bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Adiabatic Pole-to-Pole Overturning Circulation
Authors: Wolfe Christopher L. , Cessi Paola 
Published: May 2011

Abstract
The adiabatic pole-to-pole cell of the residual overturning circulation (ROC) is studied in a two-hemisphere, semienclosed basin, with a zonally reentrant channel occupying the southernmost eighth of the domain. Three different models of increasing complexity are used: a simple, analytically tractable zonally averaged model; a coarse-resolution numerical model with parameterized eddies; and an eddy-resolving general circulation model. Two elements are found to be necessary for the existence of an adiabatic pole-to-pole cell: 1) a thermally indirect, wind-driven overturning circulation in the zonally reentrant channel, analogous to the Deacon cell in the Antarctic Circumpolar Current (ACC) region, and 2) a set of outcropping isopycnals shared between the channel and the semienclosed region of the Northern Hemisphere. These points are supported by several computations varying the domain geometry, the surface buoyancy distribution, and the wind forcing. All three models give results that are qualitatively very similar, indicating that the two requirements above are general and robust.
The zonally averaged model parameterizes the streamfunction associated with adiabatic buoyancy fluxes as downgradient diffusion of buoyancy thickness, with a diffusivity in the semienclosed region of the Northern Hemisphere much larger than that in the ACC region. In the simple model, the disparity in diffusivities is necessary to obtain a substantial pole-to-pole ROC. The simple model also illustrates how the geometry of the isopycnals is shaped by the interhemispheric ROC, leading to three major thermostads, which the authors identify with the major water masses of the Atlantic: that is, North Atlantic Deep Water, Antarctic Intermediate Water, and Antarctic Bottom Water.
A Climatology of Nocturnal Warming Events Associated with Cold-Frontal Passages in Oklahoma
Authors: Nallapareddy Anita , Shapiro Alan , Gourley Jonathan J. 
Published: May 2011

AbstractA sudden increase in temperature during the nighttime hours accompanies the passages of some cold fronts. In some cold front–associated warming events, the temperature can rise by as much as 10°C and can last from a few minutes to several hours. Previous studies suggest that these events are due to the downward transport of warmer air by the strong and gusty winds associated with the cold-frontal passages. In this study, a climatology of nocturnal warming events associated with cold fronts was created using 6 yr of Oklahoma Mesonetwork (Mesonet) data from 2003 to 2008. Nocturnal warming events associated with cold-frontal passages occurred surprisingly frequently across Oklahoma. Of the cold fronts observed in this study, 91.5% produced at least one warming event at an Oklahoma Mesonet station. The winter months accounted for the most events (37.9%), and the summer months accounted for the fewest (3.8%). When normalized by the monthly number of cold-frontal passages, the winter months still had the most number of warming events. The number of warming events increased rapidly from 2300 to 0200 UTC; thereafter, the number of events gradually decreased. A spatial analysis revealed that the frequency of warming events decreased markedly from west to east across the state. In contrast, the average magnitude of the warming increased from west to east. In contrast to control periods (associated with cold-frontal passages without nocturnal warming events), warming events were associated with weaker initial winds and stronger initial temperature inversions. Moreover, the nocturnal temperature inversion weakened more during warming events than during control periods and the surface wind speeds increased more during warming events than during control periods. These results are consistent with previous studies that suggest the warming events are due to the “mixing out” of the nocturnal temperature inversion.
Poleward Shift of Subtropical Jets Inferred from Satellite-Observed Lower-Stratospheric Temperatures
Authors: Fu Qiang , Lin Pu 
Published: May 2011

Abstract
One pronounced feature in observed latitudinal dependence of lower-stratospheric temperature trends is the enhanced cooling near 30° latitude in both hemispheres. The observed phenomenon has not, to date, been explained in the literature. This study shows that the enhanced cooling is a direct response of the lower-stratospheric temperature to the poleward shift of subtropical jets. Furthermore, this enhanced lower-stratospheric cooling can be used to quantify the poleward shift of subtropical jets. Using the lower-stratospheric temperatures observed by satellite-borne microwave sounding units, it is shown that the subtropical jets have shifted poleward by 0.6° ± 0.1° and 1.0° ± 0.3° latitude in the Southern and Northern Hemispheres, respectively, in last 30 years since 1979, indicating a widening of tropical belt by 1.6° ± 0.4° latitude.
The Response of Tropical Cyclone Statistics to an Increase in CO2 with Fixed Sea Surface Temperatures
Authors: Held Isaac M. , Zhao Ming 
Published: May 2011

Abstract
The effects on tropical cyclone statistics of doubling CO2, with fixed sea surface temperatures (SSTs), are compared to the effects of a 2-K increase in SST, with fixed CO2, using a 50-km resolution global atmospheric model. Confirming earlier results of Yoshimura and Sugi, a significant fraction of the reduction in globally averaged tropical storm frequency seen in simulations in which both SST and CO2 are increased can be thought of as the effect of the CO2 increase with fixed SSTs. Globally, the model produces a decrease in tropical cyclone frequency of about 10% due to doubling of CO2 and an additional 10% for a 2-K increase in SST, resulting in roughly a 20% reduction when both effects are present. The relative contribution of the CO2 effect to the total reduction is larger in the Northern than in the Southern Hemisphere. The average intensity of storms increases in the model with increasing SST, but intensity remains roughly unchanged, or decreases slightly, with the increase in CO2 alone. As a result, when considering the frequency of more intense cyclones, the intensity increase tends to compensate for the reduced total cyclone numbers for the SST increase in isolation, but not for the CO2 increase in isolation. Changes in genesis in these experiments roughly follow changes in mean vertical motion, reflecting changes in convective mass fluxes. Discussion of one possible perspective on how changes in the convective mass flux might alter genesis rates is provided.
Implementation and Testing of Research Infrastructure for Practice‐Based Research in Hearing and Communication Disorders
Authors: Witsell David L. , Schulz Kristine A. , Moore Kathy , Tucci Debara L. 
Published: May 2011

ObjectiveTo describe site capability and experience of the CHEER network (Creating Healthcare Excellence through Education and Research) to rapidly collect descriptive data on patients with tinnitus and dizziness visiting participating CHEER sites.Study DesignProspective observational data collection study over 6 months.SettingTwenty one community otology and otolaryngology practices in the United States.Subjects and MethodsAs proof of concept, a data collection study was developed for patients with tinnitus and dizziness (presenting with or without associated migraine) through a collaborative effort of the CHEER principal investigator (PI) and co‐PIs. The 9‐page questionnaire included validated instruments and additional patient‐ and physician‐reported information. Information was captured electronically via REDCap by each site’s CHEER research coordinator. Site initiation, data entry rates, and research coordinator feedback were also collected.ResultsOf the 21 CHEER sites, 15 participated in the study. Nine sites entered a patient within the first 31 days of study initiation, and all 15 sites were entering patients and corresponding clinical data within 72 days. During the 6‐month study, 1044 patients were entered into the REDCap database. Research coordinator engagement was a major driver for success, whereas time and resources were deterrents. Incentives included altruism, professional development, and future financial opportunities.ConclusionThe CHEER research network has significant capability and infrastructure to collect prospective data in a practice‐based environment. Research coordinator engagement undergirds network success; however, future efforts will cultivate stronger collaboration of the coordinator and site PI. Central coordination of practice‐based research through a hub and spoke concept can be successful.
Repair of Large Traumatic Tympanic Membrane Perforation with a Steri‐Strips Patch
Authors: Park Moo Kyun , Kim Kyu Hoon , Lee Jong Dae , Lee Byung Don 
Published: May 2011

ObjectiveTo investigate the effects of the Steri‐Strips patch (3M) on the treatment of large traumatic tympanic membrane perforations (TMP).Study DesignProspective, randomized, controlled.SettingTertiary university hospital.Subjects and MethodsA randomized prospective analysis was performed between February 2009 and January 2011 for the treatment of traumatic TMP larger than 50% of the entire tympanic membrane. The results of closure rate, closure time, hearing gain, and rate of otorrhea between conservative observation, paper patching, and Steri‐Strips patching groups were compared.ResultsIn total, 87 patients were analyzed in this study. The closure rates of the perforations in the Steri‐Strips patching, paper patching, and observation groups were 93.3%, 84.2%, and 78.9%, respectively. There was no statistically significant difference in tympanic membrane closure rate between the 3 groups. The Steri‐Strips technique decreased the need for repeat procedures. Overall, the Steri‐Strips and paper patching groups showed shorter healing times compared with the observation group. However, there was an increased rate of otorrhea in the Steri‐Strips group compared with the observation group.ConclusionSteri‐Strips patching reduced the healing time and need for repeat procedures in patients with large traumatic TMPs. However, the occurrence of otorrhea was significantly more common in patients treated with the Steri‐Strips technique.
Carboxyhemoglobinemia in a pediatric cardiopulmonary bypass patient derived from a contaminated unit of allogenic blood
Authors: McRobb C. , Walczak R. , Lawson S. , Lodge A. , Lockhart E. , Bandarenko N. , Ing R. 
Published: May 2011

A 4.3 kg, three-month-old patient, diagnosed with a perimembranous ventricular septal defect, presented for cardiac surgery. Upon initiation of cardiopulmonary bypass (CPB), the patient developed carboxyhemoglobinemia (11.1%). Potential sources for the unexpected acquired carboxyhemoglobinemia were sought quickly. Testing of residual blood from the unit of packed red blood cells (PRBCs) used to prime the CPB circuit revealed a carboxyhemoglobin (COHb) of 15.1 %. A decrease in cerebral oximetry (rSO2) on CPB was initially felt to be a result of the elevated COHb levels. When ventilation of the oxygenator with 100% oxygen (O2) failed to decrease COHb levels, a partial exchange transfusion was performed with reduction in COHb to 7.1%. The operation was completed successfully and the patient’s COHb levels returned to normal within 75 minutes. Post case analysis of events and data collected during the case revealed a broader differential for explaining the compromised patient’s O2 delivery than the transient acquired carboxyhemoglobinemia. A partial obstruction of the superior vena cava could have triggered the drop in rSO2 on CPB. Follow-up of the donor blood confirmed the donor had previously undiagnosed carboxyhemoglobinemia as a result of chronic carbon monoxide exposure from a faulty vehicle exhaust system.
Near Infrared Spectroscopy during pediatric cardiac surgery: errors and pitfalls
Authors: Durandy Y , Rubatti M , Couturier R 
Published: May 2011

As a result of improvements in early outcomes, long-term neurologicalal outcomes are becoming a major issue in pediatric cardiac surgery. The mechanisms of brain injury are numerous, but a vast majority of injuries are impervious to therapy and only a few are modifiable. The quality of perfusion during cardiac surgery is a modifiable factor and cerebral monitoring during bypass is the way to assess the quality of intra-operative cerebral perfusion. Near infrared spectroscopy (NIRS), as a diagnostic tool, has gained in popularity within the perfusion community. However, NIRS is becoming the standard of care before its scientific validation. This manuscript relates four clinical cases, demonstrating the limitations of NIRS monitoring during pediatric cardiac surgery as well as uncertainties about the interpretation of the recorded values. The clinical relevance of cerebral oxymetry is needed before the use of NIRS as a decision making tool. Multimodal brain monitoring with NIRS, trans-cranial Doppler and electroencephalogram are currently under way in several pediatric centers. The benefit of this time-consuming and expensive monitoring system has yet to be demonstrated.
Triptan overuse in the Dutch general population: A nationwide pharmaco-epidemiology database analysis in 6.7 million people
Authors: Dekker F , Wiendels NJ , de Valk V , van der Vliet C , Neven A Knuistingh , Assendelft WJJ , Ferrari MD 
Published: May 2011

Introduction: A population-based observational study was used to assess the prevalence, demographics, risk factors, and costs of triptan overuse, defined as more than 30 (International Headache Society criteria) or 54 (stringent criteria) defined daily doses per 3 months. Methods: Analysis of the Dutch Health Care Insurance Board Database for 2005, which included prescriptions for 6.7 million people (46% of the total Dutch population). Results: Triptans were used by 85,172 (1.3%) people; of these, 8,844 (10.4%; 95% CI 10.2–10.6) were overusers by International Headache Society and 2,787 (3.3%; 95% CI 3.2–3.4) were overusers by stringent criteria. The triptan-specific odds ratios for the rate of International Headache Society overuse compared with sumatriptan were: 0.26 (95% CI 0.19–0.36) for frovatriptan; 0.34 (95% CI 0.32–0.37) for rizatriptan; 0.76 95% CI 0.68–0.85) for naratriptan; 0.86 (95% CI 0.72–1.02) for eletriptan; 0.97 (95% CI 0.88–1.06) for zolmitriptan; and 1.49 (95% CI 1.31–1.72) for almotriptan. Costs for overuse were 29.7 million euros; for the International Headache Society criteria this was 46% of total costs and for stringent criteria it was 23%. Discussion: In the Dutch general population, 1.3% used a triptan in 2005, of which 10.3% were overusers and accounted for half of the total costs of triptans. Users of frovatriptan, rizatriptan and naratriptan had a lower level of overuse.
Toward an interactive article: integrating journals and biological databases
Authors: Rangarajan Arun , Schedl Tim , Yook Karen , Chan Juancarlos , Haenel Stephen , Otis Lolly , Faelten Sharon , DePellegrin-Connelly Tracey , Isaacson Ruth , Skrzypek Marek S , Marygold Steven J , Stefancsik Raymund , Cherry J Michael , Sternberg Paul W , Müller Hans-Michael 
Published: May 2011

Abstract

Background
Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture.

Results
We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases.

Conclusions
Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.
Combining an Evolution-guided Clustering Algorithm and Haplotype-based LRT in Family Association Studies
Authors: Lee Mei-Hsien , Tzeng Jung-Ying , Huang Su-Yun , Hsiao Chuhsing Kate 
Published: May 2011

Abstract

Background
With the completion of the international HapMap project, many studies have been conducted to investigate the association between complex diseases and haplotype variants. Such haplotype-based association studies, however, often face two difficulties; one is the large number of haplotype configurations in the chromosome region under study, and the other is the ambiguity in haplotype phase when only genotype data are observed. The latter complexity may be handled based on an EM algorithm with family data incorporated, whereas the former can be more problematic, especially when haplotypes of rare frequencies are involved. Here based on family data we propose to cluster long haplotypes of linked SNPs in a biological sense, so that the number of haplotypes can be reduced and the power of statistical tests of association can be increased.

Results
In this paper we employ family genotype data and combine a clustering scheme with a likelihood ratio statistic to test the association between quantitative phenotypes and haplotype variants. Haplotypes are first grouped based on their evolutionary closeness to establish a set containing core haplotypes. Then, we construct for each family the transmission and non-transmission phase in terms of these core haplotypes, taking into account simultaneously the phase ambiguity as weights. The likelihood ratio test (LRT) is next conducted with these weighted and clustered haplotypes to test for association with disease. This combination of evolution-guided haplotype clustering and weighted assignment in LRT is able, via its core-coding system, to incorporate into analysis both haplotype phase ambiguity and transmission uncertainty. Simulation studies show that this proposed procedure is more informative and powerful than three family-based association tests, FAMHAP, FBAT, and an LRT with a group consisting exclusively of rare haplotypes.

Conclusions
The proposed procedure takes into account the uncertainty in phase determination and in transmission, utilizes the evolutionary information contained in haplotypes, reduces the dimension in haplotype space and the degrees of freedom in tests, and performs better in association studies. This evolution-guided clustering procedure is particularly useful for long haplotypes containing linked SNPs, and is applicable to other haplotype-based association tests. This procedure is now implemented in R and is free for download.
Characters of homogentisate oxygenase gene mutation and high clonality of the natural pigment-producing Vibrio choleraestrains
Authors: Wang Ruibai , Wang Hengliang , Zhou Haijian , Wang Yuelan , Yue Junjie , Diao Baowei , Kan Biao 
Published: May 2011

Abstract

Background
Some microorganisms can produce pigments such as melanin, which has been associated with virulence in the host and with a survival advantage in the environment. In Vibrio cholerae, studies have shown that pigment-producing mutants are more virulent than the parental strain in terms of increased UV resistance, production of major virulence factors, and colonization. To date, almost all of the pigmented V. cholerae strains investigated have been induced by chemicals, culture stress, or transposon mutagenesis. However, during our cholera surveillance, some nontoxigenic serogroup O139 strains and one toxigenic O1 strain, which can produce pigment steadily under the commonly used experimental growth conditions, were obtained in different years and from different areas. The genes VC1344 to VC1347, which correspond to the El Tor strain N16961 genome and which comprise an operon in the tyrosine catabolic pathway, have been confirmed to be associated with a pigmented phenotype. In the present study, we investigated the mechanism of pigment production in these strains.

Results
Sequencing of the VC1344, VC1345, VC1346, and VC1347 genes in these pigmented strains suggested that a deletion mutation in the homogentisate oxygenase gene (VC1345) may be associated with the pigmented phenotype, and gene complementation confirmed the role of this gene in pigment production. An identical 15-bp deletion was found in the VC1345 gene of all six O139 pigment-producing strains examined, and a 10-bp deletion was found in the VC1345 gene of the O1 strain. Strict sequence conservation in the VC1344 gene but higher variance in the other three genes of this operon were observed, indicating the different stress response functions of these genes in environmental adaption and selection. On the basis of pulsed-field gel electrophoresis typing, the pigment-producing O139 strains showed high clonality, even though they were isolated in different years and from different regions. Additionally all these O139 strains belong to the rb4 ribotype, which contains the O139 strains isolated from diarrheal patients, although these strains are cholera toxin negative.

Conclusion
Dysfunction of homogentisate oxygenase (VC1345) causes homogentisate accumulation and pigment formation in naturally pigmented strains of V. cholerae. The high clonality of these strains may correlate to an environmental survival advantage in the V. cholerae community due to their pigment production, and may imply a potential protective function of melanin in environmental survival of such strains.