Free-Form B-spline Deformation Model for Groupwise Registration

In this work, we extend a previously demonstrated entropy based groupwise registration method to include a free-form deformation model based on B-splines. We provide an efficient implementation using stochastic gradient descents in a multi-resolution setting. We demonstrate the method in application to a set of 50 MRI brain scans and compare the results to a pairwise approach using segmentation labels to evaluate the quality of alignment. Our results indicate that increasing the complexity of the deformation model improves registration accuracy significantly, especially at cortical regions

DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures

DNA polymerase ζ (Pol ζ) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ζ can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ζ in handling these disturbances. We show that Pol ζ/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional ‘C’ at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ζ. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ζ/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ζ

The VocalNotes Dataset

The VocalNotes dataset is a collection of audio and annotations for excerpts of vocal performances from five musical traditions - Japanese Minyo, Chinese Hebei Bangzi opera, Russian traditional singing, Alpine yodel and Jewish Romaniote chant. For each tradition the dataset contains: about 10 minutes of audio; documentation for the songs from which annotated fragments originate; f0, independent onset, offset and note pitch annotations created by two or three experts; The dataset was created as part of the VocalNotes project [1]. It is released under CC-BY-NC-SA license and can be accessed by filling out a request form

A Review of Pink Salmon in the Pacific, Arctic, and Atlantic Oceans

The Northern Hemisphere Pink Salmon Expert Group Meeting was held on October 2–3, 2022 in Vancouver, Canada, immediately preceding the International Year of the Salmon (IYS) Synthesis Symposium. The rapid expansion of pink salmon was the theme for the meeting, and experts came together to discuss the current state of knowledge for pink salmon. Specific topics of focus included the range expansion into the Atlantic and Arctic oceans, trends in distribution and abundance, research and monitoring approaches, potential inter-specific interactions, mitigation efforts, and plans for future collaborations. The outcomes of the meeting were presented at the IYS Synthesis Symposium and are further disseminated through this NPAFC Technical Report. The Executive Summary section of this report provides a brief background, a condensed overview of each topic, and concludes with overarching takeaway messages that are intended to guide future collaborations.publishedVersio

A Review of Pink Salmon in the Pacific, Arctic, and Atlantic Oceans

The Northern Hemisphere Pink Salmon Expert Group Meeting was held on October 2–3, 2022 in Vancouver, Canada, immediately preceding the International Year of the Salmon (IYS) Synthesis Symposium. The rapid expansion of pink salmon was the theme for the meeting, and experts came together to discuss the current state of knowledge for pink salmon. Specific topics of focus included the range expansion into the Atlantic and Arctic oceans, trends in distribution and abundance, research and monitoring approaches, potential inter-specific interactions, mitigation efforts, and plans for future collaborations. The outcomes of the meeting were presented at the IYS Synthesis Symposium and are further disseminated through this NPAFC Technical Report. The Executive Summary section of this report provides a brief background, a condensed overview of each topic, and concludes with overarching takeaway messages that are intended to guide future collaborations.publishedVersio

The Development and Validation of a Novel Nanobody-Based Competitive ELISA for the Detection of Foot and Mouth Disease 3ABC Antibodies in Cattle

Effective management of foot and mouth disease (FMD) requires diagnostic tests to distinguish between infected and vaccinated animals (DIVA). To address this need, several enzyme-linked immunosorbent assay (ELISA) platforms have been developed, however, these tests vary in their sensitivity and specificity and are very expensive for developing countries. Camelid-derived single-domain antibodies fragments so-called Nanobodies, have demonstrated great efficacy for the development of serological diagnostics. This study describes the development of a novel Nanobody-based FMD 3ABC competitive ELISA, for the serological detection of antibodies against FMD Non-Structural Proteins (NSP) in Uganda cattle herds. This in-house ELISA was validated using more than 600 sera from different Uganda districts, and virus serotype specificities. The evaluation of the performance of the assay demonstrated high diagnostic sensitivity and specificity of 94 % (95 % CI: 88.9–97.2), and 97.67 % (95 % CI: 94.15–99.36) respectively, as well as the capability to detect NSP-specific antibodies against multiple FMD serotype infections. In comparison with the commercial PrioCHECK FMDV NSP-FMD test, there was a strong concordance and high correlation and agreement in the performance of the two tests. This new developed Nanobody based FMD 3ABC competitive ELISA could clearly benefit routine disease diagnosis, the establishment of disease-free zones, and the improvement of FMD management and control in endemically complex environments, such as those found in Africa

The Development and Validation of a Novel Nanobody-Based Competitive ELISA for the Detection of Foot and Mouth Disease 3ABC Antibodies in Cattle

Effective management of foot and mouth disease (FMD) requires diagnostic tests to distinguish between infected and vaccinated animals (DIVA). To address this need, several enzyme-linked immunosorbent assay (ELISA) platforms have been developed, however, these tests vary in their sensitivity and specificity and are very expensive for developing countries. Camelid-derived single-domain antibodies fragments so-called Nanobodies, have demonstrated great efficacy for the development of serological diagnostics. This study describes the development of a novel Nanobody-based FMD 3ABC competitive ELISA, for the serological detection of antibodies against FMD Non-Structural Proteins (NSP) in Uganda cattle herds. This in-house ELISA was validated using more than 600 sera from different Uganda districts, and virus serotype specificities. The evaluation of the performance of the assay demonstrated high diagnostic sensitivity and specificity of 94 % (95 % CI: 88.9-97.2), and 97.67 % (95 % CI: 94.15-99.36) respectively, as well as the capability to detect NSP-specific antibodies against multiple FMD serotype infections. In comparison with the commercial PrioCHECK FMDV NSP-FMD test, there was a strong concordance and high correlation and agreement in the performance of the two tests. This new developed Nanobody based FMD 3ABC competitive ELISA could clearly benefit routine disease diagnosis, the establishment of disease-free zones, and the improvement of FMD management and control in endemically complex environments, such as those found in Africa

UniMorph 4.0:Universal Morphology

The Universal Morphology (UniMorph) project is a collaborative effort providing broad-coverage instantiated normalized morphological inflection tables for hundreds of diverse world languages. The project comprises two major thrusts: a language-independent feature schema for rich morphological annotation and a type-level resource of annotated data in diverse languages realizing that schema. This paper presents the expansions and improvements made on several fronts over the last couple of years (since McCarthy et al. (2020)). Collaborative efforts by numerous linguists have added 67 new languages, including 30 endangered languages. We have implemented several improvements to the extraction pipeline to tackle some issues, e.g. missing gender and macron information. We have also amended the schema to use a hierarchical structure that is needed for morphological phenomena like multiple-argument agreement and case stacking, while adding some missing morphological features to make the schema more inclusive. In light of the last UniMorph release, we also augmented the database with morpheme segmentation for 16 languages. Lastly, this new release makes a push towards inclusion of derivational morphology in UniMorph by enriching the data and annotation schema with instances representing derivational processes from MorphyNet