An overview of and issues with sky radiometer technology and SKYNET

This paper is an overview of the progress in sky radiometer technology and the development of the network called SKYNET. It is found that the technology has produced useful on-site calibration methods, retrieval algorithms, and data analyses from sky radiometer observations of aerosol, cloud, water vapor, and ozone. A formula was proposed for estimating the accuracy of the sky radiometer calibration constant F0 using the improved Langley (IL) method, which was found to be a good approximation to observed monthly mean uncertainty in F0, around 0.5 % to 2.4 % at the Tokyo and Rome sites and smaller values of around 0.3 % to 0.5 % at the mountain sites at Mt. Saraswati and Davos. A new cross IL (XIL) method was also developed to correct an underestimation by the IL method in cases with large aerosol retrieval errors. The root-mean-square difference (RMSD) in aerosol optical thickness (AOT) comparisons with other networks took values of less than 0.02 for λ≥500 nm and a larger value of about 0.03 for shorter wavelengths in city areas and smaller values of less than 0.01 in mountain comparisons. Accuracies of single-scattering albedo (SSA) and size distribution retrievals are affected by the propagation of errors in measurement, calibrations for direct solar and diffuse sky radiation, ground albedo, cloud screening, and the version of the analysis software called the Skyrad pack. SSA values from SKYNET were up to 0.07 larger than those from AERONET, and the major error sources were identified as an underestimation of solid viewing angle (SVA) and cloud contamination. Correction of these known error factors reduced the SSA difference to less than 0.03. Retrievals of other atmospheric constituents by the sky radiometer were also reviewed. Retrieval accuracies were found to be about 0.2 cm for precipitable water vapor amount and 13 DU (Dobson Unit) for column ozone amount. Retrieved cloud optical properties still showed large deviations from validation data, suggesting a need to study the causes of the differences. It is important that these recent studies on improvements presented in the present paper are introduced into the existing operational systems and future systems of the International SKYNET Data Center

Separated Transcriptomes of Male Gametophyte and Tapetum in Rice: Validity of a Laser Microdissection (LM) Microarray

In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on their spatial and temporal expression patterns, 140 genes which had been previously defined as anther specific were further classified as male gametophyte specific (71 genes, 51%), tapetum-specific (seven genes, 5%) or expressed in both male gametophyte and tapetum (62 genes, 44%). These results indicate that the 44K LM-microarray is a reliable tool to analyze the gene expression profiles of two important cell types in the anther, the microspore/pollen and tapetum

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Japanese TA-Like Activities in the Sectors of Medical Care, Food and Energy

Atlanta Conference on Science and Innovation Policy 2009This presentation was part of the session : Policy Actors and RelationshipsNote: This is part of the panel presentation "Knowledge Use and Exchange for Policy and Society in Japan: Concepts and Practices." Japanese TA-like activities in the sectors of medical care, food and energy Makiko Matsuo and Go Yoshizawa Given the conceptual and historical survey of TA, this presentation raises the following research questions: what kind of TA-like activities have been implemented in Japan, particularly focusing on medicine, food and energy sectors; what are the needs in these individual sectors for which institutionalization of TA would be able to meet; in which conditions fragmented or networked activities can be regarded as TA. Document analysis and interviews with relevant actors involved in the past and current TA-like activities. The approach is more like action research, by which we investigators change the context to realize the institutionalization of TA by mobilizing and networking these actors and ourselves through mutual learning. Preliminary Results Technology assessment (TA) refers to institutions and practices which support problem-definition (agenda setting) or decision-making for the development of technology and society by anticipating, at an early stage of the technology development, societal impacts of emerging technologies that are difficult to be governed by conventional research, innovation and legal systems. From this perspective, TA-like activities in the following sectors seem fragmented and less comprehensive. In the case of medical care, TA-like activities have been mostly economic assessment for the medical service payment, which is entirely focused on cost-effectiveness just for medical resource allocation, not for ethical and social implications. Advisory councils for ELSI on advanced technologies have no comprehensive discussions crossing over ministries. Inadequacy of agenda-setting also brings discussions to a deadlock - an expert panel on bioethics in the Cabinet Office has been holding years of debate on embryos. The legislation by parliamentary members is so dependent on legislative bureaus and swayed by social conditions. This entails a lack of consistency in debate as exemplified by virtually leaving discussions on transplanting organs from people 15 or younger. As to food, there are increasing applications of science and technology in this sector, such as pesticides, food additives, veterinary drugs, food irradiation, GM foods, health and dietary foods, nano foods, and cloned meat. The need for comprehensive assessment becomes more urgent, not only for social and ethical debate on GM foods and cost-benefit analysis, but also for examining how health foods affect Japanese individual dietary habits and life styles, food culture, food industry etc. Perspectives on sustainable fishery, relationship between energy and agriculture have also been dismissed. Risk assessment currently undertaken by the Food Safety Commission (FSC) is generally effectively conducted for foods subject to pre-market authorization, despite insufficient assessment of other aspects of applied technologies. The energy policy arena abounds in TA-like activities such as a number of plans, strategies, visions and roadmaps to comply with Kyoto protocol. These quantitative technical scenarios are consistent each other in number but they have hardly conducted social impact assessment. For example in the development renewable energy, there is potentially severe conflict over the renewable portfolio standard (RPS) legislation and a future distributed power supply system. There is no apparent clash, no TA-like activity, and no anticipatory governance. Other examples include an insufficient assessment on social, economic and environmental impacts of biomass fuels, the instalment of HEMS (home energy management system) and its consequence, and 24/7 convenience stores - how it affects the reduction of CO2 emissions, local retailers, regional employment, late-night criminal activities, urban life style etc. A more specific issue discussed is risks and regulations on multi-walled carbon nanotubes (MWCNT). There are controversies and confusions around scientific judgements on a couple of articles that imply this nanomaterial may causes asbestos-like mesothelioma. A precautionary but rather pointless and no evidence-based guideline announced by the Ministry of Health, Labour and Welfare (MHLW) in February 2008 has plunged the nanotechnology industry into a further confusion and nanophobia-phobia (Rip 2006). Our analysis suggests the lack of a precautionary appraisal (Stirling 2007) might be the major cause

Risk factors for neuropsychiatric symptoms in patients with Parkinson's disease during COVID-19 pandemic in Japan.

The worsening of neuropsychiatric symptoms such as depression, anxiety, and insomnia in patients with Parkinson's disease (PD) has been a concern during the COVID-19 pandemic, because most people worked in self-isolation for fear of infection. We aimed to clarify the impact of social restrictions imposed due to the COVID-19 pandemic on neuropsychiatric symptoms in PD patients and to identify risk factors associated with these symptoms. A cross-sectional, hospital-based survey was conducted from April 22, 2020 to May 15, 2020. PD patients and their family members were asked to complete paper-based questionnaires about neuropsychiatric symptoms by mail. PD patients were evaluated for motor symptoms using MDS-UPDRS part 2 by telephone interview. A total of 71 responders (39 PD patients and 32 controls) completed the study. Although there was no difference in the age distribution, the rate of females was significantly lower in PD patients (35%) than controls (84%) (P < 0.001). Participants with clinical depression (PHQ-9 score ≥ 10) were more common in PD patients (39%) than controls (6%) (P = 0.002). Multivariate logistic regression analysis revealed that an MDS-UPDRS part 2 score was correlated with the presence of clinical depression (PHQ-9 score ≥ 10) and clinical anxiety (GAD-7 score ≥ 7) (clinical depression: OR, 1.31; 95% CI, 1.04-1.66; P = 0.025; clinical anxiety: OR, 1.36; 95% CI, 1.07-1.72; P = 0.013). In the presence of social restrictions, more attention needs to be paid to the neuropsychiatric complications of PD patients, especially those with more severe motor symptoms

Enhancing Multi-Center Generalization of Machine Learning-Based Depression Diagnosis From Resting-State fMRI

esting-state fMRI has the potential to find abnormal behavior in brain activity and to diagnose patients with depression. However, resting-state fMRI has a bias depending on the scanner site, which makes it difficult to diagnose depression at a new site. In this paper, we propose methods to improve the performance of diagnosis of major depressive disorder (MDD) at an independent site by reducing the site bias effects using regression. For this, we used a subgroup of healthy subjects of the independent site to regress out site bias. We further improved the classification performance of patients with depression by focusing on melancholic depressive disorder. Our proposed methods would be useful to apply depression classifiers to subjects at completely new site

Enhancing Multi-Center Generalization of Machine Learning-Based Depression Diagnosis From Resting-State fMRI

Resting-state fMRI has the potential to help doctors detect abnormal behavior in brain activity and to diagnose patients with depression. However, resting-state fMRI has a bias depending on the scanner site, which makes it difficult to diagnose depression at a new site. In this paper, we propose methods to improve the performance of the diagnosis of major depressive disorder (MDD) at an independent site by reducing the site bias effects using regression. For this, we used a subgroup of healthy subjects of the independent site to regress out site bias. We further improved the classification performance of patients with depression by focusing on melancholic depressive disorder. Our proposed methods would be useful to apply depression classifiers to subjects at completely new sites