The whole and its parts : why and how to disentangle plant communities and synusiae in vegetation classification

Most plant communities consist of different structural and ecological subsets, ranging from cryptogams to different tree layers. The completeness and approach with which these subsets are sampled have implications for vegetation classification. Non‐vascular plants are often omitted or sometimes treated separately, referring to their assemblages as “synusiae” (e.g. epiphytes on bark, saxicolous species on rocks). The distinction of complete plant communities (phytocoenoses or holocoenoses) from their parts (synusiae or merocoenoses) is crucial to avoid logical problems and inconsistencies of the resulting classification systems. We here describe theoretical differences between the phytocoenosis as a whole and its parts, and outline consequences of this distinction for practise and terminology in vegetation classification. To implement a clearer separation, we call for modifications of the International Code of Phytosociological Nomenclature and the EuroVegChecklist. We believe that these steps will make vegetation classification systems better applicable and raise the recognition of the importance of non‐vascular plants in the vegetation as well as their interplay with vascular plants

Lineage-based identification of cellular states and expression programs

We present a method, LineageProgram, that uses the developmental lineage relationship of observed gene expression measurements to improve the learning of developmentally relevant cellular states and expression programs. We find that incorporating lineage information allows us to significantly improve both the predictive power and interpretability of expression programs that are derived from expression measurements from in vitro differentiation experiments. The lineage tree of a differentiation experiment is a tree graph whose nodes describe all of the unique expression states in the input expression measurements, and edges describe the experimental perturbations applied to cells. Our method, LineageProgram, is based on a log-linear model with parameters that reflect changes along the lineage tree. Regularization with L1 that based methods controls the parameters in three distinct ways: the number of genes change between two cellular states, the number of unique cellular states, and the number of underlying factors responsible for changes in cell state. The model is estimated with proximal operators to quickly discover a small number of key cell states and gene sets. Comparisons with existing factorization, techniques, such as singular value decomposition and non-negative matrix factorization show that our method provides higher predictive power in held, out tests while inducing sparse and biologically relevant gene sets.National Institutes of Health (U.S.) (P01-NS055923)National Institutes of Health (U.S.) (1-UL1-RR024920

Interplay between unconventional superconductivity and heavy-fermion quantum criticality: CeCu2_2Si2_2 versus YbRh2_2Si2_2

In this paper the low-temperature properties of two isostructural canonical heavy-fermion compounds are contrasted with regards to the interplay between antiferromagnetic (AF) quantum criticality and superconductivity. For CeCu$_2$Si$_2$, fully-gapped d-wave superconductivity forms in the vicinity of an itinerant three-dimensional heavy-fermion spin-density-wave (SDW) quantum critical point (QCP). Inelastic neutron scattering results highlight that both quantum critical SDW fluctuations as well as Mott-type fluctuations of local magnetic moments contribute to the formation of Cooper pairs in CeCu$_2$Si$_2$. In YbRh$_2$Si$_2$, superconductivity appears to be suppressed at $T\gtrsim~10$ mK by AF order ($T_N$ = 70 mK). Ultra-low temperature measurements reveal a hybrid order between nuclear and 4f-electronic spins, which is dominated by the Yb-derived nuclear spins, to develop at $T_A$ slightly above 2 mK. The hybrid order turns out to strongly compete with the primary 4f-electronic order and to push the material towards its QCP. Apparently, this paves the way for heavy-fermion superconductivity to form at $T_c$ = 2 mK. Like the pressure - induced QCP in CeRhIn$_5$, the magnetic field - induced one in YbRh$_2$Si$_2$ is of the local Kondo-destroying variety which corresponds to a Mott-type transition at zero temperature. Therefore, these materials form the link between the large family of about fifty low-$T$ unconventional heavy - fermion superconductors and other families of unconventional superconductors with higher $T_c$s, notably the doped Mott insulators of the cuprates, organic charge-transfer salts and some of the Fe-based superconductors. Our study suggests that heavy-fermion superconductivity near an AF QCP is a robust phenomenon.Comment: 30 pages, 7 Figures, Accepted for publication in Philosophical Magazin

Correlative analyses of RET and RAS mutations in a phase 3 trial of cabozantinib in patients with progressive, metastatic medullary thyroid cancer

BACKGROUND: Cabozantinib significantly prolonged progression-free survival (PFS) versus a placebo in patients with progressive, metastatic medullary thyroid cancer (MTC; P <.001). An exploratory analysis of phase 3 trial data evaluated the influence of rearranged during transfection (RET) and RAS (HRAS, KRAS, and NRAS) mutations on cabozantinib clinical activity. METHODS: Patients (n = 330) were randomized to cabozantinib (140 mg/day) or a placebo. The primary endpoint was PFS. Additional outcome measures included PFS, objective response rates (ORRs), and adverse events in RET and RAS mutation subgroups. RESULTS: Among all study patients, 51.2% were RET mutation–positive (38.2% with RET M918T), 34.8% were RET mutation–unknown, and 13.9% were RET mutation–negative. Sixteen patients were RAS mutation–positive. Cabozantinib appeared to prolong PFS versus the placebo in the RET mutation–positive subgroup (hazard ratio [HR], 0.23; 95% confidence interval [CI], 0.14-0.38; P <.0001), the RET mutation–unknown subgroup (HR, 0.30; 95% CI, 0.16-0.57; P =.0001), and the RAS mutation–positive subgroup (HR, 0.15; 95% CI, 0.02-1.10; P =.0317). The RET M918T subgroup achieved the greatest observed PFS benefit from cabozantinib versus the placebo (HR, 0.15; 95% CI, 0.08-0.28; P <.0001). The ORRs for RET mutation–positive, RET mutation–negative, and RAS mutation–positive patients were 32%, 22%, and 31%, respectively. No PFS benefit was observed in patients lacking both RET and RAS mutations, although the ORR was 21%. The safety profile for all subgroups was similar to that for the overall cabozantinib arm. CONCLUSIONS: These data suggest that cabozantinib provides the greatest clinical benefit to patients with MTC who have RET M918T or RAS mutations. However, a prospective trial is needed to confirm the relation between genetic variation and the response to cabozantinib. Cancer 2016;122:3856–3864. © 2016 American Cancer Society

Monte Carlo Analysis of a New Interatomic Potential for He

By means of a Quadratic Diffusion Monte Carlo method we have performed a comparative analysis between the Aziz potential and a revised version of it. The results demonstrate that the new potential produces a better description of the equation of state for liquid $^4$He. In spite of the improvement in the description of derivative magnitudes of the energy, as the pressure or the compressibility, the energy per particle which comes from this new potential is lower than the experimental one. The inclusion of three-body interactions, which give a repulsive contribution to the potential energy, makes it feasible that the calculated energy comes close to the experimental result.Comment: 36 pages, LaTex, 11 PostScript figures include

The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes

Background: The most common cause of Gram-negative bacterial neonatal meningitis is E. coli K1. It has a mortality rate of 10–15%, and neurological sequelae in 30– 50% of cases. Infections can be attributable to nosocomial sources, however the pre-colonisation of enteral feeding tubes has not been considered as a specific risk factor. Methods: Thirty E. coli strains, which had been isolated in an earlier study, from the residual lumen liquid and biofilms of neonatal nasogastric feeding tubes were genotyped using pulsed-field gel electrophoresis, and 7-loci multilocus sequence typing. Potential pathogenicity and biofilm associated traits were determined using specific PCR probes, genome analysis, and in vitro tissue culture assays. Results: The E. coli strains clustered into five pulsotypes, which were genotyped as sequence types (ST) 95, 73, 127, 394 and 2076 (Achman scheme). The extra-intestinal pathogenic E. coli (ExPEC) phylogenetic group B2 ST95 serotype O1:K1:NM strains had been isolated over a 2 week period from 11 neonates who were on different feeding regimes. The E. coli K1 ST95 strains encoded for various virulence traits associated with neonatal meningitis and extracellular matrix formation. These strains attached and invaded intestinal, and both human and rat brain cell lines, and persisted for 48 h in U937 macrophages. E. coli STs 73, 394 and 2076 also persisted in macrophages and invaded Caco-2 and human brain cells, but only ST394 invaded rat brain cells. E. coli ST127 was notable as it did not invade any cell lines. Conclusions: Routes by which E. coli K1 can be disseminated within a neonatal intensive care unit are uncertain, however the colonisation of neonatal enteral feeding tubes may be one reservoir source which could constitute a serious health risk to neonates following ingestion

The Λp\bf{\Lambda p} interaction studied via femtoscopy in p + Nb reactions at sNN=3.18 GeV\mathbf{\sqrt{s_{NN}}=3.18} ~\mathrm{\bf{GeV}}

We report on the first measurement of $p\Lambda$ and $pp$ correlations via the femtoscopy method in p+Nb reactions at $\mathrm{\sqrt{s_{NN}}=3.18} ~\mathrm{GeV}$, studied with the High Acceptance Di-Electron Spectrometer (HADES). By comparing the experimental correlation function to model calculations, a source size for $pp$ pairs of $r_{0,pp}=2.02 \pm 0.01(\mathrm{stat})^{+0.11}_{-0.12} (\mathrm{sys}) ~\mathrm{fm}$ and a slightly smaller value for $p\Lambda$ of $r_{0,\Lambda p}=1.62 \pm 0.02(\mathrm{stat})^{+0.19}_{-0.08}(\mathrm{sys}) ~\mathrm{fm}$ is extracted. Using the geometrical extent of the particle emitting region, determined experimentally with $pp$ correlations as reference together with a source function from a transport model, it is possible to study different sets of scattering parameters. The $p\Lambda$ correlation is proven sensitive to predicted scattering length values from chiral effective field theory. We demonstrate that the femtoscopy technique can be used as valid alternative to the analysis of scattering data to study the hyperon-nucleon interaction.Comment: 12 pages, 11 figure

The Hilbertian Tensor Norm and Entangled Two-Prover Games

We study tensor norms over Banach spaces and their relations to quantum information theory, in particular their connection with two-prover games. We consider a version of the Hilbertian tensor norm $\gamma_2$ and its dual $\gamma_2^*$ that allow us to consider games with arbitrary output alphabet sizes. We establish direct-product theorems and prove a generalized Grothendieck inequality for these tensor norms. Furthermore, we investigate the connection between the Hilbertian tensor norm and the set of quantum probability distributions, and show two applications to quantum information theory: firstly, we give an alternative proof of the perfect parallel repetition theorem for entangled XOR games; and secondly, we prove a new upper bound on the ratio between the entangled and the classical value of two-prover games.Comment: 33 pages, some of the results have been obtained independently in arXiv:1007.3043v2, v2: an error in Theorem 4 has been corrected; Section 6 rewritten, v3: completely rewritten in order to improve readability; title changed; references added; published versio