Indexing large genome collections on a PC

Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. Results: We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size fitting in a standard computer with 16--32\,GB, or even 8\,GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries are handled in average time of 39\,$\mu$s and with up to 3 mismatches in 373\,$\mu$s on the test PC with the index size of 13.4\,GB. For a smaller index, occupying 7.4\,GB in memory, the respective times grow to 76\,$\mu$s and 917\,$\mu$s. Availability: Software and Suuplementary material: \url{http://sun.aei.polsl.pl/mugi}

How effectively does the index of hydrogen deficiency in carbohydrates used in potassium nitrate propellant affect enthalpy change and its performance?

This work looks at the relationship between the index of hydrogen deficiency (IHD) and the enthalpy of combustion of "sugar propellant," as well as the performance of carbohydrates with similar IHD values. The study used eight different carbohydrate sources as fuels in the propellant, combined with potassium nitrate as an oxidizer in a 35:65 ratio. The IHD of the sugars ranged from 0 (polyols) to 2 (disaccharides). Different propellant mixtures (carbohydrate-KN) were tested using calorimeters and chemical analysis. The results support the hypothesis that IHD is associated with the enthalpy of combustion of sugar propellant, with polyol reactions showing the highest enthalpy change. Moreover, carbohydrates with a higher molar mass and an IHD of 2 exhibit better performance than those with an IHD of 1.Comment: 43 pages (30 pages of content, 13 pages appendices), 5 Tables, 9 figure

Data compression for sequencing data

Post-Sanger sequencing methods produce tons of data, and there is a general agreement that the challenge to store and process them must be addressed with data compression. In this review we first answer the question “why compression” in a quantitative manner. Then we also answer the questions “what” and “how”, by sketching the fundamental compression ideas, describing the main sequencing data types and formats, and comparing the specialized compression algorithms and tools. Finally, we go back to the question “why compression” and give other, perhaps surprising answers, demonstrating the pervasiveness of data compression techniques in computational biology

Interdisciplinarity in tech startups development : case study of "UniStartApp" project

Empirical data as well as scientific reports confirm that startups require diverse, in-house competencies in order to achieve market success. However, while technology-related competencies are usually brought to new tech ventures by their founders, there is a significant deficiency of market- and management-related competencies, which is reflected in the statistics of common startup failure reasons. In this context, a question arises: how interdisciplinarity of knowledge and competencies can be built into the very core of tech startups? The text addresses this question by zeroing in on the role of universities in this process. In the first part, the specificity of tech startups is analyzed. The next chapter overviews the hitherto academy-related startup education environment together with its shortcomings as far as interdisciplinarity is concerned. Finally, the case study of innovative and interdisciplinary academic ecosystem, which was built and tested within the project UniStartApp, is presented and discussed together with related lessons learned. The text is concluded with final remarks on challenges involved in embedding interdisciplinarity into startup education ecosystem

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition

Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolated from fresh venous blood (purity >99%) and used to create a spectral library covering almost 8000 proteins using strong cation exchange fractionation. Patient neutrophil samples were then analyzed by data-independent acquisition proteomics, quantifying 4154 proteins in each sample. Neutrophils with mutations in the neutrophil elastase gene ELANE showed large proteome changes that suggest these mutations may affect maturation of neutrophil granulocytes and initiate misfolded protein response and cellular stress mechanisms. In contrast, only few proteins changed in patients with leukocyte adhesion deficiency (LAD) and chronic granulomatous disease (CGD). Strikingly, neutrophil transcriptome analysis showed no correlation with its proteome. In case of two patients with undetermined genetic causes, proteome analysis guided the targeted genetic diagnostics and uncovered the underlying genomic mutations. Data-independent acquisition proteomics may help to define novel pathomechanisms in neutrophil diseases and provide a clinically useful diagnostic dimension

Perspectives of Ultra Cold Atoms Trapped in Magnetic Micro Potentials

Recent work on magnetic micro traps for ultracold atoms is briefly reviewed. The basic principles of operation are described together with the loading methods and some of the realized trap geometries. Experiments are discussed that study the interaction between atoms and the surface of micro traps as well as the dynamics of ultracold gases in wave guides are discussed. The results allow for an outlook towards future directions of research

Cosmopolitan conservation: the multi-scalar contributions of urban green infrastructure to biodiversity protection [Letter]

Urbanization is a leading cause of biodiversity loss globally. Expanding cities alter regional ecological processes by consuming habitat and modifying biogeochemical and energetic flows. Densifying cities often lose valuable intra-urban green spaces. Despite these negative impacts, novel urban ecosystems can harbor high biodiversity and provide vital ecosystem services for urban residents. Recognizing the benefits of urban ecosystems, cities across the globe are increasingly planning for urban green infrastructure (UGI). UGI as a planning concept can transform how cities integrate biodiversity into urbanized landscapes at multiple scales and contribute to conservation goals. Full operationalization of UGI concepts can also reduce urban energy and resource demands via substituting polluting technologies by UGI, further contributing to the global conservation agenda. Realizing the potential contributions of UGI to local, regional, and global conservation goals requires addressing four inter-dependent challenges: (1) expanding social-ecological-systems thinking to include connections between complex social, ecological, and technological systems (SETS), (2) explicitly addressing multi-level governance challenges, (3) adapting SETS approaches to understand the contextual and biocultural factors shaping relationships between UGI and other causal processes in cities that shape biodiversity, and (4) operationalizing UGI systems through robust modeling and design approaches. By transforming UGI policy and research through SETS approaches to explicitly integrate biodiversity we can support global conservation challenges while improving human wellbeing in cities and beyond

Radiofrequency Electromagnetic Fields Cause Non-Temperature-Induced Physical and Biological Effects in Cancer Cells

Non-temperature-induced effects of radiofrequency electromagnetic fields (RF) have been controversial for decades. Here, we established measurement techniques to prove their existence by investigating energy deposition in tumor cells under RF exposure and upon adding amplitude modulation (AM) (AMRF). Using a preclinical device LabEHY-200 with a novel in vitro applicator, we analyzed the power deposition and system parameters for five human colorectal cancer cell lines and measured the apoptosis rates in vitro and tumor growth inhibition in vivo in comparison to water bath heating. We showed enhanced anticancer effects of RF and AMRF in vitro and in vivo and verified the non-temperature-induced origin of the effects. Furthermore, apoptotic enhancement by AM was correlated with cell membrane stiffness. Our findings not only provide a strategy to significantly enhance non-temperature-induced anticancer cell effects in vitro and in vivo but also provide a perspective for a potentially more effective tumor therapy