bluuebunny/crossref_metadata_2025_split huggingface dataset:
Commercial potato production and cultural management.
Authors: Pavek M. J. 
Published: December 2014

Abstract

This chapter focuses on the principles and components key to successful commercial potato production. These include market and variety choice, pre-plant preparation, field and soil considerations, pre-plant pest management, integrated pest management, field and seedbed preparation, crop planting, propagation and seed preparation, in-row seed spacing and plant population, planting depth, planter types, planting types and post-planting tillage, growing and harvesting.
Seed potato production.
Authors: Davidson R. D. , Xie K. Y. 
Published: December 2014

Abstract

This chapter compares the formal versus informal method of seed potato production, and describes the true potato seed as well as the diseases and pests of concern. The certification process, sanitation and the early-generation stocks are discussed. Seed potato production is a complicated business. To be successful, there are basic guidelines one must follow, whether using an informal grower-saved seed source or a more formal certification programme. Production of disease-free, high-quality seed potatoes is the first and most important component in the production of high-quality, high-yielding table-stock potatoes. Poor seed quality can financially ruin commercial producers, reduce the food supply, and damage an industry.
Insect pests of potato.
Authors: Waters T. D. , Jensen A. S. 
Published: December 2014

Abstract

This chapter aims to introduce pests and categories of pests of nearly global significance, to discuss important management considerations, and to provide a set of useful references as starting points in the potato entomology literature. The four key principles to integrated pest management (IPM) programmes are described, i.e. pest identification, monitoring, control action guidelines or economic injury levels, and management of the pest. Some general concepts relative to good cultural and chemical pest management as a component of IPM are discussed. Is is suggested that a combination of the general principles of potato insect management and direct observations of local agroecosystems will give crop managers most of the knowledge necessary to minimize crop damage successfully and maintain profitability.
Fungal and bacterial disease aspects in potato production.
Authors: Kirk W. W. , Wharton P. S. 
Published: December 2014

Abstract

This chapter presents the disease cycles for various common and economically significant pathogens of the potato crop and emphasizes where in the cycle interventions are thought to be most effective. Tabulated data are provided on the important bacterial, oomycete, and fungal diseases of potato. The survival, spread and epidemiology of these diseases are described, as well as the role of the tuber in the disease cycle. Some measures to control these diseases (including foliar, seed- and soilborne fungal diseases) are provided. Future prospects, considering climate change, fungicide resistance and molecular disease diagnostics, are mentioned.
Traditional breeding and cultivar development.
Authors: Novy R. 
Published: December 2014

Abstract

This chapter details the contributions that potato breeding and cultivar development have made to the global acceptance of potato as a major food crop, the unique characteristics (including dual reproduction and tetraploidy) of potato that impact its breeding, the emerging issues of importance in cultivar development, and the methodologies used in traditional potato breeding. Traditional breeding allows for the genetic "reshuffling" of genes and their recombination into new genotypes that may carry the desired assemblage of resistance and agronomic traits (such as yield and quality) necessary for release as a new cultivar. Traditional breeding therefore remains the primary source of new potato cultivars, with a greater acceptance and adoption of them by the potato industry.
Molecular breeding of potato in the postgenomic era.
Authors: Veilleux R. E. , Boluarte-Medina T. 
Published: December 2014

Abstract

Since the potato genome was published in 2011 (Potato Genome Sequencing Consortium, 2011), with all of its associated tools, including the genome browser, blast engine, transcriptome with links to other plant genomes, the Infinium 8303 Potato Array, new possibilities have become available for potato breeding that complement the traditional approach. This chapter deals with molecular breeding of potato in the post-genomic era, discussing the development of SNP (single-nucleotide polymorphism) chip for assissting mapping, marker-assisted selection, transcriptomics, proteomics, candidate gene approach, transgenics and comparative genomics. Potato breeders have now been equipped with an enviable array of genomic technologies that can be deployed for cultivar improvement. It is likely that the genetic gains that have already been realized in other crops with more tractable breeding systems can finally become a reality for improvements to potato during the 21st century.
Sustaining soil carbon in bioenergy cropping systems of northern temperate regions.
Authors: Gul S. , Winans K. S. , Leila M. , Whalen J. K. 
Published: December 2014

Abstract

Soil organic carbon (SOC) has an essential role in controlling ecosystem functions associated with soil physical, chemical and biological properties. Maintaining the SOC pool size in agroecosystems is important to sustain food security, protect soil biodiversity and buffer environmental impacts. The SOC pool is dynamic, with losses occurring due to CO
2
mineralization and gains from microbially mediated humification of organic substrates into stable C compounds. Bioenergy production from lignocellulosic feedstock implies that greater amounts of plant residues will be removed from agroecosystems and could deplete the SOC pool, based on empirical models and experimental results from long-term field trials. In northern temperate regions, several management practices are suggested to conserve the SOC pool, such as the application of biochar, judicious use of organic and inorganic fertilizers, crop rotations that include high biomass producing non-bioenergy crops or intercropping systems that combine perennial bioenergy crops with other crops (annuals or trees). Moreover, new technologies such as genetically modified (GM) bioenergy crops are recommended to enhance bioenergy production per unit energy input. Those modifications include GM crops with higher resource-use efficiency (i.e., for water, nutrients and light), GM crops with cellulase/ligninase enzyme systems for biofuel production and GM crops with higher calorific values that release more energy during combustion.
Clinical use of cardiac troponins in dogs.
Authors: Gough A. 
Published: December 2014

Abstract
Cardiac troponins are sensitive and specific markers of myocardial damage. They have been shown to be elevated in a number of primary cardiac and non-cardiac conditions. In cardiomyopathies, they are useful for detecting occult disease, and can provide prognostic information. They can be used to detect myocardial damage caused by the administration of doxorubicin, and have been shown to be elevated in cases of intoxication, as well as after anaesthesia. Other diseases that have been shown to increase troponin levels include gastric dilatation volvulus, pyometra and brachycephalic obstructive syndrome, as well as infectious diseases, including dirofilariasias, babesiosis and ehrlichiosis.
Computational genomics of plants.
Authors: Arunachalam V. 
Published: December 2014

Abstract

This review provides a detailed outline of the developments in the field of computational genomics of plants. Emphasis is laid on research on software, databases and web tools in harnessing the genomic information of plants. The review begins with a short description of developments in complete genome sequencing technologies, platforms, assembly pitfalls and other challenges such as polyploidy and repetitive sequences. Updated literature on computational genomics of two model plants, rice and
Arabidopsis
, is given. A compilation of the available databases and genomic resources in plant families is made. Specific resources available for traits and organelles with potential to understand evolution are listed.
MACE: mutation-oriented profiling of chemical response and gene expression in cancers
Authors: Jeong Euna , He Ningning , Park Hyerin , Song Mee , Kim Nayoung , Lee Seongjoon , Yoon Sukjoon 
Published: December 2014

Abstract
Summary: The mutational status of specific cancer lineages can affect the sensitivity to or resistance against cancer drugs. The MACE database provides web-based interactive tools for interpreting large chemical screening and gene expression datasets of cancer cell lines in terms of mutation and lineage categories. GI50 data of chemicals against individual NCI60 cell lines were normalized and organized to statistically identify mutation- or lineage-specific chemical responses. Similarly, DNA microarray data on NCI60 cell lines were processed to analyze mutation- or lineage-specific gene expression signatures. A combined analysis of GI50 and gene expression data to find potential associations between chemicals and genes is also a capability of this system. This database will provide extensive, systematic information to identify lineage- or mutation-specific anticancer agents and related gene targets.
Availability and implementation: The MACE web database is available at http://mace.sookmyung.ac.kr/.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: yoonsj@sookmyung.ac.kr
Disk-based compression of data from genome sequencing
Authors: Grabowski Szymon , Deorowicz Sebastian , Roguski Łukasz 
Published: December 2014

Abstract
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be easily captured in the (relatively small) main memory. More interesting solutions for this problem are disk based, where the better of these two, from Cox et al. (2012), is based on the Burrows–Wheeler transform (BWT) and achieves 0.518 bits per base for a 134.0 Gbp human genome sequencing collection with almost 45-fold coverage.
Results: We propose overlapping reads compression with minimizers, a compression algorithm dedicated to sequencing reads (DNA only). Our method makes use of a conceptually simple and easily parallelizable idea of minimizers, to obtain 0.317 bits per base as the compression ratio, allowing to fit the 134.0 Gbp dataset into only 5.31 GB of space.
Availability and implementation: http://sun.aei.polsl.pl/orcom under a free license.
Contact: sebastian.deorowicz@polsl.pl
Supplementary information: Supplementary data are available at Bioinformatics online.
Atherogenic properties of lipoproteins in HIV patients starting atazanavir/ritonavir or darunavir/ritonavir: a substudy of the ATADAR randomized study
Authors: Saumoy Maria , Ordóñez-Llanos Jordi , Martínez Esteban , Ferrer Elena , Domingo Pere , Ribera Esteban , Negredo Eugenia , Curto Jordi , Sánchez-Quesada José Luis , Di Yacovo Silvana , González-Cordón Ana , Podzamczer Daniel 
Published: December 2014

Abstract

Objectives
To assess LDL subfraction phenotype and lipoprotein-associated phospholipase A2 (Lp-PLA2) in naive HIV-infected patients starting atazanavir/ritonavir or darunavir/ritonavir plus tenofovir/emtricitabine.

Methods
This was a substudy of a multicentre randomized study. Standard lipid parameters, LDL subfraction phenotype (by gradient gel electrophoresis) and Lp-PLA2 activity (by 2-thio-PAF) were measured at baseline and weeks 24 and 48. Multivariate regression analysis was performed. Results are expressed as the median (IQR).

Results
Eighty-six (atazanavir/ritonavir, n = 45; darunavir/ritonavir, n = 41) patients were included: age 36 (31–41) years; 89% men; CD4 319 (183–425) cells/mm3; and Framingham score 1% (0%–2%). No differences in demographics or lipid measurements were found at baseline. At week 48, a mild but significant increase in total cholesterol and HDL-cholesterol was observed in both arms, whereas LDL cholesterol increased only in the darunavir/ritonavir arm and triglycerides only in the atazanavir/ritonavir arm. The apolipoprotein A-I/apolipoprotein B ratio increased only in the atazanavir/ritonavir arm. At week 48, the LDL subfraction phenotype improved in the darunavir/ritonavir arm (increase in LDL particle size and in large LDL particles), whereas it worsened in the atazanavir/ritonavir arm (increase in small and dense LDL particles, shift to a greater prevalence of phenotype B); the worsening was related to the greater increase in triglycerides in the atazanavir/ritonavir arm. No changes in total Lp-PLA2 activity or relative distribution in LDL or HDL particles were found at week 48 in either arm.

Conclusions
In contrast with what occurred in the atazanavir/ritonavir arm, the LDL subfraction phenotype improved with darunavir/ritonavir at week 48. This difference was associated with a lower impact on plasma triglycerides with darunavir/ritonavir.
Outpatient parenteral antimicrobial therapy and antimicrobial stewardship: challenges and checklists
Authors: Gilchrist M. , Seaton R. A. 
Published: December 2014

Abstract
Outpatient parenteral antimicrobial therapy (OPAT) has become, for many countries, an established form of healthcare delivery. At the same time, there have been calls to ensure the prudent use of the existing antimicrobial armamentarium. For OPAT, this presents a dilemma. On one hand, stewardship principles look for the most effective agent with minimal collateral effects. In OPAT, whilst the aims of the service are similar, convenience of dosing to optimize early hospital discharge or admission avoidance may take precedence over an agent's spectrum of activity. This brief article aims to highlight the importance and explore the challenges of antimicrobial stewardship in the context of OPAT. Within the UK, the safe and effective use of antimicrobials is modelled around the IDSA/Society for Healthcare Epidemiology of America stewardship practice guidelines with local customization where appropriate. Current UK stewardship practice principles were compared with published good practice recommendations for OPAT to identify how OPAT could support the broader antimicrobial stewardship agenda. It is essential that antimicrobial stewardship teams should understand the challenges faced in the non-inpatient setting and the potential benefits/lower risks associated with avoided admission or shortened hospital stay in this population. Within its limitations, OPAT should practise stewardship principles, including optimization of intravenous to oral switch and the reporting of outcomes, healthcare-associated infections and re-admission rates. OPAT should report to the antimicrobial stewardship team. Ideally the OPAT team should be formally represented within the stewardship framework. A checklist has been proposed to aid OPAT services in ensuring they meet their stewardship agenda.
Seroprevalence of Human T-Cell Lymphotropic Viruses Types 1 and 2 Antibodies in Hepatitis C Virus-Positive Patients: Manitoba, Canada, 2012–2014
Authors: Kadkhoda Kamran , Smart Gerry , Bacon Diane , Casselman Adara , Malloch Laurie , Kim John 
Published: December 2014

AbstractHuman T-cell lymphotropic viruses types 1 and 2 are probably among the most neglected blood-borne pathogens that have experienced significant changes in their epidemiology since discovery, which could be attributed to globalization and intravenous drug use practices as well as enhanced screening recommendations; however, systematic prevalence studies, especially in high-risk populations in North America, are not updated.
FIELD: Automated emission line detection software for Subaru/FMOS near-infrared spectroscopy
Authors: Tonegawa Motonari , Totani Tomonori , Iwamuro Fumihide , Akiyama Masayuki , Dalton Gavin , Glazebrook Karl , Ohta Kouji , Okada Hiroyuki , Yabe Kiyoto 
Published: December 2014

Abstract
We describe the development of automated emission line detection software for the Fiber Multi-Object Spectrograph (FMOS), which is a near-infrared spectrograph fed by 400 fibers from the 0.2 deg2 prime focus field of view of the Subaru Telescope. The software, FIELD (FMOS software for Image-based Emission Line Detection), is developed and tested mainly for the FastSound survey, which is targeting Hα emitting galaxies at z ∼ 1.3 to measure the redshift space distortion as a test of general relativity beyond z ∼ 1. The basic algorithm is to calculate the line signal-to-noise ratio (S/N) along the wavelength direction, given by a 2D convolution of the spectral image and a detection kernel representing a typical emission line profile. A unique feature of FMOS is its use of OH airglow suppression masks, requiring the use of flat-field images to suppress noise around the mask regions. Bad pixels on the detectors and pixels affected by cosmic rays are efficiently removed using the information obtained from the FMOS analysis pipeline. We limit the range of acceptable line-shape parameters for the detected candidates to further improve the reliability of line detection. The final performance of line detection is tested using a subset of the FastSound data; the false detection rate of spurious objects is examined by using inverted frames obtained by exchanging object and sky frames. The false detection rate is &lt; 1% at S/N &gt; 5, allowing an efficient and objective emission line search for FMOS data at the line flux level of ≳ 1.0 × 10−16 erg cm−2 s−1.
Leaf litter nutrient uptake in an intermittent blackwater river: influence of tree species and associated biotic and abiotic drivers
Authors: Mehring Andrew S. , Kuehn Kevin A. , Thompson Aaron , Pringle Catherine M. , Rosemond Amy D. , First Matthew R. , Lowrance R Richard , Vellidis George 
Published: December 2014

Summary

Organic matter may sequester nutrients as it decomposes, increasing in total N and P mass via multiple uptake pathways. During leaf litter decomposition, microbial biomass and accumulated inorganic materials immobilize and retain nutrients, and therefore, both biotic and abiotic drivers may influence detrital nutrient content. We examined the relative importance of these types of nutrient immobilization and compared patterns of nutrient retention in recalcitrant and labile leaf litter.

Leaf packs of water oak (Quercus nigra), red maple (Acer rubrum) and Ogeechee tupelo (Nyssa ogeche) were incubated for 431 days in an intermittent blackwater stream and periodically analysed for mass loss, nutrient and metal content, and microbial biomass. These data informed regression models explaining temporal changes in detrital nutrient content. Informal exploratory models compared estimated biologically associated nutrient stocks (fungal, bacterial, leaf tissue) to observed total detrital nutrient stocks. We predicted that (i) labile and recalcitrant leaf litter would act as sinks at different points in the breakdown process, (ii) plant and microbial biomass would not account for the entire mass of retained nutrients, and (iii) total N content would be more closely approximated than total P content solely from nutrients stored in leaf tissue and microbial biomass, due to stronger binding of P to inorganic matter.

Labile litter had higher nutrient concentrations throughout the study. However, lower mass loss of recalcitrant litter facilitated greater nutrient retention over longer incubations, suggesting that it may be an important long‐term sink. N and P content were significantly related to both microbial biomass and metal content, with slightly stronger correlation with metal content over longer incubations.

Exploratory models demonstrated that a substantial portion of detrital nutrients was not accounted for by living or dead plant and microbial biomass, especially in the case of N. This suggests increased importance of both N and P sorption to inorganic matter over time, with possible additional storage of N complexed with lignin. A better understanding of the influence of these mechanisms may improve our understanding of detrital nutrient uptake, basal resource quality and retention and transport of nutrients in aquatic ecosystems.
Highway to the danger zone: exposure‐dependent costs of immunity in a vertebrate ectotherm
Authors: Brace Amber J. , Sheikali Sam , Martin Lynn B. 
Published: December 2014

Summary

Parasite exposure often causes innate immune activation, resulting in trade‐offs among physiological processes and strong selection on the parasite. Costs of immune activation vary widely among and within host populations though, likely dependent on the evolutionary history of host–parasite interactions and the environments in which they occur. For hosts, degree of exposure may drive the magnitude of costs incurred and subsequently whether hosts resist or tolerate infections.
If costs increase concomitantly with exposure, a threshold may exist where the expense of parasite resistance becomes prohibitive and parasite tolerance becomes favourable. Here, we characterized exposure‐dependent costs of an innate immune response in brown anoles (Anolis sagrei) by tracking allocation of an isotopically labelled essential amino acid (13C‐leucine), to the liver and gonads. To elicit immune responses, we used lipopolysaccharide (LPS), a strongly immunogenic molecule from Salmonella spp.
We found that both sexes paid dose‐dependent costs of SalmonellaLPS‐induced immune activation, but costs were experienced differently by the sexes, likely due to differences in life history. Males allocated more leucine to their livers in response to higher LPS doses. In females, a tendency for increased costs in response to dose was only revealed when leucine allocation ratios between lymphoid and reproductive organs were considered. We also found that regardless of dose, males always allocated more leucine to their gonads than females. Lastly, and perhaps most interestingly, cost functions in both sexes were linear, but with shallow slopes, indicating modest costs of immune activation in response to SalmonellaLPS in this species.
Altogether, our results demonstrate that costs of immunity are dose dependent in this introduced lizard species, sexes experience costs differently. Characterization of relationships between host exposure and costs of immune activation such as these can facilitate predictions about how parasites might circulate through communities.
Discovery and microbial content of the driest site of the hyperarid Atacama Desert, Chile
Authors: Azua‐Bustos Armando , Caro‐Lara Luis , Vicuña Rafael 
Published: December 2014

SummaryThe Atacama Desert is the driest and oldest desert on Earth. Eleven years ago, the Yungay region was established as the driest site of this hyperarid desert and also close to the dry limit for life on Earth. Since then, much has been published about the extraordinary characteristics of this site and its pertinence as a Mars analogue model. However, as a result of a more systematic search in the Atacama here, we describe a new site, María Elena South (MES), which is much drier than Yungay. The mean atmospheric relative humidity (RH) at MES was 17.3%, with the RH of its soils remaining at a constant 14% at the depth of 1 m, a value that matches the lowest RH measurements taken by the Mars Science Laboratory at Gale Crater. Remarkably, we found a number of viable bacterial species in the soil profile at MES using a combination of molecular dependent and independent methods, unveiling the presence of life in the driest place on the Atacama Desert reported to date.