Recognition of balance signals between healthy subjects and otoneurological patients with hidden Markov models

The objective of the present research was to investigate whether hidden Markov models can be used to recognise and classify balance signals extracted from two subject groups, the healthy and patients suffering from otoneurological vertiginous diseases. Two different testing protocols were applied: arising from a chair and standing on the force platform. Signals recorded according to these protocols were trained for models with different numbers of states to find the best choices as model structures. We found that these models with 7–15 states were able to recognise the healthy subjects from the patients with the accuracy between 70 and 90% although their balance measurements were visually very similar and difficult to separate between two groups.     

Bacteria, phages and septicemia

The use of phages is an attractive option to battle antibiotic resistant bacteria in certain bacterial infections, but the role of phage ecology in bacterial infections is obscure. Here we surveyed the phage ecology in septicemia, the most severe type of bacterial infection. We observed that the majority of the bacterial isolates from septicemia patients spontaneously secreted phages active against other isolates of the same bacterial strain, but not to the strain causing the disease. Such phages were also detected in the initial blood cultures, indicating that phages are circulating in the blood at the onset of sepsis. The fact that most of the septicemic bacterial isolates carry functional prophages suggests an active role of phages in bacterial infections. Apparently, prophages present in sepsis-causing bacterial clones play a role in clonal selection during bacterial invasion.     

Inhibition of Aurora kinases perturbs chromosome alignment and spindle checkpoint signaling in rat spermatocytes

In somatic cells, integrity of cell division is safeguarded by the spindle checkpoint, a signaling cascade that delays the separation of sister chromatids in the presence of misaligned chromosomes. Aurora kinases play important roles in this process by promoting centrosome maturation, chromosome bi-orientation, spindle checkpoint signaling, and cytokinesis. To investigate the functions of Aurora kinases in male meiosis, we applied a small molecule Aurora inhibitor, ZM447439, to seminiferous tubules in vitro. Primary and secondary spermatocytes exposed to ZM447439 exhibit defects in the spindle morphology and fail to align their chromosomes at the metaphase plate. Moreover, the treated spermatocytes undergo a forced exit from the meiotic M-phase without cytokinesis. These results suggest that the activities of Aurora kinases are required for normal spindle assembly as well as for establishment and maintenance of proper microtubule-kinetochore attachments and spindle checkpoint signaling in male mammalian meiosis.     

AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins

Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult. We describe AllerHunter, a web-based computational system for the assessment of potential allergenicity and allergic cross-reactivity in proteins. It combines an iterative pairwise sequence similarity encoding scheme with SVM as the discriminating engine. The pairwise vectorization framework allows the system to model essential features in allergens that are involved in cross-reactivity, but not limited to distinct sets of physicochemical properties. The system was rigorously trained and tested using 1,356 known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models. The system is effective for distinguishing allergens and non-allergens from allergen-like non-allergen sequences. Testing results showed that AllerHunter, with a sensitivity of 83.4% and specificity of 96.4% (accuracy = 95.3%, area under the receiver operating characteristic curve AROC = 0.928±0.004 and Matthew''s correlation coefficient MCC = 0.738), performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at http://tiger.dbs.nus.edu.sg/AllerHunter     

Real-Time Correlates of Phonological Quantity Reveal Unity of Tonal and Non-Tonal Languages

Discrete phonological phenomena form our conscious experience of language: continuous changes in pitch appear as distinct tones to the speakers of tone languages, whereas the speakers of quantity languages experience duration categorically. The categorical nature of our linguistic experience is directly reflected in the traditionally clear-cut linguistic classification of languages into tonal or non-tonal. However, some evidence suggests that duration and pitch are fundamentally interconnected and co-vary in signaling word meaning in non-tonal languages as well. We show that pitch information affects real-time language processing in a (non-tonal) quantity language. The results suggest that there is no unidirectional causal link from a genetically-based perceptual sensitivity towards pitch information to the appearance of a tone language. They further suggest that the contrastive categories tone and quantity may be based on simultaneously co-varying properties of the speech signal and the processing system, even though the conscious experience of the speakers may highlight only one discrete variable at a time.     

Monitoring the European pine sawfly with pheromone traps in maturing Scots pine stands

Abstract

• 1 During 1989–93, field studies were conducted in Finland to develop a method based on pheromone traps to monitor and forecast population levels of the European pine sawfly (Neodiprion sertifer Geoffr.) and tree defoliation.
• 2 Three traps per site were baited with 100 µg of the N. sertifer sex pheromone, the acetate ester of (2S,3S,7S)‐3,7‐dimethyl‐2‐pentadecanol (diprionol), in maturing pine stands in southern and central Finland. In addition, three different dosages (1, 10 and 100 µg) of the pheromone were tested in 1991–92.
• 3 The highest number of males was observed in traps baited with the highest dose. On average, there was a 10‐fold increase in trap catch between lure doses.
• 4 Density of overwintering eggs was used to evaluate the effectiveness of pheromone traps in predicting sawfly populations. The proportion of healthy overwintering eggs was determined each year. A model based on the number of current shoots on sample trees, diameter at breast height and tree height was formulated to estimate eggs per hectare.
• 5 Linear regression analysis produced high coefficients of determination between number of males in traps and density of total eggs in the subsequent generation, when populations were at peak densities. The relationships were not significant for low population densities. The results indicate a risk of moderate defoliation when the seasonal trap catch is 800–1000 males per trap or higher.

     

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions

Background  

Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.     

Chemical factors affecting the brown-rot decay resistance of Scots pine heartwood

The cell wall chemistry (amount of hemicellulose, f-cellulose, and total lignin) and the concentration of extractives (total acetone-soluble extractives, resin acids, pinosylvins and the total phenolics quantified as tannin acid equivalents) were studied in brown-rot resistant and susceptible juvenile heartwood of Scots pine (Pinus sylvestris L.). The study material consisted of a total of 18 trees from two 34-year-old progeny trials at Korpilahti and Kerimäki. The trees were selected from among 783 trees whose decay rate had previously been screened in a laboratory test using a brown-rot fungus, Coniophora puteana. Samples from neither location showed any significant difference in the concentration (mg/cm³) of hemicellulose, f-cellulose and total lignin between the decay resistant and susceptible trees. At both locations only the concentration of total phenolics was higher in the decay-resistant heartwood than in the decay-susceptible heartwood. At Korpilahti, the amount of acetone-soluble extractives and the concentration of pinosylvin and its derivatives were higher in the resistant than in the susceptible trees.     

Proliferation and differentiation of bovine type A spermatogonia during long-term culture

The present study was aimed at developing a method for long-term culture of bovine type A spermatogonia. Testes from 5-mo-old calves were used, and pure populations of type A spermatogonia were isolated. Cells were cultured in minimal essential medium (MEM) or KSOM (potassium-rich medium prepared according to the simplex optimization method) and different concentrations of fetal calf serum (FCS) for 2-4 wk at 32 degrees C or 37 degrees C. Culture in MEM resulted in more viable cells and more proliferation than culture in KSOM, and better results were obtained at 37 degrees C than at 32 degrees C. After 1 wk of culture in the absence of serum, only 20% of the cells were alive. However, in the presence of 2.5% FCS, approximately 80% of cells were alive and proliferating. Higher concentrations of FCS only enhanced numbers of somatic cells. In long-term culture, spermatogonia continued to proliferate, and eventually, type A spermatogonial colonies were formed. The majority of colonies consisted mostly of groups of cells connected by intercellular bridges. Most of the cells in these colonies underwent differentiation because they were c-kit positive, and ultimately, cells with morphological and molecular characteristics of spermatocytes and spermatids were formed. Occasionally, large round colonies consisting of single, c-kit-negative, type A spermatogonia (presumably spermatogonial stem cells) were observed. For the first time to our knowledge, a method has been developed to allow proliferation and differentiation of highly purified type A spermatogonia, including spermatogonial stem cells during long-term culture.