Paleoclimatic and paleoceanographic records through Marine Isotope Stage 19 at the Chiba composite section, central Japan: A key reference for the EarlyeMiddle Pleistocene Subseries boundary

Marine Isotope Stage (MIS) 19 is an important analogue for the present interglacial because of its similar orbital configuration, especially the phasing of the obliquity maximum to precession minimum. However, sedimentary records suitable for capturing both terrestrial and marine environmental changes are limited, and thus the climatic forcing mechanisms for MIS 19 are still largely unknown. The Chiba composite section, east-central Japanese archipelago, is a continuous and expanded marine sedimentary succession well suited to capture terrestrial and marine environmental changes through MIS 19. In this study, a detailed oxygen isotope chronology is established from late MIS 20 to early MIS 18, supported by a U-Pb zircon age and the presence of the Matuyama–Brunhes boundary. New pollen, marine microfossil, and planktonic foraminiferal δ18O and Mg/Ca paleotemperature records reveal the complex interplay of climatic influences. Our pollen data suggest that the duration of full interglacial conditions during MIS 19 extends from 785.0 to 775.1 ka (9.9 kyr), which offers an important natural baseline in predicting the duration of the present interglacial. A Younger Dryas-type cooling event is present during Termination IX, suggesting that such events are linked to this orbital configuration. Millennial- to multi-millennial-scale variations in our δ18O and Mg/Ca records imply that the Subarctic Front fluctuated in the northwestern Pacific Ocean during late MIS 19, probably in response to East Asian winter monsoon variability. The climatic setting at this time appears to be related to less severe summer insolation minima at 65˚N and/or high winter insolation at 50˚N. Our records do not support a recently hypothesized direct coupling between variations in the geomagnetic field intensity and global/regional climate change. Our highly resolved paleoclimatic and paleoceanographic records, coupled with a well-defined Matuyama–Brunhes boundary (772.9 ka; duration 1.9 kyr), establish the Chiba composite section as an exceptional climatic and chronological reference section for the Early–Middle Pleistocene boundary.ArticleQuaternary Science Reviews 191: 406-430(2018)journal articl

Validity of the Short Nutritional Assessment Questionnaire for Japanese Patients with Cancer Undergoing Outpatient Chemotherapy

Purpose : To investigate the utility of the Short Nutritional Assessment Questionnaire (SNAQ) in the nutritional evaluation of patients with cancer undergoing outpatient chemotherapy. Methods :We included 229 patients with cancer who were undergoing outpatient chemotherapy between October 2015 and April 2016. The SNAQ and the revised SNAQ (addition of age and body mass index) were implemented, and their relationships with Controlling Nutritional Status (CONUT), an indicator of bionutritional assessment, were examined. Results : The cutoff value of the SNAQ score corresponding to moderate-to-severe undernourishment in CONUT values was 0.5, with a sensitivity of 87.5% and a specificity of 65.9%, and the corresponding values for the revised SNAQ score were 2.5, 91.7%, and 62.9%, respectively. This cutoff value and the corresponding positive prediction value for the revised SNAQ were superior to those of SNAQ. Binary logistic regression analysis with the revised SNAQ and sex as independent variables and the CONUT value as the dependent variable revealed that the higher the SNAQ score, the more likely it was that CONUT moderate-to-severe undernourishment would be identified (odds ratio, 1.48 ; , 1.34-1.96) . Conclusion : Nutritional evaluation with the revised SNAQ can predict moderateto- severe undernourishment according to CONUT in patients with cancer undergoing outpatient chemotherapy

A reference time scale for Site U1385 (Shackleton Site) on the SW Iberian Margin

We produced a composite depth scale and chronology for Site U1385 on the SW Iberian Margin. Using log(Ca/Ti) measured by core scanning XRF at 1-cm resolution in all holes, a composite section was constructed to 166.5 meters composite depth (mcd) that corrects for stretching and squeezing in each core. Oxygen isotopes of benthic foraminifera were correlated to a stacked δ^18O reference signal (LR04) to produce an oxygen isotope stratigraphy and age model. Variations in sediment color contain very strong precession signals at Site U1385, and the amplitude modulation of these cycles provides a powerful tool for developing an orbitally-tuned age model. We tuned the U1385 record by correlating peaks in L* to the local summer insolation maxima at 37^oN. The benthic δ^18O record of Site U1385, when placed on the tuned age model, generally agrees with other time scales within their respective chronologic uncertainties. The age model is transferred to down-core data to produce a continuous time series of log(Ca/Ti) that reflect relative changes of biogenic carbonate and detrital sediment. Biogenic carbonate increases during interglacial and interstadial climate states and decreases during glacial and stadial periods. Much of the variance in the log(Ca/Ti) is explained by a linear combination of orbital frequencies (precession, tilt and eccentricity), whereas the residual signal reflects suborbital climate variability. The strong correlation between suborbital log(Ca/Ti) variability and Greenland temperature over the last glacial cycle at Site U1385 suggests that this signal can be used as a proxy for millennial-scale climate variability over the past 1.5 Ma. Millennial climate variability, as expressed by log(Ca/Ti) at Site U1385, was a persistent feature of glacial climates over the past 1.5 Ma, including glacial periods of the early Pleistocene (‘41-kyr world’) when boundary conditions differed significantly from those of the late Pleistocene (‘100-kyr world’). Suborbital variability was suppressed during interglacial stages and enhanced during glacial periods, especially when benthic δ^18O surpassed ~ 3.3-3.5‰. Each glacial inception was marked by appearance of strong millennial variability and each deglaciation was preceded by a terminal stadial event. Suborbital variability may be a symptomatic feature of glacial climate or, alternatively, may play a more active role in the inception and/or termination of glacial cycles.This research was supported by the Natural Environmental Research Council Grant NE/K005804/1 to DH and LS and NE/J017922/1 to DH.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.gloplacha.2015.07.00

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

<p>Abstract</p> <p>Background</p> <p>The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.</p> <p>Results</p> <p>Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs.</p> <p>Conclusions</p> <p>Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.</p

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Onset of Mediterranean outflow into the North Atlantic

Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics

A reference time scale for Site U1385 (Shackleton Site) on the SW Iberian Margin

Variations in sediment color contain very strong precession signals at Site U1385, and the amplitude modulation of these cycles provides a powerful tool for developing an orbitally-tuned age model. We tuned the U1385 record by correlating peaks in L* to the local summer insolation maxima at 37°N. The benthic δ18O record of Site U1385, when placed on the tuned age model, generally agrees with other time scales within their respective chronologic uncertainties. The age model is transferred to down-core data to produce a continuous time series of log(Ca/Ti) that reflect relative changes of biogenic carbonate and detrital sediment. Biogenic carbonate increases during interglacial and interstadial climate states and decreases during glacial and stadial periods. Much of the variance in the log(Ca/Ti) is explained by a linear combination of orbital frequencies (precession, tilt and eccentricity), whereas the residual signal reflects suborbital climate variability. The strong correlation between suborbital log(Ca/Ti) variability and Greenland temperature over the last glacial cycle at Site U1385 suggests that this signal can be used as a proxy for millennial-scale climate variability over the past 1.5 Ma. Millennial climate variability, as expressed by log(Ca/Ti) at Site U1385, was a persistent feature of glacial climates over the past 1.5 Ma, including glacial periods of the early Pleistocene (‘41-kyr world’) when boundary conditions differed significantly from those of the late Pleistocene (‘100-kyr world’). Suborbital variability was suppressed during interglacial stages and enhanced during glacial periods, especially when benthic δ18O surpassed ~ 3.3–3.5‰. Each glacial inception was marked by appearance of strong millennial variability and each deglaciation was preceded by a terminal stadial event. Suborbital variability may be a symptomatic feature of glacial climate or, alternatively, may play a more active role in the inception and/or termination of glacial cycles

(Table 1) Visual core description and grain size analysis from different Holes of IODP Site 339

In deep-sea sediments, contourites deposited from bottom currents mainly along slopes are associated with hemipelagites, pelagites, and sediment gravity-flow deposits. The major sedimentary facies of contourites are characterized by bioturbation and mottling and bigradational grading. However, it is difficult to discriminate muddy contourites from hemipelagites by using only these features of the lithofacies, particularly in core samples. Therefore, the present study focused on microstructure as an additional potentially diagnostic characteristic for identifying muddy contourites. Microstructures of muddy contourites, mainly from the Gulf of Cádiz, and of hemipelagites from off the West Iberian margin collected by IODP Expedition 339 were examined, along with their magnetic fabric and grain-size distribution. The results showed that the muddy contourites were composed mainly of silt grains, including plate-like silt particles that were oriented parallel or sub-parallel to the bedding plane. Some samples were composed of silt grains up to 100 µm in apparent size. In contrast, the hemipelagites were composed of calcareous nannoplankton or silt grains and randomly oriented clay particles. The magnetic fabric, as indicated by the anisotropy of magnetic susceptibility, and the grain-size distribution of the muddy contourites also differed from those of hemipelagite. On the basis of these features, the plate-like silt particles parallel or sub-parallel to the bedding plane characterizing the muddy contourites were interpreted to reflect rapid deposition from a low-concentration suspension of fine-grained particles in a weak bottom current. Although microstructural features used alone are insufficient, used in conjunction with magnetic fabric and grain-size distribution, they are expected to be a useful tool for discriminating muddy contourites from hemipelagites