dataesr/scientific-paragraphs-categorization huggingface dataset:
Our data does not exclude the possibility that AGMs might access blood material with a slower rate when compared with WAT macrophages. To gain further insight into AGM morphology in their native environment, we performed electron-microscopy analysis of adrenal glands. Macrophage presence in adrenal glands was sparse. Cells with a macrophage morphology were observed, and their surrounding cells contained lipid droplets (Figure  S5B ). Electron-microscopy analysis of purified macrophages showed that, compared with peritoneal macrophages, AGMs were enriched in structures resembling lipid droplets (Figure  S5C , red arrows). This suggests that AGMs might uptake material, likely lipid derivatives, produced and released by neighboring cells and possibly dead cells and thus contribute to tissue lipid homeostasis.
We next investigated whether AGMs might be involved in the control of norepinephrine (NE) release, a hormone produced by the adrenal gland medulla. Our scRNA-seq data indicated that AGMs express enzymes involved in NE degradation, namely monoamine oxidase (Maoa) and Comt (Figure  S5D ). Maoa expression was low in adrenal gland immune cells with only few macrophages possessing detectable Maoa mRNA (Figure  S5D ). Comt expression was detected in several populations of adrenal gland immune cells (Figure  S5D ). In our dataset, we did not detect the expression of enzymes involved in NE synthesis in immune cells (Th, Ddc, and Dbh) (data not shown). To investigate whether AGMs can degrade NE, we sorted CD64 + MerTK + cells and incubated them overnight in the presence of NE and clorgyline, a selective Maoa pharmacological inhibitor.
Nox2 was implicated in macrophage ROS generation and microbial killing  (Bedard and Krause, 2007). Furthermore, Nox2 is also involved in Cyp11b2dependent aldosterone generation by adrenal gland cortical cells  (Rajamohan et al. , 2012). Our data revelated that AGM subsets express high Cybb mRNA levels when compared with other adrenal gland immune cells (Figure  S6F ). Since macrophage depletion was correlated with a loss of adrenal Cybb mRNA expression, we decided to investigate whether local aldosterone levels were affected in macrophage-depleted adrenal glands. For this purpose, we housed mice at 4 C for 12 h. Indeed, cold exposure has been shown to trigger a stress response and increased systemic corticosterone concentration  (Williams et al. , 2017). To assess whether hormone production was modulated by macrophages in cold-challenged mice, we injected isotype control or anti-CD115-blocking Ab, and we evaluated local production and systemic levels of corticosterone and aldosterone.
During stress induction, macrophage depletion resulted in lower aldosterone local production. The very same trend was also observed for corticosterone. Increased aldosterone production leads to hypertension. Thus, controlling adrenal gland aldosterone production and release are critical to prevent hypertension. Our data suggest a role for macrophages in adrenal gland aldosterone generation. However, the administration of anti-CD115 Ab leads to macrophage depletion in multiple tissues  (Carrero et al. , 2017). Therefore, decreased aldosterone production in adrenal glands might not be a direct consequence of AGM depletion. To test the causal role of AGMs in the control of aldosterone production upon stress, one would need to selectively deplete adrenal macrophages without affecting macrophage populations in other organs.
Flow cytometry analysis Tissues were harvested and washed in PBS. Adipose depots surrounding the adrenal glands were carefully removed before shredding the tissue with scissors. Then the samples were incubated for 30 min at 37 C in PBS containing 300 mg/mL Liberase and 100 mg/mL DNAse I. The resulting suspension was homogenized using a syringe and a 20G needle, passed through a 100 mm sieve and centrifuged at 400g for 5 min. Cells were then resuspended in FACS buffer (PBS containing 0. 3 mM EDTA and 0. 06% BSA), stained for 30 min at 4 C in the dark and then washed. A viability stain (DAPI or Live/Dead fixable viability dye) was used whenever possible. Conventional cytometry data were acquired on a BD FACS Canto II or BD LSRFortessa X-20. Spectral cytometry data were acquired on a Cytek Aurora cytometer.
Serum samples and ion standard solutions were previously diluted (1/100), deproteinized by addition of acetonitrile (dilution 1:1 volume) mixed and centrifuged at 12,000g (10 min at 4 C). Ion concentrations of the supernatants were determined using an ion chromatography Dionex ICS-5000 plus system (Thermo Scientific). The system included an autosampler, pumps, eluent generator and conductivity detectors. The system is equipped with an eluent generator cartridge (Dionex EGC500MSA) and a cation column (IonPac AS-11 HC, 2 mm). Ion concentrations were determined using Chromeleon software (Thermo Scientific) by measuring surface area of the peaks and were compared to the corresponding ion standard profiles. Single-cell RNA-seq data analysis Cells were loaded on a Chromium Controller (103 Genomics) with a target output of 5000 cells per sample.
4. 3). For analysis, Seurat package (version 3. 1. 0) was used, genes which express in less than 2 cells and cells which have non-zero counts in less than 200 genes were additionally filtered from both barcode expression matrices, and the result matrices were used as analysis inputs  (Butler et al. , 2018). The fraction of mitochondrial genes was calculated for every cell, and cells with a mitochondrial fraction >1. 2% were filtered out. After all filtering procedures, 3,636 cells were left in the scRNA-seq data of the female sample, and 2,240 cells were left in scRNA-seq of the male sample. Both samples were normalized using SCTransform function with mitochondrial content as variable to regress out in a second nonregularized linear regression  (Hafemeister and Satija, 2019). For integration purpose, variable features across the samples were selected by SelectIntegrationFeatures function with the number of features equal to 2000.
Then the object was prepared for integration (PrepSCTIntegration function), the anchors were found (FindIntegrationAnchors function) and the samples were merged into the whole object (IntegrateData function)  (Stuart et al. , 2019). The dimensionality of the object was reduced by principal component analysis (PCA), and the first 20 principal components (PCs) were used further to obtain uniform manifold approximation and projection (UMAP) dimensionality reduction by RunUMAP function. Graph-based clustering was run using FindNeighbors and FindClusters with a resolution of 1. 0 and the first 20 PCs as input, and the 21 clusters were identified. Differential expression analysis was implemented using MAST package. During manual cluster annotation using canonical gene markers, a cluster corresponding to doublets of NK cells and macrophages was identified and excluded from the main figures.
ACKNOWLEDGMENTS We would like to thank the C3M animal facility for technical support and the  GIS-IBISA multi-sites platform Microscopie Imagerie Côte d'Azur (MICA ), and particularly the imaging site of  C3M  supported by  Conseil Regional, Conseil Departemental, and IBISA. We sincerely thank  Narges Khedher  and  Marie Irondelle  for their help. We would like to thank  Fabien Labbal  and  Kevin Lebrigand  and the  UCA Genomix Platform. We acknowledge the flow cytometry facility from the  ''Institut de Pharmacologie Moleculaire et Cellulaire '' part of the  MICA GIS IBiSA  labeled platform and the  UMN flow cytometry core facility. A. G. was supported by the  French government through the UCAJedi Investments  in the Future projects managed by the  National Research Agency (ANR)  ( ANR-15-IDEX-01 ).
M. M. F. and K. Z. were supported by  Government of Russian Federation  (grant  08-08 ). K. -W. K. is supported by  NIH  ( DK126753 ). R. R. G. is supported by  Centre National de la Recherche Scientifique (CNRS). L. Y. -C. is supported by  Institut National de la Santeet de la Recherche Medicale (INSERM) ,  Fondation de France  ( 00066474 ), and the  European Research Council  ( ERC) consolidator program  ( ERC2016COG724838 ). J. W. W. was supported by  National Institutes of Health  ( HL138163 ) and  American Heart Association  ( CDA 855022 ). S. I. was supported by  INSERM  and  Agence Nationale de la Recherche  ( ANR-17-CE14-0017-01  and  ANR-19-ECVD-0005-01 ). D. D. was supported by grants from the  ANR  and the  European Union :  EGID ANR-10-LABX-46. R. J. A. was supported by  ANR-20-CE-CE14-0028-01  and  CoPoC MAT-PI-17493-A-04.
37 Assessment of large genomic databases suggests an incidence of 1 per 715,000. 38 entralized diagnostics in the Netherlands for 2 decades yield an incidence of 1 per 80,000-100,000 live births and prevalence of 1. 4 per 1,000,000 without evidence of founder effects. 4 So, VWM is an ultra-rare disease, but clinical observations suggest a higher incidence than estimations based on databases. Although disease incidence is highest at young ages, prevalence is mainly attributable to adolescent and adult patients. Although two-thirds of the patients in the natural history study have an onset <6 years (Figure  5A ),  4  two-thirds of the known living patients are ≥16 years (Figure  5B ). Epidemiology varies greatly for different geographic areas (Figure  5C ). No important consanguinity or founder effects were observed, suggesting that the higher incidence observed in Europe may reflect the actual incidence and that VWM may be underdiagnosed outside Europe, especially in adults (Figure  5C ).
To reach consensus, a modified real-time (rt) Delphi procedure was executed, using EDELPHI 2021 software. 43 This online software tool allows participants to give and revise their opinion within a predefined period. A systematic literature review on VWM and a recently performed Delphi procedure among experts on MLD served as input; consortium members could add scales and questionnaires, based on individual experience. In total, 24 clinical scales and questionnaires were reviewed. The 16 recommended instruments that comprehensively assess all relevant clinical domains are presented in Table  2  and supplementary file, links. lww. com/NXG/A512. Currently, body fluid biomarkers, discussed above, and quantitative MRI parameters relevant to brain white matter integrity provide exploratory outcome measures.
Acknowledgment The authors thank  Prof. Arjen B. Brussaard , director of  Amsterdam Neuroscience, The Netherlands , for his continuous support of the VWM consortium. The authors are grateful to  Daphne Schoenmakers, MD  and PhD student at the  Department of Child Neurology, Amsterdam University Medical Center, The Netherlands , for setting up and executing the Delphi procedure. The authors thank  Menno Stellingwerff, MD  and PhD student at the  Department of Child Neurology, Amsterdam University Medical Center , for providing numbers and figures from the VWM registry. MSvdK, EB, IK-M, and  NIW  are members of the European Reference Network for Rare Neurological Disorders (ERN- RND ), project  ID 739510. AV, JLB, and AF are members of the  Global Leukodystrophy Initiative Clinical Trials Network (GLIA-CTN) ,  U54NS115052.
Study Funding No targeted funding reported. Disclosure M. S. van der Knaap is a consultant for Calico and coinvestigator for the Alexander disease trial of Ionis and received research support from the  NWO Spinoza award, ZonMw TOP  grant  91217006 ,  European Leukodystrophy Foundation  grant  2017-02712 ,  European Leukodystrophy Foundation  grant  2019-P001 ,  Hersenstichting  grant  DR-2019-00285 ,  Vanishing White Matter Foundation ,  Chloe Saxby  and VWM Disease Incorporated, and  VWM Families Foundation Inc. She has a patent P112686CA00, therapeutic effects of Guanabenz treatment in vanishing white matter, pending to  VU University Medical Center. She is principal investigator of the Guanabenz trial (EU Clinical Trials register with EudraCT number  2017-001438-25 , clinicaltrialsregister.
other possible confounders in a regression framework. Statistical methods should take into consideration the nature of the matching, with weighted least squares analysis typically required when one-to-many matching is used. Single-arm trials can be adequately powered for detection of large treatment effects. The current single-arm trial in- vestigating the efficacy of guanabenz in ambulatory patients with VWM with age at onset <6 years (clinicaltrialsregister. eu/ ctr-search/trial/2017-001438-25/NL) uses time until loss of ambulation as the primary efficacy outcome measure. To es- timate the number of patients needed, we determined that in the absence of treatment, based on the VWM natural history study, 4 the proportion of ambulatory patients 2 years after disease onset is estimated to be approximately 60%.
Whole genome sequencing and analysis Whole genome sequencing (WGS) was performed on all non-NDM isolates with SUL-DUR MIC values of ≥ 8 mg/L on a MiSeq instrument (Illumina, San Diego, CA) using the Nextera sample preparation method (2 × 300 bp paired-end reads and a coverage of ≥50X). Reads were assembled into contigs using the Shovill pipeline ( https://github. com/tseemann/shovill ) and contigs were annotated using Prokka software  [11]. Sequence types (STs), the presence of resistance genes, and the confirmation of speciation were determined using MLST (Multilocus sequence typing) 2. 0, ResFinder 4. 1  [12]  , and KmerFinder 3. 2  [13]  software available on the Center for Genomic Epidemiology platform ( https://cge. cbs. dtu. dk/services/ ). Mutations and substitutions in PBPs were identified by sequence extraction and comparison with the A.
baumannii ATCC 17978 genome (GenBank Accession No. CP018664). NCBI BLAST (National Center for Biotechnology Information Basic Local Alignment Search Tool) was used to investigate the prevalence of PBP protein sequences, and variants producing < 10 hits were considered 'uncommon'. Novel blaADC alleles, blaADC-259 and blaADC-260 , were submitted to GenBank under accession numbers OK340849 and OK396701, respectively.
Penicillin binding proteins Within the 25 SUL-DUR-resistant isolates, 17 (68%) were found to encode PBP3 and exhibit a series of substitutions comparable to those of the wildtype sequences; PBP3 was the primary target of SUL in A. baumannii  [25]. Five different PBP3 substitutions, relative to A. baumannii ATCC 17978, were identified, two of which were identified in 2 (T526S) and 12 (A515V) isolates, respectively. The latter substitutions have been previously shown to be associated with resistance to SUL-DUR  [ 19-21 , 26 ]. The remaining three isolates harbored N392T, I517N, and V565L substitutions in their PBP3 sequences which, to our knowledge, have not been previously described as a cause or contributing factor to antibiotic resistance. Because no substitutions could be identified within the PBP3 sequence compared with the reference sequence in eight isolates, the sequences of other PBPs were analyzed accordingly, and substitutions were investigated both by comparison with the reference genome ATCC 17978 and by BLAST analyses.
Six strains had substitutions in PBP2, a target for DUR  [7]  , including Q106L (n = 2), P665A (n = 3), and P662T (n = 1). However, BLAST analyses revealed that only P662T could be considered an 'uncommon' substitution if we consider < 10 BLAST hits to be 'uncommon'. Within PBP1a, another SUL target, one isolate harbored a G181S substitution and two isolates had T38A, A244T, Q644K, and T776A changes, but only the G181S and Q644K were found to be 'uncommon' when compared with sequences in GenBank. Nineteen isolates carried substitutions within PBP1b: 15 with P112S; 2 with M726V; 1 with N513H; and one isolate showing both P112S and P545L substitutions. However, only the P545L substitution could be considered potentially significant. Apart from the known PBP targets (PBP1a, 1b, 2, and 3) for SUL and DUR, one isolate (N933) harbored a transposon insertion after T302 in PBP6b.
Outer membrane proteins No significant mutations or disruptions in major porin encoding genes ( ompA, carO, ompW , and oprD) were detected by analysis of sequences obtained by WGS (data not shown). Of particular note was the high level of sequence conservation between SUL-DUR-resistant and SUL-DUR-susceptible strains for ompA , despite this porin being reported to be involved in DUR permeation into A. baumannii cells  [27]. This suggests that SUL-DUR resistance in the isolates from this study is not related to ompA -mediated uptake.
OBJECTIVES: This work aimed to investigated the changes in metabolic levels associated with natural MAP infection in infected and infectious dairy cattle METHODS: The study included sera from 23 infectious/seropositive, 10 infected but noninfectious/seronegative, and 26 negative animals. The samples were selected from a collection of samples gathered during a prospective study. The samples were analyzed by quantitative nuclear magnetic resonance (NMR) spectroscopy and routine blood chemistry. The blood indices and the 1 H NMR data were concatenated by low-level data fusion, resulting in a unique global ngerprint. Afterwards, the merged dataset was statistically analyzed by the least absolute shrinkage and selection operator (LASSO), which is a shrinkage and selection method for supervised learning.
NMR Quanti cation using MagMET For quanti cation, all 1 H-NMR spectra were processed and analyzed using a MagMET software package developed in-house  (22). MagMET allows for qualitative and quantitative analysis of an NMR spectrum by automatically tting spectral signatures from an internal database to the spectrum. Speci cally, the spectral tting for metabolites was done using the standard serum metabolite library. Typically, all of the visible peaks were assigned. Most of the visible peaks were annotated with a compound name. It has been previously shown that this tting procedure provides absolute concentration accuracy of 90% or better.
Statistical Analysis The statistical analysis was performed by using RStudio software 4. 0. 2 with caret package  (23) , a useful package for model implementation. The 1 H NMR spectra were autoscaled, while the blood chemistry data were normalized by k-nearest neighbor imputation. Afterwards, the two datasets were concatenated by low-level data fusion. Low-level data fusion is a simple concatenation of data in a unique table  (24, 25). The merged dataset was submitted to the LASSO method, a multinomial regression with L1 penalty, with the aims of i) selecting and shrinking of variables, and ii) predicting the health status of animals, i. e. negative, MAP-infected, or MAP-infectious. An expanded grid function was carried out to search and select the best penalty value. Moreover, in order to select the best classi er generated by LASSO, a 10-time repeated 5-fold cross validation was performed on the concatenated data using the retrieved informative features.
Statistical Evaluation A cumulative odds ordinal logistic regression with proportional odds was run t termine the effect of eye shape, pupillary dilation quality, and iris color on the qual the fundus assessment using the Peek Retina ®. In this analysis, the parameters for eye (left and right of each bird) were considered as independent. Odds ratios wer ported with 95% confidence intervals, and values of p < 0. 05 were considered statisti significant. All statistical tests were performed using the IBM SPSS Statistics soft (IBM Corp. Released 2017. IBM SPSS Statistics for Windows, Version 25. 0. IBM Corp monk, NY, USA).
Statistical Evaluation A cumulative odds ordinal logistic regression with proportional odds was run to determine the effect of eye shape, pupillary dilation quality, and iris color on the quality of the fundus assessment using the Peek Retina ®. In this analysis, the parameters for each eye (left and right of each bird) were considered as independent. Odds ratios were reported with 95% confidence intervals, and values of p < 0. 05 were considered statistically significant. All statistical tests were performed using the IBM SPSS Statistics software (IBM Corp. Released 2017. IBM SPSS Statistics for Windows, Version 25. 0. IBM Corp. , Armonk, NY, USA).
MATERIAL AND METHODS The protocol of the study was approved by the Ethics Committee for Animal Care and Experimentation of the Université de Sherbrooke; the experiment was performed in keeping with the recommendations of the Canadian Council on Animal Care. Sixteen full-term, male mixed-bred lambs, aged 2-4 days and weighing 3. 3 ± 0. 5 kg (range: 2. 6-4. 2 kg), were included in this crossover design study. More precisely, eight lambs were used for studying the systemic inflammation and cardiorespiratory alterations induced by Poly I:C injection, and eight control lambs were used to assess brainstem inflammation. In the first-ever study on the potential for Poly I:C injection to provide a model of early-life sepsis, we chose to include only male lambs. This is supported by literature data reporting that male sex is a well-known risk factor for SIDS  28  and might also be associated with late-onset sepsis in preterm infants.
Data analysis Video analysis of locomotor activity. The total distance traveled and the percentage of time the animal was active throughout the recordings were calculated with custom-built software, as previously described. 27 ates of alertness. Quiet and active wakefulness, as well as non-rapid eye movement (NREM) and rapid eye movement (REM) sleep were defined in keeping with standard electrophysiological and behavioral criteria. 34 rdiac and respiratory function. Electrocardiogram, arterial blood pressure and respiratory movements were continuously recorded for 6 h in both saline and Poly I:C conditions. The following variables were calculated every 15 min, as previously reported:  27  (i) respiratory frequency (f R ) averaged on 60 s, and heart rate (HR) and mean arterial pressure averaged on 30 s; (ii) the number of apneas (defined as at least two missed breaths) and total apnea duration; (iii) the number of cardiac decelerations (defined as a decrease in HR greater than 30% lasting less than 5 s); and (iv) the number of bradycardias (defined as cardiac decelerations lasting at least 5 s).
A quantitative 3Dmorphological analysis of each image was then performed with 3DMorph automatic analysis software to provide the individual volume of microglial cells as well as their total territorial volume. Real-time quantitative PCR. The medulla oblongata was kept in a TRIzol solution at -80 °C, followed by total RNA extraction and verification of RNA integrity. Reverse transcription and quantitative PCR amplification were then performed in triplicate with the appropriate primers for the earlyonset inflammatory and apoptosis mediators IL-6, IL-8, TNF-α, and caspase-3. The PCR probes and primers used are reported in Table  1  in the Supplementary Material.
Statistical analysis Statistical analyses were performed under the close guidance of the biostatistics department of our research center. All analyses were carried out on raw data for all dependent variables and expressed as median (Q1, Q3). Since all quantitative variables-rectal temperature, locomotor activity, states of alertness, apnea number, total apnea duration, cardiac deceleration and bradycardia number, total cardiac deceleration duration, heart-rate and respiratory-rate variability, cardiorespiratory interrelationsdid not follow a normal distribution (Shapiro-Wilk test), the Wilcoxon signed-rank test was used to assess the effect of Poly I:C injection for all comparisons (SPSS Statistics, version 25, Armonk, NY). A sensitivity power analysis based on a Wilcoxon signed-rank test concluded that the minimum detectable standardized difference-Cohen's d z , expressed in standard deviation units  45  -was 1.