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Practices for Braiding Indigenous Knowledges and Western Sciences for Research and Monitoring of Biodiversity in Canada
Get PDFThere has been a widespread effort to braid multiple knowledge systems in biodiversity research and monitoring, yet there is further need to consider how to do so. We interviewed Indigenous Peoples and representatives of 12 Indigenous communities, completed a systematic review of biodiversity studies that utilized Indigenous knowledges (IK) and Western sciences (WS) in Canada, and then braided the outcomes of the conversations and literature review to address if, when, and how IK and WS can be brought together for biodiversity research and monitoring in Canada. Overall, there was a great deal of support for, and desire to, braid IK and WS among interview participants. A suite of nine pillars and priorities was identified for doing so from participants' responses. These priorities included: (1) build and foster relationships; (2) IK should guide projects; (3) Indigenous communities should lead projects; (4) IK must be respected equally with WS; (5) embrace reciprocity (focus on people) and (6) embrace responsibility (focus on land) to the land and one another; (7) ensure equal gender and age representation; (8) intergenerational knowledge transfer is important; and (9) language revitalization is critical. The extent to which the pillars and priorities for braiding were reflected in the current literature varied, and we identified indicators that may help project leads choose what to prioritize in design to fulfill the pillars. These indicators included engagement, relevance, governance, and accessibility. The stages of projects at which IK and WS were brought together (i.e., design, data collection, analysis, reporting, and decision‐making), the roles for each IK and WS at various project stages, and the methods for IK collation and WS data collection varied extensively across the literature. This work deepens our understanding of the practices of knowledge braiding in biodiversity research and monitoring in Canada and offers a toolkit for doing so
Wind‐driven seed dispersal differentially promotes seed trapping and retention across alpine plants
Get PDFPremise: Seed dispersal can mediate species interactions between plants across life stages. Plants can physically stop seed movement (seed trapping) and prevent further dispersal following entrapment (seed retention). We therefore hypothesized seed trapping and retention rates depend on the physical attributes of interacting seeds and plants, including seed traits and plant length. Methods: For combinations of co‐occurring plant species in an alpine community, we experimentally measured seed trapping and retention potential. To measure seed trapping, we determined the rate at which seeds were unable to physically pass through vegetation without stopping after being launched at plants. To assess seed retention, we compared the rate that seeds left vegetation following entrapment across plant and seed species and by seed traits. Results: Seed trapping rates were higher for larger‐sized plants and differed among plant species but not seed species. Seed trapping and retention rates were higher for plant species with denser vegetation. Seeds with a pappus were retained less than seeds without, and we observed interactive effects between plant and seed species identity on retention rates. Conclusions: Seed trapping and retention rates are influenced by species identities and the physical attributes of plants and seeds. Because both processes can contribute to where a seed is ultimately dispersed, seed trapping and retention may mediate species co‐occurrence and further species interactions
Capturing gene–cell duality in a cat’s cradle
Get PDFSummary: CatsCradle is an R package for single-cell analysis that exploits the duality between cells and the genes they express. Our package provides tools to cluster genes, visualize relationships between them, and to explore relationships between gene clusters (programmes) and cell clusters (cell types). Availability and implementation: CatsCradle is available freely as an R Bioconductor package (https://bioconductor.org/packages/CatsCradle) and interfaces directly with Seurat (Hao et al. 2024) and SingleCellExperiment (Amezquita et al. 2020) data structures
A Rich Woman's World? Wealth and Gendered Paths to Office
Get PDFWe introduce and seek to explain a new and surprising fact about members of the US Congress: since at least the 1980s, Congresswomen have been substantially wealthier than Congressmen serving in the same party and decade. We articulate three mechanisms that could explain this gender wealth gap, and use new data on the backgrounds and families of members of Congress to evaluate each mechanism. We find no evidence that the wealth gap arises because districts likely to elect women also elect wealthier members, or because women had more lucrative pre‐Congressional careers. We do find evidence that the gap can be explained by women facing steeper challenges that wealth helps them overcome—particularly related to caregiving—and by Congresswomen's spouses earning more money than Congressmen's spouses. Our analysis sheds light on how obstacles facing ambitious women can lead to apparently counterintuitive advantages among the women who manage to succeed
Large‐Scale Psychometric Assessment and Validation of the Modified COVID‐19 Yorkshire Rehabilitation Scale Patient‐Reported Outcome Measure for Long COVID or Post‐COVID Syndrome
Get PDFThe C19‐YRS was the first condition‐specific for long COVID/post‐COVID syndrome. Although the original C19‐YRS evolved to the modified version (C19‐YRSm) based on psychometric evidence, clinical content relevance, as well as feedback from patients and healthcare professionals, it has not been validated through Rasch analysis. The study aim was to psychometrically assess and validate the C19‐YRSm using newly collected data from a large‐scale, multicenter study (LOCOMOTION). In total, 1278 patients (67% Female; mean age = 48.6, SD 12.7) digitally completed the C19‐YRSm. The psychometric properties of the C19‐YRSm Symptom Severity (SS) and Functional Disability (FD) subscales were assessed using a Rasch Measurement Theory framework, assessing for individual item model fit, targeting, internal consistency reliability, unidimensionality, local dependency (LD), response category functioning and differential item functioning (DIF) by age group, sex and ethnicity. Rasch analysis revealed robust psychometric properties of both subscales, with each demonstrating unidimensionality, appropriate response category structuring, no floor or ceiling effects, and minimal LD and DIF. Both subscales also displayed good targeting and reliability (SS: Person Separation Index (PSI) = 0.81, Cronbach's α = 0.82; FD: PSI = 0.76, Cronbach's α = 0.81). Although some minor anomalies are apparent, the modifications to the original C19‐YRS have strengthened its measurement characteristics and its clinical and conceptual relevance. Trial Registration: NCT05057260, ISRCTN1502230
Longitudinal analysis of neutralizing antibodies against SARS-CoV-1 and different SARS-CoV-2 strains in breakthrough and unvaccinated COVID-19 patients in Thailand (2021-2022)
Get PDFThe emergence of SARS-CoV-2 variants that evade immune responses poses challenges to effective prevention. We prospectively enrolled 111 COVID-19 patients in Thailand (2021-2022), who received homologous or heterologous vaccines or were unvaccinated. Plasma neutralizing antibody (nAb) levels against SARS-CoV-1 and 13 SARS-CoV-2 strains were measured using a multiplex surrogate virus neutralization test (sVNT) assay within a year. nAb levels increased in two weeks, showing strong inhibition against ancestral SARS-CoV-2 and non-omicron variants, but not against SAR-CoV-1 and lower responses to omicron variants. nAb levels declined by the day 60. Breakthrough patients with heterologous vaccines had higher nAb levels compared to other groups. nAb levels were lower in breakthrough patients with pneumonia than those with other conditions. Notably, breakthrough patients aged ≥60 showed rapid declines in antibody levels. Our findings highlight diverse immune responses influenced by immunization, age, and clinical conditions, underscoring the need for tailored vaccination strategies against evolving variants
A Cool Earth-sized Planet Candidate Transiting a Tenth Magnitude K-dwarf From K2
Get PDFThe transit method is currently one of our best means for the detection of potentially habitable “Earth-like” exoplanets. In principle, given sufficiently high photometric precision, cool Earth-sized exoplanets orbiting Sun-like stars could be discovered via single transit detections; however, this has not previously been achieved. In this work, we report a 10 hr long single transit event which occurred on the V = 10.1 K-dwarf HD 137010 during K2 Campaign 15 in 2017. This transit is comparatively shallow (225 ± 10 ppm) but is detected at high signal-to-noise thanks to the exceptionally high photometric precision achieved for the target. Our analysis of the K2 photometry, historical and new imaging observations, and archival radial velocities and astrometry strongly indicate that the event was astrophysical, occurred on-target, and can be best explained by a transiting planet candidate, which we designate HD 137010 b. The single observed transit implies a radius of 1.06−0.05+0.06R⊕ , and assuming negligible orbital eccentricity we estimate an orbital period of 355−59+200 days ( a=0.88−0.10+0.32 au), properties comparable to Earth. We project an incident flux of 0.29−0.13+0.11I⊕ , which would place HD 137010 b near the outer edge of the habitable zone. This is the first planet candidate with Earth-like radius and orbital properties transiting a Sun-like star bright enough for substantial follow-up observations
Revisiting uncertainty estimation and calibration of large language models
No full textAs large language models (LLMs) are increasingly deployed in high-stakes applications, robust uncertainty estimation is essential for ensuring the safe and trustworthy deployment of LLMs. We present the most comprehensive study to date of uncertainty estimation in LLMs, evaluating 80 models spanning open- and closed-source families, dense and Mixture-of-Experts (MoE) architectures, reasoning and nonreasoning modes, quantization variants and parameter scales from 0.6B to 671B. Focusing on three representative black-box single-pass methods, including token probability-based uncertainty (TPU), numerical verbal uncertainty (NVU), and linguistic verbal uncertainty (LVU), we systematically evaluate uncertainty calibration and selective classification using the challenging MMLU-Pro benchmark, which covers both reasoning-intensive and knowledge-based tasks. Our results show that LVU consistently outperforms TPU and NVU, offering stronger calibration and discrimination while being more interpretable. We also find that high accuracy does not imply reliable uncertainty, and that model scale, post-training, reasoning ability and quantization all influence estimation performance. Notably, LLMs exhibit better uncertainty estimates on reasoning tasks than on knowledge-heavy ones, and good calibration does not necessarily translate to effective error ranking. These findings highlight the need for multi-perspective evaluation and position LVU as a practical tool for improving the reliability of LLMs in real-world settings
Structural and spectroscopic studies of metal ions and metal clusters with small molecules
Get PDFGas-phase metal clusters and metal ion–ligand complexes exhibit a diverse array of structural motifs and size-dependent properties. These systems serve as valuable model platforms for exploring fundamental chemical bonding and reactivity at the molecular level. Detailed studies of such isolated clusters provide bottom-up insights into processes relevant to heterogeneous catalysis and materials chemistry, including but not limited to molecular activation at metal centres. This thesis presents experimental and computational studies on the structure and physical properties of different cluster systems of interest, as well as development work that has been completed to produce gas-phase metal clusters.Following a general introduction to the field and methods section which details the techniques that have been used to complete the studies, the experimental sections are presented in three parts. Part A presents infrared photodissociation (IRPD) studies on metal ion-ligand complexes; with Chapter 3 presenting work on cationic nitrosyl complexes, [M(NO)n] +, of Group 9 elements (Co, Rh, Ir), and Chapter 4 focusing on platinum and platinum oxide nitrosyl complexes, [PtOx(NO)n] + (x = 0, 1). In Chapter 3, spectroscopic and computational evidence suggested that (NO)2 dimer moieties form when nitric oxide (NO) molecules bind non-covalently with other molecules that are bound directly to the metal cation centre. These dimer moieties only form following the first coordination shell for these complexes being filled with nitric oxide molecules, with the number of molecules in the first shell being dependent on the metal. In Chapter 4, it was shown that up to six ligands could bind to the platinum centre in the first coordination shell before dimer moieties form. With the oxygen-rich platinum complexes, evidence of the formation of an N2O3 moiety, formed from an NO and an NO2 molecule, is presented; this is illustrated by the appearance of intense spectral features between 1900 − 2000 cm−1 in the IRPD spectra which are consistent with previous studies on [NO2(NO)n] + clusters.Part B describes infrared studies on metal clusters using free-electron laser (FEL) light. Chapter 5 describes photoionisation studies of neutral tantalum and tantalum oxide clusters, TanOx, performed using the FELICE free-electron laser at the HFML-FELIX facility in Nijmegen, The Netherlands. Preliminary calculations on cationic Ta clusters, and their reactions with nitrogen oxides (NO/N2O) are shown; with dissociative binding being predicted for all cluster sizes. In the experiment, size-dependent thermionic emission was observed with the neutral clusters, with odd-even alternations in signal intensity being caused by the clusters swapping between having open- and closed-shell electronic configurations. Ta-O stretches in the range 650 − 750 cm−1 are also observed and are in close agreement with previous studies on cationic tantalum oxide clusters. The structures of the tantalum oxide clusters that contribute towards the experimental spectra are determined using quantum chemical calculations; with the dioxide clusters shown to contain two distinct oxygen atoms, rather than molecularly bound O2 molecules.Part C focuses on in-house development work that has been completed to build and test a new cluster source. Chapter 6 presents designs, simulations, and experimental studies on an experimental setup used to characterise a new bimetallic laser ablation cluster source. Photoionisation of nitric oxide was used to determine the shape of the gas pulse generated by the new source when different configurations and conditions were used; the shape of the pulse was then compared with predictions made using a simple kinetic theory model. Subsequently, neutral and cationic gold clusters, Au0/+ n , were generated and studied using the custom built time-of-flight mass spectrometer. The source will be used in the future on existing experiments within the Mackenzie Group to investigate the role of cluster size and composition on reactivity with small molecules
Perturbations of whole-brain model reveal critical areas related to relapse of early psychosis
Get PDFOvercoming an initial psychotic episode does not always lead to recovery; relapses and subsequent psychotic episodes may happen afterward. Even if the characterization of psychotic disorders can be related to alterations in brain connectivity, clear identification of the brain areas for relapse is missing. Here, we leverage on whole-brain modeling linking anatomical structural information with functional activity as measured by MRI in 196 participants. Patients were classified into Stage II (first episode), IIIa (incomplete remission), IIIb (remission followed by one relapse), and IIIc (remission followed by several relapses), depending on the course of psychosis up to the time of the brain scan. From these data, a low-dimensional manifold reduction of the brain dynamics was obtained using deep learning variational autoencoders in which the different stages are represented, and a classification model can be trained to distinguish them. Then, a dimensionality analysis was performed to find the optimal dimension that allows the distinction between first episode and relapsing cases with high accuracy. Finally, perturbations were introduced in the model to reveal the brain regions associated with the absence of relapse, which could help predict which brain regions to target during therapy and assist the treatment of patients suffering from psychotic disorders