60. The documentation of Armenian

1. Introduction 2. The early period (5th-11th centuries) 3. The middle period (12th-16th centuries) 4. The modern period (17th-21th centuries) 5. Reference

Eznik of Kołb as a translator of Methodius of Olympus

As is well known, the de Autexusio by Methodius is one of the most relevant sources used by Eznik of Kołb in composing his treatise, conventionally known as Ełc Ałandoc‘ (Refutation of the Sects). The latter included an almost integral translation or reworking of the former, divided into two parts. This was highlighted for the first time by Father Grigoris Galēmk‘earean, who devoted to the subject the greater part of his study on Eznik’s sources, published as a monograph in 1919. In 1924–1925, Louis Mariès addressed the same topic in his work on Eznik’s text. However, in later years, the subject seems to have ceased to draw the attention of Armenologists. In this contribution, after a short summary of the contents of the works both of Methodius and Eznik, we address Eznik’s manner of selecting the sects that are the object of his criticism. We then highlight how Eznik more or less freely translates Methodius’ Greek text, providing some relevant examples

Un selfie alla cultura armena del settimo secolo: l’“Autobiografia” di Anania Širakacci

Anania Širakacci, a scientist (mathematician, cosmologist, astronomer, etc.) from the 7th century, is among the most original figures in Armenian literature. Anania Širakacci, a scientist (mathematician, cosmologist, astronomer, etc.) from the 7th century, is among the most original figures in Armenian literature. His autobiography ‒ a brief text dating back to the last phase of his scholarly activity ‒ provides a description of contemporary Armenian culture, highlighting its many deficiencies. Furthermore, it details the efforts of a brilliant man ‒ Anania himself ‒ devoted to obtaining abroad (i.e. in the Byzantine world) the knowledge and resources that were not available in his home country, and to spreading them among his compatriots. This article includes a translation of the Autobiography as well as a linguistic, historical, and philological commentary on it

Exploring the Universe of Protein Structures beyond the Protein Data Bank

It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. Beside their conceptual relevance, the new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the identification and design of novel folds

Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

Background : Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results: Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion: The predictive system are publicly available at the address http://distill.ucd.ieScience Foundation IrelandIrish Research Council for Science, Engineering and TechnologyHealth Research BoardUCD President's Award 2004au, da, ke, ab, sp - kpw30/11/1

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p

La stampa armena a Livorno - Armenian Printing in Livorno

La colonia armena di Livorno si formò progressivamente durante la seconda metà del Cinquecento ed i primi decenni del secolo successivo. L’installazione di tipografie per la stampa di libri armeni nella città labronica, per quanto temporanea essa fosse, come è logico avvenne nel periodo di maggior fioritura della comunità armeno-livornese, il Seicento, quando l’aspirante stampatore poteva trovare in città un clima relativamente aperto, le persone che gli procurassero le attrezzature e gli trasmettessero le conoscenze tecniche per la stampa, i connazionali che lo aiutassero nel lavoro o che lo finanziassero. Il lato negativo della situazione era invece una costante sorveglianza da parte di emissari della Congregazione de Propaganda Fide. Sappiamo di due tipografie armene che fecero tappa a Livorno. La prima fu fondata da Yovhannēs Ĵułayec‘i (Giovanni di Giulfa) e dai suoi torchi, nel 1644, uscì un Salterio, comprendente anche alcune preghiere, prima che lo stampatore fosse costretto ad allontanarsi in tutta fretta, per l’Oriente, portando comunque con sé l’attrezzatura tipografica. Qualche decennio dopo tre mercanti di Nuova Giulfa attivi a Livorno finanziarono la stampa della Bibbia in armeno, realizzata da Oskan Erewanc‘i ad Amsterdam tra il 1666 ed il 1668. Forse anche a seguito di questi contatti, Oskan, che aveva ereditato la stamperia intitolata a Surb Ēĵmiacin ew Surb Sargis Zōravar (Santa Ēĵmiacin e San Sergio Stratelata), decise di trasferirla a Livorno dove, tra il 1669 ed il 1672, essa produsse quattro opere, tutte di carattere religioso. Nello stesso 1672 questa tipografia venne poi trasferita a Marsiglia e, dopo quella di Oskan, non vi furono più tipografie armene a Livorno.The Armenian colony in Livorno (traditionally known as Leghorn in English) gradually developed during the second half of the sixteenth and the first decades of the seventeenth century. And it was unsurprisingly during the seventeenth century, when the community was flourishing, that a number of printing houses specializing in Armenian books were founded, even though these ventures proved short-lived. At that time, the aspirant printer was able to work in a relatively liberal environment, keeping in touch with people who could provide equipment and teach him how to use it, as well as fellow countrymen who would assist him and, most importantly, help finance the enterprise. On the downside, the operations were constantly under surveillance by agents of the Sacred Congregation for the Propagation of the Faith. To our knowledge, two Armenian printing houses were active in Livorno during this period. The first was set up by Yovhannēs Ĵułayec‘i (John of Julfa), who in 1644 managed to print a Psalter incorporating a number of prayers before he was forced to leave in a hurry, heading east and taking the whole printing press with him. A few decades later, three Livorno-based merchants, originally from New Julfa, sponsored the printing of the first Armenian Bible, which was published by Oskan Erewanc‘i in Amsterdam between 1666 and 1668. Perhaps as a result of these contacts, Oskan, who had inherited the printing house dedicated to Surb Ēĵmiacin ew Surb Sargis Zōravar (Holy Ēĵmiacin and St Sergius Stratelates), decided to move his business to Livorno. Here he published four books between 1669 and 1672, all on a religious subject. In 1672 Oskan moved his printing house once again, this time to Marseille, thus marking the demise of Armenian printing in Livorno