Parallel approach to sliding window sums

Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure

Derivatives of Isoindoline, Synthesis and Biological Activity. II. Biological Activity of Derivatives of Isoindoline

Derivati izoindolina pokazuju vrlo različita biološka djelovanja in vitro, a neki djeluju i u uvjetima in vivo. Stoga se može očekivati da će istraživanja u budućnosti dovesti i do učinkovitih lijekova za različite vrste bolesti. Pokazuju nesteroidnu protuupalnu aktivnost, antihipertenzivno djelovanje, anksiolitičko, antipsihotičko i antikonvulzivno djelovanje. Djeluju kao lokalni anestetici, vazodilatatori te se vežu na dopaminske i serotononske receptore. Ubrajaju se također u skupinu antidijabetika inhibirajući dipeptidil-peptidaze. Metalni kompleksi izoindolina i njegovih derivata djeluju poput enzima katalaze koji štiti stanice od štetnog djelovanja vodikova peroksida te djeluju i kao inhibitori protein-kinaza. Osim ostalih značajno je njihovo antitumorsko djelovanje na stanice leukemije, karcinoma debelog crijeva, epidermalnog karcinoma te karcinoma jajnika. Oni također inhibiraju enzime koji potiču rast tumorskih stanica kao što su histon deacetilaza te receptori tirozin-kinaze i krvožilnog endotelnog čimbenika rasta (VEGF-R2).Derivatives of isoindolines are a group of nitrogen heterocyclic compounds that are less represented in scientific literature than other heterocyclic compounds containing the nitrogen atom. Natural derivatives of isoindolines were first isolated in the early 1960\u27s and showed various interesting biological activity, e.g. staurosporine indicating antimicrobial, hypotensive, and cytotoxic activity, and acts as thrombocytes aggregation inhibitor and protein kinase inhibitor. Also, there are reports of their application in herbicide and dye industries. Due to these findings, isoindolines received much attention from synthetic organic chemists, and thus new synthetic methods were developed. Most of the methods include phthalaldehyde and corresponding aliphatic and aromatic amines as starting material. Products of these reactions are highly dependent on the reaction conditions, and differently substituted isoindolines are isolated. Synthetic methods starting from other compounds include phthalonitrile, phthalanhydride and phthalaldehyde acid as well as multicomponent reactions. They are also applied as ligands in coordination chemistry, which enables the modelling of three-dimensional structures with desirable areal properties

Annotated mitochondrial genome with Nanopore R9 signal for <i>Nippostrongylus brasiliensis</i>

Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data. The assembly was error-corrected using existing Illumina HiSeq reads, and annotated in full (i.e. gene boundary definitions without substantial gaps) by comparing with annotated genomes from similar parasite relatives. The mitochondrial genome has also been annotated with a preliminary electrical consensus sequence, using raw signal data generated from a Nanopore R9 flow cell

Accurate detection of complex structural variations using single-molecule sequencing

Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr ) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles ) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings

Derivatives of Isoindoline, Synthesis and Biological Activity. I. Natural and Synthetic Derivatives of Isoindoline

Derivati izoindolina pripadaju skupini dušikovih heterocikličkih spojeva koji su manje zastupljeni u literaturi od ostalih dušikovih heterocikličkih spojeva. Prvi prirodni derivati izoindolina izolirani su u drugoj polovici prošlog stoljeća te su pokazali različita interesantna biološka djelovanja, npr. staurosporin koji pokazuje antimikrobno, hipotenzivno i citotoksično djelovanje te djeluje kao inhibitor agregacije trombocita i inhibitor protein-kinaze. Zbog tih saznanja porastao je interes za kemiju izoindolina i pronađene su različite sintetske metode njihova dobivanja. Najviše su zastupljene sinteze iz ftalaldehida i odgovarajućih alifatskih i aromatskih amina kao polaznih spojeva. Sinteze iz ostalih polaznih spojeva uključuju ftalonitril, ftalanhidrid i ftalaldehidnu kiselinu te višekomponentne reakcije. Izoindolin i njegovi derivati zastupljeni su kao ligandi u kemiji metalnih kompleksa. Tako su priređeni metalni kompleksi koji omogućuju dizajniranje ciljanih trodimenzijskih struktura što se može primijeniti u raznim područjima koordinativne kemije, ali i u dizajniranju biološki aktivnih spojeva s točno određenim prostornim svojstvima.Derivatives of isoindolines are a group of nitrogen heterocyclic compounds that are less represented in scientific literature than other heterocyclic compounds containing the nitrogen atom. Natural derivatives of isoindolines were first isolated in the early 1960\u27s and showed various interesting biological activity, e.g. staurosporine indicating antimicrobial, hypotensive, and cytotoxic activity, and acts as thrombocytes aggregation inhibitor and protein kinase inhibitor. Also, there are reports of their application in herbicide and dye industries. Due to these findings, isoindolines received much attention from synthetic organic chemists, and thus new synthetic methods were developed. Most of the methods include phthalaldehyde and corresponding aliphatic and aromatic amines as starting material. Products of these reactions are highly dependent on the reaction conditions, and differently substituted isoindolines are isolated. Synthetic methods starting from other compounds include phthalonitrile, phthalanhydride and phthalaldehyde acid as well as multicomponent reactions. They are also applied as ligands in coordination chemistry, which enables the modelling of three-dimensional structures with desirable areal properties