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Apolipoprotein B messenger RNA editing in the rat liver. Modulation by fasting and refeeding a high carbohydrate diet.

Apolipoprotein B (apoB) mRNA is modified by a posttranscriptional editing reaction in which a single base (C to U) change in apoB100 mRNA modifies a glutamine (CAA) to a translational stop codon (UAA), producing apoB48 mRNA in mammalian intestine. Rat liver normally contains both edited and unedited apoB mRNAs and previous work (Davidson, N. O., Powell, L. M., Wallis, S. C., and Scott, J. (1988) J. Biol. Chem. 263, 13482-13485) has demonstrated that the introduction of a translational stop codon can be modulated by thyroid hormone. In the current study, hepatic lipogenesis was modulated in vivo by fasting and refeeding a high carbohydrate diet, a maneuver which produced a 30-fold increase in hepatic triglyceride content. In this setting, hepatic apoB100 synthesis became undetectable in animals subjected to 48 h fasting and subsequently refed a high carbohydrate diet for either 24 or 48 h. This change was accountable for by an increase in the proportion of edited apoB mRNA, as determined by primer extension analysis, from 37% UAA in fasted animals to 79 and 91% UAA at 24 and 48 h of refeeding, respectively. The effect of this regimen on the expression of other hepatic apolipoprotein genes was less dramatic. ApoA-I and apoA-IV gene expression was modulated over a 2-fold range, in contrast to the (6-14-fold) pretranslational changes induced by thyroid hormone administration. ApoCIII mRNA abundance was unaltered in the setting of either fasting and refeeding or thyroid hormone administration, while apoE gene expression demonstrated a pretranslational increase following prolonged fasting. Taken together the data provide evidence that apoB mRNA editing is modulated by alterations in hepatic lipogenesis which additionally produce effects on the expression of other hepatic apolipoprotein genes suggesting that they are not coordinately regulated in vivo.

Animals↗

1H editing of 2-deuterated exogenous and natural endogenous D-glucose in biological samples.

A spin-echo based 1H homonuclear pulse sequence, enabling the selective editing of homonuclear first-order J-multiplet types, is presented and analyzed. Its effectiveness in quantification applications is assessed. Its potential usefulness in the quantitative distinction between 2-deuterated and natural D-glucose in biological samples is briefly discussed, with emphasis on studies of hexose metabolism conducted in vitro.

Absorption↗

The National Cancer Data Base Report on poor survival of U.S. gastric carcinoma patients treated with gastrectomy: Fifth Edition American Joint Committee on Cancer staging, proximal disease, and the "different disease" hypothesis.

BACKGROUND: A high proportion of U.S. patients with gastric carcinoma do not receive surgical treatment. To sharpen staging criteria and facilitate comparisons with surgical series, an analysis of patients whose treatment included gastrectomy was undertaken. In addition, to evaluate the "different disease" hypothesis as an explanation for superior Japanese results, outcomes for Japanese Americans were examined. METHODS: Data were obtained from National Cancer Data Base (NCDB) reports of 50,169 gastric carcinoma cases diagnosed during the years 1985-1996 and treated with gastrectomy. In addition to demographic and treatment information, 5-year and 10-year relative survival rates are presented, with stage defined according to fifth edition American Joint Committee on Cancer (AJCC) staging procedures. RESULTS: Stage-stratified 5-year and 10-year relative survival rates were as follows: Stage IA, 78%/65%; Stage IB, 58%/42%; Stage II, 34%/26%; Stage IIIA, 20%/14%; Stage IIIB, 8%/3%; and Stage IV, 7%/5%. Stage-stratified survival for Japanese Americans was higher. Males had a poorer prognosis than females, and the male-to-female ratio for Japanese Americans was lower. Proximal tumors were associated with a worse prognosis than distal tumors; the proportion of Japanese Americans with proximal disease was less than in the overall patient group. Japanese Americans underwent resection of adjacent organs less frequently. In this series, adjuvant therapy did not substantially affect survival. Overall, 20% were 10-year survivors; of these, 67% were lymph node negative and 98% had </= 8 involved lymph nodes. Five-year stage-stratified survival increased for cases with >/= 15 lymph nodes analyzed. Stage migration was evident in cases with </= 15 nodes examined. CONCLUSIONS: The current AJCC/International Union Against Cancer TNM staging system fails to accommodate the effect of proximal location on prognosis. Largely because Japanese Americans present with fewer proximal tumors, have a lower male-to-female ratio, and undergo adjacent organ resection less frequently, stage- stratified survival for Japanese Americans appears to be superior. In the U.S., surgical undertreatment of patients with this disease appears to be a problem.

Aged↗

Glutamate receptor RNA editing: a molecular analysis of GluR2, GluR5 and GluR6 in human brain tissues and in NT2 cells following in vitro neural differentiation.

The properties of some glutamate receptors are modified by RNA editing. This post-transcriptional mechanism involves the enzymatic deamination of specific adenosines in the pre-mRNA of the glutamate receptors, performed by specific RNA adenosine deaminases (ADARs). This event gives rise to the substitution of a gene-encoded amino acid with a different one that modifies the physiological properties of the ion channel. Here we report an analysis of the editing levels of AMPA GluR2, and kainate GluR5 and GluR6 in a human teratocarcinoma cell line (NT2) during in vitro neural differentiation, in conjunction with an analysis of the expression levels of GluR and ADAR genes. The editing levels were analysed using a specific standardised assay based on sequence analysis. This assay can be performed on all editing sites with a high level of sensitivity and reproducibility. Whereas GluR gene expression increased during NT2 neural differentiation, the expression of ADAR genes may be detected at comparable levels even in undifferentiated NT2 cells, remaining relatively stable during the differentiation process. Furthermore, most of the glutamate receptor editing sites increased their editing levels during NT2 neural differentiation, suggesting that the level of ADAR mRNAs is not closely related to the variable editing levels detected in the GluRs analysed. In human brain tissues, the editing levels appeared finely modulated in the different areas, indicating the possible formation of ion channels with different functional properties, thus generating a complex tissue-specific regulation of receptors and modulation of excitatory stimuli.

Adenosine Deaminase↗

Two brief alcohol-screening tests From the Alcohol Use Disorders Identification Test (AUDIT): validation in a female Veterans Affairs patient population.

BACKGROUND: Primary care physicians need a brief alcohol questionnaire that identifies hazardous drinking and alcohol use disorders. The Alcohol Use Disorders Identification Test (AUDIT) questions 1 through 3 (AUDIT-C), and AUDIT question 3 alone are effective alcohol-screening tests in male Veterans Affairs (VA) patients, but have not been validated in women. METHODS: Female VA patients (n = 393) completed self-administered questionnaires, including the 10-item AUDIT and a previously proposed modification to AUDIT question 3 with a sex-specific threshold for binge drinking (>/=4 drinks/occasion), and in-person interviews with the Alcohol Use Disorder and Associated Disabilities Interview Schedule. The AUDIT-C, AUDIT question 3 alone, and the 10-item AUDIT were each evaluated with and without the sex-specific binge question and compared with past-year hazardous drinking (>7 drinks/week or >/=4 drinks/occasion) and/or active Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition alcohol abuse or dependence, based on interviews. RESULTS: Eighty-nine women (22.6%) met interview criteria for past-year hazardous drinking and/or active alcohol abuse or dependence. Standard and sex-specific AUDIT-Cs were sensitive (0.81 and 0.84, respectively) and specific (0.86 and 0.85, respectively). Their areas under the receiver operating characteristic curves were equivalent (0.91, and 0.92, respectively) and slightly higher than for the standard 10-item AUDIT (0.87). A single, sex-specific question about binge drinking (modified AUDIT question 3) had a sensitivity of 0.69 and specificity of 0.94, whereas the standard AUDIT question 3 was specific (0.96) but relatively insensitive (0.45). CONCLUSIONS: The standard and sex-specific AUDIT-Cs are effective screening tests for past-year hazardous drinking and/or active alcohol abuse or dependence in female patients in a VA study.

Adult↗

Developing a medical image content repository for e-learning.

The integration of medical informatics and e-learning systems could provide many advanced applications including training, knowledge management, telemedicine, etc. Currently, both the domains of e-learning and medical image have sophisticated specifications and standards. It is a great challenge to bring about integration. In this paper, we describe the development of a Web interface for searching and viewing medical images that are stored in standard medical image servers. With the creation of a Web solution, we have reduced the overheads of integration. We have packaged Digital Imaging and Communications in Medicine (DICOM) network services as a component that can be used via a Web server. The Web server constitutes a content repository for searching, editing, and storing Web-based medical image content. This is a simple method by which the use of Picture Archiving and Communication System (PACS) can be extended. We show that the content repository can easily interact and integrate with a learning system. With the integration, the user can easily generate and assign medical image content for e-learning. A Web solution might be the simplest way for system integration. The demonstration in this paper should be useful as a method of expanding the usage of medical information. The construction of a Web-based repository and integrated with a learning system may be also applicable to other domains.

Computer Security↗

Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization.

Large RNAs (>30 nucleotides) suffer from extensive resonance overlap that can seriously hamper unambiguous structural characterization. Here we present a set of 3D multinuclear NMR experiments with improved and optimized resolution and sensitivity for aiding with the assignment of RNA molecules. In all these experiments strong base and ribose carbon-carbon couplings are eliminated by homonuclear band-selective decoupling, leading to improved signal to noise and resolution of the C5, C6, and C1' carbon resonances. This decoupling scheme is applied to base-type selective 13C-edited NOESY, 13C-edited TOCSY (HCCH, CCH), HCCNH, and ribose H1C1C2 experiments. The 3D implementation of the HCCNH experiment with both carbon and nitrogen evolution enables direct correlation of 13C and 15N resonances at different proton resonant frequencies. The advantages of the new experiments are demonstrated on a 36 nucleotides hairpin RNA from domain 5 (D5) of the group II intron Pylaiella littoralis using an abbreviated assignment strategy. These four experiments provided additional separation for regions of the RNA that have overlapped chemical shift resonances, and enabled the assignment of critical D5 bulge nucleotides that could not be assigned using current experimental schemes.

Carbon Isotopes↗

Multidimensional assessment of acute confusion after traumatic brain injury.

OBJECTIVES: To describe the phenomenology of posttraumatic confusional state (PTCS) and to provide preliminary validation of a new procedure, the Confusion Assessment Protocol (CAP), for assessing PTCS. DESIGN: Criterion standard investigation. SETTING: Inpatient traumatic brain injury (TBI) rehabilitation program. PARTICIPANTS: Two consecutive series of patients (n=62, n=93) with TBI admitted for inpatient rehabilitation. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Clinical diagnosis of delirium based on Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV) criteria, classification of posttraumatic amnesia (PTA) based on the Galveston Orientation and Amnesia Test (GOAT), and Disability Rating Scale score at time of rehabilitation hospital discharge. Results Agreement between the diagnosis of PTCS with the CAP and DSM-IV classification of delirium was 87%, and agreement between PTCS and PTA using GOAT criteria was 90%. Patients classified as in PTCS sustained more severe injuries and required longer rehabilitation stays. Confusion status was associated with poorer functional status at rehabilitation discharge. CONCLUSIONS: The CAP is a brief, structured, repeatable measure of multiple neurobehavioral aspects of PTCS. Confusion status as determined by CAP assessment contributed to prediction of outcome at rehabilitation discharge after adjustment for other potential predictors.

Adult↗

Depression and anxiety associated with three pain conditions: results from a nationally representative sample.

Investigations of the relationship between pain conditions and psychopathology have largely focused on depression and have been limited by the use of non-representative samples (e.g. clinical samples). The present study utilized data from the Midlife Development in the United States Survey (MIDUS) to investigate associations between three pain conditions and three common psychiatric disorders in a large sample (N = 3,032) representative of adults aged 25-74 in the United States population. MIDUS participants provided reports regarding medical conditions experienced over the past year including arthritis, migraine, and back pain. Participants also completed several diagnostic-specific measures from the Composite International Diagnostic Interview-Short Form [Int. J. Methods Psychiatr. Res. 7 (1998) 171], which was based on the revised third edition of the Diagnostic and Statistical Manual of Mental Disorders [American Psychiatric Association 1987]. The diagnoses included were depression, panic attacks, and generalized anxiety disorder. Logistic regression analyses revealed significant positive associations between each pain condition and the psychiatric disorders (Odds Ratios ranged from 1.48 to 3.86). The majority of these associations remained statistically significant after adjusting for demographic variables, the other pain conditions, and other medical conditions. Given the emphasis on depression in the pain literature, it was noteworthy that the associations between the pain conditions and the anxiety disorders were generally larger than those between the pain conditions and depression. These findings add to a growing body of evidence indicating that anxiety disorders warrant further attention in relation to pain. The clinical and research implications of these findings are discussed.

Adult↗

Mood and anxiety disorders associated with chronic pain: an examination in a nationally representative sample.

Chronic pain and psychiatric disorders frequently co-occur. However, estimates of the magnitude of these associations have been biased by the use of select clinical samples. The present study utilized the National Comorbidity Survey [Arch. Gen. Psychiatry 51 (1994) 8-19] Part II data set to investigate the associations between a chronic pain condition (i.e. arthritis) and common mood and anxiety disorders in a sample representative of the general US civilian population. Participants (N=5877) completed the Composite International Diagnostic Interview [World Health Organization (1990)], a structured interview for trained non-clinician interviewers based on the revised third edition of the Diagnostic and Statistical Manual of Mental Disorders [American Psychiatric Association (1987)], and provided self-reports of pain and disability associated with a variety of medical conditions. Significant positive associations were found between chronic pain and individual 12-month mood and anxiety disorders [odds ratios (OR) ranged from 1.92 to 4.27]. The strongest associations were observed with panic disorder (OR=4.27) and post-traumatic stress disorder (OR=3.69). The presence of one psychiatric disorder was not significantly associated with pain-related disability, but the presence of multiple psychiatric disorders was significantly associated with increased disability. The findings of the present study raise the possibility that improved efforts regarding the detection and treatment of anxiety disorders may be required in pain treatment settings.

Adolescent↗

tRNA 3' processing in plants: nuclear and mitochondrial activities differ.

The nuclear tRNA 3' processing activity from wheat has been characterized and partially purified. Several characteristics of the wheat nuclear 3' processing enzyme now allow this activity to be distinguished from its mitochondrial counterpart. The nuclear enzyme is an endonuclease, which we termed nuclear RNase Z. The enzyme cleaves at the discriminator base and seems to consist only of protein subunits, since essential RNA subunits could not be detected. RNase Z leaves 5' terminal phosphoryl and 3' terminal hydroxyl groups at the processing products. It is a stable enzyme being active over broad temperature and pH ranges, with the highest activity at 35 degrees C and pH 8.4. The apparent molecular mass according to gel filtration chromatography is 122 kDa. The nuclear RNase Z does process 5' extended pretRNAs but with a much lower efficiency than 5' matured pretRNAs. Nuclear intron-containing precursor tRNAs as well as mitochondrial precursor tRNAs are efficiently cleaved by the nuclear RNase Z. Mitochondrial pretRNA(His) is processed by the nuclear RNase Z, generating a mature tRNA(His) containing an 8 base pair acceptor stem. The edited mitochondrial pretRNA(Phe) is cleaved easily, while the unedited version having a mismatch in the acceptor stem is not cleaved. Thus, an intact acceptor stem seems to be required for processing. Experiments with precursors containing mutated tRNAs showed that a completely intact anticodon arm is not necessary for processing by RNase Z. Comparison of the plant nuclear tRNA 3' processing enzyme with the plant mitochondrial one suggests that both activities are different enzymes.

Cell Nucleus↗

Analysis of conformational polymorphism in pharmaceutical solids using solid-state NMR and electronic structure calculations.

A detailed analysis of molecular structure in three polymorphic forms of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is made using a combination of multidimensional solid-state NMR (SSNMR) experiments and molecular modeling via electronic structure calculations. These compounds, collectively referred to as ROY because of their red, orange, and yellow colors, share a similar molecular structure with the exception of the dihedral angle between the phenyl and thiophene rings. The ROY materials make it possible to study the influence of nearly a single degree of freedom on the associated NMR spectra. Using the 2D PASS (Antzutkin et al. J. Magn. Reson. A 1995, 115, 7) experiment, spectral editing techniques, and DFT-based calculations of the local fields, an analysis is made of the sensitivity of all carbon and nitrogen sites to changing molecular conformation. Chemical shift and dipolar coupling information obtained from these experiments vary noticeably between forms and are subsequently used to quantitatively determine aspects of molecular structure in these materials, including the coplanar angle between the phenyl and thiophene rings. The influence of motion on the methyl and nitro chemical shifts is also investigated. The accuracy of the information obtained from local field analysis and the model structure calculation demonstrates the capabilities of SSNMR as a quantitative structural method.

Algorithms↗

Identification of spin diffusion pathways in proteins by isotope-assisted NMR cross-relaxation network editing.

A new isotope-assisted cross-relaxation editing experiment, [1H-13C]DINE-NOESY[1H-15N]HSQC (DINE=Double INEPT Edited), is proposed. It is based on the selective inversion of CH/CH3 or CH2 protons in the middle of the mixing time. The experiment sorts out the spin diffusion paths according to the principal mediators, either the CH/CH3 or the CH2 protons. This is useful in the structure refinement process, as it enables proper alignment of the aliphatic protons in the vicinity of NH protons.

Amino Acid Sequence↗

Clinical computing in a teaching hospital.

This report describes a hospital-wide clinical computing system that permits physicians, nurses, medical students, and other health workers to retrieve data from the clinical laboratories; to look up reports from the departments of radiology and pathology; to look up demographic data and outpatient visits; to look up prescriptions filled in the outpatient pharmacy; to perform bibliographic retrieval of the MEDLINE data base; to read, write, retract, edit, and forward electronic mail; and to request delivery of a patient's chart. During a one-week study period, from 300 video display terminals located throughout the hospital, 818 patient care providers used a common registry of 539,000 patients to look up clinical and laboratory data 16,768 times; 477 other hospital workers used the patient registry 46,579 times. In a separate study of 586 health care providers, 470 (80 per cent) indicated that they used computer terminals "most of the time" to look up laboratory results; in contrast, 48 (8 per cent) preferred printed reports. Of 545 hospital workers, 440 (81 per cent) indicated that the computer terminals definitely or probably made their work more accurate, and 452 (83 per cent) indicated that terminals enabled them to work faster. The large amount of use by clinicians and their judgment that the computer has been so helpful to them suggests that a reliable, comprehensive, and easy-to-use computer system can contribute substantially to the quality of patient care.

Boston↗

Different computer tasks affect the exposure of the upper extremity to biomechanical risk factors.

In order to determine differences in biomechanical risk factors across computer tasks, a repeated measures laboratory experiment was completed with 30 touch-typing adults (15 females and 15 males). The participants completed five different computer tasks: typing text, completing an html-based form with text fields, editing text within a document, sorting and resizing objects in a graphics task and browsing and navigating a series of intranet web pages. Electrogoniometers and inclinometers measured wrist and upper arm postures, surface electromyography measured muscle activity of four forearm muscles and three shoulder muscles and a force platform under the keyboard and force-sensing computer mouse measured applied forces. Keyboard-intensive tasks were associated with less neutral wrist postures, larger wrist velocities and accelerations and larger dynamic forearm muscle activity. Mouse-intensive tasks (graphics and intranet web page browsing) were associated with less neutral shoulder postures and less variability in forearm muscle activity. Tasks containing a mixture of mouse and keyboard use (form completion and text editing) were associated with higher shoulder muscle activity, larger range of motion and larger velocities and accelerations of the upper arm. Comparing different types of computer work demonstrates that mouse use is prevalent in most computer tasks and is associated with more constrained and non-neutral postures of the wrist and shoulder compared to keyboarding.

Adult↗

Data exploration tools for the Gene Ontology database.

MOTIVATION: To improve the ability of biologists (both researchers and students) to ask biologically interesting questions of the Gene Ontology (GO) database and to explore the ontologies by seeing large portions of the ontology graphs in context, along with details of individual terms in the ontologies. RESULTS: GoGet and GoView are two new tools built as part of an extensible web application system based on Java 2 Enterprise Edition technology. GoGet has a user interface that enables users to ask biologically interesting questions, such as (1) What are the DNA binding proteins involved in DNA repair, but not in DNA replication? and (2) Of the terms containing the word triphosphatase, which have associated gene products from mouse, but not fruit fly? The results of such queries can be viewed in a collapsed tabular format that eases the burden of getting through large tables of data. GoView enables users to explore the large directed acyclic graph structure of the ontologies in the GO database. The two tools are coordinated, so that results from queries in GoGet can be visualized in GoView in the ontology in which they appear, and explorations started from GoView can request details of gene product associations to appear in a result table in GoGet. AVAILABILITY: Free access to the GoGet query tool and free download of the GoView ontology viewer are provided to all users at http://db.math.macalester.edu/goproject. In addition, source code for the GoView tool is also available from this site, along with a user manual for both tools.

Algorithms↗

A DNA sequence handling program.

A computer program that aids in recording, editing, and analysis of the base sequences of DNA and RNA is presented. A tape containing copies of the program and the user manual for it are available at cost.

Base Sequence↗

Predicting the DSM-V.

Using regression estimates based upon data about past editions of the DSM, we predict various features of the DSM-V. Included in these predictions are the date of publication, number of pages, total number of categories, number of categories defined using diagnostic criteria, total number of diagnostic criteria, color of the manual, who will be in charge of the task force that creates the DSM-V, and revenues generated by the DSM-V. This article ends with comments on the changes in the editions of the DSMs and an analogy to the Sorcerer's Apprentice.

Costs and Cost Analysis↗