The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Validity of Antibodies in Lymphocyte Supernatant in Diagnosing Tuberculosis in Severely Malnourished Children Presenting with Pneumonia

BackgroundThe diagnosis of tuberculosis (TB) in young children can be challenging, especially in severely malnourished children. There is a critical need for improved diagnostics for children. Thus, we sought to evaluate the performance of a technique that measures antibodies in lymphocyte supernatant (ALS) for the diagnosis of TB in severely malnourished children presenting with suspected pneumonia.MethodsChildren less than 5 years with severe acute malnutrition and radiological features of pneumonia admitted to the Dhaka Hospital of International Centre for Diarrhoeal Disease Research, Bangladesh, were enrolled consecutively following informed written consent. In addition to clinical and radiological assessment, samples taken for TB diagnosis included gastric lavage fluid and induced sputum for microbiological confirmation. ALS was measured from venous blood, and results were evaluated in children classified as “confirmed”, “non-confirmed TB” or “not TB”.ResultsAmong 224 children who had ALS analysis, 12 (5.4%) children had microbiologically “confirmed TB”, a further 41 (18%) had clinically diagnosed “non-confirmed TB” and the remaining 168 (75%) were considered not to have TB. ALS was positive in 89 (40%) and negative in 85 (39%) of children, with a large number (47 or 21%) reported as “borderline”. These proportions were similar between the three diagnostic groups. The sensitivity and specificity of ALS when comparing “Confirmed TB” to “Not TB” was only 67% (95% CI: 31–91%) and 51% (95% CI: 42–60%), respectively.

Conclusions and Significance

Our data suggest that ALS is not sufficiently accurate to improve the diagnosis of TB in children with severe malnutrition.     

Mechanism for the posture-specific plasma volume increase after a single intense exercise protocol.

To test the hypothesis that exercise-induced hypervolemia is a posture-dependent process, we measured plasma volume, plasma albumin content, and renal function in seven healthy subjects for 22 h after single upright (Up) or supine (Sup) intense (85% peak oxygen consumption rate) exercise. This posture was maintained for 5 h after exercise. Plasma volume decreased during exercise but returned to control levels by 5 h of recovery in both postures. By 22 h of recovery, plasma volume increased 2.4 +/- 0.8 ml/kg in Up but decreased 2.1 +/- 0.8 ml/kg in Sup. The plasma volume expansion in Up was accompanied by an increase in plasma albumin content (0.11 +/- 0.04 g/kg; P < 0.05). Plasma albumin content was unchanged in Sup. Urine volume and sodium clearance were lower in Up than Sup (P < 0.05) by 5 h of recovery. These data suggest that increased plasma albumin content contributes to the acute phase of exercise-induced hypervolemia. More importantly, the mechanism by which exercise influences the distribution of albumin between extra- and intravascular stores after exercise is altered by posture and is unknown. We speculate that factors associated with postural changes (e.g., central venous pressure) modify the increase in plasma albumin content and the plasma volume expansion after exercise.     

The endocrine systems of isolated and crowded Locusta and Schistocerca in relation to oöcyte growth, and the effects of flying upon maturation

In isolated Schistocerca and crowded Locusta, oöcyte growth is slow compared with that in crowded Schistocerca and isolated Locusta. Slow oöcyte growth in both species is correlated with an accumulation of material in the pars intercerebralis-corpora cardiaca neurosecretory system. Release of neurosecretory material is prevented in isolated Schistocerca by the absence of adequate stimulation, and in crowded Locusta by the action of some inhibiting agent. Daily flying on a roundabout accelerates the rate of oöcyte growth in crowded Locusta and in isolated and crowdedSchistocerca, but apparently has little effect upon the growth of the oöcytes in isolated Locusta. Where it occurs, the increased rate of growth of the oöcytes is correlated with the more rapid release of material from the neurosecretory systems of the locusts. The effects of flying and crowding in Schistocerca together equal the stimulating effect of the male pheromone, but the effect of flying in Locusta opposes the inhibitory effect of crowding. Cyclic changes in the volumes of the corpora allata are correlated with oöcyte growth in flown and unflown, isolated and crowded Schistocerca and seem to follow upon the activity of the neurosecretory system, the greatest volume of the glands being attained sooner in the flown than in the unflown females. In isolated Locusta, the pattern of volume changes in the corpora allata is identical in both the flown and unflown females and is similar to that in Schistocerca. In unflown crowded Locusta, the corpora allata increase greatly in size without any corresponding oöcyte growth. Flying gradually reduces the size of the glands as the oöcytes develop. The enlarged glands in the unflown crowded Locusta probably represent a prolonged synthetic phase without concomitant release of hormone.     

Growth of human tumor xenografts implanted under the renal capsule of normal immunocompetent mice.

The subrenal capsule technique proved effective in demonstrating that the growth of human tumors in normal, immunocompetent animals for 6 days was quantifiable in ocular micrometer units. Positive growth was demonstrable not only with human tumors that had been established in serial transplantation in athymic nude mouse hosts, but also with primary surgical explants. Growth rates of transplantation-established xenograft systems were similar whether implanted in athymic nude or in normal immunocompetent animals indicating that the 6-day time-frame successfully evades growth inhibitory effects of immunologic origin. Immunosuppression with a single dose of cyclophosphamide did not appear to affect growth rate, but permitted the tumors to grow larger extending the time to reach peak size. Significantly, xenografts of primary surgical explants showed positive growth more frequently in 6 days (82%) in the immunocompetent animal than in 11 days (30%) in the immunodeficient athymic nude mouse.     

The Maintenance of Stable Dominance Hierarchies and the Pattern of Aggression: Support for the Suppression Hypothesis

Three hypotheses have been proposed to explain the development and maintenance of dominance hierarchies. According to the first hypothesis the dominance hierarchy is a result of the animals fighting once at their first encounter and then using the outcome of that fight to determine the rank order. The second hypothesis proposes that a dominance hierarchy reflects the fighting ability of the individuals in the group at each moment and is therefore relatively fluid with individuals continuously fighting for position. A third hypothesis, the suppression hypothesis, states that the dominance hierarchy is based to a large extent on the outcome of the first fight between the individuals but the dominant animal in each pair continuously attacks the subdominant individuals to condition them to lose in future encounters. We studied six well‐established flocks containing six adult hens each (Gallus gallus domesticus). Five of the flocks had linear hierarchies. The aggression was significantly more often directed towards the next low‐ranking individual. There was a good correlation between rank and comb size (height × width), but no significant correlation between rank and weight, or rank and level of fluctuating asymmetry. There was no significant correlation between levels of aggression and similarity of comb size for individuals of neighboring ranks. Our results tentatively support the suppression hypothesis for the maintenance of dominance hierarchies in the domestic hen.