Miracle-dz/UniFAR-FTUs huggingface dataset:
Climatic evolution of the central equatorial Pacific since the Last Glacial Maximum

This paper investigates paleoceanographic changes at a central equatorial Pacific site (6°40′N, 177°28′W) since the last glacial maximum using planktic foraminifera assemblages, together with the oxygen isotope (δ18O) and Mg/Ca compositions of three species (Globigerinoides sacculifer, Pulleniatina obliquiloculata, and Globorotalia tumida) that dwell in the mixed layer, upper thermocline, and lower thermocline, respectively. While the Mg/Ca‐derived temperatures of the mixed layer and lower thermocline varied within a narrow range from 18 ka onward, the upper thermocline temperature increased by as much as 3°C during the last deglaciation (18–12 ka) with a simultaneous decrease of δ18O. These changes are best explained by an enhanced mixing of the upper ocean and a reduced habitat depth separation between P. obliquiloculata and G. sacculifer during the 18–12 ka interval. The planktic foraminifera assemblage during the same period resembles modern composition at subtropical central Pacific sites that are strongly influenced by the northeasterly Trades and North Equatorial Current (NEC). We suggest that the study site, presently under the control of the Intertropical Convergence Zone (ITCZ)‐North Equatorial Countercurrent, had been influenced by the northeasterly Trades and NEC during the 18–12 ka interval. This interpretation is consistent with previous documentation of a more southerly location of the ITCZ during two Northern Hemisphere cooling events; the Heinrich Stadial 1 and the Younger Dryas, and implies that the mean annual position of the ITCZ was located south of the study site, by at least 2° of latitude.
Spider assemblage (Arachnida: Araneae) associated with canopies of Vochysia divergens (Vochysiaceae) in the northern region of the Brazilian Pantanal

This study describes the composition and temporal variation of the spider assemblage (Arachnida: Araneae) associated with canopies of Vochysia divergens Pohl. (Vochysiaceae) in the northern region of the Brazilian Pantanal. Three V. divergens plants were sampled in 2004, at each seasonal period of the northern Pantanal (high water, receding water, dry season and rising water), using thermonebulization of the canopies with insecticide, totaling 396 m2 of sampled canopies. Analysis of abundance and richness of spider families were based on Non-Metric Multidimensional Scaling (NMDS) and Variance Analysis (ANOVA and MANOVA). A total of 7,193 spiders were collected (6,330 immatures; 88.0%; 863 adults, 12.0%) distributed in 30 families. Araneidae (1,676 individuals), Anyphaenidae (1,631 individuals), Salticidae (1,542 individuals) and Pisauridae (906 individuals), were predominant, representing 80.0% of the sample. Ten different guilds were registered: aerial hunters, orb-weavers, nocturnal aerial runners and diurnal space web weavers dominated, sharing most ecological niches. The spider assemblage is affected by changes in the habitat structure, especially by the seasonal hydrological regime and variations in the phenology of V. divergens . The assemblage is composed of different groups of spiders. The dominant taxa and behavioral guilds differ in the different seasonal periods. Spiders were more abundant during the dry and rising water seasons, most likely reflecting a greater supply of potential prey, associated with new foliage and flowering at the canopy. The displacement of soil dwelling spiders to the trunks and canopies before and during the seasonal floods can change the structure and composition of the canopy assemblages. Oonopidae, Gnaphosidae and Caponiidae, were more frequent during the rising and high water seasons, which indicates that these taxa use the canopies of V. divergens as a refuge during the seasonal flooding in the Pantanal.
Water table management for water quality improvement

WATER quality in streams and groundwater is among the most critical environmental concerns in the United States and elsewhere. The U.S. Department of Agriculture's Agricultural Research Service (ARS), U.S. Geological Survey (USGS), Experiment Station Committee on Organization and Policy (ESCOP), and other institutions have research and extension priorities directed toward protecting surface water and groundwater resources. In the mid-1980s, ESCOP commissioned a task force to establish a groundwater quality initiative for the entire United States ( 13 ). In the report of that task force, groundwater quality issues were separated by region: West, South, North Central, and Northeast. In all areas, the top research and extension priorities included the evaluation of the source, fate, remedial treatment, and impacts of agricultural pesticides and nitrates. Agriculture is considered a major contributor to water quality problems (4, 5, 25, 35, 38, 41, 43, 51). Improved surface and subsurface drainage has been associated with water quality problems in streams and lakes (2, 9, 18, 28, 36). Research indicates that nitrogen losses increased due to drainage of relatively heavy agricultural soils in Ohio, but sediment and other nutrient losses decreased (42). Studies on a Commerce silt loam in southern Louisiana showed that …
Biomass‐burning particle measurements: Characteristic composition and chemical processing

[1] The NOAA Lockheed Orion WP-3D aircraft intercepted a forest fire plume over Utah on 19 May 2002 during the Intercontinental Transport and Chemical Transformation (ITCT) mission. Large enhancements in acetonitrile (CH3CN), carbon monoxide (CO) and particle number were measured during the fire plume interception. In the 100 s plume crossing, the Particle Analysis by Laser Mass Spectrometry (PALMS) instrument acquired 202 positive mass spectra from ionizing single particles in the 0.2–5 μm size range. These particles contained carbon, potassium, organics, and ammonium ions. No pure soot particles were sampled directly from the plume. By characterizing these particle mass spectra, a qualitative biomass-burning particle signature was developed that was then used to identify biomass-burning particles throughout ITCT. The analysis was extended to identify biomass-burning particles in four other missions, without the benefit of gas-phase biomass-burning tracers. During ITCT, approximately 33% of the particles sampled in the North American troposphere and 37% of the particles transported from Asia, not influenced by North American sources, were identified as biomass-burning particles. During the WB-57 Aerosol Mission (WAM), Atmospheric Chemistry of Combustion Emissions near the Tropopause (ACCENT) and ACCENT 2000 missions, 7% of stratospheric particles were identified as biomass-burning particles. During the Cirrus Regional Study of Tropical Anvils and Cirrus Layers – Florida Area Cirrus Experiment (CRYSTAL-FACE) this percentage increased to 52% because the regional stratosphere was strongly affected by an active fire season.
Chapter 20 Identifying linkages between rates and distributions of malaria, water-born diseases and influenza with climate variability and climate change in Vietnam

Over the last decades, there has been an increasing interest among scientists on the linkage between population health and climate and environmental factors, as well as health impacts of climate change and climate variability. Numerous studies have been done and substantial results achieved, but mostly in the developed countries, and not much quantitative evidence or assessment of the impacts at national and local levels has been provided for developing countries.
Long-term dynamics of adaptation to a warming environment is dependent on historical background

Climate change is leading to biodiversity decline at an unprecedented pace. Evolutionary responses may be crucial for organisms’ ability to cope with prolonged effects of climate change. It is thus fundamental to understand the dynamics of adaptation to warming environments in order to predict and mitigate the impacts of climate change on biodiversity. In particular, addressing how reproductive success evolves in deteriorating environments is extremely relevant, as this trait is more likely constrained at lower temperatures than upper physiological thermal limits. Experimental evolution udner a warming environment can illucidate the potential of populations to respond to rapid environmental changes. The few studies following such framework lack analysis of long-term response. We here focus on the long-term adaptive response of Drosophila subobscura populations evolving under a warming environemnt, analysing the reproductive success after 39 and 52 generations of thermal evolution. We found that long-term adaptation to higher temperatures can occur but the pace of such response is slow and likely dependent on low rates of environmental change. Furthermore, we observed that the magnitude of the response is relatively mild. In addition, the evolutionary dynamics differs between populations of distinct geographical origin, with the higher latitude populations only showing an adaptive response to the warming environment in a more advanced generation. This study reinforces the need for long-term evolution experiments to fully reveal the potential for thermal response. It also highlight that the scrutiny of several populations in this context is needed for a measure of variation within a species. Accounting for these sources of variation - both temporal and spatial - will allow for more robust assessments of climate change responses.
Division of labour underlies efficient colony defence in a clonal ant

The ecological success of social insects is often credited to the division of labour (DOL), yet empirical evidence directly linking DOL to colony efficiency is rare, in part because variation in DOL between colonies is often confounded by variation in colony traits (e.g., group size, genetic diversity) that can independently affect group efficiency. Here, we measure the link between DOL and efficiency in a crucial task, colony defence, in a social insect that affords precise experimental control over relevant individual and colony traits, the clonal raider ant (Ooceraea biroi). We find that DOL in defence behaviour emerges within colonies of near-identical workers, and is consistently associated with enhanced defence efficiency. This positive relationship is robust to variation in the social environment (group size and the presence and type of brood), indicating that the extent of behavioural variation between members of a social group can serve as a key indicator of group efficiency.
Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, can be seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea and likely reflects the importance of genome organization to gene regulatory landscapes. Here, we report a very different pattern of genome evolution in Bryozoa, an understudied yet ecologically important phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five bryozoans. We infer the ancestral bryozoan genome organization and identify multiple ancient chromosome fusions followed by gene mixing, leading to the near-complete loss of bilaterian linkage groups. A second wave of rearrangements, including chromosome fission, occurred independently in two bryozoan classes, further shuffling bryozoan genomes. We also discover nine chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional yet highly debated Lophophorata hypothesis. Finally, we show that chromosome fusion and fission processes led to the separation of bryozoan Hox clusters. These findings demonstrate how the canonical bilaterian genome structure has been lost across an entire phylum, suggest a modification to gene regulatory landscapes, and provide a powerful source of phylogenetic information.
Sub-optimal activity of gut microbiome functional pathways increases the odds of Irritable Bowel Syndrome in a large adult human population

We describe a data-driven computational approach for quantifying the microbial functional pathways in the gastrointestinal tract, based on an analysis of stool metatranscriptomic data within a large and diverse adult human population (n = 66,545). We develop a suite of eight gut microbial pathway scores, each of which represents the activity of a well-defined set of microbial functional features relevant to known gut biochemical activities. We use a normative approach within a subpopulation (n = 9,350) to determine the optimal and non-optimal levels of activity of these functional pathway scores. We hypothesize that non-optimal scores are associated with irritable bowel syndrome (IBS) and its subtypes (i.e., IBS-Constipation, IBS-Diarrhea, IBS-Mixed Type). We show that non-optimal scores within these microbial functional pathways are associated with higher odds of IBS or its subtypes within an independent cohort (n = 57,195). Given these findings, these gut pathway scores can be used to deliver meaningful health insights from simple, non-invasive stool samples, as potential molecular endpoints to measure the efficacy of practical interventions, and develop data-driven personalized algorithms aimed at providing nutritional recommendations, diagnostics, and treatments for IBS as well as related conditions. Graphical Abstract
Diverse transcriptome reprogramming trajectories underlie quantitative disease resistance at the species level

Quantitative disease resistance (QDR) is an immune response limiting the damage caused by pathogen infection in plants. It involves the transcriptomic reprogramming of numerous genes each having a weak contribution to the plant immunity phenotype. Despite QDR widespread and broad-spectrum nature, the evolution of the underlying transcriptome reprogramming remains largely uncharacterized. Here, we analyzed global gene expression in response to the necrotrophic fungus Sclerotinia sclerotiorum in 23 Arabidopsis thaliana accessions of diverse origin and contrasted QDR phenotype. Over a half of the species pan-transcriptome displayed local responses to S. sclerotiorum, with global reprogramming patterns incongruent with accessions phylogeny. Due to frequent small-amplitude variations, only ∼11% responsive genes were common to all accessions. They formed protein-protein interactions networks densely connecting both old and recent genes. Clustering of accessions based on global regulation patterns identified four subsets unrelated to QDR phenotypes, highlighting at least four distinct paths towards regulatory evolution of QDR at the species level. We identified WRKY and MYB-related DNA binding sites enriched in the 5’-regulatory regions of core and subset-specific responsive genes respectively. Our findings show that the evolution of QDR involves distinct gene reprogramming trajectories at the species level, associated with contrasted patterns of cis-regulatory variation.
Exploring anterior thalamus functional connectivity with cortical regions in prospective memory with ultra-high-field fMRI

Prospective memory (PM), or memory for future intentions, engages particular cortical regions. Lesion studies also implicate the thalamus, with PM deterioration following thalamic stroke. Neuroimaging, anatomical, and lesion studies suggest the anterior nuclei of the thalamus (ANT) in particular are involved in episodic memory, with electrophysiological studies suggesting an active role in selecting neural assemblies underlying particular memory traces. Here we hypothesized that the ANT are also engaged in realizing prospectively-encoded intentions, and that this engagement is detectable using ultra-high field strength functional MRI. Using a within-subject design, participants (N = 14; age 20-35 years) performed an n-back working memory task as the ongoing task with two cognitive loads, each with and without a PM component, during 7-Tesla functional MRI. Seed-to-voxel whole brain functional connectivity analyses were performed to establish whether including a PM component in an ongoing task results in greater connectivity between ANT and cortical regions known to be engaged in PM. Repeated measures ANOVAs were applied to behavioral and connectivity measures, with the factors Task Type (with PM or not) and N-Back (2-back or 3-back). Response accuracy was greater and reaction times faster without the PM component, and accuracy was higher in the 2-than 3-back condition. We observed a main effect of Task Type on connectivity with an ANT seed, with greater ANT–DLPFC (dorsolateral prefrontal cortex) and ANT–STG (superior temporal gyrus) connectivity when including a PM component. Post hoc testing based on a significant interaction showed greater ANT–DLPFC connectivity (p-FWE = .007) when PM was included with the low and ANT–STG connectivity (p-FWE = .019) with the high cognitive load ongoing task. These locations showed no main effect of N-Back. Connectivity based on a dorsomedial nucleus of the thalamus (DMNT) seed did not differ according to Task Type at these locations. Enhanced connectivity between the ANT and the DLPFC, a brain region with an established role in strategic monitoring for PM cues, arose with a low cognitive load ongoing task that enabled monitoring. This pattern was absent on directly increasing the cognitive load of the ongoing task without PM, suggesting specificity for PM. Greater ANT–STG connectivity on PM inclusion in the higher cognitive load ongoing task condition fits with reports of STG activation on PM through spontaneous retrieval. Differing connectivity based on a DMNT seed suggests ANT specificity. The findings fit with a coordinating role for the ANT in prospective remembering.
Functional Characterisation of the ATOH1 Molecular Subtype Indicates a Pro-Metastatic Role in Small Cell Lung Cancer

Molecular subtypes of Small Cell Lung Cancer (SCLC) have been described based on differential expression of transcription factors (TFs) ASCL1, NEUROD1, POU2F3 and immune-related genes. We previously reported an additional subtype based on expression of the neurogenic TF ATOH1 within our SCLC Circulating tumour cell- Derived eXplant (CDX) model biobank. Here we show that ATOH1 protein was detected in 7/81 preclinical models and 16/102 clinical samples of SCLC. In CDX models, ATOH1 directly regulated neurogenesis and differentiation programs consistent with roles in normal tissues. In ex vivo cultures of ATOH1-positive CDX, ATOH1 was required for cell survival. In vivo, ATOH1 depletion slowed tumour growth and suppressed liver metastasis. Our data validate ATOH1 as a bona fide oncogenic driver of SCLC with tumour cell survival and pro-metastatic functions. Further investigation to explore ATOH1 driven vulnerabilities for targeted treatment with predictive biomarkers is warranted.
Transinfection of Wolbachia wAlbB into Culex quinquefasciatus mosquitoes does not alter vector competence for Hawaiian avian malaria (Plasmodium relictum GRW4)

Avian malaria is expanding upslope with warmer temperatures and driving multiple species of Hawaiian birds towards extinction. Methods to reduce malaria transmission are urgently needed to prevent further declines. Releasing Wolbachia-infected incompatible male mosquitoes suppress mosquito populations and releasing Wolbachia-infected female mosquitoes could reduce pathogen transmission if the Wolbachia strain reduced vector competence. We cleared Culex quinquefasciatus of their natural Wolbachia pipientis wPip infection and transinfected them with Wolbachia wAlbB isolated from Aedes albopictus. We show that wAlbB infection was transmitted transovarially, and demonstrate cytoplasmic incompatibility with wild-type mosquitoes infected with wPip from Oahu and Maui, Hawaii. We measured vector competence for avian malaria, Plasmodium relictum, lineage GRW4, of seven mosquito lines (two with wAlbB; three with natural wPip infection, and two cleared of Wolbachia infection) by allowing them to feed on canaries infected with recently collected field isolates of Hawaiian P. relictum. We tested 73 groups (Ntotal = 1176) of mosquitoes for P. relictum infection in abdomens and disseminated (thorax) infections 6-14 days after feeding across a range of parasitemias from 0.028% to 2.49%, and a smaller subset of salivary glands. We found no measurable effect of Wolbachia on any endpoint, but strong effects of parasitemia, days post feeding, and mosquito strain on both abdomen infection prevalence and disseminated infection prevalence. These results suggest that releasing male wAlbB-infected C. quinquefasciatus mosquitoes could suppress wPip-infected mosquito populations, but would have little positive or negative impact on mosquito vector competence for P. relictum if wAlbB became established in local mosquito populations. More broadly, the lack of Wolbachia effects on vector competence we observed highlights the variable impacts of both native and transfected Wolbachia infections in mosquitoes.
Sex-specific fear acquisition following early life stress is linked to amygdala glutamate metabolism

Early life stress (ELS) adversely affects physiological and behavioral outcomes, increasing the vulnerability to stress-related disorders, such as post-traumatic stress disorder (PTSD). PTSD prevalence is significantly higher in women and is partially mediated by genetic risk variants. Understanding how sex influences the interaction of PTSD risk genes, such as FKBP5, with trauma-related behaviors is crucial for uncovering PTSD’s neurobiological pathways. The development of in-depth behavioral analysis tools using unsupervised behavioral classification is thereby a crucial tool to increase the understanding of the behavioral outcomes related to stress-induced fear memory formation. The current study investigates the sex-specific effects of ELS exposure by using the limited bedding and nesting (LBN) paradigm. The LBN exposure disrupted different facets of the hypothalamic-pituitary-adrenal (HPA) axis in a sex-specific manner directly after stress and at adult age. Moreover, freezing was altered by LBN exposure in both the acquisition and the retrieval of fear in a sex-dependent manner. Unsupervised behavioral analysis revealed a higher active fear response after LBN exposure during fear acquisition in females, but not in males. The regulation of the HPA axis is closely intertwined with cellular metabolism and core regulatory cascades. To investigate the impact of LBN exposure on tissue-specific metabolism, a metabolomic pathway analysis in the basolateral amygdala revealed a specific sex- and stress-dependent effect on purine, pyrimidine, and glutamate metabolism. The present study highlights the intricate interplay between metabolic pathways and the neurobiological substrates implicated in fear memory formation and stress regulation. Overall, these findings highlight the importance of considering sex-specific metabolic alterations in understanding the neurobiological mechanisms underlying stress-related disorders and offer potential avenues for targeted interventions.