bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating clonotypic B cells in classic Hodgkin lymphoma
Authors: Jones Richard J. , Gocke Christopher D. , Kasamon Yvette L. , Miller Carole B. , Perkins Brandy , Barber James P. , Vala Milada S. , Gerber Jonathan M. , Gellert Lan L. , Siedner Mark , Lemas M. Victor , Brennan Sarah , Ambinder Richard F. , Matsui William 
Published: February 2009

Abstract
Although Hodgkin and Reed-Sternberg (HRS) cells are B lymphoid cells, they are unlike any normal cells of that lineage. Moreover, the limited proliferative potential of HRS cells belies the clinical aggressiveness of Hodgkin lymphoma (HL). More than 20 years ago, the L428 HL cell line was reported to contain a small population of phenotypic B cells that appeared responsible for the continued generation of HRS cells. This observation, however, has never been corroborated, and such clonotypic B cells have never been documented in HL patients. We found that both the L428 and KM-H2 HL cell lines contained rare B-cell subpopulations responsible for the generation and maintenance of the predominant HRS cell population. The B cells within the HL cell lines expressed immunoglobulin light chain, the memory B-cell antigen CD27, and the stem cell marker aldehyde dehydrogenase (ALDH). Clonal CD27+ALDHhigh B cells, sharing immunoglobulin gene rearrangements with lymph node HRS cells, were also detected in the blood of most newly diagnosed HL patients regardless of stage. Although the clinical significance of circulating clonotypic B cells in HL remains unclear, these data suggest they may be the initiating cells for HL.
Comparison of small n statistical tests of differential expression applied to microarrays
Authors: Murie Carl , Woody Owen , Lee Anna Y , Nadon Robert 
Published: February 2009

Abstract

Background
DNA microarrays provide data for genome wide patterns of expression between observation classes. Microarray studies often have small samples sizes, however, due to cost constraints or specimen availability. This can lead to poor random error estimates and inaccurate statistical tests of differential expression. We compare the performance of the standard t-test, fold change, and four small n statistical test methods designed to circumvent these problems. We report results of various normalization methods for empirical microarray data and of various random error models for simulated data.

Results
Three Empirical Bayes methods (CyberT, BRB, and limma t-statistics) were the most effective statistical tests across simulated and both 2-colour cDNA and Affymetrix experimental data. The CyberT regularized t-statistic in particular was able to maintain expected false positive rates with simulated data showing high variances at low gene intensities, although at the cost of low true positive rates. The Local Pooled Error (LPE) test introduced a bias that lowered false positive rates below theoretically expected values and had lower power relative to the top performers. The standard two-sample t-test and fold change were also found to be sub-optimal for detecting differentially expressed genes. The generalized log transformation was shown to be beneficial in improving results with certain data sets, in particular high variance cDNA data.

Conclusion
Pre-processing of data influences performance and the proper combination of pre-processing and statistical testing is necessary for obtaining the best results. All three Empirical Bayes methods assessed in our study are good choices for statistical tests for small n microarray studies for both Affymetrix and cDNA data. Choice of method for a particular study will depend on software and normalization preferences.
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger
Authors: Wright James C , Sugden Deana , Francis-McIntyre Sue , Riba-Garcia Isabel , Gaskell Simon J , Grigoriev Igor V , Baker Scott E , Beynon Robert J , Hubbard Simon J 
Published: February 2009

Abstract

Background
Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR).

Results
405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models.

Conclusion
This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.
Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family
Authors: Augustinos Antonios A , Stratikopoulos Elias E , Drosopoulou Eleni , Kakani Evdoxia G , Mavragani-Tsipidou Penelope , Zacharopoulou Antigone , Mathiopoulos Kostas D 
Published: February 2009

Abstract

Background
The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique), albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation.

Results
Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5%) proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus.

Conclusion
Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The presented set of microsatellite markers possesses all features that would render them useful in such analyses. This could also prove helpful for species where SIT is a desired outcome, since the development of effective SIT can be aided by detailed knowledge at the genetic and molecular level. Furthermore, their presented efficacy in several other species of the Tephritidae family not only makes them useful for their analysis but also provides tools for phylogenetic comparisons among them.
Specific gene expression profiles and chromosomal abnormalities are associated with infant disseminated neuroblastoma
Authors: Lavarino Cinzia , Cheung Nai-Kong V , Garcia Idoia , Domenech Gema , de Torres Carmen , Alaminos Miguel , Rios Jose , Gerald William L , Kushner Brian , LaQuaglia Mike , Mora Jaume 
Published: February 2009

AbstractBackgroundNeuroblastoma (NB) tumours have the highest incidence of spontaneous remission, especially among the stage 4s NB subgroup affecting infants. Clinical distinction of stage 4s from lethal stage 4 can be difficult, but critical for therapeutic decisions. The aim of this study was to investigate chromosomal alterations and differential gene expression amongst infant disseminated NB subgroups.MethodsThirty-five NB tumours from patients diagnosed at < 18 months (25 stage 4 and 10 stage 4s), were evaluated by allelic and gene expression analyses.ResultsAll stage 4s patients underwent spontaneous remission, only 48% stage 4 patients survived despite combined modality therapy. Stage 4 tumours were 90% near-diploid/tetraploid, 44% MYCN amplified, 77% had 1p LOH (50% 1p36), 23% 11q and/or 14q LOH (27%) and 47% had 17q gain. Stage 4s were 90% near-triploid, none MYCN amplified and LOH was restricted to 11q. Initial comparison analyses between stage 4s and 4 < 12 months tumours revealed distinct gene expression profiles. A significant portion of genes mapped to chromosome 1 (P< 0.0001), 90% with higher expression in stage 4s, and chromosome 11 (P= 0.0054), 91% with higher expression in stage 4. Less definite expression profiles were observed between stage 4s and 4 < 18m, yet, association with chromosomes 1 (P< 0.0001) and 11 (P= 0.005) was maintained. Distinct gene expression profiles but no significant association with specific chromosomal region localization was observed between stage 4s and stage 4 < 18 months without MYCN amplification.ConclusionSpecific chromosomal aberrations are associated with distinct gene expression profiles which characterize spontaneously regressing or aggressive infant NB, providing the biological basis for the distinct clinical behaviour.
Molecular mechanisms of traumatic brain injury: the missing link in management
Authors: Veenith Tonny , Goon Serena SH , Burnstein Rowan M 
Published: February 2009

Abstract
Head injury is common, sometimes requires intensive care unit admission, and is associated with significant mortality and morbidity. A gap still remains in the understanding of the molecular mechanism of this condition. This review is aimed at providing a general overview of the molecular mechanisms involved in traumatic brain injury to a busy clinician. It will encompass the pathophysiology in traumatic brain injury including apoptosis, the role of molecules and genes, and a brief mention of possible pharmacological therapies.
Amyotrophic lateral sclerosis
Authors: Wijesekera Lokesh C , Nigel Leigh P 
Published: February 2009

Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterised by progressive muscular paralysis reflecting degeneration of motor neurones in the primary motor cortex, corticospinal tracts, brainstem and spinal cord. Incidence (average 1.89 per 100,000/year) and prevalence (average 5.2 per100,000) are relatively uniform in Western countries, although foci of higher frequency occur in the Western Pacific. The mean age of onset for sporadic ALS is about 60 years. Overall, there is a slight male prevalence (M:F ratio~1.5:1). Approximately two thirds of patients with typical ALS have a spinal form of the disease (limb onset) and present with symptoms related to focal muscle weakness and wasting, where the symptoms may start either distally or proximally in the upper and lower limbs. Gradually, spasticity may develop in the weakened atrophic limbs, affecting manual dexterity and gait. Patients with bulbar onset ALS usually present with dysarthria and dysphagia for solid or liquids, and limbs symptoms can develop almost simultaneously with bulbar symptoms, and in the vast majority of cases will occur within 1–2 years. Paralysis is progressive and leads to death due to respiratory failure within 2–3 years for bulbar onset cases and 3–5 years for limb onset ALS cases. Most ALS cases are sporadic but 5–10% of cases are familial, and of these 20% have a mutation of the SOD1 gene and about 2–5% have mutations of the TARDBP (TDP-43) gene. Two percent of apparently sporadic patients have SOD1 mutations, and TARDBP mutations also occur in sporadic cases. The diagnosis is based on clinical history, examination, electromyography, and exclusion of 'ALS-mimics' (e.g. cervical spondylotic myelopathies, multifocal motor neuropathy, Kennedy's disease) by appropriate investigations. The pathological hallmarks comprise loss of motor neurones with intraneuronal ubiquitin-immunoreactive inclusions in upper motor neurones and TDP-43 immunoreactive inclusions in degenerating lower motor neurones. Signs of upper motor neurone and lower motor neurone damage not explained by any other disease process are suggestive of ALS. The management of ALS is supportive, palliative, and multidisciplinary. Non-invasive ventilation prolongs survival and improves quality of life. Riluzole is the only drug that has been shown to extend survival.
Cocaine induces cell death and activates the transcription nuclear factor kappa-b in pc12 cells
Authors: Lepsch Lucilia B , Munhoz Carolina D , Kawamoto Elisa M , Yshii Lidia M , Lima Larissa S , Curi-Boaventura Maria F , Salgado Thais ML , Curi Rui , Planeta Cleopatra S , Scavone Cristoforo 
Published: February 2009

AbstractCocaine is a worldwide used drug and its abuse is associated with physical, psychiatric and social problems. The mechanism by which cocaine causes neurological damage is very complex and involves several neurotransmitter systems. For example, cocaine increases extracellular levels of dopamine and free radicals, and modulates several transcription factors. NF-κB is a transcription factor that regulates gene expression involved in cellular death. Our aim was to investigate the toxicity and modulation of NF-κB activity by cocaine in PC 12 cells. Treatment with cocaine (1 mM) for 24 hours induced DNA fragmentation, cellular membrane rupture and reduction of mitochondrial activity. A decrease in Bcl-2 protein and mRNA levels, and an increase in caspase 3 activity and cleavage were also observed. In addition, cocaine (after 6 hours treatment) activated the p50/p65 subunit of NF-κB complex and the pretreatment of the cells with SCH 23390, a D1 receptor antagonist, attenuated the NF-κB activation. Inhibition of NF-κB activity by using PDTC and Sodium Salicilate increased cell death caused by cocaine. These results suggest that cocaine induces cell death (apoptosis and necrosis) and activates NF-κB in PC12 cells. This activation occurs, at least partially, due to activation of D1 receptors and seems to have an anti-apoptotic effect on these cells.
Bilateral variant testicular arteries with double renal arteries
Authors: Sylvia Sarita , Kakarlapudi Sridhar Varma , Vollala Venkata Ramana , Potu Bhagath Kumar , Jetti Raghu , Bolla Srinivasa Rao , Rao Mohandas , Pamidi Narendra 
Published: February 2009

Abstract

Background
The testicular arteries normally arise from the abdominal aorta. There are reports about the variant origin of these arteries. Accessory renal arteries are also a common finding but their providing origin to testicular arteries is an important observation. The variations described here are unique and provide significant information to surgeons dissecting the abdominal cavity.

Case presentation
During routine dissection classes of abdominal region of a 60-year-old male cadaver, we observed bilateral variant testicular arteries and double renal arteries.

Conclusion
Awareness of variations of the testicular arteries such as those presented here becomes important during surgical procedures like varicocele and undescended testes.
Metastatic malignant melanoma of the conjunctiva: a case report
Authors: Manidakis Nikolaos , Polyzois Ioannis , Tsialogiannis Euaggelos , Marples Maria , Boon Andrew , Tsiridis Eleftherios 
Published: February 2009

Abstract

Background
Malignant melanoma of the conjunctiva is an extremely rare non-cutaneous neoplasm with infrequent skeletal metastatic spread.

Case presentation
We present the case of a 54 year old female Caucasian patient with osseous metastases originating from a malignant melanoma of her right conjunctiva. Metastatic deposits were identified in the left humeral diaphysis and left tibial metaphysis. Clinical, radiological and scintigraphic evaluation necessitated prompt stabilisation of both long bones. Following reamed intramedullary nailing and post-operative radiotherapy she remains asymptomatic six months post-operatively.

Conclusion
This unusual pattern of metastatic spread to the appendicular skeleton of an extremely rare melanomatous lesion requires diagnostic vigilance as well as a multidisciplinary approach for accurate diagnosis, staging and management. Due to the poor prognosis, treatment goals should be directed to palliation of symptoms and prolongation of the quality of life.
Palladium-catalyzed Decarboxylative [4+1] Cyclization of γ-Methylidene-δ-valerolactones with Isocyanides
Authors: Park Soyoung , Shintani Ryo , Hayashi Tamio 
Published: February 2009

Abstract
A palladium-catalyzed decarboxylative cyclization of γ-methylidene-δ-valerolactones with isocyanides has been developed to afford conjugated cyclopentenimines under mild conditions. Some preliminary results toward the development of an asymmetric variant have also been described.
Solvothermal Preparation and Control of Phase Composition of Nanosized Rhodium Sulfide Particles
Authors: Zhang Wu-xing , Yanagisawa Kazumichi , Kamiya Sumio , Shou Tatsuo 
Published: February 2009

Abstract
Well-crystallized Rh2S3 and Rh17S15 powders with average particle size of 100 nm were solvothermally prepared at 673 K for 10 h with S/Rh ratio of 1.65 and 0.9, respectively. The crystallinity and phase of the rhodium sulfides are closely related to the reaction temperature and the S/Rh ratio. By thermal treatment in Ar, the Rh2S3 can be transformed into Rh17S15 at 938 K by loss of sulfur.
Sulfated Zirconia-supported Palladium as a Highly Active and Highly Selective Catalyst for the Oxidation of Ethylene in the Vapor Phase
Authors: Hamada Tomoaki , Sakamoto Yoshinori , Ooka Yasunobu , Okuhara Toshio , Kamiya Yuichi 
Published: February 2009

Abstract
Pd supported on sulfated zirconia with a S/Zr ratio of 0.077 exhibited high activity and high selectivity for the oxidation of ethylene to partially oxidized products, including acetaldehyde and acetic acid, in the vapor phase.
Predictors of progression of osteoarthritis in femoroacetabular impingement
Authors: Bardakos N. V. , Villar R. N. 
Published: February 2009

Although the association between femoroacetabular impingement and osteoarthritis is established, it is not yet clear which hips have the greatest likelihood to progress rapidly to end-stage disease. We investigated the effect of several radiological parameters, each indicative of a structural aspect of the hip joint, on the progression of osteoarthritis. Pairs of plain anteroposterior pelvic radiographs, taken at least ten years apart, of 43 patients (43 hips) with a pistol-grip deformity of the femur and mild (Tönnis grade 1) or moderate (Tönnis grade 2) osteoarthritis were reviewed. Of the 43 hips, 28 showed evidence of progression of osteoarthritis. There was no significant difference in the prevalence of progression between hips with initial Tönnis grade 1 or grade 2 osteoarthritis (p = 0.31). Comparison of the hips with and without progression of arthritis revealed a significant difference in the mean medial proximal femoral angle (81° vs 87°, p = 0.004) and the presence of the posterior wall sign (39% vs 7%, p = 0.02) only. A logistic regression model was constructed to predict the influence of these two variables in the development of osteoarthritis.Mild to moderate osteoarthritis in hips with a pistol-grip deformity will not progress rapidly in all patients. In one-third, progression will take more than ten years to manifest, if ever. The individual geometry of the proximal femur and acetabulum partly influences this phenomenon. A hip with cam impingement is not always destined for end-stage arthritic degeneration.
Medical negligence in orthopaedic surgery
Authors: Gidwani S. , Zaidi S. M. R. , Bircher M. D. 
Published: February 2009

Payments by the NHS Litigation Authority continue to rise each year, and reflect an increase in successful claims for negligence against NHS Trusts. Information about the reasons for which Trusts are sued in the field of trauma and orthopaedic surgery is scarce. We analysed 130 consecutive cases of alleged clinical negligence in which the senior author had been requested to act as an expert witness between 2004 and 2006, and received information on the outcome of 97 concluded cases from the relevant solicitors. None of the 97 cases proceeded to a court hearing. Overall, 55% of cases were abandoned by the claimants’ solicitors, and the remaining 45% were settled out of court. The cases were settled for sums ranging from £4500 to £2.7 million, the median settlement being £45 000. The cases that were settled out of court were usually the result of delay in treatment or diagnosis, or because of substandard surgical technique.
Antibacterial, antiviral, and cytotoxic activities of some red and brown seaweeds from the Black Sea
Authors: Kamenarska Zornitsa , Serkedjieva Julia , Najdenski Hristo , Stefanov Kamen , Tsvetkova Iva , Dimitrova-Konaklieva Stefka , Popov Simeon 
Published: February 2009

AbstractChloroform extracts,n-butanol extracts, water extracts, and volatile compounds from seven species belonging to six Black Sea genera of brown algae and 10 species belonging to seven Black Sea genera of red algae were assessed for antibacterial, antiviral, and cytotoxic properties. Most of the extracts showed pronounced effects against the Gram (+) bacteriumStaphylococcus aureus. Activity towards the Gram (-) bacteriumEscherichia coliwas found in only few cases. A significant reduction in replication of influenza andHerpes simplexviruses in cell cultures was observed. Cytotoxic effect was established in a significant proportion of the algae investigated. The biological activities may be attributed to the presence of volatile compounds, some phenols, free fatty acids and their oxidized derivatives, eucalyptol, the methyl ester of phenyl acetic acid, and 1,2-dihydroxy ethane sulfonate.