Air-Sea Interactions in a High-Resolution Ocean-Atmosphere Simulation

During the past few years the Goddard Earth Observing System (GEOS) and Massachusetts Institute of Technology (MIT) modeling groups have produced, respectively, global atmosphere-only and ocean-only simulations with km-scale grid spacing. These simulations have proved invaluable for process studies and for the development of satellite and in-situ sampling strategies. Nevertheless, a key limitation of these "nature" simulations is the lack of interaction between the ocean and the atmosphere, which limits their usefulness for studying air-sea interactions and for designing observing missions to study these interactions. We present here results from a coupled GEOS-MIT "nature run" simulation, wherein we have coupled a cubed-sphere-720 (~ 1/8) configuration of the GEOS atmosphere to a lat-lon-cap-1080 (~ 1/12) configuration of the MIT ocean. We compare near-surface diagnostics of this fully coupled ocean-atmosphere simulation to equivalent atmosphere-only and ocean-only simulations. A particular focus of the comparisons is the coupled versus uncoupled differences in interactions between Sea Surface Temperature (SST) and ocean surface wind. We discuss, in particular, a several-day mode of temporal variability in the SST-wind cycle and how it is represented in the different model simulations and in observationally-based products. A mechanism for the cycle, which is driven by SST-wind feedback, is proposed

JAMI: a Java library for molecular interactions and data interoperability.

BACKGROUND: A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. RESULTS: A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. CONCLUSION: Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library

Shared Genetic Etiology Between Alcohol Dependence and Major Depressive Disorder

The clinical comorbidity of alcohol dependence (AD) and major depressive disorder (MDD) is well established, whereas genetic factors influencing co-occurrence remain unclear. A recent study using polygenic risk scores (PRS) calculated based on the first-wave Psychiatric Genomics Consortium MDD meta-analysis (PGC-MDD1) suggests a modest shared genetic contribution to MDD and AD. Using a (∼10 fold) larger discovery sample, we calculated PRS based on the second wave (PGC-MDD2) of results, in a severe AD case–control target sample. We found significant associations between AD disease status and MDD-PRS derived from both PGC-MDD2 (most informative P-threshold=1.0, P=0.00063, R2=0.533%) and PGCMDD1 (P-threshold=0.2, P=0.00014, R2=0.663%) metaanalyses; the larger discovery sample did not yield additional predictive power. In contrast, calculating PRS in a MDD target sample yielded increased power when using PGC-MDD2 (P-threshold=1.0, P=0.000038, R2=1.34%) versus PGC-MDD1 (P-threshold=1.0, P=0.0013, R2=0.81%). Furthermore, when calculating PGC-MDD2 PRS in a subsample of patients with AD recruited explicitly excluding comorbid MDD, significant associations were still found (n=331; P-threshold=1.0, P=0.042, R2=0.398%). Meanwhile, in the subset of patients in which MDD was not the explicit exclusion criteria, PRS predicted more variance (n=999; P-threshold=1.0, P=0.0003, R2=0.693%). Our findings replicate the reported genetic overlap between AD and MDD and also suggest the need for improved, rigorous phenotyping to identify true shared cross-disorder genetic factors. Larger target samples are needed to reduce noise and take advantage of increasing discovery sample size

Laparoscopic adjustable gastric band in an obese unrelated living donor prior to kidney transplantation: a case report

Introduction. Obese living donors who undergo donor nephrectomy have higher rates of intra-operative and post-operative complications. Many centres exclude obese donors from living donor transplant programs. Diet, exercise and medication are often ineffective weight loss interventions for donors, hence bariatric surgery should be considered. Case presentation. We report the case of a 53-year-old Caucasian woman who underwent laparoscopically adjustable gastric banding. The procedure enabled her to lose sufficient weight to gain eligibility for kidney donation. After losing weight, she had an uncomplicated laparoscopic donor nephrectomy surgery, and the recipient underwent successful kidney transplantation. Conclusion. Laparoscopically adjustable gastric banding should be considered for obese potential living kidney donors whenever transplantation units restrict access to donor nephrectomy based on the increased surgical risk for donors

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download

Variational methods

International audienceThis contribution presents derivative-based methods for local sensitivity analysis, called Variational Sensitivity Analysis (VSA). If one defines an output called the response function, its sensitivity to inputs variations around a nominal value can be studied using derivative (gradient) information. The main issue of VSA is then to provide an efficient way of computing gradients. This contribution first presents the theoretical grounds of VSA: framework and problem statement, tangent and adjoint methods. Then it covers pratical means to compute derivatives, from naive to more sophisticated approaches, discussing their various 2 merits. Finally, applications of VSA are reviewed and some examples are presented, covering various applications fields: oceanography, glaciology, meteorology

A New Atmosphere-Ocean Model for Studying Air-Sea Interactions and Coupled Data Assimilation

During the last two plus decades, The Goddard Earth Observing System (GEOS) and Massachusetts Institute of Technology (MIT) modeling groups have developed, respectively, atmosphere-only and ocean-only global general circulation models. These two models (GEOS and MITgcm) have demonstrated their data assimilation capabilities with the recent releases of the Modern Era Reanalysis for Research Applications, Version 2 (MERRA-2) atmospheric reanalysis and the Estimating the Circulation and Climate of the Ocean, Version 4 (ECCO-v4) ocean (and sea ice) state estimate. Independently, the two modeling groups have also produced global atmosphere-only and ocean-only simulations with km-scale grid spacing which proved invaluable for process studies and for the development of satellite and in-situ sampling strategies.Recently, a new effort has been made to couple these two models and to leverage their data-assimilation and high resolution capabilities (i.e., eddy-permitting ocean, cloud-permitting atmosphere). The focus in the model development is put on sub-seasonal to decadal time scales. In this talk, I discuss the new coupled model and present some first coupled simulation results. This will include a high-resolution coupled GEOS-MIT simulation, whereby we have coupled a cubed-sphere-720 (~ 1/8) configuration of the GEOS atmosphere to a lat-lon-cap-1080 (~ 1/12) configuration of the MIT ocean. We compare near-surface diagnostics of this fully coupled ocean-atmosphere set-up to equivalent atmosphere-only and ocean-only simulations. In the comparisons we focus in particular on the differences in air-sea interactions between sea surface temperature (SST) and wind for the coupled and uncoupled simulations

The Development of the New GEOS-MITgcm Atmosphere-Ocean Model for Coupled Data Assimilation System

During the last two plus decades, The Goddard Earth Observing System (GEOS) and Massachusetts Institute of Technology (MIT) modeling groups have developed, respectively, atmosphere-only and ocean-only global general circulation models. These two models (GEOS and MITgcm) have demonstrated their data assimilation capabilities with the recent releases of the Modern Era Reanalysis for Research Applications, Version 2 (MERRA-2) atmospheric reanalysis and the Estimating the Circulation and Climate of the Ocean, Version 4 (ECCO-v4) ocean (and sea ice) state estimate. Independently, the two modeling groups have also produced global atmosphere-only and ocean-only simulations with km-scale grid spacing which proved invaluable for process studies and for the development of satellite and in-situ sampling strategies.Recently, a new effort has been made to couple these two models and to leverage their data-assimilation and high resolution capabilities (i.e., eddy-permitting ocean, cloud-permitting atmosphere). The focus in the model development is put on sub-seasonal to decadal time scales. In this talk, I discuss the new coupled model and present some first coupled simulation results. This will include a high-resolution coupled GEOS-MIT simulation, whereby we have coupled a cubed-sphere-720 (~ 1/8 deg) configuration of the GEOS atmosphere to a lat-lon-cap-1080 (~ 1/12 deg) configuration of the MIT ocean. We compare near-surface diagnostics of this fully coupled ocean-atmosphere set-up to equivalent atmosphere-only and ocean-only simulations. In the comparisons we focus in particular on the differences in air-sea interactions between sea surface temperature (SST) and wind for the coupled and uncoupled simulations

An Ocean-Atmosphere Simulation for Studying Air-Sea Interactions

During the past few years the Goddard Earth Observing System (GEOS) and Massachusetts Institute of Technology (MIT) modeling groups have produced, respectively, global atmosphere-only and ocean-only simulations with km-scale grid spacing. These simulations have proved invaluable for process studies and for the development of satellite and in-situ sampling strategies. Nevertheless, a key limitation of these "nature" simulations is the lack of interaction between the ocean and the atmosphere, which limits their usefulness for studying air-sea interactions and for designing observing missions to study these interactions. To remove this limitation, we aim to perform a coupled simulation using the km-scale GEOS atmosphere and the km-scale MIT ocean models. The initial attempt at the km-scale coupled simulation resulted in computational issues which will be presented here. As a preliminary step towards the km-scale objective, we present results from a high resolution but not yet km-scale simulation, wherein we have coupled a cubed-sphere-720 (~ 1/8) configuration of the GEOS atmosphere to a lat-lon-cap-1080 (~ 1/12) configuration of the MIT ocean. We compare near-surface diagnostics of this fully coupled ocean-atmosphere set-up to equivalent atmosphere-only and ocean-only simulations. A particular focus of the comparisons is the differences in interactions between Sea Surface Temperature (SST) and ocean surface wind for the coupled and uncoupled simulations. We discuss observed and modeled high temporal variability (~days) SST-wind cycle and how it is represented in the different systems. A mechanism for the cycle, which is driven by SST-wind feedback, is proposed

Commencement Program, December (1998)

https://red.mnstate.edu/commencement/1169/thumbnail.jp