bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variability of Air–Sea Interactions over the Indian Ocean Derived from Satellite Observations
Authors: Gautier Catherine , Peterson Peter , Jones Charles 
Published: March 2011

Abstract
Novel ways of monitoring the large-scale variability of the southwest monsoon in the Indian Ocean are presented using multispectral satellite datasets. The fields of sea surface temperature (SST), surface latent heat flux (LHF), net surface solar radiation (SW), precipitation (P), and SW − LHF over the Indian Ocean are analyzed to characterize the seasonal and interannual variability with special emphasis on the period 1988–90. It is shown that satellite data are able to make a significant contribution to the multiplatform strategy necessary to describe the large-scale spatial and temporal variability of air–sea interactions associated with the Indian Ocean Monsoon. The satellite data analyzed here has shown for the first time characteristics of the interannual variability of air–sea interactions over the entire Indian Ocean. Using monthly means of SST, LHF, SW, P, and the difference SW − LHF, the main features of the seasonal and interannual variability of air–sea interactions over the Indian Ocean are characterized. It is shown that the southwest monsoon strongly affects these interactions, inducing dramatic exchanges of heat between air and sea and large temporal variations of these exchanges over relatively small timescale (with regards to typical oceanic timescales). The analyses indicate an overall good agreement between satellite and in situ (ship) estimates, except in the southern Indian Ocean, where ship sampling is minimal, the disagreement can be large. In the latitudinal band of 10°N–15°S, differences in climatological in situ estimates of surface sensible heat flux and net longwave radiation has a larger influence on the net surface heat flux than the difference between satellite and in situ estimates of SW and LHF.
Northern Hemispheric Interdecadal Variability: A Coupled Air–Sea Mode
Authors: Timmermann A. , Latif M. , Voss R. , Grötzner A. 
Published: March 2011

AbstractA coupled air–sea mode in the Northern Hemisphere with a period of about 35 years is described. The mode was derived from a multicentury integration with a coupled ocean–atmosphere general circulation model and involves interactions of the thermohaline circulation with the atmosphere in the North Atlantic and interactions between the ocean and the atmosphere in the North Pacific.The authors focus on the physics of the North Atlantic interdecadal variability. If, for instance, the North Atlantic thermohaline circulation is anomalously strong, the ocean is covered by positive sea surface temperature (SST) anomalies. The atmospheric response to these SST anomalies involves a strengthened North Atlantic Oscillation, which leads to anomalously weak evaporation and Ekman transport off Newfoundland and in the Greenland Sea, and the generation of negative sea surface salinity (SSS) anomalies. These SSS anomalies weaken the deep convection in the oceanic sinking regions and subsequently the strength of the thermohaline circulation. This leads to a reduced poleward heat transport and the formation of negative SST anomalies, which completes the phase reversal.The Atlantic and Pacific Oceans seem to be coupled via an atmospheric teleconnection pattern and the interdecadal Northern Hemispheric climate mode is interpreted as an inherently coupled air–sea mode. Furthermore, the origin of the Northern Hemispheric warming observed recently is investigated. The observed temperatures are compared to a characteristic warming pattern derived from a greenhouse warming simulation with the authors’ coupled general circulation model and also with the Northern Hemispheric temperature pattern associated with the 35-yr climate mode. It is shown that the recent Northern Hemispheric warming projects well onto the temperature pattern of the interdecadal mode under consideration.
Sensitivity of the Simulated Annual Cycle of Sea Surface Temperature in the Equatorial Pacific to Sunlight Penetration
Authors: Schneider Edwin K. , Zhu Zhengxin 
Published: March 2011

Abstract
The annual cycle of sea surface temperature (SST) in the equatorial Pacific is compared for two simulations with a coupled atmosphere–ocean general circulation model. The simulations differ only in the optical properties of the ocean: sunlight penetrates below the topmost layer of the ocean model in one case but is completely absorbed in the top layer in the other. The simulation without the sunlight penetration produces an unrealistic annual cycle of SST with a strong semiannual component in the equatorial Pacific, whereas the simulation with sunlight penetration is more realistic. The change in the character of the annual cycle results from an increase in the effective heat capacity of the ocean associated with an increase in the depth of the mixed layer directly forced by the sunlight penetration. This produces a smaller amplitude of the annual cycle of SST at latitudes close to but off the equator. The zone of intense tropical convection then remains closer to the equator, leading to a reduced semiannual cycle of zonal wind stress at the equator. The reduction in the unrealistic semiannual wind stress forcing leads to a more realistic annual cycle in SST.
The simulation of the annual mean SST is also improved by the inclusion of the sunlight penetration, with a better simulation of the warm pool in the western equatorial Pacific and associated improvements in the atmospheric circulation. This improvement is also attributed to the increase in the mixed layer depth, which changes the ocean heat flux in the western equatorial Pacific by reducing the sensitivity of SST to upwelling.
Understanding Climate Sensitivity to Tropical Deforestation in a Mechanistic Model
Authors: Zeng Ning 
Published: March 2011

Abstract
An analysis is provided to explain the sensitivity of regional climate to tropical deforestation based on an intermediate-level mechanistic model for land–atmosphere interaction. The analytical framework is made possible by the fact that feedback to local thermodynamics from large-scale dynamics is negligible, so the determining processes take place in situ. The analytical method accurately reproduces the intermediate-level numerical model results for an albedo change scenario and further provides insight into the mechanisms. A three-way balance among large-scale adiabatic cooling, moist convective heating, and radiative heating allows two positive feedback mechanisms, moisture convergence feedback and evaporation feedback, that give rise to the high sensitivity. The analysis also highlights a deficiency in column energy balance commonly used in tropical simple models, which results in a sensitivity that is likely too high. In light of these findings, some immediate needs for further advancing understanding of the problem are discussed.
The Role of Vegetation in the Dynamics of West African Monsoons
Authors: Zheng Xinyu , Eltahir Elfatih A. B. 
Published: March 2011

Abstract
The focus of this paper is the role of meridional distribution of vegetation in the dynamics of monsoons and rainfall over West Africa. A moist zonally symmetric atmospheric model coupled with a simple land surface scheme is developed to investigate these processes. Four primary experiments have been carried out to examine the sensitivity of West African monsoons to perturbations in the meridional distribution of vegetation. In the control experiment, the authors assume a distribution of vegetation that resembles the natural vegetation cover in West Africa. Each perturbation experiment is identical to the control experiment except that a change in vegetation cover is imposed for a latitudinal belt that is 10° in width. The results of the numerical experiments demonstrate that West African monsoons and therefore rainfall distribution depend critically on the location of the vegetation perturbations. Changes in vegetation cover along the border between the Sahara desert and West Africa (desertification) may have a minor impact on the simulated monsoon circulation. However, coastal deforestation may cause the collapse of the monsoon circulation and have a dramatic impact on the regional rainfall. The observed deforestation in West Africa is then likely to be a significant contributor to the observed drought.
Reconstruction of Monthly Mean 700-mb Heights from Surface Data by Reverse Specification
Authors: Klein William H. , Dai Ying 
Published: March 2011

Abstract
This paper demonstrates an objective method of computing monthly mean 700-mb height anomalies (H) at 108 grid points in the Western Hemisphere for a 40-yr period as a function of concurrent anomalies of monthly mean sea level pressure (P), at the same 108 points used for H, and monthly mean surface air temperature (T) averaged over 112 areas in North America. The authors applied a forward stepwise program to derive linear multiple regression equations that explained 81% of the variance of H by means of only 3.5 variables, averaged over all months and grid points. The stability of these equations held up well on 6 yr of independent data in terms of explained variance, root-mean-square error, and the spatial anomaly correlation coefficient. Therefore, it seems feasible to reconstruct maps of H for the first half of the twentieth century as a function of data on P and T only.
Constructing a future weather file for use in building simulation using UKCP09 projections
Authors: Watkins R. , Levermore GJ , Parkinson JB 
Published: March 2011

In the future with climate change, building designers may need to demonstrate to clients that their buildings will continue to provide a comfortable environment under future weather conditions. Building simulation modelling can be used to this end provided that suitable weather files can be constructed. This article describes the use of the latest climate projections from UKCIP (UKCP09 data) and a method of constructing an hourly weather file for the following parameters: dry-bulb temperature, relative humidity, cloud cover, solar irradiation (direct and diffuse), wind speed and wind direction. For a given future scenario, the approach used first selects appropriate months from 3000 years of UKCP09 data to construct a Test Reference Year (TRY). Unfortunately, the UKCP09 hourly data has no wind or cloud data, and the solar irradiance is uncorrected at low sun angles. This article describes algorithms for calculating wind speed and cloud cover from the UKCP09 data. From this data, a TRY can be constructed and formatted to be suitable for use with commonly used simulation packages. Practical applications: Building professionals increasingly seek reassurance on how a proposed building will perform under a future rather than historical climate. This article describes a method of processing the latest future climate projections (UKCP09 data released in June 2009) and generating a Test Reference Year (TRY) with the full complement of weather parameters suitable for use by commonly used building simulation programmes.
Development of adherence metrics for caloric restriction interventions
Authors: Pieper Carl , Redman Leanne , Racette Susan , Roberts Susan , Bhapkar Manju , Rochon James , Martin Corby , Kraus William , Das Sai , Williamson Donald , Ravussin Eric 
Published: March 2011

Background Objective measures are needed to quantify dietary adherence during caloric restriction (CR) while participants are freeliving. One method to monitor adherence is to compare observed weight loss to the expected weight loss during a prescribed level of CR. Normograms (graphs) of expected weight loss can be created from mathematical modeling of weight change to a given level of CR, conditional on the individual’s set of baseline characteristics. These normograms can then be used by counselors to help the participant adhere to their caloric target. Purpose (1) To develop models of weight loss over a year of caloric restriction-given demographics, and well-defined measurements of body mass index, total daily energy expenditure (TDEE) and %CR. (2) To utilize these models to develop normograms, given the level of caloric restriction prescribed, and measures of these variables. Methods Seventy-seven individuals completing a 6–12-month caloric restriction intervention (CALERIE) at three sites (Pennington Biomedical Research Center, Tufts University, and Washington University) and had body weight and body composition measured frequently. Energy intake (and %CR) was estimated from TDEE (by doubly labeled water) and body composition (by DXA) at baseline and months 1, 3, 6, and 12. Bodyweight was modeled to determine the predictors and distribution of the expected trajectory of percent weight change over 12 months of CR. Results As expected, CR was related to change in body weight. Controlling for time-varying measures, initially simple models of the functional form indicated that the trajectory of percent weight change was predicted by a nonlinear function of age, TDEE, %CR, and sex. Using these estimates, normograms for the weight change were developed. Our model estimates that the mean weight loss (% change from baseline weight) for an individual adherent to a 25% CR regimen is −10.9 ± 6.3% for females and −13.9 + 6.4% for men after 12 months. Limitations There are several limitations. Sample sizes are small ( n = 77), and, by design, the protocols, including prescribed CR, for the interventions differed by site, and not all subjects completed a year of follow-up. In addition, the inclusion of subjects by age and initial BMI was constricted, so that these results may not generalize to other populations including older and obese subjects. Conclusions The trajectory of percent weight change during CR interventions in the presence of well-measured covariates can be modeled using simple nonlinear functions, and is related level of CR, the percent change in TDEE, gender, and age. Displayed on a normogram, individually tailored trajectories can be used by counselors and participants to monitor weight loss and adherence to a CR regimen.
Prevalence of colonic adenomas in patients with nonalcoholic fatty liver disease
Authors: Touzin Nadege T. , Bush Kelvin N.V. , Williams Christopher D. , Harrison Stephen A. 
Published: March 2011

Background: Epidemiologic data suggest that colonic adenomas have an increased tendency to occur in patients who are obese, African American, or have a positive family history of colon cancer, or diabetes mellitus. Recent data suggest that impaired glucose tolerance, dyslipidemia, and metabolic syndrome are associated with a higher risk for colonic adenomas. Patients with nonalcoholic fatty liver disease (NAFLD) often share several of the aforementioned risk factors for colonic adenomas. However, data are lacking about the relationship between NAFLD and colonic adenomas. The aim of this study was to systematically evaluate whether NAFLD is an independent risk factor for colonic adenomas. Methods: We performed a retrospective cohort observational study on 233 patients who underwent screening colonoscopies at Brooke Army Medical Center from November 2007 to March 2010 to assess for the association between NAFLD and colonic adenomas. Patients who had previously been found to have biopsy-proven simple steatosis ( n = 65) or nonalcoholic steatohepatitis (NASH) ( n = 29) were compared with a control group without fatty liver disease on sonographic imaging ( n = 139). Patients were stratified based on gender, race, body mass index (BMI), and family history and adjusted for variables previously known to be associated with increased adenoma risk. Results: The mean age was 54.7 ± 6.0 years (48.5% women). Racial demographics were: 62.7% White, 18.5% Hispanic, 13.7%, African American, and 5.2% other. The mean BMI was 29.7 ± 5.8. The prevalence of colonic adenomas was 25.1% in the control group and 24.4% in the NAFLD group to include simple steatosis and NASH ( p = 1.00). Furthermore, when adjusting for known confounders to include race, BMI, and family history no significant differences were found ( p = 0.33). However, the ultrasound-negative patients ranked lower in the number of adenomas per person ( p = 0.016). Conclusions: There was no difference in the prevalence of colonic adenomas when comparing the NAFLD group who had undergone colonoscopy with a group of control patients without NAFLD who had undergone colonoscopy. However, patients with negative ultrasounds appeared to have a lower polyp burden.
Coexpression of Tim-3 and PD-1 identifies a CD8+ T-cell exhaustion phenotype in mice with disseminated acute myelogenous leukemia
Authors: Zhou Qing , Munger Meghan E. , Veenstra Rachelle G. , Weigel Brenda J. , Hirashima Mitsuomi , Munn David H. , Murphy William J. , Azuma Miyuki , Anderson Ana C. , Kuchroo Vijay K. , Blazar Bruce R. 
Published: March 2011

AbstractTumor-associated immune suppression can lead to defective T cell-mediated antitumor immunity. Here, we identified a unique phenotype of exhausted T cells in mice with advanced acute myelogenous leukemia (AML). This phenotype is characterized by the coexpression of Tim-3 and PD-1 on CD8+ T cells in the liver, the major first site of AML metastases. PD-1 and Tim-3 coexpression increased during AML progression. PD-1+Tim-3+ CD8+ T cells were deficient in their ability to produce IFN-γ, TNF-α, and IL-2 in response to PD-1 ligand (PDL1) and Tim-3 ligand (galectin-9) expressing AML cells. PD-1 knockout (KO), which were partially resistant to AML challenge, up-regulated Tim-3 during AML progression and such Tim-3+PD-1- KO CD8+ T cells had reduced cytokine production. Galectin-9 KO mice were more resistant to AML, which was associated with reduced T-regulatory cell accumulation and a modest induction of PD-1 and Tim-3 expression on CD8+ T cells. Whereas blocking the PD-1/PDL1 or Tim-3/galectin-9 pathway alone was insufficient to rescue mice from AML lethality, an additive effect was seen in reducing—albeit not eliminating—both tumor burden and lethality when both pathways were blocked. Therefore, combined PD-1/PDL1 and Tim-3/galectin-9 blockade may be beneficial in preventing CD8+ T-cell exhaustion in patients with hematologic malignancies such as advanced AML.
Metabolic reprogramming by HIF-1 promotes the survival of bone marrow–derived angiogenic cells in ischemic tissue
Authors: Rey Sergio , Luo Weibo , Shimoda Larissa A. , Semenza Gregg L. 
Published: March 2011

Abstract
A major obstacle to using bone marrow cell-based therapies for ischemic cardiovascular disease is that transplanted cells must survive in an ischemic microenvironment characterized by low oxygen, glucose, and pH. We demonstrate that treatment of bone marrow-derived angiogenic cells (BMDACs) with dimethyloxalylglycine, an α-ketoglutarate antagonist that induces hypoxia-inducible factor 1 (HIF-1) activity, results in metabolic reprogramming of these cells, with increased glucose uptake, decreased O2 consumption, increased lactate production, decreased reactive oxygen species, and increased intracellular pH. These effects are dependent on HIF-1, which transactivates target genes encoding metabolic enzymes and membrane transporters. Dimethyloxalylglycine-treated BMDACs have a significant survival advantage under conditions of low O2 and low pH ex vivo and in ischemic tissue. Combined HIF-1α-based gene and cell therapy reduced tissue necrosis even when BMDAC donors and ischemic recipient mice were 17 months old, suggesting that this approach may have therapeutic utility in elderly patients with critical limb ischemia.
Age-related EBV-associated lymphoproliferative disorders in the Western population: a spectrum of reactive lymphoid hyperplasia and lymphoma
Authors: Dojcinov Stefan D. , Venkataraman Girish , Pittaluga Stefania , Wlodarska Iwona , Schrager Jeffrey A. , Raffeld Mark , Hills Robert K. , Jaffe Elaine S. 
Published: March 2011

Abstract
We investigated age-related EBV+ B-cell lymphoproliferations in the Western population. The clinical features, histology, immunophenotype, EBV-encoded RNA in situ hybridization, and clonality by PCR of T-cell receptor gamma and immunoglobulin genes were categorized in 122 EBV+ lesions as follows: (1) reactive lymphoid hyperplasia; (2) polymorphic extranodal or (3) polymorphic nodal lymphoproliferative disease (LPD); and (4) diffuse large B-cell lymphoma (DLBCL). Interphase FISH for IG and PAX5 gene rearrangements was performed on 17 cases of DLBCL. The overall median age was 75 years (range, 45-101 years; 67 men, 55 women), and 67, 79, 73, and 77 years, respectively, for groups 1 through 4. Sixteen of 21 cases of polymorphic extranodal LPD were classified as EBV+ mucocutaneous ulcer. PCR for immunoglobulin genes was polyclonal in reactive lymphoid hyperplasia (84%) and monoclonal in 33%, 63%, and 56% of polymorphic extranodal and nodal LPD cases and DLBCL, respectively. All groups showed restricted/clonal T-cell receptor responses (27%-70%). By FISH, 19% of DLBCLs showed IGH@ rearrangements, but PAX5 was unaffected. Disease-specific 5-year survival was 100%, 93%, 57%, and 25% for groups 1-4, respectively, and 100% for patients with EBV+ mucocutaneous ulcer. Disease volume was predictive of therapy response (P = .0002), and pathologic subtype was predictive of overall outcome (P = .001). Age-related EBV+ B-cell LPD encompasses a wider disease spectrum than previously recognized and includes both reactive and neoplastic conditions. Reduction in the T-cell repertoire may contribute to decreased immune surveillance.
compomics-utilities: an open-source Java library for computational proteomics
Authors: Barsnes Harald , Vaudel Marc , Colaert Niklaas , Helsens Kenny , Sickmann Albert , Berven Frode S , Martens Lennart 
Published: March 2011

Abstract

Background
The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool.

Results
In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development.

Conclusions
As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics.