Determinants of social loneliness among older adults in job retirement and the role of emotional expressivity.

OBJECTIVES: The study examined the possibility that a mediating role of positive and negative emotional expressivity may contribute to understanding the associations between social loneliness and its previously identified predictors (i.e. health, age, sex, and social living situation). METHOD: Self-reported assessments were collected from community-dwelling Swedish residents (aged 65 and above) in job retirement. Structural equation modeling with manifest variables was applied to cross-sectional data (N = 601) to analyze two competing models; one main-effect regression model, examining the predictive effect of emotional expressivity (along with health and sociodemographics) on social loneliness, and one mediation model, examining the mediating effect of emotional expressivity (using the bootstrapping technique provided in Mplus). RESULTS: The results indicated that the mediation model fit the data considerably better than the main-effect regression model (Δχ2 [Δdf = 8] = 72.69, p < 0.00001), and demonstrated a good fit on its own, with CFI = 0.986 and RMSEA = 0.030. This suggests that emotional expressivity contributes to the understanding of the connection between social loneliness and its previously identified predictors. CONCLUSION: Recognizing the significance of emotional expressivity has the potential to enhance our understanding of loneliness in older adults, both in theory and in practice.

Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden.

Numerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70-95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24) gene was found. This confirms a previous finding, where changes in expression of SLC25A24 were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3 can be monitored.

Performance characterization of a prototype dual-layer cone-beam computed tomography system.

PURPOSE: Conventional cone-beam computed tomography CT (CBCT) provides limited discrimination between low-contrast tissues. Furthermore, it is limited to full-spectrum energy integration. A dual-energy CBCT system could be used to separate photon energy spectra with the potential to increase the visibility of clinically relevant features and acquire additional information relevant in a multitude of clinical imaging applications. In this work, the performance of a novel dual-layer dual-energy CBCT (DL-DE-CBCT) C-arm system is characterized for the first time. METHODS: A prototype dual-layer detector was fitted into a commercial interventional C-arm CBCT system to enable DL-DE-CBCT acquisitions. DL-DE reconstructions were derived from material-decomposed Compton scatter and photoelectric base functions. The modulation transfer function (MTF) of the prototype DL-DE-CBCT was compared to that of a commercial CBCT. Noise and uniformity characteristics were evaluated using a cylindrical water phantom. Effective atomic numbers and electron densities were estimated in clinically relevant tissue substitutes. Iodine quantification was performed (for 0.5-15 mg/ml concentrations) and virtual noncontrast (VNC) images were evaluated. Finally, contrast-to-noise ratios (CNR) and CT number accuracies were estimated. RESULTS: The prototype and commercial CBCT showed similar spatial resolution, with a mean 10% MTF of 5.98 cycles/cm and 6.28 cycles/cm, respectively, using a commercial standard reconstruction. The lowest noise was seen in the 80 keV virtual monoenergetic images (VMI) (7.40 HU) and the most uniform images were seen at VMI 60 keV (4.74 HU) or VMI 80 keV (1.98 HU), depending on the uniformity measure used. For all the tissue substitutes measured, the mean accuracy in effective atomic number was 98.2% (SD 1.2%) and the mean accuracy in electron density was 100.3% (SD 0.9%). Iodine quantification images showed a mean difference of -0.1 (SD 0.5) mg/ml compared to the true iodine concentration for all blood and iodine-containing objects. For VNC images, all blood substitutes containing iodine averaged a CT number of 43.2 HU, whereas a blood-only substitute measured 44.8 HU. All water-containing iodine substitutes measured a mean CT number of 2.6 in the VNC images. A noise-suppressed dataset showed a CNR peak at VMI 40 keV and low at VMI 120 keV. In the same dataset without noise suppression applied, a peak in CNR was obtained at VMI 70 keV and a low at VMI 120 keV. The estimated CT numbers of various clinically relevant objects were generally very close to the calculated CT number. CONCLUSIONS: The performance of a prototype dual-layer dual-energy C-arm CBCT system was characterized. Spatial resolution and noise were comparable with a commercially available C-arm CBCT system, while offering dual-energy capability. Iodine quantifications, effective atomic numbers, and electron densities were in good agreement with expected values, indicating that the system can be used to reliably evaluate the material composition of clinically relevant tissues. The VNC and monoenergetic images indicate a consistent ability to separate clinically relevant tissues. The results presented indicate that the system could find utility in diagnostic, interventional, and radiotherapy planning settings.

Lifestyle's influence on community-dwelling older adults' health: A mixed-methods study design.

BACKGROUND: Aging often involves health problems and difficulties, such as physical and psychological impairments, isolation, and loneliness, causing social and existential consequences. Studies have explored aging from different perspectives. However, few studies have examined healthy older adults' genetic backgrounds, lifestyles, and meaning in life separately or in combination. This study aims to describe how healthy older adults experience aging, health, lifestyles, and meaning in life and explore potential genetic correlations. METHODS AND DESIGN: The project will comprise three main parts: a quantitative section featuring the development and testing of a lifestyle questionnaire, a quantitative genetic analysis, and a qualitative interview study. Participants will be community-dwelling, healthy, older adults between 70 and 95 years of age. A sample size of 800 older adults will be invited to participate in seminars in collaboration with the national Swedish association Active Seniors. Data will be collected through lifestyle questionnaire, DNA extracted from saliva samples, and interviews. Based on questionnaire responses, profile groups will be created and compared statistically with variations in genetic backgrounds, providing the basis for recruiting participants to the qualitative interviews. DISCUSSION: This study's expected outcome will be to gain knowledge about variations in genetic backgrounds correlated with individual experiences regarding aging, health, and meaning in life. This knowledge can improve the understanding of motivations for healthy lifestyle changes. The results can reveal potential implications for individual prerequisites to healthy aging and how health-promoting aging and lifestyle counseling can be adjusted to meet individual needs.

Performance of dual layer dual energy CT virtual monoenergetic images to identify early ischemic changes in patients with anterior circulation large vessel occlusion.

BACKGROUND AND PURPOSE: Dual energy CT is increasingly available and used in the standard diagnostic setting of ischemic stroke patients. We aimed to evaluate how different dual energy CT virtual monoenergetic energy levels impact identification of early ischemic changes, compared to conventional polyenergetic CT images. MATERIALS AND METHODS: This retrospective single-center study included patients presenting with acute ischemic stroke caused by an occlusion of the intracranial internal carotid artery or proximal middle cerebral artery. Data was gathered on consecutive patients admitted to our institution who underwent initial diagnostic stroke imaging with dual layer dual energy CT and a subsequent follow-up CT one to three days after admission. Automated ASPECTS results from conventional polyenergetic and different virtual monoenergetic energy level reconstructions at admission were generated and compared to reference standard ASPECTS. Confidence intervals (CI) for sensitivity, specificity, negative and positive predictive value were calculated. RESULTS: A total of 24 patients were included. Virtual monoenergetic reconstructions of 70 keV had the highest region-based ASPECTS accuracy, 0.90 (sensitivity 0.82 (95% CI 0.72-0.93), specificity 0.92 (0.88-0.97), negative predictive value 0.94 (0.90-0.96)), whereas virtual monoenergetic reconstructions of 40 keV had the lowest, 0.77 (sensitivity 0.34 (0.26-0.42), specificity 0.90 (0.89-0.96), negative predictive value 0.80 (0.77-0.83)). CONCLUSIONS: Automated 70 keV ASPECTS had the highest diagnostic accuracy, sensitivity and negative predictive value overall. Our results indicate that virtual monoenergetic energy levels impact the identification of early ischemic changes on CT.

Augmented reality navigation with intraoperative 3D imaging vs fluoroscopy-assisted free-hand surgery for spine fixation surgery: a matched-control study comparing accuracy.

This study aimed to compare screw placement accuracy and clinical aspects between Augmented Reality Surgical Navigation (ARSN) and free-hand (FH) technique. Twenty patients underwent spine surgery with screw placement using ARSN and were matched retrospectively to a cohort of 20 FH technique cases for comparison. All ARSN and FH cases were performed by the same surgeon. Matching was based on clinical diagnosis and similar proportions of screws placed in the thoracic and lumbosacral vertebrae in both groups. Accuracy of screw placement was assessed on postoperative scans according to the Gertzbein scale and grades 0 and 1 were considered accurate. Procedure time, blood loss and length of hospital stay, were collected as secondary endpoints. A total of 262 and 288 screws were assessed in the ARSN and FH groups, respectively. The share of clinically accurate screws was significantly higher in the ARSN vs FH group (93.9% vs 89.6%, p < 0.05). The proportion of screws placed without a cortical breach was twice as high in the ARSN group compared to the FH group (63.4% vs 30.6%, p < 0.0001). No statistical difference was observed for the secondary endpoints between both groups. This matched-control study demonstrated that ARSN provided higher screw placement accuracy compared to free-hand.

Clinical Course in Chronic Subdural Hematoma Patients Aged 18-49 Compared to Patients 50 Years and Above: A Multicenter Study and Meta-Analysis.

Objective: Chronic Subdural Hematoma (cSDH) is primarily a disease of elderly, and is rare in patients <50 years, and this may in part be related to the increased brain atrophy from 50 years of age. This fact may also influence clinical presentation and outcome. The aim of this study was to study the clinical course with emphasis on clinical presentation of cSDH patients in the young (<50 years). Methods: A retrospective review of a population-based cohort of 1,252 patients operated for cSDH from three Scandinavian neurosurgical centers was conducted. The primary end-point was difference in clinical presentation between the patients <50 y/o and the remaining patients (≥50 y/o group). The secondary end-points were differences in perioperative morbidity, recurrence and mortality between the two groups. In addition, a meta-analysis was performed comparing clinical patterns of cSDH in the two age groups. Results: Fifty-two patients (4.2%) were younger than 50 years. Younger patients were more likely to present with headache (86.5% vs. 37.9%, p < 0.001) and vomiting (25% vs. 5.2%, p < 0.001) than the patients ≥50 y/o, while the ≥50 y/o group more often presented with limb weakness (17.3% vs. 44.8%, p < 0.001), speech impairment (5.8% vs. 26.2%, p = 0.001) and gait disturbance or falls (23.1% vs. 50.7%, p < 0.001). There was no difference between the two groups in recurrence, overall complication rate and mortality within 90 days. Our meta-analysis confirmed that younger patients are more likely to present with headache (p = 0.015) while the hemispheric symptoms are more likely in patients ≥50 y/o (p < 0.001). Conclusion: Younger patients with cSDH present more often with signs of increased intracranial pressure, while those ≥50 y/o more often present with hemispheric symptoms. No difference exists between the two groups in terms of recurrence, morbidity, and short-term mortality. Knowledge of variations in clinical presentation is important for correct and timely diagnosis in younger cSDH patients.

Pedicle Screw Placement Using Augmented Reality Surgical Navigation With Intraoperative 3D Imaging: A First In-Human Prospective Cohort Study.

STUDY DESIGN: Prospective observational study. OBJECTIVE: The aim of this study was to evaluate the accuracy of pedicle screw placement using augmented reality surgical navigation (ARSN) in a clinical trial. SUMMARY OF BACKGROUND DATA: Recent cadaveric studies have shown improved accuracy for pedicle screw placement in the thoracic spine using ARSN with intraoperative 3D imaging, without the need for periprocedural x-ray. In this clinical study, we used the same system to place pedicle screws in the thoracic and lumbosacral spine of 20 patients. METHODS: The study was performed in a hybrid operating room with an integrated ARSN system encompassing a surgical table, a motorized flat detector C-arm with intraoperative 2D/3D capabilities, integrated optical cameras for augmented reality navigation, and noninvasive patient motion tracking. Three independent reviewers assessed screw placement accuracy using the Gertzbein grading on 3D scans obtained before wound closure. In addition, the navigation time per screw placement was measured. RESULTS: One orthopedic spinal surgeon placed 253 lumbosacral and thoracic pedicle screws on 20 consenting patients scheduled for spinal fixation surgery. An overall accuracy of 94.1% of primarily thoracic pedicle screws was achieved. No screws were deemed severely misplaced (Gertzbein grade 3). Fifteen (5.9%) screws had 2 to 4 mm breach (Gertzbein grade 2), occurring in scoliosis patients only. Thirteen of those 15 screws were larger than the pedicle in which they were placed. Two medial breaches were observed and 13 were lateral. Thirteen of the grade 2 breaches were in the thoracic spine. The average screw placement time was 5.2 ±â€Š4.1 minutes. During the study, no device-related adverse event occurred. CONCLUSION: ARSN can be clinically used to place thoracic and lumbosacral pedicle screws with high accuracy and with acceptable navigation time. Consequently, the risk for revision surgery and complications could be minimized. LEVEL OF EVIDENCE: 3.

Role of antithrombotic therapy in the risk of hematoma recurrence and thromboembolism after chronic subdural hematoma evacuation: a population-based consecutive cohort study.

OBJECTIVE: To establish the risk of recurrence in patients with chronic subdural hematoma (cSDH) on antithrombotic treatment (AT, i.e., antiplatelets and anticoagulants). Secondary end points were perioperative morbidity and mortality between groups (AT vs. no-AT group) and exploration if timing of resumption of AT treatment (i.e., prophylactic early vs. late resumption) influenced the occurrence of thromboembolism and hematoma recurrence. MATERIALS: In a population-based consecutive cohort, we conducted a retrospective review of 763 patients undergoing primary burr hole procedures for cSDH between January 1, 2005, and December 31, 2010, at the Karolinska University Hospital, Stockholm, Sweden. Early AT resumption was ≤30 days and late >30 days after the procedure. RESULTS: A total of 308/763 (40.4%) cSDH patients were on AT treatment at the time of diagnosis. There was no difference in cSDH recurrence within 3 months (11.0% vs. 12.0%, p = 0.69) nor was there any difference in perioperative mortality (4.0% vs. 2.0%, p = 0.16) between those using AT compared to those who were not. However, perioperative morbidity was more common in the AT group compared to no-AT group (10.7% vs. 5.1%, p = 0.003). Comparing early vs. late AT resumption, there was no difference with respect to recurrence (7.0% vs. 13.9%, p = 0.08), but more thromboembolism in the late AT resumption group (2.0% vs. 7.0%, p < 0.01). CONCLUSION: In clinical practice, cSDH patients on AT therapy at the time of diagnosis have similar recurrence rates and mortality compared to those without AT therapy, but with higher morbidity. Early resumption was not associated with more recurrence, but with lower thromboembolic frequency. Early AT resumption seems favorable, and a prospective RCT is needed.

Predictors of Recurrence and Complications After Chronic Subdural Hematoma Surgery: A Population-Based Study.

OBJECTIVE: To investigate predictors of recurrence and moderate to severe complications after burr-hole surgery for chronic subdural hematoma (cSDH). METHODS: A retrospective review was conducted in a Scandinavian single-center population-based cohort of 759 adult patients with cSDH operated with burr-hole surgery between January 1, 2005 and December 31, 2010. Possible predictors of recurrence and complications, assessed using a standardized reporting system of adverse events, were identified and analyzed in univariable analyses. Variables with a P value < 0.10 were included in a multivariable regression model. RESULTS: Recurrence was observed in 85 patients (11.2%), whereas moderate to severe complications were observed in 35 patients (4.6%). Bilateral hematoma (odds ratio [OR], 2.05; 95% confidence interval [CI], 1.25-3.35; P < 0.01) and largest hematoma diameter in millimeters (OR, 1.05; 95% CI, 1.01-1.09; P < 0.01) were independent predictors of recurrence in the multivariable model analysis. Glasgow Coma Scale (GCS) score of <13 (OR, 6.06; 95% CI, 2.72-13.51; P < 0.01) and Charlson Comorbidity Index (CCI) >1 (OR, 2.28; 95% CI, 1.10-4.75; P = 0.03) were independent predictors of moderate to severe complications. CONCLUSIONS: Recurrence after cSDH surgery is more often encountered in patients with radiologically more extensive disease reflected by bilateral hematoma and large hematoma diameter. On the other hand, moderate to severe complications are more often seen in patients in a worse clinical condition, reflected by decreased level of consciousness and more comorbidities.

Assessment of drainage techniques for evacuation of chronic subdural hematoma: a consecutive population-based comparative cohort study.

OBJECTIVE Surgery for chronic subdural hematoma (CSDH) is one of the most common neurosurgical procedures. The benefit of postoperative passive subdural drainage compared with no drains has been established, but other drainage techniques are common, and their effectiveness compared with passive subdural drains remains unknown. METHODS In Scandinavian population-based cohorts the authors conducted a consecutive, parallel cohort study to compare different drainage techniques. The techniques used were continuous irrigation and drainage (CID cohort, n = 166), passive subdural drainage (PD cohort, n = 330), and active subgaleal drainage (AD cohort, n = 764). The primary end point was recurrence in need of reoperation within 6 months of index surgery. Secondary end points were complications, perioperative mortality, and overall survival. The analyses were based on direct regional comparison (i.e., surgical strategy). RESULTS Recurrence in need of surgery was observed in 18 patients (10.8%) in the CID cohort, in 66 patients (20.0%) in the PD cohort, and in 85 patients (11.1%) in the AD cohort (p < 0.001). Complications were more common in the CID cohort (14.5%) compared with the PD (7.3%) and AD (8.1%) cohorts (p = 0.019). Perioperative mortality rates were similar between cohorts (p = 0.621). There were some differences in baseline and treatment characteristics possibly interfering with the above-mentioned results. However, after adjusting for differences in baseline and treatment characteristics in a regression model, the drainage techniques were still significantly associated with clinical outcome (p < 0.001 for recurrence, p = 0.017 for complications). CONCLUSIONS Compared with the AD cohort, more recurrences were observed in the PD cohort and more complications in the CID cohort, also after adjustment for differences at baseline. Although the authors cannot exclude unmeasured confounding factors when comparing centers, AD appears superior to the more common PD. Clinical trial registration no.: NCT01930617 (clinicaltrials.gov).

Distribution of candidate genes for experimentally induced arthritis in rats.

BACKGROUND: Rat models are frequently used to link genomic regions to experimentally induced arthritis in quantitative trait locus (QTL) analyses. To facilitate the search for candidate genes within such regions, we have previously developed an application (CGC) that uses weighted keywords to rank genes based on their descriptive text. In this study, CGC is used for analyzing the localization of candidate genes from two viewpoints: distribution over the rat genome and functional connections between arthritis QTLs. METHODS: To investigate if candidate genes identified by CGC are more likely to be found inside QTLs, we ranked 2403 genes genome wide in rat. The number of genes within different ranges of CGC scores localized inside and outside QTLs was then calculated. Furthermore, we investigated if candidate genes within certain QTLs share similar functions, and if these functions could be connected to genes within other QTLs. Based on references between genes in OMIM, we created connections between genes in QTLs identified in two distinct rat crosses. In this way, QTL pairs with one QTL from each cross that share an unexpectedly high number of gene connections were identified. The genes that were found to connect a pair of QTLs were then functionally analysed using a publicly available classification tool. RESULTS: Out of the 2403 genes ranked by the CGC application, 1160 were localized within QTL regions. No difference was observed between highly and lowly rated genes. Hence, highly rated candidate genes for arthritis seem to be distributed randomly inside and outside QTLs. Furthermore, we found five pairs of QTLs that shared a significantly high number of interconnected genes. When functionally analyzed, most genes connecting two QTLs could be included in a single functional cluster. Thus, the functional connections between these genes could very well be involved in the development of an arthritis phenotype. CONCLUSIONS: From the genome wide CGC search, we conclude that candidate genes for arthritis in rat are randomly distributed between QTL and non-QTL regions. We do however find certain pairs of QTLs that share a large number of functionally connected candidate genes, suggesting that these QTLs contain a number of genes involved in similar functions contributing to the arthritis phenotype.

Ranking candidate genes in rat models of type 2 diabetes.

BACKGROUND: Rat models are frequently used to find genomic regions that contribute to complex diseases, so called quantitative trait loci (QTLs). In general, the genomic regions found to be associated with a quantitative trait are rather large, covering hundreds of genes. To help selecting appropriate candidate genes from QTLs associated with type 2 diabetes models in rat, we have developed a web tool called Candidate Gene Capture (CGC), specifically adopted for this disorder. METHODS: CGC combines diabetes-related genomic regions in rat with rat/human homology data, textual descriptions of gene effects and an array of 789 keywords. Each keyword is assigned values that reflect its co-occurrence with 24 different reference terms describing sub-phenotypes of type 2 diabetes (for example "insulin resistance"). The genes are then ranked based on the occurrences of keywords in the describing texts. RESULTS: CGC includes QTLs from type 2 diabetes models in rat. When comparing gene rankings from CGC based on one sub-phenotype, with manual gene ratings for four QTLs, very similar results were obtained. In total, 24 different sub-phenotypes are available as reference terms in the application and based on differences in gene ranking, they fall into separate clusters. CONCLUSION: The very good agreement between the CGC gene ranking and the manual rating confirms that CGC is as a reliable tool for interpreting textual information. This, together with the possibility to select many different sub-phenotypes, makes CGC a versatile tool for finding candidate genes. CGC is publicly available at http://ratmap.org/CGC.

RGST - Rat Gene Symbol Tracker, a database for defining official rat gene symbols.

BACKGROUND: The names of genes are central in describing their function and relationship. However, gene symbols are often a subject of controversy. In addition, the discovery of mammalian genes is now so rapid that a proper use of gene symbol nomenclature rules tends to be overlooked. This is currently the situation in the rat and there is a need for a cohesive and unifying overview of all rat gene symbols in use. Based on the experiences in rat gene symbol curation that we have gained from running the "Ratmap" rat genome database, we have now developed a database that unifies different rat gene naming attempts with the accepted rat gene symbol nomenclature rules. DESCRIPTION: This paper presents a newly developed database known as RGST (Rat Gene Symbol Tracker). The database contains rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. CONCLUSION: This database fulfils the important need of unifying rat gene symbols into an automatic and cohesive nomenclature system. The RGST database is available directly from the RatMap home page: http://ratmap.org.

A web tool for finding gene candidates associated with experimentally induced arthritis in the rat.

Rat models are frequently used for finding genes contributing to the arthritis phenotype. In most studies, however, limitations in the number of animals result in a low resolution. As a result, the linkage between the autoimmune experimental arthritis phenotype and the genomic region, that is, the quantitative trait locus, can cover several hundred genes. The purpose of this work was to facilitate the search for candidate genes in such regions by introducing a web tool called Candidate Gene Capture (CGC) that takes advantage of free text data on gene function. The CGC tool was developed by combining genomic regions in the rat, associated with the autoimmune experimental arthritis phenotype, with rat/human gene homology data, and with descriptions of phenotypic gene effects and selected keywords. Each keyword was assigned a value, which was used for ranking genes based on their description of phenotypic gene effects. The application was implemented as a web-based tool and made public at http://ratmap.org/cgc. The CGC application ranks gene candidates for 37 rat genomic regions associated with autoimmune experimental arthritis phenotypes. To evaluate the CGC tool, the gene ranking in four regions was compared with an independent manual evaluation. In these sample tests, there was a full agreement between the manual ranking and the CGC ranking for the four highest-ranked genes in each test, except for one single gene. This indicates that the CGC tool creates a ranking very similar to that made by human inspection. The exceptional gene, which was ranked as a gene candidate by the CGC tool but not in the manual evaluation, was found to be closely associated with rheumatoid arthritis in additional literature studies. Genes ranked by the CGC tools as less likely gene candidates, as well as genes ranked low, were generally rated in a similar manner to those done manually. Thus, to find genes contributing to experimentally induced arthritis, we consider the CGC application to be a helpful tool in facilitating the evaluation of large amounts of textual information.

RatMap--rat genome tools and data.

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB-Genetics at Goteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided.

Detailed chromosomal and radiation hybrid mapping in the proximal part of rat Chromosome 10 and gene order comparison with mouse and human.

The rat provides valuable and sometimes unique models of human complex diseases. To fully exploit the rat models in biomedical research, it is important to have access to detailed knowledge of the rat genome organization as well as its relation to the human genome. Rat Chromosome 10 (RNO10) harbors several important cancer-related genes. Deletions in the proximal part of RNO10 were repeatedly found in a rat model for endometrial cancer. To identify functional and positional candidate genes in the affected region, we used radiation hybrid (RH) mapping and single- and dual-color fluorescence in situ hybridization (FISH) techniques to construct a detailed chromosomal map of the proximal part of RNO10. The regional localization of 14 genes, most of them cancer-related ( Grin2a, Gspt1, Crebbp, Gfer, Tsc2, Tpsb1, Il9r, Il4, Irf1, Csf2, Sparc, Tp53, Thra1, Gh1), and of five microsatellite markers ( D10Mit10, D10Rat42, D10Rat50, D10Rat72, and D10Rat165) was determined on RNO10. For a fifteenth gene, Ppm1b, which had previously been assigned to RNO10, the map position was corrected to RNO6q12-q13.

The functional significance of absence: the chromosomal segment harboring Tp53 is absent from the T55 rat radiation hybrid mapping panel.

The T55 rat radiation hybrid (RH) mapping panel has been reported to retain the entire rat genome at retention frequencies between 22% and 37%. However, we found that a small segment of rat chromosome 10 harboring at least four different genes, including Tp53, was completely absent from the panel (retention frequency = 0%). Two other markers located in the vicinity exhibited much reduced retention (2-6%). RH clones are generated by transferring highly fragmented DNA into a recipient cell. There might be a strong selection against the transfer and retention of chromosome segments harboring an intact Tp53, as the action of this gene might prevent proliferation and establishment of the RH clone. Our finding further suggests that unexpected low retention or absence of chromosome segments in an RH panel may represent indications that the segments harbor genes with important functions in cell proliferation control.

Predictions based on the rat-mouse comparative map provide mapping information on over 6000 new rat genes.

For identification of ECS ("evolutionarily conserved segments") between rat and mouse, 893 rat-mouse orthologous gene-pairs were brought together with zoo-FISH analysis. In total, 59 autosomal ECS and 4 X-chromosomal ones were detected. Combining FISH and zoo-FISH data, the segments were anchored on the rat chromosomes, providing an improved comparative map between the two species. Since chromosomal evolution is a slow process, it is reasonable to assume that the genome organization, including gene order, is essentially conserved within the ECS. In this way we assigned tentative subchromosomal map positions to 303 rat genes, for which no regional mapping information was available. Furthermore, the concept of prediction mapping was extended to unmapped rat homologs of genes, which in the mouse are situated inside or in the vicinity of an ECS. For a total of 6669 genes, we predicted a single rat chromosomal position, whereas for another 448 genes we could predict that they were located in one of two possible positions. Thus, our study has increased the number of genes for which there is positional mapping information in the rat almost fivefold.