Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations

Summary: We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continuously updated from PubMed. These applications provide user-friendly interfaces for searching summarized information on human genetic associations, using either genes or diseases as the starting point.

Availability: Phenopedia and Genopedia can be freely accessed at http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do and http://www.hugenavigator.net/HuGENavigator/startPagePedia.do, respectively.

Contact:wby0@cdc.gov

Supplementary information:Supplementary data are available at Bioinformatics online.

Observation of the naive-T-odd Sivers effect in deep-inelastic scattering

Azimuthal single-spin asymmetries of leptoproduced pions and charged kaons were measured on a transversely polarized hydrogen target. Evidence for a naive-T-odd, transverse-momentum-dependent parton distribution function is deduced from nonvanishing Sivers effects for pi(+), pi(0), and K(+/-), as well as in the difference of the pi(+) and pi(-) cross sections.

Geometric and compositional appearance of atheroma in an angiographically normal carotid artery in patients with atherosclerosis

BACKGROUND AND PURPOSE

Arterial remodeling may enable atherosclerotic disease without luminal stenosis. We sought to assess the prevalence and characteristics of atherosclerosis in angiographically normal carotid arteries.

MATERIALS AND METHODS

Forty-six arteries with 0% stenosis by MRA were evaluated with multicontrast carotid MR imaging at 3T. For each artery, the percentage wall volume (wall volume/[lumen volume + wall volume] x 100%) and the presence versus absence of an LRNC, calcification, IPH, and fibrous cap rupture were recorded. In addition, the relative size of each plaque component (eg, percentage LRNC = LRNC volume/wall volume x 100%), when present, was calculated.

RESULTS

The mean of percentage wall volume in arteries with 0% stenosis was 43.0 +/- 6.9% with a range from 31.6% to 60.1%. An LRNC was present in 67.4% (31/46) of arteries, calcification was present in 65.2% (30/46), IPH was present in 8.7% (4/46), and fibrous cap rupture was present in 4.3% (2/46). In arteries with an LRNC (n = 31), the average percentage LRNC volume was 8.8 +/- 7.3% with a range from 1.0% to 31.5%. For calcification (n = 30), the mean percentage calcification volume was 3.8 +/- 4.2% with a range of 0.1%-17.4%. The mean percentage IPH volume (n = 4) was 2.7 +/- 1.7% with a range of 0.5%-4.1%.

CONCLUSIONS

These findings indicate that stenosis by MRA may underestimate the presence of carotid atherosclerosis, and they demonstrate the need for improved methods for accurately identifying carotid atherosclerotic plaque severity.

Effect of fat on measurement of bone mineral density

OBJECTIVE: To determine if increasing fatness interferes with the measurement of fat and bone mineral density (BMD) by dual-energy X-ray absorptiometry (Lunar iDXA). METHODS: We performed measurements of BMD and fat on a section of a beef femur defatted by prolonged boiling in detergent, completely surrounded by increasing thicknesses of lard. Initially the bone was placed in the marked spine area, overlying a 6L plastic bottle which was placed in the marked trunk area of the iDXA. The plastic bottle was then removed and further measurements were carried out with increasing thicknesses of lard surrounding the bone. Measurements were repeated 4 times. RESULTS: The reported measurement of BMD progressively increased with each increased layer of lard surrounding the bone. All the iDXA BMD measurements were significantly (P<0.01) different from one another. When surrounded by 3 layers of lard the reported BMD was 20.5% greater than the reported BMD when the bone was not surrounded by any lard. The differences between the actual amount of fat measured by chemical analysis and weighing, and the reported measurement of fat by iDXA were significant with all 3 thicknesses of lard (P<0.01); the percentage difference between the fat measured by iDXA and that measured chemically decreased as the number of layers of lard increased. CONCLUSION: We found that iDXA overestimated fat by up to 11.1%. The percentage overestimation of fat diminished as the amount of fat increased. BMD was overestimated by 20.5% when surrounded by 3 layers of fat compared to when there was no surrounding fat. In contrast to fat, the percentage overestimation of BMD increased as increasing amounts of fat surrounding the bone Using earlier generation DXAs, others have reported that measurements were ± 20-50% inaccurate and differed according to the configuration of the phantoms. The measurement of BMD and fat is the main clinical purpose of iDXA; the present experiment has shown that there are substantial inaccuracies in the measurement of BMD and fat. It is not known how these inaccuracies compare with those of earlier generations of DXA machines.

Decreased T-cell receptor excision DNA circles in peripheral blood mononuclear cells among benzene-exposed workers

Benzene is a volatile aromatic hydrocarbon solvent which is widely used in many industries. The chronic exposure of humans to benzene in the workplace has been associated with blood disorders, as well as toxicity in lymphopoiesis, including aplastic anaemia and leukaemia. However, the mechanisms of benzene-induced haematotoxicity and leukaemogenesis remain unclear. In this study, we investigated the level of T-cell receptor excision DNA circles (TRECs) in peripheral blood mononuclear cells (PBMCs) in benzene-exposed workers. This would therefore be considered as a potential marker for estimates of thymic output and an evaluation of the content of naïve T-cells. It is hoped that the data will bring a comprehensive understanding on the influence of benzene exposure in the host T-cell immune function. Quantitative detection of TRECs in DNA of PBMCs from benzene-exposed workers was preformed by real-time polymerase chain reaction using the TaqMan technique. The benzene-exposed workers were divided into four groups, and 27 normal individuals were served as controls. The result indicated that the TRECs levels of all benzene-exposed groups were significantly decreased as compared with those of controls. In conclusion, the recent thymic output function and the T-cell immune function were apparently impaired in workers after benzene exposure.

Comparison of radiography, CT and MR imaging in detection of arthropathies in patients with haemophilia

To compare magnetic resonance (MR) imaging, computed tomography (CT) and radiography for the detection of arthropathies in patients with haemophilia. Forty-one symptomatic joints in 14 men with haemophilia, ages 11-24 years (mean age 17.5 +/- 3.9 years) were examined with radiography, CT and MR. Images of each joint were acquired on the same day. The precontrast MR examination obtained coronal spin-echo T1 images and gradient echo with rephasing T2* images, as well as sagittal, axial gradient echo with rephasing T2* images using a low-field-strength 0.3-T MR imager. For the postcontrast MR examination, coronal, sagittal and axial images were acquired using the same precontrast T1 sequence. Thirteen joints were also examined on enhanced MR. The severity of damage was classified using conventional radiographical staging. Severely affected haemophilic arthropathy (HA) patients (stage 5) were excluded. Findings of soft tissue swelling, osteoporosis, epiphyseal overgrowth, joint erosion, cysts, joint space narrowing, bone marrow oedema, joint effusion, haemorrhage, synovial hypertrophy and widened intercondylar notches as well as anterior and posterior cruciate ligaments (for the knee) were used in all imaging comparisons. The joints were classified by radiographical criteria into stage 0 (n = 5), stage 1 (n = 7), stage 2 (n = 6), stage 3 (n = 8) and stage 4 (n = 15). Soft tissue swelling or joint effusion was observed in 33 joints on radiographs, in 34 on both CT and MR; joint erosions were observed in 34 joints on MR, 33 on CT and 20 on radiographs. Joint cysts appeared in 21 joints on MR, 18 on CT and 9 on radiographs. Significant differences in detection of erosion and cysts were found between radiography and CT (P < 0.05) and radiography and MR imaging (P < 0.05), not between CT and MR (P > 0.05). MR was better for detecting foci of both erosion and cysts than CT and radiography, and CT was better than radiography. MR imaging, CT and radiography were equally effective in showing the changes of epiphyseal overgrowth in 26 joints, joint space narrowing in 14 joints and widened intercondylar notches in 20 knee joints. However, only MR imaging detected tears in 17 anterior and 13 posterior cruciate ligaments in the 20 knee joints with widened intercondylar notches. Bone marrow oedema in 14 joints, haemorrhage in 34 joints and synovial hypertrophy in 27 joints were seen on MR images, but not on CT or radiography. MR imaging is superior to CT and conventional radiography for detecting abnormal changes and should be considered the first choice among imaging modalities in evaluating HAs.

Prognostic impact of the NFKB1 insertion/deletion promoter polymorphism on survival in patients with surgically resected gastric cancer

e15638

Background: The present study analyzed the functional insertion/deletion polymorphism in the promoter region of NKFB1 gene and their impact on the prognosis for patients with gastric adenocarcinoma. Methods: Five hundred and three consecutive patients with surgically resected gastric adenocarcinoma were enrolled in the present study. The genomic DNA was extracted from paraffin-embedded tissue and the -94 insertion/deletion ATTG polymorphism of NFKB1 determined using a PCR- RFLP assay. Results: The NFKB1 promoter gene polymorphism was successfully amplified in 97.8% of the cases. There were no sexual differences in relation to the genotype and allele. No correlation was observed between the frequency of the genotype or allele and the T, N, or M stage. The multivariate survival analysis showed no association between the NFKB1 -94 insertion/deletion promoter polymorphism and the disease-free survival or overall survival of the patients with gastric cancer. Conclusions: The functional NFKB1 promoter polymorphism was not found to be a prognostic marker for Korean patients with surgically resected gastric adenocarcinoma.

No significant financial relationships to disclose.

Electrical generation of pure spin currents in a two-dimensional electron gas

Pure spin currents are generated and detected in micron-wide channels of a GaAs two-dimensional electron gas, using quantum point contacts in an in-plane magnetic field as injectors and detectors. The enhanced sensitivity to spin transport offered by a nonlocal measurement geometry enables accurate spin current measurements in this widely studied physical system. The polarization of the contacts is used to extract the quantum point contact g factor and provides a test for spontaneous polarization at 0.7 structure. The spin relaxation length in the channel is 30-50 microm over the magnetic field range 3-10 T, much longer than has been reported in GaAs two-dimensional electron gases but shorter than that expected from Dyakonov-Perel relaxation.

Static magnetic order and superfluid density of RFeAs(O,F) (R=La,Nd,Ce) and LaFePO studied by muon spin relaxation: unusual similarities with the behavior of cuprate superconductors

Muon spin relaxation measurements in iron-oxypnictide systems have revealed: (1) commensurate long-range order in undoped LaFeAsO; (2) a Bessel function line shape in LaFeAs(O0.97F0.03) which indicates possible incommensurate or stripe magnetism; (3) anomalous weak magnetism existing in superconducting LaFePO, CeFeAs(O0.084F0.16), and NdFeAs(O0.88F0.12) but absent in superconducting LaFeAs(O0.92F0.08); and (4) scaling of the superfluid density with T_{c} in the Ce-, La-, and Nd-FeAs superconductors following a nearly linear relationship found in cuprates.

Nonlinear optical properties of mushroom-shaped CdSe/CdS coreshells

The third-order nonlinear optical susceptibilities of mushroom-shaped CdSe/CdS coreshells as a function of concentration have been investigated using polarization- and concentration-resolved degenerate four-wave mixing in a resonant region. The effective third-order nonlinear optical susceptibilities, /chi(3)xxxx/ and /chi(3)xyyx/ of CdSe/CdS coreshells were estimated to be approximately 1.86 x 10(-21)-1.03 x 10(-20) m2/V2, and approximately 0.45 x 10(-21)-6.15 x 10(-21) m2/V2, respectively, for various concentrations of approximately 0.64 x 10(-3)-4.95 x 10(-3) mol/m3. The second hyperpolarizabilities, /<gammah>xxxx/ and /<gammah>xyyx/, of CdSe/CdS coreshells were extracted to be approximately 2.37 x 10(-41) m5/V2 and approximately 1.29 x 10(-41) m5/V2, respectively.

Locoregional treatment of peritoneal carcinomatosis from gastric cancer

The authors reviewed the natural history and the main features of the peritoneal carcinomatosis from gastric cancer briefly and analyzed the pertinent literature concerning the locoregional modalities for prevention and for treatment. Results of the web based voting by experts were also summarized. As regards the peritoneal perfusion with cytotoxic drugs with or without hyperthermia for preventing peritoneal carcinomatosis in high risk patients, there are some randomized clinical trials and one meta-analysis supporting a benefit of the procedure. However, disparity in methodology (drugs, dosage, duration of the treatment, addition of hyperthermia, etc.) precludes the adoption of a shared protocol to be used in the clinical practice in high risk patients. Once the peritoneal carcinomatosis is established, the approach reported in literature is the peritonectomy associated with hyperthermic perfusion. However, data supporting benefits are scanty, and limited to few centers with a specific experience in this field. With regard to the main questions addressed to the experts' panel and concerning the indications for treatment and methodology, there was a general consistency among the experts and agreement with the findings of the literature. The need for a large multicenter trial to confirm the benefit and risk of intraperitoneal chemotherapy was recognized by both the experts and the authors.

Hedgehog inhibition prolongs survival in a genetically engineered mouse model of pancreatic cancer

BACKGROUND AND AIMS

Pancreatic cancer is among the most dismal of human malignancies. Current therapeutic strategies are virtually ineffective in controlling advanced, metastatic disease. Recent evidence suggests that the Hedgehog signalling pathway is aberrantly reactivated in the majority of pancreatic cancers, and that Hedgehog blockade has the potential to prevent disease progression and metastatic spread.

METHODS

Here it is shown that the Hedgehog pathway is activated in the Pdx1-Cre;LsL-Kras(G12D);Ink4a/Arf(lox/lox) transgenic mouse model of pancreatic cancer. The effect of Hedgehog pathway inhibition on survival was determined by continuous application of the small molecule cyclopamine, a smoothened antagonist. Microarray analysis was performed on non-malignant human pancreatic ductal cells overexpressing Gli1 in order to screen for downstream Hedgehog target genes likely to be involved in pancreatic cancer progression.

RESULTS

Hedgehog inhibition with cyclopamine significantly prolonged median survival in the transgenic mouse model used here (67 vs 61 days; p = 0.026). In vitro data indicated that Hedgehog activation might at least in part be ascribed to oncogenic Kras signalling. Microarray analysis identified 26 potential Hedgehog target genes that had previously been found to be overexpressed in pancreatic cancer. Five of them, BIRC3, COL11A1, NNMT, PLAU and TGM2, had been described as upregulated in more than one global gene expression analysis before.

CONCLUSION

This study provides another line of evidence that Hedgehog signalling is a valid target for the development of novel therapeutics for pancreatic cancer that might be worth evaluating soon in a clinical setting.

Comfort evaluation of maternity support garments in a wear trial

This study aims to evaluate the wear comfort of eight commercially available maternity support garments. The thermophysiological, sensory/tactile and movement comfort were assessed in a wear trial using a 19-item questionnaire. Fourteen pregnant Chinese women aged 32.3 +/- 4.2 years were recruited from a local obstetric clinic. The results show that the tested garments generally provided greater sensory comfort than thermophysiological comfort. The thermophysiological comfort was mainly influenced by the fibre contents and breathability. Significant linear relationships were found between material appearance and hand feel (r = 0.86, p < 0.001), and between non-itchiness and no red mark (r = 0.78, p < 0.001). Movement comfort was influenced by the garment type and style features. Overall, the soft, good-fit, cotton/elastane maternity brief was perceived as the best product. The findings of comfort needs in pregnant women and the effects of various garment attributes would be helpful for the development of maternity support garment design criteria that are required to satisfy critical ergonomic needs. Low back pain during pregnancy is a common and significant health problem. A maternity support garment is regarded as a convenient and safe device to stabilise the lumbar spine so as to relieve pain. However, patient compliance is likely to be affected by discomfort and inconvenience. The results of this study provide guidance for the optimal design of maternity support clothing.