Recent Submissions

  • High-Throughput Screening of Metal-Organic Frameworks for Kinetic Separation of Propane and Propene

    Pramudya, Yohanes; Bonakala, Satyanarayana; Antypov, Dmytro; Bhatt, Prashant; Shkurenko, Aleksander; Eddaoudi, Mohamed; Rosseinsky, Matthew J.; Dyer, Matthew S (Physical Chemistry Chemical Physics, Royal Society of Chemistry (RSC), 2020-10-06) [Article]
    We apply molecular simulations to screen a database of reported metal-organic framework structures from the Computation-Ready, Experimental (CoRE) MOF database to identify materials potentially capable of separating propane and propene...
  • Programmable constant phase element realization with crossbar arrays

    Fouda, M. E.; AbdelAty, A. M.; Elwakil, A. S.; Radwan, A. G.; Eltawil, Ahmed (Journal of Advanced Research, Elsevier BV, 2020-08-26) [Article]
    In this paper, we propose a new programmable Constant Phase Element (CPE) realization using resistive crossbar arrays. The programmability of the resistive devices is used to program the CPE. Due to the structure of the crossbar, a new approximation of the CPE element is investigated. The approximation consists of parallel branches where each one can be seen as a weighted sum of low and high pass filters having the same cut-off frequency (i.e., Lapicque model). The closed-form approximation expression is derived, and then the Flower Pollination Algorithm (FPA) is used to find the optimal values of the network components. Different design examples are given over the frequency range of 106-109 rad/s to prove the ability of this realization to achieve any fractional order with less than 5% relative error in both phase and pseudo-capacitance and to demonstrate its programmability. Monte-Carlo simulations are performed to evaluate the sensitivity of the proposed realization against device variability. In addition, the proposed realization is compared with two other state-of-art realizations showing comparable results as standalone realization and within fractional-order relaxation oscillator application.
  • Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

    Fan, Guangyi; Song, Yue; Yang, Liandong; Huang, Xiaoyun; Zhang, Suyu; Zhang, Mengqi; Yang, Xianwei; Chang, Yue; Zhang, He; Li, Yongxin; Liu, Shanshan; Yu, Lili; Chu, Jeffery; Seim, Inge; Feng, Chenguang; Near, Thomas J; Wing, Rod Anthony; Wang, Wen; Wang, Kun; Wang, Jing; Xu, Xun; Yang, Huanming; Liu, Xin; Chen, Nansheng; He, Shunping (GigaScience, Oxford University Press (OUP), 2020-08-18) [Article]
    Background With more than 30,000 species, fish—including bony, jawless, and cartilaginous fish—are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Results Here, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies. Conclusions To illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.
  • Metastatic State of Colorectal Cancer can be Accurately Predicted with Methylome

    Albaradei, Somayah; Thafar, Maha; Van Neste, Christophe; Essack, Magbubah; Bajic, Vladimir B. (ACM, 2020-05-04) [Conference Paper]
    Colorectal cancer (CRC) appears to be the third most common cancer as well as the fourth most common cause of cancer deaths in the world. Its most lethal states are when it becomes metastatic. It is of interest to find tests that can quickly and accurately determine if the patient has already developed metastasis. Changes in methylation profiles have been found to be characteristic of cancers at different stages and can therefore be used to develop diagnostic panels. We developed a deep learning (DL) model (Deep2Met) using methylation profiles of patients with CRC to predict if the cancer is in its metastatic state. Results suggest that our method achieves an AUPR and an average F-score of 96.99% and 94.71%, respectively, making Deep2Met potentially useful for diagnostic purposes. The DL model Deep2Met we developed, shows promise in the diagnosis of CRC based on methylation profiles of individual patients.
  • CCDC 1838597: Experimental Crystal Structure Determination

    Zinser, Caroline M.; Nahra, Fady; Falivene, Laura; Brill, Marcel; Cordes, David B.; Slawin, Alexandra M. Z.; Cavallo, Luigi; Cazin, Catherine S. J.; Nolan, Steven P. (Cambridge Crystallographic Data Centre, 2019) [Dataset]
  • Supplementary material from "Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome"

    Carvalho, Susana; Aylagas, Eva; Villalobos, Rodrigo; Kattan, Yasser; Berumen, Michael L.; Pearman, John K. (figshare, 2019) [Dataset]
    In an era of coral reef degradation, our knowledge of ecological patterns in reefs is biased towards large conspicuous organisms. The majority of biodiversity, however, inhabits small cryptic spaces within the framework of the reef. To assess this biodiverse community, which we term the ‘reef cryptobiome’, we deployed 87 autonomous reef monitoring structures (ARMS), on 22 reefs across 16 degrees latitude of the Red Sea. Combining ARMS with metabarcoding of the mitochondrial cytochrome oxidase I gene, we reveal a rich community, including the identification of 14 metazoan phyla within 10 416 operational taxonomic units (OTUs). While mobile and sessile subsets were similarly structured along the basin, the main environmental driver was different (particulate organic matter and sea surface temperature, respectively). Distribution patterns of OTUs showed that only 1.5% were present in all reefs, while over half were present in a single reef. On both local and regional scales, the majority of OTUs were rare. The high heterogeneity in community patterns of the reef cryptobiome has implications for reef conservation. Understanding the biodiversity patterns of this critical component of reef functioning will enable a sound knowledge of how coral reefs will respond to future anthropogenic impacts.