Immunoglobulin variable-region gene mutational lineage tree analysis: application to autoimmune diseases

Lineage trees have frequently been drawn to illustrate diversification, via somatic hypermutation (SHM), of immunoglobulin variable-region (IGV) genes. In order to extract more information from IGV sequences, we developed a novel mathematical method for analyzing the graphical properties of IgV gene lineage trees, allowing quantification of the differences between the dynamics of SHM and antigen-driven selection in different lymphoid tissues, species, and disease situations. Here, we investigated trees generated from published IGV sequence data from B cell clones participating in autoimmune responses in patients with Myasthenia Gravis (MG), Rheumatoid Arthritis (RA), and Sjögren's Syndrome (SS). At present, as no standards exist for cell sampling and sequence extraction methods, data obtained by different research groups from two studies of the same disease often vary considerably. Nevertheless, based on comparisons of data groups within individual studies, we show here that lineage trees from different individual patients are often similar and can be grouped together, as can trees from two different tissues in the same patient, and even from IgG- and IgA-expressing B cell clones. Additionally, lineage trees from most studies reflect the chronic character of autoimmune diseases

QuickCut Waterjet Cutter

The QuickCut Waterjet Cutter was created in 2019 as a senior design project. This is the third iteration of the waterjet cutter. The goal of this project was to create an operable CNC waterjet cutter that is able to cut 1/16” tensile specimens consisting of nonferrous metal or plastic. This machine will be utilized in the Manufacturing Laboratory at the University of Akron to provide education to interested students on the waterjet cutting process, how it operates, and industrial application of the technology. Waterjet cutting is a subtractive manufacturing process which is recognized for its specialized applications such as cutting dangerous materials or preserving heat treatment. Waterjet cutting utilizes high pressurized water with entrained garnet to cut through materials with precision and accuracy. The QuickCut Waterjet Cutter aims to bring the applications of industrial waterjet cutting operations to the smaller, tabletop scale to cut softer materials with precision. This report goes in depth on what defines an abrasive waterjet cutter, important components and the benefits of the waterjet cutting process. Detailed steps on how the newest rendition of the Quickcut Waterjet Cutter was created are covered. This includes brainstorming, design of components, design of controls, manufacturing process, as well as testing and future work to be completed

Canonical extension and canonicity via DCPO presentations

The canonical extension of a lattice is in an essential way a two-sided completion. Domain theory, on the contrary, is primarily concerned with one-sided completeness. In this paper, we show two things. Firstly, that the canonical extension of a lattice can be given an asymmetric description in two stages: a free co-directed meet completion, followed by a completion by \emph{selected} directed joins. Secondly, we show that the general techniques for dcpo presentations of dcpo algebras used in the second stage of the construction immediately give us the well-known canonicity result for bounded lattices with operators.Comment: 17 pages. Definition 5 was revised slightly, without changing any of the result

A Monte Carlo Method to Estimate Radiation Dose from Cone Beam Computed Tomography

Objectives: This study compares effective dose determination of four large field of view CBCT units (NewTom-3G, Galileos Comfort Plus, CS-9300, iCat-FLX,) using a Monte Carlo software analysis method (PCXMC) and dosimetry using anthropomorphic phantoms. Methods: Previous research provided phantom effective dose comparisons. Field-of-view and phantom positioning were duplicated in the software. Software and phantom dosimetry values were compared. Descriptive statistics, chi-square, and logistic regression, were used to analyze the data. The null-hypothesis that there is no statistically significant difference between the dosimetry values of the anthropomorphic phantom and the calculated values of the PCXMC software was tested. Results: PCXMC simulated scans produced dose values within 20% of the phantom dosimetry 48-58% of the time. Conclusions: While the software calculations are simpler to perform than phantom dosimetry, imprecise calculated results make this program less effective for CBCT dosimetry in dentistry.Master of Scienc

The coevolution of play and the cortico-cerebellar system in primates.

Primates are some of the most playful animals in the natural world, yet the reason for this remains unclear. One hypothesis posits that primates are so playful because playful activity functions to help develop the sophisticated cognitive and behavioural abilities that they are also renowned for. If this hypothesis were true, then play might be expected to have coevolved with the neural substrates underlying these abilities in primates. Here, we tested this prediction by conducting phylogenetic comparative analyses to determine whether play has coevolved with the cortico-cerebellar system, a neural system known to be involved in complex cognition and the production of complex behaviour. We used phylogenetic generalised least squares analyses to compare the relative volume of the largest constituent parts of the primate cortico-cerebellar system (prefrontal cortex, non-prefrontal heteromodal cortical association areas, and posterior cerebellar hemispheres) to the mean percentage of time budget spent in play by a sample of primate species. Using a second categorical data set on play, we also used phylogenetic analysis of covariance to test for significant differences in the volume of the components of the cortico-cerebellar system among primate species exhibiting one of three different levels of adult-adult social play. Our results suggest that, in general, a positive association exists between the amount of play exhibited and the relative size of the main components of the cortico-cerebellar system in our sample of primate species. Although the explanatory power of this study is limited by the correlational nature of its analyses and by the quantity and quality of the data currently available, this finding nevertheless lends support to the hypothesis that play functions to aid the development of cognitive and behavioural abilities in primates

Halo: Estimation and Reduction of Hallucinations in Open-Source Weak Large Language Models

Large Language Models (LLMs) have revolutionized Natural Language Processing (NLP). Although convenient for research and practical applications, open-source LLMs with fewer parameters often suffer from severe hallucinations compared to their larger counterparts. This paper focuses on measuring and reducing hallucinations in BLOOM 7B, a representative of such weaker open-source LLMs that are publicly available for research and commercial applications. We introduce HaloCheck, a lightweight BlackBox knowledge-free framework designed to quantify the severity of hallucinations in LLMs. Additionally, we explore techniques like knowledge injection and teacher-student approaches to alleviate hallucinations in low-parameter LLMs. Our experiments effectively demonstrate the reduction of hallucinations in challenging domains for these LLMs

The effect of anthropogenic noise on foraging and vigilance in zoo housed pied tamarins

The phenomenon of human-induced rapid environmental change (HIREC) is a great challenge in the modern world that presents a threat to all species. Research on the effect of anthropogenic noise on free-living wildlife is increasing but the effect of anthropogenic noise on the behaviour and welfare of captive wildlife has received limited attention, even though captive settings are full of human activity and a wide range of sounds. Moreover, studies in captivity tend to classify noise subjectively by volume according to human hearing and as part of the overall ‘visitor effect’ rather than a stressor in its own right. Research on free-living wildlife suggests that anthropogenic noise can negatively impact foraging behaviour; similar impacts in captive species could have a detrimental effect on their health and welfare if animals cannot perform functional feeding behaviours and access adequate nutrition. In the current study, we designed a forage box experiment for captive pied tamarins, a Critically Endangered callitrichid primate species that is prone to poor physical health and breeding success in captivity. Ten pairs of tamarins housed at Jersey Zoo were provided with a forage box containing cryptic (hidden) prey items (waxworms). Using a within-subjects design, tamarins were provided access to the forage box in noise and non-noise conditions of anthropogenic noise (machinery used for gardening in the zoo). Both active (foraging with the hands) and observational (looking into the forage box) foraging were significantly less frequent in the presence of anthropogenic noise; however, there was no difference in the duration of these behaviours or in foraging success. Furthermore, the presence of anthropogenic noise did not significantly affect vigilance behaviour. We found no sex differences in the effect of noise, and our results suggest that the anthropogenic noise we tested was only a minimal distractor for tamarins. However, large individual differences in foraging suggest that other factors may have a larger impact on foraging than the anthropogenic noise used in this experiment. More research into how captive animals may respond to the presence of anthropogenic noise is needed

Resistance to antibiotics of clinical relevance in the fecal microbiota of Mexican wildlife.

There are a growing number of reports of antibiotic resistance (ATBR) in bacteria living in wildlife. This is a cause for concern as ATBR in wildlife represents a potential public health threat. However, little is known about the factors that might determine the presence, abundance and dispersion of ATBR bacteria in wildlife. Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys (Alouatta palliata), spider monkeys (Ateles geoffroyi), tapirs (Tapirus bairdii) and felids (jaguars, Panthera onca; pumas, Puma concolor; jaguarundis, Puma yagouaroundi; and ocelots, Leopardus pardalis) living freely in two regions of the Mexican state of Veracruz under different degrees of human influence. Overall, our study shows that ATBR is commonplace in bacteria isolated from wildlife in southeast Mexico. Most of the resistances were towards old and naturally occurring antibiotics, but we also observed resistances of potential clinical significance. We found that proximity to humans positively affected the presence of ATBR and that ATBR was higher in terrestrial than arboreal species. We also found evidence suggesting different terrestrial and aerial routes for the transmission of ATBR between humans and wildlife. The prevalence and potential ATBR transfer mechanisms between humans and wildlife observed in this study highlight the need for further studies to identify the factors that might determine ATBR presence, abundance and distribution.The authors acknowledge the National Council of Science of Technology (CONACYT) in Mexico and the Veracruz State Government for providing partial financial support to JCA (Grant Number 108990). JCD was supported by grants from the Isaac Newton Trust and The Cambridge Humanities Research Grant Scheme. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.This is the final published version. It originally appeared in PLOS One at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0107719