An active texture-based digital atlas enables automated mapping of structures and markers across brains.

Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.

Laminin targeting of a peripheral nerve-highlighting peptide enables degenerated nerve visualization.

Target-blind activity-based screening of molecular libraries is often used to develop first-generation compounds, but subsequent target identification is rate-limiting to developing improved agents with higher specific affinity and lower off-target binding. A fluorescently labeled nerve-binding peptide, NP41, selected by phage display, highlights peripheral nerves in vivo. Nerve highlighting has the potential to improve surgical outcomes by facilitating intraoperative nerve identification, reducing accidental nerve transection, and facilitating repair of damaged nerves. To enable screening of molecular target-specific molecules for higher nerve contrast and to identify potential toxicities, NP41's binding target was sought. Laminin-421 and -211 were identified by proximity-based labeling using singlet oxygen and by an adapted version of TRICEPS-based ligand-receptor capture to identify glycoprotein receptors via ligand cross-linking. In proximity labeling, photooxidation of a ligand-conjugated singlet oxygen generator is coupled to chemical labeling of locally oxidized residues. Photooxidation of methylene blue-NP41-bound nerves, followed by biotin hydrazide labeling and purification, resulted in light-induced enrichment of laminin subunits α4 and α2, nidogen 1, and decorin (FDR-adjusted P value < 10-7) and minor enrichment of laminin-γ1 and collagens I and VI. Glycoprotein receptor capture also identified laminin-α4 and -γ1. Laminins colocalized with NP41 within nerve sheath, particularly perineurium, where laminin-421 is predominant. Binding assays with phage expressing NP41 confirmed binding to purified laminin-421, laminin-211, and laminin-α4. Affinity for these extracellular matrix proteins explains the striking ability of NP41 to highlight degenerated nerve "ghosts" months posttransection that are invisible to the unaided eye but retain hollow laminin-rich tubular structures.

Linking Load, Fuel, and Emission Controls to Photochemical Production of Secondary Organic Aerosol from a Diesel Engine.

Diesel engines are important sources of fine particle pollution in urban environments, but their contribution to the atmospheric formation of secondary organic aerosol (SOA) is not well constrained. We investigated direct emissions of primary organic aerosol (POA) and photochemical production of SOA from a diesel engine using an oxidation flow reactor (OFR). In less than a day of simulated atmospheric aging, SOA production exceeded POA emissions by an order of magnitude or more. Efficient combustion at higher engine loads coupled to the removal of SOA precursors and particle emissions by aftertreatment systems reduced POA emission factors by an order of magnitude and SOA production factors by factors of 2-10. The only exception was that the retrofitted aftertreatment did not reduce SOA production at idle loads where exhaust temperatures were low enough to limit removal of SOA precursors in the oxidation catalyst. Use of biodiesel resulted in nearly identical POA and SOA compared to diesel. The effective SOA yield of diesel exhaust was similar to that of unburned diesel fuel. While OFRs can help study the multiday evolution, at low particle concentrations OFRs may not allow for complete gas/particle partitioning and bias the potential of precursors to form SOA.

Primary and Secondary Sources of Gas-Phase Organic Acids from Diesel Exhaust.

Organic acids have primary and secondary sources in the atmosphere, impact ecosystem health, and are useful metrics for identifying gaps in organic oxidation chemistry through model-measurement comparisons. We photooxidized (OH oxidation) primary emissions from diesel and biodiesel fuel types under two engine loads in an oxidative flow reactor. formic, butyric, and propanoic acids, but not methacrylic acid, have primary and secondary sources. Emission factors for these gas-phase acids varied from 0.3-8.4 mg kg-1 fuel. Secondary chemistry enhanced these emissions by 1.1 (load) to 4.4 (idle) × after two OH-equivalent days. The relative enhancement in secondary organic acids in idle versus loaded conditions was due to increased precursor emissions, not faster reaction rates. Increased hydrocarbon emissions in idle conditions due to less complete combustion (associated with less oxidized gas-phase molecules) correlated to higher primary organic acid emissions. The lack of correlation between organic aerosol and organic acid concentrations downstream of the flow reactor indicates that the secondary products formed on different oxidation time scales and that despite being photochemical products, organic acids are poor tracers for secondary organic aerosol formation from diesel exhaust. Ignoring secondary chemistry from diesel exhaust would lead to underestimates of both organic aerosol and gas-phase organic acids.

Anthropogenic Sulfur Perturbations on Biogenic Oxidation: SO2 Additions Impact Gas-Phase OH Oxidation Products of α- and ß-Pinene.

In order to probe how anthropogenic pollutants can impact the atmospheric oxidation of biogenic emissions, we investigated how sulfur dioxide (SO2) perturbations impact the oxidation of two monoterpenes, α-and ß-pinene. We used chemical ionization mass spectrometry to examine changes in both individual molecules and gas-phase bulk properties of oxidation products as a function of SO2 addition. SO2 perturbations impacted the oxidation systems of α-and ß-pinene, leading to an ensemble of products with a lesser degree of oxygenation than unperturbed systems. These changes may be due to shifts in the OH:HO2 ratio from SO2 oxidation and/or to SO3 reacting directly with organic molecules. Van Krevelen diagrams suggest a shift from gas-phase functionalization by alcohol/peroxide groups to functionalization by carboxylic acid or carbonyl groups, consistent with a decreased OH:HO2 ratio. Increasing relative humidity dampens the impact of the perturbation. This decrease in oxygenation may impact secondary organic aerosol formation in regions dominated by biogenic emissions with nearby SO2 sources. We observed sulfur-containing organic compounds following SO2 perturbations of monoterpene oxidation; whether these are the result of photochemistry or an instrumental artifact from ion-molecule clustering remains uncertain. However, our results demonstrate that the two monoterpene isomers produce unique suites of oxidation products.

In vivo quantitative proteomics of somatosensory cortical synapses shows which protein levels are modulated by sensory deprivation.

Postnatal bilateral whisker trimming was used as a model system to test how synaptic proteomes are altered in barrel cortex by sensory deprivation during synaptogenesis. Using quantitative mass spectrometry, we quantified more than 7,000 synaptic proteins and identified 89 significantly reduced and 161 significantly elevated proteins in sensory-deprived synapses, 22 of which were validated by immunoblotting. More than 95% of quantified proteins, including abundant synaptic proteins such as PSD-95 and gephyrin, exhibited no significant difference under high- and low-activity rearing conditions, suggesting no tissue-wide changes in excitatory or inhibitory synaptic density. In contrast, several proteins that promote mature spine morphology and synaptic strength, such as excitatory glutamate receptors and known accessory factors, were reduced significantly in deprived synapses. Immunohistochemistry revealed that the reduction in SynGAP1, a postsynaptic scaffolding protein, was restricted largely to layer I of barrel cortex in sensory-deprived rats. In addition, protein-degradation machinery such as proteasome subunits, E2 ligases, and E3 ligases, accumulated significantly in deprived synapses, suggesting targeted synaptic protein degradation under sensory deprivation. Importantly, this screen identified synaptic proteins whose levels were affected by sensory deprivation but whose synaptic roles have not yet been characterized in mammalian neurons. These data demonstrate the feasibility of defining synaptic proteomes under different sensory rearing conditions and could be applied to elucidate further molecular mechanisms of sensory development.

Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture.

We review the organizational principles of the cortical vasculature and the underlying patterns of blood flow under normal conditions and in response to occlusion of single vessels. The cortex is sourced by a two-dimensional network of pial arterioles that feeds a three-dimensional network of subsurface microvessels in close proximity to neurons and glia. Blood flow within the surface and subsurface networks is largely insensitive to occlusion of a single vessel within either network. However, the penetrating arterioles that connect the pial network to the subsurface network are bottlenecks to flow; occlusion of even a single penetrating arteriole results in the death of a 500 µm diameter cylinder of cortical tissue despite the potential for collateral flow through microvessels. This pattern of flow is consistent with that calculated from a full reconstruction of the angioarchitecture. Conceptually, collateral flow is insufficient to compensate for the occlusion of a penetrating arteriole because penetrating venules act as shunts of blood that flows through collaterals. Future directions that stem from the analysis of the angioarchitecture concern cellular-level issues, in particular the regulation of blood flow within the subsurface microvascular network, and system-level issues, in particular the role of penetrating arteriole occlusions in human cognitive impairment.

Early detection of thrombin activity in neuroinflammatory disease.

Although multiple sclerosis (MS) has been associated with the coagulation system, the temporal and spatial regulation of coagulation activity in neuroinflammatory lesions is unknown. Using a novel molecular probe, we characterized the activity pattern of thrombin, the central protease of the coagulation cascade, in experimental autoimmune encephalomyelitis. Thrombin activity preceded onset of neurological signs, increased at disease peak, and correlated with fibrin deposition, microglial activation, demyelination, axonal damage, and clinical severity. Mice with a genetic deficit in prothrombin confirmed the specificity of the thrombin probe. Thrombin activity might be exploited for developing sensitive probes for preclinical detection and monitoring of neuroinflammation and MS progression.

CellBoost: A pipeline for machine assisted annotation in Neuroanatomy.

One of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression of fluorescent proteins. Modern scanning microscopes allow high resolution multi-channel imaging of the mechanically or optically sectioned brain with thousands of marked cells per square millimeter. Manual identification of all marked cells is prohibitively time consuming. At the same time, simple segmentation algorithms suffer from high error rates and sensitivity to variation in fluorescent intensity and spatial distribution. We present a methodology that combines human judgement and machine learning that serves to significantly reduce the labor of the anatomist while improving the consistency of the annotation. As a demonstration, we analyzed murine brains with marked premotor neurons in the brainstem. We compared the error rate of our method to the disagreement rate among human anatomists. This comparison shows that our method can reduce the time to annotate by as much as ten-fold without significantly increasing the rate of errors. We show that our method achieves significant reduction in labor while achieving an accuracy that is similar to the level of agreement between different anatomists.

A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules.

How transient hyperglycemia contributes to cerebro-vascular disease has been a challenge to study under controlled physiological conditions. We use amplified, ultrashort laser-pulses to physically disrupt brain-venule endothelium at targeted locations. This vessel disruption is performed in conjunction with transient hyperglycemia from a single injection of metabolically active D-glucose into healthy mice. The observed real-time responses to laser-induced disruption include rapid serum extravasation, platelet aggregation, and neutrophil recruitment. Thrombo-inflammation is pharmacologically ameliorated by a platelet inhibitor, by a scavenger of reactive oxygen species, and by a nitric oxide donor. As a control, vessel thrombo-inflammation is significantly reduced in mice injected with metabolically inert L-glucose. Venules in mice with diabetes show a similar response to laser-induced disruption and damage is reduced by restoration of normo-glycemia. Our approach provides a controlled method to probe synergies between transient metabolic and physical vascular perturbations and can reveal new aspects of brain pathophysiology.

Thrombin activity associated with neuronal damage during acute focal ischemia.

Mechanisms of ischemic neuronal and vascular injury remain obscure. Here we test the hypothesis that thrombin, a blood-borne coagulation factor, contributes to neurovascular injury during acute focal ischemia. Stroke was induced in adult Sprague Dawley rats by occluding the middle cerebral artery. Intra-arterial thrombin infusion during ischemia significantly increased vascular disruption and cellular injury. Intravenous infusion of argatroban, a direct thrombin inhibitor, alleviated neurovascular injury. Immunostaining showed thrombin on neurons in the ischemic core. Using an activatable cell-penetrating peptide engineered to detect thrombin activity, we discovered that thrombin proteolytic activity was specifically associated with neuronal damage during ischemia. Protease activated receptor-1, the presumptive thrombin receptor, appeared to mediate ischemic neurovascular injury. Furthermore, rats receiving thrombin during ischemia showed cognitive deficit, whereas rats receiving argatroban retained intact learning and memory. These results suggest a potential role for thrombin contributing to neurovascular injury and several potential avenues for neuroprotection.

Fluorescent ligand for human progesterone receptor imaging in live cells.

We employed molecular modeling to design and then synthesize fluorescent ligands for the human progesterone receptor. Boron dipyrromethene (BODIPY) or tetramethylrhodamine were conjugated to the progesterone receptor antagonist RU486 (Mifepristone) through an extended hydrophilic linker. The fluorescent ligands demonstrated comparable bioactivity to the parent antagonist in live cells and triggered nuclear translocation of the receptor in a specific manner. The BODIPY labeled ligand was applied to investigate the dependency of progesterone receptor nuclear translocation on partner proteins and to show that functional heat shock protein 90 but not immunophilin FKBP52 activity is essential. A tissue distribution study indicated that the fluorescent ligand preferentially accumulates in tissues that express high levels of the receptor in vivo. The design and properties of the BODIPY-labeled RU486 make it a potential candidate for in vivo imaging of PR by positron emission tomography through incorporation of (18)F into the BODIPY core.

Ratiometric activatable cell-penetrating peptides provide rapid in vivo readout of thrombin activation.

In real time: thrombin activation in vivo can be imaged in real time with ratiometric activatable cell penetrating peptides (RACPPs). RACPPs are designed to combine 1) dual-emission ratioing, 2) far red to infrared wavelengths for in vivo mammalian imaging, and 3) cleavage-dependent spatial localization. The most advanced RACPP uses norleucine (Nle)-TPRSFL as a linker that increases sensitivity to thrombin by about 90-fold.

Re-engineering the coding workflow: assessing today with an eye toward tomorrow.

EHRs, CAC, ICD-10--coding is in the midst of profound change. Which makes this the best time to re-engineer coding workflow. Five steps help HIM professionals assess and evolve coding workflows with an eye toward tomorrow.

Brain microvasculature has a common topology with local differences in geometry that match metabolic load.

The microvasculature underlies the supply networks that support neuronal activity within heterogeneous brain regions. What are common versus heterogeneous aspects of the connectivity, density, and orientation of capillary networks? To address this, we imaged, reconstructed, and analyzed the microvasculature connectome in whole adult mice brains with sub-micrometer resolution. Graph analysis revealed common network topology across the brain that leads to a shared structural robustness against the rarefaction of vessels. Geometrical analysis, based on anatomically accurate reconstructions, uncovered a scaling law that links length density, i.e., the length of vessel per volume, with tissue-to-vessel distances. We then derive a formula that connects regional differences in metabolism to differences in length density and, further, predicts a common value of maximum tissue oxygen tension across the brain. Last, the orientation of capillaries is weakly anisotropic with the exception of a few strongly anisotropic regions; this variation can impact the interpretation of fMRI data.

Constructing an adult orofacial premotor atlas in Allen mouse CCF.

Premotor circuits in the brainstem project to pools of orofacial motoneurons to execute essential motor action such as licking, chewing, breathing, and in rodent, whisking. Previous transsynaptic tracing studies only mapped orofacial premotor circuits in neonatal mice, but the adult circuits remain unknown as a consequence of technical difficulties. Here, we developed a three-step monosynaptic transsynaptic tracing strategy to identify premotor neurons controlling vibrissa, tongue protrusion, and jaw-closing muscles in the adult mouse. We registered these different groups of premotor neurons onto the Allen mouse brain common coordinate framework (CCF) and consequently generated a combined 3D orofacial premotor atlas, revealing unique spatial organizations of distinct premotor circuits. We further uncovered premotor neurons that simultaneously innervate multiple motor nuclei and, consequently, are likely to coordinate different muscles involved in the same orofacial motor actions. Our method for tracing adult premotor circuits and registering to Allen CCF is generally applicable and should facilitate the investigations of motor controls of diverse behaviors.

Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels.

It is well known that the density of neurons varies within the adult brain. In neocortex, this includes variations in neuronal density between different lamina as well as between different regions. Yet the concomitant variation of the microvessels is largely uncharted. Here, we present automated histological, imaging, and analysis tools to simultaneously map the locations of all neuronal and non-neuronal nuclei and the centerlines and diameters of all blood vessels within thick slabs of neocortex from mice. Based on total inventory measurements of different cortical regions ( approximately 10(7) cells vectorized across brains), these methods revealed: (1) In three dimensions, the mean distance of the center of neuronal somata to the closest microvessel was 15 mum. (2) Volume samples within lamina of a given region show that the density of microvessels does not match the strong laminar variation in neuronal density. This holds for both agranular and granular cortex. (3) Volume samples in successive radii from the midline to the ventral-lateral edge, where each volume summed the number of cells and microvessels from the pia to the white matter, show a significant correlation between neuronal and microvessel densities. These data show that while neuronal and vascular densities do not track each other on the 100 mum scale of cortical lamina, they do track each other on the 1-10 mm scale of the cortical mantle. The absence of a disproportionate density of blood vessels in granular lamina is argued to be consistent with the initial locus of functional brain imaging signals.

Source apportionment of PM2.5 at two Seattle chemical speciation sites.

Positive Matrix Factorization analysis of PM2.5 chemical speciation data collected from 2015-2017 at Washington State Department of Ecology's urban NCore (Beacon Hill) and near-road (10th and Weller) sites found similar PM2.5 sources at both sites. Identified factors were associated with gasoline exhaust, diesel exhaust, aged and fresh sea salt, crustal, nitrate-rich, sulfur-rich, unidentified urban, zinc-rich, residual fuel oil, and wood smoke. Factors associated with vehicle emissions were the highest contributing sources at both sites. Gasoline exhaust emissions comprised 26% and 21% of identified sources at Beacon Hill and 10th and Weller, respectively. Diesel exhaust emissions comprised 29% of identified sources at 10th and Weller but only 3% of identified sources at Beacon Hill. Correlation of the diesel exhaust factor with measured concentrations of black carbon and nitrogen oxides at 10th and Weller suggests a method to predict PM2.5 from diesel exhaust without a full chemical speciation analysis. While most PM2.5 sources exhibit minimal change over time, primary PM2.5 from gasoline emissions is increasing on average 0.18 µg m-3 per year in Seattle. IMPLICATIONS: This study utilizes Positive Matrix Factorization to determine PM2.5 sources from chemical speciation measurements at two urban Seattle sites from 2015-2017. The paper reports PM2.5 source trends, and extends previous source apportionment analyses in Seattle to the present day. The study also quantifies diesel PM2.5 at a near-road site, and describes a predictive model that allows estimation of the contribution of diesel PM2.5 to the total measured PM2.5 at near-road sites across the country without a full chemical speciation analysis.