The effect of organic matter management on the productivity of Eucalyptus globulus stands in Spain and Portugal: tree growth and harvest residue decomposition in relation to site and treatment

Sustainable management of forest resources, including nutrient retention and protection of the soil structure, is required to ensure long-term soil fertility and productivity of later rotations. Potential depletion of soil nutrients is particularly likely in production systems based on fast-growing trees, such as eucalypts. We have studied production of second rotation Eucalyptus globulus stands at two sites in northern Spain and two in central Portugal, after replanting or coppicing, under four treatments, in which plant residues from the ®rst crop were utilised. The residues were either removed from the sites (Treatment R), spread over the soil surface (Treatments S, uniform spreading, and W, in which the woody debris was con®ned to rows between the trees) or incorporated into the soil by harrowing to 15-cm depth (Treatment I). We measured tree height and girth at intervals over three growing seasons, and root biomass at the Portuguese sites. Decomposition of three residue components: leaves-plus-bark, twigs and branches, was measured in litter bags placed in the position corresponding to the placement of the organic residues. By the end of the experiment, tree height was signi®cantly greater in Treatment I than in Treatment R at both Spanish sites, if planted as seedlings, with intermediate growth in S and W. In Portugal, tree height was smaller in R, though not signi®cantly. DBH showed similar trends, although treatment differences were not signi®cant. Coppiced trees grew faster than seedling trees, but a signi®cant treatment effect on the growth was only observed at the inland Portuguese site, where it was better in Treatment I by the end of the experiment. The residues decomposed signi®cantly faster in I than S or W at the Portuguese sites, but not in Spain. Leaves-plus-bark decomposed faster than twigs, and twigs faster than branches. The results are discussed in relation to recommended management option

PhyleasProg: a user-oriented web server for wide evolutionary analyses

Evolutionary analyses of biological data are becoming a prerequisite in many fields of biology. At a time of high-throughput data analysis, phylogenetics is often a necessary complementary tool for biologists to understand, compare and identify the functions of sequences. But available bioinformatics tools are frequently not easy for non-specialists to use. We developed PhyleasProg (http://phyleasprog.inra.fr), a user-friendly web server as a turnkey tool dedicated to evolutionary analyses. PhyleasProg can help biologists with little experience in evolutionary methodologies by analysing their data in a simple and robust way, using methods corresponding to robust standards. Via a very intuitive web interface, users only need to enter a list of Ensembl protein IDs and a list of species as inputs. After dynamic computations, users have access to phylogenetic trees, positive/purifying selection data (on site and branch-site models), with a display of these results on the protein sequence and on a 3D structure model, and the synteny environment of related genes. This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins

Time-Expanded F-OTDR based on binary sequences

In this paper, the capabilities of time-expanded phase-sensitive optical time-domain reflectometry (TE F-OTDR) using binary sequences are demonstrated. We present a highly flexible and integrable TE F-OTDR approach that allows a customized distributed optical fiber sensor (range, spatial resolution, and acoustic sampling) by simply changing the length of the binary sequence and the reference clock frequencies of the binary sequence generators. The here presented architecture eliminates the need for the cumbersome arbitrary signal generators used to date to create the dual-comb spectra for interrogating the fiber. In this approach, the use of large binary sequences allows us to obtain dual combs in a simple and cost-effective way. Spatial resolution of ~1 cm is achieved, attaining ~15, 000 independent measurements points along the interrogated fiber, with a capability of sensing ~30, 000 measurements points

Multi-Harmony: detecting functional specificity from sequence alignment

Many protein families contain sub-families with functional specialization, such as binding different ligands or being involved in different protein–protein interactions. A small number of amino acids generally determine functional specificity. The identification of these residues can aid the understanding of protein function and help finding targets for experimental analysis. Here, we present multi-Harmony, an interactive web sever for detecting sub-type-specific sites in proteins starting from a multiple sequence alignment. Combining our Sequence Harmony (SH) and multi-Relief (mR) methods in one web server allows simultaneous analysis and comparison of specificity residues; furthermore, both methods have been significantly improved and extended. SH has been extended to cope with more than two sub-groups. mR has been changed from a sampling implementation to a deterministic one, making it more consistent and user friendly. For both methods Z-scores are reported. The multi-Harmony web server produces a dynamic output page, which includes interactive connections to the Jalview and Jmol applets, thereby allowing interactive analysis of the results. Multi-Harmony is available at http://www.ibi.vu.nl/ programs/shmrwww

Cholestasis associated to inborn errors in bile acid synthesis

Several metabolic pathways are involved in the biotransformation of C27 neutral cholesterol to C24 primary bile acids (BAs), mainly cholic acid (CA) and chenodeoxycholic acid (CDCA), which are then conjugated with glycine or taurine. This process can start with the modification of the steroid ring or the shortening of the side chain and involves enzymes present in different subcellular compartments. Inborn errors affecting the biogenesis of organelles, such as peroxisomes, or the expression or function of specific enzymes of these convergent routes result in: i) the lack of mature C24-BAs, with the subsequent impairment in digestion and absorption of dietary fat and liposoluble vitamins, such as vitamin K, which may account for a deficient hepatic synthesis of several coagulation factors; ii) the accumulation of intermediate metabolites, which may affect hepatocyte physiology, causing cholestasis as a commonly shared alteration besides other deleterious hepatic events; and iii) extrahepatic clinical manifestations due to accumulation of toxic metabolites in other territories, such as the nervous system, causing neurological disorders. In general, diseases whose primary alteration is a genetic defect in BA synthesis are diagnosed in children or young individuals with a very low incidence. The symptomatology can markedly vary among individuals, ranging from mild to severe conditions. Oral therapy, based on the enrichment of the BA pool with natural C24-BAs, such as CA, CDCA, glyco-CA, or ursodeoxycholic acid (UDCA), depending on the exact deficiency causing the disease, may be beneficial in preventing life-threatening situations. In contrast, in other cases, a liver transplant is the only option for these patients. This review describes the updated information on the genetic and molecular bases of these diseases and the current approaches to achieve a selective diagnosis and specific treatment

Impact of Liver Inflammation on Bile Acid Side Chain Shortening and Amidation

Bile acid (BA) synthesis from cholesterol by hepatocytes is inhibited by inflammatory cytokines. Whether liver inflammation also affects BA side chain shortening and conjugation was investigated. In human liver cell lines (IHH, HepG2, and HepaRG), agonists of nuclear receptors including the farnesoid X receptor (FXR), liver X receptor (LXR), and peroxisome proliferator-activated receptors (PPARs) did not affect the expression of BA-related peroxisomal enzymes. In contrast, hepatocyte nuclear factor 4? (HNF4?) inhibition down-regulated acyl-CoA oxidase 2 (ACOX2). ACOX2 was repressed by fibroblast growth factor 19 (FGF19), which was prevented by extracellular signal-regulated kinase (ERK) pathway inhibition. These changes were paralleled by altered BA synthesis (HPLC-MS/MS). Cytokines able to down-regulate cholesterol-7?-hydroxylase (CYP7A1) had little effect on peroxisomal enzymes involved in BA synthesis except for ACOX2 and bile acid-CoA:amino acid N-acyltransferase (BAAT), which were down-regulated, mainly by oncostatin M (OSM). This effect was prevented by Janus kinase (JAK) inhibition, which restored BA side chain shortening and conjugation. The binding of OSM to the extracellular matrix accounted for a persistent effect after culture medium replacement. In silico analysis of four databases (n = 201) and a validation cohort (n = 90) revealed an inverse relationship between liver inflammation and ACOX2/BAAT expression which was associated with changes in HNF4? levels. In conclusion, BA side chain shortening and conjugation are inhibited by inflammatory effectors. However, other mechanisms involved in BA homeostasis counterbalance any significant impact on the serum BA profile

Providing Personalized Guidance in Arithmetic Problem Solving

Supervising a student's resolution of an arithmetic word problem is a cumbersome task. Di erent students may use di erent lines of reasoning to reach the nal solution, and the assistance provided should be consistent with the resolution path that the student has in mind. In addition, further learning gains can be achieved if the previous student's background is also considered in the process. In this paper, we outline a relatively simple method to adapt the hints given by an Intelligent Tutoring System to the line of reasoning that the student is currently following. We also outline possible extensions to build a model of the student's most relevant skills, by tracking user's actions

Maintenance therapy of patients with recurrent epithelial ovarian carcinoma with the anti-tumor-associated-mucin-1 antibody gatipotuzumab: results from a double-blind, placebo-controlled, randomized, phase II study

BACKGROUND: Gatipotuzumab is a humanized monoclonal antibody recognizing the carbohydrate-induced epitope of the tumor-associated mucin-1 (TA-MUC1). This study aimed to evaluate the efficacy and safety of switch maintenance therapy with gatipotuzumab in patients with TA-MUC1-positive recurrent ovarian, fallopian tube, or primary high-grade serous peritoneal cancer. PATIENTS AND METHODS: In this double-blind, randomized, placebo-controlled, phase II trial, patients with at least stable disease (SD) following chemotherapy were randomized 2:1 to receive intravenous gatipotuzumab (500 mg followed by 1700 mg 1 week later) or placebo every 3 weeks until tumor progression or unacceptable toxicity occurred. Stratification factors were the number of prior chemotherapy lines (2 versus 3-5), response versus SD after the most recent chemotherapy, and progression-free survival (PFS) <6 versus 6-12 months following the prior therapy. Primary endpoint was PFS according to modified immune-related RECIST 1.1 response criteria. Secondary endpoints were PFS at 6 months, safety, overall response rate, CA-125 progression, overall survival, quality of life, and pharmacokinetics. RESULTS: Overall, 216 patients were randomized to gatipotuzumab (n  =  151) or placebo (n  =  65). Median PFS with gatipotuzumab was 3.5 months as compared with 3.5 months with placebo (hazard ratio 0.96, 95% confidence interval 0.69-1.33, P  =  0.80). No advantage for gatipotuzumab over placebo was seen in the secondary efficacy endpoints or in any stratified subgroups. Gatipotuzumab was well tolerated, with mild to moderate infusion-related reactions being the most common adverse events. CONCLUSIONS: Gatipotuzumab switch maintenance therapy does not improve outcome in TA-MUC1-positive ovarian cancer patients. TRIAL REGISTRATION: ClinicalTrials.govNCT01899599; https://clinicaltrials.gov/ct2/show/NCT01899599

DOMMINO: a database of macromolecular interactions

With the growing number of experimentally resolved structures of macromolecular complexes, it becomes clear that the interactions that involve protein structures are mediated not only by the protein domains, but also by various non-structured regions, such as interdomain linkers, or terminal sequences. Here, we present DOMMINO (http://dommino.org), a comprehensive database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides. The database complements SCOP domain annotations with domain predictions by SUPERFAMILY and is automatically updated every week. The database interface is designed to provide the user with a three-stage pipeline to study macromolecular interactions: (i) a flexible search that can include a PDB ID, type of interaction, SCOP family of interacting proteins, organism name, interaction keyword and a minimal threshold on the number of contact pairs; (ii) visualization of subunit interaction network, where the user can investigate the types of interactions within a macromolecular assembly; and (iii) visualization of an interface structure between any pair of the interacting subunits, where the user can highlight several different types of residues within the interfaces as well as study the structure of the corresponding binary complex of subunits