Miracle-dz/UniFAR-FTUs huggingface dataset:
Restoring grasslands in southern Ontario sandpits : plant and soil food web responses to arbuscular mycorrhizal fungal inoculum, biochar, and municipal compost

Habitat destruction and land use change are among the anthropogenic influences affecting many ecosystems. Sandpit mining often restricts grassland plant restoration efforts due to the abioticially stressed mine substrate, a lack of viable plant symbionts, and disrupted multi–trophic interactions in soil food webs. Recently excavated sandpits can be ameliorated with soil amendments and arbuscular mycorrhizal fungal inoculum to address these degraded substrate conditions, potentially improving plant performance and accelerating soil food web development. This dissertation describes the results of a multi–year grassland restoration project established in southern Ontario that optimized industrial–scale grassland restoration protocol in post–extraction sandpits. This research tested the effect of soil amendment rate (municipal compost, biochar) and arbuscular mycorrhizal (AM) fungal inoculum (Rhizophagus irregularis) in a grassland plant plug trial and a seed application trial. In the plant plug trial, the multi–year effects of the experimental treatments on plant growth, AM fungal colonization of roots, soil microbial biomass (i.e. bacteria and fungi) and soil animal abundance (i.e. nematodes, Collembola, and mites) were explored over two growing seasons. In the plant plug trial, 20 T ha−1 (tons hectare−1) of compost mixed with a low rate of biochar (10 T ha−1) yielded the largest positive effect on total plant biomass, microbial community biomass, and soil animal abundance after two growing seasons. AM fungal inoculation did not influence total plant biomass or soil food web development during this trial. In the seed application trial, the multi–year effects of increasing rates of compost and biochar (0 T ha−1 to 40 T ha−1) were explored for total plant cover over three growing seasons. AM fungal inoculation combined with high rates of compost (20 T ha−1 and 40 T ha−1) and biochar (20 T ha−1 and 40 T ha−1) resulted in the highest plant cover over three growing seasons compared to controls. Our results indicate that: (1) co–amending mine substrates with compost, biochar, and AM fungal inoculum are practical land management tools that improve grassland plant growth while increasing soil food web development, (2) AM fungal inoculum increases plant cover when applying seed with high rates of compost + biochar, and (3) amending post–mine substrates with biochar as a solitary amendment may increase biotic stress in the sandpit environment during restoration. I suggest that restoration practitioners emphasize soil community development in tandem with plant community growth when restoring sandpits to maximize restoration success.
Transitioning to a Commercial Dashboarding System: Socio-Technical Observations and Opportunities

Many long-established, traditional manufacturing businesses are becoming more digital and data-driven to improve their production. These companies are embracing visual analytics in these transitions through their adoption of commercial dashboarding systems. Although a number of studies have looked at the technical challenges of adopting these systems, very few have focused on the socio-technical issues that arise. In this paper, we report on the results of an interview study with 17 participants working in a range of roles at a long-established, traditional manufacturing company as they adopted Microsoft Power BI. The results highlight a number of socio-technical challenges the employees faced, including difficulties in training, using and creating dashboards, and transitioning to a modern digital company. Based on these results, we propose a number of opportunities for both companies and visualization researchers to improve these difficult transitions, as well as opportunities for rethinking how we design dashboarding systems for real-world use.
Microbial carbonates: the geological record of calcified bacterial–algal mats and biofilms

Deposits produced by microbial growth and metabolism have been important components of carbonate sediments since the Archaean. Geologically best known in seas and lakes, microbial carbonates are also important at the present day in fluviatile, spring, cave and soil environments. The principal organisms involved are bacteria, particularly cyanobacteria, small algae and fungi, that participate in the growth of microbial biofilms and mats. Grain‐trapping is locally important, but the key process is precipitation, producing reefal accumulations of calcified microbes and enhancing mat accretion and preservation. Various metabolic processes, such as photosynthetic uptake of CO2 and/or HCO3– by cyanobacteria, and ammonification, denitrification and sulphate reduction by other bacteria, can increase alkalinity and stimulate carbonate precipitation. Extracellular polymeric substances, widely produced by microbes for attachment and protection, are important in providing nucleation sites and facilitating sediment trapping.
Variantes genéticas implicadas en la susceptibilidad del osteosarcoma pediátrico

El osteosarcoma (OS) es el c? ncer ? seo primario m? s com? n que se da principalmente en ni? os, adolescentes y adultos j? venes. El hecho de que el OS se produzca a una edad temprana sugiere que existe un fuerte componente gen? tico en su origen. Diversos estudios han sugerido que la susceptibilidad a desarrollar OS se debe a peque? as variantes comunes de baja penetrancia, como los SNPs. La implicaci? n de las variantes gen? ticas comunes en la susceptibilidad a desarrollar c? ncer ya se ha demostrado en diversos estudios.
Association Between Triglycerides and Risk of Dementia in Community-Dwelling Older Adults

Background and Objectives It has been suggested that higher triglyceride levels were associated with a lower risk of Alzheimer disease. This study aimed to examine the association of triglycerides with dementia and cognition change in community-dwelling older adults. Methods This prospective longitudinal study used data from the Aspirin in Reducing Events in the Elderly (ASPREE) randomized trial of adults aged 65 years or older without dementia or previous cardiovascular events at enrollment. The main outcome was incident dementia. Other outcomes included changes in composite cognition and domain-specific cognition (global cognition, memory, language and executive function, and psychomotor speed). The association between baseline triglycerides and dementia risk was estimated using Cox proportional hazard models adjusting for relevant risk factors. Linear mixed models were used to investigate cognitive change. The analysis was repeated in a subcohort of participants with available APOE-ε4 genetic data with additional adjustment for APOE-ε4 carrier status and an external cohort (UK Biobank) with similar selection criteria applied. Results This study included 18,294 ASPREE participants and 68,200 UK Biobank participants (mean age: 75.1 and 66.9 years; female: 56.3% and 52.7%; median [interquartile range] triglyceride: 106 [80–142] mg/dL and 139 [101–193] mg/dL), with dementia recorded in 823 and 2,778 individuals over a median follow-up of 6.4 and 12.5 years, respectively. Higher triglyceride levels were associated with lower dementia risk in the entire ASPREE cohort (hazard ratio [HR] with doubling of triglyceride: 0.82, 95% CI 0.72–0.94). Findings were similar in the subcohort of participants with APOE-ε4 genetic data (n = 13,976) and in the UK Biobank cohort (HR was 0.82 and 0.83, respectively, all p ≤ 0.01). Higher triglycerides were also associated with slower decline in composite cognition and memory over time (p ≤ 0.05). Discussion Older adults with higher triglyceride levels within the normal to high-normal range had a lower dementia risk and slower cognitive decline over time compared with individuals with lower triglyceride levels. Higher triglyceride levels may be reflective of better overall health and/or lifestyle behaviors that would protect against dementia development. Future studies are warranted to investigate whether specific components within the total circulating pool of plasma triglycerides may promote better cognitive function, with the hope of informing the development of new preventive strategies.
CD57 T cells associated with immunosenescence in adults living with HIV or AIDS

Despite the advancement of human immunodeficiency virus (HIV)‐related discoveries, new HIV infections still persist. With the advent of antiretroviral therapy, prognosis has migrated from acute to chronic HIV infection and inflammation, with the possibility of increased immune aging. We aimed to assess such immunosenescence by analysing CD27 and CD57 expression on the surface of T cells. This cross‐sectional study was conducted between 2017 and 2018 on people living with HIV/AIDS (PLWHA) who attended an outpatient clinic of the Infectious Diseases Service of a university hospital and a geriatric reference service in Brazil. A standardized interview was conducted, and venous peripheral blood was collected for flow cytometry analysis. To assess immunosenescence, we compared CD27 and CD57 expression on the surface of T cells between adult and elderly individuals without HIV and adult PLWHA. All results for cells in terminal senescent stages in adult PLWHA more closely resembled those of elderly than adult participants without HIV (p > 0.05). The presence of CD27+ cells did not differ statistically among the three study groups when comparing immunological responders (IR) and immunological non‐responders (INR); for the entire CD4+ T‐cell population (including CD4 + CD8+ and CD4 + CD8– cells), the median count (25–75th) was higher in the INR (79.6%) than the IR (68.0%) group. HIV‐infected individuals possessed a higher number of T lymphocytes with a molecular phenotype associated with immunosenescence, a lower proportion of T cells in the early stages of senescence (median 25–75th: 27.0%), and a higher proportion of T cells in the intermediate and final stages of senescence (median 25–75th: 16.1%) than adults without HIV (median 25–75th: 42.0% and 18.4%, respectively). Considering the higher number of senescent T lymphocytes, we observed in our PLWHA population—especially in the INR group (CD8CD57+ cells: 39.3% INR vs. 23.4% IR; CD4CD57+ cells: 44.0% INR vs. 27.7% IR)—may indicate a similar mortality risk phenotype from immune‐preventable diseases
Occurrence of a melange along the Malakand pass north of Dargai, northern Pakistan

An ophiolitic melange has been identified along the Malakand pass north of Dargai. The melange is characterized by exotic blocks of talc-carbonate, talc actinolite schist, greenschist and plagio-granite in a matrix of graphitic schist of the Saidu formation. It has an northeast southwest extension. The melange is considered as imbrication of the MMT zone along the Kishora thrust.
Regional seismic variations in the inner core under the North Pacific

An asymmetry between a nearly isotropic, faster 'eastern' hemisphere and an anisotropic, slower 'western' hemisphere in Earth's inner core has been revealed by previous seismic studies. However, it remains unclear if division of the inner core into just two hemispheres is too simplistic. Here, we carry out regional-scale tomography using a new body wave data set to study the hemisphere boundary region beneath the northern and central Pacific Ocean and North America. If anisotropy is not considered, then a hemispherical pattern seems to be present in the study region, though the hemisphere boundary appears to be irregular. However, once the presence of anisotropy is permitted we find that this region cannot be simply separated into an anisotropic western hemisphere and an isotropic eastern hemisphere; instead the strength of the anisotropy varies regionally. The global hemispherical pattern is not observed here, instead the strongest anisotropy is observed in the centre and south west of the study region. Some of the strongest anisotropy appears to be in the -eastern' inner core, while part of the inner core assumed to be in the western hemisphere shows weaker anisotropy. Thus, this part of the inner core displays complex variations in anisotropy which differ from a simple hemispherical division. We suggest that a long-lived global heterogeneity, such as uneven heat flow through the core-mantle boundary over a period of hundreds of millions of years, may be responsible for the observed pattern of inner core anisotropy.
Systematic discovery of gene-environment interactions underlying the human plasma proteome in UK Biobank

Understanding how gene-environment interactions (GEIs) influence the circulating proteome could aid in biomarker discovery and validation. The presence of GEIs can be inferred from single nucleotide polymorphisms that associate with phenotypic variability - termed variance quantitative trait loci (vQTLs). Here, vQTL association studies are performed on plasma levels of 1,468 proteins in 53,752 UK Biobank participants. A set of 683 independent vQTLs are identified across 571 proteins, all of which are newly discovered. They include 65 variants that lack conventional additive main effects on protein levels. Over 1,400 GEIs are identified between 142 proteins and 101 lifestyle and metabolic exposures. GEI analyses uncover biological mechanisms that explain why 13/65 vQTL-only sites lack corresponding main effects. Stratified analyses also highlight how age, sex and genotype can interact to modify relationships between biomarkers and health-related traits. This study establishes the most comprehensive database yet of vQTLs and GEIs for the human proteome.
Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection

Background. Acute kidney injury (AKI) is common in hospitalized patients with SARS-CoV2 infection despite vaccination and leads to long-term kidney dysfunction. However, peripheral blood molecular signatures in AKI from COVID-19 and their association with long-term kidney dysfunction are yet unexplored. Methods. In patients hospitalized with SARS-CoV2, we performed bulk RNA sequencing using peripheral blood mononuclear cells (PBMCs). We applied linear models accounting for technical and biological variability on RNA-Seq data accounting for false discovery rate (FDR) and compared the functional enrichment and pathway results to a historical sepsis-AKI cohort. Finally, we evaluated the association of these signatures with long-term trends in kidney function. Results. Of 283 patients, 106 had AKI. After adjustment for sex, age, mechanical ventilation, and chronic kidney disease (CKD), we identified 2635 significant differential gene expressions at FDR<0.05. Top canonical pathways were EIF2 signaling, oxidative phosphorylation, mTOR signaling, and Th17 signaling, indicating mitochondrial dysfunction and endoplasmic reticulum (ER) stress. Comparison with sepsis associated AKI showed considerable overlap of key pathways (48.14%). Using follow-up estimated glomerular filtration rate (eGFR) measurements from 115 patients, we found that 164/2635 (6.2%) of the significantly differentiated genes were associated with overall decrease in long-term kidney function. The strongest associations were autophagy, renal impairment via fibrosis and cardiac structure/function. Conclusions. We show that AKI in SARS-CoV2 is a multifactorial process with mitochondrial dysfunction driven by ER stress whereas long-term kidney function decline is associated with cardiac structure and function, and immune dysregulation. Functional overlap with sepsis-AKI also highlights common signatures indicating generalizability in therapeutic approaches.
GENIPOSIDE IMPROVES CLP-INDUCED SEPSIS MODEL PROGNOSIS BY UPREGULATING PPARγ TO MODULATE MONOCYTE PHENOTYPE AND CYTOKINE NETWORK

ABSTRACT Background: We explored the efficacy and main biological mechanism of geniposide intervention in sepsis. Methods: A sepsis model was established in male BALB/c mice through cecal ligation and puncture (CLP). Different doses of geniposide (20 or 40 mg/kg) were administered intravenously at 0 and/or 24 h after CLP surgery. The survival rate of different groups was observed. In addition, the expression levels of CD16 and major histocompatibility complex class II in monocytes were assessed using flow cytometry. The concentrations of TNF-α, IL-1β, IL-6, and IL-10 in the serum were measured by ELISA. We also observed the biological effects of geniposide on CD16 and MHC-II expression levels in RAW264.7 cells, as well as the secretion of TNF-α, IL-1β, IL-6, and IL-10 in the LPS-induced RAW264.7 cell model. The PPARγ levels were determined using western blot analysis. Results: Intravenous administration of 40 mg/kg of geniposide at 0 h after CLP significantly improved the survival outcomes in the septic mouse model, with no significant benefits from low dosing (20 mg/kg) or delayed administration (24 h). The effective dose of geniposide significantly decreased the serum cytokine TNF-α, IL-1β, IL-6, and IL-10 concentrations in septic mice (P < 0.05). Notably, in vitro assays showed that geniposide specifically increased the IL-10 level. Geniposide significantly reduced the CD16 expression (P < 0.05) and increased MHC-II expression in monocytes (P < 0.05). In addition, geniposide elevated the PPARγ level in monocytes (P < 0.05). Conclusions: High-dose early-stage geniposide administration significantly improved the survival rate in a CLP mouse sepsis model by modulating the monocyte phenotype and regulating the cytokine network (IL-6/IL-10 levels). The pharmacological mechanism of geniposide action might be exerted primarily through PPARγ upregulation.
Patient and caregiver experiences of living with dementia in Tanzania

Introduction: Tanzania is a low-income country with an increasing prevalence of dementia, which provides challenges for the existing healthcare system. People with dementia often don’t receive a formal diagnosis, and with a lack of formal healthcare, are often predominantly supported by family relatives. There are very few published data relating to lived experiences of people with dementia in Tanzania. This study aimed to understand people with dementia, and their caregivers’ experiences of living with dementia in Tanzania and the perceived needs of people with dementia. Methods: Qualitative, semi-structured interviews were conducted with 14 people with dementia and 12 caregivers in Moshi, Tanzania. Interviews were audio-recorded, translated, transcribed and analysed using a Framework Analysis approach. Results: Three sub-themes were identified within data describing the experience of ‘Living with Dementia in Tanzania’: ‘Deteriorations in Health’, ‘Challenges to living with Dementia in Tanzanian Culture’, and ‘Lack of Support’: people with dementia faced challenges due to social isolation, stigmatisation, and lack of caregiver knowledge on how best to provide support. Collectively, these impacted on both the physical and mental health of people with dementia. Misconceptions about dementia aetiology related to age, stresses of daily life and other co-morbidities. People with dementia were motivated to access treatment, exhibiting pluralistic health-seeking behaviours. There was an overall preference for non-pharmacological interventions over medication, with high levels of trust in medical professional opinions. Conclusions: Living with dementia in Tanzania is influenced by both cultural and religious factors. More work is needed to target supplementary healthcare (with efforts to promote accessibility), support for caregivers and public health education about dementia to overcome existent misconceptions and stigma.
One hundred and six years of change in a Sonoran Desert plant community: Impact of climate anomalies and trends in species sensitivities.

A major restriction in predicting plant community response to future climate change is a lack of long-term data needed to properly assess species and community response to climate and identify a baseline to detect climate anomalies. Here, we use a 106-year dataset on a Sonoran Desert plant community to test the role of extreme temperature and precipitation anomalies on community dynamics at the decadal scale and over time. Additionally, we test the climate sensitivity of 39 desert plant species and whether sensitivity is associated with growth form, longevity, geographic range, or local dominance. We find that desert plant communities have shifted directionally over the 106 years, but the climate had little influence on this directional change primarily due to non-linear shifts in precipitation anomalies. Decadal-scale climate had the largest impact on species richness, species relative density, and total plant cover, explaining up to 26, 45, and 55% of the variance in each, respectively. Drought and the interaction between the frequency of freeze events and above-average summer precipitation were among the most influential climate factors. Increased drought frequency and wetter periods with frequent freeze events led to larger reductions in total plant cover, species richness, and the relative densities of dominant subshrubs Ambrosia deltoidea and Encelia farinosa. Over 80% of the tested species were sensitive to climate, where sensitivity was related to a species' local dominance but not longevity, geographic range, or growth form. Dominant species appear to exhibit demographic buffering. They were more sensitive to drought but better able to take advantage of hot and wet conditions than subdominant species. Overall, our results suggest that while decadal-scale climate variation substantially impacts these desert plant communities, directional change in temperature over the last century has had little impact due to the relative importance of precipitation and drought. With projections of increased drought in this region, we may see reductions in total vegetation cover and species richness due to the loss of dominant species, possibly through a breakdown in their ability to demographically buffer climatic variation, potentially changing community dynamics through a change in facilitative and competitive processes. This article is protected by copyright. All rights reserved.
WHY DO MEYER SETS DIFFRACT?

Abstract. Given a weak model setfpW q in a locally compact Abelian group we construct a relatively dense set of common Bragg peaks for all subsets Λ Ď fpW q with non-trivial Bragg spectrum. Next, for each ε ą 0 we construct a relatively dense set Pε which are common ε-norm almost periods for the diffraction, pure point, absolutely continuous and singular continuous spectrum, respectively, for all subsets Λ Ď fpW q. We use the Fibonacci model set to illustrate these phenomena, and extend the results to arbitrary weighted Dirac combs with weak Meyer set support. We complete the paper by discussing some extensions of the existence of the generalized Eberlein decomposition for measures with weak Meyer set support.