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DATASET: Alpha version 2010 and 2014 estimates of numbers of people per grid square, with national totals adjusted to match UN population division estimates (http://esa.un.org/wpp/). REGION: Africa SPATIAL RESOLUTION: 0.00833333 decimal degrees (approx 100m at the equator) PROJECTION: Geographic, WGS84 UNITS: Estimated persons per grid square MAPPING APPROACH: Land cover based, as described in: Linard, C., Gilbert, M., Snow, R.W., Noor, A.M. and Tatem, A.J., 2012, Population distribution, settlement patterns and accessibility across Africa in 2010, PLoS ONE, 7(2): e31743. FORMAT: Geotiff (zipped using 7-zip (open access tool): www.7-zip.org) FILENAMES: Example - AGO10adjv4.tif = Angola (AGO) population count map for 2010 (10) adjusted to match UN national estimates (adj), version 4 (v4). Population maps are updated to new versions when improved census or other input data become available. DATE OF PRODUCTION: January 2013

* These data represent: Raw data presented in Sluijs et al., 2020 (Climate of the Past)- Peak areas of GDGTs and GMGTs peaks across the late Paleocene - early Eocene of Hole 4 of the Arctic Coring EXpecition (ACEX).- Abundances of isoGDGTs and and chrenarchaeol in the modern peat dataset.* whereThe data were generated on sediment samples taken from drill cores retreived from Lomonosov Ridge, Arctic Ocean, 2004 by the Integrated Ocean Drilling Program, stored in the Bremen Core Repository. For the present paper, we analyzed organic lipid extracts previously documented by Sluijs et al., (2006; 2008; 2009) using the current methodological standards.* when and howThe lipid extracts were analyzed in 2018 in the organic geochemical laboratory at Utrecht University using Ultra High Performance liquid chromatography and atmospheric pressure chemical ionization mass spectrometry using an Agilent 1260 Infinity series HPLC system coupled to an Agilent 6130 single-quadrupole mass spectrometer (methods follow Hopmans et al., 2016)* whyWe re-analyzed the extracts because analytical methodology has improved since the generation of the original datasets and because the dataset from the Arctic is crucial for Paleocene-Eocene climatology.

Supplement to: Howe, Jacob N W; Piotrowski, Alexander M; Noble, Taryn L; Mulitza, Stefan; Chiessi, Cristiano Mazur; Bayon, Germain (2016): North Atlantic Deep Water Production during the Last Glacial Maximum. Nature Communications, 7, 11765 Neodymium isotopes measured on chemically uncleaned planktic foraminifera from cores throughout the Atlantic Ocean. Samples are Holocene and Last Glacial Maximum in age.

On the basis of two sedimentary records from the central Sea of Okhotsk, we reconstruct the closely coupled glacial/interglacial changes in terrigenous flux, marine productivity, and sea ice coverage over the past 1.1 Myr. The correspondance of our sedimentary records to the China loess grain size record (China loess particle timescale, CHILOPARTS) suggests that environmental changes in both the Sea of Okhotsk area and in SE Asia were closely related via the Siberian atmospheric high-pressure cell. During full glacial times our records point to a strong Siberian High causing northerly wind directions, the extension of the sea ice cover, and a reduced Amur River discharge. Deglacial maxima of terrigenous flux were succeeded by or synchronous to high-productivity events. Marine productivity was strengthened during glacial terminations because of an effective nutrient utilization at times of enhanced water column stratification and high nutrient supply from fluvial runoff and sea ice thawing. During interglacials, SE monsoonal winds prevailed, analogous to today's summer situation of a pronounced Mongolian Heat Low and a strong Hawaiian High. Strong freshwater discharge induced by high precipitation rates in the Amur drainage area and a seasonally reduced and mobile sea ice cover favored marine productivity (although being considerably lower than during the terminations) and a lowered flux of ice-rafted detritus. Supplement to: Nürnberg, Dirk; Tiedemann, Ralf (2004): Environmental change in the Sea of Okhotsk during the last 1.1 million years. Paleoceanography, 19(4), PA4011

Objectives: Natural language processing (NLP) and machine learning approaches were used to build classifiers to identify genomic-related treatment changes in the free-text visit progress notes of cancer patients. Methods: We obtained 5,889 de-identified progress reports (2,439 words on average) for 755 cancer patients who have undergone a clinical Next Generation Sequencing (NGS) testing in Wake Forest Baptist Comprehensive Cancer Center for our data analyses. An NLP system was implemented to process the free-text data and extract NGS-related information. Three types of recurrent neural network (RNN) namely, gated recurrent unit (GRU), long-short term memory (LSTM), and bidirectional LSTM (LSTM_Bi) were applied to classify documents to the treatment-change and no-treatment-change groups. Further, we compared the performances of RNNs to five machine learning algorithms including Naive Bayes (NB), K-nearest Neighbor (KNN), Support Vector Machine for classification (SVC), Random Forest (RF), and Logistic Regression (LR). Results: Our results suggested that, overall, RNNs outperformed traditional machine learning algorithms, and LSTM_Bi showed the best performance among the RNNs in terms of accuracy, precision, recall, and F1 score. In addition, pre-trained word embedding can improve the accuracy of LSTM by 3.4% and reduce the training time by more than 60%. Discussion and Conclusion: NLP and RNN-based text mining solutions have demonstrated advantages in information retrieval and document classification tasks for unstructured clinical progress notes. NLP_Report_Process_cleanPython code to process raw clinical report.NonDL_models_cleanPython file used to perform classification with non-RNN models.LSTM_keras_03012018_cleanPython code to perform RNN models.visualizeModels_cleanPython code to create visualizations.

The boron isotope composition (d11B) of planktic foraminiferal calcite, which reflects seawater pH, is a well-established proxy for reconstructing palaeo-atmospheric CO2 and seawater carbonate chemistry. However, to translate d11B measurements determined in calcareous fossils into pH we need to know the boron isotope composition of the parent seawater (d11Bsw). While a number of d11Bsw reconstructions exist, the discrepancies between them reveals uncertainties and deficiencies that need to be addressed. Here we present a new d11Bsw record based on the d11B difference between planktic and benthic foraminifera and an estimate of the pH gradient between surface and deep water. We then calculate d11Bsw two different ways. One variant of our method assumes that the pH gradient between surface and deep has remained the same as today over the past 23 Ma; the other uses the d13C gradient between surface and deep to represent change in the pH gradient through time. The results of these two methods of calculating d11Bsw are broadly consistency with each other, however, based on extensive carbon cycle modelling using CYCLOPS and GENIE we favour the d13C gradient method. In our favoured d11Bsw reconstruction, d11Bsw is around 2 per mil lower than today at ~37.5 per mil during the early and middle Miocene and increases to the modern value (39.61 per mil) by ~5 Ma. A similar pattern of change is evident in the seawater composition of three other stable isotope systems, Mg, Li and Ca. Concurrent shifts in the seawater isotopic composition of all four of these elements during the late Miocene, suggest a common forcing mechanism. We hypothesise the most likely cause of these shifts is a change in the isotopic composition of the riverine input, potentially driven by an increase in secondary mineral formation since ~15 Ma. Supplement to: Greenop, Rosanna; Hain, Mathis P; Sosdian, Sindia M; Oliver, Kevin I C; Goodwin, Philip; Chalk, Thomas B; Lear, Caroline H; Wilson, Paul A; Foster, Gavin L (2017): A record of Neogene seawate d11B reconstructed from paired d11B analyses on benthic and planktic foraminifera. Climate of the Past, 13(2), 149-170

Eosinophil results by foragingData necessary to run analysis on the influence of foraging on eosinophil concentrations. Given small population sizes all data have been randomised to protect individuals identity.eosfarm.csvEosinophil results by settlementData necessary to run analysis on the influence of settlement on eosinophil concentrations. Given small population sizes all data have been randomised to protect individuals identity.eosset.csvFertility by foragingData necessary to run analysis on the influence of foraging on fertility. Given small population sizes all data have been randomised to protect individuals identity.fertfarm.csvFertility by settlementData required for analysis of fertility and mobility.fertset.csvLymphocytosis by foragingData necessary to run analysis on the influence of foraging on Lymphocytosis. Given small population sizes all data have been randomised to protect individuals identity.lymfarm.csvLymphocytosis by settlementData necessary to run analysis on the influence of settlement on Lymphocytosis. Given small population sizes all data have been randomised to protect individuals identity.lymset.csvMortality by foragingData necessary to run analysis on the influence of foraging on mortality. Given small population sizes all data have been randomised to protect individuals identity.mortfarm.csvMortality by settlementData necessary to run analysis on the influence of settlement on mortality. Given small population sizes all data have been randomised to protect individuals identity.mortset.csvNeutrophilia by foragingData necessary to run analysis on the influence of foraging on Neutrophilia. Given small population sizes all data have been randomised to protect individuals identity.neufarm.csvNeutrophilia by settlementData necessary to run analysis on the influence of settlement on Neutrophilia. Given small population sizes all data have been randomised to protect individuals identity.neuset.csvParasite loadData necessary to run analysis on the influence of settlement on parasite burdenparaload.csvReproductive success and foragingData necessary to run analysis on the influence of foraging on RS. Given small population sizes all data have been randomised to protect individuals identity.rsfarm.csvReproductive success and settlementData necessary to run analysis on the influence of settlement on RS. Given small population sizes all data have been randomised to protect individuals identity.rsset.csv The Neolithic demographic transition remains a paradox, because it is associated with both higher rates of population growth and increased morbidity and mortality rates. Here we reconcile the conflicting evidence by proposing that the spread of agriculture involved a life history quality–quantity trade-off whereby mothers traded offspring survival for increased fertility, achieving greater reproductive success despite deteriorating health. We test this hypothesis by investigating fertility, mortality, health, and overall reproductive success in Agta hunter-gatherers whose camps exhibit variable levels of sedentarization, mobility, and involvement in agricultural activities. We conducted blood composition tests in 345 Agta and found that viral and helminthic infections as well as child mortality rates were significantly increased with sedentarization. Nonetheless, both age-controlled fertility and overall reproductive success were positively affected by sedentarization and participation in cultivation. Thus, we provide the first empirical evidence, to our knowledge, of an adaptive mechanism in foragers that reconciles the decline in health and child survival with the observed demographic expansion during the Neolithic.