Manipulating Multiple Order Parameters via Oxygen Vacancies: The case of Eu0.5Ba0.5TiO3-{\delta}

Controlling functionalities, such as magnetism or ferroelectricity, by means of oxygen vacancies (VO) is a key issue for the future development of transition metal oxides. Progress in this field is currently addressed through VO variations and their impact on mainly one order parameter. Here we reveal a new mechanism for tuning both magnetism and ferroelectricity simultaneously by using VO. Combined experimental and density-functional theory studies of Eu0.5Ba0.5TiO3-{\delta}, we demonstrate that oxygen vacancies create Ti3+ 3d1 defect states, mediating the ferromagnetic coupling between the localized Eu 4f7 spins, and increase an off-center displacement of Ti ions, enhancing the ferroelectric Curie temperature. The dual function of Ti sites also promises a magnetoelectric coupling in the Eu0.5Ba0.5TiO3-{\delta}.Comment: Accepted by Physical Review B, 201

Genome Assembly for a Yunnan-Guizhou Plateau “3E” Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications

A Yunnan-Guizhou Plateau fish, the Kanglang white minnow (Anabarilius grahami), is a typical “3E” (Endangered, Endemic, and Economic) species in China. Its distribution is limited to Fuxian Lake, the nation’s second deepest lake, with a significant local economic value but a drastically declining wild population. This species has been evaluated as VU (Vulnerable) in the China Species Red List. As one of the “Four Famous Fish” in Yunnan province, the artificial breeding has been achieved since 2003. It has not only re-established its wild natural populations by reintroduction of the artificial breeding stocks, but also brought a wide and popular utilization of this species to the local fish farms. A. grahami has become one of the main native aquaculture species in Yunnan province, and the artificial production has been emerging in steady growth each year. To promote the conservation and sustainable utilization of this fish, we initiated its whole genome sequencing project using an Illumina Hiseq2500 platform. The assembled genome size of A. grahami is 1.006 Gb, accounting for 98.63% of the estimated genome size (1.020 Gb), with contig N50 and scaffold N50 values of 26.4 kb and 4.41 Mb, respectively. Approximately about 50.38% of the genome was repetitive. A total of 25,520 protein-coding genes were subsequently predicted. A phylogenetic tree based on 4,580 single-copy genes from A. grahami and 18 other cyprinids revealed three well-supported subclades within the Cyprinidae. This is the first inter-subfamily relationship of cyprinids at genome level, providing a simple yet useful framework for understanding the traditional but popular subfamily classification systems. Interestingly, a further population demography of A. grahami uncovered a historical relationship between this fish and Fuxian Lake, suggesting that range expansion or shrinkage of the habitat has had a remarkable impact on the population size of endemic plateau fishes. Additionally, a total of 33,836 simple sequence repeats (SSR) markers were identified, and 11 loci were evaluated for a preliminary genetic diversity analysis in this study, thus providing another useful genetic resource for studying this “3E” species

The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

Phylogeography and Demographic History of Babina pleuraden (Anura, Ranidae) in Southwestern China

Factors that determine genetic structure of species in southwestern China remain largely unknown. In this study, sequences of two mitochondrial genes (COI and cyt b) were determined to investigate the phylogeography and demography of Babina pleuraden, a pond frog endemic to southwestern China. A total of 262 individuals from 22 populations across the entire range of the species were collected. Our results indicate that B. pleuraden comprises five well-supported mitochondrial lineages roughly corresponding to five geographical areas. The phylogeographic structure of B. pleuraden has been shaped primarily by the unique regional responses of the Yunnan Plateau to the rapid uplift of the Qinghai-Tibetan Plateau occurred c. 2.5 Mya (B phrase of Qingzang Movement) and climatic oscillation during middle Pleistocene (c. 0.64–0.36 Mya), rather than by the paleo-drainage systems. The present wide distribution of the species has resulted from recent population expansion (c. 0.053–0.025 Mya) from multiple refugia prior to the Last Glacial Maximum, corresponding to the scenario of “refugia within refugia”

A New Strategy of Drug Delivery: Electric Field Distribution in Brain Tumor Due to Electroporation

As the second leading cause of cancer-related deaths in children under 20, and the second leading cause of cancer-related deaths in males aged 20–39, there is a need to seek an effective treatment for brain tumors. While there may be various drugs for brain tumors, the problem is the lack of effective methods of delivery through cell membranes at a very specified and confined region. In order to tackle this specific problem of drug delivery, electroporation is introduced. Electroporation, the local application of electrical pulses, renders the cell membranes permeable to otherwise impermeable or poorly permeable anticancer drugs, thereby facilitating a potent localized cytotoxic effect. For effective electroporation-based drug uptake, the electric field distribution is critical. If the electric field intensity is too low, it will not open up the pores; if the electric field intensity is too high, it will kill the cells. This study investigated how the applied electric field varied in a 2-D model of a brain slice both with and without tumors, as well as in a simple 3-D model. With a critical field strength at around 1,200 V/cm, simulated electric fields were observed and compared under various conditions. The software utilized was ElecNet, an electric field simulation tool, by which the model was constructed with variable parameters, such as material conductivity and permittivity. Under various conditions, data were collected consistently at relative locations—barely outside, barely inside, and at the center of the tumor—for comparison and analysis. Results in the 2-D model showed the most optimal effect with an 8-needle array electrode, and suggested an enlarged needle array electrode for a large tumor. In 3-D, the critical strength and confined effect were observed at various depths. These results were consistent with previous studies of electroporation on breast tumors, which demonstrated similar electric behaviors. Based on our study, electroporation is a potential therapeutic strategy for treatment of brain tumors. Future investigation of a more sophisticated 3-D model is expected to confirm these findings with other preclinical studies using electroporation

Modeling Cortical Visual Processing With Recurrent Neural Network

Human vision is enabled by a cascade of visual processes in the brain. On the other hand, deep neural networks have also enabled computer vision to recognize images to a human-like level. Bearing on this similarity, it has recently attracted interests in using deep neural networks for modeling the human visual cortex with fMRI imaging. Studies have shown convolutional neural networks (CNNs) predicted the cortical activity during subjects viewing natural images. Besides, CNNs revealed the spatial hierarchy of visual processing in the cortex. Yet, neither the brain nor our visual world is static. Therefore, we acquired fMRI data during subjects watching natural movies. We used both a CNN, and a recurrent neural network (RNN) extended upon the CNN, for modeling and understanding the workings of the visual cortex during natural vision. Using neural encoding as the common metric, we found that these models predicted widespread cortical activity. Moreover, the RNN, exploiting temporal structures, was superior to the CNN in a number of aspects. It not only predicted more about the cortical activity and mapped the spatial hierarchy, but also reported the temporal hierarchy in the visual processing for the first time. Our results cast light on the future studies of systems neuroscience using computational models

Community Detection Using Robust Label Propagation Algorithm

Because there is so much randomness, the robustness of label propagation algorithm (LPA) is severely hampered. To reduce the randomness, a label propagation algorithm based on degree (LPAD) is proposed. Only the node with extreme degree is labeled initially, and the label is updated according to the sum degree of its neighbors during iteration. The results show that the randomness of LPAD is reduced greatly, the robustness of community partition is improved significantly, and the convergence is speeded up too