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At least 271 records · Page 15Linked to original sources
PubMed1995

Assessing the quality of randomized controlled trials: an annotated bibliography of scales and checklists.

Assessing the quality of randomized controlled trials (RCTs) is important and relatively new. Quality gives us an estimate of the likelihood that the results are a valid estimate of the truth. We present an annotated bibliography of scales and checklists developed to assess quality. Twenty-five scales and nine checklists have been developed to assess quality. The checklists are most useful in providing investigators with guidelines as to what information should be included in reporting RCTs. The scales give readers a quantitative index of the likelihood that the reported methodology and results are free of bias. There are several shortcomings with these scales. Future scale development is likely to be most beneficial if questions common to all trials are assessed, if the scale is easy to use, and if it is developed with sufficient rigor.

Bias↗
PubMed2026

Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.

Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.

Antibiotic resistance genes↗
PubMed1992

Annotated tray lists save time, decrease errors.

We have achieved more consistency in instrument processing by using the annotated tray lists. This improved consistency has resulted in fewer errors and damaged instruments. Important tasks, such as lubricating the instruments, are not being overlooked inadvertently or performed incorrectly by staff. Productivity has increased because information is available when questions arise. Technicians do not have to look through large procedure manuals or ask other technicians to identify instruments and perform specific procedures. While the tray lists do not replace formal procedure manuals, they are helpful adjuncts for personnel who prepare the surgical trays.

Central Supply, Hospital↗
PubMed1996

Rhythm annotation and interobserver reproducibility of measures of heart rate variability.

Interobserver reproducibility is high for time domain and power spectral measures of heart rate variability, with greater reproducibility for low-frequency measures, and especially for the standard deviation of the 5-minute RR intervals over 24 hours, than for high-frequency measures. Overall interobserver variability of < 8% for these measures is largely (50% to 75%) explained by interobserver differences in annotation of supraventricular ectopy and sinus arrhythmia.

Adult↗
PubMed1998

The complete genome of Bacillus subtilis: from sequence annotation to data management and analysis.

The completion of the entire 4.2-Mb genome sequence of the gram-positive bacterium Bacillus subtilis has been a milestone for biological studies on this model organism. This paper describes bioinformatics work related to this joint European and Japanese project: methods and strategies for gene annotation and detection of sequencing errors, using an integrated cooperative computer environment (Imagene); construction of a specialized database for data management and a WWW server for data retrieval (SubtiList); DNA sequence analysis, yielding striking results on oligonucleotide bias, repeated sequences, and codon usage, all landmarks of evolutionary events shaping the B. subtilis genome.

Amino Acid Sequence↗
PubMed1998

Computational analyses and annotations of the Arabidopsis peroxidase gene family.

Classical heme-containing plant peroxidases have been ascribed a wide variety of functional roles related to development, defense, lignification, and hormonal signaling. More than 40 peroxidase genes are now known in Arabidopsis thaliana for which functional association is complicated by a general lack of peroxidase substrate specificity. Computational analysis was performed on 30 near full-length Arabidopsis peroxidase cDNAs for annotation of start codons and signal peptide cleavage sites. A compositional analysis revealed that 23 of the 30 peroxidase cDNAs have 5' untranslated regions containing 40-71% adenine, a rare feature observed also in cDNAs which predominantly encode stress-induced proteins, and which may indicate translational regulation.

Adenine↗
PubMedDate not supplied

An annotated bibliography for ethics training in consultation-liaison psychiatry.

The expanding field of bioethics has created a need in psychiatry for rapid access to the complex bioethics literature. This is especially true in consultation-liaison work. An annotated bibliography was created by a task force of the Academy of Psychosomatic Medicine charged with exploring how psychiatrists function on bioethics committees. The bibliography is organized into headings that reflect how bioethical problems came to the attention of psychiatrists. Introductory references allow the reader an overview of the history of bioethics and a selection of useful textbooks. References are provided explaining how ethical principles are used. References are also organized by areas of medical work frequently visited by consultation-liaison psychiatrists.

Bioethics↗
PubMed2001

Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome.

Computational methods for automated genome annotation are critical to understanding and interpreting the bewildering mass of genomic sequence data presently being generated and released. A neural network model of the structural and compositional properties of a eukaryotic core promoter region has been developed and its application for analysis of the Drosophila melanogaster genome is presented. The model uses a time-delay architecture, a special case of a feed-forward neural network. The structure of this model allows for variable spacing between functional binding sites, which is known to play a key role in the transcription initiation process. Application of this model to a test set of core promoters not only gave better discrimination of potential promoter sites than previous statistical or neural network models, but also revealed indirectly subtle properties of the transcription initiation signal. When tested in the Adh region of 2.9 Mbases of the Drosophila genome, the neural network for promoter prediction (NNPP) program that incorporates the time-delay neural network model gives a recognition rate of 75% (69/92) with a false positive rate of 1/547 bases. The present work can be regarded as one of the first intensive studies that applies novel gene regulation technologies to the identification of the complex gene regulation sites in the genome of Drosophila melanogaster.

Animals↗
PubMed2001

A status report on the sequencing and annotation of the P. falciparum genome.

Almost 5 years ago, an international consortium of sequencing centers and funding agencies was formed to sequence the genome of the human malaria parasite Plasmodium falciparum. A novel chromosome by chromosome shotgun strategy was devised to sequence this very AT-rich genome. Two of the 14 chromosomes have been completed and the remaining chromosomes are in the final stages of gap closure. The consortium recently developed plans for the annotation and analysis of the complete genome sequence and its publication in 2002.

Animals↗
PubMed1992

Geriatric emergency care: an annotated bibliography.

This annotated bibliography provides selected references to journal articles addressing general issues of the care of elderly patients in the emergency department. The bibliography was compiled by the Society for Academic Emergency Medicine Geriatric Emergency Medicine Task Force. Because the literature pertinent to geriatrics has continued to grow rapidly, only key articles of general interest to the clinician and academician are included in the bibliography. Preference is given to recent publications; most references date from the past five years. The articles cited are primarily concerned with the delivery of emergency care to geriatric patients; economic, legal, ethical, and sociological topics receive limited coverage. Some articles were selected to highlight current controversies or changes in viewpoint. Aging physiology, atypical characteristics of illness, and disease processes have been addressed elsewhere (J Am Geriatr Soc 1989;37:894-910).

Aged↗
PubMed1998

An annotated checklist by genus and species of 93 species level names for 51 recognized species of small strongyles (Nematoda: Strongyloidea: Cyathostominea) of horses, asses and zebras of the world.

The results of an international collaborative effort to prepare a recommended list of scientific names for the small strongyles (Nematoda: Strongyloidea: Cyathostominea) of horses, donkeys and zebras are reported. Fifty-one valid species are recognized in 13 genera, including Cyathostomum, Coronocyclus, Cylicodontophorus, Cylicocyclus, Cylicostephanus, Skrjabinodentus, Tridentoinfundibulum, Petrovinema, Poteriostomum, Parapoteriostomum, Hsiungia, Cylindropharynx and Caballonema. In addition, 42 other species level names are listed as synonyms of the 51 recognized species or as species inquirendae (10 species) or nomen nudum (one species). Numerous annotations provide information on the nomenclatural and systematics history, current status and additional studies needed.

Animals↗
PubMed2001

Whole-genome analysis: annotations and updates.

The most important advances in the field of genome annotation over the past two years involve the use of cDNA sequences, protein structures and gene expression data to predict genes. These types of information not only improve gene identification, but they also give insights into variation in gene structure and function.

Alternative Splicing↗
PubMed1998

Joint Task Force Algorithm and Annotations for Diagnosis and Management of Rhinitis.

The algorithm and text annotations in this document are intended to assist clinical decision making about patients who present with symptoms of rhinitis. This document complements the Executive Summary of Joint Task Force Practice Parameters for Diagnosis and Management of Rhinitis (Ann Allergy, Asthma, Immunol 1998; 81:463-468) and Diagnosis and Management of Rhinitis: Complete Guidelines of the Joint Task Force on Practice Parameters in Allergy, Asthma and Immunology (Ann Allergy, Asthma, Immunol 1998;81:478-578). The Joint Task Force on Practice Parameters in Allergy, Asthma and Immunology is co-sponsored by the American Academy of Allergy, Asthma and Immunology, the American College of Allergy, Asthma and Immunology and the Joint Council of Allergy, Asthma and Immunology.

Algorithms↗
PubMed2003

Comparison of rice and Arabidopsis annotation.

Several versions of the rice genome were published in 2002, providing a first overview of the genome content of this model monocot. At the same time, the genome of the model dicot, Arabidopsis thaliana, reached a new level of annotation as thousands of full-length cDNA sequences were integrated with the genome sequence.

Arabidopsis↗
PubMed2002

Semantic annotation for concept-based cross-language medical information retrieval.

We present a framework for concept-based cross-language information retrieval in the medical domain, which is under development in the MUCHMORE project. Our approach is based on using the Unified Medical Language System (UMLS) as the primary source of semantic data. Documents and queries are annotated with multiple layers of linguistic information. Linguistic processing includes part-of-speech tagging, morphological analysis, phrase recognition and the identification of medical terms and semantic relations between them. The paper describes experiments in monolingual and cross-language document retrieval, performed on a corpus of medical abstracts. Results show that linguistic processing, especially lemmatization and compound analysis for German, is a crucial step in achieving a good baseline performance. On the other hand, they show that semantic information, specifically the combined use of concepts and relations, increases the performance in monolingual and cross-language retrieval.

Humans↗
PubMed2000

Types of corrosion in removable appliances: annotated cases and preventative measures.

Three different types of electrochemical corrosion cells are discussed - composition, concentration, and stress cells. Annotated cases are presented for each type of corrosion cell in removable appliances using conventional photography, scanning electron microscopy, and X-ray elemental analyses. The complexity that corrosion can attain is illustrated via the case of a palatal expansion device. Specific examples of galvanic cells, which are possible in orthodontic practice, are summarized in terms of the anodic and cathodic half-cells. These include material differences, oxygen gradients, presence of debris, changes in pH, induced stress levels, changes in stress states, and variations in as-received history. A galvanic series is constructed from the orthodontist's perspective that includes titanium, nickel-titanium, cobalt-chromium, and stainless steel alloys, as well as glass-fiber-reinforced polymer-matrix composites. Preventative measures are presented from the perspectives of the raw material manufacturers, the dental laboratories, the chair-side practitioner, and the patient. A list of materials is provided, which are known to promote corrosion in the event that stainless steels are sensitized as a consequence of improper handling. In the final analysis, however, retainers and removable appliances are reliable if corrosion cells are conscientiously averted and preventative measures are routinely employed.

Journal Article↗