Nondeterministic self-assembly of two tile types on a lattice.

Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of important functions in the cell, whereas protein aggregation is the hallmark of a number of diseases and represents a nondeterministic self-assembly process. Here we build on previous work on a lattice model of deterministic self-assembly to investigate nondeterministic self-assembly of single lattice tiles and mixtures of two tiles at varying relative concentrations. Despite limiting the simplicity of the model to two interface types, which results in 13 topologically distinct single tiles and 106 topologically distinct sets of two tiles, we observe a wide variety of concentration-dependent behaviors. Several two-tile sets display critical behaviors in the form of a sharp transition from bound to unbound structures as the relative concentration of one tile to another increases. Other sets exhibit gradual monotonic changes in structural density, or nonmonotonic changes, while again others show no concentration dependence at all. We catalog this extensive range of behaviors and present a model that provides a reasonably good estimate of the critical concentrations for a subset of the critical transitions. In addition, we show that the structures resulting from these tile sets are fractal, with one of two different fractal dimensions.This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by the American Physical Society

Determinism and boundedness of self-assembling structures.

Self-assembly processes are widespread in nature and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the determinism and boundedness of the self-assembly. The former tells us whether the same set of building blocks always generates the same structure, and the latter whether it grows indefinitely. These properties are highly relevant in the context of protein structures, as the difference between deterministic protein self-assembly and nondeterministic protein aggregation is central to a number of diseases. Here we introduce a graph theoretical approach that can determine the determinism and boundedness for several geometries and dimensionalities of self-assembly more accurately and quickly than conventional methods. We apply this methodology to a previously studied lattice self-assembly model and discuss generalizations to a wide range of other self-assembling systems

Nondeterministic self-assembly with asymmetric interactions.

We investigate general properties of nondeterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides insights into the study of diseases caused by protein aggregation.Winton Programme for the Physics of Sustainability, Gates Cambridge, Oppenheimer PhD studentship, NanoDTC Cambridge (Grant ID: EP/L015978/1), Engineering and Physical Sciences Research Council (Grant ID: EP/L504920/1), Royal SocietyThis is the author accepted manuscript. The final version is available from the American Physical Society via http://dx.doi.org/10.1103/PhysRevE.94.02240

Land use change in a pericolonial society: intensification and diversification in Ifugao, Philippines between 1570 and 1800 CE

Land use modelling is increasingly used by archaeologists and palaeoecologists seeking to quantify and compare the changing influence of humans on the environment. In Southeast Asia, the intensification of rice agriculture and the arrival of European colonizers have both been seen as major catalysts for deforestation, soil erosion, and biodiversity change. Here we consider the Tuwali-Ifugao people of the Cordillera Central (Luzon, Philippines), who resisted Spanish colonial subjugation from the 16th to the mid-nineteenth century, in part through the development of a world-renowned system of intensive wet-rice terrace agriculture. To quantify changes in how the Tuwali-Ifugao used their environment, we model land use in Old Kiyyangan Village, a long-inhabited settlement, at two timepoints: circa 1570 CE, prior to the Spanish arrival in Luzon, and circa 1800 CE, before the village was sacked by Spanish military expeditions. Our model demonstrates that between 1570 and 1800 the adoption of rice as a staple and the corresponding expansion in terrace agriculture, along with a general diversification of diet and land use, enabled the village’s population to double without increasing total land use area. Further, this major intensification led to the solidification of social hierarchies and occurred without a proportional increase in deforestation.Introduction Methodology - Models in Ifugao: The History and Socio-Ecology of the Region - The Historical Land Use Model - Model Calculations for OKV - Population and Boble (Settled Area) at OKV - Payo (Terraces) - Uma (Swidden Fields) - Muyong (Private Forests) - Domesticated Animals - Hunting, Foraging, and Fishing - Fuel and Resource Extraction - Commerce - Agricultural Productivity and Nutritional Value - Dietary Proportions Results - 1800 - 1570 - Exploring Social Difference: Kadangyan and Nawotwot Land Use in 1800 Discussio

Year-round multi-scale habitat selection by Crested Tit (Lophophanes cristatus) in lowland mixed forests (northern Italy)

Determining how animals respond to resource availability across spatial and temporal extents is crucial to understand ecological processes underpinning habitat selection. Here, we used a multi-scale approach to study the year-round habitat selection of the Crested Tit (Lophophanes cristatus) in a semi-natural lowland woodland of northern Italy, analysing different habitat features at each scale. We performed Crested Tit censuses at three different spatial scales. At the macrohabitat scale, we used geolocalized observations of individuals to compute Manly's habitat selection index, based on a detailed land-use map of the study area. At the microhabitat scale, the trees features were compared between presence and absence locations. At the foraging habitat scale, individual foraging birds and their specific position on trees were recorded using focal animal sampling. Censuses were performed during both the breeding (March to May) and wintering (December to January) seasons. At the macrohabitat scale, the Crested Tits significantly selected pure and mixed pine forests and avoided woods of alien plant species, farmlands and urban areas. At the microhabitat scale, old pine woods with dense cover were selected, with no significant difference in the features of tree selection between the two phenological phases. At the foraging habitat scale, the species was observed spending more time foraging in the canopies than in the understorey, using mostly the portion of Scots Pine (Pinus sylvestris) canopies closer to the trunk in winter, while during the breeding period, the whole canopy was visited. Overall, breeding and wintering habitats largely overlapped in the Crested Tit. Based on our findings, lowland Crested Tits can be well defined as true habitat specialists: they are strictly related to some specific coniferous woodland features. Noteworthily, compared to other tit species, which normally show generalist habits during winter, the Crested Tit behaves as a habitat specialist also out of the breeding season. Our study stressed the importance of considering multi-scale (both spatial and phenological) habitat selection in birds

Development and Validation of a Reversed-Phase HPLC Method with UV Detection for the Determination of L-Dopa in Vicia faba L. Broad Beans

L-Dopa (LD), a substance used medically in the treatment of Parkinson's disease, is found in several natural products, such as Vicia faba L., also known as broad beans. Due to its low chemical stability, LD analysis in plant matrices requires an appropriate optimization of the chosen analytical method to obtain reliable results. This work proposes an HPLC-UV method, validated according to EURACHEM guidelines as regards linearity, limits of detection and quantification, precision, accuracy, and matrix effect. The LD extraction was studied by evaluating its aqueous stability over 3 months. The best chromatographic conditions were found by systematically testing several C-18 stationary phases and acidic mobile phases. In addition, the assessment of the best storage treatment of Vicia faba L. broad beans able to preserve a high LD content was performed. The best LD determination conditions include sun-drying storage, extraction in HCl 0.1 M, chromatographic separation with a Discovery C-18 column, 250 x 4.6 mm, 5 mu m particle size, and 99% formic acid 0.2% v/v and 1% methanol as the mobile phase. The optimized method proposed here overcomes the problems linked to LD stability and separation, thus contributing to the improvement of its analytical determination

Effect of awake prone position on diaphragmatic thickening fraction in patients assisted by noninvasive ventilation for hypoxemic acute respiratory failure related to novel coronavirus disease

Background: Awake prone position is an emerging rescue therapy applied in patients undergoing noninvasive ventilation (NIV) for acute hypoxemic respiratory failure (ARF) related to novel coronavirus disease (COVID-19). Although applied to stabilize respiratory status, in awake patients, the application of prone position may reduce comfort with a consequent increase in the workload imposed on respiratory muscles. Thus, we primarily ascertained the effect of awake prone position on diaphragmatic thickening fraction, assessed through ultrasound, in COVID-19 patients undergoing NIV. Methods: We enrolled all COVID-19 adult critically ill patients, admitted to intensive care unit (ICU) for hypoxemic ARF and undergoing NIV, deserving of awake prone positioning as a rescue therapy. Exclusion criteria were pregnancy and any contraindication to awake prone position and NIV. On ICU admission, after NIV onset, in supine position, and at 1\ua0h following awake prone position application, diaphragmatic thickening fraction was obtained on the right side. Across all the study phases, NIV was maintained with the same setting present at study entry. Vital signs were monitored throughout the entire study period. Comfort was assessed through numerical rating scale (0 the worst comfort and 10 the highest comfort level). Data were presented in median and 25th\u201375th percentile range. Results: From February to May 2021, 20 patients were enrolled and finally analyzed. Despite peripheral oxygen saturation improvement [96 (94\u201397)% supine vs 98 (96\u201399)% prone, p = 0.008], turning to prone position induced a worsening in comfort score from 7.0 (6.0\u20138.0) to 6.0 (5.0\u20137.0) (p = 0.012) and an increase in diaphragmatic thickening fraction from 33.3 (25.7\u201340.5)% to 41.5 (29.8\u201350.0)% (p = 0.025). Conclusions: In our COVID-19 patients assisted by NIV in ICU, the application of awake prone position improved the oxygenation at the expense of a greater diaphragmatic thickening fraction compared to supine position. Trial registration ClinicalTrials.gov, number NCT04904731. Registered on 05/25/2021, retrospectively registered. https://clinicaltrials.gov/ct2/show/NCT04904731

Does Syphilis Increase the Risk of HIV-RNA Elevation >200 Copies/mL in HIV-Positive Patients Under Effective Antiretroviral Treatment? Data From the ICONA Cohort

BACKGROUND: To assess the impact of syphilis infection on the risk of HIV-RNA elevation in people living with HIV (PLWH) with current HIV-RNA ≤50 copies/mL. SETTING: The Italian Cohort Naïve Antiretrovirals (ICONA). METHODS: All PLWH (2009-2020) under antiretroviral treatment with at least 2 consecutive HIV-RNA values ≤50 copies/mL before the date of syphilis diagnosis and at least one HIV-RNA determination after the syphilis event were enrolled. A control group of PLWH without syphilis was matched for mode of HIV transmission. Outcomes were defined using the first HIV-RNA measure in the time window ranging between -2 and +6 months of the diagnosis/index date. The primary outcome used a single value>200 copies/mL to define HIV-RNA elevation associated with risk of transmission. The association between syphilis infection and the protocol defined outcome was evaluated using logistic regression analysis. RESULTS: Nine hundred and twenty-six PLWH with a syphilis event were enrolled and matched with a random sample of 1370 PLWH without syphilis. Eighteen of the 926 (1.9%) with syphilis had ≥1 HIV-RNA>200 copies/mL in the window vs. 29/1370 (2.1%) of the not exposed (p=0.77). In the multivariable analysis adjusted for age, year of diagnosis/index date and clinical site, syphilis infection was not associated with the risk of HIV-RNA >200 copies/mL [adjusted Odds Ratio 0.81; 95% confidence interval 0.43-1.52, p=0.508]. CONCLUSIONS: We did not find any evidence for an association between syphilis infection and viral elevation >200 copies/mL