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- Deans, Andrew R, et al.
(author)
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Finding Our Way through Phenotypes.
- 2015
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In: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
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Journal article (peer-reviewed)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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- Giosan, Liviu, et al.
(author)
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Fluvial landscapes of the Harappan civilization
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:26, s. E1688-E1694
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Journal article (peer-reviewed)abstract
- The collapse of the Bronze Age Harappan, one of the earliest urban civilizations, remains an enigma. Urbanism flourished in the western region of the Indo-Gangetic Plain for approximately 600 y, but since approximately 3,900 y ago, the total settled area and settlement sizes declined, many sites were abandoned, and a significant shift in site numbers and density towards the east is recorded. We report morphologic and chronologic evidence indicating that fluvial landscapes in Harappan territory became remarkably stable during the late Holocene as aridification intensified in the region after approximately 5,000 BP. Upstream on the alluvial plain, the large Himalayan rivers in Punjab stopped incising, while downstream, sedimentation slowed on the distinctive mega-fluvial ridge, which the Indus built in Sindh. This fluvial quiescence suggests a gradual decrease in flood intensity that probably stimulated intensive agriculture initially and encouraged urbanization around 4,500 BP. However, further decline in monsoon precipitation led to conditions adverse to both inundation- and rain-based farming. Contrary to earlier assumptions that a large glacier-fed Himalayan river, identified by some with the mythical Sarasvati, watered the Harappan heartland on the interfluve between the Indus and Ganges basins, we show that only monsoonal-fed rivers were active there during the Holocene. As the monsoon weakened, monsoonal rivers gradually dried or became seasonal, affecting habitability along their courses. Hydroclimatic stress increased the vulnerability of agricultural production supporting Harappan urbanism, leading to settlement downsizing, diversification of crops, and a drastic increase in settlements in the moister monsoon regions of the upper Punjab, Haryana, and Uttar Pradesh.
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- Lundberg, Hans, et al.
(author)
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High-gain Soft-x-ray Pumped Photoionization Laser in Zinc Vapor
- 1984
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 45:4
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Journal article (peer-reviewed)abstract
- Large inversion densities in Zn+ have been produced by photoionizing inner #x2010;shell d electrons with the broadband soft #x2010;x #x2010;ray flux from a 1.06 #x2010; #x3bc;m laser #x2010;produced plasma. This pumping scheme is an effective technique for rapidly producing large population densities (5 #xd7;1013 cm-3) in the 3d9 #x2009;4s2 #x2009;2D5/2 upper laser level. These large densities (a) produced laser action on a two #x2010;electron transition from the d #x2010;electron manifold to the outer #x2010;electron manifold at 7478 #xc5;, (b) allowed the isotope shifts on this relatively weak transition to be measured, and (c) may eventually be transferred to other high lying states in Zn+ to produce vacuum ultraviolet lasers.
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- Macklin, P. A., et al.
(author)
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Carbon dioxide dynamics in a tropical estuary over seasonal and rain-event time scales
- 2020
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In: Continental Shelf Research. - : Elsevier BV. - 0278-4343. ; 206
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Journal article (peer-reviewed)abstract
- Tropical estuaries may release large amounts of carbon dioxide to the atmosphere, but remain understudied relative to temperate systems. Here, we investigate hydrological drivers of pCO(2) along similar to 22 km of an aquatic continuum from the mountain river to the coastal ocean, including highly modified aquaculture and urban zones (Perancak Estuary, Ijo Gading River, Bali, Indonesia). We report seasonal spatial surveys (n = 8) and stationary time series observations (n = 4 days) during a rain event. Overall, pCO(2) ranged from 330 mu atm to 12,126 mu atm, with the lowest values observed near the estuary mouth and in the river upstream of the urban zone, and the highest values in the upper estuary where radon (Rn-222, a natural groundwater tracer) revealed elevated groundwater discharge. Average atmospheric CO2 fluxes in the upper estuary (107.3 mmol m(-2 )d(-1)) were -5-fold greater than in the lower estuary (19.1 mmol m(-2 )d(-1)), while the river was a minor atmospheric CO2 sink (-0.2 mmol m(-2 )d(-1)). Overall, the estuary was a source of CO2 to the atmosphere with area-weighted emissions of similar to 67 mmol m(-2 )d(-1). Seasonal spatial surveys revealed strong correlations between antecedent rainfall and pCO(2) and Rn-222 in the estuary, implying pCO(2) responds to delayed groundwater discharge. A detailed 4-day time series covering an episodic flooding event revealed sharp transitions in CO2 drivers, including dilution by rainfall followed by inputs of CO2-enriched groundwater. Groundwater discharge, as traced by radon, explained most of pCO(2) variability in dry and wet conditions. Overall, we highlight the importance of seasonal and episodic rainfall and how delayed groundwater seepage may drive CO2 distribution in a highly modified tropical estuary.
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- Sanders, Luciana M., et al.
(author)
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Carbon accumulation in Amazonian floodplain lakes : A significant component of Amazon budgets?
- 2017
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In: Limnology and Oceanography Letters. - : Wiley. - 2378-2242. ; 2:1, s. 29-35
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Journal article (peer-reviewed)abstract
- The Amazon floodplains cover approximately 10% of the Amazon Basin and are composed of predominantly anoxic sediments that may store large amounts of carbon. Our study combines Pb-210 derived sedimentation rates from four recently analyzed sediment cores (n = 4) with previously published organic carbon (OC) burial estimates (n = 18) to provide a broad, first order estimate of carbon accumulation in Amazon floodplain lakes. The OC burial rates were 266 +/- 57 g C m(-2) yr(-1). This rate is several folds greater than those reported for lakes in arctic, boreal, temperate, and tropical regions. The large amount and spatial variation of OC burial rates in these floodplain lakes highlights the need for increased sampling efforts to better measure these potentially important components of the Amazon Basin carbon budget.
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- van den Berg, Leonard H., et al.
(author)
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Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials
- 2019
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In: Neurology. - : Wolters Kluwer. - 0028-3878 .- 1526-632X. ; 92:14, s. E1610-E1623
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Journal article (peer-reviewed)abstract
- Objective: To revise the 1999 Airlie House consensus guidelines for the design and implementation of preclinical therapeutic studies and clinical trials in amyotrophic lateral sclerosis (ALS).Methods: A consensus committee comprising 140 key members of the international ALS community (ALS researchers, clinicians, patient representatives, research funding representatives, industry, and regulatory agencies) addressed 9 areas of need within ALS research: (1) preclinical studies; (2) biological and phenotypic heterogeneity; (3) outcome measures; (4) disease-modifying and symptomatic interventions; (5) recruitment and retention; (6) biomarkers; (7) clinical trial phases; (8) beyond traditional trial designs; and (9) statistical considerations. Assigned to 1 of 8 sections, committee members generated a draft set of guidelines based on a “background” of developing a (pre)clinical question and a “rationale” outlining the evidence and expert opinion. Following a 2-day, face-to-face workshop at the Airlie House Conference Center, a modified Delphi process was used to develop draft consensus research guidelines, which were subsequently reviewed and modified based on comments from the public. Statistical experts drafted a separate document of statistical considerations (section 9).Results: In this report, we summarize 112 guidelines and their associated backgrounds and rationales. The full list of guidelines, the statistical considerations, and a glossary of terms can be found in data available from Dryad (appendices e-3–e-5, doi.org/10.5061/dryad.32q9q5d). The authors prioritized 15 guidelines with the greatest potential to improve ALS clinical research.Conclusion: The revised Airlie House ALS Clinical Trials Consensus Guidelines should serve to improve clinical trial design and accelerate the development of effective treatments for patients with ALS.
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