Joint supervised and self-supervised learning for 3D real world challenges

Point cloud processing and 3D shape understanding are challenging tasks for which deep learning techniques have demonstrated great potentials. Still further progresses are essential to allow artificial intelligent agents to interact with the real world. In many practical conditions the amount of annotated data may be limited and integrating new sources of knowledge becomes crucial to support autonomous learning. Here we consider several scenarios involving synthetic and real world point clouds where supervised learning fails due to data scarcity and large domain gaps. We propose to enrich standard feature representations by leveraging self-supervision through a multi-task model that can solve a 3D puzzle while learning the main task of shape classification or part segmentation. An extensive analysis investigating few-shot, transfer learning and cross-domain settings shows the effectiveness of our approach with state-of-the-art results

Dietary alpha-lactalbumin alters energy balance, gut microbiota composition and intestinal nutrient transporter expression in high-fat diet fed mice

peer-reviewedRecently there has been a considerable rise in the frequency of metabolic diseases, such as obesity, due to changes in lifestyle and resultant imbalances between energy intake and expenditure. Whey proteins are considered as potentially important components of a dietary solution to the obesity problem. However, the roles of individual whey proteins in energy balance remain poorly understood. This study investigated the effects of a high fat diet (HFD) containing alphalactalbumin (LAB), a specific whey protein, or the non-whey protein casein (CAS), on energy balance, nutrient transporters expression, and enteric microbial populations. C57BL/6J mice (n = 8) were given a HFD containing either 20% CAS or LAB as protein sources or a low-fat diet (LFD) containing CAS for 10 weeks. HFD-LAB fed mice showed a significant increase in cumulative energy intake (P=0.043), without differences in body weight, energy expenditure, locomotor activity, respiratory exchange ratio or subcutaneous and epididymal adipose tissue weight. HFD-LAB intake led to a decrease in the expression of glucose transporter glut2 in the ileum (P=0.05)and in the fatty acid transporter cd36 (P<0.001) in both ileum and jejunum. This suggests a reduction of absorption efficiency within the small intestine in the HFD-LAB group. DNA from faecal samples was used for 16S rRNA-based assessment of intestinal microbiota populations; the genera Lactobacillus, Parabacteroides and Bifidobacterium were present in significantly higher proportions in the HFD-LAB group. These data indicate a possible functional relationship between gut microbiota, intestinal nutrient transporters and energy balance, with no impact on weight gain

Depletion of the gut microbiota differentially affects the impact of whey protein on high-fat diet-induced obesity and intestinal permeability

Acknowledgement: The authors thank Fiona Crispie and Amanda Brechon from Teagasc Moorepark Food Research Centre for their assistance in 16S library preparation and sequencing. The authors thank Thomaz Bastiaanssen for generating the pictures for caecal metabolomics analysis. The authors thank Joana Pereira, Eoin Sherwin and Marina Shverer for helping with the Ussing chambers experiment. S. B. was funded under the Teagasc Walsh Fellowship scheme (grant number 2016007). K. N. N. was supported by Teagasc, Ireland and in part by a research grant from Science Foundation Ireland (SFI) under grant numbers SFI/16/BBSRC/3389 and BBSRC under the grant number BB/P009875/1 (to K.N.N. and J.R.S). Funding information Teagasc Walsh Fellowship Programme, Grant/Award Number: 2016007; Science Foundation Ireland, Grant/Award Number: SFI/16/BBSRC/3389; Biotechnology and Biological Sciences Research Council, Grant/Award Number: BB/P009875/1Peer reviewedPublisher PD

Geometric deep learning

The goal of these course notes is to describe the main mathematical ideas behind geometric deep learning and to provide implementation details for several applications in shape analysis and synthesis, computer vision and computer graphics. The text in the course materials is primarily based on previously published work. With these notes we gather and provide a clear picture of the key concepts and techniques that fall under the umbrella of geometric deep learning, and illustrate the applications they enable. We also aim to provide practical implementation details for the methods presented in these works, as well as suggest further readings and extensions of these ideas

Whey protein effects on energy balance link the intestinal mechanisms of energy absorption with adiposity and hypothalamic neuropeptide gene expression

peer-reviewedWe tested the hypothesis that dietary whey protein isolate (WPI) affects the intestinal mechanisms related to energy absorption and that the resulting energy deficit is compensated by changes in energy balance to support growth. C57BL/6 mice were provided a diet enriched with WPI with varied sucrose content, and the impact on energy balance-related parameters was investigated. As part of a high-sucrose diet, WPI reduced the hypothalamic expression of pro-opiomelanocortin gene expression and increased energy intake. The energy expenditure was unaffected, but epididymal weight was reduced, indicating an energy loss. Notably, there was a reduction in the ileum gene expression for amino acid transporter SLC6a19, glucose transporter 2, and fatty acid transporter 4. The composition of the gut microbiota also changed, where Firmicutes were reduced. The above changes indicated reduced energy absorption through the intestine. We propose that this mobilized energy in the adipose tissue and caused hypothalamic changes that increased energy intake, acting to counteract the energy deficit arising in the intestine. Lowering the sucrose content in the WPI diet increased energy expenditure. This further reduced epididymal weight and plasma leptin, whereupon hypothalamic ghrelin gene expression and the intestinal weight were both increased. These data suggest that when the intestine-adipose-hypothalamic pathway is subjected to an additional energy loss (now in the adipose tissue), compensatory changes attempt to assimilate more energy. Notably, WPI and sucrose content interact to enable the component mechanisms of this pathway

Targeted delivery of photosensitizers: efficacy and selectivity issues revealed by multifunctional ORMOSIL nanovectors in cellular systems

PEGylated and non-PEGylated ORMOSIL nanoparticles prepared by microemulsion condensation of vinyltriethoxy-silane (VTES) were investigated in detail for their micro-structure and ability to deliver photoactive agents. With respect to pure silica nanoparticles, organic modification substantially changes the microstructure and the surface properties. This in turn leads to a modulation of both the photophysical properties of embedded photosensitizers and the interaction of the nanoparticles with biological entities such as serum proteins. The flexibility of the synthetic procedure allows the rapid preparation and screening of multifunctional nanosystems for photodynamic therapy (PDT). Selective targeting of model cancer cells was tested by using folate, an integrin specific RGD peptide and anti-EGFR antibodies. Data suggest the interference of the stealth-conferring layer (PEG) with small targeting agents, but not with bulky antibodies. Moreover, we showed that selective photokilling of tumour cells may be limited even in the case of efficient targeting because of intrinsic transport limitations of active cellular uptake mechanisms or suboptimum localization

Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes

ACKNOWLEDGMENTS This work was supported by a research grant from Science Foundation Ireland (SFI) under grant SFI/16/BBSRC/3389, BBSRC under grant number BB/ P009875/1 (to K.N.N. and J.R.S.), and in part by SFI and the Department of Agriculture, Food and Marine under grant 16/RC/3835 (to VistaMilk). We thank Conall Strain, David Mannion, and John Leech for contributing to the metabolomics analysis. We thank Alina Kondrashina for help with the Milliplex system.Peer reviewedPublisher PD

Top-down synthesis of multifunctional iron oxide nanoparticles formacrophage labelling and manipulation

Multifunctional iron oxide (FeOx) magnetic nanoparticles (MNPs) are promising items for biomedical applications. They are studied as theranostic agents for cancer treatment, selective probes for bioanalytical assays, controllable carriers for drug delivery and biocompatible tools for cell sorting or tissue repair. Here we report a new method for the synthesis in water of FeOx–MNPs via a top-down physical technique consisting in Laser Ablation Synthesis in Solution (LASiS). LASiS is a green method that does not require chemicals or stabilizers, because nanoparticles are directly obtained in water as a stable colloidal system. A gamut of characterization techniques was used for investigating the structure of FeOx–MNPs that have a polycrystalline structure prevalently composed of magnetite (ca. 75%) and hematite (ca. 22%). The FeOx–MNPs exhibit very good magnetic properties if compared to what is usually reported for iron oxide nanoparticles, with saturation magnetization close to the bulk value (ca. 80 emu g1) and typical signatures of the coexistence of ferrimagnetic and antiferromagnetic phases in the same particle. The functionalization of FeOx–MNPs after the synthesis was possible with a variety of ligands. In particular, we succeeded in the functionalization of FeOx–MNPs with carboxylated phosphonates, fluorescent alkylamines, fluorescent isothiocyanates and bovine serum albumin. Our FeOx–MNPs showed excellent biocompatibility. Multifunctional FeOx–MNPs were exploited for macrophage cell labelling with fluorescent probes as well as for cell sorting and manipulation by external magnetic fields