Miracle-dz/UniFAR-FTUs huggingface dataset:
Relative importance of bacterivorous mixotrophs in an estuary-coast environment

Mixotrophic eukaryotes are important bacterivores in oligotrophic open oceans, but their significance as grazers in more nutrient-rich waters is less clear. Here we investigated the bacterivory partition between mixotrophs and heterotrophs in a productive, estuary-influenced coastal region in East China Sea. We found ubiquitous, actively feeding phytoplankton populations and taxa with mixotrophic potential, by identifying ingestion of fluorescent prey surrogate and analyzing community 18S rRNA gene amplicons. Potential and active mixotrophs accounted for 10-63% of total eukaryotic community and 17-69% of bacterivores observed, respectively, contributing 6-48% of estimated in situ bacterivory. The much higher mixotroph fitness outside of the turbid plume were potentially driven by increased light and decreased nutrients availability. Our results suggest that, although heterotrophs dominated overall in situ bacterivory, mixotrophs were abundant and important bacterivores in this low-latitude mesotrophic coastal region. Scientific Significance Statement Mixotrophy, the combing of photosynthetic and phagotrophic nutrition, can dramatically increase primary production and alter material movements in aquatic food webs. Understanding the distribution and fitness of phagotrophic mixotrophs in a range of habitats are therefore critical to properly understand the biogeochemical cycles of the ocean. We developed a robust method to estimate active mixotrophs in situ and demonstrate rapid shifts of bacterivory partition between mixotrophs and heterotrophs across an estuary-coast environment in East China Sea. Our results help fill the knowledge gap of mixotroph niches in mesotrophic coastal environments that are impacted by riverine discharge, shedding light on relationships among mixotrophy, light and nutrient conditions.
The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chronic Trypanosoma brucei infection

The meningeal space is a critical brain structure providing immunosurveillance for the central nervous system, but the impact of infections on the meningeal immune landscape is far from being fully understood. The extracellular protozoan parasite Trypanosoma brucei, which causes Human African Trypanosomiasis (HAT) or sleeping sickness, accumulates in the meningeal spaces, ultimately inducing severe meningitis and resulting in death if left untreated. Thus, sleeping sickness represents an attractive model to study immunological dynamics in the meninges during infection. Here, by combining single cell transcriptomics and mass cytometry by time of flight (CyTOF) with in vivo interventions, we found that chronic T. brucei infection triggers the development of ectopic lymphoid aggregates (ELAs) in the murine meninges. These infection-induced ELAs were defined by the presence of ER-TR7+ fibroblastic reticular cells, CD21/35+ follicular dendritic cells, CXCR5+ PD1+ T follicular helper-like phenotype, GL7+ CD95+ GC-like B cells, and plasmablasts/plasma cells. Furthermore, the B cells found in the infected meninges produced high-affinity autoantibodies able to recognise mouse brain antigens, in a process dependent on LTβ signalling. A mid-throughput screening identified several host factors recognised by these autoantibodies, including myelin basic protein (MBP), coinciding with cortical demyelination and brain pathology. In humans, we identified the presence of autoreactive IgG antibodies in the cerebrospinal fluid of second stage HAT patients that recognised human brain lysates and MBP, consistent with our findings in experimental infections. Lastly, we found that the pathological B cell responses we observed in the meninges required the presence of T. brucei in the CNS, as suramin treatment before the onset of the CNS stage prevented the accumulation of GL7+ CD95+ GC-like B cells and brain-specific autoantibody deposition. Taken together, our data provide evidence that the meningeal immune response during chronic T. brucei infection results in the acquisition of lymphoid tissue-like properties, broadening our understanding of meningeal immunity in the context of chronic infections. These findings have wider implications for understanding the mechanisms underlying the formation ELAs during chronic inflammation resulting in autoimmunity in mice and humans, as observed in other autoimmune neurodegenerative disorders, including neuropsychiatric lupus and multiple sclerosis.
Impact of whole-genome duplications on structural variant evolution in the plant genus Cochlearia

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genus Cochlearia (Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome for Cochlearia, we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.
Evaluation of miniature temperature‐loggers to monitor snowpack evolution at mountain permafrost sites, northwestern Canada

A technique to monitor snowpack development using miniature temperature‐loggers mounted in a vertical array is evaluated from nearly 100 site‐years of measurements in northwestern Canada. The method shows good agreement between interpreted values and actual snow depths checked during site visits. Inferred snowpack build‐up and ablation follow the patterns recorded at nearby climatological stations while absolute amounts and the duration of snow cover vary with elevation and vegetation type. Interpretation of snowpack evolution was possible at 93 per cent of the monitoring sites, a success rate that is judged to be acceptable given the low costs of the technique and the difficulty of obtaining the same information through other methods. Copyright © 2008 John Wiley & Sons, Ltd.
MALDI-IM-MS Imaging of Brain Sterols and Lipids in a Mouse Model of Smith-Lemli-Opitz Syndrome

Smith-Lemli-Opitz syndrome (SLOS) is a neurodevelopmental disorder caused by genetic mutations in the DHCR7 gene, encoding the enzyme 3β-hydroxysterol-Δ7-reductase (DHCR7) that catalyzes the last step of cholesterol synthesis. The resulting deficiency in cholesterol and accumulation of its precursor, 7-dehydrocholesterol (7-DHC), have a profound impact on brain development, which manifests as developmental delay, cognitive impairment, and behavioral deficits. To understand how the brain regions are differentially affected by the defective Dhcr7, we aim to map the regional distribution of sterols and other lipids in neonatal brains from a Dhcr7-KO mouse model of SLOS, using mass spectrometry imaging (MSI). MSI enables spatial localization of biomolecules in situ on the surface of a tissue section, which is particularly useful for mapping the changes that occur within a metabolic disorder such as SLOS, and in an anatomically complex organ such as the brain. In this work, using MALDI-ion mobility (IM)-MSI, we successfully determined the regional distribution of features that correspond to cholesterol, 7-DHC/desmosterol, and the precursor of desmosterol, 7-dehydrodesmosterol, in WT and Dhcr7-KO mice. Interestingly, we also observed m/z values that match the major oxysterol metabolites of 7-DHC (DHCEO and hydroxy-7-DHC), which displayed similar patterns as 7-DHC. We then identified brain lipids using m/z and CCS at the Lipid Species-level and curated a database of MALDI-IM-MS-derived lipid CCS values. Subsequent statistical analysis of regions-of-interest allowed us to identify differentially expressed lipids between Dhcr7-KO and WT brains, which could contribute to defects in myelination, neurogenesis, neuroinflammation, and learning and memory in SLOS.
Learning patterns of HIV-1 co-resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning

The ability to predict HIV-1 resistance to broadly neutralizing antibodies (bnAbs) will increase bnAb therapeutic benefits. Machine learning is a powerful approach for such prediction. One challenge is that some HIV-1 subtypes in currently available training datasets are underrepresented, which likely affects models’ generalizability across subtypes. A second challenge is that combinations of bnAbs are required to avoid the inevitable resistance to a single bnAb, and computationally determining optimal combinations of bnAbs is an unsolved problem. Recently, machine learning models trained using resistance outcomes for multiple antibodies at once, a strategy called multi-task learning (MTL), have been shown to achieve better performance in several cases than previous approaches. We develop a new model and show that, beyond the boost in performance, MTL also helps address the previous two challenges. Specifically, we demonstrate empirically that MTL can mitigate bias from underrepresented subtypes, and that MTL allows the model to learn patterns of co-resistance between antibodies, thus providing tools to predict antibodies’ epitopes and to potentially select optimal bnAb combinations. Our analyses, publicly available at https://github.com/iaime/LBUM, can be adapted to other infectious diseases that are treated with antibody therapy.
Title: Origin of hexagonal metric of grid cells in navigating spaces

To achieve the computational goal of navigating both natural and mental spaces, the brain adopts a hexagonal metric of grid cells in the entorhinal cortex (ERC) to chart the spaces. However, little is known about how and why the hexagonal metric emerges. Here we designed an object matching task where participants adjusted two parts of object variants to match their prototype in fMRI scanner. Unbeknownst to the participants, the object variants were arranged on a ring centering on the prototype in an object space constructed by the object parts. When the participants navigated from a location in the ring to the center in the space, we observed hexagonal signals in the ERC, and more importantly, a spatial rhythm of 3Hz in the hippocampus (HPC). Accordingly, we built a computational model depicting the spatial rhythm of 3Hz as scaffolds to transform discrete spatial locations into structured states of cognitive map that allows continuous updates of location estimates with each movement made. The formal proof shows that to support the cognitive map in the HPC, the spatial input from the ERC must be in a hexagonal pattern. To further examine the biological plausibility of the model, we built various forms of neural networks in their simplest architecture to transform locations in space
Observed and Computed M2 Tidal Currents in the North Sea

Abstract M2 tidal elevations and currents have been computed using a three-dimensional hydrodynamic numerical model of the northwest European shelf. These have been compared with observational data from tide gages and current meter rigs moored in different positions in the North Sea. The observed and computed current ellipse parameters (semi-major and semi-minor axes, axis orientation and sense of rotation) are tabulated and compared, and found to be in good agreement with each other. An analysis of amplitude errors derived from computed and observed M2 tidal elevations shows a marked difference in the distribution of phase errors, as derived, on the one hand, from the present three-dimensional model and, on the other hand, from an earlier two-dimensional model covering the same region.
Detection of infrasonic pulses from thunderclouds

Acoustic data obtained from thunderstorm observations during 1975 near Socorro, New Mexico, and during 1976 at J. F. Kennedy Space Center, Florida, exhibited single, infrasonic pulses superimposed on the thunder signals arriving from the cloud in each of several thunder records. Only the Socorro data have been quantitatively analysed thus far. These data show infrasonic pulses with periods of about 0.5 sec and amplitudes of about 0.1 N/m². We argue that these pulses were not generated by lightning channel heating. The pulse waveform is characterized by an initial compression followed by a rarefaction. Acoustic source reconstruction place the origins of these pulses in the cloud within essentially the same volume of space as the horizontal portions of the lightning channels. This volume is presumably the storage region for the charge participating in the lightning events. If the pulses are electrostatic in origin as predicted by Dessler [1973], then the data indicate a rapid (0.5 sec) intensification of the field prior to discharge.
Prograde, peak, and retrograde P–T paths from aluminium in orthopyroxene: High‐temperature contact metamorphism in the aureole of the Makhavinekh Lake Pluton, Nain Plutonic Suite, Labrador

Static heating during intrusion of the Makhavinekh Lake Pluton (MLP) caused replacement of garnet in the adjacent country rocks (Tasiuyak Gneiss) by coronal assemblages of orthopyroxene + cordierite. Thermometry based on Al solubility in orthopyroxene, applied to relict garnet and neighbouring orthopyroxene, preserves a temperature gradient from 700 to 900 °C at distances between 5750 and 20 m from the intrusion, reaffirming the robustness of this thermometry technique. Intracrystalline and intergranular variations of Al zoning in orthopyroxene are well‐preserved, suggesting that little diffusional modification of Al growth zoning occurred. Maximum Al2O3 in orthopyroxene ranges from c. 2.0 wt% at 5750 m from the intrusion to a maximum of 4.3 wt% at the contact. Individual orthopyroxene grains show decreasing Al from core to rim in samples < 500 m from the intrusion, while those at greater distances show an increase from core to rim. These features are interpreted with the aid of numerical models for conductive heat flow in the aureole. Coronas in samples close to the intrusion grew at high temperatures and along T‐t paths dominated by cooling, so maximum Al content in orthopyroxene in these samples occurs in the cores of grains that grew during the earliest stages of garnet consumption. In contrast, the corona‐forming reactions in rocks further from the contact proceeded along prograde heating paths, so maximum Al content in orthopyroxene occurs in the rims of grains that grew during the final stages of garnet consumption. These results document the ability of Al‐in‐orthopyroxene thermometry to preserve a detailed record of thermal histories in contact‐metamorphic granulites; they suggest that similar intracrystalline and intergranular variations of Al zoning in orthopyroxene in regional granulites may also preserve portions of both the prograde and peak‐T evolution.
Giant trilobites and trilobite clusters from the Ordovician of Portugal

Large quarrying surfaces of roofi ng slate in the Arouca Geopark (northern Portugal), formed under oxygen-depleted conditions, have yielded a unique Ordovician fossil lagerstatte that reveals new information on the social behavior of trilobites. It provides several of the world’s largest trilobite specimens (some reaching 70 cm), showing evidence of possible polar gigantism in six different species, as well as numerous examples of monotaxic and polytaxic size-segregated autochthonous trilobite clusters, some of which contain as many as 1000 specimens. These reveal a very diverse social behavior, which includes temporary refuge from predation and synchronous molting and reproduction, demonstrated for the fi rst time in fi contemporary families of three different trilobite orders from a single formation.
EXTENSIONAL EVOLUTION OF THE GULF OF MEXICO BASIN AND THE DEPOSITION OF TERTIARY EVAPORITES

Current interpretations of the evolution of the Gulf of Mexico Basin are guided by the critical assumption that all the salt in this huge basin is Jurassic and time‐equivalent to the Louann salt of the interior evaporite basins of Texas, Louisiana and Mississippi. This assumption forces the interpretation that extensive salt sheets that now reside within Eocene to Plio‐Pleistocene stratigraphic levels are allochthonous, having been emplaced by several episodes of Jurassic salt piercement and horizontal flow as shallow salt sills or sub‐aqueous salt glaciers during Tertiary sedimentation.
Greenhouse Gas Emissions from Dairy Farms

The reduction of greenhouse gas emissions is becoming more important world-wide. Although research suggests that farmland can serve as a sink for carbon, agriculture is also an important source of emissions. As a sector, agriculture is reported to be the greatest contributor of nitrous oxide and the third greatest contributor of methane in the U.S. Thus, strategies must be designed to reduce or eliminate net emissions of greenhouse gases. Before these strategies can be developed, we must first understand typical emission ranges from each source at the farm level in order to focus on the processes with the greatest emissions. Sources on dairy farms include soil, growing crops, feed storage, animals, and manure in animal housing facilities, during storage, and following field application. Other countries, particularly in Europe, have quantified emission ranges, although these data are less established within the U.S. An extensive literature review was conducted to determine the major processes contributing to greenhouse gas emissions from dairy farms and to quantify typical emission levels. From these typical levels, emissions were estimated for a representative dairy farm. This review and farm analysis will help direct modeling efforts by determining the important physical processes that drive emissions of carbon dioxide, methane, and nitrous oxide in dairy production. The review also expands the knowledge base of researchers, farm planners, and policymakers as they work to develop and maintain sustainable farming systems.
The Geology of Northern Ireland: Our Natural Foundation

This New Regional Geology Guide to Northern Ireland (second edition) provides a comprehensive account of the geology of the region. Northern Ireland represents a small area of the Earth's surface, but contains a huge variety of rock types, representing many different geological ages which are reflected in the sheer variety of landscape. Landscape reflects the interaction of rock type and geological processes which give rise to the environmental niches supporting the varied flora and fauna to be found in Northern Ireland. This book presents detailed, comprehensive information in a user-friendly way; sites of national or international significance are described and illustrated through photographs and large-scale maps. Published by the Geological Survey of Northern Ireland, 298pp plus index, full colour.
A high resolution optical dating study of the Mostiştea loess-palaeosol sequence (SE Romania) using sand-sized quartz

We report on SAR-OSL dating of closely-spaced samples from the loess-palaeosol sequence near Mostiştea lake (Danube Plain, SE Romania). We used sand-sized quartz and a SAR protocol that involved a preheat of 10s at 220°C and a test dose cutheat to 180°C. It is shown that these thermal pretreatments isolate a quartz OSL signal that is dominated by the fast component. The behaviour of this signal in the SAR protocol is then documented. The ratio of the measured to given dose tends to lie slightly but systematically above unity (∼5% on average) and the recycling ratio below unity (∼6% on average); for all samples, the recuperated signal is negligible. Within analytical uncertainty, the nineteen optical ages are internally consistent and agree with the predictions from a palaeomagnetic age-depth model. Although it may be possible to optimize the SAR measurement procedure, the optical ages already confirm the chronostratigraphic position of the uppermost welldeveloped palaeosol in that it formed during MIS 5. The established chronology allows correlating the sequence near Mostiştea lake with that near Mircea VodĂ that we investigated earlier.
The influence of mesoscale and submesoscale heterogeneity on ocean biogeochemical reactions

The oceanic circulation in the meso to submesoscale regime generates heterogeneity in the concentrations of biogeochemical components over these scales, horizontally between 1 and 100 km. Due to nonlinearities in the biogeochemical reactions, such as phytoplankton primary production and zooplankton grazing, this small‐scale heterogeneity can lead to departure from the mean field approximation, whereby plankton reactions are evaluated from mean distributions at coarser scale. Here we explore the magnitude of these eddy reactions and compare their strength to those of the more widely studied eddy transports. We use the term eddy to denote effects arising from scales smaller than ∼ 100 km. This is done using a submesoscale permitting biogeochemical model, representative of the seasonally varying subtropical and subpolar gyres. We found that the eddy reactions associated with primary production and grazing account for ±5–30% of productivity and grazing, respectively, depending on location and time of year, and are scale dependent: two thirds are due to heterogeneities at scales 30–100 km and one third to those at scales below 30 km. Moreover, eddy productivities are systematically negative, implying that production tends to be reduced by nonlinear interactions at the mesoscale and smaller. The opposite result is found for eddy grazing, which is generally positive. The contrasting effects result from vertical advection, which negatively correlates phytoplankton and nutrients and positively correlates phytoplankton and zooplankton in the meso to submesoscale range. Moreover, our results highlight the central role played by eddy reactions for ecological aspects and the distribution of organisms and by eddy transport for biogeochemical aspects and nutrient budgets.