A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation.

Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo. In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison of neuroanatomy from different subjects in a common coordinate frame. High-resolution, digital atlases derived from histology (e.g., Allen atlas [7], BigBrain [13], Julich [15]), are currently the state of the art and provide exquisite 3D cytoarchitectural maps, but lack probabilistic labels throughout the whole brain. Here we present NextBrain, a next-generation probabilistic atlas of human brain anatomy built from serial 3D histology and corresponding highly granular delineations of five whole brain hemispheres. We developed AI techniques to align and reconstruct ~10,000 histological sections into coherent 3D volumes with joint geometric constraints (no overlap or gaps between sections), as well as to semi-automatically trace the boundaries of 333 distinct anatomical ROIs on all these sections. Comprehensive delineation on multiple cases enabled us to build the first probabilistic histological atlas of the whole human brain. Further, we created a companion Bayesian tool for automated segmentation of the 333 ROIs in any in vivo or ex vivo brain MRI scan using the NextBrain atlas. We showcase two applications of the atlas: automated segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimer's disease and healthy brain ageing based on ~4,000 publicly available in vivo MRI scans. We publicly release: the raw and aligned data (including an online visualisation tool); the probabilistic atlas; the segmentation tool; and ground truth delineations for a 100 µm isotropic ex vivo hemisphere (that we use for quantitative evaluation of our segmentation method in this paper). By enabling researchers worldwide to analyse brain MRI scans at a superior level of granularity without manual effort or highly specific neuroanatomical knowledge, NextBrain holds promise to increase the specificity of MRI findings and ultimately accelerate our quest to understand the human brain in health and disease.

Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology.

We present open-source tools for three-dimensional (3D) analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (1) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (2) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimer's Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between post mortem confirmed Alzheimer's disease cases and controls. The tools are available in our widespread neuroimaging suite 'FreeSurfer' (https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools).

Every year, thousands of human brains are donated to science. These brains are used to study normal aging, as well as neurological diseases like Alzheimer's or Parkinson's. Donated brains usually go to 'brain banks', institutions where the brains are dissected to extract tissues relevant to different diseases. During this process, it is routine to take photographs of brain slices for archiving purposes. Often, studies of dead brains rely on qualitative observations, such as 'the hippocampus displays some atrophy', rather than concrete 'numerical' measurements. This is because the gold standard to take three-dimensional measurements of the brain is magnetic resonance imaging (MRI), which is an expensive technique that requires high expertise ­ especially with dead brains. The lack of quantitative data means it is not always straightforward to study certain conditions. To bridge this gap, Gazula et al. have developed an openly available software that can build three-dimensional reconstructions of dead brains based on photographs of brain slices. The software can also use machine learning methods to automatically extract different brain regions from the three-dimensional reconstructions and measure their size. These data can be used to take precise quantitative measurements that can be used to better describe how different conditions lead to changes in the brain, such as atrophy (reduced volume of one or more brain regions). The researchers assessed the accuracy of the method in two ways. First, they digitally sliced MRI-scanned brains and used the software to compute the sizes of different structures based on these synthetic data, comparing the results to the known sizes. Second, they used brains for which both MRI data and dissection photographs existed and compared the measurements taken by the software to the measurements obtained with MRI images. Gazula et al. show that, as long as the photographs satisfy some basic conditions, they can provide good estimates of the sizes of many brain structures. The tools developed by Gazula et al. are publicly available as part of FreeSurfer, a widespread neuroimaging software that can be used by any researcher working at a brain bank. This will allow brain banks to obtain accurate measurements of dead brains, allowing them to cheaply perform quantitative studies of brain structures, which could lead to new findings relating to neurodegenerative diseases.

Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology.

We present open-source tools for 3D analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (i) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (ii) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimer's Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between post mortem confirmed Alzheimer's disease cases and controls. The tools are available in our widespread neuroimaging suite "FreeSurfer" ( https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools ).

Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length.

Manual segmentation of stacks of 2D biomedical images (e.g., histology) is a time-consuming task which can be sped up with semi-automated techniques. In this article, we present a suggestive deep active learning framework that seeks to minimise the annotation effort required to achieve a certain level of accuracy when labelling such a stack. The framework suggests, at every iteration, a specific region of interest (ROI) in one of the images for manual delineation. Using a deep segmentation neural network and a mixed cross-entropy loss function, we propose a principled strategy to estimate class probabilities for the whole stack, conditioned on heterogeneous partial segmentations of the 2D images, as well as on weak supervision in the form of image indices that bound each ROI. Using the estimated probabilities, we propose a novel active learning criterion based on predictions for the estimated segmentation performance and delineation effort, measured with average Dice scores and total delineated boundary length, respectively, rather than common surrogates such as entropy. The query strategy suggests the ROI that is expected to maximise the ratio between performance and effort, while considering the adjacency of structures that may have already been labelled - which decrease the length of the boundary to trace. We provide quantitative results on synthetically deformed MRI scans and real histological data, showing that our framework can reduce labelling effort by up to 60-70% without compromising accuracy.

A multimodal computational pipeline for 3D histology of the human brain.

Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors.

Divisional review of the nurse specialist role.

Nurse specialists have been described as providing an optimal return on investment for income generation, patient safety, cost savings, and improvements in patient care and experience. However, there is often a lack of understanding of the nurse specialist role and how such nurses support improved patient outcomes. To assess the effect of the nurse specialist in a division of one large NHS trust, a review of the nurse specialist role was undertaken within eight specialties. This review profiled nurse specialists' roles in terms of their activity, income generation and quality, with the aim of producing specialist job plans to accurately reflect their roles. Nurse specialists were provided with a job-planning template and face-to-face sessions on how to complete it. The returned job plans were reviewed by a panel consisting of nursing management, lead clinical nurse specialists and representatives from finance. The results were used to generate three generic nurse specialist job plans that recognised the core elements of the role. The division intends to undertake a further review of nurse specialists, which aims to explore the role in further detail, including identifying their development needs. Having examined the effects of the nurse specialist role, the division needs to ensure that nurse specialists are resourced to reach their full potential.

LMTK2 binds to kinesin light chains to mediate anterograde axonal transport of cdk5/p35 and LMTK2 levels are reduced in Alzheimer's disease brains.

Cyclin dependent kinase-5 (cdk5)/p35 is a neuronal kinase that regulates key axonal and synaptic functions but the mechanisms by which it is transported to these locations are unknown. Lemur tyrosine kinase-2 (LMTK2) is a binding partner for p35 and here we show that LMTK2 also interacts with kinesin-1 light chains (KLC1/2). Binding to KLC1/2 involves a C-terminal tryptophan/aspartate (WD) motif in LMTK2 and the tetratricopeptide repeat (TPR) domains in KLC1/2, and this interaction facilitates axonal transport of LMTK2. Thus, siRNA loss of KLC1 or mutation of the WD motif disrupts axonal transport of LMTK2. We also show that LMTK2 facilitates the formation of a complex containing KLC1 and p35 and that siRNA loss of LMTK2 disrupts axonal transport of both p35 and cdk5. Finally, we show that LMTK2 levels are reduced in Alzheimer's disease brains. Damage to axonal transport and altered cdk5/p35 are pathogenic features of Alzheimer's disease. Thus, LMTK2 binds to KLC1 to direct axonal transport of p35 and its loss may contribute to Alzheimer's disease.

Initial experience of an algorithm-based protocol for the community follow-up of men with prostate cancer.

OBJECTIVE: To evaluate the implementation of a novel algorithm-based discharge programme for the community follow-up of men with prostate cancer. PATIENTS AND METHODS: Men with prostate cancer considered suitable for discharge were identified from consultant-led and clinical nurse-specialist telephone clinics at Nottingham University Hospitals National Health Service Trust. Patients were discharged on to one of four discharge pathways: watchful waiting, androgen-deprivation therapy (ADT), post-prostatectomy, and post-radiotherapy. Primary care providers were asked to adhere to specific surveillance measures and refer patients back to secondary care after breach of pre-defined prostate-specific antigen (PSA) level threshold criteria. Reasons for non-compliance, re-referral, and cause of death were determined for all discharged men. RESULTS: In all, 573 men were discharged across all four pathways; 169 on the watchful-waiting pathway, 229 on the ADT pathway, 95 on the post-prostatectomy pathway, and 80 on the post-radiotherapy pathway. All patients had ≥12 months of follow-up. In all, 48 of 54 (88.9%) men were re-referred promptly after a PSA-threshold breach. Of the remaining six patients there were three refusals, one unrelated death before referral, and two late referrals at 4 months. Three patients were lost to follow-up due to database non-registration and were subsequently recalled, none of whom had a PSA-threshold breach. There were three unexpected deaths attributed to prostate cancer: two were community deaths with no biochemical or clinical evidence of prostate cancer progression, while one was due to a likely progressive PSA non-secreting tumour. CONCLUSION: Initial results suggest the algorithm-based protocol is a viable, effective, and oncologically safe method for the controlled discharge of men from secondary to primary care. Longer-term follow-up, patient satisfaction and cost-effectiveness data are required to assess the true impact of the initiative.

Selective pressurized liquid extraction of pesticides, polychlorinated biphenyls and polybrominated diphenyl ethers in a whale earplug (earwax): a novel method for analyzing organic contaminants in lipid-rich matrices.

Lipid-rich matrices are often sinks for lipophilic contaminants, such as pesticides, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs). Typically methods for contaminant extraction and cleanup for lipid-rich matrices require multiple cleanup steps; however, a selective pressurized liquid extraction (SPLE) technique requiring no additional cleanup has been developed for the simultaneous extraction and cleanup of whale earwax (cerumen; a lipid-rich matrix). Whale earwax accumulates in select whale species over their lifetime to form wax earplugs. Typically used as an aging technique in cetaceans, layers or laminae that comprise the earplug are thought to be associated with annual or semiannual migration and feeding patterns. Whale earplugs (earwax) represent a unique matrix capable of recording and archiving whales' lifetime contaminant profiles. This study reports the first analytical method developed for identifying and quantifying lipophilic persistent organic pollutants (POPs) in a whale earplug including organochlorine pesticides, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs). The analytical method was developed using SPLE to extract contaminants from ∼0.25 to 0.5g aliquots of each lamina of sectioned earplug. The SPLE was optimized for cleanup adsorbents (basic alumina, silica gel, and Florisil(®)), adsorbent to sample ratio, and adsorbent order. In the optimized SPLE method, the earwax homogenate was placed within the extraction cell on top of basic alumina (5g), silica gel (15g), and Florisil(®) (10g) and the target analytes were extracted from the homogenate using 1:1 (v/v) dichloromethane:hexane. POPs were analyzed using gas chromatography-mass spectrometry with electron capture negative ionization and electron impact ionization. The average percent recoveries for the POPs were 91% (±6% relative standard deviation), while limits of detection and quantification ranged from 0.00057 to 0.96ngg(-1) and 0.0017 to 2.9ngg(-1), respectively. Pesticides, PCBs, and PBDEs, were measured in a single blue whale (Balaenoptera musculus) cerumen lamina at concentrations ranging from 0.11 to 150ng g(-1).

Blue whale earplug reveals lifetime contaminant exposure and hormone profiles.

Lifetime contaminant and hormonal profiles have been reconstructed for an individual male blue whale (Balaenoptera musculus, Linnaeus 1758) using the earplug as a natural aging matrix that is also capable of archiving and preserving lipophilic compounds. These unprecedented lifetime profiles (i.e., birth to death) were reconstructed with a 6-mo resolution for a wide range of analytes including cortisol (stress hormone), testosterone (developmental hormone), organic contaminants (e.g., pesticides and flame retardants), and mercury. Cortisol lifetime profiles revealed a doubling of cortisol levels over baseline. Testosterone profiles suggest this male blue whale reached sexual maturity at approximately 10 y of age, which corresponds well with and improves on previous estimates. Early periods of the reconstructed contaminant profiles for pesticides (such as dichlorodiphenyltrichloroethanes and chlordanes), polychlorinated biphenyls, and polybrominated diphenyl ethers demonstrate significant maternal transfer occurred at 0-12 mo. The total lifetime organic contaminant burden measured between the earplug (sum of contaminants in laminae layers) and blubber samples from the same organism were similar. Total mercury profiles revealed reduced maternal transfer and two distinct pulse events compared with organic contaminants. The use of a whale earplug to reconstruct lifetime chemical profiles will allow for a more comprehensive examination of stress, development, and contaminant exposure, as well as improve the assessment of contaminant use/emission, environmental noise, ship traffic, and climate change on these important marine sentinels.

Uptake and metabolism of individual polybrominated diphenyl ether congeners by embryonic zebrafish.

Embryonic zebrafish were used to compare the uptake and metabolism of six polybrominated diphenyl ether (PBDE) congeners (BDEs 28, 47, 99, 100, 153, and 183) and identified metabolites from static exposures at 24 and 120 h postfertilization (hpf). An inverse relationship was observed between uptake of PBDEs and their octanol-water partitioning coefficients (uptake of BDEs 28 and 47>99 and 100>153 and 183). Debromination metabolites were identified in all congeners (excluding BDE 28) tested in the 120-hpf tissue samples. Interestingly, BDE 153 underwent meta-debromination, forming BDEs 47 and 99. Gene transcription analysis was conducted at 120 hpf to identify potential metabolic pathways for the PBDEs examined in the present study (gstpi, deiodinases 1 and 2, cyp1a1, cyp1b1, and ugt5g). The greatest induction was of ugt5g for all congeners and deiodinase transcription was also upregulated by BDEs 28, 47, and 183. The cyp1a1 and cyp1b1 were upregulated by BDEs 28, 47, 99, and 183. The least alterations in gene transcription were in the BDE 153-exposed embryos. A clear primary pathway of debromination metabolism was not identified; however, upregulation of these different genes indicated that fish were responding to exposure of PBDEs. Furthermore, the present study demonstrated that the most bioavailable congeners are also those with the highest reported toxicity.

Assessment of legacy and emerging persistent organic pollutants in Weddell seal tissue (Leptonychotes weddellii) near McMurdo Sound, Antarctica.

Muscle samples were collected from pup, juvenile and adult Weddell seals (Leptonychotes weddellii) near McMurdo Sound, Antarctica during the austral summer of 2006. Blubber samples were collected from juvenile and adult seals. Samples were analyzed for emerging and legacy persistent organic pollutants (POPs) including current and historic-use organochlorine pesticides, polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs). Of the 41 target analytes, 28 contaminants were recovered from the Weddell seal blubber, in this order of prevalence: p,p'-DDE, p,p'-DDT, trans-nonachlor, mirex, cis-nonachlor, PCB 153, PCB 138, dieldrin, heptachlor epoxide, nonachlor III, PCB 187, oxychlordane, cis-chlordane, PCB 118, PBDE 47, PCB 156, PCB 149, PCB 180, PCB 101, PCB 170, PCB 105, o,p'-DDT, PCB 99, trans-chlordane, PCB 157, PCB 167, PCB 189, and PCB 114. Fewer POPs were found in the muscle samples, but were similar in the order of prevalence to that of the blubber: p,p'-DDE, o,p'-DDT, trans-nonachlor, nonachlor III, oxychlordane, p,p'-DDT, dieldrin, mirex, cis-nonachlor, PCB 138, and PCB 105. Besides differences in toxicant concentrations reported between the muscle and blubber, we found differences in POP levels according to age class and suggest that differences in blubber storage and/or mobilization of lipids result in age class differences in POPs. To our knowledge, such ontogenetic associations are novel. Importantly, data from this study suggest that p,p'-DDT is becoming less prevalent temporally, resulting in an increased proportion of its metabolite p,p'-DDE in the tissues of this top predator. In addition, this study is among the first to identify a PBDE congener in Weddell seals near the McMurdo Station. This may provide evidence of increased PBDE transport and encroachment in Antarctic wildlife.

PBDE developmental effects on embryonic zebrafish.

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous environmental contaminants with potential for bioaccumulation and maternal-fetal transfer that has led to regulatory bans and/or phasing out of several technical mixtures of PBDEs. In the present study, six PBDE congeners (BDE 28, BDE 47, BDE 99, BDE 100, BDE 153, BDE 183) were evaluated for developmental effects on embryonic zebrafish. These congeners were chosen because they are environmentally relevant and cover a wide range of physical-chemical properties. Alterations in behavior, physical malformations, and mortality were scored daily until 168 h postfertilization (hpf). A concentration-dependent increase in spontaneous movement indicated an early onset of behavioral responses to PBDE exposures. Spontaneous movement was affected the most by BDE 47 and BDE 28, whereas BDE 183 did not alter behavior at any concentration tested. Swimming rates were significantly increased by BDE 28 at 96 and 120 hpf, but decreased swimming activity at 168 hpf. Additionally, BDE 47 significantly decreased the swimming rate at 168 hpf. Other endpoints included malformations and mortality. Congeners with fewer bromines (BDE 28, 47, 99, and 100) also induced a curved body axis starting around 120 hpf, which was followed by mortality. BDEs 153 and 183, however, did not elicit these adverse effects. A relationship was found between log K(OW) and median lethal concentration (LC50) and median effective concentration (EC50). Structure-activity relationships in this study suggest that PBDE acute toxicity results from a receptor-mediated effect and further studies are necessary to determine these pathways.