Observer-oriented approach improves species distribution models from citizen science data

Citizen science platforms are increasingly growing, and, storing a huge amount of data on species locations, they provide researchers with essential information to develop sound strategies for species conservation. However, the lack of information on surveyed sites (i.e., where the observers did not record the target species) and sampling effort (e.g., the number of surveys at a given site, by how many observers, and for how much time) strongly limit the use of citizen science data. Thus, we examined the advantage of using an observer-oriented approach (i.e., considering occurrences of species other than the target species collected by the observers of the target species as pseudo-absences and additional predictors relative to the total number of observations, observers, and days in which locations were collected in a given sampling unit, as proxies of sampling effort) to develop species distribution models. Specifically, we considered 15 mammal species occurring in Italy and compared the predictive accuracy of the ensemble predictions of nine species distribution models carried out considering random pseudo-absences versus observer-oriented approach. Through cross-validations, we found that the observer-oriented approach improved species distribution models, providing a higher predictive accuracy than random pseudo-absences. Our results showed that species distribution modeling developed using pseudo-absences derived citizen science data outperform those carried out using random pseudo-absences and thus improve the capacity of species distribution models to accurately predict the geographic range of species when deriving robust surrogate of sampling effort

Networks from gene expression time series: characterization of correlation patterns

This paper describes characteristic features of networks reconstructed from gene expression time series data. Several null models are considered in order to discriminate between informations embedded in the network that are related to real data, and features that are due to the method used for network reconstruction (time correlation).Comment: 10 pages, 3 BMP figures, 1 Table. To appear in Int. J. Bif. Chaos, July 2007, Volume 17, Issue

Tihonov theory and center manifolds for inhibitory mechanisms in enzyme kinetics

Abstract In this paper we study the chemical reaction of inhibition, determine the appropriate parameter ε for the application of Tihonov's Theorem, compute explicitly the equations of the center manifold of the system and find sufficient conditions to guarantee that in the phase space the curves which relate the behavior of the complexes to the substrates by means of the tQSSA are asymptotically equivalent to the center manifold of the system. Some numerical results are discussed

Influence of the synthetic procedure on the properties of three Ziegler-Natta catalysts with the same 1,3-diether internal donor

Being the main responsible for the huge production of polyolefins, heterogeneous Ziegler-Natta catalysts are among the most important catalysts in the chemical industry and they have been optimized over the years since their discovery in 1953 crossing many different generations. Lastly, catalysts of the 5th generation are characterized by the introduction in the pre-catalyst of 1,3-diether compounds as internal electron donors, which are stable in the presence of AlR3 activators and do not require the further addition of external donors during the following steps of the catalytic process to control the activity and selectivity. In this work, we synthetized and systematically investigated by a multi-technique approach three Ziegler-Natta catalysts characterized by the same 1,3-diether donor, but differing in the synthesis route. We found that the synthetic route influences the MgCl2 particle size, as well as the properties of the Ti species. In particular, the reprecipitation method brings the smallest MgCl2 particles and the most positive Ti4+ sites in the pre-catalyst, but also the largest amount of accessible Ti3+ sites after TEAl activation. These structural and spectroscopic data correlate pretty well with the kinetic of gas-phase propylene polymerization in very mild conditions

Molecular Interaction Studies of HIV-1 Matrix Protein p17 and Heparin: IDENTIFICATION OF THE HEPARIN-BINDING MOTIF OF p17 AS A TARGET FOR THE DEVELOPMENT OF MULTITARGET ANTAGONISTS

Once released by HIV cells, p17 binds heparan sulfate proteoglycans (HSPGs) and CXCR1 on leukocytes causing their dysfunction. By exploiting an approach integrating computational modeling, site-directed mutagenesis of p17, chemical desulfation of heparin, and surface plasmon resonance, we characterized the interaction of p17 with heparin, a HSPG structural analog, and CXCR1. p17 binds to heparin with an affinity (Kd 190 nM) that is similar to those of other heparin-binding viral proteins. Two stretches of basic amino acids (basic motifs) are present in p17 N and C termini. Neutralization (Arg3Ala substitution) of the N-terminal, but not of the C-terminal basic motif, causes the loss of p17 heparin-binding capacity. The N-terminal heparin-binding motif of p17 partially overlaps the CXCR1-binding domain. Accordingly, its neutralization prevents also p17 binding to the chemochine receptor. Competition experiments demonstrated that free heparin and heparan sulfate (HS), but not selectively 2-O-, 6-O-, and N-O desulfated heparins, prevent p17 binding to substrate-immobilized heparin, indicating that the sulfate groups of the glycosaminoglycan mediate p17 interaction. Evaluation of the p17 antagonist activity of a panel of biotechnological heparins derived by chemical sulfation of the Escherichia coli K5 polysaccharide revealed that the highlyN,O-sulfated derivative prevents the binding of p17 to both heparin and CXCR1, thus inhibiting p17-driven chemotactic migration of human monocytes with an efficiency that is higher than those of heparin and HS. Here, we characterized at a molecular level the interaction of p17 with its cellular receptors, laying the basis for the development of heparin-mimicking p17 antagonists

Singularities and closed time-like curves in type IIB 1/2 BPS geometries

We study in detail the moduli space of solutions discovered in LLM relaxing the constraint that guarantees the absence of singularities. The solutions fall into three classes, non-singular, null-singular and time machines with a time-like naked singularity. We study the general features of these metrics and prove that there are actually just two generic classes of space-times - those with null singularities are in the same class as the non-singular metrics. AdS/CFT seems to provide a dual description only for the first of these two types of space-time in terms of a unitary CFT indicating the possible existence of a chronology protection mechanism for this class of geometries.Comment: 34 pages, 7 figures, LaTeX. References adde

Virtual Drug Repositioning as a Tool to Identify Natural Small Molecules That Synergize with Lumacaftor in F508del-CFTR Binding and Rescuing

Cystic fibrosis is a hereditary disease mainly caused by the deletion of the Phe 508 (F508del) of the cystic fibrosis transmembrane conductance regulator (CFTR) protein that is thus withheld in the endoplasmic reticulum and rapidly degraded by the ubiquitin/proteasome system. Cystic fibrosis remains a potentially fatal disease, but it has become treatable as a chronic condition due to some CFTR-rescuing drugs that, when used in combination, increase in their therapeutic effect due to a synergic action. Also, dietary supplementation of natural compounds in combination with approved drugs could represent a promising strategy to further alleviate cystic fibrosis symptoms. On these bases, we screened by in silico drug repositioning 846 small synthetic or natural compounds from the AIFA database to evaluate their capacity to interact with the highly druggable lumacaftor binding site of F508del-CFTR. Among the identified hits, nicotinamide (NAM) was predicted to accommodate into the lumacaftor binding region of F508del-CFTR without competing against the drug but rather stabilizing its binding. The effective capacity of NAM to bind F508del-CFTR in a lumacaftor-uncompetitive manner was then validated experimentally by surface plasmon resonance analysis. Finally, the capacity of NAM to synergize with lumacaftor increasing its CFTR-rescuing activity was demonstrated in cell-based assays. This study suggests the possible identification of natural small molecules devoid of side effects and endowed with the capacity to synergize with drugs currently employed for the treatment of cystic fibrosis, which hopefully will increase the therapeutic efficacy with lower doses

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range

RGS2 expression predicts amyloid-β sensitivity, MCI and Alzheimer's disease: genome-wide transcriptomic profiling and bioinformatics data mining

Alzheimer's disease (AD) is the most frequent cause of dementia. Misfolded protein pathological hallmarks of AD are brain deposits of amyloid-β (Aβ) plaques and phosphorylated tau neurofibrillary tangles. However, doubts about the role of Aβ in AD pathology have been raised as Aβ is a common component of extracellular brain deposits found, also by in vivo imaging, in non-demented aged individuals. It has been suggested that some individuals are more prone to Aβ neurotoxicity and hence more likely to develop AD when aging brains start accumulating Aβ plaques. Here, we applied genome-wide transcriptomic profiling of lymphoblastoid cells lines (LCLs) from healthy individuals and AD patients for identifying genes that predict sensitivity to Aβ. Real-time PCR validation identified 3.78-fold lower expression of RGS2 (regulator of G-protein signaling 2; P=0.0085) in LCLs from healthy individuals exhibiting high vs low Aβ sensitivity. Furthermore, RGS2 showed 3.3-fold lower expression (P=0.0008) in AD LCLs compared with controls. Notably, RGS2 expression in AD LCLs correlated with the patients' cognitive function. Lower RGS2 expression levels were also discovered in published expression data sets from postmortem AD brain tissues as well as in mild cognitive impairment and AD blood samples compared with controls. In conclusion, Aβ sensitivity phenotyping followed by transcriptomic profiling and published patient data mining identified reduced peripheral and brain expression levels of RGS2, a key regulator of G-protein-coupled receptor signaling and neuronal plasticity. RGS2 is suggested as a novel AD biomarker (alongside other genes) toward early AD detection and future disease modifying therapeutics