The OpenAIRE guide for research institutions

Çelik, Sönmez (Dogus Author)Bu metin, Araştırma Kurumlarına yardımcı olmak için 13.04.2011 tarihinde yayımlanan OpenAIRE Kılavuzu’nun çevirisidir. Çeviri, ANKOS Açık Erişim ve Kurumsal Arşivler Grubu üyeleri ve İYTE Kütüphanesi tarafından yürütülen OpenAIREplus Projesi, Türkiye Yardım Masası destek ekibinin işbirliği ile yapılmıştır. OpenAIRE Projesi, bir Avrupa Yardım Masası Sistemi aracılığıyla araştırmacılara Avrupa Komisyonu Yedinci Çerçeve Programıyla uyumlu bir destek sağlamayı; araştırmacıları, bu çerçeve program kapsamında fon desteği alan çalışmalarına ait çıktılarını OpenAIRE Portalı’na dahil bir kurumsal veya konusal arşivde yayımlamaları için desteklemeyi hedeflemektedir. OpenAIRE Projesinin devamı niteliğinde olacak bir proje olan OpenAIREplus’ın temel amacı ise, hakemli bilimsel yayınlara ve ilişkili veri setlerine sağlam çapraz bağlantılar sağlamaktır.This text is transcript of OpenAIRE Guide which is prepared in order to help research institutions was released on 13.04.2011and translated with the cooperation of ANKOS Open Access and Institutional Repositories Grup members and OpenAIREplus project team of Turkey which is coordinated from Izmir Institute of Technology Library. OpenAIRE Project aims to support researchers in complying with the European Commission Seventh Framework Programme Open Access Pilot through a European Helpdesk System; support researchers in depositing their research publications in an institutional or disciplinary repository; build up an OpenAIRE portal and e-infrastructure for repository networks. The project will work in tadem with OpeanAIREplus Project which has the principal goal of creating a robust, participatory service for the cross-linking of peer-reviewed scientific publications and associated datasets

Open Access and DSpace Institutional Repository System

Çelik, Sönmez (Dogus Author)Akademik camiada ortak çıkarların yaratılması amacıyla bilginin paylaşılmasına armağan edilmiş toplumsal bir hareket olan Açık Erişim, bugün dünyada pek çok bilim insanı, yayınevi ve araştırmacı tarafından desteklenmektedir. Açık erişimin temelini oluşturan kurumsal arşiv sistemleri için kullanılan yazılımlar, ücretsiz olan açık kaynak kodlu yazılımlar ve çeşitli firmalar tarafından geliştirilen ücretli paket programlardan oluşmaktadır. İlk sürümü 2002 yılında kullanıma sunulan DSpace Massachusetts Teknoloji Enstitüsü (MIT) ve Hewlett Packard (HP) işbirliğiyle geliştirilmiş açık kaynak kodlu kurumsal arşiv yazılımıdır ve Kasım 2012 itibarıyla dünyada 1.360’tan fazla kurum tarafından kullanılmaktadır. Bu çalışmada, açık erişim ve kurumsal arşivler üzerinde durularak, DSpace kurumsal arşiv yazılımının özellikleri ve açık erişim girişimlerine olan katkısı vurgulanmaya çalışılmıştır.The Open Access movement is a social movement in academia, dedicated to the principle of open access - to information - sharing for the common good and is being supported by many scientists, publishers, and researchers in the world, today. The software that is used to operate the institutional archive systems which are the basis of the Open Access, are divided into two forms of some free open source software and paid package programs which were developed by some corporates. DSpace, whose first version was presented to use in 2002, is an open source archive software which was developed with the co-operation of Massachusetts Institute of Technology and Hewlett Packard and is being used by more than 1.360 institutions all over the world as of November, 2012. The aim of this study is to highlight the features of the DSpace institutional archive software and its contributions to the open access initiatives by emphasizing the open access and institutional archive

Accuracy Boosters: Epoch-Driven Mixed-Mantissa Block Floating-Point for DNN Training

The unprecedented growth in DNN model complexity, size and the amount of training data have led to a commensurate increase in demand for computing and a search for minimal encoding. Recent research advocates Hybrid Block Floating-Point (HBFP) as a technique that minimizes silicon provisioning in accelerators by converting the majority of arithmetic operations in training to 8-bit fixed-point. In this paper, we perform a full-scale exploration of the HBFP design space including minimal mantissa encoding, varying block sizes, and mixed mantissa bit-width across layers and epochs. We propose Accuracy Boosters, an epoch-driven mixed-mantissa HBFP that uses 6-bit mantissa only in the last epoch and converts $99.7\%$ of all arithmetic operations in training to 4-bit mantissas. Accuracy Boosters enable reducing silicon provisioning for an HBFP training accelerator by $16.98\times$ as compared to FP32, while preserving or outperforming FP32 accuracy

The role of cavity residue leucine 95 and channel residues glutamine 204, aspartic acid 211, and phenylalanine 269 on toluene o-xylene monooxygenase activity and regiospecificity

The biocatalyst toluene-o-xylene monooxygenase (ToMO) of Pseudomonas sp. OX1 belongs to a remarkable family of bacterial multicomponent monooxygenases and has been shown to have a great potential for biotechnological and environmental applications. Structural analysis of ToMO hydroxylase revealed the presence of three hydrophobic cavities, a channel, and a pore leading from the protein surface to the active site. A structural study with the related enzyme toluene-4-monooxygenase (T4MO) hydroxylase with its respective regulatory protein confirmed that the channel undergoes extensive structural changes upon binding of the regulatory protein and transiently opens and closes during catalysis (Figure 1). Here, saturation mutagenesis was used to investigate the catalytic roles of alpha-subunit (TouA) second cavity residue L95 and TouA channel residues Q204, D211, and F269. By testing the substrates toluene, phenol, nitrobenzene, and/or naphthalene, these positions were found to influence the catalytic activity of ToMO. Several regiospecific variants were identified from TouA positions Q204, F269, and L95. For example, TouA variant Q204H had the regiospecificity of nitrobenzene changed significantly from 30 to 61 % p-nitrophenol. Interestingly, a combination of mutations at Q204H and A106V altered the regiospecificity of nitrobenzene back to 27 % p-nitrophenol. TouA variants F269Y, F269P, Q204E, and L95D improved the meta-hydroxylating capability of nitrobenzene by producing 87, 85, 82, and 77 % m-nitrophenol, respectively. Here, two additional TouA residues, S222 and A106, were also identified that may have important roles in catalysis. Most of the isolated variants from D211 remained active, whereas having a hydrophobic residue at this position appeared to diminish the catalytic activity toward naphthalene. The mutational effects on the ToMO regiospecificity described here suggest that it is possible to further fine tune and engineer the reactivity of multicomponent diiron monooxygenases toward different substrates at positions that are relatively distant from the active site. Please click Additional Files below to see the full abstract

Criteria for Open Access and Publishing

Bu makale DOAJ’ın tarihsel gelişimi ve bugünkü durumuna ilişkin genel bir değerlendirme sunmaktadır. Makalede DOAJ tarihine kısaca değinildikten sonra DOAJ’ın açık erişim, fikri mülkiyet hakları ve kuşku uyandıran yayıncılarla ilgili politikaları detaylı biçimde anlatılmaktadır. Makalenin büyük bir kısmını, DOAJ’ın açık erişim dergi değerlendirme sürecinde yeni belirlenen değerlendirme kriterlerinin nasıl kullanıldığına ilişkin açıklamalar ve DOAJ Seal’ı nitelendirmek için seçilen yedi yeni değerlendirme kriterinin arkasında yatan gerekçeler oluşturmaktadır. Son bölüm, DOAJ’ın yakında akademisyen ve yayıncılara sunacağı veri tabanı arama ve üst veri yükleme ile ilgili genişletilmiş seçeneklere ayrılmıştır. Sonuç, daha güçlü bir platform ve daha istikrarlı bir veri tabanı sunan, yükleme ve üst verinin derlenebilmesi için gelişmiş hizmetlere izin veren yenilenmiş bir DOAJ’dır.This article gives an overview of the history and current status of the DOAJ. After a brief historical overview, DOAJ policies regarding open access, intellectual property rights and questionable publishers are explained in detail. The larger part of this article is a much requested explanation on how DOAJ uses its new set of criteria for the evaluation of open access journals and the rationale behind choosing the seven extra criteria that qualify for the DOAJ Seal. A final section is devoted to the extended possibilities that DOAJ will be offering shortly to scholars and publishers for searching the database and for uploading metadata. The result is a renewed DOAJ that offers a more robust platform, a more stable database and enhanced services to allow the upload and collection of metadata

A novel B,O,N-doped mesogen with narrowband MR-TADF emission

The St Andrews team would also like to thank EPSRC (EP/P010482/1, EP/W015137/1, EP/W007517/1) for financial support. E.Z.-C. was a Royal Society Leverhulme Trust Senior Research Fellow (SRF\R1\201089).Modification of an unsymmetric B,O,N-doped aromatic core with peripheral mesogenic units triggers self-assembly into a columnar hexagonal mesophase, which is stable between 22 and 144 °C. The columnar assembly is preserved in a glassy state below 22 °C. The B,O,N-doped mesogen displays narrowband sky-blue multiresonance thermally activated delayed fluorescence (MR-TADF) under diluted conditions and bright excimer emission in condensed phase. Our combined experimental and theoretical approach provides insight into the development of strongly aggregating liquid crystalline MR-TADF emitters.Peer reviewe

Araştırma Kurumları İçin OpenAIRE Kılavuzu

This text is transcript of OpenAIRE Guide which is prepared in order to help research institutions was released on 13.04.2011and translated with the cooperation of ANKOS Open Access and Institutional Repositories Grup members and OpenAIREplus project team of Turkey which is coordinated from Izmir Institute of Technology Library.OpenAIRE Project aims to support researchers in complying with the European Commission Seventh Framework Programme Open Access Pilot through a European Helpdesk System; support researchers in depositing their research publications in an institutional or disciplinary repository; build up an OpenAIRE portal and e-infrastructure for repository networks. The project will work in tadem with OpeanAIREplus Project which has the principal goal of creating a robust, participatory service for the cross-linking of peer-reviewed scientific publications and associated datasets.Bu metin, Araştırma Kuramlarına yardımcı olmak için 13.04.2011 tarihinde yayımlanan OpenAIRE Kılavuzu’nun çevirisidir. Çeviri, ANKOS Açık Erişim ve Kuramsal Arşivler Gruba üyeleri ve İYTE Kütüphanesi tarafından yürütülen OpenAIREplas Projesi, Türkiye Yardım Masası destek ekibinin işbirliği ile yapılmıştır.OpenAIRE Projesi, bir Avrupa Yardım Masası Sistemi aracılığıyla araştırmacılara Avrupa Komisyonu Yedinci Çerçeve Programıyla uyumlu bir destek sağlamayı; araştırmacıları, bu çerçeve program kapsamında fon desteği alan çalışmalarına ait çıktılarını OpenAIRE Portalı’na dahil bir kurumsal veya konusal arşivde yayımlamaları için desteklemeyi hedeflemektedir. OpenAIRE Projesinin devamı niteliğinde olacak bir proje olan OpenAIREplus’ın temel amacı ise, hakemli bilimsel yayınlara ve ilişkili veri setlerine sağlam çapraz bağlantılar sağlamaktır

Açık bilimsel bilgi dünyası

Çelik, Sönmez (Dogus Author)25-27 Nisan 2013 tarihinde Antalya Maritim Kongre Merkezi'nde gerçekleştirilen ANKOSLink 2013 konferansında ANKOS Açık Erişim ve Kurumsal Arşivler Grubunun yapmışolduğu sunumun görselleridir. Sunumda, açık erişim, kurumsal arşivler ile AEKA grubunun faaliyetleri anlatılmıştır

New CagL amino acid polymorphism patterns of helicobacter pylori in peptic ulcer and non-ulcer dyspepsia

Background and Objectives: Helicobacter pylori infection is associated with chronic gastritis, ulcers, and gastric cancer. The H. pylori Type 4 secretion system (T4SS) translocates the CagA protein into host cells and plays an essential role in initiating gastric carcinogenesis. The CagL protein is a component of the T4SS. CagL amino acid polymorphisms are correlated with clinical outcomes. We aimed to study the association between CagL amino acid polymorphisms and peptic ulcer disease (PUD) and non-ulcer dyspepsia (NUD). Materials and Methods: A total of 99 patients (PUD, 46; NUD, 53) were enrolled and screened for H. pylori by qPCR from antrum biopsy samples. The amino acid polymorphisms of CagL were analyzed using DNA sequencing, followed by the MAFFT sequence alignment program to match the amino acid sequences. Results: Antrum biopsy samples from 70 out of 99 (70.7%) patients were found to be H. pylori DNA-positive. A positive band for cagL was detected in 42 out of 70 samples (PUD, 23; NUD, 19), and following this, these 42 samples were sequenced. In total, 27 different polymorphisms were determined. We determined three CagL amino acid polymorphism combinations, which were determined to be associated with PUD and NUD. Pattern 1 (K35/N122/V134/T175/R194/E210) was only detected in PUD patient samples and was related to a 1.35-fold risk (p = 0.02). Patterns 2 (V41/I134) and 3 (V41/K122/A171/I174) were found only in NUD patient samples and were linked to a 1.26-fold increased risk (p = 0.03). Conclusions: We observed three new patterns associated with PUD and NUD. Pattern 1 is related to PUD, and the other two patterns (Patterns 2 and 3) are related to NUD. The patterns that we identified include the remote polymorphisms of the CagL protein, which is a new approach. These patterns may help to understand the course of H. pylori infection.Istanbul Aydin University Scientific Research Projects Uni