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OPTIMISING SAMPLE PREPARATION FOR MASS SPECTOMETRY PROTEOMIC BIOMARKER DISCOVERY IN SYNOVIAL FLUID
No full textRefining asymptotic complexity bounds for nonconvex optimization methods, including why steepest descent is o(eps^{-2}) rather than O(eps^{-2})
Get PDFWe revisit the standard ``telescoping sum'' argument ubiquitous in the final steps of analyzing evaluation complexity of algorithms for smooth nonconvex optimization, and obtain a refined formulation of the resulting bound as a function of the requested accuracy eps. While bounds obtained using the standard argument typically are of the form O(eps^{-\alpha}) for some positive alpha, the refined results are of the form o(eps^{-\alpha}). We then explore to which known algorithms our refined bounds are applicable and finally describe an example showing how close the standard and refined bounds can be
European mammal turnover driven by a global rapid warming event preceding the Paleocene–Eocene Thermal Maximum
No full textA brief global warming event known as the Pre-Onset Excursion (POE) occurred just before the Paleocene–Eocene Thermal Maximum (PETM, 56 Mya). The deconvolution of the evolutionary consequences of these two hyperthermal events is puzzling because of their close temporal proximity and the lack of comprehensive, well-calibrated paleontological records, especially in terrestrial environments. As a consequence, the impact of the POE on mammalian evolution and its role in shaping PETM faunas remains unclear. Here, we report from France a mammalian fauna, named Albas, which is interpreted to postdate the POE and predate the PETM. The absence of artiodactyls, perissodactyls, and euprimates at Albas lends support to the controversial hypothesis that these “modern” mammal groups appeared in the European fossil record during the PETM. In contrast, Albas yielded the European first definitive Paleocene record of metatherians, paromomyid primates, “creodonts,” and rodents, challenging the assumption that these groups migrated into Europe during the PETM. Because the majority of them originated from North American pre-POE species, we tentatively suggest that these “precursor” dispersers entered Europe during the POE. Similar to the modern orders during the PETM, these “precursor” dispersers likely entered Europe through corridors in the continuous evergreen forest belt at high latitudes. Our findings highlight how a brief warming event in the Arctic during the latest Paleocene, such as the POE (which could result in a release of carbon into the atmosphere similar to cumulative ongoing anthropogenic emissions), significantly influenced the evolutionary dynamics of European mammals.</p
A Network History of Historical Network Analysis:Using a Citation Network to Explore Historiography
No full textTamL is a Key Player of the Outer Membrane Homeostasis in Bacteroidota
Get PDFIn Proteobacteria, the outer membrane protein TamA and the inner membrane-anchored protein TamB form the Translocation and Assembly Module (TAM) complex, which facilitates the transport of autotransporters, virulence factors, and likely lipids across the two membranes. In Bacteroidota, TamA is replaced by TamL, a TamA-like lipoprotein with a lipid modification at its N-terminus that likely anchors it to the outer membrane. This structural difference suggests that TamL may have a distinct function compared to TamA. However, the role of TAM in bacterial phyla other than Proteobacteria remains unexplored. Our study aimed to elucidate the function of TamL in Flavobacterium johnsoniae, an environmental Bacteroidota. Unlike its homologs in Proteobacteria, we found that TamL and TamB are essential in F. johnsoniae. Through genetic, phenotypic, proteomic, and lipidomic analyses, we show that TamL depletion severely compromises outer membrane integrity, as evidenced by reduced cell viability, altered cell shape, increased susceptibility to membrane-disrupting agents, and elevated levels of outer membrane lipoproteins. Notably, we did not observe an overall decrease in the levels of β-barrel outer membrane proteins, nor substantial alterations in outer membrane lipid composition. By pull-down assays, we found TamL co-purifying with TamB in F. johnsoniae, suggesting an interaction. Furthermore, we found that while TamL and TamB monocistronic genes are conserved among Bacteroidota, only some species encode multiple TamL, TamB and TamA proteins. To our knowledge, this study is the first to provide functional insights into a TAM subunit beyond Proteobacteria.</p
Higher-order Laplacian renormalization
No full textThe renormalization group is a pillar of the theory of scaling, scale invariance and universality in physics. Recently, this tool has been adapted to complex networks with pairwise interactions through a scheme based on diffusion dynamics. However, as the importance of polyadic interactions in complex systems becomes more evident, there is a pressing need to extend the renormalization group methods to higher-order networks. Here we fill this gap and propose a Laplacian renormalization group scheme for arbitrary higher-order networks. At the heart of our approach is the introduction of cross-order Laplacians, which generalize existing higher-order Laplacians by allowing the description of diffusion processes that can happen on hyperedges of any order via hyperedges of any other order. This approach enables us to probe higher-order structures, define scale invariance at various orders and propose a coarse-graining scheme. We validate our approach on controlled synthetic higher-order systems and then use it to detect the presence of order-specific scale-invariant profiles of real-world complex systems from multiple domains.</p
Pharmaceutical pollution influences river-to-sea migration in Atlantic salmon (Salmo salar)
No full textDespite the growing threat of pharmaceutical pollution, we lack an understanding of whether and how such pollutants influence animal behavior in the wild. Using laboratory- and field-based experiments across multiple years in Atlantic salmon (Salmo salar; n = 730), we show that the globally detected anxiolytic pollutant clobazam accumulates in the brain of exposed fish and influences river-to-sea migration success. Clobazam exposure increased the speed with which fish passed through two hydropower dams along their migration route, resulting in more clobazam-exposed fish reaching the sea compared with controls. We argue that such effects may arise from altered shoaling behavior in fish exposed to clobazam. Drug-induced behavioral changes are expected to have wide-ranging consequences for the ecology and evolution of wild populations
