Miracle-dz/UniFAR-FTUs huggingface dataset:
Plastic pollution in croplands threatens long‐term food security

Plastic pollution is a global concern given its prevalence in aquatic and terrestrial ecosystems. Studies have been conducted on the distribution and impact of plastic pollution in marine ecosystems, but little is known on terrestrial ecosystems. Plastic mulch has been widely used to increase crop yields worldwide, yet the impact of plastic residues in cropland soils to soil health and crop production in the long term remained unclear. In this paper, using a global meta‐analysis, we found that the use of plastic mulch can indeed increase crop yields on average by 25%–42% in the immediate season due to the increase of soil temperature (+8%) and moisture (+17%). However, the unabated accumulation of film residues in the field negatively impacts its physicochemical properties linked to healthy soil and threatens food production in the long term. It has multiple negative impacts on plant growth including crop yield (at the mean rate of −3% for every additional 100 kg/ha of film residue), plant height (−2%) and root weight (−5%), and soil properties including soil water evaporation capacity (−2%), soil water infiltration rate (−8%), soil organic matter (−0.8%) and soil available phosphorus (−5%) based on meta‐regression. Using a nationwide field survey of China, the largest user of plastic mulch worldwide, we found that plastic residue accumulation in cropland soils has reached 550,800 tonnes, with an estimated 6%–10% reduction in cotton yield in some polluted sites based on current level of plastic residue content. Immediate actions should be taken to ensure the recovery of plastic film mulch and limit further increase in film residue loading to maintain the sustainability of these croplands.
Effect of different molecular weight PLGA on flurbiprofen nanoparticles: formulation, characterization, cytotoxicity, and in vivo anti-inflammatory effect by using HET-CAM assay

Abstract Objective: The effect of polymers used in nanoparticle (NP) production on the formulation properties is one of the few studied issues. Therefore, this study aims to formulate flurbiprofen (FLB) loaded NPs with different molecular weight (Mw) poly lactic-co-glycolic acid (PLGA) and investigate the effect of Mw on NP character. One of the most important objectives is to provide a high anti-inflammatory effect with a low dose and the anti-inflammatory efficacy of the selected optimal formulation is to be determined by in vivo hen’s egg test on Chorioallantoic Membrane (HET-CAM) analysis that a new, popular and in vivo animal experiment alternative method. Significance: To determine the anti-inflammatory efficacy of the optimum formulation by HET-CAM analysis. To the best of our knowledge, this is the first report on the in vivo anti-inflammatory evaluation of FLB-loaded PLGA NP using the in vivo HET-CAM assay. Methods: Blank and FLB-loaded PLGA NPs were prepared using a nanoprecipitation technique. The cell viability test for all formulation was performed with MTT in the NIH-3T3 mouse embryonic fibroblast cell line. The anti-inflammatory activity of optimum formulation (A6) was examined using the in vivo HET-CAM assay. Results: The particle sizes (PSs) of the FLB-loaded PLGA NPs were between 175 and 198 nm. The encapsulation efficiency (EE%) was a range of 82–93%. In vitro release of NPs showed extended-release up to 144 h. The release kinetics were fitted to the Peppas–Sahlin and Weibull models. The results showed that PS, PDI, EE%, and release rates of NPs were directly related to the Mw of PLGA. There is no statistically significant difference in cell viability study was observed between blank and FLB-loaded PLGA NPs. The in vivo anti-inflammatory activity results indicated that A6 coded formulation was showed significantly good anti-inflammatory potential at low dose. Conclusions: It could be concluded that FLB-loaded NPs seem to be a promising extended-release drug delivery system for oral administration with a low dose and high efficiency.
Ex vivo antioxidant preconditioning improves the survival rate of bone marrow stem cells in the presence of wound fluid

The advancement of autologous mesenchymal stem cell (MSC) therapy for the treatment of non‐healing diabetic wounds is hampered by endogenous MSC dysfunction and limited viability of cells post‐transplantation into the pathological wound environment. The development of effective strategies to restore the functional capabilities of these impaired MSCs prior to transplantation may be a key to their ultimate success as wound repair mediators. The current study therefore investigated whether antioxidant preconditioning [7.5 mM N‐acetylcysteine (NAC) + 0.6 mM ascorbic 2‐phosphate (AAP)] could restore the growth rate, migration ability and viability of impaired MSCs and whether this restored state is maintained in the presence of diabetic wound fluid (DWF). Healthy control (source: wild type, C57BL/6J mice) (n = 12) and impaired/diabetic MSCs (source: obese prediabetic, B6.Cg‐Lepob/J mice) (n = 12) were isolated from the bone marrow of mice. Treatment groups post‐isolation were as follow: (a) No treatment (baseline phenotype): MSCs expanded in standard growth media (SGM) (±8 days) and only exposed to growth media. (b) DWF (baseline response): MSCs expanded in SGM (±8 days) followed by exposure to DWF (24 hours, 48 hours, 96 hours). (c) Antioxidant preconditioning (preconditioned phenotype): MSCs expanded in the presence of NAC/AAP (±8 days). (d) Antioxidant preconditioning + DWF (preconditioned response): MSCs expanded in the presence of NAC/AAP (±8 days) followed by exposure to DWF (24 hours, 48 hours, 96 hours). The results demonstrated that expansion of MSCs (both healthy control and impaired diabetic) in the presence of combined NAC/AAP treatment improved ex vivo MSC viability and protected MSCs in the presence of DWF. Despite improved viability, AAP/NAC could however not rescue the reduced proliferation and migration capacity of impaired diabetic MSCs. The protective effect of NAC/AAP preconditioning against the toxicity of DWF could however be a potential strategy to improve cell number post‐transplantation.
Mechanical roles of anterograde and retrograde intestinal peristalses after feeding in a larval fish (Danio rerio).

Transport in gut is important not only for digestion, metabolism and nutrient uptake but also for microbiotic circumstance in the digestive tract, however, the effects of mixing and pumping in the intestine have not been fully clarified. Therefore, in this study, we quantitatively explored intestinal mixing and pumping represented using a dispersion coefficient and pressure rise in zebrafish larvae, which is a model organism for vertebrate digestive studies, over time by measuring transport phenomena after feeding. Here we provide the first quantitative evidence of the roles of anterograde and retrograde intestinal peristalses in the larval fish of Danio rerio after feeding in terms of digestive pumping and mixing functions by an in vivo imaging of intestinal propagation waves in the larval intestine. Peristaltic velocities in the anterior and posterior intestines change considerably after feeding for 5 hours, while the intervals and amplitudes remain almost constant. The intestinal transport is successively visualized after feeding to elimination. Moreover, the particle tracking velocimetry in the chyme leads our quantitative understanding of outstanding mixing and pumping functions in the anterior and posterior intestines by adopting physical parameters of diffusivity and pressure rise, respectively. From scaling analysis, we found that the anterior intestine maintains mixing for 5 hours from feeding, whereas the posterior intestine activates gradually pumping up. These results suggest that time change of pumping and mixing functions of intestinal peristalsis could considerably influence the nutrient uptake and microbiotic circumstance in the larval fish intestine.
Reduction by Lie Group Symmetries in Diffeomorphic Image Registration and Deformation Modelling

We survey the role of reduction by symmetry in the large deformation diffeomorphic metric mapping framework for registration of a variety of data types (landmarks, curves, surfaces, images and higher-order derivative data). Particle relabelling symmetry allows the equations of motion to be reduced to the Lie algebra allowing the equations to be written purely in terms of the Eulerian velocity field. As a second use of symmetry, the infinite dimensional problem of finding correspondences between objects can be reduced for a range of concrete data types, resulting in compact representations of shape and spatial structure. Using reduction by symmetry, we describe these models in a common theoretical framework that draws on links between the registration problem and geometric mechanics. We outline these constructions and further cases where reduction by symmetry promises new approaches to the registration of complex data types.
Temporal lags in observed and dark diversity in the Anthropocene

Understanding biodiversity changes in the Anthropocene (e.g. due to climate and land‐use change) is an urgent ecological issue. This important task is challenging because global change effects and species responses are dependent on the spatial scales considered. Furthermore, responses are often not immediate. However, both scale and time delay issues can be tackled when, at each study site, we consider dynamics in both observed and dark diversity. Dark diversity includes those species in the region that can potentially establish and thrive in the local sites’ conditions but are currently locally absent. Effectively, dark diversity connects biodiversity at the study site to the regional scales and defines the site‐specific species pool (observed and dark diversity together). With dark diversity, it is possible to decompose species gains and losses into two space‐related components: one associated with local dynamics (species moving from observed to dark diversity and vice versa) and another related to gains and losses of site‐specific species pool (species moving to and from the pool after regional immigration, regional extinction or change in local ecological conditions). Extinction debt and immigration credit are useful to understand dynamics in observed diversity, but delays might happen in species pool changes as well. In this opinion piece we suggest that considering both observed and dark diversity and their temporal dynamics provides a deeper understanding of biodiversity changes. Considering both observed and dark diversity creates opportunities to improve conservation by allowing to identify species that are likely to go regionally extinct as well as foreseeing which of the species that newly arrive to the region are more likely to colonize local sites. Finally, by considering temporal lags and species gains and losses in observed and dark diversity, we combine phenomena at both spatial and temporal scales, providing a novel tool to examine biodiversity change in the Anthropocene.
Screening Assay Protocols Targeting the Nav1.7 Channel Using Qube High‐Throughput Automated Patch‐Clamp System

This article describes the basic procedure for setting up the screening protocol and recording data for Nav1.7 on a Qube automated patch‐clamp system. Three protocols along with step‐by‐step details are provided. First, we describe a protocol to estimate Vhalf, the voltage at which half of the channels are inactivated, using traditional steady‐state inactivation measurement as well as a new adaptive online estimation. Second, we establish a state‐dependent protocol using adaptive online Vhalf measurement to obtain a concentration response curve (CRC) on known reference blockers. Last, we introduce a use‐dependent protocol. In our hands, the sample reference demonstrated good state‐ and use‐dependent inhibition of Nav1.7. © 2020 by John Wiley & Sons, Inc.
The sequence and thresholds of leaf hydraulic traits underlying grapevine varietal differences in drought tolerance

Abstract Adapting agriculture to climate change is driving the need for the selection and breeding of drought-tolerant crops. The aim of this study was to identify key drought tolerance traits and determine the sequence of their water potential thresholds across three grapevine cultivars with contrasting water use behaviors, Grenache, Syrah, and Semillon. We quantified differences in water use between cultivars and combined this with the determination of other leaf-level traits (e.g. leaf turgor loss point, π TLP), leaf vulnerability to embolism (P50), and the hydraulic safety margin (HSM P50). Semillon exhibited the highest maximum transpiration (Emax), and lowest sensitivity of canopy stomatal conductance (Gc) to vapor pressure deficit (VPD), followed by Syrah and Grenache. Increasing Emax was correlated with more negative water potential at which stomata close (Pgs90), π TLP, and P50, suggesting that increasing water use is associated with hydraulic traits allowing gas exchange under more negative water potentials. Nevertheless, all the cultivars closed their stomata prior to leaf embolism formation. Modeling simulations demonstrated that despite a narrower HSM, Grenache takes longer to reach thresholds of hydraulic failure due to its conservative water use. This study demonstrates that the relationships between leaf hydraulic traits are complex and interactive, stressing the importance of integrating multiple traits in characterizing drought tolerance.
Nucleus segmentation of cervical cytology images based on multi-scale fuzzy clustering algorithm

ABSTRACT In the screening of cervical cancer cells, accurate identification and segmentation of nucleus in cell images is a key part in the early diagnosis of cervical cancer. Overlapping, uneven staining, poor contrast, and other reasons present challenges to cervical nucleus segmentation. We propose a segmentation method for cervical nuclei based on a multi-scale fuzzy clustering algorithm, which segments cervical cell clump images at different scales. We adopt a novel interesting degree based on area prior to measure the interesting degree of the node. The application of these two methods not only solves the problem of selecting the categories number of the clustering algorithm but also greatly improves the nucleus recognition performance. The method is evaluated by the IBSI2014 and IBSI2015 public datasets. Experiments show that the proposed algorithm has greater advantages than the state-of-the-art cervical nucleus segmentation algorithms and accomplishes high accuracy nucleus segmentation results. Graphical abstract
RpoN1 and RpoN2 play different regulatory roles in virulence traits, flagellar biosynthesis, and basal metabolism in Xanthomonas campestris

Abstract Homologous regulatory factors are widely present in bacteria, but whether homologous regulators synergistically or differentially regulate different biological functions remains mostly unknown. Here, we report that the homologous regulators RpoN1 and RpoN2 of the plant pathogen Xanthomonas campestris pv. campestris (Xcc) play different regulatory roles with respect to virulence traits, flagellar biosynthesis, and basal metabolism. RpoN2 directly regulated Xcc fliC and fliQ to modulate flagellar synthesis in X. campestris, thus affecting the swimming motility of X. campestris. Mutation of rpoN2 resulted in reduced production of biofilms and extracellular polysaccharides in Xcc. These defects may together cause reduced virulence of the rpoN2 mutant against the host plant. Moreover, we demonstrated that RpoN1 could regulate branched‐chain fatty acid production and modulate the synthesis of diffusible signal factor family quorum sensing signals. Although RpoN1 and RpoN2 are homologues, the regulatory roles and biological functions of these proteins were not interchangeable. Overall, our report provides new insights into the two different molecular roles that form the basis for the transcriptional specialization of RpoN homologues.
Understanding generation and regeneration of pancreatic β cells from a single-cell perspective

ABSTRACT Understanding the mechanisms that underlie the generation and regeneration of β cells is crucial for developing treatments for diabetes. However, traditional research methods, which are based on populations of cells, have limitations for defining the precise processes of β-cell differentiation and trans-differentiation, and the associated regulatory mechanisms. The recent development of single-cell technologies has enabled re-examination of these processes at a single-cell resolution to uncover intermediate cell states, cellular heterogeneity and molecular trajectories of cell fate specification. Here, we review recent advances in understanding β-cell generation and regeneration, in vivo and in vitro, from single-cell technologies, which could provide insights for optimization of diabetes therapy strategies. Summary: This Review summarizes recent advances in the use of single-cell based technologies to understand intermediate cell states, cellular heterogeneity and molecular trajectories of β-cell generation and regeneration.
Off-Label studies on anakinra in dermatology: a review

Abstract Purpose Anakinra (Kineret®) is an interleukin-1 receptor antagonist (IL-1Ra) FDA approved for use in rheumatoid arthritis and in neonatal-onset multisystem inflammatory disease (NOMID). It has been used off-label for a variety of dermatologic conditions. A review of the available studies and cases of these off-label uses would be valuable to the dermatologist considering alternative treatments for these oftentimes poorly studied conditions. Materials and methods The PubMed/MEDLINE, EMBASE, Scopus, and ClinicalTrials.gov databases were searched with the term ‘anakinra. ’ Results were manually screened to identify published data on off-label uses of anakinra in dermatologic conditions and systemic conditions with prominent dermatologic manifestations. Results Anakinra appears to show efficacy for numerous dermatologic conditions, with the strongest evidence for hidradenitis suppurativa, Bechet’s disease, Muckle-Wells syndrome, and SAPHO syndrome. Case reports and case series data are available for numerous other dermatologic conditions. Conclusion Anakinra is a potential option for patients with certain difficult-to-treat dermatologic diseases, given its relatively benign adverse effect profile and its effectiveness in a wide array of conditions. Overall, anakinra appears to be a promising option in the treatment of numerous dermatologic inflammatory conditions refractory to first line therapies, but further and higher-quality data is needed to clarify its therapeutic role.
Acute phase response to exertional heat stroke in mice

What is the central question of this study? Exertional heat stroke is accompanied by a marked inflammatory response. In this study, we explored the time course of acute phase proteins during recovery from severe heat stress in mice and the potential role of skeletal muscles as their source. What is the main finding and its importance? Exertional heat stroke transiently increased expression of acute phase proteins in mouse liver and plasma and depleted liver and plasma fibrinogen, a typical response to severe trauma. In contrast, skeletal muscle fibrinogen production was stimulated by heat stroke, which can provide an additional reservoir for fibrinogen supply to maintain the clotting potential throughout the body and locally within the muscle.
Contextually Constrained Deep Networks for Scene Labeling

Learning using deep learning architectures is a difficult problem: the complexity of the prediction model and the difficulty of solving non-convex optimization problems inherent to most learning algorithms can both lead to overfitting phenomena and bad local optima. To overcome these problems we would like to constraint parts of the network using some semantic context to 1) control its capacity while still allowing complex functions to be learned 2) obtain more meaningful layers. We first propose to learn a weak convolutional network which would provide us rough label maps over the neighborhood of a pixel. Then, we incorporate this weak learner in a bigger network. This iterative process aims at increasing the interpretability by constraining some feature maps to learn precise contextual information. Using Stanford and SIFT Flow scene labeling datasets, we show how this contextual knowledge improves accuracy of state-of-the-art architectures. The approach is generic and can be applied to similar networks where contextual cues are available at training time.
Spiral Phases in Doped Antiferromagnets

One can create high-temperature superconductors by doping antiferromagnets with holes or electrons. The effective theory that describes such materials in a low-energy regime is the condensed matter analog of chiral perturbation theory in QCD. Using this theory in this work, we study different phases of doped antiferromagnets depending on the values of the low-energy parameters. In order to do so, we investigate the effects of different periodic background field configurations with piecewise constant potentials and compare them to existing results for constant background fields. It will turn out that the energetically most favorable cases are in fact the configurations with constant background fields that were known before. Ist nicht der Anfang und das Ende jeder Wissenschaft in Dunkel gehüllt? Heinrich von Kleist, Letter to Adolfine von Werdeck
Analytical perspectives on performance-based management: an outline of theoretical assumptions in the existing literature

Abstract Performance-based management (PBM) has become a dominant form of governance in health care and there is a need for careful assessment of its function and effects. This article contains a cross-disciplinary literature synthesis of current studies of PBM. Literature was retrieved by database searches and categorized according to analytical differences and similarities concerning (1) purpose and (2) governance mechanism of PBM. The literature could be grouped into three approaches to the study of PBM, which we termed: the ‘functionalist’, the ‘interpretive’ and the ‘post-modern’ perspective. In the functionalist perspective, PBM is perceived as a management tool aimed at improving health care services by means of market-based mechanisms. In the interpretive perspective, the adoption of PBM is understood as consequence of institutional and individual agents striving for public legitimacy. In the post-modern perspective, PBM is analysed as a form of governance, which has become so ingrained in Western culture that health care professionals internalize and understand their own behaviour and goals according to the values expressed in these governance systems. The recognition of differences in analytical perspectives allows appreciation of otherwise implicit assumptions and potential implications of PBM. Reflections on such differences are important to ensure vigilant appropriation of shifting management tools in health quality governance.
Fast and Robust Normal Estimation for Point Clouds with Sharp Features

This paper presents a new method for estimating normals on unorganized point clouds that preserves sharp features. It is based on a robust version of the Randomized Hough Transform (RHT). We consider the filled Hough transform accumulator as an image of the discrete probability distribution of possible normals. The normals we estimate corresponds to the maximum of this distribution. We use a fixed‐size accumulator for speed, statistical exploration bounds for robustness, and randomized accumulators to prevent discretization effects. We also propose various sampling strategies to deal with anisotropy, as produced by laser scans due to differences of incidence. Our experiments show that our approach offers an ideal compromise between precision, speed, and robustness: it is at least as precise and noise‐resistant as state‐of‐the‐art methods that preserve sharp features, while being almost an order of magnitude faster. Besides, it can handle anisotropy with minor speed and precision losses.