Directly Observing the Reversible Unfolding and Refolding of an Alpha/Beta Protein by Single-Molecule Atomic Force Microscopy

Digitalitzat per Artypla

1st ICLR International Workshop on Privacy, Accountability, Interpretability, Robustness, Reasoning on Structured Data (PAIR^2Struct)

Recent years have seen advances on principles and guidance relating to accountable and ethical use of artificial intelligence (AI) spring up around the globe. Specifically, Data Privacy, Accountability, Interpretability, Robustness, and Reasoning have been broadly recognized as fundamental principles of using machine learning (ML) technologies on decision-critical and/or privacy-sensitive applications. On the other hand, in tremendous real-world applications, data itself can be well represented as various structured formalisms, such as graph-structured data (e.g., networks), grid-structured data (e.g., images), sequential data (e.g., text), etc. By exploiting the inherently structured knowledge, one can design plausible approaches to identify and use more relevant variables to make reliable decisions, thereby facilitating real-world deployments

Bidirectional Inference Networks: A Class of Deep Bayesian Networks for Health Profiling

We consider the problem of inferring the values of an arbitrary set of variables (e.g., risk of diseases) given other observed variables (e.g., symptoms and diagnosed diseases) and high-dimensional signals (e.g., MRI images or EEG). This is a common problem in healthcare since variables of interest often differ for different patients. Existing methods including Bayesian networks and structured prediction either do not incorporate high-dimensional signals or fail to model conditional dependencies among variables. To address these issues, we propose bidirectional inference networks (BIN), which stich together multiple probabilistic neural networks, each modeling a conditional dependency. Predictions are then made via iteratively updating variables using backpropagation (BP) to maximize corresponding posterior probability. Furthermore, we extend BIN to composite BIN (CBIN), which involves the iterative prediction process in the training stage and improves both accuracy and computational efficiency by adaptively smoothing the optimization landscape. Experiments on synthetic and real-world datasets (a sleep study and a dermatology dataset) show that CBIN is a single model that can achieve state-of-the-art performance and obtain better accuracy in most inference tasks than multiple models each specifically trained for a different task.Comment: Appeared at AAAI 201

Types of Tags for Annotating Academic Blogs

Academic blog sites are popular academic information exchange platforms, and they have been widely used in recent years. Blogs in those sites are often annotated with tags, and the tags can help to describe, organize and retrieve these blogs. However, it is still unknown what types of tags are frequently adopted for annotating academic blogs. In this poster, we present survey results for detecting the usage of tag types, and its changes with the bloggers' demographic information. We believe that our study can benefit users in their access to academic blogs and help the academic blog websites improve their services

Boosting freshwater fish conservation with high-resolution distribution mapping across a large territory

The lack of high-resolution distribution maps for freshwater species across large extents fundamentally challenges biodiversity conservation worldwide. We devised a simple framework to delineate the distributions of freshwater fishes in a high-resolution drainage map based on stacked species distribution models and expert information. We applied this framework to the entire Chinese freshwater fish fauna (>1600 species) to examine high-resolution biodiversity patterns and reveal potential conflicts between freshwater biodiversity and anthropogenic disturbances. The correlations between spatial patterns of biodiversity facets (species richness, endemicity, and phylogenetic diversity) were all significant (r = 0.43–0.98, p < 0.001). Areas with high values of different biodiversity facets overlapped with anthropogenic disturbances. Existing protected areas (PAs), covering 22% of China's territory, protected 25–29% of fish habitats, 16–23% of species, and 30–31% of priority conservation areas. Moreover, 6–21% of the species were completely unprotected. These results suggest the need for extending the network of PAs to ensure the conservation of China's freshwater fishes and the goods and services they provide. Specifically, middle to low reaches of large rivers and their associated lakes from northeast to southwest China hosted the most diverse species assemblages and thus should be the target of future expansions of the network of PAs. More generally, our framework, which can be used to draw high-resolution freshwater biodiversity maps combining species occurrence data and expert knowledge on species distribution, provides an efficient way to design PAs regardless of the ecosystem, taxonomic group, or region considered.Strategic Priority Research Program of Chinese Academy of Sciences XDB31000000Second Tibetan PlateauScientific Expedition Program 2019QZKK0304, 2019QZKK05010102National Key Research and Devel-opment Program of China 2021YFC3200300103National Natural Science Foundation of China 32070436, 4207744

Cadmium suppresses the proliferation of piglet Sertoli cells and causes their DNA damage, cell apoptosis and aberrant ultrastructure

<p>Abstract</p> <p>Objective</p> <p>Very little information is known about the toxic effects of cadmium on somatic cells in mammalian testis. The objective of this study is to explore the toxicity of cadmium on piglet Sertoli cells.</p> <p>Methods</p> <p>Sertoli cells were isolated from piglet testes using a two-step enzyme digestion and followed by differential plating. Piglet Sertoli cells were identified by oil red O staining and Fas ligand (FasL) expression as assayed by immunocytochemistry and expression of transferrin and androgen binding protein by RT-PCR. Sertoli cells were cultured in DMEM/F12 supplemented with 10% fetal calf serum in the absence or presence of various concentrations of cadmium chloride, or treatment with p38 MAPK inhibitor SB202190 and with cadmium chloride exposure. Apoptotic cells in seminiferous tubules of piglets were also performed using TUNEL assay in vivo.</p> <p>Results</p> <p>Cadmium chloride inhibited the proliferation of Piglet Sertoli cells as shown by MTT assay, and it increased malondialdehyde (MDA) but reduced superoxide dismutase (SOD) and Glutathione peroxidase (GSH-Px) activity. Inhibitor SB202190 alleviated the proliferation inhibition of cadmium on piglet Sertoli cells. Comet assay revealed that cadmium chloride caused DNA damage of Piglet Sertoli cells and resulted in cell apoptosis as assayed by flow cytometry. The in vivo study confirmed that cadmium induced cell apoptosis in seminiferous tubules of piglets. Transmission electronic microscopy showed abnormal and apoptotic ultrastructure in Piglet Sertoli cells treated with cadmium chloride compared to the control.</p> <p>Conclusion</p> <p>cadmium has obvious adverse effects on the proliferation of piglet Sertoli cells and causes their DNA damage, cell apoptosis, and aberrant morphology. This study thus offers novel insights into the toxicology of cadmium on male reproduction.</p

Convolutional Neural Networks Facilitate River Barrier Detection and Evidence Severe Habitat Fragmentation in the Mekong River Biodiversity Hotspot

Construction of river infrastructure, such as dams and weirs, is a global issue for ecosystem protection due to the fragmentation of river habitat and hydrological alteration it causes. Accurate river barrier databases, increasingly used to determine river fragmentation for ecologically sensitive management, are challenging to generate. This is especially so in large, poorly mapped basins where only large dams tend to be recorded. The Mekong is one of the world's most biodiverse river basins but, like many large rivers, impacts on habitat fragmentation from river infrastructure are poorly documented. To demonstrate a solution to this, and enable more sensitive basin management, we generated a whole‐basin barrier database for the Mekong, by training Convolutional Neural Network (CNN)–based object detection models, the best of which was used to identify 10,561 previously unrecorded barriers. Combining manual revision and merged with the existing barrier database, our new barrier database for the Mekong Basin contains 13,054 barriers. Existing databases for the Lower Mekong documented under ∼3% of the barriers recorded by CNN combined with manual checking. The Nam Chi/Nam Mun region, eastern Thailand, is the most fragmented area within the basin, with a median [95% CI] barrier density of 15.53 [0.00–49.30] per 100 km, and Catchment Area‐based Fragmentation Index value, calculated in an upstream direction, of 1,178.67 [0.00–6,418.46], due to the construction of dams and sluice gates. The CNN‐based object detection framework is effective and potentially can transform our ability to identify river barriers across many large river basins and facilitate ecologically‐sensitive management

Ultra-Conformal Skin Electrodes With Synergistically Enhanced Conductivity For Long-Time and Low-Motion Artifact Epidermal Electrophysiology

Accurate and imperceptible monitoring of electrophysiological signals is of primary importance for wearable healthcare. Stiff and bulky pregelled electrodes are now commonly used in clinical diagnosis, causing severe discomfort to users for long-time using as well as artifact signals in motion. Here, we report a ~100 nm ultra-thin dry epidermal electrode that is able to conformably adhere to skin and accurately measure electrophysiological signals. It showed low sheet resistance (~24 Ω/sq, 4142 S/cm), high transparency, and mechano-electrical stability. The enhanced optoelectronic performance was due to the synergistic effect between graphene and poly (3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), which induced a high degree of molecular ordering on PEDOT and charge transfer on graphene by strong π-π interaction. Together with ultra-thin nature, this dry epidermal electrode is able to accurately monitor electrophysiological signals such as facial skin and brain activity with low-motion artifact, enabling human-machine interfacing and long-time mental/physical health monitoring

DNA damage and decrease of cellular oxidase activity in piglet sertoli cells exposed to gossypol

The study was designated to explore the toxic effects of gossypol on piglet sertoli cells. Sertoli cells were isolated from piglet testes using a two-step enzyme digestion and followed by differential plating. Piglet sertoli cells were cultured and classified into five groups, that is, group A, the control without gossypol, group B with 2.5 μg/ml gossypol, group C with 5 μg/ml gossypol, group D with 10 μg/ml gossypol and group E with 20 μg/ml gossypol. We found that sertoli cells’ growth was inhibited by gossypol at dose 2.5 μg/ml when compared with the control group. The oxidase activity of sertoli cell also decreased at 2.5 μg/m gossypol. Moreover, DNA damage of sertoli cells was observed at 5 μg/ml gossypol. Putting this into consideration, our study suggests that exposure of gossypol to sertoli cells leads to an inhibition of sertoli cell growth and oxidase activity of sertoli cells at a low concentration, whereas gossypol results in DNA damage of sertoli cells at a higher concentration.Keywords: Gossypol, sertoli cells, oxidase, DNA damag

Single-cell transcriptomic analysis identifies downregulated phosphodiesterase 8B as a novel oncogene in IDH-mutant glioma

IntroductionGlioma, a prevalent and deadly brain tumor, is marked by significant cellular heterogeneity and metabolic alterations. However, the comprehensive cell-of-origin and metabolic landscape in high-grade (Glioblastoma Multiforme, WHO grade IV) and low-grade (Oligoastrocytoma, WHO grade II) gliomas remains elusive.MethodsIn this study, we undertook single-cell transcriptome sequencing of these glioma grades to elucidate their cellular and metabolic distinctions. Following the identification of cell types, we compared metabolic pathway activities and gene expressions between high-grade and low-grade gliomas.ResultsNotably, astrocytes and oligodendrocyte progenitor cells (OPCs) exhibited the most substantial differences in both metabolic pathways and gene expression, indicative of their distinct origins. The comprehensive analysis identified the most altered metabolic pathways (MCPs) and genes across all cell types, which were further validated against TCGA and CGGA datasets for clinical relevance.DiscussionCrucially, the metabolic enzyme phosphodiesterase 8B (PDE8B) was found to be exclusively expressed and progressively downregulated in astrocytes and OPCs in higher-grade gliomas. This decreased expression identifies PDE8B as a metabolism-related oncogene in IDH-mutant glioma, marking its dual role as both a protective marker for glioma grading and prognosis and as a facilitator in glioma progression