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PubMedDate not supplied

Digitization of medical documents: an X-Windows application for fast scanning.

This paper deals with digitization, using a commercial scanner, of medical documents as still images for introduction into a computer-based Information System. Document management involves storing, editing and transmission. This task has usually been approached from the perspective of the difficulties posed by radiologic images because of their indisputable qualitative and quantitative significance. However, healthcare activities require the management of many other types of documents and involve the requirements of numerous users. One key to document management will be the availability of a digitizer to deal with the greatest possible number of different types of documents. This paper describes the relevant aspects of documents and the technical specifications that digitizers must fulfill. The concept of document type is introduced as the ideal set of digitizing parameters for a given document. The use of document type parameters can drastically reduce the time the user spends in scanning sessions. Presentation is made of an application based on Unix, X-Windows and OSF/Motif, with a GPIB interface, implemented around the document type concept. Finally, the results of the evaluation of the application are presented, focusing on the user interface, as well as on the viewing of color images in an X-Windows environment and the use of lossy algorithms in the compression of medical images.

Database Management Systems↗
PubMed2005

Editing of plastid RNA in Arabidopsis thaliana ecotypes.

Post-transcriptional maturation of plastid-encoded mRNAs from land plants includes editing by making cytidine to uridine alterations at highly specific positions; this usually restores codon identities for conserved amino acids that are important for the proper function of the affected proteins. In contrast to the rather constant number of editing sites their location varies greatly, even between closely related taxa. Here, we experimentally determined the specific pattern of editing sites (the editotype) of the plastid genome of Arabidopsis thaliana ecotype Columbia (Col-0). Based on phylogenetic analyses of plastid open reading frames, we identified 28 editing sites. Two editing events in the genes matK and ndhB seem to have evolved late during the evolution of flowering plants. Strikingly, they are embedded in almost identical sequence elements and seem to be phylogenetically co-processed. This suggests that the two sites are recognized by the same trans-factor, which could help to explain the hitherto enigmatic gain of editing sites in evolution. In order to trace variations in editotype at the subspecies level we examined two other A. thaliana accessions, Cape Verde Islands (Cvi-0) and Wassilewskija (Ws-2), for the Col-0 editing sites. Both Cvi-0 and Ws-2 possess and process the whole set of editing sites as determined in Col-0, but the consequences of RNA editing differ at one position between the ecotypes.

Amino Acid Sequence↗
PubMed2005

Medicare and Medicaid programs; fire safety requirements for certain health care facilities; amendment. Interim final rule with comment period.

This interim final rule with comment period adopts the substance of the April 15, 2004 temporary interim amendment (TIA) 00-1 (101), Alcohol Based Hand Rub Solutions, an amendment to the 2000 edition of the Life Safety Code, published by the National Fire Protection Association (NFPA). This amendment will allow certain health care facilities to place alcohol-based hand rub dispensers in egress corridors under specified conditions. This interim final rule with comment period also requires that nursing facilities install smoke detectors in resident rooms and public areas if they do not have a sprinkler system installed throughout the facility or a hard-wired smoke detection system in those areas.

Alcohols↗
PubMed2000

Extradural neural axis compartment.

The lengthy, continuous, slender extradural neural axis compartment (EDNAC), which extends from the coccyx to the orbit, has been not so much discovered as recognized. Through this compartment run arteries, myelinated and unmyelinated nerves, and valveless veins. Adipose tissue is abundant in the orbital and spinal segments, possibly due to movement requirements, although it is very sparse in the skull base segment, the last segment to be recognized as a continuation of the EDNAC, which connects Breschet's veins to the orbit. The lateral sellar compartment (in older terminology, the cavernous sinus) is an enlarged segment of this EDNAC along the skull base connecting the orbit with the extradural space through the superior orbital fissure and down the dorsum to Breschet's veins of the basilar process of the occipital bone. Understanding the continuity of the EDNAC should help the student understand any segment, particularly the skull base. As Batson noted, "Living anatomy is slowly editing and replacing the anatomy of the dead room."

Adipose Tissue↗
PubMed2026

Markerless gene deletion in Porphyromonas gingivalis using a pheS*-based counterselection system.

Porphyromonas gingivalis is an oral pathobiont implicated in periodontitis and several systemic diseases and serves as an important model organism. However, the routine generation of markerless mutants in P. gingivalis has remained challenging due to the lack of an efficient counterselection system for the double cross-over approach. Markerless gene deletion is crucial for bacterial genetic manipulations, in particular for generating multiple gene deletions or introducing point mutations. In this study, a counterselection system for P. gingivalis was established by placing the pheS* gene under the control of a P. gingivalis promoter enabling efficient expression. The construct was delivered to P. gingivalis via a suicide plasmid by conjugation. Using PG0719 as a representative target gene, first cross-over recombinants were selected using erythromycin resistance encoded on the suicide plasmid. Cells were then subjected to counterselection in the presence of p-chloro-phenylalanine (p-Cl-Phe). Retention of pheS* in the genome reduced viability, thereby enriching recombinants that had undergone a second recombination event and loss of the plasmid sequence. Candidate clones were screened by colony PCR analysis to confirm the loss of the gene of interest. A markerless PG0719 mutant was generated and further validated by Sanger sequencing, demonstrating a practical approach for markerless gene deletion in P. gingivalis and providing a framework for further genome modifications in the organism.IMPORTANCEAlthough Porphyromonas gingivalis is a widely studied model organism, the genetic manipulation of this bacterium has remained limited by the lack of efficient tools for markerless genome editing. Here, we established a counterselection system based on pheS∗ that enables markerless gene deletion in P. gingivalis. This approach addresses a technical limitation in the field and provides a practical and broadly applicable framework for advanced genetic manipulation in this important oral pathobiont.

Porphyromonas gingivalis↗
PubMed2000

A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.

Small hemoproteins displaying amino acid sequences 20-40 residues shorter than (non-)vertebrate hemoglobins (Hbs) have recently been identified in several pathogenic and non-pathogenic unicellular organisms, and named 'truncated hemoglobins' (trHbs). They have been proposed to be involved not only in oxygen transport but also in other biological functions, such as protection against reactive nitrogen species, photosynthesis or to act as terminal oxidases. Crystal structures of trHbs from the ciliated protozoan Paramecium caudatum and the green unicellular alga Chlamydomonas eugametos show that the tertiary structure of both proteins is based on a 'two-over-two' alpha-helical sandwich, reflecting an unprecedented editing of the classical 'three-over-three' alpha-helical globin fold. Based on specific Gly-Gly motifs the tertiary structure accommodates the deletion of the N-terminal A-helix and replacement of the crucial heme-binding F-helix with an extended polypeptide loop. Additionally, concerted structural modifications allow burying of the heme group and define the distal site, which hosts a TyrB10, GlnE7 residue pair. A set of structural and amino acid sequence consensus rules for stabilizing the fold and the bound heme in the trHbs homology subfamily is deduced.

Amino Acid Motifs↗
PubMedDate not supplied

Evaluation of consumer drug information databases.

OBJECTIVES: To evaluate prescription drug information contained in six consumer drug information databases available on CD-ROM, and to make health care professionals aware of the information provided, so that they may appropriately recommend these databases for use by their patients. DESIGN: Observational study of six consumer drug information databases: The Corner Drug Store, Home Medical Advisor, Mayo Clinic Family Pharmacist, Medical Drug Reference, Mosby's Medical Encyclopedia, and PharmAssist. SETTING: Not applicable. PATIENTS OR OTHER PARTICIPANTS: Not applicable. INTERVENTIONS: Information on 20 frequently prescribed drugs was evaluated in each database. The databases were ranked using a point-scale system based on primary and secondary assessment criteria. MAIN OUTCOME MEASURES: For the primary assessment, 20 categories of information based on those included in the 1998 edition of the USP DI Volume II, Advice for the Patient: Drug Information in Lay Language were evaluated for each of the 20 drugs, and each database could earn up to 400 points (for example, 1 point was awarded if the database mentioned a drug's mechanism of action). For the secondary assessment, the inclusion of 8 additional features that could enhance the utility of the databases was evaluated (for example, 1 point was awarded if the database contained a picture of the drug), and each database could earn up to 8 points. RESULTS: The results of the primary and secondary assessments, listed in order of highest to lowest number of points earned, are as follows: Primary assessment--Mayo Clinic Family Pharmacist (379), Medical Drug Reference (251), PharmAssist (176), Home Medical Advisor (113.5), The Corner Drug Store (98), and Mosby's Medical Encyclopedia (18.5); secondary assessment--The Mayo Clinic Family Pharmacist (8), The Corner Drug Store (5), Mosby's Medical Encyclopedia (5), Home Medical Advisor (4), Medical Drug Reference (4), and PharmAssist (3). CONCLUSION: The Mayo Clinic Family Pharmacist was the most accurate and complete source of prescription drug information based on the USP DI Volume II and would be an appropriate database for health care professionals to recommend to patients.

CD-I↗
PubMed2002

[Internet: an infrastructure of evidence-based medicine in neurology].

EBM is a cyclic process. Medical evidences are created in clinical trials, which are published in medical literatures. The medical literatures are converted to literature database, from which clinical practice guidelines are made. They are provided to the clinicians, from whom a new clinical research is born again. Information technology, especially the use of internet has deeply related to every process of EBM, which is shown above. In clinical trials, data are accumulated through internet and the process is controlled by a coordinator using internet. In Japan, University Hospital Medical Information System (UMIN) has successfully provided such a tool to the clinical researchers. For the literature search. IT is mandatory and clinical practice guidelines are created on the base of various secondary information database, which are edited using advanced information technology Clinical practice guidelines are provided to hospitals through internet and they reach to the clinicians using a function of hospital information system, especially electronic medical record. In recent days, IT is an indispensable tool for daily practice of evidence-based medicine. However, in Japan the evidence has not been accumulated in national level, and for the future, the creation of national database of medical data should be explored.

Evidence-Based Medicine↗
PubMed1994

A DNA-polymerase-related reading frame (pol-r) in the mtDNA of Secale cereale.

Mitochondrial (mt)DNA of Secale cereale contains an open reading frame (pol-r), the potential translation product of which shows significant homology to the type-B DNA polymerase encoded by the S1 plasmid of Zea mays; it contains the highly-conserved domains IIa to V of family B polymerases. The pol-r ORF is transcribed, as proven by RT-PCR, but the transcript is not edited. Upstream of the putative start codon a potential promoter motif was detected, fitting well into the postulated consensus sequence of the transcription initiation regions of Z. mays and Triticum aestivum. The pol-r ORF occurs in mtDNA of the fertile rye variety "Halo" and the cytoplasmic male-sterile (CMS) line "Pampa". Both ORFs are almost identical, apart from the 3' terminus; pol-r from Halo can code for 289 amino acids, pol-r from Pampa for 312 amino acids. Based on codon usage and the lack of editing, pol-r is considered to be a "young" gene, probably introduced in the mtDNA of rye by recombination with an mt plasmid.

Amino Acid Sequence↗
PubMed2005

Cleavage of dsRNAs hyper-edited by ADARs occurs at preferred editing sites.

Long double-stranded RNAs (dsRNAs) may undergo covalent modification (hyper-editing) by adenosine deaminases that act on RNA (ADARs), whereby up to 50-60% of adenosine residues are converted to inosine. Previously, we have described a ribonuclease activity in various cell extracts that specifically targets dsRNAs hyper-edited by ADARs. Such a ribonuclease may play an important role in viral defense, or may alternatively be involved in down-regulation of other RNA duplexes. Cleavage of hyper-edited dsRNA occurs within sequences containing multiple IU pairs but not in duplexes that contain either isosteric GU pairs or Watson-Crick base pairs. Here, we describe experiments aimed at further characterizing cleavage of hyper-edited dsRNA. Using various inosine-containing dsRNAs we show that cleavage occurs preferentially at a site containing both IU and UI pairs, and that inclusion of even a single GU pair inhibits cleavage. We also show that cleavage occurs on both strands within a single dsRNA molecule and requires a 2'-OH group. Strikingly, we show that ADAR1, ADAR2 or dADAR all preferentially generate the preferred cleavage site when hyper-editing a long dsRNA.

Adenosine Deaminase↗
PubMed1997

Controlled vocabulary and design of laboratory results displays.

Traditional data-review displays are driven by the ancillary systems that produced the data. A different paradigm is being used at Columbia-Presbyterian Medical Center (CPMC) where a controlled medical vocabulary-the Medical Entities Dictionary (MED) is the driving force behind laboratory data-review displays. Using hierarchical and semantic networks the authors have constructed a Web-based tool that considerably simplifies the MED-editing task required to create new displays. The tool uses knowledge in the MED to extract contextually relevant hierarchic and semantic sub-nets from the MED. The tool has a sensitivity of 92.2% and a relevance of 94.7% for retrieval of terms from the MED. Based on these results and given sufficient domains' structure within controlled vocabularies, we conclude that similar algorithms will enable applications to design and generate customized displays on-the-fly.

Algorithms↗
PubMed2005

The effect of support group on the mental health and quality of life for mothers with autistic children.

BACKGROUND: The purpose of this study was to explore the effect of support groups on the mental health and quality of life for mothers with autistic children. METHOD: A quasi-experimental pre-post control group design was used in this study. The mothers had children without chronic diseases diagnosed as autistic based on Diagnostic and Statistical Manual of Mental Disorder-Fourth Edition (DSM-IV) and were their primary caregivers. The mothers were assigned to control or intervention groups based on their willingness. The 10 weeks of the support group programme served as an intervention. There were three waves of data collection: pre-test, post-test, and after 1 month follow-up. A total of 27 mothers with autistic children were assigned into experimental and control groups. In total, there were eight mothers in the experimental group and 19 mothers served as the control group. RESULTS: The results of this study showed that mental health had not significantly improved in the intervention group compared to those in the control group at the end of the first month during follow-up. However, the subjective well-being and employment status had an effect on their mental health. Only the subjective well-being had an effect on their quality of life. CONCLUSION: According to the results of this study, recommendations included (1) regularly promulgating a caregiver support group, (2) the advancement of training skills within the group, and (3) upgrading and promoting nurses' ability to lead support groups in the future.

Adult↗
PubMed2026

AI-driven CRISPR screening: optimizing gene editing through automation and intelligent decision support.

BACKGROUND: CRISPR-based genetic screening has become a central methodology in functional genomics, enabling systematic interrogation of gene function, genetic interactions and context-dependent vulnerabilities at scale. However, the rapid expansion of screening modalities-including multi-condition designs, combinatorial perturbations, in vivo applications and single-cell readouts-has exposed fundamental limitations of heuristic-driven experimental design and post hoc statistical analysis. MAIN BODY: This Review synthesizes how artificial intelligence is reshaping CRISPR screening by introducing predictive, adaptive and system-level intelligence across the experimental lifecycle. We organize recent advances into two tightly coupled modules. First, machine learning and deep learning (ML/DL) methods optimize experimental design by learning context-dependent perturbation behavior, anticipating confounding effects and enabling iterative, information-efficient screening strategies. Second, large language model-agent (LLM-agent) systems complement these advances by externalizing scientific reasoning, integrating biological knowledge at scale and coordinating analysis and decision-making in human-in-the-loop workflows. CONCLUSIONS: Together, ML/DL and LLM-agent approaches reframe CRISPR screening from a static analytical pipeline into an intelligent experimental system, with important implications for robustness, scalability and biological discovery.

Artificial Intelligence↗
PubMed2001

Specific cleavage of hyper-edited dsRNAs.

Extended double-stranded DNA (dsRNA) duplexes can be hyper-edited by adenosine deaminases that act on RNA (ADARs). Long uninterrupted dsRNA is relatively uncommon in cells, and is frequently associated with infection by DNA or RNA viruses. Moreover, extensive adenosine to inosine editing has been reported for various viruses. A number of cellular antiviral defence strategies are stimulated by dsRNA. An additional mechanism to remove dsRNA from cells may involve hyper-editing of dsRNA by ADARs, followed by targeted cleavage. We describe here a cytoplasmic endonuclease activity that specifically cleaves hyper-edited dsRNA. Cleavage occurs at specific sites consisting of alternating IU and UI base pairs. In contrast, unmodified dsRNA and even deaminated dsRNAs that contain four consecutive IU base pairs are not cleaved. Moreover, dsRNAs in which alternating IU and UI base pairs are replaced by isomorphic GU and UG base pairs are not cleaved. Thus, the cleavage of deaminated dsRNA appears to require an RNA structure that is unique to hyper-edited RNA, providing a molecular target for the disposal of hyper-edited viral RNA.

Adenosine Deaminase↗
PubMed1997

RNA editing: getting U into RNA.

RNA editing in kinetoplastid protozoa remodels the sequences of mitochondrial pre-mRNAs by the precise insertion and deletion of uridylate residues. These sequence changes are directed by small trans-acting RNAs, termed guide RNAs. The basic mechanistic pathway by which edited RNA is generated has recently been elucidated using in vitro systems capable of a full round of guide-RNA-directed editing.

Base Sequence↗
PubMed1995

Apolipoprotein B messenger RNA editing: an update.

Apolipoprotein (apo) B mRNA editing consists of a C-->U conversion of the first base of the codon CAA encoding glutamine 2153 in apoB mRNA to UAA, a stop codon. The cDNA for an apoB mRNA editing protein was recently cloned in rat and human. The human protein contains 236 amino acid residues and exists as a homodimer. The editing protein edits apoB mRNA in vitro only in the presence of tissue complementation factors. There is a leucine-rich motif spanning residues 173-210 of the protein which may be involved in homodimer formation and/or interaction with complementation factors. The requirements for these factors support the existence of an editosome involved in apoB mRNA editing.

APOBEC-1 Deaminase↗
PubMed2026

Multichannel genomic recording of biological information with ENGRAM.

Molecular recording is an emerging paradigm for measuring biology over time. Enhancer-mediated genomic recording of activity in multiplex (ENGRAM) is a recently described synthetic biology circuit architecture that converts the transient activity of cis-regulatory elements (CREs) into stable genomic records that can be retrospectively recovered via DNA sequencing. Here we provide a step-by-step protocol for conducting ENGRAM experiments and analyzing the resulting data. We also describe key design considerations for ENGRAM recorders, summarize the strengths and limitations of ENGRAM, and highlight applications, including multiplex signal recording and high-throughput CRE screening. In contrast to other systems for DNA-based recording in mammalian systems, ENGRAM relies on prime editing-mediated insertions to record the activity of a given CRE, such that it is inherently multiplexable-for example, four-base-pair insertions can represent the activities of up to 256 distinct CREs. A further contrast lies with ENGRAM's compatibility with DNA Typewriter, which facilitates the capture of signal order. For users with basic skills in molecular biology, mammalian cell culture and DNA sequencing analysis, ENGRAM experiments can typically be completed within 5-6 weeks.

Genomics↗
PubMed1983

GOG meets RPMIS. Experience with computerized data management in a cooperative group setting.

The Gynecologic Oncology Group (GOG) is a multiinstitutional, multidisciplinary cooperative group. Its clinical trials encompass the planning, initiation, execution, analysis, and presentation of results of management and treatment of patients with gynecologic cancer. The GOG Statistical Office, located at Roswell Park Memorial Institute, is responsible for data management and analysis of all patients entered into GOG protocols. Present annual accrual is approximately 1,600 patients; 37 protocols are active, while follow-up continues on 9 studies that are closed to patient entry. RPMIS is a formatted video-based system of programs for file creation, data entry, editing, updating, retrieval, and report generation. It has been utilized in more than 500 intrainstitutional research studies at Roswell Park. In the past, data management for the GOG had been based on computer entry via punched cards, and on hand-filled reports. The switch to RPMIS used required major reorganization of the data-handling process and was first attempted on a limited basis. As the advantages of RPMIS became evident, the whole data management operation was gradually converted to the new system. In this paper, batch processing and RPMIS utilization are compared and contrasted in terms of time saved, human engineering, quality control, and satisfaction of information requests.

Antineoplastic Agents↗