bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pacific Decadal Variability: Paced by Rossby Basin Modes?
Authors: Weijer Wilbert , Muñoz Ernesto , Schneider Niklas , Primeau François 
Published: August 2012

Abstract
A systematic study is presented of decadal climate variability in the North Pacific. In particular, the hypothesis is addressed that oceanic Rossby basin modes are responsible for enhanced energy at decadal and bidecadal time scales. To this end, a series of statistical analyses are performed on a 500-yr control integration of the Community Climate System Model, version 3 (CCSM3). In particular, a principal oscillation pattern (POP) analysis is performed to identify modal behavior in the subsurface pressure field.
It is found that the dominant energy of sea surface temperature (SST) variability at 25 yr (the model equivalent of the Pacific decadal oscillation) cannot be explained by the resonant excitation of an oceanic basin mode. However, significant energy in the subsurface pressure field at time scales of 17 and 10 yr appears to be related to internal ocean oscillations. However, these oscillations lack the characteristics of the classical basin modes, and must either be deformed beyond recognition by the background circulation and inhomogeneous stratification or have another dynamical origin altogether. The 17-yr oscillation projects onto the Pacific decadal oscillation and, if present in the real ocean, has the potential to enhance the predictability of low-frequency climate variability in the North Pacific.
Systematic Patterns of the Inconsistency between Snow Water Equivalent and Accumulated Precipitation as Reported by the Snowpack Telemetry Network
Authors: Meyer Jonathan D. D. , Jin Jiming , Wang Shih-Yu 
Published: August 2012

Abstract
The authors investigated the accuracy of snow water equivalent (SWE) observations compiled by 748 Snowpack Telemetry stations and attributed the systematic bias introduced to SWE measurements to drifting snow. Often observed, SWE outpaces accumulated precipitation (AP), which can be statistically and physically explained through 1) precipitation undercatchment and/or 2) drifting snow. Forty-four percent of the 748 stations reported at least one year where the maximum SWE was greater than AP, while 16% of the stations showed this inconsistency for at least 20% of the observed years. Regions with a higher likelihood of inconsistency contained drier snow and are exposed to higher winds speeds, both of which are positively correlated to drifting snow potential as well as gauge undercatch. Differentiating between gauge undercatch and potential drifting scenarios, days when SWE increased but AP remained zero were used. These drift days occurred on an average of 13.3 days per year for all stations, with 31% greater wind speeds at 10 m for such days (using reanalysis winds). Findings suggest marked consistency between SWE and AP throughout the Cascade Mountains and lower elevations of the interior west while indicating notable inconsistency between these two variables throughout the higher elevations of the Rocky Mountains, Utah mountain ranges, and the Sierra Nevada.
Sea Surface Temperature and Wind Stress Curl Variability near a Cape
Authors: Castelao Renato M. 
Published: August 2012

Abstract
The coupling between sea surface temperature (SST), SST gradients, and wind stress curl variability near a cape off Brazil is investigated using satellite observations and several different SST high-resolution analyses. The cape is characterized by strong SST fronts year-round, associated with upwelling and advection of warm water offshore in a western boundary current. Observations reveal a strong coupling between crosswind SST gradients and wind stress curl variability, with the predominantly negative crosswind gradients leading to negative, upwelling favorable wind stress curl anomalies. The spatial correlation between empirical orthogonal functions (EOF) of those variables is ~0.6, while the correlation between the EOF amplitude time series of the wind stress curl and crosswind SST gradients is larger than 0.7. The coupling occurs during summer and winter and is strongly modulated by variations in the wind stress directional steadiness. The intensity of the coupling is weaker than around capes on the California Current system, presumably because of higher variability in wind direction off Brazil. During periods of high wind stress directional steadiness off Cape Frio, the coupling is intensified by up to 40%–75%. Wind stress curl is also correlated with SST itself, especially in the vicinity of the cape, although not as strongly as with crosswind SST gradients. The analyses suggest that the observed wind stress curl anomalies can lead to surface cooling of as much as 1°C. If the enhanced upwelling leads to further strengthening of the upwelling front, negative wind stress curl anomalies may be intensified in a positive feedback mechanism.
On Fitting a Straight Line to Data when the “Noise” in Both Variables Is Unknown*
Authors: Clarke Allan J. , Van Gorder Stephen 
Published: August 2012

Abstract
In meteorology and oceanography, and other fields, it is often necessary to fit a straight line to some points and estimate its slope. If both variables corresponding to the points are noisy, the slope as estimated by the ordinary least squares regression coefficient is biased low; that is, for a large enough sample, it always underestimates the true regression coefficient between the variables. In the common situation when the relative size of the noise in the variables is unknown, an appropriate regression coefficient is plus or minus the ratio of the standard deviations of the variables, the sign being determined by the sign of the correlation coefficient. For this case of unknown noise, the authors here obtain the probability density function (pdf) for the true regression coefficient divided by the appropriate regression coefficient just mentioned. For the case when the number of data is very large, a simple analytical expression for this pdf is obtained; for a finite number of data points the relevant pdfs are obtained numerically. The pdfs enable the authors to provide tables for confidence intervals for the true regression coefficient. Using these tables, the end result of this analysis is a simple practical way to estimate the true regression coefficient between two variables given their standard deviations, the sample correlation, and the number of independent data.
CheapAML: A Simple, Atmospheric Boundary Layer Model for Use in Ocean-Only Model Calculations
Authors: Deremble Bruno , Wienders N. , Dewar W. K. 
Published: August 2012

Abstract
A model of the marine atmospheric boundary layer is developed for ocean-only modeling in order to better represent air–sea exchanges. This model computes the evolution of the atmospheric boundary layer temperature and humidity using a prescribed wind field. These quantities react to the underlying ocean through turbulent and radiative fluxes. With two examples, the authors illustrate that this formulation is accurate for regional and global modeling purposes and that turbulent fluxes are well reproduced in test cases when compared to reanalysis products. The model builds upon and is an extension of Seager et al.
Impact of Flow Dependence, Column Covariance, and Forecast Model Type on Surface-Observation Assimilation for Probabilistic PBL Profile Nowcasts
Authors: Rostkier-Edelstein Dorita , Hacker Joshua P. 
Published: August 2012

Abstract
A probabilistic verification and factor-separation analysis (FSA) elucidate skillful nowcasts of planetary boundary layer (PBL) temperature, moisture, and wind profiles with a single-column model (SCM) and ensemble filter (EF) assimilation of surface observations. Recently, an FSA showed the importance of surface assimilation versus advection and radiation on ensemble-mean skill. That work addressed the necessary complexity of the model and assimilation scheme for improving PBL nowcasts, relative to deterministic-mesoscale predictions. Here, probabilistic ensemble-based SCM forecasts are compared to a simple probabilistic postprocessing scheme termed climatological dressing (CD). CD adjusts a deterministic mesoscale forecast using surface-atmosphere 3D-climatological covariances, a 30-min persistence model, and surface-forecast errors. It also dresses the adjusted profile with an in-sample uncertainty distribution (obtained from archives) scaled by the 30-min forecast error. Superior deterministic skill from SCM/EF results during night when flow-dependent covariances are more accurate than climatological covariances. CD is deterministically more skillful for temperature and moisture profiles during daytime because SCM/PBL parameterization yields biased covariances. SCM/EF is most probabilistically skillful because (a) the EF covariances accommodate large seasonal variability, (b) the 30-min error persistence assumption fails during nighttime, and (c) vertical error covariance estimates from archived forecasts are generally poor estimates of actual error covariances. A probabilistic FSA of the SCM/EF shows the relative importance of surface assimilation, radiation parameterization, and advection during night. Results confirm surface assimilation as the most important factor. A factor can be deterministically beneficial and probabilistically detrimental, or vice versa, depending on its role in reducing mean error or improving sharpness. Assimilation results in notable probabilistic improvement for nowcasts of low-level jet structures.
Evaluation of the Storm Prediction Center’s Day 1 Convective Outlooks
Authors: Hitchens Nathan M. , Brooks Harold E. 
Published: August 2012

Abstract
The Storm Prediction Center has issued daily convective outlooks since the mid-1950s. This paper represents an initial effort to examine the quality of these forecasts. Convective outlooks are plotted on a latitude–longitude grid with 80-km grid spacing and evaluated using storm reports to calculate verification measures including the probability of detection, frequency of hits, and critical success index. Results show distinct improvements in forecast performance over the duration of the study period, some of which can be attributed to apparent changes in forecasting philosophies.
Adherence to adjuvant endocrine therapy in women with breast cancer
Authors: Danilak Melanie , Chambers Carole R 
Published: August 2012

Purpose: To determine how many breast cancer patients who initiated adjuvant endocrine therapy discontinued early and to evaluate adherence in patients who persisted with therapy. Secondary objectives were to explore possible trends to see if certain factors may correlate to early discontinuation of therapy. Methods: A retrospective review of charts and pharmacy dispensing records was conducted, including patients who initiated adjuvant endocrine therapy for breast cancer at the Cross Cancer Institute from 1 January to 31 December, 2006. Results: Out of 346 patients, 81 (22%) discontinued therapy within 2 years. Adherence rates calculated for the 265 patients who remained on therapy beyond 2 years showed that 247 (93%) of these patients had 80% or better adherence. Patients who did not undergo chemotherapy and patients with Cross Cancer Institute follow-up times of less than 1 year were significantly more likely to discontinue therapy early. Conclusions: The majority of patients who were prescribed adjuvant endocrine therapy for breast cancer at the Cross Cancer Institute remained on therapy for at least 2 years and were adherent. Longer follow-up by Cross Cancer Institute practitioners may help decrease discontinuation rates.
Phase 2 study of subcutaneous omacetaxine mepesuccinate after TKI failure in patients with chronic-phase CML with T315I mutation
Authors: Cortes Jorge , Lipton Jeff H. , Rea Delphine , Digumarti Raghunadharao , Chuah Charles , Nanda Nisha , Benichou Annie-Claude , Craig Adam R. , Michallet Mauricette , Nicolini Franck E. , Kantarjian Hagop 
Published: August 2012

AbstractChronic myeloid leukemia (CML) patients with the BCR-ABL T315I mutation do not benefit from therapy with currently approved tyrosine kinase inhibitors. Omacetaxine mepesuccinate is a protein synthesis inhibitor that has demonstrated activity in cells harboring the T315I mutation. This phase 2 trial assessed the efficacy of omacetaxine in CML patients with T315I and tyrosine kinase inhibitor failure. Patients received subcutaneous omacetaxine 1.25 mg/m2 twice daily, days 1-14, every 28 days until hematologic response or a maximum of 6 cycles, and then days 1-7 every 28 days as maintenance. Results for patients treated in chronic phase are reported here. Patients (n = 62) received a median of 7 (range, 1-41) cycles. Complete hematologic response was achieved in 48 patients (77%; 95% lower confidence limit, 65%); median response duration was 9.1 months. Fourteen patients (23%; 95% lower confidence limit, 13%) achieved major cytogenetic response, including complete cytogenetic response in 10 (16%). Median progression free-survival was 7.7 months. Grade 3/4 hematologic toxicity included thrombocytopenia (76%), neutropenia (44%), and anemia (39%) and was typically manageable by dose reduction. Nonhematologic adverse events were mostly grade 1/2 and included infection (42%), diarrhea (40%), and nausea (34%). Omacetaxine may provide a safe and effective treatment for CML patients with T315I mutation. This study is registered at www.clinicaltrials.gov as NCT00375219.
Nontranscriptional activation of PI3K/Akt signaling mediates hypotensive effect following activation of estrogen receptor β in the rostral ventrolateral medulla of rats
Authors: Wu Kay LH , Chen Chen-Hsiu , Shih Cheng-Dean 
Published: August 2012

Abstract

Background
Estrogen acts on the rostral ventrolateral medulla (RVLM), where sympathetic premotor neurons are located, to elicit vasodepressor effects via an estrogen receptor (ER)β-dependent mechanism. We investigated in the present study nontranscriptional mechanism on cardiovascular effects following activation of ERβ in the RVLM, and delineated the involvement of phosphatidylinositol 3-kinase (PI3K)/serine/threonine kinase (Akt) signaling pathway in the effects.

Methods
In male Sprague–Dawley rats maintained under propofol anesthesia, changes in arterial pressure, heart rate and sympathetic neurogenic vasomotor tone were examined after microinjection bilaterally into RVLM of 17β-estradiol (E2β) or a selective ERα or ERβ agonist. Involvement of ER subtypes and PI3K/Akt signaling pathway in the induced cardiovascular effects were studied using pharmacological tools of antagonists or inhibitors, gene manipulation with antisense oligonucleotide (ASON) or adenovirus-mediated gene transfection.

Results
Similar to E2β (1 pmol), microinjection of ERβ agonist, diarylpropionitrile (DPN, 1, 2 or 5 pmol), into bilateral RVLM evoked dose-dependent hypotension and reduction in sympathetic neurogenic vasomotor tone. These vasodepressive effects of DPN (2 pmol) were inhibited by ERβ antagonist, R,R-tetrahydrochrysene (50 pmol), ASON against ERβ mRNA (250 pmol), PI3K inhibitor LY294002 (5 pmol), or Akt inhibitor (250 pmol), but not by ERα inhibitor, methyl-piperidino-pyrazole (1 nmol), or transcription inhibitor, actinomycin D (5 or 10 nmol). Gene transfer by microinjection into bilateral RVLM of adenovirus encoding phosphatase and tensin homologues deleted on chromosome 10 (5 × 108 pfu) reversed the vasodepressive effects of DPN.

Conclusions
Our results indicate that vasodepressive effects following activation of ERβ in RVLM are mediated by nongenomic activation of PI3K/Akt signaling pathway. This study provides new insight in the intracellular signaling cascades involved in central vasodepressive functions of estrogen.
Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates
Authors: Wang Jinkai , Cao Xiangyu , Zhang Yanfeng , Su Bing 
Published: August 2012

Abstract

Background
The highly improved cognitive function is the most significant change in human evolutionary history. Recently, several large-scale studies reported the evolutionary roles of DNA methylation; however, the role of DNA methylation on brain evolution is largely unknown.

Results
To test if DNA methylation has contributed to the evolution of human brain, with the use of MeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis to identify differentially methylated regions (DMRs) in the brain between humans and rhesus macaques. We first identified a total of 150 candidate DMRs by the MeDIP-Chip method, among which 4 DMRs were confirmed by the MassARRAY analysis. All 4 DMRs are within or close to the CpG islands, and a MIR3 repeat element was identified in one DMR, but no repeat sequence was observed in the other 3 DMRs. For the 4 DMR genes, their proteins tend to be conserved and two genes have neural related functions. Bisulfite sequencing and phylogenetic comparison among human, chimpanzee, rhesus macaque and rat suggested several regions of lineage specific DNA methylation, including a human specific hypomethylated region in the promoter of K6IRS2 gene.

Conclusions
Our study provides a new angle of studying human brain evolution and understanding the evolutionary role of DNA methylation in the central nervous system. The results suggest that the patterns of DNA methylation in the brain are in general similar between humans and non-human primates, and only a few DMRs were identified.
Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens
Authors: Cui Huan-Xian , Liu Ran-Ran , Zhao Gui-Ping , Zheng Mai-Qing , Chen Ji-Lan , Wen Jie 
Published: August 2012

Abstract

Background
Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been determined. In this study, a systematic identification of candidate genes and new pathways related to IMF deposition in chicken breast tissue has been made using gene expression profiles of two distinct breeds: Beijing-you (BJY), a slow-growing Chinese breed possessing high meat quality and Arbor Acres (AA), a commercial fast-growing broiler line.

Results
Agilent cDNA microarray analyses were conducted to determine gene expression profiles of breast muscle sampled at different developmental stages of BJY and AA chickens. Relative to d 1 when there is no detectable IMF, breast muscle at d 21, d 42, d 90 and d 120 (only for BJY) contained 1310 differentially expressed genes (DEGs) in BJY and 1080 DEGs in AA. Of these, 34–70 DEGs related to lipid metabolism or muscle development processes were examined further in each breed based on Gene Ontology (GO) analysis. The expression of several DEGs was correlated, positively or negatively, with the changing patterns of lipid content or breast weight across the ages sampled, indicating that those genes may play key roles in these developmental processes. In addition, based on KEGG pathway analysis of DEGs in both BJY and AA chickens, it was found that in addition to pathways affecting lipid metabolism (pathways for MAPK & PPAR signaling), cell junction-related pathways (tight junction, ECM-receptor interaction, focal adhesion, regulation of actin cytoskeleton), which play a prominent role in maintaining the integrity of tissues, could contribute to the IMF deposition.

Conclusion
The results of this study identified potential candidate genes associated with chicken IMF deposition and imply that IMF deposition in chicken breast muscle is regulated and mediated not only by genes and pathways related to lipid metabolism and muscle development, but also by others involved in cell junctions. These findings establish the groundwork and provide new clues for deciphering the molecular mechanisms underlying IMF deposition in poultry. Further studies at the translational and posttranslational level are now required to validate the genes and pathways identified here.
The polyphenol oxidase gene family in land plants: Lineage-specific duplication and expansion
Authors: Tran Lan T , Taylor John S , Constabel C Peter 
Published: August 2012

Abstract

Background
Plant polyphenol oxidases (PPOs) are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals.

Results
Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens, contained 13 PPO genes and Selaginella moellendorffii (spike moss) and Glycine max (soybean) each had 11 genes. Populus trichocarpa (poplar) contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO- like sequences were identified in several chlorophyte (green algae) genomes or Arabidopsis (A. lyrata and A. thaliana). We found that many PPOs contained one or two introns often near the 3’ terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes.

Conclusion
Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data. The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
Authors: Dhamgaye Sanjiveeni , Bernard Maria , Lelandais Gaelle , Sismeiro Odile , Lemoine Sophie , Coppée Jean-Yves , Le Crom Stéphane , Prasad Rajendra , Devaux Frédéric 
Published: August 2012

Abstract

Background
Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart.

Results
RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of β-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator.

Conclusion
Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.