bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moist Dynamical Linkage between the Equatorial Indian Ocean and the South Asian Monsoon Trough*
Authors: Annamalai H. 
Published: October 2009

Abstract
During boreal summer, both the monsoon trough and the equatorial Indian Ocean (EIO) receive intense climatological precipitation. At various time scales, EIO sea surface temperature (SST) and/or precipitation variations interact with rainfall along the trough. For instance, during July–August in strong Indian Ocean dipole/zonal mode (IODZM) years, EIO experiences below-normal rainfall while regions along the monsoon trough receive above-normal rainfall. A lack of spatial coherency between SST and precipitation variations is noted in both regions. This paper posits the hypothesis that interaction between equatorial waves and moist physics is important in determining precipitation anomalies over these regions and in setting up the teleconnection. The hypothesis is tested using a linear baroclinic model (LBM). IODZM-related SST anomalies derived from multicentury integrations of the Geophysical Fluid Dynamics Laboratory coupled model (GFDL CM2.1) are used to force the LBM. Consistent with observations and CM2.1 composites of strong IODZM events, steady-state LBM solutions simulate zonally oriented negative (positive) precipitation anomalies over the EIO (along the monsoon trough). To identify the processes simulated in the LBM, moisture and moist static energy budgets are examined. Over both regions, analyses reveal that moisture advection contributes the most to the LBM budget, with advection of climatological moisture by the anomalous wind being the principal factor. Specifically, in response to cold SST anomalies in the EIO, moist stability due to surface fluxes increases, giving rise to below-normal rainfall. These conditions produce anomalous anticyclonic circulation as a Rossby wave response in the lower troposphere. Over the central-eastern EIO, this anomalous circulation advects climatological air of lower moisture content from the subtropics. In addition, advection of anomalous moisture by both climatological and anomalous wind results in anomalous dry conditions over the entire EIO. In contrast, anomalous divergent circulations that emanate from the EIO advect climatological air of higher moisture content from the equatorial region, amplifying rainfall along the monsoon trough. Consequently, the two regions are connected by a thermally driven overturning meridional circulation. Budget diagnostics performed with CM2.1 composites and the ECMWF interim reanalysis for observed IODZM events support the hypothesis. The results here imply that in coupled models, realistic representation of the basic state and details of the moist processes are necessary for successful monsoon prediction.
Simulating the IHOP_2002 Fair-Weather CBL with the WRF-ARW–Noah Modeling System. Part I: Surface Fluxes and CBL Structure and Evolution along the Eastern Track
Authors: LeMone Margaret A. , Chen Fei , Tewari Mukul , Dudhia Jimy , Geerts Bart , Miao Qun , Coulter Richard L. , Grossman Robert L. 
Published: October 2009

AbstractFair-weather data from the May–June 2002 International H2O Project (IHOP_2002) 46-km eastern flight track in southeast Kansas are compared to simulations using the advanced research version of the Weather Research and Forecasting model coupled to the Noah land surface model (LSM), to gain insight into how the surface influences convective boundary layer (CBL) fluxes and structure, and to evaluate the success of the modeling system in representing CBL structure and evolution. This offers a unique look at the capability of the model on scales the length of the flight track (46 km) and smaller under relatively uncomplicated meteorological conditions.It is found that the modeled sensible heat flux H is significantly larger than observed, while the latent heat flux (LE) is much closer to observations. The slope of the best-fit line ΔLE/ΔH to a plot of LE as a function of H, an indicator of horizontal variation in available energy H + LE, for the data along the flight track, was shallower than observed. In a previous study of the IHOP_2002 western track, similar results were explained by too small a value of the parameter C in the Zilitinkevich equation used in the Noah LSM to compute the roughness length for heat and moisture flux from the roughness length for momentum, which is supplied in an input table; evidence is presented that this is true for the eastern track as well. The horizontal variability in modeled fluxes follows the soil moisture pattern rather than vegetation type, as is observed; because the input land use map does not capture the observed variation in vegetation. The observed westward rise in CBL depth is successfully modeled for 3 of the 4 days, but the actual depths are too high, largely because modeled H is too high. The model reproduces the timing of observed cumulus cloudiness for 3 of the 4 days.Modeled clouds lead to departures from the typical clear-sky straight line relating surface H to LE for a given model time, making them easy to detect. With spatial filtering, a straight slope line can be recovered. Similarly, larger filter lengths are needed to produce a stable slope for observed fluxes when there are clouds than for clear skies.
Simulating the IHOP_2002 Fair-Weather CBL with the WRF-ARW–Noah Modeling System. Part II: Structures from a Few Kilometers to 100 km across
Authors: LeMone Margaret A. , Chen Fei , Tewari Mukul , Dudhia Jimy , Geerts Bart , Miao Qun , Coulter Richard L. , Grossman Robert L. 
Published: October 2009

Abstract
Fair-weather data along the May–June 2002 International H2O Project (IHOP_2002) eastern track and the nearby Argonne Boundary Layer Experiments (ABLE) facility in southeast Kansas are compared to numerical simulations to gain insight into how the surface influences convective boundary layer (CBL) structure, and to evaluate the success of the modeling system in replicating the observed behavior. Simulations are conducted for 4 days, using the Advanced Research version of the Weather Research and Forecasting (WRF) model coupled to the Noah land surface model (LSM), initialized using the High-Resolution Land Data Assimilation System (HRLDAS). Because the observations focus on phenomena less than 60 km in scale, the model is run with 1-km grid spacing, offering a critical look at high-resolution model behavior in an environment uncomplicated by precipitation.
The model replicates the type of CBL structure on scales from a few kilometers to ∼100 km, but some features at the kilometer scales depend on the grid spacing. Mesoscale (tens of kilometers) circulations were clearly evident on 2 of the 4 days (30 May and 20 June), clearly not evident on 1 day (22 June), with the situation for the fourth day (17 June) ambiguous. Both observed and modeled surface-heterogeneity-generated mesoscale circulations are evident for 30 May. On the other hand, 20 June satellite images show north-northwest–south-southeast cloud streets (rolls) modulated longitudinally, presumably by tropospheric gravity waves oriented normal to the roll axis, creating northeast–southwest ridges and valleys spaced 50–100 km apart. Modeled cloud streets showed similar longitudinal modulation, with the associated two-dimensional structure having maximum amplitude above the CBL and no relationship to the CBL temperature distribution; although there were patches of mesoscale vertical velocity correlated with CBL temperature. On 22 June, convective rolls were the dominant structure in both model and observations.
For the 3 days for which satellite images show cloud streets, WRF produces rolls with the right orientation and wavelength, which grows with CBL depth. Modeled roll structures appeared for the range of CBL depth to Obukhov length ratios (−zi/L) associated with rolls. However, sensitivity tests show that the roll wavelength is also related to the grid spacing, and the modeled convection becomes more cellular with smaller grid spacing.
Patterns of Precipitation and Mesolow Evolution in Midlatitude Mesoscale Convective Vortices
Authors: James Eric P. , Johnson Richard H. 
Published: October 2009

Abstract
Surface pressure manifestations of mesoscale convective vortices (MCVs) that traversed Oklahoma during the periods May–August 2002–05 are studied using the Weather Surveillance Radar-1988 Doppler (WSR-88D), the Oklahoma Mesonet, and the NOAA Profiler Network data. Forty-five MCVs that developed from mesoscale convective systems (MCSs) have been investigated, 28 (62%) of which exhibit mesolows detectable at the surface. Within this group, three distinct patterns of precipitation organization and associated mesolow evolution have been identified. The remaining 17 (38%) of the cases do not contain a surface mesolow. Two repeating patterns of precipitation organization are identified for the latter group.
The three categories of MCVs possessing a surface mesolow are as follows. Nineteen are classified as “rear-inflow-jet MCVs,” and tend to form within large and intense asymmetric MCSs. Rear inflow into the MCS, enhanced by the development of an MCV on the left-hand side relative to system motion, produces a rear-inflow notch and a distinct surface wake low at the back edge of the stratiform region. Hence, the surface mesolow and MCV are displaced from one another. Eight are classified as “collapsing-stratiform-region MCVs.” These MCVs arise from small asymmetric MCSs. As the stratiform region of the MCS weakens, a large mesolow appears beneath its dissipating remnants due to broad subsidence warming, and at the same time the midlevel vortex spins up due to column stretching. One case, called a “vertically coherent MCV,” contains a well-defined surface mesolow and associated cyclonic circulation, apparently due to the strength of the midlevel warm core and the weakness of the low-level cold pool. In these latter two cases, the surface mesolow and MCV are approximately collocated.
Within the group of MCVs without a surface mesolow, 14 are classified as “remnant-circulation MCVs” containing no significant precipitation or surface pressure effects. Finally, three are classified as “cold-pool-dominated MCVs;” these cases contain significant precipitation but no discernible surface mesolow.
This study represents the first systematic analysis of the surface mesolows associated with MCVs. The pattern of surface pressure and winds accompanying MCVs can affect subsequent convective development in such systems. Extension of the findings herein to tropical oceans may have implications regarding tropical cyclogenesis.
Challenges in the design of a Home Telemanagement Trial for patients with ulcerative colitis
Authors: Cross Raymond K , Finkelstein Joseph 
Published: October 2009

Background Nonadherence, inadequate monitoring, and side-effects result in suboptimal outcomes in ulcerative colitis (UC). We hypothesize that telemanagement for UC will improve symptoms, quality of life, adherence, and decrease costs. Purpose This article describes the challenges encountered in the design of the home telemanagement in patients with UC trial. Methods In a randomized trial to assess the effectiveness of telemanagement for UC compared to best available care, 100 patients will be enrolled. Subjects in the intervention arm will complete self-testing with telemanagement weekly; best available care subjects will receive scheduled follow up, educational fact sheets, and written action plans. Telemanagement consists of a home-unit, decision support server, and web-based clinician portal. The home-unit includes a scale and laptop. Subjects will respond to questions about symptoms, side-effects, adherence, and knowledge weekly; subjects will receive action plans after self-testing. Outcome variables to be assessed every 4 months include: disease activity, using the Seo index; quality of life, using the Inflammatory Bowel Disease Questionnaire; adherence, using pharmacy refill data and the Morisky Medication Adherence Scale; utilization of healthcare resources, using urgent care visits and hospitalizations. Results We encountered several challenges during design and implementation of our trial. First, we selected a randomized controlled trial design. We could have selected a quasiexperimental design to decrease the sample size needed and costs. Second, identification of a control group was challenging. Telemanagement patients received self-care plans and an educational curriculum. Since controls would not receive these interventions, we thought our results would be biased in favor of telemanagement. In addition, we wanted to evaluate the mode of delivery of these components of care. Therefore, we included written action plans and educational materials for patients in the control group (‘best available care’). Third, we could not blind subjects to group assignment. In an attempt to decrease bias, staff was masked to group assignment to decrease measurement bias. Fourth, we selected outcome measures that were not invasive to decrease risks to subjects and to enhance recruitment. Limitations Our results may not be generalizable as our program is a tertiary center. Further, subjects are not blinded to the intervention potentially resulting in bias; we attempt to minimize this bias by having staff masked to treatment group at the time of assessment of outcome measures. Conclusions To the best of our knowledge, our trial will be the first randomized controlled trial to evaluate telemedicine in subjects with gastrointestinal disease. We describe several issues encountered in design and implementation of our trial that will aid investigators when planning telemedicine trials in inflammatory bowel disease. Clinical Trials 2009; 6: 649–657. http://ctj.sagepub.com
Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes
Authors: Gazave Eve , Lapébie Pascal , Richards Gemma S , Brunet Frédéric , Ereskovsky Alexander V , Degnan Bernard M , Borchiellini Carole , Vervoort Michel , Renard Emmanuelle 
Published: October 2009

Abstract

Background
Of the 20 or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. One of these is the Notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. In light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway.

Results
We searched for 22 components of the Notch pathway in 35 different species that represent 8 major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor Notch and its ligands Delta/Jagged. We confirm that a Notch pathway, with true receptors and ligands is specific to the Metazoa. This study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. The origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. In addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies.

Conclusion
The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.
A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life
Authors: Haas Crysten E , Rodionov Dmitry A , Kropat Janette , Malasarn Davin , Merchant Sabeeha S , de Crécy-Lagard Valérie 
Published: October 2009

AbstractBackgroundCOG0523 proteins are, like the nickel chaperones of the UreG family, part of the G3E family of GTPases linking them to metallocenter biosynthesis. Even though the first COG0523-encoding gene,cobW, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family.ResultsBased on a combination of comparative genomics, literature and phylogenetic analyses and experimental validations, the COG0523 family can be separated into at least fifteen subgroups. The CobW subgroup involved in cobalamin synthesis represents only one small sub-fraction of the family. Another, larger subgroup, is suggested to play a predominant role in the response to zinc limitation based on the presence of the corresponding COG0523-encoding genes downstream from putative Zur binding sites in many bacterial genomes. Zur binding sites in these genomes are also associated with candidate zinc-independent paralogs of zinc-dependent enzymes. Finally, the potential role of COG0523 in zinc homeostasis is not limited to Bacteria. We have predicted a link between COG0523 and regulation by zinc in Archaea and show that two COG0523 genes are induced upon zinc depletion in a eukaryotic reference organism,Chlamydomonas reinhardtii.ConclusionThis work lays the foundation for the pursuit by experimental methods of the specific role of COG0523 members in metal trafficking. Based on phylogeny and comparative genomics, both the metal specificity and the protein target(s) might vary from one COG0523 subgroup to another. Additionally, Zur-dependent expression ofCOG0523and putative paralogs of zinc-dependent proteins may represent a mechanism for hierarchal zinc distribution and zinc sparing in the face of inadequate zinc nutrition.
Combination of interferon-alpha and 5-fluorouracil inhibits endothelial cell growth directly and by regulation of angiogenic factors released by tumor cells
Authors: Wada Hiroshi , Nagano Hiroaki , Yamamoto Hirofumi , Noda Takehiro , Murakami Masahiro , Kobayashi Shogo , Marubashi Shigeru , Eguchi Hidetoshi , Takeda Yutaka , Tanemura Masahiro , Umeshita Koji , Doki Yuichiro , Mori Masaki 
Published: October 2009

Abstract

Background
The combination therapy of interferon (IFN)-alpha and 5-fluorouracil (5-FU) improved the prognosis of the patients with hepatocellular carcinoma (HCC). To determine the molecular mechanisms of the anti-tumor and anti-angiogenic effects, we examined the direct anti-proliferative effects on human umbilical vein endothelial cells (HUVEC) and indirect effects by regulating secretion of angiogenic factors from HCC cells.

Methods
The direct effects on HUVEC were examined by TUNEL, Annexin-V assays and cell cycles analysis. For analysis of the indirect effects, the apoptosis induced by the conditioned medium from HCC cell treated by IFN-alpha/5-FU and expression of angiogenic factors was examined.

Results
IFN-alpha and 5-FU alone had anti-proliferative properties on HUVEC and their combination significantly inhibited the growth (compared with control, 5-FU or IFN alone). TUNEL and Annexin-V assays showed no apoptosis. Cell cycle analysis revealed that IFN-alpha and 5-FU delayed cell cycle progression in HUVEC with S-phase accumulation. The conditioned medium from HuH-7 cells after treatment with IFN/5-FU significantly inhibited HUVEC growth and induced apoptosis, and contained high levels of angiopoietin (Ang)-1 and low levels of vascular endothelial growth factor (VEGF) and Ang-2. Knockdown of Ang-1 in HuH-7 cells abrogated the anti-proliferative effects on HUVEC while knockdown of Ang-2 partially rescue the cells.

Conclusion
These results suggested that IFN-alpha and 5-FU had direct growth inhibitory effects on endothelial cells, as well as anti-angiogenic effects through regulation of angiogenic factors released from HCC cells. Modulation of VEGF and Angs secretion by IFN-alpha and 5-FU may contribute to their anti-angiogenic and anti-tumor effects on HCC.
Right atrium myxoma coexisting with antiphospholipid syndrome: a case report
Authors: Pliakos Christos , Alexiadou Eleni , Metallidis Symeon , Papavramidis Theodossis S , Kapoulas Stergios , Sapalidis Konstantinos , Nikolaidis Pavlos 
Published: October 2009

Abstract
In this case report we describe a rare case of right atrium myxoma that coexisted with antiphospholipid syndrome in a young woman. We describe the unusual findings and diagnostic challenges combined with a review of the literature.
Laparoscopic conservative management of ureteral endometriosis: a survey of eighty patients submitted to ureterolysis
Authors: Camanni Marco , Bonino Luca , Delpiano Elena Maria , Berchialla Paola , Migliaretti Giuseppe , Revelli Alberto , Deltetto Francesco 
Published: October 2009

Abstract

Background
this study aims to evaluate the effectiveness and safety of laparoscopic conservative management of ureteral endometriosis.

Methods
Eighty cases of histologically confirmed endometriosis affecting the ureter, 10 of which with bladder involvement were prospectively studied. In detail, patients were 13 women with ureteral stenosis (7 with hydronephrosis), 32 with circular lesions totally encasing the ureter, and 35 with endometriotic foci on the ureteral wall, but not completely encasing it. They were submitted to laparoscopic ureterolysis with or without partial cystectomy, ureteroneocistostomy. The rate of surgical complications, the recurrence rate, the patients' satisfaction rate was assessed during 22 months (median) follow-up.

Results
Laparoscopic ureterolysis was employed for all patients and set free the ureter from the disease in 95% of cases, whereas ureteroneocystostomy was necessary for 4 patients showing severe stenosis with hydronephrosis, among which 2 had intrinsic endometriosis of the ureteral muscularis. Three post-surgery ureteral fistulae occurred in cases with ureteral involvement longer than 4 cm: two cases were successfully treated placing double J catheter, the third needed ureteroneocistostomy. During follow-up, ureteral endometriosis recurred in 2 patients who consequently underwent ureteroneocystostomy. Most patients expressed high satisfaction rate throughout the whole follow-up period.

Conclusion
laparoscopic ureterolysis is effective and well tolerated in most cases of ureteral endometriosis. Ureteroneocystostomy is a better strategy for patients with extended (more than 4 cm) ureteral involvement or with severe stenosis with or without hydronephrosis.