bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of cervical lymph node metastasis in head and neck cancer patients with clinically N0 neck—a meta-analysis comparing different imaging modalities
Authors: Liao Li-Jen , Lo Wu-Chia , Hsu Wan-Lun , Wang Chi-Te , Lai Mei-Shu 
Published: June 2012

Abstract

Background
How to properly manage clinically negative neck of head and neck cancer patients is a controversial topic. Research is now directed toward finding a method sensitive enough to bring the risk of occult metastases below 20%. The aim of this review was to compare the diagnostic accuracy of different imaging modalities, including CT, MRI, PET and US, in clinically N0 head and neck cancer patients.

Methods
For this systematic review and meta-analysis, PubMed and the Cochrane Database were searched for relevant original articles published up to May 2011. Inclusion criteria were as follows: articles were reported in English; CT, MRI, PET or US were performed to identify cervical metastases in clinically N0 head and neck squamous cell carcinoma; and data were sufficient for the calculation of true-positive or false-negative values. A bivariate random effect model was used to obtain pooled sensitivity and specificity. The positive and negative test probability of neck metastasis was generated based on Bayesian theory and collected data for different pre-test possibilities.

Results
Of the 168 identified relevant articles, 7 studies fulfilled all inclusion criteria for CT, 6 studies for MRI, 11 studies for PET and 8 studies for US. There was no difference in sensitivity and specificity among these imaging modalities, except CT was superior to US in specificity. The pooled estimates for sensitivity were 52% (95% confidence interval [CI], 39% ~ 65%), 65% (34 ~ 87%) 66% (47 ~ 80%), and 66% (45 ~ 77%), on a per-neck basis for CT, MRI, PET and US, respectively. The pooled estimates for specificity were 93% (87% ~ 97%), 81% (64 ~ 91%), 87% (77 ~ 93%), and 78% (71 ~ 83%) for CT, MRI, PET and US, respectively. With pre-examination nodal metastasis probabilities set at 10%, 20% and 30%, the post-exam probabilities of positive nodal metastasis rates were 47%, 66% and 77% for CT; 27%, 46% and 59% for MRI; 36%, 56% and 69% for PET; and 25%, 42% and 56% for US, respectively. Negative nodal metastasis probabilities were 95%, 89% and 82% for CT; 95%, 90% and 84% for MRI; 96%, 91% and 86% for PET; and 95%, 90% and 84% for US, respectively.

Conclusions
Modern imaging modalities offer similar diagnostic accuracy to define and diagnose clinically N0 neck. Minimizing morbidity and avoiding elective neck dissection is acceptable in some select cases.
Li-Fraumeni-like syndrome associated with a large BRCA1 intragenic deletion
Authors: Silva Amanda Gonçalves , Ewald Ingrid Petroni , Sapienza Marina , Pinheiro Manuela , Peixoto Ana , de Nóbrega Amanda França , Carraro Dirce M , Teixeira Manuel R , Ashton-Prolla Patricia , Achatz Maria Isabel W , Rosenberg Carla , Krepischi Ana C V 
Published: June 2012

Abstract

Background
Li-Fraumeni (LFS) and Li-Fraumeni-like (LFL) syndromes are associated to germline TP53 mutations, and are characterized by the development of central nervous system tumors, sarcomas, adrenocortical carcinomas, and other early-onset tumors. Due to the high frequency of breast cancer in LFS/LFL families, these syndromes clinically overlap with hereditary breast cancer (HBC). Germline point mutations in BRCA1, BRCA2, and TP53 genes are associated with high risk of breast cancer. Large rearrangements involving these genes are also implicated in the HBC phenotype.

Methods
We have screened DNA copy number changes by MLPA on BRCA1, BRCA2, and TP53 genes in 23 breast cancer patients with a clinical diagnosis consistent with LFS/LFL; most of these families also met the clinical criteria for other HBC syndromes.

Results
We found no DNA copy number alterations in the BRCA2 and TP53 genes, but we detected in one patient a 36.4 Kb BRCA1 microdeletion, confirmed and further mapped by array-CGH, encompassing exons 9–19. Breakpoints sequencing analysis suggests that this rearrangement was mediated by flanking Alu sequences.

Conclusion
This is the first description of a germline intragenic BRCA1 deletion in a breast cancer patient with a family history consistent with both LFL and HBC syndromes. Our results show that large rearrangements in these known cancer predisposition genes occur, but are not a frequent cause of cancer susceptibility.
Prognostic factors of successful tympanoplasty in pediatric patients: a cohort study
Authors: Boronat-Echeverría Nuria Esperanza , Reyes-García Esmeralda , Sevilla-Delgado Yolanda , Aguirre-Mariscal Héctor , Mejía-Aranguré Juan Manuel 
Published: June 2012

Abstract

Background
Tympanoplasty in children is a current and controversial theme. The success of tympanoplasty traditionally has been measured only by the post-operative integrity of the graft. Yet, there are other variables that may be used to determine success. The objectives of the present work were to analyze which factors are predictive of successful tympanoplasty in pediatric patients and to construct and validate a prognostic index that could be used as a tool to predict the success of tympanoplasty in children.

Methods

Setting. Department of Pediatric Otorhinolaryngology, tertiary-care hospital, Mexico City. Patients. Forty-eight patients, who were older that five years of age, had persistent perforation of the tympanic membrane, and had undergone tympanoplasty (January 2005–June 2008), were followed for a year. Main Outcome Measures. The factors tested for their value as predictors were the following: age at time of surgery, state of contralateral ear, previous adenoidectomy, cause of perforation, size of perforation, infection at the time of surgery, state of mucosa, age at first occurrence of perforation, presence of craniofacial dysmorphia, and surgical technique. These factors were compared with the criterion, success, which was defined as attaining three positive outcomes: 1) integrity of the implant or membrane; 2) minimum of 10-dB gain in the auditory threshold or, in the case of normal hearing, conservation of same; and 3) air-filled space in the middle ear. The best model was obtained through logistic regression analysis; the model was validated.

Results
The most balanced prediction model was that in which the three success criteria were included, with age, surgical technique, and infection at surgery being excluded as variables. The additional 12 pediatric cases used in the validation had a probability of success >0.425 (best cut-off level); two patients (17%) had poor evolution.

Conclusions
This is the first study that validated a predictive index of the result of tympanoplasty in children. This index predicted 81% of the successful outcomes.
Prevalence of molecular markers of Plasmodium falciparum drug resistance in Dakar, Senegal
Authors: Wurtz Nathalie , Fall Bécaye , Pascual Aurélie , Diawara Silmane , Sow Kowry , Baret Eric , Diatta Bakary , Fall Khadidiatou B , Mbaye Pape S , Fall Fatou , Diémé Yaya , Rogier Christophe , Bercion Raymond , Briolant Sébastien , Wade Boubacar , Pradines Bruno 
Published: June 2012

Abstract

Background
As a result of the widespread resistance to chloroquine and sulphadoxine-pyrimethamine, artemisinin-based combination therapy (ACT) (including artemether-lumefantrine and artesunate-amodiaquine) has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Intermittent preventive treatments with anti-malarial drugs based on sulphadoxine-pyrimethamine are also given to children or pregnant women once per month during the transmission season. Since 2006, there have been very few reports on the susceptibility of Plasmodium falciparum to anti-malarial drugs. To estimate the prevalence of resistance to several anti-malarial drugs since the introduction of the widespread use of ACT, the presence of molecular markers associated with resistance to chloroquine and sulphadoxine-pyrimethamine was assessed in local isolates at the military hospital of Dakar.

Methods
The prevalence of genetic polymorphisms in genes associated with anti-malarial drug resistance, i.e., Pfcrt, Pfdhfr, Pfdhps and Pfmdr1, and the copy number of Pfmdr1 were evaluated for a panel of 174 isolates collected from patients recruited at the military hospital of Dakar from 14 October 2009 to 19 January 2010.

Results
The Pfcrt 76T mutation was identified in 37.2% of the samples. The Pfmdr1 86Y and 184F mutations were found in 16.6% and 67.6% of the tested samples, respectively. Twenty-eight of the 29 isolates with the 86Y mutation were also mutated at codon 184. Only one isolate (0.6%) had two copies of Pfmdr1. The Pfdhfr 108N/T, 51I and 59R mutations were identified in 82.4%, 83.5% and 74.1% of the samples, respectively. The double mutant (108N and 51I) was detected in 83.5% of the isolates, and the triple mutant (108N, 51I and 59R) was detected in 75.3%. The Pfdhps 437G, 436F/A and 613S mutations were found in 40.2%, 35.1% and 1.8% of the samples, respectively. There was no double mutant (437G and 540E) or no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E). The prevalence of the quadruple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G) was 36.5%.

Conclusions
Since 2004, the prevalence of chloroquine resistance had decreased. The prevalence of isolates with high-level pyrimethamine resistance is 83.5%. The prevalence of isolates resistant to sulphadoxine is 40.2%. However, no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E), which is associated with a high level of sulphadoxine-pyrimethamine resistance, has been identified to date. The resistance to amodiaquine remains moderate.
The RASSF gene family members RASSF5, RASSF6 and RASSF7 show frequent DNA methylation in neuroblastoma
Authors: Djos Anna , Martinsson Tommy , Kogner Per , Carén Helena 
Published: June 2012

AbstractBackgroundHypermethylation of promotor CpG islands is a common mechanism that inactivates tumor suppressor genes in cancer. Genes belonging to theRASSFgene family have frequently been reported as epigenetically silenced by promotor methylation in human cancers. Two members of this gene family,RASSF1AandRASSF5Ahave been reported as methylated in neuroblastoma. Data from our previously performed genome-wide DNA methylation array analysis indicated that other members of theRASSFgene family are targeted by DNA methylation in neuroblastoma.ResultsIn the current study, we found that several of theRASSFfamily genes (RASSF2,RASSF4,RASSF5,RASSF6,RASSF7, andRASSF10) to various degrees were methylated in neuroblastoma cell lines and primary tumors. In addition, several of theRASSFfamily genes showed low or absent mRNA expression in neuroblastoma cell lines.RASSF5andRASSF6were to various degrees methylated in a large portion of neuroblastoma tumors andRASSF7was heavily methylated in most tumors. Further, CpG methylation sites in the CpG islands of someRASSFfamily members could be used to significantly discriminate between biological subgroups of neuroblastoma tumors. For example,RASSF5methylation highly correlated toMYCNamplification and INRG stage M. Furthermore, high methylation ofRASSF6was correlated to unfavorable outcome, 1p deletion andMYCNamplification in our tumor material.In conclusionThis study shows that several genes belonging to theRASSFgene family are methylated in neuroblastoma. The genesRASSF5,RASSF6andRASSF7stand out as the most promising candidate genes for further investigations in neuroblastoma.
Role of glycogen synthase kinase-3 beta in the inflammatory response caused by bacterial pathogens
Authors: Cortés-Vieyra Ricarda , Bravo-Patiño Alejandro , Valdez-Alarcón Juan J , Juárez Marcos Cajero , Finlay B Brett , Baizabal-Aguirre Víctor M 
Published: June 2012

Abstract
Glycogen synthase kinase 3β (GSK3β) plays a fundamental role during the inflammatory response induced by bacteria. Depending on the pathogen and its virulence factors, the type of cell and probably the context in which the interaction between host cells and bacteria takes place, GSK3β may promote or inhibit inflammation. The goal of this review is to discuss recent findings on the role of the inhibition or activation of GSK3β and its modulation of the inflammatory signaling in monocytes/macrophages and epithelial cells at the transcriptional level, mainly through the regulation of nuclear factor-kappaB (NF-κB) activity. Also included is a brief overview on the importance of GSK3 in non-inflammatory processes during bacterial infection.
Comparative proteomic analysis of transition of saccharomyces cerevisiae from glucose-deficient medium to glucose-rich medium
Authors: Giardina Bennett J , Stanley Bruce A , Chiang Hui-Ling 
Published: June 2012

Abstract

Background
When glucose is added to Saccharomyces cerevisiae grown in non-fermentable carbon sources, genes encoding ribosomal, cell-cycle, and glycolytic proteins are induced. By contrast, genes involved in mitochondrial functions, gluconeogenesis, and the utilization of other carbon sources are repressed. Glucose also causes the activation of the plasma membrane ATPase and the inactivation of gluconeogenic enzymes and mitochondrial enzymes. The goals of this study were to use the iTRAQ-labeling mass spectrometry technique to identify proteins whose relative levels change in response to glucose re-feeding and to correlate changes in protein abundance with changes in transcription and enzymatic activities. We used an experimental condition that causes the degradation of gluconeogenic enzymes when glucose starved cells are replenished with glucose. Identification of these enzymes as being down-regulated by glucose served as an internal control. Furthermore, we sought to identify new proteins that were either up-regulated or down-regulated by glucose.

Results
We have identified new and known proteins that change their relative levels in cells that were transferred from medium containing low glucose to medium containing high glucose. Up-regulated proteins included ribosomal subunits, proteins involved in protein translation, and the plasma membrane ATPase. Down-regulated proteins included small heat shock proteins, mitochondrial proteins, glycolytic enzymes, and gluconeogenic enzymes. Ach1p is involved in acetate metabolism and is also down-regulated by glucose.

Conclusions
We have identified known proteins that have previously been reported to be regulated by glucose as well as new glucose-regulated proteins. Up-regulation of ribosomal proteins and proteins involved in translation may lead to an increase in protein synthesis and in nutrient uptake. Down-regulation of glycolytic enzymes, gluconeogenic enzymes, and mitochondrial proteins may result in changes in glycolysis, gluconeogenesis, and mitochondrial functions. These changes may be beneficial for glucose-starved cells to adapt to the addition of glucose.
EQ-5D™-derived utility values for different levels of migraine severity from a UK sample of migraineurs
Authors: Stafford Megan R , Hareendran Asha , Ng-Mak Daisy S , Insinga Ralph P , Xu Ruifeng , Stull Donald E 
Published: June 2012

Abstract

Background
To estimate utility values for different levels of migraine pain severity from a United Kingdom (UK) sample of migraineurs.

Methods
One hundred and six migraineurs completed the EQ-5D to evaluate their health status for mild, moderate and severe levels of migraine pain severity for a recent migraine attack, and for current health defined as health status within seven days post-migraine attack. Statistical tests were used to evaluate differences in mean utility scores by migraine severity.

Results
Utility scores for each health state were significantly different from 1.0 (no problems on any EQ-5D dimension) (p < 0.0001) and one another (p < 0.0001). The lowest mean utility, − 0.20 (95% confidence interval [CI]: -0.27 – -0.13), was for severe migraine pain. The smallest difference in mean utility was between mild and moderate migraine pain (0.13) and the largest difference in mean utility was between current health (without migraine) and severe migraine pain (1.07).

Conclusions
Results indicate that all levels of migraine pain are associated with significantly reduced utility values. As severity worsened, utility decreased and severe migraine pain was considered a health state worse than death. Results can be used in cost-utility models examining the relative economic value of therapeutic strategies for migraine in the UK.
Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac
Authors: Brandariz-Nuñez Alberto , Valle-Casuso Jose Carlos , White Tommy E , Laguette Nadine , Benkirane Monsef , Brojatsch Jurgen , Diaz-Griffero Felipe 
Published: June 2012

AbstractBackgroundSAMHD1 is a nuclear protein that blocks lentiviral infection before reverse transcription in macrophages and dendritic cells. The viral accessory protein Vpx overcomes the SAMHD1-mediated lentiviral block by inducing its proteasomal degradation.ResultsHere, we identified the nuclear localization signal (NLS) of SAMHD1, and studied its contribution to restriction of HIV-1 and SIVmac. By studying the cellular distribution of different SAMHD1 variants, we mapped the nuclear localization of SAMHD1 to residues11KRPR14. Mutagenesis of these residues changed the cellular distribution of SAMHD1 from the nucleus to the cytoplasm. SAMHD1 mutants that lost nuclear localization restricted HIV-1 and SIV as potently as the wild type protein. Interestingly, SAMHD1 mutants that localized to the cytoplasm were not degraded by nuclear Vpx alleles. Therefore, nuclear Vpx alleles require nuclear localization of SAMHD1 in order to induce its degradation. In agreement, SIVmac viruses encoding Vpx did not overcome the restriction imposed by the cytoplasmic variants of SAMHD1.ConclusionsWe mapped the NLS of SAMHD1 to residues11KRPR14and studied the contribution of SAMHD1 nuclear localization to restriction of HIV-1 and SIV. These experiments demonstrate that cytoplasmic variants of SAMHD1 potently block lentiviral infection and are resistant to Vpx-mediated degradation. The nuclear Vpx alleles studied here are only capable of degrading a nuclearly localized SAMHD1 suggesting that Vpx-mediated degradation of SAMHD1 is initiated in the nucleus.
Loop-mediated isothermal amplification for the detection of goose circovirus
Authors: Woźniakowski Grzegorz , Kozdruń Wojciech , Samorek-Salamonowicz Elżbieta 
Published: June 2012

Abstract

Background
Goose circovirus (GCV) presents an immunosuppressive problem in production of geese. The infection’s clinical symptoms include growth retardation or feathering disorders but the infection process may remain non-symptomatic what makes the infected birds more susceptible for secondary viral, bacterial and fungal infections. Diagnosis of GCV infection is made by histopathological examination, dot blot hybridization, polymerase chain reaction (PCR) and real-time PCR. However these techniques require application of thermocyclers and qualified staff which may be cost-consuming for some diagnostic units. The aim of this study was to develop loop-mediated isothermal amplification assay (LAMP) as a simple method of GCV detection.

Results
The presented study has shown LAMP as a rapid tool of detecting DNA of goose circovirus (GCV) as soon in 30 min time. The method used three sets of primers: two outer primers (F3 and B3), two inner primers (FIP and BIP) and two loop primers (FL and BL) to accelerate the reaction. The optimum reaction temperature and the time were 61°C for 30 min, respectively. The results were analysed using SYBR Green dye and GelRedTM solutions. Thirty-eight isolates of GCV collected from geese flocks in Poland were examined. For comparison, real-time polymerase chain reaction with F3 and B3 primers and SYBR Green dye was conducted. The obtained results have shown GCV-LAMP as a sensitive, rapid and specific assay and alternative for PCR-based methods.

Conclusions
The developed technique due to its simplicity may be applied by any veterinary laboratory or even mobile diagnostics units for the routine detection of GCV.
Rapid Detection of high-level oncogene amplifications in ultrasonic surgical aspirations of brain tumors
Authors: Truong Long N , Patil Shashikant , Martin Sherry S , LeBlanc Jay F , Nanda Anil , Nordberg Mary L , Beckner Marie E 
Published: June 2012

AbstractBackgroundGenomic tumor information, such as identification of amplified oncogenes, can be used to plan treatment. The two sources of a brain tumor that are commonly available include formalin-fixed, paraffin-embedded (FFPE) sections from the small diagnostic biopsy and the ultrasonic surgical aspiration that contains the bulk of the tumor. In research centers, frozen tissue of a brain tumor may also be available. This study compared ultrasonic surgical aspiration and FFPE specimens from the same brain tumors for retrieval of DNA and molecular assessment of amplified oncogenes.MethodsSurgical aspirations were centrifuged to separate erythrocytes from the tumor cells that predominantly formed large, overlying buffy coats. These were sampled to harvest nuclear pellets for DNA purification. Four glioblastomas, 2 lung carcinoma metastases, and an ependymoma were tested. An inexpensive PCR technique, multiplex ligation-dependent probe amplification (MLPA), quantified 79 oncogenes using 3 kits. Copy number (CN) results were normalized to DNA from non-neoplastic brain (NB) in calculated ratios, [tumor DNA]/[NB DNA]. Bland-Altman and Spearman rank correlative comparisons were determined. Regression analysis identified outliers.ResultsPurification of DNA from ultrasonic surgical aspirations was rapid (<3 days) versus FFPE (weeks) and yielded greater amounts in 6 of 7 tumors. Gene amplifications up to 15-fold corresponded closely between ultrasonic aspiration and FFPE assays in Bland-Altman analysis. Correlation coefficients ranged from 0.71 to 0.99 using 3 kit assays per tumor. Although normalized CN ratios greater than 2.0 were more numerous in FFPE specimens, some were found only in the ultrasonic surgical aspirations, consistent with tumor heterogeneity. Additionally, CN ratios revealed 9 high-level (≥ 6.0) gene amplifications in FFPE of which 8 were also detected in the ultrasonic aspirations at increased levels. The ultrasonic aspiration levels of these amplified genes were also greater than 6.0 CN ratio, except in one case (3.53 CN ratio). Ten of 17 mid-level (≥3.0 & <6.0 CN ratio) amplifications detected in FFPE were also detected as being increased (≥ 2.0 CN ratio) in the aspirations.ConclusionsBuffy coats of centrifuged ultrasonic aspirations contained abundant tumor cells whose DNA permitted rapid, multiplex detection of high-level oncogene amplifications that were confirmed in FFPE.Virtual slideshttp://www.diagnosticpathology.diagnomx.eu/vs/1883718801686466