bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant parasitic nematodes of potato.
Authors: Palomares-Rius J. E. , Oliveira C. M. G. , Blok V. C. 
Published: December 2014

Abstract

This chapter describes the current main nematode parasites of potato, which include the potato cyst nematodes (Globodera rostochiensis, G. pallida and G. ellingtonae), root-knot nematodes (Meloidogyne spp.), false root-knot nematodes (Nacobbus aberrans), root-lesion nematodes (Pratylenchus spp.), stubby-root nematodes (Paratrichodorus spp. and Trichodorus spp.), potato rot nematode or potato tuber nematode (Ditylenchus destructor), and the yam nematode (Scutellonema bradys). Some management options are presented, including crop rotation, early harvesting, green manure amendments, trap cropping, host plant resistance, application of nematicides, biological control agents, and transgenic plant strategy. The development of nematode integrated management programmes is also mentioned.
Virus disease problems facing potato industries worldwide: viruses found, climate change implications, rationalizing virus strain nomenclature, and addressing the Potato virus Y issue.
Authors: Jones R. A. C. 
Published: December 2014

Abstract

This chapter emphasizes recent information or aspects previously not addressed fully regarding potato viruses. It starts by discussing briefly the viruses known to infect the crop, their relative importance, and the likelihood that more than the 50 or so currently known viruses will emerge as potato is increasingly grown in warmer, food-insecure parts of the world. It then discusses what is currently known about the likely influences of climate change in exacerbating the future incidence of potato virus diseases and altering their distributions in different potato growing regions. An analysis is provided of the current disagreement between biological and phylogenetic nomenclature systems for different strains of common potato viruses and how to approach a resolution, especially regarding Potato virus Y (PVY) strain group classification. The chapter then focuses on the reasons for the recent upsurge of problems with PVY in potato crops in many countries and what can be done to address this. Finally, it emphasizes areas where research on potato viruses is needed in the future, the need for surveillance over the emergence of additional potato viruses, and the importance of improving the effectiveness of seed potato health, especially in developing countries.
Weed control strategies for potato (Solanum tuberosum).
Authors: Burke I. C. , Everman W. J. 
Published: December 2014

Abstract

This chapter describes some common and troublesome weeds in potato, and their management. Integrated weed management is discussed, which can be divided into three phases: seedbank management, minimization of seedling establishment, and reduction of weed-crop interference. It is suggested that management of weeds in potato should be performed within a larger integrated pest management context that considers the long-term impacts and profitability of control inputs and the consequence of failures. Growers are advised to always combine cultural, mechanical, and chemical methods of weed management with knowledge of weed biology in an integrated approach to manage weeds in potato successfully.
Postharvest storage and physiology.
Authors: Bethke P. C. 
Published: December 2014

Abstract

This chapter begins by describing briefly the purpose and value of potato storage, and some of the many options available for storing the crop. Tuber respiration is discussed, with an emphasis on how storage duration and temperature impact respiration rates. The effects of respiration on crop value and potato storage management are illustrated. The mechanism of tuber water loss is described, and the relative importance of water loss through the periderm, lenticels, wounds, and sprouts is considered. Sprout control is essential to maintain crop value, and as such, options for residue-free, organic, and synthetic sprout control are presented. Finally, guidelines for the storage of potatoes in bulk bins are provided, in order to give a general understanding of how potatoes in large, ventilated storage facilities are managed.
Potato flavor.
Authors: Taylor M. A. 
Published: December 2014

Abstract

Despite the increasing importance of potato flavour to consumers, there is still much to be learned about the complex flavour trait and the key components that contribute to it. Means of determining flavour analytically that can be applied efficiently to germplasm are obvious requirements for improvement of the potato crop. Additionally, breeders require clear target phenotypes for flavour, as preferences are likely to vary depending on consumer groups, market classes, and cooking methods. This chapter reviews the progress that has been made in understanding these complex traits, and the opportunities that are arising from advances in analytical chemistry, sensory science, and genomic and metabolomic technologies that are now being applied to potato.
Impact of global warming on European cereal production.
Authors: Höhn J. G. , Rötter R. P. 
Published: December 2014

Abstract

This review examines relevant impact assessments identified by a literature search from 1991 to date. A bibliographic search was applied to the CAB Abstracts database with a given search string. Resultant papers were checked for relevance, based on expert judgment. This yielded 91 papers, which were subjected to further analysis. Firstly, publication intensity over time and distribution by geographic location and cereal crop were examined. Next, for a given crop, the assessments and their outcomes were grouped by type and number of the change variables considered - that is, effects of climate change only, elevated CO
2
and technological progress (improved breeds, management). Finally, separately for individual countries/subregions and Europe as a whole, we examined whether and to what extent study results have changed over time, for example become more positive/negative. Based on our sample, we found that publication intensity increased exponentially during the last 4 years, the majority of studies are Europe-wide, but some concentrated on a few countries (Italy, Spain and UK), whereby studies on wheat are clearly most popular. Taking the factor of technological progress into account has an overruling influence on results. Finally, over time, projected yield impacts have become more negative. This is in line with finding from global analyses, as reflected by the most recent comparison of agricultural impact chapters, of the 4th and 5th Assessment Reports of Intergovernmental Panel on Climate Change, Working Group II. In the future, there is particular need to consider impacts under various incremental and transformational adaptation measures in more depth (e.g. their interconnections across scales) and with more breadth (e.g. anticipated new breeds). Follow-up reviews should also examine how projected impacts are changing with the new climate scenario data sets (CMIP5) and with improved impact models and assessment approaches.
Impact of lighting on poultry reproduction and recent advances.
Authors: Reddy I. J. , Sukanto Mondal Sukanto Mondal , Ashish Mishra Ashish Mishra , Gorti RaviKiran Gorti RaviKiran 
Published: December 2014

Abstract
Different wavelengths of visible light spectrum influence the reproductive system of domestic avian species. Light perceived by the retina is involved in growth and behaviour whereas light perceived by the hypothalamus is involved in reproduction through photosensitive cells in the brain (extra-retinal photoreceptors) and it varies with intensity of different wavelengths of light. Red spectrum of light with 675 nm of wavelengths is more gonadostimulatory than shorter wavelengths of 450-475 nm of light. Recent studies indicate that the hypothalamic opsins are involved in avian photoreception. Non-mammalian vertebrates detect light by deep brain photoreceptors that lie outside the retina and pineal gland to regulate seasonal cycle of reproduction. It was reported that opsin is a deep-brain photoreceptive molecule in the avian brain that regulate seasonal reproduction in birds. Lighting recommendations should be based on local environmental conditions, house type, light requirements for pullets, growers, broilers, layers and overall stockman objectives. Lighting programmes that are inappropriately employed may impair average daily gain and compromise flock performance. Careful observations of flock performance, nutrient density and intake are also important in designing lighting programmes in broilers. Layer and broiler lighting programmes in concert with the proper genetics, environment, nutrition and management create the best in welfare for the animal and performance for the integrator. Light-emitting diode (LED) lighting in poultry facilities is cost effective and could increase egg production in layers and early body weight gain in broilers exposed to red and green LED light, respectively.
NO synthase in plants?
Authors: Hancock J. T. , Neill S. J. 
Published: December 2014

Abstract
Nitric oxide (NO) is a key signalling molecule in plants. Although the early work was in animals, it is clear that in plants too NO is involved in the regulation of a range of physiological events, including root growth and stomatal closure. The responses to stress challenges are some of the major events mediated by NO. NO will work in interaction with other signalling components, and it has been proposed that in plants NO is generated by the use of a nitric oxide synthase (NOS) enzyme. Such an enzyme is often the primary source of NO in animals, but is such an enzyme present in plants? Recently a NOS enzyme has been shown to be encoded in the genome of the algae Ostreococcus, and this may be seen as supporting optimism for finding a NOS in a higher plant. However, the methods used to assay NO generation and NOS activity in plants are often not as robust as they need to be. Furthermore there are several other enzymes which are found in plants that may also produce NO. There is no evidence of genes encoding a NOS enzyme in several plant genomes studied, and although it can not be ruled out, despite the report of the algal NOS, it is now likely that future work searching for a NOS in higher plants may not be beneficial.
Human health consequences of reducing emissions of climate altering pollutants.
Authors: Robinson D. L. 
Published: December 2014

Abstract

Efforts to reduce global warming often generate significant health benefits. For example, 16 measures recommended by the UN Environment Program and World Meteorological Association (UNEP/WMO) to reduce short-lived greenhouse pollutants (methane (CH
4
), black carbon (BC) and ozone precursors) are predicted to avoid 2.4 million premature deaths from air pollution and reduce future warming by 0.4-0.5°C. Key UNEP/WMO recommendations include replacing traditional biomass and coal stoves in developing countries with clean-burning ones, recovery and use of vented gas during oil and gas production, reducing gas pipeline leaks, collection and utilization of CH
4
from landfills, and separation and treatment of biodegradable waste (recycling, composting and anaerobic digestion) instead of sending it to landfill. Reducing major sources of particulate pollution (diesel engines, coal-fired power and domestic wood-heaters) partly through increased energy efficiency, and encouraging walking and cycling to replace short car journeys are also predicted to improve health and reduce global warming. Compared with climate benefits, the health co-benefits are more local and can be achieved more quickly and directly, making them more tangible and attractive to policymakers and the public. For electricity, estimated health benefits considerably offset the cost of greenhouse-gas mitigation, especially in India, which has high pollution and low mitigation costs. In Australia, improved efficiency, better regulation and replacing coal-fired power with renewables are also estimated to cost less than pollution from coal-fired power. The total health and environmental cost of not addressing global warming are generally considered to exceed the cost of researching, developing and implementing effective measures to reduce climate change.
Invasive alien plant management.
Authors: Auld B. A. , Johnson S. B. 
Published: December 2014

Abstract
A number of policies, strategies and tools are available for the management of invasive alien plants. This review considers these and their suitability in the light of developing theory and practical experience. Policies range from quarantine and eradication to containment and asset protection. While there is scope for modelling the potential spread and impact of invasive plants, these factors are invariably species-specific and a land manager is typically faced with the problem of dealing with several species simultaneously. Weed risk management systems have been developed to prioritize species management actions. These systems will be improved by further efforts to encompass uncertainty. Most management actions require long time-frames, and institutional commitment, as well as stakeholder involvement for successful outcomes.
Antibiotic policies in acute English NHS trusts: implementation of ‘Start Smart—Then Focus’ and relationship with Clostridium difficile infection rates
Authors: Llewelyn Martin J. , Hand Kieran , Hopkins Susan , Walker A. Sarah 
Published: December 2014

Abstract

Objectives
The objective of this study was to establish how antibiotic prescribing policies at National Health Service (NHS) hospitals match the England Department of Health ‘Start Smart—Then Focus’ recommendations and relate to Clostridium difficile infection (CDI) rates.

Methods
Antibiotic pharmacists were surveyed regarding recommendations for empirical treatment of common syndromes (‘Start Smart’) and antimicrobial prescription reviews (‘Focus’) at their hospital trusts. If no response was provided, policy data were sought from trust websites and the MicroGuide app (Horizon Strategic Partners, UK). Empirical treatment recommendations were categorized as broad spectrum (a β-lactam penicillin/β-lactamase inhibitor, cephalosporin, quinolone or carbapenem) or narrow spectrum. CDI rates were gathered from the national mandatory surveillance system.

Results
Data were obtained for 105/145 English acute hospital trusts (72%). β-Lactam/β-lactamase inhibitor combinations were recommended extensively. Only for severe community-acquired pneumonia and pyelonephritis were narrow-spectrum agents recommended first line at a substantial number of trusts [42/105 (40%) and 50/105 (48%), respectively]. Policies commonly recommended dual therapy with aminoglycosides and β-lactams for abdominal sepsis [40/93 trusts (43%)] and undifferentiated severe sepsis [54/94 trusts (57%)]. Most policies recommended treating for ≥7 days for most indications. Nearly all policies [100/105 trusts (95%)] recommended antimicrobial prescription reviews, but only 46/96 respondents (48%) reported monitoring compliance. Independent predictors of higher CDI rates were recommending a broad-spectrum regimen for community-acquired pneumonia (P = 0.06) and, counterintuitively, a recommended treatment duration of &lt;48 h for nosocomial pneumonia (P = 0.01).

Conclusions
Hospital antibiotic policies in the NHS ‘Start Smart’ by recommending broad-spectrum antibiotics for empirical therapy, but this may have the unintended potential to increase the use of broad-spectrum antibiotics and risk of CDI unless better mechanisms are in place to improve ‘Focus’.
Acquisition of high-level mupirocin resistance in CoNS following nasal decolonization with mupirocin
Authors: Hetem David J. , Vogely H. Charles , Severs Tim T. , Troelstra Annet , Kusters Johannes G. , Bonten Marc J. M. 
Published: December 2014

Abstract

Objectives
The association between mupirocin use and plasmid-based high-level resistance development mediated through mupA in CoNS has not been quantified. We determined acquisition of mupirocin resistance in Staphylococcus aureus and CoNS in surgery patients treated peri-operatively with mupirocin.

Patients and methods
Patients admitted for surgery were treated with nasal mupirocin ointment and chlorhexidine soap for 5 days, irrespective of S. aureus carrier status. Nasal swabs were obtained before decolonization (T1) and 4 days after surgery (T2) and were inoculated onto agars containing 8 mg/L mupirocin. Staphylococci were identified by MALDI-TOF MS and mupirocin resistance was confirmed by Etest.

Results
Among 1578 surgical patients, 936 (59%) had nasal swabs obtained at T1 and T2; 192 (21%) patients carried mupirocin-resistant CoNS at T1 and 406 (43%) at T2 (P &lt; 0.001). Of 744 patients not colonized at T1, 277 acquired resistance (37%), corresponding to an acquisition rate of 7.4/100 patient days at risk. In all, 588 (97%) of 607 mupirocin-resistant CoNS had an MIC &gt;256 mg/L (high level) and 381 of 383 (99.5%) were mupA positive. No acquisition of mupirocin resistance was observed in S. aureus.

Conclusions
Acquisition of mupirocin resistance following decolonization was widespread in CoNS and absent in S. aureus. As almost all isolates harboured the mupA gene, monitoring resistance development in S. aureus when decolonization strategies containing mupirocin are used is recommended.
Implementing a Large-Scale Systematic Tuberculosis Screening Program in Correctional Facilities in South Africa
Authors: Zishiri Vincent , Charalambous Salome , Shah Maunank R. , Chihota Violet , Page-Shipp Liesl , Churchyard Gavin J. , Hoffmann Christopher J. 
Published: December 2014

Abstract
Background.  Tuberculosis (TB) prevalence is high in correctional facilities in southern Africa. With support from local South African nongovernmental organizations, the South African Department of Correctional Services initiated a program of systematically screening newly admitted and current inmates for symptoms followed by GeneXpert Mycobacterium tuberculosis (MTB)/rifampicin (Rif) for microbiologic testing of symptomatic inmates.
Methods.  We conducted a program evaluation during a 5-month window describing program reach, effectiveness, adoption within the facilities, cost, and opportunities for sustainability. This evaluation included 4 facilities (2 large and 2 smaller) with a total daily census of 20 700 inmates.
Results.  During the 5-month evaluation window from May to September 2013, 7426 inmates were screened at the 4 facilities. This represents screening 87% of all new admits (the remaining new admits were screened by correctional staff only and are not included in these statistics) and 23% of the daily inmate census, reaching 55% of the overall screening target as calculated per annum. The reach ranged from 57% screened during these 5 months at one of the smaller facilities to 13% at the largest facility. Two hundred one cases of pulmonary TB were diagnosed, representing 2.1% of the screened population; 93% had documented initiation of TB treatment. The cost per TB case identified was $1513, excluding treatment costs (with treatment costs it was $1880).
Conclusions.  We reached a large number of inmates with high-volume screening and effectively used GeneXpert MTB/Rif to diagnose pulmonary TB and rapidly initiate treatment. The cost was comparable to other screening programs.
Public good diffusion limits microbial mutualism
Authors: Menon Rajita , Korolev Kirill S. 
Published: December 2014

Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using game theory with parameters renormalized by diffusion. Contrary to expectations, greater sharing of metabolites reduces the strength of cooperation and leads to species extinction via a nonequilibrium phase transition. We report analytic results for the critical diffusivity and the length scale of species intermixing. We also show that fitness nonlinearities suppress mutualism and favor the species producing slower nutrients.PACS numbers: 87.23.Cc, 87.23.Kg, 87.15.Zg, 64.60.ah
Mapping bias overestimates reference allele frequencies at theHLAgenes in the 1000 Genomes Project phase I data
Authors: Brandt Débora Y. C. , Aguiar Vitor R. C. , Bitarello Bárbara D. , Nunes Kelly , Goudet Jérôme , Meyer Diogo 
Published: December 2014

AbstractNext Generation Sequencing (NGS) technologies have become the standard for data generation in studies of population genomics, as the 1000 Genomes Project (1000G). However, these techniques are known to be problematic when applied to highly polymorphic genomic regions, such as the Human Leukocyte Antigen (HLA) genes. Because accurate genotype calls and allele frequency estimations are crucial to population ge-nomics analises, it is important to assess the reliability of NGS data. Here, we evaluate the reliability of genotype calls and allele frequency estimates of the SNPs reported by 1000G (phase I) at fiveHLAgenes (HLA-A,-B,-C,-DRB1,-DQB1). We take advantage of the availability ofHLASanger sequencing of 930 of the 1,092 1000G samples, and use this as a gold standard to benchmark the 1000G data. We document that 18.6% of SNP genotype calls inHLAgenes are incorrect, and that allele frequencies are estimated with an error higher than ±0.1 at approximately 25% of the SNPs inHLAgenes. We found a bias towards overestimation of reference allele frequency for the 1000G data, indicating mapping bias is an important cause of error in frequency estimation in this dataset. We provide a list of sites that have poor allele frequency estimates, and discuss the outcomes of including those sites in different kinds of analyses. Since theHLAregion is the most polymorphic in the human genome, our results provide insights into the challenges of using of NGS data at other genomic regions of high diversity.Data available in public repositorieshttps://github.com/deboraycb/reliability_hla_1000g
The Neural Marketplace: I. General Formalism and Linear Theory
Authors: Lewis Sarah N. , Harris Kenneth D. 
Published: December 2014

AbstractWe propose a mathematical theory for how networks of neurons in the brain self-organize into functional networks, similarly to the self-organization of supply networks in a free-market economy. The theory is inspired by recent experimental results showing how information about changes to output synapses can travel backward along axons to affect a neuron’s inputs. In neuronal development, competition for such “retroaxonal” signals determines which neurons live and which die. We suggest that in adults, an analogous form of competition occurs between neurons, to supply their targets with appropriate information in exchange for a “payment” returned to them backward along the axon. We review experimental evidence suggesting that neurotrophins may constitute such a signaling pathway in the adult brain.We construct a mathematical model, in which a small number of “consumer” neurons receive explicit fast error signals while a larger number of “producer” neurons compete to supply them with information, guided by retroaxonal signals from the consumers and from each other. We define a loss function to measure network performance and define the “worth” of a producer to be the increase in loss that would result if that neuron were to fall silent. We show how slow retroaxonal signals can allow producers to estimate their worth, and how these estimates allow the network to perform a form of parallel search over multiple producer cells. We validate our approximations and demonstrate the proposed learning rule using simulations.