A machine learning decision criterion for reducing scan time for hyperspectral neutron computed tomography systems.

We present the first machine learning-based autonomous hyperspectral neutron computed tomography experiment performed at the Spallation Neutron Source. Hyperspectral neutron computed tomography allows the characterization of samples by enabling the reconstruction of crystallographic information and elemental/isotopic composition of objects relevant to materials science. High quality reconstructions using traditional algorithms such as the filtered back projection require a high signal-to-noise ratio across a wide wavelength range combined with a large number of projections. This results in scan times of several days to acquire hundreds of hyperspectral projections, during which end users have minimal feedback. To address these challenges, a golden ratio scanning protocol combined with model-based image reconstruction algorithms have been proposed. This novel approach enables high quality real-time reconstructions from streaming experimental data, thus providing feedback to users, while requiring fewer yet a fixed number of projections compared to the filtered back projection method. In this paper, we propose a novel machine learning criterion that can terminate a streaming neutron tomography scan once sufficient information is obtained based on the current set of measurements. Our decision criterion uses a quality score which combines a reference-free image quality metric computed using a pre-trained deep neural network with a metric that measures differences between consecutive reconstructions. The results show that our method can reduce the measurement time by approximately a factor of five compared to a baseline method based on filtered back projection for the samples we studied while automatically terminating the scans.

Morphological diversity of Paramoeba perurans trophozoites and their interaction with Atlantic salmon, Salmo salar L., gills.

Amoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans affects several cultured marine fish species worldwide. In this study, the morphology and ultrastructure of P. perurans in vitro and in vivo was investigated using scanning and transmission electron microscopy (SEM and TEM, respectively). Amoebae cultures contained several different morphologies ranging from a distinct rounded cell structure and polymorphic cells with pseudopodia of different lengths and shapes. SEM studies of the gills of AGD-affected Atlantic salmon, Salmo salar L., revealed the presence of enlarged swellings in affected gill filaments and fusion of adjacent lamellae. Spherical amoebae appeared to embed within the epithelium, and subsequently leave hemispherical indentations with visible fenestrations in the basolateral surface following their departure. These fenestrated structures corresponded to the presence of pseudopodia which could be seen by TEM to penetrate into the epithelium. The membrane-membrane interface contained an amorphous and slightly fibrous matrix. This suggests the existence of cellular glycocalyces and a role for extracellular products in mediating pathological changes in amoebic gill disease.

Co-infection of Nucleospora cyclopteri (Microsporidia) and Kudoa islandica (Myxozoa) in farmed lumpfish, Cyclopterus lumpus L., in Norway: a case report.

This study describes a co-infection of Kudoa islandica (Myxozoa) and Nucleospora cyclopteri (Microsporida) in farmed lumpfish, Cyclopterus lumpus L., in Norway. Several other parasites (Cryptocotyle sp., protozoan ciliates and Gyrodactylus sp.) were also found in gills. In June 2013, the mortality in a farmed lumpfish population increased to 65%. Lumpfish showed erratic swimming behaviour and loss of weight. At necropsy, nodules in the kidney were the only visible lesions. Histologically, all fish showed severe changes with gill inflammation and necrosis in the spleen, kidney and liver. Haemorrhages and necrosis were observed in some hearts. Intracellular microsporidians associated with the lesions were detected in most organs using histological examination and Calcofluor White. Kudoa spores were diagnosed in the skeletal muscle, but no inflammatory response was associated with the presence of the plasmodia. Comparison of 18S ribosomal DNA sequences showed 100% similarity to Kudoa islandica and Nucleospora cyclopteri. Kudoa islandica and N. cyclopteri have previously been described associated with lesions in wild lumpfish in Iceland. In the present case, N. cyclopteri is believed to be the main cause of systemic pathology. This is the first description of K. islandica and N. cyclopteri causing pathology in farmed lumpfish in Norway.

Measurement of intracellular calcium concentration and plasma membrane potential in human spermatozoa using flow cytometry.

We report 2 novel approaches using flow cytometry to measure intracellular calcium concentration and plasma membrane potential in human spermatozoa. Both approaches have the potential to measure different responses in subpopulations of cells, which is particularly useful when studying heterogeneous populations such as human spermatozoa. Intracellular calcium concentration ([Ca2+]i) was measured using the probe indo-1/AM. This allowed measurements to be made that were independent of variation in cell size and dye loading. It also enabled dead cells to be directly identified and excluded from the analyses without the need for counterstaining. Mean basal [Ca2+]i was determined as 50 nM (25-75 nM range) and, in response to the agonist progesterone (20 microM), this increased transiently to 195 nM (125-285 nM range) before declining to approximately half the maximal level within 2 minutes (values in parentheses correspond to the range of values typically found within a sperm population from 1 sample). These results are comparable with previously published data on whole sperm populations. Sperm membrane potential (VM) was assayed using the probe DiOC6(3). In carefully controlled experiments, a marked depolarization of the plasma membrane potential of capacitated spermatozoa was observed in response to progesterone (20 microM). Following in vitro capacitation, the sperm plasma membrane potential became hyperpolarized compared with the noncapacitated state. Therefore, this technique may be used to assay for sperm capacitation in vitro.

Continuous assessment of human spermatozoa viability during cryopreservation.

Cryomicroscopy has enabled direct observation of freezing and thawing of human spermatozoa. When used with a fluorescent viability kit, sperm membrane damage was not apparent down to temperatures of -5 degrees C, but significant damage occurred after thawing (55% of spermatozoa had damaged membranes). Semen samples were cooled or frozen to temperatures (at decrements of 10 degrees C) from 0 degree C to -110 degrees C. At all these temperatures the proportion of live to membrane-damaged cells remained constant. Samples held at temperatures above -30 degrees C were not adversely affected. Below -30 degrees C there was a gradual increase in the proportion of membrane-damaged cells on thaw and a decrease in the number of live cells recovering motility. At temperatures between -50 degrees C and -60 degrees C there was an equal proportion of live motile, immotile, and membrane-damaged cells. It is concluded that some irreversible damage to spermatozoa was a result of freezing processes in cells frozen to -30 degrees C or less, but most of the cryodamage was incurred during thawing, possibly due to recrystallization.

Direct assessment of cryopreservation of human spermatozoa using a cryomicroscope and computer-aided sperm analysis.

Use of a cryostage has enabled direct observation of human spermatozoa as they are cryopreserved and thawed. Crystallization and recrystallization events are readily observed. In combination with computer-aided semen analysis (CASA) equipment it was possible to determine the consequence of altering the cooling, freezing and thawing rates of a temperature-rate profile on sperm motility. Increasing the cooling rate to 50 degrees C/min resulted in significantly lower pre-freeze to post-thaw ratios for average path velocity (VAP, 13%), mean straight line velocity (VSL, 35%), mean linearity (LIN, 28%) and straightness (STR, 24%), while the ratio of the number of cells crossing the field of view (NCF) significantly increased (30%) compared to a standard freeze-thaw temperature rate profile. The NCF pre-freeze to post-thaw ratio was associated with the percentage of cell recovery after cryopreservation. Faster thaw rates resulted in better survival of the cells, perhaps due to the shorter time during which recrystallization occurred. The NCF ratios were significantly higher (33 and 30% for thaw rates of 50 and 100 degrees C/min respectively) than for the standard profile samples. Previous studies on cell survival have shown a link between the cooling and thaw rates. The cryostage should prove invaluable in future studies to identify the causes of cryodamage to spermatozoa. When used in combination with CASA, changes to sperm function during cryopreservation can be accurately measured.

High-luminosity blue and blue-green gallium nitride light-emitting diodes.

Compact and efficient sources of blue light for full color display applications and lighting eluded and tantalized researchers for many years. Semiconductor light sources are attractive owing to their reliability and amenability to mass manufacture. However, large band gaps are required to achieve blue color. A class of compound semiconductors formed by metal nitrides, GaN and its allied compounds AIGaN and InGaN, exhibits properties well suited for not only blue and blue-green emitters, but also for ultraviolet emitters and detectors. What thwarted engineers and scientists from fabricating useful devices from these materials in the past was the poor quality of material and lack of p-type doping. Both of these obstacles have recently been overcome to the point where highluminosity blue and blue-green light-emitting diodes are now available in the marketplace.

Psychiatric morbidity: prevalence, associated factors and significance.

A cross-sectional observational systematic study was carried out on ambulatory patients at a tertiary care hospital to determine the probable prevalence, associated factors and significance of psychiatric morbidity by using an Urdu translation of the hospital anxiety and depression (HAD) scale over a period of 6 days in a week. Results showed a prevalence of 38.4% which is slightly higher than what has been generally reported (30%). Two variables, i.e., female sex and being a housewife were significantly related with the outcome. An attempt has been made to identify the probable reasons for this and some suggestions laid down for further work.

Relative roles of K region and bay region towards determining the carcinogenic potencies of polycyclic aromatic hydrocarbons.

Using the quantum mechanical MINDO/3 method a bond reactivity index based on superdelocalization of electrons in a compound has been formulated in order to estimate the relative carcinogenic properties of polycyclic aromatic hydrocarbons. The values of the index calculated for the K region as well as the bay region suggest that a knowledge of the reactivities of both regions is necessary for a reasonable estimation of the relative carcinogenic potencies of PAHs. However, no direct relationship between the two reactivity indices was observed in the calculations. It was found that the results for the bay-region reactivity index correlated well with the relative carcinogenic potencies of the molecules.

A quantum mechanical approach to the theory of cancer from polynuclear compounds. Metabolic activation and carcinogenicity of extended anilines and aminoazo compounds.

Calculations have been carried out of the electronic structure and molecular properties in relation to metabolic activation and carcinogenic activities of polycyclic aromatic amines (PAAs). Quantum mechanical molecular orbital method MINDO/3 is employed in the calculations mainly on anilines, extended anilines, and aminoazo and other azo compounds. The calculations, in agreement with findings of Arcos and Argus, indicate that for the highest level of carcinogenic activity obtainable with the dicyclic aromatic amines, the amino substituent must be introduced at the terminal carbon atom of the longest conjugate chain. In the case of monocyclic compounds, in particular, charge distribution of the amino substitution aids in identifying the carcinogenic character of the PAAs. Our results demonstrate that ring hydroxylation leads to detoxification of the compounds. However, the major pathway leading to carcinogenic activity involves transformation to hydroxylamines and subsequently to electrophilic arylnitrenium ions (ANIs). These are in line with findings from experiments. Calculations of certain electronic parameters give expected relative carcinogenic potencies. In all cases the ANIs function as ambient electrophiles which can undergo both electrostatic and covalent binding with nucleophilic centers of proteins and DNA bases.