Higher-Order Demand-Driven Program Analysis (Artifact)

This artifact is a proof-of-concept implementation of DDPA, an on-demand program analysis for higher-order functional programs. The implementation, written in OCaml, includes a parser, evaluator, and DDPA analysis for the language defined in the companion paper (including the proper record semantics extension). The analysis may be performed using different levels of precision as specified by the user and is capable of rendering the control flow graphs and pushdown systems using the GraphViz language DOT. This artifact was used to verify the conclusions of the companion paper and produces visualizations matching those figures in the companion paper\u27s overview

Diverged composition and regulation of the Trypanosoma brucei origin recognition complex that mediates DNA replication initiation

Initiation of DNA replication depends upon recognition of genomic sites, termed origins, by AAA+ ATPases. In prokaryotes a single factor binds each origin, whereas in eukaryotes this role is played by a six-protein origin recognition complex (ORC). Why eukaryotes evolved a multisubunit initiator, and the roles of each component, remains unclear. In Trypanosoma brucei, an ancient unicellular eukaryote, only one ORC-related initiator, TbORC1/CDC6, has been identified by sequence homology. Here we show that three TbORC1/CDC6-interacting factors also act in T. brucei nuclear DNA replication and demonstrate that TbORC1/CDC6 interacts in a high molecular complex in which a diverged Orc4 homologue and one replicative helicase subunit can also be found. Analysing the subcellular localization of four TbORC1/CDC6-interacting factors during the cell cycle reveals that one factor, TbORC1B, is not a static constituent of ORC but displays S-phase restricted nuclear localization and expression, suggesting it positively regulates replication. This work shows that ORC architecture and regulation are diverged features of DNA replication initiation in T. brucei, providing new insight into this key stage of eukaryotic genome copying

A Case for Online Algorithms

Cyberneticists agree that metamorphic communication are an interesting new topic in the field of robotics, and mathematicians concur. After years of appropriate research into XML, we verify the simulation of cache coherence, demonstrates the appropriate importance of software engineering. Our focus in this position paper is not on whether suffix trees and multicast algorithms are often incompatible, but rather on constructing an adaptive tool for controlling IPv6 (Chalcocite)

Excitonic Resonances in Coherent Anti-Stokes Raman Scattering from Single Wall Carbon Nanotubes

In this work we investigate the role of exciton resonances in coherent anti-Stokes Raman scattering (er-CARS) in single walled carbon nanotubes (SWCNTs). We drive the nanotube system in simultaneous phonon and excitonic resonances, where we observe a superior enhancement by orders of magnitude exceeding non-resonant cases. We investigated the resonant effects in five $(n,m)$ chiralities and find that the er-CARS intensity varies drastically between different nanotube species. The experimental results are compared with a perturbation theory model. Finally, we show that such giant resonant non-linear signals enable rapid mapping and local heating of individualized CNTs, suggesting easy tracking of CNTs for future nanotoxology studies and therapeutic application in biological tissues.Comment: 17 pages, 6 figure

Prognostic significance of TRAIL-R3 and CCR-2 expression in tumor epithelial cells of patients with early breast cancer

Tumor epithelial cells (TEpCs) and spindle-shaped stromal cells, not associated with the vasculature, of patients with early breast cancer express osteoprotegerin (OPG), tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), receptor activator of nuclear factor kappa B ligand, stromal cell derived factor-1, interleukin-6, macrophage colony stimulating factor, chemokine (C-C motif) ligand-2 (CCL-2) and their receptors at significantly higher levels compared with non-neoplastic breast tissues. We evaluated the clinicopathological significance of these ligands and receptors in TEpC and spindle-shaped stromal cells, not associated with the vasculature, to determine their impact on prognosis of patients with early-stage breast cancer.Fil: Labovsky, Vivian. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Martinez, Leandro Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Davies, Kevin Mauro. Hospital Italiano; ArgentinaFil: de Luján Calcagno, María. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: García Rivello, Hernán. Hospital Italiano; ArgentinaFil: Wernicke, Alejandra. Hospital Italiano; ArgentinaFil: Feldman, Leonardo. Fundación Favaloro; ArgentinaFil: Matas, Ayelen. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Giorello, María Belén. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Borzone, Francisco Raúl. Ministerio de Salud. Instituto Nacional del Cancer; ArgentinaFil: Choi, Hosoon. Central Texas Veterans Research Foundation; Estados UnidosFil: Howard, Scott C.. University of Tennessee; Estados UnidosFil: Chasseing, Norma Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentin

Lack of Aquaporin 3 in bovine erythrocyte membranes correlates with low glycerol permeation

NOTICE: this is the author’s version of a work that was accepted for publication in Biochemical and Biophysical Research Communications. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biochemical and Biophysical Research Communications. May 2011; 408 (3): 477-481.In general, erythrocytes are highly permeable to water, urea and glycerol. However, expression of aquaporin isoforms in erythrocytes appears to be species characteristic. In the present study, human (hRBC) and bovine (bRBC) erythrocytes were chosen for comparative studies due to their significant difference in membrane glycerol permeability. Osmotic water permeability (Pf) at 23 ºC was (2.89 ± 0.37) × 10-2 and (5.12 ± 0.61) × 10-2 cm s-1 for human and bovine cells respectively, with similar activation energies for water transport. Glycerol permeability (Pgly) for human ((1.37 ± 0.26) × 10-5 cm s-1) differed in three orders of magnitude from bovine erythrocytes ((5.82 ± 0.37) ×10-8 cm s-1) that also showed higher activation energy for glycerol transport. When compared to human, bovine erythrocytes showed a similar expression pattern of AQP1 glycosylated forms on immunoblot analysis, though in slight higher levels, which could be correlated with the 1.5-fold larger Pf found. However, AQP3 expression was not detectable. Immunofluorescence analysis confirmed the absence of AQP3 expression in bovine erythrocyte membranes. In conclusion, lack of AQP3 in bovine erythrocytes points to the lipid pathway as responsible for glycerol permeation and explains the low glycerol permeability and high Ea for transport observed in ruminants

“Revisiting the Past”: A Redescription of \u3ci\u3ePhysaloptera retusa\u3c/i\u3e (Nemata, Physalopteridae) from Material Deposited in Museums and New Material from Amazon Lizards = “Revisitando o passado”: Uma redescrição de \u3ci\u3ePhysaloptera retusa\u3c/i\u3e (Nemata, Physalopteridae) a partir de material depositado em museus e novo material de lagartos amazônicos

Abstract Physaloptera Rudolphi, 1819 is a genus of nematodes that includes approximately 100 species parasitic in vertebrates around the world. From these, approximately 30 occur in the Neotropical region, with nine reported from neotropical reptiles. Physaloptera spp. are recognized by their distinct morphology of the apical end and characters of the reproductive system. However, despite the fact that the morphological characters for species diagnosis have been firmly established, we frequently find identification problems regarding poorly detailed descriptions and poorly preserved specimens. These may lead to taxonomic incongruencies. Physaloptera retusa (Rudolphi, 1819) is the most common species of the genus and has been reported from several species of neotropical reptiles. Based on our reexaminations of nematode specimens identified as P. retusa from different museum collections, we provide a detailed redescription including the type material, voucher specimens and new specimens recovered currently and showed in this study with new morphological data obtained using light and scanning electron microscopy tools. Keywords: Helminths of reptiles, Amazon, taxonomical identification, morphology, scanning electron microscopy. Resumo Physaloptera Rudolphi, 1819 é um gênero de nematódeos que inclui aproximadamente 100 espécies parasitárias em vertebrados em todo o mundo. Destes, aproximadamente 30 ocorrem na região Neotropical, e nove foram reportados para répteis neotropicais. Physaloptera spp. são reconhecidas por sua morfologia distinta na extremidade apical e por caracteres do sistema reprodutivo, especialmente nos machos. No entanto, embora os caracteres morfológicos para o diagnóstico de espécies tenham sido estabelecidos, frequentemente são encontrados problemas de identificação em relação a descrições pouco detalhadas e espécimes mal preservados. Isto pode levar a incongruências taxonômicas e erros de identificação. Physaloptera retusa (Rudolphi, 1819) é a espécie mais comum do gênero e tem sido reportada para várias espécies de répteis neotropicais. Com base nos estudos das revisões de espécimes de nematódeos, identificados como P. retusa de diferentes coleções de museus, foi providenciada uma redescrição detalhada, incluindo-se o material-tipo, espécimes “voucher” e novos espécimes obtidos neste estudo com novos dados morfológicos, obtidos a partir de microscopia eletrônica de luz e varredura

Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies

BACKGROUND: Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases. Despite the advent of next-generation sequencing technologies, Sanger sequencing is still the most popular approach in population genetics studies because of the widespread availability of automatic sequencers based on capillary electrophoresis and because it is still less prone to sequencing errors, which is critical in population genetics studies. Two popular software applications for re-sequencing studies are Phred-Phrap-Consed-Polyphred, which performs base calling, alignment, graphical edition and genotype calling and DNAsp, which performs a set of population genetics analyses. These independent tools are the start and end points of basic analyses. In between the use of these tools, there is a set of basic but error-prone tasks to be performed with re-sequencing data. RESULTS: In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp. CONCLUSION: We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation

Erratum: Author Correction: Midbrain Circuit Regulation of Individual Alcohol Drinking Behaviors in Mice (Nature Communications (2017) 8 1 (2220))

The original version of this Article contained an error in the spelling of the author Scott Edwards, which was incorrectly given as Scott Edward. This has now been corrected in both the PDF and HTML versions of the Article