Analysis of the HLA class I associated peptide repertoire in a hepatocellular carcinoma cell line reveals tumor-specific peptides as putative targets for immunotherapy

HLA class I molecules present peptides on the cell surface to CD8(+) T cells. The repertoire of peptides that associate to class I molecules represents the cellular proteome. Therefore, cells expressing different proteomes could generate different class I-associated peptide repertoires. A large number of peptides have been sequenced from HLA class I alleles, mostly from lymphoid cells. On the other hand, T cell immunotherapy is a goal in the fight against cancer, but the identification of T cell epitopes is a laborious task. Proteomic techniques allow the definition of putative T cell epitopes by the identification of HLA natural ligands in tumor cells. In this study, we have compared the HLA class I-associated peptide repertoire from the hepatocellular carcinoma (HCC) cell line SK-Hep-1 with that previously described from lymphoid cells. The analysis of the peptide pool confirmed that, as expected, the peptides from SK-Hep-1 derive from proteins localized in the same compartments as in lymphoid cells. Within this pool, we have identified 12 HLA class I peptides derived from HCC-related proteins. This confirms that tumor cell lines could be a good source of tumor associated antigens to be used, together with MS, to define putative epitopes for cytotoxic T cells from cancer patients.     

Ontology-based semantic similarity: A new feature-based approach

Estimation of the semantic likeness between words is of great importance in many applications dealing with textual data such as natural language processing, knowledge acquisition and information retrieval. Semantic similarity measures exploit knowledge sources as the base to perform the estimations. In recent years, ontologies have grown in interest thanks to global initiatives such as the Semantic Web, offering an structured knowledge representation. Thanks to the possibilities that ontologies enable regarding semantic interpretation of terms many ontology-based similarity measures have been developed. According to the principle in which those measures base the similarity assessment and the way in which ontologies are exploited or complemented with other sources several families of measures can be identified. In this paper, we survey and classify most of the ontology-based approaches developed in order to evaluate their advantages and limitations and compare their expected performance both from theoretical and practical points of view. We also present a new ontology-based measure relying on the exploitation of taxonomical features. The evaluation and comparison of our approach’s results against those reported by related works under a common framework suggest that our measure provides a high accuracy without some of the limitations observed in other works.     

CMOS-SOI platform for monolithic integration of crystalline silicon MEMS

A new platform for the fabrication of crystalline micro- and nano-electromechanical systems fully integrable with CMOS is presented. A pre-CMOS process on SOI wafers allows bulk silicon areas for standard CMOS processing and areas with a stack layer of silicon and silicon oxide to be obtained, in which a set of microelectromechanical devices can be fabricated. An integrated resonant beam system with electrical actuation and detection fabricated according to the presented approach is provided.     

Deletions and loss of expression of p16INK4a and p21Waf1 genes are associated with aggressive variants of mantle cell lymphomas

Mantle cell lymphoma (MCL) is molecularly characterized by bcl-1 rearrangement and cyclin D1 gene overexpression. Some aggressive variants of MCL have been described with blastic or large cell morphology, higher proliferative activity, and shorter survival. The cyclin-dependent kinase inhibitors (CDKIs) p21Waf1 and p16INK4a have been suggested as candidates for tumor-suppressor genes. To determine the role of p21Waf1 and p16INK4a gene alterations in MCLs, we examined the expression, deletions, and mutations of these genes in a series of 24 MCLs, 18 typical, and 6 aggressive variants. Loss of expression and/or deletions of p21Waf1 and p16INK4a genes were detected in 4 (67%) aggressive MCLs but in none of the typical variants. Two aggressive MCLs showed a loss of p16INK4a expression. These cases showed homozygous deletions of p16INK4a gene by Southern blot analysis. An additional aggressive MCL in which expression could not be examined showed a hemizygous 9p12 deletion. Loss of p21Waf1 expression at both protein and mRNA levels was detected in an additional aggressive MCL. No p21Waf1 gene deletions or mutations were found in this case. The p21Waf1 expression in MCLs was independent of p53 mutations. The two cases with p53 mutations showed p21Waf1 and p16INK4a expression whereas the 4 aggressive MCLs with p16INK4a and p21Waf1 gene alterations had a wild-type p53. p21Waf1 and p16INK4a were expressed at mRNA and protein levels in all typical MCLs examined. No gene deletions or point mutations were found in typical variants. Two typical MCLs showed an anomalous single-stranded conformation polymorphism corresponding to the known polymorphisms at codon 148 of p16INK4a gene and codon 31 of p21Waf1 gene. These findings indicate that p21Waf1 and p16INK4a alterations are rare in typical MCLs but the loss of p21Waf1 and p16INK4a expression, and deletions of p16INK4a gene are associated with aggressive variants of MCLs, and they occur in a subset of tumors with a wild-type p53 gene.     

Establishing In-House Cutoffs of CSF Alzheimer’s Disease Biomarkers for the AT(N) Stratification of the Alzheimer Center Barcelona Cohort

Background: Clinical diagnosis of Alzheimer’s disease (AD) increasingly incorporates CSF biomarkers. However, due to the intrinsic variability of the immunodetection techniques used to measure these biomarkers, establishing in-house cutoffs defining the positivity/negativity of CSF biomarkers is recommended. However, the cutoffs currently published are usually reported by using cross-sectional datasets, not providing evidence about its intrinsic prognostic value when applied to real-world memory clinic cases. Methods: We quantified CSF Aβ1-42, Aβ1-40, t-Tau, and p181Tau with standard INNOTEST^® ELISA and Lumipulse G^® chemiluminescence enzyme immunoassay (CLEIA) performed on the automated Lumipulse G600II. Determination of cutoffs included patients clinically diagnosed with probable Alzheimer’s disease (AD, n = 37) and subjective cognitive decline subjects (SCD, n = 45), cognitively stable for 3 years and with no evidence of brain amyloidosis in 18F-Florbetaben-labeled positron emission tomography (FBB-PET). To compare both methods, a subset of samples for Aβ1-42 (n = 519), t-Tau (n = 399), p181Tau (n = 77), and Aβ1-40 (n = 44) was analyzed. Kappa agreement of single biomarkers and Aβ1-42/Aβ1-40 was evaluated in an independent group of mild cognitive impairment (MCI) and dementia patients (n = 68). Next, established cutoffs were applied to a large real-world cohort of MCI subjects with follow-up data available (n = 647). Results: Cutoff values of Aβ1-42 and t-Tau were higher for CLEIA than for ELISA and similar for p181Tau. Spearman coefficients ranged between 0.81 for Aβ1-40 and 0.96 for p181TAU. Passing–Bablok analysis showed a systematic and proportional difference for all biomarkers but only systematic for Aβ1-40. Bland–Altman analysis showed an average difference between methods in favor of CLEIA. Kappa agreement for single biomarkers was good but lower for the Aβ1-42/Aβ1-40 ratio. Using the calculated cutoffs, we were able to stratify MCI subjects into four AT(N) categories. Kaplan–Meier analyses of AT(N) categories demonstrated gradual and differential dementia conversion rates (p = 9.815⁻²⁷). Multivariate Cox proportional hazard models corroborated these findings, demonstrating that the proposed AT(N) classifier has prognostic value. AT(N) categories are only modestly influenced by other known factors associated with disease progression. Conclusions: We established CLEIA and ELISA internal cutoffs to discriminate AD patients from amyloid-negative SCD individuals. The results obtained by both methods are not interchangeable but show good agreement. CLEIA is a good and faster alternative to manual ELISA for providing AT(N) classification of our patients. AT(N) categories have an impact on disease progression. AT(N) classifiers increase the certainty of the MCI prognosis, which can be instrumental in managing real-world MCI subjects.     

Detection of anisakids in fish and seafood products by real-time PCR

Anisakids are a group of widely distributed nematodes which have acquired high social relevance due to their involvement in foodborne infections caused by consumption of raw or undercooked seafood. A TaqMan^®-LNA probe real-time assay targeting the cytochrome oxidase subunit I (COI) was developed allowing the simultaneous detection of the most important anisakids species present in fish and seafood products.The determination of the detection limit in terms of ppm was 1 ppmFor the validation of method developed, twenty fish and cephalopod samples were experimentally contaminated with anisakid. It was checked that in cases in any anisakids species was present, it was detected because the Ct was always less than 35 and did not produce any case false negatives. The main novelty of this work lies in the fact that it can be applied to all kinds of processed products, including those undergoing intensive processes of transformation, as for instance canned foods. The proposed methodology is rapid, robust, highly sensitive and readily adaptable in routine molecular diagnostic laboratories, and can be employed as molecular screening method in order to assess the food security.     

Web-Based Semantic Similarity: An Evaluation in the Biomedical Domain

Computation of semantic similarity between concepts is a very common problem in many language related tasks and knowledge domains. In the biomedical field, several approaches have been developed to deal with this issue by exploiting the structured knowledge available in domain ontologies (such as SNOMED-CT or MeSH) and specific, closed and reliable corpora (such as clinical data). However, in recent years, the enormous growth of the Web has motivated researchers to start using it as the corpus to assist semantic analysis of language. This paper proposes and evaluates the use of the Web as background corpus for measuring the similarity of biomedical concepts. Several ontology-based similarity measures have been studied and tested, using a benchmark composed by biomedical terms, comparing the results obtained when applying them to the Web against approaches in which specific clinical data were used. Results show that the similarity values obtained from the Web for ontology-based measures are at least and even more reliable than those obtained from specific clinical data, showing the suitability of the Web as information corpus for the biomedical domain.     

Addition of a reactive diluent to a catalyzed epoxy-anhydride system. I. Influence on the cure kinetics

The effect of a reactive diluent (RD) on the kinetics of the curing of an epoxy resin, based on diglycidyl ether of bisphenol A (DGEBA), with a carboxylic anhvdride derived from methyl-tetrahydrophthalic anhydride (MTHPA) catalyzed by a tertiary amine has been studied. The reactive diluent was a low-viscosity aliphatic diglycidyl ether, and the compositions per 100 parts by weight (pbw) of DGEBA were 10, 30, and 50 pbw of RD with the stoichiometric quantity of MTHPA and 1 pbw of catalyst. The curing kinetics was monitored by differential scanning calorimetry (DSC), and the kinetic parameters were determined from the nonisothermal DSC curves by the method described by Málek. The kinetic analysis suggests that the two-parameter autocatalytic model is the more appropriate to describe the kinetics of the curing reaction of this epoxy-anhydride system. The kinetic parameters thus derived satisfactorily simulate both the nonisothermal DSC curves and the isothermal conversion-time plots. Increasing the RD content leads to a small increase in both the nonisothermal and the isothermal heats of curing and has a slight effect on the kinetic parameters E, ln A, m, and n, and, consequently, on the overall reactivity of the system. On the other hand, the increase of the RD content significantly affects the structure of the crosslinked epoxy. It is confirmed that the introduction of aliphatic chains in the structure of the epoxy increases the mobility of the segmental chains in the glass transition region. The consequence of this chemical modification is a decrease of the glass transition temperature, T_g. © 1996 John Wiley & Sons, Inc.     

Physical aging in polymers: Comparison of two ways of determining narayanaswamy's parameter

In this work, we have investigated by differential scanning calorimetry the enthalpy relaxation of two poly[methyl(α-n-alkyl)acrylates] in which it is possible to change the length of the two alkyl chains. In particular, we have evaluated the Narayanaswamy parameter, which controls relative contribution of temperature and of structure to the relaxation times, by two methods: Grenet's method (GM) and the peak-shift method (PSM). The data obtained show that both methods lead to equivalent results. Nevertheless, PSM requires fewer experiments than GM, and PSM appears to be more practical. The results obtained on the two acrylates show that the parameter x increases with the lateral chain length, that is to say, that the temperature effects increase as the length of the alkyl chain is increased.