bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA)
Authors: Engel Annette Summers , Meisinger Daniela B , Porter Megan L , Payn Robert A , Schmid Michael , Stern Libby A , Schleifer K H , Lee Natuschka M 
Published: August 2009

Abstract
Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.
Robot‐assisted laparoscopic myomectomy; a feasible technique for removal of unfavorably localized myomas
Authors: LÖNNERFORS CELINE , PERSSON JAN 
Published: August 2009

AbstractObjective. To describe the feasibility of robot‐assisted laparoscopic myomectomy for unfavorably localized myomas using the da Vinci surgical system. Design. Prospective observational. Setting. University hospital. Method. Between April 2006 and March 2008, a robot‐assisted laparoscopic myomectomy was performed on 13 women selected for having deep intramural myomas with probable impact on fertility and/or later pregnancy. The alternative surgical approach for all 13 was myomectomy via laparotomy. A transvaginal ultrasonography (TVUS) mapping of the myomas was performed to enable an optimal approach during surgery. Using a prospective protocol, relevant times at the operating theater as well as postoperative and follow‐up data, were obtained. Results. Median time for surgery was 132 minutes (range 94–209 minutes). Median blood loss was 50 ml (range 25–200 ml). No significant complication occurred during or after surgery. Median postoperative hospital stay was one day (range 1–3 days). At follow‐up, including TVUS, no unexpected residual myomas larger than 5 mm were identified. Of eight women with an active wish for conception, six have become pregnant a median time of 15 months after surgery. All additional symptoms associated with the myomas were alleviated. Conclusion. Robot‐assisted laparoscopic myomectomy is a feasible technique for removal of deep intramural myomas unfavorably localized for traditional laparoscopy. The properties of the da Vinci robot facilitate dissection and suturing comprising the major surgical parts of myomectomy.
Severe physical violence among intimate partners: a risk factor for vaginal bleeding during gestation in less privileged women?
Authors: MORAES CLAUDIA LEITE , REICHENHEIM MICHAEL , NUNES ANTÔNIO PAULO 
Published: August 2009

AbstractObjectives. To evaluate the role of severe physical violence within intimate partners on the occurrence of vaginal bleeding during gestation in less privileged women. Design. Health service survey. Setting. Three large public maternities in the city of Rio de Janeiro, Brazil. Sample. Five hundred and twenty‐eight women who gave birth to full‐term newborn infants were selected at random among the births that took place during the six months of fieldwork. Methods. Information on vaginal bleeding during gestation was obtained from medical records, pre‐natal cards, and by means of a questionnaire addressed to the women giving birth. To collect severe physical violence data, use was made of the Portuguese version of the instrument Revised Conflict Tactics Scales, formally adapted for use in Brazil. Main outcome measures. Vaginal bleeding during gestation. Results. After accounting for socio‐economic, demographic, reproductive, and pregnant women's life‐style variables, women who had been victims of two or more acts of severe physical violence were 2.74 (95% CI: 1.37–5.48) times more liable to present with vaginal bleeding during pregnancy than those who did not. Conclusion. Our findings suggest that physical violence increases the risk of vaginal bleeding in pregnancy. This result should encourage studies on whether intervention in violent relationships can reduce the risk of vaginal bleeding and other pregnancy complications.
Effect of Treatment on Weight Gain and Metabolic Abnormalities in Patients with First-Episode Psychosis
Authors: Verma Swapna , Liew Alvin , Subramaniam Mythily , Poon Lye Yin 
Published: August 2009

Objective: The aim of the present prospective and naturalistic study was to examine the effects of antipsychotic medication on weight and serum levels of lipids, glucose and insulin in first-episode psychosis patients. Method: Fifty-six patients admitted to the Singapore Early Psychosis Intervention Programme participated in this study. They were assessed at baseline (i.e. within 72 h of starting antipsychotics), and 6 months later. Weight (kg) and height (m) were measured and body mass index (BMI) was calculated. Blood samples were taken after a 12 h overnight fast. Choice of antipsychotics was based on the treating physician's clinical decision. Total cumulative Chlorpromazine (CPZ) equivalent of antipsychotic exposure during the 6 months was calculated. Statistical analyses were carried out for comparisons between baseline and 6 months, and for the two outcome event groups of ≥7% versus <7% weight gain. Where appropriate, confounders were controlled. Results and conclusion: There were significant increases in BMI, serum levels of triglyceride, low-density lipoprotein and total cholesterol from baseline to 6 months. Mean increase in weight was 6.2±7.0 kg (p < 0.05) and 65% of the patients had clinically significant weight gain (i.e. ≥7% increase from baseline). On logistic regression lower baseline BMI, female gender, and younger age, were associated with clinically significant weight gain.
Improving efficiency and robustness of the doubly robust estimator for a population mean with incomplete data
Authors: Cao Weihua , Tsiatis Anastasios A. , Davidian Marie 
Published: August 2009

Abstract
Considerable recent interest has focused on doubly robust estimators for a population mean response in the presence of incomplete data, which involve models for both the propensity score and the regression of outcome on covariates. The usual doubly robust estimator may yield severely biased inferences if neither of these models is correctly specified and can exhibit nonnegligible bias if the estimated propensity score is close to zero for some observations. We propose alternative doubly robust estimators that achieve comparable or improved performance relative to existing methods, even with some estimated propensity scores close to zero.
Parading as Millionaires: Montana Bankers and the Panic of 1893
Authors: Petrik Paula 
Published: August 2009

One day two swindlers came to this city; they made people believe that they were weavers, and declared they could manufacture the finest cloth to be imaginedHistorians, in general, and historians of the trans-Mississippi West, in particular, have paid scant attention to the Panic of 1893 except to summarize its highlights: the silver-mining industry collapsed; banks and businesses failed; unemployment increased; labor rebelled—sometimes violently; and the Populists gained political ground. Some historians of the American West have given the panic a miss entirely
Prediction of benthic biotopes on a Norwegian offshore bank using a combination of multivariate analysis and GIS classification
Authors: Buhl-Mortensen Pål , Dolan Margaret , Buhl-Mortensen Lene 
Published: August 2009

Abstract
Mortensen, P. B., Dolan, M., and Buhl-Mortensen, L. 2009. Prediction of benthic biotopes on a Norwegian offshore bank using a combination of multivariate analysis and GIS classification. – ICES Journal of Marine Science, 66: 2026–2032. This study is part of the multidisciplinary seabed mapping programme MAREANO (Marine AREAdatabase for NOrwegian coast and sea areas). The mapping programme includes acquisition of multibeam bathymetry and acoustic backscatter data together with a comprehensive, integrated biological and geological sampling programme. The equipment used includes underwater video, boxcorer, grab, hyperbenthic sled, and beam trawl. The Tromsøflaket offshore bank was used as a case-study area to develop suitable methods for mapping habitats and biotopes. A procedure for producing maps of predicted biotopes is described that combined information on the distribution of biological communities with environmental factors and indicators. Detrended correspondence analysis (DCA) was used to relate bottom environment [including multiscale physical descriptors of the seabed derived from multibeam echosounder (MBES) data] and faunal distribution to find the best physical biotope descriptors. DCA of 252 video samples (sequences 200 m long) revealed six groups of locations representing different biotopes. These were characterized by different compositions of species, substrata, depths, and values for terrain parameters. Prediction of biotope distribution was performed using a supervised GIS classification with the MBES-derived physical seabed descriptors with the strongest explanatory ability (depth, backscatter, and broad-scale bathymetric position index) identified by the DCA. The species diversity of the identified biotopes was described from the content of the bottom samples. For future MAREANO cruises, an important task will be to ground-truth predictions of habitat and biotopes and to test the reliability of these predictions in the wider MAREANO area.
The fishery for whiteweed, Sertularia cupressina (Cnidaria, Hydrozoa), in the Wadden Sea, Germany: history and anthropogenic effects
Authors: Wagler H. , Berghahn R. , Vorberg R. 
Published: August 2009

Abstract
Wagler, H., Berghahn, R., and Vorberg, R. 2009. The fishery for whiteweed, Sertularia cupressina (Cnidaria, Hydrozoa), in the Wadden Sea, Germany: history and anthropogenic effects. – ICES Journal of Marine Science, 66: 2116–2120. The whiteweed fishery in the German Wadden Sea did not close as a consequence of the loss of whiteweed beds, but rather because of declining markets. To this day, neither the assumed disappearance of whiteweed beds nor the assumed decrease in whiteweed abundance has been substantiated. Even if such a decrease were to be demonstrated, the causes for the decline would more likely have been eutrophication and anthropogenic changes in the hydrodynamics of the Wadden Sea than the activities of the shrimp and mussel fisheries or the former whiteweed fishery.
Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize
Authors: Kronmiller Brent A. , Wise Roger P. 
Published: August 2009

Abstract
The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961- and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.
Plastidial Glyceraldehyde-3-Phosphate Dehydrogenase Deficiency Leads to Altered Root Development and Affects the Sugar and Amino Acid Balance in Arabidopsis
Authors: Muñoz-Bertomeu Jesús , Cascales-Miñana Borja , Mulet Jose Miguel , Baroja-Fernández Edurne , Pozueta-Romero Javier , Kuhn Josef M. , Segura Juan , Ros Roc 
Published: August 2009

AbstractGlycolysis is a central metabolic pathway that, in plants, occurs in both the cytosol and the plastids. The glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate with concomitant reduction of NAD+ to NADH. Both cytosolic (GAPCs) and plastidial (GAPCps) GAPDH activities have been described. However, the in vivo functions of the plastidial isoforms remain unresolved. In this work, we have identified two Arabidopsis (Arabidopsis thaliana) chloroplast/plastid-localized GAPDH isoforms (GAPCp1 and GAPCp2). gapcp double mutants display a drastic phenotype of arrested root development, dwarfism, and sterility. In spite of their low gene expression level as compared with other GAPDHs, GAPCp down-regulation leads to altered gene expression and to drastic changes in the sugar and amino acid balance of the plant. We demonstrate that GAPCps are important for the synthesis of serine in roots. Serine supplementation to the growth medium rescues root developmental arrest and restores normal levels of carbohydrates and sugar biosynthetic activities in gapcp double mutants. We provide evidence that the phosphorylated pathway of Ser biosynthesis plays an important role in supplying serine to roots. Overall, these studies provide insights into the in vivo functions of the GAPCps in plants. Our results emphasize the importance of the plastidial glycolytic pathway, and specifically of GAPCps, in plant primary metabolism.
Rapid Screening for Temperature-Sensitive Alleles in Plants
Authors: Vidali Luis , Augustine Robert C. , Fay Scotty N. , Franco Paula , Pattavina Kelli A. , Bezanilla Magdalena 
Published: August 2009

Abstract
We developed a simple and fast method to identify temperature-sensitive alleles of essential plant genes. We used primary and tertiary structure information to identify residues in the core of the protein of interest. These residues were mutated and tested for temperature sensitivity, taking advantage of the exceptionally rapid 1-week complementation assay in the moss Physcomitrella patens. As test molecules, we selected the actin-binding proteins profilin and actin-depolymerizing factor, because they are essential and their loss-of-function phenotype can be fully rescued. Screening a small number of candidate mutants, we successfully identified temperature-sensitive alleles of both profilin and actin-depolymerizing factor. Plants harboring these alleles grew well at the permissive temperature of 20°C to 25°C but showed a complete loss of function at the restrictive temperature of 32°C. Notably, the profilin mutation identified in the moss gene can be transferred to profilins from other plant species, also rendering them temperature sensitive. The ability to routinely generate temperature-sensitive alleles of essential plant proteins provides a powerful tool for the study of gene function in plants.
Starch Granule Initiation inArabidopsisRequires the Presence of Either Class IV or Class III Starch Synthases
Authors: Szydlowski Nicolas , Ragel Paula , Raynaud Sandy , Lucas M. Mercedes , Roldán Isaac , Montero Manuel , Muñoz Francisco José , Ovecka Miroslav , Bahaji Abdellatif , Planchot Véronique , Pozueta-Romero Javier , D'Hulst Christophe , Mérida Ángel 
Published: August 2009

AbstractThe mechanisms underlying starch granule initiation remain unknown. We have recently reported that mutation of soluble starch synthase IV (SSIV) in Arabidopsis thaliana results in restriction of the number of starch granules to a single, large, particle per plastid, thereby defining an important component of the starch priming machinery. In this work, we provide further evidence for the function of SSIV in the priming process of starch granule formation and show that SSIV is necessary and sufficient to establish the correct number of starch granules observed in wild-type chloroplasts. The role of SSIV in granule seeding can be replaced, in part, by the phylogenetically related SSIII. Indeed, the simultaneous elimination of both proteins prevents Arabidopsis from synthesizing starch, thus demonstrating that other starch synthases cannot support starch synthesis despite remaining enzymatically active. Herein, we describe the substrate specificity and kinetic properties of SSIV and its subchloroplastic localization in specific regions associated with the edges of starch granules. The data presented in this work point to a complex mechanism for starch granule formation and to the different abilities of SSIV and SSIII to support this process in Arabidopsis leaves.
Abscisic Acid Represses Growth of theArabidopsisEmbryonic Axis after Germination by Enhancing Auxin Signaling
Authors: Belin Christophe , Megies Christian , Hauserová Eva , Lopez-Molina Luis 
Published: August 2009

AbstractUnder unfavorable environmental conditions, the stress phytohormone ABA inhibits the developmental transition from an embryo in a dry seed into a young seedling. We developed a genetic screen to isolate Arabidopsis thaliana mutants whose early seedling development is resistant to ABA. Here, we report the identification of a recessive mutation in AUXIN RESISTANT1 (AUX1), encoding a cellular auxin influx carrier. Although auxin is a major morphogenesis hormone in plants, little is known about ABA–auxin interactions during early seedling growth. We show that aux1 and pin2 mutants are insensitive to ABA-dependent repression of embryonic axis (hypocotyl and radicle) elongation. Genetic and physiological experiments show that this involves auxin transport to the embryonic axis elongation zone, where ABA enhances the activity of an auxin-responsive promoter. We propose that ABA represses embryonic axis elongation by potentiating auxin signaling in its elongation zone. This involves repression of the AUXIN INDUCIBLE (Aux/IAA) gene AXR2/IAA7, encoding a key component of ABA- and auxin-dependent responses during postgerminative growth.
SUMO E3 Ligase HIGH PLOIDY2 Regulates Endocycle Onset and Meristem Maintenance inArabidopsis
Authors: Ishida Takashi , Fujiwara Sumire , Miura Kenji , Stacey Nicola , Yoshimura Mika , Schneider Katja , Adachi Sumiko , Minamisawa Kazunori , Umeda Masaaki , Sugimoto Keiko 
Published: August 2009

AbstractEndoreduplication involves a doubling of chromosomal DNA without corresponding cell division. In plants, many cell types transit from the mitotic cycle to the endoreduplication cycle or endocycle, and this transition is often coupled with the initiation of cell expansion and differentiation. Although a number of cell cycle regulators implicated in endocycle onset have been identified, it is still largely unknown how this transition is developmentally regulated at the whole organ level. Here, we report that a nuclear-localized SUMO E3 ligase, HIGH PLOIDY2 (HPY2), functions as a repressor of endocycle onset in Arabidopsis thaliana meristems. Loss of HPY2 results in a premature transition from the mitotic cycle to the endocycle, leading to severe dwarfism with defective meristems. HPY2 possesses an SP-RING domain characteristic of MMS21-type SUMO E3 ligases, and we show that the conserved residues within this domain are required for the in vivo and in vitro function of HPY2. HPY2 is predominantly expressed in proliferating cells of root meristems and it functions downstream of meristem patterning transcription factors PLETHORA1 (PLT1) and PLT2. These results establish that HPY2-mediated sumoylation modulates the cell cycle progression and meristem development in the PLT-dependent signaling pathway.
Milankovitch and sub‐Milankovitch forcing of the Oxfordian (Late Jurassic) Terres Noires Formation (SE France) and global implications
Authors: Boulila S. , Galbrun B. , Hinnov L. A. , Collin P.‐Y. , Ogg J. G. , Fortwengler D. , Marchand D. 
Published: August 2009

ABSTRACTHigh‐resolution analysis (2277 samples) of magnetic susceptibility (MS) was performed on ∼700‐m‐thick Early–Middle Oxfordian marine marls of the Terres Noires Formation, SE France. MS variations within these sediments record sub‐Milankovitch to Milankovitch frequencies with long‐term eccentricity (405 kyr and ∼2 Myr) being the most prominent. The 405 kyr cycle was used as a high‐resolution geochronometer for astronomical calibration of this poorly constrained interval of Late Jurassic time. The estimated duration of this Early–Middle Oxfordian interval concurs with the current International Geologic Time Scale GTS2004 (∼4 Myr), but the estimated durations of the corresponding ammonite zones are notably different. The calibration improves the resolution and accuracy of the M‐sequence magnetic anomaly block model that was previously used to establish the Oxfordian time scale. Additionally, the 405 kyr cyclicity is linked to third‐order sea‐level depositional sequences observed for Early–Middle Oxfordian time. Strong ∼2 Myr cycles are consistent with long‐term eccentricity modulation predicted for the Late Jurassic. These cycles do not match second‐order sequences that have been documented for European basins; this raises questions about the definition and hierarchy of depositional sequences in the Mesozoic eustatic chart. Our results require substantial revisions to the chart, which is frequently used as a reference for the correlation of widely separated palaeogeographic domains. Finally, a long‐term trend in the MS data reflects a progressive carbonate enrichment of the marls expressing an Early Oxfordian global cooling followed gradually by a warming in the Middle Oxfordian. This trend also records a major transgressive interval likely peaking at the Transversarium ammonite zone of the Middle Oxfordian.