Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Tillage and Crop Rotation on Aggregate-Associated Carbon in Two Oxisols

In temperate regions, the adoption of no-tillage (NT) often stimulates the sequestration of soil C and N and improves soil structural stability. The aim of this study was to investigate if NT has similar impacts on the stability of water-stable aggregates and C and N stabilization in two Oxisols (Typic Haplorthox) under different crop rotations. Slaking-resistant aggregates were isolated by wet sieving and analyzed for C and N concentrations at two agricultural experiment sites (Passo Fundo and Londrina) in southern Brazil. At both sites, the total organic C and N in the 0- to 5-cm depth interval, decreased in order native vegetation (NV) > NT > conventional tillage (CT). The mean weight diameter (MWD) of the aggregates was on average 0.5 mm greater under NT compared with CT, and was also greater (approximately 0.2 mm) under more diverse rotations, which included a leguminous green-manure crop, in comparison with continuous wheat (Triticam aestivum)-soybean (Glycine Max L.). The aggregate-size distribution was dominated (60-90%) by macroaggregates (> 250 mu m). At both sites, CT decreased the proportion of the largest macroaggregate class (> 2000 mu m) by approximately 10% in comparison with NT management, and there was a corresponding increase in the proportion of the 53- to 250-mu m aggregate class. In the 0- to 5-cm soil layer of both sites, the C and N concentrations were significantly higher in the macroaggregates of the NT than of the CT systems. The lack of differences in C, N content, and ON ratio across aggregate-size classes indicated that these soils dominated by 1:1 clays and Fe/Al oxides do not express an aggregate hierarchy and that an increase in aggregation does not explain the increase in C and N under NT. In conclusion, CT decreased aggregation similarly in Oxisols as in temperate soils, but this decrease does not explain the loss of C and N because the tight feedback between soil organic matter (SOM) and aggregate stability (i.e., SOM being a major binding agent) observed for temperate soils was not found for Oxisols.
Exosomal circ-0020887 and circ-0009590 as novel biomarkers for the diagnosis and prediction of short-term adverse cardiovascular outcomes in STEMI patients

Abstract This study attempted to identify exosomal circular RNAs (circRNAs) as diagnostic and prognostic biomarkers for patients with ST-segment elevation myocardial infarction (STEMI). The differentially expressed exosomal circRNAs (DEECs) were screened from microarray dataset (GSE160717 and GSE197137) and RNA-Seq dataset (GSE208194), and the expression levels of DEECs in patients with STEMI were validated using reverse transcription and quantitative real-time PCR. The diagnostic value of DEECs was assessed using receiver operating characteristic curves. The major adverse cardiovascular event (MACE)-free 1-year survival rate was evaluated using the Kaplan–Meier method, and the factors affecting prognosis were determined using Cox regression model analysis. Results showed that four DEECs were screened including exo-circ-0001490, exo-circ-0020887, exo-circ-0009590, and exo-circ-0055440, and only upregulated exo-circ-0020887 and exo-circ-0009590 expression was validated in patients with STEMI. The exo-circ-0020887 and exo-circ-0009590 expression was positively correlated with hs-CRP, LDL-C, cTnI, and CK-MB. The exo-circ-0020887 and exo-circ-0009590 showed good diagnostic efficacy to distinguish STEMI patients from healthy controls (area under the curves: 0.85 and 0.80). STEMI patients with high levels of exo-circ-0020887 and exo-circ-0009590 had lower MACE-free 1-year survival rate, and exo-circ-0020887 and exo-circ-0009590 expression was independent risk factors for adverse prognosis. In summary, upregulation of plasma exo-circ-0020887 and exo-circ-0009590 might act as potential biomarkers for the diagnosis and prediction of short-term adverse cardiovascular outcomes in patients with STEMI.
Optimum nutrition and nitrogen saturation in Scots pine stands

Long-term field experiments are described, in which nitrogen and other plant nutrients were added regularly to young Scots pine stands at two sites in Sweden, Lisselbo (1969-1988) and Norrliden (1971-1989; some treatments still in progress). A main aim was to establish a range of needle nitrogen concentration levels, as stable as possible, and to study the effects of these and of other factors (other added nutrients, soil acidity changes, irrigation) on tree growth and tree nutrient status. The results confirmed previous experience that nitrogen supply normally is a growth-limiting factor in boreal forest, but showed that regular nitrogen additions can induce boron and magnesium deficiency, and low internal concentrations in the trees, e.g. of potassium and phosphorus. Other aspects of ecosystem functioning at varied nitrogen supply-biomass production, nutrient balances for several elements; vegetation changes, soil acidity changes, nitrification, studied by ourselves or by cooperating research groups-are reviewed. The importance of long-term field experiments in the study of urgent environmental problems, such as nitrogen saturation and soil acidification, is discussed.
Structure and Plant Species Dominance in North Queensland Wet Sclerophyll Forests

The wet sclerophyll forests of north Queensland were mapped for Vegetation Type from aerial photographs taken in 1990-94. These forests occur to the west of the crest of the Great Dividing Range, where altitudes exceed 500m, between latitudes 16.13 - 19.05 S (percentage degrees) i.e. approx. 450km in length. The Vegetation Types form bands orientated north-south, along the western flank of the Range. The bands reflect the decreasing moisture regime with declining altitude in the rainshadow of the Range. This entire ecotone is usually less than 20km in width. Nine segments of this ecotone were selected for groundtruthing. The segments accounted for 26% of the total area. Each segment extended from rainforest, near the crest of the Range, westwards through six types of wet sclerophyll forest to dry, Eucalyptus woodland. Ground surveys recorded physical features, dominant plants and vegetation cover and structure on 3,224 plots of dimensions 20_20m. Tree and herb species showed a marked response to the rainfall/altitude gradient but shrub species were relatively insensitive. Abundance and frequency measures for the commonest species are recorded by Vegetation Type and confirm the vegetation classification based on aerial photos. Eucalyptus grandis was dominant in the overstorey and virtually confined to the most mesic part of the ecotone, which covered 8% of the area. E. resinifera was not dominant in, but was largely restricted to, the next band, which covered 36% of the area. E. acmenoides and E. crebra were defining species for the driest band of forest before the tree canopy opened up into woodland. Other common tree species were more widespread but nonetheless showed significant peaks in particular bands. Size structure is presented for populations of the major tree species and demonstrates that the smallest size classes of most Eucalyptus species are suppressed where rainforest has established. Rainforest establishment also suppresses grasses, at first in favour of sedges and at a later stage even they disappear. Rainforest invasion was restricted to E. grandis (80%) and E. resinifera forest types and had occurred on a significantly higher percentage of granitic substrate than on basaltic soil. If these invaded areas progress to mature rainforest the overall survival of wet sclerophyll biota in north Queensland will be endangered. These data and maps establish a baseline against which future changes can be measured.
Cue-specific neuronal ensembles span intermittent rate coding of working memory

Persistent, memorandum-specific neuronal spiking activity has long been hypothesized to underlie working memory. However, emerging evidence suggests a possible role for ‘activity-silent’ synaptic mechanisms. This issue remains controversial because evidence for either view has largely depended on datasets that fail to capture single-trial population dynamics or on indirect measures of neuronal spiking. We addressed this by examining the dynamics of mnemonic information on single trials obtained from large, local populations of prefrontal neurons recorded simultaneously in monkeys performing a working memory task. We show that mnemonic information does not persist in the spiking activity of prefrontal neurons, but instead alternates between ‘On’ and ‘Off’ periods during memory delays. At the level of single neurons, Off periods are driven by a coordinated loss of selectivity for memoranda and a return of firing rates to baseline levels. Further exploiting the large-scale recordings, we asked whether the functional connectivity among large neuronal ensembles depended on information held in working memory. We show that mnemonic information is available in the pattern of ensemble connectivity during the memory delay in both On and Off periods of neuronal activity. Intermittent epochs of memoranda-specific spiking therefore coexist with activity-silent mechanisms to span memory delays.
Biomarker discovery in progressive supranuclear palsy from human cerebrospinal fluid using mass spectrometry-based proteomics

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder that is often misdiagnosed as Parkinson’s Disease (PD) because of shared symptoms. PSP is characterized by the accumulation of tau protein in specific brain regions, which results in loss of balance, gaze impairment, and dementia. Diagnosing PSP is often challenging, and there’s a significant demand for reliable biomarkers. However, existing biomarkers, including tau protein and neurofilament light chain (NfL) levels in cerebrospinal fluid (CSF), show inconsistencies in distinguishing PSP from other neurodegenerative disorders. To overcome these limitations, we conducted a comprehensive proteome analysis for CSF samples from 40 PSP, 40 PD, and healthy controls (HC) using the tandem mass tag-based quantification method, identifying 3,653 unique proteins. Our statistical analysis identified 190, 152, and 247 differentially expressed proteins when comparing PSP vs. HC, PSP vs. PD, and PSP against both PD and HC, respectively. Gene set enrichment analysis and interactome analysis conducted with the differentially expressed proteins in PSP CSF indicated that most of them were implicated in cell adhesion, cholesterol metabolism, and glycan biosynthesis. Cell-type enrichment analysis revealed that neuronally-derived proteins were predominant among the differentially expressed proteins. Potential biomarker classification performance showed that ATP6AP2 (reduced in PSP) had the highest AUC (0.922), followed by NEFM, EFEMP2, LAMP2, CHST12, FAT2, B4GALT1, LCAT, CBLN3, FSTL5, ATP6AP1, and GGH. This is the first large-scale mass spectrometry-based proteome analysis to discover CSF PSP biomarkers differentiating from both controls and PD, thereby laying a foundation for further development and validation.
RNA structure modulates Cas13 activity and enables mismatch detection

The RNA-targeting CRISPR nuclease Cas13 has emerged as a powerful tool for applications ranging from nucleic acid detection to transcriptome engineering and RNA imaging1–6. Cas13 is activated by the hybridization of a CRISPR RNA (crRNA) to a complementary single-stranded RNA (ssRNA) protospacer in a target RNA1,7. Though Cas13 is not activated by double-stranded RNA (dsRNA) in vitro, it paradoxically demonstrates robust RNA targeting in environments where the vast majority of RNAs are highly structured2,8. Understanding Cas13’s mechanism of binding and activation will be key to improving its ability to detect and perturb RNA; however, the mechanism by which Cas13 binds structured RNAs remains unknown9. Here, we systematically probe the mechanism of LwaCas13a activation in response to RNA structure perturbations using a massively multiplexed screen. We find that there are two distinct sequence-independent modes by which secondary structure affects Cas13 activity: structure in the protospacer region competes with the crRNA and can be disrupted via a strand-displacement mechanism, while structure in the region 3’ to the protospacer has an allosteric inhibitory effect. We leverage the kinetic nature of the strand displacement process to improve Cas13-based RNA detection, enhancing mismatch discrimination by up to 50-fold and enabling sequence-agnostic mutation identification at low (<1%) allele frequencies. Our work sets a new standard for CRISPR-based nucleic acid detection and will enable intelligent and secondary-structure-guided target selection while also expanding the range of RNAs available for targeting with Cas13.
Rapid evolution of pesticide resistance via adaptation and interspecific introgression in a major North American crop pest

Insect crop pests threaten global food security. This threat is amplified through the spread of non-native species and the evolution of pesticide resistance, which can be introduced to a population though de novo mutation or gene flow. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has rapidly evolved resistance to several pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid resistance gene CYP337B3 to South American H. zea via introgression. To understand whether this contributes to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites in the US. First, we report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4Mbp region containing CYP337B3. Second, we show that the remarkable dispersal ability of H. zea results in a panmictic North American population. Third, we detect signatures of selection in non-admixed H. zea, identifying a selective sweep at a second pesticide resistance locus with a similar name: CYP333B3. We estimate that its derived allele conferred a ∼4.9% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Our results show that pesticide resistance in H. zea evolved rapidly and recently via two independent mechanisms: interspecific introgression and rapid intraspecific adaptation.
Heterologous booster with a novel formulation containing glycosylated trimeric S protein is effective against Omicron

In this study, we evaluated the efficacy of a heterologous three-dose vaccination schedule against the Omicron BA.1 SARS-CoV-2 variant infection using a mouse intranasal challenge model. The vaccination schedules tested in this study consisted of a primary series of 2 doses covered by two commercial vaccines: an mRNA-based vaccine (mRNA1273) or a non-replicative vector-based vaccine (AZD1222/ChAdOx1, hereafter referred to as AZD1222). These were followed by a heterologous booster dose using one of the two vaccine candidates previously designed by us: one containing the glycosylated and trimeric spike protein (S) from the ancestral virus (SW-Vac 2μg), and the other from the Delta variant of SARS-CoV-2 (SD-Vac 2μg), both formulated with Alhydrogel as an adjuvant. For comparison purposes, homologous three-dose schedules of the commercial vaccines were used. The mRNA-based vaccine, whether used in heterologous or homologous schedules, demonstrated the best performance, significantly increasing both humoral and cellular immune responses. In contrast, for the schedules that included the AZD1222 vaccine as the primary series, the heterologous schemes showed superior immunological outcomes compared to the homologous 3-dose AZD1222 regimen. For these schemes no differences were observed in the immune response obtained when SW-Vac 2μg or SD-Vac 2μg were used as a booster dose. Neutralizing antibody levels against Omicron BA.1 were low, especially for the schedules using AZD1222. However, a robust Th1 profile, known to be crucial for protection, was observed, particularly for the heterologous schemes that included AZD1222. All the tested schedules were capable of inducing populations of CD4 T effector, memory, and follicular helper T lymphocytes. It is important to highlight that all the evaluated schedules demonstrated a satisfactory safety profile and induced multiple immunological markers of protection. Although the levels of these markers were different among the tested schedules, they appear to complement each other in conferring protection against intranasal challenge with Omicron BA.1 in K18-hACE2 mice. In summary, the results highlight the potential of using the S protein (either ancestral Wuhan or Delta variant)-based vaccine formulation as heterologous boosters in the management of COVID-19, particularly for certain commercial vaccines currently in use.
Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
Beyond human-likeness: Socialness is more influential when attributing mental states to robots

We sought to replicate and expand previous work showing that the more human-like a robot appears, the more willing people are to attribute mind-like capabilities and socially engage with it. Forty-two participants played games against a human, a humanoid robot, a mechanoid robot, and a computer algorithm while undergoing functional neuroimaging. Replicating previous studies, we confirmed that the more human-like the agent, the more participants attributed a mind to them. However, exploratory analyses revealed that beyond humanness, the perceived socialness of an agent appeared to be as important, if not more so, for mind attribution. Our findings suggest that top-down knowledge cues are just as important, if not more so, than bottom-up stimulus cues when exploring mind attribution in non-human agents. While further work is now required to test this hypothesis directly, these preliminary findings hold important implications for robotic design and to understand and test the flexibility of human social cognition when people engage with artificial agents.
Mitochondrial background can explain variable costs of immune deployment

Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet, immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology), or to a sterile control, and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation between lifespan and the proportion of time cybrids spent moving while alive. Our results suggests that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host-pathogen interactions.
A comparative approach for selecting orthologous candidate genes underlying signal in genome-wide association studies across multiple species

Advances in quantitative genetics have enabled researchers to identify genomic regions associated with changes in phenotype. However, genomic regions can contain hundreds to thousands of genes, and progressing from genomic regions to candidate genes is still challenging. In genome-wide association studies (GWAS) measuring elemental accumulation (ionomic) traits, a mere 5% of loci are associated with a known ionomic gene - indicating that many causal genes are still unknown. To select candidates for the remaining 95% of loci, we developed a method to identify conserved genes underlying GWAS loci in multiple species. For 19 ionomic traits, we identified 14,336 candidates across Arabidopsis, soybean, rice, maize, and sorghum. We calculated the likelihood of candidates with random permutations of the data and determined that most of the top 10% of candidates were orthologous genes linked to GWAS loci across all five species. The candidate list also includes orthologous genes with previously established ionomic functions in Arabidopsis and rice. Our methods highlight the conserved nature of ionomic genetic regulators and enable the identification of previously unknown ionomic genes. Author summary Identifying the genes contributing to changes in a given trait is challenging. Many genes can be near the region of interest, but proximity does not always translate to causality. We use other methods to narrow our focus to the genes most likely involved in our trait of interest before confirming their involvement through confirmation experiments. However, these other methods are often time, labor, and resource-consuming. We developed an approach to narrow these gene lists before these laborious methods are required. Through testing with genetic markers for elemental (i.e., calcium, iron, zinc) uptake, we found that comparing markers across multiple species for nearby evolutionarily conserved genes is a successful approach. We’ve produced a list of candidate genes likely to be involved in elemental uptake traits, including previously known elemental uptake genes and genes whose potential elemental uptake function has yet to be observed. Some of these genes would not have been considered according to the significance threshold within a single GWAS, but combining comparable datasets across species has collectively boosted their signal. Methods like our approach are useful for reducing candidate lists to conserve resources spent in functional characterization experiments and encouraging the discovery of new functional roles of these genes.