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The creatine-phosphocreatine cycle serves as a crucial temporary energy buffering system in the brain, regulated by brain creatine kinase (CKB), in maintaining Adenosine triphosphate (ATP) levels. Alzheimer's disease (AD) has been linked to increased CKB oxidation and loss of its regulatory function, although specific pathological processes and affected cell types remain unclear. In our study, cerebral cortex samples from individuals with AD, dementia with Lewy bodies (DLB), and age-matched controls were analyzed using antibody-based methods to quantify CKB levels and assess alterations associated with disease processes. Two independently validated antibodies exclusively labeled astrocytes in the human cerebral cortex. Combining immunofluorescence (IF) and mass spectrometry (MS), we explored CKB availability in AD and DLB cases. IF and Western blot analysis demonstrated a loss of CKB immunoreactivity correlated with increased plaque load, severity of tau pathology, and Lewy body pathology. However, transcriptomics data and targeted MS demonstrated unaltered total CKB levels, suggesting posttranslational modifications (PTMs) affecting antibody binding. This aligns with altered efficiency at proteolytic cleavage sites indicated in the targeted MS experiment. These findings highlight that the proper function of astrocytes, understudied in the brain compared with neurons, is highly affected by PTMs. Reduction in ATP levels within astrocytes can disrupt ATP-dependent processes, such as the glutamate-glutamine cycle. As CKB and the creatine-phosphocreatine cycle are important in securing constant ATP availability, PTMs in CKB, and astrocyte dysfunction may disturb homeostasis, driving excitotoxicity in the AD brain. CKB and its activity could be promising biomarkers for monitoring early-stage energy deficits in AD., (© 2024 The Author(s). GLIA published by Wiley Periodicals LLC.)

Direct nitrous oxide (N 2 O) emissions from fertilizer application are the largest anthropogenic source of global N 2 O, but the factors influencing these emissions remain debated. Here, we compile 1134 observations of fertilizer-induced N 2 O emission factor (EF) from 229 publications, covering various regions and crops globally. We then employ an interpretable machine learning model to investigate the driving factors of fertilizer-induced N 2 O emissions. Our results reveal that pH, soil organic carbon, precipitation, and temperature are the most influential factors, overweighing the impacts of management practices. Nitrogen application rate has a positive impact on the EF, but the effect diminishes as nitrogen application rate increases, which has been overestimated in previous studies. Soil pH has three-stage influence on EF: positive when 7.3 ≤ pH ≤ 8.7, significantly negative between 6.8 and 7.3, and insignificant at lower pH levels (4.7 ≤ pH ≤ 6.8). Moreover, we confirm the nonlinear contributions of temperature and precipitation to EF, which may cause an unexpected increase in N 2 O emission under climate change. Our research provides crucial insights for global N 2 O modeling and mitigation strategies.

Dissolved organic carbon (DOC) dynamics are critical to carbon cycling in forest ecosystems and sensitive to global change. Our study, spanning from 2001 to 2020 in a headwater catchment in subtropical China, analyzed DOC and water chemistry of throughfall, litter leachate, soil waters at various depths, and streamwater. We focused on DOC transport through hydrological pathways and assessed the long-term trends in DOC dynamics amidst environmental and climatic changes. Our results showed that the annual DOC deposition via throughfall and stream outflow was 14.2 ± 2.2 and 1.87 ± 0.83 g C m -2 year -1 , respectively. Notably, there was a long-term declining trend in DOC deposition via throughfall (-0.195 mg C L -1 year -1 ), attributed to reduced organic carbon emissions from clean air actions. Conversely, DOC concentrations in soil waters and stream waters showed increasing trends, primarily due to mitigated acid deposition. Moreover, elevated temperature and precipitation could partly explain the long-term rise in DOC leaching. These trends in DOC dynamics have significant implications for the stability of carbon sink in terrestrial, aquatic, and even oceanic ecosystems at regional scales.

Although biochar application to soils has been found to increase soil quality and crop yield, the biochar dispersion extent and its impacts on native soil organic carbon (SOC) has received relatively little attention. Here, the vertical and lateral migration of fine, intermediate and coarse-sized biochar (<0.5, 0.5-1 and 1-5 mm, respectively), applied at low and high doses (1.5-2 and 3-4% w/w, respectively), was tracked using stable isotope methods, along with its impact on native SOC stocks. Biochar was homogeneously mixed into the surface layer (0-7 cm depth) of a loamy sandy Acrisol in Zambia. After 4.5 y, 38-75% of the biochar carbon (BC) was lost from the applied layer and 4-25% was detected in lower soil layers (7-30 cm). Estimating BC mineralization to be no more than 8%, 25-60% was likely transported laterally out of the experimental plots. This conclusion was supported by observations of BC in the control plot and in soils up to 2 m outside of the experimental plots. These processes were likely progressive as recovery of BC in similar plots 1 year after application was greater in both surface and lower soil layers than after 4.5 y. Fine and intermediate-sized BC displayed the greatest downward migration (25.3 and 17.9%, respectively), particularly when applied at lower doses, suggesting its movement through soil inter-particle spaces. At higher dosages, fine and intermediate-sized particles may have clogged pore, so coarse biochar displayed the greatest downward migration when biochar was applied at higher doses. In the BC treatment plot soil profiles, native SOC stocks were reduced by 2.8 to 24.5% (18.4% on average), i.e. positive priming. However, some evidence suggested that the soils may switch to negative priming over time. The dispersion of biochar in soil should be considered when evaluating biochar's agronomic benefits and environmental effects., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Obia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

China currently has the highest acid deposition globally, yet research on its status, impacts, causes and controls is lacking. Here, we compiled data and calculated critical loads regarding acid deposition. The results showed that the abatement measures in China have achieved a sharp decline in the emissions of acidifying pollutants and a continuous recovery of precipitation pH, despite the drastic growth in the economy and energy consumption. However, the risk of ecological acidification and eutrophication showed no significant decrease. With similar emission reductions, the decline in areas at risk of acidification in China (7.0%) lags behind those in Europe (20%) or the USA (15%). This was because, unlike Europe and the USA, China's abatement strategies primarily target air quality improvement rather than mitigating ecological impacts. Given that the area with the risk of eutrophication induced by nitrogen deposition remained at 13% of the country even under the scenario of achieving the dual targets of air quality and carbon dioxide mitigation in 2035, we explored an enhanced ammonia abatement pathway. With a further 27% reduction in ammonia by 2035, China could largely eliminate the impacts of acid deposition. This research serves as a valuable reference for China's future acid deposition control and for other nations facing similar challenges., (© The Author(s) 2024. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.)

Major depressive disorder (MDD) is a serious disease and a burden to patients, families and society. Rodent experiments and human studies suggest that several neuropeptide systems are involved in mood regulation. The aim of this study is two-fold: (i) to monitor, with qPCR, transcript levels of the substance P/tachykinin (TAC), NPY and CCK systems in bulk samples from control and suicide subjects, targeting five postmortem brain regions including locus coeruleus (LC); and (ii) to analyse expression of neuropeptide family transcripts in LC neurons of 'normal' postmortem brains by using laser capture microdissection with Smart-Seq2 RNA sequencing. qPCR revealed distinct regional expression patterns in male and female controls with higher levels for the TAC system in the dorsal raphe nucleus and LC, versus higher transcripts levels of the NPY and CCK systems in prefrontal cortex. In suicide patients, TAC, TAC receptors and a few NPY family transcript levels were increased mainly in prefrontal cortex and LC. The second study on 'normal' noradrenergic LC neurons revealed expression of transcripts for GAL, NPY, TAC1, CCK, and TACR1 and many other peptides (e.g. Cerebellin4 and CARTPT) and receptors (e.g. Adcyap1R1 and GPR173). These data and our previous results on suicide brains indicates that the tachykinin and galanin systems may be valid targets for developing antidepressant medicines. Moreover, the perturbation of neuropeptide systems in MDD patients, and the detection of further neuropeptide and receptor transcripts in LC, shed new light on signalling in noradrenergic LC neurons and on mechanisms possibly associated with mood disorders., Competing Interests: Conflict of interest T.H. owns stock in H. Lundbeck A/S. All the other authors declare no conflict of interest., (Copyright © 2023. Published by Elsevier B.V.)

Background and Purpose: COVID-19 is associated with multiple neurological manifestations. The clinical presentation, trajectory, and treatment response for three cases of myoclonus during COVID-19 infection, with no previous neurological disease, are decsribed., Metods: Analysis of cerebrospinal fluid from the cases using indirect immunohistochemistry., Results: Antibodies against rodent brain tissue, and similarities in staining patterns were observed, indicating the presence of antineuronal immunoglobulin G autoantibodies targeting astrocytes in the hippocampus., Conclusion: Our results demontrate cerebrospinal fluid antineuronal antibodies indicating an an autoimmune involvment in the pathogenesis in COVID-19 associated myoclonus., (© 2023 The Authors. European Journal of Neurology published by John Wiley & Sons Ltd on behalf of European Academy of Neurology.)

Elucidating the cellular organization of the cerebral cortex is critical for understanding brain structure and function. Using large-scale single-nucleus RNA sequencing and spatial transcriptomic analysis of 143 macaque cortical regions, we obtained a comprehensive atlas of 264 transcriptome-defined cortical cell types and mapped their spatial distribution across the entire cortex. We characterized the cortical layer and region preferences of glutamatergic, GABAergic, and non-neuronal cell types, as well as regional differences in cell-type composition and neighborhood complexity. Notably, we discovered a relationship between the regional distribution of various cell types and the region's hierarchical level in the visual and somatosensory systems. Cross-species comparison of transcriptomic data from human, macaque, and mouse cortices further revealed primate-specific cell types that are enriched in layer 4, with their marker genes expressed in a region-dependent manner. Our data provide a cellular and molecular basis for understanding the evolution, development, aging, and pathogenesis of the primate brain., Competing Interests: Declaration of interests Stereo-seq is covered in pending patents. BGI employees hold company stock., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

An accurate depiction of mercury (Hg) reduction is important to predict Hg biogeochemistry in both aquatic and soil systems. Although the photoreduction of Hg is well documented, reduction in the dark is poorly known and is thus the focus of this work. Black carbon (BC), an important constituent of organic matter in environments, can reduce Hg 2+ in dark and oxygen-deficient conditions. Fast removal of Hg 2+ in BC/Hg 2+ solution was observed, with 4.99-86.88 L mg -1 h -1 of the reaction rate constant, which could be ascribed to the combined actions of adsorption and reduction. Meanwhile, slow Hg reduction was obtained, compared to Hg removal, with 0.06-2.16 L mg -1 h -1 of the reaction rate constant. Thus, in the initial stage, Hg 2+ removal was mainly triggered by adsorption, rather than reduction. Afterward, the adsorbed Hg 2+ on black carbon was converted into Hg 0 . Dissolved black carbon and aromatic CH on particulate black carbon were dominant triggers of Hg reduction for black carbon. During Hg reduction, the intastable intermediate, formed in the complex between aromatic CH and Hg 2+ , behaved as persistent free radicals, which could be detected by in situ electron paramagnetic resonance. Subsequently, the intastable intermediate was mainly converted into CO on black carbon and Hg 0 . Corresponding results of the present study highlight the important role of black carbon in the Hg biogeochemical cycle., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Here, we assess the effects of gypsum and local organic waste as amendments to non-weathered, filter-pressed bauxite residue (BR) to improve its properties and support plant growth. In addition, we monitored the leachate quality of the amended BR under progressive leaching that simulated precipitation conditions in Northern Brazil. Free-draining column tests consisting of BR amended with gypsum and organic waste, at 5% and 10% w/w, respectively, were leached for 8 weeks to assess the effects on the chemical composition of BR and the leachates. Adding gypsum to BR reduced the exchangeable sodium (Na) percentage (ESP) from approximately 79%-48%, whereas adding only organic waste had smaller effects on ESP (from ∼79% to ∼ 70%). The mean leachate pH ranged from 8.7 to 9.4 for the gypsum, and organic waste amended BR, while this was 10.3 in the leachate of the unamended BR. The treatments had similar trends of electrical conductivity throughout the experiments and were below 2 dS/cm after 8 weeks, when ∼1.700 mm simulated precipitation had leached. Aluminium (Al), Arsenic (As), and Vanadium (V) concentrations in leachates of BR with gypsum, either alone or in combination with organic waste, were significantly lowered than in leachate of non-amended BR. By contrast, metal concentrations increased if organic waste was added to BR. We conclude that amending BR with gypsum, in combination with organic waste, significantly improves the chemical properties of the solid phase and achieved rehabilitation goals for SAR and EC of the leachates after 8 weeks of leaching. However, despite high leaching rates, rehabilitation goals for pH and ESP were not achieved with gypsum either alone or combined with organic waste., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Yuuki Silveira Miura reports financial support and equipment or supplies were provided by Norsk Hydro ASA. Yuuki Silveira Miura reports a relationship with Norsk Hydro ASA that includes: employment., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The rapid growth of energy-intensive and high-emission industries has propelled China's economy but has also led to massive levels of air pollutant emissions and ecological problems, such as acid deposition. Despite recent declines, atmospheric acid deposition in China is still severe. Long-term exposure to high levels of acid depositions has a substantial negative impact on the ecosystem. Evaluating these hazards and incorporating this issue into planning and decision-making processes is critical to achieving sustainable development goals in China. However, the long-term economic loss caused by atmospheric acid deposition and its temporal and spatial variation in China is unclear. Hence, the aim of this study was to assess the environmental cost of acid deposition in the agriculture, forestry, construction, and transportation industries from 1980 to 2019, using long-term monitoring, integrated data, and the dose-response method with localization parameters. The results showed that the estimated cumulative environmental cost of acid deposition was USD 230 billion, representing 0.27% of the gross domestic product (GDP) in China. This cost, was particularly high for building materials, followed by crops, forests, and roads. Temporally, the environmental cost and the ratio of environmental cost to GDP decreased from their peaks by 43% and 91%, respectively, because of emission controls targeting acidifying pollutants and promotion of clean energy. Spatially, the largest environmental cost occurred in developing provinces, indicating that more stringent emission reduction measures should be implemented in these regions. These findings highlight the huge environmental costs behind rapid development; however, the implementation of reasonable emission reduction measures can effectively reduce these environmental costs, providing a promising paradigm for other undeveloped and developing countries., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Background: A large proportion of people who sustain a whiplash injury will have persistent pain, disability, and participation problems. Several prognostic factors for functional recovery have been reported in the literature but these factors are often evaluated based on differing implementations in clinical practice. Additionally, physiotherapists also rely on their clinical intuition to estimate the functional prognosis of their patients, but this is seldom measured in experimental research. Furthermore, no study to date has explored the associations between clinical intuition, clinically estimated factors, and objectively measured factors for functional recovery of patients with Whiplash-Associated Disorders (WAD)., Aim: The aim of this exploratory study is to evaluate associations between prognostic factors for functional recovery, based on routinely collected data in a specialized primary care physiotherapy practice in a consecutive sample of patients (n = 523) with WAD., Methods: Three sources of prognostic factors were selected: (1) physiotherapists' synthesis of clinical intuition in terms of high-risk, inconclusive risk, or low-risk for functional recovery, (2) patient-registered factors from history taking, and (3) patient-reported prognostic factors derived from questionnaires. Prognostic factors were selected based on the literature, recommendations in Dutch clinical practice guidelines, and consensus between experts. Spearman's rank correlation coefficients were calculated to explore the associations between sources of prognostic factors, using a cutoff ≥0.25 for acceptable association., Results: Associations between physiotherapists' intuitive synthesis and patient-registered variables were substantial ( r s = 0.86), between patient-registered variables and patient-reported variables fair (ranging from 0.30 to 0.41) to substantial (ranging from 0.69 to 0.73), and between physiotherapists intuitive synthesis and patient-reported variables fair (ranging from 0.30 to 0.37)., Conclusion: When estimating prognosis for functional recovery using clinical reasoning, physiotherapists should integrate patients' registered experience of their course of recovery, as well as the timeline after an accident, with their own synthesis of clinical intuition regarding prognostic factors in patients with WAD., Competing Interests: The authors report no conflict of interest in this work.

Tau pathology of the noradrenergic locus coeruleus (LC) is a hallmark of several age-related neurodegenerative disorders, including Alzheimer's disease. However, a comprehensive neuropathological examination of the LC is difficult due to its small size and rod-like shape. To investigate the LC cytoarchitecture and tau cytoskeletal pathology in relation to possible propagation patterns of disease-associated tau in an unprecedented large-scale three-dimensional view, we utilized volume immunostaining and optical clearing technology combined with light sheet fluorescence microscopy. We examined AT8 + pathological tau in the LC/pericoerulear region of 20 brains from Braak neurofibrillary tangle (NFT) stage 0-6. We demonstrate an intriguing morphological complexity and heterogeneity of AT8 + cellular structures in the LC, representing various intracellular stages of NFT maturation and their diverse transition forms. We describe novel morphologies of neuronal tau pathology such as AT8 + cells with fine filamentous somatic protrusions or with disintegrating soma. We show that gradual dendritic atrophy is the first morphological sign of the degeneration of tangle-bearing neurons, even preceding axonal lesions. Interestingly, irrespective of the Braak NFT stage, tau pathology is more advanced in the dorsal LC that preferentially projects to vulnerable forebrain regions in Alzheimer's disease, like the hippocampus or neocortical areas, compared to the ventral LC projecting to the cerebellum and medulla. Moreover, already in the precortical Braak 0 stage, 3D analysis reveals clustering tendency and dendro-dendritic close appositions of AT8 + LC neurons, AT8 + long axons of NFT-bearing cells that join the ascending dorsal noradrenergic bundle after leaving the LC, as well as AT8 + processes of NFT-bearing LC neurons that target the 4th ventricle wall. Our study suggests that the unique cytoarchitecture, comprised of a densely packed and dendritically extensively interconnected neuronal network with long projections, makes the human LC to be an ideal anatomical template for early accumulation and trans-neuronal spreading of hyperphosphorylated tau., (© 2022. The Author(s).)

Human prefrontal cortex (hPFC) is a complex brain region involved in cognitive and emotional processes and several psychiatric disorders. Here, we present an overview of the distribution of the peptidergic systems in 17 subregions of hPFC and three reference cortices obtained by microdissection and based on RNA sequencing and RNAscope methods integrated with published single-cell transcriptomics data. We detected expression of 60 neuropeptides and 60 neuropeptide receptors in at least one of the hPFC subregions. The results reveal that the peptidergic landscape in PFC consists of closely located and functionally different subregions with unique peptide/transmitter-related profiles. Neuropeptide-rich PFC subregions were identified, encompassing regions from anterior cingulate cortex/orbitofrontal gyrus. Furthermore, marked differences in gene expression exist between different PFC regions (>5-fold; cocaine and amphetamine-regulated transcript peptide) as well as between PFC regions and reference regions, for example, for somatostatin and several receptors. We suggest that the present approach allows definition of, still hypothetical, microcircuits exemplified by glutamatergic neurons expressing a peptide cotransmitter either as an agonist (hypocretin/orexin) or antagonist (galanin). Specific neuropeptide receptors have been identified as possible targets for neuronal afferents and, interestingly, peripheral blood-borne peptide hormones (leptin, adiponectin, gastric inhibitory peptide, glucagon-like peptides, and peptide YY). Together with other recent publications, our results support the view that neuropeptide systems may play an important role in hPFC and underpin the concept that neuropeptide signaling helps stabilize circuit connectivity and fine-tune/modulate PFC functions executed during health and disease.

Soil acidification along with base cations loss degrades soil quality and is a major environmental problem, especially in agroecosystems with extensive nitrogen (N) fertilization. So far, the rates of proton (H + ) production and real soil acidification (loss of base cations) remain unclear in subtropical agricultural watersheds. To assess the current status and future risk of soil acidification in subtropical red soil region of China, a two-year monitoring was conducted in a typical agricultural watershed with upland, paddy fields, and orchards where high N fertilizers are applied (320 kg N ha -1 yr -1 ). H + production, neutralization and base cations losses were quantified based on the inputs (rainwater, inflow of water, and fertilizer) and outputs (outflow of water, groundwater drainage, and plant uptake) of major elements (K + , Ca 2+ , Na + , Mg 2+ , Al 3+ , NH 4 + , NO 3 - , SO 4 2- , Cl - , and H + ). The result showed that total H + production in the watershed was 5152 mol c ha -1 yr -1 . N transformation was the most important H + source (68%), followed by excess plant uptake of cations (25%) and H + deposition (7%). Base cations exchange and weathering of minerals (3842 mol c ha -1 yr -1 ) dominated H + neutralization, followed by SO 4 2- adsorption (1081 mol c ha -1 yr -1 ), while H + and Al 3+ leaching amounted to 431 mol c ha -1 yr -1 , only. These results state clearly that despite significant soil acidification, the acidification of surface waters is minor, implying that soils have buffered substantially the net H + addition. As a result of soil buffering, there was abundant loss of base cations, whose rate is significantly higher than the previously reported weathering rate of minerals in red soils (3842 vs 230-1080 mol c ha -1 yr -1 ). This suggests that the pool of exchangeable base cations is being depleted in the watershed, increasing the vulnerability of the watershed, and posing a serious threat to future recovery of soils from acidification., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-β, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia., (© 2022. The Author(s).)

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development., Competing Interests: Declaration of interests The chip, procedure, and applications of Stereo-seq are covered in pending patents. J.W. and H.Y. are founders of BGI-Shenzhen, and employees of BGI have stock holdings in BGI., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Nitrogen (N)-induced soil acidification has received much attention worldwide. Nitrification and soil N mineralization are two key N cycle processes that affect soil acidification. However, the seasonal dynamics of soil pH under their combined influence is unclear. We studied the effect of N fertilization on soil pH and N transformations using 15 N tracing in field lysimeters with soils developed from different parent materials (Quaternary red clay, sandstone, and basalt). Maize was planted with 200 kg N ha -1  yr -1 15 N-labeled urea addition. During 7-45 days after fertilization, proton (H + ) production due to nitrification of fertilizer N, nitrate (NO 3 - ) leaching, and plant uptake exceeded H + consumption by base cations mobilization and leaching, resulting in a significant soil pH decline. When nitrification activity decreased (after 45 days), due to exhausted ammonium (NH 4 + ) availability, soil pH rose again. During the fallow period, acid neutralization due to base cation mobilization, and ammonification of soil organic N (SON) offset H + production caused by nitrification of mineralized SON, leading to a sustained rise in soil pH. After the one-year experiment, no significant soil pH decrease was observed in any of the soils. Parent material had little effect on the seasonal dynamics of soil acidification, which appeared to be controlled by fertilization, environmental factors (temperature and moisture), and plant uptake. In subtropical regions, monitoring of soil pH on an annual basis may mask the effect of N fertilization on soil acidification., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Nitrate (NO 3 - ) loss and enrichment in water bodies caused by fertilization are a major environmental problem in agricultural areas. However, the quantitative contribution of different NO 3 - sources, especially chemical fertilizers (CF) and soil organic nitrogen (SON), to NO 3 - runoff loss remains unclear. In this study, a systematic investigation of NO 3 - runoff and its sources was conducted in a subtropical agricultural watershed located in Yujiang County, Jiangxi Province, China. A semi-monthly sampling was performed at the inlet and outlet from March 2018 to February 2019. Hydrochemical and dual NO 3 - isotope ( 15  N and 18 O) approaches were combined to estimate the NO 3 - runoff loss and quantify the contribution of different sources with a Bayesian isotope mixing model. Source apportionment by Stable Isotope Analysis in R (SIAR) suggested that NO 3 - in runoff was mainly derived from nitrification of ammonium (NH 4 + ) mineralized from SON (37-52%) and manure/sewage (M&S) (25-47%), while the contribution of CF was relatively small (14-25%). The contribution of various sources showed seasonal variations, with a greater contribution of CF in the wet growing season (March to August). Compared with the inlet which contributed 37-40% to runoff NO 3 - , SON contributed more at the outlet (49-52%). Denitrification in the runoff was small and appeared to be confined to the dry season (September to February), with an estimated NO 3 - loss of 2.73 kg N ha -1 . The net NO 3 - runoff loss of the watershed was 34.5 kg N ha -1  yr -1 , accounting for 15% of the annual fertilization rate (229 kg N ha -1  yr -1 ). Besides M&S (22%), fertilization and remineralization of SON (CF + SON) were the main sources for the NO 3 - runoff loss (78%), suggesting accelerated nitrification of NH 4 + from CF (24%) and SON mineralization (54%). Our study indicates that NO 3 - runoff loss in subtropical agricultural watersheds is dominated by nonpoint source pollution from fertilization. SON played a more important role than CF. Besides, the contribution of sewage should not be neglected. Our data suggest that a combination of more rational fertilizer N application (CF), better management of SON, and better treatment of domestic sewage could alleviate NO 3 - pollution in subtropical China., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Background: There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs., Results: An open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented., Conclusions: Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs., (© 2022. The Author(s).)

Uterine sarcomas are rare but deadly malignancies without effective treatment. Immunotherapy is a promising new approach to treat these tumors but has shown heterogeneous effects in sarcoma patients. With the goal of identifying key factors for improved patient treatment, we characterized the tumor immune landscape in 58 uterine sarcoma cases with full clinicopathological annotation. Immune cell characterization revealed the overall prevalence of FOXP3+ cells and pro-tumor M2-like macrophages. Hierarchical clustering of patients showed four tumor type-independent immune signatures, where infiltration of FOXP3+ cells and M1-like macrophages associated with favorable prognosis. High CD8+/FOXP3+ ratio in UUS and ESS correlated with poor survival, upregulation of immunosuppressive markers, extracellular matrix (ECM)-related genes and proteins, and YAP activation. This study shows that uterine sarcomas present distinct immune signatures with prognostic value, independent of tumor type, and suggests that targeting the ECM could be beneficial for future treatments., (© 2021. The Author(s).)

On the cultivated slopes of the highlands of southwest Ethiopia, soil degradation due to water erosion is a challenge for crop production. To limit surface runoff and soil erosion, soil bunds often in combination with trenches, constructed along contour lines, are common. In addition to the interception of surface runoff, soil bunds may affect crop yield. Here, we evaluate effect of soil bunds on surface runoff and maize yield, using FAO's AquaCrop model, calibrated based on field experiments in the Bokole-Karetha watershed, in SW Ethiopia. Experiments were conducted in 2018 and 2019 on three neighboring fields, each comprising plots in triplicate without and with soil bunds. Experimental data from 2018 to 2019, which were average and above average with respect to rainfall, indicate that water availability was sufficient or even in excess for maize production. Soil bunds significantly (p < 0.05) reduced surface runoff, but maize yield did not differ significantly. In plots without soil bunds, the AquaCrop model described surface runoff satisfactorily after slight adjustment of the curve number (related to infiltration capacity) in one of the three fields. Maize yields were reproduced adequately after calibrating soil fertility and adjusting water productivity. After calibration and validation, the AquaCrop model was used to hindcast surface runoff and grain yield from 1999 to 2017, given available climatic data for the region. Hindcasts show that maize yield in the Bokole-Karetha watershed, with its relatively high rainfall, is not significantly affected by rainfall in two of the three fields. In the third field maize yield decreases slightly, but significantly (p < 0.05) with rainfall. In the short run, yield differences between plots with and without soil bunds are not significant. However, eventually high surface runoff from plots without soil bunds are expected to result in unsustainable crop production, due to significant erosion and degradation of the often nutrient-poor soils. Implementation of soil and water management techniques, combined with fertilization, are important to prevent soil degradation and nutrient stress on sloping land., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Hepatic nerves have a complex role in synchronizing liver metabolism. Here, we used three-dimensional (3D) immunoimaging to explore the integrity of the hepatic nervous system in experimental and human nonalcoholic fatty liver disease (NAFLD). We demonstrate parallel signs of mild degeneration and axonal sprouting of sympathetic innervations in early stages of experimental NAFLD and a collapse of sympathetic arborization in steatohepatitis. Human fatty livers display a similar pattern of sympathetic nerve degeneration, correlating with the severity of NAFLD pathology. We show that chronic sympathetic hyperexcitation is a key factor in the axonal degeneration, here genetically phenocopied in mice deficient of the Rac-1 activator Vav3. In experimental steatohepatitis, 3D imaging reveals a severe portal vein contraction, spatially correlated with the extension of the remaining nerves around the portal vein, enlightening a potential intrahepatic neuronal mechanism of portal hypertension. These fundamental alterations in liver innervation and vasculature uncover previously unidentified neuronal components in NAFLD pathomechanisms., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Purpose: To analyze biopsy samples from the subscapularis tendon and from the joint capsule from male patients with subacromial impingement syndrome and compare them with samples from male patients with post-traumatic recurrent shoulder instability, to detect increased inflammatory activity that might be present inside the humeroscapular joint., Methods: Twenty male patients scheduled for surgery for either subacromial decompression or Bankart reconstruction were included. Four biopsies from each patient were obtained during surgery from the capsule and the subscapularis tendon. Each specimen was analyzed for TNF-α, IL-6, CD-3 and CD-72. Multiplex fluorescence immunohistochemistry was performed on histological samples from the capsule and tendon to demonstrate the level of inflammatory markers. Fluorescence microscope images were acquired using an automated scanning system. On each slide, the number of pixels was registered and used in the analyses., Results: The subacromial impingement syndrome group comprised eight patients, median age 53 (45-74) years, while the instability group 12, median age 27 (22-48) years (p < 0.00001). The amount of IL-6 and TNF-α was significantly higher in the subscapularis tendon of the patients with subacromial impingement syndrome compared with instability patients (p = 0.0015 and p = 0.0008 respectively). In the capsular samples, significantly higher amount of TNF-α and CD-72 was found in patients with subacromial impingement syndrome compared with instability patients (p < 0.0001 for both). On the other hand, the amount of CD-3 was significantly higher in the instability group (p = 0.0013)., Conclusions: This study provides evidence that an extended inflammatory process is present, not only in the subacromial bursa but also in the glenohumeral joint in patients with subacromial impingement syndrome., Level of Evidence: Level III., Clinical Relevance: To develop a treatment targeted towards intra-articular inflammatory cytokines appears appealing.

Forest soils in the warm-humid tropics significantly contribute to the regional greenhouse gas (GHG) budgets. However, spatial heterogeneity of GHG fluxes is often overlooked. Here, we present a study of N 2 O and CH 4 fluxes over 1.5 years, along a topographic gradient in a rainforest catchment in Xishuangbanna, SW China. From the upper hillslope to the foot of the hillslope, and further to the flat groundwater discharge zone, we observed a decrease of N 2 O emission associated with an increase of soil water-filled-pore-space (WFPS), which we tentatively attribute to more complete denitrification to N 2 at larger WFPS. In the well-drained soils on the hillslope, denitrification at anaerobic microsites or under transient water-saturation was the potential N 2 O source. Negative CH 4 fluxes across the catchment indicated a net soil CH 4 sink. As the oxidation of atmospheric CH 4 is diffusion-limited, soil CH 4 consumption rates were negatively related to WFPS, reflecting the topographic control. Our observations also suggest that during dry seasons N 2 O emission was significantly dampened (<10 μg N 2 O-N m -2  h -1 ) and CH 4 uptake was strongly enhanced (83 μg CH 4 -C m -2  h -1 ) relative to wet seasons (17 μg N 2 O-N m -2  h -1 and 56 μg CH 4 -C m -2  h -1 ). In a post-drought period, several rain episodes induced exceptionally high N 2 O emissions (450 μg N 2 O-N m -2  h -1 ) in the groundwater discharge zone, likely driven by flushing of labile organic carbon accumulated during drought. Considering the global warming potential associated with both GHGs, we found that N 2 O emissions largely offset the C sink contributed by CH 4 uptake in soils (more significant in the groundwater discharge zone). Our study illustrates important topographic controls on N 2 O and CH 4 fluxes in forest soils. With projected climate change in the tropics, weather extremes may interact with these controls in regulating forest GHG fluxes, which should be accounted for in future studies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA-editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. Although potential data biases caused by age, sex or health status are not considered, this study provides a rich resource to better understand the evolutionary importance of post-transcriptional RNA editing.

Alzheimer's disease (AD) is the most prevalent form of dementia and is characterized by abnormal extracellular aggregates of amyloid-β and intraneuronal hyperphosphorylated tau tangles and neuropil threads. Microglia, the tissue-resident macrophages of the central nervous system (CNS), are important for CNS homeostasis and implicated in AD pathology. In amyloid mouse models, a phagocytic/activated microglia phenotype has been identified. How increasing levels of amyloid-β and tau pathology affect human microglia transcriptional profiles is unknown. Here, we performed snRNAseq on 482,472 nuclei from non-demented control brains and AD brains containing only amyloid-β plaques or both amyloid-β plaques and tau pathology. Within the microglia population, distinct expression profiles were identified of which two were AD pathology-associated. The phagocytic/activated AD1-microglia population abundance strongly correlated with tissue amyloid-β load and localized to amyloid-β plaques. The AD2-microglia abundance strongly correlated with tissue phospho-tau load and these microglia were more abundant in samples with overt tau pathology. This full characterization of human disease-associated microglia phenotypes provides new insights in the pathophysiological role of microglia in AD and offers new targets for microglia-state-specific therapeutic strategies.

PET hypoxia imaging can assess tissue viability in acute ischemic stroke (AIS). [ 18 F]FMISO is an established tracer but requires substantial accumulation time, limiting its use in hyperacute AIS. [ 64 Cu]CuATSM requires less accumulation time and has shown promise as a hypoxia tracer. We compared these tracers in a M2-occlusion model (M2CAO) with preserved collateral blood flow. Rats underwent M2CAO and [ 18 F]FMISO ( n  = 12) or [ 64 Cu]CuATSM ( n  = 6) examinations. [ 64 Cu]CuATSM animals were also examined with MRI. Pimonidazole was used as a surrogate for [ 18 F]FMISO in an immunofluorescence analysis employed to profile levels of hypoxia in neurons (NeuN) and astrocytes (GFAP). There was increased [ 18 F]FMISO uptake in the M2CAO cortex. No increase in [ 64 Cu]CuATSM activity was found. The pimonidazole intensity of neurons and astrocytes was increased in hypoxic regions. The pimonidazole intensity ratio was higher in neurons than in astrocytes. In the majority of animals, immunofluorescence revealed a loss of astrocytes within the core of regions with increased pimonidazole uptake. We conclude that [ 18 F]FMISO is superior to [ 64 Cu]CuATSM in detecting hypoxia in AIS, consistent with an earlier study. [ 18 F]FMISO may provide efficient diagnostic imaging beyond the hyperacute phase. Results do not provide encouragement for the use of [ 64 Cu]CuATSM in experimental AIS.

On the steep hill slopes of southwest Ethiopia, soil erosion may cause significant declines in soil organic carbon (SOC) and nutrients, negatively affecting cropland productivity. Soil bunds are advised as an effective means to reduce surface runoff and soil erosion. However, the effects on SOC and nutrients are rarely quantified. The objective of this study was to assess the quantitative effect of soil bunds on surface runoff as well as soil and nutrients losses from cropland in the region. Data was collected from experimental fields on three farms (fields 1, 2 and 3) in the Omo-Gibe River basin in southwest Ethiopia. On each farm, effects of soil bunds on runoff and erosion were investigated and compared with adjacent plots without soil bunds in the 2018 and 2019 growing seasons. Soil bunds effectively reduced surface runoff (by 80-92%). Without soil bunds, soil losses in the growing season were 5-22 t ha -1 in 2018 and 15-43 t ha -1 in 2019, on average removing 1.3-4 mm soil per year. Soil bunds decreased soil losses by about 96%. Observed soil losses from fields without soil bunds were well described by the Universal Soil Loss Equation (USLE; R 2  = 0.92; p < 0.01). Of the total soil loss, 47-69% was removed in suspended form. Suspended material had significantly larger (p < 0.05) SOC, and plant available potassium (K) and phosphorus (P) concentrations than coarser, rapidly settling sediment and bulk soil. In 2019, up to 733 kg SOC ha -1 , 77 kg total nitrogen ha -1 and 21 kg K ha -1 were lost per season from plots without soil bunds. For SOC this amounts to 6% of its stocks in the topsoil. Soil bunds are important controls on surface runoff, strongly limiting losses of SOC and nutrients in sloping croplands of southwest Ethiopia., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

In recent years, studies have shown higher prevalence of autoantibodies in patients with schizophrenia compared to healthy individuals. This study applies an untargeted and a targeted affinity proteomics approach to explore and characterize the autoantibody repertoire in brain tissues from 73 subjects diagnosed with schizophrenia and 52 control subjects with no psychiatric or neurological disorders. Selected brain tissue lysates were first explored for IgG reactivity on planar microarrays composed of 11,520 protein fragments representing 10,820 unique proteins. Based on these results of ours and other previous studies of autoantibodies related to psychosis, we selected 226 fragments with an average length of 80 amino acids, representing 127 unique proteins. Tissue-based analysis of IgG reactivities using antigen suspension bead arrays was performed in a multiplex and parallel fashion for all 125 subjects. Among the detected autoantigens, higher IgG reactivity in subjects with schizophrenia, as compared to psychiatrically healthy subjects, was found against the glutamate ionotropic receptor NMDA type subunit 2D (anti-GluN2D). In a separate cohort with serum samples from 395 young adults with a wider spectrum of psychiatric disorders, higher levels of serum autoantibodies targeting GluN2D were found when compared to 102 control individuals. By further validating GluN2D and additional potential autoantigens, we will seek insights into how these are associated with severe mental illnesses.

A multi-season field trial was carried out to investigate the effect of the amendment of biochar, lime, ash and washed biochar on the growth of maize. A degraded, strongly acidic Ultisol (pH KCl 3.60), with a relatively high exchangeable aluminium content (2.4 cmol c /kg) and a low exchangeable calcium content (0.99 cmol c /kg), was used. Soil was treated once at the beginning of the field trial and crop growth was monitored over seven planting seasons (PS). All treatments increased maize yield. The average increases were; seven times for biochar, five times for lime, five times for washed biochar and eight times for ash treatment, when compared to the control across all PS. The effect of biochar, lime and ash treatments on maize yield were sustained over the seven PS. Soil pH KCl was significantly increased (p < 0.05 level) following the addition of all of the amendment materials. All treatments significantly reduced the concentration of Al 3+ when compared to the control (p < 0.05), with the lowest concentrations for the lime and ash treatments. The ash treatment also increased the concentration of macronutrients (K, P and Mg) to the greatest extent. Results showed that there was a clear liming effect at play. The better performance of biochar compared to lime, despite lime having the highest pH and the lowest Al 3+ concentration, can be explained by the additional K, Mg and P the biochar adds to the soil. Results also showed a clear nutrient addition effect where ash added the most nutrients. Overall, this work supports the fact that small scale farmers in Indonesia should produce biochar from their waste agricultural materials. Doing so not only provides an increase in crop productivity, but also sequesters carbon resulting in the best overall environmental benefit., Competing Interests: Declaration of competing interest The authors declare no conflicts of interest., (Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Neurodegenerative diseases feature stereotypical deposits of protein aggregates that selectively accumulate in vulnerable cells. The ability to simultaneously localize multiple targets in situ is critical to facilitate discovery and validation of pathogenic molecular pathways. Immunostaining methods enable in situ detection of specific targets. Effective stripping of antibodies, allowing successive rounds of staining while maintaining tissue adhesion and antigen integrity, is the main roadblock for enabling multiplex immunostaining in standard labs. Furthermore, stripping techniques require antibody-specific optimization, validation, and quality control steps., New Method: Aiming to create protocols for multiplex localization of neurodegenerative-related processes, without the need for specialized equipment, we evaluated several antibody stripping techniques. We also recommend quality control steps to validate stripping efficacy and ameliorate concerns of cross-reactivity and false positives based on extensive testing., Results: A protocol using β-mercaptoethanol and SDS consistently enables reliable antibody stripping across multiple rounds of staining and minimizes the odds of cross-reactivity while preserving tissue adhesion and antigen integrity in human postmortem tissue., Comparison With Existing Methods: Our proposed method is optimal for standard lab settings and shows consistent efficacy despite the intricacies of suboptimal human postmortem tissue and the need to strip markers bound to highly aggregated proteins. Additionally, it incorporates quality control steps to validate antibody stripping., Conclusions: Multiplex immunofluorescence methods for studying neurodegenerative diseases in human postmortem tissue are feasible even in standard laboratories. Nevertheless, evaluation of stripping parameters during optimization and validation phases of experiments is prudent., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Cadmium (Cd) is an on-going environmental pollutant associated with hindered plant growth. In response, plants possess various strategies to alleviate Cd stress, including reactive oxygen species (ROS) scavenging and chelation-mediated Cd detoxification. The present study examined the Cd defense mechanism of perennial ryegrass (Lolium perenne L.), taking into account the effect of exogenous phosphorus (P) input. It was found that despite triggering antioxidant enzyme activity, Cd stress heightened lipid peroxidation levels. Exogenous P input partially mitigated the lipid peroxidation impact and decreased the levels of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) antioxidant enzymes, revealing reduced ROS-scavenging activity. Importantly, notable relationships were determined between the amount of Cd uptake in the root and the amount of non-protein thiols (R 2  = 0.914), glutathione (R 2  = 0.805) and phytochelatins (R 2  = 0.904) in proportion to the amount of exogenous P applied. The levels of amino acids proline and cysteine were also enhanced by exogenous P input showing their influence in alleviating Cd stress. Overall, it is reported that Cd detoxification in ryegrass plants can be stimulated by exogenous P input, which facilitates chelation-mediated Cd detoxification processes., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Rationale: Acidic subtropical forest soils that receive high atmospheric nitrogen (N) deposition have been identified as important sources of nitric oxide (NO). The relative importance of major processes producing NO is unclear., Methods: To partition NO sources, we conducted an in situ tracing experiment with 15 NH 4 NO 3 and NH 4 15 NO 3 in well-drained acid soils of an N-saturated subtropical forest in Chongqing, southwest China., Results: In the 15 NH 4 NO 3 treatment, the 15 N signature of NO emitted from the foot of the hillslope (Lower site) was similar to that of the NH 4 + pool, indicating predominant autotrophic nitrification for NO formation. In the NH 4 15 NO 3 treatment, the 15 N enrichment of NO was smaller than that of the NO 3 - pool, suggesting minor contribution of denitrification to NO production (~15%)., Conclusions: Nitrification is the main process responsible for NO emissions, even in monsoonal summers when soil water-filled pore space values are relatively high., (© 2019 John Wiley & Sons, Ltd.)

The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Background: G protein-gated inwardly rectifying potassium (GIRK) channels are involved in the regulation of neuronal excitability. Four GIRK subunits (GIRK1-4) are expressed in rat dorsal root ganglia (DRGs). Recently, we have characterized the expression of GIRK1 and -2, and both are downregulated in rat DRGs and spinal cord after a complete sciatic nerve transection (axotomy). Here, we aimed to study the neurochemical characteristics of GIRK3, and its regulation in rat DRGs and spinal cord induced by nerve injury., Methods: A sciatic nerve axotomy was performed to study the influences of injury on GIRK3 expression in DRGs and spinal cord. A dorsal root rhizotomy and a sciatic nerve crush were employed to study the axonal transport of GIRK3 protein, respectively. Immunohistochemistry analysis was employed for investigating the neurochemical characteristics of GIRK3., Results: In control DRGs, ~18% of neuron profiles (NPs) were GIRK3-positive ( + ), and ~41%, ~48% and ~45% of GIRK3 + NPs were CGRP + , IB4 + and NF200 + , respectively. GIRK3-like immunoreactivity was observed in glabrous skin of hind paws and axons originating from DRG neurons. Fourteen days after axotomy, more than one-third of DRG NPs were GIRK3 + , and among these ~51% and ~56% coexpressed galanin and neuropeptide Y, respectively. In control animals, a small group of interneurons found in the dorsal horn was GIRK3 + . In addition, GIRK3 + processes could be observed in superficial laminae of spinal dorsal horn. After nerve injury, the intensity of GIRK3-like immunoreactivity in the superficial layers was increased. Evidence based on rhizotomy and sciatic nerve crush indicated both anterograde and retrograde transport of GIRK3., Conclusion: Our study demonstrates that GIRK3 is expressed in sensory neurons and spinal cord. GIRK3 has both anterograde and retrograde axonal transport. GIRK3 expression can be regulated by peripheral nerve injury., Competing Interests: The authors report no conflicts of interest in this work., (© 2020 Lyu et al.)

Conservation farming (CF), involving basin tillage, residue retention and crop rotation, combined with biochar may help to mitigate negative impacts of conventional agriculture. In this study, the effects of CF on the amount and quality of soil organic matter (SOM) and potential nitrogen (N) mineralization were investigated in a maize-soya-maize rotation in an Acrisol in Zambia. A large field was run under CF for 7 years and in the subsequent three growing seasons (2015-2018), four management practices were introduced to study effects on soil characteristics and crop yield. We tested i) a continuation of regular CF (CF-NORM) ii) CF without residue retention (CF-NO-RES); iii) Conventional (CONV), with full tillage and removal of residues; and iv) CF with 4 ton ha-1 pigeon pea biochar inside basins and residue retention (CF-BC). The experiment involved the addition of fertilizer only to maize, while soya received none. Soya yield was significantly higher in CF systems than in CONV. Maize yields were not affected by the different management practices probably due to the ample fertilizer addition. CF-NORM had a higher stock of soil organic carbon (SOC), higher N mineralization rates, more hot-water extractable carbon (HWEC; labile SOC) and particulate organic matter (POM) inside basins compared to the surrounding soil (outside basins). Our results suggest that the input of roots inside basins are more effective increasing SOM and N mineralization, than the crop residues that are placed outside basins. CONV reduced both quality and quantity of SOM and N mineralization as compared to CF inside basins. CF-BC increased the amount of SOC as compared with CF-NORM, whereas N mineralization rate and HWEC remained unaffected. The results suggest benefits on yield of CF and none of biochar; larger impact of root biomass on the build-up of SOM than crop residues; and high stability of biochar in soil., Competing Interests: The authors have declared that no competing interests exist.

FRMD6, a member of the group of FERM-domain proteins, is involved both in communication between cells, interactions with extracellular matrix, cellular apoptotic and regenerative mechanisms. FRMD6 was first discovered in the rodent sciatic nerve, and in the present immunohistochemical study we investigated the distribution of FRMD6 in the dorsal root ganglia (DRGs), sciatic nerve and spinal cord following sciatic nerve injury. FRMD6-immunoreactivity was found in the cytoplasm, nucleus or both, and in a majority of DRG neurons. FRMD6-immunoreactivity co-existed with several well-known neuronal markers, including calcitonin gene-related peptide, isolectin B4 and neurofilament 200 in mouse DRGs. After peripheral nerve injury, the FRMD6 mRNA levels and the overall percentage of FRMD6-positive neuron profiles (NPs) were decreased in ipsilateral lumbar DRGs, the latter mainly affecting small size neurons with cytoplasmic localization. Conversely, the proportion of NPs with nuclear FRMD6-immunoreactivity was significantly increased. In the sciatic nerve, FRMD6-immunoreactivity was observed in non-neuronal cells and in axons, and accumulated proximally to a ligation of the nerve. In the spinal cord FRMD6-immunoreactivity was detected in neurons in both dorsal and ventral horns, and was upregulated in ipsilateral dorsal horn after peripheral nerve axotomy. Our results demonstrate that FRMD6 is strictly regulated by peripheral nerve injury at the spinal level.

Maternal drug abuse during pregnancy is a rapidly escalating societal problem. Psychostimulants, including amphetamine, cocaine, and methamphetamine, are amongst the illicit drugs most commonly consumed by pregnant women. Neuropharmacology concepts posit that psychostimulants affect monoamine signaling in the nervous system by their affinities to neurotransmitter reuptake and vesicular transporters to heighten neurotransmitter availability extracellularly. Exacerbated dopamine signaling is particularly considered as a key determinant of psychostimulant action. Much less is known about possible adverse effects of these drugs on peripheral organs, and if in utero exposure induces lifelong pathologies. Here, we addressed this question by combining human RNA-seq data with cellular and mouse models of neuroendocrine development. We show that episodic maternal exposure to psychostimulants during pregnancy coincident with the intrauterine specification of pancreatic β cells permanently impairs their ability of insulin production, leading to glucose intolerance in adult female but not male offspring. We link psychostimulant action specifically to serotonin signaling and implicate the sex-specific epigenetic reprogramming of serotonin-related gene regulatory networks upstream from the transcription factor Pet1/Fev as determinants of reduced insulin production., (© 2019 The Authors. Published under the terms of the CC BY 4.0 license.)

Purpose: To compare the 2-year cumulative survival rates of class II restorations made according to Atraumatic Restorative Treatment (ART) with axial grooves and the high-viscosity glass-ionomer cement (HVGIC) Equia Fil (GC) and the conventional method using the resin composite Filtek Z250 (3M Oral Care). Materials and Methods: A parallel-group study design and a stratified randomization process (DMFS count and cavity size) were applied. Restorations were evaluated according to the ART restoration and USPHS criteria. Data were statistically analyzed using the proportional hazard rate regression model with frailty correction. Results: 272 class II restorations were placed in 131 people (mean age 26.2 years) by two dentists. The dropout rate of restorations was 2.6%. According to ART restoration and USPHS criteria, the 2-year cumulative survival rates of class II ART/HVGIC restorations were 96.2% and 97.0%, respectively, and 97.8% and 98.5%, respectively, for the conventional class II resin-composite restorations. No differences were observed in the cumulative survival rates between the two treatment groups at 2 years (ART criteria: p=0.26; USPHS criteria p=0.23). Conclusion: HVGIC Equia Fil used in the ART method with axial grooves and Filtek Z250 in the conventional method provided high survival rates for restoring class II cavities over 2 years.

Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The aim of this clinical trial was to compare the 5-year cumulative survival of atraumatic restorative treatment restorations using high-viscosity glass-ionomer restorations (ART/HVGIC) and conventional resin composite restorations (CRT) placed in patients with intellectual and/or physical disability. Patients referred for restorative care to a special care service in Córdoba, Argentina, were recruited. Patients and/or caregivers were provided with written and verbal information regarding treatment options and selected the alternative they preferred. The treatment protocols were ART (hand instruments/HVGIC) in the clinic or CRT (rotary instrumentation/resin composite) in the clinic or under general anaesthesia (GA). Two independent, trained and calibrated examiners evaluated restoration survival using established ART codes after 6, 12, 24, 36 and 60 months. The proportional hazard model with frailty corrections provided survival estimates. Jackknife errors were used to test 5-year results. Sixty-six patients (13.6 ± 7.8 years) with 16 different medical conditions participated. CRT in the clinic proved feasible for five patients (13%), and 14 patients received CRT under GA (21%). ART was provided for 47 patients (71.2%). A total number of 298 dentine carious lesions were restored in primary and permanent teeth (182 ART; 116 CRT). Four patients died between the 3 and 5-year follow up. Percentage survival and jackknife standard error were calculated and were significantly higher for all ART/HVGIC restorations (90.2% ± 2.6) than for all CRT restorations (82.8% ± 5.3), 5 years after placement (p=0.044). These 5-year follow-up results confirm that ART/HVGIC is an effective treatment protocol for patients with disability, equal to that of conventional resin composite restoration. The results of this clinical trial support the use of ART as an evidence-based treatment resource contributing to the reduction of inequalities in access to oral health care among people with disability.

Background: A better definition of biomarkers and biological processes related to local recurrence and disease progression is highly warranted for ductal breast carcinoma in situ (DCIS). Stromal-epithelial interactions are likely of major importance for the biological, clinical, and pathological distinctions between high- and low-risk DCIS cases., Methods: Stromal platelet derived growth factor receptor (PDGFR) was immunohistochemically assessed in two DCIS patient cohorts (n = 458 and n = 80). Cox proportional hazards models were used to calculate the hazard ratios of recurrence. The molecular mechanisms regulating stromal PDGFR expression were investigated in experimental in vitro co-culture systems of DCIS cells and fibroblasts and analyzed using immunoblot and quantitative real-time PCR. Knock-out of JAG1 in DCIS cells and NOTCH2 in fibroblasts was obtained through CRISPR/Cas9. Experimental data were validated by mammary fat pad injection of DCIS and DCIS-JAG1 knock-out cells (10 mice per group). All statistical tests were two-sided., Results: PDGFRα(low)/PDGFRβ(high) fibroblasts were associated with increased risk for recurrence in DCIS (univariate hazard ratio = 1.59, 95% confidence interval [CI] = 1.02 to 2.46; P = .04 Wald test; multivariable hazard ratio = 1.78, 95% CI = 1.07 to 2.97; P = .03). Tissue culture and mouse model studies indicated that this fibroblast phenotype is induced by DCIS cells in a cell contact-dependent manner. Epithelial Jagged1 and fibroblast Notch2 were identified through loss-of-function studies as key juxtacrine signaling components driving the formation of the poor prognosis-associated fibroblast phenotype., Conclusions: A PDGFRα(low)/PDGFRβ(high) fibroblast subset was identified as a marker for high-risk DCIS. The Jagged-1/Notch2/PDGFR stroma-epithelial pathway was described as a novel signaling mechanism regulating this poor prognosis-associated fibroblast subset. In general terms, the study highlights epithelial-stromal crosstalk in DCIS and contributes to ongoing efforts to define clinically relevant fibroblast subsets and their etiology., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)