bluuebunny/crossref_metadata_2025_split huggingface dataset:
A BACH2‐BCL2L1 fusion gene resulting from a t(6;20)(q15;q11.2) chromosomal translocation in the lymphoma cell line BLUE‐1
Authors: Türkmen Seval , Riehn Mathias , Klopocki Eva , Molkentin Mara , Reinhardt Richard , Burmeister Thomas 
Published: March 2011

AbstractAbnormalities of the long arm of chromosome 6 are a common feature in various B‐cell malignancies. In most cases, the genes involved have not yet been clearly identified. We have molecularly characterized the recently established Burkitt lymphoma cell line BLUE‐1 that carries a t(6;20)(q15;q11.2) rearrangement in addition to the typical t(8;14) with MYC‐IGH fusion. To identify the gene loci involved on both chromosomes we applied a sequential BAC clone mapping strategy. By using RT‐PCR we were finally able to detect a chimeric mRNA transcript showing a fusion of the first (non‐coding) exon of BACH2 (BTB and CNC homology 1, basic leucine zipper transcription factor 2) on 6q15 to the second exon of BCL2L1 (BCL‐X) on 20q11. Various fusion transcripts were detected for different BCL2L1 (BCL‐XL) isoforms. The fusion ultimately results in strong expression of the BCL2L1 (BCL‐XL) anti‐apoptosis protein, as demonstrated by immunoblotting. This is the first report that shows the involvement of both BCL2L1 and the transcription factor BACH2 in a chromosomal rearrangement. It points to BACH2 as a possibly important target in lymphomas with 6q aberrations, although other genes on 6q are probably also involved in these cases. Moreover, it suggests that members of the BCL2 anti‐apoptosis gene family other than BCL2 itself might also be involved in lymphoma. © 2011 Wiley‐Liss, Inc.
Genomic aberrations in diffuse low‐grade gliomas
Authors: Dahlback Hanne‐Sofie S. , Gorunova Ludmila , Brandal Petter , Scheie David , Helseth Eirik , Meling Torstein R. , Heim Sverre 
Published: March 2011

AbstractThe current classification of diffuse low‐grade gliomas is based mainly on histopathological criteria, which cannot accurately predict the highly variable clinical course observed in patients with such tumors. In an attempt to increase pathogenetic understanding of these tumors, we investigated 38 WHO Grade II astrocytomas, oligodendrogliomas, and oligoastrocytomas using a combination of G‐band chromosome analysis and high‐resolution comparative genomic hybridization (HR‐CGH). Abnormal karyotypes were found in 41% of tumors. Karyotypes of astrocytomas and oligodendrogliomas were near‐diploid whereas oligoastrocytomas also displayed near‐tetraploid clones. The most common aberrations were losses of chromosomes X, Y, 3, 4, 6, and 11 and gains of chromosomes 8 and 12. The only recurrent structural rearrangement was del(6)(q21). HR‐CGH analysis verified karyotyping findings but also revealed frequent losses at 1p, 17q, and 19q and gains of 7q, 10p, 11q, and 20p. Among the tumors were two gemistocytic astrocytomas, a subgroup of diffuse astrocytomas with a particular predisposition for progression but not studied cytogenetically before; one showed a near‐diploid, complex karyotype with structural aberrations of chromosomes 1, 3, and 11 whereas both displayed simple aberrations including loss of 11p by HR‐CGH. Our findings suggest that within diffuse low‐grade gliomas are genetically distinct entities that do not fit the currently used classification. In addition, tumors with complex chromosomal aberrations had a higher tendency for aggressive tumor behavior (shorter progression‐free survival) than tumors displaying simple aberrations only (P= 0.07). This could help identify genetic subsets of patients with low‐grade glioma who might benefit from early antineoplastic therapy. © 2011 Wiley‐Liss, Inc.
Downregulation of methylthioadenosin phosphorylase by homozygous deletion in gastric carcinoma
Authors: Kim Jin , Kim Min A , Min Sun Young , Jee Chang Do , Lee Hee Eun , Kim Woo Ho 
Published: March 2011

AbstractThe methylthioadenosine phosphorylase (MTAP) gene is located on 9p21 telomeric to the CDKN2A tumor suppressor gene. Loss of MTAP gene is frequently associated with CDKN2A homozygous deletion. Although the homozygous deletion of MTAP has been reported in various human cancers, its function in gastric carcinogenesis is unknown. Here, we determined the status of the MTAP gene by using a combination of array‐based comparative genomic hybridization and oligonucleotide microarray. It was found that MTAP was deleted and downregulated in 2 of 10 gastric cancer cell lines. Of the 494 primary gastric carcinomas examined, MTAP expression at the protein level was reduced in 59 (11.9%). Furthermore, a lack of MTAP expression was found to be associated with poor survival (P = 0.038). The genomic loss of MTAP and CDKN2A in gastric carcinomas was investigated by quantitative real‐time PCR. Among 20 gastric carcinomas, two cases showed deletion of both MTAP and CDKN2A, and three samples showed homozygous deletion of MTAP, but not of CDKN2A. An analysis of gastric carcinomas revealed that reduced MTAP expression correlated significantly with a genomic deletion. Furthermore, functional assays by transfecting the siRNA or the expressional cDNA into gastric cancer cell lines demonstrated that MTAP regulates cell growth and invasion. The present study suggests that MTAP plays an important role in the regulation of gastric carcinogenesis and, in particular, that MTAP loss is implicated in some way with tumor growth via the modulation of cellular properties, which, in turn, suggests that MTAP has therapeutic applications. © 2011 Wiley‐Liss, Inc.
Scale invariance and self‐similarity in kinematic wave overland flow in space and time
Authors: Haltas I. , Kavvas M. L. 
Published: March 2011

AbstractFractals are famous for their self‐similar nature at different spatial scales. Similar to fractals, solutions of scale invariant processes are self‐similar at different space–time scales. This unique property of scale‐invariant processes can be utilized to translate the solution of the processes at a much larger or smaller space–time scale (domain) based on the solution calculated on the original space–time scale. This study investigates scale invariance conditions of kinematic wave overland flow process in one‐parameter Lie group of point transformations framework. Scaling (stretching) transformation is one of the one‐parameter Lie group of point transformations and it has a unique importance among the other transformations, as it leads to the scale invariance or scale dependence of a process. Scale invariance of a process yields a self‐similar solution at different space–time scales. However, the conditions for the process to be scale invariant usually dictate various relationships between the scaling coefficients of the dependent and independent variables of the process. Therefore, the scale invariance of a process does not assure a self‐similar solution at any arbitrary space and time scale. The kinematic wave overland flow process is modelled mathematically as initial‐boundary value problem. The conditions to be satisfied by the system of governing equations as well as the initial and boundary conditions of the kinematic wave overland flow process are established in order for the process to be scale invariant. Also, self‐similarity of the solution of the kinematic wave overland flow under the established invariance conditions is demonstrated by various numerical example problems. Copyright © 2011 John Wiley & Sons, Ltd.
Toxicity studies of nonylphenol and octylphenol: hormonal, hematological and biochemical effects inClarias gariepinus
Authors: Senthil Kumaran Satyanarayanan , Kavitha Chokkalingam , Ramesh Mathan , Grummt Tamara 
Published: March 2011

ABSTRACTAmong the numerous chemicals discharged into aquatic ecosystems, nonylphenol (NP) and octylphenol (OP) have been shown to have a potent effect on the endocrine system of fish; this issue has been clearly dealt with in several studies. The objective of this study was to assess and compare the general toxicity of these estrogenic chemicals individually onClarias gariepinus. Fish were exposed to different concentrations of both NP and OP (250, 500, 750 and 1000 μg l−1) under semi‐static conditions for a period of 7 days. The adverse effect was evaluated with use of blood cell counting, hemoglobin (Hb), hematocrit (HCT), hematimetric indices, bilirubin, protein, glucose, serum transaminases, serum phosphatases, lactate dehydrogenase and cortisol. The results showed a clear indication of anemia, increases in leukocyte count and bilirubin content and a reduction in plasma protein levels with higher concentrations of both the toxicants compared with controls. Furthermore, with all the concentrations the inevitable increase in serum cortisol and plasma glucose showed primary and secondary stress responses. Moreover, probable tissue damage gave rise to a series of fluctuations of enzyme levels at lower concentrations, but a decrease with higher concentrations showed the severity of the effect. Depending on the parameters examined, OP had a relatively greater effect than NP. Overall, these two chemicals seemingly affected hematology and the activity of some enzymes, leading to serious impairment of the metabolism and physiology ofC.gariepinus. Copyright © 2011 John Wiley & Sons, Ltd.
Computational chemistry, systems biology and toxicology. Harnessing the chemistry of life: revolutionizing toxicology. A commentary
Authors: Kimber Ian , Humphris Colin , Westmoreland Carl , Alepee Nathalie , Negro Gianni Dal , Manou Irene 
Published: March 2011

ABSTRACTThere is a continuing interest in, and increasing imperatives for, the development of alternative methods for toxicological evaluations that do not require the use of animals. Although a significant investment has resulted in some achievements, progress has been patchy and there remain many challenges. Among the most significant hurdles is developing non‐animal methods that would permit assessment of the potential for a chemical or drug to cause adverse health effects following repeated systemic exposure. Developing approaches to address this challenge has been one of the objectives of the European Partnership for Alternative Approaches to Animal Testing (EPAA). The EPAA is a unique partnership between the European Commission and industry that has interests in all aspects of reducing, refining and replacing the use of animals (the ‘3Rs’). One possible strategy that emerged from a broad scientific debate sponsored by the EPAA was the opportunity for developing entirely new paradigms for toxicity testing based upon harnessing the increasing power of computational chemistry in combination with advanced systems biology. This brief commentary summarizes a workshop organized by the EPAA in 2010, that had the ambitious title of ‘Harnessing the Chemistry of Life: Revolutionizing Toxicology’. At that workshop international experts in chemistry, systems biology and toxicology sought to map out how best developments in these sciences could be exploited to design new strategies for toxicity testing using adverse effects in the liver as an initial focus of attention. Here we describe the workshop design and outputs, the primary purpose being to stimulate debate about the need to align different areas of science with toxicology if new and truly innovative approaches to toxicity testing are to be developed. Copyright © 2011 John Wiley & Sons, Ltd.
Employment of single‐strand conformation polymorphism analysis in screening for α‐1,3 glucosyltransferase gene mutation A333V in Croatian population
Authors: Goreta Sandra Supraha , Dabelic Sanja , Dumic Jerka 
Published: March 2011

AbstractCongenital disorder of glycosylation type Ic (CDG‐Ic) is caused by mutations in hALG6 gene encoding α‐1,3 glucosyltransferase (NP_037471.2), an enzyme that catalyzes the addition of the first glucose residue to the growing lipid‐linked oligosaccharide precursor in N‐glycosylation process. The most frequent mutation in hALG6 gene causing CDG‐Ic is c.998C>T that results in p.A333V substitution. Up‐to‐date, no CDG‐Ic patient has been detected in Croatia. However, as a part of the comprehensive project undertaken with the aim to estimate the frequencies of the carriers for specific mutations and polymorphisms related to particular CDGs in Croatian population, we screened genomic DNA samples obtained from 600 healthy nonconsanguineous Croatian residents to determine the frequency of the A333V mutation. For that purpose, we established the conditions for polymerase chain reaction‐based single‐strand conformation polymorphism analysis that is suitable for primary screening and in population studies, especially when the initial sample volume is small or DNA quantity is limited. None of the analyzed samples carried this mutation, indicating that the frequency of the patients carrying this homozygous mutation in Croatian population would be <1 in 1.4×106. J. Clin. Lab. Anal. 25:65;–70, 2011. © 2011 Wiley‐Liss, Inc.
Clinical applicability of single‐tube multiplex reverse‐transcriptase PCR in dengue virus diagnosis and serotyping
Authors: Mishra Bajayantimala , Sharma Mirnalini , Pujhari Sujit Kumar , Appannanavar Suma B. , Ratho Radha Kanta 
Published: March 2011

AbstractThis study has evaluated the clinical applicability of a single‐tube multiplex RT‐ PCR as compared with a two‐step nested RT‐PCR for the diagnosis as well as serotyping of dengue virus in patient's samples. Seventy‐six acute phase blood samples collected from clinically suspected dengue patients during the 2008 outbreak were subjected to two‐step nested RT‐PCR and single‐tube multiplex RT‐PCR for dengue diagnosis and serotyping. Of the 76 samples, 17 (22.4%) were positive for dengue viral RNA. Single dengue virus infection was found in 16 cases and 1 had concurrent infection with two serotypes (3&1). Dengue serotype 3 was the predominant serotype (70.5%), followed by serotype 1 (23.5%). Single‐tube multiplex PCR had concordant result with that of two‐step nested RT‐PCR including the one with concomitant infection. This study reveals the predominance of dengue serotype 3 in North India in addition to the co‐circulation of multiple serotypes and concomitant infection. The rapid and accurate diagnostic capability of single‐tube multiplex RT‐PCR used in the study appears to be promising enough to be commonly used for dengue viral detection as well as serotyping. J. Clin. Lab. Anal. 25:76–78, 2011. © 2011 Wiley‐Liss, Inc.
Comparison of RNA extraction methods to augment the sensitivity for the differentiation of vesicular stomatitis virus Indiana1 and New Jersey
Authors: Arshed Muhammad Javed , Magnuson Roberta J. , Triantis Joni , Abubakar Muhammad , Campen Hana Van , Salman Mo 
Published: March 2011

AbstractTwo methods for the extraction of RNA of vesicular stomatitis virus (VSV) Indiana1 and New Jersey and their simultaneous amplification by one‐step polymerase chain reaction using reverse transcriptase were evaluated. A guanidine‐thiocyanate‐based RNA extraction (Qiagen RNeasy Mini Kit, Qiagen, Valencia, CA ) followed by column‐based purification coupled with one‐step RT‐PCR proved to be a simple, safe, practicable, and reliable tool for rapid, highly sensitive, and specific differential diagnosis of both types of VSV in cell lysate and spiked tissue samples as compared with the tri‐phasic extraction method (Tri‐reagent method). When RNA was extracted either from VSV cell culture stock or from VSV spiked bovine lymph nodes by using Qiagen RNeasy Mini Kit, the detection limit in the multiplex RT‐PCR was as low as 0.505 to 2.84 TCID50 for VSV‐IND and VSV‐NJ, respectively. The multiplex RT‐PCR consistently detected VSV‐IND and NJ RNA in as little as 0.1–1.0 fg of total RNA from spiked BHK‐21 cell suspension when Qiagen RNeasy mini kit was used. The multiplex RT‐PCR assay was capable of detecting both types of VSV in a one‐step reaction tube. The minimum sensitivity of this assay in various experiments was 0.1683 TCID50 (IND), 0.0946 TCID50 (NJ), and 0.057 fg (IND and NJ) per 2 µl PCR sample, which is significantly more sensitive than reported previously (0.28–2.8 TCID50/1 µl). So the present study improved the sensitivity of previously reported multiplex RT‐PCR for the detection and differentiation of VSV‐IND and VSV‐NJ in a single assay. J. Clin. Lab. Anal. 25:95–99, 2011. © 2011 Wiley‐Liss, Inc.
Fetal RHD genotyping by analysis of maternal plasma in a mixed population
Authors: Amaral Daphne R.T. , Credidio Débora C. , Pellegrino Jordão , Castilho Lilian 
Published: March 2011

AbstractBackground: Maternal plasma analysis for the determination of the fetal RHD status is an exciting tool for the management of RhD‐negative pregnant women, specially sensitized women. We assessed the accuracy of fetal RHD genotyping by analysis of maternal plasma in a multi‐ethnic population. Methods: We analyzed plasma samples from 88 RhD‐negative pregnant women between 11 and 39 weeks of gestation, median age of 28 years old to determine the fetal RHD genotype. This population was from Southeastern Brazil with high mixed ethnic background. Fourteen patients (16%) had anti‐D alloantibody. We used Taqman primers and probes to detect by real‐time PCR, exons 4, 5, and 10 of RHD. As internal controls we used primers/probes sets to SRY and CCR5. Peripheral or umbilical cord bloods from respective nenonates were collected during delivery and hemagglutination was performed. Results: Fifty‐eight samples (66%) were genotyped as RHD+, 27 samples (31%) showed complete absence of RHD and 3 samples (3 %) presented a D variant (RHDψ). All the results agreed with the neonatal typing, including the three fetuses with the RHDψ, phenotyped as RhD‐negative. Thus, the accuracy of the fetal RHD genotyping in this mixed population was 100%. The earliest pregnancy in which fetal RHD was detected was 11 weeks. Conclusion: Our findings indicate that the accuracy of RHD gene using three regions (exons 4, 5, and 10) can be sufficient for clinical application in a multi‐ethnic population. This knowledge helped us on the development of a feasible protocol for fetal RHD genotyping on DNA from maternal plasma for our population. J. Clin. Lab. Anal. 25:100–104, 2011. © 2011 Wiley‐Liss, Inc.
Analysis of the temperature affects on leukocyte surface antigen expression
Authors: Jämsä Joel , Huotari Virva , Savolainen Eeva‐Riitta , Syrjälä Hannu , Ala‐Kokko Tero 
Published: March 2011

AbstractFlow cytometric analysis of leukocyte surface antigens has been used to characterize infectious and septic processes in patients. We wanted to investigate how the sampling and processing temperature, the anticoagulant used, and the storage of the sample influence leukocyte immunophenotyping. Four blood samples, two using acid citrate dextrose and two using heparin as an anticoagulant, were taken from five intensive‐care unit patients with severe sepsis and five healthy volunteers. The samples were collected, stored, and processed either at +4°C or at room temperature (RT). The samples were processed for flow cytometric analysis within 1 hr of collection or after 6 or 24 hr storage. The surface antigens of interest were neutrophilic CD11b and CD64, monocytic CD11b, CD14, CD40, CD64, CD80 and HLA‐DR, and lymphocytic CD69 (separately in CD4+ and CD8+ T cells, B cells, and natural killer cells). The fluorescence intensities were higher at RT than at +4°C. During storage the intensities increased at RT, but at +4°C there were only minor changes. The effects were similar with both anticoagulants studied. According to our results, flow cytometric analysis of leukocyte surface antigen expressions should be performed using +4°C temperature throughout the process and within 6 hr. J. Clin. Lab. Anal. 25:118–125, 2011. © 2011 Wiley‐Liss, Inc.
Analytical quality goals for 25‐vitamin D based on biological variation
Authors: Viljoen Adie , Singh Dhruv K. , Farrington Ken , Twomey Patrick J. 
Published: March 2011

AbstractBackground: Measurement of 25‐hydroxyvitamin D, (25D) is central in the investigation of pathologies of bone and mineral ion metabolism and in determining a patient's vitamin D status. More recently much research interest has lead to investigating the role it can play in decreasing the risk of many chronic illnesses, including common cancers, autoimmune diseases, infectious diseases, and cardiovascular disease. Knowledge of the biological variation of an analyte forms an essential part of evaluating a new analyte enabling the objective assessment of the changes in serial results, the utility of reference intervals as well as establishing laboratory quality specifications. Methods: This study determined the biological variation of 25D in 20 healthy individuals that was calculated according to the familiar methods outlined by Fraser and Harris. Results: The within‐subject variation was 12.1% and the between subject variation was 40.3%. The critical difference for sequential values significant at P<0.05 was calculated as 38.4%. The within‐subject variation forms a relatively small part of the reference interval shown by the low index of individuality of 0.3. Objective analytical quality goals have also been established which have shown achievable minimum performance for imprecision of ∼6%. The desirable analytical bias goal was ∼10%. Conclusion: This study has objectively shown that the analytical precision of current instruments is being achieved contrary to the known problems surrounding the analytical bias for 25D assays. The limitations of using reference intervals for 25D, both in diagnoses and monitoring are shown. J. Clin. Lab. Anal. 25:130–133, 2011. © 2011 Wiley‐Liss, Inc.
Evaluation of saliva specimens as an alternative sampling method to detect hepatitis B surface antigen
Authors: Cruz Helena Medina , da Silva Elisangela Ferreira , Villela‐Nogueira Cristiane A. , Nabuco Letícia C. , Rodrigues do Ó Kycia Maria , Lewis‐Ximenez Lia Laura , Tachibana Yoshida Clara Fumiko , Lampe Elisabeth , Villar Livia Melo 
Published: March 2011

AbstractIn this study, a modified enzyme immunoassay (EIA) was evaluated for the Hepatitis B surface antigen (HBsAg) among whole saliva and oral fluid samples. Specimens were collected from 115 individuals who gave serum and oral fluid using Salivette (Sarstedt, Nümbrecht, Germany) and whole saliva. Saliva specimens were tested following a modified ELISA, and the results were compared with paired serum specimens that were tested according to the supplier's instructions. Transport buffer for the oral fluids, sample volume for assay, incubation period of sample with conjugate as well as cut‐off values were evaluated to optimize the assay. The highest sensitivity and specificity were obtained by increasing the incubation of sample and conjugate to 16 hr and using the area under the receiver operating characteristic curve to calculate cut‐off values. HBsAg was detected in 40 oral fluids and 44 whole saliva samples out of 47 paired positive serum specimens and not detected in 64 oral fluids and 63 whole saliva samples out of 68 matched negative sera samples by the ELISA assay. There was excellent agreement between the results for the serum and saliva specimens kappa value (κ): 0.80 for oral fluid and κ: 0.87 for whole saliva and there was excellent reproducibility. Using an optimized protocol, the sensitivities of whole saliva and oral fluid were 93.6 and 85.1%, respectively, whereas specificities of whole saliva and oral fluid were 92.6 and 94.1%, respectively. Our data showed a significant promise for the use of whole saliva and oral fluid together with the modified commercial EIA for Hepatitis B virus infection surveillance. J. Clin. Lab. Anal. 25:134–141, 2011. © 2011 Wiley‐Liss, Inc.
An efficient synthesis of pyrrolo[1,2‐a]quinazolin‐5(1H)‐one derivatives with the aid of low‐valent titanium reagent
Authors: Zhao Xuan , Shi Da‐Qing 
Published: March 2011

AbstractA short and facile synthesis of 2,3,3a,4‐tetrahydropyrrolo[1,2‐a]quinazolin‐5(1H)‐ones and 2,3,3a,4‐tetrahydropyrrolo[1,2‐a]quinazoline‐1,5‐diones in good yields via the novel reductive cyclization of 2‐nitrobenzamides with haloketones or 4‐oxopentanoic acid promoted by low‐valent titanium reagent is described. J. Heterocyclic Chem., (2011).