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  • 1
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    Online Resource
    Anatomically interpretable deep learning of brain age captures domain-specific cognitive impairment
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 2 ( 2023-01-10)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 2 ( 2023-01-10)
    Abstract: The gap between chronological age (CA) and biological brain age, as estimated from magnetic resonance images (MRIs), reflects how individual patterns of neuroanatomic aging deviate from their typical trajectories. MRI-derived brain age (BA) estimates are often obtained using deep learning models that may perform relatively poorly on new data or that lack neuroanatomic interpretability. This study introduces a convolutional neural network (CNN) to estimate BA after training on the MRIs of 4,681 cognitively normal (CN) participants and testing on 1,170 CN participants from an independent sample. BA estimation errors are notably lower than those of previous studies. At both individual and cohort levels, the CNN provides detailed anatomic maps of brain aging patterns that reveal sex dimorphisms and neurocognitive trajectories in adults with mild cognitive impairment (MCI, N  = 351) and Alzheimer’s disease (AD, N  = 359). In individuals with MCI (54% of whom were diagnosed with dementia within 10.9 y from MRI acquisition), BA is significantly better than CA in capturing dementia symptom severity, functional disability, and executive function. Profiles of sex dimorphism and lateralization in brain aging also map onto patterns of neuroanatomic change that reflect cognitive decline. Significant associations between BA and neurocognitive measures suggest that the proposed framework can map, systematically, the relationship between aging-related neuroanatomy changes in CN individuals and in participants with MCI or AD. Early identification of such neuroanatomy changes can help to screen individuals according to their AD risk.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2214634120
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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  • 2
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    Multiple constraints cause positive and negative feedbacks limiting grassland soil CO 2 efflux under CO 2 enrichment
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 2 ( 2021-01-12)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 2 ( 2021-01-12)
    Abstract: Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO 2 that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO 2 efflux, J CO2 , a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO 2 enrichment gradient (250 to 500 µL L −1 ) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of J CO2 responses and feedbacks from other resources, plant diversity [effective species richness, exp(H)], and community change (plant species turnover). We found linear increases in J CO2 on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modeling identified CO 2 as the dominant limitation on J CO2 on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear J CO2 response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic J CO2 response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2008284117
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 3
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    Increased stray gas abundance in a subset of drinking water wells near Marcellus shale gas extraction
    Proceedings of the National Academy of Sciences ; 2013
    In:  Proceedings of the National Academy of Sciences Vol. 110, No. 28 ( 2013-07-09), p. 11250-11255
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 110, No. 28 ( 2013-07-09), p. 11250-11255
    Abstract: Horizontal drilling and hydraulic fracturing are transforming energy production, but their potential environmental effects remain controversial. We analyzed 141 drinking water wells across the Appalachian Plateaus physiographic province of northeastern Pennsylvania, examining natural gas concentrations and isotopic signatures with proximity to shale gas wells. Methane was detected in 82% of drinking water samples, with average concentrations six times higher for homes 〈 1 km from natural gas wells ( P = 0.0006). Ethane was 23 times higher in homes 〈 1 km from gas wells ( P = 0.0013); propane was detected in 10 water wells, all within approximately 1 km distance ( P = 0.01). Of three factors previously proposed to influence gas concentrations in shallow groundwater (distances to gas wells, valley bottoms, and the Appalachian Structural Front, a proxy for tectonic deformation), distance to gas wells was highly significant for methane concentrations ( P = 0.007; multiple regression), whereas distances to valley bottoms and the Appalachian Structural Front were not significant ( P = 0.27 and P = 0.11, respectively). Distance to gas wells was also the most significant factor for Pearson and Spearman correlation analyses ( P 〈 0.01). For ethane concentrations, distance to gas wells was the only statistically significant factor ( P 〈 0.005). Isotopic signatures (δ 13 C-CH 4 , δ 13 C-C 2 H 6 , and δ 2 H-CH 4 ), hydrocarbon ratios (methane to ethane and propane), and the ratio of the noble gas 4 He to CH 4 in groundwater were characteristic of a thermally postmature Marcellus-like source in some cases. Overall, our data suggest that some homeowners living 〈 1 km from gas wells have drinking water contaminated with stray gases.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1221635110
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2013
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  • 4
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    Noble gases identify the mechanisms of fugitive gas contamination in drinking-water wells overlying the Marcellus and Barnett Shales
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 39 ( 2014-09-30), p. 14076-14081
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 39 ( 2014-09-30), p. 14076-14081
    Abstract: Horizontal drilling and hydraulic fracturing have enhanced energy production but raised concerns about drinking-water contamination and other environmental impacts. Identifying the sources and mechanisms of contamination can help improve the environmental and economic sustainability of shale-gas extraction. We analyzed 113 and 20 samples from drinking-water wells overlying the Marcellus and Barnett Shales, respectively, examining hydrocarbon abundance and isotopic compositions (e.g., C 2 H 6 /CH 4 , δ 13 C-CH 4 ) and providing, to our knowledge, the first comprehensive analyses of noble gases and their isotopes (e.g., 4 He, 20 Ne, 36 Ar) in groundwater near shale-gas wells. We addressed two questions. ( i ) Are elevated levels of hydrocarbon gases in drinking-water aquifers near gas wells natural or anthropogenic? ( ii ) If fugitive gas contamination exists, what mechanisms cause it? Against a backdrop of naturally occurring salt- and gas-rich groundwater, we identified eight discrete clusters of fugitive gas contamination, seven in Pennsylvania and one in Texas that showed increased contamination through time. Where fugitive gas contamination occurred, the relative proportions of thermogenic hydrocarbon gas (e.g., CH 4 , 4 He) were significantly higher ( P 〈 0.01) and the proportions of atmospheric gases (air-saturated water; e.g., N 2 , 36 Ar) were significantly lower ( P 〈 0.01) relative to background groundwater. Noble gas isotope and hydrocarbon data link four contamination clusters to gas leakage from intermediate-depth strata through failures of annulus cement, three to target production gases that seem to implicate faulty production casings, and one to an underground gas well failure. Noble gas data appear to rule out gas contamination by upward migration from depth through overlying geological strata triggered by horizontal drilling or hydraulic fracturing.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1322107111
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
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  • 5
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    Elevated levels of diesel range organic compounds in groundwater near Marcellus gas operations are derived from surface activities
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 43 ( 2015-10-27), p. 13184-13189
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 43 ( 2015-10-27), p. 13184-13189
    Abstract: Hundreds of organic chemicals are used during natural gas extraction via high-volume hydraulic fracturing (HVHF). However, it is unclear whether these chemicals, injected into deep shale horizons, reach shallow groundwater aquifers and affect local water quality, either from those deep HVHF injection sites or from the surface or shallow subsurface. Here, we report detectable levels of organic compounds in shallow groundwater samples from private residential wells overlying the Marcellus Shale in northeastern Pennsylvania. Analyses of purgeable and extractable organic compounds from 64 groundwater samples revealed trace levels of volatile organic compounds, well below the Environmental Protection Agency’s maximum contaminant levels, and low levels of both gasoline range (0–8 ppb) and diesel range organic compounds (DRO; 0–157 ppb). A compound-specific analysis revealed the presence of bis(2-ethylhexyl) phthalate, which is a disclosed HVHF additive, that was notably absent in a representative geogenic water sample and field blanks. Pairing these analyses with ( i ) inorganic chemical fingerprinting of deep saline groundwater, ( ii ) characteristic noble gas isotopes, and ( iii ) spatial relationships between active shale gas extraction wells and wells with disclosed environmental health and safety violations, we differentiate between a chemical signature associated with naturally occurring saline groundwater and one associated with alternative anthropogenic routes from the surface (e.g., accidental spills or leaks). The data support a transport mechanism of DRO to groundwater via accidental release of fracturing fluid chemicals derived from the surface rather than subsurface flow of these fluids from the underlying shale formation.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1511474112
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
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  • 6
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    Large stocks of peatland carbon and nitrogen are vulnerable to permafrost thaw
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 34 ( 2020-08-25), p. 20438-20446
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 34 ( 2020-08-25), p. 20438-20446
    Abstract: Northern peatlands have accumulated large stocks of organic carbon (C) and nitrogen (N), but their spatial distribution and vulnerability to climate warming remain uncertain. Here, we used machine-learning techniques with extensive peat core data ( n 〉 7,000) to create observation-based maps of northern peatland C and N stocks, and to assess their response to warming and permafrost thaw. We estimate that northern peatlands cover 3.7 ± 0.5 million km 2 and store 415 ± 150 Pg C and 10 ± 7 Pg N. Nearly half of the peatland area and peat C stocks are permafrost affected. Using modeled global warming stabilization scenarios (from 1.5 to 6 °C warming), we project that the current sink of atmospheric C (0.10 ± 0.02 Pg C⋅y −1 ) in northern peatlands will shift to a C source as 0.8 to 1.9 million km 2 of permafrost-affected peatlands thaw. The projected thaw would cause peatland greenhouse gas emissions equal to ∼1% of anthropogenic radiative forcing in this century. The main forcing is from methane emissions (0.7 to 3 Pg cumulative CH 4 -C) with smaller carbon dioxide forcing (1 to 2 Pg CO 2 -C) and minor nitrous oxide losses. We project that initial CO 2 -C losses reverse after ∼200 y, as warming strengthens peatland C-sinks. We project substantial, but highly uncertain, additional losses of peat into fluvial systems of 10 to 30 Pg C and 0.4 to 0.9 Pg N. The combined gaseous and fluvial peatland C loss estimated here adds 30 to 50% onto previous estimates of permafrost-thaw C losses, with southern permafrost regions being the most vulnerable.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1916387117
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 7
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    Peak grain forecasts for the US High Plains amid withering waters
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 42 ( 2020-10-20), p. 26145-26150
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 42 ( 2020-10-20), p. 26145-26150
    Abstract: Irrigated agriculture contributes 40% of total global food production. In the US High Plains, which produces more than 50 million tons per year of grain, as much as 90% of irrigation originates from groundwater resources, including the Ogallala aquifer. In parts of the High Plains, groundwater resources are being depleted so rapidly that they are considered nonrenewable, compromising food security. When groundwater becomes scarce, groundwater withdrawals peak, causing a subsequent peak in crop production. Previous descriptions of finite natural resource depletion have utilized the Hubbert curve. By coupling the dynamics of groundwater pumping, recharge, and crop production, Hubbert-like curves emerge, responding to the linked variations in groundwater pumping and grain production. On a state level, this approach predicted when groundwater withdrawal and grain production peaked and the lag between them. The lags increased with the adoption of efficient irrigation practices and higher recharge rates. Results indicate that, in Texas, withdrawals peaked in 1966, followed by a peak in grain production 9 y later. After better irrigation technologies were adopted, the lag increased to 15 y from 1997 to 2012. In Kansas, where these technologies were employed concurrently with the rise of irrigated grain production, this lag was predicted to be 24 y starting in 1994. In Nebraska, grain production is projected to continue rising through 2050 because of high recharge rates. While Texas and Nebraska had equal irrigated output in 1975, by 2050, it is projected that Nebraska will have almost 10 times the groundwater-based production of Texas.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2008383117
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
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  • 8
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    Curbing the U.S. carbon deficit
    Proceedings of the National Academy of Sciences ; 2004
    In:  Proceedings of the National Academy of Sciences Vol. 101, No. 45 ( 2004-11-09), p. 15827-15829
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 101, No. 45 ( 2004-11-09), p. 15827-15829
    Abstract: The U.S. emitted ≈1.58 petagrams (Pg) of fossil fuel carbon in 2001, approximately one-quarter of global CO 2 production. With climate change increasingly likely, strategies to reduce carbon emissions and stabilize climate are needed, including greater energy efficiency, renewable energy sources, geoengineering, decarbonization, and geological and biological sequestration. Two of the most commonly proposed biological strategies are restoring organic carbon in agricultural soils and using plantations to sequester carbon in soils and wood. Here, we compare scenarios of land-based sequestration to emissions reductions arising from increased fuel efficiency in transportation, targeting ways to reduce net U.S. emissions by 10% (≈0.16 Pg of carbon per year). Based on mean sequestration rates, converting all U.S. croplands to no-till agriculture or retiring them completely could sequester ≈0.059 Pg of carbon per year for several decades. Summary data across a range of plantations reveal an average rate of carbon storage an order of magnitude larger than in agricultural soils; in consequence, one-third of U.S. croplands or 44 million hectares would be needed for plantations to reach the target of ≈0.16 Pg of carbon per year. For fossil fuel reductions, cars and light trucks generated ≈0.31 Pg of carbon in U.S. emissions in 2001. To reduce net emissions by 0.16 Pg of carbon per year, a doubling of fuel efficiency for cars and light trucks is needed, a change feasible with current technology. Issues of permanence, leakage, and economic potentials are discussed briefly, as is the recognition that such scenarios are only a first step in addressing total U.S. emissions.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0403631101
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2004
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  • 9
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    Reply to Pierret and Lacombe: Global controls on maximum rooting depths remain important
    Proceedings of the National Academy of Sciences ; 2018
    In:  Proceedings of the National Academy of Sciences Vol. 115, No. 12 ( 2018-03-20)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 115, No. 12 ( 2018-03-20)
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1801899115
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2018
    detail.hit.zdb_id: 209104-5
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  • 10
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    Geochemical evidence for possible natural migration of Marcellus Formation brine to shallow aquifers in Pennsylvania
    Proceedings of the National Academy of Sciences ; 2012
    In:  Proceedings of the National Academy of Sciences Vol. 109, No. 30 ( 2012-07-24), p. 11961-11966
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 30 ( 2012-07-24), p. 11961-11966
    Abstract: The debate surrounding the safety of shale gas development in the Appalachian Basin has generated increased awareness of drinking water quality in rural communities. Concerns include the potential for migration of stray gas, metal-rich formation brines, and hydraulic fracturing and/or flowback fluids to drinking water aquifers. A critical question common to these environmental risks is the hydraulic connectivity between the shale gas formations and the overlying shallow drinking water aquifers. We present geochemical evidence from northeastern Pennsylvania showing that pathways, unrelated to recent drilling activities, exist in some locations between deep underlying formations and shallow drinking water aquifers. Integration of chemical data (Br, Cl, Na, Ba, Sr, and Li) and isotopic ratios ( 87 Sr/ 86 Sr, 2 H/H, 18 O/ 16 O, and 228 Ra/ 226 Ra) from this and previous studies in 426 shallow groundwater samples and 83 northern Appalachian brine samples suggest that mixing relationships between shallow ground water and a deep formation brine causes groundwater salinization in some locations. The strong geochemical fingerprint in the salinized (Cl  〉  20 mg/L) groundwater sampled from the Alluvium, Catskill, and Lock Haven aquifers suggests possible migration of Marcellus brine through naturally occurring pathways. The occurrences of saline water do not correlate with the location of shale-gas wells and are consistent with reported data before rapid shale-gas development in the region; however, the presence of these fluids suggests conductive pathways and specific geostructural and/or hydrodynamic regimes in northeastern Pennsylvania that are at increased risk for contamination of shallow drinking water resources, particularly by fugitive gases, because of natural hydraulic connections to deeper formations.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1121181109
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2012
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