bluuebunny/crossref_metadata_2025_split huggingface dataset:
TBL1XR1/TP63: a novel recurrent gene fusion in B-cell non-Hodgkin lymphoma
Authors: Scott David W. , Mungall Karen L. , Ben-Neriah Susana , Rogic Sanja , Morin Ryan D. , Slack Graham W. , Tan King L. , Chan Fong Chun , Lim Raymond S. , Connors Joseph M. , Marra Marco A. , Mungall Andrew J. , Steidl Christian , Gascoyne Randy D. 
Published: April 2012

Abstract
Recently, the landscape of single base mutations in diffuse large B-cell lymphoma (DLBCL) was described. Here we report the discovery of a gene fusion between TBL1XR1 and TP63, the only recurrent somatic novel gene fusion identified in our analysis of transcriptome data from 96 DLBCL cases. Based on this cohort and a further 157 DLBCL cases analyzed by FISH, the incidence in de novo germinal center B cell–like (GCB) DLBCL is 5% (6 of 115). The fusion appears exclusive to GCB and was not seen in 138 non-GCB cases examined (P = .008, Fisher exact test) but was present at low incidence in follicular lymphoma (1 of 81). In all 7 cases identified, the 3′ end of the fusion consists of exons 4 and onwards of TP63. The recurrence, subtype enrichment, and the remarkably conserved nature of the TP63 portion of the fusion suggest an important functional role in the lymphomas that harbor this event.
Selectivity by host plants affects the distribution of arbuscular mycorrhizal fungi: evidence from ITS rDNA sequence metadata
Authors: Yang Haishui , Zang Yanyan , Yuan Yongge , Tang Jianjun , Chen Xin 
Published: April 2012

Abstract

Background
Arbuscular mycorrhizal fungi (AMF) can form obligate symbioses with the vast majority of land plants, and AMF distribution patterns have received increasing attention from researchers. At the local scale, the distribution of AMF is well documented. Studies at large scales, however, are limited because intensive sampling is difficult. Here, we used ITS rDNA sequence metadata obtained from public databases to study the distribution of AMF at continental and global scales. We also used these sequence metadata to investigate whether host plant is the main factor that affects the distribution of AMF at large scales.

Results
We defined 305 ITS virtual taxa (ITS-VTs) among all sequences of the Glomeromycota by using a comprehensive maximum likelihood phylogenetic analysis. Each host taxonomic order averaged about 53% specific ITS-VTs, and approximately 60% of the ITS-VTs were host specific. Those ITS-VTs with wide host range showed wide geographic distribution. Most ITS-VTs occurred in only one type of host functional group. The distributions of most ITS-VTs were limited across ecosystem, across continent, across biogeographical realm, and across climatic zone. Non-metric multidimensional scaling analysis (NMDS) showed that AMF community composition differed among functional groups of hosts, and among ecosystem, continent, biogeographical realm, and climatic zone. The Mantel test showed that AMF community composition was significantly correlated with plant community composition among ecosystem, among continent, among biogeographical realm, and among climatic zone. The structural equation modeling (SEM) showed that the effects of ecosystem, continent, biogeographical realm, and climatic zone were mainly indirect on AMF distribution, but plant had strongly direct effects on AMF.

Conclusion
The distribution of AMF as indicated by ITS rDNA sequences showed a pattern of high endemism at large scales. This pattern indicates high specificity of AMF for host at different scales (plant taxonomic order and functional group) and high selectivity from host plants for AMF. The effects of ecosystemic, biogeographical, continental and climatic factors on AMF distribution might be mediated by host plants.
Antidepressant-like effects of methanol extract of Hibiscus tiliaceus flowers in mice
Authors: Vanzella Cláudia , Bianchetti Paula , Sbaraini Sabrina , Vanzin Samanta Inês , Melecchi Maria Inês Soares , Caramão Elina Bastos , Siqueira Ionara Rodrigues 
Published: April 2012

Abstract

Background

Hibiscus tiliaceus L. (Malvaceae) is used in postpartum disorders. Our purpose was to examine the antidepressant, anxiolytic and sedative actions of the methanol extract of H. tiliaceus flowers using animal models.

Methods
Adult male Swiss albino mice were treated with saline, standard drugs or methanol extract of H. tiliaceus and then subjected to behavioral tests. The forced swimming and tail suspension tests were used as predictive animal models of antidepressant activity, where the time of immobility was considered. The animals were submitted to the elevated plus-maze and ketamine-induced sleeping time to assess anxiolytic and sedative activities, respectively.

Results
Methanol extract of H. tiliaceus significantly decreased the duration of immobility in both animal models of antidepressant activity, forced swimming and tail suspension tests. This extract did not potentiate the effect of ketamine-induced hypnosis, as determined by the time to onset and duration of sleeping time.

Conclusion
Our results indicate an antidepressant-like profile of action for the extract of Hibiscus tiliaceus without sedative side effect.
Impact of psychological problems in chemical warfare survivors with severe ophthalmologic complication, a cross sectional study
Authors: Ghaedi Gholamhosein , Ghasemi Hassan , Mousavi Batool , Soroush Mohammad Reza , Rahnama Parvin , Jafari Farhad , Afshin-Majd Siamak , Sadeghi Naeeni Maryam , Naghizadeh Mohammad Mehdi 
Published: April 2012

Abstract

Background
Sulfur mustard (SM) has been used as a chemical warfare agent since the early twentieth century. Despite the large number of studies that have investigated SM induced ocular injuries, few of those studies have also focused on the psychological health status of victims. This study has evaluated the most prominent influences on the psychological health status of patients with severe SM induced ocular injuries.

Methods
This descriptive study was conducted on 149 Iranian war veterans with severe SM induced eye injuries. The psychological health status of all patients was assessed using the Iranian standardized Symptom Check List 90-Revised (SCL90-R) questionnaire. The results of patients' Global Severity Index (GSI) were compared with the optimal cut-off point of 0.4 that has previously been calculated for GSI in Iranian community. The Mann-Whitney U test, T tests and effect sizes (using Cohen's d) were employed as statistical methods. Data were analyzed using SPSS software.

Results
The mean age of patients was 44.86 (SD = 8.7) and mean duration of disease was 21.58 (SD = 1.20) years. Rate of exposure was once in 99 (66.4%) cases. The mean GSI (1.46) of the study group was higher compared to standardized cut off point (0.4) of the Iranian community. The results of this study showed that the mean of total GSI score was higher in participants with lower educational levels (effect size = 0.507), unemployment (effect size = 0.464) and having more than 3 children (effect size = 0.62). Among the participants, 87 (58.4%) cases had a positive psychological history for hospitalization or receiving outpatient cares previously and 62 (41.6%) cases had a negative psychological history. In addition, the mean of GSI in participants with negative psychological history was lower than those with positive psychological history (Mean Change Difference = -0.621 with SD = 0.120). There was a significant difference between positive and negative psychological history with respect to GSI (P < 0.001).

Conclusion
The study showed that severe ophthalmologic complications in chemical survivors are accompanied with destructive effects on psychological health status. Appropriate management may improve psychological health status in these patients.
Bending effects of ZnO nanorod metal–semiconductor–metal photodetectors on flexible polyimide substrate
Authors: Chen Tse-Pu , Young Sheng-Joue , Chang Shoou-Jinn , Hsiao Chih-Hung , Hsu Yu-Jung 
Published: April 2012

Abstract
The authors report the fabrication and I-V characteristics of ZnO nanorod metal–semiconductor–metal photodetectors on flexible polyimide substrate. From field-emission scanning electron microscopy and X-ray diffraction spectrum, ZnO nanorods had a (0002) crystal orientation and a wurtzite hexagonal structure. During the I-V and response measurement, the flexible substrates were measured with (i.e., the radius of curvatures was 0.2 cm) and without bending. From I-V results, the dark current decreased, and the UV-to-visible rejection ratio increased slightly in bending situation. The decreasing tendency of the dark current under bending condition may be attributed to the increase of the Schottky barrier height.
Novel therapeutic strategies targeting HIV integrase
Authors: Quashie Peter K , Sloan Richard D , Wainberg Mark A 
Published: April 2012

Abstract
Integration of the viral genome into host cell chromatin is a pivotal and unique step in the replication cycle of retroviruses, including HIV. Inhibiting HIV replication by specifically blocking the viral integrase enzyme that mediates this step is an obvious and attractive therapeutic strategy. After concerted efforts, the first viable integrase inhibitors were developed in the early 2000s, ultimately leading to the clinical licensure of the first integrase strand transfer inhibitor, raltegravir. Similarly structured compounds and derivative second generation integrase strand transfer inhibitors, such as elvitegravir and dolutegravir, are now in various stages of clinical development. Furthermore, other mechanisms aimed at the inhibition of viral integration are being explored in numerous preclinical studies, which include inhibition of 3' processing and chromatin targeting. The development of new clinically useful compounds will be aided by the characterization of the retroviral intasome crystal structure. This review considers the history of the clinical development of HIV integrase inhibitors, the development of antiviral drug resistance and the need for new antiviral compounds.
Sporadic haemangioblastoma of the kidney with rhabdoid features and focal CD10 expression: report of a case and literature review
Authors: Yin Wei-hua , Li Jian , Chan John KC 
Published: April 2012

Abstract
We present here an intriguing case of sporadic renal haemangioblastoma occurring in a 61-year-old male. The tumor consisted of nests of polygonal cells and abundant capillary networks. The neoplastic cells generally showed abundant eosinophilic cytoplasm and prominent eccentric nuclei, resembling the rhabdoid cells. Pronounced intranuclear cytoplasmic pseudoinclusions were another significant feature seen. NSE, a-inhibin and S100 were positive in tumor cells and particularly, focal CD10 expressions were observed. This is possibly the first reported case of a haemangioblastoma showing a rhabdoid phenotype and CD10 immunopositivity. Malignant rhabdoid tumor and renal cell carcinoma with rhabdoid features were probably the most challenging mimics need to be differentiated. The result of focal CD10 staining in our case may further lead to confusion with renal cell carcinoma. To avoid misdiagnosis, more considerations should be attached to the rare neoplasm.

Virtual Slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1068858553657049
DNA methylation differences at growth related genes correlate with birth weight: a molecular signature linked to developmental origins of adult disease?
Authors: Turan Nahid , Ghalwash Mohamed F , Katari Sunita , Coutifaris Christos , Obradovic Zoran , Sapienza Carmen 
Published: April 2012

AbstractBackgroundInfant birth weight is a complex quantitative trait associated with both neonatal and long-term health outcomes. Numerous studies have been published in which candidate genes (IGF1, IGF2, IGF2R, IGFbinding proteins,PHLDA2andPLAGL1) have been associated with birth weight, but these studies are difficult to reproduce in man and large cohort studies are needed due to the large inter individual variance in transcription levels. Also, very little of the trait variance is explained. We decided to identify additional candidates without regard for what is known about the genes. We hypothesize that DNA methylation differences between individuals can serve as markers of gene "expression potential" at growth related genes throughout development and that these differences may correlate with birth weight better than single time point measures of gene expression.MethodsWe performed DNA methylation and transcript profiling on cord blood and placenta from newborns. We then used novel computational approaches to identify genes correlated with birth weight.ResultsWe identified 23 genes whose methylation levels explain 70-87% of the variance in birth weight. Six of these (ANGPT4, APOE, CDK2, GRB10, OSBPL5andREG1B) are associated with growth phenotypes in human or mouse models. Gene expression profiling explained a much smaller fraction of variance in birth weight than did DNA methylation. We further show that two genes, the transcriptional repressorMSX1and the growth factor receptor adaptor proteinGRB10, are correlated with transcriptional control of at least seven genes reported to be involved in fetal or placental growth, suggesting that we have identified important networks in growth control.GRB10methylation is also correlated with genes involved in reactive oxygen species signaling, stress signaling and oxygen sensing and more recent data implicateGRB10in insulin signaling.ConclusionsSingle time point measurements of gene expression may reflect many factors unrelated to birth weight, while inter-individual differences in DNA methylation may represent a "molecular fossil record" of differences in birth weight-related gene expression. Finding these "unexpected" pathways may tell us something about the long-term association between low birth weight and adult disease, as well as which genes may be susceptible to environmental effects. These findings increase our understanding of the molecular mechanisms involved in human development and disease progression.
Occupational Status and Health Transitions
Authors: Morefield Brant , Ribar David C. , Ruhm Christopher J. 
Published: April 2012

Abstract
We use longitudinal data from the 1984-2007 waves of the Panel Study of Income Dynamics to examine how occupational status is related to the health transitions of 30-59 year-old U.S. males. A recent history of blue-collar employment predicts a substantial increase in the probability of transitioning from very good into bad self-assessed health, relative to white-collar employment, but with no evidence of a difference in movements from bad to very good health. Service work is also associated with a higher probability of transitioning into bad health and possibly with a lower probability of recovery. These findings suggest that blue-collar and service workers “wear out” faster with age because they are more likely than their white-collar counterparts to experience negative health shocks. There is also evidence that this partly reflects differences in the physical demands of jobs.
Challenges in nutrition-related DNA methylation studies
Authors: Niculescu Mihai D. 
Published: April 2012

AbstractThe rapid progress in nutritional epigenetics allowed for a much better understanding of the mechanisms involved in gene-nutrient interactions and the roles that nutrition has in transgenerational inheritance of acquired epigenetic traits. Studies indicated that a considerable number of nutrients or diet types are capable of inducing epimutations. In parallel, the rapid development of genome-wide DNA methylation detection methods allowed for a broader image on how nutrition impacts the epigenetic status in human and animal models. But this increased complexity in the epigenetic field and also brought important challenges that need resolution, or it suggests that some of the initial epigenetic paradigms have to be revisited or reconsidered. The aim of this review is to discuss the inherent challenges that need to be resolved, from both practical and theoretical aspects, stemming from the rapid progress in the field of nutritional epigenetics, with a focus on DNA methylation. Because such challenges are present at every stage of study development, the review systematically discusses the most common issues relevant to DNA methylation in a nutritional context. Various types of challenges and potential bias generators are discussed within study design, sample quality, detection methods, data processing, and statistical and bioinformatic analysis. Additional aspects to be considered include epigenetic heterogeneity of treatment groups, the role of genomic variability in introducing measurement bias and errors in interpretation of changes, and issues related to the final interpretation of results and in assigning functional significance. It is also posited that all these issues will be largely resolved within the next decade.
Viperin: a radical response to viral infection
Authors: Duschene Kaitlin S. , Broderick Joan B. 
Published: April 2012

AbstractOne of the first lines of defense of the host immune response to infection is upregulation of interferons, which play a vital role in triggering the early nonspecific antiviral state of the host. Interferons prompt the generation of numerous downstream products, known as interferon-stimulated genes (ISGs). One such ISG found to be either directly induced by type I, II, and III interferons or indirectly through viral infection is the ‘virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible’ protein, or viperin. Not only is viperin capable of combating a wide array of viral infections but its upregulation is also observed in the presence of endotoxins, various bacterial infections, or even in response to other immune stimuli, such as atherosclerotic lesions. Recent advances in the understanding of possible mechanisms of action of viperin involve, but are perhaps not limited to, interaction with farnesyl pyrophosphate synthase and disruption of lipid raft domains to prevent viral bud release, inhibition of hepatitis C virus secretory proteins, and coordination to lipid droplets and inhibition of viral replication. Unexpectedly, new insight into the human cytomegalovirus induction of this antiviral protein demonstrates that mitochondrial viperin plays a necessary and beneficial role for viral propagation.
The epsin protein family: coordinators of endocytosis and signaling
Authors: Sen Arpita , Madhivanan Kayalvizhi , Mukherjee Debarati , Aguilar R. Claudio 
Published: April 2012

AbstractThe epsins are a conserved family of endocytic adaptors essential for cell viability in yeast and for embryo development in higher eukaryotes. Epsins function as adaptors by recognizing ubiquitinated cargo and as endocytic accessory proteins by contributing to endocytic network stability/regulation and membrane bending. Importantly, epsins play a critical role in signaling by contributing to epidermal growth factor receptor downregulation and the activation of notch and RhoGTPase pathways. In this review, we present an overview of the epsins and emphasize their functional importance as coordinators of endocytosis and signaling.
Cyanobacteria and macroalgae from an arid environment mangrove on the east coast of the Baja California Peninsula
Authors: Pérez-Estrada Claudia J. , León-Tejera Hilda , Serviere-Zaragoza Elisa 
Published: April 2012

Abstract
We describe the assemblage of cyanobacteria and macroalgae on Avicennia germinans pneumatophores, Rhizophora mangle aerial roots, and within the tidal channel of a mangrove located in a lagoon bordering the east coast of the Baja California Peninsula, from samples collected every 2 months from May 2005 to May 2006. A total of 68 species were found: 21 cyanobacteria, 1 Xanthophyta, 25 Chlorophyta, 1 Ochrophyta-Phaeophyceae, 19 Rhodophyta, and 1 Anthophyta. Species richness varied between habitats; pneumatophores supported 29 species of algae, aerial roots supported 20 species of algae, and the channel bottom supported 46 species. Taxa common to the three habitats were Lyngbya sp., Vaucheria sp., Boodleopsis pusilla, Rhizoclonium riparium, and Bostrychia radicans. Mean wet weight algal biomasses on aerial roots and in the channel were 494 g root-1and 12,924 g m-2, respectively. The dominant species on aerial roots and on the channel bottom were Caulerpa sertularioides, Gracilariopsis lemaneiformis, and Spyridia filamentosa. The channel bottom also had Vaucheria sp. and two cyanobacteria (Oscillatoria sp. and Lyngbya sp.). Morphotypes of two cyanobacteria (Heteroleibleinia sp. and Johanesbaptistia sp.) are recorded in this habitat for the first time.
A facile and efficient synthesis of 1-trichloromethyl-1,2-dihydrobenzo[b][1,6]naphthyridines via three-component reaction among 2-alkynylquinoline-3-carbaldehydes, primary amines, and chloroform
Authors: Bukšnaitienė Rita , Čikotienė Inga 
Published: April 2012

Abstract
A three-component reaction among 2-alkynylquinoline-3-carbaldehydes, primary amines, and chloroform leading to novel 1-(trichloromethyl)-1,2-dihydrobenzo[b][1,6]naphthyridines was developed using microwave initiation in an absence of any catalysts. This method provides a facile approach to the title compounds with moderate to higher yields.
Synthesis and characterization of magnetite nanoparticles modified with PEG-based amphiphilic copolymers
Authors: Kasuya Ryo , Kikuchi Teppei , Balachandran Jeyadevan , Tai Yutaka 
Published: April 2012

ABSTRACTAn aqueous magnetic suspension was prepared by dispersing amphiphilic co-polymer (ACP) coated monodispersed magnetite nanoparticles (MNPs) synthesized through thermal decomposition of iron(III) acetylacetonate in a mixture of oleic acid and oleylamine. ACP composed of poly (maleic anhydride-alt-1-octadecene) and polyethylene glycol methyl ether was applied to disperse MNPs in water and buffer solution. The average diameter of MNPs increased from 6.6 to 12.5 nm with increasing reaction temperature from 200 to 250°C. Infrared spectra and elemental analysis revealed that the surface modified MNPs contain carboxyl groups originated from oleic acid and ACP. The conjugation of MNPs and bovine serum albumin (BSA) antibody was examined. As a result, the as-synthesized MNPs adsorbed BSA antibody effectively than the surface modified MNPs: the BSA antibody adsorption decreased with increasing cross-linker concentration.
The Impact of PCAOB Auditing Standard No. 5 on Audit Fees and Audit Quality
Authors: Wang Dechun , Zhou Jian 
Published: April 2012

SYNOPSIS
We investigate the impact of the Public Company Accounting Oversight Board (PCAOB) Auditing Standard No. 5 (AS5) on audit fees and audit quality. AS5 supersedes Auditing Standard No. 2 (AS2), and became effective for audits for accelerated filers for fiscal years ending on or after November 15, 2007. Using a large sample of accelerated filers subject to AS5, we find evidence that audit fees decrease upon the adoption of AS5. More importantly, even though AS5 adoption reduces audit fees for our test sample, we find no evidence of a decrease in audit quality. In summary, we document evidence that AS5 improves the efficiency of internal control audits.
JEL Classifications: M41.
Impact of Job Complexity and Performance on CFO Compensation
Authors: Balsam Steven , Irani Afshad J. , Yin Qin Jennifer 
Published: April 2012

SYNOPSIS
This study investigates the impact of job complexity and firm, as well as CFO-specific performance, on CFO compensation. We find job complexity and overall firm performance affects both CFO salary and bonus, while CFO-specific performance affects CFO bonus. Specifically, we find that CFOs are not only rewarded when their firms meet or beat earnings targets, but they get incremental rewards for managing earnings and/or expectations to allow their firms to meet or just beat those targets.