The onset time of Fermi's golden rule

Fermi's golden rule describes the decay dynamics of unstable quantum systems coupled to a reservoir, and predicts a linear decay in time. Although it arises at relatively short times, the Fermi regime does not take hold in the earliest stages of the quantum dynamics. The standard criterion in the literature for the onset time of the Fermi regime is $t_F\sim1/\Delta\omega$, with $\Delta\omega$ the frequency interval around the resonant transition frequency $\omega_0$ of the system, over which the coupling to the reservoir does not vary appreciably. In this work, this criterion is shown to be inappropriate in general for broadband reservoirs, where the reservoir coupling spectrum takes the form $R\left(\omega\right)\propto\omega^\eta$, and for which it is found that for $\eta>1$, the onset time of the Fermi regime is given by $t_F\propto\left(\omega_{\mathrm{X}}/\omega_0\right)^{\eta-1}\times1/\omega_0$ where $\omega_{\mathrm{X}}$ is the high-frequency cutoff of the reservoir. Therefore, the onset of the Fermi regime can take place at times orders of magnitude larger than those predicted by the standard criterion. This phenomenon is shown to be related to the excitation of the off-resonant frequencies of the reservoir at short times. For broadband reservoirs with $\eta\leq1$, and for narrowband reservoirs, it is shown that the standard criterion is correct. Our findings revisit the conditions of applicability of Fermi's golden rule and improve our understanding of the dynamics of unstable quantum systems

Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres

TPMS: a set of utilities for querying collections of gene trees

Background: The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. Results: In this paper, we present TPMS (Tree Pattern-Matching Suite), a set of programs for handling and retrieving gene trees according to different criteria. The programs from the suite include utilities for tree collection building, specific tree-pattern search strategies and tree rooting. Use of TPMS is illustrated through three examples: systematic search for incongruencies in a large tree collection, a short study on the Coelomata/Ecdysozoa controversy and an evaluation of the level of support for a recently published Mammal phylogeny. Conclusion: TPMS is a powerful suite allowing to quickly retrieve sets of trees matching complex patterns in large collection or to root trees using more rigorous approaches than the classical midpoint method. As it is made of a set of command-line programs, it can be easily integrated in any sequence analysis pipeline for an automated use

2-{(E)-N-[2-(1H-Inden-3-yl)eth­yl]imino­meth­yl}-1H-imidazole

The asymmetric unit of the title compound, C15H15N3, contains two crystallographically independent mol­ecules with very similar geometries. The imidazole and indenyl planes are approximately orthogonal, making dihedral angles of 88.21 (9) and 83.08 (9)%deg; in the two independent molecules. In the crystal, the imidazole units are linked by N—H⋯N hydrogen bonds into chains parallel to the 101) plane stretched in the diagonal direction [translation vector (,1,0); C(4) motif]. Within a chain, there are two types of symmetrically non-equivalent alternating H-bonds which slightly differ in their parameters

Precision measurements of the top quark mass from the Tevatron in the pre-LHC era

The top quark is the heaviest of the six quarks of the Standard Model. Precise knowledge of its mass is important for imposing constraints on a number of physics processes, including interactions of the as yet unobserved Higgs boson. The Higgs boson is the only missing particle of the Standard Model, central to the electroweak symmetry breaking mechanism and generation of particle masses. In this Review, experimental measurements of the top quark mass accomplished at the Tevatron, a proton-antiproton collider located at the Fermi National Accelerator Laboratory, are described. Topologies of top quark events and methods used to separate signal events from background sources are discussed. Data analysis techniques used to extract information about the top mass value are reviewed. The combination of several most precise measurements performed with the two Tevatron particle detectors, CDF and \D0, yields a value of \Mt = 173.2 \pm 0.9 GeV/$c^2$.Comment: This version contains the most up-to-date top quark mass averag

Quantum Calogero-Moser Models: Integrability for all Root Systems

The issues related to the integrability of quantum Calogero-Moser models based on any root systems are addressed. For the models with degenerate potentials, i.e. the rational with/without the harmonic confining force, the hyperbolic and the trigonometric, we demonstrate the following for all the root systems: (i) Construction of a complete set of quantum conserved quantities in terms of a total sum of the Lax matrix (L), i.e. (\sum_{\mu,\nu\in{\cal R}}(L^n)_{\mu\nu}), in which ({\cal R}) is a representation space of the Coxeter group. (ii) Proof of Liouville integrability. (iii) Triangularity of the quantum Hamiltonian and the entire discrete spectrum. Generalised Jack polynomials are defined for all root systems as unique eigenfunctions of the Hamiltonian. (iv) Equivalence of the Lax operator and the Dunkl operator. (v) Algebraic construction of all excited states in terms of creation operators. These are mainly generalisations of the results known for the models based on the (A) series, i.e. (su(N)) type, root systems.Comment: 45 pages, LaTeX2e, no figure

Uncoupling of the endocannabinoid signalling complex in a mouse model of fragile X syndrome

Fragile X syndrome, the most commonly known genetic cause of autism, is due to loss of the fragile X mental retardation protein, which regulates signal transduction at metabotropic glutamate receptor-5 in the brain. Fragile X mental retardation protein deletion in mice enhances metabotropic glutamate receptor-5-dependent long-term depression in the hippocampus and cerebellum. Here we show that a distinct type of metabotropic glutamate receptor-5-dependent long-term depression at excitatory synapses of the ventral striatum and prefrontal cortex, which is mediated by the endocannabinoid 2-arachidonoyl-sn-glycerol, is absent in fragile X mental retardation protein-null mice. In these mutants, the macromolecular complex that links metabotropic glutamate receptor-5 to the 2-arachidonoyl-sn-glycerolproducing enzyme, diacylglycerol lipase-α (endocannabinoid signalosome), is disrupted and metabotropic glutamate receptor-5-dependent 2-arachidonoyl-sn-glycerol formation is compromised. These changes are accompanied by impaired endocannabinoid-dependent long-term depression. Pharmacological enhancement of 2-arachidonoyl-sn-glycerol signalling normalizes this synaptic defect and corrects behavioural abnormalities in fragile X mental retardation protein-deficient mice. The results identify the endocannabinoid signalosome as

Association of combined PD- L1 expression and tumour- infiltrating lymphocyte features with survival and treatment outcomes in patients with metastatic melanoma

BackgroundRecent advances obtained with immune checkpoint inhibitors (ICIs) targeting the programmed cell death- 1 (PD- 1) protein have significantly improved the outcome of patients with metastatic melanoma. The PD- L1 expression in tumour cells as detected by immunohistochemistry is a predictive biomarker in some solid tumours, but appears insufficient as prognostic or predictive factor of response to ICIs in metastatic melanomas.ObjectivesWe investigated whether the presence and the features of pretreatment CD8+tumour- infiltrating T lymphocytes (TILs) could be a complementary prognostic or predictive biomarker in patients with metastatic melanoma.MethodsIn this retrospective study, we evaluated the association of PD- L1 expression - ¥5% of tumour cells combined with TIL features (CD8, CD28, Ki67) with the overall survival (OS) among 51 patients treated with ICIs and 54 patients treated with other treatment options (non- ICIs).ResultsPD- L1 positivity was observed in 33% and 39% of primary melanomas and matched metastases, respectively, with, however, poor concordance between the primary and the matched metastatic site (κ = 0.283). No significant association was noted between PD- L1 expression and CD8+TIL profile analysed as single markers and OS or response to immunotherapy. Instead, their combined analysis in primary melanoma samples showed that the PD- L1- /CD8+status was significantly associated with prolonged OS in the whole population (P = 0.04) and in the subgroup treated with non- ICIs (P = 0.009). Conversely, the PD- L1+/CD8+ status was a good prognostic factor in patients treated with ICIs (P = 0.022), whereas was significantly associated with poor prognosis in patients treated with non- ICIs (P = 0.014). While the expression of CD28 was not related to outcome, the Ki67 expression was significantly associated with poor OS in the subgroup CD8+TIL+/PD- L1- (P = 0.02).ConclusionsThe pretreatment combination of PD- L1 expression with the level of CD8+TILs could better assess OS and predict therapeutic response of patients with metastatic melanoma treated by either immunotherapy or other treatment regimens.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155478/1/jdv16016_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155478/2/jdv16016.pd

Safety and diagnostic yield of renal biopsy in the intensive care unit

Purpose Renal biopsy (RB) is occasionally performed in critically ill patients. The safety and impact of RB in this setting have not been reported. Methods A 10-year (2000–2009) retrospective multicentre study was conducted in ten French intensive care units (ICU) on patients who underwent RB during their management. Medical files were retrieved for data analysis. Results Seventy-seven patients underwent an RB of which 68 (88 %) were on a native kidney and 9 (12 %) on a transplanted kidney. Percutaneous ultrasound-guided RB was used in most cases (87 %). Fifty-seven per cent of the patients were on mechanical ventilation at the time of RB. RB-related complications occurred in 17 (22 %) patients, two were graded as severe (requirement for kidney embolization, eventually successful). In 35 (51 %) non-transplanted patients, RB established a specific diagnosis other than acute tubular necrosis (ATN), which was diagnosed in only 18 % of patients. In the remaining patients, only non-specific lesions were observed. Therapeutic modifications followed RB in 14 (21 %) non-transplanted patients. Presence of signs of systemic disease involving the renal tract, occurrence of renal failure before hospital admission, and absence of any factor usually associated with ATN significantly predicted the presence of a specific diagnosis at RB other than ATN. Conclusions In this cohort, the contribution of RB to diagnosis and treatment was undeniable, but at the expense of frequent adverse events although most of them were not considered severe