DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors

Motivation: DNA copy number gains and losses are commonly found in tumor tissue, and some of these aberrations play a role in tumor genesis and development. Although high resolution DNA copy number data can be obtained using array-based techniques, no single method is widely used to distinguish between recurrent and sporadic copy number aberrations

The hydrology of the humid tropics

Hydrological processes in the humid tropics differ from other regions in having greater energy inputs and faster rates of change, including human-induced change. Human influences on population growth, land use and climate change will profoundly influence tropical hydrology, yet understanding of key hydrological interactions is limited. We propose that efforts to collect tropical data should explicitly emphasize characterizing moisture and energy fluxes from below the ground surface into the atmosphere. Research needs to chiefly involve field-based characterizations and modelling of moisture cycling and catchment processes, as well as long-term data acquisition and organization

Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes

2007, Physical and genetic structure of the maize genome reflects its complex evolutionary history, PLoS

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes. Citation: Wei F, Coe E, Nelson W, Bharti AK, Engler F, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3(7): e123

The Science Performance of JWST as Characterized in Commissioning

This paper characterizes the actual science performance of the James Webb Space Telescope (JWST), as determined from the six month commissioning period. We summarize the performance of the spacecraft, telescope, science instruments, and ground system, with an emphasis on differences from pre-launch expectations. Commissioning has made clear that JWST is fully capable of achieving the discoveries for which it was built. Moreover, almost across the board, the science performance of JWST is better than expected; in most cases, JWST will go deeper faster than expected. The telescope and instrument suite have demonstrated the sensitivity, stability, image quality, and spectral range that are necessary to transform our understanding of the cosmos through observations spanning from near-earth asteroids to the most distant galaxies.Comment: 5th version as accepted to PASP; 31 pages, 18 figures; https://iopscience.iop.org/article/10.1088/1538-3873/acb29

Participatory evaluation of integrated pest and soil fertility management options using ordered categorical data analysis

Maize is becoming the major food crop around Lake Victoria. Major constraints to its production are Striga, stem borer, and declining soil fertility. Innovative integrated technologies have been developed: the 'push-pull' system (intercropping with Desmodium and surrounded by Napier grass), soybean and Crotalaria rotations, and imidazolinone-resistant (IR) maize seed. In 12 demonstration trials in four villages in Siaya and Vihiga districts (Kenya) and two villages in Busia (Uganda) in 2003 and 2004, 504 farmers evaluated all cropping systems and a mono-cropped continuous maize, each cropped with IR or local maize, and supplemented or not with fertilizer, totaling 16 treatments. Farmers evaluated all treatments for yield, resistance to Striga and stem borer, improvement of soil fertility, and provided an overall evaluation score, using an ordered scale of 1 (very poor) to 5 (very good). Data were analyzed using ordinal regression, estimating log odds ratios. The results show significant preferences for all treatments over the control. Push-pull with IR and fertilizer had the highest log odds ratio (2.93), so the odds of farmers preferring this treatment are 18.7 times the odds that farmers prefer the control. The odds ratios for the other push-pull combinations were generally highest (9-15), followed by the rotation systems with Crotalaria (3.5-7.0), and soybeans, especially with IR maize and fertilizer (odds ratio of 5.7). In mono-cropping systems, IR maize was only appreciated in combination with fertilizer, and then only in 2004. Push-pull and Crotalaria were more appreciated in 2004 than in 2003. Farmers in Vihiga had a stronger preference for push-pull, and those in Busia for soybean rotations. Significant differences among farmers were observed, but the effects were small. Women appreciated push-pull more than men, while other technologies were gender-neutral. Older farmers were more likely to prefer push-pull and Crotalaria with fertilizer. Livestock ownership was not found to have an effect on technology preferences. Measured yield, stem borer and Striga infestation all had significant but small effects, although their inclusion did not eliminate the treatment effects, indicating that other factors are still important. OLS of the scores for different criteria on the overall score shows yield to be the most important criterion (coefficient of 0.40), followed by soil fertility enhancement (0.25) and Striga resistance (0.13). Labor saving (0.09) and stem borer resistance (0.03) are relatively minor criteria. This research shows that scoring and analysis with ordinal regression is a convenient way to solicit and analyze farmers' preferences for new technologies, with wide applicability in farming systems and participatory research. Its application here shows that farmers like the new technologies, especially push-pull, but that there are substantial differences between years, sites and farmers. The use of this method can be very helpful to define and focus further research and formulate specific and targeted recommendations for agricultural extension.Maize Imidazolinone-resistant maize Ordinal regression Participatory evaluation Striga Stem borer