bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss to follow‐up before and after delivery among women testing HIV positive during pregnancy in Johannesburg, South Africa
Authors: Clouse Kate , Pettifor Audrey , Shearer Kate , Maskew Mhairi , Bassett Jean , Larson Bruce , Van Rie Annelies , Sanne Ian , Fox Matthew P. 
Published: February 2013

AbstractObjectiveHIV‐positive pregnant women are at heightened risk of becoming lost to follow‐up (LTFU) from HIV care. We examined LTFU before and after delivery among pregnant women newly diagnosed with HIV.MethodsObservational cohort study of all pregnant women ≥18 years (N = 300) testing HIV positive for the first time at their first ANC visit between January and June 2010, at a primary healthcare clinic in Johannesburg, South Africa. Women (n = 27) whose delivery date could not be determined were excluded.ResultsMedian (IQR) gestation at HIV testing was 26 weeks (21–30). Ninety‐eight per cent received AZT prophylaxis, usually started at the first ANC visit. Of 139 (51.3%) patients who were ART eligible, 66.9% (95% CI 58.8–74.3%) initiated ART prior to delivery; median (IQR) ART duration pre‐delivery was 9.5 weeks (5.1–14.2). Among ART‐eligible patients, 40.5% (32.3–49.0%) were cumulatively retained through 6 months on ART. Of those ART‐ineligible patients at HIV testing, only 22.6% (95% CI 15.9–30.6%) completed CD4 staging and returned for a repeat CD4 test after delivery. LTFU (≥1 month late for last scheduled visit) before delivery was 20.5% (95% CI 16.0–25.6%) and, among those still in care, 47.9% (95% CI 41.2–54.6%) within 6 months after delivery. Overall, 57.5% (95% CI 51.6–63.3%) were lost between HIV testing and 6 months post‐delivery.ConclusionsOur findings highlight the challenge of continuity of care among HIV‐positive pregnant women attending antenatal services, particularly those ineligible for ART.
Microtubules in viral replication and transport
Authors: Niehl Annette , Peña Eduardo J. , Amari Khalid , Heinlein Manfred 
Published: February 2013

SummaryViruses use and subvert host cell mechanisms to support their replication and spread between cells, tissues and organisms. Microtubules and associated motor proteins play important roles in these processes in animal systems, and may also play a role in plants. Although transport processes in plants are mostly actin based, studies, in particular with Tobacco mosaic virus (TMV) and its movement protein (MP), indicate direct or indirect roles of microtubules in the cell‐to‐cell spread of infection. Detailed observations suggest that microtubules participate in the cortical anchorage of viral replication complexes, in guiding their trafficking along the endoplasmic reticulum (ER)/actin network, and also in developing the complexes into virus factories. Microtubules also play a role in the plant‐to‐plant transmission of Cauliflower mosaic virus (CaMV) by assisting in the development of specific virus‐induced inclusions that facilitate viral uptake by aphids. The involvement of microtubules in the formation of virus factories and of other virus‐induced inclusions suggests the existence of aggresomal pathways by which plant cells recruit membranes and proteins into localized macromolecular assemblies. Although studies related to the involvement of microtubules in the interaction of viruses with plants focus on specific virus models, a number of observations with other virus species suggest that microtubules may have a widespread role in viral pathogenesis.
ABA inhibits entry into stomatal‐lineage development in Arabidopsis leaves
Authors: Tanaka Yoko , Nose Tomoe , Jikumaru Yusuke , Kamiya Yuji 
Published: February 2013

SummaryThe number and density of stomata are controlled by endogenous and environmental factors. Despite recent advances in our understanding of stomatal development, mechanisms which prevent stomatal‐lineage entry remain unclear. Here, we propose that abscisic acid (ABA), a phytohormone known to induce stomatal closure, limits initiation of stomatal development and induces enlargement of pavement cells in Arabidopsis cotyledons. An ABA‐deficient aba2‐2 mutant had an increased number/proportion of stomata within a smaller cotyledon, as well as reduced expansion of pavement cells. This tendency was reversed after ABA application or in an ABA over‐accumulating cyp707a1cyp707a3 doublemutant. Our time course analysis revealed that aba2‐2 shows prolonged formation of meristemoids and guard mother cells, both precursors of stoma. This finding is in accordance with prolonged gene expression of SPCH and MUTE, master regulators for stomatal formation, indicating that ABA acts upstream of these genes. Only aba2‐2 mute, but not aba2‐2 spch double mutant showed additive phenotypes and displayed inhibition of pavement cell enlargement with increased meristemoid number, indicating that ABA action on pavement cell expansion requires the presence of stomatal‐lineage cells.
A Predominant Reversal in the Relationship between the SAM and East Antarctic Temperatures during the Twenty-First Century
Authors: Marshall Gareth J. , Orr Andrew , Turner John 
Published: February 2013

Abstract
The scientific literature portrays a temporally invariant spatial relationship between the phase of the southern annular mode (SAM) and the sign of surface air temperature (SAT) anomalies across Antarctica. However, here the authors describe a predominant switch from a negative to positive SAM–temperature relationship (STR) across East Antarctica in austral summer/autumn during the first decade of the twenty-first century, when the SAM was generally weakly positive. Of the nine years that had a positive regional STR from 1957 to 2010, seven occurred during the last decade. This reversal appears to be a response to anomalous high pressure over East Antarctica, resulting from variability in the phase and amplitude of the local component of the zonal wavenumber 3 pressure pattern. In years when a reversed (positive) regional STR exists the anomalous circulation is such that there is greater energy flux into the region, while enhanced katabatic drainage across the continental interior disrupts the surface temperature inversion leading to warmer SATs inland, too. The average summer/autumn SAT increase across East Antarctica for years with reversed versus standard STR is ~1°C. Anthropogenically forced models fail to reproduce the trend toward the anomalous high pressure pattern so it is likely that the STR switch is due to natural internal climate variability. That such broadscale STR reversals can take place on decadal time scales needs to be considered when detecting and attributing recent Antarctic climate change and when utilizing isotope data from the East Antarctic ice core record to provide a proxy SAM index prior to the instrumental record.
The Impact of Precipitation Type Discrimination on Hydrologic Simulation: Rain–Snow Partitioning Derived from HMT-West Radar-Detected Brightband Height versus Surface Temperature Data
Authors: Mizukami Naoki , Koren Victor , Smith Michael , Kingsmill David , Zhang Ziya , Cosgrove Brian , Cui Zhengtao 
Published: February 2013

Abstract
Hourly surface precipitation type (Ptype) grids (a total of 408 h from 1 December 2005 through April 20, 2006) were generated by mapping the elevation of the radar-detected brightband height (BBH) to terrain elevation during the 2005/06 observation period of the western Hydrometeorology Testbed (HMT-West) in the North Fork American River basin. BBH Ptype grids were compared to those derived by the standard National Weather Service (NWS) temperature threshold method. In this method, a fixed threshold temperature separating rain and snow was applied to hourly 4-km gridded temperature data. The BBH Ptype grids agreed well (&gt;90%) with the temperature threshold–based grids below an elevation of 1524 m. The agreement dropped to below 60% above this elevation, and BBH Ptype produced more rainfall than the temperature-based Ptype. Continuous hourly streamflow simulations were generated using spatially lumped and distributed hydrologic models with and without the BBH Ptype data from 1 October 2005 through 30 September 2006. Simple insertion of BBH Ptype data did not always improve streamflow simulations for the 11 events examined relative to corresponding simulations using temperature threshold–derived precipitation type, possibly because of the use of the models calibrated with the temperature-based Ptype. The simple sensitivity test indicated simulations of both peak flows from midwinter storms and spring snowmelt runoff are affected by errors in precipitation type estimates.
Geostationary Enhanced Temporal Interpolation for CERES Flux Products
Authors: Doelling David R. , Loeb Norman G. , Keyes Dennis F. , Nordeen Michele L. , Morstad Daniel , Nguyen Cathy , Wielicki Bruce A. , Young David F. , Sun Moguo 
Published: February 2013

Abstract
The Clouds and the Earth’s Radiant Energy System (CERES) instruments on board the Terra and Aqua spacecraft continue to provide an unprecedented global climate record of the earth’s top-of-atmosphere (TOA) energy budget since March 2000. A critical step in determining accurate daily averaged flux involves estimating the flux between CERES Terra or Aqua overpass times. CERES employs the CERES-only (CO) and the CERES geostationary (CG) temporal interpolation methods. The CO method assumes that the cloud properties at the time of the CERES observation remain constant and that it only accounts for changes in albedo with solar zenith angle and diurnal land heating, by assuming a shape for unresolved changes in the diurnal cycle. The CG method enhances the CERES data by explicitly accounting for changes in cloud and radiation between CERES observation times using 3-hourly imager data from five geostationary (GEO) satellites. To maintain calibration traceability, GEO radiances are calibrated against Moderate Resolution Imaging Spectroradiometer (MODIS) and the derived GEO fluxes are normalized to the CERES measurements. While the regional (1° latitude × 1° longitude) monthly-mean difference between the CG and CO methods can exceed 25 W m−2 over marine stratus and land convection, these regional biases nearly cancel in the global mean. The regional monthly CG shortwave (SW) and longwave (LW) flux uncertainty is reduced by 20%, whereas the daily uncertainty is reduced by 50% and 20%, respectively, over the CO method, based on comparisons with 15-min Geostationary Earth Radiation Budget (GERB) data.
Joint Impact of Forecast Tendency and State Error Biases in Ensemble Kalman Filter Data Assimilation of Inner-Core Tropical Cyclone Observations
Authors: Vukicevic Tomislava , Aksoy Altuğ , Reasor Paul , Aberson Sim D. , Sellwood Kathryn J. , Marks Frank 
Published: February 2013

Abstract
In this study the properties and causes of systematic errors in high-resolution data assimilation of inner-core tropical cyclone (TC) observations were investigated using the Hurricane Weather Research and Forecasting (HWRF) Ensemble Data Assimilation System (HEDAS). Although a recent study by Aksoy et al. demonstrated overall good performance of HEDAS for 83 cases from 2008 to 2011 using airborne observations from research and operational aircraft, some systematic errors were identified in the analyses with respect to independent observation-based estimates. The axisymmetric primary circulation intensity was underestimated for hurricane cases and the secondary circulation was systematically weaker for all cases. The diagnostic analysis in this study shows that the underestimate of primary circulation was caused by the systematic spindown of the vortex core in the short-term forecasts during the cycling with observations. This tendency bias was associated with the systematic errors in the secondary circulation, temperature, and humidity. The biases were reoccurring in each cycle during the assimilation because of the inconsistency between the strength of primary and secondary circulation during the short-term forecasts, the impact of model error in planetary boundary layer dynamics, and the effect of forecast tendency bias on the background error correlations. Although limited to the current analysis the findings in this study point to a generic problem of mutual dependence of short-term forecast tendency and state estimate errors in the data assimilation of TC core observations. The results indicate that such coupling of errors in the assimilation would also lead to short-term intensity forecast bias after the assimilation for the same reasons.
Circulations, Bounded Weak Echo Regions, and Horizontal Vortices Observed within Long-Lake-Axis-Parallel–Lake-Effect Storms by the Doppler on Wheels*
Authors: Steiger Scott M. , Schrom Robert , Stamm Alfred , Ruth Daniel , Jaszka Keith , Kress Timothy , Rathbun Brett , Frame Jeffrey , Wurman Joshua , Kosiba Karen 
Published: February 2013

Abstract
The eastern Great Lakes (Erie and Ontario) are often affected by intense lake-effect snowfalls. Lake-effect storms that form parallel to the major axes of these lakes can strongly impact communities by depositing more than 100 cm of snowfall in less than 24 h. Long-lake-axis-parallel (LLAP) storms are significantly different in structure and dynamics compared to the much more studied wind-parallel roll storms that typically form over the western Great Lakes. A Doppler on Wheels (DOW) mobile radar sampled several of these storms at fine spatial and temporal resolutions (and close to the surface) during the winter of 2010–11 over and downwind of Lake Ontario to document and improve understanding of how these storms develop. Over 1100 observations of vortices were catalogued within the 16 December 2010 and 4–5 January 2011 events. The majority of these vortices were less than 1 km in diameter with a statistical modal difference in Doppler velocity (delta-V) value across the vortex of 11 m s−1. Vortices developed along boundaries, which formed within the bands, suggesting horizontal shear instability was the main cause. Other features noted in the DOW observations included bounded weak echo regions, anvils, and horizontal vortices, typically on the south side of west–east-oriented LLAP bands. The reflectivity and velocity structure of LLAP bands were found to be much more complex than previously thought, which may impact localized precipitation amounts and errors in forecast location/intensity.
An Inner-Shelf Wave Forecasting System for the U.S. Pacific Northwest
Authors: García-Medina Gabriel , Özkan-Haller H. Tuba , Ruggiero Peter , Oskamp Jeffrey 
Published: February 2013

Abstract
An operational inner-shelf wave forecasting system was implemented for the Oregon and southwest Washington coast in the U.S. Pacific Northwest (PNW). High-resolution wave forecasts are useful for navigational planning, identifying wave energy resources, providing information for site-specific coastal flood models, and having an informed recreational beach user group, among other things. This forecasting model is run once a day at 1200 UTC producing 84-h forecasts. A series of nested grids with increasing resolution shoreward are implemented to achieve a 30-arc-second resolution at the shelf level. This resolution is significantly higher than what the current operational models produce, thus improving the ability to quantify the alongshore variations of wave conditions on the PNW coast. Normalized root-mean-squared errors in significant wave height and mean wave period range from 0.13 to 0.24 and from 0.13 to 0.26, respectively. Visualization of the forecasts is made available online and is presently being used by recreational beach users and the scientific community. A series of simulations, taking advantage of having a validated shelf-scale numerical wave model, suggests that neither dissipation due to bottom friction nor wind generation is important in the region at this scale for wave forecasting and hindcasting when considering bulk parameters as opposed to the processes of refraction and shoaling. The Astoria and McArthur Canyons; the Stonewall, Perpetua, and Heceta Banks; and Cape Blanco are significant bathymetric features that are shown to be capable of producing alongshore variability of wave heights on the shelf.
Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli
Authors: Hofsteenge Niels , van Nimwegen Erik , Silander Olin K 
Published: February 2013

Abstract

Background
Bacterial persistence describes a phenomenon wherein a small subpopulation of cells is able to survive a challenge with high doses of an antibiotic (or other stressor) better than the majority of the population. Previous work has shown that cells that are in a dormant or slow-growing state are persistent to antibiotic treatment and that populations with higher fractions of dormant cells exhibit higher levels of persistence. These data suggest that a major determinant of the fraction of persisters within a population is the rate at which cells enter and exit from dormancy. However, it is not known whether there are physiological changes in addition to dormancy that influence persistence. Here, we use quantitative measurements of persister fractions in a set of environmental isolates of E. coli together with a mathematical model of persister formation to test whether a single general physiological change, such as cell dormancy, can explain the differences in persister phenotypes observed in different strains.

Results
If a single physiological change (e.g. cell dormancy) underlies most persister phenotypes, then strains should exhibit characteristic fractions of persister cells: some strains will consistently have high fractions of persisters (dormant cells), whereas others will have low fractions. Although we found substantial variation in the fraction of persisters between different environmental isolates of E. coli, these fractions were not correlated across antibiotics. Some strains exhibited high persister fractions in one antibiotic, but low persister fractions in a second antibiotic. Surprisingly, no correlation in persister fractions was observed between any two drugs, even for antibiotics with nearly identical modes of action (ciprofloxacin and nalidixic acid).

Conclusions
These data support the hypothesis that there is no single physiological change that determines the persistence level in a population of cells. Instead, the fraction of cells that survive antibiotic treatment (persist) depends critically on the specific antibiotic that is used, suggesting that physiological changes in addition to dormancy can underlie persister phenotypes.
Transcriptome analysis of embryo maturation in maize
Authors: Teoh Keat Thomas , Requesens Deborah Vicuna , Devaiah Shivakumar P , Johnson Daniel , Huang Xiuzhen , Howard John A , Hood Elizabeth E 
Published: February 2013

AbstractBackgroundMaize is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of maize grain (as well as rice, wheat and other grains) will be critical. Maize grain development is understood from the perspective of morphology, hormone responses, and storage reserve accumulation. This includes various studies on gene expression during embryo development and maturation but a global study of gene expression of the embryo has not been possible until recently. Transcriptome analysis is a powerful new tool that can be used to understand the genetic basis of embryo maturation.ResultsWe undertook a transcriptomic analysis of normal maturing embryos at 15, 21 and 27 days after pollination (DAP), of one elite maize germplasm line that was utilized in crosses to transgenic plants. More than 19,000 genes were analyzed by this method and the challenge was to select subsets of genes that are vitally important to embryo development and maturation for the initial analysis. We describe the changes in expression for genes relating to primary metabolic pathways, DNA synthesis, late embryogenesis proteins and embryo storage proteins, shown through transcriptome analysis and confirmed levels of transcription for some genes in the transcriptome using qRT-PCR.ConclusionsNumerous genes involved in embryo maturation have been identified, many of which show changes in expression level during the progression from 15 to 27 DAP. An expected array of genes involved in primary metabolism was identified. Moreover, more than 30% of transcripts represented un-annotated genes, leaving many functions to be discovered. Of particular interest are the storage protein genes, globulin-1, globulin-2 and an unidentified cupin family gene. When expressing foreign proteins in maize, the globulin-1 promoter is most often used, but this cupin family gene has much higher expression and may be a better candidate for foreign gene expression in maize embryos. Results such as these allow identification of candidate genes and promoters that may not otherwise be available for use. mRNA seq data archived in NCBI SRA; Accession number: ACC=SRA060791 subid=108584.
Single-cell-based system to monitor carrier driven cellular auxin homeostasis
Authors: Barbez Elke , Laňková Martina , Pařezová Markéta , Maizel Alexis , Zažímalová Eva , Petrášek Jan , Friml Jiří , Kleine-Vehn Jürgen 
Published: February 2013

Abstract

Background
Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.

Results
We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.

Conclusions
This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.