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1.  Synergistic interactions between sorafenib and everolimus in pancreatic cancer xenografts in mice 
Cancer chemotherapy and pharmacology  2013;71(5):1231-1240.
Purpose
Molecular targeting of cellular signaling pathways is a promising approach in cancer therapy, but often fails to achieve sustained benefit because of the activation of collateral cancer cell survival and proliferation pathways. We tested the hypothesis that a combination of targeted agents that inhibit compensatory pathways would be more effective than single agents in controlling pancreatic cancer cell growth. We investigated whether everolimus, an mTOR inhibitor, and sorafenib, a multi-kinase inhibitor, would together inhibit growth of low-passage, patient-derived pancreatic cancer xenografts in mice more efficaciously than either agent alone.
Methods
Tumor volume progression was measured following treatment with both drugs as single agents, in combination, and at multiple doses. Pharmacokinetics in tumors and other tissues was also assessed. Pharmacodynamic interactions were evaluated quantitatively.
Results
A 5-week regimen of daily oral doses of 10 mg/kg sorafenib and 0.5 mg/kg everolimus, alone and in combination, did not achieve significant tumor growth inhibition. Higher doses (20 mg/kg of sorafenib and 1 mg/kg of everolimus) inhibited tumor growth significantly when given alone and caused complete inhibition of growth when given in combination. Tumor volume progression was described by a linear growth model, and drug effects were described by Hill-type inhibition. Using population modeling approaches, dual-interaction parameter estimates indicated a highly synergistic pharmacodynamic interaction between the two drugs.
Conclusions
The results indicate that combinations of mTOR and multi-kinase inhibitors may offer greater efficacy in pancreatic cancer than either drug alone. Drug effects upon tumor stromal elements may contribute to the enhanced anti-tumor efficacy.
doi:10.1007/s00280-013-2117-x
PMCID: PMC3752659  PMID: 23455452
Everolimus; Sorafenib; Xenografts; Non-competitive interaction model; PBPK-PD; Pancreatic cancer
2.  Physiologically based pharmacokinetic models for everolimus and sorafenib in mice 
Cancer chemotherapy and pharmacology  2013;71(5):1219-1229.
Purpose
Everolimus is a mammalian target of rapamycin (mTOR) inhibitor approved as an immunosuppressant and for second-line therapy of hepatocellular carcinoma (HCC) and renal cell carcinoma (RCC). Sorafenib is a multikinase inhibitor used as first-line therapy in HCC and RCC. This study assessed the pharmacokinetics (PK) of everolimus and sorafenib alone and in combination in plasma and tissues, developed physiologically based pharmacokinetic (PBPK) models in mice, and assessed the possibility of PK drug interactions.
Methods
Single and multiple oral doses of everolimus and sorafenib were administered alone and in combination in immunocompetent male mice and to severe combined immune-deficient (SCID) mice bearing low-passage, patient-derived pancreatic adenocarcinoma in seven different studies. Plasma and tissue samples including tumor were collected over a 24-h period and analyzed by liquid chromatography-tandem mass spectrometry (LC–MS/MS). Distribution of everolimus and sorafenib to the brain, muscle, adipose, lungs, kidneys, pancreas, spleen, liver, GI, and tumor was modeled as perfusion rate-limited, and all data from the diverse studies were fitted simultaneously using a population approach.
Results
PBPK models were developed for everolimus and sorafenib. PBPK analysis showed that the two drugs in combination had the same PK as each drug given alone. A twofold increase in sorafenib dose increased tumor exposure tenfold, thus suggesting involvement of transporters in tumor deposition of sorafenib.
Conclusions
The developed PBPK models suggested the absence of PK interaction between the two drugs in mice. These studies provide the basis for pharmacodynamic evaluation of these drugs in patient-derived primary pancreatic adenocarcinomas explants.
doi:10.1007/s00280-013-2116-y
PMCID: PMC3755750  PMID: 23455451
Everolimus; Sorafenib; Pancreatic cancer; PBPK; Patient-derived pancreatic adenocarcinoma
3.  Evaluation of GWAS-identified genetic variants for age at menarche among Chinese women 
Human Reproduction (Oxford, England)  2013;28(4):1135-1143.
STUDY QUESTION
Do genetic polymorphisms which influence age at menarche in women of European ancestry also influence women of Chinese ancestry?
SUMMARY ANSWER
Many genetic variants influencing age at menarche in European populations appear to impact Chinese populations in a similar manner.
WHAT IS KNOWN AND WHAT THIS PAPER ADDS
Prior genome-wide association studies have uncovered 42 SNPs associated with age at menarche in European populations. This study is the first to demonstrate that many of the genetic determinants of age at menarche are shared between European and Chinese women.
PARTICIPANTS AND SETTING
We evaluated 37 of 42 SNPs identified as associated with age at menarche from a recent, large meta-analysis, consisting primarily of women of European ancestry, in a population of 6929 Chinese women from Shanghai, China. We also constructed weighted genetic risk scores (GRSs) combining the number of effect variants for all 37 SNPs, or only the SNPs associated with age at menarche among our study population, to evaluate their joint influence on age at menarche.
MAIN RESULTS
For 32 of the 37 evaluated variants, the direction of the allele associations were the same between women of European ancestry and women of Chinese ancestry (P = 3.71 × 10−6, binomial sign test); 9 of these were statistically significant. Subjects in the highest quintile of GRSs began menarche ∼5 months later than those in the lowest quintile.
BIAS, LIMITATIONS AND GENERALIZABILITY TO OTHER POPULATIONS
Age at menarche was obtained by self-report, which can be subject to recall errors. The current analysis was restricted to loci which met or approached GWAS significance thresholds and did not evaluate loci which may act predominantly or exclusively in the Chinese population. The smaller sample size for our meta-analysis compared with meta-analyses conducted in European populations reduced the power to detect significant results.
STUDY FUNDING/COMPETING INTERESTS
This study was supported, in part, by grants from US National Institutes of Health (grants R01CA124558, R01CA090899, R01CA070867; R01CA064277 and R01CA092585 and UL1 RR024975), Ingram professorship funds and Allen Foundation funds. There are no competing interests to declare.
doi:10.1093/humrep/det011
PMCID: PMC3600840  PMID: 23406970
menarche; genome-wide association study; genetics; reproductive endocrinology
4.  Interactions of Everolimus and Sorafenib in Whole Blood Lymphocyte Proliferation 
Pharmaceutical research  2012;30(3):707-713.
Purpose
Everolimus is an immunosuppressant that blocks growth factor-mediated proliferation of hematopoietic cells by targeting the mammalian target of rapamycin (mTOR). Sorafenib is a multikinase inhibitor that inhibits cell proliferation by arresting cells in the G0–G1 phase of the cell cycle. These agents are under investigation as combination therapy for various cancers. Because the two drugs individually inhibit lymphocyte proliferation, this study examined the effects of everolimus and sorafenib on lymphocyte proliferation in order to anticipate possible immunosuppression.
Methods
Inhibition of lymphocyte proliferation was evaluated ex vivo over a range of concentrations of these drugs, alone and in combination. Data analysis, using a population approach to characterize interactions, employed the Ariens noncompetitive interaction model, which was modified to accommodate interactions of the two drugs.
Results
Everolimus alone caused partial inhibition of lymphocyte proliferation, with a mean IC50 of 4.5 nM for females and 10.5 nM in males. Sorafenib alone caused complete inhibition, with a mean IC50 of 11.4 µM and no difference between genders.
Conclusion
The population estimate for the interaction term was greater than 1, suggesting that the two drugs exert slight antagonism in terms of inhibition of lymphocyte proliferation.
doi:10.1007/s11095-012-0909-z
PMCID: PMC3726064  PMID: 23151723
everolimus; lymphocyte proliferation; modeling interactions; population analysis; sorafenib
5.  Interactions of Everolimus and Sorafenib in Pancreatic Cancer Cells 
The AAPS Journal  2012;15(1):78-84.
Everolimus targets the mammalian target of rapamycin, a kinase that promotes cell growth and proliferation in pancreatic cancer. Sorafenib inhibits the Raf-mitogen-activated protein kinase, vascular endothelial growth factor, and platelet-derived growth factor pathways, thus inhibiting cell growth and angiogenesis. Combinations of these two agents are under evaluation for therapy of several cancers. This study examined the effects of everolimus and sorafenib on proliferation of the pancreatic cancer cell lines MiaPaCa-2 and Panc-1. Cell growth inhibition was evaluated in vitro for a range of concentrations of the drugs alone and in combination. Maximum inhibition capacity (Imax) and potency (IC50) were determined. The data were analyzed to characterize drug interactions using two mathematical analysis techniques. The Ariens noncompetitive interaction model and Earp model were modified to accommodate alterations in the inhibition parameters of one drug in the presence of another. Sorafenib alone inhibited growth of both cell lines completely (Imax = 1), with an IC50 of 5–8 μM. Maximal inhibition by everolimus alone was only 40% (Imax = 0.4) in both cell lines, with an IC50 of 5 nM. Slight antagonistic interaction occurred between the drugs; both analytic methods estimated the interaction term Ψ as greater than 1 for both cell lines. The in vitro data for two pancreatic cancer cell lines suggest that a combination of these two drugs would be no more efficacious than the individual drugs alone, consistent with the drug interaction analysis that indicated slight antagonism for growth inhibition.
doi:10.1208/s12248-012-9417-7
PMCID: PMC3535103  PMID: 23054975
everolimus; MiaPaCa-2; modeling interactions; Panc-1; sorafenib
6.  Adepth: new representation and its implications for atomic depths of macromolecules 
Nucleic Acids Research  2013;41(Web Server issue):W412-W416.
We applied the signed distance function (SDF) for representing the depths of atoms in a macromolecule. The calculations of SDF values were performed on grid points in a rectangular box that accommodates the macromolecule. The depth for an atom inside the molecule was then obtained as a result of tri-linear interpolation of SDF values at the nearest grid points surrounding the atom. For testing the performance of present program Adepth, we have constructed an artificial molecule whose atomic depths are known as the gold standard for accuracy assessments. On average, our results showed that Adepth reached an accuracy of 1.6% at 0.5 Å of grid spacing, whereas the current reference server DEPTH reached 7.5%. The Adepth program provides both depth and height representations; it is capable of computing iso-surfaces for atomic depths and presenting graphical view of macromolecular shape at some distance away from the surface. Web interface is available at http://biodev.cea.fr/adepth.
doi:10.1093/nar/gkt299
PMCID: PMC3692060  PMID: 23609539
7.  Isoform-specific palmitoylation of JNK regulates axonal development 
Cell Death and Differentiation  2011;19(4):553-561.
The c-jun N-terminal kinase (JNK) proteins are encoded by three genes (Jnk1–3), giving rise to 10 isoforms in the mammalian brain. The differential roles of JNK isoforms in neuronal cell death and development have been noticed in several pathological and physiological contexts. However, the mechanisms underlying the regulation of different JNK isoforms to fulfill their specific roles are poorly understood. Here, we report an isoform-specific regulation of JNK3 by palmitoylation, a posttranslational modification, and the involvement of JNK3 palmitoylation in axonal development and morphogenesis. Two cysteine residues at the COOH-terminus of JNK3 are required for dynamic palmitoylation, which regulates JNK3's distribution on the actin cytoskeleton. Expression of palmitoylation-deficient JNK3 increases axonal branching and the motility of axonal filopodia in cultured hippocampal neurons. The Wnt family member Wnt7a, a known modulator of axonal branching and remodelling, regulates the palmitoylation and distribution of JNK3. Palmitoylation-deficient JNK3 mimics the effect of Wnt7a application on axonal branching, whereas constitutively palmitoylated JNK3 results in reduced axonal branches and blocked Wnt7a induction. Our results demonstrate that protein palmitoylation is a novel mechanism for isoform-specific regulation of JNK3 and suggests a potential role of JNK3 palmitoylation in modulating axonal branching.
doi:10.1038/cdd.2011.124
PMCID: PMC3307970  PMID: 21941371
c-Jun N-terminal kinase/JNK; palmitoylation; axonal branching; isoform regulation; cytoskeleton; Wnt pathway
8.  Computational reconstruction of multidomain proteins using atomic force microscopy data 
Structure(London, England:1993)  2012;20(1):113-120.
Summary
Classical structural biology techniques face a great challenge to determine the structure at the atomic level of large and flexible macromolecules. We present a novel methodology that combines high-resolution AFM topographic images with atomic coordinates of proteins to assemble very large macromolecules or particles. Our method uses a two-step protocol: atomic coordinates of individual domains are docked beneath the molecular surface of the large macromolecule, and then each domain is assembled using a combinatorial search. The protocol was validated on three test cases: a simulated system of antibody structures; and two experimentally-based test cases: Tobacco mosaic virus, a rod-shaped virus; and aquaporin Z, a bacterial membrane protein. We have shown that AFM-intermediate resolution topography and partial surface data are useful constraints for building macromolecular assemblies. The protocol is applicable to multi-component structures connected in the polypeptide chain or as disjoint molecules. The approach effectively increases the resolution of AFM beyond topographical information down to atomic-detail structures.
doi:10.1016/j.str.2011.10.023
PMCID: PMC3264848  PMID: 22244760
AFM; protein structure; integrative modeling; molecular assembly; super-complexes; computational biology
9.  Resonant waveguide sensing made robust by on-chip peak tracking through image correlation 
Biomedical Optics Express  2012;3(10):2436-2451.
We demonstrate a solution to make resonant-waveguide-grating sensing both robust and simpler to optically assess, in the spirit of biochips. Instead of varying wavelength or angle to track the resonant condition, the grating itself has a step-wise variation with typically few tens of neighboring “micropads.” An image capture with incoherent monochromatic light delivers spatial intensity sequences from these micropads. Sensitivity and robustness are discussed using correlation techniques on a realistic model (Fano shapes with noise and local distortion contributions). We confirm through fluid refractive index sensing experiments an improvement over the step-wise maximum position tracking by more than 2 orders of magnitude, demonstrating sensitivity down to 2 × 10−5 RIU, giving high potential development for bioarray imaging.
doi:10.1364/BOE.3.002436
PMCID: PMC3469982  PMID: 23082286
(280.1415) Biological sensing and sensors; (310.2785) Guided wave applications; (050.5745) Resonance domain; (110.2960) Image analysis; (070.6110) Spatial filtering
10.  Neutralizing human monoclonal antibodies binding multiple serotypes of botulinum neurotoxin 
Botulism, a disease of humans characterized by prolonged paralysis, is caused by botulinum neurotoxins (BoNTs), the most poisonous substances known. There are seven serotypes of BoNT (A–G) which differ from each other by 34–64% at the amino acid level. Each serotype is uniquely recognized by polyclonal antibodies, which originally were used to classify serotypes. To determine if there existed monoclonal antibodies (mAbs) capable of binding two or more serotypes, we evaluated the ability of 35 yeast-displayed single-chain variable fragment antibodies generated from vaccinated humans or mice for their ability to bind multiple BoNT serotypes. Two such clonally related human mAbs (1B18 and 4E17) were identified that bound BoNT serotype A (BoNT/A) and B or BoNT/A, B, E and F, respectively, with high affinity. Using molecular evolution techniques, it proved possible to both increase affinity and maintain cross-serotype reactivity for the 4E17 mAb. Both 1B18 and 4E17 bound to a relatively conserved epitope at the tip of the BoNT translocation domain. Immunoglobulin G constructed from affinity matured variants of 1B18 and 4E17 were evaluated for their ability to neutralize BoNT/B and E, respectively, in vivo. Both antibodies potently neutralized BoNT in vivo demonstrating that this epitope is functionally important in the intoxication pathway. Such cross-serotype binding and neutralizing mAbs should simplify the development of antibody-based BoNT diagnostics and therapeutics.
doi:10.1093/protein/gzq111
PMCID: PMC3038462  PMID: 21149386
botulism; botulinum neurotoxin; molecular evolution; single-chain Fv; yeast display
11.  Association of genetic variation in FTO with risk of obesity and type 2 diabetes with data from 96,551 East and South Asians 
Diabetologia  2011;55(4):981-995.
Aims/hypothesis
FTO harbours the strongest known obesity-susceptibility locus in Europeans. While there is growing evidence for a role for FTO in obesity risk in Asians, its association with type 2 diabetes, independently of BMI, remains inconsistent. To test whether there is an association of the FTO locus with obesity and type 2 diabetes, we conducted a meta-analysis of 32 populations including 96,551 East and South Asians.
Methods
All studies published on the association between FTO-rs9939609 (or proxy [r2 > 0.98]) and BMI, obesity or type 2 diabetes in East or South Asians were invited. Each study group analysed their data according to a standardised analysis plan. Association with type 2 diabetes was also adjusted for BMI. Random-effects meta-analyses were performed to pool all effect sizes.
Results
The FTO-rs9939609 minor allele increased risk of obesity by 1.25-fold/allele (p = 9.0 × 10−19), overweight by 1.13-fold/allele (p = 1.0 × 10−11) and type 2 diabetes by 1.15-fold/allele (p = 5.5 × 10−8). The association with type 2 diabetes was attenuated after adjustment for BMI (OR 1.10-fold/allele, p = 6.6 × 10−5). The FTO-rs9939609 minor allele increased BMI by 0.26 kg/m2 per allele (p = 2.8 × 10−17), WHR by 0.003/allele (p = 1.2 × 10−6), and body fat percentage by 0.31%/allele (p = 0.0005). Associations were similar using dominant models. While the minor allele is less common in East Asians (12–20%) than South Asians (30–33%), the effect of FTO variation on obesity-related traits and type 2 diabetes was similar in the two populations.
Conclusions/interpretation
FTO is associated with increased risk of obesity and type 2 diabetes, with effect sizes similar in East and South Asians and similar to those observed in Europeans. Furthermore, FTO is also associated with type 2 diabetes independently of BMI.
Electronic supplementary material
The online version of this article (doi:10.1007/s00125-011-2370-7) contains peer-reviewed but unedited supplementary material, which is available to authorised users.
doi:10.1007/s00125-011-2370-7
PMCID: PMC3296006  PMID: 22109280
Asians; FTO; Meta-analysis; Obesity; Type 2 diabetes
12.  Emerging therapies in pancreas cancer 
Pancreas cancer has a grave prognosis and treatment options remain limited despite advancement in anti-cancer chemotherapeutics. This review provides an overview of the emerging therapies for pancreas cancer, focusing on novel signal transduction inhibitors (insulin-like growth factor receptor, hedgehog/Smo, PI3k/Akt/mTOR) and cytotoxics (nab-paclitaxel) that are currently in clinical development. Despite the impact molecularly targeted agents have on other tumor types, their application without cytotoxics in pancreas cancer remains limited. In addition, recent report of the superiority of an intensive cytotoxic regimen using fluorouracil, irinotecan and oxaliplatin (FOLFIRINOX) over gemcitabine reminded us of the importance of cytotoxics in this disease. As such, the future of pancreas cancer therapy may be combination regimens consisting of cytotoxics and molecularly targeted agents.
doi:10.3978/j.issn.2078-6891.2011.002
PMCID: PMC3397600  PMID: 22811835
Pancreas cancer; chemotherapy; target therapy
13.  Affinity maturation of human botulinum neurotoxin antibodies by light chain shuffling via yeast mating 
Botulism is caused by the botulinum neurotoxins (BoNTs), the most poisonous substance known. Because of the high potency of BoNT, development of diagnostic and therapeutic antibodies for botulism requires antibodies of very high affinity. Here we report the use of yeast mating to affinity mature BoNT antibodies by light chain shuffling. A library of immunoglobulin light chains was generated in a yeast vector where the light chain is secreted. The heavy chain variable region and the first domain of the constant region (VH–CH1) from a monoclonal antibody was cloned into a different yeast vector for surface display as a fusion to the Aga2 protein. Through yeast mating of the two haploid yeasts, a library of light chain-shuffled Fab was created. Using this approach, the affinities of one BoNT/A and two BoNT/B scFv antibody fragments were increased from 9- to more than 77-fold. Subcloning the V-genes from the affinity-matured Fab yielded fully human IgG1 with equilibrium binding constants for BoNT/A and BoNT/B of 2.51 × 10−11 M or lower for all three monoclonal antibodies. This technique provides a rapid route to antibody affinity maturation.
doi:10.1093/protein/gzq001
PMCID: PMC2841544  PMID: 20156888
antibody engineering; botulinum neurotoxin; FACS; molecular evolution; yeast mating
14.  DeStripe: frequency-based algorithm for removing stripe noises from AFM images 
Background
Atomic force microscopy (AFM) is a relatively recently developed technique that shows a promising impact in the field of structural biology and biophysics. It has been used to image the molecular surface of membrane proteins at a lateral resolution of one nanometer or less. An immediate obstacle of characterizing surface features in AFM images is stripe noise. To better interpret structures at a sub-domain level, pre-processing of AFM images for removing stripe noises is necessary. Noise removal can be performed in either spatial or frequency domain. However, denoising processing in the frequency domain is a better solution for preserving edge sharpness.
Results
We have developed a denoising protocol, called DeStripe, for AFM bio-molecular images that are contaminated with heavy and fine stripes. This program adopts a divide-and-conquer approach by dividing the Fourier spectrum of the image into central and off-center regions for noisy pixels detection and intensity restoration; it is also applicable to other images interfered with high-density stripes such as those acquired by the scanning electron microscope. The denoising effect brought by DeStripe provides better visualization for image objects without introducing additional artifacts into the restored image.
Conclusions
The DeStripe denoising effect on AFM images is illustrated in the present work. It allows extracting extended information from the topographic measurements and implicitly enhances the molecular features in the image. All the presented images were processed by DeStripe with the raw image as the only input without any requirement for other prior information. A web service, http://biodev.cea.fr/destripe, is available for running DeStripe.
doi:10.1186/1472-6807-11-7
PMCID: PMC3749244  PMID: 21281524
15.  White matter hyperintensities are related to physical disability and poor motor function 
Objective: To determine the impact of white matter hyperintensities (WMHs) on physical health and cognitive function in 60–64 year old individuals residing in the community.
Methods: A subsample of 478 persons aged 60–64 from a larger community sample underwent brain magnetic resonance imaging (MRI) scans. WMHs on T2 weighted FLAIR (fluid attenuated inversion recovery) MRI scans were assessed using an automated procedure. Subjects were assessed for global cognitive function, episodic memory, working memory (digit span), information processing speed (Symbol Digit Modalities Test; SDMT), fine motor dexterity (Purdue Pegboard), and grip strength, and completed the Physical Component Summary of the Short Form Health Survey (SF-12). Regression analyses were used to examine the effect of WMHs on physical and cognitive function.
Results: Deep and periventricular WMHs were present in all subjects, with women having slightly more lesions than men. WMHs were significantly associated with poorer reported physical health on the SF-12 scale, after adjusting for depression, cognitive function, and brain atrophy. WMHs were also related to lower scores on the Purdue Pegboard test, grip strength, choice reaction time, and SDMT, but not on tests of episodic memory, working memory, general intellectual function, and global cognitive function. On regression analyses, the Purdue Pegboard test and grip strength were related to physical disability.
Conclusion: WMHs are common, albeit mild, in middle adult life. They are associated with physical disability, possibly through reduced speed, fine motor coordination, and muscular strength. They are also related to slowed information processing speed but not other cognitive functions.
doi:10.1136/jnnp.2004.042945
PMCID: PMC1739526  PMID: 15716527
16.  Longest held occupation in a lifetime and risk of disability in activities of daily living 
OBJECTIVES—To examine the association between the longest held occupation in a lifetime and risk of disability in activities of daily living (ADL) among elderly people (65 years and older) in northern Taiwan.
METHODS—A case-control design was used nested within two cohorts of a total of 2198 elderly people who had been followed up either between 1993 and 1997 or between 1996 and 1997. Cases were 360 elderly people with ADL disability within the study period. For each case, two sex matched controls were randomly sampled from the pool of elderly people free from ADL disability. Occupational data were collected through interviews conducted in 1997. Performed job contents were classified into occupational categories and occupation based social classes. Unconditional logistic regression techniques were used to estimate relative risk and 95% confidence intervals (95% CIs) of ADL disability.
RESULTS—Compared with people who were former legislators, government administrators, or business executives and managers, workers in agriculture, animal husbandry, forestry, or fishing (odds ratio (OR) 1.9, 95% CI 1.1 to 3.5) and workers in craft and related trades (OR 1.9, 95% CI 1.1 to 3.4) had significantly increased risks of subsequent ADL disability. Differential risks of ADL disability were found across social classes, with a significant dose-response trend in which unskilled blue collar workers had an 1.8 times higher risk of ADL disability than higher social classes of white collar workers.
CONCLUSIONS—After adjustment for education, there was still an inverse relation between risk of ADL disability and social class. Although total control for all the known risk factors for ADL disability among elderly people was impossible, the results tend to suggest a potential for an effect of longest held occupation in a lifetime on risk of ADL disability.


Keywords: activity of daily living; occupation; socioeconomic status
doi:10.1136/oem.57.8.550
PMCID: PMC1739999  PMID: 10896962
17.  Patterns of infection and day care utilization and risk of childhood acute lymphoblastic leukaemia 
British Journal of Cancer  1999;82(1):234-240.
To investigate if decreased exposure to common childhood infections is associated with risk of childhood acute lymphoblastic leukaemia (ALL) we conducted a case–control study of 1842 newly diagnosed and immunophenotypically defined cases of ALL under age 15, and 1986 matched controls in the US. Data regarding day care, sibship size and common childhood infections were obtained through parental interviews. Data were analysed stratified by leukaemia lineage and separately for ‘common’ childhood ALL (age 2–5 years, CD19, CD10-positive). Neither attendance at day care nor time at day care was associated with risk of ALL overall or ‘common’ ALL. Ear infections during infancy were less common among cases, with odds ratios of 0.86, 0.83, 0.71 and 0.69 for 1, 2–4, 5+ episodes, and continuous infections respectively (trend P = 0.026). No effect of sibship size or birth interval was seen. With one exception (ear infections), these data do not support the hypothesis that a decrease in the occurrence of common childhood infection increases risk of ALL. © 2000 Cancer Research Campaign
doi:10.1054/bjoc.1999.0905
PMCID: PMC2363184  PMID: 10638995
childhood acute lymphoblastic leukaemia; infections; day care
19.  Trends and variations in length of hospital stay for childbirth in Canada 
BACKGROUND: Early discharge after childbirth is widely reported. In this study the authors examined trends in maternal length of hospital stay in Canada from fiscal year 1984-85 through fiscal year 1994-95. They also examined variations in length of stay in 1994-95 in most of the Canadian provinces and the territories. METHODS: Epidemiologic analyses of the temporal and geographic variations in maternal length of hospital stay in Canada from 1984-85 to 1994-95 (even years only), based on hospital discharge data collected by the Canadian Institute for Health Information, with a total of 1,456,800 women for the 6 study years. RESULTS: Mean length of hospital stay decreased during the decade, from 5.3 days in 1984-85 to 3.0 days in 1994-95, with similar trends for both cesarean and vaginal delivery. The decrease resulted from both increasing rates of short stay (less than 2 days) and decreasing rates of long stay (more than 4 days). Substantial temporal and interprovincial variations in several medical and obstetric complications were also observed but did not explain the corresponding variations in length of stay. The reduction in length of hospital stay was not restricted to uncomplicated cases: there was an equivalent decrease in cases with complications. In 1994-95 the average length of hospital stay in Alberta was 2.6 days, 0.3 to 1.7 days shorter than in the other provinces and the territories. INTERPRETATION: Length of hospital stay for childbirth has decreased substantially in Canada in recent years, but there remain important interprovincial variations. These trends and variations are not likely due to changes or differences in patient-specific factors.
PMCID: PMC1229182  PMID: 9559012
20.  Hospital volume, calendar age, and short term outcomes in patients undergoing repair of abdominal aortic aneurysms: the Ontario experience, 1988-92. 
OBJECTIVE: To determine, for abdominal aortic aneurysm surgery, whether a previously reported relationship between hospital case volume and mortality rate was observed in Ontario hospitals and to assess the potential impact of age on the mortality rate for elective surgery. DESIGN: Population based observational study using administrative data. SETTING: All Ontario hospitals where repair of abdominal aortic aneurysm as a primary procedure was performed during 1988-92. PATIENTS: These comprised 5492 patients with unruptured abdominal aortic aneurysms and 1203 patients with ruptured abdominal aortic aneurysms admitted to hospital between 1988-92 for repair of abdominal aortic aneurysm as a primary procedure. MAIN OUTCOMES: In-hospital death and length of in-hospital stay. RESULTS: The case fatality rate was 3.8% for unruptured abdominal aortic aneurysms and 40.0% for ruptured abdominal aortic aneurysms. For unruptured cases, after adjustment for patient and hospital covariates, each 10 case per year increase in hospital volume was related to a 6% reduction in relative odds of death (odds ratio (OR) 0.94, 95% confidence intervals 0.88, 0.99) and 0.29 days reduction (95% CI -0.22, -0.35) in postoperative in-hospital stay. Female sex (OR 1.53, 95% CI 1.08, 2.18) and transfer from another acute care hospital (OR 4.37, 95% CI 2.62, 7.29) were associated with increased case fatality rates among patients in the unruptured category. For ruptured cases, neither the case fatality rate nor postoperative in-hospital stay were significantly related to hospital volume. The case fatality rates increased linearly and substantially with advancing age both for unruptured and ruptured aneurysms, and the excess risk of postoperative death in ruptured as compared to unruptured aneurysms was substantially higher in older patients. CONCLUSION: The relationship between hospital volume and mortality or morbidity was very modest and observed only for elective surgery. Case fatality rates in patients with ruptured abdominal aortic aneurysms remained 10 times higher than for patients with unruptured abdominal aortic aneurysms, despite improvements in overall mortality in comparison to previously published data. More effective detection of aneurysms, including elective repair for those once considered "high risk" older patients, might further reduce the toll from ruptured aortic aneurysms.
PMCID: PMC1060254  PMID: 8762390
21.  Favorable left ventricular remodeling following large myocardial infarction by exercise training. Effect on ventricular morphology and gene expression. 
Journal of Clinical Investigation  1995;96(2):858-866.
Continued adverse remodeling of myocardium after infarction may lead to progressive ventricular dilation and heart failure. We tested the hypothesis that exercise training in a healed myocardial infarction-dysfunction rat model can favorably modify the adverse effects of ventricular remodeling including attenuation of abnormal myosin gene expression. Sprague-Dawley rats were subjected to either proximal LAD ligation or sham operation. At 5 wk after the operation, animals were randomly assigned to sedentary conditions or 6 wk of graduated swim training, creating four experimental groups: infarct sedentary (IS), infarct exercise (IE), sham sedentary (SS), and sham exercise (SE). At 11 wk all rats were sacrificed and analyzed. Compared to sedentary infarct controls, exercise training attenuated left ventricular (LV) dilation and allowed more hypertrophy of the non infarct wall. The exercise-trained hearts also showed a reduction in the estimated peak wall tension. Northern blot analysis showed an increase in beta-myosin heavy chain expression in the hearts of the sedentary infarction group soon after infarction when compared to sham controls. However, with exercise training, there was a significant attenuation of the beta-myosin heavy chain expression in the myocardium. Exercise training in a model of left ventricular dysfunction after healed myocardial infarction can improve the adverse remodeling process by attenuating ventricular dilation and reducing wall tension. The abnormal beta-myosin expression was also attenuated in the exercise trained group. This is evidence that abnormal gene expression following severe myocardial infarction dysfunction can be favorably modified by an intervention.
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PMCID: PMC185272  PMID: 7635980
22.  Diagnostic accuracy and short-term surgical outcomes in cases of suspected acute appendicitis. 
OBJECTIVE: To test the hypothesis that, with modern diagnostic methods and antibiotics, more conservative use of surgery in cases of suspected appendicitis would not result in increased rates of short-term complications in confirmed cases. DESIGN: Population-based observational study using administrative data. SETTING: All Ontario hospitals in which primary appendectomy was performed from Apr. 1, 1981, to Mar. 31, 1992. PATIENTS: All 126,815 patients admitted to hospital for a primary appendectomy during the study period. OUTCOME MEASURES: Diagnostic accuracy rate (acute appendicitis as the primary diagnosis), perforation rate, in-hospital death rate and length of stay. RESULTS: The diagnostic accuracy rate among the male patients was stable throughout the decade; among the female patients it rose significantly, from 71.7% in 1981 to 75.3% in 1991 (p < 0.01). The perforation rates increased significantly among both the female and male patients (p < 0.01), whereas the mean length of stay decreased (p < 0.05). Despite sex-related differences in the accuracy rates, the male and female patients had similar in-hospital death rates and mean lengths of stay. The institutional diagnostic accuracy rates, as determined from data for 1989-90 to 1991-92, ranged from 50.0% to 96.7%. Multivariate analyses of 27,189 confirmed cases of appendicitis at 175 hospitals revealed that perforation was a strong predictor of in-hospital death (odds ratio [OR] 2.46, 95% confidence interval [CI] 1.24 to 4.88), but comorbidity was the strongest predictor (OR 11.50, 95% CI 5.96 to 22.10). For each 10% increase in the diagnostic accuracy rate, the perforation rate increased 14% (OR 1.14, 95% CI 1.10 to 1.19), but the accuracy rate was not significantly related to the in-hospital death rate or the length of stay. CONCLUSION: A higher diagnostic accuracy rate is associated with more perforated appendixes. Although perforation itself leads to adverse outcomes, a higher accuracy rate does not. This suggests that hospitals with higher accuracy rates incur more perforations, but, with close observation, timely laparotomy and the use of modern antibiotics, these patients have favourable outcomes. This contrasts with adverse effects of perforation among patients at high risk for perforation (especially very young children and elderly people) in centres at all accuracy levels. The variation in hospitals' diagnostic accuracy rates suggests that some proportion of appendectomies could be safely avoided.
PMCID: PMC1337858  PMID: 7743448
23.  A refractory phase in cyclic AMP-responsive transcription requires down regulation of protein kinase A. 
Molecular and Cellular Biology  1995;15(3):1826-1832.
Cyclic AMP (cAMP) stimulates the expression of numerous genes through the protein kinase A (PK-A)-mediated phosphorylation of the nuclear factor CREB at Ser-133 (G. A. Gonzalez and M. R. Montminy, Cell 59:675-680, 1989). Like other signal transduction pathways, cAMP induces gene expression with burst-attenuation kinetics; cAMP-dependent transcription and CREB phosphorylation peak within 30 min and decline steadily over the next 4 to 6 h via the protein phosphatase 1-mediated dephosphorylation of CREB (M. Hagiwara, A. Alberts, P. Brindle, J. Meinkoth, J. Feramisco, T. Deng, M. Karin, S. Shenolikar, and M. Montminy, Cell 70:105-113, 1992). Here we characterize a third phase in cAMP-responsive transcription--a refractory period during which hormone-treated cells become transcriptionally unresponsive to subsequent stimulation by cAMP. This refractory period begins 6 to 8 h after stimulation and lasts 3 to 5 days after the removal of hormone. In contrast to the earlier attenuation phase, transcription of cAMP-responsive genes during the refractory period is not restored by inhibitors of protein phosphatase 1 activity. Rather, the establishment and maintenance of this phase rely on a marked reduction in PK-A catalytic subunit expression at the translational level. As overexpression of C-subunit protein can reactive transcription of cAMP-responsive genes during the refractory period, our results suggest that hormone-responsive cells may stimulate, attenuate, and then silence signal-dependent genes through distinct regulatory mechanisms.
PMCID: PMC230407  PMID: 7862172
24.  Inhibition of thyrotropin-stimulated DNA synthesis by microinjection of inhibitors of cellular Ras and cyclic AMP-dependent protein kinase. 
Molecular and Cellular Biology  1993;13(8):4477-4484.
Microinjection of a dominant interfering mutant of Ras (N17 Ras) caused a significant reduction in thyrotropin (thyroid-stimulating hormone [TSH])-stimulated DNA synthesis in rat thyroid cells. A similar reduction was observed following injection of the heat-stable protein kinase inhibitor of the cyclic AMP-dependent protein kinase. Coinjection of both inhibitors almost completely abolished TSH-induced DNA synthesis. In contrast to TSH, overexpression of cellular Ras protein did not stimulate the expression of a cyclic AMP response element-regulated reporter gene. Similarly, injection of N17 Ras had no effect on TSH-stimulated reporter gene expression. Moreover, overexpression of cellular Ras protein stimulated similar levels of DNA synthesis in the presence or absence of the heat-stable protein kinase inhibitor. Together, these results suggest that in Wistar rat thyroid cells, a full mitogenic response to TSH requires both Ras and cyclic APK-dependent protein kinase.
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PMCID: PMC360056  PMID: 8336696
25.  Movement of the free catalytic subunit of cAMP-dependent protein kinase into and out of the nucleus can be explained by diffusion. 
Molecular Biology of the Cell  1993;4(10):993-1002.
The catalytic (C) subunit of cyclic AMP (cAMP) dependent protein kinase (PKA) has previously been shown to enter and exit the nucleus of cells when intracellular cAMP is raised and lowered, respectively. To determine the mechanism of nuclear translocation, fluorescently labeled C subunit was injected into living REF52 fibroblasts either as free C subunit or in the form of holoenzyme (PKA) in which the catalytic and regulatory subunits were labeled with fluorescein and rhodamine, respectively. Quantification of nuclear and cytoplasmic fluorescence intensities revealed that free C subunit nuclear accumulation was most similar to that of macromolecules that diffuse into the nucleus. A glutathione S-transferase-C subunit fusion protein did not enter the nucleus following cytoplasmic microinjection. Puncturing the nuclear membrane did not decrease the nuclear concentration of C subunit, and C subunit entry into the nucleus did not appear to be saturable. Cooling or depleting cells of energy failed to block movement of C subunit into the nucleus. Photobleaching experiments showed that even after reaching equilibrium at high [cAMP], individual molecules of C subunit continued to leave the nucleus at approximately the same rate that they had originally entered. These results indicate that diffusion is sufficient to explain most aspects of C subunit subcellular localization.
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PMCID: PMC275733  PMID: 8298196

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