Deblocking of interacting particle assemblies: from pinning to jamming

A wide variety of interacting particle assemblies driven by an external force are characterized by a transition between a blocked and a moving phase. The origin of this deblocking transition can be traced back to the presence of either external quenched disorder, or of internal constraints. The first case belongs to the realm of the depinning transition, which, for example, is relevant for flux-lines in type II superconductors and other elastic systems moving in a random medium. The second case is usually included within the so-called jamming scenario observed, for instance, in many glassy materials as well as in plastically deforming crystals. Here we review some aspects of the rich phenomenology observed in interacting particle models. In particular, we discuss front depinning, observed when particles are injected inside a random medium from the boundary, elastic and plastic depinning in particle assemblies driven by external forces, and the rheology of systems close to the jamming transition. We emphasize similarities and differences in these phenomena.Comment: 20 pages, 8 figures, submitted for a special issue of the Brazilian Journal of Physics entitled: Statistical Mechanics of Irreversible Stochastic Models - I

Identification of novel stem cell markers using gap analysis of gene expression data

A method for the detection of marker genes in large heterogeneous collections of gene expression data is described and applied to DNA microarray data generated from 83 mouse stem cell-related samples

Pseudogenes as an alternative source of natural antisense transcripts

<p>Abstract</p> <p>Background</p> <p>Naturally occurring antisense transcripts (NATs) are non-coding RNAs that may regulate the activity of sense transcripts to which they bind because of complementarity. NATs that are not located in the gene they regulate (trans-NATs) have better chances to evolve than cis-NATs, which is evident when the sense strand of the cis-NAT is part of a protein coding gene. However, the generation of a trans-NAT requires the formation of a relatively large region of complementarity to the gene it regulates.</p> <p>Results</p> <p>Pseudogene formation may be one evolutionary mechanism that generates trans-NATs to the parental gene. For example, this could occur if the parental gene is regulated by a cis-NAT that is copied as a trans-NAT in the pseudogene. To support this we identified human pseudogenes with a trans-NAT to the parental gene in their antisense strand by analysis of the database of expressed sequence tags (ESTs). We found that the mutations that appeared in these trans-NATs after the pseudogene formation do not show the flat distribution that would be expected in a non functional transcript. Instead, we found higher similarity to the parental gene in a region nearby the 3' end of the trans-NATs.</p> <p>Conclusions</p> <p>Our results do not imply a functional relation of the trans-NAT arising from pseudogenes over their respective parental genes but add evidence for it and stress the importance of duplication mechanisms of genetic material in the generation of non-coding RNAs. We also provide a plausible explanation for the large transcripts that can be found in the antisense strand of some pseudogenes.</p

A time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities

We present an efficient perturbative method to obtain both static and dynamic polarizabilities and hyperpolarizabilities of complex electronic systems. This approach is based on the solution of a frequency dependent Sternheimer equation, within the formalism of time-dependent density functional theory, and allows the calculation of the response both in resonance and out of resonance. Furthermore, the excellent scaling with the number of atoms opens the way to the investigation of response properties of very large molecular systems. To demonstrate the capabilities of this method, we implemented it in a real-space (basis-set free) code, and applied it to benchmark molecules, namely CO, H2O, and paranitroaniline (PNA). Our results are in agreement with experimental and previous theoretical studies, and fully validate our approach.Comment: 9 pages, 4 figure

Amplification of the Gene Ontology annotation of Affymetrix probe sets

BACKGROUND: The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable for microarray experiment evaluation. RESULTS: Here we present a protocol to amplify the set of Gene Ontology annotations associated to Affymetrix DNA microarray probe sets using information from related databases. CONCLUSION: Predicted novel annotations and the evidence producing them can be accessed at Probe2GO: . Scripts are available on demand

The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons

Almost 50 years following the discovery of the prokaryotic operon, the functional relevance of gene order within operons remains unclear. In this work, we take advantage of the eroded genome of Mycobacterium leprae to add evidence supporting the notion that functionally less important genes have a tendency to be located at the end of its operons. M. leprae’s genome includes 1133 pseudogenes and 1614 protein-coding genes and can be compared with the close genome of M. tuberculosis. Assuming M. leprae’s pseudogenes to represent dispensable genes, we have studied the position of these pseudogenes in the operons of M. leprae and of their orthologs in M. tuberculosis. We observed that both tend to be located in the 3′ (downstream) half of the operon (P-values of 0.03 and 0.18, respectively). Analysis of pseudogenes in all available prokaryotic genomes confirms this trend (P-value of 7.1 × 10−7). In a complementary analysis, we found a significant tendency for essential genes to be located at the 5′ (upstream) half of the operon (P-value of 0.006). Our work provides an indication that, in prokarya, functionally less important genes have a tendency to be located at the end of operons, while more relevant genes tend to be located toward operon starts

Atividade antifúngica in vivo do extrato bruto da Lobelia langeana Dusén, Campanelaceae, frente a um patógeno da erva-mate (Ilex paraguariensis St. Hil.).

Dentre as espécies vegetais da flora nativa brasileira, encontra-se a Lobelia langeana Dusén, erva comum nos estados do Paraná e Santa Catarina, conhecida como “lobélia”. Esta planta possui várias propriedades terapêuticas, inclusive a de substituto do tabaco. Um estudo foi desenvolvido para determinar sua fungitoxicidade, para participar de métodos alternativos de controle de fitopatógenos. Neste ensaio preliminar, avaliou-se o efeito de um extrato bruto da lobélia sobre a formação de lesões foliares causadas por Cylindrocladium spathulatum, em folhas destacadas de erva-mate. O extrato da lobélia inibiu em 48,9 % o desenvolvimento das lesões foliares. Este resultado mostrou que o extrato desta planta pode ser testado para o controle da pinta-preta da erva-mate, em condições de campo

Study of the efficacy of Korean Red Ginseng in the treatment of erectile dysfunction

Aim: To examine the treatment efficacy of Korean Red Ginseng (KRG) in impotent men with erectile dysfunction (ED). Methods: A total of 60 patients presenting mild or mild to moderate ED were enrolled in a double-blind, placebo-controlled study in which the efficacies of KRG and a placebo were compared. the patients received either 1 000 mg (3 times daily) of KRG or a placebo. Results: the five-item version of the International Index of Erectile Function (IIEF-5) score after the treatment was significantly higher in the KRG group compared with that before the treatment (from 16.4 +/- 2.9 to 21.0 +/- 6.3, P 0.05). in the KRG group, 20 patients (66.6%), reported improved erection, significant in the global efficacy question (P 0.05). Conclusion: Our data show that KRG can be an effective alternative to the invasive approaches for treating male ED.Univ São Paulo, Div Urol Clin, Sector Sexual Med, São Paulo, BrazilUniversidade Federal de São Paulo, Discipline Urol, São Paulo, BrazilUniversidade Federal de São Paulo, Discipline Urol, São Paulo, BrazilWeb of Scienc

Viral diagnosis in cultivars of Ipomoea batatas (L.) Lam

Ipomoea batatas (L.) Lam. commonly known as sweet potato, is an important staple food worldwide, mainly due to its high nutritional value and yield. However, vegetative reproduction of sweet potato makes it more susceptible to viral infections, which threatens its productivity, quality, and difficult long-term preservation in germplasm banks. Also, it can act as a virus reservoir infecting the rest of the plant accessions in the bank collections. Hence, this work aimed to screen Begomovirus, Potyvirus, and Carlavirus infections in 16 traditional sweet potato cultivars from the germplasm collection of the ISOPlexis Germplasm Bank, Madeira, Portugal. The infection prevalence by these viruses among cultivars was 81.25%, 25.00%, and 6.25%, respectively; being ISOP1011 the only accession coinfected by Potyvirus and Carlavirus. The accessions ISOP1006, ISOP1010, and ISOP1047 were also coinfected by Begomovirus and Potyvirus, highlighting their vulnerability to viral infections. The ISOP1005 and ISOP1027 accessions were the only ones not infected by any of these viruses. The analysis of the partial sequence obtained from the Carlavirus detected in the accession ISOP1011, revealed the existence of an ORF that encodes for 93 amino acids of the catalytic domain of an RNA-directed RNA polymerase related to the Tymovirus protein family, as could be confirmed by comparison with proteins stored in UniProtKB. Multiple sequence alignment with these proteins showed that Motifs A and B of the catalytic domain were conserved. The search for sequence similarity with sequences deposited in GenBank reported a high sequence identity with Sweet potato yellow mottle virus (SPYMV) and Sweet potato chlorotic fleck virus (SPCFV). However, the 9-11% discrepancy in nucleotide sequence identity and a phylogenetic analysis carried out using the maximum probability method suggests the virus isolated from ISOP1011 is a new divergent strain of the SPCFV species.info:eu-repo/semantics/publishedVersio