Reducibility, Degree Spectra, and Lowness in Algebraic Structures

This dissertation addresses questions in computable structure theory, which is a branch of mathematical logic hybridizing computability theory and the study of familiar mathematical structures. We focus on algebraic structures, which are standard topics of discussion among model theorists. The structures examined here are fields, graphs, trees under a predecessor function, and Boolean algebras. For a computable field F, the splitting set SF of F is the set of polynomials in F[X] which factor over F, and the root set RF of F is the set of polynomials in F[X] which have a root in F. Results of Fröhlich and Shepherdson from 1956 imply that for a computable field F, the splitting set SF and the root set RF are Turing-equivalent. Much more recently, in 2010, R. Miller showed that for algebraic fields, if we use a finer measure, the root set actually has slightly higher complexity: for algebraic fields F, it is always the case that SF ≤1 RF, but there are algebraic fields F where we have RF \nleq1 SF . In the first chapter, we compare the splitting set and the root set of a computable algebraic field under a different reduction: the bounded Turing (bT) reduction. We construct a computable algebraic field for which RN \lneq1bT SF. We also define a Rabin embedding g of a field into its algebraic closure, and for a computable algebraic field F, we compare the relative complexities of RF, SF, and g(F) under m-reducibility and under bT-reducibility. Work by R. Miller in 2009 proved several theorems about algebraic fields and computable categoricity. Also in 2009, A. Frolov, I. Kalimullin, and R. Miller proved some results about the degree spectrum of an algebraic field when viewed as a subfield of its algebraic closure. In the second chapter, we show that the same computable categoricity results also hold for finite-branching trees under the predecessor function and for connected, finitevalence, pointed graphs, and we show that the degree spectrum results do not hold for these trees and graphs. We also offer an explanation for why the degree spectrum results distinguish these classes of structures: although all three structures are algebraic structures, the fields are what we call effectively algebraic. Every lown Boolean algebra, for 1 ≤ n ≤ 4, is isomorphic to a computable Boolean algebra. It is not yet known whether the same is true for n \u3e 4. However, it is known that there exists a low5 subalgebra of the computable atomless Boolean algebra which, when viewed as a relation on the computable atomless Boolean algebra, does not have a computable copy. In the third chapter, we adapt the proof of this recent result to show that there exists a low4 subalgebra of the computable atomless Boolean algebra B which, when viewed as a relation on B, has no computable copy. This result provides a sharp contrast with the one which shows that every low4 Boolean algebra has a computable copy. That is, the spectrum of the subalgebra as a unary relation can contain a low4 degree without containing the degree 0, even though no spectrum of a Boolean algebra (viewed as a structure) can do the same. We also point out that unlike Boolean algebras as structures, which cannot have nth-jump degree above 0(n), subalgebras of B considered as relations on B can have nth-jump degree strictly bigger than 0(n)

Classifications of Computable Structures

Let K be a family of structures, closed under isomorphism, in a fixed computable language. We consider effective lists of structures from K such that every structure in K is isomorphic to exactly one structure on the list. Such a list is called a computable classification of K, up to isomorphism. Using the technique of Friedberg enumeration, we show that there is a computable classification of the family of computable algebraic fields, and that with a 0\u27-oracle, we can obtain similar classifications of the families of computable equivalence structures and of computable finite-branching trees. However, there is no computable classification of the latter, nor of the family of computable torsion-free abelian groups of rank 1, even though these families are both closely allied with computable algebraic fields

FARS2 mutations presenting with pure spastic paraplegia and lesions of the dentate nuclei.

Mutations in FARS2, the gene encoding the mitochondrial phenylalanine-tRNA synthetase (mtPheRS), have been linked to a range of phenotypes including epileptic encephalopathy, developmental delay, and motor dysfunction. We report a 9-year-old boy with novel compound heterozygous variants of FARS2, presenting with a pure spastic paraplegia syndrome associated with bilateral signal abnormalities in the dentate nuclei. Exome sequencing identified a paternal nonsense variant (Q216X) lacking the catalytic core and anticodon-binding regions, and a maternal missense variant (P136H) possessing partial enzymatic activity. This case confirms and expands the phenotype related to FARS2 mutations with regards to clinical presentation and neuroimaging findings

Wide-Area Geolocalization with a Limited Field of View Camera in Challenging Urban Environments

Cross-view geolocalization, a supplement or replacement for GPS, localizes an agent within a search area by matching ground-view images to overhead images. Significant progress has been made assuming a panoramic ground camera. Panoramic cameras' high complexity and cost make non-panoramic cameras more widely applicable, but also more challenging since they yield less scene overlap between ground and overhead images. This paper presents Restricted FOV Wide-Area Geolocalization (ReWAG), a cross-view geolocalization approach that combines a neural network and particle filter to globally localize a mobile agent with only odometry and a non-panoramic camera. ReWAG creates pose-aware embeddings and provides a strategy to incorporate particle pose into the Siamese network, improving localization accuracy by a factor of 100 compared to a vision transformer baseline. This extended work also presents ReWAG*, which improves upon ReWAG's generalization ability in previously unseen environments. ReWAG* repeatedly converges accurately on a dataset of images we have collected in Boston with a 72 degree field of view (FOV) camera, a location and FOV that ReWAG* was not trained on.Comment: 10 pages, 16 figures. Extension of ICRA 2023 paper arXiv:2209.1185

Multi-state open robust design applied to opportunistic data reveals dynamics of wide-ranging taxa: The sperm whale case.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Boys, R. M., Oliveira, C., Perez-Jorgeo, S., Prieto, R., Steiner, L., & Silva, M. A. Multi-state open robust design applied to opportunistic data reveals dynamics of wide-ranging taxa: The sperm whale case. Ecosphere, 10(3), (2019):e02610, doi:10.1002/ecs2.2610.Capture–mark–recapture methods have been extensively used to estimate abundance, demography, and life history parameters of populations of several taxa. However, the high mobility of many species means that dedicated surveys are logistically complicated and expensive. Use of opportunistic data may be an alternative, if modeling takes into account the inevitable heterogeneity in capture probability from imperfect detection and incomplete sampling, which can produce significant bias in parameter estimates. Here, we compare covariate‐based open Jolly‐Seber models (POPAN) and multi‐state open robust design (MSORD) models to estimate demographic parameters of the sperm whale population summering in the Azores, from photo‐identification data collected opportunistically by whale‐watching operators and researchers. The structure of the MSORD also allows for extra information to be obtained, estimating temporary emigration and improving precision of estimated parameters. Estimates of survival from both POPAN and MSORD were high, constant, and very similar. The POPAN model, which partially accounted for heterogeneity in capture probabilities, estimated an unbiased super‐population of ~1470 whales, with annual abundance showing a positive trend from 351 individuals (95% CI: 234–526) in 2010 to 718 (95% CI: 477–1082) in 2015. In contrast, estimates of abundance from MSORD models that explicitly incorporated imperfect detection due to temporary emigration were less biased, more precise, and showed no trend over years, from 275 individuals (95% CI: 188–404) in 2014 to 367 (95% CI: 248–542) in 2012. The MSORD estimated short residence time and an even‐flow temporary emigration, meaning that the probability of whales emigrating from and immigrating to the area was equal. Our results illustrate how failure to account for transience and temporary emigration can lead to biased estimates and trends in abundance, compromising our ability to detect true population changes. MSORD models should improve inferences of population dynamics, especially when capture probability is low and highly variable, due to wide‐ranging behavior of individuals or to non‐standardized sampling. Therefore, these models should provide less biased estimates and more accurate assessments of uncertainty that can inform management and conservation measures.We acknowledge IFAW for providing photo‐identification data from the early period of the study (1987–1993), Biosphere Expeditions and clients of Whale Watch Azores for making data collection possible. We thank Sara Magalhães, Tiago Sá, João Medeiros, Yves Cuenot, Pablo Chevallard Navarro, and numerous volunteers that over the years helped with data collection and organization of the photo‐identification catalogue. We are deeply grateful to Gary White, Bill Kendall, Jim Hines, James Nichols, Paul Conn, and Olivier Gimenez for offering guidance and advice on CMR modeling. We thank Jonathan Gordon for his comments on an earlier version of the manuscript. We are thankful to the three anonymous reviewers for providing very helpful comments. This work was supported by Fundação para a Ciência e Tecnologia (FCT), Azores 2020 Operational Programme, and Fundo Regional da Ciência e Tecnologia (FRCT) through research projects FCT‐Exploratory project (IF/00943/2013/CP1199/CT0001), WATCH IT (Acores‐01‐0145‐FEDER‐000057), and MISTIC SEAS II (GA11.0661/2017/750679/SUB/ENV.C2) co‐funded by FEDER, COMPETE, QREN, POPH, ESF, Portuguese Ministry for Science and Education, and EU‐DG/ENV. The Azores 2020 Operational Programme is funded by the community structural funds ERDF and ESF. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013. Rebecca M Boys is supported by an Estagiar L scholarship, Cláudia Oliveira by a research assistant contract from WATCH IT and Mónica A Silva by an FCT‐Investigator contract (IF/00943/2013), and Rui Prieto by an FCT postdoctoral grant (SFRH/BPD/108007/2015). Mónica A Silva conceptualized the project, acquired funding, administered, and supervised the project. Lisa Steiner, Cláudia Oliveira, Rebecca M Boys, and Mónica A Silva involved in data curation. Rebecca M Boys, Mónica A Silva, Sergi Pérez‐Jorge, and Cláudia Oliveira involved in formal analysis, investigation, and methodology. Rebecca M Boys preparation and visualization of the data. Rebecca M Boys, Mónica A Silva, Sergi Pérez‐Jorge, Rui Prieto wrote the original draft of the manuscript. Rebecca M Boys, Mónica A Silva, Rui Prieto, Sergi Pérez‐Jorge, Cláudia Oliveira, and Lisa Steiner wrote, reviewed, and edited the manuscript

\u3cem\u3eFARS2\u3c/em\u3e Mutations Presenting with Pure Spastic Paraplegia and Lesions of the Dentate Nuclei

Mutations in FARS2, the gene encoding the mitochondrial phenylalanine‐tRNA synthetase (mtPheRS), have been linked to a range of phenotypes including epileptic encephalopathy, developmental delay, and motor dysfunction. We report a 9‐year‐old boy with novel compound heterozygous variants of FARS2, presenting with a pure spastic paraplegia syndrome associated with bilateral signal abnormalities in the dentate nuclei. Exome sequencing identified a paternal nonsense variant (Q216X) lacking the catalytic core and anticodon‐binding regions, and a maternal missense variant (P136H) possessing partial enzymatic activity. This case confirms and expands the phenotype related to FARS mutations with regards to clinical presentation and neuroimaging findings

Oxidation Alters the Architecture of the Phenylalanyl-tRNA Synthetase Editing Domain to Confer Hyperaccuracy

High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection

The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB

The polysaccharide Bep is essential for in vitro biofilm formation of the opportunistic pathogen Burkholderia cenocepacia. We found that the Burkholderia diffusible signaling factor (BDSF) quorum sensing receptor RpfR is a negative regulator of the bep gene cluster in B. cenocepacia. An rpfR mutant formed wrinkled colonies, whereas additional mutations in the bep genes or known bep regulators like berA and berB restored the wild-type smooth colony morphology. We found that there is a good correlation between intracellular c-di-GMP levels and bep expression when the c-di-GMP level is increased or decreased through ectopic expression of a diguanylate cyclase or a c-di-GMP phosphodiesterase, respectively. However, when the intracellular c-di-GMP level is changed by site directed mutagenesis of the EAL or GGDEF domain of RpfR there is no correlation between intracellular c-di-GMP levels and bep expression. Except for rpfR, deletion mutants of all 25 c-di-GMP phosphodiesterase and diguanylate cyclase genes encoded by B. cenocepacia showed no change to berA and bep gene expression. Moreover, bacterial two-hybrid assays provided evidence that RpfR and BerB physically interact and give specificity to the regulation of the bep genes. We suggest a model where RpfR binds BerB at low c-di-GMP levels to sequester this RpoN-dependent activator to an RpfR/RpfF complex. If the c-di-GMP levels rise, possibly by the enzymatic action of RpfR, BerB binds c-di-GMP and is released from the RpfR/RpfF complex and associates with RpoN to activate transcription of berA, and the BerA protein subsequently activates transcription of the bep genes

Antenatal depression, treatment with selective serotonin reuptake inhibitors, and neonatal brain structure: A propensity-matched cohort study

The aim of this propensity-matched cohort study was to evaluate the impact of prenatal SSRI exposure and a history of maternal depression on neonatal brain volumes and white matter microstructure. SSRI-exposed neonates (n = 27) were matched to children of mothers with no history of depression or SSRI use (n=54). Additionally, neonates of mothers with a history of depression, but no prenatal SSRI exposure (n=41), were matched to children of mothers with no history of depression or SSRI use (n=82). Structural magnetic resonance imaging and diffusion weighted imaging scans were acquired with a 3T Siemens Allegra scanner. Global tissue volumes were characterized using an automatic, atlas-moderated expectation maximization segmentation tool. Local differences in gray matter volumes were examined using deformation-based morphometry. Quantitative tractography was performed using an adaptation of the UNC-Utah NA-MIC DTI framework. SSRI-exposed neonates exhibited widespread changes in white matter microstructure compared to matched controls. Children exposed to a history of maternal depression but no SSRIs showed no significant differences in brain development compared to matched controls. No significant differences were found in global or regional tissue volumes. Additional research is needed to clarify whether SSRIs directly alter white matter development or whether this relationship is mediated by depressive symptoms during pregnancy