bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translocations activating IRF4 identify a subtype of germinal center-derived B-cell lymphoma affecting predominantly children and young adults
Authors: Salaverria Itziar , Philipp Claudia , Oschlies Ilske , Kohler Christian W. , Kreuz Markus , Szczepanowski Monika , Burkhardt Birgit , Trautmann Heiko , Gesk Stefan , Andrusiewicz Miroslaw , Berger Hilmar , Fey Miriam , Harder Lana , Hasenclever Dirk , Hummel Michael , Loeffler Markus , Mahn Friederike , Martin-Guerrero Idoia , Pellissery Shoji , Pott Christiane , Pfreundschuh Michael , Reiter Alfred , Richter Julia , Rosolowski Maciej , Schwaenen Carsten , Stein Harald , Trümper Lorenz , Wessendorf Swen , Spang Rainer , Küppers Ralf , Klapper Wolfram , Siebert Reiner ,   for the Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe,   the German High-Grade Lymphoma Study Group,   the Berlin-Frankfurt-Münster-NHL trial group
Published: April 2011

Abstract
The prognosis of germinal center–derived B-cell (GCB) lymphomas, including follicular lymphoma and diffuse large-B-cell lymphoma (DLBCL), strongly depends on age. Children have a more favorable outcome than adults. It is not known whether this is because of differences in host characteristics, treatment protocols, or tumor biology, including the presence of chromosomal alterations. By screening for novel IGH translocation partners in pediatric and adult lymphomas, we identified chromosomal translocations juxtaposing the IRF4 oncogene next to one of the immunoglobulin (IG) loci as a novel recurrent aberration in mature B-cell lymphoma. FISH revealed 20 of 427 lymphomas to carry an IG/IRF4-fusion. Those were predominantly GCB-type DLBCL or follicular lymphoma grade 3, shared strong expression of IRF4/MUM1 and BCL6, and lacked PRDM1/BLIMP1 expression and t(14;18)/BCL2 breaks. BCL6 aberrations were common. The gene expression profile of IG/IRF4-positive lymphomas differed from other subtypes of DLBCL. A classifier for IG/IRF4 positivity containing 27 genes allowed accurate prediction. IG/IRF4 positivity was associated with young age and a favorable outcome. Our results suggest IRF4 translocations to be primary alterations in a molecularly defined subset of GCB-derived lymphomas. The probability for this subtype of lymphoma significantly decreases with age, suggesting that diversity in tumor biology might contribute to the age-dependent differences in prognosis of lymphoma.
Risk factors for arterial and venous thrombosis in WHO-defined essential thrombocythemia: an international study of 891 patients
Authors: Carobbio Alessandra , Thiele Juergen , Passamonti Francesco , Rumi Elisa , Ruggeri Marco , Rodeghiero Francesco , Randi Maria Luigia , Bertozzi Irene , Vannucchi Alessandro M. , Antonioli Elisabetta , Gisslinger Heinz , Buxhofer-Ausch Veronika , Finazzi Guido , Gangat Naseema , Tefferi Ayalew , Barbui Tiziano 
Published: April 2011

Abstract
In an international collaborative study, a central histologic review identified 891 patients with essential thrombocythemia, strictly defined by World Health Organization criteria. After a median follow-up of 6.2 years, 109 (12%) patients experienced arterial (n = 79) or venous (n = 37) thrombosis. In multivariable analysis, predictors of arterial thrombosis included age more than 60 years (P = .03; hazard ratio [HR] = 1.7), thrombosis history (P = .003; HR = 2.1), cardiovascular risk factors including tobacco use, hypertension, or diabetes mellitus (P = .007; HR = 1.9), leukocytosis (> 11 × 109/L; P = .04; HR = 1.7), and presence of JAK2V617F (P = .009; HR = 2.6). In contrast, only male gender predicted venous thrombosis. Platelet count more than 1000 × 109/L was associated with a lower risk of arterial thrombosis (P = .007; HR = 0.4). These associations, except the one with leukocytosis, remained significant (or near significant) when analysis was restricted to JAK2V617F-positive cases. The current study clarifies the contribution of specific disease and host characteristics to the risk of arterial versus venous thrombosis in essential thrombocythemia.
Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba
Authors: Bortolotto Erica , Bucklin Ann , Mezzavilla Massimo , Zane Lorenzo , Patarnello Tomaso 
Published: April 2011

Abstract

Background
Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill Euphausia superba using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range.

Results
MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter g (a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion.

Conclusions
The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, versus sedentary benthic shelf species.
EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species.
Copy number variation of microRNA genes in the human genome
Authors: Marcinkowska Malgorzata , Szymanski Maciej , Krzyzosiak Wlodzimierz J , Kozlowski Piotr 
Published: April 2011

Abstract
Background
MicroRNAs (miRNAs) are important genetic elements that regulate the expression of thousands of human genes. Polymorphisms affecting miRNA biogenesis, dosage and target recognition may represent potentially functional variants. The functional consequences of single nucleotide polymorphisms (SNPs) within critical miRNA sequences and outside of miRNA genes were previously demonstrated using both experimental and computational methods. However, little is known about how copy number variations (CNVs) affect miRNA genes.

Results
In this study, we analyzed the co-localization of all miRNA loci with known CNV regions. Using bioinformatic tools we identified and validated 209 copy number variable miRNA genes (CNV-miRNAs) in CNV regions deposited in Database of Genomic Variations (DGV) and 11 CNV-miRNAs in two sets of CNVs defined as highly polymorphic. We propose potential mechanisms of CNV-mediated variation of functional copies of miRNAs (dosage) for different types of CNVs overlapping miRNA genes. We also showed that, consistent with their essential biological functions, miRNA loci are underrepresented in highly polymorphic and well-validated CNV regions.

Conclusion
We postulate that CNV-miRNAs are potential functional variants and should be considered high priority candidate variants in genotype-phenotype association studies.
Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers
Authors: Gao Lei , Zhou Yuan , Wang Zhi-Wei , Su Ying-Juan , Wang Ting 
Published: April 2011

Abstract

Background
The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization.

Results
A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns.

Conclusions
Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS.
Rapid identification of allergenic and pathogenic molds in environmental air by an oligonucleotide array
Authors: Hung Wen-Tsung , Su Shu-Li , Shiu Lin-Yi , Chang Tsung C 
Published: April 2011

Abstract

Background
Airborne fungi play an important role in causing allergy and infections in susceptible people. Identification of these fungi, based on morphological characteristics, is time-consuming, expertise-demanding, and could be inaccurate.

Methods
We developed an oligonucleotide array that could accurately identify 21 important airborne fungi (13 genera) that may cause adverse health problems. The method consisted of PCR amplification of the internal transcribed spacer (ITS) regions, hybridization of the PCR products to a panel of oligonucleotide probes immobilized on a nylon membrane, and detection of the hybridization signals with alkaline phosphatase-conjugated antibodies.

Results
A collection of 72 target and 66 nontarget reference strains were analyzed by the array. Both the sensitivity and specificity of the array were 100%, and the detection limit was 10 pg of genomic DNA per assay. Furthermore, 70 fungal isolates recovered from air samples were identified by the array and the identification results were confirmed by sequencing of the ITS and D1/D2 domain of the large-subunit RNA gene. The sensitivity and specificity of the array for identification of the air isolates was 100% (26/26) and 97.7% (43/44), respectively.

Conclusions
Identification of airborne fungi by the array was cheap and accurate. The current array may contribute to decipher the relationship between airborne fungi and adverse health effect.
Health-related Quality of life in 640 head and neck cancer survivors after radiotherapy using EORTC QLQ-C30 and QLQ-H&N35 questionnaires
Authors: Wan Leung Stephen , Lee Tsair-Fwu , Chien Chih-Yen , Chao Pei-Ju , Tsai Wen-Ling , Fang Fu-Min 
Published: April 2011

Abstract

Background
With the advances in modern radiotherapy (RT), many patients with head and neck cancer (HNC) can be effectively cured, and their health-related quality of life (HR-QoL) has become an important issue. In this study, we evaluated the prognosticators of HR-QoL in a large cohort of HNC patients, with a focus on the result from technological advances in RT.

Methods
A cross-sectional investigation was conducted to assess the HR-QoL of 640 HNC patients with cancer-free survival of more than 2 years. Among them, 371 patients were treated by two-dimensional RT (2DRT), 127 by three-dimensional conformal RT (3DCRT), and 142 by intensity-modulated RT (IMRT). The EORTC QLQ-C30 questionnaire and QLQ-H&N35 module were used. A general linear model multivariate analysis of variance was used to analyze the prognosticators of HR-QoL.

Results
By multivariate analysis, the variables of gender, annual family income, tumor site, AJCC stage, treatment methods, and RT technique were prognosticators for QLQ-C30 results, so were tumor site and RT technique for H&N35. Significant difference (p < 0.05) of HR-QoL outcome by different RT techniques was observed at 2 of the 15 scales in QLQ-C30 and 10 of the 13 scales in H&N35. Compared with 2DRT, IMRT had significant better outcome in the scales of global QoL, physical functioning, swallowing, senses (taste/smell), speech, social eating, social contact, teeth, opening mouth, dry mouth, sticky saliva, and feeling ill.

Conclusions
The technological advance of RT substantially improves the head-and-neck related symptoms and broad aspects of HR-QoL for HNC survivors.
Chronic occupational exposure to hexavalent chromium causes DNA damage in electroplating workers
Authors: Zhang Xu-Hui , Zhang Xuan , Wang Xu-Chu , Jin Li-Fen , Yang Zhang-Ping , Jiang Cai-Xia , Chen Qing , Ren Xiao-Bin , Cao Jian-Zhong , Wang Qiang , Zhu Yi-Min 
Published: April 2011

Abstract

Background
Occupational exposure to chromium compounds may result in adverse health effects. This study aims to investigate whether low-level hexavalent chromium (Cr(VI)) exposure can cause DNA damage in electroplating workers.

Methods
157 electroplating workers and 93 control subjects with no history of occupational exposure to chromium were recruited in Hangzhou, China. Chromium levels in erythrocytes were determined by graphite furnace atomic absorption spectrophotometer. DNA damage in peripheral lymphocytes was evaluated with the alkaline comet assay by three parameters: Olive tail moment, tail length and percent of DNA in the comet tail (tail DNA%). Urinary 8-OHdG levels were measured by ELISA.

Results
Chromium concentration in erythrocytes was about two times higher in electroplating workers (median: 4.41 μg/L) than that in control subjects (1.54 μg/L, P < 0.001). The medians (range) of Olive tail moment, tail length and tail DNA% in exposed workers were 1.13 (0.14-6.77), 11.17 (3.46-52.19) and 3.69 (0.65-16.20), and were significantly higher than those in control subjects (0.14 (0.01-0.39), 3.26 (3.00-4.00) and 0.69 (0.04-2.74), P < 0.001). Urinary 8-OHdG concentration was 13.65 (3.08-66.30) μg/g creatinine in exposed workers and 8.31 (2.94-30.83) μg/g creatinine in control subjects (P < 0.001). The differences of urinary 8-OHdG levels, Olive tail moment, tail length and tail DNA% between these two groups remained significant (P < 0.001) even after stratification by potential confounding factors such as age, gender, and smoking status. Chromium exposure was found to be positively associated with chromium levels in erythrocytes, urinary 8-OHdG levels, Olive tail moment, tail length and tail DNA%. Positive dose-response associations were also found between chromium levels in erythrocytes and Olive tail moment, tail length and tail DNA%.

Conclusion
The findings in this study indicated that there was detectable chromium exposure in electroplating workers. Low-level occupational chromium exposure induced DNA damage.
Gα16 interacts with tetratricopeptide repeat 1 (TPR1) through its β3 region to activate Ras independently of phospholipase Cβ signaling
Authors: Liu Andrew MF , Lo Rico KH , Guo Emily X , Ho Maurice KC , Ye Richard D , Wong Yung H 
Published: April 2011

AbstractBackgroundG protein-coupled receptors constitute the largest family of cell surface receptors in the mammalian genome. As the core of the G protein signal transduction machinery, the Gα subunits are required to interact with multiple partners. The GTP-bound active state of many Gα subunits can bind a multitude of effectors and regulatory proteins. Yet it remains unclear if the different proteins utilize distinct or common structural motifs on the Gα subunit for binding. Using Gα16as a model, we asked if its recently discovered adaptor protein tetratricopeptide repeat 1 (TPR1) binds to the same region as its canonical effector, phospholipase Cβ (PLCβ).ResultsWe have examined the specificity of Gα16/TPR1 association by testing a series of chimeras between Gα16and Gαz. TPR1 co-immunoprecipitated with Gα16and more tightly with its constitutively active Gα16QL, but not Gαz. Progressive replacement of Gα16sequence with the corresponding residues of Gαzeventually identified a stretch of six amino acids in the β3 region of Gα16which are responsible for TPR1 interaction and the subsequent Ras activation. Insertion of these six residues into Gαzallowed productive TPR1-interaction. Since the β3 region only minimally contributes to interact with PLCβ, several chimeras exhibited differential abilities to stimulate PLCβ and Ras. The ability of the chimeras to activate downstream transcription factors such as signal transducer and activator of transcription 3 and nuclear factor κB appeared to be associated with PLCβ signaling.ConclusionsOur results suggest that Gα16can signal through TPR1/Ras and PLCβ simultaneously and independently. The β3 region of Gα16is essential for interaction with TPR1 and the subsequent activation of Ras, but has relatively minor influence on the PLCβ interaction. Gα16may utilize different structural domains to bind TPR1 and PLCβ.
Impaired lipid metabolism in idiopathic pulmonary alveolar proteinosis
Authors: Tian Xinlun , Luo Jinmei , Xu Kai-Feng , Wang Lan , Zhou Jiong , Feng Ruie , Gui Yaosong , Wang Juan , Xu Wenbing , Xiao Yi , Zhu Yuanjue 
Published: April 2011

Abstract

Background
It is well known that lipids abnormally accumulate in the alveoli during idiopathic pulmonary alveolar proteinosis (PAP). It is unclear, however, whether lipids also abnormally accumulate in serum. This study investigated the serum lipid panels in idiopathic PAP patients and explored the relationships between serum levels and the severity of idiopathic PAP.

Methods and Results
Clinical data including the level of serum lipids were evaluated in 33 non-diabetic idiopathic PAP patients and 157 healthy volunteers. Serum levels of triglyceride were higher in PAP patients than in healthy subjects (median: 192.00 mg/dl (P
25: 104.36, P
75: 219.00) vs 119.56 mg/dl (P
25: 78.81, P
75: 193.03), P < 0.05), while high-density lipoprotein cholesterol (HDL-C) levels were lower in patients than in the control group (42.50 ± 10.30 vs 51.34 ± 12.06 mg/dl, P < 0.01). Forced expiratory volume in one second and forced vital capacity in hypertriglyceridemia patients were lower than those in patients with normal triglyceride. Serum LDL-C and HDL-C ratio correlated negatively with PaO2 (r = -0.403, P < 0.05) and positively with lactate dehydrogenase (r = 0.381, P < 0.05).

Conclusions
PAP associates with high triglyceride and low HDL levels in the serum, and these lipids provide potential intervention strategy for treatment.
Spontaneous intraperitoneal rupture of pyonephrosis in a patient with unknown kidney carcinosarcoma: a case report
Authors: Quaresima Silvia , Manzelli Antonio , Ricciardi Edoardo , Petrou Athanasios , Brennan Nicholas , Mauriello Alessandro , Rossi Piero 
Published: April 2011

Abstract
Seventeen cases of peritonitis due to rupture of a pyonephrosis have been reported. The majority of these cases occur secondary to renal stones. Only two cases of ruptured pyonephrosis with concurrent kidney neoplasm have been described and only one of these presented as an acute peritonitis. In this presentation we discuss an unusual case of a 68 year old man with a chronic history of bilateral nephrolithiasis and recent pyonephrosis. He presented acutely with peritonitis and was later found to have a carcinosarcoma of the kidney. The case highlights the importance of recognizing the possibility of underling renal carcinoma in patients presenting with a ruptured pyonephrosis and discuss steps to avoid this serious complication.
One-step synthesis of PbSe-ZnSe composite thin film
Authors: Abe Seishi 
Published: April 2011

AbstractThis study investigates the preparation of PbSe-ZnSe composite thin films by simultaneous hot-wall deposition (HWD) from multiple resources. The XRD result reveals that the solubility limit of Pb in ZnSe is quite narrow, less than 1 mol%, with obvious phase-separation in the composite thin films. A nanoscale elemental mapping of the film containing 5 mol% PbSe indicates that isolated PbSe nanocrystals are dispersed in the ZnSe matrix. The optical absorption edge of the composite thin films shifts toward the low-photon-energy region as the PbSe content increases. The use of a phase-separating PbSe-ZnSe system and HWD techniques enables simple production of the composite package.
Herpes simplex virus type 2 infection increases human immunodeficiency virus type 1 entry into human primary macrophages
Authors: Sartori Elena , Calistri Arianna , Salata Cristiano , Del Vecchio Claudia , Palù Giorgio , Parolin Cristina 
Published: April 2011

AbstractEpidemiological and clinical data indicate that genital ulcer disease (GUD) pathogens are associated with an increased risk of human immunodeficiency virus type 1 (HIV-1) acquisition and/or transmission. Among them, genital herpes simplex virus type 2 (HSV-2) seems to play a relevant role. Indeed, the ability of HSV-2 to induce massive infiltration at the genital level of cells which are potential targets for HIV-1 infection may represent one of the mechanisms involved in this process. Here we show that infection of human primary macrophages (MDMs) by HSV-2 results in an increase of CCR5 expression levels on cell surface and allows higher efficiency of MDMs to support entry of R5 HIV-1 strains. This finding could strengthen, at the molecular level, the evidence linking HSV-2 infection to an increased susceptibility to HIV-1 acquisition.