bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease
Authors: Dobrin Radu , Zhu Jun , Molony Cliona , Argman Carmen , Parrish Mark L , Carlson Sonia , Allan Mark F , Pomp Daniel , Schadt Eric E 
Published: May 2009

Abstract
Background
Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level.

Results
To provide an inter-tissue view of obesity with respect to molecular states that are associated with physiological states, we developed a framework for constructing tissue-to-tissue coexpression networks between genes in the hypothalamus, liver or adipose tissue. These networks have a scale-free architecture and are strikingly independent of gene-gene coexpression networks that are constructed from more standard analyses of single tissues. This is the first systematic effort to study inter-tissue relationships and highlights genes in the hypothalamus that act as information relays in the control of peripheral tissues in obese mice. The subnetworks identified as specific to tissue-to-tissue interactions are enriched in genes that have obesity-relevant biological functions such as circadian rhythm, energy balance, stress response, or immune response.

Conclusions
Tissue-to-tissue networks enable the identification of disease-specific genes that respond to changes induced by different tissues and they also provide unique details regarding candidate genes for obesity that are identified in genome-wide association studies. Identifying such genes from single tissue analyses would be difficult or impossible.
Phylogenetic classification of Escherichia coliO157:H7 strains of human and bovine origin using a novel set of nucleotide polymorphisms
Authors: Clawson Michael L , Keen James E , Smith Timothy PL , Durso Lisa M , McDaneld Tara G , Mandrell Robert E , Davis Margaret A , Bono James L 
Published: May 2009

Abstract
Background
Cattle are a reservoir of Shiga toxin-producing Escherichia coli O157:H7 (STEC O157), and are known to harbor subtypes not typically found in clinically ill humans. Consequently, nucleotide polymorphisms previously discovered via strains originating from human outbreaks may be restricted in their ability to distinguish STEC O157 genetic subtypes present in cattle. The objectives of this study were firstly to identify nucleotide polymorphisms in a diverse sampling of human and bovine STEC O157 strains, secondly to classify strains of either bovine or human origin by polymorphism-derived genotypes, and finally to compare the genotype diversity with pulsed-field gel electrophoresis (PFGE), a method currently used for assessing STEC O157 diversity.

Results
High-throughput 454 sequencing of pooled STEC O157 strain DNAs from human clinical cases (n = 91) and cattle (n = 102) identified 16,218 putative polymorphisms. From those, 178 were selected primarily within genomic regions conserved across E. coli serotypes and genotyped in 261 STEC O157 strains. Forty-two unique genotypes were observed that are tagged by a minimal set of 32 polymorphisms. Phylogenetic trees of the genotypes are divided into clades that represent strains of cattle origin, or cattle and human origin. Although PFGE diversity surpassed genotype diversity overall, ten PFGE patterns each occurred with multiple strains having different genotypes.

Conclusions
Deep sequencing of pooled STEC O157 DNAs proved highly effective in polymorphism discovery. A polymorphism set has been identified that characterizes genetic diversity within STEC O157 strains of bovine origin, and a subset observed in human strains. The set may complement current techniques used to classify strains implicated in disease outbreaks.
Worldwide patterns of haplotype diversity at 9p21.3, a locus associated with type 2 diabetes and coronary heart disease
Authors: Silander Kaisa , Tang Hua , Myles Sean , Jakkula Eveliina , Timpson Nicholas J , Cavalli-Sforza Luigi , Peltonen Leena 
Published: May 2009

AbstractA 100 kb region on 9p21.3 harbors two major disease susceptibility loci: one for type 2 diabetes (T2D) and one for coronary heart disease (CHD). The single nucleotide polymorphisms (SNPs) associated with these two diseases in Europeans reside on two adjacent haplotype blocks with independent effects on disease. To help delimit the regions that likely harbor the disease-causing variants in populations of non-European origin, we studied the haplotype diversity and allelic history of the 9p21.3 region using 938 unrelated individuals from 51 populations (Human Genome Diversity Panel). We used SNP data from Illumina's 650Y SNP arrays supplemented with five additional SNPs within the region of interest. Haplotype frequencies were analyzed with the EM algorithm implemented in PLINK. For the T2D locus, the TT risk haplotype of SNPs rs10811661 and rs10757283 was present at similar frequencies in all global populations, while a shared 6-SNP haplotype that carries the protective C allele of rs10811661 was found at a frequency of 2.9% in Africans and 41.3% in East Asians and was associated with low haplotype diversity. For the CHD locus, all populations shared a core risk haplotype spanning >17.5 kb, which shows dramatic increase in frequency between African (11.5%) and Middle Eastern (63.7%) populations. Interestingly, two SNPs (rs2891168 and rs10757278) tagging this CHD risk haplotype are most strongly associated with CHD disease status according to independent clinical fine-mapping studies. The large variation in linkage disequilibrium patterns identified between the populations demonstrates the importance of allelic background data when selecting SNPs for replication in global populations. Intriguingly, the protective allele for T2D and the risk allele for CHD show an increase in frequency in non-Africans compared to Africans, implying different population histories for these two adjacent disease loci.
Fibroblast Growth Factor 21 Controls Glycemia via Regulation of Hepatic Glucose Flux and Insulin Sensitivity
Authors: Berglund Eric D. , Li Candice Y. , Bina Holly A. , Lynes Sara E. , Michael M. Dodson , Shanafelt Armen B. , Kharitonenkov Alexei , Wasserman David H. 
Published: May 2009

AbstractFibroblast growth factor 21 (FGF21) is a novel metabolic regulator shown to improve glycemic control. However, the molecular and functional mechanisms underlying FGF21-mediated improvements in glycemic control are not completely understood. We examined FGF21 effects on insulin sensitivity and glucose fluxes upon chronic (daily injection for 8 d) and acute (6 h infusion) administration in ob/+ and ob/ob mice. Results show that chronic FGF21 ameliorated fasting hyperglycemia in ob/ob mice via increased glucose disposal and improved hepatic insulin sensitivity. Acute FGF21 suppressed hepatic glucose production, increased liver glycogen, lowered glucagon, and improved glucose clearance in ob/+ mice. These effects were blunted in ob/ob mice. Neither chronic nor acute FGF21 altered skeletal muscle or adipose tissue glucose uptake in either genotype. In conclusion, FGF21 has potent glycemic effects caused by hepatic changes in glucose flux and improved insulin sensitivity. Thus, these studies define mechanisms underlying anti-hyperglycemic actions of FGF21 and support its therapeutic potential.
Apurinic/Apyrimidinic Endonuclease 1 Alters Estrogen Receptor Activity and Estrogen-Responsive Gene Expression
Authors: Curtis Carol D. , Thorngren Daniel L. , Ziegler Yvonne S. , Sarkeshik Ali , Yates John R. , Nardulli Ann M. 
Published: May 2009

AbstractApurinic/apyrimidinic endonuclease 1 or redox factor-1 (Ape1/Ref-1) is a pleiotropic cellular protein involved in DNA repair and, through its redox activity, enhances the binding of a select group of transcription factors to their cognate recognition sequences in DNA. Thus, we were intrigued when we identified Ape1/Ref-1 and a number of DNA repair and oxidative stress proteins in a complex associated with the DNA-bound estrogen receptor α (ERα). Because Ape1/Ref-1 interacts with a number of transcription factors and influences their activity, we determined whether it might also influence ERα activity. We found that endogenously expressed Ape1/Ref-1 and ERα from MCF-7 human breast cancer cells interact and that Ape1/Ref-1 enhances the interaction of ERα with estrogen-response elements (EREs) in DNA. More importantly, Ape1/Ref-1 alters expression of the endogenous, estrogen-responsive progesterone receptor and pS2 genes in MCF-7 cells and associates with ERE-containing regions of these genes in native chromatin. Interestingly, knocking down Ape1/Ref-1 expression or inhibiting its redox activity with the small molecule inhibitor E3330 enhances estrogen responsiveness of the progesterone receptor and pS2 genes but does not alter the expression of the constitutively active 36B4 gene. Additionally, the reduced form of Ape1/Ref-1 increases and E3330 limits ERα-ERE complex formation in vitro and in native chromatin. Our studies demonstrate that Ape1/Ref-1 mediates its gene-specific effects, in part, by associating with endogenous, estrogen-responsive genes and that the redox activity of Ape1/Ref-1 is instrumental in altering estrogen-responsive gene expression.
Acute unilateral cataract in a postpartum adolescent with poorly-controlled type 1 diabetes
Authors: Ahmad S S , Misra A , Glenn A , Temple R C 
Published: May 2009

Acute cataract is recognized as a rare complication in adolescents with type 1 diabetes mellitus and may be associated with rapid improvement in glycaemia in patients with newly diagnosed diabetes. Transient cataracts, which resolve following improved metabolic control, and irreversible cataracts requiring surgery have also previously been documented. Development or progression of retinopathy may complicate pregnancy in women with diabetes. To our knowledge, we present the first case report of an acute cataract developing postpartum in a woman with type 1 diabetes. This rare case serves to demonstrate a possible association between acute cataract and altered glycaemic control in pregnancy. Acute cataract should be considered in any woman with diabetes who develops sudden visual loss following pregnancy.
Correlations of Free Thyroid Hormones Measured by Tandem Mass Spectrometry and Immunoassay with Thyroid-Stimulating Hormone across 4 Patient Populations
Authors: Jonklaas Jacqueline , Kahric-Janicic Natasa , Soldin Offie P , Soldin Steven J 
Published: May 2009

AbstractBackground: Accurate measurement of free thyroid hormones is important for managing thyroid disorders. Ultrafiltration liquid chromatography tandem mass spectrometry (LC-MS/MS) can reliably measure the concentrations of small molecules, including thyroid hormones. Our study was designed to compare free thyroid hormone measurements performed with immunoassay and LC-MS/MS.Methods: We studied the performance of LC-MS/MS in 4 different populations comprising pediatric patients, euthyroid adults, and healthy nonpregnant and pregnant women. The samples obtained from each population numbered 38, 200, 28, and 128, respectively. Free thyroxine, free triiodothyronine, and thyroid-stimulating hormone (TSH) concentrations were documented.Results: LC-MS/MS measurement of free thyroid hormones provided better correlation with log-transformed serum TSH in each population and also the populations combined. The correlations between free thyroxine measured by LC-MS/MS and log TSH in the pediatric outpatients and healthy adults were −0.90 and −0.77, respectively. The correlations for immunoassay were −0.82 and −0.48. The correlations between free triiodothyronine measured by LC-MS/MS and TSH for both pediatric and healthy adult populations were −0.72 and −0.68, respectively.Conclusions: Free thyroid hormone concentrations measured by LC-MS/MS correlate to a greater degree with log TSH values compared to concentrations measured by immunoassay. This correlation was maintained across the patient populations we studied and may reflect the accuracy and specificity of LC-MS/MS. The superior ability of LC-MS/MS to enable documentation of the well-known thyroid hormone–TSH relationship supports the use of this measurement technique in a variety of clinical situations.
Impact of Left Ventricular End-Diastolic Wall Stress on Plasma B-Type Natriuretic Peptide in Heart Failure with Chronic Kidney Disease and End-Stage Renal Disease
Authors: Niizuma Shinichiro , Iwanaga Yoshitaka , Yahata Takaharu , Tamaki Yodo , Goto Yoichi , Nakahama Hajime , Miyazaki Shunichi 
Published: May 2009

AbstractBackground: Plasma B-type natriuretic peptide (BNP) is a diagnostic and prognostic marker in heart failure (HF). Although renal function is reported as an important clinical determinant, precise evaluations of the relationships of renal function with hemodynamic factors in determining BNP have not been performed. Therefore, we evaluated the association of plasma BNP concentrations with LV end-diastolic wall stress (EDWS) in a broad range of HF patients including those with chronic kidney disease (CKD) and end-stage renal disease (ESRD).Methods: In 156 consecutive HF patients including those with CKD and ESRD, we measured plasma BNP and performed echocardiography and cardiac catheterization. LV EDWS was calculated as a crucial hemodynamic determinant of BNP.Results: Plasma BNP concentrations increased progressively with decreasing renal function across the groups (P &lt; 0.01) and were correlated with LV EDWS (r = 0.47) in the HF patients overall. This relationship was also present when patients were subdivided into systolic and diastolic HF (P &lt; 0.01). In multivariable analysis, higher EDWS was associated with increased BNP concentration independently of renal dysfunction (P &lt; 0.01). Anemia, systolic HF, and decreased BMI also contributed to increased BNP concentrations.Conclusions: These results suggest that LV EDWS is a strong determinant of BNP even in patients with CKD and ESRD. Anemia, obesity, and HF type (systolic or diastolic) should also be considered in interpreting plasma BNP concentrations in HF patients. These findings may contribute to the clinical management of HF patients, especially those complicated with CKD and ESRD.
Perfluorinated phosphonic acids in Canadian surface waters and wastewater treatment plant effluent: Discovery of a new class of perfluorinated acids
Authors: D'eon Jessica C. , Crozier Patrick W. , Furdui Vasile I. , Reiner Eric J. , Libelo E. Laurence , Mabury Scott A. 
Published: May 2009

Abstract
The environmental prevalence of a new class of perfluorinated acids, the perfluorinated phosphonic acids (PFPAs), was determined in Canadian surface waters and wastewater treatment plant (WWTP) effluent. For quality control and comparison, the C8- to C11-perfluorinated carboxylic acids and perfluorooctane sulfonic acid were included in the analysis. Water samples were extracted using weak anion-exchange solid-phase extraction cartridges. Perfluorinated phosphonic acids were observed in 80% of surface water samples and in six of the seven WWTP effluent samples. The C8-PFPA was observed at concentrations ranging from 88 ± 33 to 3,400 ± 900 pg/L in surface waters and from 760 ± 270 to 2,500 ± 320 pg/L in WWTP effluent. To our knowledge, this is the first observation of PFPAs in the environment. Given their structural similarities with perfluorinated carboxylic and sulfonic acids, PFPAs are expected to be persistent. The observation of PFPAs in the majority of samples analyzed here suggests they are prevalent environmental contaminants and should be considered in future environmental monitoring campaigns to better understand the total burden of fluorinated materials in the environment.
The Asian clam Corbicula fluminea as a biomonitor of trace element contamination: Accounting for different sources of variation using an hierarchical linear model
Authors: Shoults-Wilson W. Aaron , Peterson James T. , Unrine Jason M. , Rickard James , Black Marsha C. 
Published: May 2009

Abstract
In the present study, specimens of the invasive clam, Corbicula fluminea, were collected above and below possible sources of potentially toxic trace elements (As, Cd, Cr, Cu, Hg, Pb, and Zn) in the Altamaha River system (Georgia, USA). Bioaccumulation of these elements was quantified, along with environmental (water and sediment) concentrations. Hierarchical linear models were used to account for variability in tissue concentrations related to environmental (site water chemistry and sediment characteristics) and individual (growth metrics) variables while identifying the strongest relations between these variables and trace element accumulation. The present study found significantly elevated concentrations of Cd, Cu, and Hg downstream of the outfall of kaolin-processing facilities, Zn downstream of a tire cording facility, and Cr downstream of both a nuclear power plant and a paper pulp mill. Models of the present study indicated that variation in trace element accumulation was linked to distance upstream from the estuary, dissolved oxygen, percentage of silt and clay in the sediment, elemental concentrations in sediment, shell length, and bivalve condition index. By explicitly modeling environmental variability, the Hierarchical linear modeling procedure allowed the identification of sites showing increased accumulation of trace elements that may have been caused by human activity. Hierarchical linear modeling is a useful tool for accounting for environmental and individual sources of variation in bioaccumulation studies.
Distribution of Albian clastic deposits in the Benguela basin (Angola): evidence of a Benguela palaeocurrent?
Authors: Quesne Didier , Buta-Neto André , Benard Dominique , Guiraud Michel 
Published: May 2009

Abstract
The Albian clastic Tuenza Formation of the Benguela basin (south Angola) is described and its geographic distribution analysed in detail. From these observations, the existence of an Albian “PalaeoBenguela current” is proposed. This would imply that a marine longshore current reworked the sand transported by palaeorivers and settled it northward along the coast of the young Atlantic Ocean (during the Albian). A parallel between Albian clastic deposits and the modern sediments deposited by the Benguela current is drawn, focusing on the striking resemblance between the two currents, i.e. the actual Benguela current and the Albian marine current, and the associated sedimentary bodies.
Distribution of living benthic foraminifera in relation with environmental variables within the Aiguillon cove (Atlantic coast, France): improving knowledge for paleoecological interpretation
Authors: du Chatelet Eric Armynot , Degre Delphine , Sauriau Pierre-Guy , Debenay Jean-Pierre 
Published: May 2009

AbstractSearch for bioindicators in marine environments has provided new tools for monitoring global and local natural changes. Among these tools, benthic foraminifera play a central role. More accurate paleogeographical and paleoecological reconstructions become possible on the basis of the ecology of recent foraminifera. Nevertheless, factors acting on foraminiferal assemblages are still partially understood. The aim of this study is to correlate the distribution patterns of living (stained) benthic foraminifera with environmental variables such as tidal elevation, interstitial pore water salinity, organic matter content of the sediment, pheopigments, chlorophyll a, carbonate contents and grain size distribution of the sediment from 86 samples collected in the Aiguillon cove (France). In this paralic environment, sediment grain size, salinity and tidal elevation are fundamental factors that drive the distribution of the most abundant species i.e. Brizalina variabilis, Cribroelphidium excavatum and Haynesina germanica. Organic matter also influences the distribution patterns of benthic foraminifera: the relative abundance of Ammonia tepida is typically favored by an increase of total organic matter food resources. Chlorophyll a and pheopigments, as indicators of organic matter quality however may not be limiting in the proportion present in the Aiguillon cove. Carbonate proportions do not limit benthic foraminifera of the Aiguillon cove essentially with carbonaceous shells.
An Analysis of the Evaporation Method for Determining Interstitial Water
Authors: Dodd Charles G. 
Published: May 2009

Abstract
A theoretical study of the principles of evaporation of liquids from large pores in petroleum reservoir rock core samples has resulted in the development of a working hypothesis to explain the application of evaporation measurements to the determination of minimum interstitial-water content. Rate-determining factors that control kinetics of evaporation processes have been considered in evolving the new hypothesis. Variations in temperature during evaporation experiments are found to have a negligibly small effect on evaporation interstitial-water measurements. Determination of complete capillary-pressure curves by evaporation measurements is discussed briefly. Theoretical calculations indicate that minimum interstitial-water saturations determined by the evaporation method should correspond quantitatively with water saturations above transition zones in petroleum reservoirs. Experimental comparisons between the evaporation method and the well-accepted porous-disk method demonstrate excellent agreement.

Introduction
A new procedure for determining the "irreducible minimum"interstitial-water content of petroleum reservoir rock has been described recently by Messer. The essential novelty of Messer's experimental approach, as compared with methods previously proposed, lies in the displacement of a saturating liquid by evaporation rather than by the pressure of a second immiscible fluid or centrifugal force. Probably the major advantage of the evaporation process, especially when applied to routine core analyses, is its speed. In addition, it is applicable to drill cuttings. A third advantage, not suggested by Messer, results from using a saturating liquid known to wet the laboratory-extracted core with a zero contact angle.
Experience with the evaporation method has demonstrated that about 20 core samples may be run in eight hours. The porous-disk procedure of Rose and Bruce and the mercury pressuring method of Purcell permit the analysis of about two samples per day if the use of four cells each holding eight samples is assumed in the case of the former, and one piece of apparatus in the case of the latter. The centrifugal method of Slobod, Chambers, and Prehn is as rapid as the evaporation method when applied to "looser" cores of moderately high permeability, but is as slow as the other methods when relatively"tight" cores having permeabilities of a few millidarcys are analyzed.