An Efficient Local Search for Partial Latin Square Extension Problem

A partial Latin square (PLS) is a partial assignment of n symbols to an nxn grid such that, in each row and in each column, each symbol appears at most once. The partial Latin square extension problem is an NP-hard problem that asks for a largest extension of a given PLS. In this paper we propose an efficient local search for this problem. We focus on the local search such that the neighborhood is defined by (p,q)-swap, i.e., removing exactly p symbols and then assigning symbols to at most q empty cells. For p in {1,2,3}, our neighborhood search algorithm finds an improved solution or concludes that no such solution exists in O(n^{p+1}) time. We also propose a novel swap operation, Trellis-swap, which is a generalization of (1,q)-swap and (2,q)-swap. Our Trellis-neighborhood search algorithm takes O(n^{3.5}) time to do the same thing. Using these neighborhood search algorithms, we design a prototype iterated local search algorithm and show its effectiveness in comparison with state-of-the-art optimization solvers such as IBM ILOG CPLEX and LocalSolver.Comment: 17 pages, 2 figure

Atividade antimicrobiana de subfrações padronizadas da planta Arrabidaea chica Verl.

Este estudo analisou o potencial terapêutico de extratos e subfrações padronizadas da planta amazônica Arrabidaea chica, visando seu uso tópico como medicamento e eficácia comprovada em doenças cutâneas

Biologically driven DOC release from peatlands during recovery from acidification

Peatlands recovering from acidification release dissolved organic carbon (DOC), but no biological role has yet been identified in this process. Here, the authors show that pH increases enhance phenol oxidase activity, pore-water DOC concentrations and lead to greater abundances in Actinobacteria and fungi

Evaluation of Dynamic Cell Processes and Behavior Using Video Bioinformatics Tools

Just as body language can reveal a person’s state of well-being, dynamic changes in cell behavior and morphology can be used to monitor processes in cultured cells. This chapter discusses how CL-Quant software, a commercially available video bioinformatics tool, can be used to extract quantitative data on: (1) growth/proliferation, (2) cell and colony migration, (3) reactive oxygen species (ROS) production, and (4) neural differentiation. Protocols created using CL-Quant were used to analyze both single cells and colonies. Time-lapse experiments in which different cell types were subjected to various chemical exposures were done using Nikon BioStations. Proliferation rate was measured in human embryonic stem cell colonies by quantifying colony area (pixels) and in single cells by measuring confluency (pixels). Colony and single cell migration were studied by measuring total displacement (distance between the starting and ending points) and total distance traveled by the colonies/cells. To quantify ROS production, cells were pre-loaded with MitoSOX Red™, a mitochondrial ROS (superoxide) indicator, treated with various chemicals, then total intensity of the red fluorescence was measured in each frame. Lastly, neural stem cells were incubated in differentiation medium for 12 days, and time lapse images were collected daily. Differentiation of neural stem cells was quantified using a protocol that detects young neurons. CLQuant software can be used to evaluate biological processes in living cells, and the protocols developed in this project can be applied to basic research and toxicological studies, or to monitor quality control in culture facilities

Functional studies of signaling pathways in peri-implantation development of the mouse embryo by RNAi

BACKGROUND: Studies of gene function in the mouse have relied mainly on gene targeting via homologous recombination. However, this approach is difficult to apply in specific windows of time, and to simultaneously knock-down multiple genes. Here we report an efficient method for dsRNA-mediated gene silencing in late cleavage-stage mouse embryos that permits examination of phenotypes at post-implantation stages. RESULTS: We show that introduction of Bmp4 dsRNA into intact blastocysts by electroporation recapitulates the genetic Bmp4 null phenotype at gastrulation. It also reveals a novel role for Bmp4 in the regulation the anterior visceral endoderm specific gene expression and its positioning. We also show that RNAi can be used to simultaneously target several genes. When applied to the three murine isoforms of Dishevelled, it leads to earlier defects than previously observed in double knock-outs. These include severe delays in post-implantation development and defects in the anterior midline and neural folds at headfold stages. CONCLUSION: Our results indicate that the BMP4 signalling pathway contributes to the development of the anterior visceral endoderm, and reveal an early functional redundancy between the products of the murine Dishevelled genes. The proposed approach constitutes a powerful tool to screen the functions of genes that govern the development of the mouse embryo

Disruption of the temporally regulated cloaca endodermal B-catenin signaling causes anorectal malformations

published_or_final_versio

New 14C Determinations from Lake Suigetsu, Japan:12,000 to 0 Cal BP

Calibration is a fundamental stage of the radiocarbon (14C) dating process if one is to derive meaningful calendar ages from samples’ 14C measurements. For the first time, the IntCal09 calibration curve (Reimer et al. 2009) provided an internationally ratified calibration data set across almost the complete range (0 to 50,000 cal BP) of the 14C timescale. However, only the last 12,550 cal yr of this record are composed of terrestrial data, leaving approximately three quarters of the 14C timescale necessarily calibrated via less secure, marine records (incorporating assumptions pertaining to the temporally variable “marine reservoir effect”). The predominantly annually laminated (varved) sediment profile of Lake Suigetsu, central Japan, offers an ideal opportunity to derive an extended terrestrial record of atmospheric 14C across the entire range of the method, through pairing of 14C measurements of terrestrial plant macrofossil samples (extracted from the sediment) with the independent chronology provided through counting of its annual laminations. This paper presents new data (182 14C determinations) from the upper (largely non-varved) 15 m of the Lake Suigetsu (SG06) sediment strata. These measurements provide evidence of excellent coherence between the Suigetsu 14C data and the IntCal09 calibration curve across the last ~12,000 cal yr (i.e. the portion of IntCal based entirely on terrestrial data). Such agreement demonstrates that terrestrial plant material picked from the Lake Suigetsu sediment provides a reliable archive of atmospheric 14C, and therefore supports the site as being capable of providing a high-resolution extension to the “wholly terrestrial” (i.e. non-reservoir-corrected) calibration curve beyond its present 12,550 cal BP limit

Event layers in the Japanese Lake Suigetsu 'SG06' sediment core:Description, interpretation and climatic implications

Event layers in lake sediments are indicators of past extreme events, mostly the results of floods or earthquakes. Detailed characterisation of the layers allows the discrimination of the sedimentation processes involved, such as surface runoff, landslides or subaqueous slope failures. These processes can then be interpreted in terms of their triggering mechanisms. Here we present a 40 ka event layer chronology from Lake Suigetsu, Japan. The event layers were characterised using a multi-proxy approach, employing light microscopy and μXRF for microfacies analysis. The vast majority of event layers in Lake Suigetsu was produced by flood events (362 out of 369), allowing the construction of the first long-term, quantitative (with respect to recurrence) and well dated flood chronology from the region. The flood layer frequency shows a high variability over the last 40 ka, and it appears that extreme precipitation events were decoupled from the average long-term precipitation. For instance, the flood layer frequency is highest in the Glacial at around 25 ka BP, at which time Japan was experiencing a generally cold and dry climate. Other cold episodes, such as Heinrich Event 1 or the Late Glacial stadial, show a low flood layer frequency. Both observations together exclude a simple, straightforward relationship with average precipitation and temperature. We argue that, especially during Glacial times, changes in typhoon genesis/typhoon tracks are the most likely control on the flood layer frequency, rather than changes in the monsoon front or snow melts. Spectral analysis of the flood chronology revealed periodic variations on centennial and millennial time scales, with 220 yr, 450 yr and a 2000 yr cyclicity most pronounced. However, the flood layer frequency appears to have not only been influenced by climate changes, but also by changes in erosion rates due to, for instance, earthquakes