Digital Vapor Trails: Using Website Behavior to Nowcast Entrepreneurial Activity

[EN] Following recent research, we explore virtually contemporaneous, and geographically granular, user online activity related to entrepreneurship. In this paper, we present evidence that data harvested by Dstillery can complement efforts of, and data collected by, government agencies and organizations advocating for entrepreneurship, business formation and economic growth, e.g., the Kauffman Foundation. Our website-based behavior data is close to real time and at a geographically granular level. We find that the concentration of a region’s visits to website resources for entrepreneurship and business development are statistically related to business start-up and, particularly, growth activity. Visits to websites related to entrepreneurship are more strongly associated with growth entrepreneurship, in contrast to start-up entrepreneurship. While data capture and analysis related to entrepreneurship website activity is in its infancy, this analysis points to the potential of this data source to nowcast business formation and growth at a regional level.Slaper, T.; Bianco, A.; Lenz, P. (2018). Digital Vapor Trails: Using Website Behavior to Nowcast Entrepreneurial Activity. En 2nd International Conference on Advanced Reserach Methods and Analytics (CARMA 2018). Editorial Universitat Politècnica de València. 107-113. https://doi.org/10.4995/CARMA2018.2018.8327OCS10711

Third Places and Art Spaces: Using Web Activity to Differentiate Cultural Dimensions of Entrepreneurship Across U.S. Regions

[EN] We use unconventional, web-based user data to assess regional entrepreneurial activity and regional variations in characteristics and culture that drive differences in business formation. Using geographically granular, user-online activity to estimate a region’s proclivity for entrepreneurship, we assess the statistical relationship between business formation, operationalized as establishment births, and a region’s general interest in “third places” – informal gathering and mixing locations – and websites related to arts, music and design – “arts spaces.” We operationalize interest in, or intention to patronize, third places and arts spaces by individuals within a geographical unit of analysis (U.S. counties) who access website information and resources related to those third places. Controlling for regional interest in entrepreneurship related web resources, we find that interest in third places and art spaces is strongly associated with regional variation in business formation. This work corroborates research showing that regions with a high concentration of interest (and participation) in third places and art spaces may attract the attention of would be entrepreneurs as desirable places to live, work and explore business opportunities, and help identify and address a critical missing ingredient in regions that have lower rates of start-ups and business growth.Slaper, T.; Bianco, A.; Lenz, P. (2020). Third Places and Art Spaces: Using Web Activity to Differentiate Cultural Dimensions of Entrepreneurship Across U.S. Regions. Editorial Universitat Politècnica de València. https://doi.org/10.4995/CARMA2020.2020.11638OCS23924

Cation effects on the folding of ribosomal RNA

Folding of ribonucleic acids (RNAs), including those which constitute the functional components of the ribosome, invariably involves positively charged metal ions (cations). Here, we explore the intricate relationships between divalent cations and ribosomal structure, origins, and evolution. We develop and test a model of an ancestral ribosomal RNA which, despite extensive deletions, retains the ability to fold into its predicted secondary structure and associate specifically with Mg2+ ions. These results support that the functional core of the ribosome is an ancient assembly that has remained largely static over billions of years of evolution. We also find that modern protein-free ribosomal RNA exhibits widely-dispersed conformational changes upon association with Mg2+, consistent with global collapse to a near-native conformation containing many native tertiary interactions. By inference, the structural effects of ribosomal proteins are largely assumed to be local and nominal. We perform experiments designed to examine the structure of ribosomal RNA under plausible early earth conditions, particularly in presence of Fe2+, to study the emergence of the translation apparatus under relevant geochemical conditions. Our results suggest atomic-level mimicry of Fe2+ for Mg2+ in extant and ancient protein-free ribosomal RNA structures, both of which fold more readily in presence of Fe2+ than Mg2+. We discuss the observation of experimental patterns for certain RNA motifs, and the potential utility of these types of patterns in improving RNA structure prediction and validation.Ph.D

Multiple prebiotic metals mediate translation.

Today, Mg2+ is an essential cofactor with diverse structural and functional roles in life's oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, and high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) was used to compare the effect of Mg2+, Fe2+, and Mn2+ on the tertiary structure of rRNA. Then, we used in vitro translation reactions to test whether Fe2+ or Mn2+ could mediate protein production, and quantified ribosomal metal content. We found that (i) Mg2+, Fe2+, and Mn2+ had strikingly similar effects on rRNA folding; (ii) Fe2+ and Mn2+ can replace Mg2+ as the dominant divalent cation during translation of mRNA to functional protein; and (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+ and Mn2+ were abundant, these findings suggest that Fe2+ and Mn2+ played a role in early ribosomal evolution

Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

A significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome only 2% have been experimentally verified and over 6,000 are hypothetical. Here, we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.DFG, 325093850, Open Access Publizieren 2017 - 2018 / Technische Universität BerlinEC/FP7/607332/EU/Quantitative Biology for Fungal Secondary Metabolite Producers/QuantFun

Near-uniform internal rotation of the main-sequence γ Doradus pulsator KIC 7661054

We used Kepler photometry to determine the internal rotation rate of KIC 7661054, a chemically normal γ Dor star on the main sequence at spectral type F2.5 V. The core rotation period of 27.25 ± 0.06 d is obtained from the rotational splittings of a series of dipole g modes. The surface rotation period is calculated from a spectroscopic projected rotation velocity and a stellar radius computed from models. Literature data, obtained without inclusion of macroturbulence as a line-broadening mechanism, imply that the surface rotates much more quickly than the core, while our detailed analysis suggests that the surface may rotate slightly more quickly than the core and that the rotation profile is uniform within the 1-σ uncertainties. We discuss the pitfalls associated with the determination of surface rotation rates of slow rotators from spectroscopy in the absence of asteroseismic constraints. A broad signal is observed at low frequency, which we show cannot be attributed to rotation, contrary to previous suggestions concerning the origin of such signals

Grouping of UVCB substances with dose-response transcriptomics data from human cell-based assays

The application of in vitro biological assays as new approach methodologies (NAMs) to support grouping of UVCB (unknown or variable composition, complex reaction products, and biological materials) substances has recently been demonstrated. In addition to cell-based phenotyping as NAMs, in vitro transcriptomic profiling is used to gain deeper mechanistic understanding of biological responses to chemicals and to support grouping and read-across. However, the value of gene expression profiling for characterizing complex substances like UVCBs has not been explored. Using 141 petroleum substance extracts, we performed dose-response transcriptomic profiling in human induced pluripotent stem cell (iPSC)-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, as well as cell lines MCF7 and A375. The goal was to determine whether transcriptomic data can be used to group these UVCBs and to further characterize the molecular basis for in vitro biological responses. We found distinct transcriptional responses for petroleum substances by manufacturing class. Pathway enrichment informed interpretation of effects of substances and UVCB petroleum-class. Transcriptional activity was strongly correlated with concentration of polycyclic aromatic compounds (PAC), especially in iPSC-derived hepatocytes. Supervised analysis using transcriptomics, alone or in combination with bioactivity data collected on these same substances/cells, suggest that transcriptomics data provide useful mechanistic information, but only modest additional value for grouping. Overall, these results further demonstrate the value of NAMs for grouping of UVCBs, identify informative cell lines, and provide data that could be used for justifying selection of substances for further testing that may be required for registration

Periodicities in the high-mass X-ray binary system RXJ0146.9+6121/LSI+61 235

The high-mass X-ray binary RX J0146.9+6121, with optical counterpart LS I+61°235 (V831 Cas), is an intriguing system on the outskirts of the open cluster NGC 663. It contains the slowest Be type X-ray pulsar known with a pulse period of around 1400 s and, primarily from the study of variation in the emission line profile of Hα, it is known to have a Be decretion disc with a one-armed density wave period of approximately 1240 d. Here we present the results of an extensive photometric campaign, supplemented with optical spectroscopy, aimed at measuring short time-scale periodicities. We find three significant periodicities in the photometric data at, in order of statistical significance, 0.34, 0.67 and 0.10 d. We give arguments to support the interpretation that the 0.34 and 0.10 d periods could be due to stellar oscillations of the B-type primary star and that the 0.67 d period is the spin period of the Be star with a spin axis inclination of 23+10−8 degrees. We measured a systemic velocity of −37.0 ± 4.3 km s−1 confirming that LS I+61°235 has a high probability of membership in the young cluster NGC 663 from which the system's age can be estimated as 20–25 Myr. From archival RXTE All Sky Monitor (ASM) data we further find ‘super’ X-ray outbursts roughly every 450 d. If these super outbursts are caused by the alignment of the compact star with the one-armed decretion disc enhancement, then the orbital period is approximately 330 d