A tutorial on information retrieval: basic terms and concepts

This informal tutorial is intended for investigators and students who would like to understand the workings of information retrieval systems, including the most frequently used search engines: PubMed and Google. Having a basic knowledge of the terms and concepts of information retrieval should improve the efficiency and productivity of searches. As well, this knowledge is needed in order to follow current research efforts in biomedical information retrieval and text mining that are developing new systems not only for finding documents on a given topic, but extracting and integrating knowledge across documents.     

A new sterilization and inoculation method in silage research

The study aimed at evaluating an effective sterilization–inoculation technique to facilitate silage research on the effect of forage microflora on fermentation variables. The sterilization effect of heating at 60°C for 3 h + 103°C for 15 h was tested on samples of grass, grass–clover, white clover and maize, pre‐dried at 60°C to a dry‐matter (DM) content >900 g kg^?1. The ensilability of treated samples, reconstituted to original DM concentration (250–390 g kg^?1), was assessed by inoculation with microfloras extracted from the original samples. Microfloral inoculants were obtained by a combination of centrifugation (15 500  g for 40 min) and filtration (0·45 and 0·22 μm pore sizes) of the supernatant. The sterilization treatment effectively sterilized the forage samples but decreased water soluble carbohydrates by 49% and N buffer solubility by 22% and increased the acid detergent insoluble N proportion of total N by 53% (P < 0·05). The reconstituted silages had 18% less lactic acid, 20% less ethanol and 37% less ammonia‐N (P < 0·05), but volatile fatty acids and 2,3‐butanediol did not differ from the untreated silages (P > 0·05). Counts of lactic acid bacteria, enterobacteria, clostridia, yeasts and moulds in the two silage treatments were also similar (P > 0·05). It is concluded that, despite causing chemical and physical alterations, the sterilization–inoculation technique evaluated could be a useful tool for future studies on the effects of microflora on ensiling results.     

Oryza pan-genomics:A new foundation for future rice research and improvement

The wild rice species in the genus Oryza harbor a large amount of genetic diversity that has been untapped for rice improvement. Pan-genomics has revolutionized...     

陆地棉新品系农艺性状的配合力及杂种优势研究

研究了自育的几个陆地棉新品系的一般配合力效应及组配杂种优势的潜力。结果表明，研究的几个陆地棉新品系中，以品系99-54、99-20、96-7的一般配合力较高．所配组合的杂种竞争优势籽、皮棉产量分别达到16．21％、12．18％和11．38％、7．68％．而品系98-19和00-99一般配合力较差。在亲本选择和杂种优势利用中，应用99-54、99-20、96-7较其它四个品系k4、k6、98-19、00-99为优。     

The new (challenging) role of academia in biomaterial translational research and medical device development

With the ever-changing landscape of translational research, the medical device and pharmaceutical industries increasingly license technologies with the added value of clinical and/or pre-clinical data rather than those in earlier stages of development. Universities have the potential to fill the gap in product development from academic laboratories through enhanced student training and increased implementation of some development and manufacturing activities that are traditionally found only in the private sector. A development roadmap is described from initial product feasibility through commercialization in the context of efficient development practices. The specific challenges in the design and development of biomaterial-based medical devices are described in the context of this development path with an emphasis on unique challenges for academic laboratories.     

Sea Urchin Pigments: Echinochrome A and Its Potential Implication in the Cytokine Storm Syndrome

Background: Echinochrome A (EchA) is a pigment from sea urchins. EchA is a polyhydroxylated 1,4-naphthoquinone that contains several hydroxyl groups appropriate for free-radical scavenging and preventing redox imbalance. EchA is the most studied molecule of this family and is an active principle approved to be used in humans, usually for cardiopathies and glaucoma. EchA is used as a pharmaceutical drug. Methods: A comprehensive literature and patent search review was undertaken using PubMed, as well as Google Scholar and Espacenet search engines to review these areas. Conclusions: In the bloodstream, EchA can mediate cellular responses, act as a radical scavenger, and activate the glutathione pathway. It decreases ROS imbalance, prevents and limits lipid peroxidation, and enhances mitochondrial functions. Most importantly, EchA contributes to the modulation of the immune system. EchA can regulate the generation of regulatory T cells, inhibit pro-inflammatory IL-1β and IL-6 cytokine production, while slightly reducing IL-8, TNF-α, INF-α, and NKT, thus correcting immune imbalance. These characteristics suggest that EchA is a candidate drug to alleviate the cytokine storm syndrome (CSS).     

高校地域性校园绿地空间与景观格局分析——以海南大学为例

运用景观生态学原理和传统造景艺术手法,分析海南大学校园绿地景观格局分布特点和造景特色。结果表明,海南大学校园绿地景观特色突出,景观多样性较高,具有明显的异质性;同时造景形式多样,体现出强烈的热带滨海校园风光和浓郁的地域性特征。但同类型绿地斑块之间应该加强内部联系;在植物造景突出校园热带特色的同时,应把握其自然性与人工性的结合。     

Sprout inhibition in storage: Current status, new chemistries and natural compounds

A major component of managing potato quality in storage is effective sprout inhibition. Sprouting causes increased weight loss, reduced tuber quality and impedes air movement through the potato pile. The primary method to control sprouting in storage is with postharvest applications of isopropylN-(3-chlorophenyl) carbamate (chlorpropham; CIPC). CIPC inhibits sprout development by interfering with cell division. However, a recent Environmental Protection Agency mandate, from the requirements of the Food Quality Protection Act (FQPA) of 1996, resulted in a reduction in allowable CIPC residue on fresh potatoes in the United States from 50 ppm to 30 ppm. This mandate coincides with tolerance reductions or restrictions for use of CIPC in other parts of the world. CIPC is an effective sprout inhibitor although factors such as storage conditions, application technology, and cultivar can impact that effectiveness. Alternative sprout inhibitors to CIPC continue to be evaluated. Essential oils (e.g., caraway, peppermint, spearmint, clove) or their components (e.g., s-carvone, eugenol), and hydrogen peroxide-based materials, physically damage the developing sprout and suppress sprout elongation. However, repeated or continuous application of these compounds may be necessary for efficacy. Substituted naphthalenes (e.g., dimethyl naphthalene, diisopropyl naphthalene) may help reduce the amount of CIPC applied and/or our dependency on CIPC for sprout suppression in storage. The objective of this review is to summarize the current use of CIPC for potato sprout inhibition in storage and to review the status of current research on other postharvest applied compounds or materials that may be used as alternatives for CIPC.     

Potato germplasm collecting expedition to Mexico in 1997: Taxonomy and new germplasm resources

Wild potato (Solanum sect.Petota) germplasm has been collected in Mexico on nine major expeditions, as determined by 20 collections or more from each expedition currently at the United States potato genebank, the National Research Support Program-6 (NRSP-6). These have resulted in 609 accessions with good collection data. In addition, NRSP-6 has germplasm of approximately 90 other Mexican collections that are unspecific regarding date or place of collection. This expedition was funded to collect those remaining collections with no or little germplasm:Solanum clarum,S. xedinense, S. hintonii, S. hjertingii var.physaloides, S. leptosepalum, S. lesteri, S. macropilosum, S. xmichoacanum, S. xsambucinum, andS. stenophyllidium. In addition, some species and species groups (species groups indicated in parentheses) have unresolved taxonomic problems that needed clarification by additional field collections. These are (S. agrimonifolium and S.oxycarpum), (S. brachycarpum, S. guerreroense, S. hougasii, andS. iopetalum - theS. brachycarpum complex), (S. fendleri, S. papita, S. stoloniferum - theS. stoloniferum complex),S. leptosepalum, andS. macropilosum. We conducted a wild potato germplasm collecting expedition in Mexico from August 22 to October 31, 1997. Our 103 collections, 71 as germplasm collections, provide the first germplasm samples forS. hjertingii var.physaloides,S. leptosepalum, andS. macropilosum. They provide additional germplasm of the rare speciesS. clarum, S. xedinense, S. lesteri, S. xmichoacanum, S. xsambucinum, andS. stenophyllidium. We additionally gathered germplasm and field data to help resolve taxonomic difficulties inS. agrimonifolium andS. oxycarpum, theS. brachycarpum complex, and theS. stoloniferum complex.     

Deoxynivalenol in wheat milling fractions: A critical evaluation regarding ongoing and new legislation limits

New maximum limits (ML) for deoxynivalenol (DON) in wheat and its products were set in Brazil in 2017, and new changes are scheduled for 2019. The concentration of DON in wheat and milling fractions (bran, shorts, break flour, reduction flour) was evaluated in samples from commercial fields to discuss the effects of the new legislation. Cleaned wheat samples contaminated with DON had concentrations ranging from 308 to 2373 ng g⁻¹ (n = 29), and one sample had a concentration of 3426 ng g⁻¹. DON concentration obtained in bran and shorts were significantly higher than that of the flours. Compared to the initial concentration in cleaned wheat, DON relative concentrations were 73 and 35% higher in bran and shorts, respectively, and 67% lower in the straight run flour (break plus reduction flour). The bran and straight run flour contained DON concentrations that were 62.1 and 17.2% respectively higher than that of the ML set in Brazil in 2017; additionally, these values would reach 65.5 and 34.5%, respectively, according to the changes to be in effect in 2019. The present study demonstrates DON distribution in wheat milling fractions, thus, providing updated information for the management of DON contamination for the industry and policymakers.     

Annual forage legumes in dryland agricultural systems of the West Asia and North Africa Regions: research achievements and future perspective

Forage legumes are vitally important to animal production in the dryland farming systems of the Mediterranean region. Of the diverse forage‐legume species adapted to the Mediterranean climate, vetches, (Vicia spp.), chicklings (Lathyrus spp.), annual medics (Medicago spp), clovers (Trifolium spp.) and species of the Lupinus, Lotus, Onobrychis, Hedysarum and Ornithopus genera are considered to be the most agronomically important and economically valuable species for the region. Adoption of perennial self‐regenerating medic (Medicago spp.) has been limited because of technical difficulties, but annual vetch (Vicia spp.) has the greatest potential as a viable animal‐feed source and a rotation crop with cereals. Some forage legumes survive harsh conditions by their unique underground growth habit, for example, V. amphicarpa and Lathyrus ciliolatus. Efforts to improve forage legumes have been based on both management/cultural factors and breeding. Research based on several long‐term barley‐ and wheat‐based rotation trials has demonstrated the viability of forage legumes, especially vetch, in the region's improved farming system. An additional benefit to such legumes is the enhancement of soil quality, that is, soil fertility, soil organic matter and soil physical properties. Thus, the development of forage legumes is essential to agricultural sustainability in the Mediterranean region and in other dryland cereal‐growing areas of the world where grazing livestock is a dominant enterprise. To build upon the considerable research conducted on forages, intensified efforts are needed to develop locally adapted forage cultivars, to provide economic assessment of forages in cropping systems and to promote technology transfer at the farm and community level.     

Trends in literature on new oilseed crops and related species: Seeking evidence of increasing or waning interest

Bibliographic records on eight new crop species Camelina, Crambe, Cuphea, Physaria, Limnanthes, Stokesia, Thlaspi, and Vernonia from Agricola, CAB Abstracts, Scopus, and Web of Science were analyzed for historical and recent trends on the areas of research, author distribution, and quantity and impact of publications. A total of 6786 non-redundant bibliographic records were curated and used in the analyses with about 59% of the records pertaining to the primary oilseed species. The highest number of records was found to be on Thlaspi while the least on Stokesia. Authors representing a total of 110 countries were determined to have worked in these new crops and their relative species during the past six decades with those from United States contributing about 27% in the total number of publications. There was an increase of more than ten-fold in the number of publications on new crops and relatives from 1950 to 2010 and this was paralleled by a similar increase on articles in popular and news media. The h-index values, indicating the collective impact of publications by researchers in the crop groups, show an increasing trend until the year 2000 then followed by a decline. It was determined that in recent times, there are fewer papers in the areas of chemistry, agronomy and horticulture, and more publications dealing with genetics and plant biology.     

Grazing legumes in Europe: a review of their status, management, benefits, research needs and future prospects

In many parts of Europe there has been a net decline in the use of forage legumes since the 1980s, despite the reputed value of legumes for low‐input livestock production systems. The political environment within which livestock farming in much of Europe operates (Common Agricultural Policy) is shifting the balance of economic advantage towards legumes and away from high usage of inorganic fertilizer. This has already been found for legume and grass–legume silages when compared with grass silages with a potential economic gain for farmers averaging 137 € ha^?1, corresponding to an annual benefit for the European livestock farming sector of as much as € 1300 million. Recent literature has shown that legume‐based grazing systems have the ability to reduce environmental problems by increasing the efficiency of N use and by avoiding a high transient surplus of soil mineral N. From the perspective of livestock nutrition, when forage legumes contain moderate levels of secondary compounds, such as condensed tannins and flavonoids, they offer considerable advantages including increased efficiency of N utilization within the digestive tract, reduced incidence of bloat hazard and higher resilience to parasites. Nevertheless, these benefits are partially counterbalanced in both temperate and Mediterranean regions by difficulties in establishment, maintenance and management under grazing. To gain knowledge on mixed grass–legume pastures, further research is required on: (i) the development of sustainable systems of livestock production which can maintain sward persistence and agricultural production under environmental stress; (ii) increasing knowledge of soil–plant–animal relations for a wide range of leguminous species, and under different soil types and climatic situations; and (iii) the benefits for consumers of food produced from low‐input livestock production systems.     

Optimising harvest date in sugar production: A case study for the Mossman mill region in Australia: I. Development of operations research model and solution

Cane and sugar yields within a sugar mill region can vary with geographical location, harvest date, harvest age, variety and crop class. It is not possible, due to limited mill capacity, to harvest all cane when maximum yields are attained. Given a prolonged harvest season, an important question is how the harvest of individual paddocks of cane should be scheduled so as to maximise net revenue for the entire mill region. This paper presents the application of an optimisation model to the Mossman mill region with the objectives of maximising sugar yield and net revenue in relation to harvest date and crop age. Six years of block productivity data classified according to district, crop class, variety, harvest date, harvest age, cane yield and sugar yield, were used to generate the input parameters for the model. Other inputs were sugar price, growing and milling costs, and transport and crushing capacity. With current crushing capacity and harvest season lengths, an application of the model to maximise sugar yield showed a 4% increase in sugar yield compared to current practice, but a 23% decrease in net revenue due to a shorter crop cycle with less ratoons before replanting. Optimising with respect to net revenue, gave a 3% gain in sugar yield with an 8% gain in net revenue. When crushing capacity was allowed to increase for current season lengths, the model showed a 14% gain in net revenue given fixed milling costs. It is concluded that there is scope for optimising harvest date to improve profitability in this mill region given current harvest season lengths and land area.     

Correction to: A new and simple method for measuring in situ field-saturated hydraulic conductivity using a falling-head single cylinder

Paddy and Water Environment - Hydraulic properties of soil play important roles in water and temperature regimes. Measuring hydraulic properties has been studied for decades in the laboratory and...     

CAP Analysis of the Distribution of the Introduced Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex in Xinjiang,China and the Southerly Expansion of the Mediterranean Species

Bemisia tabaci (Gennadius) cryptic complex has invaded Xinjiang, China, since 1998. The distribution of Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1) B. tabaci substrains has been gradually identified due to the development of molecular technology. In this study, the distribution of MED and MEAM1 in Xinjiang was determined by cleaved amplified polymorphic sequence (CAPs). Results showed that MED dominated in northern Xinjiang (84%), whereas MEAM1 was dominant in southern Xinjiang (72%). Five pairs of simple sequence repeat (SSR) primers were used to analyze the genetic diversity of B. tabaci among 36 geographic populations. The genetic diversity of MED and MEAM1was low and varied little among populations in Xinjiang (0.09 ± 0.14 and 0.09 ± 0.13, respectively). Based on ∆K statistic, 13 populations of MEAM1 could be classified into two subgroups at K = 2, whereas the 23 populations of MED could be classified into four subgroups at K = 4. However, Mantel t-test demonstrated no correlation between geographical and genetic distances among B. tabaci complex (R = 0.42, P = 1.00). Neighbor-joining and principal coordinate analysis showed that geographical isolation and interspecific differences were the main causes of the genetic variation. Gene flow predicted that MEAM1 was most likely introduced from Urumqi to the southern Xinjiang. Meanwhile, a large proportion of MED in Kashi region came from Changji and Yining. To block ongoing dispersal, strict detection and flower quarantine regulations need to be enforced.     

Seminole: A new variety of potato combining good chipping characteristics with good field performance in Alabama,Florida, and North Carolina

Seminole (FL282 or B4469-7) is a new potato variety, named and released by the Research and Farm Departments of Frito-Lay, Inc. Its medium-early tubers are round to oblong with smooth, light cream-buff skin color. The eyes are shallow and pink. It was selected on the Research Farm, Rhinelander, Wisconsin from family line B4469, one of 399 family lines received from the National Potato Breeding Program, Beltsville, Maryland. Tested for its reaction to Verticillium wilt, it was one of the most resistant among 1,190 seedlings. It proved superior to many named and numbered varieties in specific gravity and chip color. In Alabama, Seminole produced relatively high yields of tubers with unusually high specific gravity. Tests in Florida and North Carolina gave similar results. In the South, Seminole is usually 7–10 days earlier than Sebago, and produces higher yields of tubers with higher specific gravity. Unlike Sebago, its tubers separate readily from the vines preventing losses in mechanical harvesting.