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1.  Cognitive and psychomotor responses to high-altitude exposure in sea level and high-altitude residents of Ecuador 
Background
High-altitude inhabitants have cardiovascular and respiratory adaptations that are advantageous for high-altitude living, but they may have impaired cognitive function. This study evaluated the influence of altitude of residence on cognitive and psychomotor function upon acute exposure to very high altitude.
Findings
Ecuadorians (31 residing at 0–1,500 m [LOW], 78 from 1,501–3,000 m [MOD], and 23 living >3,000 m [HIGH]) were tested upon their arrival to a hut at 4,860 m on Mount Chimborazo. Cognitive/psychomotor measurements included a go-no-go test (responding to a non-visual stimulus), a verbal fluency test (verbalizing a series of words specific to a particular category), and a hand movement test (rapidly repeating a series of hand positions). Mean differences between the three altitude groups on these cognitive/psychomotor tests were evaluated with one-way ANOVA. There were no significant differences (p = 0.168) between LOW, MOD, and HIGH for the verbal fluency test. However, the go-no-go test was significantly lower (p < 0.001) in the HIGH group (8.8 ± 1.40 correct responses) than the LOW (9.8 ± 0.61) or MOD (9.8 ± 0.55) groups, and both MOD (97.9 ± 31.2) and HIGH (83.5 ± 26.7) groups completed fewer correct hand movements than the LOW (136.6 ± 37.9) subjects (p < 0.001).
Conclusions
Based on this field study, high-altitude residents appear to have some impaired cognitive function suggesting the possibility of maladaptation to long-term exposure to hypobaric hypoxia.
doi:10.1186/s40101-014-0039-x
PMCID: PMC4320830  PMID: 25649647
Altitude; Adaptation; High-altitude natives; Cognitive function
2.  Robotic or open radical prostatectomy after previous open surgery in the pelvic region 
Korean Journal of Urology  2015;56(2):131-137.
Purpose
We sought to evaluate the feasibility and safety of open or robotic radical prostatectomy (RP) after rectum, sigmoid, or colon surgery.
Materials and Methods
Sixty-four patients with a median age of 65 years (range, 46-73 years) who underwent RP after previous pelvic surgery were included. Twenty-four patients (38%) underwent robotic RP and 40 patients (62%) underwent open RP. Bilateral lymph node dissection and nerve preservation were performed in 50 patients (78%) and 35 patients (55%), respectively. Variables evaluated included demographic characteristics, perioperative complications, and functional and oncological outcomes. The median hospitalization and follow-up periods were 2 days (range, 1-12 days) and 21 months (range, 1-108 months), respectively.
Results
No conversions from robotic to open surgery were performed and there were no intraoperative complications. Surgical margins were positive in 13 patients (20%), seminal vesicle involvement was detected in 6 patients (9%), and lymph node involvement was found in 2 patients (3%). Postoperative complications included lymphocele in 1 patient, urethral stricture in 1 patient, and bowel obstruction and persistent bladder leakage in 2 patients. Eighty-eight percent of the patients were continent at 7 months and 80% of patients were able to achieve erection with or without medical aid.
Conclusions
Open or robotic RP can be done safely and effectively in patients who have previously undergone pelvic surgery. Although prior pelvic surgery of the large intestine was associated with increased morbidity, it should not be considered a contraindication for robotic or open RP.
doi:10.4111/kju.2015.56.2.131
PMCID: PMC4325117
Prostate; Prostate neoplasms; Prostatectomy; Robotics; Surgery
3.  YAP Regulates Cell Proliferation, Migration, and Steroidogenesis in Adult Granulosa Cell Tumors 
Endocrine-related cancer  2014;21(2):297-310.
The Hippo signaling pathway has been implicated as a conserved regulator of organ size in both Drosophila and mammals. Yes associated protein (YAP), the central component of the Hippo signaling cascade, functions as an oncogene in several malignancies. Ovarian granulosa cell tumors (GCT) are characterized by enlargement of ovary, excess production of estrogen, high frequency of recurrence and potential of malignancy and metastasis. Whether the Hippo pathway plays a role in the pathogenesis of GCT is unknown. This study was conducted to examine the expression of YAP in human adult GCTs and to determine the role of YAP in the proliferation and steroidogenesis of GCT cells. Compared with age-matched normal human ovaries, GCT tissues exhibited higher levels of YAP expression. YAP protein was predominantly expressed in the nucleus of tumor cells, whereas the non-tumor ovarian stromal cells expressed very low levels of YAP. YAP was also expressed in cultured primary human granulosa cells and in KGN and COV434 GCT cell lines. siRNA-mediated knockdown of YAP in KGN cells resulted in a significant reduction in cell proliferation (P<0.001). Conversely, overexpression of wild-type YAP or a constitutively active YAP mutant resulted in a significant increase in KGN cell proliferation and migration. Moreover, YAP knockdown reduced FSH-induced aromatase (CYP19A1) protein expression and estrogen production in KGN cells. These results demonstrate that YAP plays an important role in regulating GCT cell proliferation, migration and steroidogenesis. Targeting the Hippo/YAP pathway may provide a novel therapeutic approach for GCT.
doi:10.1530/ERC-13-0339
PMCID: PMC4222524  PMID: 24389730
Hippo/YAP pathway; granulosa cell tumor; cell proliferation; steroidogenesis; migration
4.  Efficacy and safety of pateclizumab (anti-lymphotoxin-α) compared to adalimumab in rheumatoid arthritis: a head-to-head phase 2 randomized controlled study (The ALTARA Study) 
Introduction
Tumor necrosis factor (TNF) and, possibly, lymphotoxin alpha (LTα) signaling contribute to inflammation and rheumatoid arthritis (RA) pathogenesis. Pateclizumab (anti-lymphotoxin- alpha; MLTA3698A) is a humanized monoclonal antibody that blocks and depletes anti-LTα. This phase 2, randomized, head-to-head, active- and placebo-controlled trial examined the safety and efficacy of pateclizumab compared to adalimumab in RA patients with an inadequate response to disease-modifying antirheumatic drugs (DMARD-IR).
Methods
Patients (n = 214) with active RA (≥6 swollen and tender joints, C-reactive protein ≥10 mg/L) on oral DMARDs were randomized (2:2:1) to receive pateclizumab 360 mg, adalimumab 40 mg, or placebo subcutaneously every 2 weeks. The primary endpoint, 4-variable, 28-joint disease activity score erythrocyte sedimentation rate (DAS28(4)-ESR) response, was evaluated at 12 weeks using an analysis of covariance (ANCOVA) model with adjustments for concomitant DMARD use and geographic region. Secondary efficacy endpoints included American College of Rheumatology (ACR) 20, ACR50, and ACR70 responses at Day 85. Pharmacokinetics, pharmacodynamics, and immunogenicity of pateclizumab were assessed.
Results
Pateclizumab reduced the DAS28(4)-ESR response (−1.89) at 12 weeks, however, this did not reach statistical significance compared to placebo (−1.54), while adalimumab (−2.52) differed significantly from both placebo and pateclizumab. Pateclizumab 12-week ACR20, ACR50 and ACR70 response rates (64%, 33%, and 14%) suggested clinical activity but were not statistically significant compared to placebo rates (46%, 24%, and 8%, respectively). CXCL13 serum levels decreased significantly following pateclizumab and adalimumab administration, demonstrating pharmacological target engagement by both drugs. Overall, adverse events (AEs) were comparable among all cohorts. Infections were the most common AE, occurring with comparable frequency in all groups. Serious AEs occurred in 0% of pateclizumab, 5.9% of adalimumab, and 2.3% of placebo patients, with serious infection in 2.3% of adalimumab patients and none in pateclizumab and placebo patients.
Conclusions
Pateclizumab had a good safety profile in patients inadequately responsive to DMARDs, but no statistically significant improvement in RA signs and symptoms after 12 weeks of treatment. Adalimumab demonstrated efficacy and safety comparable to published results in this head-to-head comparison in DMARD-IR RA patients.
Trial registration
ClinicalTrials.gov NCT01225393, Registered 18 October 2010.
doi:10.1186/s13075-014-0467-3
PMCID: PMC4243296  PMID: 25359150
5.  Prostate-specific antigen is unlikely to be a suitable biomarker of semen exposure from recent unprotected receptive anal intercourse in men who have sex with men 
Sexually transmitted diseases  2014;41(6):377-379.
A biomarker of unprotected receptive anal intercourse (RAI) could improve validity of sexual behavior measurement. We quantified prostate-specific antigen (PSA) from rectal swabs from men who have sex with men (MSM). One swab was PSA-positive. Using current methods, PSA is an inadequate biomarker of recent unprotected RAI in MSM.
doi:10.1097/OLQ.0000000000000129
PMCID: PMC4206185  PMID: 24825334
MSM; Receptive anal intercourse; Prostate specific antigen (PSA); Measurement; Validity; biomarker
6.  Rheumatoid Arthritis and Cardiovascular Disease 
American heart journal  2013;166(4):622-628.e1.
Background
Rheumatic disease and heart disease share common underpinnings involving inflammation. The high levels of inflammation that characterize rheumatic diseases provide a “natural experiment” to help elucidate the mechanisms by which inflammation accelerates heart disease. Rheumatoid arthritis (RA) is the most common of the rheumatic diseases and has the best studied relationships with heart disease.
Methods
Review of current literature on heart disease and rheumatoid arthritis
Results
Patients with RA have an increased risk of developing heart disease that is not fully explained by traditional cardiovascular risk factors. Therapies used to treat RA may also affect the development of heart disease; by suppressing inflammation, they may also reduce the risk of heart disease. However, their other effects, as in the case of steroids, may increase heart disease risk.
Conclusions
Investigations of the innate and adaptive immune responses occurring in RA may delineate novel mechanisms in the pathogenesis of heart disease, and help identify novel therapeutic targets for the prevention and treatment of heart disease.
doi:10.1016/j.ahj.2013.07.010
PMCID: PMC3890244  PMID: 24093840
7.  Accelerated Aging Influences Cardiovascular Disease Risk in Rheumatoid Arthritis 
Arthritis and rheumatism  2013;65(10):2562-2566.
OBJECTIVE
To determine whether the impact of aging on cardiovascular disease (CVD) risk in the general population (as estimated by the Framingham risk score [FRS]) differs in patients with rheumatoid arthritis (RA).
METHODS
A population-based inception cohort of Olmsted County, Minnesota residents aged ≥30 years who fulfilled 1987 ACR criteria for RA in 1988–2008 was assembled and followed until death, migration, or 7-1-2012. Data on CVD events were collected by medical record review. The 10-year FRS for CVD was calculated. Cox models adjusted for FRS were used to examine the influence of age on CVD risk.
RESULTS
The study included 563 patients with RA without prior CVD (mean age: 55 years, 72% women; 69% seropositive [i.e., rheumatoid factor and/or anti-citrullinated protein antibody positive]). During a mean follow-up of 8.2 years, 98 patients developed CVD (74 seropositive and 24 seronegative), but FRS predicted only 59.7 events (35.4 seropositive and 24.3 seronegative). The gap between observed and predicted CVD risk increased exponentially across age, and the age effect on CVD risk in seropositive RA was nearly double its effect in the general population with additional log(age) coefficients of 2.91 for women (p=0.002) and 2.06 for men (p=0.027).
CONCLUSION
Age exerts an exponentially increasing effect on CVD risk in seropositive RA, but no increased effect among seronegative patients. The causes of accelerated aging in patients with seropositive RA deserve further investigation.
doi:10.1002/art.38071
PMCID: PMC3966134  PMID: 23818136
accelerated aging; rheumatoid arthritis; cardiovascular disease
10.  Longitudinal Performance of a Surgically Implanted Neuroprosthesis for Lower Extremity Exercise, Standing, and Transfers after Spinal Cord Injury 
Objective
To investigate the longitudinal performance of a surgically implanted neuroprosthesis for lower extremity exercise, standing, and transfers after spinal cord injury.
Design
Case series.
Setting
Research or outpatient physical therapy departments of four academic hospitals.
Participants
15 subjects with thoracic or low-cervical level spinal cord injuries who had received the 8-channel neuroprosthesis for exercise and standing.
Interventions
After completing rehabilitation with the device, the subjects were discharged to unrestricted home use of the system. A series of assessments were performed before discharge and at a follow-up appointment approximately one year later.
Main Outcome Measure(s)
Neuroprosthesis usage, maximum standing time, body weight support, knee strength, knee fatigue index, electrode stability, and component survivability.
Results
Levels of maximum standing time, body weight support, knee strength, and knee fatigue index were not statistically different from discharge to follow-up (p > 0.05). Additionally, neuroprosthesis usage was consistent with subjects choosing to use the system on approximately half of the days during each monitoring period. Although the number of hours using the neuroprosthesis remained constant, subjects shifted their usage to more functional standing versus more maintenance exercise, suggesting that the subjects incorporated the neuroprosthesis into their lives. Safety and reliability of the system were demonstrated by electrode stability and a high component survivability rate (>90%).
Conclusions
This group of 15 subjects is the largest cohort of implanted lower extremity neurorprosthetic exercise and standing system users. The safety and efficiency data from this group, and acceptance of the neuroprosthesis as demonstrated by continued usage, indicate that future efforts towards commercialization of a similar device may be warranted.
doi:10.1016/j.apmr.2012.01.001
PMCID: PMC4111081  PMID: 22541312
Electrical Stimulation; Exercise; Neural Prostheses; Spinal Cord Injuries; Weight-Bearing
11.  Rheumatoid Arthritis is Associated with Left Ventricular Concentric Remodeling: Results of a Population-based Cross-sectional Study 
Arthritis and rheumatism  2013;65(7):1713-1718.
Objective
To study left ventricular (LV) geometry in patients with rheumatoid arthritis (RA) who have no heart failure (HF) versus subjects without either RA or HF, and to determine the impact of RA on LV remodeling.
Methods
A cross-sectional, community-based study was conducted among adult (≥50 years) RA patients and age- and sex-matched non-RA subjects without a history of HF. All participants underwent a standard 2D/Doppler echocardiography. LV geometry was classified into four categories based on relative wall thickness and sex-specific cut-offs for LV mass index: concentric remodeling, concentric hypertrophy, eccentric hypertrophy, or normal geometry.
Results
The study included 200 RA patients and 600 matched non-RA subjects (mean age 65; 74% female in both cohorts). RA patients were significantly more likely to have abnormal LV geometry than non-RA subjects (odds ratio [OR] 1.44; 95% confidence interval [CI] 1.03, 2.00), adjusting for cardiovascular risk factors and comorbidities. Among those with abnormal LV geometry, RA patients had significantly increased odds of concentric LV remodeling (OR 4.73; 95% CI 2.85, 7.83). In linear regression analyses, LV mass index appeared to be lower in RA patients currently using corticosteroids (Beta +/− standard error: −0.082 +/− 0.027; p=0.002), adjusting for cardiovascular risk factors and comorbidities.
Conclusion
RA was strongly associated with abnormal LV remodeling, particularly, with concentric LV remodeling, among patients without HF. This association was significant beyond adjustment for cardiovascular risk factors and comorbidities. RA disease related factors may promote changes in LV geometry. The biological mechanisms underlying LV remodeling warrant further investigation.
doi:10.1002/art.37949
PMCID: PMC3914147  PMID: 23553738
rheumatoid arthritis; left ventricular remodeling; risk factors
12.  Many young men with prostate-specific antigen (PSA) screen-detected prostate cancers may be candidates for active surveillance 
BJU international  2013;111(6):934-940.
SUMMARY
Objective
To identify a population of young men (aged < 55 years at diagnosis) with very-low-risk prostate cancer (stage cT1c, with prostate-specific antigen [PSA] density of < 0.15 ng/mL/g, Gleason score ≤ 6, and ≤ 2 positive biopsy cores with < 50% tumour involvement) that may be candidates for active surveillance (AS).
Patients and methods
We queried a Department of Defense tumor registry and hard-copy records for servicemen diagnosed with prostate cancer from 1987 to 2010.
Statistical analyses were undertaken using Fisher's exact and chi-square testing.
Results
From 1987–1991 and 2007–2010, PSA screen-detected tumours diagnosed in men aged ≤ 55 years > 30-fold.
Data for a subset of men (174) with PSA screen-detected cancer were evaluable for disease risk assessment.
Of the 174 men with screen-detected disease, 81 (47%) had very-low-risk disease.
Of that group, 96% (78/81) selected treatment and, of 57 men undergoing radical prostatectomy (RP), the tumours of 49 (86%) carried favourable pathology (organ confined, < 10% gland involvement, Gleason ≤ 6).
Conclusions
Nearly half of young men with PSA screen-detected prostate cancer are AS candidates but the overwhelming majority seek treatment.
Considering that many tumours show favourable pathology at RP, there is a possibility that these patients may benefit from AS management.
doi:10.1111/j.1464-410X.2012.11768.x
PMCID: PMC3637421  PMID: 23350937
very-low-risk prostatic neoplasms; active surveillance; risk assessment; overtreatment
13.  EPIGENETIC MODIFICATIONS OF GABAERGIC INTERNEURONS ARE ASSOCIATED WITH THE SCHIZOPHRENIA-LIKE PHENOTYPE INDUCED BY PRENATAL STRESS IN MICE 
Neuropharmacology  2012;68:184-194.
Human studies suggest that a variety of prenatal stressors are related to high risk for cognitive and behavioral abnormalities associated with psychiatric illness (Markham and Koenig, 2011). Recently, a down-regulation in the expression of GABAergic genes (i.e., glutamic acid decarboxylase 67 and reelin) associated with DNA methyltransferase (DNMT) overexpression in GABAergic neurons has been regarded as a characteristic phenotypic component of the neuropathology of psychotic disorders (Guidotti et al., 2011).
Here, we characterized mice exposed to prenatal restraint stress (PRS) in order to study neurochemical and behavioral abnormalities related to development of schizophrenia in the adult. Offspring born from non-stressed mothers (control mice) showed high levels of DNMT1 and 3a mRNA expression in the frontal cortex at birth, but these levels progressively decreased at post-natal days (PND) 7, 14, and 60. Offspring born from stressed mothers (PRS mice) showed increased levels of DNMTs compared to controls at all time-points studied including at birth and at PND 60. Using GAD67-GFP transgenic mice, we established that, in both control and PRS mice, high levels of DNMT1 and 3a were preferentially expressed in GABAergic neurons of frontal cortex and hippocampus. Importantly, the overexpression of DNMT in GABAergic neurons was associated with a decrease in reelin and GAD67 expression in PRS mice in early and adult life. PRS mice also showed an increased binding of DNMT1 and MeCP2, and an increase in 5-methylcytosine and 5-hydroxymethylcytosine in specific CpG-rich regions of the reelin and GAD67 promoters. Thus, the epigenetic changes in PRS mice are similar to changes observed in the post-mortem brains of psychiatric patients. Behaviorally, adult PRS mice showed hyperactivity and deficits in social interaction, prepulse inhibition, and fear conditioning that were corrected by administration of valproic acid (a histone deacetylase inhibitor) or clozapine (an atypical antipsychotic with DNA-demethylation activity). Taken together, these data show that prenatal stress in mice induces abnormalities in the DNA methylation network and in behaviors indicative of a schizophrenia-like phenotype. Thus, PRS mice may be a valid model for the investigation of new drugs for schizophrenia treatment targeting DNA methylation.
doi:10.1016/j.neuropharm.2012.04.013
PMCID: PMC3433586  PMID: 22564440
schizophrenia; DNA methyltransferase; prenatal stress; epigenetic; antipsychotic; valproic acid
14.  Learning Curve Assessment of Robot-Assisted Radical Prostatectomy Compared with Open-Surgery Controls from the Premier Perspective Database 
Journal of Endourology  2014;28(5):560-566.
Abstract
Introduction: The primary aims of this study were to assess the learning curve effect of robot-assisted radical prostatectomy (RARP) in a large administrative database consisting of multiple U.S. hospitals and surgeons, and to compare the results of RARP with open radical prostatectomy (ORP) from the same settings.
Materials and Methods: The patient population of study was from the Premier Perspective Database (Premier, Inc., Charlotte, NC) and consisted of 71,312 radical prostatectomies performed at more than 300 U.S. hospitals by up to 3739 surgeons by open or robotic techniques from 2004 to 2010. The key endpoints were surgery time, inpatient length of stay, and overall complications. We compared open versus robotic, results by year of procedures, results by case volume of specific surgeons, and results of open surgery in hospitals with and without a robotic system.
Results: The mean surgery time was longer for RARP (4.4 hours, standard deviation [SD] 1.7) compared with ORP (3.4 hours, SD 1.5) in the same hospitals (p<0.0001). Inpatient stay was shorter for RARP (2.2 days, SD 1.9) compared with ORP (3.2 days, SD 2.7) in the same hospitals (p<0.0001). The overall complications were less for RARP (10.6%) compared with ORP (15.8%) in the same hospitals, as were transfusion rates. ORP results in hospitals without a robot were not better than ORP with a robot, and pretreatment co-morbidity profiles were similar in all cohorts. Trending of results by year of procedure showed no differences in the three cohorts, but trending of RARP results by surgeon experience showed improvements in surgery time, hospital stay, conversion rates, and complication rates.
Conclusions: During the initial 7 years of RARP development, outcomes showed decreased hospital stay, complications, and transfusion rates. Learning curve trends for RARP were evident for these endpoints when grouped by surgeon experience, but not by year of surgery.
doi:10.1089/end.2013.0534
PMCID: PMC3995359  PMID: 24350787
15.  FUNCTIONAL LIMITATIONS DUE TO AXIAL AND PERIPHERAL JOINT IMPAIRMENTS IN PATIENTS WITH ANKYLOSING SPONDYLITIS: ARE FOCUSED MEASURES MORE INFORMATIVE? 
Arthritis care & research  2013;65(4):607-614.
Objective
Functional limitations in ankylosing spondylitis (AS) may be due to peripheral joint or axial involvement. To determine if the Bath AS Functional Index (BASFI), an axial-focused measure, can detect limitations related to peripheral joint involvement equally well as the Health Assessment Questionnaire modified for the Spondyloarthropathies (HAQ-S), a peripheral arthritis-focused measure, and vice versa, we compared associations of each questionnaire with spinal and hip range of motion, peripheral arthritis, and enthesitis in patients with AS.
Methods
We examined patients every 4 to 6 months in this prospective longitudinal study. We used mixed linear models to examine associations between ten physical examination measures and the BASFI and HAQ-S.
Results
We studied 411 patients for a median of 1.5 years (3 visits). In multivariate analyses, cervical rotation, chest expansion, lateral thoracolumbar flexion, hip motion, tender joint count, and tender enthesis count were equally strongly associated with the BASFI and HAQ-S. Peripheral joint swelling was more strongly associated with the HAQ-S. Individual items of the BASFI were more likely than items of the HAQ-S to be associated with unrelated physical exam measures (e.g. association between difficulty rising from a chair and cervical rotation), which may have diminished the axial/peripheral distinction for the BASFI.
Conclusions
The BASFI and HAQ-S had similar associations with impairments in axial measures, while the HAQ-S had stronger associations with the number of swollen peripheral joints. The HAQ-S should be considered for use in studies focused on spondyloarthritis with peripheral joint involvement.
doi:10.1002/acr.21878
PMCID: PMC3567248  PMID: 23097327
Ankylosing spondylitis; functional limitations; metrology
16.  Personality, Behavior and Environmental Features Associated with OXTR Genetic Variants in British Mothers 
PLoS ONE  2014;9(3):e90465.
Background
It is assumed that the oxytocin receptor gene (OXTR) is associated with factors that are related to features of reproduction as well as the currently emerging fields of mood and emotional response.
Methods
We analysed data from over 8000 mothers who participated in the Avon Longitudinal Study of Parents and Children (ALSPAC). We determined reproductive, emotional and personality differences related to the two SNPs rs53576 and rs2254298 of the oxytocin receptor gene to determine whether there was evidence in this population for: (i) associations with emotional and personality differences, and (ii) behavioural or environmental links with these SNPs using a hypothesis free approach with over 1000 types of exposure.
Results
Our analyses of 7723 women showed that there were no differences in 11 mood, social or relationship characteristics associated with the rs2254298, and just one with rs53576 (with emotional loneliness) – one statistically significant out of 22 tests is no more than would be expected by chance. There were no interactions with childhood abuse. Using a hypothesis-free approach we found few indicators of environmental or behavioural differences associated with rs2254298, but there was an excess of associations with eating habits with rs53576. The findings included an association with dieting to lose weight, and habits typical of bulimia for the women with GG. The nutrition of the women also showed negative associations of the GG genotype with 13 nutrients, including vitamins D, B12 and retinol, and intake of calcium, potassium and iodine.
Conclusions
We conclude that this large database of pregnant women was unable to provide confirmation of the types of personality associated with these two OXTR SNPs, but we have shown some evidence of eating differences in those with GG on rs53576. Confirmation of our hypothesis free associations using other data sets is important.
doi:10.1371/journal.pone.0090465
PMCID: PMC3951216  PMID: 24621820
17.  Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies 
Genome Biology  2014;15(3):R59.
Background
The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.
Results
We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.
Conclusions
In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.
doi:10.1186/gb-2014-15-3-r59
PMCID: PMC4053751  PMID: 24647006
18.  Sequence motifs associated with hepatotoxicity of locked nucleic acid—modified antisense oligonucleotides 
Nucleic Acids Research  2014;42(8):4882-4891.
Fully phosphorothioate antisense oligonucleotides (ASOs) with locked nucleic acids (LNAs) improve target affinity, RNase H activation and stability. LNA modified ASOs can cause hepatotoxicity, and this risk is currently not fully understood. In vitro cytotoxicity screens have not been reliable predictors of hepatic toxicity in non-clinical testing; however, mice are considered to be a sensitive test species. To better understand the relationship between nucleotide sequence and hepatotoxicity, a structure–toxicity analysis was performed using results from 2 week repeated-dose-tolerability studies in mice administered LNA-modified ASOs. ASOs targeting human Apolipoprotien C3 (Apoc3), CREB (cAMP Response Element Binding Protein) Regulated Transcription Coactivator 2 (Crtc2) or Glucocorticoid Receptor (GR, NR3C1) were classified based upon the presence or absence of hepatotoxicity in mice. From these data, a random-decision forest-classification model generated from nucleotide sequence descriptors identified two trinucleotide motifs (TCC and TGC) that were present only in hepatotoxic sequences. We found that motif containing sequences were more likely to bind to hepatocellular proteins in vitro and increased P53 and NRF2 stress pathway activity in vivo. These results suggest in silico approaches can be utilized to establish structure–toxicity relationships of LNA-modified ASOs and decrease the likelihood of hepatotoxicity in preclinical testing.
doi:10.1093/nar/gku142
PMCID: PMC4005641  PMID: 24550163
19.  REGIONAL RADIOGRAPHIC DAMAGE AND FUNCTIONAL LIMITATIONS IN PATIENTS WITH ANKYLOSING SPONDYLITIS: DIFFERENCES IN EARLY AND LATE DISEASE 
Arthritis care & research  2013;65(2):257-265.
Objective
Radiographic damage and functional limitations both increase with the duration of ankylosing spondylitis (AS). We examined whether radiographic damage contributed more to functional limitations in late AS than in early AS, and if the strength of association varied with the anatomic region of damage.
Methods
In this cross-sectional study of 801 patients with AS, we examined associations of the lumbar modified Stoke AS Spine Score (mSASSS), cervical mSASSS, lumbar posterior fusion, cervical posterior fusion, and hip arthritis with the Bath AS Functional Index (BASFI) and the Health Assessment Questionnaire (HAQ-S).
Results
Higher lumbar and cervical mSASSS were associated with more functional limitations, but there was an interaction between mSASSS and the duration of AS such that the strength of their association with functional limitations decreased with increasing duration of AS. Cervical posterior fusion was associated with worse functioning independent of mSASSS. Hip arthritis was significantly associated with functional limitations independent of measures of spinal damage. Among patients with AS ≥ 40 years, the number of comorbid conditions accounted for most of the variation in functioning. Results were similar for both the BASFI and HAQ-S.
Conclusions
Although both radiographic damage and functional limitations increase over time in AS, the relative contribution of radiographic damage to functional limitations is lower among patients with longstanding AS than early AS, suggesting patients may accommodate to limited flexibility. Damage in different skeletal regions impacts functioning over the duration of AS. Functional limitations due to comorbidity supervene in late AS.
doi:10.1002/acr.21821
PMCID: PMC3541454  PMID: 23042639
Ankylosing spondylitis; radiographic damage; functional limitations
20.  Cellular steatosis in ethanol oxidizing-HepG2 cells is partially controlled by the transcription factor, early growth response-1 
Recent studies have shown that the transcription factor early growth response-1 (Egr-1) regulates ethanol-induced fatty liver. However, the mechanism(s) through which ethanol oxidation controls Egr-1 is unknown. Here, using recombinant hepatoma (HepG2; VL-17A) cells that metabolize ethanol, we show that alcohol dehydrogenase catalysis of ethanol oxidation and subsequent acetaldehyde production controls Egr-1 expression. Further, the induction of Egr-1 enhances expression of other steatosis-related genes, resulting in triglyceride accumulation. Ethanol exposure increased Egr-1 promoter activity, messenger RNA and Egr-1 protein levels in VL-17A cells. Elevated Egr-1 protein was sustained by an ethanol-induced decrease in proteasome activity, thereby stabilizing the Egr-1 protein. Egr-1 induction depended on ethanol oxidation, as it was prevented when ethanol oxidation was blocked. Ethanol exposure induced Egr-1 and triglyceride accumulation only in alcohol dehydrogenase-expressing cells that produced acetaldehyde. Such induction did not occur in parental, non-metabolizing HepG2 cells or in cells that express only cytochrome P450 2E1. However, direct exposure of HepG2 cells to acetaldehyde induced both Egr-1 protein and triglycerides. Egr-1 over-expression elevated triglyceride levels, which were augmented by ethanol exposure. However, these triglyceride levels did not exceed those in ethanol-exposed cells that had normal Egr-1 expression. Conversely, Egr-1 knockdown by siRNA only partially blocked ethanol-induced triglyceride accumulation and was associated not only with lower Egr-1 expression but also attenuation of SREBP1c and TNF-α mRNAs. Double knockdown of both Egr-1 and SREBP-1c abolished ethanol-elicited steatosis. Collectively, our findings provide important new insights into the temporal regulation by ethanol oxidation of Egr-1 and cellular steatosis.
doi:10.1016/j.biocel.2012.10.002
PMCID: PMC3549023  PMID: 23103837
acetaldehyde; oxidant stress; cytochrome P450 2E1; proteasome; cellular steatosis
21.  Contribution of Obesity to the Rise in Incidence of Rheumatoid Arthritis 
Arthritis care & research  2013;65(1):71-77.
OBJECTIVE
To determine whether the “obesity epidemic” could explain the recent rise in the incidence of RA.
BACKGROUND
Obesity is an under-recognized risk factor for RA. In recent years both the prevalence of obesity and the incidence of RA have been rising.
METHODS
An inception cohort of Olmsted County, Minnesota residents who fulfilled 1987 American College of Rheumatology criteria for RA in 1980–2007 was compared to population-based controls (matched on age, sex and calendar year). Heights, weights and smoking status were collected from medical records. Obesity was defined as body mass index (BMI) ≥ 30 kg/m2. Conditional logistic regression was used to assess the influence of obesity on developing RA. Population attributable risk was used to estimate the incidence of RA in the absence of obesity.
RESULTS
The study included 813 patients with RA and 813 controls. Both groups had extensive medical history available prior to incidence/index date (mean 32.2 years), and approximately 30% of each group were obese at incidence/index date. The history of obesity was a significantly associated with developing RA (OR:1.24; 95 % CI: 1.01, 1.53 adjusted for smoking status). In 1985–2007 the incidence of RA rose by an increment of 9.2 per 100,000 among women. Obesity accounted for 4.8 per 100,000 (or 52%) of this increase.
CONCLUSION
Obesity is associated with a modest risk for developing RA. Given the rapidly increasing prevalence of obesity, this has had a significant impact on RA incidence and may account for much of the recent increase in incidence of RA.
doi:10.1002/acr.21660
PMCID: PMC3707391  PMID: 22514156
rheumatoid arthritis; obesity; incidence; population attributable risk; body mass index
22.  Duplications and losses in gene families of rust pathogens highlight putative effectors 
Rust fungi are a group of fungal pathogens that cause some of the world's most destructive diseases of trees and crops. A shared characteristic among rust fungi is obligate biotrophy, the inability to complete a lifecycle without a host. This dependence on a host species likely affects patterns of gene expansion, contraction, and innovation within rust pathogen genomes. The establishment of disease by biotrophic pathogens is reliant upon effector proteins that are encoded in the fungal genome and secreted from the pathogen into the host's cell apoplast or within the cells. This study uses a comparative genomic approach to elucidate putative effectors and determine their evolutionary histories. We used OrthoMCL to identify nearly 20,000 gene families in proteomes of 16 diverse fungal species, which include 15 basidiomycetes and one ascomycete. We inferred patterns of duplication and loss for each gene family and identified families with distinctive patterns of expansion/contraction associated with the evolution of rust fungal genomes. To recognize potential contributors for the unique features of rust pathogens, we identified families harboring secreted proteins that: (i) arose or expanded in rust pathogens relative to other fungi, or (ii) contracted or were lost in rust fungal genomes. While the origin of rust fungi appears to be associated with considerable gene loss, there are many gene duplications associated with each sampled rust fungal genome. We also highlight two putative effector gene families that have expanded in Cqf that we hypothesize have roles in pathogenicity.
doi:10.3389/fpls.2014.00299
PMCID: PMC4071342  PMID: 25018762
effectors; rust pathogens; secretome; genome evolution; comparative genomics
23.  Vesicular Stomatitis Virus Variants Selectively Infect and Kill Human Melanomas but Not Normal Melanocytes 
Journal of Virology  2013;87(12):6644-6659.
Metastatic malignant melanoma remains one of the most therapeutically challenging forms of cancer. Here we test replication-competent vesicular stomatitis viruses (VSV) on 19 primary human melanoma samples and compare these infections with those of normal human melanocyte control cells. Even at a low viral concentration, we found a strong susceptibility to viral oncolysis in over 70% of melanomas. In contrast, melanocytes displayed strong resistance to virus infection and showed complete protection by interferon. Several recombinant VSVs were compared, and all infected and killed most melanomas with differences in the time course with increasing rates of melanoma infection, as follows: VSV-CT9-M51 < VSV-M51 < VSV-G/GFP < VSV-rp30. VSV-rp30 sequencing revealed 2 nonsynonymous mutations at codon positions P126 and L223, both of which appear to be required for the enhanced phenotype. VSV-rp30 showed effective targeting and infection of multiple subcutaneous and intracranial melanoma xenografts in SCID mice after tail vein virus application. Sequence analysis of mutations in the melanomas used revealed that BRAF but not NRAS gene mutation status was predictive for enhanced susceptibility to infection. In mouse melanoma models with specific induced gene mutations including mutations of the Braf, Pten, and Cdkn2a genes, viral infection correlated with the extent of malignant transformation. Similar to human melanocytes, mouse melanocytes resisted VSV-rp30 infection. This study confirms the general susceptibility of the majority of human melanoma types for VSV-mediated oncolysis.
doi:10.1128/JVI.03311-12
PMCID: PMC3676084  PMID: 23552414
24.  Child care in general practice 
doi:10.3399/bjgp12X659169
PMCID: PMC3505388  PMID: 23211237
25.  Immune response profiling in early rheumatoid arthritis: discovery of a novel interaction of treatment response with viral immunity 
Arthritis Research & Therapy  2013;15(6):R199.
Introduction
It remains challenging to predict the outcomes of therapy in patients with rheumatoid arthritis (RA). The objective of this study was to identify immune response signatures that correlate with clinical treatment outcomes in patients with RA.
Methods
A cohort of 71 consecutive patients with early RA starting treatment with disease-modifying antirheumatic drugs (DMARDs) was recruited. Disease activity at baseline and after 21 to 24 weeks of follow-up was measured using the Disease Activity Score in 28 joints (DAS28). Immune response profiling was performed by analyzing multi-cytokine production from peripheral blood cells following incubation with a panel of stimuli, including a mixture of human cytomegalovirus (CMV) and Epstein-Barr virus (EBV) lysates. Profiles identified via principal components analysis (PCA) for each stimulus were then correlated with the ΔDAS28 from baseline to follow-up. A clinically meaningful improvement in the DAS28 was defined as a decrease of ≥1.2.
Results
A profile of T-cell cytokines (IL-13, IL-4, IL-5, IL-2, IL-12, and IFN-γ) produced in response to CMV/EBV was found to correlate with the ΔDAS28 from baseline to follow-up. At baseline, a higher magnitude of the CMV/EBV immune response profile predicted inadequate DAS28 improvement (mean PCA-1 scores: 65.6 versus 50.2; P = 0.029). The baseline CMV/EBV response was particularly driven by IFN-γ (P = 0.039) and IL-4 (P = 0.027). Among patients who attained clinically meaningful DAS28 improvement, the CMV/EBV PCA-1 score increased from baseline to follow-up (mean +11.6, SD 25.5), whereas among patients who responded inadequately to DMARD therapy, the CMV/EBV PCA-1 score decreased (mean -12.8, SD 25.4; P = 0.002). Irrespective of the ΔDAS28, methotrexate use was associated with up-regulation of the CMV/EBV response. The CMV/EBV profile was associated with positive CMV IgG (P <0.001), but not EBV IgG (P = 0.32), suggesting this response was related to CMV exposure.
Conclusions
A profile of T-cell immunity associated with CMV exposure influences the clinical response to DMARD therapy in patients with early RA. Because CMV latency is associated with greater joint destruction, our findings suggest that changes in T-cell immunity mediated by viral persistence may affect treatment response and possibly long-term outcomes of RA.
doi:10.1186/ar4389
PMCID: PMC3978471  PMID: 24267267

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