Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonequilibrium equation of state in suspensions of active colloids

Active colloids constitute a novel class of materials composed of colloidal-scale particles locally converting chemical energy into motility, mimicking micro-organisms. Evolving far from equilibrium, these systems display structural organizations and dynamical properties distinct from thermalized colloidal assemblies. Harvesting the potential of this new class of systems requires the development of a conceptual framework to describe these intrinsically nonequilibrium systems. We use sedimentation experiments to probe the nonequilibrium equation of state of a bidimensional assembly of active Janus microspheres, and conduct computer simulations of a model of self-propelled hard disks. Self-propulsion profoundly affects the equation of state, but these changes can be rationalized using equilibrium concepts. We show that active colloids behave, in the dilute limit, as an ideal gas with an activity-dependent effective temperature. At finite density, increasing the activity is similar to increasing adhesion between equilibrium particles. We quantify this effective adhesion and obtain a unique scaling law relating activity and effective adhesion in both experiments and simulations. Our results provide a new and efficient way to understand the emergence of novel phases of matter in active colloidal suspensions.
How Load-Carrying Ants Avoid Falling Over: Mechanical Stability during Foraging in Atta vollenweideri Grass-Cutting Ants

Background Foraging workers of grass-cutting ants (Atta vollenweideri) regularly carry grass fragments larger than their own body. Fragment length has been shown to influence the ants’ running speed and thereby the colony’s food intake rate. We investigated whether and how grass-cutting ants maintain stability when carrying fragments of two different lengths but identical mass. Principal Findings Ants carried all fragments in an upright, backwards-tilted position, but held long fragments more vertically than short ones. All carrying ants used an alternating tripod gait, where mechanical stability was increased by overlapping stance phases of consecutive steps. The overlap was greatest for ants carrying long fragments, resulting in more legs contacting the ground simultaneously. For all ants, the projection of the total centre of mass (ant and fragment) was often outside the supporting tripod, i.e. the three feet that would be in stance for a non-overlapping tripod gait. Stability was only achieved through additional legs in ground contact. Tripod stability (quantified as the minimum distance of the centre of mass to the edge of the supporting tripod) was significantly smaller for ants with long fragments. Here, tripod stability was lowest at the beginning of each step, when the center of mass was near the posterior margin of the supporting tripod. By contrast, tripod stability was lowest at the end of each step for ants carrying short fragments. Consistently, ants with long fragments mainly fell backwards, whereas ants carrying short fragments mainly fell forwards or to the side. Assuming that transporting ants adjust neither the fragment angle nor the gait, they would be less stable and more likely to fall over. Conclusions In grass-cutting ants, the need to maintain static stability when carrying long grass fragments has led to multiple kinematic adjustments at the expense of a reduced material transport rate.
lncRNA Gene Signatures for Prediction of Breast Cancer Intrinsic Subtypes and Prognosis

Background: Breast cancer is intrinsically heterogeneous and is commonly classified into four main subtypes associated with distinct biological features and clinical outcomes. However, currently available data resources and methods are limited in identifying molecular subtyping on protein-coding genes, and little is known about the roles of long non-coding RNAs (lncRNAs), which occupies 98% of the whole genome. lncRNAs may also play important roles in subgrouping cancer patients and are associated with clinical phenotypes. Methods: The purpose of this project was to identify lncRNA gene signatures that are associated with breast cancer subtypes and clinical outcomes. We identified lncRNA gene signatures from The Cancer Genome Atlas (TCGA )RNAseq data that are associated with breast cancer subtypes by an optimized 1-Norm SVM feature selection algorithm. We evaluated the prognostic performance of these gene signatures with a semi-supervised principal component (superPC) method. Results: Although lncRNAs can independently predict breast cancer subtypes with satisfactory accuracy, a combined gene signature including both coding and non-coding genes will give the best clinically relevant prediction performance. We highlighted eight potential biomarkers (three from coding genes and five from non-coding genes) that are significantly associated with survival outcomes. Conclusion: Our proposed methods are a novel means of identifying subtype-specific coding and non-coding potential biomarkers that are both clinically relevant and biologically significant.
Adult onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) and Nasu-Hakola disease: Lesion staging and dynamic changes of axons and microglial subsets

The brains of 10 Japanese patients with adult onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) encompassing hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) and pigmentary orthochromatic leukodystrophy (POLD) and eight Japanese patients with Nasu–Hakola disease (N‐HD) and five age‐matched Japanese controls were examined neuropathologically with special reference to lesion staging and dynamic changes of microglial subsets. In both diseases, the pathognomonic neuropathological features included spherically swollen axons (spheroids and globules), axon loss and changes of microglia in the white matter. In ALSP, four lesion stages based on the degree of axon loss were discernible: Stage I, patchy axon loss in the cerebral white matter without atrophy; Stage II, large patchy areas of axon loss with slight atrophy of the cerebral white matter and slight dilatation of the lateral ventricles; Stage III, extensive axon loss in the cerebral white matter and dilatation of the lateral and third ventricles without remarkable axon loss in the brainstem and cerebellum; Stage IV, devastated cerebral white matter with marked dilatation of the ventricles and axon loss in the brainstem and/or cerebellum. Internal capsule and pontine base were relatively well preserved in the N‐HD, even at Stage IV, and the swollen axons were larger with a higher density in the ALSP. Microglial cells immunopositive for CD68, CD163 or CD204 were far more obvious in ALSP, than in N‐HD, and the shape and density of the cells changed in each stage. With progression of the stage, clinical symptoms became worse to apathetic state, and epilepsy was frequently observed in patients at Stages III and IV in both diseases. From these findings, it is concluded that (i) shape, density and subsets of microglia change dynamically along the passage of stages and (ii) increase of IBA‐1‐, CD68‐, CD163‐ and CD204‐immunopositive cells precedes loss of axons in ALSP.
Re‐evaluation of stannous chloride (E 512) as food additive

Abstract The Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re‐evaluating the safety of stannous chloride and stannous chloride dihydrate (E 512) as food additives. The Panel considered that adequate exposure and toxicity data were available. Stannous chloride is only permitted as food additives in one food category and no reply on the actual use level of stannous chloride (E 512) as a food additive and on its concentration in food was provided by any interested party. According to the Mintel's Global New Products Database (GNPD), stannous chloride was not labelled on any products in the EU nor in Norway. The regulatory maximum level exposure assessment scenario is based on the maximum permitted levels (MPLs) for stannous chloride (E 512), which is 25 mg Sn/kg. The mean exposure to stannous chloride (E 512) from its use as a food additive was below 1.3 μg Sn/kg body weight (bw) per day for all age groups. The 95th percentile of exposure to stannous chloride (E 512) ranged from 0.0 μg Sn/kg bw per day in all groups to 11.2 μg Sn/kg bw per day in adults. Absorption of stannous chloride from the gastrointestinal tract is low there is no concern with respect to carcinogenicity and genotoxicity. Gastrointestinal irritation was reported in humans after ingestion of a bolus dose of 40 mg Sn. The Panel concluded that stannous chloride (E 512) is of no safety concern in this current authorised use and use levels.
LncRNA‐RP11‐296A18.3/miR‐138/HIF1A Pathway Regulates the Proliferation ECM Synthesis of Human Nucleus Pulposus Cells (HNPCs)

During the process of Intervertebral disc degeneration (IDD), nucleus pulposus apoptosis increases, extracellular matrix (ECM) alters and/or degrades, abnormal proliferation of cells forms cell clusters, and the expression of various inflammatory factors increases. Thus, regulation of human nucleus pulposus cell (HNPC) proliferation and ECM synthesis present promising strategies for IDD treatment. Accumulating evidence indicates that non‐coding RNAs are involved in various cellular processes, including cell proliferation, differentiation, apoptosis, and metastasis. High expression of long non‐coding RNA (lncRNA) RP11‐296A18.3, as well as a low expression of miR‐138 during the IDD process has been reported; yet their functional roles in HNPC proliferation and ECM synthesis still remain unclear. MTT and BrdU assays showed that knockdown of RP11‐296A18.3 inhibited the proliferation of HNPC. The ECM marker, MMP‐13 and Collagen I expressions were also reduced. Bioinformatics target prediction, qPCR, and luciferase assays identified LncRNA‐RP11‐296A18.3 interacted with miR‐138. Moreover, RP11‐296A18.3 regulates HNPC proliferation and ECM synthesis through miR‐138. As the target gene of miR‐138, hypoxia‐inducible factor 1‐alpha (HIF1A) was closely associated with cell proliferation which was also regulated by RP11‐296A18.3 via miR‐138. Immunochemistry and qPCR results showed that miR‐138 expression was inversely correlated to RP11‐296A18.3 and HIF1A in IDD tissues, respectively; RP11‐296A18.3 was positively correlated to HIF1A. We revealed that RP11‐296A18.3 promote HIF1A expression through sponging miR‐138, thus to promote HNPC proliferation and ECM synthesis. Targeting RP11‐296A18.3 to rescue miR‐138 expression in HNPCs and IDD tissues presents a promising strategy for IDD improvement. J. Cell. Biochem. 118: 4862–4871, 2017. © 2017 Wiley Periodicals, Inc.
The Impact of Phosphorus Supply on Selenium Uptake During Hydroponics Experiment of Winter Wheat (Triticum aestivum) in China

Selenium (Se) is a necessary trace element for humans and animals, and Se fertilization is an efficient way to increase Se concentration in the edible parts of crops, thus enhance the beneficiary effects of Se in human and animal health. Due to the similarity of physical and chemical properties between phosphate () and selenite (), phosphorus (P) supply often significantly impacts the absorption of Se in plants, but little is known about how P supply influences the subcellular distribution and chemical forms of Se. In this study, the effects of P supply on subcellular distribution and chemical forms of Se in winter wheat were investigated in a hydroponic trial with medium Se level (0.1 mg Se L-1). P was applied with three concentrations (0.31, 3.1, and 31 mg P L-1) in the experiment. The results showed that increasing P supply significantly decreased the concentration and accumulation of Se in the roots, stems, and leaves of winter wheat. An increase in P supply significantly inhibited Se accumulation in the root cell wall, but enhanced Se distribution in the organelles and soluble fraction of root cells. These findings suggest that increased P supply inhibited the root-to-shoot transport of Se. An increase in P supply enhanced Se accumulation in the cell wall of plant stems (both apical and axillary stem) and cell organelles of plants leaves, but inhibited Se distribution in the soluble fraction of stems and leaves. This suggests that P supply enhances Se transportation across the cell membrane in shoots of winter wheat. In addition, increased P supply also altered the chemical forms of Se in tissues of winter wheat. These findings will help in understanding of the regulation grain Se accumulation and provide a practical way to enhance Se intake for humans inform Se-enriched grains.
3 D Exterior Soundfield Capture Using Pressure and Gradient Microphone Array on 2 D Plane

Two-dimensional (2D) planar array of first order microphones have been utilised in spherical harmonic decomposition based interior soundfield analysis. This paper proposes an efficient method in designing two-dimensional planar arrays of first order microphones that are capable of completely capturing three-dimensional (3D) spatial exterior soundfields. First order microphones are utilised within the array for measurements of pressure gradients, allowing the microphone array to capture soundfield components that conventional planar omni-directional microphone arrays are unable to detect. While spherical microphone arrays are capable of detecting all soundfield components, they have drawbacks in feasibility due to their 3D geometric configuration. The proposed planar array of first-order microphone provides the same functionality as a large spherical array which needs to encompass all sound sources while having a scalable geometry that lies purely in a two-dimensional horizontal plane. Simulations show the accuracy and feasibility of the proposed microphone array design in capturing a fully developed exterior soundfield.
The Role of Below-Ground Processes in Mediating Plant Invasions Local dominance of exotic plants declines with residence time : a role for plant – soil feedback ?

Recent studies have shown that introduced exotic plant species may be released from their native soilborne pathogens, but that they become exposed to increased soil pathogen activity in the new range when time since introduction increases. Other studies have shown that introduced exotic plant species become less dominant when time since introduction increases, and that plant abundance may be controlled by soil-borne pathogens; however, no study yet has tested whether these soil effects might explain the decline in dominance of exotic plant species following their initial invasiveness. Here we determine plant–soil feedback of 20 plant species that have been introduced into The Netherlands. We tested the hypotheses that (i) exotic plant species with a longer residence time have a more negative soil feedback and (ii) greater local dominance of the introduced exotic plant species correlates with less negative, or more positive, plant–soil feedback. Although the local dominance of exotic plant species decreased with time since introduction, there was no relationship of local dominance with plant–soil feedback. Plant–soil feedback also did not become more negative with increasing time since introduction. We discuss why our results may deviate from some earlier published studies and why plant–soil feedback may not in all cases, or not in all comparisons, explain patterns of local dominance of introduced exotic plant species.
Distributed greedy sparse learning over doubly stochastic networks

In this paper, we develop a greedy algorithm for sparse learning over a doubly stochastic network. In the proposed algorithm, nodes of the network perform sparse learning by exchanging their individual intermediate variables. The algorithm is iterative in nature. We provide a restricted isometry property (RIP)-based theoretical guarantee both on the performance of the algorithm and the number of iterations required for convergence. Using simulations, we show that the proposed algorithm provides good performance.
Supervised Rank Aggregation for Predicting Influence in Networks

Much work in Social Network Analysis has focused on the identification of the most important actors in a social network. This has resulted in several measures of influence and authority. While most of such sociometrics (e.g., PageRank) are driven by intuitions based on an actors location in a network, asking for the "most influential" actors in itself is an ill-posed question, unless it is put in context with a specific measurable task. Constructing a predictive task of interest in a given domain provides a mechanism to quantitatively compare different measures of influence. Furthermore, when we know what type of actionable insight to gather, we need not rely on a single network centrality measure. A combination of measures is more likely to capture various aspects of the social network that are predictive and beneficial for the task. Towards this end, we propose an approach to supervised rank aggregation, driven by techniques from Social Choice Theory. We illustrate the effectiveness of this method through experiments on Twitter and citation networks.
Cryptography through Interpolation, Approximation and Computational Intelligence Methods

Recently, numerous techniques and methods have been proposed to address hard and complex algebraic and number theoretical problems related to cryptography. We review several interpolation and approximation techniques. In particular, we discuss techniques related to polynomial interpolation, discrete Fourier transforms, as well as, polynomial approximation. Subsequently, we focus on a recently proposed approach to tackle these problems based on computational intelligence methods. More specifically, a study of the neural network approach to address the discrete logarithm problem, the Diffie-Hellman mapping problem, and the factorization problem related to the RSA cryptosystem,
The Morphology and Adhesion Mechanism of Octopus vulgaris Suckers

The octopus sucker represents a fascinating natural system performing adhesion on different terrains and substrates. Octopuses use suckers to anchor the body to the substrate or to grasp, investigate and manipulate objects, just to mention a few of their functions. Our study focuses on the morphology and adhesion mechanism of suckers in Octopus vulgaris. We use three different techniques (MRI, ultrasonography, and histology) and a 3D reconstruction approach to contribute knowledge on both morphology and functionality of the sucker structure in O. vulgaris. The results of our investigation are two-fold. First, we observe some morphological differences with respect to the octopus species previously studied (i.e., Octopus joubini, Octopus maya, Octopus bimaculoides/bimaculatus and Eledone cirrosa). In particular, in O. vulgaris the acetabular chamber, that is a hollow spherical cavity in other octopuses, shows an ellipsoidal cavity which roof has an important protuberance with surface roughness. Second, based on our findings, we propose a hypothesis on the sucker adhesion mechanism in O. vulgaris. We hypothesize that the process of continuous adhesion is achieved by sealing the orifice between acetabulum and infundibulum portions via the acetabular protuberance. We suggest this to take place while the infundibular part achieves a completely flat shape; and, by sustaining adhesion through preservation of sucker configuration. In vivo ultrasonographic recordings support our proposed adhesion model by showing the sucker in action. Such an underlying physical mechanism offers innovative potential cues for developing bioinspired artificial adhesion systems. Furthermore, we think that it could possibly represent a useful approach in order to investigate any potential difference in the ecology and in the performance of adhesion by different species.
Dual role of intravitreous infliximab in experimental choroidal neovascularization: effect on the expression of sulfated glycosaminoglycans.

PURPOSE To determine effects of intravitreous anti-TNF-alpha (infliximab) in a laser-induced choroidal neovascularization (CNV) model by fluorescein angiogram (FA), immunofluorescence, ELISA, and glycosaminoglycan analyses. METHODS CNV induction was performed using argon laser. Rats were divided into eight groups (no-laser no-infliximab; laser; laser with 10, 20, 40, 80, or 320 microg infliximab; and isotype-matched IgG). After 3 weeks, CNV area was measured by FA and von Willebrand factor (vWF) immunofluorescence. VEGF, TGF-beta, and syndecan-4 were evaluated by ELISA and immunofluorescence. Glycosaminoglycan expression was determined in retina and choroid of animals metabolically labeled with [(35)S]-sulfate. Cytotoxicity was investigated using ARPE-19 and endothelial cells. RESULTS FA showed significant reduction in the low-dose infliximab groups (10-40 microg), confirmed by vWF immunofluorescence that showed 49% decrease in the CNV. VEGF and TGF-beta decreased expression detected by ELISA and immunofluorescence paralleled these results. Similar data were observed for syndecan-4. The expression of these molecules in the neovascularization area using 320 microg was similar to the no-infliximab laser group or laser with isotype-matched IgG. Heparan sulfate expression in retina and choroid paralleled the observed effects on angiogenesis. Increased expression of chondroitin sulfate in retina and dermatan sulfate in choroid reflects the effects of injury and fibrosis using high doses of anti-TNF-alpha. Infliximab showed no cytotoxic effect in ARPE-19 cells, whereas high doses led to 20% decrease in endothelial cell viability. CONCLUSIONS Intravitreal infliximab shows dual effect on the development of laser-induced CNV. It reduces angiogenesis and glycosaminoglycan expression at low doses, whereas opposite effects are observed at high doses.
Detection and Strain Typing of Ancient Mycobacterium leprae from a Medieval Leprosy Hospital

Nine burials excavated from the Magdalen Hill Archaeological Research Project (MHARP) in Winchester, UK, showing skeletal signs of lepromatous leprosy (LL) have been studied using a multidisciplinary approach including osteological, geochemical and biomolecular techniques. DNA from Mycobacterium leprae was amplified from all nine skeletons but not from control skeletons devoid of indicative pathology. In several specimens we corroborated the identification of M. leprae with detection of mycolic acids specific to the cell wall of M. leprae and persistent in the skeletal samples. In five cases, the preservation of the material allowed detailed genotyping using single-nucleotide polymorphism (SNP) and multiple locus variable number tandem repeat analysis (MLVA). Three of the five cases proved to be infected with SNP type 3I-1, ancestral to contemporary M. leprae isolates found in southern states of America and likely carried by European migrants. From the remaining two burials we identified, for the first time in the British Isles, the occurrence of SNP type 2F. Stable isotope analysis conducted on tooth enamel taken from two of the type 3I-1 and one of the type 2F remains revealed that all three individuals had probably spent their formative years in the Winchester area. Previously, type 2F has been implicated as the precursor strain that migrated from the Middle East to India and South-East Asia, subsequently evolving to type 1 strains. Thus we show that type 2F had also spread westwards to Britain by the early medieval period.