Annotated Version Research Articles

G. A. Dzagurov and the Japhetic theory of academician N. Ya. Marr: Commented re-edition of the text

The present work introduces to the annotated re-edition of an article written by the prominent Ossetian scientist, folklorist and teacher Grigory Alekseevich Dzagurov (1888–1979), which was published in 1924 under the title “The Japhetic Theory of Academician N. Ya. Marr and the Question of the Origin of the Ossetians”. The text, reproduced in a new annotated version with identification of the sources used by the author, introduces to the new linguistic theory promoted by Academician N. Ya. Marr (1864–1934), postulating the relationship between Hamito-Semitic and Kartvelian languages as well as the idea of linguistic mixing and crossing. By deliberately overusing direct quotations from the works of the creator of Japhetic linguistics, Dzagurov gives a brief overview of the main provisions of Marr’s linguistic theory, showing its direct relation to the question of the dual nature, Indo-European (Iranian) and Japhetic, of Ossetic. At that time, as is well known, linguistic arguments were readily provided when discussing thorny questions about the ethnogenesis of peoples. Overall, Dzagurov’s article has historical significance in many respects. Firstly, it testifies to the reception of the Japhetic stage of Marr’s linguistic theory (that is, before the emergence of the New Doctrine of Language) with respect to the study of the Iranian linguistic world in the Northern Caucasus. Secondly, such ideas about the phenomena of the Caucasian substrate and language mixing were skillfully developed over the following decades by one of the best students of Marr, V. A. Abaev (1900–2001), who identified numerous Caucasian elements in the Ossetian language at all language levels. Finally, it is interesting to notice that it was Dzagurov who gave a recommendation on Abaev’s application for admission to the Petrograd State University, thus indirectly contributing to the onset of an important stage in the history of Ossetian studies and, in general, Soviet linguistics.

Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus.

This study identified a novel SNP and developed a highly efficient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties. Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype-phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specific PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efficient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specific trait (Q) and validating them with commercial varieties (V). The identified SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.

Hijrah and changing religious preferences in contemporary Islamic legal practice

This research examines how urban Muslim communities in Purwokerto understand and practice religion in the area of muamalah (social relationships between people). Religious practice in urban Muslim communities is different from other religious communities. The intersection between the reality of modernity, Islamicity, and identity provides a model for distinguishing contemporary Muslim religious practices. This study is based on field research employing a phenomenological approach. Participatory observation was used to collect data from two mosques in Purwokerto City: the General Soedirman Grand Mosque and the Gelora Indah Mosque. Both mosques serve as the hub of religious discourse for Purwokerto's urban Muslim community, and they host a variety of religious studies on a regular basis. In-depth interviews were performed with worshippers from the two mosques by the researchers. Secondary data is derived from studies, journals, books, and other sources. This article concludes that urban Muslim identity is manifested in the shift away from usury practices and the choice of halal products. Studies in urban mosques and social media cannot isolate the rhetoric from the social formation of urban Muslims. In this environment, hijrah (shifting paradigm) has emerged as one of the trends that give rise to new nuances and views of any Islamic legal concept that is an annotated version of older works. Because of these shifts in preferences, the discipline of Islamic law, particularly fiqh muamalah, has become one of the most important areas for the expression of religious experience in the lives of urban Muslims

강독 수업과 연계한 판소리계 소설 교재 제작 및 활용 방안 연구

In the classical novel reading class, which is a major subject of Korean language and literature department and Korean language education department, pansori novels are frequently dealt with. At this time, it is necessary to set the standard of what to select as a reading class textbook among various annotated versions and check the use of textbooks for effective operation of the reading class. These days, annotated versions of classical novels are largely divided into modern translations for general readers and original texts for professional researchers. In the case of the reading class, students begin to read classical novels as general readers at the introduction stage, but ultimately they are aimed at having the ability to decipher original texts as major students. Therefore, it is necessary to utilize modern translations and original texts hierarchically. To do this, first of all, it should be clarified that the essence of the reading of the original text pursued by the reading class is the oral recitation in the community unit, and that the function of oral recitation is in expressing and deepening the emotional response of the audience to classical novels. Next, the class process should be hierarchized so that students who are still unfamiliar with oral recitation can get used to reading aloud by using the familiar silent reading method. At the beginning of the reading class, it is necessary to use the modern translation versions to focus on the contents through the silent reading, but it is necessary to gradually induce the students to experience the rich auditory elements contained in the original text and to increase the utilization of the original text. At the first stage of silent reading, focusing on imagining the emotion and atmosphere of the characters rather than acquiring detailed information is more important so that the result of silent reading can be the basis for coordinating the voice according to the emotional meaning of the scenes in the next stage of oral reading. Finally, the purpose of each step should be reflected in the production of textbooks. The modern translation versions that will be used in the silent reading stage should be able to stimulate the reader’s imagination and emotional responses by containing various image materials and presenting appropriate additional information in the quotations of poems. Based on this, it is necessary for students to reflect on their reading and to activate mutual criticism by making the textbook in the form of an audio file to be used in the oral reading stage of original texts.

“Funeral oration and prayer” – From the 12th century to the present

AbstractThis study is a representative text written as part of the project “Hungarian Literary Culture in a Transcultural Perspective”. It aims to convey to readers versed in other cultures the effects of the first complete text in the Hungarian language, the “Funeral Oration and Prayer” (Halotti Beszéd és Könyörgés), as an element of the living literary tradition manifesting in writing and reading. The study consists in a commented and annotated version of the basic text that will serve as a basis for the chapters adapted to the specificities of the different language versions of the book. The text gives a brief overview of 12th century Hungarian texts, and then introduces several 20th century Hungarian poems that share as their precursor the “Funeral Oration and Prayer”.

PEATmoss: A Gene Expression Atlas for Bryophytes.

PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data from multiple gene annotation versions. This atlas includes more than 100 experiments of P. patens, is expanding to host Anthoceros agrestis and Marchantia polymorpha, and aims to host data from more species in the future. PEATmoss has multiple visualization methods and tools for data downloading and is connected to the Physcomitrium patens Gene Model Lookup DB (PpGML DB), which links P. patens genes to annotations and resources from several databases and contains tools for gene version lookup and sequence and annotation extraction. Among the new features available in PEATmoss are dataset privacy control, multispecies menu, interactive color scale, co-expression network visualization, and replicate data downloading.

EasyGDB: a low-maintenance and highly customizable system to develop genomics portals.

SummaryEasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects.Availability and implementation The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb.

Is IDO1 an adequate target for treatment in glioblastoma?

e14039 Background: Glioblastoma (GB) is the most prevalent primary brain tumor in adults. The first-line treatment is based on standard brain surgery and adjuvant radio-chemotherapy. Indoleamine 2,3-dioxygenase 1 (IDO1) is a catabolic enzyme that plays a role in the metabolism of tryptophan (Trp), thereby promoting a state of immunosuppression. New treatments inhibiting this pathway are being tested in GB. This study aims to assess the expression of IDO in GB patients to determine whether this enzyme may be an actionable target for the treatment of GB. Methods: This is a retrospective transversal study whose database comes from the GLIOCAT project. Expression of IDO protein and mRNA was evaluated in tumor specimens of newly diagnosed GB patients by immunohistochemistry (IHC) (percentage of positive tumor cells) with an antibody anti-IDO1 (Sigma-Aldrich Cat#HPA027772) and by RNA sequencing (RNA-seq). RNA-seq (IIlumina HiSeq2000) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4). Reads were mapped to the human reference genome version hg38 with STAR. Genes were quantified with RSEM using gencode annotation version 24. Normalization of gene expression was performed with the trimmed-mean of M values (TMM) method. IDO gene expression values of -6 logCPM were considered as not expressed. Results: From the 255 samples assessed by IHC, 199 patients (78%) did not express IDO1 protein (mean 0.8±2.73, range 0-21%). From the 139 samples assessed by RNA-seq, TMM values, were negative for 49.6%, while low expression was detected for the other samples (mean -3.36 +/- 3.15 logCPM, range -6.12-4.32). Conclusions: Although IDO1 is barely expressed in normal brain tissue, certain studies show that its expression is upregulated in GB, either by tumor cells or indirectly induced in host antigen presenting cells, leading to immune evasion. Therefore, the metabolism of Trp is an attractive pathway to be targeted for the treatment of GB; however, our results show that IDO may not be the main target to be inhibited due to its undetectable or very low levels of expression.

Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing.

The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing (AS) events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the untranslated regions (UTRs) of 20,340 annotated genes and corrected 886 wrongly spliced genes. We also identified 28,564 AS events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.

ILoci: robust evaluation of genome content and organization for provisional and mature genome assemblies.

We introduce a new framework for genome analyses based on parsing an annotated genome assembly into distinct interval loci (iLoci), available as open-source software as part of the AEGeAn Toolkit (https://github.com/BrendelGroup/AEGeAn). We demonstrate that iLoci provide an alternative coordinate system that is robust to changes in assembly and annotation versions and facilitates granular quality control of genome data. We discuss how statistics computed on iLoci reflect various characteristics of genome content and organization and illustrate how these statistics can be used to establish a baseline for assessment of the completeness and accuracy of the data. We also introduce a well-defined measure of relative genome compactness and compute other iLocus statistics that reveal genome-wide characteristics of gene arrangements in the whole genome context. Given the fast pace of assembly/annotation updates, our AEGeAn Toolkit fills a niche in computational genomics based on deriving persistent and species-specific genome statistics. Gene structure model-centric iLoci provide a precisely defined coordinate system that can be used to store assembly/annotation updates that reflect either stable or changed assessments. Large-scale application of the approach revealed species- and clade-specific genome organization in precisely defined computational terms, promising intriguing forays into the forces of shaping genome structure as more and more genome assemblies are being deposited.

Annotation and Textual Criticism of the Chapter on “ Emperor Hongzhi and his Ministers” in the Major Events of Ming History

<p>本文逐條校讀《明史紀事本末‧弘治君臣》的文本，註出其可能的史源，並以史源校正文本之訛誤。並以校注結果，兼談作者的編纂水平與史學。今尋其史源，以《皇明大政紀》為最主要史源，全書只有三條文本沒有參考引用《皇明大政紀》。不少條文本，其他史書皆不載，獨《皇明大政紀》載之；是獨家史源。由於編者未參考《明實錄》，全篇99條，時間錯置多達47處。而人名、官名和文字缺漏亦有18處，是本篇缺點。但作者能根據私家史書撰寫一些官方史書忌諱的史事，是本篇優點。其敘事完全配合「谷應泰論贊」對弘治朝政治的評價，論述其君臣之互動，大臣不斷進諫，弘治帝也能採納。對於朝政的負面現象，也不迴避。就此而論，《明史紀事本末‧弘治君臣》仍不失為一篇良史之作。</p> <p> </p><p>This is an annotated version of the chapter on “ Emperor Hongzhi and his Ministers” in the Major Events of Ming History, tracing the likely sources upon which the account was based, and using the sources to correct errors in the text. And the essay will further discuss the editorial and historiographical abilities of the compiler. The Chronicle of Major Political Events of the Ming Dynasty was the most important source for this work. In the entire volume, there were only three entries that did not cite the Chronicle of Major Political Events of the Ming Dynasty. Several of the entries cited no historical sources other than the Chronicle of Major Political Events of the Ming Dynasty, and hence it could be the only source. Because the compiler did not consult the Ming Veritable Records, among the ninety-nine entries in the volume, there were as many as forty-seven errors in dates. And there were eighteen errors in names and titles of individuals. These are the weaknesses of this volume. However, the compiler was able to draw upon works by private historians to recount historical events omitted from the official records. This is the strength of this volume. The narrative completely matches the evaluation in “Gu Yingtai’s Assessment” on the Hongzhi reign regarding the interactions between the Hongzhi emperor and his ministers, that the high officials made endless admonitions of the emperor and the emperor was fairly receptive to their opinions. As for the negative aspects of governance during this reign, the work does not avoid them. And hence, the “Emperor Hongzhi and his Ministers” chapter in the Major Events of Ming History can be regarded as a fine historical record.</p> <p> </p>

EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control

In many research areas, scientific progress is accelerated by multidisciplinary access to image data and their interdisciplinary annotation. However, keeping track of these annotations to ensure a high-quality multi-purpose data set is a challenging and labour intensive task. We developed the open-source online platform EXACT (EXpert Algorithm Collaboration Tool) that enables the collaborative interdisciplinary analysis of images from different domains online and offline. EXACT supports multi-gigapixel medical whole slide images as well as image series with thousands of images. The software utilises a flexible plugin system that can be adapted to diverse applications such as counting mitotic figures with a screening mode, finding false annotations on a novel validation view, or using the latest deep learning image analysis technologies. This is combined with a version control system which makes it possible to keep track of changes in the data sets and, for example, to link the results of deep learning experiments to specific data set versions. EXACT is freely available and has already been successfully applied to a broad range of annotation tasks, including highly diverse applications like deep learning supported cytology scoring, interdisciplinary multi-centre whole slide image tumour annotation, and highly specialised whale sound spectroscopy clustering.

Jefferson Takes on Buffon: The Polemic on American Animals in <em>Notes on the State of Virginia</em>

In Query 6 of Notes on the State of Virginia, Thomas Jefferson’s only published book, he made a spirited argument against the theories of the leading French naturalist Georges-Louis Leclerc, comte de Buffon, who believed the Americas had fewer species and smaller animals than in the Old World. Many historians and biographers have championed Jefferson’s patriotic defense of American nature, but few have recognized how closely Jefferson relied on Buffon even as he tried to refute his theories. This article examines the composition of NSV’s Query 6 based on the archived manuscript and notes held at the Massachusetts Historical Society, as well as the French translation published in Paris in 1786. It includes an annotated version of one of Jefferson’s several tables of American animals, cross-referencing it to sources in Buffon and to modern species names. Whereas many assume that Jefferson got the better of Buffon, in fact the latter’s evidence for a decline in the size of large quadruped species was accurate. Jefferson’s paper about an animal he called the megalonyx, which he read to the American Philosophical Society in 1797, revisited the debate, added high-quality engravings of fossil bones, and—because Jefferson argued that the mammoth and the megalonyx still lived in North America—reiterated his difficulties in taking on Buffon.

Is there any intron sliding in mammals?

BackgroundEukaryotic protein-coding genes consist of exons and introns. Exon–intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group.ResultsWe didn’t find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data.ConclusionsWe assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation.

#UsToo: A Musical Comedy about Sexual Assault and Harassment

#UsToo debuted at the 39th Annual Conference of the North American Drama Therapy Association. It was written and performed by the author as an autoethnographic therapeutic theatre performance investigating her experiences with sexual assault and harassment perpetrated by members of the drama therapy community. This article includes an annotated version of the script with a discussion on form, content, aesthetic choices and embodiment. This article concludes with a synthesis of authorial learnings and outcomes throughout the devising, rehearsal and performance processes.

Text-Mining Services of the Swiss Variant Interpretation Platform for Oncology.

The Swiss Variant Interpretation Platform for Oncology is a centralized, joint and curated database for clinical somatic variants piloted by a board of Swiss healthcare institutions and operated by the SIB Swiss Institute of Bioinformatics. To support this effort, SIB Text Mining designed a set of text analytics services. This report focuses on three of those services. First, the automatic annotations of the literature with a set of terminologies have been performed, resulting in a large annotated version of MEDLINE and PMC. Second, a generator of variant synonyms for single nucleotide variants has been developed using publicly available data resources, as well as patterns of non-standard formats, often found in the literature. Third, a literature ranking service enables to retrieve a ranked set of MEDLINE abstracts given a variant and optionally a diagnosis. The annotation of MEDLINE and PMC resulted in a total of respectively 785,181,199 and 1,156,060,212 annotations, which means an average of 26 and 425 annotations per abstract and full-text article. The generator of variant synonyms enables to retrieve up to 42 synonyms for a variant. The literature ranking service reaches a precision (P10) of 63%, which means that almost two-thirds of the top-10 returned abstracts are judged relevant. Further services will be implemented to complete this set of services, such as a service to retrieve relevant clinical trials for a patient and a literature ranking service for full-text articles.

Complete Genome Sequence of Plant Growth-Promoting Rhizobacterium Pseudomonas protegens SN15-2.

We report the complete genome sequence of Pseudomonas protegens SN15-2, which was isolated from the rhizosphere of tomato roots in Shanghai, China, and can be used in the biological control of phytopathogens. This annotated version will be the basis for upcoming genomic studies.

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens.

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de.

Mark-up and Annotation in the Corpus of Historical English Law Reports (CHELAR): Potential for Historical Genre Analysis

Adding annotation and mark-up to linguistic corpora has become a standard practice in corpus building over the past few decades as a way to facilitate data extraction and at the same time guarantee that new corpora are compatible with existing and future tools. The purpose of this article is twofold. First, we provide an overview of the main forms of annotation and mark-up available to the research community and how they have been applied to the Corpus of Historical English Law Reports 1535-1999 (CHELAR), a specialized corpus consisting of law reports or records of judicial decisions. Second, we give an account of preliminary research based on the annotated versions of CHELAR, which so far has been primarily aimed at identifying the distinctive linguistic characteristics of law reports, as well as at investigating how the language of law reports has evolved over a time span of almost five centuries. Our article illustrates the multiple advantages of applying a simple annotation schema to a corpus and how this can enhance the potential of a corpus for historical genre analysis.

Updated Genome Sequence and Annotation for the Full Genome of Pseudomonas protegens CHA0.

Minor differences in the previously obtained genome of Pseudomonas protegens CHA0 were detected after resequencing the strain. Based on this, the genome size slightly increased. Additionally, we performed a manual annotation of genes involved in biocontrol and insect pathogenicity. This annotation version will be the basis for upcoming genome studies.