bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alternative expression of TCRζ related genes in patients with chronic myeloid leukemia
Authors: Zha Xianfeng , Yan Xiaojuan , Shen Qi , Zhang Yuping , Wu Xiuli , Chen Shaohua , Li Bo , Yang Lijian , Geng Suxia , Weng Jianyu , Du Xin , Li Yangqiu 
Published: December 2012

AbstractA previous study has demonstrated a significant decrease in the TCRζ gene expression level in chronic myeloid leukemia (CML); thus, we further investigated the expression of TCRζ-regulating factors, the distribution of the TCRζ 3' untranslated region (3'-UTR) splice variants, and the expression level and correlation of the alternative splicing factor/splicing factor 2 (ASF/SF-2), FcεRIγ and ZAP-70 genes. TCRζ 3'-UTR splice variants were identified in peripheral blood mononuclear cells (PBMCs) from 14 healthy individuals, 40 patients with CML and 22 patients with CML in complete remission (CML-CR) by RT-PCR. The expression level of the TCRζ, FcεRIγ, ASF/SF-2 and ZAP-70 genes was analyzed by real-time quantitative PCR. While the expression of TCRζ gene in the CML group was significantly lower than that in the healthy individual and CML-CR groups, a significantly higher expression of the FceRIγ and ASF/SF-2 genes was found in the CML group. Two types of splicing forms were detected in all of the healthy individual CML-CR cases: wild type (WT) TCRζ 3'-UTR and alternatively splieced (AS) TCRζ 3'-UTR which have been alternatively splieced in the WT TCRζ 3'-UTR . However, 35% of the CML cases contained only the wild type TCRζ 3'-UTR isoform. Based on the TCRζ 3'-UTR isoform expression characteristic, we divided the patients with CML into two subgroups: the WT+AS-CML group, containing patients that express only the wild type TCRζ 3'-UTR, and the WT+AS+CML group, which contained patients that expressed two TCRζ 3'-UTR isoforms. A significantly different ASF/SF-2 and FcεRIγ gene expression pattern was found between the WT+AS-and WT+AS+CML groups. We concluded that defective TCRζ expression may be characterized in the WT+AS-and WT+AS+CML subgroups by the different gene expression pattern. The overexpression of ASF/SF2, which alternatively splices the TCRζ 3’-UTR, is thought to participate in feedback regulation. The characteristics of TCRζ 3'-UTR alternative splicing may be a novel immunological marker for the evaluation of the CML immune status.
Unusual osseous presentation of blastomycosis in an immigrant child: a challenge for European pediatricians
Authors: Codifava Margherita , Guerra Azzurra , Rossi Giulio , Paolucci Paolo , Iughetti Lorenzo 
Published: December 2012

Abstract

Background
Blastomycosis, caused by the thermally dimorphic fungus Blastomyces dermatitidis is a systemic pyogranulomatous infection, endemic in United States and Canada, with few reported cases in Africa and Asia. It is uncommon among children and adolescents, ranging from 3% to 10%. Clinical features vary from asymptomatic spontaneously healing pneumonia, through acute or chronic pneumonia, to a malignant appearing lung mass. Blastomycosis can originate a "metastatic disease" in the skin, bones, genitourinary tract and central nervous system. Bone is the third most common site of blastomycotic lesions, after lung and skin. Bones may be involved in 14-60% of cases of blastomycosis. Direct visualization of single broadbased budding yeast with specific stains in sputum or tissue samples at microscopy is the primary method for diagnosis, while culture is timeconsuming and other methods are unreliable.

Case presentation
We report a case of severe osteoarticular Blastomycosis occurring in a 3-years-old presented to our Emergency Department with pain and swelling of the left knee, successfully treated with surgical curettage and antifungal therapy. To our knowledge this is the first case reported in Europe.

Conclusions
Blastomycosis represents a challenge for European physicians, and it should be included in the differential diagnosis of unexplained infections in patients coming from endemic areas.
Access to kidney transplantation: outcomes of the non-referred
Authors: AlBugami Meteb M , Panek Romuald , Soroka Steven , Tennankore Karthik , Kiberd Bryce A 
Published: December 2012

Abstract

Background
There is a concern that some, especially older people, are not referred and could benefit from transplantation.

Methods
We retrospectively examined consecutive incident end stage renal disease (ESRD) patients at our center from January 2006 to December 2009. At ESRD start, patients were classified into those with or without contraindications using Canadian eligibility criteria. Based on referral for transplantation, patients were grouped as CANDIDATE (no contraindication and referred), NEITHER (no contraindication and not referred) and CONTRAINDICATION. The Charlson Comorbidity Index (CCI) was used to assess comorbidity burden.

Results
Of the 437 patients, 133 (30.4%) were CANDIDATE (mean age 50 and CCI 3.0), 59 (13.5%) were NEITHER (age 76 and CCI 4.4), and 245 (56.1%) were CONTRAINDICATION (age 65 and CCI 5.5). Age was the best discriminator between NEITHER and CANDIDATES (c-statistic 0.96, P <0.0001) with CCI being less discriminative (0.692, P <0.001). CANDIDATES had excellent survival whereas those patients designated NEITHER and CONTRAINDICATION had high mortality rates. NEITHER patients died or developed a contraindication at very high rates. By 1.5 years 50% of the NEITHER patients were no longer eligible for a transplant.

Conclusions
There exists a relatively small population of incident patients not referred who have no contraindications. These are older patients with significant comorbidity who have a small window of opportunity for kidney transplantation.
Effects of EPA supplementation on plasma fatty acids composition in hypertriglyceridemic subjects with FABP2 and PPARα genotypes
Authors: Pishva Hamideh , Amini Mohsen , Eshraghian Mohammad Reza , Hosseini Saeed , Mahboob Soltan Ali 
Published: December 2012

Abstract
Background
Fatty acid binding protein 2 (FABP2) and peroxisome proliferator-activated receptor α (PPARα) are involved in cellular uptake and metabolism of fatty acids. Polymorphism of FABP2 and PPARα may influence plasma levels of fatty acids in those who take supplemental eicosapentaenoic acid (EPA). The purpose of this study was to study the potential associations between the Ala54/Thr polymorphism in FABP2 protein and the Leu162/Val in exon 5 and G/C in intron 7 of PPARα with plasma fatty acids composition after EPA supplementation.

Methods
Twenty three FABP2 Ala54 and twenty three Thr54 carriers with hypertriglyceridemia were enrolled in this study. Participants took 2 g of pure EPA daily for 8 wks. Plasma fatty acids composition was determined and changes from the baseline were measured.

Results
Although EPA supplementation increased the level of plasma EPA and ω-3 fatty acids in both carriers of FABP2 and PPARα genes, these effects were more pronounced in Thr54 and Val162 carriers. EPA supplementation decreased the level of some n-6 fatty acids such as arachidonic acid.

Conclusion
EPA consumption has more favorable effects on blood n-3 fatty acids and can change the level of plasma n-3 fatty acids, particularly EPA. Because the FABP2 Thr54 polymorphism appears to be prevalent in hypertriglyceridemic subjects, increasing EPA intake in these subjects could be an effective strategy for preventing cardiovascular diseases. Finally, diets and micronutrient recommendations should be individualized for high risk people.
Citrullinated fibronectin inhibits apoptosis and promotes the secretion of pro-inflammatory cytokines in fibroblast-like synoviocytes in rheumatoid arthritis
Authors: Fan Lieying , Wang Qiang , Liu Rongqing , Zong Ming , He Dongyi , Zhang Hui , Ding Yuanyuan , Ma Jianwei 
Published: December 2012

Abstract
Introduction
Rheumatoid arthritis (RA) is characterized by synovial lining hyperplasia, in which there may be an imbalance between the growth and death of fibroblast-like synoviocytes (FLSs). Antibodies against citrullinated proteins are proposed to induce RA. This study aimed to investigate the pathogenic role of citrullinated fibronectin (cFn) in RA.

Methods
The distribution of fibronectin (Fn) and cFn in synovial tissues from RA and osteoarthritis (OA) patients was examined by immunohistochemical and double immunofluorescence analysis. FLSs were isolated from RA and OA patients and treated with Fn or cFn. Apoptosis was detected by flow cytometry and TUNEL assay. The expression of survivin, caspase-3, cyclin-B1, Bcl-2 and Bax was detected by real-time PCR. The secretion of proinflammatory cytokines was measured by ELISA.

Results
Fn formed extracellular aggregates that were specifically citrullinated in synovial tissues of RA patients, but no Fn deposits were observed in those of OA patients. Fn induced the apoptosis of RA and OA FLSs while cFn inhibited the apoptosis of RA and OA FLSs. Fn significantly increased the expression of caspase-3 and decreased the expression of survivin and cyclin-B1 in FLSs from RA and OA patients. cFn significantly increased the expression of survivin in RA FLSs. Furthermore, cFn increased the secretion of TNF-α and IL-1 by FLSs.

Conclusions
cFn plays a potential pathophysiologic role in RA by inhibiting apoptosis and increasing proinflammatory cytokine secretion of FLSs.
Silencing of microRNA-101 prevents IL-1β-induced extracellular matrix degradation in chondrocytes
Authors: Dai Linghui , Zhang Xin , Hu Xiaoqing , Zhou Chunyan , Ao Yingfang 
Published: December 2012

Abstract
Introduction
Extracellular matrix (ECM) degradation leads to malfunction of the cartilage in osteoarthritis (OA). Inflammatory cytokine interleukin-1 beta (IL-1β) functions in ECM degradation and prevents ECM synthesis by down-regulating the key transcription factor, Sox9, and consequently inhibiting ECM gene expression. Evidence reveals that microRNAs (miRNA) have been associated with OA, but little is known of their function in chondrocyte ECM degradation. This study aimed to identify possible miRNAs that mediate IL-1β-induced down-regulation of Sox9 as well as its known down-stream genes, collagen type II and aggrecan.

Methods
The miRNAs were predicted based on three classical databases. The expression levels of the predicted miRNAs were assessed in IL-1β stimulated chondrocytes by real-time PCR. A luciferase reporter was used to test the binding of the miRNAs to the 3' untranslated regions (3'UTR) of Sox9. The predicted miRNAs were transfected into chondrocytes to validate their relationship with Sox9. Functional analysis of the miRNAs on chondrocytes ECM degradation was performed at both the mRNA and protein levels after miRNA transfection and IL-1β treatment.

Results
Six miRNAs were predicted to target Sox9, and their expression in IL-1β-stimulated chondrocytes was revealed by real-time PCR. The luciferase reporter assay indicated that only miR-101 could bind to the 3'UTR of Sox9. The expression of Sox9 was likewise negatively regulated by miR-101 in rat chondrocytes. Functional analysis showed that miR-101 could aggravate chondrocyte ECM degradation, whereas miR-101 inhibition could reverse IL-1β-induced ECM degradation.

Conclusion
miR-101 participates in IL-1β-induced chondrocyte ECM degradation. Down-regulating miR-101 expression can prevent the IL-1β-induced ECM degradation in chondrocytes. miR-101 probably functions by directly targeting Sox9 mRNA.
Derivation of HLA types from shotgun sequence datasets
Authors: Warren René L , Choe Gina , Freeman Douglas J , Castellarin Mauro , Munro Sarah , Moore Richard , Holt Robert A 
Published: December 2012

AbstractThe human leukocyte antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. We describe HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets (http://www.bcgsc.ca/platform/bioinfo/software/hlaminer). This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.
Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat
Authors: Pérez-Rodríguez Paulino , Gianola Daniel , González-Camacho Juan Manuel , Crossa José , Manès Yann , Dreisigacker Susanne 
Published: December 2012

AbstractIn genome-enabled prediction, parametric, semi-parametric, and non-parametric regression models have been used. This study assessed the predictive ability of linear and non-linear models using dense molecular markers. The linear models were linear on marker effects and included the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B. The non-linear models (this refers to non-linearity on markers) were reproducing kernel Hilbert space (RKHS) regression, Bayesian regularized neural networks (BRNN), and radial basis function neural networks (RBFNN). These statistical models were compared using 306 elite wheat lines from CIMMYT genotyped with 1717 diversity array technology (DArT) markers and two traits, days to heading (DTH) and grain yield (GY), measured in each of 12 environments. It was found that the three non-linear models had better overall prediction accuracy than the linear regression specification. Results showed a consistent superiority of RKHS and RBFNN over the Bayesian LASSO, Bayesian ridge regression, Bayes A, and Bayes B models.
Natural Variation in the Yeast Glucose-Signaling Network Reveals a New Role for the Mig3p Transcription Factor
Authors: Lewis Jeffrey A , Gasch Audrey P 
Published: December 2012

AbstractThe Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors. While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered, despite numerous investigations of laboratory yeast strains. Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains. We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment. Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard vs. stress conditions and that this function has been largely lost in the lab strains. Population analysis suggests that the lab strain and several wild strains harbor mutations that diminish Mig3p function. Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response.
Differentiation-Driven Nucleolar Association of the Mouse Imprinted Kcnq1 Locus
Authors: Fedoriw Andrew M , Calabrese J Mauro , Mu Weipeng , Yee Della , Magnuson Terry 
Published: December 2012

Abstract
The organization of the genome within the mammalian nucleus is nonrandom, with physiologic processes often concentrated in specific three-dimensional domains. This organization may be functionally related to gene regulation and, as such, may play a role in normal development and human disease processes. However, the mechanisms that participate in nuclear organization are poorly understood. Here, we present data characterizing localization of the imprinted Kcnq1 alleles. We show that nucleolar association of the paternal allele (1) is stimulated during the differentiation of trophoblast stem cells, (ii) is dependent upon the Kcnq1ot1 noncoding RNA, (3) does not require polycomb repressive complex 2, and (4) is not sufficient to preclude transcription of imprinted genes. Although nucleolar positioning has been proposed as a mechanism to related to gene silencing, we find that silencing and perinucleolar localization through the Kcnq1ot1 noncoding RNA are separable events.
Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression
Authors: Elmore Martha H , Gibbons John G , Rokas Antonis 
Published: December 2012

AbstractCopy number polymorphisms of nucleotide tandem repeat (TR) regions, such as microsatellites and minisatellites, are mutationally reversible and highly abundant in eukaryotic genomes. Studies linking TR polymorphism to phenotypic variation have led some to suggest that TR variation modulates and majorly contributes to phenotypic variation; however, studies in which the authors assess the genome-wide impact of TR variation on phenotype are lacking. To address this question, we quantified relationships between polymorphism levels in 143 genome-wide promoter region TRs across 16 isolates of the filamentous fungus Aspergillus flavus and its ecotype Aspergillus oryzae with expression levels of their downstream genes. We found that only 4.3% of relationships tested were significant; these findings were consistent with models in which TRs act as “tuning,” “volume,” or “optimality” “knobs” of phenotype but not with “switch” models. Furthermore, the promoter regions of differentially expressed genes between A. oryzae and A. flavus did not show TR enrichment, suggesting that genome-wide differences in molecular phenotype between the two species are not significantly associated with TRs. Although in some cases TR polymorphisms do contribute to transcript abundance variation, these results argue that at least in this case, TRs might not be major modulators of variation in phenotype.
A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder
Authors: Prasad Aparna , Merico Daniele , Thiruvahindrapuram Bhooma , Wei John , Lionel Anath C , Sato Daisuke , Rickaby Jessica , Lu Chao , Szatmari Peter , Roberts Wendy , Fernandez Bridget A , Marshall Christian R , Hatchwell Eli , Eis Peggy S , Scherer Stephen W 
Published: December 2012

Abstract
The identification of rare inherited and de novo copy number variations (CNVs) in human subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD cases using a high-resolution one-million feature CGH microarray, the majority of which were previously genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array data sets on the ASD cohort and CGH data on an additional 1000 control samples. Of the 615 ASD cases analyzed on both SNP and CGH arrays, we found that 13,572 of 21,346 (64%) of the CNVs were exclusively detected by the CGH array. Several of the CGH-specific CNVs are rare in population frequency and impact previously reported ASD genes (e.g., NRXN1, GRM8, DPYD), as well as novel ASD candidate genes (e.g., CIB2, DAPP1, SAE1), and all were inherited except for a de novo CNV in the GPHN gene. A functional enrichment test of gene-sets in ASD cases over controls revealed nucleotide metabolism as a potential novel pathway involved in ASD, which includes several candidate genes for follow-up (e.g., DPYD, UPB1, UPP1, TYMP). Finally, this extensively phenotyped and genotyped ASD clinical cohort serves as an invaluable resource for the next step of genome sequencing for complete genetic variation detection.
Nuclear Gene Variation in Wild Brown Rats
Authors: Ness Rob W , Zhang Yao-Hua , Cong Lin , Wang Yu , Zhang Jian-Xu , Keightley Peter D 
Published: December 2012

AbstractAlthough the brown rat (Rattus norvegicus) is widely used as a model mammal throughout biological sciences, little is known about genetic variation in wild rat populations or the relationship of commonly used inbred strains to their wild relatives. We sampled wild brown rats from the species’ presumed ancestral range in NW China and from a derived population in the UK and estimated nucleotide diversity and population subdivision, based on the sequences of 30 autosomal protein-coding loci. Neutral genetic diversity was close to 0.2% in both populations, which is about five times lower than diversity at the orthologous sites in a population of wild house mice from the species’ putative ancestral range in India. We found significant population differentiation between UK and Chinese populations, as assessed by Fst and the program STRUCTURE. Based on synonymous diversity and divergence between the brown rat and house mouse, we estimate that the recent effective population size in brown rats is approximately 130,000 (approximate 95% confidence interval 85,000-184,000), about fivefold lower than wild house mice.
Synthesis and Physical Properties of Skutterudite Superlattices
Authors: Williams Joshua R. , Johnson David C. , Kaeser Michael , Tritt Terry , Nolas George , Nelson E. 
Published: December 2012

ABSTRACTPredicted and observed reductions in thermal conductivity of materials with superlattice structure have prompted interesting research into the possibility of using these materials as higher efficiency thermoelectrics. Synthesis of superlattice materials is challenging however, as the structure itself is generally not very stable at high temperatures as it is prone to interdiffusion. Presented here is the successful synthesis and characterization of a superlattice composed of two materials with the skutterudite structure, IrSb3 and CoSb3.
Removal of Total Organics and Grease from Oil Production Effluents by an Adsorption Process
Authors: Moore Lucas R. , Cardoso Cynthia , Costa Marcelo , Mahmoudkhani Amir 
Published: December 2012

Abstract
Oilfield produced water accounts for 98% of all waste generated in oil and gas exploration and processing. This process water may contain up to 1000 ppm total oil and grease, which must be treated prior to discharge. A novel inorganic adsorbent was designed to have high affinity towards such organics. Lab scale evaluations of this adsorbent on production effluents obtained from an onshore site consistently yields TOG removal &gt; 96%. This was found to be a significant improvement over the chemically assisted DAF at 74% in similar lab scale evaluations. This novel technology has the potential to provide a substancial reduction in capital and operating costs for water treatment.