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At least 289 records · Page 16Linked to original sources
PubMed2002

An integrated, functionally annotated gene map of the DXS8026-ELK1 interval on human Xp11.3-Xp11.23: potential hotspot for neurogenetic disorders.

Human chromosome Xp11.3-Xp11.23 encompasses the map location for a growing number of diseases with a genetic basis or genetic component. These include several eye disorders, syndromic and nonsyndromic forms of X-linked mental retardation (XLMR), X-linked neuromuscular diseases and susceptibility loci for schizophrenia, type 1 diabetes, and Graves' disease. We have constructed an approximately 2.7-Mb high-resolution physical map extending from DXS8026 to ELK1, corresponding to a genetic distance of approximately 5.5 cM. A combination of chromosome walking and sequence-tagged site (STS)-content mapping resulted in an integrated framework and transcript map, precisely positioning 10 polymorphic microsatellites (one of which is novel), 16 ESTs, and 12 known genes (RP2, PCTK1, UHX1, UBE1, RBM10, ZNF157, SYN1, ARAF1, TIMP1, PFC, ELK1, UXT). The composite map is currently anchored with 89 STSs to give an average resolution of approximately 1 STS every 30 kb. By a combination of EST database searches and in silico detection of UniGene clusters within genomic sequence generated from this template map, we have mapped several novel genes within this interval: a Na+/H+ exchanger (SLC9A7), at least two zincfinger transcription factors (KIAA0215 and Hs.68318), carbohydrate sulfotransferase-7 (CHST7), regucalcin (RGN), inactivation-escape-1 (INE1), the human ortholog of mouse neuronal protein 15.6, and four putative novel genes. Further genomic analysis enabled annotation of the sequence interval with 20 predicted pseudogenes and 21 UniGene clusters of unknown function. The combined PAC/BAC transcript map and YAC scaffold presented here clarifies previously conflicting data for markers and genes within the Xp11.3-Xp11.23 interval and provides a powerful integrated resource for functional characterization of this clonally unstable, yet gene-rich and clinically significant region of proximal Xp.

Chromosome Mapping↗
PubMed1994

On teaching bedside diagnostic and therapeutic procedures to medical students: an annotated bibliography of audiovisual materials.

OBJECTIVE: The teaching of procedures that involve risk of pain or morbidity deserves special care. The author set out to develop a teaching program for medical students to ensure quality control of bedside diagnostic and therapeutic procedures. DESIGN: A bibliography of available videotapes and related audiovisual teaching materials on 15 common bedside procedures was assembled following requests for materials from all U.S. medical schools. Audiovisual materials from nine institutions were reviewed. SETTING: Medical schools and teaching institutions. PARTICIPANTS: Medical schools and libraries. MAIN RESULTS: Seventy-three percent (24/33) of responding schools had no visual material on the procedures. There was ten times more material on physical diagnosis than on bedside procedures. About 20 videotapes were reviewed in an annotated bibliography. Some videos contained valuable insights on how to make good teaching materials. A set of criteria for quality videotapes is listed. CONCLUSIONS: Considerable work needs to be done to develop audiovisual materials and curricula for teaching bedside procedures. Videotape is a valuable medium for introducing procedures and ensuring uniformity of technique. After reviewing all available videotapes, the author decided that videotapes should be the initial part of a multidimensional program for teaching procedures.

Audiovisual Aids↗
PubMed2003

Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants.

The type I MADS-box genes constitute a largely unexplored subfamily of the extensively studied MADS-box gene family, well known for its role in flower development. Genes of the type I MADS-box subfamily possess the characteristic MADS box but are distinguished from type II MADS-box genes by the absence of the keratin-like box. In this in silico study, we have structurally annotated all 47 members of the type I MADS-box gene family in Arabidopsis thaliana and exerted a thorough analysis of the C-terminal regions of the translated proteins. On the basis of conserved motifs in the C-terminal region, we could classify the gene family into three main groups, two of which could be further subdivided. Phylogenetic trees were inferred to study the evolutionary relationships within this large MADS-box gene subfamily. These suggest for plant type I genes a dynamic of evolution that is significantly different from the mode of both animal type I (SRF) and plant type II (MIKC-type) gene phylogeny. The presence of conserved motifs in the majority of these genes, the identification of Oryza sativa MADS-box type I homologues, and the detection of expressed sequence tags for Arabidopsis thaliana and other plant type I genes suggest that these genes are indeed of functional importance to plants. It is therefore even more intriguing that, from an experimental point of view, almost nothing is known about the function of these MADS-box type I genes.

Amino Acid Motifs↗
PubMed2000

Comparative analysis of the PCOLCE region in Fugu rubripes using a new automated annotation tool.

The Japanese pufferfish Fugu rubripes with a genome of about 400 Mb is becoming increasingly recognized as a vertebrate model organism for comparative gene analysis (see Elgar 1996 for review). We have isolated and sequenced two Fugu cosmids spanning a genomic region of 66 kb containing the Fugu homolog to the human PCOLCE-I (Glöckner et al. 1998). We then examined if RUMMAGE-DP, a newly developed analysis tool for gene discovery which was designed for human and mouse genomic DNA, can be used for automatic annotation of Fugu genomic sequence. The exon prediction programs contained in RUMMAGE-DP performed better overall for the human sequence than for the Fugu contig. The GENSCAN program was the only exon prediction programme that performed equally well for both organisms. We show that RUMMAGE-DP is very useful in automatic analysis of Fugu sequences. Comparative analysis of the genomic structure of the PCOLCE-I genes in Fugu and human reveals that the exon/intron structure throughout the protein coding region is almost identical. We defined an additional domain based on the high degree of similarity of 26 aa between mammals and Fugu. The PCOLCE-I protein in both organisms contains two highly conserved CUB domains. Exons 6 and 7 are the only coding exons that differ in length between the two species. We assume that these exons do not code for any catalytic domain of the protein. Analysis of the remaining five Fugu genes within the 66 kb interval revealed no conserved synteny with the corresponding human 7q22 region.

Amino Acid Sequence↗
PubMed2002

Image annotation with Adobe Photoshop.

The authors relate the basic steps used to annotate grayscale cross sectional images with keyboard characters, arrowheads, and arrows using Adobe Photoshop 6.0 and 7.0.

Humans↗
PubMed1987

An annotated interview with Giuseppe Moruzzi, 1910-1986. Interview by Louise M. Marshall.

Utilizing three modes of information exchange, this "annotated autobiography" presents in perspective a picture of an eminent neuroscientist of the 20th century. The reminiscences of Guiseppe Moruzzi, Director of the Institute of Physiology of the University of Pisa for more than thirty years, were combined with contemporary tributes, a review of his major published work, and comments of friends and associates. Such a three-dimensional view of a scientific career illustrates the possibilities of "the medium is the message."

Belgium↗
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↗