Trapped ion chain as a neural network

We demonstrate the possibility of realizing a neural network in a chain of trapped ions with induced long range interactions. Such models permit to store information distributed over the whole system. The storage capacity of such network, which depends on the phonon spectrum of the system, can be controlled by changing the external trapping potential and/or by applying longitudinal local magnetic fields. The system properties suggest the possibility of implementing robust distributed realizations of quantum logic.Comment: 4 pages, 3 figure

Double Fe-impurity charge state in the topological insulator Bi2_2Se3_3

The influence of individual impurities of Fe on the electronic properties of topological insulator Bi$_2$Se$_3$ is studied by Scanning Tunneling Microscopy. The microscope tip is used in order to remotely charge/discharge Fe impurities. The charging process is shown to depend on the impurity location in the crystallographic unit cell, on the presence of other Fe impurities in the close vicinity, as well as on the overall doping level of the crystal. We present a qualitative explanation of the observed phenomena in terms of tip-induced local band bending. Our observations evidence that the specific impurity neighborhood and the position of the Fermi energy with respect to the Dirac point and bulk bands have both to be taken into account when considering the electron scattering on the disorder in topological insulators.Comment: 10 pages, accepted for publication in Applied Physics Letters, minor bugs were correcte

Cooling of Neutron Stars: Two Types of Triplet Neutron Pairing

We consider cooling of neutron stars (NSs) with superfluid cores composed of neutrons, protons, and electrons (assuming singlet-state pairing of protons, and triplet-state pairing of neutrons). We mainly focus on (nonstandard) triplet-state pairing of neutrons with the $|m_J| = 2$ projection of the total angular momentum of Cooper pairs onto quantization axis. The specific feature of this pairing is that it leads to a power-law (nonexponential) reduction of the emissivity of the main neutrino processes by neutron superfluidity. For a wide range of neutron critical temperatures $T_{cn}$, the cooling of NSs with the $|m_J| = 2$ superfluidity is either the same as the cooling with the $m_J = 0$ superfluidity, considered in the majority of papers, or much faster. The cooling of NSs with density dependent critical temperatures $T_{cn}(\rho)$ and $T_{cp}(\rho)$ can be imitated by the cooling of the NSs with some effective critical temperatures $T_{cn}$ and $T_{cp}$ constant over NS cores. The hypothesis of strong neutron superfluidity with $|m_J| = 2$ is inconsistent with current observations of thermal emission from NSs, but the hypothesis of weak neutron superfluidity of any type does not contradict to observations.Comment: 10 pages, 6 figure

UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets

Background: Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently representative of real datasets. Results: Here, we propose an unsupervised method for the unification of clustering results from multiple datasets using external specifications (UNCLES). This method has the ability to identify the subsets of genes consistently co-expressed in a subset of datasets while being poorly co-expressed in another subset of datasets, and to identify the subsets of genes consistently co-expressed in all given datasets. We also propose the M-N scatter plots validation technique and adopt it to set the parameters of UNCLES, such as the number of clusters, automatically. Additionally, we propose an approach for the synthesis of gene expression datasets using real data profiles in a way which combines the ground-truth-knowledge of synthetic data and the realistic expression values of real data, and therefore overcomes the problem of faithfulness of synthetic expression data modelling. By application to those datasets, we validate UNCLES while comparing it with other conventional clustering methods, and of particular relevance, biclustering methods. We further validate UNCLES by application to a set of 14 real genome-wide yeast datasets as it produces focused clusters that conform well to known biological facts. Furthermore, in-silico-based hypotheses regarding the function of a few previously unknown genes in those focused clusters are drawn. Conclusions: The UNCLES method, the M-N scatter plots technique, and the expression data synthesis approach will have wide application for the comprehensive analysis of genomic and other sources of multiple complex biological datasets. Moreover, the derived in-silico-based biological hypotheses represent subjects for future functional studies.The National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0310-1004)

Ontogenetic changes in leaf traits of tropical rainforest trees differing in juvenile light requirement

Relationships between leaf traits and the gap dependence for regeneration, and ontogenetic changes therein, were investigated in juvenile and adult tropical rainforest tree species. The juveniles of the 17 species included in the study were grown in high light, similar to the exposed crowns of the adult trees. The traits were structural, biomechanical, chemical and photosynthetic. With increasing species gap dependence, leaf mass per area (LMA) decreased only slightly in juveniles and remained constant in adults, whereas punch strength together with tissue density decreased, and photosynthetic capacity and chlorophyll increased. Contrary to what has been mostly found in evergreen tropical rainforest, the trade-off between investment in longevity and in productivity was evident at an essentially constant LMA. Of the traits pertaining to the chloroplast level, photosynthetic capacity per unit chlorophyll increased with gap dependence, but the chlorophyll a/b ratio showed no relationship. Adults had a twofold higher LMA, but leaf strength was on average only about 50% larger. Leaf tissue density, and chlorophyll and leaf N per area were also higher, whereas chlorophyll and leaf N per unit dry mass were lower. Ranking of the species, relationships between traits and with the gap dependence of the species were similar for juveniles and adults. However, the magnitudes of most ontogenetic changes were not clearly related to a species’ gap dependence. The adaptive value of the leaf traits for juveniles and adults is discussed

Metabolic profiling of sourdough fermented wheat and rye bread

Sourdough fermentation by lactic acid bacteria is commonly used in bread baking, affecting several attributes of the final product. We analyzed whole-grain wheat and rye breads and doughs prepared with baker's yeast or a sourdough starter including Candida milleri, Lactobacillus brevis and Lactobacillus plantarum using non-targeted metabolic profiling utilizing LC-QTOF-MS. The aim was to determine the fermentation-induced changes in metabolites potentially contributing to the health-promoting properties of whole-grain wheat and rye. Overall, we identified 118 compounds with significantly increased levels in sourdough, including branched-chain amino acids (BCAAs) and their metabolites, small peptides with high proportion of BCAAs, microbial metabolites of phenolic acids and several other potentially bioactive compounds. We also identified 69 compounds with significantly decreased levels, including phenolic acid precursors, nucleosides, and nucleobases. Intensive sourdough fermentation had a higher impact on the metabolite profile of whole-grain rye compared to milder whole-grain wheat sourdough fermentation. We hypothesize that the increased amount of BCAAs and potentially bioactive small peptides may contribute to the insulin response of rye bread, and in more general, the overall protective effect against T2DM and CVD.Peer reviewe

Normal reference values of strength in pelvic floor muscle of women: a descriptive and inferential study

Background: To describe the clinical, functional and quality of life characteristics in women with Stress Urinary Incontinence (SUI). In addition, to analyse the relationship between the variables reported by the patients and those informed by the clinicians, and the relationship between instrumented variables and the manual pelvic floor strength assessment.Methods: Two hundred and eighteen women participated in this observational, analytical study. An interview about Urinary Incontinence and the quality of life questionnaires (EuroQoL-5D and SF-12) were developed as outcomes reported by the patients. Manual muscle testing and perineometry as outcomes informed by the clinician were assessed. Descriptive and correlation analysis were carried out.Results: The average age of the subjects was (39.93 ± 12.27 years), (24.49 ± 3.54 BMI). The strength evaluated by manual testing of the right levator ani muscles was 7.79 ± 2.88, the strength of left levator ani muscles was 7.51 ± 2.91 and the strength assessed with the perineometer was 7.64 ± 2.55. A positive correlation was found between manual muscle testing and perineometry of the pelvic floor muscles (p < .001). No correlation was found between outcomes of quality of life reported by the patients and outcomes of functional capacity informed by the physiotherapist.Conclusion: A stratification of the strength of pelvic floor muscles in a normal distribution of a large sample of women with SUI was done, which provided the clinic with a baseline. There is a relationship between the strength of the pelvic muscles assessed manually and that obtained by a perineometer in women with SUI. There was no relationship between these values of strength and quality of life perceived

An Earthworm Riddle: Systematics and Phylogeography of the Spanish Lumbricid Postandrilus

As currently defined, the genus Postandrilus Qui and Bouché, 1998, (Lumbricidae) includes six earthworm species, five occurring in Majorca (Baleares Islands, western Mediterranean) and another in Galicia (NW Spain). This disjunct and restricted distribution raises some interesting phylogeographic questions: (1) Is Postandrilus distribution the result of the separation of the Baleares-Kabylies (BK) microplate from the proto-Iberian Peninsula in the Late Oligocene (30-28 Mya)--vicariant hypothesis? (2) Did Postandrilus diversify in Spain and then colonize the Baleares during the Messinian salinity crisis (MSC) 5.96-5.33 Mya--dispersal hypothesis? (3) Is the distribution the result of a two-step process--vicariance with subsequent dispersal?To answer these questions and assess Postandrilus evolutionary relationships and systematics, we collected all of the six Postandrilus species (46 specimens - 16 locations) and used Aporrectodea morenoe and three Prosellodrilus and two Cataladrilus species as the outgroup. Regions of the nuclear 28S rDNA and mitochondrial 16S rDNA, 12S rDNA, ND1, COII and tRNA genes (4,666 bp) were sequenced and analyzed using maximum likelihood and Bayesian methods of phylogenetic and divergence time estimation. The resulting trees revealed six new Postandrilus species in Majorca that clustered with the other five species already described. This Majorcan clade was sister to an Iberian clade including A. morenoe (outgroup) and Postandrilus bertae. Our phylogeny and divergence time estimates indicated that the split between the Iberian and Majorcan Postandrilus clades took place 30.1 Mya, in concordance with the break of the BK microplate from the proto-Iberian Peninsula, and that the present Majorcan clade diversified 5.7 Mya, during the MSC.Postandrilus is highly diverse including multiple cryptic species in Majorca. The genus is not monophyletic and invalid as currently defined. Postandrilus is of vicariant origin and its radiation began in the Late Oligocene