bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Signatures of Equatorial and Extratropical Wave Forcing in Tropical Tropopause Layer Temperatures
Authors: Grise Kevin M. , Thompson David W. J. 
Published: December 2012

Abstract
Temperatures in the tropical tropopause layer (TTL) play an important role in stratosphere–troposphere exchange and in the formation and maintenance of thin cirrus clouds. Many previous studies have examined the contributions of extratropical and equatorial waves to the TTL using coarse-vertical-resolution satellite and reanalysis data. In this study, the authors provide new insight into the role of extratropical and equatorial waves in the TTL using high-vertical-resolution GPS radio occultation data.
The results examine the influence of four different wave forcings on the TTL: extratropical waves that propagate vertically into the stratosphere, extratropical waves that propagate meridionally into the subtropical stratosphere, extratropical waves that propagate meridionally into the subtropical troposphere, and the equatorial planetary waves. The vertically and meridionally propagating extratropical stratospheric waves are associated with deep, zonally symmetric temperature anomalies that extend and amplify with height throughout the lower-to-middle tropical stratosphere. In contrast, the extratropical tropospheric waves and the equatorial planetary waves are associated with tropical temperature anomalies that are confined below 20-km altitude. The equatorial planetary waves dominate the zonally asymmetric component of the TTL temperature field, and both the equatorial planetary waves and the extratropical tropospheric waves are linked to large temperature variability in a 1–2-km-deep layer near the tropical tropopause. The fine vertical scale of the TTL temperature features associated with the equatorial planetary waves and the extratropical tropospheric waves is only readily apparent in high-vertical-resolution data.
Sensitivity of Twenty-First-Century Global-Mean Steric Sea Level Rise to Ocean Model Formulation
Authors: Hallberg Robert , Adcroft Alistair , Dunne John P. , Krasting John P. , Stouffer Ronald J. 
Published: December 2012

AbstractTwo comprehensive Earth system models (ESMs), identical apart from their oceanic components, are used to estimate the uncertainty in projections of twenty-first-century sea level rise due to representational choices in ocean physical formulation. Most prominent among the formulation differences is that one (ESM2M) uses a traditional z-coordinate ocean model, while the other (ESM2G) uses an isopycnal-coordinate ocean. As evidence of model fidelity, differences in twentieth-century global-mean steric sea level rise are not statistically significant between either model and observed trends. However, differences between the two models’ twenty-first-century projections are systematic and both statistically and climatically significant. By 2100, ESM2M exhibits 18% higher global steric sea level rise than ESM2G for all four radiative forcing scenarios (28–49 mm higher), despite having similar changes between the models in the near-surface ocean for several scenarios. These differences arise primarily from the vertical extent over which heat is taken up and the total heat uptake by the models (9% more in ESM2M than ESM2G). The fact that the spun-up control state of ESM2M is warmer than ESM2G also contributes by giving thermal expansion coefficients that are about 7% larger in ESM2M than ESM2G. The differences between these models provide a direct estimate of the sensitivity of twenty-first-century sea level rise to ocean model formulation, and, given the span of these models across the observed volume of the ventilated thermocline, may also approximate the sensitivities expected from uncertainties in the characterization of interior ocean physical processes.
Current Capability of Operational Numerical Models in Predicting Tropical Cyclone Intensity in the Western North Pacific
Authors: Yu Hui , Chen Peiyan , Li Qingqing , Tang Bi 
Published: December 2012

Abstract
Forecasts of tropical cyclone (TC) intensity from six operational models (three global models and three regional models) during 2010 and 2011 are assessed to study the current capability of model guidance in the western North Pacific. The evaluation is performed on both Vmax and Pmin from several aspects, including the relative error, skill assessment, category score, the hitting rate of trend, and so on. It is encouraging to see that the models have had some skills in the prediction of TC intensity, including that two of them are better than a statistical baseline in Vmax at several lead times and three of them show some skill in intensity change. With dissipated cases included, all the models have skills in category and trend forecasting at lead times longer than 24 h or so. The model forecast errors are found to be significantly correlated with initial error and the observed initial intensity. A statistical calibration scheme for model forecasting is proposed based on such an attribute, which is more effective for Pmin than Vmax. The statistically calibrated model forecasts are important in setting up a skillful multimodel consensus, for either the mean or the statistically weighted mean. The Vmax forecasts converted from the calibrated Pmin consensus based on a statistical wind–pressure relationship show significant skill over the baseline and a skillful scheme is also proposed to deal with the delay of the model forecasts in operation.
Hurricane Eyewall Slope as Determined from Airborne Radar Reflectivity Data: Composites and Case Studies
Authors: Hazelton Andrew T. , Hart Robert E. 
Published: December 2012

Abstract
Understanding and predicting the evolution of the tropical cyclone (TC) inner core continues to be a major research focus in tropical meteorology. Eyewall slope and its relationship to intensity and intensity change is one example that has been insufficiently studied. Accordingly, in this study, radar reflectivity data are used to quantify and analyze the azimuthal average and variance of eyewall slopes from 124 flight legs among 15 Atlantic TCs from 2004 to 2011. The slopes from each flight leg are averaged into 6-h increments around the best-track times to allow for a comparison of slope and best-track intensity. A statistically significant relationship is found between both the azimuthal mean slope and pressure and between slope and wind. In addition, several individual TCs show higher correlation between slope and intensity, and TCs with both relatively high and low correlations are examined in case studies. In addition, a correlation is found between slope and radar-based eye size at 2 km, but size shows little correlation with intensity. There is also a tendency for the eyewall to tilt downshear by an average of approximately 10°. In addition, the upper eyewall slopes more sharply than the lower eyewall in about three-quarters of the cases. Analysis of case studies discusses the potential effects on eyewall slope of both inner-core and environmental processes, such as vertical shear, ocean heat content, and eyewall replacement cycles. These results indicate that eyewall slope is an important measure of TC inner-core structure, and may prove useful for future study of the processes that drive changes in the TC core.
Quantitation of hematogones at the time of engraftment is a useful prognostic indicator in allogeneic hematopoietic stem cell transplantation
Authors: Shima Takahiro , Miyamoto Toshihiro , Kikushige Yoshikane , Mori Yasuo , Kamezaki Kenjiro , Takase Ken , Henzan Hideho , Numata Akihiko , Ito Yoshikiyo , Takenaka Katsuto , Iwasaki Hiromi , Kamimura Tomohiko , Eto Tetsuya , Nagafuji Koji , Teshima Takanori , Kato Koji , Akashi Koichi 
Published: December 2012

Key PointsQuantitation of hematogones at engraftment is useful to predict prognosis of patients treated with allogeneic stem cell transplantation.
Retinoid agonist Am80-enhanced neutrophil bactericidal activity arising from granulopoiesis in vitro and in a neutropenic mouse model
Authors: Ding Wanjing , Shimada Hiroyuki , Li Lin , Mittal Rahul , Zhang Xiaokun , Shudo Koichi , He Qiaojun , Prasadarao Nemani V. , Wu Lingtao 
Published: December 2012

Key PointsNeutrophils mobilized by Am80 display greater bactericidal activity than those by G-CSF. These findings suggest a molecular rationale for developing new therapy for neutropenia by using Am80 as a cost-effective treatment option.
Risk factors for secondary transmission of Shigellainfection within households: implications for current prevention policy
Authors: Boveé Lian , Whelan Jane , Sonder Gerard JB , van Dam Alje P , van den Hoek Anneke 
Published: December 2012

Abstract

Background
Internationally, guidelines to prevent secondary transmission of Shigella infection vary widely. Cases, their contacts with diarrhoea, and those in certain occupational groups are frequently excluded from work, school, or daycare. In the Netherlands, all contacts attending pre-school (age 0–3) and junior classes in primary school (age 4–5), irrespective of symptoms, are also excluded pending microbiological clearance. We identified risk factors for secondary Shigella infection (SSI) within households and evaluated infection control policy in this regard.

Methods
This retrospective cohort study of households where a laboratory confirmed Shigella case was reported in Amsterdam (2002–2009) included all households at high risk for SSI (i.e. any household member under 16 years). Cases were classified as primary, co-primary or SSIs. Using univariable and multivariable binomial regression with clustered robust standard errors to account for household clustering, we examined case and contact factors (Shigella serotype, ethnicity, age, sex, household size, symptoms) associated with SSI in contacts within households.

Results
SSI occurred in 25/ 337 contacts (7.4%): 20% were asymptomatic, 68% were female, and median age was 14 years (IQR: 4–38). In a multivariable model adjusted for case and household factors, only diarrhoea in contacts was associated with SSI (IRR 8.0, 95% CI:2.7-23.8). In a second model, factors predictive of SSI in contacts were the age of case (0–3 years (IRRcase≥6 years:2.5, 95% CI:1.1-5.5) and 4–5 years (IRRcase≥6 years:2.2, 95% CI:1.1-4.3)) and household size (>6 persons (IRR2-4 persons 3.4, 95% CI:1.2-9.5)).

Conclusions
To identify symptomatic and asymptomatic SSI, faecal screening should be targeted at all household contacts of preschool cases (0–3 years) and cases attending junior class in primary school (4–5 years) and any household contact with diarrhoea. If screening was limited to these groups, only one asymptomatic adult carrier would have been missed, and potential exclusion of 70 asymptomatic contacts <6 years old from school or daycare, who were contacts of cases of all ages, could have been avoided.
Human amniotic epithelial cells differentiate into cells expressing germ cell specific markers when cultured in medium containing serum substitute supplement
Authors: Evron Ayelet , Goldman Shlomit , Shalev Eliezer 
Published: December 2012

Abstract

Background
Human amniotic epithelial cells (hAECs) maintain the plasticity of pregastrulation embryonic cells, having the potential to differentiate into all three germ layers. The potential of these cells to differentiate into cells expressing germ cell specific markers has never been described before.

Methods
In the present study, hAECs were cultured in medium containing serum substitute supplement (SSS). Gene and protein expression of germ cell and oocyte specific markers was assessed by reverse transcription-polymerase chain reaction (RT-PCR), immunofluorescence staining and flow activated cell sorter analysis (FACS) in hAECs at different time points during the differentiation into cells expressing germ cell specific markers.

Results
When cultured with SSS, already at passage 1, hAECs start to express the germ cell specific genes C-KIT, DAZL, VASA and ZP3 and at passage 5 large round cells, resembling oocytes, appeared. The cells express the germ cell specific marker DAZL, the oocyte specific markers GDF9 and ZP3 and the meiosis specific markers DMC1 and SCP3 at the protein level.

Conclusions
From our preliminary results we can conclude that hAECs have the potential to differentiate into cells expressing germ cell specific markers.
The chemokine, macrophage inflammatory protein-2γ, reduces the expression of glutamate transporter-1 on astrocytes and increases neuronal sensitivity to glutamate excitotoxicity
Authors: Fang Jie , Han Deping , Hong Jinsheng , Tan Qi , Tian Yeping 
Published: December 2012

AbstractBackgroundChanges in glutamatergic neurotransmission via decreased glutamate transporter (GLT) activity or expression contributes to multiple neurological disorders. Chemokines and their receptors are involved in neurological diseases but the role of chemokines in the expression of glutamate transporters is unclear.MethodsPrimary astrocytes were prepared from neonatal (<24 hours old) SJL/J mouse brains and incubated with 5 μg/ml lipopolysaccharide (LPS) or 50 ng/ml tumor necrosis factor α (TNF-α) for 24 hours. Soluble macrophage inflammatory protein-2γ (MIP-2γ) in culture supernatants was determined using a sandwich ELISA. The MIP-2γ effect on the expression of GLT-1 was measured by quantitative RT-PCR, flow cytometric analysis or western blot assay. Detergent-resistant membranes from astrocytes were isolated on the basis of their ability to float in density gradients. Raft-containing fractions were tracked by the enrichment of caveolin-1 and the dendritic lipid raft marker, flotillin-1. Cell viability was determined by measuring either the leakage of lactate dehydrogenase or the reduction of 3-(4,5-dimethylthiazol-2-yl)- 2,5-diphenyltetrazolium bromide by viable cells and confirmed by visual inspection.ResultsThe production of the chemokine MIP-2γ by mouse cortical astrocytes increased significantly after stimulation with LPS or TNF-αin vitro. Astrocytes over-expressing MIP-2γ down-regulated the expression of GLT-1 at the mRNA and protein level and caused redistribution of GLT-1 out of the lipid rafts that mediate glutamate uptake. We used pharmacological inhibitors to identify the downstream signaling pathways underlying MIP-2γ activity. We also found complementary results by knocking down MIP-2γ activity in astrocytes with MIP-2γ small interfering RNA (siRNA). MIP-2γ overexpression in astrocytes enhanced the neuronal toxicity of glutamate by decreasing GLT-1 activity, but MIP-2γ itself was not toxic to neurons.ConclusionsThese results suggest that MIP-2γ mediates the pathogenesis of central nervous system disorders associated with neutrophil infiltration in the brain and decreased GLT-1 activity.
Phenotype prediction from genome-wide association studies: application to smoking behaviors
Authors: Yoon Dankyu , Kim Young Jin , Park Taesung 
Published: December 2012

Abstract

Background
A great success of the genome wide association study enabled us to give more attention on the personal genome and clinical application such as diagnosis and disease risk prediction. However, previous prediction studies using known disease associated loci have not been successful (Area Under Curve 0.55 ~ 0.68 for type 2 diabetes and coronary heart disease). There are several reasons for poor predictability such as small number of known disease-associated loci, simple analysis not considering complexity in phenotype, and a limited number of features used for prediction.

Methods
In this research, we investigated the effect of feature selection and prediction algorithm on the performance of prediction method thoroughly. In particular, we considered the following feature selection and prediction methods: regression analysis, regularized regression analysis, linear discriminant analysis, non-linear support vector machine, and random forest. For these methods, we studied the effects of feature selection and the number of features on prediction. Our investigation was based on the analysis of 8,842 Korean individuals genotyped by Affymetrix SNP array 5.0, for predicting smoking behaviors.

Results
To observe the effect of feature selection methods on prediction performance, selected features were used for prediction and area under the curve score was measured. For feature selection, the performances of support vector machine (SVM) and elastic-net (EN) showed better results than those of linear discriminant analysis (LDA), random forest (RF) and simple logistic regression (LR) methods. For prediction, SVM showed the best performance based on area under the curve score. With less than 100 SNPs, EN was the best prediction method while SVM was the best if over 400 SNPs were used for the prediction.

Conclusions
Based on combination of feature selection and prediction methods, SVM showed the best performance in feature selection and prediction.
Miniature array analysis of microtremors
Authors: Cho Ikuo , Senna Shigeki , Fujiwara Hiroyuki 
Published: December 2012

We suggest observing microtremors by using a miniature array consisting of vertical-component seismometers that are placed at the center and on the circumference of a circle with a radius of several tens of centimeters, for identifying the phase velocities of Rayleigh waves with wavelengths exceeding several tens or a hundred meters. We present, as tools for the analysis, a set comprised of the analysis methods for the phase velocity and the evaluation method for the analysis limit, which were recently developed by the authors on the basis of a rigorous theory derived by generalizing a spatial autocorrelation method. We conducted miniature-array observations using four or six servo-type seismometers, JU-215 manufactured by Hakusan Corporation, at about 50 observation points throughout a test site and urban areas in Tsukuba City and its surroundings, which have various topographical and geologic environments. The time required from arrival at an observation point to retrieval averaged about 30 min. We could determine the phase velocities of Rayleigh waves with wavelengths of 40 and 100 m at 91% and 51% of all the observation points, respectively. Miniature array analyses can significantly improve the mobility of observation to infer shallow subsurface velocity structures to the depth of several tens of meters.
Prognostic Significance of Progesterone Receptor–Positive Tumor Cells Within Immunohistochemically Defined Luminal A Breast Cancer
Authors: Prat Aleix , Cheang Maggie Chon U. , Martín Miguel , Parker Joel S. , Carrasco Eva , Caballero Rosalía , Tyldesley Scott , Gelmon Karen , Bernard Philip S. , Nielsen Torsten O. , Perou Charles M. 
Published: December 2012

Purpose Current immunohistochemical (IHC)-based definitions of luminal A and B breast cancers are imperfect when compared with multigene expression-based assays. In this study, we sought to improve the IHC subtyping by examining the pathologic and gene expression characteristics of genomically defined luminal A and B subtypes. Patients and Methods Gene expression and pathologic features were collected from primary tumors across five independent cohorts: British Columbia Cancer Agency (BCCA) tamoxifen-treated only, Grupo Español de Investigación en Cáncer de Mama 9906 trial, BCCA no systemic treatment cohort, PAM50 microarray training data set, and a combined publicly available microarray data set. Optimal cutoffs of percentage of progesterone receptor (PR) –positive tumor cells to predict survival were derived and independently tested. Multivariable Cox models were used to test the prognostic significance. Results Clinicopathologic comparisons among luminal A and B subtypes consistently identified higher rates of PR positivity, human epidermal growth factor receptor 2 (HER2) negativity, and histologic grade 1 in luminal A tumors. Quantitative PR gene and protein expression were also found to be significantly higher in luminal A tumors. An empiric cutoff of more than 20% of PR-positive tumor cells was statistically chosen and proved significant for predicting survival differences within IHC-defined luminal A tumors independently of endocrine therapy administration. Finally, no additional prognostic value within hormonal receptor (HR) –positive/HER2-negative disease was observed with the use of the IHC4 score when intrinsic IHC-based subtypes were used that included the more than 20% PR-positive tumor cells and vice versa. Conclusion Semiquantitative IHC expression of PR adds prognostic value within the current IHC-based luminal A definition by improving the identification of good outcome breast cancers. The new proposed IHC-based definition of luminal A tumors is HR positive/HER2 negative/Ki-67 less than 14%, and PR more than 20%.
Consultations Between Patients With Breast Cancer and Surgeons: A Pathway From Patient-Centered Communication to Reduced Hopelessness
Authors: Robinson Jeffrey D. , Hoover Donald R. , Venetis Maria K. , Kearney Thomas J. , Street Richard L. 
Published: December 2012

PurposePatient-centered communication (PCC) affects psychosocial health outcomes of patients. However, these effects are rarely direct, and our understanding of such effects are largely based on self-report (v observational) data. More information is needed on the pathways by which concrete PCC behaviors affect specific psychosocial outcomes in cancer care. We hypothesized that PCC behaviors increase the satisfaction of patients with surgeons, which, in turn, reduces the postconsultation hopelessness of patients.Patients and MethodsIn Portland, OR, we videotaped consultations between 147 women newly diagnosed with breast cancer and nine surgeons and administered surveys to participants immediately preconsultation and postconsultation. Consultations were coded for PCC behaviors. Multivariate regression models analyzed the association between PCC and the satisfaction of patients and between satisfaction and hopelessness.ResultsLevels of hopelessness of patients significantly decreased from preconsultation to postconsultation (P < .001). Two PCC behaviors (ie, patient asserting treatment preference [odds ratio {OR}, 1.50/log unit; 95% CI, 1.01 to 2.23/log unit; P = .042] and surgeon providing good/hopeful news [OR, 1.62/log unit; 95% CI, 1.01 to 2.60/log unit; P = .047]) were independently significantly associated with the satisfaction of patients with surgeons, which, in turn, independently predicted reduced levels of postconsultation hopelessness (linear change, −0.78; 95% CI, 1.44 to −0.12; P = .02).ConclusionAlthough additional research is needed with larger and more-diverse data sets, these findings suggest the possibility that concrete and trainable PCC behaviors can lower the hopelessness of patients with breast cancer indirectly through their effects on patient satisfaction with care.