Exploration of biological network centralities with CentiBiN

Background  

The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements. Centrality analysis ranks network elements according to their importance within the network structure and different centrality measures focus on different importance concepts. Central elements of biological networks have been found to be, for example, essential for viability.     

Effect of endurance flight on haematocrit in migrating birds

The effects of an endurance flight on the haematocrit, the percentage of packed red blood cells per blood volume, were examined within the framework of six possible factors explaining possible changes in the haematocrit. Two approaches were adopted: (1) the haematocrit was studied in four species of passerine birds which landed on an Italian island after having crossed the Mediterranean Sea on their spring migration in a non-stop flight; (2) the haematocrit was evaluated in six individual red knots after a flight of 1, 2, 4 and 10 h in a wind tunnel and the data thus obtained compared with data on resting birds with or without food. In the four passerine species, the haematocrit decreased from 51% in fat birds to 48% in lean birds. In lean birds, the haematocrit dropped from 48% in birds with well-developed breast muscles to 36% in birds with emaciated breast muscles. In the red knots, the haematocrit was dependent on body mass in flying and resting birds. The haematocrit decreased from about 51% pre-flight to about 49% within 1 h of flight and remained at this level for up to 10 h of flight. Taking the results from the passerines and the red knots together, it seems that the haematocrit drops by a few percentage points within 1 h after the onset of flight, decreases very slowly with decreasing body mass and decreases more steeply in very lean birds having entered stage III of fasting. This indicates that dehydration is not an underlying factor in decreased haematocrit because if this were the case we would expect an increase with endurance flight. We found no effect of the presence of blood parasites on haematocrit. With the onset of flight, haemodilution may be adaptive, because it reduces blood viscosity and, thereby, energy expenditure by the heart, or it may be a sign of water conservation as an insurance against the risk of dehydration during long non-stop flights. During endurance flight, a reduction in the haematocrit may be adaptive, in that oxygen delivery capacity is adjusted to the decreased oxygen needs as body mass decreases. A decreasing haematocrit would also allow birds to reduce heart beat frequency and/or heart size, because blood viscosity decreases disproportionally with decreasing haematocrit. However, when energy stores are about to come to an end and birds increase protein breakdown, the haematocrit decreases even further, and birds probably become anaemic due to a reduced erythropoiesis.     

Auditory lateralization in bushcrickets: a new dichotic paradigm

Pair formation in the bushcricket Gampsocleis gratiosa is achieved through acoustic signalling by the male and phonotactic approaches of the female towards the calling song. On a walking belt in the free sound field, females tracked the position of the speaker broadcasting the male calling song with a remarkable precision, deviating by no more than 10 cm in either direction from the ideal course. Starting with stimulus angles of 6–10° the females significantly turned to the correct side, and with stimulus angles greater than 25° no incorrect turns were made. Using neurophysiological data on the directionality of the ear we calculated that with such stimulus angles the available binaural intensity difference is in the order of 1–2 dB. We developed a dichotic ear stimulation device for freely moving females with a cross-talk barrier of about 50 dB, which allowed to precisely apply small binaural intensity differences. In such a dichotic stimulation paradigm, females on average turned to the tronger stimulated side starting with a 1 dB difference between both ears. The significance of such a reliable lateralization behaviour with small interaural intensity differences for phonotactic behaviour under natural conditions is discussed.     

Effects of Landscape Elements on the Distribution of the Rare Bumblebee Species Bombus muscorum in an Agricultural Landscape

The regional distribution pattern of Bombus muscorum was studied in an agricultural landscape of central Germany, one of two remaining areas with the occurrence of this nationally endangered species in the Land Hesse. To determine the landscape characteristics that facilitate the occurrence of B. muscorum, grid-based observation records were analysed in a GIS environment at a regional scale. A significantly negative effect of the number of trees on the occurrence of B. muscorum and a significantly positive one of the proportion of arable land, strongly support the species’ preference for open landscapes. Yet, apart from open landscapes additional landscape features were shown to be important. A significantly positive effect of ditches in the final model revealed the importance of this landscape element for the occurrence of B. muscorum. This finding was additionally supported by recordings of nest-searching queens, nests, and flower visits along dithes. The positive effects of clover and fallow land indicate the species’ need for suitable food resources throughout the season. Because B. muscorum exhibits small foraging ranges, it is essential that landscape elements that provide nesting sites, foraging habitats and undisturbed hibernation structures are next to each other. The low numbers of individuals of B. muscorum recorded indicate that the supply of these habitat elements may have reached a critical threshold in the study region.     

Improved variance estimation of classification performance via reduction of bias caused by small sample size

Background  

Supervised learning for classification of cancer employs a set of design examples to learn how to discriminate between tumors. In practice it is crucial to confirm that the classifier is robust with good generalization performance to new examples, or at least that it performs better than random guessing. A suggested alternative is to obtain a confidence interval of the error rate using repeated design and test sets selected from available examples. However, it is known that even in the ideal situation of repeated designs and tests with completely novel samples in each cycle, a small test set size leads to a large bias in the estimate of the true variance between design sets. Therefore different methods for small sample performance estimation such as a recently proposed procedure called Repeated Random Sampling (RSS) is also expected to result in heavily biased estimates, which in turn translates into biased confidence intervals. Here we explore such biases and develop a refined algorithm called Repeated Independent Design and Test (RIDT).