Search

In this paper, a novel approach is proposed based on the accurate computation of the inaccessible volume and the corresponding surface area which is defined by the locus of points where a ligand molecule can be placed so that it “touches” a protein molecule at a preset minimum interatomic distance without resulting in overlaps between the atoms of the protein and the atoms of the ligand. The proposed approach can be considered an extension of the widely used concept of the solvent accessible surface area (SASA). The SASA is defined as the surface where a solvent molecule can be in contact with the initial one without any overlaps. This excluded volume interaction is evaluated by treating atoms as hard core spheres, with the limitation of the solvent molecule being represented as a single sphere. In the proposed concepts of the molecular accessible surface (MASA) and the molecular inaccessible volume (MIV) we have practically removed this limitation and all atoms, both in the initial and the “inserted” molecules, are represented as hard spheres. In this paper we focus our examples on biological systems, especially on studying protein–ligand systems, since we expect that this will be one of the most promising fields of applications where the MASA and MIV extensions of the SASA will be of practical and immediate use. Therefore, the MASA and MIV are evaluated based on the surface generated by the ligand while it is being rolled over on all the atoms of the protein without penetrating them. Identification of the inaccessible volume of each candidate protein–ligand pair is also provided in the context of this study, along with the boundary surface where the ligand can be placed so as to be in “contact” with the protein. The proposed concepts of the MASA and MIV are expected to significantly enhance the ability to investigate specific protein–drug interactions by explicitly taking into account the polyatomic nature of a ligand. Several trials have been conducted using the analytical method of Dodd and Theodorou leading to accurate volume and surface area measurements of an arbitrary set of fused spheres in systems of various scales.

In this work, a novel approach is proposed based on the accurate computation of a protein’s inaccessible volume as regards to a ligand, plus the corresponding surface area, where the ligand can be placed in order to “touch” the protein without any overlaps. The proposed approach can be thought as an extension of the widely used concept of the Solvent-Accessible Surface Area (SASA), evaluating the surface generated by the ligand while being rolled over all the atoms of the protein without penetrating them. Identification of the inaccessible volume of each candidate protein-ligand pair is also provided in the context of this study, along with the boundary surface where the ligand can be placed so as to be in “contact” with the protein, which is expected to significantly enhance the ability to investigate specific protein drug interactions.

Introduction Accurate determination of low-density lipoprotein cholesterol (LDL) is important for coronary heart disease (CHD) risk assessment among others. A low-cost method used is the Friedewald equation, calculating LDL from total cholesterol after subtracting high-density lipoprotein cholesterol (HDL) and triglycerides divided by 5. A new calculation method has been proposed where the value of 5 is not fixed but depends on the values of the other parameters. Results We validated this method in a Greek population sample, by comparing direct LDL, the Friedewald equation and the novel method. Some clinical laboratories use the direct determination when TG > 200 mg/dl (2.26 mmol/lt). We performed segmented linear regression to check if this value makes sense. Bayesian linear regression was performed to compare the direct determination to the Friedewald and novel one. Conclusions We found that TG > 200 mg/dl is a sensible threshold value since it is a saddle point for the standard error of the regression. For Bayesian linear regression, the results were inconclusive. When the LDL values were used for classification of CHD, it turned out that the novel method was better than the Friedewald equation at correctly classifying LDL levels for CHD risk assessment.

The increased computational power of modern embedded devices with the widespread development of Internet infrastructure has brought the Internet of Things (IoT) era closest than ever. Recent market researches indicate that IoT product and relevant service suppliers will generate revenue exceeding $300 billion and the interconnected devices will grow to 26 billion [1, 2]. One field that can be benefited from the common advantages of IoT systems, (real time monitoring, large scale deployment etc.) is the Logistics area. In this paper we investigate a common problem in the logistics which is the automating object counting. We concentrate on uniform, disposable products stored on a pile, queue or a stack (e.g., a shelf) and examine a number of different technologies for sensing input and output through a gate to the storage area and how we can integrate them in an IoT environment. We define a set of comparison criteria with practical flavor in order to examine and evaluate twelve different types of sensors 3. The intention for our study is to form a baseline for anyone needing to implement gate-based input/output control.

The present study was conducted to investigate the prognostic significance of co-expression patterna of HER-2, IL-6, TNF-a and TGF-β1 in breast cancer, by correlating the number of markers with positive expression with clinicopathological characteristics indicative of tumor progression and overall survival. One hundred thirty consecutive patients with primary breast cancer were prospectively included and evaluated. Serum concentrations of the above markers were measured by ELISA. Median split was used to subdivide patients with marker positive or negative expression. The presence of ≥ 3 positive markers was independently associated with extended lymph node (>3) involvement (aOR, 11.94, p=0.001) and lymphovascular invasion (aOR, 12.04, p=0.018), increasing the prognostic significance of each marker considered separately. Additional prognostic information regarding survival was also provided; as the number of positive markers increased, a gradually reduction of survival time was observed. In addition, patients with 4 positive markers had significantly shorter survival (25 vs 39 months, p=0.006) and a more than 4 fold increased risk of death (aHR, 4.35, p=0.003) compared to patients with 3 positive markers. Our findings suggest that the coexpression pattern of these four markers could be used clinically as a useful marker for tumor extension and outcome of breast cancer.

A decade of screening (years 2000 to 2010) for hemoglobinopathies in 3,931 patients was performed at the General Hospital of Poligiros, Halkidiki, Northern Greece. Among the patients examined, 10.8% heterozygotes for β-thalassemia (β-thal) were found, as well as 4.1% with sickle cell disease and 1.2% with double β-thal/Hb S [β6(A3)Glu→Val] heterozygosity. Iron deficiency was observed in 23.4%. The geographical distribution in the region revealed a substantial incidence of hemoglobinopathies even in mountainous areas. This pattern did not follow the typical distribution according to the malaria hypothesis, as incidence did not dovetail with swamp locations recorded in the past. The HBB gene mutations for 85 patients were also analyzed. Most prevalent in Halkidiki, Northern Greece, was the codon 39 (CT) mutation (27.1%) followed by the IVS-I-110 (GA) mutation (22.4%); this was in direct contrast to the current distribution of the same mutations seen in the rest of Greece (Greek National Genetic Database, GNGD). This frequency inversion was statistically significant, with the difference from the GNGD being 20.6% for the IVS-I-110 mutation (p0.0005) and 7.6% for the codon 39 mutation (p = 0.0238). The history of Halkidiki, denoting a clear example of geographical isolation from the rest of the country, may possibly account for a potentially diverse genetical identity of the disease in this region.

Objectives: The analytical performance of the TOSOH HLC-723G7 hemoglobin HPLC analyzer and the effect of the presence of HbS in the determination of HbA2 using HPLC and manual column methods. Design and methods: The performance characteristics of the TOSOH HLC-723G7 analyzer in the determination of HbA2 were compared to those of the HELENA Beta-Thal Quik column. The effect of HbS presence in the samples was quantified using the HELENA SAS-MX alkaline gel electrophoresis kit as the reference method. Results: Within-run and between-run CVs for HbA2 were better for the TOSOH HPLC analyzer than for the HELENA manual column method. The presence of HbS in the samples produces a strong positive bias in the %HbA2 values when using both the HPLC and manual column methods, compared to the alkaline electrophoresis gel. Conclusion: Both the TOSOH HPLC and the manual column are reliable methods for %HbA2 determination when no HbS is detectable in the samples. When HbS is present, the gel electrophoresis method gives more accurate results.

While technical internships as a scheme are considered positive for both the intern and the hosting organisation, carrying out a successful internship session is not neither easy nor trivial. Towards managing an internship, we adopt an Agile-based framework that consists of four phases with a mixture of research, technical and communication tasks and covers the full project lifecycle providing good exposure to a range of professional practices. This framework is flexible to accommodate changes in preferences of an intern and includes a large variety of communication tasks such as project plan generation, technical progress reporting, generation and presentation of ideas and competitive analysis, along with technical tasks for instance Test Driven design and programming, development with C++ and code revision. Apart from interns, the hosting body benefits from the work of the interns which is reliable and of acceptable quality.

Although internships contribute to the professional development of a junior engineer, it is not straightforward to achieve a fruitful outcome for either the intern or the hosting the organisation. We discuss a structured framework based on Agile and Scrum concepts with the goal of providing in a flexible manner a mixture of communication, technical and research skills. Not only interns get hands-on exposure to the aforementioned skills but the organisation can make use of their deliverables.

Contextual data monitoring plays an important role in increasing the quality of life of humans. Sensors observing specific activities report contextual data to a central system capable of situational reasoning. The system responds to any event related to the observed phenomenon. We propose an intelligent mechanism that builds on top of sensors measurements and derives the appropriate decisions for immediate identification of events. The mechanism adopts multivariate data fusion, time-series prediction, and consensus theory for aggregating measurements. We adopt Fuzzy Logic for handling the induced uncertainty in the decision making on the derived alerts. Simulations over real contextual data showcase the advantages and disadvantages of our monitoring mechanism.

Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains regions interpretable either as RNA chains or as protein motifs. To assist phasing at higher resolution we introduced recombinant methods aimed at extensive selenation for MAD phasing. We are focusing on several ribosomal proteins that can be quantitatively detached by chemical means. These proteins can be modified and subsequently reconstituted into depleted ribosomal cores. They also can be used for binding heavy atoms, by incorporating chemically reactive binding sites, such as -SH groups, into them. In parallel we are co-crystallizing the ribosomal particles with tailor made ligands, such as antibiotics or cDNA to which heavy-atoms have been attached or diffuse the latter compounds into already formed crystals.

Crystals of small and large ribosomal subunits from thermophilic and halophilic bacteria, diffracting to 3 A, are being subjected to structural analysis with synchrotron radiation. The bright beam necessary for detecting and collecting the diffraction at the higher-resolution shell causes significant decay even at 25 K. Nevertheless, data collected from native and heavy-atom-derivatized crystals led to the construction of electron density maps of both ribosomal subunits, showing recognizable morphologies and internal features similar to those observed by EM reconstructions of the corresponding ribosomal particle. The main features of these maps include elongated dense regions traceable as well separated RNA duplexes or single strands. Also seen are globular patches of lower density, readily distinguishable from the above, in which folds observed by NMR or crystallography in isolated ribosomal proteins at atomic resolution were detected. The intercomponents contacts identified so far reveal diverse modes of recognition. Metal clusters, attached at selected sites on the particles, are being exploited to facilitate unbiased map interpretation. In this way, two surface proteins were located and several surface RNA strands were targeted.

Objectives: The effect of the presence of HbS in the determination of HbA 2 using the Biorad Variant II analyzer. Design and methods: The effect of HbS presence in the samples was quantified using the HELENA SAS-MX alkaline gel electrophoresis kit as the reference method. Results: The %HbA 2 values from the Variant II analyzer and the HELENA SAS-MX alkaline gel electrophoresis kit show a good linear correlation in the absence of HbS. A strong positive bias in the %HbA 2 values from the Variant II is apparent in the presence of HbS in the samples, when compared to the alkaline electrophoresis gel. Conclusion: The Variant II analyzer gives reliable results for %HbA 2 determination when no HbS is detectable in the samples. When HbS is present, the gel electrophoresis method gives more accurate results.

Presented study was conducted to investigate the prognostic significance of the coexpression of serum interleukin-6 (IL-6) and tumor necrosis factor-a (TNF-a) in breast cancer, by correlating their presence with clinicopathological characteristics indicative of tumor progression and the overall survival of breast cancer patients. One hundred twelve consecutive patients with primary breast cancer were prospectively included and evaluated. Serum concentrations of IL-6 and TNF-a were measured by quantitative sandwich enzyme immunoassay (ELISA). Median split was used to subdivide patients with low or high IL-6 and TNF-a levels. A positive association between the expression of the two cytokines was found. The coexpression of high IL-6 and TNF-α was independently associated with extended lymph node (>3) involvement (aOR, 7.8) and lymphovascular invasion (aOR, 14.1), increasing the prognostic significance of each cytokine separately; it also provided additional prognostic information regarding survival, defining a high-risk subgroup of patients with significantly shorter survival and higher risk of death compared to patients with both cytokines low (aHR, 4.45) and patients with only one cytokine high (aHR, 3.63). Our findings suggest that the coexpression of these two cytokines could be used clinically as a useful tumor marker for the extension and the outcome of the disease.

Preliminary phases were determined by the application of the isomorphous replacement method at low and intermediate resolution for structure factor amplitudes collected from crystals of large and small ribosomal subunits from halophilic and thermophilic bacteria. Derivatization was performed with dense heavy atom clusters, either by soaking or by specific covalent binding prior to the crystallization. The resulting initial electron density maps contain features comparable in size to those expected for the corresponding particles. The packing arrangements of these maps have been compared with motifs observed by electron microscopy in positively stained thin sections of embedded three-dimensional as well as with phase sets obtained by ab-initio computations. Aimed at higher resolution phasing, procedures are being developed for multi-site binding of relatively small dense metal clusters at selected locations. Potential sites are being inserted either by mutagenesis or by chemical modifications to facilitate cluster binding to the large halophilic and the small thermophil!c ribosomal subunits which yield crystals diffracting to the highest resolution obtained so far for ribosomes, 2.9 and 7.3 A, respectively. For this purpose the surfaces of these ribosomal particles have been characterized and conditions for quantitative reversible detachment of selected ribosomal proteins have been found. The corresponding genes are being cloned, sequenced, mutated to introduce the reactive side-groups (mainly cysteines) and overexpressed. To assist the interpretation of the anticipated electron density maps, sub-ribosomal stable complexes were isolated from H50S. One of these complexes is composed of two proteins and the other is made of a stretch of the rRNA and a protein. For exploiting the exposed parts of the surface of these complexes for heavy atom binding and for attempting the determination of their three-dimensional structure, their components are being produced genetically. The low resolution models reconstructed from tilt series of crystalline arrays of ribosomal particles are being employed for initial phasing. The tentative functional interpretation of these models stimulated the design and the crystallization of complexes mimicking

Lebanon nowadays faces critical power generation shortages and energy security problems due to almost full dependence on imported oil and chronic economic deficit of Electricite du Liban(EDL). Since these problems persist, now is the time for Lebanon to formulate a firm policy and action plans for attracting investments in renewable energy and energy efficiency. The paper examines key donor activities and projects and their results in the introduction of renewables and energy efficiency technologies as well as creating the respective legislative and institutional framework in Lebanon. Conclusions discuss proposals for the further improvement of renewables and energy efficiency, the most important being the political commitment to promote these technologies and reform the energy sector, the set up of fiscal incentives and financing mechanisms, the right use of subsidies and the establishment of the institutional framework of the energy sector with clear roles.

It is known that the presence of hemoglobin S (HbS) affects the determination of hemoglobin A(2) (HbA(2)) levels in clinical samples. We quantitated this effect using the Menarini HA-8160 analyzer and compared with other instruments (HELENA beta-thal quik column, TOSOH HLC-723G7 and BIORAD Variant II) using the HELENA SAS-MX alkaline gel electrophoresis kit as the reference method. The %HbA(2) values from the HA-8160 analyzer and the alkaline gel electrophoresis show a good linear correlation in the absence of HbS. A strong positive bias in the %HbA(2) values from the HA-8160 is apparent in the presence of HbS in the samples, when compared with the alkaline electrophoresis. The analytical imprecision and bias of the three HPLC instruments are comparable both in the presence and absence of HbS. The manual column method shows a lower bias in the absence of HbS but is more affected when HbS is present in the samples.

Procedures were developed exploiting organometallic clusters and coordination compounds in combination with heavy metal salts for derivatization of ribosomal crystals. These enabled the construction of multiple isomorphous replacement (MIR) and multiple isomorphous replacement combined with anomalous scattering medium-resolution electron density maps for the ribosomal particles that yield the crystals diffracting to the highest resolution, 3 A, of the large subunit from Haloarcula marismortui and the small subunit from Thermus thermophilus. The first steps in the interpretation of the 7.3-A MIR map of the small subunit were made with the aid of a tetrairidium cluster that was covalently attached to exposed sulfhydryls on the particle’s surface prior to crystallization. The positions of these sulfhydryls were localized in difference Fourier maps that were constructed with the MIR phases. r 1999 Academic Press

Abstract 1899 Poster Board I-922 Background-Aim: Ph negative MPNs comprise a heterogeneous group of disorders in which activation of JAK and other downstream signaling pathways can occur in a varying degree, yielding several different phenotypes. The identification of the somatic point mutation in the JAK2 gene (JAK2V617F) as a key pathogenetic mechanism has further assisted in classification and diagnosis, in conjunction with clinical, morphological and biological characteristics of the various disease categories. The aim of this study was to investigate the presence of the mutation in association with the previously recognized as abnormal TIMP/MMP ratio in MPNs. This imbalance appears to favor inhibitory rather than proteolytic activity, resulting in tissue and bone marrow reforming processes to progress towards fibrosis instead of matrix proteins degradation. Subjects and Methods: In a case-control study, 64 consecutive patients (27 males; mean age 61.62 ± 16.64 years) who met WHO and PVSG criteria for polycythemia vera (PV), essential thrombocytosis (ET) and idiopathic myelofibrosis (IMF), were prospectively included and evaluated. The control group consisted of 74 healthy individuals (54 males; mean age 52.76 ± 15.54 years). Allele specific PCR was used for JAK2 mutation detection in peripheral and/or bone marrow derived DNA. Serum concentrations of MMP-2, MMP-9, TIMP-1 and TIMP-2 were measured by quantitative sandwich enzyme immunoassay (ELISA). The levels of these parameters were expressed as mean ± SE and assessed with analysis of covariance (ANCOVA), adjusted for gender, age and co-morbidity. Results: Patients were classified as follows: PV n:37, ET n:20, IMF n:7. V617F mutational frequency was 81% [nPV:35 (94%) with exon 12 lesion identified in 2 patients, nET:12 (60%) and nIMF:5 (71%)]. The presence of the mutation was significantly associated with splenomegaly (p=0.018) and age at diagnosis (p=0.004). Regardless of JAK2 status, all patients showed significantly lower MMP-2 levels (181.62 ± 8.00 vs 237.15 ± 7.33, p Conclusions: In the particular group of patients studied, the identification of an abnormal TIMP/MMP ratio in all disease categories, regardless of JAK2 mutation status, supports the notion that BCR ABL negative MPNs are invariably characterised by bone marrow stroma remodelling, more likely as a consequence of continuous inhibition of matrix degradation with subsequent displacement, at a variable degree, by fibrotic tissue. Presence of JAK2V617F, being associated with even lower levels of MMP2, appears to be a concurring participant in this process. Further study will enable to delineate whether abnormal ratios are more prevalent in patients with thrombotic complications and perhaps document changes at different time points during treatment. Possible correlates with V617F allelic burden, especially towards thrombosis or fibrotic transformation, also remain to be elucidated. Disclosures: No relevant conflicts of interest to declare.