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PubMed2000

A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains.

Members of the double-stranded RNA- (dsRNA) specific adenosine deaminase gene family convert adenosine residues into inosines in dsRNA and are involved in A-to-I RNA editing of transcripts of glutamate receptor (GluR) subunits and serotonin receptor subtype 2C (5-HT(2C)R). We have isolated hADAR3, the third member of this class of human enzyme and investigated its editing site selectivity using in vitro RNA editing assay systems. As originally reported for rat ADAR3 or RED2, purified ADAR3 proteins could not edit GluR-B RNA at the "Q/R" site, the "R/G" site, and the intronic "hot spot" site. In addition, ADAR3 did not edit any of five sites discovered recently within the intracellular loop II region of 5-HT(2C)R RNAs, confirming its total lack of editing activity for currently known substrate RNAs. Filter-binding analyses revealed that ADAR3 is capable of binding not only to dsRNA but also to single-stranded RNA (ssRNA). Deletion mutagenesis identified a region rich in arginine residues located in the N-terminus that is responsible for binding of ADAR3 to ssRNA. The presence of this ssRNA-binding domain as well as its expression in restricted brain regions and postmitotic neurons make ADAR3 distinct from the other two ADAR gene family members, editing competent ADAR1 and ADAR2. ADAR3 inhibited in vitro the activities of RNA editing enzymes of the ADAR gene family, raising the possibility of a regulatory role in RNA editing.

Adenosine Deaminase↗
PubMed2003

Modulation of RNA editing by functional nucleolar sequestration of ADAR2.

The adenosine deaminases that act on RNA (ADARs) catalyze the site-specific conversion of adenosine to inosine (A to I) in primary mRNA transcripts, thereby affecting the splicing pattern or coding potential of mature mRNAs. Although the subnuclear localization of A-to-I editing has not been precisely defined, ADARs have been shown to act before splicing, suggesting that they function near nucleoplasmic sites of transcription. Here we demonstrate that ADAR2, a member of the vertebrate ADAR family, is concentrated in the nucleolus, a subnuclear domain disparate from the sites of mRNA transcription. Selective inhibition of ribosomal RNA synthesis or the introduction of mutations in the double-stranded RNA-binding domains within ADAR2 results in translocation of the protein to the nucleoplasm, suggesting that nucleolar association of ADAR2 depends on its ability to bind to ribosomal RNA. Fluorescence recovery after photobleaching reveals that ADAR2 can shuttle rapidly between subnuclear compartments. Enhanced translocation of endogenous ADAR2 from the nucleolus to the nucleoplasm results in increased editing of endogenous ADAR2 substrates. These observations indicate that the nucleolar localization of ADAR2 represents an important mechanism by which RNA editing can be modulated by the sequestration of enzymatic activity from potential RNA substrates in the nucleoplasm.

Adenosine Deaminase↗
PubMed1994

Glutamate receptor update.

The past year has seen significant advances in matching the actions of recombinant glutamate receptors with the actions of native receptors, and in mapping their distribution and regulation. The discovery of a novel RNA editing mechanism for AMPA receptors and a revised view of the transmembrane topology of the NMDA receptor subunit, NR1, are particularly noteworthy. Seven metabotropic glutamate receptor subtypes have been identified with several interesting expression patterns and transduction mechanisms; results from work on these subtypes has led to a provocative model of the ligand-binding site. Functional studies of metabotropic receptors have been enhanced by the development of the first subtype-specific antagonist.

Animals↗
PubMedDate not supplied

Screening for family and intimate partner violence: recommendation statement.

This statement summarizes the U.S. Preventive Services Task Force (USPSTF) recommendations on screening for family and intimate partner violence based on the USPSTF's examination of evidence specific to family and intimate partner violence. It updates the 1996 recommendations contained in the Guide to Clinical Preventive Services, second edition. In 1996, the USPSTF found insufficient evidence to recommend for or against the use of specific instruments to detect domestic violence (a "C" recommendation according to 1996 grade definitions). The Task Force now uses an explicit process in which the balance of benefits and harms is determined exclusively by the quality and magnitude of the evidence. As a result, current letter grades are based on different criteria than those in 1996. Current explanations of the ratings and of the strength of overall evidence are given in Appendix A and in Appendix B, respectively. The complete information on which this statement is based, including evidence tables and references, is available in the summary article and in the Systematic Evidence Review, "Screening for Family and Intimate Partner Violence: Systematic Evidence Review for the U.S. Preventive Services Task Force." The USPSTF recommendations, the accompanying summary article, and complete Systematic Evidence Review are available through the USPSTF web site (http://www.preventiveservices.ahrq.gov). The summary article and the USPSTF recommendation statement are available in print through the AHRQ Publications Clearinghouse (call 1-800-358-9295 or e-mail ahrqpubs@ahrq.gov).

Adolescent↗
PubMed2000

Improving social adjustment in children with attention-deficit/hyperactivity disorder.

OBJECTIVE: To determine if sending motivational letters would improve peer relations in children with social maladjustment and attention-deficit/hyperactivity disorder (ADHD). DESIGN: From a consecutive sample, a case series was followed up for 2 years. SETTING: Primary care, private physician, office-based practice. PATIENTS: Ninety-five children diagnosed as having ADHD by Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria made up the consecutive sample. Twenty-one children qualified with a comorbid social maladjustment disorder with baseline t scores of 1.5 SDs or greater above the mean on the asocial domain of the Conners' Teacher Rating Scale. Seventeen children completed the study. There were no significant differences between these patients and those who did not complete the study (P = .55 for baseline score differences and P = .85 for age). INTERVENTIONS: In addition to conventional therapy for ADHD when children achieved a goal, such as an improved report card or better conduct, a personal letter about their success was mailed to them. Letters averaged 5 per student per year. MAIN OUTCOME MEASURES: The asocial domain of the Conners' Teacher Rating Scale was repeated during the next 2 school years for comparison. Statistical analysis was by a repeated-measures analysis of variance and Helmert contrasts. RESULTS: Of 17 students who completed the study, 16 improved on the Conners' Teacher Rating Scale asocial domain, and the results were statistically significant (P<.001). CONCLUSIONS: Difficulties with peer relations are commonly seen in children with ADHD. Sending motivational letters correlated with improved social adjustment in these children. The data suggest that busy practitioners might consider incorporating this successful, and time-efficient, intervention into their ADHD treatment regimens.

Adolescent↗
PubMed2004

Risk and incidence of dementia in a cohort of older subjects with Parkinson's disease in the United Kingdom.

To determine the incidence and possible risk factors for dementia in patients with clinically probable Parkinson's disease (PD), a cohort (n = 86) of nondemented patients over 65 years of age with PD fulfilling the PD Brain Bank clinical diagnostic criteria were determined from community records. A similarly aged group of control subjects (n = 102) were recruited from the same area. Both groups were assessed at baseline and approximately 4 years later for cognition, mood, and motor function (PD patients only). The presence and severity of cognitive impairments was based on subject and informant interview, neuropsychological assessment based on the Cambridge Cognitive Examination (CAMCOG) and the application of the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV). At 4 years, 51 (59%) of the PD and 72 (71%) of the control cohort were available for reassessment. Of the PD cohort, 18 (35.3%) had developed dementia and 5 (9.4%) had evidence of mild cognitive impairments. In the control group, 5 (7%) had developed dementia. The incidence of dementia per 1,000 person-years in the PD cohort was 107.1 (95% confidence interval [CI], 59.9-159.8) and in the control group was 17.9 (95% CI, 5.8-31.9). The relative risk of patients developing dementia was 5.1 times that of the controls (95% CI, 2.1-12.5). Increasing age, later age of onset of PD, longer duration of PD symptoms, the presence of hallucinations, and impairment of memory and language function were all predictive factors for the development of dementia (P < 0.05). Dementia was also found to be a significant predictor for institutional placement in the PD group. Compared with similarly aged controls, patients with clinically probable PD have a fivefold-increased risk of developing dementia. This finding has significant implications for successful clinical management of this condition.

Aged↗
PubMedDate not supplied

Editing of rps3/rpl16 transcripts creates a premature truncation of the rpl16 open reading frame.

Overlapping open reading frames corresponding to maize mitochondrial genes rps3 and rpl16 have been found in Petunia mitochondrial DNA. The DNA region associated with these two genes is part of the Petunia mitochondrial recombination repeat and is iterated three times. Analysis of transcripts from these genes shows that there is RNA editing of the coding regions and that one of the editing sites detected in the open reading frame overlap creates a premature stop codon in the rpl16 sequence. No transcripts were detected that were unedited at this site. Thus, in Petunia editing of rpl16 appears to render this gene nonfunctional.

Amino Acid Sequence↗
PubMed2003

A novel inducible element, activated by contact with Rathke's pouch, is present in the regulatory region of the Rpx/Hesx1 homeobox gene.

Reciprocal inductive interactions are postulated to play a role in the determination and differentiation of the pituitary gland and the ventral hypothalamus. The homeobox gene Rpx/Hesxl is expressed during gastrulation in the anterior endoderm, prechordal plate, and the prospective cephalic neural plate, and at later stages of development in Rathke's pouch, the primordium of the pituitary. We have defined the regulatory elements necessary for proper spatial and temporal expression during development in transgenic mice using lacZ reporter genes. Proper spatial and temporal expression in the anterior endoderm prechordal plate and anterior neural plate can be recapitulated with as little as 568 bp of upstream sequence and intragenic sequence containing the first exon and intron. Late-stage expression in Rathke's pouch requires additional negative and positive regulatory elements. Interestingly, deletion analysis uncovered an element that directs transgene expression to a region of the hypothalamus that lies in direct contact with Rathke's pouch. In vitro tissue recombination experiments have established that this expression is induced by contact with the pouch. We propose that this element may be present in other genes that normally respond to signals emanating from the pouch during the development of the hypothalamic-pituitary axis. The Rpx-lacZ transgenic mice provide a novel model system for the molecular dissection of inductive cell signaling during pituitary development.

Animals↗
PubMed2003

Headache and facial pain in children and adolescents.

Headaches commonly affect children and adolescents. Proper diagnosis and management is dependent on thorough history taking and a comprehensive physical and neurological examination. Additional diagnostic testing is indicated in some cases. The second edition of the headache classification system by the International Headache Society has recently become available. The classification system is primarily based on adults, but we discussed the subtle distinctions made regarding children. In addition to the primary headache types of migraine, tension-type, and cluster headaches, we discussed selected symptomatic headaches. Emphasis was placed on migraine and tension-type headaches because these are the most common pediatric headache types. We briefly discussed genetic aspects of headaches. Genetic factors have been hypothesized for chronic tension headache and other forms of migraine, but genetic linkage has only been established for familial hemiplegic migraine. We reviewed the nonpharmacologic and pharmacologic therapies, including abortive and prophylactic medications for various age groups. Unlike headaches, facial neuralgias are rare in otherwise healthy children. Facial pain may be neurological, vascular, or dental in origin. We focused on trigeminal neuralgia, glossopharyngeal neuralgia, occipital neuralgia, and Bell's palsy as neurological causes of facial pain in children.

Adolescent↗
PubMedDate not supplied

Using lexical disambiguation and named-entity recognition to improve spelling correction in the electronic patient record.

In this article, we show how a set of natural language processing (NLP) tools can be combined to improve the processing of clinical records. The study concentrates on improving spelling correction, which is of major importance for quality control in the electronic patient record (EPR). As first task, we report on the design of an improved interactive tool for correcting spelling errors. Unlike traditional systems, the linguistic context (both semantic and syntactic) is used to improve the correction strategy. The system is organized along three modules. Module 1 is based on a classical spelling checker, it means that it is context-independent and simply measures a string-edit-distance between a misspelled word and a list of well-formed words. Module 2 attempts to rank more relevantly the set of candidates provided by the first module using morpho-syntactic disambiguation tools. Module 3 processes words with the same part-of-speech (POS) and apply word-sense (WS) disambiguation in order to rerank the set of candidates. As second task, we show how this improved interactive spell checker can be cast as a fully automatic system by adjunction of another NLP module: a named-entity (NE) extractor, i.e. a tool able to identify words as such patient and physician names. This module is used to avoid replacement of named-entities when the system is not used in an interactive mode. Results confirm that using the linguistic context can improve interactive spelling correction, and justify the use of named-entity recognizer to conduct fully automatic spelling correction. It is concluded that NLP is mature enough to help information processing in EPR.

Artificial Intelligence↗
PubMed1999

Stereolithographic biomodelling in cranio-maxillofacial surgery: a prospective trial.

Stereolithographic (SL) biomodelling is a new technology that allows three-dimensional (3-D) computed tomography (CT) data to be used to manufacture solid plastic replicas of anatomical structures (biomodels). A prospective trial with the objective of assessing the utility of biomodelling in complex surgery has been performed. Forty-five patients with craniofacial, maxillofacial, skull base cervical spinal pathology were selected. 3-D CT or MR scanning was performed and the data of interest were edited and converted into a form acceptable to the rapid prototyping technology SL. The data were used to guide a laser to selectively polymerize photosensitive resin to manufacture biomodels. The biomodels were used by surgeons for patient education, diagnosis and operative planning. An assessment protocol was used to test the hypothesis that 'biomodels in addition to standard imaging had greater utility in the surgery performed than the standard imaging alone'. Biomodels significantly improved operative planning (images 44.09%, images with biomodel 82.21%, P < .01) and diagnosis (images 65.63%, images with biomodel 95.23%, P < .01). Biomodels were found to improve measurement accuracy significantly (image measurement error 44.14%, biomodel measurement error 7.91%, P < .05). Surgeons estimated that the use of biomodels reduced operating time by a mean of 17.63% and were cost effective at a mean price of $1031 AUS. Patients found the biomodels to be helpful for informed consent (images 63.53%, biomodels 88.54%, P < .001). Biomodelling is an intuitive, user-friendly technology that facilitated diagnosis and operative planning. Biomodels allowed surgeons to rehearse procedures readily and improved communication between colleagues and patients.

Cephalometry↗
PubMed2002

Determining foot and ankle impairments by the AMA fifth edition guides.

The fifth edition of the Guides has been criticized for its failure to provide a comprehensive, valid, reliable, unbiased, and evidenced-based system for rating impairments and the way in which workers' compensation systems use the ratings, resulting in inappropriate compensation [8]. The lower extremity chapter utilizes numerous functional and anatomic methods of assessment, as well as diagnosis-based estimates. Though this process of using multiple approaches to measure impairment increases the chances that an underlying physical impairment may be detected, it is time-consuming and may increase rating variability [9]. McCarthy et al studied the correlation between measures of impairment for patients with fractures of the lower extremity. They found that the anatomic approach of evaluation was better correlated than functional and diagnostic methods with measures of task performance based on direct observations as well as the patient's own assessment of activity limitation and disability. Also, muscle strength assessment as described in the Guides was a more sensitive measure of impairment than range of motion [9]. The most elusive part of the foot and ankle evaluation is the inability to capture the added impairment burden caused by pain. The assessment of pain is the most problematic part of any evaluation. Pain is considered and incorporated into the impairment ratings found in the foot and ankle section, as well as the other individual chapters. Chronic pain is often not adequately accounted for, however, and the examiner must evaluate permanent impairment from chronic pain separately. The examiner has the ability to increase the percentage of organ system impairment from 1% to 3% if there is pain-related impairment that increases the burden of illness slightly. If there is significant pain-related impairment, a formal pain assessment is performed. Chapter 18 provides guidance in making these determinations. Impairments for Complex Regional Pain syndrome (CRPS), type 1 (reflex sympathetic dystrophy), and CRPS, type 2 (causalgia) should incorporate the use of a formal pain assessment in addition to the standard methods of assessment. The formal pain evaluation relies mostly on self-reports from the individual and is most heavily weighted for ADL deficits. The physician must make assessments of the individual's pain behavior and credibility for this evaluation. The formal pain assessment classifies the pain-related impairment into categories of mild, moderate, moderately severe, or severe and determines whether this impairment is ratable or not. These categories do not have impairment percentages associated with them. The individual's symptoms or presentation should match known conditions or syndromes in order to be ratable. If not ratable, the examiner should report that the individual has apparent impairment that is not ratable on the basis of current medical knowledge. In the end, pain evaluations are used administratively and, depending on the situation, may be given equal weight with the standard evaluation or may be totally disregarded.

American Medical Association↗
PubMed2026

Translating functional molecular knowledge into crop-breeding success.

Historical plant breeding, which optimizes phenotypes through selective crossing guided by phenotypic evaluation and molecular markers, is limited by evolutionary constraints that hinder rapid crop improvement. A new paradigm, precision breeding, circumvents these limitations by targeting genetic variants through functional molecular knowledge. To generate this knowledge at scale, sequence-based deep learning leverages high-quality genome sequence data to predict variant effects at base-pair resolution. When linked to agronomically important traits, these predictions enable breeders to prioritize variants for precision selection or editing. Although it is still in the early stages of development, we foresee three key applications for this approach: introgressing genes from distant breeding pools, purging deleterious mutations and designing new plant ideotypes. Looking ahead, refined computational models will facilitate targeted editing and the systematic redesign of complex physiological processes to address emerging breeding goals under shifting environmental conditions.

Crops, Agricultural↗
PubMed2026

Spatially guided in vivo single-cell functional genomics of postnatal heart.

Understanding how spatial organization and cell-cell interactions shape gene regulatory programs is central to decoding tissue development and function. The transition at birth, marked by increased circulatory demands and rapid tissue growth, requires precise spatiotemporal coordination of cardiac maturation. In this study, we generated a high-resolution spatial and temporal atlas of the postnatal mouse heart by integrating single-nucleus RNA sequencing with image-based spatial transcriptomics. This framework revealed dynamic cellular interactions, niche-specific signaling and transcriptional programs guiding cardiomyocyte maturation. To functionally test prioritized regulators in vivo and at scale, we developed PIP-seq (probe-based indel-detectable Perturb-seq), a high-throughput platform that detects single guide RNA identity, infers gene editing and profiles transcription from fixed nuclei. Applying PIP-seq to the developing postnatal heart, we identified 21 previously uncharacterized regulators of cardiomyocyte maturation, including genes essential for sarcomere assembly, metabolic reprogramming and electrophysiological transitions. Together, our findings define how microenvironmental signals and intrinsic gene programs cooperate to guide heart maturation and establish a broadly applicable framework for functional genomics in complex tissues.

Animals↗
PubMed2000

Altered G protein-coupling functions of RNA editing isoform and splicing variant serotonin2C receptors.

Different isoforms of serotonin subtype 2C receptor (5-HT(2C)R) with altered G protein-coupling efficacy are generated by RNA editing, which converts genomically encoded adenosine residues into inosines. In combination, editing of five sites all located within the second intracellular loop region of 5-HT(2C)R mRNA changes the gene-encoded Ile, Asn, and Ile at positions 156, 158, and 160, respectively. We analyzed the G protein-coupling functions of previously unreported editing isoform receptors. An approximately 13-fold reduction in the agonist potency for G protein-coupling stimulation as well as a significantly reduced basal level activity was observed with the thalamus-specific isoform carrying Ile156, Gly158, and Val160 (5-HT(2C)R-IGV). In contrast, the agonist was four- to five-fold less potent with 5-HT(2C)R-MSV and -IDV, detected in the amygdala and choroid plexus, respectively, indicating a dominant role for the amino acid residue at position 158 in receptor functions. We also identified a splicing variant receptor with a truncated C terminus that displayed no ligand binding capacity or G protein-coupling activity. Examination of the alternatively spliced RNA encoding this truncated receptor suggests that editing of this variant RNA occurs after completion of splicing, resulting in complete editing at all five sites.

3T3 Cells↗
PubMedDate not supplied

Chronic peritoneal dialysis patients diagnosed with clinical depression: results of pharmacologic therapy.

Depression has been documented as the most frequently encountered psychological problem in end-stage renal disease (ESRD) patients and has been correlated with both mortality and morbidity in these patients. Previous work by our group has shown that clinical depression is treatable with psychotropic medications in these patients, but that only a limited number of ESRD patients with depression will successfully complete a course of pharmacologic therapy. From July 1997 to October 2002, all chronic peritoneal dialysis (PD) patients in our facility were encouraged to be screened for depression utilizing the self-administered Beck Depression Inventory (BDI) questionnaire. Based on previous work, a score > or =11 on this questionnaire was used to indicate a possible diagnosis of clinical depression; patients with BDI scores > or =11 were encouraged to complete a more formal evaluation for the presence of clinical depression. A total of 320 BDI questionnaires were completed during the study period: 134 patients. (42%) scored > or =11 on the BDI, 69 of the 134 patients (51%) with BDI scores > or =11 agreed to further evaluation. Sixty of these 69 patients (87%) were diagnosed with clinical depression based on scores > or =18 on the Hamilton Depression Scale and standard Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) criteria. Forty-four patients with clinical depression agreed to pharmacologic treatment. However, only 23 of the 44 patients (52%) successfully completed a 12-week course of drug therapy. Two unit social work reviewers systematically reviewed the records of these 21 patients who did not complete therapy and assessed the reasons for their inability to complete treatment. Reasons identified included eight patients who experienced acute medical problems, three who were active substance abusers, and two who reported medication side effects. The remaining eight patients who did not complete the 12 weeks of therapy were examined by applying the axis 1 and axis 2 DSM-IV criteria. Axis 1 is used to diagnose clinical disorders and axis 2 is used to diagnose personality disorders. While all these patients met the DSM-IV axis 1 criteria for clinical depression, eight of these patients met axis 2 criteria for personality disorders; five patients had borderline personality disorders, one had a narcissistic personality disorder, one had a factitious disorder, and one had features of avoidant personality disorder. While some chronic PD patients can be successfully treated for clinical depression with psychotropic medication prescribed by the dialysis medical team, not all patients will agree to be evaluated for clinical depression and accept pharmacologic treatment. Others cannot or will not complete treatment when additional psychiatric disorders exist. These patients may require additional intervention when diagnosed with clinical depression and a personality disorder. Further trials are warranted.

Antidepressive Agents↗
PubMed1999

Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.

Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.

Amino Acid Sequence↗
PubMed2000

15N-enriched 5-fluorocytosine as a probe for examining unusual DNA structures.

A new method is presented for the synthesis of oligonucleotides containing 15N-enriched 5-fluorocytosine (FC). Due to the reduced pK of FC, the amino protons of an unpaired FC residue may be observed at lower values of solution pH. The labeled FC residue has been placed as a template base at a model DNA replication fork. The amino protons of the FC residue have been identified in isotope-edited NMR spectra. Data is presented for a template FC residue unpaired, paired with guanine, and mispaired with adenine. These studies demonstrate the utility of labeled FC in examining unusual DNA structures.

DNA↗