This paper deals with the phrase intonation of the Southern Russian dialect spoken in the village of Rogovatoe, in the Starooskol'sky district of the Belgorod region. The study is devoted to the ...analysis of the prosodic structure of various communicative categories: statements, yes-no questions, wh-questions, non-finality, imperative, and vocative. Based on the examination of more than 7000 sentences, I argue that the dialect of Rogovatoe uses only two monotonal pitch accents - H* and L* - as opposed to three bitonal accents of Modern Standard Russian. I also postulate two final boundary tones - H% and L% - for this dialect, while no proof of a phonological distinction between the high and the low phrase accents was found. Finally, the idiom of Rogovatoe employs the phonological distinction between the high and the low initial boundary tone - %H and %L. Therefore, the prosodic system of this Southern Russian dialect is much more focused on the level tones than Modern Standard Russian utilizing predominantly contour (rising and falling) tones.
This paper analyzes prosodic phrasing in Northern Russian dialects spoken in the Pinezhsky, Plesetsky, Verkhnetoemsky, Mezensky, Leshukonsky, Konoshsky, and Vinogradovsky districts of Arkhangelsk ...Oblast based on the material of dialectal speech corpora and the author's tape recordings of dialectal speech made in 1987–1999 (49 hours in total). It deals primarily with the issues related to the local markers of prosodic phrasing, their hierarchy and phonetic means of realization. Based on the performed analysis, I suggest the following break index scale in Arkhangelsk dialects: 0 - break index showing strongest cohesion (absence of prosodic break), typical of boundaries internal to prosodic words (e.g., boundaries between clitics and hosts); 1 - break index marking prosodic word boundaries: marked on the right edge of a prosodic word followed by another prosodic word within the same accentual phrase (by means of reset of the word's rhythmical structure); 2 - break index marking accentual phrase boundaries: marked on the right edge of an accentual phrase followed by another accentual phrase within the same intermediate phrase (phonetically manifested as a significant - more than 1.5 semitones - tonal drop on a voiced consonant and/or on a poststressed vowel); 3 - break index marking a boundary between an intermediate phrase with nuclear pitch accent and an accentual phrase with non-nuclear pitch accent within the same intonational phrase (using a long, 300–1500 ms, interruption in articulation and high or low boundary tone); 4 - break index marking intermediate phrase boundaries: marked on the right edge of an intonational phrase (by means of high or low boundary tone and an optional pause); 5 - break index marking intonational phrase boundaries: marked on the right edge of an intonational phrase (by means of low boundary tone and an optional pause). The most characteristic features of Arkhangelsk dialects from the perspective of prosodic phrasing are 1) the accommodation of microprosodic features (tonal drop on voiced consonants) for macroprosodic purposes (marking accentual phrase boundaries); 2) the use of lasting physical breaks in articulation to mark prosodic phrasing within an intonational phrase; 3) the absence of a sraightforward correlation between the pause duration and the depth of prosodic breaks.
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with ...technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.
This paper deals with the phrase intonation of two neighboring Eastern Middle-Russian dialects with okan’je and akan’je spoken in Melenki and Gus’-Khrustal’ny districts of Vladimir region. The study, ...based on the material of dialectal speech recordings made in the 2008 and 2009 (nine speakers born in 1914–1940, total duration — 19 hours), reveals that the prosodic system of these dialects is relatively similar to that one of the Modern Standard Russian, sharing with it most pitch accents (L*, H*+L, L*+H) and association of tonal structures with the basic communicative categories — statements, yes-no questions, wh-question, non-finality, commands and requests. The main distinctive properties of the Vladimir dialect as compared to Standard Russian are: 1) phonological distinction between two rising pitch accents — L*+H and L+H*; 2) probable H* pitch accents in dialects with akan’je; 3) “falling set-up” on pretonic syllable for rising pitch accents; 4) earlier timing of rising L*+H and falling H*+L pitch accents; 5) phonological distinction between two initial boundary tones — %L and %H; 6) the wide distribution of falling final boundary tone HL%; 7) some traces of ‘word-to-word’ tonal prominence. Meanwhile, the difference between the two Vladimir dialects themselves is not that noticeable and lies in the domain of phonetic realization and the degree of manifestation of particular elements of prosodic structure, as well as in the degree of their prevalence rather than in the set of prosodic units.
RNA viruses mutate at extremely high rates, forming an intra-host viral population of closely related variants, which allows them to evade the host's immune system and makes them particularly ...dangerous. Viral outbreaks pose a significant threat for public health, and, in order to deal with it, it is critical to infer transmission clusters, i.e., decide whether two viral samples belong to the same outbreak. Next-generation sequencing (NGS) can significantly help in tackling outbreak-related problems. While NGS data is first obtained as short reads, existing methods rely on assembled sequences. This requires reconstruction of the entire viral population, which is complicated, error-prone and time-consuming.
The experimental validation using sequencing data from HCV outbreaks shows that the proposed algorithm can successfully identify genetic relatedness between viral populations, infer transmission direction, transmission clusters and outbreak sources, as well as decide whether the source is present in the sequenced outbreak sample and identify it.
Introduced algorithm allows to cluster genetically related samples, infer transmission directions and predict sources of outbreaks. Validation on experimental data demonstrated that algorithm is able to reconstruct various transmission characteristics. Advantage of the method is the ability to bypass cumbersome read assembly, thus eliminating the chance to introduce new errors, and saving processing time by allowing to use raw NGS reads.
Outbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software ...that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. We developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. MicrobeTrace is a web-based, client-side, JavaScript application (
https://microbetrace.cdc.gov
) that runs in Chromium-based browsers and remains fully operational without an internet connection. Using publicly available data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. Users can email
microbetrace@cdc.gov
for support. The source code is available at
https://github.com/cdcgov/microbetrace
.
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, ...facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.
RNA viruses such as HCV and HIV mutate at extremely high rates, and as a result, they exist in infected hosts as populations of genetically related variants. Recent advances in sequencing ...technologies make possible to identify such populations at great depth. In particular, these technologies provide new opportunities for inference of relatedness between viral samples, identification of transmission clusters and sources of infection, which are crucial tasks for viral outbreaks investigations.
We present (i) an evolutionary simulation algorithm Viral Outbreak InferenCE (VOICE) inferring genetic relatedness, (ii) an algorithm MinDistB detecting possible transmission using minimal distances between intra-host viral populations and sizes of their relative borders, and (iii) a non-parametric recursive clustering algorithm Relatedness Depth (ReD) analyzing clusters' structure to infer possible transmissions and their directions. All proposed algorithms were validated using real sequencing data from HCV outbreaks.
All algorithms are applicable to the analysis of outbreaks of highly heterogeneous RNA viruses. Our experimental validation shows that they can successfully identify genetic relatedness between viral populations, as well as infer transmission clusters and outbreak sources.
The requirements of new intensive technologies for newly created varieties of berry crops are increasing every year. Therefore, there is a need to involve new donors and sources of economically ...valuable traits in the breeding process. The successful implementation of the breeding program is largely determined by the correct selection of parental forms, and for the successful solution of this task, constant screening of both newly created material and existing material is necessary. Over the years of research, work has been done to obtain, study and isolate the most promising genotypes of black currant for use in breeding for resistance to biotic factors. The article presents the results of the evaluation of potential black currant donors of the VNIISPK selection. As a result of the study, donors were identified not only with complex resistance to biotic factors, but also donors with high productivity.
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to ...dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, and neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. The results highlight that while benchmarks often make code available and are in principle reproducible, they remain difficult to extend, for example, as new methods and new ways to assess methods emerge. In addition, embracing containerization and workflow systems would enhance reusability of intermediate benchmarking results, thus also driving wider adoption.
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