A framework for benchmarking of homogenisation algorithm performance on the global scale

The International Surface Temperature Initiative (ISTI) is striving towards substantively improving our ability to robustly understand historical land surface air temperature change at all scales. A key recently completed first step has been collating all available records into a comprehensive open access, traceable and version-controlled databank. The crucial next step is to maximise the value of the collated data through a robust international framework of benchmarking and assessment for product intercomparison and uncertainty estimation. We focus on uncertainties arising from the presence of inhomogeneities in monthly mean land surface temperature data and the varied methodological choices made by various groups in building homogeneous temperature products. The central facet of the benchmarking process is the creation of global-scale synthetic analogues to the real-world database where both the "true" series and inhomogeneities are known (a luxury the real-world data do not afford us). Hence, algorithmic strengths and weaknesses can be meaningfully quantified and conditional inferences made about the real-world climate system. Here we discuss the necessary framework for developing an international homogenisation benchmarking system on the global scale for monthly mean temperatures. The value of this framework is critically dependent upon the number of groups taking part and so we strongly advocate involvement in the benchmarking exercise from as many data analyst groups as possible to make the best use of this substantial effort.

Quantifying the improvement in sepsis diagnosis, documentation, and coding: the marginal causal effect of year of hospitalization on sepsis diagnosis.

PURPOSE To quantify the coinciding improvement in the clinical diagnosis of sepsis, its documentation in the electronic health records, and subsequent medical coding of sepsis for billing purposes in recent years. METHODS We examined 98,267 hospitalizations in 66,208 patients who met systemic inflammatory response syndrome criteria at a tertiary care center from 2008 to 2012. We used g-computation to estimate the causal effect of the year of hospitalization on receiving an International Classification of Diseases, Ninth Revision, Clinical Modification discharge diagnosis code for sepsis by estimating changes in the probability of getting diagnosed and coded for sepsis during the study period. RESULTS When adjusted for demographics, Charlson-Deyo comorbidity index, blood culture frequency per hospitalization, and intensive care unit admission, the causal risk difference for receiving a discharge code for sepsis per 100 hospitalizations with systemic inflammatory response syndrome, had the hospitalization occurred in 2012, was estimated to be 3.9% (95% confidence interval [CI], 3.8%-4.0%), 3.4% (95% CI, 3.3%-3.5%), 2.2% (95% CI, 2.1%-2.3%), and 0.9% (95% CI, 0.8%-1.1%) from 2008 to 2011, respectively. CONCLUSIONS Patients with similar characteristics and risk factors had a higher of probability of getting diagnosed, documented, and coded for sepsis in 2012 than in previous years, which contributed to an apparent increase in sepsis incidence.

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.

Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Effect of the REG1 anticoagulation system versus bivalirudin on outcomes after percutaneous coronary intervention (REGULATE-PCI): a randomised clinical trial.

BACKGROUND REG1 is a novel anticoagulation system consisting of pegnivacogin, an RNA aptamer inhibitor of coagulation factor IXa, and anivamersen, a complementary sequence reversal oligonucleotide. We tested the hypothesis that near complete inhibition of factor IXa with pegnivacogin during percutaneous coronary intervention, followed by partial reversal with anivamersen, would reduce ischaemic events compared with bivalirudin, without increasing bleeding. METHODS We did a randomised, open-label, active-controlled, multicentre, superiority trial to compare REG1 with bivalirudin at 225 hospitals in North America and Europe. We planned to randomly allocate 13,200 patients undergoing percutaneous coronary intervention in a 1:1 ratio to either REG1 (pegnivacogin 1 mg/kg bolus [>99% factor IXa inhibition] followed by 80% reversal with anivamersen after percutaneous coronary intervention) or bivalirudin. Exclusion criteria included ST segment elevation myocardial infarction within 48 h. The primary efficacy endpoint was the composite of all-cause death, myocardial infarction, stroke, and unplanned target lesion revascularisation by day 3 after randomisation. The principal safety endpoint was major bleeding. Analysis was by intention to treat. This trial is registered at ClinicalTrials.gov, identifier NCT01848106. The trial was terminated early after enrolment of 3232 patients due to severe allergic reactions. FINDINGS 1616 patients were allocated REG1 and 1616 were assigned bivalirudin, of whom 1605 and 1601 patients, respectively, received the assigned treatment. Severe allergic reactions were reported in ten (1%) of 1605 patients receiving REG1 versus one (<1%) of 1601 patients treated with bivalirudin. The composite primary endpoint did not differ between groups, with 108 (7%) of 1616 patients assigned REG1 and 103 (6%) of 1616 allocated bivalirudin reporting a primary endpoint event (odds ratio [OR] 1·05, 95% CI 0·80-1·39; p=0·72). Major bleeding was similar between treatment groups (seven [<1%] of 1605 receiving REG1 vs two [<1%] of 1601 treated with bivalirudin; OR 3·49, 95% CI 0·73-16·82; p=0·10), but major or minor bleeding was increased with REG1 (104 [6%] vs 65 [4%]; 1·64, 1·19-2·25; p=0·002). INTERPRETATION The reversible factor IXa inhibitor REG1, as currently formulated, is associated with severe allergic reactions. Although statistical power was limited because of early termination, there was no evidence that REG1 reduced ischaemic events or bleeding compared with bivalirudin. FUNDING Regado Biosciences Inc.

Modern and fossil corals from Palmyra and Christmas islands

The relationship between decadal to centennial changes in ocean circulation and climate is difficult to discern using the sparse and discontinuous instrumental record of climate and, as such, represents a large uncertainty in coupled ocean-atmosphere general circulation models. We present new modern and fossil coral radiocarbon (D14C) records from Palmyra (6°N, 162°W) and Christmas (2°N, 157°W) islands to constrain central tropical Pacific ocean circulation changes during the last millennium. Seasonally to annually resolved coral D14C measurements from the 10th, 12th-17th, and 20th centuries do not contain significant interannual to decadal-scale variations, despite large changes in coral d18O on these timescales. A centennial-scale increase in coral radiocarbon from the Medieval Climate Anomaly (~900-1200 AD) to the Little Ice Age (~1500-1800) can be largely explained by changes in the atmospheric D14C, as determined with a box model of Palmyra mixed layer D14C. However, large 12th century depletions in Palmyra coral D14C may reflect as much as a 100% increase in upwelling rates and/or a significant decrease in the D14C of higher-latitude source waters reaching the equatorial Pacific during this time. SEM photos reveal evidence for minor dissolution and addition of secondary aragonite in the fossil corals, but our results suggest that coral D14C is only compromised after moderate to severe diagenesis for these relatively young fossil corals.

Pliocene stable isotope and carbonate stratigraphy at DSDP Holes 85-572C and 85-573A

Holes 572C and 573A provide high resolution (about 5000-yr. sampling interval) records of oxygen and carbon isotope stratigraphy (Globigerinoides sacculifera) and carbonate stratigraphy for the Pliocene of the equatorial Pacific. These data enable detailed correlation of carbonate events between sites and provide additional resolution to the previous carbonate stratigraphy. Comparison of calcium carbonate and d18O data reveal a "Pacific-type" carbonate stratigraphy throughout the Pliocene. The d18O data have two modes of variability with a boundary at 2.9 Ma. The planktonic d18O record does not have a steplike enrichment at 3.2 Ma, which is observed in benthic records elsewhere, suggesting that this event does not represent the proposed initiation of northern hemispheric glaciation. Hole 572C does record a distinct d18O enrichment event at about 2.4 Ma, which has been previously associated with the onset of major ice rafting in the North Atlantic.

Calcium carbonate, sedimentation and mass accumulation rates at DSDP Site 85-572

At Site 572, located at 1°N, 114° W (3903 m water depth), we recovered a continuous hydraulic piston cored section of upper Miocene to upper Pleistocene pelagic sediments. The sediment is composed of biogenic carbonate and silica with nonbiogenic material as a minor component. Detailed analysis of the calcium carbonate content shows that the degree of variability in carbonate deposition apparently changed markedly between the late Miocene and Pliocene at this equatorial Pacific site. During this interval carbonate mass accumulation rates decreased from 2.6 to 0.8 g/cm**2 per 10**3 yr. If we assume that variations in CaCO3 content reflect changes in the degree of dissolution, then the detailed carbonate analysis would suggest that the degree of variability in carbonate deposition decreases by a factor of 5 as the dominant wavelength of variations increases significantly. However, if the variability in carbonate concentration is described in terms of changes in mean mass accumulation, calculations then suggest that relatively small changes in noncarbonate rates may be important in controlling the observed carbonate records. In addition, the analysis suggests that the degree of variability observed in pelagic carbonate data may in part reflect total accumulation rates. Intervals with high sedimentation rates show lower amplitude variations in concentration than intervals with lower sedimentation rates for the same degree of change in the carbonate accumulation rate.

(Table 2) Stratigraphic position of midpoints of reddish and beige layers of lithologic cycles in the Loulja-A Section and their astronomical ages after tuning to the ETP and Summer Insolation Curves of the La2004 solution

An integrated high-resolution stratigraphy and orbital tuning is presented for the Loulja sections located in the Bou Regreg area on the Atlantic side of Morocco. The sections constitute the upward continuation of the upper Messinian Ain el Beida section and contain a well-exposed, continuous record of the interval straddling the Miocene-Pliocene (M-P) boundary. The older Loulja-A section, which covers the interval from ~5.59 to 5.12 Ma, reveals a dominantly precession-controlled color cyclicity that allows for a straightforward orbital tuning of the boundary interval and for detailed cyclostratigraphic correlations to the Mediterranean; the high-resolution and high-quality benthic isotope record allows us to trace the dominantly obliquity-controlled glacial history. Our results reveal that the M-P boundary coincides with a minor, partly precession-related shift to lighter "interglacial" values in d18O. This shift and hence the M-P boundary may not correlate with isotope stage TG5, as previously thought, but with an extra (weak) obliquity-controlled cycle between TG7 and TG5. Consequently, the M-P boundary and basal Pliocene flooding of the Mediterranean following the Messinian salinity crisis are not associated with a major deglaciation and glacio-eustatic sea level rise, indicating that other factors, such as tectonics, must have played a fundamental role. On the other hand, the onset of the Upper Evaporites in the Mediterranean marked by hyposaline conditions coincides with the major deglaciation step between marine isotope stage TG12 and TG11, suggesting that the associated sea level rise is at least partly responsible for the apparent onset of intermittently restricted marine conditions following the main desiccation phase. Finally, the Loulja-A section would represent an excellent auxiliary boundary stratotype for the M-P boundary as formally defined at the base of the Trubi marls in the Eraclea Minoa section on Sicily.

Planktic foraminifera from ODP Hole 117-723B

Upwelling occurs during the summer off the coast of Oman when the Asian monsoon produces strong southwest winds in the northern Arabian Sea. Ekman transport driven by the southwest monsoon winds upwells cool nutrient-rich waters along the coast which contrast with the warmer, less productive waters offshore. The spatial pattern of foraminifers in the sediments corresponds with the coastal environmental gradient. The upwelling species Globigerina bulloides dominates the sediment assemblage on the continental margin, while Globigerinita glutinata is more abundant offshore, creating a coastal gradient in fauna. We reconstructed the upwelling faunal gradient using high resolution oxygen isotope stratigraphy to correlate between Hole 723B on the Oman Margin, and a core from the Owen Ridge (RC2761), adjacent Site 722. A gradient similar in magnitude to the present, implying upwelling conditions similar to today existed during each interglacial time during the late Pleistocene interval from 0 to 300 k.y. The gradient was reduced or absent during glacial times implying diminshed southwest winds along the coast of Oman, not strong enough to produce an environmental gradient between the coast and offshore sites.

Age determination and stable isotope record of sediment cores at 9°S in the Indian Ocean

A continuous 10-m-long section consisting of roughly two thirds Ethmodiscus rex (a diatom) and one third mixed planktonic foraminifera was identified in a core from 3800 m depth at 9°S on the Indian Ocean's 90°E Ridge. Radiocarbon dates place the onset of deposition of this layer at >30,000 years B.P. and its termination at close to 11,000 years B.P. However, precise dating of the foraminifera from the Ethmodiscus layer itself proved to be impossible owing to the presence of secondary calcite presumably precipitated from the pore waters. During the Holocene, high calcium carbonate content ooze free of diatoms was deposited at this locale. As the site currently lies beneath the pathway taken by upper ocean waters entering the Indian Ocean from the Pacific (via the Indonesian Straits), it appears that during glacial time, thermocline waters moving along this same path provided the silica and other nutrients required by these diatoms.

Stable oxygen and carbon isotope record of foraminifera of ODP SIte 184-1146

Ocean Drilling Program Site 1146 was drilled within a small rift basin on the midcontinental slope of the northern South China Sea. It is located at 19°27.4'N, 116°16.37'E, in 2092 m water depth. This site was drilled to recover records of Asian monsoon variability into the middle Miocene with temporal resolution sufficient for orbital-scale analyses. Here we present oxygen and carbon isotopic measurements of planktonic foraminifers (Globigerinoides ruber) and benthic foraminifers (Uvigerina peregrina and Cibicides wuellerstorfi) as well as a preliminary age model for the top 185 meters composite depth (mcd).

Stable oxygen isotope record and lithogenic composition of ODP Hole 117-722B

The upper 38 m of Hole 722B sediments (Owen Ridge, northwest Arabian Sea) was sampled at 20 cm intervals and used to develop records of lithogenic percent, mass accumulation rate, and grain size spanning the past 1 m.y. Over this interval, the lithogenic component of Owen Ridge sediments can be used to infer variability in the strength of Arabian Sea summer monsoon winds (median grain size) and the aridity of surrounding dust source-areas (mass accumulation rate; MAR in g/cm**2/k.y). The lithogenic MAR has strong 100, 41, and 23 k.y. cyclicities and is forced primarily by changes in source-area aridity associated with glacial-interglacial cycles. The lithogenic grain size, on the other hand, exhibits higher frequency variability (23 k.y.) and is forced by the strength of summer monsoon winds which, in turn, are forced by the effective sensible heating of the Indian-Asian landmass and by the availability of latent heat from the Southern Hemisphere Indian Ocean. These forcing mechanisms combine to produce a wind-strength record which has no strong relationship to glacial-interglacial cycles. Discussion of the mechanisms responsible for production of primary Milankovitch cyclicities in lithogenic records from the Owen Ridge is presented elsewhere (Clemens and Prell, 1990, doi:10.1029/PA005i002p00109). Here we examine the 1 m.y. record from Hole 722B focusing on different aspects of the lithogenic components including an abrupt change in the monsoon wind-strength record at 500 k.y., core-to-core reproducibility, comparison with magnetic susceptibility, coherency with a wind-strength record from the Pacific Ocean, and combination frequencies in the wind-strength record. The Hole 722B lithogenic grain-size record shows an abrupt change at 500 k.y. possibly indicating decreased monsoon wind-strength over the interval from 500 k.y. to present. The grain-size decrease appears to be coincident with a loss of spectral power near the 41 k.y. periodicity. However, the grain-size decrease is not paralleled in the Globigerina bulloides upwelling record, an independent record of summer monsoon wind-strength (Prell, this volume). These observations leave us with competing hypotheses possibly involving: (1) a decrease in the sensitivity of monsoon windstrength to obliquity forcing, (2) decoupling of the grain size and G. bulloides records via a decoupling of the nutrient supply from wind-driven upwelling, and/or (3) a change in dust source-area or the patterns of dust transporting winds. Comparison of the lithogenic grain size and weight percent records from Hole 722B with those from a nearby core shows that the major and most minor events are well replicated. These close matches establish our confidence in the lithogenic extraction techniques and measurements. Further, reproducibility on a core-to-core scale indicates that the eolian depositional signal is regionally strong, coherent, and well preserved. The lithogenic weight percent and magnetic susceptibility are extremely well correlated in both the time and frequency domains. From this we infer that the magnetically susceptible component of Owen Ridge sediments is of terrestrial origin and transported to the Owen Ridge via summer monsoon winds. Because of the high correlation with the lithogenic percent record, the magnetic susceptibility record can be cast in terms of lithogenic MAR and used as a high resolution proxy for continental aridity. In addition to primary Milankovitch periodicities, the Hole 722B grain-size record exhibits periodicity at 52 k.y. and at 29 k.y. Both periodicities are also found in the grain-size record from piston core RC11-210 in the equatorial Pacific Ocean. Comparison of the two grain-size records shows significant coherence and zero phase relationships over both the 52 and 29 k.y. periodicities suggesting that the strengths of the Indian Ocean monsoon and the Pacific southeasterly trade winds share common forcing mechanisms. Two possible origins for the 52 and 29 k.y. periodicities in the Hole 722B wind-strength record are (1) direct Milankovitch forcing (54 and 29 k.y. components of obliquity) and (2) combination periodicities resulting from nonlinear interactions within the climate system. We find that the 52 and 29 k.y. periodicities show stronger coherency with crossproducts of eccentricity and obliquity (29 k.y.) and precession and obliquity (52 k.y.) than with direct obliquity forcing. Our working hypothesis attributes these periodicities to nonlinear interaction between external insolation forcing and internal climatic feedback mechanisms involving an interdependence of continental snow/ice-mass (albedo) and the hydrological cycle (latent heat availability).