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PubMed2006

Machine learning techniques in disease forecasting: a case study on rice blast prediction.

BACKGROUND: Diverse modeling approaches viz. neural networks and multiple regression have been followed to date for disease prediction in plant populations. However, due to their inability to predict value of unknown data points and longer training times, there is need for exploiting new prediction softwares for better understanding of plant-pathogen-environment relationships. Further, there is no online tool available which can help the plant researchers or farmers in timely application of control measures. This paper introduces a new prediction approach based on support vector machines for developing weather-based prediction models of plant diseases. RESULTS: Six significant weather variables were selected as predictor variables. Two series of models (cross-location and cross-year) were developed and validated using a five-fold cross validation procedure. For cross-year models, the conventional multiple regression (REG) approach achieved an average correlation coefficient (r) of 0.50, which increased to 0.60 and percent mean absolute error (%MAE) decreased from 65.42 to 52.24 when back-propagation neural network (BPNN) was used. With generalized regression neural network (GRNN), the r increased to 0.70 and %MAE also improved to 46.30, which further increased to r = 0.77 and %MAE = 36.66 when support vector machine (SVM) based method was used. Similarly, cross-location validation achieved r = 0.48, 0.56 and 0.66 using REG, BPNN and GRNN respectively, with their corresponding %MAE as 77.54, 66.11 and 58.26. The SVM-based method outperformed all the three approaches by further increasing r to 0.74 with improvement in %MAE to 44.12. Overall, this SVM-based prediction approach will open new vistas in the area of forecasting plant diseases of various crops. CONCLUSION: Our case study demonstrated that SVM is better than existing machine learning techniques and conventional REG approaches in forecasting plant diseases. In this direction, we have also developed a SVM-based web server for rice blast prediction, a first of its kind worldwide, which can help the plant science community and farmers in their decision making process. The server is freely available at http://www.imtech.res.in/raghava/rbpred/.

Agriculture↗

PubMed2006

Plant Methods moves to fund open-access publishing.

As an Open Access journal dedicated to promoting technological innovation in plant biology, Plant Methods occupies a unique niche amongst plant journals. To fund its open access policy, and to enable it to continue to serve the plant sciences community, Plant Methods will be introducing an article processing charge (APC) from March 1st 2006. This charge will cover the costs of making the article freely and universally accessible online and the costs involved in its inclusion in PubMed and its archiving in public repositories. In some circumstances, waivers of the APC may be granted and authors whose institutions are BioMed Central members will incur no, or reduced, charges.

Journal Article↗

PubMed1999

Pharmaceuticals and personal care products in the environment: agents of subtle change?

During the last three decades, the impact of chemical pollution has focused almost exclusively on the conventional "priority" pollutants, especially those acutely toxic/carcinogenic pesticides and industrial intermediates displaying persistence in the environment. This spectrum of chemicals, however, is only one piece of the larger puzzle in "holistic" risk assessment. Another diverse group of bioactive chemicals receiving comparatively little attention as potential environmental pollutants includes the pharmaceuticals and active ingredients in personal care products (in this review collectively termed PPCPs), both human and veterinary, including not just prescription drugs and biologics, but also diagnostic agents, "nutraceuticals," fragrances, sun-screen agents, and numerous others. These compounds and their bioactive metabolites can be continually introduced to the aquatic environment as complex mixtures via a number of routes but primarily by both untreated and treated sewage. Aquatic pollution is particularly troublesome because aquatic organisms are captive to continual life-cycle, multigenerational exposure. The possibility for continual but undetectable or unnoticed effects on aquatic organisms is particularly worrisome because effects could accumulate so slowly that major change goes undetected until the cumulative level of these effects finally cascades to irreversible change--change that would otherwise be attributed to natural adaptation or ecologic succession. As opposed to the conventional, persistent priority pollutants, PPCPs need not be persistent if they are continually introduced to surface waters, even at low parts-per-trillion/parts-per-billion concentrations (ng-microg/L). Even though some PPCPs are extremely persistent and introduced to the environment in very high quantities and perhaps have already gained ubiquity worldwide, others could act as if they were persistent, simply because their continual infusion into the aquatic environment serves to sustain perpetual life-cycle exposures for aquatic organisms. This review attempts to synthesize the literature on environmental origin, distribution/occurrence, and effects and to catalyze a more focused discussion in the environmental science community.

Cosmetics↗

PubMed1993

Introducing health sciences librarians to the Internet.

The Internet is no longer just for the adventurous explorers or the technical experts--it has found its way into the mainstream of librarianship. New users are coming onto "the net" in droves. A wealth of information is currently available dealing with the mechanics of the Internet and there are general guides to the available resources. More work needs to be done, however, in developing subject specific materials. This paper will report on the strategy that Scott Memorial Library, Thomas Jefferson University, has employed to develop staff skills and awareness and to take advantage of the resources and opportunities that the network provides for the health sciences community.

Academic Medical Centers↗

PubMed1999

On the trabecular "thickness"-number problem.

The decrease in trabecular number with aging and in osteoporosis seems to be naturally irreversible. In one view the resulting loss of bone strength would be irreversible too, but in another view the remaining trabeculae could increase their strength, chiefly by thickening. Whether that can occur has become important for osteoporosis research and management as well as for some biomechanical issues. This article reviews evidence and ideas that concern that matter. It suggests why the second view could be correct although previous studies did not detect it. However, that view still needs the kind of proof the general skeletal science community could accept.

Aging↗

PubMed2002

Rural reforms and changes in land management and attitudes: a case study from inner Mongolia, China.

The international science community stresses the importance of the local perspective in the context of dryland degradation. This paper explores changes in management and attitudes in a mixed farming system in northern China, since the introduction of the economic reforms in the early 1980s, and the following changes in land-use rights. The area encompasses a dune landscape scattered with crop-land, as well as the Daqinggou Nature Reserve, an area of natural vegetation. According to farmers new varieties of maize in combination with increased use of fertilizers have improved yields, though high yield variability persists due to erratic rainfall. Farmers acknowledge the importance of the 30-year contract on cultivated land in 1997 for their investment in long-term management, but emphasize the importance of chemical fertilizers for short-term economic survival. The farmers stressed the negative impact of grazing and cultivation on soil erosion and stated that differences in vegetation composition and cover in the nature reserve are due to anthropogenic factors.

Adult↗

PubMed2004

Biotechnology to improve health in developing countries -- a review.

The growing health disparities between the developing and the developed world call for urgent action from the scientific community. Science and technology have in the past played a vital role in improving public health. Today, with the tremendous potential of genomics and other advances in the life sciences, the contribution of science to improve public health and reduce global health disparities is more pertinent than ever before. Yet the benefits of modern medicine still have not reached millions of people in developing countries. It is crucial to recognize that science and technology can be used very effectively in partnership with public health practices in developing countries and can enhance their efficacy. The fight to improve global health needs, in addition to effective public health measures, requires rapid and efficient diagnostic tools; new vaccines and drugs, efficient delivery methods and novel approaches to therapeutics; and low-cost restoration of water, soil and other natural resources. In 2002, the University of Toronto published a report on the "Top 10 Biotechnologies for Improving Health in Developing Countries". Here we review these new and emerging biotechnologies and explore how they can be used to support the goals of developing countries in improving health.

Biotechnology↗

PubMedDate not supplied

Soil quality in New Zealand: policy and the science response.

Soil depletion and degradation have been increasingly recognized as important environmental issues in many parts of the world. Over the last decade a number of political and legislative measures have been introduced to encourage and enforce sustainable soil management in New Zealand. Application of the new legislation has highlighted gaps in our knowledge of soil quality and a lack of scientific methods to assess and monitor soil quality. This paper describes the legislative measures and outlines the sdentific response to the needs of regulatory agencies responsible for maintaining environmental quality. The research recommended a set of indicators to assess soil quality. Each soil quality attribute has an associated "target range" defining the acceptable value for the attribute. The paper also discusses the communication of results to end-users, including the development of a computerized assessment tool. The legislative measures and scientific response have fostered a closer relationship between the policy and science communities, leading to more well-focused research, but greater collaboration is still required.

Agriculture↗

PubMed1998

Toward a pluralistic animal science: postliberal feminist perspectives.

Women have not had the authority to define the conditions of animal agriculture or to develop strategies for addressing its problems because the field of animal science has been and remains dominated by men. Therefore, criteria for assessing the professional performance of animal scientists reflect the views of men and the experiences of masculinity. Recent attempts to improve the retention rates of women in the animal science profession have focused on socializing female protégés to the norms and expectations of the discipline. This approach is based on traditional liberal beliefs that all humans are essentially alike and that embodiment and(or) social location are irrelevant in understanding the world. Such socialization assumes that problems of gender inequity can be solved by providing opportunities for women to succeed in the existing system, with its existing norms. This approach ignores the possibility that the structure of women's lives and the normative commitments arising from women's experiences may be quite different from those of men. Professional reward structures that favor the life experiences and perspectives of men and ignore those of women coerce women into adopting values that may be incompatible with their identities. This not only devalues their perspectives and contributions, it forces them to commit self-betrayal. This is both harmful and antithetical to the idea of an empirically relevant science that blends multiple perspectives and understands diverse values. Substantive diversity in the animal science community requires standards that reflect and accommodate the pluralism in which we live.

Animal Husbandry↗

PubMed2004

Assessing the informational value of parameter estimates in cognitive models.

Mathematical models of cognition often contain unknown parameters whose values are estimated from the data. A question that generally receives little attention is how informative such estimates are. In a maximum likelihood framework, standard errors provide a measure of informativeness. Here, a standard error is interpreted as the standard deviation of the distribution of parameter estimates over multiple samples. A drawback to this interpretation is that the assumptions that are required for the maximum likelihood framework are very difficult to test and are not always met. However, at least in the cognitive science community, it appears to be not well known that standard error calculation also yields interpretable intervals outside the typical maximum likelihood framework. We describe and motivate this procedure and, in combination with graphical methods, apply it to two recent models of categorization: ALCOVE (Kruschke, 1992) and the exemplar-based random walk model (Nosofsky & Palmeri, 1997). The applications reveal aspects of these models that were not hitherto known and bring a mix of bad and good news concerning estimation of these models.

Algorithms↗

PubMed1998

Improving patient satisfaction through focus group interviews.

Long used by the social science community, focus groups have been increasingly used by nursing leaders to obtain information and feedback. Use of the focus group interview (FGI), a qualitative research method, allows the nurse executive the opportunity to obtain data on a variety of topics. In order for the findings to be meaningful, however, the researcher must adhere to basic FGI design and data analysis. Like other research methodologies, the focus group offers advantages and disadvantages that must be evaluated for appropriateness and feasibility. The article illustrates the use of the FGI to spark the creation of patient-focused care and significant increases in patient satisfaction in an academic medical center.

Data Interpretation, Statistical↗

PubMed2000

A rare mutation in the amelogenin gene and its potential investigative ramifications.

Over the past few years, the Australian forensic science community has adopted a common methodology and technology in the application of DNA profiling for investigative and forensic purposes. The ultimate objective of this initiative is the establishment of a national DNA database similar to that used in the UK. An integral part of this methodology is the use of "Profiler Plus," a nonaplex of STRs combined with amelogenin, a locus utilized for sex determination. This paper reports the results from a case where a mutation in the annealing region of the amelogenin primers appears to have resulted in the failure to amplify the amelogenin Y-homolog from a phenotypically normal male. The result was confirmed using two different primer sets that amplify different regions of the amelogenin gene. This situation suggests that the genetic determination of sex based on the amelogenin sequences from specimens of unknown origin, such as crime scene samples, should not be considered infallible.

Amelogenin↗

PubMed2002

TWGDAM validation of AmpFlSTR PCR amplification kits for forensic DNA casework.

Laboratory procedures used in short tandem repeat (STR) analysis were subjected to various scenarios that assessed reliability and identified potential limitations. These validation studies were designed as recommended by the Technical Working Group on DNA Analysis Methods (TWGDAM) and the DNA Advisory Board (DAB) (17,18). Various DNA samples were amplified by the polymerase chain reaction (PCR) using AmpFlSTR PCR Amplification Kits (i.e., AmpFlSTR Green I, Profiler, Profiler Plus, and COfiler kits), detected with ABI Prism instrumentation, and analyzed using GeneScan and Genotyper software. Data acquired in these studies reinforced an existing body of knowledge and expertise regarding application and interpretation of STR typing in the forensic science community. Consistent STR genotypes were detected in various body tissues and fluids. Inter-laboratory comparisons produced concordant genotype results. Quantitative interpretational aids for DNA mixtures were characterized. Ability of the typing systems to type potentially compromised samples reliably was evaluated. Nonprobative case evidentiary DNA was successfully amplified, genotyped, and interpreted. Potential limitations or cautionary factors in the interpretation of minimal fluorescence intensity were demonstrated. Differential amplification between loci was observed when PCR was inhibited; preferential amplification typically was not. Single AmpFlSTR locus amplification did not offer consistent benefit over AmpFlSTR multiplexing, even in cases of DNA degradation or PCR inhibition. During rigorous evaluation, AmpFlSTR PCR Amplification Kits reproducibly yielded sensitive and locus-specific results, as required in routine forensic analyses.

DNA↗

PubMed2003

Gene expression databases and data mining.

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.

Breast Neoplasms↗

PubMed2003

Components of gene therapy experimentation that contribute to relative risk.

Gene therapy is the purposeful delivery of genetic material to somatic cells for the purpose of treating disease or biomedical investigation. Either viral or non-viral vector methods can be used. The risk of collateral exposure of laboratory animal care personnel to gene therapy vectors is dependent on a number of factors. These factors are intrinsic to the gene therapy vector (the vehicle for genetic conveyance), product encoded by the genetic construct delivered, method of delivery, and immune status of the recipient. The component risks of gene therapy experiments can be analyzed to surmise the overall relative risk of the experiment. Knowledge of the components that contribute potential hazardous risk to a study can assist animal care staff in identifying area(s) where prudent practices should be focused. Gene therapy experiments involving viral vectors are generally performed at either biosafety level 2 or 3. The objective of this review is to report on various components of gene therapy experiments, focusing on characteristics of viral and non-viral vectors, to assist the laboratory animal science community in determining prudent biosafety practices.

Animal Technicians↗

PubMed1992

[Ewald Hering's opponent colors. History of an idea].

Ewald Hering (1834-1918) was one of the founders of modern visual science. Among his contributions, his color concept gave rise to mostly fruitless controversies, because it appeared to be incompatible with the trivariance of vision theory put forward by Young and Helmholtz. It is now clear that the two color concepts can be reconciled with one another. Hering's theory is based upon an analysis of visual perception. Experience indicates that a conscious subject needs four unique colors in order to characterize perception: blue, yellow, red and green. Usually, two of these hues, but never more, constitute a color sensation, e.g., orange contains red and yellow while blue and green are the components of turquoise. The central idea in Hering's concept was that red and green are opposite hues because they are never elicited simultaneously by a color stimulus; the same is true for blue and yellow. Hering also postulated that the perception of opponent colors is mediated by opponent processes in certain elements of the nervous system, i.e., that there are neurons that respond in a qualitatively different way to spectral stimuli of different frequencies. Today we know that, in fact, the majority of neurons in the retina and the visual pathway is capable of opponent-type responses as anticipated by Hering. It was, however, a long way until his concept was understood and finally accepted by the science community. Among those who helped to acknowledge it were the German physiologist von Kries, the Austrian physicist Schrödinger, the Finnish neurophysiologist Svaetichin, and the American psychophysicists Hurvich and Jameson. In 1906, the German Ophthalmological Society honored Ewald Hering by awarding him the Albrecht von Graefe Medal.

Color Perception↗

PubMed1992

Sexual assault: review of a national model protocol for forensic and medical evaluation. New Hampshire Sexual Assault Medical Examination Protocol Project Committee.

A national hospital/community model protocol was developed for the forensic and medical examination of victims of sexual assault. This review is designed to assist states in the development of sexual assault protocols. Controversial issues were addressed, including the collection of hair evidence, the importance of semen, mandatory reporting, pregnancy testing and prophylaxis, and sexually transmitted diseases including human immunodeficiency virus. The current role of DNA profiling is reviewed. These issues at the interface of medicine, forensic science, victim advocacy, and the law are analyzed. Representatives of the medical, legal, law enforcement, victim advocacy, and forensic science communities contributed to the development of the protocols at the national and state levels. The importance of a collaborative effort is emphasized. The broad protocol goals are to minimize the physical and psychological trauma to the victim while maximizing the probability of collecting and preserving physical evidence for potential use in the legal system.

Clinical Protocols↗

PubMed2005

The visible human and digital anatomy learning initiative.

A collaborative initiative is starting within the Internet2 Health Science community to explore the development of a framework for providing access to digital anatomical teaching resources over Internet2. This is a cross-cutting initiative with broad applicability and will require the involvement of a diverse collection of communities. It will seize an opportunity created by a convergence of needs and technical capabilities to identify the technologies and standards needed to support a sophisticated collection of tools for teaching anatomy.

Anatomy↗