Predictive models in ecology: Comparison of performances and assessment of applicability

Ecological systems are governed by complex interactions which are mainly nonlinear. In order to capture the inherent complexity and nonlinearity of ecological, and in general biological systems, empirical models recently gained popularity. However, although these models, particularly connectionist approaches such as multilayered backpropagation networks, are commonly applied as predictive models in ecology to a wide variety of ecosystems and questions, there are no studies to date aiming to assess the performance, both in terms of data fitting and generalizability, and applicability of empirical models in ecology. Our aim is hence to provide an overview for nature of the wide range of the data sets and predictive variables, from both aquatic and terrestrial ecosystems with different scales of time-dependent dynamics, and the applicability and robustness of predictive modeling methods on such data sets by comparing different empirical modeling approaches. The models used in this study range from predicting the occurrence of submerged plants in shallow lakes to predicting nest occurrence of bird species from environmental variables and satellite images. The methods considered include k-nearest neighbor (k-NN), linear and quadratic discriminant analysis (LDA and QDA), generalized linear models (GLM) feedforward multilayer backpropagation networks and pseudo-supervised network ARTMAP.Our results show that the predictive performances of the models on training data could be misleading, and one should consider the predictive performance of a given model on an independent test set for assessing its predictive power. Moreover, our results suggest that for ecosystems involving time-dependent dynamics and periodicities whose frequency are possibly less than the time scale of the data considered, GLM and connectionist neural network models appear to be most suitable and robust, provided that a predictive variable reflecting these time-dependent dynamics included in the model either implicitly or explicitly. For spatial data, which does not include any time-dependence comparable to the time scale covered by the data, on the other hand, neighborhood based methods such as k-NN and ARTMAP proved to be more robust than other methods considered in this study. In addition, for predictive modeling purposes, first a suitable, computationally inexpensive method should be applied to the problem at hand a good predictive performance of which would render the computational cost and efforts associated with complex variants unnecessary.     

Renoprotective Effects of Alpha Lipoic Acid on Iron Overload-Induced Kidney Injury in Rats by Suppressing NADPH Oxidase 4 and p38 MAPK Signaling

Biological Trace Element Research - We aimed to investigate the protective effect of alpha lipoic acid (ALA), a powerful antioxidant, against oxidative kidney damage induced by iron overload in...     

Deficiency in Origin Licensing Proteins Impairs Cilia Formation: Implications for the Aetiology of Meier-Gorlin Syndrome

Mutations in ORC1, ORC4, ORC6, CDT1, and CDC6, which encode proteins required for DNA replication origin licensing, cause Meier-Gorlin syndrome (MGS), a disorder conferring microcephaly, primordial dwarfism, underdeveloped ears, and skeletal abnormalities. Mutations in ATR, which also functions during replication, can cause Seckel syndrome, a clinically related disorder. These findings suggest that impaired DNA replication could underlie the developmental defects characteristic of these disorders. Here, we show that although origin licensing capacity is impaired in all patient cells with mutations in origin licensing component proteins, this does not correlate with the rate of progression through S phase. Thus, the replicative capacity in MGS patient cells does not correlate with clinical manifestation. However, ORC1-deficient cells from MGS patients and siRNA–mediated depletion of origin licensing proteins also have impaired centrosome and centriole copy number. As a novel and unexpected finding, we show that they also display a striking defect in the rate of formation of primary cilia. We demonstrate that this impacts sonic hedgehog signalling in ORC1-deficient primary fibroblasts. Additionally, reduced growth factor-dependent signaling via primary cilia affects the kinetics of cell cycle progression following cell cycle exit and re-entry, highlighting an unexpected mechanism whereby origin licensing components can influence cell cycle progression. Finally, using a cell-based model, we show that defects in cilia function impair chondroinduction. Our findings raise the possibility that a reduced efficiency in forming cilia could contribute to the clinical features of MGS, particularly the bone development abnormalities, and could provide a new dimension for considering developmental impacts of licensing deficiency.     

Synthesis, biological activity and molecular modelling studies of tricyclic alkylimidazo-, pyrimido- and diazepinopurinediones

Syntheses and biological activities of imidazo-, pyrimido- and diazepino[2,1-f]purinediones containing N-alkyl substituents (with straight, branched or unsaturated chains) are described. Tricyclic derivatives were synthesized by the cyclization of 8-bromo-substituted 7-(2-bromoethyl)-, 7-(3-chloropropyl)- or 7-(4-bromobutyl)-theophylline with primary amines under various conditions. Compound 22 with an ethenyl substituent was synthesized by dehydrohalogenation of 9-(2-bromoethyl)-1,3-dimethyltetrahydropyrimido[2,1-f]purinedione. The obtained derivatives (5–35) were initially evaluated for their affinity at rat A₁ and A_2A adenosine receptors (AR), showing moderate affinity for both adenosine receptor subtypes. The best ligands were diazepinopurinedione 28 (K_i = 0.28 μM) with fivefold A_2A selectivity and the non-selective A₁/A_2A AR ligand pyrimidopurinedione 35 (K_i A₁ = 0.28 μM and K_i A_2A = 0.30 μM). The compounds were also evaluated for their affinity at human A₁, A_2A, A_2B and A₃ ARs. All of the obtained compounds were docked to the A_2A AR X-ray structure in complex with the xanthine-based, potent adenosine receptor antagonist—XAC. The likely interactions of imidazo-, pyrimido- and diazepino[2,1-f]purinediones with the residues forming the A_2A binding pocket were discussed. Furthermore, the new compounds were tested in vivo as anticonvulsants in maximal electroshock, subcutaneous pentylenetetrazole (ScMet) and TOX tests in mice (i.p.). Pyrimidopurinediones showed anticonvulsant activity mainly in the ScMet test. The best derivative was compound 11, showing 100 % protection at a dose of 100 mg/kg without symptoms of neurotoxicity. Compounds 6, 7, 8 and 14 with short substituents showed neurotoxicity and caused death. In rat tests (p.o.), 9 was characterized by a high protection index (>13.3). AR affinity did not apparently correlate with the antiepileptic potency of the compounds.

Electronic supplementary material

The online version of this article (doi:10.1007/s11302-013-9358-3) contains supplementary material, which is available to authorized users.     

Cladistic and phylogenetic analyses of the genus Cicer in Turkey

Fifteen taxa of the genus Cicer L. growing naturally in Turkey and out-groups were classified by phylogenetic and cladistic analysis. Taxa of the genus Cicer and the out-group taxa belonging to the closest genera Phaseolus L., Vicia L., Lathyrus L. and Ononis L., which are placed in Phaseoleae, Vicieae and Ononideae tribes, respectively, were used in molecular studies in order to derive their phylogenetic relationships. Morphological, palynological and seed characters were used on the basis of 143 traits. The micromorphological characters of seed and pollen grains were revealed by SEM. Lathyrus L. and Vicia L. species were used as out-groups for numerical analysis. Ten specimens were used for the measurements of metric characters related to the morphological structures of the taxa used for statistical analysis via PAUP and NTSYS-pc packages. Phylogenetic relationships between species and populations of the same species growing in different locations and their variations were determined using molecular methods performed on regions of the Inter Simple Sequence Repeat (ISSR). DNA was isolated from the collected samples, using modified CTAB protocols. ISSR was used for phylogenetic fingerprinting. The data were analyzed with NTSYS-pc package. Standardized data were used to generate a dendrogram that revealed the phylogenetic relationships of the taxa. Geographic distribution of the Cicer taxa appears to be closely related to the Anatolian Diagonal. As a result of this study, four new endemic taxa were added and evaluated for the first time.     

Synthesis,crystal structure and antibacterial activity of new highly functionalized ionic compounds based on the imidazole nucleus

Several new highly functionalized imidazolium derivatives were synthesized, via appropriate synthetic routes, using imidazole, 1-methylimidazole and 2-phenyl-1-methylimidazole as key intermediates. The antibacterial activity of the prepared compounds was evaluated against: Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella thipymurium using disk-diffusion and MIC methods. Crystal X-ray structures are reported for six compounds.     

Sphingosine-1-phosphate lyase deficiency produces a pro-inflammatory response while impairing neutrophil trafficking

Sphingosine-1-phosphate (S1P) lyase catalyzes the degradation of S1P, a potent signaling lysosphingolipid. Mice with an inactive S1P lyase gene are impaired in the capacity to degrade S1P, resulting in highly elevated S1P levels. These S1P lyase-deficient mice have low numbers of lymphocytes and high numbers of neutrophils in their blood. We found that the S1P lyase-deficient mice exhibited features of an inflammatory response including elevated levels of pro-inflammatory cytokines and an increased expression of genes in liver associated with an acute-phase response. However, the recruitment of their neutrophils into inflamed tissues was impaired and their neutrophils were defective in migration to chemotactic stimulus. The IL-23/IL-17/granulocyte-colony stimulating factor (G-CSF) cytokine-controlled loop regulating neutrophil homeostasis, which is dependent on neutrophil trafficking to tissues, was disturbed in S1P lyase-deficient mice. Deletion of the S1P4 receptor partially decreased the neutrophilia and inflammation in S1P lyase-deficient mice, implicating S1P receptor signaling in the phenotype. Thus, a genetic block in S1P degradation elicits a pro-inflammatory response but impairs neutrophil migration from blood into tissues.     

A rare tumor of the lung: inflammatory myofibroblastic tumor

ABSTRACT: Inflammatory myofibroblastic tumor is a rare benign lesion whose tumor origin is now proven. It represents 0.7% of all lung tumors. We report the case of a three-year-old child who suffered from a chronic cough with recurrent respiratory infections. Chest X-ray and computed tomography revealed the presence of a left lower lobe lung mass. After pneumonectomy, histological examination combined with immunohistochemical study discovered an inflammatory myofibroblastic tumor. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/8722069326962972.     

Homozygous M694V as a risk factor for amyloidosis in Turkish FMF patients

Secondary amyloidosis is the most severe complication of familial Mediterranean fever (FMF). Since the M694V mutation was associated with clinical severity, it was expected to be associated with amyloidosis as well. However, a number of contradicting reports have been published, especially pertinent to Turkish patients nearly 10 years ago. The aim of this study was to analyze recent data regarding the association between M694V mutation and amyloidosis among FMF patients in Turkey.We conducted a comprehensive review of the literature regarding the role of M694V mutation in the development of amyloidosis secondary to FMF. Twenty-seven papers from 20 centers including 3505 Turkish subjects were reviewed.Four-hundred patients had amyloidosis and homozygous M694V was detected in 189 (47%) of the 400 amyloidotic patients which was significantly higher than that in the FMF patients not developing amyloidosis (p < 0.0001).In the presented analysis we were able to reach a patient number of 400 which is much higher than all those published hitherto. Our findings confirmed that homozygous M694V is associated with amyloidosis in the Turkish population as well similar to Armenia, Israel, and Arabian countries. The necessity to treat asymptomatic or mildly symptomatic FMF patients with this genotype, even in countries where amyloidosis is rare, should be considered carefully.