Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

Small non-coding RNAs (ncRNAs) such as microRNAs, snoRNAs and tRNAs are a diverse collection of molecules with several important biological functions. Current methods for high-throughput sequencing for the first time offer the opportunity to investigate the entire ncRNAome in an essentially unbiased way. However, there is a substantial need for methods that allow a convenient analysis of these overwhelmingly large data sets. Here, we present DARIO, a free web service that allows to study short read data from small RNA-seq experiments. It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates. The DARIO web site can be accessed at http://dario.bioinf.uni-leipzig.de/

The words leader/líder and their resonances in an Italo-Latin American multinational corporation

© 2017, © The Author(s) 2017. The problems of ‘lost in translation’ are well known. Yet some terms of English managerial vocabulary, which are perfectly translatable in other languages, remain untranslated. One explanation of this phenomenon is what Linguistic anthropology call negative semantic resonances. Semantic resonances focused on the issue of which meanings can or cannot be expressed by a single word in different cultures. In this paper, based on an organisational ethnography of Latin American expatriates working for an Italo-Latin-American multinational corporation (Tubworld), we analyse the resonances of the word leader/líder and director, direttore, capo, guida, coordinador, caudillo among a group of expatriates; all Italian, Spanish or multilingual speakers who use English as a second language in their everyday interactions. The paper explains how the different uses contribute to create a meaning of what a leader should and should not be; someone who leads without leading, sometimes a manager. The authors, an Italian native speaker who learnt Spanish during childhood and use English as his everyday language and a Spanish native speaker, argue that Italian or Spanish speakers not only avoid the words duce and caudillo (the vernacular vocabulary for leader, not in use due to the political and cultural meaning) but also the word leader/líder itself, as it resonate to the other two (violent, authoritarian, autocratic, antidemocratic leadership) but furthermore because the word, a lexical loan from English, failed to encapsulate the complexity of leading multilingual organisations like Tubworld

Evidence for cognitive vestibular integration impairment in idiopathic scoliosis patients

<p>Abstract</p> <p>Background</p> <p>Adolescent idiopathic scoliosis is characterized by a three-dimensional deviation of the vertebral column and its etiopathogenesis is unknown. Various factors cause idiopathic scoliosis, and among these a prominent role has been attributed to the vestibular system. While the deficits in sensorimotor transformations have been documented in idiopathic scoliosis patients, little attention has been devoted to their capacity to integrate vestibular information for cognitive processing for space perception. Seated idiopathic scoliosis patients and control subjects experienced rotations of different directions and amplitudes in the dark and produced saccades that would reproduce their perceived spatial characteristics of the rotations (vestibular condition). We also controlled for possible alteration of the oculomotor and vestibular systems by measuring the subject's accuracy in producing saccades towards memorized peripheral targets in absence of body rotation and the gain of their vestibulo-ocular reflex.</p> <p>Results</p> <p>Compared to healthy controls, the idiopathic scoliosis patients underestimated the amplitude of their rotations. Moreover, the results revealed that idiopathic scoliosis patients produced accurate saccades to memorized peripheral targets in absence of body rotation and that their vestibulo-ocular reflex gain did not differ from that of control participants.</p> <p>Conclusion</p> <p>Overall, results of the present study demonstrate that idiopathic scoliosis patients have an alteration in cognitive integration of vestibular signals. It is possible that severe spine deformity developed partly due to impaired vestibular information travelling from the cerebellum to the vestibular cortical network or alteration in the cortical mechanisms processing the vestibular signals.</p

Gender and line size factors modulate the deviations of the subjective visual vertical induced by head tilt

<p>Abstract</p> <p>Background</p> <p>The subjective visual vertical (SVV, the visual estimation of gravitational direction) is commonly considered as an indicator of the sense of orientation. The present study examined the impact of two methodological factors (the angle size of the stimulus and the participant's gender) on deviations of the SVV caused by head tilt. Forty healthy participants (20 men and 20 women) were asked to make visual vertical adjustments of a light bar with their head held vertically or roll-tilted by 30° to the left or to the right. Line angle sizes of 0.95° and 18.92° were presented.</p> <p>Results</p> <p>The SVV tended to move in the direction of head tilt in women but away from the direction of head tilt in men. Moreover, the head-tilt effect was also modulated by the stimulus' angle size. The large angle size led to deviations in the direction of head-tilt, whereas the small angle size had the opposite effect.</p> <p>Conclusions</p> <p>Our results showed that gender and line angle size have an impact on the evaluation of the SVV. These findings must be taken into account in the growing body of research that uses the SVV paradigm in disease settings. Moreover, this methodological issue may explain (at least in part) the discrepancies found in the literature on the head-tilt effect.</p

Third Report on Chicken Genes and Chromosomes 2015

Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned