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Diamond Blackfan Anemia (DBA) is a rare disease characterized by anemia secondary to impaired red blood cell production from bone marrow failure. We present a case of infantile hypothermia and shock caused by this clinical pathology. A seven-week-old infant was brought to the emergency department by the father with the chief complaint of abnormal breathing and low activity level throughout the day. Medical history was unremarkable for both the patient and the family. On examination, the infant was breathing 30 breaths per minutes, had a heart rate of 116, and a core temperature of 33 degrees Celsius. The infant was ashen in color, limp, with grunted breathing and minimal movement. Numerous abnormal laboratory readings were reported, with the most significant being a hemoglobin of 1.7 and a hematocrit of 7.4. Emergent blood transfusion was initiated, and the patient was eventually air-lifted to a pediatric hospital two hours away. This case highlights the imperative of a thorough history and examination and consideration of a broad differential for neonatal hypothermia and shock, especially in the setting of no obvious bleeding.
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Tracking climatic conditions throughout the year is often assumed to be an adaptive behaviour underlying seasonal migration patterns in animal populations. We investigate this hypothesis using genetic markers data to map migratory connectivity for 27 genetically distinct bird populations from 7 species. We found that the variation in seasonal climate tracking across our suite of populations at a continental scale is more likely a consequence, rather than a direct driver, of migratory connectivity, which is primarily shaped by energy efficiency-i.e., optimizing the balance between accessing available resources and movement costs. However, our results also suggest that regional-scale seasonal precipitation tracking affects population migration destinations, thus revealing a potential scale dependency of ecological processes driving migration. Our results have implications for the conservation of these migratory species under climate change, as populations tracking climate seasonally are potentially at higher risk if they adapt to a narrow range of climatic conditions.
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Migración Animal , Aves , Cambio Climático , Estaciones del Año , Animales , Aves/fisiología , ClimaRESUMEN
Accurate mapping and monitoring of tropical forests aboveground biomass (AGB) is crucial to design effective carbon emission reduction strategies and improving our understanding of Earth's carbon cycle. However, existing large-scale maps of tropical forest AGB generated through combinations of Earth Observation (EO) and forest inventory data show markedly divergent estimates, even after accounting for reported uncertainties. To address this, a network of high-quality reference data is needed to calibrate and validate mapping algorithms. This study aims to generate reference AGB datasets using field inventory plots and airborne LiDAR data for eight sites in Central Africa and five sites in South Asia, two regions largely underrepresented in global reference AGB datasets. The study provides access to these reference AGB maps, including uncertainty maps, at 100 m and 40 m spatial resolutions covering a total LiDAR footprint of 1,11,650 ha [ranging from 150 to 40,000 ha at site level]. These maps serve as calibration/validation datasets to improve the accuracy and reliability of AGB mapping for current and upcoming EO missions (viz., GEDI, BIOMASS, and NISAR).
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Bosques , Árboles , Clima Tropical , África Central , Sur de Asia , Biomasa , Reproducibilidad de los ResultadosRESUMEN
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
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Genoma , Pájaros Cantores , Animales , Pájaros Cantores/genética , Femenino , California , Flujo GénicoRESUMEN
The white-bellied pangolin (Phataginus tricuspis) is the world's most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales from Asia between 2012 and 2018, we found that poaching pressures shifted over time from West to Central Africa. Recently, Cameroon's southern border has emerged as a site of intense poaching. Using data from seizures representing nearly 1 million African pangolins, we identified Nigeria as one important hub for trafficking, where scales are amassed and transshipped to markets in Asia. This origin-to-destination approach offers new opportunities to disrupt the illegal wildlife trade and to guide anti-trafficking measures.
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Crimen , Extinción Biológica , Genómica , Pangolines , Comercio de Vida Silvestre , Animales , Asia , Genoma , Nigeria , Crimen/prevención & control , CamerúnRESUMEN
Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, with the former being genetically structured and the latter exhibiting no signs of structure. Among resident populations, we observed significantly higher genetic differentiation, significant isolation-by-distance, and significantly elevated inbreeding. Among migratory breeding groups, on the other hand, we observed lower genetic differentiation, no isolation-by-distance, and substantially lower inbreeding. Using genotype-environment association analysis, we find significant evidence for relationships between migratory phenotypes (i.e., migrant versus resident) and environmental variation associated with cold temperatures during the winter and barren, open habitats. In the regions of the genome most differentiated between migrants and residents, we find significant enrichment for genes associated with the metabolism of fats. This may be linked to the increased pressure on migrants to process and store fats more efficiently in preparation for and during migration. Our results provide a significant contribution toward understanding the evolution of migratory behavior and vital insight into ongoing conservation and management efforts for the western burrowing owl.
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Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.
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Passeriformes , Pájaros Cantores , Humanos , Animales , Estados Unidos , Migración Animal , Passeriformes/genética , Pájaros Cantores/genética , Secuenciación Completa del Genoma , Región del CaribeRESUMEN
Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting data from wildlife remains (when negative interactions occur) at energy installations can act as a first step regarding the study of species and communities interacting with facilities. In the case of avian species, samples can be collected relatively easily (as compared to other sampling methods), but may only be able to be identified when morphological characteristics are diagnostic for a species. Therefore, many samples that appear as partial remains, or "feather spots"-known to be of avian origin but not readily assignable to species via morphology-may remain unidentified, reducing the efficiency of sample collection and the accuracy of patterns observed. To obtain data from these samples and ensure their identification and inclusion in subsequent analyses, we applied, for the first time, a DNA barcoding approach that uses mitochondrial genetic data to identify unknown avian samples collected at solar facilities to species. We also verified and compared identifications obtained by our genetic method to traditional morphological identifications using a blind test, and discuss discrepancies observed. Our results suggest that this genetic tool can be used to verify, correct, and supplement identifications made in the field and can produce data that allow accurate comparisons of avian interactions across facilities, locations, or technology types. We recommend implementing this genetic approach to ensure that unknown samples collected are efficiently identified and contribute to a better understanding of wildlife impacts at renewable energy projects.
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Energía Solar , Animales , Energía Renovable , Animales Salvajes , Aves/genética , Cambio ClimáticoRESUMEN
Biallelic hypomorphic variants in PRORP have been recently described as causing the autosomal recessive disorder combined oxidative phosphorylation deficiency type 54 (COXPD54). COXPD54 encompasses a phenotypic spectrum of sensorineural hearing loss and ovarian insufficiency (Perrault syndrome) to leukodystrophy. Here, we report three additional families with homozygous missense PRORP variants with pleiotropic phenotypes. Each missense variant altered a highly conserved residue within the metallonuclease domain. In vitro mitochondrial tRNA processing assays with recombinant TRMT10C, SDR5C1 and PRORP indicated two COXPD54-associated PRORP variants, c.1159A>G (p.Thr387Ala) and c.1241C>T (p.Ala414Val), decreased pre-tRNAIle cleavage, consistent with both variants impacting tRNA processing. No significant decrease in tRNA processing was observed with PRORP c.1093T>C (p.Tyr365His), which was identified in an individual with leukodystrophy. These data provide independent evidence that PRORP variants are associated with COXPD54 and that the assessment of 5' leader mitochondrial tRNA processing is a valuable assay for the functional analysis and clinical interpretation of novel PRORP variants.
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Pérdida Auditiva Sensorineural , Enfermedades Mitocondriales , Ribonucleasa P , Femenino , Humanos , Genotipo , Pérdida Auditiva Sensorineural/genética , Homocigoto , Enfermedades Mitocondriales/genética , ARN de Transferencia , Ribonucleasa P/genéticaRESUMEN
Ecosystems function in a series of feedback loops that can change or maintain vegetation structure. Vegetation structure influences the ecological niche space available to animals, shaping many aspects of behaviour and reproduction. In turn, animals perform ecological functions that shape vegetation structure. However, most studies concerning three-dimensional vegetation structure and animal ecology consider only a single direction of this relationship. Here, we review these separate lines of research and integrate them into a unified concept that describes a feedback mechanism. We also show how remote sensing and animal tracking technologies are now available at the global scale to describe feedback loops and their consequences for ecosystem functioning. An improved understanding of how animals interact with vegetation structure in feedback loops is needed to conserve ecosystems that face major disruptions in response to climate and land-use change.
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Ecosistema , Tecnología de Sensores Remotos , Animales , Retroalimentación , Ecología , Clima , Cambio ClimáticoRESUMEN
We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.
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Mamíferos , Pangolines , Animales , Masculino , Femenino , Pangolines/genética , Mamíferos/genética , Genoma , Cromosomas/genéticaRESUMEN
Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly Bicyclus dorothea originating from rainforest and ecotone habitats in Cameroon under common garden conditions. We also sampled wild-caught butterflies from forest and ecotone sites and used RADseq to explore genome-wide population differentiation. We found differences in the level of phenotypic plasticity across habitats. Specifically, ecotone populations exhibited greater sensitivity in wing eyespot features with variable development temperatures relative to rainforest populations. Known adaptive roles of wing eyespots in Bicyclus species suggest that this morphological plasticity is likely under divergent selection across environmental gradients. However, we found no distinct population structure of genome-wide variation between habitats, suggesting high level of ongoing gene flow between habitats is homogenizing most parts of the genome.
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Mariposas Diurnas , Animales , Mariposas Diurnas/fisiología , Bosque Lluvioso , Ecosistema , Bosques , Adaptación Fisiológica , Alas de Animales/anatomía & histología , Pigmentación/genéticaRESUMEN
Technological advances in migratory tracking tools have revealed a remarkable diversity in migratory patterns. One such pattern is leapfrog migration, where individuals that breed further north migrate to locations further south. Here, we analyzed migration patterns in the Painted Bunting (Passerina ciris) using a genetic-based approach. We started by mapping patterns of genetic variation across geographic space (called a genoscape) using 386 individuals from 25 populations across the breeding range. We then genotyped an additional 230 samples from 31 migration stopover locations and 178 samples from 16 wintering locations to map patterns of migratory connectivity. Our analyses of genetic variation across the breeding range show the existence of four genetically distinct groups within the species: Eastern, Southwestern, Louisiana, and Central groups. Subsequent assignment of migrating and wintering birds to genetic groups illustrated that birds from the Central group migrated during the fall via western Mexico or southern Texas, spent the winter from northeastern Mexico to Panama, and migrated north via the Gulf Coast of Mexico. While Louisiana birds overlapped with Central birds on their spring migratory routes along the Gulf Coast, we found that Louisiana birds had a more restricted wintering distribution in the Yucatan Peninsula and Central America. Further estimation of the straight-line distance from the predicted breeding location to the wintering location revealed that individuals sampled at lower winter latitudes traveled to greater distances (i.e., the predicted breeding area was further north; p > .001), confirming that these species exhibit a leapfrog migration pattern. Overall, these results demonstrate the utility of a genoscape-based approach for identifying range-wide patterns of migratory connectivity such as leapfrog migration with a high degree of clarity.
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Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
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Lagartos , Bosque Lluvioso , Animales , Pradera , Ecosistema , Frecuencia de los Genes , Biodiversidad , Lagartos/genética , Especiación GenéticaRESUMEN
The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.
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Genoma , Pájaros Cantores , Pájaros Cantores/genética , Animales , Conservación de los Recursos NaturalesRESUMEN
Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide-ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype-environment associations in the hermit thrush (Catharus guttatus), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype-environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature-associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature-related barriers to gene flow and/or temperature-driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype-environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population-level sensitivity to climate change and other stressors.
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BACKGROUND AND OBJECTIVE: We evaluated the metabolomic profile in CSF, serum and urine of participants with idiopathic intracranial hypertension (IIH) compared to controls and measured changes in metabolism associated with clinical markers of disease activity and treatment. METHODS: A case-control study compared women aged 18-55 years with active IIH (Friedman diagnostic criteria), to a sex, age and body mass index matched control group. IIH participants were identified from neurology and ophthalmology clinics from National Health Service hospitals and underwent a prospective intervention to induce disease remission through weight loss with re-evaluation at 12 months. Clinical assessments included lumbar puncture, headache, papilledema and visual measurements. Spectra of CSF, serum and urine metabolites were acquired utilizing proton nuclear magnetic resonance spectroscopy. RESULTS: Urea was lower in IIH (CSF; controls median ±IQR 0.196 ±0.008, IIH 0.058 ±0.059, p<0.001, urine; controls 5971.370 ±3021.831, IIH 4691.363 ±1955.774, p=0.009), correlated with ICP (urine p=0.019) and headache severity (CSF p=0.031) and increased by 12 months (CSF 12 months; 0.175 ±0.043, p=0.004, urine; 5210.874 ±1825.302, p=0.043). The lactate:pyruvate ratio was increased compared to controls (CSF; controls 49.739 ±19.523, IIH 113.114 ±117.298, p=0.023, serum; controls 38.187 ±13.392, IIH 54.547 ±18.471, p=0.004) and decreased at 12 months (CSF; 113.114 ±117.298, p<0.001). Baseline acetate was higher in IIH (CSF; controls 0.128 ±0.041, IIH 0.192 ±0.151, p=0.008), correlated with headache severity (p = 0.030) and headache disability (p = 0.003) and was reduced at 12 months (0.160 ±0.060, p = 0.007). Ketones 3-hydroxybutyrate and acetoacetate were altered in CSF at baseline in IIH (3-hydroxybutyrate; controls 0.074 ±0.063, IIH 0.049 ±0.055, p = 0.019, acetoacetate; controls 0.013 ±0.007, IIH 0.017 ±0.010, p = 0.013) and normalized at 12 months (0.112 ±0.114, p = 0.019, 0.029 ±0.017, p = 0.015 respectively). DISCUSSION: We observed metabolic disturbances that are evident in CSF, serum and urine of IIH participants, suggesting global metabolic dysregulation. Altered ketone body metabolites normalized following therapeutic weight loss. CSF:serum urea ratio was altered which may influence ICP dynamics and headache. Elevated CSF acetate, known to stimulate trigeminal sensitization, was associated with headache morbidity. These alterations of metabolic pathways specific to IIH provide biological insight and warrants mechanistic evaluation.
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The topological structure associated with the branch point singularity around an exceptional point (EP) can provide tools for controlling the propagation of light. Through use of graphene-based devices, we demonstrate the emergence of EPs in an electrically controlled interaction between light and a collection of organic molecules in the terahertz regime at room temperature. We show that the intensity and phase of terahertz pulses can be controlled by a gate voltage, which drives the device across the EP. Our electrically tunable system allows reconstruction of the Riemann surface associated with the complex energy landscape and provides topological control of light by tuning the loss imbalance and frequency detuning of interacting modes. Our approach provides a platform for developing topological optoelectronics and studying the manifestations of EP physics in light-matter interactions.
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Human genetic studies have linked rare coding variants in microglial genes, such as TREM2, and more recently PLCG2 to Alzheimer's disease (AD) pathology. The P522R variant in PLCG2 has been shown to confer protection for AD and to result in a subtle increase in enzymatic activity. PLCγ2 is a key component of intracellular signal transduction networks and induces Ca2+ signals downstream of many myeloid cell surface receptors, including TREM2. To explore the relationship between PLCγ2 and TREM2 and the role of PLCγ2 in regulating immune cell function, we generated human induced pluripotent stem cell (iPSC)- derived macrophages from isogenic lines with homozygous PLCG2 knockout (Ko). Stimulating TREM2 signalling using a polyclonal antibody revealed a complete lack of calcium flux and IP1 accumulation in PLCγ2 Ko cells, demonstrating a non-redundant role of PLCγ2 in calcium release downstream of TREM2. Loss of PLCγ2 led to broad changes in expression of several macrophage surface markers and phenotype, including reduced phagocytic activity and survival, while LPS-induced secretion of the inflammatory cytokines TNFα and IL-6 was unaffected. We identified additional deficits in PLCγ2- deficient cells that compromised cellular adhesion and migration. Thus, PLCγ2 is key in enabling divergent cellular functions and might be a promising target to increase beneficial microglial functions.