Miracle-dz/UniFAR-FTUs huggingface dataset:
Kin recognition in an annual plant

Kin recognition is important in animal social systems. However, though plants often compete with kin, there has been as yet no direct evidence that plants recognize kin in competitive interactions. Here we show in the annual plant Cakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.
Leaf anatomy enables more equal access to light and CO2 between chloroplasts

The function of a leaf is photosynthesis, which requires the interception of light and access to atmospheric CO2 while controlling water loss. This paper examines the influence of leaf anatomy on both light capture and CO2 diffusion. As photosynthetic metabolism is spread between many chloroplasts, a leaf faces the challenge of matching light capture by a given chloroplast with the metabolic capacity of that chloroplast. Chloroplasts nearest the leaf surface receive the greatest irradiance and therefore absorb more light per unit chlorophyll than chloroplasts in the centre of a leaf. Electron transport and carbon fixation capacities per unit of chlorophyll decline with increasing depth in the leaf, to compensate for the decline in light absorbed per unit chlorophyll. Many key photosynthetic protein complexes in chloroplasts have nuclear encoded genetic information. Consequently, all chloroplasts within a given cell have a similar metabolic complement, which limits the potential gradient of photosynthetic capacity per unit chlorophyll across the leaf. A simple model couples light absorption through the leaf (based on the Beer–Lambert law) with the profile of chlorophyll through a leaf and the gradient in photosynthetic capacity. It is validated by comparison with 14CO2 fixation profiles through spinach leaves obtained in various studies. The model can account for published 14C fixation profiles obtained with blue, red and green light of different irradiances and white light applied in different combinations to the adaxial and abaxial surfaces of spinach leaves. The model confirms that spongy mesophyll increases the apparent extinction coefficient of chlorophyll compared to palisade tissue. The palisade tissue nearest the surface which receives light facilitates the penetration of light to a greater depth, while spongy mesophyll promotes scattering to enhance light absorption, thus reducing the gradient in light absorbed per unit chlorophyll through a leaf. CO2 fixation faces a diffusional limitation, which necessitates Rubisco to be spread evenly across the cell walls exposed to intercellular airspace. Mesophyll cell structure reflects the need to have a large cell surface per unit volume exposed to airspaces. The regular array of columnar cells in palisade tissue, or cell lobing in monocot leaves, results in greater exposed surface per unit tissue volume than spongy mesophyll. The exposed surface area per unit leaf area scales with photosynthetic capacity such that the difference in CO2 partial pressure between substomatal cavities and the sites of carboxylation within chloroplasts is, on average, independent of photosynthetic capacity of the leaf. However, Rubisco specific activity declines as the Rubisco content per unit leaf area increases due to greater internal diffusional limitations.
Design for Mood: Twenty Activity-Based Opportunities to Design for Mood Regulation

This paper introduces a theory-based approach to design for mood regulation. The main proposition is that design can best influence mood by enabling and stimulating people to engage in a broad range of mood-regulating activities. The first part of the manuscript reviews state-of-the art mood-focused design research initiatives, grouped into four basic intentions, exploring how technology can measure, express, adapt to, or influence mood. The second part provides a functional explanation of the mood phenomenon, addressing how mood can be described, the function of mood, manifestations of mood, and how mood differs from emotion. The third and final part of the manuscript introduces an overview of novel mood-regulation strategies, and explores how these strategies can inspire design interventions. Twenty activity-based opportunities to design for mood regulation are grouped into three main focal categories: seeking relief, restoring balance, and building resilience.
Influence of epoxy, polytetrafluoroethylene (PTFE) and rhodium surface coatings on surface roughness, nano-mechanical properties and biofilm adhesion of nickel titanium (Ni-Ti) archwires

Aim. To investigate the effect of epoxy, polytetrafluoroethylene (PTFE) and rhodium surface coatings on surface roughness, nano-mechanical properties and biofilm adhesion of nickel titanium (Ni-Ti) archwires Methods. Three different coated (Epoxy, polytetrafluoroethylene (PTFE) and rhodium) and one uncoated Ni-Ti archwires were evaluated in the present study. Surface roughness (Ra) was assessed using a non-contact surface profilometer. The mechanical properties (nano-hardness and elastic modulus) were measured using a nanoindenter. Bacterial adhesion assays were performed using Streptococcus mutans (MS) and streptococcus sobrinus (SS) in an in-vitro set up. The data obtained were analyzed using analyses of variance, Tukey’s post hoc test and Pearson’s correlation coefficient test. Result. The highest Ra values (1.29 ± 0.49) were obtained for epoxy coated wires and lowest Ra values (0.29 ± 0.16) were obtained for the uncoated wires. No significant differences in the Ra values were observed between the rhodium coated and uncoated archwires (P > 0.05). The highest nano-hardness (3.72 ± 0.24) and elastic modulus values (61.15 ± 2.59) were obtained for uncoated archwires and the lowest nano-hardness (0.18 ± 0.10) and elastic modulus values (4.84 ± 0.65) were observed for epoxy coated archwires. No significant differences in nano-hardness and elastic modulus values were observed between the coated archwires (P > 0.05). The adhesion of Streptococcus mutans (MS) to the wires was significantly greater than that of streptococcus sobrinus (SS). The epoxy coated wires demonstrated an increased adhesion of MS and SS and the uncoated wires demonstrated decreased biofilm adhesion. The Spearman correlation test showed that MS and SS adhesion was positively correlated with the surface roughness of the wires. Conclusion. The different surface coatings significantly influence the roughness, nano-mechanical properties and biofilm adhesion parameters of the archwires. The evaluated parameters were most influenced by epoxy coating followed by PTFE and rhodium coating. A positive correlation was detected between surface roughness and biofilm adhesion.
Axial and radial water flow in the trunks of oak trees: a quantitative and qualitative analysis.

Axial water flow in the trunks of mature oak trees (Quercus petraea (Matt.) Liebl. and Q. robur L. ) was studied by four independent techniques: water absorption from a cut trunk, sap flowmeters, heat pulse velocity (HPV) and thermoimaging. Estimation of the total water flow with sap flowmeters, HPV and water absorption yielded comparable results. We concluded from dye colorations, thermograms and axial profiles of sap flow and heat pulse velocity that, in intact trunks, most of the flow occurred in the current-year ring, where early-wood vessels in the outermost ring were still functional. Nevertheless, there was significant flow in the older rings of the xylem. Total water flow through the trunk was only slightly reduced when air embolisms were artificially induced in early-wood vessels, probably because there was little change in hydraulic conductance in the root-leaf sap pathway. Embolization of the current-year vessels reactivated transport in the older rings.
Ubiquity and Diversity of Heterotrophic Bacterial nasA Genes in Diverse Marine Environments

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.
Spatial loading based on channel covariance feedback and channel estimates

Transmission schemes for flat multi-input, multi-output (MIMO) channels are well established for the cases where perfect channel state information or no channel state information is available at the transmitter. However, communication over channels where the transmitter has access to partial or imperfect information has received less attention. If exploited, such information has the potential of improving system performance and reducing the bandwidth requirements of feedback links or the required quality of channel estimates. Herein, a simple design scheme is introduced, that approximately maximizes the data rates of MIMO communication systems where the transmitter has access to partial channel state information in the form of covariance feedback or erroneous channel estimates. An algorithm is presented which is computationally attractive and performance gains are shown when compared to systems not using this information.
Wastewater Irrigation: The State of Play

As demand for fresh water intensifies, wastewater is frequently being seen as a valuable resource. Furthermore, wise reuse of wastewater alleviates concerns attendant with its discharge to the environment. Globally, around 20 million ha of land are irrigated with wastewater, and this is likely to increase markedly during the next few decades as water stress intensifies. In 1995, around 2.3 billion people lived in water‐stressed river basins and this could increase to 3.5 billion by 2025. We review the current status of wastewater irrigation by providing an overview of the extent of the practice throughout the world and through synthesizing the current understanding of factors influencing sustainable wastewater irrigation. A theme that emerges is that wastewater irrigation is not only more common in water‐stressed regions such as the Near East, but the rationale for the practice also tends to differ between the developing and developed worlds. In developing nations, the prime drivers are livelihood dependence and food security, whereas environmental agendas appear to hold greater sway in the developed world. The following were identified as areas requiring greater understanding for the long‐term sustainability of wastewater irrigation: (i) accumulation of bioavailable forms of heavy metals in soils, (ii) environmental fate of organics in wastewater‐irrigated soils, (iii) influence of reuse schemes on catchment hydrology, including transport of salt loads, (iv) risk models for helminth infections (pertinent to developing nations), (v) microbiological contamination risks for aquifers and surface waters, (vi) transfer efficiencies of chemical contaminants from soil to plants, (vii) health effects of chronic exposure to chemical contaminants, and (viii) strategies for engaging the public.
Impact of Currently Marketed Tampons and Menstrual Cups on Staphylococcus aureus Growth and Toxic Shock Syndrome Toxin 1 Production In Vitro

ABSTRACT Fifteen currently marketed intravaginal protection products (11 types of tampon and 4 types of menstrual cup) were tested by the modified tampon sac method to determine their effect on Staphylococcus aureus growth and toxic shock syndrome toxin 1 (TSST-1) production. Most tampons reduced S. aureus growth and TSST-1 production, with differences based on brand and composition, and the level of S. aureus growth was higher in destructured than in unaltered tampons. We observed higher levels of S. aureus growth and toxin production in menstrual cups than in tampons, potentially due to the additional air introduced into the bag by cups, with differences based on cup composition and size. IMPORTANCE Menstrual toxic shock syndrome is a rare but severe disease. It occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock syndrome toxin 1 using intravaginal protection, such as tampons or menstrual cups. Intravaginal protection induces TSS by the collection of catamenial products, which act as a growth medium for S. aureus. Previous studies evaluated the impact of tampon composition on S. aureus producing toxic shock syndrome toxin 1, but they are not recent and did not include menstrual cups. This study demonstrates that highly reproducible results for S. aureus growth and TSST-1 production can be obtained by using a simple protocol that reproduces the physiological conditions of tampon and cup usage as closely as possible, providing recommendations for tampon or cup use to both manufacturers and consumers. Notably, our results do not show that menstrual cups are safer than tampons and suggest that they require similar precautions.
Influence of structure of grain boundaries and size distribution of grains on the yield strength at quasistatic and dynamical loading

Dependences of the yield strength of metals on the grain size and the dispersion of the grain size are discussed for quasistatic and dynamic conditions of loading. In these two cases, the size distribution of grains influences differently on the slope of the Hall–Petch curve. The presence of wide size distribution of grains shifts the maximal yield strength to smaller grains, which can obstruct an observation of the inverse Hall–Petch effect. According to our analyses, the role of the grain boundary structure is significant both at low strain rate in the coarse-grained materials and at high strain rate in the fine-grained materials.
Modeling and Estimation of Cardiorespiratory Function, with Application to Mechanical Ventilation

Modeling and Estimation of Cardiorespiratory Function, with Application to Mechanical Ventilation Nikolaos Karamolegkos Evidence-based medicine is at the heart of current medical practice where clinical decisions are driven by research data. However, most current therapy recommendations follow generalized protocols and guidelines that are based on epidemiological (population) studies and thus not suited for the individual patient’s demands. Patient-tailored therapies are considered, hence, an unmet clinical need. We believe that mathematical models of the physiology can attend to such a clinical need, because they can be tuned to the individual patient. Such models provide a sound mathematical framework for personalized clinical decisions. In particular, physiological models in medicine can serve the following two purposes: 1) They can be an efficient tool to quantify cardiopulmonary dynamics, conduct virtual clinical/physiological experiments, and investigate the effects of specific treatments. 2) Model-based estimation techniques can assess physiological parameters or variables, which are otherwise impractical or dangerous to measure; they can effectively tune a generic model to become patient-specific, able to mimic the behavior of a particular patient. In this thesis, we propose a series of modifications to a previously developed cardiopulmonary model (CP Model) in order to better replicate heart-lung interaction phenomena that are typically observed under mechanical ventilation, hence allowing for a more accurate analysis of ventilation-induced changes in cardiac function. The response of this modified model is validated with experimental data collected during mechanical ventilation conditions. Further, as an industrial application of mathematical models, we present a patient emulator system that comprises the modified CP Model, a physical ventilator, and a piston-cylinder arrangement that serves as an electrical-to-hydraulic transducer. The modified CP Model then serves as the virtual patient that is being ventilated, where disease conditions can be instilled. Such a system is designed to offer a well-controlled experimental environment for ventilator manufacturers to efficaciously test and compare ventilation modalities and therapies, thereby enhancing their verification and validation manufacturing processes. Finally, we develop a model-based approach to estimate (noninvasively) the function of the cardiovascular system, in terms of cardiac performance (i.e., cardiac output) and the dynamics of the systemic arterial tree (i.e., time constant). With this technique, we envision to provide continuous and real-time bedside monitoring of changes in cardiovascular function, such as those induced by changes in ventilator settings.
CFD Characterization of a Wet Foam Flow Rheological Behavior

In some industrial processes, aqueous foams flow presents an important phase of the process, whereas, they cause pressure drop when designing and dimensioning systems. Identifying the different rheological parameters of foam flow is an interest key to understanding the interfacial phenomena. Actually, the difficulty to model the rheological parameters of foam flow is a major challenge. In this study, we present a robust model to describe the foam fluid inside horizontal channels by the reverse approach of a numerical simulation (Computational Fluid Dynamics: CFD), based on the behavior laws of the Herschel-Bulkley type, for the non-Newtonian fluids. This reverse method starts from experimental (deduced from Particle Image Velocimetry (PIV) technique) results of the previous experimental work of Chovet (2015). The pressure losses measurements near-wall velocity fields, velocity profiles and the wall shear stress evolution including the void fraction from 55% to 85%, are considered in order to identify the different parameters of the developed model to determine the nature of the flow, the foams rheological behavior and the foam flow regime along the length of the channel. The numerical study (CFD) is applied for two conditions: the first one for a wet foam flow with a void fraction of 70% and a foam flow velocity of 2cm/s (one-dimensional regime) and the second one, for a foam quality of 55% and a flow rate of 6cm/s. The numerical evolutions are identical to experimental ones for these same conditions. Therefore, we can conclude that the Herschel-Bulkley rheological model can correctly describe the aqueous foams fix behavior.
A protein phosphorylation/dephosphorylation network regulates a plant potassium channel

Potassium (K+) is an essential nutrient for plant growth and development. Plants often adapt to low K+ conditions by increasing their K+ uptake capability. Recent studies have led to the identification of a calcium signaling pathway that enables plants to act in this capacity. Calcium is linked to two calcineurin B-like calcium sensors (CBLs) and a target kinase (CBL-interacting protein kinase 23 or CIPK23) that, in turn, appears to phosphorylate and activate the potassium channel, Arabidopsis K+ transporter 1 (AKT1), responsible for K+ uptake in roots. Here, we report evidence that this regulatory mechanism is more elaborate than earlier envisaged. The recently described pathway is part of an extensive network whereby several CBLs interact with multiple CIPKs in the activation of the potassium channel, AKT1. The physical interactions among the CBL, CIPK, and AKT1 components provide a mechanism for specifying the members of the CBL and CIPK families functional in AKT1 regulation. The interaction between the CIPKs and AKT1 was found to involve the kinase domain of the CIPK component and the ankyrin repeat domain of the channel. Furthermore, we identified a 2C-type protein phosphatase that physically interacts and inactivates the AKT1 channel. These findings provide evidence that the calcium-sensitive CBL and CIPK families together with 2C-type protein phosphatases form a protein phoshporylation/dephosphorylation network that regulates the AKT1 channel for K+ transport in plants.
Aposematism increases acoustic diversification and speciation in poison frogs

Multimodal signals facilitate communication with conspecifics during courtship, but they can also alert eavesdropper predators. Hence, signallers face two pressures: enticing partners to mate and avoiding detection by enemies. Undefended organisms with limited escape abilities are expected to minimize predator recognition over mate attraction by limiting or modifying their signalling. Alternatively, organisms with anti-predator mechanisms such as aposematism (i.e. unprofitability signalled by warning cues) might elaborate mating signals as a consequence of reduced predation. We hypothesize that calls diversified in association with aposematism. To test this, we assembled a large acoustic signal database for a diurnal lineage of aposematic and cryptic/non-defended taxa, the poison frogs. First, we showed that aposematic and non-aposematic species share similar extinction rates, and aposematic lineages diversify more and rarely revert to the non-aposematic phenotype. We then characterized mating calls based on morphological (spectral), behavioural/physiological (temporal) and environmental traits. Of these, only spectral and temporal features were associated with aposematism. We propose that with the evolution of anti-predator defences, reduced predation facilitated the diversification of vocal signals, which then became elaborated or showy via sexual selection.