A review on the use of artificial intelligence for medical imaging of the lungs of patients with coronavirus disease 2019

The results of research on the use of artificial intelligence (AI) for medical imaging of the lungs of patients with coronavirus disease 2019 (COVID-19) has been published in various forms. In this study, we reviewed the AI for diagnostic imaging of COVID-19 pneumonia. PubMed, arXiv, medRxiv, and Google scholar were used to search for AI studies. There were 15 studies of COVID-19 that used AI for medical imaging. Of these, 11 studies used AI for computed tomography (CT) and 4 used AI for chest radiography. Eight studies presented independent test data, 5 used disclosed data, and 4 disclosed the AI source codes. The number of datasets ranged from 106 to 5941, with sensitivities ranging from 0.67–1.00 and specificities ranging from 0.81–1.00 for prediction of COVID-19 pneumonia. Four studies with independent test datasets showed a breakdown of the data ratio and reported prediction of COVID-19 pneumonia with sensitivity, specificity, and area under the curve (AUC). These 4 studies showed very high sensitivity, specificity, and AUC, in the range of 0.9–0.98, 0.91–0.96, and 0.96–0.99, respectively

Functional Ingredients Extraction from Garcinia mangostana Pericarp by Liquefied Dimethyl Ether

The mangosteen (Garcinia mangostana Linn.) pericarp contains rich xanthone, a one kind of the polyphenols in the non-edible portion. In recent years, xanthones have been noted as a functionality such as anti-cancer effect and is expected as pharmaceuticals and health supplements. In this work, extraction of xanthones from mangosteen pericarp by using liquefied DME were investigated. Wet powder and cube samples were used as a raw material. Experimental conditions were 35°C, 0.8 MPa with various amounts of sample (1, 3, 6 g). Extracted components were analyzed by using high performance liquid chromatography (HPLC). As a result, it was confirmed that eight kinds of xanthones such as alpha-mangostin, 3-Isomangostin, Mangostanol, 8-Desoxygartanin, Gartanin, Garcinone E, 9-Hydroxycalabaxanthone, beta-Mangostin were extracted. The highest yield of alpha-mangostin (42.9 mg/g_dry sample) was obtained with a powder sample of 6 g loaded. Final alpha-magostin corresponded to about 104% of the ethanol extraction with wet mangosteen pericarp, and 72% of the dried sample. Therefore, it was considered that in the extraction of xanthones from the mangosteen, liquefied DME extraction was valid

A Report on Overseas Teaching Practicum by Graduate Students in Elementary/Secondary Schools in the United States （XII）

This paper reports on the overseas teaching practicum in the U.S., which was supposed to be the 12th time this year. Eight students joined this year’s program and they prepared for the practicum in the U.S. They met regularly to discuss the lesson plans and deepen their understanding on how to create a lesson and what scaffolding steps they should prepare for conveying messages to American children who know little about Japanese culture and having different background from us. Unfortunately, just a few days before the departure, we had to give up our visit to the U.S. since there was a high chance of a hurricane hitting the area we were to visit. Though we could not make our visit in September, instead we held a forum in November and exchanged discussion on the impact of the program to the participants and the schools which accept us. The details of the lesson plans and the forum are reported in this paper

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map

Following recent advances in high-throughput mass spectrometry (MS)–based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining of yeast multi-omics data. First, new phosphoproteome data on yeast cells were obtained by MS-based proteomics and unified with publicly available yeast phosphoproteome data. This revealed that nearly 60% of ∼6,000 yeast genes encode phosphoproteins. We mapped these unified phosphoproteome data on a yeast protein–protein interaction (PPI) network with other yeast multi-omics datasets containing information about proteome abundance, proteome disorders, literature-derived signaling reactomes, and in vitro substratomes of kinases. In the phospho-PPI, phosphoproteins had more interacting partners than nonphosphoproteins, implying that a large fraction of intracellular protein interaction patterns (including those of protein complex formation) is affected by reversible and alternative phosphorylation reactions. Although highly abundant or unstructured proteins have a high chance of both interacting with other proteins and being phosphorylated within cells, the difference between the number counts of interacting partners of phosphoproteins and nonphosphoproteins was significant independently of protein abundance and disorder level. Moreover, analysis of the phospho-PPI and yeast signaling reactome data suggested that co-phosphorylation of interacting proteins by single kinases is common within cells. These multi-omics analyses illuminate how wide-ranging intracellular phosphorylation events and the diversity of physical protein interactions are largely affected by each other

A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks

Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks. The currently available large-scale PPI data sets only contain information on interaction partners. The data presented in this study also include the sequences involved in the interactions (i.e., the interacting regions, IRs) suggested to correspond to functional and structural domains. Here we present the first large-scale IR data set obtained using mRNA display for 50 human transcription factors (TFs), including 12 transcription-related proteins. The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners. Furthermore, these IRs were preferentially associated with intrinsic disorder. This finding supports the hypothesis that intrinsically disordered regions play a major role in the dynamics and diversity of TF networks through their ability to structurally adapt to and bind with multiple partners. Accordingly, this domain-based interaction resource represents an important step in refining protein interactions and networks at the domain level and in associating network analysis with biological structure and function

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Orofacial somatosensory inputs change the auditory categorization in perceptual adaptation training

International audienceOrofacial somatosensory system intervenes in the perception of speech sounds. Recent study also showed that somatosensory input during speech motor learning can play an important role in the change of speech perception. However, it is still unclear that repeated exposure of somatosensory stimulation during speech perception can also induce an adaptive change of speech representation. This study examined whether speech perception system can be modified by perceptual training involving repeated exposure of orofacial somatosensory stimulation. We focused on the perceptual threshold between /e/ and /a/, and examined whether this perceptual threshold is changed between prior to and following the perceptual adaptation training. We tested 15 native speakers of French. The experiment consisted of three sessions. The first session was the test to measure baseline level of perceptual threshold. The second session was the perceptual adaptation training with somatosensory stimulation associated with facial skin deformation. The third session was the perceptual test again to measure aftereffects of the training. In the first and the third session, we applied an adaptive method based on the maximum-likelihood procedure to detect perceptual threshold by small number of trials. Seventeen trials are used to determine a perceptual threshold. We repeated four times of this test in one session. In the second session, we applied method of constant stimuli using 10 continuum between /e/ and /a/ in order to be exposed all stimulus variants equal number of times. We presented each stimulus in a pseudo-random order for 50 times. In this session, we also applied somatosensory stimulation when the stimulus sound was presented. Given that the target vowels (/e/ and /a/) are characterized by articulatory vertical movements, facial skin deformation was applied in the upward direction. In all sessions, subjects’ task was to identify whether the presented sound was /e/ or /a/ by pressing a key on a keyboard as quickly as possible. The stimuli were presented through headphones at a comfortable volume level. Perceptual thresholds between /e/ and /a/ were identified as the 50% point of the psychometric function estimated by fitting a logistic function. The threshold prior to perceptual adaption was obtained using responses of the last two blocks in the first session and the one following adaptation was obtained using the first two blocks in the third session. Two subjects were excluded since their changes were out of the range for average ± 3SD of the rest of group. When we compared perceptual thresholds prior to and following perceptual adaptation, the threshold changed to the direction of /e/ (-5.46 ± 1.04, average ± s.e.), indicating that the subjects perceived /a/ more than /e/ as an aftereffect of training. One-way ANOVA showed significantly different between sessions prior to and following the training (F(1, 12) = 27.83, p < 0.001). Our data suggest that repetitive exposure of somatosensory inputs during speech perception changes perceptual system and can support the idea that somatosensory input plays a role in speech adaptation