Toward a generalizable machine learning workflow for neurodegenerative disease staging with focus on neurofibrillary tangles.

Machine learning (ML) has increasingly been used to assist and expand current practices in neuropathology. However, generating large imaging datasets with quality labels is challenging in fields which demand high levels of expertise. Further complicating matters is the often seen disagreement between experts in neuropathology-related tasks, both at the case level and at a more granular level. Neurofibrillary tangles (NFTs) are a hallmark pathological feature of Alzheimer disease, and are associated with disease progression which warrants further investigation and granular quantification at a scale not currently accessible in routine human assessment. In this work, we first provide a baseline of annotator/rater agreement for the tasks of Braak NFT staging between experts and NFT detection using both experts and novices in neuropathology. We use a whole-slide-image (WSI) cohort of neuropathology cases from Emory University Hospital immunohistochemically stained for Tau. We develop a workflow for gathering annotations of the early stage formation of NFTs (Pre-NFTs) and mature intracellular (iNFTs) and show ML models can be trained to learn annotator nuances for the task of NFT detection in WSIs. We utilize a model-assisted-labeling approach and demonstrate ML models can be used to aid in labeling large datasets efficiently. We also show these models can be used to extract case-level features, which predict Braak NFT stages comparable to expert human raters, and do so at scale. This study provides a generalizable workflow for various pathology and related fields, and also provides a technique for accomplishing a high-level neuropathology task with limited human annotations.

The conditional growth suppressor E7.25d.7 is an allele of the sterile-20 kinase misshapen.

The notion of a two-hit or multi-hit model of carcinogenesis dates to at least the 1970's and work done by Alfred Knudson. This concept was considered in the design and execution of a previous FLP/FRT screen in Drosophila melanogaster for conditional growth suppressors. During the course of this work, the lethal allele E7.25D.7 was identified as being of phenotypic interest. Here we report the genetic mapping of E7.25D.7, an allele of the sterile-20 kinase misshapen (msn).

The level of oncogenic Ras determines the malignant transformation of Lkb1 mutant tissue in vivo.

The genetic and metabolic heterogeneity of RAS-driven cancers has confounded therapeutic strategies in the clinic. To address this, rapid and genetically tractable animal models are needed that recapitulate the heterogeneity of RAS-driven cancers in vivo. Here, we generate a Drosophila melanogaster model of Ras/Lkb1 mutant carcinoma. We show that low-level expression of oncogenic Ras (RasLow) promotes the survival of Lkb1 mutant tissue, but results in autonomous cell cycle arrest and non-autonomous overgrowth of wild-type tissue. In contrast, high-level expression of oncogenic Ras (RasHigh) transforms Lkb1 mutant tissue resulting in lethal malignant tumors. Using simultaneous multiview light-sheet microcopy, we have characterized invasion phenotypes of Ras/Lkb1 tumors in living larvae. Our molecular analysis reveals sustained activation of the AMPK pathway in malignant Ras/Lkb1 tumors, and demonstrate the genetic and pharmacologic dependence of these tumors on CaMK-activated Ampk. We further show that LKB1 mutant human lung adenocarcinoma patients with high levels of oncogenic KRAS exhibit worse overall survival and increased AMPK activation. Our results suggest that high levels of oncogenic KRAS is a driving event in the malignant transformation of LKB1 mutant tissue, and uncovers a vulnerability that may be used to target this aggressive genetic subset of RAS-driven tumors.

Tunable Mechanical and Optoelectronic Properties of Organic Cocrystals by Unexpected Stacking Transformation from H- to J- and X-Aggregation.

Molecular stacking modes, generally classified as H-, J-, and X-aggregation, play a key role in determining the optoelectronic properties of organic crystals. However, the control of stacking transformation of a specific molecule is an unmet challenge, and a priori prediction of the performance in different stacking modes is extraordinarily difficult to achieve. In particular, the existence of hybrid stacking modes and their combined effect on physicochemical properties of molecular crystals are not fully understood. Herein, unexpected stacking transformation from H- to J- and X-aggregation is observed in the crystal structure of a small heterocyclic molecule, 4,4'-bipyridine (4,4'-Bpy), upon coassembly with N-acetyl-l-alanine (AcA), a nonaromatic amino acid derivative. This structural transformation into hybrid stacking mode improves physicochemical properties of the cocrystals, including a large red-shifted emission, enhanced supramolecular chirality, improved thermal stability, and higher mechanical properties. While a single crystal of 4,4'-Bpy shows good optical waveguiding and piezoelectric properties due to the uniform elongated needles and low symmetry of crystal packing, the significantly lower band gap and resistance of the cocrystal indicate improved conductivity. This study not only demonstrates cocrystallization-induced packing transformation between H-, J-, and X-aggregations in the solid state, leading to tunable mechanical and optoelectronic properties, but also will inspire future molecular design of organic functional materials by the coassembly strategy.

Human grooming in comparative perspective: People in six small-scale societies groom less but socialize just as much as expected for a typical primate.

OBJECTIVES: Grooming has important utilitarian and social functions in primates but little is known about grooming and its functional analogues in traditional human societies. We compare human grooming to typical primate patterns to test its hygienic and social functions. MATERIALS AND METHODS: Bayesian phylogenetic analyses were used to derive expected human grooming time given the potential associations between grooming, group size, body size, terrestriality, and several climatic variables across 69 primate species. This was compared against observed times dedicated to grooming, other hygienic behavior, and conversation among the Maya, Pumé, Sanöma, Tsimane', Yanomamö, and Ye'kwana (mean number of behavioral scans = 23,514). RESULTS: Expected grooming time for humans was 4% (95% Credible Interval = 0.07%-14%), similar to values observed in primates, based largely on terrestriality and phylogenetic signal (mean λ = 0.56). No other covariates strongly associated with grooming across primates. Observed grooming time across societies was 0.8%, lower than 89% of the expected values. However, the observed times dedicated to any hygienic behavior (3.0%) or "vocal grooming," that is conversation (7.3%), fell within the expected range. CONCLUSIONS: We found (i) that human grooming may be a (recent) phylogenetic outlier when defined narrowly as parasite removal but not defined broadly as personal hygiene, (ii) there was no support for thermoregulatory functions of grooming, and (iii) no support for the "vocal grooming" hypothesis of language having evolved as a less time-consuming means of bonding. Thus, human grooming reflects decreased hygienic needs, but similar social needs compared to primate grooming.