Automatic analysis of silver-stained comets by CellProfiler software

The comet assay is one of the most widely used methods to evaluate DNA damage and repair in eukaryotic cells. The comets can be measured by software, in a semi-automatic or automatic process. In this paper, we apply the CellProfiler open-source software for automatic analysis of comets from digitized images, reporting the percentage of tail DNA. A side-by-side comparison of CellProfiler with CASP software demonstrated good agreement between the two packages. Our work demonstrates that automatic measurement of silver-stained comets with open-source software is possible, providing significant time savings.

Metastatic lymph node ratio versus number of metastatic lymph nodes as a prognostic factor in gastric cancer

OBJECTIVE

Knowledge of prognostic factors in gastric cancer is essential to decide on single patient management. We aim to establish the value of lymph node ratio compared to lymph node involvement in the prediction of gastric cancer survival and treatment approach.

METHODS

Charts of ninety-six consecutive patients undergoing gastrectomy for resectable gastric cancer were reviewed between January 1996 and December 2005. Receiver operating characteristic (ROC) curves were plotted to verify the accuracy of metastatic lymph node ratio (MLNR) and number of metastatic lymph node (NMLN) cut-off values for survival prediction. Patients were divided into two groups according to ROC curve cut-offs and accuracy in prognosis was reviewed.

RESULTS

ROC curves showed that 5 metastatic nodes and a node ratio value of 20% had the best survival prognostic correlation. The median survival of patients with MLNR and NMLN were similar according to cut-off determinations (≤ 5/> 5 metastatic nodes and ≤20/>20% lymph node ratio). Five-year survival rates were 70.9% vs 17.1% and 72.4% vs 15.6%, respectively (p < 0.001). Positive correlation coefficient was found between the number of excised nodes and the number of metastatic nodes.

CONCLUSION

Number of metastatic lymph nodes showed greater accuracy than lymph node ratio for survival prediction in gastric cancer.

Laser emission from mirrorless waveguides based on photosensitized polymers incorporating POSS

Laser emission from leaky waveguides based in dye-doped organic gain media incorporating Polyhedral Oligomeric Silsesquioxanes (POSS) nanoparticles is reported. The samples consist of thin film gain media deposited onto glass substrate defining a planar asymmetric slab waveguide, which does not incorporate any resonant substructure. The presence of POSS results in additional amplified spontaneous emission (ASE) spectral narrowing, and conditions have been found for which directional multimode laser emission is achieved. The spectral narrowing is ascribed to the photon path enlargement caused by a non-resonant feedback mechanism provided by individual scatterers, which enhances incoherently the magnitude of the amplification process. On the contrary, the appearance of multimode lasing is attributed to coherent random lasing from a many scatterers collective effect.

[Evidence-based ophthalmology: critical evaluation of the literature in relation to diagnostic tests]

PURPOSE

In general, articles on diagnostic tests have a very poor methodological quality. If we translate their conclusions to daily practice without a proper analysis it is easy to see a typical trend: physicians use new (and expensive) tests without increasing diagnostic capacity; they only increase the health budget. Evidence-based medicine (EBM) consists of using the best evidence in decision-making. It deals with selected and relevant information, supported by data obtained through the most rigorous scientific method: epidemiology and statistics. Critical evaluation of papers related to diagnostic tests is our aim. We provide with basic skills for evaluation and analysis of papers by means of simple topics on statistics, design of clinical assays and clinical epidemiology.

METHODS

Review of the medical literature.

RESULTS

To evaluate papers on diagnostic tests and to use a test correctly, it is necessary to know its diagnostic capacity, the level of certainty to start treatment, the probability of having the disease before using the test and the test capacity to change that probability.

CONCLUSIONS

The maximum performance of a test is reached when it is used in a maximum uncertainty situation (disease probability 50%). Its highest usefulness is obtained when pre-test probability is maximal, after a careful review of the patient's history and a complete patient examination.

Amplified spontaneous emission and optical gain measurements from pyrromethene 567--doped polymer waveguides and quasi-waveguides

Amplified spontaneous emission from planar waveguides and quasi-waveguides based on Pyrromethene 567-doped poly(methyl methacrylate) thin films deposited onto quartz and glass substrates is investigated. Films with different thickness were prepared and pumped optically at 532 nm with pulses of up to 8 MW/cm(2). Pump thresholds for the onset of ASE emission, optical gains and losses were assessed. Net gain coefficients were estimated by fitting the data provided by variable stripe length measurements with a theoretical expression which takes into account saturation. In this way, net gain coefficients of up to 56 +/- 9 cm(-1) at a pump intensity of 5.3 MW/cm(2) for quasi-waveguides and up to 20.6 +/- 2.7 cm(-1) at a pump intensity of 3.4 MW/cm2 for waveguides, were obtained. Loss coefficients in the waveguides were estimated to be 3.8 +/- 0.4 cm-1 and 6.1 +/- 1.3 cm(-1) for 15 microm and 5 microm thick films, respectively. The results obtained seem to indicate a stronger self-mode-restriction capability in the quasiwaveguides than in conventional total internal-reflection waveguides.

Synthesis, structure, and physical properties of hybrid nanocomposites for solid-state dye lasers

We report on the synthesis, structural characterization, physical properties, and lasing action of two organic dyes, Rhodamine 6G (Rh6G) and Pyrromethene 597 (PM597), incorporated into new hybrid organic-inorganic materials, where the organic component was either poly(2-hydroxyethyl-methacrylate) (PHEMA) or copolymers of HEMA with methyl methacrylate (MMA), and the inorganic counterpart consisted of silica derived from hydrolysis-condensation of methyltriethoxysilane (TRIEOS) in weight proportion of up to 30%. Lasing efficiencies of up 23% and high photostabilities, with no sign of degradation in the initial laser output after 100 000 pump pulses at 10 Hz, were demonstrated when pumping the samples transversely at 534 nm with 5.5 mJ/pulse. A direct relationship could be established between the structure of the hybrid materials, analyzed by solid-state NMR, and their laser behavior. An inorganic network dominated by di-/tri- substituted silicates in a proportion approximately 35:65, corresponding to samples of HEMA with 15 and 20 wt % proportion of TRIEOS, optimizes the lasing photostability. The thermal properties of these materials, together with the high homogeneity revealed by atomic force microscopy (AFM) images, even in compounds with high silica content, indicate their microstructure to be a continuous phase, corresponding to the polymer matrix, which "traps" the silica components at molecular level via covalent bonding, with few or no silica islands.

Allele frequencies of six miniSTR loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) in a Spanish population

Allele frequencies and forensic parameters for six miniSTR autosomal loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) were obtained from a sample of 264 unrelated individuals from Spain. No significant deviations from Hardy-Weinberg expectations were found. Due to the small PCR products (<125 bp), the use of these non-CODIS (NC) miniSTRs can increase the probability that a degraded sample can be typed. Additionally, these systems can be used in routine paternity analyses where more markers are needed to increase the power of exclusion or in complex paternity cases (e.g. involving closely related individuals).

Population genetic data for 18 STR loci in Costa Rica

Allele frequencies for 18 STR autosomal loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, CSF1PO, Penta D, Penta E, D19S433, D2S1338 and SE33) were obtained from a sample of 191-500 unrelated individuals from Costa Rica, Central America.

STR data for 11 autosomal STR markers from Costa Rica, Central America

Allele frequencies for 11 STR autosomal loci (F13A01, F13B, FESFPS, LPL, CSF1PO, TH01, TPOX, VWA, D16S539, D7S820 and D13S317) were obtained from a sample of 200 unrelated individuals from Costa Rica, Central America.

Mitochondrial DNA haplotyping revealed the presence of mixed up benign and neoplastic tissue sections from two individuals on the same prostatic biopsy slide

DNA typing was requested to investigate a presumptive cancer diagnosis error by confirming whether benign and cancerous prostatic tissue in the same presurgical haematoxylin and eosin stained slide belonged to the same person. After independent histological re-examination of the slide by a pathologist, manual slide dissection was used to guarantee independent and high recovery DNA isolation from each tissue section, avoiding carryover and background contamination. Nuclear DNA quantification performed by real time polymerase chain reaction (PCR) revealed the absence of human DNA for short tandem repeat (STR) typing. Mitochondrial DNA was only obtained by performing PCR of very short fragments ( approximately 100 bp), indicating high DNA degradation. Different low frequency hypervariable region I haplotypes were obtained from each tissue section (normal tissue section haplotype: 16224C, 16234T, 16311C, 16356C; cancer tissue section haplotype: 16256T, 16270T, 16293G). Only the normal tissue section haplotype matched that obtained from the patient's blood sample, indicating that the cancer tissue section originated from an unknown patient. These results supported the hypothesis of sample mix up during block processing or slide preparation by a carryover mechanism. Mitochondrial genetic typing is recommended to exclude the possibility of carryover artefacts when low DNA content and high degradation compromise conventional STR typing.

Polymer-Filled Nanoporous Silica Aerogels as Hosts for Highly Stable Solid-State Dye Lasers

New hybrid solid-state dye laser materials based on highly porous silica aerogels have been synthesized. The open porous network of the aerogel was saturated with laser dyes dissolved in appropriate organic monomers, and polymerization took place inside the silica structure. The resulting polymer-filled nanoporous aerogel (PFNPA) was cast in a cylindrical shape, forming monoliths that were used as gain media in solid-state dye lasers. When the PFNPA incorporated pyrromethene dyes, highly photostable laser emission with good lasing efficiency was obtained. Under the demanding conditions of tightly focused transversal pumping with 532 nm, 5 mJ pulses at 10 Hz repetition rate, the commercial dye Pyrromethene 567 exhibited laser action with only a 10% drop in the laser output after 10(6) pump pulses in the same position of the sample.

The efficiency of titanocene as photoinitiator in the polymerization of dental formulations

A comparative kinetic study of the polymerization of tetraethyleneglycol dimethacrylate (TEEGDM) under visible light irradiation was carried out in order to determine the effectiveness of titanocene as photoinitiator in this process. The pair camphorquinone/dimethylaminoethyl methacrylate, CQ/DMAEMA (0.5/0.5%, by weight), was used as a reference photoinitiatior system. The reactions were carried out both in the presence and absence of oxygen (in N2) and with variable and constant titanocene concentration and incident light intensity. It was observed that in both atmospheres the polymerization reaction commenced rapidly and its initial rate was comparable with that obtained in the presence of the classic initiation system. However, after reacting for a few seconds this process suffered abrupt deactivation, this tendency being more noticeable at low titanocene concentrations. To explain the observed kinetic behavior, the study of the photofragmentation of titanocene upon irradiation with visible light in both atmospheres was carried out. The quantum yield calculated in the presence of O2 (phifr = 8 at 465 nm) suggests the existence of a chain reaction with participation of oxygen, and this explains, in turn, the high value of the initial rate of polymerization and also the rapid disappearance of the photoinitiator. In an inert atmosphere the photofragmentation occurs in a conventional way, this being a very effective process with quantum yield of 0.7 at 465 nm. However, it seems that only a small part of the active species acts as initiating radicals and these are not sufficient to achieve the appropriate monomer conversion.

Strategies for neuroprotection against L-trans-2,4-pyrrolidine dicarboxylate-induced neuronal damage during energy impairment in vitro

Increased levels of extracellular excitatory amino acids and failure of energy metabolism are two conditions associated with brain ischemia. In the present study we have combined the simultaneous inhibition of glutamate uptake and mitochondrial electron transport chain to simulate neuronal damage associated with brain ischemia. Results show that cerebellar granule neurons are not vulnerable to transient glutamate uptake inhibition by L-trans-pyrrolidine-2,4-dicarboxylate (PDC) despite the increase in the extracellular concentration of glutamate, unless they are simultaneously exposed to the mitochondrial toxins 3-nitropropionic acid (3-NP) or sodium azide. Cell damage was assessed by light microscopy observation, by reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and by the fluorescent markers for live and dead cells, calcein and ethidium homodimer, respectively. The protective effect of alternative energy substrates, such as pyruvate, acetoacetate, and beta-hydroxybutyrate against PDC-induced neuronal death during 3-NP exposure was studied and compared to the effects of the antioxidant vitamin E, the spin trapper alpha-phenyl-N-tert-butylnitrone (PBN), voltage-dependent calcium channel antagonists, and glutamate receptor antagonists. Results show that neuronal damage can be efficiently prevented in the presence of pyruvate and the N-methyl-D-aspartate (NMDA) receptor antagonist MK-801, whereas the non-NMDA receptor antagonist NBQX, acetoacetate, vitamin E, and PBN showed partial protection. In contrast, beta-hydroxybutyrate and voltage-dependent calcium channels blockers did not show any protective effect at the concentrations tested.