Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Editorial: On Poverty and Its Eradication

The Research Topic "On poverty and its eradication" was inspired by the International Day for the Eradication of Poverty, first commemorated in Paris in 1987 and formally designated by the United Nations. This day is dedicated to renewing the commitment to universal human development, enabling all individuals to achieve their highest potential, and reflecting on how poverty hinders this progress. The urgency of addressing poverty has increased after the COVID-19 pandemic, which exacerbated existing issues and highlighted the critical need for effective poverty eradication strategies. The studies included in this Research Topic aim to expand knowledge about poverty, its causes, consequences, and connections to crises, inequality, and fairness, and to assess policy measures for poverty reduction. The included contributions use various theoretical, empirical, quantitative, and qualitative approaches to drive sociological and policy-related discussions and initiatives, promoting fair and inclusive societies

Spinal epidural abscess: a rare complication of olecranon bursitis

Spinal epidural abscess is a rare but potentially fatal condition if left untreated. We report the case of a 67-year old man who presented to the Accident and Emergency department complaining of acute onset of inter-scapular back pain, left leg weakness and loss of sensation in the left foot. On examination he was found to be pyrexial with long tract signs in the left lower leg. In addition he had a left sided olecranon bursitis of three weeks duration. Blood tests revealed raised inflammatory markers and a staphylococcal bacteremia. Magnetic resonance imaging (MRI) confirmed the diagnosis of spinal epidural abscess and he subsequently underwent a three level laminectomy with good resolution of his back pain and neurological symptoms. He has made a complete recovery with a prolonged course of intravenous antibiotics

The suitability of the IEC 61400-2 wind model for small wind turbines operating in the built environment

This paper investigates the applicability of the assumed wind fields in International Electrotechnical Commission (IEC) standard 61400 Part 2, the design standard for small wind turbines, for a turbine operating in the built environment, and the effects these wind fields have on the predicted performance of a 5 kW Aerogenesis turbine using detailed aeroelastic models developed in Fatigue Aerodynamics Structures and Turbulence (FAST). Detailed wind measurements were acquired at two built environment sites: from the rooftop of a Bunnings Ltd. warehouse at Port Kennedy (PK) (Perth, Australia) and from the small wind turbine site at the University of Newcastle at Callaghan (Newcastle, Australia). For both sites, IEC 61400-2 underestimates the turbulence intensity for the majority of the measured wind speeds. A detailed aeroelastic model was built in FAST using the assumed wind field from IEC 61400-2 and the measured wind fields from PK and Callaghan as an input to predict key turbine performance parameters. The results of this analysis show a modest increase in the predicted mean power for the higher turbulence regimes of PK and Callaghan as well as higher variation in output power. Predicted mean rotor thrust and blade flapwise loading showed a minor increase due to higher turbulence, with mean predicted torque almost identical but with increased variations due to higher turbulence. Damage equivalent loading for the blade flapwise moment was predicted to be 58% and 11% higher for a turbine operating at Callaghan and PK respectively, when compared with IEC 61400-2 wind field. Time series plots for blade flapwise moments and power spectral density plots in the frequency domain show consistently higher blade flapwise bending moments for the Callaghan site with both the sites showing a once-per-revolution response

Enabled Negatively Regulates Diaphanous-Driven Actin Dynamics In Vitro and In Vivo

Actin regulators facilitate cell migration by controlling cell protrusion architecture and dynamics. As the behavior of individual actin regulators becomes clear, we must address why cells require multiple regulators with similar functions and how they cooperate to create diverse protrusions. We characterized Diaphanous (Dia) and Enabled (Ena) as a model, using complementary approaches: cell culture, biophysical analysis, and Drosophila morphogenesis. We found that Dia and Ena have distinct biochemical properties that contribute to the different protrusion morphologies each induces. Dia is a more processive, faster elongator, paralleling the long, stable filopodia it induces in vivo, while Ena promotes filopodia with more dynamic changes in number, length, and lifetime. Acting together, Ena and Dia induce protrusions distinct from those induced by either alone, with Ena reducing Dia-driven protrusion length and number. Consistent with this, EnaEVH1 binds Dia directly and inhibits DiaFH1FH2-mediated nucleation in vitro. Finally, Ena rescues hemocyte migration defects caused by activated Dia

Responsible agriculture must adapt to the wetland character of mid‐latitude peatlands

Drained, lowland agricultural peatlands are greenhouse gas (GHG) emission hotspots and a large but vulnerable store of irrecoverable carbon. They exhibit soil loss rates of ~2.0 cm yr−1 and are estimated to account for 32% of global cropland emissions while producing only 1.1% of crop kilocalories. Carbon dioxide emissions account for >80% of their terrestrial GHG emissions and are largely controlled by water table depth. Reducing drainage depths is, therefore, essential for responsible peatland management. Peatland restoration can substantially reduce emissions. However, this may conflict with societal needs to maintain productive use, to protect food security and livelihoods. Wetland agriculture strategies will, therefore, be required to adapt agriculture to the wetland character of peatlands, and balance GHG mitigation against productivity, where halting emissions is not immediately possible. Paludiculture may substantially reduce GHG emissions but will not always be viable in the current economic landscape. Reduced drainage intensity systems may deliver partial reductions in the rate of emissions, with smaller modifications to existing systems. These compromise systems may face fewer hurdles to adoption and minimize environmental harm until societal conditions favour strategies that can halt emissions. Wetland agriculture will face agronomic, socio-economic and water management challenges, and careful implementation will be required. Diversity of values and priorities among stakeholders creates the potential for conflict. Successful implementation will require participatory research approaches and co-creation of workable solutions. Policymakers, private sector funders and researchers have key roles to play but adoption risks would fall predominantly on land managers. Development of a robust wetland agriculture paradigm is essential to deliver resilient production systems and wider environmental benefits. The challenge of responsible use presents an opportunity to rethink peatland management and create thriving, innovative and green wetland landscapes for everyone's future benefit, while making a vital contribution to global climate change mitigation

Modeling phase behavior for quantifying micro-pervaporation experiments

We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS membrane to build up a solute concentration profile inside a long microfluidic channel. We simplify the evolution of this profile in binary mixtures to a one-dimensional model which comprises two concentration-dependent coefficients. The model then provides a link between directly accessible experimental observations, such as the widths of dense phases or their growth velocity, and the underlying chemical potentials and phenomenological coefficients. It shall thus be useful for quantifying the thermodynamic and dynamic properties of dilute and dense binary mixtures.Comment: to be published in EPJ-

Genomic and transcriptional analysis of protein heterogeneity of the honeybee venom allergen Api m 6

Several components of honeybee venom are known to cause allergenic responses in humans and other vertebrates. One such component, the minor allergen Api m 6, has been known to show amino acid variation but the genetic mechanism for this variation is unknown. Here we show that Api m 6 is derived from a single locus, and that substantial protein-level variation has a simple genome-level cause, without the need to invoke multiple loci or alternatively spliced exons. Api m 6 sits near a misassembled section of the honeybee genome sequence, and we propose that a substantial number of indels at and near Api m 6 might be the root cause of this misassembly. We suggest that genes such as Api m 6 with coding-region or untranslated region indels might have had a strong effect on the assembly of this draft of the honeybee genome

Upper estimate of martingale dimension for self-similar fractals

We study upper estimates of the martingale dimension $d_m$ of diffusion processes associated with strong local Dirichlet forms. By applying a general strategy to self-similar Dirichlet forms on self-similar fractals, we prove that $d_m=1$ for natural diffusions on post-critically finite self-similar sets and that $d_m$ is dominated by the spectral dimension for the Brownian motion on Sierpinski carpets.Comment: 49 pages, 7 figures; minor revision with adding a referenc