University of Los Andes

About: University of Los Andes is a education organization based out in Bogotá, Colombia. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 17616 authors who have published 25555 publications receiving 413463 citations.

An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays.

Abstract: In vitro scratch wound healing assay, a simple and low-cost technique that works along with other image analysis tools, is one of the most widely used 2D methods to determine the cellular migration and proliferation in processes such as regeneration and disease. There are open-source programs such as imageJ to analyze images of in vitro scratch wound healing assays, but these tools require manual tuning of various parameters, which is time-consuming and limits image throughput. For that reason, we developed an optimized plugin for imageJ to automatically recognize the wound healing size, correct the average wound width by considering its inclination, and quantify other important parameters such as: area, wound area fraction, average wound width, and width deviation of the wound images obtained from a scratch/ wound healing assay. Our plugin is easy to install and can be used with different operating systems. It can be adapted to analyze both individual images and stacks. Additionally, it allows the analysis of images obtained from bright field, phase contrast, and fluorescence microscopes. In conclusion, this new imageJ plugin is a robust tool to automatically standardize and facilitate quantification of different in vitro wound parameters with high accuracy compared with other tools and manual identification.

Combination of the top-quark mass measurements from the Tevatron collider

Abstract: We thank the Fermilab staff and technical staffs of the participating institutions for their vital contributions and acknowledge support from the DOE and NSF (USA), ARC (Australia), CNPq, FAPERJ, FAPESP, and FUNDUNESP (Brazil), NSERC (Canada), NSC, CAS, and CNSF (China), Colciencias (Colombia), MSMT and GACR (Czech Republic), the Academy of Finland, CEA, and CNRS/IN2P3 (France), BMBF and DFG (Germany), DAE and DST (India), SFI (Ireland), INFN (Italy), MEXT (Japan), the Korean World Class University Program and NRF (Korea), CONACyT (Mexico), FOM (Netherlands), MON, NRC KI, and RFBR (Russia), the Slovak R&D Agency, the Ministerio de Ciencia e Innovacio´n, and Programa Consolider-Ingenio 2010 (Spain), The Swedish Research Council (Sweden), SNSF (Switzerland), STFC and the Royal Society (United Kingdom), and the A. P. Sloan Foundation (USA).

Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

Abstract: Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.

Prompt and non-prompt J/ψ production in pp collisions at √s = 7 TeV

Abstract: The production of J/psi mesons is studied in pp collisions at sqrt(s)=7 TeV with the CMS experiment at the LHC. The measurement is based on a dimuon sample corresponding to an integrated luminosity of 314 inverse nanobarns. The J/psi differential cross section is determined, as a function of the J/psi transverse momentum, in three rapidity ranges. A fit to the decay length distribution is used to separate the prompt from the non-prompt (b hadron to J/psi) component. Integrated over J/psi transverse momentum from 6.5 to 30 GeV/c and over rapidity in the range |y| < 2.4, the measured cross sections, times the dimuon decay branching fraction, are 70.9 \pm 2.1 (stat.) \pm 3.0 (syst.) \pm 7.8(luminosity) nb for prompt J/psi mesons assuming unpolarized production and 26.0 \pm 1.4 (stat.) \pm 1.6 (syst.) \pm 2.9 (luminosity) nb for J/psi mesons from b-hadron decays.

Anelastic Earth structure from the coherency of the ambient seismic field

Abstract: [1] Cross correlation of the ambient seismic field is now routinely used to measure seismic wave travel times; however, relatively little attention has been paid to other information that could be extracted from these signals. In this paper we demonstrate the relationship between the spatial coherency of the ambient field and the elastodynamic Green's function in both time and frequency domains. Through measurement of the frequency domain coherency as a function of distance, we sequentially recover phase velocities and attenuation coefficients. From these measurements we generate 1-D shear wave velocity and attenuation models for southern California. The ambient field measurements of attenuation and the exceptional path coverage that results from the many possible interstation measurements allow us to extend Q estimates over a range of frequencies that has previously been difficult to analyze using earthquake data. Measurements from paths that cross major sedimentary basins show both lower wave speeds and lower-quality factors than other paths, as expected. Our results indicate that there is a wealth of information available in the spatial coherency of the ambient seismic field.