Cavity approach for modeling and fitting polymer stretching

The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly studied force--elongation relation is typically hard. Here we draw from techniques developed in the context of disordered systems to solve models for single and double--stranded DNA stretching in the limit of a long polymeric chain. Since we directly derive the marginals for the molecule local orientation, our approach allows us to readily calculate the experimental elongation as well as other observables at wish. As an example, we evaluate the correlation length as a function of the stretching force. Furthermore, we are able to fit successfully our solution to real experimental data. Although the model is admittedly phenomenological, our findings are very sound. For single--stranded DNA our solution yields the correct (monomer) scale and, yet more importantly, the right persistence length of the molecule. In the double--stranded case, our model reproduces the well-known overstretching transition and correctly captures the ratio between native DNA and overstretched DNA. Also in this case the model yields a persistence length in good agreement with consensus, and it gives interesting insights into the bending stiffness of the native and overstretched molecule, respectively.Comment: 12 pages; 3 figures; 1 tabl

The luminosity evolution over the EQuiTemporal Surfaces in the prompt emission of Gamma-Ray Bursts

Due to the ultrarelativistic velocity of the expanding "fireshell" (Lorentz gamma factor \gamma \sim 10^2 - 10^3), photons emitted at the same time from the fireshell surface do not reach the observer at the same arrival time. In interpreting Gamma-Ray Bursts (GRBs) it is crucial to determine the properties of the EQuiTemporal Surfaces (EQTSs): the locus of points which are source of radiation reaching the observer at the same arrival time. In the current literature this analysis is performed only in the latest phases of the afterglow. Here we study the distribution of the GRB bolometric luminosity over the EQTSs, with special attention to the prompt emission phase. We analyze as well the temporal evolution of the EQTS apparent size in the sky. We use the analytic solutions of the equations of motion of the fireshell and the corresponding analytic expressions of the EQTSs which have been presented in recent works and which are valid for both the fully radiative and the adiabatic dynamics. We find the novel result that at the beginning of the prompt emission the most luminous regions of the EQTSs are the ones closest to the line of sight. On the contrary, in the late prompt emission and in the early afterglow phases the most luminous EQTS regions are the ones closest to the boundary of the visible region. This transition in the emitting region may lead to specific observational signatures, i.e. an anomalous spectral evolution, in the rising part or at the peak of the prompt emission. We find as well an expression for the apparent radius of the EQTS in the sky, valid in both the fully radiative and the adiabatic regimes. Such considerations are essential for the theoretical interpretation of the prompt emission phase of GRBs.Comment: 11 pages, 5 figures, in the Proceedings of the 1st Galileo-Xu GuangQi Meeting, October 26-30, 2009, Shangha

Mapping international research output within ethical, legal, and social implications (ELSI) of assisted reproductive technologies

Research about ethical, legal, and social implications (ELSI) of assisted reproductive technologies (ART) is infuenced by cultural and value-based perspectives. It impacts regulations, funding, and clinical practice, and shapes the perception of ART in society. We analyze trends in the global literature on ELSI of ART between 1999 and 2019. As most output is produced by North America, Western Europe, and Australia, we focus on international research, i.e., academic articles studying a diferent country than that of the corresponding author. Methods The corpus, extracted from PubMed, Web of Science, and Scopus, includes 7714 articles, of which 1260 involved international research. Analysis is based on titles, abstracts and keywords, classifcation into ART felds and Topic Modeling, the countries of corresponding author, and countries mentioned in abstracts. Results An absolute increase in the number of international studies, and their relative proportion. Trends of decentralization are apparent, yet geographic centralization remains, which refects an unequal distribution of research funds across countries and may result in fndings that do not refect global diversity of norms and values. Preference for studying conceptual challenges through philosophical analysis, and for felds that concern only a portion of ART cycles. Less attention was dedicated to economic analysis and barriers to access, or to knowledge of and attitudes. International studies provide an opportunity to expand and diversify the scope of ELSI research. Conclusion We call on the research community to promote international collaborations, focus on less explored regions, and divert more attention to questions of cost, access, knowledge, and attitude

Mapping ethical, legal, & social implications (ELSI) of assisted reproductive technologies

Purpose A signifcant portion of the research on assisted reproductive technologies explores ethical, legal, and social implications. It has an impact on social perceptions, the evolution of norms of clinical practices, regulations and public funding. This paper reviews and maps the geographical distribution to test the hypothesis of geographical concentration and classifes the output by felds and topics. Methods We queried PubMed, Scopus and the Web of Science for documents published between 1999 and 2019, excluding clinical trials and medical case reports. Documents were analyzed according to their titles, abstracts and keywords and were classifed to assisted reproductive felds and by Topic Modeling. We analyzed geographic distribution. Results Research output increased nearly tenfold. We show a trend towards decentralization of research, although at a slower rate compared with clinical assisted reproduction research. While the U.S. and the U.K.’s share has dropped, North America and Western Europe are still responsible for more than 70%, while China and Japan had limited participation in the global discussion. Fertility preservation and surrogacy have emerged as the most researched categories, while research about genetics was less prominent. Conclusions We call to enrich researchers’ perspectives by addressing local issues in ways that are tailored to local cultural values, social and economic contexts, and diferently structured healthcare systems. Researchers from wealthy centers should conduct international research, focusing on less explored regions and topics. More research on fnancial issues and access is required, especially regarding regions with limited public fundin

Mapping Climate Change Research via Open Repositories & AI: advantages and limitations for an evidence-based R&D policy-making

In the last few years, several initiatives have been starting to offer access to research outputs data and metadata in an open fashion. The platforms developed by those initiatives are opening up scientific production to the wider public and they can be an invaluable asset for evidence-based policy-making in Science, Technology and Innovation (STI). These resources can indeed facilitate knowledge discovery and help identify available R&D assets and relevant actors within specific research niches of interest. Ideally, to gain a comprehensive view of entire STI ecosystems, the information provided by each of these resources should be combined and analysed accordingly. To ensure so, at least a certain degree of interoperability should be guaranteed across data sources, so that data could be better aggregated and complemented and that evidence provided towards policy-making is more complete and reliable. Here, we study whether this is the case for the case of mapping Climate Action research in the whole Denmark STI ecosystem, by using 4 popular open access STI data sources, namely OpenAire, Open Alex, CORDIS and Kohesio.Comment: This is an extended version of paper 10.1007/978-3-031-16802-4_52, which was accepted at the International Conference on Theory and Practice of Digital Libraries (TPDL) 2022. arXiv admin note: text overlap with arXiv:2209.0892

V-ATPase, a master effector of E2F1-mediated lysosomal trafficking, mTORC1 activation and autophagy

In addition to being a master regulator of cell cycle progression, E2F1 regulates other associated biological processes, including growth and malignancy. Here, we uncover a regulatory network linking E2F1 to lysosomal trafficking and mTORC1 signaling that involves v-ATPase regulation. By immunofluorescence and time-lapse microscopy we found that E2F1 induces the movement of lysosomes to the cell periphery, and that this process is essential for E2F1-induced mTORC1 activation and repression of autophagy. Gain- and loss-of-function experiments reveal that E2F1 regulates v-ATPase activity and inhibition of v-ATPase activity repressed E2F1-induced lysosomal trafficking and mTORC1 activation. Immunoprecipitation experiments demonstrate that E2F1 induces the recruitment of v-ATPase to lysosomal RagB GTPase, suggesting that E2F1 regulates v-ATPase activity by enhancing the association of V0 and V1 v-ATPase complex. Analysis of v-ATPase subunit expression identified B subunit of V0 complex, ATP6V0B, as a transcriptional target of E2F1. Importantly, ATP6V0B ectopic-expression increased v-ATPase and mTORC1 activity, consistent with ATP6V0B being responsible for mediating the effects of E2F1 on both responses. Our findings on lysosomal trafficking, mTORC1 activation and autophagy suppression suggest that pharmacological intervention at the level of v-ATPase may be an efficacious avenue for the treatment of metastatic processes in tumors overexpressing E2F1