Structural and magnetic instabilities of layered magnetic systems

We present a study of the magnetic order and the structural stability of two-dimensional quantum spin systems in the presence of spin-lattice coupling. For a square lattice it is shown that the plaquette formation is the most favourable form of static two-dimensional dimerization. We also demonstrate that such distortions may coexist with long range magnetic order, in contrast to the one-dimensional case. Similarly, the coupling to Einstein phonons is found to reduce, but not to eliminate the staggered magnetic moment. In addition, we consider the renormalization of the square lattice phonon spectrum due to spin-phonon coupling in the adiabatic approximation. Towards low temperatures significant softening mainly of zone boundary phonons is found, especially around the $(\pi,0)$ point of the Brillouin zone. This result is compatible with the tendency to plaquette formation in the static limit. We also point out the importance of a "magnetic pressure" on the lattice due to spin-phonon coupling. At low temperatures, this results in a tendency towards shear instabilities of the lattice

The cytotoxicity of fatty acid/α-lactalbumin complexes depends on the amount and type of fatty acid

peer-reviewedComplexes of the milk protein, α-lactalbumin, and the fatty acid, oleic acid, have previously been shown to be cytotoxic. Complexes of α-lactalbumin and five different fatty acids (vaccenic, linoleic, palmitoleic, stearic, and elaidic acid) were prepared and compared to those formed with oleic acid. All complexes were cytotoxic to human promyelocytic leukemia-derived (HL-60) cells but to different degrees depending on the fatty acid. The amount of fatty acid per α-lactalbumin molecule was found to correlate with the cytotoxicity; the higher the number of fatty acids per protein, the more cytotoxic the complex. Importantly, all the tested fatty acids were also found to be cytotoxic on their own in a concentration dependent manner. The cytotoxic effect of complexes between α-lactalbumin and linoleic acid, vaccenic acid, or oleic acid was further investigated using flow cytometry and found to induce cell death resembling apoptosis on Jurkat cells. Practical applications: Cytotoxic complexes of α-lactalbumin and several different fatty acids could be produced. The cytotoxicity of all the variants is similar to that previously determined for α-lactalbumin/oleic acid complexes.This work was supported by the Food Institutional Research Measure (FIRM, project no. 08RDTMFRC650) of the Department of Agriculture, Fisheries, and Food, Ireland

Thermodynamic properties of the two-dimensional S=1/2 Heisenberg antiferromagnet coupled to bond phonons

By applying a quantum Monte Carlo procedure based on the loop algorithm we investigate thermodynamic properties of the two-dimensional antiferromagnetic S=1/2 Heisenberg model coupled to Einstein phonons on the bonds. The temperature dependence of the magnetic susceptibility, mean phonon occupation numbers and the specific heat are discussed in detail. We study the spin correlation function both in the regime of weak and strong spin phonon coupling (coupling constants g=0.1, w=8J and g=2, w=2J, respectively). A finite size scaling analysis of the correlation length indicates that in both cases long range Neel order is established in the ground state.Comment: 10 pages, 13 figure

Investigation of Correlation Functions in Low-Dimensional Quantum Antiferromagnets by Quantum Monte Carlo Methods

In this thesis the quantum Monte Carlo loop algorithm is applied to study the properties of correlation functions in low-dimensional quantum antiferromagnets. Two different types of lattice models are investigated. The first system is the quantum critical XXZ chain. The second class of models emerges when coupling the square lattice Heisenberg model to phonons. In case of the quantum critical XXZ chain, the loop algorithm is used to compute the two-point spin and dimer correlation functions at low temperatures. Starting from the well-known asymptotic expressions from conformal field theory for the decay of the correlations, the crossover from the finite-temperature to the ground state behavior is investigated. In addtion, the Monte Carlo data are used to extract numerical estimates for the correlation amplitudes. The deviations from asymptotic scaling at low finite temperatures and intermediate distances are examined. The results are also used to study the algebraic and logarithmic corrections in the ground state. The method is further applied to compute the low-temperature spin correlations of the square lattice Heisenberg model coupled to dispersionless Einstein phonons. Also, statically dimerized Heisenberg models in two dimensions are investigated. Here the quantum Monte Carlo technique is used to determine the specific pattern of dimerized bonds which has the largest gain in the magnetic energy. A direct comparison of ground state energies is only possible for a small number of dimerized systems. For this reason an alternative approach is developed, which allows to study a significantly larger class of models. Starting from a Landau expansion of the free energy, this amounts to a computation of specific structure factors of the dimer correlations of the uniform Heisenberg model. As a consequence, a Landau theory for the two-dimensional counterpart of the spin-Peierls transition is established. This adiabatic approach also applies to the Heisenberg model coupled to dispersive phonons. In this case the data for the dimer correlations are used to study the impact of the spin-phonon coupling on the phonon dispersion relations. In particular, the softening of phonon modes is investigated, which is relevant for experimental studies on substances with a quasi two-dimensional magnetic structure

Lysosomal protease deficiency or substrate overload induces an oxidative-stress mediated STAT3-dependent pathway of lysosomal homeostasis

How cells regulate their lysosomal proteolytic capacity is only partly understood. Here, the authors show that lysosomal protease deficiency or substrate overload induces lysosomal stress leading to activation of a STAT3-dependent, TFEB-independent pathway of lysosomal hydrolase expression

Stat3 controls cell death during mammary gland involution by regulating uptake of milk fat globules and lysosomal membrane permeabilization.

We have previously demonstrated that Stat3 regulates lysosomal-mediated programmed cell death (LM-PCD) during mouse mammary gland involution in vivo. However, the mechanism that controls the release of lysosomal cathepsins to initiate cell death in this context has not been elucidated. We show here that Stat3 regulates the formation of large lysosomal vacuoles that contain triglyceride. Furthermore, we demonstrate that milk fat globules (MFGs) are toxic to epithelial cells and that, when applied to purified lysosomes, the MFG hydrolysate oleic acid potently induces lysosomal leakiness. Additionally, uptake of secreted MFGs coated in butyrophilin 1A1 is diminished in Stat3-ablated mammary glands and loss of the phagocytosis bridging molecule MFG-E8 results in reduced leakage of cathepsins in vivo. We propose that Stat3 regulates LM-PCD in mouse mammary gland by switching cellular function from secretion to uptake of MFGs. Thereafter, perturbation of lysosomal vesicle membranes by high levels of free fatty acids results in controlled leakage of cathepsins culminating in cell death.This work was supported by a grant from the Medical Research Council programme grant no. MR/J001023/1 (T.J.S. and B. L-L.) and a Cancer Research UK Cambridge Cancer Centre PhD studentship (H.K.R.).This is the accepted manuscript. The final version is available from Nature Publishing at http://www.nature.com/ncb/journal/vaop/ncurrent/full/ncb3043.html

Emerging concepts about NAIP/NLIRC4 inflammasomes

Neuronal apoptosis inhibitory protein (NAIP)/NOD-like receptor (NLR) containing a caspase activating and recruitment domain (CARD) 4 (NLRC4) inflammasome complexes are activated in response to proteins from virulent bacteria that reach the cell cytosol. Specific NAIP proteins bind to the agonists and then physically associate with NLRC4 to form an inflammasome complex able to recruit and activate pro-caspase-1. NAIP5 and NAIP6 sense flagellin, component of flagella from motile bacteria, whereas NAIP1 and NAIP2 detect needle and rod components from bacterial type III secretion systems, respectively. Active caspase-1 mediates the maturation and secretion of the pro-inflammatory cytokines, 11,113 and 11,18, and is responsible for the induction of pyroptosis, a pro-inflammatory form of cell death. in addition to these well-known effector mechanisms, novel roles have been described for NAIP/NLRC4 inflammasomes, such as phagosomal maturation, activation of inducible nitric oxide synthase, regulation of autophagy, secretion of inflammatory mediators, antibody production, activation of T cells, among others. These effector mechanisms mediated by NAIP/NLRC4 inflammasomes have been extensively studied in the context of resistance of infections and the potential of their agonists has been exploited in therapeutic strategies to non-infectious pathologies, such as tumor protection. Thus, this review will discuss current knowledge about the activation of NAIP/NLRC4 inflammasomes and their effector mechanisms.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)INCTVUniversidade Federal de São Paulo, Ctr Terapia Celulare & Mol CTC Mol, BR-04044010 São Paulo, SP, BrazilUniversidade Federal de São Paulo, Dept Ciencias Biol, BR-04044010 São Paulo, SP, BrazilUniversidade Federal de São Paulo, Ctr Terapia Celulare & Mol CTC Mol, BR-04044010 São Paulo, SP, BrazilUniversidade Federal de São Paulo, Dept Ciencias Biol, BR-04044010 São Paulo, SP, BrazilFAPESP: 2013/16010-5Web of Scienc

EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical Text

Background Medical research generates millions of publications and it is a great challenge for researchers to utilize this information in full since its scale and complexity greatly surpasses human reading capabilities. Automated text mining can help extract and connect information spread across this large body of literature but this technology is not easily accessible to life scientists. Results Here, we developed an easy-to-use end-to-end pipeline for deep learning- and dictionary-based named entity recognition (NER) of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19. Conclusions The NER pipeline we present is applicable in a variety of medical research settings and makes customizable text mining accessible to life scientists

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10-11 to 5.0 × 10-21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10-6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation