Miracle-dz/UniFAR-FTUs huggingface dataset:
Affine-invariant skeleton of 3D shapes

Different application fields have shown increasing interest in shape description oriented to recognition and similarity issues. Beyond the application aims, the capability of handling details separating them from building elements, the invariance to a set of geometric transformations, the uniqueness and stability to noise represent fundamental properties of each proposed model. This paper defines an affine-invariant skeletal representation; starting from global features of a 3D shape, located by curvature properties, a Reeb graph is defined using the topological distance as a quotient function. If the mesh has uniformly spaced vertices, this Reeb graph can also be rendered as a geometric skeleton defined by the barycenters of pseudo-geodesic circles sequentially expanded from all the feature points.
Phenotypic Plasticity in Adult Life‐History Strategies Compensates for a Poor Start in Life in Trinidadian Guppies (Poecilia reticulata)

Low food availability during early growth and development can have long‐term negative consequences for reproductive success. Phenotypic plasticity in adult life‐history decisions may help to mitigate these potential costs, yet adult life‐history responses to juvenile food conditions remain largely unexplored. I used a food‐manipulation experiment with female Trinidadian guppies (Poecilia reticulata) to examine age‐related changes in adult life‐history responses to early food conditions, whether these responses varied across different adult food conditions, and how these responses affected overall reproductive success. Guppy females reared on low food as juveniles matured at a later age, at a smaller size, and with less energy reserves than females reared on high food as juveniles. In response to this setback, they changed their investment in growth, reproduction, and fat storage throughout the adult stage such that they were able to catch up in body size, increase their reproductive output, and restore their energy reserves to levels comparable to those of females reared on high food as juveniles. The net effect was that adult female guppies did not merely mitigate but surprisingly were able to fully compensate for the potential long‐term negative effects of poor juvenile food conditions on reproductive success.
Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia)

One way to build larger, more comprehensive phylogenies is to combine the vast amount of phylogenetic information already available. We review the two main strategies for accomplishing this (combining raw data versus combining trees), but employ a relatively new variant of the latter: supertree construction. The utility of one supertree technique, matrix representation using parsimony analysis (MRP), is demonstrated by deriving a complete phylogeny for all 271 extant species of the Garnivora from 177 literature sources. Beyond providing a ‘consensus’ estimate of carnivore phylogeny, the tree also indicates taxa for which the relationships remain controversial (e.g. the red panda; within canids, felids, and hyaenids) or have not been studied in any great detail (e.g. herpestids, viverrids, and intrageneric relationships in the procyonids). Times of divergence throughout the tree were also estimated from 74 literature sources based on both fossil and molecular data. We use the phylogeny to show that some lineages within the Mustelinae and Canidae contain significantly more species than expected for their age, illustrating the tree's utility for studies of macroevolution. It will also provide a useful foundation for comparative and conservational studies involving the carnivores.
SimPhospho: a software tool enabling confident phosphosite assignment

Motivation: Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site‐specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. Results: We present SimPhospho, a fast and user‐friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans‐Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. Availability and implementation: SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user's manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/. Supplementary information: Supplementary data are available at Bioinformatics online.
Glycosylphosphatidylinositol Anchors from Galactomannan and GPI-Anchored Protein Are Synthesized by Distinct Pathways in Aspergillus fumigatus

Glycosylphosphatidylinositols (GPIs) are lipid anchors allowing the exposure of proteins at the outer layer of the plasma membrane. In fungi, a number of GPI-anchored proteins (GPI-APs) are involved in the remodeling of the cell wall polymers. GPIs follow a specific biosynthetic pathway in the endoplasmic reticulum. After the transfer of the protein onto the GPI-anchor, a lipid remodeling occurs to substitute the diacylglycerol moiety by a ceramide. In addition to GPI-APs, A. fumigatus produces a GPI-anchored polysaccharide, the galactomannan (GM), that remains unique in the fungal kingdom. To investigate the role of the GPI pathway in the biosynthesis of the GM and cell wall organization, the deletion of PER1—coding for a phospholipase required for the first step of the GPI lipid remodeling—was undertaken. Biochemical characterization of the GPI-anchor isolated from GPI-APs showed that the PER1 deficient mutant produced a lipid anchor with a diacylglycerol. The absence of a ceramide on GPI-anchors in the Δper1 mutant led to a mislocation of GPI-APs and to an alteration of the composition of the cell wall alkali-insoluble fraction. On the other hand, the GM isolated from the Δper1 mutant membranes possesses a ceramide moiety as the parental strain, showing that GPI anchor of the GM follow a distinct unknown biosynthetic pathway.
Maternal hatching synchronization in a subsocial burrower bug mitigates the risk of future sibling cannibalism

Abstract Sibling cannibalism—the killing and consumption of conspecifics within broods—carries a high risk of direct and inclusive fitness loss for parents and offspring. We reported previously that a unique vibrational behavior shown by the mother of the subsocial burrower bug, Adomerus rotundus (Heteroptera: Cydnidae), induced synchronous hatching. Maternal regulation may be one of the most effective mechanisms for preventing or limiting sibling cannibalism. Here, we tested the hypothesis that synchronous hatching induced by maternal vibration in A. rotundus prevents sibling cannibalism. Mothers and their mature egg masses were allocated to three groups: synchronous hatching by maternal vibration (SHmv), synchronous hatching by artificial vibration (SHav), and asynchronous hatching (AH). We then investigated the influence of each hatching strategy on the occurrence of sibling cannibalism of eggs and early‐instar nymphs in the laboratory. No difference in the proportion of eggs cannibalized was observed among the three groups. However, the proportion of nymphs cannibalized was higher in the AH group than in the SHmv group. The difference in the number of days to first molting within clutch was significantly higher in the AH group than in the SHmv group. Junior nymphs were sometimes eaten by senior nymphs. However, immediately after molting, senior nymphs were at a high risk of being eaten by junior nymphs. Our results indicate that synchronous hatching of A. rotundus is necessary to mitigate the risk of sibling cannibalism.
THERMAL-MECHANICAL BEHAVIOR OF SILICA-BASED GEOPOLYMER - CARBON COMPOSITE

Thermal silica-based geopolymer composites reinforced by approximately 35 weight or 53 volume percentage of unidirectional carbon fiber HTS 5631 1600tex 24K were synthesized and fabricated at optimal range of c uring conditions, and the effects of calcination in a furnace at high temperatures up to 1000 o C for 1 hour on the thermal-mechanical properties were studied. The fle xural properties of the resulting composites were d etermined on a universal testing machine under three-point be nding mode in accordance with ASTM C 1341 ‐ 06 and the results show that the flexural strength of geocompo sites after calcination at 1000 o C still remained nearly 50 % compared with that of at 20 o C. The microstructure of composites were analyzed by means of Scanning Electron Microscope (SEM), after calcination at temperature higher than 800 o C the microstructure of geocomposite looks like foamed composites and the adhesion between the fiber and matrix still show very well. Energy Disp ersive Xray Analysis (EDX) was used to determine the initia l reaction layer on the fiber will be presentes as well.
The Fine Structure of Preferential Attachment Graphs I: Somewhere-Denseness

Preferential attachment graphs are random graphs designed to mimic properties of typical real world networks. They are constructed by a random process that iteratively adds vertices and attaches them preferentially to vertices that already have high degree. We use improved concentration bounds for vertex degrees to show that preferential attachment graphs contain asymptotically almost surely (a.a.s.) a one-subdivided clique of size at least $(\log n)^{1/4}$. Therefore, preferential attachment graphs are a.a. s somewhere-dense. This implies that algorithmic techniques developed for sparse graphs are not directly applicable to them. The concentration bounds state: Assuming that the exact degree $d$ of a fixed vertex (or set of vertices) at some early time $t$ of the random process is known, the probability distribution of $d$ is sharply concentrated as the random process evolves if and only if $d$ is large at time $t$.
Alteration of gene expression by intestinal epithelial cells precedes colitis in interleukin-2-deficient mice.

Intestinal epithelial cells may be actively involved in the immunoregulatory pathways leading to intestinal inflammation. The aim of this study was to assess expression by intestinal epithelial cells of cytokines with potential involvement in the development of intestinal inflammation in interleukin (IL)-2-deficient [(-/-)] mice. Wild-type mice, mice heterozygous for the disrupted IL-2 gene, and IL-2(-/-) mice were studied at 6, 16, and 24 wk of age. The mRNA levels of transforming growth factor-β1 (TGF-β1), tumor necrosis factor-α (TNF-α), IL-1β, IL-6, IL-15, KC, JE, and CD14 in colonic and small intestinal epithelial cells were assessed by Northern blot analysis. CD14 was also measured by Western blotting and reverse transcriptase polymerase chain reaction (RT-PCR). TGF-β1 mRNA was constitutively expressed in both colonic and small intestinal epithelial cells with increased expression in the colonic epithelium of colitic mice. CD14 was detected only in colonic epithelial cells, and mRNA levels increased severalfold in IL-2(-/-) mice with colitis. Northern analysis demonstrated increased levels of TGF-β1 and CD14 mRNA in colonic epithelial cells of IL-2(-/-) mice before the development of signs of colitis. CD14 mRNA and protein expression in the epithelial cells of colitic mice were confirmed by RT-PCR and Western blot analysis of isolated cells. In addition, IL-2(-/-) mice also expressed increased levels of IL-15 mRNA in small intestinal and colonic epithelial cells compared with heterozygous control mice. TNF-α, IL-1β, IL-6, KC, and JE mRNAs were only detectable in colonic epithelial cells of mice after the onset of colitis. Enhanced expression of TGF-β1, IL-15, and CD14 by colonic epithelial cells may play a role in the subsequent development of colitis in IL-2(-/-) mice.
Resource Discovery in a Dynamic Grid Environment

Resource discovery in a grid environment is a critical problem, as a typical grid system includes a very large number of resources, which must be readily identified and accessed to run applications. Traditional grid discovery algorithms perform poorly, as they do not scale, nor allow grid-enabled applications to transparently query the whole set of grid resources. Peer-to-peer (P2P) has been argued as a suitable distributed paradigm that not only overcomes the issues of scalability of such discovery systems, but also better supports the discovery of resources in a context of dynamicity of resources and associated information. In this paper we propose a P2P system for indexing and discovering grid resources. We assume that grid resources are characterized by a set of attributes, and our system can be queried for resources satisfying arbitrary range conditions on these attributes. Note that traditional P2P searching techniques can not be directly applied in this case, since they work well mostly for static content and exact queries. Simulation results show that the system provides an adequate degree of scalability
A generic model of multi-class support vector machine

Roughly speaking, there is one main model of pattern recognition support vector machine, with several variants of lower popularity. On the contrary, among the different multi-class support vector machines which can be found in literature, none is clearly favoured. On the one hand, they exhibit distinct statistical properties. On the other hand, multiple comparative studies between multi-class support vector machines and decomposition methods have highlighted the fact that in practice, each model has its advantages and drawbacks. In this article, we introduce a generic model of multi-class support vector machine. It provides the first unifying definition of all the machines of this kind published so far. This contribution makes it possible to devise new machines meeting specific requirements as well as to analyse globally the statistical properties of the multi-class support vector machines.
The Effects of Cryotherapy on Knee Joint Position Sense and Force Production Sense in Healthy Individuals

Abstract The proprioceptive information received from mechanoreceptors is potentially responsible for controlling the joint position and force differentiation. However, it is unknown whether cryotherapy influences this complex mechanism. Previously reported results are not universally conclusive and sometimes even contradictory. The main objective of this study was to investigate the impact of local cryotherapy on knee joint position sense (JPS) and force production sense (FPS). The study group consisted of 55 healthy participants (age: 21 ± 2 years, body height: 171.2 ± 9 cm, body mass: 63.3 ± 12 kg, BMI: 21.5 ± 2.6). Local cooling was achieved with the use of gel-packs cooled to -2 ± 2.5°C and applied simultaneously over the knee joint and the quadriceps femoris muscle for 20 minutes. JPS and FPS were evaluated using the Biodex System 4 Pro apparatus. Repeated measures analysis of variance (ANOVA) did not show any statistically significant changes of the JPS and FPS under application of cryotherapy for all analyzed variables: the JPS’s absolute error (p = 0.976), its relative error (p = 0.295), and its variable error (p = 0.489); the FPS’s absolute error (p = 0.688), its relative error (p = 0.193), and its variable error (p = 0.123). The results indicate that local cooling does not affect proprioceptive acuity of the healthy knee joint. They also suggest that local limited cooling before physical activity at low velocity did not present health or injury risk in this particular study group.
Enhanced triglyceride clearance with intraperitoneal human acylation stimulating protein in C57BL/6 mice.

Acylation stimulating protein (ASP), a novel adipocyte-derived autocrine protein, stimulates triglyceride synthesis and glucose transport in vitro in human and murine adipocytes. In vitro, chylomicrons increase ASP and precursor complement C3 production in adipocytes. Furthermore, in vivo, ASP production from human adipose tissue correlates positively with triglyceride clearance postprandially. The aim of the present study was to determine if intraperitoneally injected ASP accelerated triglyceride clearance in vivo after a fat load in C57Bl/6 mice. ASP increased the triglyceride clearance with a reduction of the triglyceride area under the curve over 6 h (AUC0-6) from 102.6 ± 30.0 to 61.0 ± 14.5 mg ⋅ dl-1 ⋅ h-1( P < 0.05), especially in the latter postprandial period (AUC3-6; 56.2 ± 18.0 vs. 24.9 ± 8.9 mg ⋅ dl-1 ⋅ h-1, P < 0.025). ASP also reduced plasma glucose both in the mice with accelerated plasma triglyceride clearance and in those with relatively delayed triglyceride clearance ( P < 0.025). Therefore, ASP alters postprandial triglyceride and glucose metabolism.
Trastuzumab- and Fab′ fragment-modified curcumin PEG-PLGA nanoparticles: preparation and evaluation in vitro and in vivo

Introduction Nanoparticles (NPs) modified with bio-ligands represent a promising strategy for active targeted drug delivery to tumour. However, many targeted ligands, such as trastuzumab (TMAB), have high molecular weight, limiting their application for targeting. In this study, we prepared Fab’ (antigen-binding fragments cut from TMAB)-modified NPs (Fab′-NPs) with curcumin (Cur) as a model drug for more effective targeting of human epidermal growth factor receptor 2 (HER2/ErbB2/Neu), which is overexpressed on breast cancer cells. Material and methods The release kinetics was conducted by dialysis bags. The ability to kill HER2-overexpressing BT-474 cells of Fab′-Cur-NPs compared with TMAB-Cur-NPs was conducted by cytotoxicity experiments. Qualitative and quantitative cell uptake studies using coumarin-6 (fluorescent probe)-loaded NPs were performed by fluorescence microscopy and flow cytometry. Pharmacokinetics and biodistribution experiments in vivo were assessed by liquid chromatography–tandem mass spectrometry (LC-MS/MS). Results The release kinetics showed that both Fab′-Cur-NPs and TMAB-Cur-NPs provided continuous, slow release of curcumin for 72 h, with no significant difference. In vitro cytotoxicity experiments showed that Fab′-Cur-NPs manifested prominent ability to kill HER2-overexpressing BT-474 cells compared with TMAB-Cur-NPs. Qualitative and quantitative cell uptake studies indicated that the accumulation of Fab′-NPs was greater than that of TMAB-NPs in BT-474 (HER2+) cells; However, there was no significant difference in MDA-MB-231 (HER2−) cells. Pharmacokinetics and biodistribution experiments in vivo demonstrated that the half-life (t1/2) and area under the blood concentration-time curve (AUC0-t) of Fab′-Cur-NPs increased 5.30-fold and 1.76-fold relative to those of TMAB-Cur-NPs, respectively. Furthermore, the tumor accumulation of Fab′-Cur-NPs was higher than that of TMAB-Cur-NPs. Conclusion Fab′ fragment has greater capacity than the intact antibody to achieve tumor targeting through NP-based delivery.
Structure-based discovery of glycomimetic FmlH ligands as inhibitors of bacterial adhesion during urinary tract infection

Significance The emergence of multidrug-resistant bacteria, including uropathogenic Escherichia coli (UPEC), makes the development of targeted antivirulence therapeutics a critical focus of research. During urinary tract infections (UTIs), UPEC uses chaperone–usher pathway pili tipped with an array of adhesins that recognize distinct receptors with sterochemical specificity to facilitate persistence in various tissues and habitats. We used an interdisciplinary approach driven by structural biology and synthetic glycoside chemistry to design and optimize glycomimetic inhibitors of the UPEC adhesin FmlH. These inhibitors competitively blocked FmlH in vitro, in in vivo mouse UTI models, and in ex vivo healthy human kidney tissue. This work demonstrates the utility of structure-driven drug design in the effort to develop antivirulence therapeutic compounds. Treatment of bacterial infections is becoming a serious clinical challenge due to the global dissemination of multidrug antibiotic resistance, necessitating the search for alternative treatments to disarm the virulence mechanisms underlying these infections. Uropathogenic Escherichia coli (UPEC) employs multiple chaperone–usher pathway pili tipped with adhesins with diverse receptor specificities to colonize various host tissues and habitats. For example, UPEC F9 pili specifically bind galactose or N-acetylgalactosamine epitopes on the kidney and inflamed bladder. Using X-ray structure-guided methods, virtual screening, and multiplex ELISA arrays, we rationally designed aryl galactosides and N-acetylgalactosaminosides that inhibit the F9 pilus adhesin FmlH. The lead compound, 29β-NAc, is a biphenyl N-acetyl-β-galactosaminoside with a Ki of ∼90 nM, representing a major advancement in potency relative to the characteristically weak nature of most carbohydrate–lectin interactions. 29β-NAc binds tightly to FmlH by engaging the residues Y46 through edge-to-face π-stacking with its A-phenyl ring, R142 in a salt-bridge interaction with its carboxylate group, and K132 through water-mediated hydrogen bonding with its N-acetyl group. Administration of 29β-NAc in a mouse urinary tract infection (UTI) model significantly reduced bladder and kidney bacterial burdens, and coadministration of 29β-NAc and mannoside 4Z269, which targets the type 1 pilus adhesin FimH, resulted in greater elimination of bacteria from the urinary tract than either compound alone. Moreover, FmlH specifically binds healthy human kidney tissue in a 29β-NAc–inhibitable manner, suggesting a key role for F9 pili in human kidney colonization. Thus, these glycoside antagonists of FmlH represent a rational antivirulence strategy for UPEC-mediated UTI treatment.
Vision-based MAV Navigation: Implementation Challenges Towards a Usable System in Real-Life Scenarios

In this workshop, we share our experience on autonomous flights with a MAV using a monocular camera as the only exteroceptive sensor. We developed a flexible and modular framework for realtime onboard MAV navigation fusing visual data with IMU at a rate of 1 kHz. We aim to provide a detailed insight of how our modules work and how they are used in our system. Using this framework, we achieved unprecedented MAV navigation autonomy, with flights of more than 350 m length at altitudes between 0 m and 70 m, in previously unknown Areas while global signals as GPS were not used.