Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110

Small open reading frames (sORFs) and genes for non-coding RNAs are poorly investigated components of most genomes. Our analysis of 1391 ORFs recently annotated in the soybean symbiont Bradyrhizobium japonicum USDA 110 revealed that 78% of them contain less than 80 codons. Twenty-one of these sORFs are conserved in or outside Alphaproteobacteria and most of them are similar to genes found in transposable elements, in line with their broad distribution. Stabilizing selection was demonstrated for sORFs with proteomic evidence and bll1319_ISGA which is conserved at the nucleotide level in 16 alphaproteobacterial species, 79 species from other taxa and 49 other Proteobacteria. Further we used Northern blot hybridization to validate ten small RNAs (BjsR1 to BjsR10) belonging to new RNA families. We found that BjsR1 and BjsR3 have homologs outside the genus Bradyrhizobium, and BjsR5, BjsR6, BjsR7, and BjsR10 have up to four imperfect copies in Bradyrhizobium genomes. BjsR8, BjsR9, and BjsR10 are present exclusively in nodules, while the other sRNAs are also expressed in liquid cultures. We also found that the level of BjsR4 decreases after exposure to tellurite and iron, and this down-regulation contributes to survival under high iron conditions. Analysis of additional small RNAs overlapping with 3’-UTRs revealed two new repetitive elements named Br-REP1 and Br-REP2. These REP elements may play roles in the genomic plasticity and gene regulation and could be useful for strain identification by PCR-fingerprinting. Furthermore, we studied two potential toxin genes in the symbiotic island and confirmed toxicity of the yhaV homolog bll1687 but not of the newly annotated higB homolog blr0229_ISGA in E. coli. Finally, we revealed transcription interference resulting in an antisense RNA complementary to blr1853, a gene induced in symbiosis. The presented results expand our knowledge on sORFs, non-coding RNAs and repetitive elements in B. japonicum and related bacteria

Empowering domain experts in developing AI: challenges of bottom-up ML development platforms

Recent trends in AI development, exemplified by innovations like automated machine learning and generative AI, have significantly increased the bottom-up organizational deployment of AI. No- and low-code AI tools empower domain experts to develop AI and thus foster organizational innovation. At the same time, the inherent opaqueness of AI, complemented by the abandonment of requirement to follow rigorous IS development and implementation methods, implies a loss of oversight over the IT for individual domain experts and their organization, and inability to account for the regulatory requirements on AI use. We build on expert knowledge of no- and low-code AI deployment in different types of organizations, and the emerging theorizing on weakly structured systems (WSS) to argue that conventional methods of software engineering and IS deployment can’t help organizations harness the risks of innovation-fostering bottom-up developments of ML tools by domain experts. In this research in progress paper we review the inherent risks and limitations of AI - opacity, explainability, bias, and controllability - in the context of ethical and regulatory requirements. We argue that maintaining human oversight is pivotal for the bottom-up ML developments to remain “under control” and suggest directions for future research on how to balance the innovation potential and risk in bottom-up ML development projects

Empowering Domain Experts in Developing AI: Challenges of bottom-up ML development platforms

Recent trends in AI development, exemplified by innovations like automated machine learning and generative AI, have significantly increased the bottom-up organizational deployment of AI. No- and low-code AI tools empower domain experts to develop AI and thus foster organizational innovation. At the same time, the inherent opaqueness of AI, complemented by the abandonment of requirement to follow rigorous IS development and implementation methods, implies a loss of oversight over the IT for individual domain experts and their organization, and inability to account for the regulatory requirements on AI use. We build on expert knowledge of no- and low-code AI deployment in different types of organizations, and the emerging theorizing on weakly structured systems (WSS) to argue that conventional methods of software engineering and IS deployment can’t help organizations harness the risks of innovation-fostering bottom-up developments of ML tools by domain experts. In this research in progress paper we review the inherent risks and limitations of AI - opacity, explainability, bias, and controllability - in the context of ethical and regulatory requirements. We argue that maintaining human oversight is pivotal for the bottom-up ML developments to remain “under control” and suggest directions for future research on how to balance the innovation potential and risk in bottom-up ML development projects

Stable Real-Time Interaction Between Virtual Humans and Real Scenes

We present an augmented reality system that relies on purely passive techniques to solve the real-time registration problem. It can run on a portable PC and does not require engineering of the environment, for example by adding markers. To achieve this result, we have integrated robust computer vision techniques into a powerful VR framework. The resulting AR system allows us to produce complex rendering and animation of virtual human characters, and to blend them into the real world. The system tracks the 3D camera position by means of a natural features tracker, which, given a rough CAD model, can deal with complex 3D objects. The tracking method can handle both large camera displacements and aspect changes. We will show that our system works in the cluttered environment of a real industrial facility and can, therefore, be used to enhance manufacturing and industrial processe

Real-time augmented face

This real-time augmented reality demonstration relies on our tracking algorithm described in V. Lepetit et al (2003). This algorithm considers natural feature points, and then does not require engineering of the environment. It merges the information from preceding frames in traditional recursive tracking fashion with that provided by a very limited number of reference frames. This combination results in a system that does not suffer from jitter and drift, and can deal with drastic changes. The tracker recovers the full 3D pose of the tracked object, allowing insertion of 3D virtual objects for augmented reality application

Phase Diagram Of A Hard-sphere System In A Quenched Random Potential: A Numerical Study

We report numerical results for the phase diagram in the density-disorder plane of a hard sphere system in the presence of quenched, random, pinning disorder. Local minima of a discretized version of the Ramakrishnan-Yussouff free energy functional are located numerically and their relative stability is studied as a function of the density and the strength of disorder. Regions in the phase diagram corresponding to liquid, glassy and nearly crystalline states are mapped out, and the nature of the transitions is determined. The liquid to glass transition changes from first to second order as the strength of the disorder is increased. For weak disorder, the system undergoes a first order crystallization transition as the density is increased. Beyond a critical value of the disorder strength, this transition is replaced by a continuous glass transition. Our numerical results are compared with those of analytical work on the same system. Implications of our results for the field-temperature phase diagram of type-II superconductors are discussed.Comment: 14 pages, 10 postscript figures (included), submitted to Phys. Rev.

Accreting Protoplanets in the LkCa 15 Transition Disk

Exoplanet detections have revolutionized astronomy, offering new insights into solar system architecture and planet demographics. While nearly 1900 exoplanets have now been discovered and confirmed, none are still in the process of formation. Transition discs, protoplanetary disks with inner clearings best explained by the influence of accreting planets, are natural laboratories for the study of planet formation. Some transition discs show evidence for the presence of young planets in the form of disc asymmetries or infrared sources detected within their clearings, as in the case of LkCa 15. Attempts to observe directly signatures of accretion onto protoplanets have hitherto proven unsuccessful. Here we report adaptive optics observations of LkCa 15 that probe within the disc clearing. With accurate source positions over multiple epochs spanning 2009 - 2015, we infer the presence of multiple companions on Keplerian orbits. We directly detect H{\alpha} emission from the innermost companion, LkCa 15 b, evincing hot (~10,000 K) gas falling deep into the potential well of an accreting protoplanet.Comment: 35 pages, 3 figures, 1 table, 9 extended data item