How to collect high quality segmentations: use human or computer drawn object boundaries?

High quality segmentations must be captured consistently for applications such as biomedical image analysis. While human drawn segmentations are often collected because they provide a consistent level of quality, computer drawn segmentations can be collected efficiently and inexpensively. In this paper, we examine how to leverage available human and computer resources to consistently create high quality segmentations. We propose a quality control methodology. We demonstrate how to apply this approach using crowdsourced and domain expert votes for the "best" segmentation from a collection of human and computer drawn segmentations for 70 objects from a public dataset and 274 objects from biomedical images. We publicly share the library of biomedical images which includes 1,879 manual annotations of the boundaries of 274 objects. We found for the 344 objects that no single segmentation source was preferred and that human annotations are not always preferred over computer annotations. These results motivated us to examine the traditional approach to evaluate segmentation algorithms, which involves comparing the segmentations produced by the algorithms to manual annotations on benchmark datasets. We found that algorithm benchmarking results change when the comparison is made to consensus-voted segmentations. Our results led us to suggest a new segmentation approach that uses machine learning to predict the optimal segmentation source and a modified segmentation evaluation approach.National Science Foundation (IIS-0910908

EFFECT OF CONSTANT VOLUME STRUCTURE PARAMETERS ON GRAIN VENTILATION DRYING

ABSTRACT The structural parameters of a grain dryer are directly related to the its energy consumption and quality formation. Therefore, based on the Ergun model, air state parameters and uniformity evaluation method, the effect of changes in the ventilation area on grain airflow resistance, drying energy consumption, drying efficiency and uniformity are theoretically and experimentally studied in this work under the same initial grain weight and air flux. The results show that under the conditions of air temperatures 35℃ and 70℃, the weight of paddy 8.547 kg and the air flux 12.3 m3·h-1, hot air introduced into the drying chamber with cross-sectional areas of S1 and S2 respectively, the ventilation area enlarged by 2.328 times, the grain airflow resistance decreased by 7.17 and 6.99 times. Enlarging the ventilation area effectively improved the drying rate of paddy, especially at 70℃, while the unit energy consumption was the opposite. It also accelerated the moving speed of the saturated humidity line in the drying layer and improved the drying uniformity of the paddy. These experimental results are in agreement with the theoretical analysis, which provides a reference for the design of grain drying equipment and technology

Comparison of in vitro Neuronal Differentiation Capacity Between Mouse Epiblast Stem Cells Derived From Nuclear Transfer and Naturally Fertilized Embryos

Somatic cell nuclear transfer (SCNT) can give rise to fertile adults, but the successful perinatal and postnatal developmental rates are inefficient, including delayed developmental behaviors, and respiratory failure. However, the molecular and cellular mechanisms remain elusive. Mouse epiblast stem cells (mEpiSCs) from E5.5-6.5 epiblasts share defining features with human embryonic stem cells (hESCs), providing a new opportunity to study early mammalian development in vitro. In this study, mEpiSCs were established from naturally fertilized mouse embryos (F-mEpiSCs) and SCNT mouse embryos (NT-mEpiSCs). Also, the in vitro neuronal differentiation capacity of F-mEpiSCs and NT-mEpiSCs was compared. Morphology analysis showed less and smaller neurospheres formation and lower percentage of early neurons generation in NT-mEpiSCs. The immunocytochemical analysis and altered mRNA expression levels of the neuronal markers in differentiated cells further confirmed that neurogenesis was slower in NT-mEpiSCs than in F-mEpiSCs. Moreover, neuronal differentiation capacity was correlated with the basal expression levels of Atox1 and Vinculin but not Brachyury and Otx2, emphasizing that developmental aberrations in neurogenesis were associated with the NT technique but not random variations between clones. This study provided an important in vitro platform using mEpiSCs to study early epigenetic and developmental processes associated with neurogenesis

Depiction of immune heterogeneity of peripheral blood from patients with type II diabetic nephropathy based on mass cytometry

Diabetic nephropathy (DN) is the most prominent cause of chronic kidney disease and end-stage renal failure. However, the pathophysiology of DN, especially the risk factors for early onset remains elusive. Increasing evidence has revealed the role of the innate immune system in developing DN, but relatively little is known about early immunological change that proceeds from overt DN. Herein, this work aims to investigate the immune-driven pathogenesis of DN using mass cytometry (CyTOF). The peripheral blood mononuclear lymphocytes (PBMC) from 6 patients with early-stage nephropathy and 7 type II diabetes patients without nephropathy were employed in the CyTOF test. A panel that contains 38 lineage markers was designed to monitor immune protein levels in PBMC. The unsupervised clustering analysis was performed to profile the proportion of individual cells. t-Distributed Stochastic Neighbor Embedding (t-SNE) was used to visualize the differences in DN patients’ immune phenotypes. Comprehensive immune profiling revealed substantial immune system alterations in the early onset of DN, including the significant decline of B cells and the marked increase of monocytes. The level of CXCR3 was dramatically reduced in the different immune cellular subsets. The CyTOF data classified the fine-grained differential immune cell subsets in the early stage of DN. Innovatively, we identified several significant changed T cells, B cell, and monocyte subgroups in the early-stage DN associated with several potential biomarkers for developing DN, such as CTLA-4, CXCR3, PD-1, CD39, CCR4, and HLA-DR. Correlation analysis further demonstrated the robust relationship between above immune cell biomarkers and clinical parameters in the DN patients. Therefore, we provided a convincible view of understanding the immune-driven early pathogenesis of DN. Our findings exhibited that patients with DN are more susceptible to immune system disorders. The classification of fine-grained immune cell subsets in this present research might provide novel targets for the immunotherapy of DN

A Cu2+ (S = 1/2) Kagom\'e Antiferromagnet: MgxCu4-x(OH)6Cl2

Spin-frustrated systems are one avenue for inducing macroscopic quantum states in materials. However, experimental realization of this goal has been difficult because of the lack of simple materials and, if available, the separation of the unusual magnetic properties arising from exotic magnetic states from behavior associated with chemical disorder, such as site mixing. Here we report the synthesis and magnetic properties of a new series of magnetically frustrated materials, MgxCu4-x(OH)6Cl2. Because of the substantially different ligand-field chemistry of Mg2+ and Cu2+, site disorder within the kagom\'e layers is minimized, as directly measured by X-ray diffraction. Our results reveal that many of the properties of these materials and related systems are not due to disorder of the magnetic lattice but rather reflect an unusual ground state.Comment: Accepted for publication in J. Am. Chem. Soc

Opposing effects of final population density and stress on Escherichia coli mutation rate

Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis-SIM) and decrease at high final population density (density-associated mutation-rate plasticity-DAMP). We hypothesised that these two forms of mutation-rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM results in a mutation rate minimum at intermediate nutrient levels (which can support 7 × 10  cells ml ). These findings demonstrate a strikingly close and nuanced relationship of ecological factors-stress and population density-with mutation, the fuel of all evolution

Molecular effects of resistance elicitors from biological origin and their potential for crop protection

Plants contain a sophisticated innate immune network to prevent pathogenic microbes from gaining access to nutrients and from colonising internal structures. The first layer of inducible response is governed by the plant following the perception of microbe- or modified plant-derived molecules. As the perception of these molecules results in a plant response that can provide efficient resistance towards non-adapted pathogens they can also be described as ‘defence elicitors’. In compatible plant/microbe interactions, adapted microorganisms have means to avoid or disable this resistance response and promote virulence. However, this requires a detailed spatial and temporal response from the invading pathogens. In agricultural practice, treating plants with isolated defence elicitors in the absence of pathogens can promote plant resistance by uncoupling defence activation from the effects of pathogen virulence determinants. The plant responses to plant, bacterial, oomycete or fungal-derived elicitors are not, in all cases, universal and need elucidating prior to the application in agriculture. This review provides an overview of currently known elicitors of biological rather than synthetic origin and places their activity into a molecular context

The 2022 China report of the Lancet Countdown on health and climate change: leveraging climate actions for healthy ageing

A health-friendly, climate resilient, and carbon-neutral pathway would deliver major benefits to people's health and wellbeing in China, especially for older populations, while simultaneously promoting high-quality development in the long run. This report is the third China Lancet Countdown report, led by the Lancet Countdown Regional Centre based in Tsinghua University. With the contributions of 73 experts from 23 leading institutions, both within China and globally, this report tracks progress through 27 indicators in the following five domains: (1) climate change impacts, exposure, and vulnerability; (2) adaptation, planning, and resilience for health; (3) mitigation actions and health co-benefits; (4) economics and finance; and (5) public and political engagement. From 2021 to 2022, two new indicators have been added, and methods have been improved for many indicators. Specifically, one of the new indicators measures how heat affects the hours that are safe for outdoor exercise, an indicator of particular relevance given the boom in national sports triggered by the summer and winter Olympics. Findings in this report, which coincide with the UN Framework Convention on Climate Change 27th Conference of the Parties (COP27) hosted in Egypt (where much attention is being focused on adaptation for clinically vulnerable populations), expose the urgency for accelerated adaptation and mitigation efforts to minimise the health impacts of the increasing climate change hazards in China