University of Zagreb

About: University of Zagreb is a education organization based out in Zagreb, Grad Zagreb, Croatia. It is known for research contribution in the topics: Population & European union. The organization has 21769 authors who have published 50267 publications receiving 783239 citations. The organization is also known as: Zagreb University & Sveučilište u Zagrebu.

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Abstract: Realizing the democratic promise of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics. Here we present GraphMap, a mapping algorithm designed to analyse nanopore sequencing reads, which progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long reads with speed and high precision (>95%). Evaluation on MinION sequencing data sets against short- and long-read mappers indicates that GraphMap increases mapping sensitivity by 10–80% and maps >95% of bases. GraphMap alignments enabled single-nucleotide variant calling on the human genome with increased sensitivity (15%) over the next best mapper, precise detection of structural variants from length 100 bp to 4 kbp, and species and strain-specific identification of pathogens using MinION reads. GraphMap is available open source under the MIT license at https://github.com/isovic/graphmap.

The External RNA Controls Consortium: a progress report.

Abstract: Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.

Prenatal development of neurons in the human prefrontal cortex. II. A quantitative Golgi study.

Abstract: The quantitative development of neurons in the human dorsolateral and lateral prefrontal cortex was studied in Golgi-impregnated tissue from postmortem brains ranging from 13.5 weeks of gestation up to the second postnatal month. Pyramidal neurons in the future layers III and V of the cortical plate, as well as different types of neurons in the transient subplate zone, were studied. The basal dendrites of the future layer III and V pyramidal neurons show a slow increase during the first two-thirds of the period of gestation. From 27-32 weeks of gestation on, there is a rapid increase in the length of basal dendrites of layer III and V pyramidal neurons, while the number of basal dendrites per pyramidal neuron appears to stabilize at 26/27 weeks of gestation. The increase in total length of basal dendrites per pyramidal neuron is mainly due to an increase in the number of bifurcations and the growth of terminal segments. Throughout the whole period studied, the size of the layer III pyramidal basal dendritic tree was smaller than that of layer V pyramidal neurons. Thus, not until postnatal life do the layer III pyramidal basal dendrites become larger than those of layer V. No statistically significant differences were found for data of the pyramidal neurons between the superior and middle frontal gyri. The dendritic size of subplate neurons, except for the subplate inverted pyramidal neurons, significantly exceeds the size of the basal dendrites of the pyramidal neurons up to the seventh gestational month, which indicates an earlier maturation of these subplate neurons. During the period examined, no clear decrease in the size of the subplate neurons was observed. The present study shows that the dendritic parameters of either subplate or cortical plate pyramidal neurons rapidly increase during the periods of ingrowth of afferent fibers into the subplate zone and cortical plate, respectively. In the Golgi preparations of the prefrontal cortex, the size of the subplate neurons does not show any clearly regressive changes at the end of the prenatal period.

Exotic modes of excitation in atomic nuclei far from stability

Abstract: We review recent studies of the evolution of collective excitations in atomic nuclei far from the valley of β-stability. Collective degrees of freedom govern essential aspects of nuclear structure, and for several decades the study of collective modes such as rotations and vibrations has played a vital role in our understanding of complex properties of nuclei. The multipole response of unstable nuclei and the possible occurrence of new exotic modes of excitation in weakly bound nuclear systems, present a rapidly growing field of research, but only few experimental studies of these phenomena have been reported so far. Valuable data on the evolution of the low-energy dipole response in unstable neutron-rich nuclei have been gathered in recent experiments, but the available information is not sufficient to determine the nature of observed excitations. Even in stable nuclei various modes of giant collective oscillations had been predicted by theory years before they were observed, and for that reason it is very important to perform detailed theoretical studies of the evolution of collective modes of excitation in nuclei far from stability. We therefore discuss the modern theoretical tools that have been developed in recent years for the description of collective excitations in weakly bound nuclei. The review focuses on the applications of these models to studies of the evolution of low-energy dipole modes from stable nuclei to systems near the particle emission threshold, to analyses of various isoscalar modes, those for which data are already available, as well as those that could be observed in future experiments, to a description of charge-exchange modes and their evolution in neutron-rich nuclei, and to studies of the role of exotic low-energy modes in astrophysical processes.