagnosis,and the treatment of esophagogastric junction *** there are discrepancies in the treatment strategy between Asian and Western countries,surgery remains the mainstay of treatment for esophagogastric junction *** developments of perioperative multidisciplinary treatment may lead to better therapeutic effect,higher complete resection rate,and better control of the residual diseases,thus result in prolonged *** this review,we will focus on the treatment of locally advanced resectable esophagogastric junction cancer,and discuss the current status and future perspectives of the perioperative treatment including chemotherapy,radiation therapy,and immunotherapy,as well as the surgical *** understanding of the latest treatment strategy and future overlook may enable to standardize and individualize the treatment for esophagogastric junction cancer,thus leading to better prognosis for those patients.

关键词： Esophagogastric junction cancer Perioperative therapy Neoadjuvant therapy Surgery Multidisciplinary treatment

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Hepcidin/ferroportin expression levels involve efficacy of pegylated-interferon plus ribavirin in hepatitis C virusinfected liver

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World Journal of Gastroenterology 2015年第11期21卷 3291-3299页

作者： Motoyuki Kohjima Tsuyoshi Yoshimoto Munechika Enjoji Nobuyoshi Fukushima Kunitaka Fukuizumi Tsukasa nakamura miho Kurokawa Nao Fujimori Yusuke Sasaki Yasushi Shimonaka Yusuke Murata Susumu Koyama Ken Kawabe Kazuhiro Haraguchi Yorinobu Sumida Naohiko Harada Masaki Kato Kazuhiro Kotoh Makoto Nakamuta Department of Gastroenterology and Clinical Research Center National Hospital Organization Kyushu Medical Center Health Care Center Fukuoka University Product Research Department Chugai Pharmaceutical Co.Ltd. Department of Medicine and Bioregulatory Science Kyushu University

AIM:To investigate the relationship between the ironmetabolism-related gene expression profiles and efficacy of antiviral therapy in chronic hepatitis C ***:The hepatic expression profile of ironmetabolism-related genes was analyzed and its association with virological response to pegylated-interferon plus ribavirin combination therapy was evaluated.A hundred patients with chronic hepatitis C(genotype1b,n = 50; genotype 2,n = 50) were enrolled and retrospectively *** biopsy samples were subjected to quantitative polymerase chain reaction for iron-metabolismrelated genes and protein expression(Western blotting analysis) for *** a control,normal liver tissue was obtained from 18 living donors of liver *** hepcidin level was measured by sensitive liquid chromatography/electrospray ionization tandem mass ***:Iron overload is associated with liver damage by increasing oxidative stress and hepatitis C virus(HCV)is reported to induce iron accumulation in hepatocytes in ***,iron administration suppresses HCV replication in ***,the association between HCV infection and iron metabolism remains *** with controls,patients had significantly higher gene expression for transferrin,iron-regulatoryproteins 1 and 2,divalent metal transporter 1,and ferroportin,but similar for transferrin receptors 1 and2,and *** the expression profiles were compared between sustained virological response(SVR)and non-SVR patients,the former showed significantly lower transcription and protein expression of hepcidin and *** of hepcidin-regulating genes,BMPR1,BMPR2,and hemojuvelin,was significantly increased,whereas BMP2 was decreased in HCV-infected ***2 and hemojuvelin expression was significantly lower in the SVR than non-SVR *** infection affects the expression of iron-metabolism-related genes,leading to iron accumulation in ***:Decrea

关键词： Chronic hepatitis C Iron-metabolism Hepcidin Ferro

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