Computer-based malignancy grading of astrocytomas employing a support vector machine classifier, the WHO grading system and the regular hematoxylin-eosin diagnostic staining procedure

OBJECTIVE: To investigate and develop an automated technique for astrocytoma malignancy grading compatible with the clinical routine. STUDY DESIGN: One hundred forty biopsies of astrocytomas were collected from 2 hospitals. The degree of tumor malignancy was defined as low or high according to the World Health Organization grading system. From each biopsy, images were digitized and segmented to isolate nuclei from background tissue. Morphologic and textural nuclear features were quantified to encode tumor malignancy. Each case was represented by a 40-dimensional feature vector. An exhaustive search procedure in feature space was utilized to determine the best feature combination that resulted in the smallest classification error. Low and high grade tumors were discriminated using support vector machines (SVMs). To evaluate the system performance, all available data were split randomly into training and test sets. RESULTS: The best vector combination consisted of 3 textural and 2 morphologic features. Low and high grade cases were discriminated with an accuracy of 90.7% and 88.9%, respectively, using an SVM classifier with polynomial kernel of degree 2. CONCLUSION: The proposed methodology was based on standards that are common in daily clinical practice and might be used in parallel with conventional grading as a second-opinion tool to reduce subjectivity in the classification of astrocytomas.     

Utilization of household food waste for the production of ethanol at high dry material content

Background

Environmental issues and shortage of fossil fuels have turned the public interest to the utilization of renewable, environmentally friendly fuels, such as ethanol. In order to minimize the competition between fuels and food production, researchers are focusing their efforts to the utilization of wastes and by-products as raw materials for the production of ethanol. household food wastes are being produced in great quantities in European Union and their handling can be a challenge. Moreover, their disposal can cause severe environmental issues (for example emission of greenhouse gasses). On the other hand, they contain significant amounts of sugars (both soluble and insoluble) and they can be used as raw material for the production of ethanol.

Results

Household food wastes were utilized as raw material for the production of ethanol at high dry material consistencies. A distinct liquefaction/saccharification step has been included to the process, which rapidly reduced the viscosity of the high solid content substrate, resulting in better mixing of the fermenting microorganism. This step had a positive effect in both ethanol production and productivity, leading to a significant increase in both values, which was up to 40.81% and 4.46 fold, respectively. Remaining solids (residue) after fermentation at 45% w/v dry material (which contained also the unhydrolyzed fraction of cellulose), were subjected to a hydrothermal pretreatment in order to be utilized as raw material for a subsequent ethanol fermentation. This led to an increase of 13.16% in the ethanol production levels achieving a final ethanol yield of 107.58 g/kg dry material.

Conclusions

In conclusion, the ability of utilizing household food waste for the production of ethanol at elevated dry material content has been demonstrated. A separate liquefaction/saccharification process can increase both ethanol production and productivity. Finally, subsequent fermentation of the remaining solids could lead to an increase of the overall ethanol production yield.     

Socioeconomic Deprivation and the Incidence of 12 Cardiovascular Diseases in 1.9 Million Women and Men: Implications for Risk Prediction and Prevention

Background

Recent experimental evidence suggests that socioeconomic characteristics of neighbourhoods influence cardiovascular health, but observational studies which examine deprivation across a wide range of cardiovascular diseases (CVDs) are lacking.

Methods

Record-linkage cohort study of 1.93 million people to examine the association between small-area socioeconomic deprivation and 12 CVDs. Health records covered primary care, hospital admissions, a myocardial infarction registry and cause-specific mortality in England (CALIBER). Patients were aged ≥30 years and were initially free of CVD. Cox proportional hazard models stratified by general practice were used.

Findings

During a median follow-up of 5.5 years 114,859 people had one of 12 initial CVD presentations. In women the hazards of all CVDs except abdominal aortic aneurysm increased linearly with higher small-area socioeconomic deprivation (adjusted HR for most vs. least deprived ranged from 1.05, 95%CI 0.83–1.32 for abdominal aortic aneurysm to 1.55, 95%CI 1.42–1.70 for heart failure; I² = 81.9%, τ² = 0.01). In men heterogeneity was higher (HR ranged from 0.89, 95%CI 0.75–1.06 for cardiac arrest to 1.85, 95%CI 1.67–2.04 for peripheral arterial disease; I² = 96.0%, τ² = 0.06) and no association was observed with stable angina, sudden cardiac death, subarachnoid haemorrhage, transient ischaemic attack and abdominal aortic aneurysm. Lifetime risk difference between least and most deprived quintiles was most marked for peripheral arterial disease in women (4.3% least deprived, 5.8% most deprived) and men (4.6% least deprived, 7.8% in most deprived); but it was small or negligible for sudden cardiac death, transient ischaemic attack, abdominal aortic aneurysm and ischaemic and intracerebral haemorrhage, in both women and men.

Conclusions

Associations of small-area socioeconomic deprivation with 12 types of CVDs were heterogeneous, and in men absent for several diseases. Findings suggest that policies to reduce deprivation may impact more strongly on heart failure and peripheral arterial disease, and might be more effective in women.     

Asymmetric loading of Kar9 onto spindle poles and microtubules ensures proper spindle alignment

Spindle alignment is the process in which the two spindle poles are directed toward preselected and opposite cell ends. In budding yeast, the APC-related molecule Kar9 is required for proper alignment of the spindle with the mother-bud axis. We find that Kar9 localizes to the prospective daughter cell spindle pole. Kar9 is transferred from the pole to cytoplasmic microtubules, which are then guided in a myosin-dependent manner to the bud. Clb4/Cdc28 kinase phosphorylates Kar9 and accumulates on the pole destined to the mother cell. Mutations that block phosphorylation at Cdc28 consensus sites result in localization of Kar9 to both poles and target them both to the bud. Thus, Clb4/Cdc28 prevents Kar9 loading on the mother bound pole. In turn, asymmetric distribution of Kar9 ensures that only one pole orients toward the bud. Our results indicate that Cdk1-dependent spindle asymmetry ensures proper alignment of the mitotic spindle with the cell division axis.     

The effect of model approximations on single-collision distributions of low-energy electrons in liquid water

The development of cross sections for the inelastic interaction of low-energy electrons with condensed tissue-like media is best accomplished within the framework of the dielectric theory. In this work we investigate the degree to which various model approximations, used in the above methodology, influence electron single-collision distributions. These distributions are of major importance to Monte Carlo track structure codes, namely, the energy-loss spectrum, the inelastic inverse mean free path, and the ionization efficiency. In particular, we make quantitative assessment of the influence of (1) the optical data set, (2) the dispersion algorithm, and (3) the perturbation and exchange Born corrections. It is shown that, although the shape and position of the energy-loss spectrum remains almost fixed, its peak height may vary by up to a factor of 1.5. Discrepancies in the calculated inelastic inverse mean free path are largely within 20-30% above 100 eV; they increase drastically, though, at lower energies. Exchange and perturbation Born corrections increase gradually below 1 keV leading to a approximately 30 to 40% reduction of the inverse mean free path at 100 eV. The perturbation effect contributes more than the exchange effect to this reduction. Similar to the dispersion situation, the effect of Born corrections at lower energies is also unclear since the models examined disagree strongly below 100 eV. In comparison, the vapor data are higher than the liquid calculations by 20 to 50% as the energy decreases from 1 to 0.1 keV, respectively. The excitation contribution is the main cause of this difference, since the ionization efficiency in the liquid levels off at approximately 90%, whereas the plateau value for the vapor is approximately 70%. It is concluded that electron inelastic distributions for liquid water, although in some respects distinctively different from the vapor phase, have associated uncertainties that are comparable in magnitude to the phase differences. The situation below 100 eV is uncertain.     

Combinatorial de novo design and application of a biomimetic affinity ligand for the purification of human anti‐HIV mAb 4E10 from transgenic tobacco

Monoclonal anti‐HIV antibody 4E10 (mAb 4E10) is one of the most broadly neutralizing antibodies against HIV, directed against a specific epitope on envelope protein gp41. In the present study, a combinatorial de novo design approach was used for the development of a biomimetic ligand for the affinity purification of mAb 4E10 from tobacco transgenic extract in a single chromatographic step. The biomimetic ligand (4E10lig) was based on a L ‐Phe/β‐Ala bi‐substituted 1,3,5‐triazine (Trz) scaffold (β‐Ala‐Trz‐L ‐Phe, 4E10lig) which potentially mimics the more pronounced electrostatic and hydrophobic interactions of mAb 4E10‐binding sequence determined by screening of a random peptide library. This library was comprised of Escherichia coli cells harboring a plasmid (pFlitrx) engineered to express a fusion protein containing random dodecapeptides that were inserted into the active loop of thioredoxin, which itself was inserted into the dispensable region of the flagellin gene. Adsorption equilibrium studies with this biomimetic ligand and mAb 4E10 determined a dissociation constant (K_D) of 0.41 ± 0.05 µM. Molecular modeling studies of the biomimetic ligand revealed that it can potentially occupy the same binding site as the natural binding core peptide epitope. The biomimetic affinity adsorbent was exploited in the development of a facile mAb 4E10 purification protocol, affording mAb 4E10 of high purity (approximately 95%) with good overall yield (60–80%). Analysis of the antibody preparation by SDS‐PAGE, enzyme‐linked immunosorbent assays (ELISA), and western blot showed that the mAb 4E10 was fully active and free of degraded variants, polyphenols, and alkaloids. Copyright © 2009 John Wiley & Sons, Ltd.