bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguishing adrenal cortical carcinomas and adenomas: a study of clinicopathological features and biomarkers
Authors: Wang Cuiping , Sun Yang , Wu Huanwen , Zhao Dachun , Chen Jie 
Published: September 2013

AimsTo determine clinicopathological criteria and molecular markers helpful in distinguishing adrenocortical carcinomas (ACCs) from adrenocortical adenomas (ACAs).Methods and resultsWe analysed retrospectively the clinical and pathological features of 50 adrenal cortical tumours, and tested the expression of miR483‐3p by in‐situ hybridization as well as the expression of IGF2 and Smad4 by immunohistochemistry. We found that tumour size, tumour weight, hormonal function and the Weiss system are all high‐efficacy criteria for differentiating malignant from benign tumours (P < 0.001). MiR483‐3p was overexpressed in 68% (17 of 25) of ACCs compared to 12% (three of 25) of ACAs (P < 0.05). Using a combination of miR483‐3p and Smad4 improved diagnostic accuracy. Molecular markers were then tested in an independent set of 15 borderline tumours. We confirmed that the combined use of miR483‐3p and Smad4 immunochemistry can complement the Weiss score in the diagnosis of ACC in cases that display borderline histology.ConclusionsTumour size, tumour weight, hormonal function and the Weiss system are useful clinicopathological criteria that can result in accurate diagnosis of most ACCs and ACAs. In challenging cases, miR483‐3p and Smad4 expression may help in distinguishing these two entities.
Complete Genome Sequence of Antarctic Bacterium
Psychrobacter
sp. Strain G
Authors: Che Shuai , Song Lai , Song Weizhi , Yang Meng , Liu Guiming , Lin Xuezheng 
Published: September 2013

ABSTRACT

Here, we report the complete genome sequence of
Psychrobacter
sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus.
Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia
Authors: Sheh Alexander , Piazuelo M. Blanca , Wilson Keith T. , Correa Pelayo , Fox James G. 
Published: September 2013

ABSTRACT

The draft genome sequences of six Colombian
Helicobacter pylori
strains are presented. These strains were isolated from patients from regions of high and low gastric cancer risk in Colombia and were characterized by multilocus sequence typing. The data provide insights into differences between
H. pylori
strains of different phylogeographic origins.
Draft Genome Sequence of Sphingobium lactosutens Strain DS20
T
, Isolated from a Hexachlorocyclohexane Dumpsite
Authors: Kumar Roshan , Dwivedi Vatsala , Negi Vivek , Khurana J. P. , Lal Rup 
Published: September 2013

ABSTRACT

Sphingobium lactosutens
DS20
T
has been isolated from the hexachlorocyclohexane (HCH) dumpsite in Lucknow, India, but does not degrade any of the HCH isomers. Here, we present the ~5.36-Mb draft genome sequence of strain DS20
T
, which consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.
Complete Genome Sequence of a Channel Catfish Epidemic Isolate, Aeromonas hydrophila Strain ML09-119
Authors: Tekedar Hasan C. , Waldbieser Geoffrey C. , Karsi Attila , Liles Mark R. , Griffin Matt J. , Vamenta Stefanie , Sonstegard Tad , Hossain Mohammad , Schroeder Steven G. , Khoo Lester , Lawrence Mark L. 
Published: September 2013

ABSTRACT

Aeromonas hydrophila
is a Gram-negative, rod-shaped, mesophilic bacterium that infects both aquatic poikilothermic animals and mammals, including humans. Here, we present the complete genome sequence of
Aeromonas hydrophila
strain ML09-119, which represents a clonal group of
A. hydrophila
isolates causing outbreaks of bacterial septicemia in channel catfish since 2009.
Oestrogen receptor polymorphisms are an associated risk factor for mild cognitive impairment and Alzheimer disease in women APOE ɛ4 carriers: a case–control study
Authors: Fernández-Martínez Manuel , Elcoroaristizabal Martín Xabier , Blanco Martín Elisa , Galdos Alcelay Luis , Ugarriza Serrano Iratxe , Gómez Busto Fernando , Álvarez-Álvarez Maite , Molano Salazar Ana , Bereincua Gandarias Rocio , Inglés Borda Sandra , Uterga Valiente Juan María , Indakoetxea Juanbeltz Begoña , Gómez Beldarraín María Ángeles , Moraza López Josefa , Barandiarán Amillano Myriam , M de Pancorbo Marian 
Published: September 2013

ObjectivesExamine the role of single nucleotide polymorphisms (SNPs) in the oestrogen receptor (ER) genes: rs9340799, rs2234693, rs2228480 (in theESR1gene) and rs4986938 (in theESR2gene) as a risk factor for amnesic mild cognitive impairment (MCIa) and Alzheimer's disease (AD) and its possible association with the apolipoprotein E (APOE)gene.DesignWe have investigated the independent and combined association of different alleles of the oestrogen receptor genes and APOE*ɛ4 allele with cognitive impairment using a case–control design.SettingParticipants were prospectively recruited from the neurology departments of several Basque Country hospitals.ParticipantsThis study comprised 816 Caucasian participants who were aged 50 years and older: 204 MCIa, 350 sporadic patients with AD and 262 healthy controls.Primary and secondary outcome measuresClinical criteria and neuropsychological tests were used to establish the diagnostic groups (MCIa, AD and healthy controls). A dichotomous variable was used for each allele and genotype and the association with MCIa and AD was established using Logistic Regression Models.ResultsNeither alleles nor genotypes of SNPs rs9340799, rs2234693, rs2228480 and rs4986938 of oestrogen receptor genes (ESR1andESR2) are independently associated with the risk of MCIa or AD. However, the genetic profile created with the combination of the less represented alleles of these SNPs (expressed as XPAA) was associated with an increased risk for MCIa (OR=3.30, 95% CI 1.28 to 8.54, p=0.014) and AD (OR=5.16, 95% CI 2.19 to 12.14, p<0.001) in women APOE*ɛ4 allele carriers.ConclusionsThe less represented alleles of SNPs studied are associated with MCIa and AD in APOE*E4 carriers. In particular, the genetic profile created with the less represented alleles ofESR1andESR2SNPs are associated with an increased risk for MCIa and AD in women APOEɛ4 allele carriers.
Predicting adult obesity from measures in earlier life
Authors: Potter Caroline M , Ulijaszek Stanley J 
Published: September 2013

BackgroundAs most obese adults were not overweight as children, the prediction of adult obesity from childhood body size alone is limited. We constructed a two-way, multifactor risk assessment framework for predicting adult obesity during childhood using the Foresight Obesity System Map and tested it against longitudinal data from the 1958 National Child Development Study.MethodsThe framework divided study participants according to two categories of risk: ‘conditioning factors’ (past/fixed events and conditions) and ‘intervention factors’ (present and modifiable). At the age of 11 years, conditioning factors were ‘low/high birth weight’ and ‘absence of breastfeeding’, and intervention factors were ‘low childhood activity level’ and ‘having at least one obese parent’. From a composite score of all four variables, study participants were assigned to one of the four risk groups: low risk, past ‘conditioning’ risk only, present ‘intervention’ risk only and high combined risk. ORs and relative risks for the development of future overweight/obesity at ages 23, 33 and 42 years were calculated for each risk group.ResultsThose identified in the highest risk category at the age of 11 were around twice as likely to become overweight (body mass index (BMI)≥25 kg/m2) by the age of 23 years, and obese (BMI≥30 kg/m2) by ages 33 and 42 years, in comparison to their low-risk peers (total sample, N=11 752). Increased prevalence of future obesity was also observed for high-risk children who were not already overweight at the age of 11 (filtered sample, N=9549).ConclusionsThis framework identifies a greater proportion of the population that is at risk for future obesity than does childhood weight assessment alone.
Functional Heterogeneity of Cancer-Associated Fibroblasts from Human Colon Tumors Shows Specific Prognostic Gene Expression Signature
Authors: Herrera Mercedes , Islam Abul B.M.M.K. , Herrera Alberto , Martín Paloma , García Vanesa , Silva Javier , Garcia Jose M. , Salas Clara , Casal Ignacio , de Herreros Antonio García , Bonilla Félix , Peña Cristina 
Published: September 2013

Abstract
Purpose: Cancer-associated fibroblasts (CAF) actively participate in reciprocal communication with tumor cells and with other cell types in the microenvironment, contributing to a tumor-permissive neighborhood and promoting tumor progression. The aim of this study is the characterization of how CAFs from primary human colon tumors promote migration of colon cancer cells.
Experimental design: Primary CAF cultures from 15 primary human colon tumors were established. Their enrichment in CAFs was evaluated by the expression of various epithelial and myofibroblast specific markers. Coculture assays of primary CAFs with different colon tumor cells were performed to evaluate promigratory CAF-derived effects on cancer cells. Gene expression profiles were developed to further investigate CAF characteristics.
Results: Coculture assays showed significant differences in fibroblast-derived paracrine promigratory effects on cancer cells. Moreover, the association between CAFs' promigratory effects on cancer cells and classic fibroblast activation or stemness markers was observed. CAF gene expression profiles were analyzed by microarray to identify deregulated genes in different promigratory CAFs. The gene expression signature, derived from the most protumorogenic CAFs, was identified. Interestingly, this “CAF signature” showed a remarkable prognostic value for the clinical outcome of patients with colon cancer. Moreover, this prognostic value was validated in an independent series of 142 patients with colon cancer, by quantitative real-time PCR (qRT-PCR), with a set of four genes included in the “CAF signature.”
Conclusions: In summary, these studies show for the first time the heterogeneity of primary CAFs' effect on colon cancer cell migration. A CAF gene expression signature able to classify patients with colon cancer into high- and low-risk groups was identified. Clin Cancer Res; 19(21); 5914–26. ©2013 AACR.
Targeting Fibroblast Growth Factor Pathways in Prostate Cancer
Authors: Corn Paul G. , Wang Fen , McKeehan Wallace L. , Navone Nora 
Published: September 2013

AbstractAdvanced prostate cancer carries a poor prognosis and novel therapies are needed. Research has focused on identifying mechanisms that promote angiogenesis and cellular proliferation during prostate cancer progression from the primary tumor to bone—the principal site of prostate cancer metastases. One candidate pathway is the fibroblast growth factor (FGF) axis. Aberrant expression of FGF ligands and FGF receptors leads to constitutive activation of multiple downstream pathways involved in prostate cancer progression including mitogen-activated protein kinase, phosphoinositide 3-kinase, and phospholipase Cγ. The involvement of FGF pathways in multiple mechanisms relevant to prostate tumorigenesis provides a rationale for the therapeutic blockade of this pathway, and two small-molecule tyrosine kinase inhibitors—dovitinib and nintedanib—are currently in phase II clinical development for advanced prostate cancer. Preliminary results from these trials suggest that FGF pathway inhibition represents a promising new strategy to treat castrate-resistant disease. Clin Cancer Res; 19(21); 5856–66. ©2013 AACR.
5′-AMP–Activated Protein Kinase–Activating Transcription Factor 1 Cascade Modulates Human Monocyte–Derived Macrophages to Atheroprotective Functions in Response to Heme or Metformin
Authors: Wan Xinyi , Huo Yilin , Johns Michael , Piper Emma , Mason Justin C. , Carling David , Haskard Dorian O. , Boyle Joseph J. 
Published: September 2013

Objective—
Intraplaque hemorrhage (IPH) is an important driver of the progression of atherosclerotic plaques. Recently, we characterized Mhem as a novel macrophage phenotype that limits the atherogenicity of IPH. Mhem are directed by activating transcription factor 1 (ATF1), which is activated by phosphorylation. A better understanding of the counteratherogenic ATF1–Mhem pathway may facilitate antiatherosclerotic therapies.

Approach and Results—
We tested the hypothesis that heme in pathologically relevant concentrations activates the ATF1–Mhem pathway via 5′-AMP–activated protein kinase (AMPK) in primary human monocyte–derived macrophages and mouse bone marrow macrophages. We found that heme (10 μmol/L) activates AMPK, and downstream ATF1-mediated coinduction of heme oxygenase and liver X receptor that characterize Mhem. Heme increased macrophage phospho-AMPK, phospho-ATF1, and its target genes, and these effects were inhibited by the AMPK antagonist dorsomorphin, or by AMPK-knockdown with small inhibitory ribonucleic acid. The AMPK-activating oral hypoglycemic agent metformin also induced and phosphorylated ATF1 at a clinically relevant concentration (10 μmol/L). Functional effects of heme and metformin were inhibited by AMPK-knockdown and included suppression of macrophage oxidative stress; increased cholesterol export; protection from foam-cell formation; and suppression of macrophage inflammatory activation (human leukocyte antigen type DR expression).

Conclusions—
Our data indicate that heme activates the ATF1 pathway in human macrophages via AMPK, and that a similar response occurs after treatment of cells with metformin. Our results suggest an in vitro mechanism that may explain the clinical evidence that metformin has vascular protective effects beyond its role in treating hyperglycemia.
Inducible Overexpression of GLUT1 Prevents Mitochondrial Dysfunction and Attenuates Structural Remodeling in Pressure Overload but Does Not Prevent Left Ventricular Dysfunction
Authors: Pereira Renata O. , Wende Adam R. , Olsen Curtis , Soto Jamie , Rawlings Tenley , Zhu Yi , Anderson Steven M. , Dale Abel E. 
Published: September 2013

Background

Increased glucose transporter 1 (
GLUT1
) expression and glucose utilization that accompany pressure overload‐induced hypertrophy (
POH
) are believed to be cardioprotective. Moreover, it has been shown that lifelong transgenic overexpression of
GLUT1
in the heart prevents cardiac dysfunction after aortic constriction. The relevance of this model to clinical practice is unclear because of the life‐long duration of increased glucose metabolism. Therefore, we sought to determine if a short‐term increase in
GLUT1
‐mediated myocardial glucose uptake would still confer cardioprotection if overexpression occurred at the onset of
POH
.

Methods and Results

Mice with cardiomyocyte‐specific inducible overexpression of a hemagglutinin (
HA
)‐tagged
GLUT1
transgene (G1HA) and their controls (Cont) were subjected to transverse aortic constriction (
TAC
) 2 days after transgene induction with doxycycline (
DOX
). Analysis was performed 4 weeks after
TAC
. Mitochondrial function, adenosine triphosphate (
ATP
) synthesis, and
mRNA
expression of oxidative phosphorylation (
OXPHOS
) genes were reduced in Cont mice, but were maintained in concert with increased glucose utilization in G1HA following
TAC
. Despite attenuated adverse remodeling in G1HA relative to control
TAC
mice, cardiac hypertrophy was exacerbated in these mice, and positive dP/dt (in vivo) and cardiac power (ex vivo) were equivalently decreased in Cont and G1HA
TAC
mice compared to shams, consistent with left ventricular dysfunction. O‐GlcNAcylation of Ca
2+
cycling proteins was increased in G1HA
TAC
hearts.

Conclusions

Short‐term cardiac specific induction of
GLUT1
at the onset of
POH
preserves mitochondrial function and attenuates pathological remodeling, but exacerbates the hypertrophic phenotype and is insufficient to prevent
POH
‐induced cardiac contractile dysfunction, possibly due to impaired calcium cycling.
Evaluation of Satellite-Retrieved Extreme Precipitation over Europe using Gauge Observations
Authors: Lockhoff M. , Zolina O. , Simmer C. , Schulz J. 
Published: September 2013

Abstract
Climate change is expected to change precipitation characteristics and particularly the frequency and magnitude of precipitation extremes. Satellite observations form an important part of the observing system necessary to monitor both temporal and spatial patterns of precipitation variability and extremes. As satellite-based precipitation estimates are generally only indirect, however, their reliability has to be verified.
This study evaluates the ability of the satellite-based Global Precipitation Climatology Project One-Degree Daily (GPCP1DD) dataset to reliably reproduce precipitation variability and extremes over Europe compared to the European Daily High-resolution Observational Gridded Dataset (E-OBS). The results show that the two datasets agree reasonably well not only when looking at climatological statistics such as climatological mean, number of wet days (rain rates 1 mm), and mean intensity (i.e., mean over all wet days) but also with respect to their distributions. The results also reveal a pronounced seasonal cycle in the performance of GPCP1DD that is worse in winter and spring. Both deterministic and fuzzy verification methods are used to assess the ability of the GPCP1DD dataset to capture extremes. Fuzzy methods prove to be the better suited evaluation approach for such a highly variable parameter as precipitation because it compensates for slight spatial and temporal displacements. Whereas the deterministic diagnostics confirm previous findings on the deficiencies of satellite products, the “fuzzy” results show that at larger spatiotemporal scales (e.g., 3°/5 days) GPCP1DD has useful skill and is able to reliably represent the spatial and temporal variability of extremes.
Delayed Southern Hemisphere Climate Change Induced by Stratospheric Ozone Recovery, as Projected by the CMIP5 Models
Authors: Barnes Elizabeth A. , Barnes Nicholas W. , Polvani Lorenzo M. 
Published: September 2013

AbstractStratospheric ozone is expected to recover by the end of this century because of the regulation of ozone-depleting substances by the Montreal Protocol. Targeted modeling studies have suggested that the climate response to ozone recovery will greatly oppose the climate response to rising greenhouse gas (GHG) emissions. However, the extent of this cancellation remains unclear since only a few such studies are available. Here, a much larger set of simulations performed for phase 5 of the Coupled Model Intercomparison Project is analyzed, which includes ozone recovery. It is shown that the closing of the ozone hole will cause a delay in summertime [December–February (DJF)] Southern Hemisphere climate change between now and 2045. Specifically, it is found that the position of the jet stream, the width of the subtropical dry zones, the seasonality of surface temperatures, and sea ice concentrations all exhibit significantly reduced summertime trends over the first half of the twenty-first century as a consequence of ozone recovery. After 2045, forcing from GHG emissions begins to dominate the climate response. Finally, comparing the relative influences of future GHG emissions and historic ozone depletion, it is found that the simulated DJF tropospheric circulation changes between 1965 and 2005 (driven primarily by ozone depletion) are larger than the projected changes in any future scenario over the entire twenty-first century.
Generation and Separation of Mesoscale Eddies from Surface Ocean Fronts
Authors: Manucharyan Georgy E. , Timmermans Mary-Louise 
Published: September 2013

Abstract
This study is motivated by Arctic Ocean observations of sub–mixed layer eddies found at large distances from their assumed formation region of a surface ocean front. Eddy formation is explored through high-resolution numerical simulations of surface fronts, separating two mixed layers, with a range of configurations similar to those observed in the Arctic Ocean. This study finds that frontal instabilities lead to the development of self-propagating dipoles, which have the potential to propagate far from the front if interactions with other eddies are avoided. However, most dipoles are unbalanced, consisting of a dominating surface cyclone and a weaker anticyclone below, and thus propagate on curved trajectories with eventual recirculation back to the front. Their maximum separation distance from the front depends on the ratio of self-advecting velocities ϵ; balanced dipoles that have ϵ ≈ 1, and the ability to propagate far from the front. For dipoles generated numerically, this study estimates ϵ using analytical solutions of a 2½-layer quasigeostrophic model for Gaussian vortices. The distribution of the ratio ϵ for these dipoles is found to be skewed toward higher values (i.e., cyclones are dominant in dipoles). Sensitivity experiments suggest that shallow fronts that separate mixed layers of approximately equal depths favor the development of balanced dipoles that can self-propagate over long distances.
Time-Varying Biases in U.S. Total Cloud Cover Data
Authors: Free Melissa , Sun Bomin 
Published: September 2013

AbstractThis paper presents evidence of significant discontinuities in U.S. cloud cover data from the Integrated Surface Database (ISD) and its predecessor datasets. While long-term U.S. cloud records have some well-known homogeneity problems related to the introduction of the Automated Surface Observing System (ASOS) in the 1990s, the change to the international standard reporting format [aviation routine weather report (METAR)] in the United States in July 1996 introduces an additional inhomogeneity at many of the stations where humans still make or supplement cloud observations. This change is associated with an upward shift in total cloud of 0.1%–10%, statistically significant at 95 of 172 stations. The shift occurs at both National Weather Service and military weather stations, producing a mean increase in total cloud of 2%–3%. This suggests that the positive trends in U.S. cloud cover reported by other researchers for recent time periods may be exaggerated, a conclusion that is supported by comparisons with precipitation and diurnal temperature range data.Additional discontinuities exist at other times in the frequency distributions of fractional cloud cover at the majority of stations, many of which may be explained by changes in the sources and types of data included in ISD. Some of these result in noticeable changes in monthly-mean total cloud. The current U.S. cloud cover database needs thorough homogeneity testing and adjustment before it can be used with confidence for trend assessment or satellite product validation.
An Objective Analysis of Tornado Risk in the United States
Authors: Coleman Timothy A. , Dixon P. Grady 
Published: September 2013

Abstract
In this paper, an objective analysis of spatial tornado risk in the United States is performed, using a somewhat different dataset than in some previous tornado climatologies. The focus is on significant tornadoes because their reporting frequency has remained fairly stable for several decades. Also, data before 1973 are excluded, since those tornadoes were rated after the fact and were often overrated. Tornado pathlength within the vicinity of a grid point is used to show tornado risk, as opposed to tornado days or the total number of reported tornadoes. The possibility that many tornadoes in the Great Plains were underrated due to the lack of damage indicators, causing a low bias in the number of significant tornadoes there, is mostly discounted through several analyses. The kernel density analysis of 1973–2011 significant tornadoes performed herein shows that the area of highest risk for tornadoes in the United States extends roughly from Oklahoma to Tennessee and northwestern Georgia, with the highest risk in the southeastern United States, from central Arkansas across most of Mississippi and northern Alabama.