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1.
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2.
  • Arndt, D. S., et al. (author)
  • State of the Climate in 2016
  • 2017
  • In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280
  • Journal article (peer-reviewed)abstract
    • In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
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3.
  • Arndt, D. S., et al. (author)
  • STATE OF THE CLIMATE IN 2017
  • 2018
  • In: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 99:8, s. S1-S310
  • Research review (peer-reviewed)
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4.
  • Blunden, Jessica, et al. (author)
  • State of the Climate in 2012
  • 2013
  • In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 94:8, s. S1-S258
  • Journal article (peer-reviewed)abstract
    • For the first time in serveral years, the El Nino-Southern Oscillation did not dominate regional climate conditions around the globe. A weak La Ni a dissipated to ENSOneutral conditions by spring, and while El Nino appeared to be emerging during summer, this phase never fully developed as sea surface temperatures in the eastern conditions. Nevertheless, other large-scale climate patterns and extreme weather events impacted various regions during the year. A negative phase of the Arctic Oscillation from mid-January to early February contributed to frigid conditions in parts of northern Africa, eastern Europe, and western Asia. A lack of rain during the 2012 wet season led to the worst drought in at least the past three decades for northeastern Brazil. Central North America also experienced one of its most severe droughts on record. The Caribbean observed a very wet dry season and it was the Sahel's wettest rainy season in 50 years. Overall, the 2012 average temperature across global land and ocean surfaces ranked among the 10 warmest years on record. The global land surface temperature alone was also among the 10 warmest on record. In the upper atmosphere, the average stratospheric temperature was record or near-record cold, depending on the dataset. After a 30-year warming trend from 1970 to 1999 for global sea surface temperatures, the period 2000-12 had little further trend. This may be linked to the prevalence of La Ni a-like conditions during the 21st century. Heat content in the upper 700 m of the ocean remained near record high levels in 2012. Net increases from 2011 to 2012 were observed at 700-m to 2000-m depth and even in the abyssal ocean below. Following sharp decreases in to the effects of La Ni a, sea levels rebounded to reach records highs in 2012. The increased hydrological cycle seen in recent years continued, with more evaporation in drier locations and more precipitation in rainy areas. In a pattern that has held since 2004, salty areas of the ocean surfaces and subsurfaces were anomalously salty on average, while fresher areas were anomalously fresh. Global tropical cyclone activity during 2012 was near average, with a total of 84 storms compared with the 1981-2010 average of 89. Similar to 2010 and 2011, the North Atlantic was the only hurricane basin that experienced above-normal activity. In this basin, Sandy brought devastation to Cuba and parts of the eastern North American seaboard. All other basins experienced either near-or below-normal tropical cyclone activity. Only three tropical cyclones reached Category 5 intensity-all in Bopha became the only storm in the historical record to produce winds greater than 130 kt south of 7 N. It was also the costliest storm to affect the Philippines and killed more than 1000 residents. Minimum Arctic sea ice extent in September and Northern Hemisphere snow cover extent in June both reached new record lows. June snow cover extent is now declining at a faster rate (-17.6% per decade) than September sea ice extent (-13.0% per decade). Permafrost temperatures reached record high values in northernmost Alaska. A new melt extent record occurred on 11-12 July on the Greenland ice sheet; 97% of the ice sheet showed some form of melt, four times greater than the average melt for this time of year. The climate in Antarctica was relatively stable overall. The largest maximum sea ice extent since records begain in 1978 was observed in September 2012. In the stratosphere, warm air led to the second smallest ozone hole in the past two decades. Even so, the springtime ozone layer above Antarctica likely will not return to its early 1980s state until about 2060. Following a slight decline associated with the global 2 emissions from fossil fuel combustion and cement production reached a record 9.5 +/- 0.5 Pg C in 2011 and a new record of 9.7 +/- 0.5 Pg C is estimated for 2012. Atmospheric CO2 concentrations increased by 2.1 ppm in 2012, to 392.6 ppm. In spring 2012, 2 concentration exceeded 400 ppm at 7 of the 13 Arctic observation sites. Globally, other greenhouse gases including methane and nitrous oxide also continued to rise in concentration and the combined effect now represents a 32% increase in radiative forcing over a 1990 baseline. Concentrations of most ozone depleting substances continued to fall.
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6.
  • Klionsky, Daniel J., et al. (author)
  • Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
  • 2008
  • In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
  • Research review (peer-reviewed)abstract
    • Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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8.
  • Ades, M., et al. (author)
  • Global Climate : in State of the climate in 2019
  • 2020
  • In: Bulletin of The American Meteorological Society - (BAMS). - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 101:8, s. S17-S127
  • Journal article (peer-reviewed)
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9.
  • Ades, M., et al. (author)
  • GLOBAL CLIMATE
  • 2020
  • In: BULLETIN OF THE AMERICAN METEOROLOGICAL SOCIETY. - 0003-0007 .- 1520-0477. ; 101:8
  • Journal article (peer-reviewed)
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10.
  • Gavin, Michael C., et al. (author)
  • Process-based modelling shows how climate and demography shape language diversity
  • 2017
  • In: Global Ecology and Biogeography. - : WILEY. - 1466-822X .- 1466-8238. ; 26:5, s. 584-591
  • Journal article (peer-reviewed)abstract
    • AimTwo fundamental questions about human language demand answers: why are so many languages spoken today and why is their geographical distribution so uneven? Although hypotheses have been proposed for centuries, the processes that determine patterns of linguistic and cultural diversity remain poorly understood. Previous studies, which relied on correlative, curve-fitting approaches, have produced contradictory results. Here we present the first application of process-based simulation modelling, derived from macroecology, to examine the distribution of human groups and their languages. LocationThe Australian continent is used as a case study to demonstrate the power of simulation modelling for identifying processes shaping the diversity and distribution of human languages. MethodsProcess-based simulation models allow investigators to hold certain factors constant in order to isolate and assess the impact of modelled processes. We tested the extent to which a minimal set of processes determines the number and spatial distribution of languages on the Australian continent. Our model made three basic assumptions based on previously proposed, but untested, hypotheses: groups fill unoccupied spaces, rainfall limits population density and groups divide after reaching a maximum population. ResultsRemarkably, this simple model accurately predicted the total number of languages (average estimate 406, observed 407), and explained 56% of spatial variation in language richness on the Australian continent. Main conclusionsOur results present strong evidence that current climatic conditions and limits to group size are important processes shaping language diversity patterns in Australia. Our study also demonstrates how simulation models from macroecology can be used to understand the processes that have shaped human cultural diversity across the globe.
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11.
  • Gavin, Michael C., et al. (author)
  • Toward a Mechanistic Understanding of Linguistic Diversity
  • 2013
  • In: BioScience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 63:7, s. 524-535
  • Journal article (peer-reviewed)abstract
    • Our species displays remarkable linguistic diversity. Although the uneven distribution of this diversity demands explanation, the drivers of these patterns have not been conclusively determined. We address this issue in two steps: First, we review previous empirical studies whose authors have suggested environmental, geographical, and sociocultural drivers of linguistic diversification. However, contradictory results and methodological variation make it difficult to draw general conclusions. Second, we outline a program for future research. We suggest that future analyses should account for interactions among causal factors, the lack of spatial and phylogenetic independence of the data, and transitory patterns. Recent analytical advances in biogeography and evolutionary biology, such as simulation modeling of diversity patterns, hold promise for testing four key mechanisms of language diversification proposed here: neutral change, population movement, contact, and selection. Future modeling approaches should also evaluate how the outcomes of these processes are influenced by demography, environmental heterogeneity, and time.
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12.
  • Schweinsberg, Martin, et al. (author)
  • Same data, different conclusions : Radical dispersion in empirical results when independent analysts operationalize and test the same hypothesis
  • 2021
  • In: Organizational Behavior and Human Decision Processes. - : Elsevier BV. - 0749-5978 .- 1095-9920. ; 165, s. 228-249
  • Journal article (peer-reviewed)abstract
    • In this crowdsourced initiative, independent analysts used the same dataset to test two hypotheses regarding the effects of scientists' gender and professional status on verbosity during group meetings. Not only the analytic approach but also the operationalizations of key variables were left unconstrained and up to individual analysts. For instance, analysts could choose to operationalize status as job title, institutional ranking, citation counts, or some combination. To maximize transparency regarding the process by which analytic choices are made, the analysts used a platform we developed called DataExplained to justify both preferred and rejected analytic paths in real time. Analyses lacking sufficient detail, reproducible code, or with statistical errors were excluded, resulting in 29 analyses in the final sample. Researchers reported radically different analyses and dispersed empirical outcomes, in a number of cases obtaining significant effects in opposite directions for the same research question. A Boba multiverse analysis demonstrates that decisions about how to operationalize variables explain variability in outcomes above and beyond statistical choices (e.g., covariates). Subjective researcher decisions play a critical role in driving the reported empirical results, underscoring the need for open data, systematic robustness checks, and transparency regarding both analytic paths taken and not taken. Implications for orga-nizations and leaders, whose decision making relies in part on scientific findings, consulting reports, and internal analyses by data scientists, are discussed.
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13.
  • Aaron-Morrison, Arlene P., et al. (author)
  • State of the climate in 2014
  • 2015
  • In: Bulletin of the American Meteorological Society. - : American Meteorological Society. - 0003-0007 .- 1520-0477. ; 96
  • Journal article (peer-reviewed)abstract
    • Most of the dozens of essential climate variables monitored each year in this report continued to follow their long-term trends in 2014, with several setting new records. Carbon dioxide, methane, and nitrous oxide-the major greenhouse gases released into Earth's atmosphere-once again all reached record high average atmospheric concentrations for the year. Carbon dioxide increased by 1.9 ppm to reach a globally averaged value of 397.2 ppm for 2014. Altogether, 5 major and 15 minor greenhouse gases contributed 2.94 W m-2 of direct radiative forcing, which is 36% greater than their contributions just a quarter century ago. Accompanying the record-high greenhouse gas concentrations was nominally the highest annual global surface temperature in at least 135 years of modern record keeping, according to four independent observational analyses. The warmth was distributed widely around the globe's land areas, Europe observed its warmest year on record by a large margin, with close to two dozen countries breaking their previous national temperature records; many countries in Asia had annual temperatures among their 10 warmest on record; Africa reported above-average temperatures across most of the continent throughout 2014; Australia saw its third warmest year on record, following record heat there in 2013; Mexico had its warmest year on record; and Argentina and Uruguay each had their second warmest year on record. Eastern North America was the only major region to observe a below-average annual temperature. But it was the oceans that drove the record global surface temperature in 2014. Although 2014 was largely ENSO-neutral, the globally averaged sea surface temperature (SST) was the highest on record. The warmth was particularly notable in the North Pacific Ocean where SST anomalies signaled a transition from a negative to positive phase of the Pacific decadal oscillation. In the winter of 2013/14, unusually warm water in the northeast Pacific was associated with elevated ocean heat content anomalies and elevated sea level in the region. Globally, upper ocean heat content was record high for the year, reflecting the continued increase of thermal energy in the oceans, which absorb over 90% of Earth's excess heat from greenhouse gas forcing. Owing to both ocean warming and land ice melt contributions, global mean sea level in 2014 was also record high and 67 mm greater than the 1993 annual mean, when satellite altimetry measurements began. Sea surface salinity trends over the past decade indicate that salty regions grew saltier while fresh regions became fresher, suggestive of an increased hydrological cycle over the ocean expected with global warming. As in previous years, these patterns are reflected in 2014 subsurface salinity anomalies as well. With a now decade-long trans-basin instrument array along 26°N, the Atlantic meridional overturning circulation shows a decrease in transport of-4.2 ± 2.5 Sv decade-1. Precipitation was quite variable across the globe. On balance, precipitation over the world's oceans was above average, while below average across land surfaces. Drought continued in southeastern Brazil and the western United States. Heavy rain during April-June led to devastating floods in Canada's Eastern Prairies. Above-normal summer monsoon rainfall was observed over the southern coast of West Africa, while drier conditions prevailed over the eastern Sahel. Generally, summer monsoon rainfall over eastern Africa was above normal, except in parts of western South Sudan and Ethiopia. The south Asian summer monsoon in India was below normal, with June record dry. Across the major tropical cyclone basins, 91 named storms were observed during 2014, above the 1981-2010 global average of 82. The Eastern/Central Pacific and South Indian Ocean basins experienced significantly above-normal activity in 2014; all other basins were either at or below normal. The 22 named storms in the Eastern/Central Pacific was the basin's most since 1992. Similar to 2013, the North Atlantic season was quieter than most years of the last two decades with respect to the number of storms, despite the absence of El Niño conditions during both years. In higher latitudes and at higher elevations, increased warming continued to be visible in the decline of glacier mass balance, increasing permafrost temperatures, and a deeper thawing layer in seasonally frozen soil. In the Arctic, the 2014 temperature over land areas was the fourth highest in the 115-year period of record and snow melt occurred 20-30 days earlier than the 1998-2010 average. The Greenland Ice Sheet experienced extensive melting in summer 2014. The extent of melting was above the 1981-2010 average for 90% of the melt season, contributing to the second lowest average summer albedo over Greenland since observations began in 2000 and a record-low albedo across the ice sheet for August. On the North Slope of Alaska, new record high temperatures at 20-m depth were measured at four of five permafrost observatories. In September, Arctic minimum sea ice extent was the sixth lowest since satellite records began in 1979. The eight lowest sea ice extents during this period have occurred in the last eight years. Conversely, in the Antarctic, sea ice extent countered its declining trend and set several new records in 2014, including record high monthly mean sea ice extent each month from April to November. On 20 September, a record large daily Antarctic sea ice extent of 20.14 × 106 km2 occurred. The 2014 Antarctic stratospheric ozone hole was 20.9 million km2 when averaged from 7 September to 13 October, the sixth smallest on record and continuing a decrease, albeit statistically insignificant, in area since 1998.
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14.
  • Akbari, Parsa, et al. (author)
  • Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity
  • 2021
  • In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 373:6550
  • Journal article (peer-reviewed)abstract
    • Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ∼4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.
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15.
  • Blunden, Jessica, et al. (author)
  • State of the climate in 2013
  • 2014
  • In: Bulletin of the American Meteorological Society. - 0003-0007. ; 95
  • Journal article (peer-reviewed)abstract
    • © 2014, American Meteorological Society. All rights reserved. In 2013, the vast majority of the monitored climate variables reported here maintained trends established in recent decades. ENSO was in a neutral state during the entire year, remaining mostly on the cool side of neutral with modest impacts on regional weather patterns around the world. This follows several years dominated by the effects of either La Niña or El Niño events. According to several independent analyses, 2013 was again among the 10 warmest years on record at the global scale, both at the Earth’s surface and through the troposphere. Some regions in the Southern Hemisphere had record or near-record high temperatures for the year. Australia observed its hottest year on record, while Argentina and New Zealand reported their second and third hottest years, respectively. In Antarctica, Amundsen-Scott South Pole Station reported its highest annual temperature since records began in 1957. At the opposite pole, the Arctic observed its seventh warmest year since records began in the early 20th century. At 20-m depth, record high temperatures were measured at some permafrost stations on the North Slope of Alaska and in the Brooks Range. In the Northern Hemisphere extratropics, anomalous meridional atmospheric circulation occurred throughout much of the year, leading to marked regional extremes of both temperature and precipitation. Cold temperature anomalies during winter across Eurasia were followed by warm spring temperature anomalies, which were linked to a new record low Eurasian snow cover extent in May. Minimum sea ice extent in the Arctic was the sixth lowest since satellite observations began in 1979. Including 2013, all seven lowest extents on record have occurred in the past seven years. Antarctica, on the other hand, had above-average sea ice extent throughout 2013, with 116 days of new daily high extent records, including a new daily maximum sea ice area of 19.57 million km2 reached on 1 October. ENSO-neutral conditions in the eastern central Pacific Ocean and a negative Pacific decadal oscillation pattern in the North Pacific had the largest impacts on the global sea surface temperature in 2013. The North Pacific reached a historic high temperature in 2013 and on balance the globally-averaged sea surface temperature was among the 10 highest on record. Overall, the salt content in nearsurface ocean waters increased while in intermediate waters it decreased. Global mean sea level continued to rise during 2013, on pace with a trend of 3.2 mm yr-1 over the past two decades. A portion of this trend (0.5 mm yr-1) has been attributed to natural variability associated with the Pacific decadal oscillation as well as to ongoing contributions from the melting of glaciers and ice sheets and ocean warming. Global tropical cyclone frequency during 2013 was slightly above average with a total of 94 storms, although the North Atlantic Basin had its quietest hurricane season since 1994. In the Western North Pacific Basin, Super Typhoon Haiyan, the deadliest tropical cyclone of 2013, had 1-minute sustained winds estimated to be 170 kt (87.5 m s-1) on 7 November, the highest wind speed ever assigned to a tropical cyclone. High storm surge was also associated with Haiyan as it made landfall over the central Philippines, an area where sea level is currently at historic highs, increasing by 200 mm since 1970. In the atmosphere, carbon dioxide, methane, and nitrous oxide all continued to increase in 2013. As in previous years, each of these major greenhouse gases once again reached historic high concentrations. In the Arctic, carbon dioxide and methane increased at the same rate as the global increase. These increases are likely due to export from lower latitudes rather than a consequence of increases in Arctic sources, such as thawing permafrost. At Mauna Loa, Hawaii, for the first time since measurements began in 1958, the daily average mixing ratio of carbon dioxide exceeded 400 ppm on 9 May. The state of these variables, along with dozens of others, and the 2013 climate conditions of regions around the world are discussed in further detail in this 24th edition of the State of the Climate series.
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16.
  • Campbell, Brittany B., et al. (author)
  • Comprehensive Analysis of Hypermutation in Human Cancer
  • 2017
  • In: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 171:5
  • Journal article (peer-reviewed)abstract
    • © 2017 Elsevier Inc. We present an extensive assessment of mutation burden through sequencing analysis of > 81,000 tumors from pediatric and adult patients, including tumors with hypermutation caused by chemotherapy, carcinogens, or germline alterations. Hypermutation was detected in tumor types not previously associated with high mutation burden. Replication repair deficiency was a major contributing factor. We uncovered new driver mutations in the replication-repair-associated DNA polymerases and a distinct impact of microsatellite instability and replication repair deficiency on the scale of mutation load. Unbiased clustering, based on mutational context, revealed clinically relevant subgroups regardless of the tumors' tissue of origin, highlighting similarities in evolutionary dynamics leading to hypermutation. Mutagens, such as UV light, were implicated in unexpected cancers, including sarcomas and lung tumors. The order of mutational signatures identified previous treatment and germline replication repair deficiency, which improved management of patients and families. These data will inform tumor classification, genetic testing, and clinical trial design. A large-scale analysis of hypermutation in human cancers provides insights into tumor evolution dynamics and identifies clinically actionable mutation signatures.
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17.
  • Liu, Shanlin, et al. (author)
  • Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
  • 2021
  • In: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
  • Journal article (peer-reviewed)abstract
    • Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (similar to 16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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19.
  • Niemi, MEK, et al. (author)
  • 2021
  • swepub:Mat__t
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20.
  • Kanai, M, et al. (author)
  • 2023
  • swepub:Mat__t
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21.
  • Agrawal, Ganesh Kumar, et al. (author)
  • Boosting the Globalization of Plant Proteomics through INPPO : Current Developments and Future Prospects
  • 2012
  • In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 12:3, s. 359-368
  • Journal article (peer-reviewed)abstract
    • The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO's official launch in 2011 via its website (www.inppo.com) and publication of the 'Viewpoint paper' in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) to achieve INPPO objectives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO's primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a section dedicated to plant proteomics has been introduced starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January and July) newsletter entitled 'INPPO Express: News & Views' with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, and Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO community, and also due to the wide encouragement and support from the communities (scientific and non-scientific).
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22.
  • Agrawal, Ganesh Kumar, et al. (author)
  • INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics : Change of Guard, INPPO Update, and Upcoming Activities
  • 2013
  • In: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 13:21, s. 3093-3100
  • Journal article (other academic/artistic)abstract
    • The International Plant Proteomics Organization (INPPO) is a non-profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.
  •  
23.
  • Allassonniere-Tang, Marc, et al. (author)
  • The evolutionary trends of grammatical gender in Indo-Aryan languages
  • 2021
  • In: Language Dynamics and Change. - : Brill Academic Publishers. - 2210-5824 .- 2210-5832. ; 11:2, s. 211-240
  • Journal article (peer-reviewed)abstract
    • This paper infers the processes of development and change of grammatical gender in Indo-Aryan languages using phylogenetic comparative methods. 48 Indo-Aryan languages are coded based on 44 presence-absence features relating to gender marking on the verbs, adjectives, personal pronouns, demonstrative pronouns, and possessive pronouns. A Bayesian Reverse Jump Hyper Prior analysis, which infers the evolutionary dynamics of changes between feature values, gives results that are consistent with historical linguistic and typological studies on gender systems in Indo-Aryan languages and predicts the evolutionary trends of the features included in the dataset.
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24.
  • Beger, Richard D., et al. (author)
  • Metabolomics enables precision medicine : "A White Paper, Community Perspective"
  • 2016
  • In: Metabolomics. - : Springer. - 1573-3882 .- 1573-3890. ; 12:10
  • Journal article (peer-reviewed)abstract
    • INTRODUCTION BACKGROUND TO METABOLOMICS: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates.OBJECTIVES OF WHITE PAPER—EXPECTED TREATMENT OUTCOMES AND METABOLOMICS ENABLING TOOL FOR PRECISION MEDICINE: We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject's response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient's metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine.CONCLUSIONS KEY SCIENTIFIC CONCEPTS AND RECOMMENDATIONS FOR PRECISION MEDICINE: Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
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25.
  • Birchall, Joshua, et al. (author)
  • A combined comparative and phylogenetic analysis of the Chapacuran language family
  • 2016
  • In: International Journal of American Linguistics. - 0020-7071 .- 1545-7001. ; 82:3, s. 255-284
  • Journal article (peer-reviewed)abstract
    • The Chapacuran language family, with three extant members and nine historically attested lects, has yet to be classified following modern standards in historical linguistics. This paper presents an internal classification of these languages by combining both the traditional comparative method (CM) and Bayesian phylogenetic inference (BPI). We identify multiple systematic sound correspondences and 285 cognate sets of basic vocabulary using the available documentation. These allow us to reconstruct a large portion of the Proto-Chapacuran phonemic inventory and identify tentative major subgroupings. The cognate sets form the input for the BPI analysis, which uses a stochastic Continuous-Time Markov Chain to model the change of these cognate sets over time. We test various models of lexical substitution and evolutionary clocks, and use ethnohistorical information and data collection dates to calibrate the resulting trees. The CM and BPI analyses produce largely congruent results, suggesting a division of the family into three different clades.
  •  
26.
  • Bouckaert, Remco, et al. (author)
  • Mapping the Origins and Expansion of the Indo-European Language Family
  • 2012
  • In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 337:6097, s. 957-960
  • Journal article (peer-reviewed)abstract
    • There are two competing hypotheses for the origin of the Indo-European language family. The conventional view places the homeland in the Pontic steppes about 6000 years ago. An alternative hypothesis claims that the languages spread from Anatolia with the expansion of farming 8000 to 9500 years ago. We used Bayesian phylogeographic approaches, together with basic vocabulary data from 103 ancient and contemporary Indo-European languages, to explicitly model the expansion of the family and test these hypotheses. We found decisive support for an Anatolian origin over a steppe origin. Both the inferred timing and root location of the Indo-European language trees fit with an agricultural expansion from Anatolia beginning 8000 to 9500 years ago. These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory.
  •  
27.
  • Buchanan, Andrew, et al. (author)
  • Fire safety in timber buildings
  • 2022
  • In: Fire Safe Use of Wood in Buildings. - Boca Raton : CRC Press. - 9781032040394 - 9781032040417 - 9781003190318 ; , s. 33-62
  • Book chapter (peer-reviewed)abstract
    • This chapter provides an overall description of the strategy for delivering fire safety in timber buildings. As in the design of all buildings, the goals are to provide life safety for occupants, safe access for firefighters and protection of affected property. It is essential to control the severity and duration of any accidental fire and prevent it from spreading elsewhere in the building. An important design objective for timber buildings is to control the burning or charring of exposed timber or protected timber, because this can add to the fuel load, and it will reduce the load capacity of structural timber members due to loss of cross-section. Many of the topics introduced here are expanded on in the following chapters.
  •  
28.
  • Burenhult, Niclas, et al. (author)
  • Language history and culture groups among Austroasiatic-speaking foragers of the Malay Peninsula
  • 2011
  • In: Dynamics of human diversity: the case of Mainland Southeast Asia. ; , s. 257-275
  • Book chapter (peer-reviewed)abstract
    • The Malay Peninsula is a crossroads for people, languages and cultural influences, apparent in today's vibrant mix of Malay, Chinese, Indian, Thai and European. Yet this modern state of affairs all but conceals signals of much older situations of diversity. Thus, some 140,000 people grouped together under the label Orang Asli (Malay for 'aboriginal people') represent a range of cultural and biological adaptations and linguistic diversifications with roots far back in prehistory. These 20-plus ethnolinguistic groups represent a unique and vanishing window on the history of human diversity in the region, and they offer intriguing examples relevant to more general issues of the dynamics of human societies. By synthesising the current ethnographic, linguistic and genetic body of knowledge about these groups with our own quantitative analyses of new lexical data from 27 language varieties, we explore the local historical relationships and interaction between languages and cultures. Specifically, we look at the relationship between a particular subsistence mode, namely nomadic foraging, and the Aslian branch of the Austroasiatic language stock. While foraging has been considered in many previous accounts to have a historically close connection to one particular sub branch of Aslian (Northern Aslian), we highlight several mismatches in this correlation and take a step toward disentangling a complex picture of linguistic history and contact.
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29.
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30.
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31.
  • Dagenais, Christian, et al. (author)
  • Fire Safe Use of Wood in Buildings : Global Design Guide
  • 2023
  • In: World Conference on Timber Engineering. - : World Conference on Timber Engineering (WCTE). - 9781713873297 ; , s. 4627-4635
  • Conference paper (peer-reviewed)abstract
    • Building codes around the globe dictate the design and construction of buildings. For most buildings, designers will follow prescriptive code provisions to demonstrate code compliance. However, some buidling codes allow the use of performance-based design to demonstrate code compliance. Performance-based design is usually more complex but allows for greater flexibility in the use of materials and systems. Regardless of the code compliance methods, the combustibility of timber structures and wood products needs to be well understood and properly accounted for in building designs. This paper describes the develpment of a new international guidance document on fire safety in timber building within the Fire Safe Use of Wood (FSUW) network, written by 13 lead authors assisted by more than 20 experts in over a dozen different countries.
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32.
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33.
  • de Heer, Mervi, et al. (author)
  • Loanwords in Basic Vocabulary as an Indicator of Borrowing Profiles
  • 2024
  • In: Journal of Language Contact. - : Brill Academic Publishers. - 1877-4091 .- 1955-2629. ; 16:1, s. 54-103
  • Journal article (peer-reviewed)abstract
    • Loanwords carry information on linguistic interactions, and can also reveal (pre-)historicalpopulation contacts. The contact history of a particular language family is an essential component of historical linguistics, but it is also illuminating for integrative studies of the human past. However, data availability and the time-consuming nature of etymology mean that comprehensive research on loanword layers exists for relatively few languages, forcing us to rely on limited material for others. This paper compares the loanword layers in the basic and total vocabulary of six well-studied Uralic languages, assessing how accurately the borrowing profile in basic vocabulary reflects the full profile of a language. We define “borrowing profile” as the known contact history of a language reflected by its loanword layers. We demonstrate that the loanword layers in basic vocabulary provide an adequate cross-section of the full borrowing profile, although basic vocabulary manifests prehistoric contacts more strongly than more recent contacts.
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34.
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35.
  • Dunn, Gabriel, et al. (author)
  • Selective Insulation of Carbon nanotubes
  • 2017
  • In: Physica status solidi. B, Basic research. - : Wiley-VCH Verlagsgesellschaft. - 0370-1972 .- 1521-3951. ; 254:11
  • Journal article (peer-reviewed)abstract
    • We demonstrate a method for the selective encapsulation of carbonnanotubes in thin parylene films using iron as a sacrificial lift-off layer. Theiron serves as an inhibitor of parylene deposition and prevents the parylenemolecules from linking, thus facilitating selective area coating after lift-off.
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36.
  •  
37.
  • Dunn, Michael, et al. (author)
  • Aslian linguistic prehistory: a case study in computational phylogenetics
  • 2011
  • In: Diachronica. - : John Benjamins Publishing Company. - 0176-4225 .- 1569-9714. ; 28:3, s. 291-323
  • Journal article (peer-reviewed)abstract
    • This paper analyzes newly collected lexical data from 26 languages of the Aslian subgroup of the Austroasiatic language family using computational phylogenetic methods. We show the most likely topology of the Aslian family tree, discuss rooting and external relationships to other Austroasiatic languages, and investigate differences in the rates of diversification of different branches. Evidence is given supporting the classification of Jah Hut as a fourth top level subgroup of the family. The phylogenetic positions of known geographic and linguistic outlier languages are clarified, and the relationships of the little studied Aslian languages of Southern Thailand to the rest of the family are explored.
  •  
38.
  • Dunn, Michael, et al. (author)
  • Assessing the lexical evidence for a Central Solomons Papuan family using the Oswalt Monte Carlo Test
  • 2012
  • In: Diachronica. - : John Benjamins Publishing Company. - 0176-4225 .- 1569-9714. ; 29:1, s. 1-27
  • Journal article (peer-reviewed)abstract
    • In the absence of comparative method reconstruction, high rate of lexical cognate candidates is often used as evidence for relationships between languages. This paper uses the Oswalt Monte Carlo Shift test (a variant of Oswalt 1970) to explore the statistical basis of the claim that the four Papuan languages of the Solomon Islands have greater than chance levels of lexical similarity. The results of this test initially appear to show that the lexical similarities between the Central Solomons Papuan languages are statistically significant, but the effect disappears when known Oceanic loanwords are removed. The Oswalt Monte Carlo test is a useful technique to test a claim of greater than chance similarity between any two word lists — with the proviso that undetected loanwords strongly increase the chance of spurious identification.
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39.
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40.
  • Dunn, Michael, et al. (author)
  • Dative sickness : Aphylogenetic analysis of argument structure evolution in Germanic
  • 2017
  • In: Language. - : Project Muse. - 0097-8507 .- 1535-0665. ; 93:1, s. E1-E22
  • Journal article (peer-reviewed)abstract
    • A major argument against the feasibility of reconstructing syntax for proto-stages is the widely discussed lack of directionality of syntactic change. In a recent typology of changes in argument structure constructions based on Germanic (Barodal 2015), several different, yet opposing, changes are reported. These include, among others, processes sometimes called dative sickness, nominative sickness, and accusative sickness. In order to tease apart the roles of the different processes, we have carried out a phylogenetic trait analysis on a predefined data set of twelve predicates found across the Germanic phyla using the MULTISTATE method. This is, as far as we are aware, the first application of the MULTISTATE method (Pagel et al. 2004) in historical syntax. The results clearly favor one of the models, the dative sickness model, over any other model, as this model is the only one that can accurately account for both the observed diversity of case frames and the independently proposed philological reconstructions. Methods of evolutionary trait analysis can be used to model evolutionary paths of argument structure constructions, and they provide the perfect testing ground for hypotheses arrived at through philological reconstruction, based on classical historical-comparative methods.
  •  
41.
  • Dunn, Michael, et al. (author)
  • Evolution and Spread of Politeness Systems in Indo-European
  • 2023
  • In: Transactions of the Philological Society. - : John Wiley & Sons. - 0079-1636 .- 1467-968X. ; 121:1, s. 152-167
  • Journal article (peer-reviewed)abstract
    • In this paper, we investigate the phenomenon of pronominal politeness in the Indo-European languages and demonstrate that the processes of change of pronominal systems related to politeness follow two evolutionary regimes, one inside the 'Standard Average European' (SAE) linguistic area and another outside of it. Historical processes of language change differ at different levels of linguistic structure. In general, we presume that lower level, unconscious aspects of language change slowly over phylogenetic time, giving rise to patterns of relationship that can often be described as a family tree. Aspects of language that are consciously manipulated by speakers are expected to vary at a faster rate and to diffuse within areas of contact. Politeness is a social phenomenon, so we expect these systems to be highly susceptible to areal norms of interaction. We show that the similarities of SAE politeness systems can be accounted for with a model of convergence due to parallel evolution in a shared (social-demographic) environment, rather than by genealogical relatedness or borrowing. By quantifying and testing factors determining rates of structural change, we offer a novel and realistic approach that can explain similarities between distantly related languages sharing the same environment.
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42.
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43.
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44.
  • Dunn, Michael (author)
  • From effluvia to chemicals : techniques of self and somatic ethics in tropical health travel narratives
  • 2021
  • In: Studia Neophilologica. - : Taylor & Francis. - 0039-3274 .- 1651-2308. ; 93:2, s. 155-172
  • Journal article (peer-reviewed)abstract
    • Recent environmental humanities scholarship has argued that environmental illness memoirs perform important cultural work by recasting health as an environmental issue. In this article, I show how EI autobiography hearkens back to a longer tradition of health travel with deep colonial resonances. I explore such connections by means of a comparative analysis of two health travel narratives: The first, A winter in the West Indies and Florida, is an anonymous tract by a self-described 'northern invalid' dealing with his travels to the Caribbean as a remedy for his chronic pulmonary problems during the late 1830s. The second, drawn from a collection by disability activist Aurora Levins Morales, details the author's healing journey to Cuba during the summer of 2009. I argue that, while A Winter points forward to modern sociobiology, Levins Morales's narrative should be read as issuing from a biosocial community of EI sufferers. Finally, attending to the continuities and differences between EI autobiographies may deepen current debates on trans-corporeality, which tend to assume a direct relation between non-dualistic epistemologies and somatic ethics. In this sense, the article can be read as a commentary on overly rights-based approaches to illness and Q1 disability in the present biochemical age.
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45.
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46.
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47.
  • Dunn, Matt J, et al. (author)
  • Minimal reporting guideline for research involving eye tracking (2023 edition)
  • In: Behavior Research Methods. - 1554-3528.
  • Journal article (peer-reviewed)abstract
    • A guideline is proposed that comprises the minimum items to be reported in research studies involving an eye tracker and human or non-human primate participant(s). This guideline was developed over a 3-year period using a consensus-based process via an open invitation to the international eye tracking community. This guideline will be reviewed at maximum intervals of 4 years.
  •  
48.
  • Dunn, Michael (author)
  • Language phylogenies
  • 2015
  • In: The Routledge Handbook of Historical Linguistics. - : Routledge. ; , s. 190-211
  • Book chapter (peer-reviewed)
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49.
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50.
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