Quality assessment of higher resolution images and videos with remote testing.

In many research fields, human-annotated data plays an important role as it is used to accomplish a multitude of tasks. One such example is in the field of multimedia quality assessment where subjective annotations can be used to train or evaluate quality prediction models. Lab-based tests could be one approach to get such quality annotations. They are usually performed in well-defined and controlled environments to ensure high reliability. However, this high reliability comes at a cost of higher time consumption and costs incurred. To mitigate this, crowd or online tests could be used. Usually, online tests cover a wider range of end devices, environmental conditions, or participants, which may have an impact on the ratings. To verify whether such online tests can be used for visual quality assessment, we designed three online tests. These online tests are based on previously conducted lab tests as this enables comparison of the results of both test paradigms. Our focus is on the quality assessment of high-resolution images and videos. The online tests use AVrate Voyager, which is a publicly accessible framework for online tests. To transform the lab tests into online tests, dedicated adaptations in the test methodologies are required. The considered modifications are, for example, a patch-based or centre cropping of the images and videos, or a randomly sub-sampling of the to-be-rated stimuli. Based on the analysis of the test results in terms of correlation and SOS analysis it is shown that online tests can be used as a reliable replacement for lab tests albeit with some limitations. These limitations relate to, e.g., lack of appropriate display devices, limitation of web technologies, and modern browsers considering support for different video codecs and formats.

Effect of therapeutic hypothermia on chromosomal aberration in perinatal asphyxia.

INTRODUCTION: Perinatal asphyxia is a major cause for neonatal mortality and morbidity around the world. The reduction of O2 results in the generation of reactive oxygen species which interact with nucleic acid and make alteration in the structure and functioning of the genome. We studied the effect of therapeutic hypothermia on chromosomes with karyotyping. SUBJECTS AND METHODS: Babies in the hypothermia group were cooled for the first 72 h, using gel packs. Rectal temperature of 33-34°C was maintained. Blood sample was collected after completion of therapeutic hypothermia for Chromosomal analysis. It was done with IKAROS Karyotyping system, Metasystems, based on recommendations of International system of human cytogenetic nomenclature. RESULTS: The median chromosomal aberration was lower in hypothermia [2(0-5)] than control group [4(1-7)] and chromatid breakage was commonest aberration seen. Chromosomal aberration was significantly higher in severe encephalopathy group than moderate encephalopathy group. CONCLUSION: We conclude that the TH significantly reduces DNA damage in perinatal asphyxia.

Effect of therapeutic hypothermia on DNA damage and neurodevelopmental outcome among term neonates with perinatal asphyxia: a randomized controlled trial.

OBJECTIVE: To study the effect of therapeutic hypothermia (TH) on deoxyribonucleic acid (DNA) damage and the neurodevelopmental outcome in term babies with perinatal asphyxia. METHODS: Babies in the hypothermia group were cooled for the first 72 h, using gel packs. Rectal temperature of 33-34°C was maintained. Blood sample was collected before, at 36 h and after completion of TH for assessment of comet assay and 8-hydroxy2-deoxyguanosine (8-OHdG). Infants were followed up till 12 months. RESULTS: Baseline parameters were similar. After 72 h, the hypothermia group showed lower olive tail moment (12.88 ± 2.14) than the control group (22.16 ± 5.26) (p < 0.001). 8-HDG levels increased significantly in the control group (1252.87 ± 357.07) as compared to the hypothermia group (757.03 ± 198.49) (p < 0.001). Neurodevelopmental assessment at 12 months showed significantly low motor and mental developmental quotient in the control than hypothermia group. CONCLUSIONS: TH reduces oxidative stress-induced DNA damage and improves neurodevelopmental outcome.

A latest and promising approach for prediction of viral load in hepatitis B virus infected patients.

INTRODUCTION: Designing a rapid, reliable and sensitive assay for detection of hepatitis B virus (HBV) variants by real-time PCR is challenging at best. A recent approach for quantifying the viral load using a sensitive fluorescent principle was brushed in this study. MATERIALS AND METHODS: : A total of 250 samples were collected from the outpatient unit, CLRD. Complete Human HBVDNA sequences (n = 944) were selected from the National Centre for Biotechnology Information (NCBI), primers and probes were designed and synthesized from the core, surface, and x region. Real-time based quantification was carried out using a standard kit and in-house generated standards and RT-PCR protocols. RESULTS AND DISCUSSION: The standard calibration curve was generated by using serial dilution 10(2) to 10(8). The calibration curve was linear in a range from 10(2) to 10(8) copies/ml, with an R(2) value of 0.999. Reproducibility as measured by dual testing of triplicates of serum samples was acceptable, with coefficients of variation at 6.5%, 7.5%, and 10.5%. Our results showed that amplification performance was good in the case of the x-region-based design (98%). Out of 100 negative samples screened by enzyme linked immunosorbent assay and the standard RT-PCR kit, one sample was detected as positive with the in-house developed RT-PCR assay, the positivity of the sample was confirmed by sequencing the amplified product, NCBI accession EU684022. CONCLUSION: This assay is reproducible showing limited inter- and intra-assay variability. We demonstrate that the results of our assay correlated well with the standard kit for the HBV viral load monitor.

DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables.

The diversity of breast cancers reflects variations in underlying biology and affects the clinical implications for patients. Gene expression studies have identified five major subtypes- Luminal A, Luminal B, basal-like, ErbB2+ and Normal-Like. We set out to determine the role of DNA methylation in subtypes by performing genome-wide scans of CpG methylation in breast cancer samples with known expression-based subtypes. Unsupervised hierarchical clustering using a set of most varying loci clustered the tumors into a Luminal A majority (82%) cluster, Basal-like/ErbB2+ majority (86%) cluster and a non-specific cluster with samples that were also inconclusive in their expression-based subtype correlations. Contributing methylation loci were both gene associated loci (30%) and non-gene associated (70%), suggesting subtype dependant genome-wide alterations in the methylation landscape. The methylation patterns of significant differentially methylated genes in luminal A tumors are similar to those identified in CD24 + luminal epithelial cells and the patterns in basal-like tumors similar to CD44 + breast progenitor cells. CpG islands in the HOXA cluster and other homeobox (IRX2, DLX2, NKX2-2) genes were significantly more methylated in Luminal A tumors. A significant number of genes (2853, p < 0.05) exhibited expression-methylation correlation, implying possible functional effects of methylation on gene expression. Furthermore, analysis of these tumors by using follow-up survival data identified differential methylation of islands proximal to genes involved in Cell Cycle and Proliferation (Ki-67, UBE2C, KIF2C, HDAC4), angiogenesis (VEGF, BTG1, KLF5), cell fate commitment (SPRY1, OLIG2, LHX2 and LHX5) as having prognostic value independent of subtypes and other clinical factors.

Volatile oil composition of Pogostemon heyneanus and comparison of its composition with patchouli oil.

The volatile oil of the leaves of Pogostemon heyneanus Benth. (Lamiaceae) was analyzed by GC and GC-MS. Twenty-six components representing 96.0% of the oil were identified. The major components of the oil were acetophenone (51.0%), beta-pinene (5.3%), (E)-nerolidol (5.4%), and patchouli alcohol (14.0%). Comparison of the compositions of the oils of P. heyneanus and P. cablin (Blanco) Benth. (Patchouli oil) showed wide variation between them. Though 13 sesquiterpenes and oxygenated sesquiterpenes were detected in both oils, their concentrations in the oils differed widely. Acetophenone, benzoyl acetone and (E)-nerolidol present in the oil of P. heyneanus were not detected in patchouli oil.

Stochastic approach to data analysis in fluorescence correlation spectroscopy.

Fluorescence correlation spectroscopy (FCS) has emerged as a powerful technique for measuring low concentrations of fluorescent molecules and their diffusion constants. In FCS, the experimental data is conventionally fit using standard local search techniques, for example, the Marquardt-Levenberg (ML) algorithm. A prerequisite for these categories of algorithms is the sound knowledge of the behavior of fit parameters and in most cases good initial guesses for accurate fitting, otherwise leading to fitting artifacts. For known fit models and with user experience about the behavior of fit parameters, these local search algorithms work extremely well. However, for heterogeneous systems or where automated data analysis is a prerequisite, there is a need to apply a procedure, which treats FCS data fitting as a black box and generates reliable fit parameters with accuracy for the chosen model in hand. We present a computational approach to analyze FCS data by means of a stochastic algorithm for global search called PGSL, an acronym for Probabilistic Global Search Lausanne. This algorithm does not require any initial guesses and does the fitting in terms of searching for solutions by global sampling. It is flexible as well as computationally faster at the same time for multiparameter evaluations. We present the performance study of PGSL for two-component with triplet fits. The statistical study and the goodness of fit criterion for PGSL are also presented. The robustness of PGSL on noisy experimental data for parameter estimation is also verified. We further extend the scope of PGSL by a hybrid analysis wherein the output of PGSL is fed as initial guesses to ML. Reliability studies show that PGSL and the hybrid combination of both perform better than ML for various thresholds of the mean-squared error (MSE).

Fast focus field calculations.

We present a fast calculation of the electromagnetic field near the focus of an objective with a high numerical aperture (NA). Instead of direct integration, the vectorial Debye diffraction integral is evaluated with the fast Fourier transform for calculating the electromagnetic field in the entire focal region. We generalize this concept with the chirp z transform for obtaining a flexible sampling grid and an additional gain in computation speed. Under the conditions for the validity of the Debye integral representation, our method yields the amplitude, phase and polarization of the focus field for an arbitrary paraxial input field on the objective. We present two case studies by calculating the focus fields of a 40 x 1.20 NA water immersion objective for different amplitude distributions of the input field, and a 100 x 1.45 NA oil immersion objective containing evanescent field contributions for both linearly and radially polarized input fields.

Total internal reflection fluorescence correlation spectroscopy (TIR-FCS) with low background and high count-rate per molecule.

We designed a fluorescence correlation spectroscopy (FCS) system for measurements on surfaces. The system consists of an objective-type total internal reflection fluorescence (TIRF) microscopy setup, adapted to measure FCS. Here, the fluorescence exciting evanescent wave is generated by epi-illumination through the periphery of a high NA oil-immersion objective. The main advantages with respect to conventional FCS systems are an improvement in terms of counts per molecule (cpm) and a high signal to background ratio. This is demonstrated by investigating diffusion as well as binding and release of single molecules on a glass surface. Furthermore, the size and shape of the molecule detection efficiency (MDE) function was calculated, using a wave-vectorial approach and taking into account the influence of the dielectric interface on the emission properties of fluorophores.