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At least 19 records

Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013

Mass spectrometry special interest group (MS-SIG) aims to bring together experts from the global research community to discuss highlights and challenges in the field of mass spectrometry (MS)-based proteomics and computational biology. The rapid echnological developments in MS-based proteomics have enabled the generation of a large amount of meaningful information on hundreds to thousands of proteins simultaneously from a biological sample; however, the complexity of the MS data require sophisticated computational algorithms and software for data analysis and interpretation. This year’s MS-SIG meeting theme was ‘Beyond the Proteome’ with major focuses on improving protein identification/quantification and using proteomics data to solve interesting problems in systems biology and clinical research.

Ryu, Soyoung↗

CLARIFYING THE NEXUS BETWEEN LIFE CYCLE ASSESSMENT AND CIRCULARITY INDICATORS: A SETAC/ACLCA INTEREST GROUP

Purpose Improving the circularity of resources is important to the sustainability of consumer goods. Current research has indicated that circularity practices and circular economy (CE) methods do not always reduce environmental impacts. The aim of this research is to investigate the adoption of the life cycle assessment (LCA) methodology to improve the environmental impacts of circularity practices. Methods As part of the Society for Environmental Toxicology And Chemistry (SETAC) forum, an interest group (IG) on Circularity and LCA was formed in partnership with the American Center for Life Cycle Assessment (ACLCA) to tackle methodological and technical issues related to circularity in LCA. The IG’s research approach is summarized in four key steps: defining goals and objectives, literature review and gap analysis, ideation, and experimentation. The twelve active persons within this IG meet monthly and have been divided into four sub-working groups (sub-WGs) so that complementary tasks can be completed concurrently in an effective manner. Each sub-WG meets monthly and reports back to the main group for collaboration and brainstorming to meet the research objectives. Results and discussion First, the sub-WG #1, focusing on the “pool of circularity and LCA-based indicators”, analyzed the complementarity between two of the most used circularity indicators and LCA. Second, the sub-WG #2, working on the “evaluation of CE loops performance through LCA”, built a mind map of pain points that reflect the challenges that the LCA practitioners face when combining LCA with CE approaches. Third, the sub-WG #3, dealing with the “trade-offs between circularity and sustainability”, highlighted key alignments and/or conflicts between circularity and sustainability performance depending on the scope, product, industry, or system of analysis. Fourth, the sub-WG #4, focusing on “business and industrial cases”, plans to leverage the knowledge base developed within this IG to develop use cases documenting the benefits and challenges associated with CE-related loops modeling in LCA. Conclusions The first findings of this SETAC/ACLCA IG provide a state-of-the-art overview of the synergists of LCA methodology and the CE measurement frameworks reported in the literature. To move forward and capitalize on the first findings, one valuable point will be to discuss and provide concrete solutions to the pain points that emerged when considering circularity in LCA. Eventually, the knowledge base and resources created within this IG ultimately aim to support the proper application of LCA for practitioners in CE contexts, and could provide relevant inputs for the ISO Technical Committee ISO/TC 323 working on the upcoming standard for the measurement of CE performance.

Life cycle assessment, circular economy, circulari↗

Focused Interest Groups Propel Innovation in the Emerging Data-Driven Hardware Ecosystem

Over the past several decades, the science of electron microscopy (EM) has risen to become one of the cornerstone approaches to understanding material structure, chemistry, and defects at exceptional spatial resolution. This rise can be attributed to the hard work of researchers and companies who have pushed the bounds of instrumentation and analysis, but it is also the result of advocacy by members of professional societies. Furthermore, such advocacy is exemplified by the Aberration Corrected EM (ACEM) focused interest group (FIG) of the Microscopy Society of America (MSA), which has played an important role in facilitating new hardware developments, promoting the exchange of ideas to catalyze discovery, and building the next generation of leaders in electron microscopy. From the early 2000s to the present, aberration correction has moved from proof-of-concept instrumentation to an established technique, providing unprecedented improvements in spatial and chemical resolution for breakthroughs in chemistry, physics, and materials science.

47 OTHER INSTRUMENTATION↗

The research data alliance photon and neutron science interest group

Scientific research data provides unique challenges that are distinct from classic “Big Data” sources. One common element in research data is that the experiment, observations, or simulation were designed, and data were specifically acquired, to shed light on an open scientific question. The data and methods are usually “owned” by the researcher(s) and the data itself might not be viewed to have long-term scientific significance after the results have been published. Often, the data volume was relatively low, with data sometimes easier to reproduce than to catalog and store. Some data and meta-data were not collected in a digital form, or were stored on antiquated or obsolete media. Generally speaking, policies, tools, and management of digital research data have reflected an ad hoc approach that varies domain by domain and research group by research group. This model, which treats research data as disposable, is proving to be a serious limitation as the volume and complexity of research data explodes. Changes are required at every level of scientific research: within the individual groups, and across scientific domains and interdisciplinary collaborations. Enabling researchers to learn about available tools, processes, and procedures should encourage a spirit of cooperation and collaboration, allowing researchers to come together for the common good. In conclusion, these community-oriented efforts provide the potential for targeted projects with high impact.

97 MATHEMATICS AND COMPUTING↗

New England Wind Energy Education Project (NEWEEP) (Final Technical Report)

Project objective is to develop and disseminate accurate, objective information on critical wind energy issues impacting market acceptance of hundreds of land-based projects and vast off-shore wind developments proposed in the 6-state New England region, thereby accelerating the pace of wind installation from today's 140 MW towards the region's 20% by 2030 goals of 12,500 MW. Methodology: This objective will be accomplished by accumulating, developing, assembling timely, accurate, objective and detailed information representing the 'state of the knowledge' on critical wind energy issues impacting market acceptance, and widely disseminating such information. The target audience includes state agencies and local governments; utilities and grid operators; wind developers; agricultural and environmental groups and other NGOs; research organizations; host communities and the general public, particularly those in communities with planned or operating wind projects. Information will be disseminated through: (a) a series of topic-specific web conference briefings; (b) a one-day NEWEEP conference, back-to-back with a Utility Wind Interest Group one-day regional conference organized for this project; (c) posting briefing and conference materials on the New England Wind Forum (NEWF) web site and featuring the content on NEWF electronic newsletters distributed to an opt-in list of currently over 5000 individuals; (d) through interaction with and participation in Wind Powering America (WPA) state Wind Working Group meetings and WPA's annual All-States Summit, and (e) through the networks of project collaborators. Sustainable Energy Advantage, LLC (lead) and the National Renewable Energy Laboratory will staff the project, directed by an independent Steering Committee composed of a collaborative regional and national network of organizations. Major Participants - the Steering Committee: In addition to the applicants, the initial collaborators committing to form a Steering Committee consists of the Massachusetts Renewable Energy Trust; Maine Public Utilities Commission; New Hampshire office of Energy & Planning, the Connecticut Clean Energy Fund;, ISO New England; Utility Wind Interest Group; University of Massachusetts Wind Energy Center; Renewable Energy New England (a new partnership between the renewable energy industry and environmental public interest groups), and Lawrence Berkeley National Laboratory (conditionally). The Steering Committee will: (1) identify and prioritize topics of greatest interest or concern where detailed, objective and accurate information will advance the dialogue in the region; (2) identify critical outreach venues, influencers and experts; (3) direct and coordinate project staff; (4) assist project staff in planning briefings and conferences described below; (5) identify topics needing additional research or technical assistance and (6) identify and recruit additional steering committee members. Impacts/Benefits/Outcomes: By cutting through the clutter of competing and conflicting information on critical issues, this project is intended to encourage the market's acceptance of appropriately-sited wind energy generation.

14 SOLAR ENERGY↗

Compensatory mitigation and screening rules in environmental impact assessment

Concerns about the effectiveness of environmental impact assessment (EIA) have prompted proposals to improve its performance by limiting the discretion of decision-makers in screening. To investigate whether such proposals are likely to generate the desired results, we conducted an evaluation of the screening process under the Australian government's EIA regime from its introduction on 16 July 2000 to 30 June 2013 (study period). Almost 1 in 5 ‘particular manner’ decisions—a type of screening decision under the regime—were found to be unlawful. The extent of non-compliance is explained on the basis of convenience. The department was required to assess a large number of projects under tight timeframes and with limited resources, while being pressured by proponents to allow their projects to bypass EIA. These pressures resulted in the development of an informal custom whereby the formal compensatory mitigation restrictions were frequently ignored. The results highlight the relative significance of formal and informal institutions in EIA. Formal EIA rules typically provide a mere outline of the process. The informal institutions adopted by administrators often have a greater influence on how the process operates and what it achieves. - Highlights: • Concerns about the effectiveness of environmental impact assessment (EIA) have prompted proposals to improve its performance by limiting the discretion of decision-makers in screening. • To investigate whether such proposals are likely to generate the desired results, we conducted an evaluation of the Australian government's screening process, looking at the extent of compliance with a formal prohibition on the consideration of compensatory mitigation. • Almost 1 in 5 ‘particular manner’ decisions – a type of screening decision under the regime – were found to be unlawful (with a 95% confidence interval of between 1:4 and 1:7) because of a failure to abide by the compensatory mitigation restrictions. For urban development actions, the ratio between lawful and unlawful particular manner decisions was worse than 1:1. • The extent of non-compliance is explained on the basis of convenience. Budget and interest group pressures resulted in the development of an informal custom whereby the formal compensatory mitigation restrictions were ignored. • The results highlight the relative significance of formal and informal institutions in EIA. Formal EIA rules typically provide a mere outline of the process. The informal institutions adopted by administrators often have a greater influence on how the process operates and what it achieves.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Aleutian Pribilof Islands Wind Energy Feasibility Study

Under this project, the Aleutian Pribilof Islands Association (APIA) conducted wind feasibility studies for Adak, False Pass, Nikolski, Sand Point and St. George. The DOE funds were also be used to continue APIA's role as project coordinator, to expand the communication network quality between all participants and with other wind interest groups in the state and to provide continued education and training opportunities for regional participants. This DOE project began 09/01/2005. We completed the economic and technical feasibility studies for Adak. These were funded by the Alaska Energy Authority. Both wind and hydro appear to be viable renewable energy options for Adak. In False Pass the wind resource is generally good but the site has high turbulence. This would require special care with turbine selection and operations. False Pass may be more suitable for a tidal project. APIA is funded to complete a False Pass tidal feasibility study in 2012. Nikolski has superb potential for wind power development with Class 7 wind power density, moderate wind shear, bi-directional winds and low turbulence. APIA secured nearly $\$$1M from the United States Department of Agriculture Rural Utilities Service Assistance to Rural Communities with Extremely High Energy Costs to install a 65kW wind turbine. The measured average power density and wind speed at Sand Point measured at 20m (66ft), are 424 W/m2 and 6.7 m/s (14.9 mph) respectively. Two 500kW Vestas turbines were installed and when fully integrated in 2012 are expected to provide a cost effective and clean source of electricity, reduce overall diesel fuel consumption estimated at 130,000 gallons/year and decrease air emissions associated with the consumption of diesel fuel. St. George Island has a Class 7 wind resource, which is superior for wind power development. The current strategy, led by Alaska Energy Authority, is to upgrade the St. George electrical distribution system and power plant. Avian studies in Nikolski and Sand Point have allowed for proper wind turbine siting without killing birds, especially endangered species and bald eagles. APIA continues coordinating and looking for funding opportunities for regional renewable energy projects. An important goal for APIA has been, and will continue to be, to involve community members with renewable energy projects and energy conservation efforts.

17 WIND ENERGY↗

Constraints on the Parameterization of Convective Cloud Systems from Analyses of ARM Observations and Models

Anthony D. Del Genio has served as principal investigator since the inception of ASR in 2009 as co-chair of the Cloud Lifecycle Working Group (CLWG) and in connection with that as a member of the ASR Science and Infrastructure Steering Committee. In this role he has been intimately involved with oversight of existing and proposed ASR Focus Groups (Vertical Velocity, QUICR, Ice Properties) and thematic interest groups (Mesoscale Organized Convection, Warm Low Clouds, Mixed-Phase Clouds, MJO, Entrainment) whose activities fall under the purview of CLWG. The PI actively participates himself in the Mesoscale Organized Convection and MJO groups, is a Co-Investigator on two successfully implemented IOPs (AMIE, MC3E), and was an unfunded Collaborator on the recently completed FASTER project at BNL under the DOE Modeling Program. The PI has also spent the past three years as a member of the ARM Science Board, which reviews proposals to conduct IOPs at the permanent ARM sites and to deploy the ARM Mobile Facilities. Finally, the PI was a participant in the first ARM-European workshop in 2012 that eventually led to the creation of the SGP supersite concept. This report includes an annotated list of published research results.

54 ENVIRONMENTAL SCIENCES↗

Filling-enforced obstructed atomic insulators

Topological band theory has achieved great success in the high-throughput search for topological band structures both in paramagnetic and magnetic crystal materials. However, a significant proportion of materials are topologically trivial insulators at the Fermi level. In this paper, we show that, remarkably, for a subset of the topologically trivial insulators, knowing only their electron number and the Wyckoff positions of the atoms we can separate them into two groups: the obstructed atomic insulator (OAI) and the atomic insulator (AI). The interesting group, the OAI, have a center of charge not localized on the atoms. Using the theory of topological quantum chemistry, in this work we first derive the necessary and sufficient conditions for a topologically trivial insulator to be a filling enforced obstructed atomic insulator (feOAI) in the 1651 Shubnikov space groups. Remarkably, the filling enforced criteria enable the identification of obstructed atomic bands without knowing the representations of the band structures. Hence, no calculations are needed for the filling enforced criteria, although they are needed to obtain the band gaps. With the help of the Topological Quantum Chemistry website, we have performed a high-throughput search for feOAIs and have found that 957 ICSD entries (638 unique materials) are paramagnetic feOAIs, among which 738 (475) materials have an indirect gap. The metallic obstructed surface states of feOAIs are also showcased by several material examples. Published by the American Physical Society 2024

Materials Science↗

Development and implementation of energy efficiency standards and labeling programs in China: Progress and challenges

Over the last twenty years, with growing policy emphasis on improving energy efficiency and reducing environmental pollution and carbon emissions, China has implemented a series of new minimum energy performance standards (MEPS) and mandatory and voluntary energy labels to improve appliance energy efficiency. As China begins planning for the next phase of standards and labeling (S&L) program development under the 12th Five Year Plan, an evaluation of recent program developments and future directions is needed to identify gaps that still exist when compared with international best practices. The review of China’s S&L program development and implementation in comparison with major findings from international experiences reveal that there are still areas of improvement, particularly when compared to success factors observed across leading international S&L program. China currently lacks a formalized regulatory process for standard-setting and do not have any legal or regulatory guidance on elements of S&L development such as stakeholder participation or the issue of legal precedence between conflicting national, industrial and local standards. Consequently, China’s laws regarding standard-setting and management of the mandatory energy label program could be updated, as they have not been amended or revised recently and no longer reflects the current situation. While China uses similar principles for choosing target products as the U.S., Australia, EU and Japan, including high energy-consumption, mature industry and testing procedure and stakeholder support, recent MEPS revisions have generally aimed at only eliminating the bottom 20% efficiency of the market. Setting a firm principle based on maximizing energy savings that are technically feasible and economically justified may help improve the stringency of China’s MEPS program and reduce the need for frequent revisions. China also lacks robust survey data and relies primarily on market research data in relatively simple techno-economic analyses used to determine its efficiency standards levels rather than the specific sets of analyses and tools used internationally. Based on international experiences, inclusion of more detailed energy consumption surveys in the Chinese national census surveys and statistical reporting systems could help provide the necessary data for more comprehensive standard-setting analyses. In terms of stakeholder participation in the standards development process, stakeholder participation in China is limited to membership on technical committees responsible for developing or revising standards and generally do not include environmental groups, consumer associations, utilities and other NGOs. Increasing stakeholder involvement to broader interest groups could help garner more support and feedback in the S&L implementation process. China has emerged as a leader in a national verification testing scheme with complementary pilot checktesting projects, but it still faces challenges with insufficient funding, low local awareness amongst some regulatory agencies and resistance to check-testing by some manufacturers, limited product sampling scope, and testing inconsistency and incomparability of results. Thus, further financial and staff resources and capacity building will be needed to overcome these remaining challenges and to expand impacts evaluations to assess the actual effectiveness of implementation and enforcement.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Elevated levels of plasma Big endothelin-1 and its relation to hypertension and skin lesions in individuals exposed to arsenic

Chronic arsenic (As) exposure affects the endothelial system causing several diseases. Big endothelin-1 (Big ET-1), the biological precursor of endothelin-1 (ET-1) is a more accurate indicator of the degree of activation of the endothelial system. Effect of As exposure on the plasma Big ET-1 levels and its physiological implications have not yet been documented. We evaluated plasma Big ET-1 levels and their relation to hypertension and skin lesions in As exposed individuals in Bangladesh. A total of 304 study subjects from the As-endemic and non-endemic areas in Bangladesh were recruited for this study. As concentrations in water, hair and nails were measured by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS). The plasma Big ET-1 levels were measured using a one-step sandwich enzyme immunoassay kit. Significant increase in Big ET-1 levels were observed with the increasing concentrations of As in drinking water, hair and nails. Further, before and after adjusting with different covariates, plasma Big ET-1 levels were found to be significantly associated with the water, hair and nail As concentrations of the study subjects. Big ET-1 levels were also higher in the higher exposure groups compared to the lowest (reference) group. Interestingly, we observed that Big ET-1 levels were significantly higher in the hypertensive and skin lesion groups compared to the normotensive and without skin lesion counterpart, respectively of the study subjects in As-endemic areas. Thus, this study demonstrated a novel dose–response relationship between As exposure and plasma Big ET-1 levels indicating the possible involvement of plasma Big ET-1 levels in As-induced hypertension and skin lesions. -- Highlights: ► Plasma Big ET-1 is an indicator of endothelial damage. ► Plasma Big ET-1 level increases dose-dependently in arsenic exposed individuals. ► Study subjects in arsenic-endemic areas with hypertension have elevated Big ET-1 levels. ► Study subjects with arsenic-induced skin lesions show elevated plasma Big ET-1 levels. ► Arsenic-induced hypertension and skin lesions may be linked to plasma Big ET-1 levels.

54 ENVIRONMENTAL SCIENCES↗

The 2016 Bioinformatics Open Source Conference (BOSC)

The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC (http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

59 BASIC BIOLOGICAL SCIENCES↗