bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Atmospheric Changes in Spatially and Temporally Averaged Infrared Spectra Observed from Space
Authors: Kato Seiji , Wielicki Bruce A. , Rose Fred G. , Liu Xu , Taylor Patrick C. , Kratz David P. , Mlynczak Martin G. , Young David F. , Phojanamongkolkij Nipa , Sun-Mack Sunny , Miller Walter F. , Chen Yan 
Published: July 2011

Abstract
Variability present at a satellite instrument sampling scale (small-scale variability) has been neglected in earlier simulations of atmospheric and cloud property change retrievals using spatially and temporally averaged spectral radiances. The effects of small-scale variability in the atmospheric change detection process are evaluated in this study. To simulate realistic atmospheric variability, top-of-the-atmosphere nadir-view longwave spectral radiances are computed at a high temporal (instantaneous) resolution with a 20-km field-of-view using cloud properties retrieved from Moderate Resolution Imaging Spectroradiometer (MODIS) measurements, along with temperature humidity profiles obtained from reanalysis. Specifically, the effects of the variability on the necessary conditions for retrieving atmospheric changes by a linear regression are tested. The percentage error in the annual 10° zonal mean spectral radiance difference obtained by assuming linear combinations of individual perturbations expressed as a root-mean-square (RMS) difference computed over wavenumbers between 200 and 2000 cm−1 is 10%–15% for most of the 10° zones. However, if cloud fraction perturbation is excluded, the RMS difference decreases to less than 2%. Monthly and annual 10° zonal mean spectral radiances change linearly with atmospheric property perturbations, which occur when atmospheric properties are perturbed by an amount approximately equal to the variability of the10° zonal monthly deseasonalized anomalies or by a climate-model-predicted decadal change. Nonlinear changes in the spectral radiances of magnitudes similar to those obtained through linear estimation can arise when cloud heights and droplet radii in water cloud change. The spectral shapes computed by perturbing different atmospheric and cloud properties are different so that linear regression can separate individual spectral radiance changes from the sum of the spectral radiance change. When the effects of small-scale variability are treated as noise, however, the error in retrieved cloud properties is large. The results suggest the importance of considering small-scale variability in inferring atmospheric and cloud property changes from the satellite-observed zonally and annually averaged spectral radiance difference.
A Model Study of the Air–Sea Interaction Associated with the Climatological Aspects and Interannual Variability of the South Asian Summer Monsoon Development
Authors: Lau Ngar-Cheung , Nath Mary Jo 
Published: July 2011

Abstract
The climatological characteristics and interannual variations of the development of the South Asian summer monsoon (SASM) in early summer are studied using output from a 200-yr simulation of a coupled atmosphere–ocean general circulation model (CM2.1). Some of the model results are compared with corresponding observations. Climatological charts of the model and observational data at pentadal intervals indicate that both the precipitation and SST signals exhibit a tendency to migrate northward. Enhanced monsoonal precipitation at a given site is accompanied by a reduction in incoming shortwave radiation and intensification of upward latent heat flux, and by oceanic cooling.
An extended empirical orthogonal function analysis is used to identify the dates for initiation of the northward march of SASM in individual summers. It is noted that early monsoon development prevails after the mature phase of La Niña events, whereas delayed development occurs after El Niño.
Sensitivity experiments based on the atmospheric component of CM2.1 indicate that the effects of SST forcings in the tropical Pacific (TPAC) and Indian Ocean (IO) on monsoon development are opposite to each other. During El Niño events, the atmospheric response to remote TPAC forcing tends to suppress or postpone monsoon development over South Asia. Conversely, the warm SST anomalies in IO, which are generated by the “atmospheric bridge” mechanism in El Niño episodes, lead to accelerated monsoon development. The net result of these two competing effects is an evolution scenario with a timing that is intermediate between the response to TPAC forcing only and the response to IO forcing only.
Observations of Wintertime U.S. West Coast Precipitating Systems with W-Band Satellite Radar and Other Spaceborne Instruments
Authors: Matrosov Sergey Y. 
Published: July 2011

Abstract
The potential of CloudSat W-band radar for observing wintertime storms affecting the West Coast of North America is evaluated. Storms having high hydrological impact often result from landfalls of “atmospheric rivers” (“ARs”), which are the narrow elongated regions of water vapor transport from the tropics. CloudSat measurements are used for retrievals of rain rate R and cloud ice water path (IWP) along the satellite ground track over ocean and land. These retrievals present quasi-instantaneous vertical cross sections of precipitating systems with high-resolution information about hydrometeors. This information is valuable in coastal areas with complex terrain where observations with existing instrumentation, including ground-based radars, are limited. CloudSat reflectivity enhancements [i.e., bright band (BB)] present a way to estimate freezing levels, indicating transitions between rainfall and snowfall. CloudSat estimates of these levels were validated using data from radiosonde soundings and compared to model and microwave sounder data. Comparisons of CloudSat retrievals of rain rates with estimates from ground-based radars in the areas where measurements from these radars were available indicated an agreement within retrieval uncertainties, which were around 50%. The utility of CloudSat was illustrated for case studies of pronounced AR events at landfall and over ocean. Initial analysis of CloudSat crossings of ARs during the 2006/07 season were used for rainfall regime prevalence assessment. It indicated that stratiform rain, which often had BB features, warm rain, and mixed rain were observed with about 26%, 24%, and 50% frequency. Stratiform regions generally had higher rain rates. Significant correlation (~0.72) between mean values of IWP and rain rate was observed for stratiform rainfall.
The Impact of Airmass Boundaries on the Propagation of Deep Convection: A Modeling-Based Study in a High-CAPE, Low-Shear Environment
Authors: Houston Adam L. , Wilhelmson Robert B. 
Published: July 2011

Abstract
A suite of experiments conducted using a cloud-resolving model is examined to assess the role that preexisting airmass boundaries can play in regulating storm propagation. The 27 May 1997 central Texas tornadic event is used to guide these experiments. The environment of this event was characterized by multiple preexisting airmass boundaries, large CAPE, and weak vertical shear.
Only the experiments with preexisting airmass boundaries produce back-building storm propagation (storm motion in opposition to the mean wind). When both the cold front and dryline are present, storm maintenance occurs through the quasi-continuous maintenance of a set of long-lived updrafts and not through discrete updraft redevelopment. Since the cold front is not required for back building, it is clear that back building in this environment does not require quasi-continuous updraft maintenance. The back-building storm simulated with both the cold front and dryline is found to be anchored to the boundary zipper (the intersection of the cold front and dryline). However, multiple preexisting airmass boundaries are not required for back building since experiments with only a dryline also support back building. A conceptual model of back building and boundary zippering is developed that highlights the important role that preexisting boundaries can play in back-building propagation.
Evaluation of Tools Used for Monitoring and Forecasting Flash Floods in the United States
Authors: Gourley Jonathan J. , Erlingis Jessica M. , Hong Yang , Wells Ernest B. 
Published: July 2011

Abstract
This paper evaluates, for the first time, flash-flood guidance (FFG) values and recently developed gridded FFG (GFFG) used by the National Weather Service (NWS) to monitor and predict imminent flash flooding, which is the leading storm-related cause of death in the United States. It is envisioned that results from this study will be used 1) to establish benchmark performance of existing operational flash-flood prediction tools and 2) to provide information to NWS forecasters that reveals how the existing tools can be readily optimized. Sources used to evaluate the products include official reports of flash floods from the NWS Storm Data database, discharge measurements on small basins available from the U.S. Geological Survey, and witness reports of flash flooding collected during the Severe Hazards Analysis and Verification Experiment. Results indicated that the operational guidance values, with no calibration, were marginally skillful, with the highest critical success index of 0.20 occurring with 3-h GFFG. The false-alarm rates fell and the skill improved to 0.34 when the rainfall was first spatially averaged within basins and then reached 50% of FFG for 1-h accumulation and exceeded 3-h FFG. Although the skill of the GFFG values was generally lower than that of their FFG counterparts, GFFG was capable of detecting the spatial variability of reported flash flooding better than FFG was for a case study in an urban setting.
Sleep Medicine Clinical and Surgical Training during Otolaryngology Residency
Authors: Shen Tianjie , Shimahara Erika , Cheng Jing , Capasso Robson 
Published: July 2011

ObjectiveThe authors sought to assess the otolaryngology residency training experiences in adult sleep medicine and sleep surgery in the United States.Study DesignInternet survey.SettingUS academic otolaryngology residency programs.Subjects and MethodsThis Internet survey was emailed to the program directors of 103 US Accreditation Council for Graduate Medical Education (ACGME)–approved otolaryngology residency programs in 2010.ResultsA total of 47 program directors responded, representing 46% of programs surveyed. In 59% of these programs, there was at least 1 faculty member with clinical practice dedicated to adult medicine. Most commonly, these clinicians spent less than 50% of their clinical time on adult sleep medicine. While most otolaryngology residents were reported being well trained in commonly performed procedures such as septoplasty and uvulopalatopharyngoplasty (UPPP), the training on hypopharyngeal or multilevel surgeries, such as partial glossectomy, tongue base resection, hyoid or tongue suspension, or geniotubercle advancement, was considered less frequent. The overall exposure to education regarding the interpretation of original data of laboratory‐based sleep studies or portable home monitoring devices was infrequent. A significant portion of respondents indicated that they would like to expand their residents’ exposure to adult sleep medicine and sleep surgery.ConclusionThis survey provides a starting point to further assess the rigor of sleep medicine/sleep surgery training in US residency programs. Continued assessment and strengthening of the current curriculum are crucial to keep residents up to date with this evolving field. This result calls attention to the importance of bolstering sleep medicine and surgery curriculum to meet the academic requirements of otolaryngology training.
Microbiological Evaluation of Indoor Air of Kindergartens in Fatih District of Istanbul
Authors: Önoğlu Nazan , Önal Ayşe Emel , Güngör Günay , Ayvaz Özkan , Özel Sevda 
Published: July 2011

Objective: The aim of this study was to determine the total mould and bacteria levels in the kindergartens in Istanbul City, Fatih District. Materials: This is a cross sectional study and was performed in 15 preschool institutions in Fatih district in May 2007. Methods: Merck Air Sampler Mas 100 was used for measurements. Results: The total amounts of bacteria grown in the stations measured (classroom, lunch room, kitchen and toilets) were as follows: 946.43 ± 1033.79 CFU·m−3 in the morning and 849.29 ± 594 CFU·m−3 in the afternoon. Total mould numbers were 489.64 ± 441.25 CFU·m−3 in the morning and 993.39 ± 1013.52 CFU·m−3 in the afternoon. Cladosporium spp. and Aspergillus spp. were found to be the most commonly reproduced mould species. The total mould levels were found to be higher in stations with aluminium window framing and floor carpeting. Furthermore, when compared in terms of total mould levels, there was no difference between concrete and brick buildings; and also, total bacteria count was higher in brick buildings during the morning measurements. Conclusion: For providing a better indoor air quality in kindergartens, natural ventilation, polyvinyl chloride windows, concrete building, minimum furniture and textile materials (sofas, cushions, curtains and kids’ clothing) are preferable.
Identification of a specific intronic PEAR1 gene variant associated with greater platelet aggregability and protein expression
Authors: Faraday Nauder , Yanek Lisa R. , Yang Xiao Ping , Mathias Rasika , Herrera-Galeano J. Enrique , Suktitipat Bhoom , Qayyum Rehan , Johnson Andrew D. , Chen Ming-Huei , Tofler Geoffrey H. , Ruczinski Ingo , Friedman Alan D. , Gylfason Arnaldur , Thorsteinsdottir Unnur , Bray Paul F. , O'Donnell Christopher J. , Becker Diane M. , Becker Lewis C. 
Published: July 2011

Abstract
Genetic variation is thought to contribute to variability in platelet function; however, the specific variants and mechanisms that contribute to altered platelet function are poorly defined. With the use of a combination of fine mapping and sequencing of the platelet endothelial aggregation receptor 1 (PEAR1) gene we identified a common variant (rs12041331) in intron 1 that accounts for ≤ 15% of total phenotypic variation in platelet function. Association findings were robust in 1241 persons of European ancestry (P = 2.22 × 10−8) and were replicated down to the variant and nucleotide level in 835 persons of African ancestry (P = 2.31 × 10−27) and in an independent sample of 2755 persons of European descent (P = 1.64 × 10−5). Sequencing confirmed that variation at rs12041331 accounted most strongly (P = 2.07 × 10−6) for the relation between the PEAR1 gene and platelet function phenotype. A dose-response relation between the number of G alleles at rs12041331 and expression of PEAR1 protein in human platelets was confirmed by Western blotting and ELISA. Similarly, the G allele was associated with greater protein expression in a luciferase reporter assay. These experiments identify the precise genetic variant in PEAR1 associated with altered platelet function and provide a plausible biologic mechanism to explain the association between variation in the PEAR1 gene and platelet function phenotype.
Mouse embryonic stem cell-derived thymic epithelial cell progenitors enhance T-cell reconstitution after allogeneic bone marrow transplantation
Authors: Lai Laijun , Cui Cheng , Jin Jingjun , Hao Zhifang , Zheng Qiuhong , Ying Mingang , Boyd Richard , Zhao Yong 
Published: July 2011

AbstractWe have reported that mouse embryonic stem cells (mESCs) can be selectively induced in vitro to differentiate into thymic epithelial cell progenitors (TEPs). When placed in vivo, these mESC-derived TEPs differentiate into cortical and medullary thymic epithelial cells, reconstitute the normal thymic architecture, and enhance thymocyte regeneration after syngeneic BM transplantation (BMT). Here, we show that transplantation of mESC-derived TEPs results in the efficient establishment of thymocyte chimerism and subsequent generation of naive T cells in both young and old recipients of allo-geneic BM transplant. GVHD was not induced, whereas graft-versus-tumor activity was significantly enhanced. Importantly, the reconstituted immune system was tolerant to host, mESC, and BM transplant donor antigens. Therefore, ESC-derived TEPs may offer a new approach for the rapid and durable correction of T-cell immune deficiency after BMT, and the induction of tolerance to ESC-derived tissue and organ transplants. In addition, ESC-derived TEPs may also have use as a means to reverse age-dependent thymic involution, thereby enhancing immune function and decreasing infection rates in the elderly.
Homeostatic cytokines orchestrate the segregation of CD4 and CD8 memory T-cell reservoirs in mice
Authors: Yang Lili , Yu Yang , Kalwani Manorama , Tseng Tai-Wei Joy , Baltimore David 
Published: July 2011

Abstract
Memory T cells (TMs) have been detected in many tissues but their quantitative distribution remains largely undefined. We show that in mice there is a remarkably biased accumulation of long-term CD4 TMs into mucosal sites (mainly gut, especially Peyer patches), and CD8 TMs into lymph nodes and spleen (in particular, peripheral lymph nodes [PLNs]). This distinction correlates with their differentiated expression of PLN- and gut-homing markers. CD8 and CD4 TMs selectively require the expression of PLN-homing marker CCR7 or gut-homing marker α4β7 for maintenance. PLNs and gut supply CD8 and CD4 TMs with their individually favored homeostatic cytokine, IL-15, or IL-7. Cytokine stimulation in turn regulates the different gut-homing marker expression on CD4 and CD8 TMs. IL-15 plays a major role in vivo regulating CD8 TMs homing to PLNs. Thus, the reservoir segregation of CD4 and CD8 TMs meets their individual needs for homeostatic cytokines and is under feedback control of cytokine stimulation.
IRF4 mutations in chronic lymphocytic leukemia
Authors: Havelange Violaine , Pekarsky Yuri , Nakamura Tatsuya , Palamarchuk Alexey , Alder Hansjuerg , Rassenti Laura , Kipps Thomas , Croce Carlo M. 
Published: July 2011

Abstract
Interferon regulatory factor 4 (IRF4) is a member of the interferon regulatory factor family of transcription factors and has been shown to have critical functions at several stages of B-cell development. Genome-wide association study identified a polymorphism in the 3′ untranslated region of IRF4 as a chronic lymphocytic leukemia risk locus. In this study, we report a recurrent heterozygous somatic mutation in the DNA-binding domain of IRF4 detected in 7 of 457 chronic lymphocytic leukemia patients (1.5%). Patients with IRF4 mutation have a good prognosis, and 4 of 6 have a trisomy 12. We also found that IRF4 mRNA expression is higher in the patients with the mutation.
The PI3K pathway drives the maturation of mast cells via microphthalmia transcription factor
Authors: Ma Peilin , Mali Raghuveer Singh , Munugalavadla Veerendra , Krishnan Subha , Ramdas Baskar , Sims Emily , Martin Holly , Ghosh Joydeep , Li Shuo , Chan Rebecca J. , Krystal Gerald , Craig Andrew W. , Takemoto Clifford , Kapur Reuben 
Published: July 2011

Abstract
Mast cell maturation is poorly understood. We show that enhanced PI3K activation results in accelerated maturation of mast cells by inducing the expression of microphthalmia transcription factor (Mitf). Conversely, loss of PI3K activation reduces the maturation of mast cells by inhibiting the activation of AKT, leading to reduced Mitf but enhanced Gata-2 expression and accumulation of Gr1+Mac1+ myeloid cells as opposed to mast cells. Consistently, overexpression of Mitf accelerates the maturation of mast cells, whereas Gata-2 overexpression mimics the loss of the PI3K phenotype. Expressing the full-length or the src homology 3– or BCR homology domain–deleted or shorter splice variant of the p85α regulatory subunit of PI3K or activated AKT or Mitf in p85α-deficient cells restores the maturation but not growth. Although deficiency of both SHIP and p85α rescues the maturation of SHIP−/− and p85α−/− mast cells and expression of Mitf; in vivo, mast cells are rescued in some, but not all tissues, due in part to defective KIT signaling, which is dependent on an intact src homology 3 and BCR homology domain of p85α. Thus, p85α-induced maturation, and growth and survival signals, in mast cells can be uncoupled.
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments
Authors: ÓhÉigeartaigh Seán S , Armisén David , Byrne Kevin P , Wolfe Kenneth H 
Published: July 2011

Abstract

Background
In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically.

Results
We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis.

Conclusions
SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external information has been added may prove useful in other settings.