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At least 613 records · Page 34Linked to original sources

PubMed2006

Genes expressed during the development and ripening of watermelon fruit.

A normalized cDNA library was constructed using watermelon flesh mRNA from three distinct developmental time-points and was subtracted by hybridization with leaf cDNA. Random cDNA clones of the watermelon flesh subtraction library were sequenced from the 5' end in order to identify potentially informative genes associated with fruit setting, development, and ripening. One-thousand and forty-six 5'-end sequences (expressed sequence tags; ESTs) were assembled into 832 non-redundant sequences, designated as "EST-unigenes". Of these 832 "EST-unigenes", 254 ( approximately 30%) have no significant homology to sequences published so far for other plant species. Additionally, 168 "EST-unigenes" ( approximately 20%) correspond to genes with unknown function, whereas 410 "EST-unigenes" ( approximately 50%) correspond to genes with known function in other plant species. These "EST-unigenes" are mainly associated with metabolism, membrane transport, cytoskeleton synthesis and structure, cell wall formation and cell division, signal transduction, nucleic acid binding and transcription factors, defense and stress response, and secondary metabolism. This study provides the scientific community with novel genetic information for watermelon as well as an expanded pool of genes associated with fruit development in watermelon. These genes will be useful targets in future genetic and functional genomic studies of watermelon and its development.

Citrullus↗

PubMed2005

Combining microscience and neurobiology.

There is a wide range of literature on soft lithography, organic surface science (especially self-assembled monolayers of organic thiols adsorbed on gold) and microfluidics. These areas have developed in the fields of physical and surface chemistry, materials science and condensed matter physics, but they offer broad new capabilities in the development of relevant micro- and nanosystems to users in biology in general, and in cell biology in particular. The ability to integrate these techniques for fabricating materials and for controlling the chemistry of surfaces with electrical and electrochemical measurements should be especially relevant in neurobiology. The major impediment to the development of a field of 'microfabrication and measurement' in neuroscience is the absence of effective collaborative interactions between the communities of fabricators and neurobiologists.

Cell Culture Techniques↗

PubMed1998

Construction of the gyrB Database for the Identification and Classification of Bacteria.

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. We have therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. We chose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.

Journal Article↗

PubMedDate not supplied

The United Nations: the embarrassment of international law.

The United Nations should be working towards an international community living in peace under the aegis of international law. Although progress was made in its early years, notably in decolonization, with its membership increased from 50 to 189, major inequalities remain between its nations and their peoples. The Security Council, and in particular its five permanent members (P5), has been guilty of double standards in enforcing international law. Investment should create prosperity and not increase demand for arms. Independent oversight of the UN, and particularly the Security Council, by civil society is needed. If the legitimacy of the UN is to be restored, the Security Council should become more representative, the power of the General Assembly should be restored and the role of the International Court of Justice should be increased. All members of the UN, especially the PS, must respect international law as enshrined in the UN Charter and Conventions.

Conflict, Psychological↗

PubMed2004

Americo Negrette (1924 to 2003): diagnosing Huntington disease in Venezuela.

OBJECTIVE: To elucidate the role of Dr. Americo Negrette in diagnosing and reclassifying the dancing mania in Maracaibo, Venezuela as Huntington disease (HD). METHODS: All of the medical and nonmedical books and articles by Negrette were collected and reviewed. Personal interviews with Negrette were performed to confirm the details of his life and original work. His childhood, medical education, and contribution to HD, as well as contributions to medicine, art, and poetry, were covered in interview sessions. Excerpts from his autobiography, Ciudad de Fuego, were translated into English for publication. A complete bibliography of 70 books and research articles authored by Negrette was assembled. Negrette himself reviewed the compilation of this manuscript just days before his sudden death on September 14, 2003. RESULTS: Americo Negrette, a Venezuelan physician, biochemist, artist, and poet, observed a dancing epidemic in 1952. He acquired, through interviews with locals, the knowledge that there were two other small towns along Lake Maracaibo devastated by a syndrome called el mal (the bad). Negrette changed the diagnosis of these patients from a dancing mania to what he believed was Huntington chorea, later termed HD. He presented his findings at the Venezuelan Sixth Congress of Medical Science in 1955. He was met with reluctance in the local scientific community and a passive ear from government authorities. His description, written in Spanish, was not widely distributed beyond Venezuela, and its importance would have to wait until one of his students shared his observations (more than a decade later) with the HD research community and the rest of the world. CONCLUSION: The "dancing mania" of Maracaibo, because of the work of Americo Negrette, has been reclassified as Huntington disease.

Attitude to Health↗

PubMed1991

Views and reflections on anti-malaria programmes in the world.

The certification of achieved malaria eradication from Taiwan in 1965, and the maintenance of malaria-free status of the country for 25 years, do prove the soundness of the malaria eradication adopted in 1955 by the World Health Assembly, but only when this policy is well understood and well implemented. Certain unique features of Taiwan eradication programme that ultimately lead to its success are cited. The worsening of the malaria situation in the world, and the dismantling of the vertical malaria structures in many countries were highlighted in an article entitled "Malaria Programme from Euphoria to Anarchy" in the WHO forum of 1980. Since then another decade of indifference to the rising tide of malaria, brought about an alarming situation that elicited the 1989 World Health Assembly's resolution on Malaria Control. The underlying causes of this indifference by governments and international bodies concerned with health and socioeconomic development are presented to apprise governments of malarious countries of certain imperative facts that have to be accepted when seriously considering malaria control schemes in their health plans. The need for training future generations of seasoned malariologists is stressed, as well as the need to develop new curricula comprising the experience gained in this field since the dawn of this century. A stress is made on the importance of promoting research, not only on technical problems but also on the social behaviour of rural communities in relation to the acceptance and participation in malaria control programmes. The role of Tropical Diseases Institutes and Research Centres in promoting basic and practical research in the field of malaria is underlined.

Humans↗

PubMed2001

DNA sequence quality trimming and vector removal.

MOTIVATION: Most sequence comparison methods assume that the data being compared are trustworthy, but this is not the case with raw DNA sequences obtained from automatic sequencing machines. Nevertheless, sequence comparisons need to be done on them in order to remove vector splice sites and contaminants. This step is necessary before other genomic data processing stages can be carried out, such as fragment assembly or EST clustering. A specialized tool is therefore needed to solve this apparent dilemma. RESULTS: We have designed and implemented a program that specifically addresses the problem. This program, called LUCY, has been in use since 1998 at The Institute for Genomic Research (TIGR). During this period, many rounds of experience-driven modifications were made to LUCY to improve its accuracy and its ability to deal with extremely difficult input cases. We believe we have finally obtained a useful program which strikes a delicate balance among the many issues involved in the raw sequence cleaning problem, and we wish to share it with the research community. AVAILABILITY: LUCY is available directly from TIGR (http://www.tigr.org/softlab). Academic users can download LUCY after accepting a free academic use license. Business users may need to pay a license fee to use LUCY for commercial purposes. CONTACT: Questions regarding the quality assessment module of LUCY should be directed to Michael Holmes (mholmes@tigr.org). Questions regarding other aspects of LUCY should be directed to Hui-Hsien Chou (hhchou@iastate.edu).

Algorithms↗

PubMed2005

First nuclear DNA amounts in more than 300 angiosperms.

BACKGROUND AND AIMS: Genome size (DNA C-value) data are key biodiversity characters of fundamental significance used in a wide variety of biological fields. Since 1976, Bennett and colleagues have made scattered published and unpublished genome size data more widely accessible by assembling them into user-friendly compilations. Initially these were published as hard copy lists, but since 1997 they have also been made available electronically (see the Plant DNA C-values database http://www.kew.org/cval/homepage.html). Nevertheless, at the Second Plant Genome Size Meeting in 2003, Bennett noted that as many as 1000 DNA C-value estimates were still unpublished and hence unavailable. Scientists were strongly encouraged to communicate such unpublished data. The present work combines the databasing experience of the Kew-based authors with the unpublished C-values produced by Zonneveld to make a large body of valuable genome size data available to the scientific community. METHODS: C-values for angiosperm species, selected primarily for their horticultural interest, were estimated by flow cytometry using the fluorochrome propidium iodide. The data were compiled into a table whose form is similar to previously published lists of DNA amounts by Bennett and colleagues. KEY RESULTS AND CONCLUSIONS: The present work contains C-values for 411 taxa including first values for 308 species not listed previously by Bennett and colleagues. Based on a recent estimate of the global published output of angiosperm DNA C-value data (i.e. 200 first C-value estimates per annum) the present work equals 1.5 years of average global published output; and constitutes over 12 % of the latest 5-year global target set by the Second Plant Genome Size Workshop (see http://www.kew.org/cval/workshopreport.html). Hopefully, the present example will encourage others to unveil further valuable data which otherwise may lie forever unpublished and unavailable for comparative analyses.

Cell Nucleus↗

PubMed2003

A latent variable model approach for assembling and scoring screening tests for dementia.

In dementia studies, the diagnosis of dementia often relies on results of screening tests aimed at measuring various dimensions of cognitive functions. The current practice of scoring a screening test involves simply summing the correct responses from each item. However, this method may be imprecise and inefficient in the predictive power of the score for dementia. We propose a latent variable model approach for the scoring and item selection of such tests. We model the item responses to be random variables based on latent variables. We also model the disease outcomes to be a function of the latent variables. Maximum likelihood estimates are obtained by maximizing the joint likelihood functions of disease and the item responses over a specified distribution function for the latent variables. Variances of model parameters are estimated using a nonparametric bootstrap method. We illustrate the approach using a screening test for dementia from a community-based study.

Aged↗

PubMed2026

The genome sequence of the Golden Plusia, Polychrysia moneta (Fabricius, 1787) (Lepidoptera: Noctuidae).

We present a genome assembly from a male specimen of Polychrysia moneta (Golden Plusia; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 430.64 megabases and 425.60 megabases. Most of haplotype 1 (98.46%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.26 kilobases. This work is part of Project Psyche, a collaborative programme generating genomes for European butterflies and moths.

Polychrysia moneta; Golden Plusia; genome sequence↗

PubMed1998

The bio-objects project. Part I: the object data model core elements.

MOTIVATION: Scientific data reside in a number of different data sources, both public and commercial, and are accessible through various software applications. Data and software interoperability is becoming a critical issue in the research community. In our opinion, the need to develop a unified object model for biotechnology must be recognized. Herein, we present a prototype and core elements for the Object Data Model, a central part of our future commercial product development. RESULTS: We have designed a first layer of the Object Data Model that will be used for further commercial application development. The CBioBase object was designed as a citable, stable and core data element for the Object Data Model. General relationships between objects and application components were established. AVAILABILITY: Software tools will be provided with a future DNASIS product to access various elements of the Object Model. We are planning to assemble C++ libraries and Java binary files into BioObjects SDK (software development kit) for those interested in software implementation using the described object model. CONTACT: smaltch@msn.com or smaltch@hitachi-soft.com

Biotechnology↗

PubMed2003

Child health indicators for Europe: a priority for a caring society.

BACKGROUND: Measurement of children's health is important for two reasons: first, because young people are citizens in their own right, yet largely unable to act as self-advocates, particularly at the population level; and second, because their health determines the health of the future population. Indicators based on measurements of child health are important for identifying progress, problems and priorities, changes over time, and newly emergent issues. The European Community Health Monitoring Programme (HMP) is a comprehensive programme to develop and implement a set of national-level indicators. The Child Health Indicators of Life and Development (CHILD) project is the only population group-specific project, seeking to determine a holistic set of measures. METHODS: The project endeavoured to address all aspects of child health and its determinants, balancing positive and negative aspects. It undertook a structured search of published evidence to seek to identify, and validate, indicators of health and illness, health determinants and challenges to health, quality of healthcare support and health-promoting national policies. A systematic approach was used in identifying valid indicators, and in assembling a balanced composite list. All ages from infancy to adolescence were covered. RESULTS: The project's final report identifies 38 core desirable national indicators, citing purpose and evidence for each. Of equal importance, it also identifies 17 key child health topics on which further research work is needed in order to identify and validate indicators appropriate across different national settings.

Adolescent↗

PubMed2004

Crystal structure of leucotoxin S component: new insight into the Staphylococcal beta-barrel pore-forming toxins.

Staphylococcal leucocidins and gamma-hemolysins (leucotoxins) are bi-component toxins that form lytic transmembrane pores. Their cytotoxic activities require the synergistic association of a class S component and a class F component, produced as water-soluble monomers that form hetero-oligomeric membrane-associated complexes. Strains that produce the Panton-Valentine leucocidin are clinically associated with cutaneous lesions and community-acquired pneumonia. In a previous study, we determined the crystal structure of the F monomer from the Panton-Valentine leucocidin. To derive information on the second component of the leucotoxins, the x-ray structure of the S protein from the Panton-Valentine leucocidin was solved to 2.0 angstrom resolution using a tetragonal crystal form that contains eight molecules in the asymmetric unit. The structure demonstrates the different conformation of the domain involved in membrane contacts and illustrates sequence and tertiary structure variabilities of the pore-forming leucotoxins. Mutagenesis studies at a key surface residue (Thr-28) further support the important role played by these microheterogeneities for the assembly of the bipartite leucotoxins.

Amino Acid Sequence↗

PubMed2004

In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database.

An extensive analysis of the Arabidopsis thaliana peripheral and integral thylakoid membrane proteome was performed by sequential extractions with salt, detergent, and organic solvents, followed by multidimensional protein separation steps (reverse-phase HPLC and one- and two-dimensional electrophoresis gels), different enzymatic and nonenzymatic protein cleavage techniques, mass spectrometry, and bioinformatics. Altogether, 154 proteins were identified, of which 76 (49%) were alpha-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein. The data were integrated with our analysis of the lumenal-enriched proteome. We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis. The high coverage of the photosynthetic apparatus and the identification of known hydrophobic proteins with low expression levels, such as cpSecE, Ohp1, and Ohp2, indicate an excellent dynamic resolution of the analysis. The sequential extraction process proved very helpful to validate transmembrane prediction. Our data also were cross-correlated to chloroplast subproteome analyses by other laboratories. All data are deposited in a new curated plastid proteome database (PPDB) with multiple search functions (http://cbsusrv01.tc.cornell.edu/users/ppdb/). This PPDB will serve as an expandable resource for the plant community.

Amino Acid Sequence↗

PubMed2002

Recommendations for improving the quality of care through stroke centers and systems: an examination of stroke center identification options: multidisciplinary consensus recommendations from the Advisory Working Group on Stroke Center Identification Options of the American Stroke Association.

BACKGROUND AND PURPOSE: The American Stroke Association (ASA) assembled a multidisciplinary group of experts to develop recommendations regarding the potential effectiveness of establishing an identification program for stroke centers and systems. "Identification" refers to the full spectrum of models for assessing and recognizing standards of quality care (self-assessment, verification, certification, and accreditation). A primary consideration is whether stroke center identification might improve patient outcomes. METHODS: In February 2001, ASA, with the support of the Stroke Council's Executive Committee, decided to embark on an evaluation of the potential impact of stroke center identification. HealthPolicy R&D was selected to prepare a comprehensive report. The investigators reported on models outside the area of stroke, ongoing initiatives within the stroke community (such as Operation Stroke), and state and federal activities designed to improve care for stroke patients. The investigators also conducted interviews with thought leaders in the stroke community, representing a diverse sampling of specialties and affiliations. In October 2001, the Advisory Working Group on Stroke Center Identification developed its consensus recommendations. This group included recognized experts in neurology, emergency medicine, emergency medical services, neurological surgery, neurointensive care, vascular disease, and stroke program planning. RESULTS: There are a variety of existing identification programs, generally falling within 1 of 4 categories (self-assessment, verification, certification, and accreditation) along a continuum with respect to intensity and scope of review and consumption of resources. Ten programs were evaluated, including Peer Review Organizations, trauma centers, and new efforts by the National Committee on Quality Assurance and the Joint Commission on the Accreditation of Healthcare Organizations to identify providers and disease management programs. The largest body of literature on clinical outcomes associated with identification programs involves trauma centers. Most studies support that trauma centers and systems lead to improved mortality rates and patient outcomes. The Advisory Working Group felt that comparison to the trauma model was most relevant given the need for urgent evaluation and treatment of stroke. The literature in other areas generally supports the positive impact of identification programs, although patient outcomes data have less often been published. In the leadership interviews, participants generally expressed strong support for pursuing some form of voluntary identification program, although concerns were raised that this effort could meet with some resistance. CONCLUSIONS: Identification of stroke centers and stroke systems competencies is in the best interest of stroke patients in the United States, and ASA should support the development and implementation of such processes. The purpose of a stroke center/systems identification program is to increase the capacity for all hospitals to treat stroke patients according to standards of care, recognizing that levels of involvement will vary according to the resources of hospitals and systems.

Accreditation↗

PubMed2026

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗

PubMedDate not supplied

The surgeon as a scientific writer.

The skills of a surgeon as a scientific writer are many and sophisticated. Recognizing the essential elements of research, learning how to plan and execute the idea, and finally assembling and reporting the data in a coherent and intelligent manner are all critical elements in successfully writing a publication. But writing a research paper is a demanding process that young surgeons are often ill-equiped to address. It consists of many complex tasks and inevitable difficulties that confront every researcher. From undergraduate programs through residency, more attention must be given to cultivate writing skills, especially within the scientific realm. In this article we specifically address these shortcomings while identifying solutions for and attributes of sound scientific writing. When we can manage the parts, we can manage the whole, and look forward to more research with greater confidence. Those who want to join communities that depend on research, such as surgical and medical communities, have to demonstrate not only that they can give good answers to hard questions, but also that they can report their results in ways that are useful to their community, and that means in ways that are apparent, accessible, and recognizable. Being a scientific writer allows him or her to clearly express and effectively convey the importance of worthwhile research. Only when someone has experienced the process of doing his or her own research can one intelligently evaluate the research of others.

Biomedical Research↗

PubMed2006

Multisegmented one-dimensional nanorods prepared by hard-template synthetic methods.

In the science and engineering communities, the nanoscience revolution is intensifying. As many types of nanomaterials are becoming more reliably synthesized, they are being used for novel applications in all branches of nanoscience and nanotechnology. Since it is sometimes desirable for single nanomaterials to perform multiple functions simultaneously, multicomponent nanomaterials, such as core-shell, alloyed, and striped nanoparticles, are being more extensively researched. Nanoscientists hope to design multicomponent nanostructures and exploit their inherent multiple functionalities for use in many novel applications. This review highlights recent advances in the synthesis of multisegmented one-dimensional nanorods and nanowires with metal, semiconductor, polymer, molecular, and even gapped components. It also discusses the applications of these multicomponent nanomaterials in magnetism, self-assembly, electronics, biology, catalysis, and optics. Particular emphasis is placed on the new materials and devices achievable using these multicomponent, rather than single-component, nanowire structures.

Electrochemistry↗