bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Detection of Climate Change and Observing Biases in a Network with Incomplete Sampling
Authors: Sherwood Steven C. 
Published: August 2007

AbstractAll instrumental climate records are affected by instrumentation changes and variations in sampling over time. While much attention has been paid to the problem of detecting “change points” in time series, little has been paid to the statistical properties of climate signals that result after adjusting (“homogenizing”) the data—or to the effects of the irregular sampling and serial correlation exhibited by real climate records. These issues were examined here by simulating multistation datasets. Simple homogenization methods, which remove apparent artifacts and then calculate trends, tended to remove some of the real signal. That problem became severe when change-point times were not known a priori, leading to significant underestimation of real and/or artificial trends. A key cause is false detection of change points, even with nominally strict significance testing, due to serial correlation in the data. One conclusion is that trends in previously homogenized radiosonde datasets should be viewed with caution.Two-phase regression reduced but did not resolve this problem. A new approach is proposed in which trends, change points, and natural variability are estimated simultaneously. This is accomplished here for the case of incomplete data from a fixed station network by an adaptation of the “iterative universal Kriging” method, which converges to maximum-likelihood parameters by iterative imputation of missing values. With careful implementation this method’s trend estimates had low random errors and were nearly unbiased in these tests. It is argued that error-free detection of change points is neither realistic nor necessary, and that success should be measured instead by the integrity of climate signals.
Midsummer Gap Winds and Low-Level Circulation over the Eastern Tropical Pacific
Authors: Romero-Centeno Rosario , Zavala-Hidalgo Jorge , Raga G. B. 
Published: August 2007

AbstractThe low-level seasonal and intraseasonal wind variability over the northeastern tropical Pacific (NETP), its relationship with other variables, and the connection with large- and middle-scale atmospheric patterns are analyzed using a suite of datasets. Quick Scatterometer (QuikSCAT) wind data show that the low-level circulation over the NETP is mainly affected by the northerly trades, the southerly trades, and the wind jets crossing through the Tehuantepec, Papagayo, and Panama mountain gaps. The seasonal and intraseasonal evolution of these wind systems determines the circulation patterns over the NETP, showing predominant easterly winds in winter and early spring and wind direction reversals in summer over the central region of the NETP. During summer, when southerly trades are the strongest and reach their maximum northward penetration, weak westerlies are observed in June, easterlies in July–August, despite that strong southerlies tend to turn eastward, and again westerlies in September–October. This circulation pattern appears to be related to the Tehuantepec and Papagayo jets, which slightly strengthen during midsummer favored by the westward elongation and intensification of the Azores–Bermuda high (ABH). This ABH evolution induces an across-gap pressure gradient over the Isthmus of Tehuantepec favoring the generation of the jet and a meridional sea level pressure (SLP) gradient in the western Caribbean that favors the funneling of the trade winds through the Papagayo gap. The SLP pattern causing the gap winds in winter is different than in midsummer, being the southeastward intrusion of high pressure systems coming from the northwest, the main cause of the large meridional SLP gradients in Tehuantepec and the western Caribbean.The westward low-level circulation observed over the central-eastern region of the NETP during midsummer induces westward moisture fluxes in the lower layers of the atmosphere, displaces convergence areas away from the coasts, and confines the relatively strong convergence in the easternmost NETP to the south of the area of influence of the wind jets and associated easterlies, contributing to the development of the midsummer drought observed in southern Mexico and Central America.
Climate and Vegetation in the Middle East: Interannual Variability and Drought Feedbacks
Authors: Zaitchik Benjamin F. , Evans Jason P. , Geerken Roland A. , Smith Ronald B. 
Published: August 2007

Abstract
The Euphrates Plain (EP) experiences large interannual variability in vegetation cover, especially in areas of marginal rain-fed agriculture. Vegetation in this region is primarily limited by available soil moisture, as determined by winter precipitation, spring precipitation, and air temperature. Satellite analyses indicate that the springtime normalized difference vegetation index (NDVI) is negatively correlated with surface albedo, and that interannual variability in albedo in the EP produces an estimated forcing on the radiation balance that peaks at 16.0 W m−2 in May.
Simulations with a regional climate model indicate that surface energy fluxes during a drought year (1999) differed substantially from those during a year with normal precipitation (2003). These differences were geographically specific, with the EP exhibiting increased albedo and decreased sensible heat flux while the neighboring Zagros Plateau region showed no albedo effect, a large increase in sensible heat flux, and an offsetting reduction in latent heat flux. In both the EP and the Zagros there was a potential for positive feedbacks on temperature and drought in late spring, though the most likely feedback mechanisms differed between the two regions: in the EP surface brightening leads to cooling and reduced turbulent heat flux, while in the Zagros region reduced latent heat flux leads to warming and a deepening of the planetary boundary layer.
Coupling of Vegetation Growing Season Anomalies and Fire Activity with Hemispheric and Regional-Scale Climate Patterns in Central and East Siberia
Authors: Balzter Heiko , Gerard France , George Charles , Weedon Graham , Grey Will , Combal Bruno , Bartholomé Etienne , Bartalev Sergey , Los Sietse 
Published: August 2007

Abstract
An 18-yr time series of the fraction of absorbed photosynthetically active radiation (fAPAR) taken in by the green parts of vegetation data from the NOAA Advanced Very High Resolution Radiometer (AVHRR) instrument series was analyzed for interannual variations in the start, peak, end, and length of the season of vegetation photosynthetic activity in central and east Siberia. Variations in these indicators of seasonality can give important information on interactions between the biosphere and atmosphere. A second-order local moving window regression model called the “camelback method” was developed to determine the dates of phenological events at subcontinental scale. The algorithm was validated by comparing the estimated dates to phenological field observations. Using spatial correlations with temperature and precipitation data and climatic oscillation indices, two geographically distinct mechanisms in the system of climatic controls of the biosphere in Siberia are postulated: central Siberia is controlled by an “Arctic Oscillation–temperature mechanism,” while east Siberia is controlled by an “El Niño–precipitation mechanism.” While the analysis of data from 1982 to 1991 indicates a slight increase in the length of the growing season for some land-cover types due to an earlier beginning of the growing season, the overall trend from 1982 to 1999 is toward a slightly shorter season for some land-cover types caused by an earlier end of season. The Arctic Oscillation tended toward a more positive phase in the 1980s leading to enhanced high pressure system prevalence but toward a less positive phase in the 1990s. The results suggest that the two mechanisms also control the fire regimes in central and east Siberia. Several extreme fire years in central Siberia were associated with a highly positive Arctic Oscillation phase, while several years with high fire damage in east Siberia occurred in El Niño years. An analysis of remote sensing data of forest fire partially supports this hypothesis.
Tropical Rainfall Variability on Interannual-to-Interdecadal and Longer Time Scales Derived from the GPCP Monthly Product
Authors: Gu Guojun , Adler Robert F. , Huffman George J. , Curtis Scott 
Published: August 2007

Abstract
Global and large regional rainfall variations and possible long-term changes are examined using the 27-yr (1979–2005) Global Precipitation Climatology Project (GPCP) monthly dataset. Emphasis is placed on discriminating among variations due to ENSO, volcanic events, and possible long-term climate changes in the Tropics. Although the global linear change of precipitation in the dataset is near zero during the time period, an increase in tropical rainfall is noted in the dataset, with a weaker decrease over Northern Hemisphere middle latitudes. Focusing on the Tropics (25°S–25°N), the dataset indicates an upward linear change (0.06 mm day−1 decade−1) and a downward linear change (−0.01 mm day−1 decade−1) over tropical ocean and land, respectively. This corresponds to an about 5.5% increase (ocean) and 1% decrease (land) during the entire 27-yr time period. The year 2005 has the largest annual tropical total precipitation (land plus ocean) for the GPCP record. The five highest years are (in descending order) 2005, 2004, 1998, 2003, and 2002. For tropical ocean the five highest years are 1998, 2004, 2005, 2002, and 2003.
Techniques are applied to isolate and quantify variations due to ENSO and two major volcanic eruptions during the time period (El Chichón, March 1982; Mount Pinatubo, June 1991) in order to examine longer-time-scale changes. The ENSO events generally do not impact the tropical total rainfall, but rather induce significant anomalies with opposite signs over tropical land and ocean. The impact of the two volcanic eruptions is estimated to be about a 5% reduction in tropical rainfall over both land and ocean. A modified dataset (with ENSO and volcano effects removed) retains the same approximate linear change slopes, but with reduced variances, thereby increasing the statistical significance levels associated with the long-term rainfall changes in the Tropics. However, although care has been taken to ensure that this dataset is as homogeneous as possible, firm establishment of the existence of the discussed changes as long-term trends may require continued analysis of the input datasets and a lengthening of the observation period.
Statistical Tropical Cyclone Wind Radii Prediction Using Climatology and Persistence
Authors: Knaff John A. , Sampson Charles R. , DeMaria Mark , Marchok Timothy P. , Gross James M. , McAdie Colin J. 
Published: August 2007

Abstract
An operational model used to predict tropical cyclone wind structure in terms of significant wind radii (i.e., 34-, 50-, and 64-kt wind radii, where 1 kt = 0.52 m s−1) at the National Oceanic and Atmospheric Administration/National Hurricane Center (NHC) and the Department of Defense/Joint Typhoon Warning Center (JTWC) is described. The statistical-parametric model employs aspects of climatology and persistence to forecast tropical cyclone wind radii through 5 days. Separate versions of the model are created for the Atlantic, east Pacific, and western North Pacific by statistically fitting a modified Rankine vortex, which is generalized to allow wavenumber-1 asymmetries, to observed values of tropical cyclone wind radii as reported by NHC and JTWC. Descriptions of the developmental data and methods used to formulate the model are given. A 2-yr verification and comparison with operational forecasts and an independently developed wind radii forecast method that also employs climatology and persistence suggests that the statistical-parametric model does a good job of forecasting wind radii. The statistical-parametric model also provides reliable operational forecasts that serve as a baseline for evaluating the skill of operational forecasts and other wind radii forecast methods in these tropical cyclone basins.
Une ontologie réaliste pour la sociologie: système, morphogenèse et collectifs
Authors: Vandenberghe Frédéric 
Published: August 2007

English After presenting French readers with the main ideas of Roy Bhaskar's critical realism and of Margaret Archer's morphogenetic theory, the article sets out a complex and stratified ontology for sociology that makes it possible to displace, if not surpass, the former opposition between individualism and collectivism, while avoiding the twin stumbling blocks of reification and reduction. The article next introduces collective actors into society and thus develops a realistic dialectical analysis of collective subjectivity. Symbolic identification, socio-technical mediation and political representation are identified as three stages of group structuration, which gradually transform categories into structured, mobilisable groups capable of action. French Tout en présentant les lignes de force du réalisme critique de Roy Bhaskar et de la théorie morphogénétique de Margaret Archer aux lecteurs francophones, l’article propose une ontologie complexe et stratifiée pour la sociologie qui permet de déplacer, si ce n’est de dépasser, l’ancienne opposition entre l’individualisme et le collectivisme en évitant le double écueil de la réification et de la réduction. En introduisant, ensuite, les acteurs collectifs dans la société, l’article développe une analyse réaliste et dialectique des subjectivités collectives. L’identification symbolique, la médiation sociotechnique et la représentation politique sont identifiées comme trois moments de la structuration des collectifs qui transforment progressivement les catégories en groupes structurés, mobilisables et capables d’action.
Friend retrovirus infection of myeloid dendritic cells impairs maturation, prolongs contact to naïve T cells, and favors expansion of regulatory T cells
Authors: Balkow Sandra , Krux Frank , Loser Karin , Becker Jan U. , Grabbe Stephan , Dittmer Ulf 
Published: August 2007

AbstractRetroviruses have developed immunmodulatory mechanisms to avoid being attacked by the immune system. The mechanisms of this retrovirus-associated immune suppression are far from clarified. Dendritic cells (DCs) have been attributed a decisive role in these pathogenic processes. We have used the Friend retrovirus (FV) mouse model in order to acquire further knowledge about the role of infection of DCs in virus-induced immunosuppression. About 20% of the myeloid DCs that were generated from the bone marrow of FV-infected mice carried FV proteins. The infection was productive, and infected DCs transmitted the virus in cell culture and in vivo. FV infection of DCs led to a defect in DC maturation, as infected cells expressed very little costimulatory molecules. Live imaging analysis of the cell contact between DCs and T cells revealed prolonged contacts of T cells with infected DCs compared with uninfected DCs. Although naive T cells were still activated by FV-infected DCs, this activation did not result in antigen-specific T-cell proliferation. Interestingly, infected DCs expanded a population of Foxp3+ regulatory T cells with immunosuppressive potential, suggesting that the contact between naive T cells and retrovirus-infected DCs results in tolerance rather than immunity. Thus, retroviral infection of DCs leads to an expansion of regulatory T cells, which might serve as an immune escape mechanism of the virus.
The transcriptional coactivator Maml1 is required for Notch2-mediated marginal zone B-cell development
Authors: Wu Lizi , Maillard Ivan , Nakamura Makoto , Pear Warren S. , Griffin James D. 
Published: August 2007

Abstract
Signaling mediated by various Notch receptors and their ligands regulates diverse biological processes, including lymphoid cell fate decisions. Notch1 is required during T-cell development, while Notch2 and the Notch ligand Delta-like1 control marginal zone B (MZB) cell development. We previously determined that Mastermind-like (MAML) transcriptional coactivators are required for Notchinduced transcription by forming ternary nuclear complexes with Notch and the transcription factor CSL. The 3 MAML family members (MAML1-MAML3) are collectively essential for Notch activity in vivo, but whether individual MAMLs contribute to the specificity of Notch functions is unknown. Here, we addressed this question by studying lymphopoiesis in the absence of the Maml1 gene. Since Maml1−/− mice suffered perinatal lethality, hematopoietic chimeras were generated with Maml1−/−, Maml1+/−, or wild-type fetal liver progenitors. Maml1 deficiency minimally affected T-cell development, but was required for the development of MZB cells, similar to the phenotype of Notch2 deficiency. Moreover, the number of MZB cells correlated with Maml1 gene dosage. Since all 3 Maml genes were expressed in MZB cells and their precursors, these results suggest that Maml1 is specifically required for Notch2 signaling in MZB cells.
Thiamine diphosphate adenylyl transferase from E. coli: functional characterization of the enzyme synthesizing adenosine thiamine triphosphate
Authors: Makarchikov Alexander F , Brans Alain , Bettendorff Lucien 
Published: August 2007

Abstract

Background
We have recently identified a new thiamine derivative, adenosine thiamine triphosphate (AThTP), in E. coli. In intact bacteria, this nucleotide is synthesized only in the absence of a metabolizable carbon source and quickly disappears as soon as the cells receive a carbon source such as glucose. Thus, we hypothesized that AThTP may be a signal produced in response to carbon starvation.

Results
Here we show that, in bacterial extracts, the biosynthesis of AThTP is carried out from thiamine diphosphate (ThDP) and ADP or ATP by a soluble high molecular mass nucleotidyl transferase. We partially purified this enzyme and characterized some of its functional properties. The enzyme activity had an absolute requirement for divalent metal ions, such as Mn2+ or Mg2+, as well as for a heat-stable soluble activator present in bacterial extracts. The enzyme has a pH optimum of 6.5–7.0 and a high K
m for ThDP (5 mM), suggesting that, in vivo, the rate of AThTP synthesis is proportional to the free ThDP concentration. When ADP was used as the variable substrate at a fixed ThDP concentration, a sigmoid curve was obtained, with a Hill coefficient of 2.1 and an S
0.5 value of 0.08 mM. The specificity of the AThTP synthesizing enzyme with respect to nucleotide substrate is restricted to ATP/ADP, and only ThDP can serve as the second substrate of the reaction. We tentatively named this enzyme ThDP adenylyl transferase (EC 2.7.7.65).

Conclusion
This is the first demonstration of an enzyme activity transferring a nucleotidyl group on thiamine diphosphate to produce AThTP. The existence of a mechanism for the enzymatic synthesis of this compound is in agreement with the hypothesis of a non-cofactor role for thiamine derivatives in living cells.
Regionalisation of the mouse visceral endoderm as the blastocyst transforms into the egg cylinder
Authors: Perea-Gomez Aitana , Meilhac Sigolène M , Piotrowska-Nitsche Karolina , Gray Dionne , Collignon Jérôme , Zernicka-Goetz Magdalena 
Published: August 2007

Abstract

Background
Reciprocal interactions between two extra-embryonic tissues, the extra-embryonic ectoderm and the visceral endoderm, and the pluripotent epiblast, are required for the establishment of anterior-posterior polarity in the mouse. After implantation, two visceral endoderm cell types can be distinguished, in the embryonic and extra-embryonic regions of the egg cylinder. In the embryonic region, the specification of the anterior visceral endoderm (AVE) is central to the process of anterior-posterior patterning. Despite recent advances in our understanding of the molecular interactions underlying the differentiation of the visceral endoderm, little is known about how cells colonise the three regions of the tissue.

Results
As a first step, we performed morphological observations to understand how the extra-embryonic region of the egg cylinder forms from the blastocyst. Our analysis suggests a new model for the formation of this region involving cell rearrangements such as folding of the extra-embryonic ectoderm at the early egg cylinder stage. To trace visceral endoderm cells, we microinjected mRNAs encoding fluorescent proteins into single surface cells of the inner cell mass of the blastocyst and analysed the distribution of labelled cells at E5.0, E5.5 and E6.5. We found that at E5.0 the embryonic and extra-embryonic regions of the visceral endoderm do not correspond to distinct cellular compartments. Clusters of labelled cells may span the junction between the two regions even after the appearance of histological and molecular differences at E5.5. We show that in the embryonic region cell dispersion increases after the migration of the AVE. At this time, visceral endoderm cell clusters tend to become oriented parallel to the junction between the embryonic and extra-embryonic regions. Finally we investigated the origin of the AVE and demonstrated that this anterior signalling centre arises from more than a single precursor between E3.5 and E5.5.

Conclusion
We propose a new model for the formation of the extra-embryonic region of the egg cylinder involving a folding of the extra-embryonic ectoderm. Our analyses of the pattern of labelled visceral endoderm cells indicate that distinct cell behaviour in the embryonic and extra-embryonic regions is most apparent upon AVE migration. We also demonstrate the polyclonal origin of the AVE. Taken together, these studies lead to further insights into the formation of the extra-embryonic tissues as they first develop after implantation.
Modeling HIV quasispecies evolutionary dynamics
Authors: Sguanci Luca , Bagnoli Franco , Liò Pietro 
Published: August 2007

Abstract

Background
During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been correlated with a faster progression of the disease to the AIDS phase. As several pharmaceutical companies are starting large phase III trials for R5 and X4 drugs, models are needed to predict the co-evolutionary and competitive dynamics of virus strains.

Results
We present a model of HIV early infection which describes the dynamics of R5 quasispecies and a model of HIV late infection which describes the R5 to X4 switch. We report the following findings: after superinfection (multiple infections at different times) or coinfection (simultaneous infection by different strains), quasispecies dynamics has time scales of several months and becomes even slower at low number of CD4+ T cells. Phylogenetic inference of chemokine receptors suggests that viral mutational pathway may generate a large variety of R5 variants able to interact with chemokine receptors different from CXCR4. The decrease of CD4+ T cells, during AIDS late stage, can be described taking into account the X4-related Tumor Necrosis Factor dynamics.

Conclusion
The results of this study bridge the gap between the within-patient and the inter-patients (i.e. world-wide) evolutionary processes during HIV infection and may represent a framework relevant for modeling vaccination and therapy.