On dendrograms, ordinations and functional spaces: Methodo-logical choices or pitfalls?

A number of concerns persist regarding (i) how functional spaces should be quantified, (ii) how phylogenetic richness should be calculated, (iii) and how functional beta diversity should be calculated. Because all current methods have their shortcomings we think that analytical choices are as much a matter of knowing the limitations of the data and knowing the working hypothesis. Only then can one follow their personal choice, weighing up the shortcomings of different methods that, at the end of the day, usually produce qualitatively similar results

Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages

The ratio of species extinctions to introductions has been comparable for many insular assemblages, suggesting that introductions could have ‘compensated’ for extinctions. However, the capacity for introduced species to replace ecological roles and evolutionary history lost following extinction is unclear. We investigated changes in bird functional and phylogenetic diversity in the wake of extinctions and introductions across a sample of 32 islands worldwide. We found that extinct and introduced species have comparable functional and phylogenetic alpha diversity. However, this was distributed at different positions in functional space and in the phylogeny, indicating a ‘false compensation’. Introduced and extinct species did not have equivalent functional roles nor belong to similar lineages. This makes it unlikely that novel island biotas composed of introduced taxa will be able to maintain ecological roles and represent the evolutionary histories of pre-disturbance assemblages and highlights the importance of evaluating changes in alpha and beta diversity concurrently

Fetal growth and glycemic control in type 1 diabetes pregnancy

INTRODUCTION: Conflicting results have been reported with respect to the relationship between direct or indirect measures of glycemic control in mothers with type 1 diabetes and macrosomia. OBJECTIVE: To evaluate the frequency of LGA babies in type 1 diabetic pregnancies and analyse the influence of some maternal characteristics and glucose control in oversized babies. MATERIAL AND METHODS: A retrospective study of 18 pregnant women with type 1 diabetes mellitus was performed. It was divided in two groups: group 1 (G1- n=9)--pregnant women with LGA babies and group 2 (G2- n=9)--pregnant women with AGA (Appropriate weight for gestational age) babies. We evaluate the follow parameters: HbA1c in the third trimester of pregnancy, fasting and 1 h postprandial capillary glucose levels, pregestational BMI, maternal age, duration of Diabetes mellitus, weight gain during pregnancy, microvascular diabetes complications (retinopathy and nefropathy), and type of delivery. We defined LGA birth weight over the 90 centile. RESULTS: LGA babies occurred in 50% of gestations. We did not find any statistical differences in maternal age, diabetes mellitus duration, pregestational BMI, weight gain during pregnancy, microvascular diabetes complications, HbA1c levels (medium value in the two groups 6,5%). The glucose fasting values were higher in G1: 95,7 +/- 31.7 mg/ dl, vs G2: 83.3 +/- 17.1 mg/dl without, however, reaching statistically significant differences. There was statically differences in postprandial glucose values G1: 160.3 +/- 60.2 mg/dl vs G2: 111.9 +/- 27.1 mg/dl -- p= 0.043. CONCLUSIONS: The frequency of LGA babies was elevated 50% in type 1 diabetic pregnancies, although normal HbA1c values. Thus we conclude that the 1 h postprandial glucose levels should be considered a strong predictor of fetal growth

Nanostructured 3D Constructs Based on Chitosan and Chondroitin Sulphate Multilayers for Cartilage Tissue Engineering

Nanostructured three-dimensional constructs combining layer-by-layer technology (LbL) and template leaching were processed and evaluated as possible support structures for cartilage tissue engineering. Multilayered constructs were formed by depositing the polyelectrolytes chitosan (CHT) and chondroitin sulphate (CS) on either bidimensional glass surfaces or 3D packet of paraffin spheres. 2D CHT/CS multi-layered constructs proved to support the attachment and proliferation of bovine chondrocytes (BCH). The technology was transposed to 3D level and CHT/CS multi-layered hierarchical scaffolds were retrieved after paraffin leaching. The obtained nanostructured 3D constructs had a high porosity and water uptake capacity of about 300%. Dynamical mechanical analysis (DMA) showed the viscoelastic nature of the scaffolds. Cellular tests were performed with the culture of BCH and multipotent bone marrow derived stromal cells (hMSCs) up to 21 days in chondrogenic differentiation media. Together with scanning electronic microscopy analysis, viability tests and DNA quantification, our results clearly showed that cells attached, proliferated and were metabolically active over the entire scaffold. Cartilaginous extracellular matrix (ECM) formation was further assessed and results showed that GAG secretion occurred indicating the maintenance of the chondrogenic phenotype and the chondrogenic differentiation of hMSCs

Rise and Demise of Bioinformatics? Promise and Progress

The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself

An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved

Bacterial type IV secretion systems (T4SSs) comprise a diverse transporter family functioning in conjugation, competence, and effector molecule (DNA and/or protein) translocation. Thirteen genome sequences from Rickettsia, obligate intracellular symbionts/pathogens of a wide range of eukaryotes, have revealed a reduced T4SS relative to the Agrobacterium tumefaciens archetype (vir). However, the Rickettsia T4SS has not been functionally characterized for its role in symbiosis/virulence, and none of its substrates are known.Superimposition of T4SS structural/functional information over previously identified Rickettsia components implicate a functional Rickettsia T4SS. virB4, virB8 and virB9 are duplicated, yet only one copy of each has the conserved features of similar genes in other T4SSs. An extraordinarily duplicated VirB6 gene encodes five hydrophobic proteins conserved only in a short region known to be involved in DNA transfer in A. tumefaciens. virB1, virB2 and virB7 are newly identified, revealing a Rickettsia T4SS lacking only virB5 relative to the vir archetype. Phylogeny estimation suggests vertical inheritance of all components, despite gene rearrangements into an archipelago of five islets. Similarities of Rickettsia VirB7/VirB9 to ComB7/ComB9 proteins of epsilon-proteobacteria, as well as phylogenetic affinities to the Legionella lvh T4SS, imply the Rickettsiales ancestor acquired a vir-like locus from distantly related bacteria, perhaps while residing in a protozoan host. Modern modifications of these systems likely reflect diversification with various eukaryotic host cells.We present the rvh (Rickettsiales vir homolog) T4SS, an evolutionary conserved transporter with an unknown role in rickettsial biology. This work lays the foundation for future laboratory characterization of this system, and also identifies the Legionella lvh T4SS as a suitable genetic model

Observation of Two New Excited Ξb0 States Decaying to Λb0 K-π+

Two narrow resonant states are observed in the Λb0K-π+ mass spectrum using a data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the LHCb experiment and corresponding to an integrated luminosity of 6 fb-1. The minimal quark content of the Λb0K-π+ system indicates that these are excited Ξb0 baryons. The masses of the Ξb(6327)0 and Ξb(6333)0 states are m[Ξb(6327)0]=6327.28-0.21+0.23±0.12±0.24 and m[Ξb(6333)0]=6332.69-0.18+0.17±0.03±0.22 MeV, respectively, with a mass splitting of Δm=5.41-0.27+0.26±0.12 MeV, where the uncertainties are statistical, systematic, and due to the Λb0 mass measurement. The measured natural widths of these states are consistent with zero, with upper limits of Γ[Ξb(6327)0]<2.20(2.56) and Γ[Ξb(6333)0]<1.60(1.92) MeV at a 90% (95%) credibility level. The significance of the two-peak hypothesis is larger than nine (five) Gaussian standard deviations compared to the no-peak (one-peak) hypothesis. The masses, widths, and resonant structure of the new states are in good agreement with the expectations for a doublet of 1D Ξb0 resonances

Measurement of the CKM angle γ\gamma using B0→DK∗0B^0 \rightarrow D K^{*0} with D→KS0π+π−D \rightarrow K^0_S \pi^+ \pi^- decays

A model-dependent amplitude analysis of the decay $B^0\rightarrow D(K^0_S\pi^+\pi^-) K^{*0}$ is performed using proton-proton collision data corresponding to an integrated luminosity of 3.0fb$^{-1}$, recorded at $\sqrt{s}=7$ and $8 TeV$ by the LHCb experiment. The CP violation observables $x_{\pm}$ and $y_{\pm}$, sensitive to the CKM angle $\gamma$, are measured to be \begin{eqnarray*} x_- &=& -0.15 \pm 0.14 \pm 0.03 \pm 0.01, y_- &=& 0.25 \pm 0.15 \pm 0.06 \pm 0.01, x_+ &=& 0.05 \pm 0.24 \pm 0.04 \pm 0.01, y_+ &=& -0.65^{+0.24}_{-0.23} \pm 0.08 \pm 0.01, \end{eqnarray*} where the first uncertainties are statistical, the second systematic and the third arise from the uncertainty on the $D\rightarrow K^0_S \pi^+\pi^-$ amplitude model. These are the most precise measurements of these observables. They correspond to $\gamma=(80^{+21}_{-22})^{\circ}$ and $r_{B^0}=0.39\pm0.13$, where $r_{B^0}$ is the magnitude of the ratio of the suppressed and favoured $B^0\rightarrow D K^+ \pi^-$ decay amplitudes, in a $K\pi$ mass region of $\pm50 MeV$ around the $K^*(892)^0$ mass and for an absolute value of the cosine of the $K^{*0}$ decay angle larger than $0.4$.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-007.htm

Search for dark photons produced in 13 TeV pppp collisions

Searches are performed for both promptlike and long-lived dark photons, A 0 , produced in proton-proton collisions at a center-of-mass energy of 13 TeV, using A 0 → μ þ μ − decays and a data sample corresponding to an integrated luminosity of 1 . 6 fb − 1 collected with the LHCb detector. The promptlike A 0 search covers the mass range from near the dimuon threshold up to 70 GeV, while the long-lived A 0 search is restricted to the low-mass region 214 <m ð A 0 Þ < 350 MeV. No evidence for a signal is found, and 90% confidence level exclusion limits are placed on the γ – A 0 kinetic-mixing strength. The constraints placed on promptlike dark photons are the most stringent to date for the mass range 10 . 6 <m ð A 0 Þ < 70 GeV, and are comparable to the best existing limits for m ð A 0 Þ < 0 . 5 GeV. The search for long-lived dark photons is the first to achieve sensitivity using a displaced-vertex signature